evolution of consciousness (Introduction)
by George Jelliss 
, Crewe, Saturday, July 29, 2017, 17:19 (2672 days ago)
Came across this and thought of you:
https://www.theatlantic.com/science/archive/2016/06/how-consciousness-evolved/485558/
All sounds quite plausible to me.
--
GPJ
evolution of consciousness
by David Turell , Sunday, July 30, 2017, 02:02 (2672 days ago) @ George Jelliss
George: Came across this and thought of you:
https://www.theatlantic.com/science/archive/2016/06/how-consciousness-evolved/485558/
All sounds quite plausible to me.
We all appreciate your thinking of us and providing this very well done explanation of the evolution of the human brain. I don't think he hasn't given us a good explanation of consciousness, but has afforded a good description as to how we arrived at the state of being conscious and responsive. Well worth reading.
evolution of consciousness
George: Came across this and thought of you:
https://www.theatlantic.com/science/archive/2016/06/how-consciousness-evolved/485558/
All sounds quite plausible to me.
DAVID: We all appreciate your thinking of us and providing this very well done explanation of the evolution of the human brain. I don't think he hasn't given us a good explanation of consciousness, but has afforded a good description as to how we arrived at the state of being conscious and responsive. Well worth reading.
I add my delight at hearing from you again, George, and for a change I agree with David. Good history, but absolutely no explanation of consciousness. The essence of the whole thing seems to me to lie in this section. A talking crocodile might say:
“I’ve got something intangible inside me. It’s not an eyeball or a head or an arm. It exists without substance. It’s my mental possession of things. It moves around from one set of items to another. When that mysterious process in me grasps hold of something, it allows me to understand, to remember, and to respond.”
The crocodile would be wrong, of course. Covert attention isn’t intangible. It has a physical basis, but that physical basis lies in the microscopic details of neurons, synapses, and signals. The brain has no need to know those details. The attention schema is therefore strategically vague. It depicts covert attention in a physically incoherent way, as a non-physical essence. And this, according to the theory, is the origin of consciousness. We say we have consciousness because deep in the brain, something quite primitive is computing that semi-magical self-description.
There is no theory of the origin of consciousness here. Merely the author’s contention that the crocodile is wrong, and it’s all due to neurons, synapses and signals, which is the standard materialist explanation. He may be right, but nobody in the world knows how it works or how it originated.
evolution: development of neurons
by David Turell , Tuesday, February 20, 2018, 22:25 (2466 days ago) @ dhw
They are such complex cells, did they evolve or were they designed:
https://darwins-god.blogspot.com/2018/02/this-didnt-evolve-few-mutations-at-time.html
"Nerve cells have a long tail which carries an electronic impulse. The tail can be several feet long and its signal might stimulate a muscle to action, control a gland, or report a sensation to the brain.
"Early researchers considered that perhaps the electronic impulse traveled along the nerve cell tail like electricity in a wire. But they soon realized that the signal in nerve cells is too weak to travel very far. The nerve cell would need to boost the signal along the way for it to travel along the tail.
"After years of research it was discovered that the signal is boosted by membrane proteins. First, there is a membrane protein that simultaneously pumps two potassium ions into the cell and three sodium ions out of the cell. This sets up a chemical gradient across the membrane. There is more potassium inside the cell than outside, and there is more sodium outside than inside. Also, there are more negatively charged ions inside the cell so there is a voltage drop (50-100 millivolt) across the membrane.
"In addition to the sodium-potassium pump, there are also sodium channels and potassium channels. These membrane proteins allow sodium and potassium, respectively, to pass through the membrane. They are normally closed, but when the decaying electronic impulse travels along the nerve cell tail, it causes the sodium channels to quickly open. Sodium ions outside the cell then come streaming into the cell down the electro-chemical gradient. As a result, the voltage drop is reversed and the decaying electronic impulse, which caused the sodium channels to open, is boosted as it continues on its way along the nerve cell tail.
"When the voltage goes from negative to positive inside the cell, the sodium channels slowly close and the potassium channels open. Hence the sodium channels are open only momentarily, and now with the potassium channels open, the potassium ions concentrated inside the cell come streaming out down their electro-chemical gradient. As a result the original voltage drop is reestablished.
"This process repeats itself as the electronic impulse travels along the tail of the nerve cell, until the impulse finally reaches the end of the nerve cell. Although we’ve left out many details, it should be obvious that the process depends on the intricate workings of the three membrane proteins. The sodium-potassium pump helps set up the electro-chemical gradient, the electronic impulse is strong enough to activate the sodium channel, and then the sodium and potassium channels open and close with precise timing.
"How, for example, are the channels designed to be ion-selective? Sodium is about 40% smaller than potassium so the sodium channel can exclude potassium if it is just big enough for sodium. Random mutations must have struck on an amino acid sequence that would fold up just right to provide the right channel size.
"The potassium channel, on the other hand is large enough for both potassium, and sodium, yet it is highly efficient. It somehow excludes sodium almost perfectly (the potassium to sodium ratio is about 10000), yet allows potassium to pass through almost as if there were nothing in the way."
"Nerve cells are constantly firing off in your body. They control your eyes as you read these words, and they send back the images you see on this page to your brain. They, along with chemical signals, control a multitude of processes in our bodies, and there is no scientific reason to think they gradually evolved, one mutation at time.
"Indeed, that idea contradicts everything we know from the science. And yet this is what evolutionists believe. Let me repeat that: evolutionists believe nerve cells and their action potential designs evolved one mutation at time. Indeed, evolutionists believe this is a proven fact, beyond all reasonable doubt."
Comment: Hunter then goes on to dissect an evolution-science paper about how neurons evolved and demonstrates how it is filled with wishful thinking., not fact A neuron appears in evolution from no predecessors and had to be designed to be this complex.
evolution: pressure-sensing proteins
by David Turell , Wednesday, August 21, 2019, 23:49 (1919 days ago) @ David Turell
Absolutely necessary for complex organisms who need to feel bowel and bladder pressure, control of blood pressure, touch, etc. Specialized complex proteins must b e developed and employed:
https://phys.org/news/2019-08-scientists-basics-pressure-sensing-piezo-proteins.html
"A team of scientists from Weill Cornell Medicine and The Rockefeller University has illuminated the basic mechanism of Piezo proteins, which function as sensors in the body for mechanical stimuli such as touch, bladder fullness, and blood pressure.
***
"They confirmed this complex protein's structure and showed essentially how it can convert mechanical stimuli into an electrical signal.
"'Our analysis shows that tension on the cell membrane in which Piezo1 is embedded can flatten and widen the protein's structure," said co-senior author Dr. Simon Scheuring,
***
"Piezo1 and Piezo2 are very large and complex proteins with unique structures. They are embedded within the membranes of certain cell types, and their function is to transduce mechanical force on cells into electrical signals that alter cell activity. Piezo1 proteins work for example in bladder cells to detect when the bladder is full, and in blood vessel-lining cells to detect and help regulate changes in blood pressure. Piezo2 proteins work in sensory nerve endings in the skin and joints, helping to mediate the senses of touch, pain, and proprioception—the sense of how one's limbs are arranged.
"Advances in imaging techniques have enabled scientists in recent years to determine the basic structure of Piezo1—a structure that Piezo2 is thought to mostly share. From above this structure has a three-armed, propeller or "triskelion" appearance. (my bold)
"From the side it looks like a shallow bowl embedded in the cell membrane, with an ion channel at its center. The latter, when opened, allows a flow of calcium and other positively charged ions into the cell.
***
"They showed with these methods that Piezo1 is a springy structure that normally bends the cell membrane where it sits, but will flatten out when, for example, a mechanical force is applied to the cell membrane.
"'As the membrane tension increases, the structure of Piezo1 flattens and stretches out to occupy a larger area, which in turn opens the ion channel," Dr. Scheuring said.
"He noted the possibility that other stimuli that stretch and flatten the Piezo1 structure, such as a pulling force on its arms from the inside or on an external domain called the CED from the outside the cell, in principle could open the ion channel—making it a suitably versatile mechanism for the wide range of cell types and physiological functions in which it works."
Comment: This three-armed propeller-like shape is an extremely specialized construction. It absolutely has to have been designed. Chance would never discover this form and its electrical functionality. Bipedal walking would be impossible without proprioceptive sensors placed throughout the body. Not by Darwin.
evolution: finding useful proteins
by David Turell , Monday, October 21, 2019, 22:20 (1858 days ago) @ David Turell
Folded proteins of large size are necessary because they have specific functions in the biochemistry of life and are absolutely vital for life to exist. they are why the Darwin theory does not work:
https://www.asiatimes.com/2019/09/opinion/pseudo-science-the-bible-and-human-freedom/
"An enormous literature documents the collapse of Charles Darwin’s theory in light of evidence (or lack of it), artfully summarized in Claremont Review of Books by the distinguished computer scientist David Gelernter. The Cambrian explosion of new species, Darwin’s critics observe, should have been preceded by pre-Cambrian forms, but those simply do not exist:
“'The trunk was supposed to branch into many different species, each species giving rise to many genera, and towards the top of the tree you would find so much diversity that you could distinguish separate phyla – the large divisions (sponges, mosses, mollusks, chordates, and so on) that comprise the kingdoms of animals, plants, and several others – take your pick. But, as [David] Berlinski points out, the fossil record shows the opposite: ‘representatives of separate phyla appearing first followed by lower-level diversification on those basic themes.’ In general, ‘most species enter the evolutionary order fully formed and then depart unchanged.’ The incremental development of new species is largely not there.”
"And that is not the worst of it. The new science of DNA proves mathematically that the odds of a random mutation leading to an improvement in the adaptability of a living organism are effectively zero, Gelernter shows. Even a small protein molecule has a chain of 150 amino acids. If we rearrange them at random we mostly obtain gibberish. In fact, “of all 150-link amino acid sequences, 1 in 1074 will be capable of folding into a stable protein. To say that your chances are 1 in 1074 is no different, in practice, from saying that they are zero. It’s not surprising that your chances of hitting a stable protein that performs some useful function, and might therefore play a part in evolution, are even smaller,” Gelernter explains. That is Establishment science, not the murmurings of the Creationist fringe. (my bold)
"In short, the evolutionary biologists can’t explain how animal life made the great leap from protozoans to arthropods in the Cambrian Explosion, let alone how natural selection through random mutation might have shaped the human mind. Biologists do brilliant and important research, to be sure, and the profession should not be blamed for the exaggerated claims made by a few publicists like Harari or Harvard’s Steven Pinker."
Comment: the bolded paragraph shows why Darwin's materialistic chance mutation type evolution cannot work. these special large molecules must be designed. See the next entry about how tiny proteins also play a role in the so-called 'junk' areas of DNA.
evolution: finding tiny proteins
by David Turell , Monday, October 21, 2019, 22:37 (1858 days ago) @ David Turell
The last entry discussed large complex protein molecules. This describes new;y discovered tiny proteins taht seem to have enormous influence on large protein functions:
https://www.sciencemag.org/news/2019/10/new-universe-miniproteins-upending-cell-biology...
"On a treadmill, the mice could scurry up a steep 10% grade for about 90 minutes before faltering, 31% longer than other rodents. Those iron mice differed from counterparts in just one small way—the researchers had genetically altered the animals to lack one muscle protein. That was enough to unleash superior muscle performance. "It's like you've taken the brakes off," Olson says.
"Just as startling was the nature of the crucial protein. Muscles house some gargantuan proteins. Dystrophin, a structural protein whose gene can carry mutations that cause muscular dystrophy, has more than 3600 amino acids. Titin, which acts like a spring to give muscles elasticity, is the biggest known protein, with more than 34,000 amino acids. The protein disabled in the mice has a paltry 46. Although researchers have probed how muscles work for more than 150 years, they had completely missed the huge impact this tiny protein, called myoregulin, has on muscle function.
***
"Biologists are just beginning to delve into the functions of those molecules, called microproteins, micropeptides, or miniproteins. But their small size seems to allow them to jam the intricate workings of larger proteins, inhibiting some cellular processes while unleashing others. Early findings suggest microproteins bolster the immune system, control destruction of faulty RNA molecules, protect bacteria from heat and cold, dictate when plants flower, and provide the toxic punch for many types of venom. "There's probably going to be small [proteins] involved in all biological processes. We just haven't looked for them before," says biochemist Alan Saghatelian of the Salk Institute for Biological Studies in San Diego, California.
"Small proteins also promise to revise the current understanding of the genome. Many appear to be encoded in stretches of DNA—and RNA—that were not thought to help build proteins of any sort. Some researchers speculate that the short stretches of DNA could be newborn genes, on their way to evolving into larger genes that make full-size proteins. Thanks in part to small proteins, "We need to rethink what genes are," says microbiologist and molecular biologist Gisela Storz. (my bold)
***
"Being small limits a protein's capabilities. Larger proteins fold into complex shapes suited for a particular function, such as catalyzing chemical reactions. Proteins smaller than about 50 to 60 amino acids probably don't fold, says chemist Julio Camarero of the University of Southern California in Los Angeles. So they probably aren't suited to be enzymes or structural proteins.
"However, their diminutive size also opens up opportunities. "They are tiny enough to fit into nooks and crannies of larger proteins that function as channels and receptors," Olson says. Small proteins often share short stretches of amino acids with their larger partners and can therefore bind to and alter the activity of those proteins. Bound microproteins can also shepherd bigger molecules to new locations—helping them slip into cell membranes, for instance."
Comment: short modifications of large proteins, by having the small proteins inserted into larger ones is a neatly designed way to alter function on the fly. Further note these are the result of DNA and RNA work considered to come from 'junk' DNA, again reducing the amount of so-called junk DNA. Discoveries like this are pointing to the necessary conclusion that it is all designed.
Evolution: bacteria's' role
by David Turell , Wednesday, January 08, 2020, 00:48 (1780 days ago) @ David Turell
They were at the start of life and have continued to support life as it evolved:
https://cosmosmagazine.com/biology/birds-bats-and-bacteria?utm_source=Cosmos+-+Master+M...
"Their study, published in the journal mBio, has upended current thinking about microbial similarities between related species by revealing that, unlike other mammals, bats have unpredictable gut bacteria much like birds.
"This suggests that evolving to fly may have a dramatic impact on the gut microbiome, raising questions about how evolution impacts microbial communities.
"Research has established that gut microbes co-evolved with mammals – including humans – over millions of years and are intimately connected to diet and wellbeing.
"But the new study implies that mammals’ reliance on their microscopic friends may be unique, according to co-first author Se Jin Song, from the University of California San Diego.
“'This represents a paradigm shift in how we think about animals and the relationships they have with their microbes,” he says.
***
“What was shocking,” he says, “was that we didn’t find that birds and bats share a similar microbiome per se, but rather that both lack a specific relationship with microbes.”
"While all mammals showed clear patterns of bacteria in closely related groups, those found in flying birds and bats were virtually unpredictable.
“'It’s almost like they’re just picking up whatever’s around them and they don’t really need their microbes to help them in ways that we do,” says co-author Holly Lutz from UC San Diego and Chicago’s Field Museum.
"Micro-organisms might, therefore, have less importance for supporting healthy digestion in bats and birds, possibly an adaptive response to taking flight.
***
"By learning more about the microbiomes of different animals, the researchers hope to understand more about our own; in this case species that don’t rely on their gut bacteria could provide unique insights.
“'If we are ever putting ourselves in some kind of extreme situation where we’re disrupting our microbiome,” says Lutz, “there is something that we can learn from animals that don’t need their microbiomes as much.'”
Comment: They were there at the start of life and have stayed around to serve other purposes in support of life in various ways. They are one type of organism which never went extinct. Why? As Shapiro noted, they have great transformative abilities, because they are free living individuals, and they can respond to groups of other bacteria for more protection by acting in concert. Looks like a good plan to me by the designer.
Evolution: bacteria's' role
DAVID: They were there at the start of life and have stayed around to serve other purposes in support of life in various ways. They are one type of organism which never went extinct. Why? As Shapiro noted, they have great transformative abilities, because they are free living individuals, and they can respond to groups of other bacteria for more protection by acting in concert. Looks like a good plan to me by the designer.
Yes, Shapiro thinks they are intelligent, and you agree that outwardly they show all the signs of intelligence. This theory does not in any way preclude the possibility that your God designed their intelligence as part of whatever his plan was. But you believe that 3.8 billion years ago your God preprogrammed all their intelligent responses to every single problem and/or opportunity they would encounter for the rest of time. Your alternative is that he comes down and gives them private tuition (= dabbles). The programmes or private lessons are what you call "guidelines". Just clarifying.
Evolution: bacteria's' role
by David Turell , Thursday, January 09, 2020, 00:49 (1779 days ago) @ dhw
DAVID: They were there at the start of life and have stayed around to serve other purposes in support of life in various ways. They are one type of organism which never went extinct. Why? As Shapiro noted, they have great transformative abilities, because they are free living individuals, and they can respond to groups of other bacteria for more protection by acting in concert. Looks like a good plan to me by the designer.
dhw: Yes, Shapiro thinks they are intelligent, and you agree that outwardly they show all the signs of intelligence. This theory does not in any way preclude the possibility that your God designed their intelligence as part of whatever his plan was. But you believe that 3.8 billion years ago your God preprogrammed all their intelligent responses to every single problem and/or opportunity they would encounter for the rest of time. Your alternative is that he comes down and gives them private tuition (= dabbles). The programmes or private lessons are what you call "guidelines". Just clarifying.
Our disagrees are clear.
Evolution: bacteria's' role in plant biomes
by David Turell , Monday, April 13, 2020, 19:47 (1683 days ago) @ David Turell
We are finding that controlled beneficial biomes are everywhere. New plant research:
https://www.sciencedaily.com/releases/2020/04/200413103534.htm
"Michigan State University scientists show how plant genes select which microbes get to live inside their leaves in order to stay healthy.
"This is the first study to show a causal relationship between plant health and assembly of the microbial community in the phyllosphere -- the total above-ground portions of plants. The work suggests that organisms, from plants to animals, may share a similar strategy to control their microbiomes.
***
"'If everything is allowed to grow in the plants, it would probably be a mess. We want to know if the numbers and types of microbes matter, if there is a perfect composition of microbes. If so, do plants have a genetic system to host and nurture the right microbiome?"
"It seems plants do. The newly discovered mechanism involves two genetic networks. One involves the plant immune system and the other controls hydration levels inside leaves. Both networks work together to select which microbes survive inside of plant leaves.
***
"'Very few people have grown a sterile plant in sterile, organic-rich material," He said. "Our system uses a peat-based soil-like substrate, basically greenhouse potting soil. We use heat and pressure to kill all the germs in the soil, and the plants can grow under this germ-free condition."
"Researchers can then introduce microbes in a controlled fashion, into this environment.
"'You can add one, two, or even a community of bacteria," He said. "In our study, we extracted a community of bacteria from dysbiotic, or sick, plants and introduced them to our healthy plants, and vice-versa. We found that both the microbiome composition and the plant genetic systems are required for plant health."
"For example, a plant with defective genetics could not take advantage of a microbiome transplanted from a healthy plant. The microbiome slowly reverted to the state that caused sickness.
"On the other end, a healthy plant exposed to a sick plant's microbiome also suffered. Although it had the genetic tools to select the right microbes, microbe availability was limited and abnormal. The plant couldn't fix the situation.
"It turns out that increased microbiome diversity correlates with plant health. Somehow, plant genes are gatekeepers that encourage this diversity.
***
"In the sick plants, proteobacteria strains -- many of which are harmful to plants -- jumped from two-thirds the composition of a healthy microbiome to 96% in the abnormal population. Fermicutes strains, many which may be helpful to plants, went down in numbers.
"'Perhaps, when the population of microbiome is abnormally higher in that sick plant, the microbes are physically too close to each other," He said. "Suddenly, they fight over resources, and the aggressive -- in this case harmful -- ones unfortunately win. Healthy plants seem to prevent this takeover from happening."
"The study is yet another example of how diversity is important to support healthy living systems. Each type of microbe might impart different benefits to plants, such as increased immunity, stress tolerance or nutrient absorption."
Comment: Once again we see how important bacteria are in the scheme of livings things and their continuing health. God knows what He is doing, despite dhw's doubts. We wondered, early on, why bacteria survived all the extinctions and are still here. they were meant to be a major help all along. God knows His plans for the future, from the beginning.
Evolution: bacteria's' role in plant biomes
QUOTE: "The study is yet another example of how diversity is important to support healthy living systems. Each type of microbe might impart different benefits to plants, such as increased immunity, stress tolerance or nutrient absorption."
DAVID: Once again we see how important bacteria are in the scheme of livings things and their continuing health. God knows what He is doing, despite dhw's doubts. We wondered, early on, why bacteria survived all the extinctions and are still here. they were meant to be a major help all along. God knows His plans for the future, from the beginning.
Of course they’re important, and I’ve never questioned that. Nor have I ever questioned that if God exists, he knows what he’s doing! The question which you simply refuse to face up to is why, if his one and only purpose was to specially design H. sapiens, he specially designed billions of now extinct non-human life forms and their econiches and their lifestyles and their strategies and other natural wonders. You cannot find a single reason why he should have done so. Bacteria are essential to all forms of life, and food is essential to all forms of life. That doesn’t mean that all forms of life are/were essential to enable him to specially design humans! “See David’s theory of evolution”.
Evolution: bacteria's' role in plant biomes
by David Turell , Tuesday, April 14, 2020, 19:13 (1682 days ago) @ dhw
QUOTE: "The study is yet another example of how diversity is important to support healthy living systems. Each type of microbe might impart different benefits to plants, such as increased immunity, stress tolerance or nutrient absorption."
DAVID: Once again we see how important bacteria are in the scheme of livings things and their continuing health. God knows what He is doing, despite dhw's doubts. We wondered, early on, why bacteria survived all the extinctions and are still here. they were meant to be a major help all along. God knows His plans for the future, from the beginning.
dhw: Of course they’re important, and I’ve never questioned that. Nor have I ever questioned that if God exists, he knows what he’s doing! The question which you simply refuse to face up to is why, if his one and only purpose was to specially design H. sapiens, he specially designed billions of now extinct non-human life forms and their econiches and their lifestyles and their strategies and other natural wonders. You cannot find a single reason why he should have done so. Bacteria are essential to all forms of life, and food is essential to all forms of life. That doesn’t mean that all forms of life are/were essential to enable him to specially design humans! “See David’s theory of evolution”.
The same old false problem which is your illogical invention, taken from a human view of an imagined humanized god. Why do you state: Nor have I ever questioned that if God exists, he knows what he’s doing! , if you then reverse course and wonder why He chose to evolve us over time, which is exactly what history tells us He did! Swiss cheese thinking at best.
Evolution: bacteria's' role in human biomes
by David Turell , Tuesday, July 21, 2020, 19:52 (1584 days ago) @ David Turell
Our gut is filled with beneficial bacteria and viruses, and they survive attacks:
https://phys.org/news/2020-07-viruses-bacteria-gut-microbiome.html
"The adage 'all things in moderation' applies not to just to food and drink, but also to the legions of bacteria inside our guts helping us digest that food and drink. It turns out the rule may also extend to the lesser understood bacteriophages, which are viruses that infect the bacteria living inside us.
"Like Russian nesting dolls, our bodies host close to 100 trillion bacterial cells that make up our microbiomes—and those bacterial cells have their own inhabitants.
"'We're appreciating more and more that the most abundant microbial entities in the human gut are actually viruses," says Eric Martens, Ph.D.
***
"His team has been exploring the puzzling way bacteria and their viruses appear to coexist inside the human gut. The secret may lie in a hairy-looking sugar coating bacteria used to defend not only against attacks from the human immune system, but also from various viruses seeking a way in.
"Using a common gut bacteria Bacteroides thetaiotaomicron, or BT for short, Martens' team began to look at the complex interaction between BT and viruses, by pitting them against each other in the lab.
"When challenged with viruses, or phages, collected from waste water, some of the bacteria were able to resist infection while some were not. "When a particular phage comes along that can kill certain members of the population, it does so and the resistant bacteria quickly grow out," says Martens.
"However, instead of permanently altering the receptor that allowed the viral penetration, and potentially harming itself, some of the bacteria temporarily turn on a resistant state through a reversible process called a phase variation. But some of members of the bacterial population, unaware of the phage's continued presence, turn off this resistance switch, leaving them susceptible to infection...and on and on.
"The team genetically engineered the BT strain to express just one of eight chemically-distinct capsules and a version with no coating at all. In all cases, infection could be blocked by some, but not all, of the capsules. Surprisingly, the researchers noted that the bald bacteria were also able to evade infection. "We were intrigued to see we could take away all of the capsules and still infect it with these phages and the bacteria could still survive, which necessitates that they have a backup mechanism in place," Martens says.
"The interplay between the gut microbiome and their phages could have implications for human disease. "One of our hypotheses is that individuals carry different types of viral loads in their guts. Some could be more or less immunogenic, interacting with our immune system to cause inflammation. But they also might modify the physiology of the bacteria that are there by forcing them to express certain functions/capsules that we also know interact with the immune system," says Martens.
"He says the study helps explain this age old observation that these bacteria coexist with their viruses. Notes Martens, "Neither side necessarily wins out over the other." As such, bacterial viruses could offer a way of beneficially altering the gut microbiome for the treatment of disease."
Comment: As noted before, bacteria have survived forever and this useful behavior shows why.
Evolution: t he gut has its own independent neuron network
by David Turell , Friday, December 25, 2020, 15:57 (1427 days ago) @ David Turell
100 billion neurons connected to send signals to the brain by the vagus nerve while running the digestive processes:
https://mindmatters.ai/2020/12/did-you-know-you-have-a-second-brain/
"Our huge gastrointestinal tracts operate their own nervous system, using neurons that follow different principles from those of brain neurons, according to recent findings:
"Our approximately seven-meter long gastrointestinal (GI) tract has its own functionally distinct neurons. Since this enteric nervous system (ENS) operates autonomously, it is sometimes referred to as the “second” or “abdominal” brain. While the ENS controls muscle movement (peristalsis) in the gut and its fluid balance and blood flow, it also communicates with the immune system and microbiome.
"The Karolinska researchers made progress in studying the little-understood second brain by mapping the neuron types in the digestive systems of mice. The human gut is estimated to contain an independent network of over 100 billion neurons that not only control digestion but work with the immune system to fight a constant war with hostile bacteria.
"These neurons help account for the curious sensation of “butterflies in the stomach.”
***
"...scientists were shocked to learn that about 90 percent of the fibers in the primary visceral nerve, the vagus, carry information from the gut to the brain and not the other way around. “Some of that info is decidedly unpleasant,” Gershon says.
"The second brain informs our state of mind in other more obscure ways, as well. “A big part of our emotions are probably influenced by the nerves in our gut,” Mayer says. Butterflies in the stomach—signaling in the gut as part of our physiological stress response, Gershon says—is but one example. Although gastrointestinal (GI) turmoil can sour one’s moods, everyday emotional well-being may rely on messages from the brain below to the brain above. For example, electrical stimulation of the vagus nerve—a useful treatment for depression—may mimic these signals, Gershon says."
Comment: The vagus nerve, the tenth cranial nerve, directly connected to the brain keeps tabs on what is going on but the system really is autonomous and runs the show. This is not new knowledge. I learned this in medical school. The details are new, especially the new findings that the gut biome can affect our emotions. The design is not by chance.
Evolution: bacteria's' role in human biomes
by David Turell , Monday, July 12, 2021, 19:09 (1228 days ago) @ David Turell
It seems our gut biome is influences by our genome:
https://www.sciencedaily.com/releases/2021/07/210708170331.htm
"...a University of Notre Dame study has found a much greater genetic component at play than was once known.
"In the study, published recently in Science, researchers discovered that most bacteria in the gut microbiome are heritable after looking at more than 16,000 gut microbiome profiles collected over 14 years from a long-studied population of baboons in Kenya's Amboseli National Park. However, this heritability changes over time, across seasons and with age. The team also found that several of the microbiome traits heritable in baboons are also heritable in humans.
***
"The gut microbiome performs several jobs. In addition to helping with food digestion, it creates essential vitamins and assists with training the immune system. This new research is the first to show a definitive connection with heritability.
***
'The research team found that 97 percent of microbiome traits, including overall diversity and the abundance of individual microbes, were significantly heritable
***
"The team did find evidence that environmental factors influence trait heritability in the gut microbiome. Microbiome heritability was typically 48 percent higher in the dry season than in the wet, which may be explained by the baboons' more diverse diet during the rainy season. Heritability also increased with age, according to the study.
"Because the research also showed the significant impact of environment on the gut microbiomes in baboons, their findings agreed with previous studies showing that environmental effects on the variation in the gut microbiome play a larger role than additive genetic effects. Combined with their discovery of the genetic component, the team plans to refine its understanding of the environmental factors involved."
Comment: More evidence that bacteria must be here and have a strong role to play, even if some act badly at times.
Evolution: bacteria's' role in human therapy
by David Turell , Monday, July 12, 2021, 19:17 (1228 days ago) @ David Turell
we can modify friendly bacteria to stop pathogenic bacteria:
https://www.sciencedaily.com/releases/2021/07/210712122106.htm
"A recent trial has shown that nose drops of modified 'friendly' bacteria may protect against meningitis.
***
"Around 10% of adults carry N. meningitidis in the back of their nose and throat with no signs or symptoms. However, in some people it can invade the bloodstream. That can lead to life-threatening conditions including meningitis and blood poisoning ('septicaemia).
"The 'friendly' bacteria Neisseria lactamica (N. lactamica) also lives in some people's noses naturally. By occupying the nose, it protects from a severe type of meningitis. It does so by denying a foothold to its close cousin Neisseria meningitidis (N. meningitidis).
"The new data build on the team's previous work aiming to exploit this natural phenomenon. That study showed nose drops of N. lactamica prevented N. meningitidis from settling in 60% of participants.
"For those people, N. lactamica had locked out its deadly cousin. That drove work to make N. lactamica even more effective in displacing N. meningitidis.
"The team did so by handing it one of N. meningitidis' key weapons; a 'sticky' surface protein that grips the cells lining the nose. By inserting a copy of the gene for this protein into N. lactamica's DNA, it could also it -- levelling the playing field.
"As well as inducing a stronger immune response, those modified bacteria stayed longer. Present for at least 28 days, with most participants (86%) still carrying it at 90 days, it caused no adverse symptoms."
Comment: We humans can use our God-given brains to use bacteria for our benefit.
Evolution: can work in reverse
by David Turell , Saturday, August 21, 2021, 19:22 (1188 days ago) @ David Turell
Newly found Cambrian fossils make the point:
https://phys.org/news/2021-08-rare-cambrian-fossils-utah-reveal.html
"Ctenophores, also known as comb jellies, are a group of over 200 living species of invertebrate animals with a transparent gelatinous body superficially resembling that of a jellyfish. There is much interest in ctenophore evolution in recent years as their controversial phylogenetic position in the animal tree of life has prompted conflicting hypotheses. While some studies suggest they might represent the earliest branching animals, others suggest a more traditional position as close relatives of jellyfish.
***
"Despite their importance for understanding animal evolution, most information about ctenophores comes from living species alone as fossil comb jellies are extremely rare due to their gelatinous bodies. However, some fossil ctenophores have been discovered in early and middle Cambrian sites (about 520-500 million years ago) with exceptional preservation. These fossilized specimens, found around the world in sites including Burgess Shale in Canada and Chengjiang in South China, show that Cambrian ctenophores are a bit different from living representatives. The fossils include features such as a skeleton that supported the ctenes, or comb rows, as well as up to 24 comb rows—many more than the eight comb rows possessed by living species.
***
"The first species, Ctenorhabdotus campanelliformis, has a small bell-shaped body with up to 24 comb rows and a wavy mouth opening. Intriguingly, this species shows two important features. First, there is a rigid capsule that protects the sensory apical organ, which represents the remains of the skeleton found in older ctenophores from the early Cambrian. Secondly, this species also shows a preserved nervous system. The nerves are long, and connect with a ring around the mouth. "This was quite an unexpected finding, as only one species (Euplokamis) of comb jellies today has comparable long nerves. Most modern comb jellies have a diffuse nervous net, and not well-defined long nerves," said senior author Professor Javier Ortega-Hernández, the Department of Organismic and Evolutionary Biology, Harvard University.
"The second species, Thalassostaphylos elegans, has a rounder appearance, approximately 16 comb rows, and a wavy mouth opening. Although this species does not show fossilized nerves, it has an important feature known as the "polar fields", which can be seen as two small dots on top of the apical organ. "These are also important for sensing the environment in living comb jellies, and finding evidence for them in the Cambrian is significant for understanding their evolution," said Ortega-Hernández. "Interestingly, Thalassostaphylos elegans does not have a rigid capsule, indicating that the skeleton found in early Cambrian ctenophores was already lost in some representatives by the mid-Cambrian."
***
"The researchers conclude that Cambrian ctenophores had more complex nervous systems compared to those observed today. Living species of comb jellies have a diffuse nervous system similar to the structure of chicken wire, but very thin and transparent. Cambrian ctenophores' nervous systems were condensed with specific nerve tracks that basically ran along the length of the body and then as a ring around the mouth. This complex system is only seen in one living species, the Euplokamis, which is regarded as potentially being an early branching ctenophore living today. However, while Euplokamis has this elongated nerve structure that runs the length of the body, it does not have the ring around the mouth, so it too is simpler compared to Cambrian ctenophores.
"To better understand the evolution of this group, the team performed phylogenetic analysis which suggests the condensed nervous system is actually the ancestral condition and that only modern ctenophores have lost this complex nervous system and instead favored a more diffuse nerve net.
***
"'This discovery means that there has a been a secondary simplification of comb jellies during their evolution, first losing the rigid skeleton, and then the discrete nerves observed in the fossils," said Dr. Luke A. Parry, Department of Earth Sciences, University of Oxford, UK. "These are insights that would be impossible to obtain from only studying living comb jellies, so the fossil record is providing a valuable glimpse into the evolution of these enigmatic animals." (my bold)
"Ortega-Hernández agreed, "In this context, Euplokamis would be showing a sort of vestigial organization of the nervous system, which are not seen in other living ctenophores. Ctenophores have a more complex evolutionary history than what can be reconstructed from their living representatives alone. Fossils allow us to understand the morphology that developed first and how it has changed through time.'"
Comment: these simple forms are nowhere like the complex animals that make the Cambrian Explosion such a huge gap in evolution. As simple forms they actually lost complexity over time. Evolution can run in reverse on very limited occasions. In Darwinist terms, it is obvious advanced complexification through natural selection isn't required. Animals can get by with less complexity than previously present.
Evolution: can work at high speed
by David Turell , Monday, August 23, 2021, 18:51 (1186 days ago) @ David Turell
Shown in a study of transition from fish to land tetrapods:
https://phys.org/news/2021-08-speedy-evolution-sustained-fast-tetrapods.html
"This "fish-to-tetrapod" transition took place somewhere between the Middle and Late Devonian (~400-360 million years ago) and represents the onset of a major environmental shift, when vertebrates first walked onto land. Yet, some of the most fundamental questions regarding the dynamics of this transition have remained unresolved for decades.
***
"'The study also innovates by combining data from fossil footprints and body fossils to pinpoint the time of origin of the tetrapods. "Normally footprint data shows up after body fossils of their track makers. In this case, we have tetrapod footprints much older than the first body fossils by several million years, which is extremely unusual. By combining both footprint and body fossils, we could search for a more precise age for the rise of tetrapods," said Pierce. (my bold)
"'We were able to provide a very precise age for the origin of tetrapods at approximately 390 million years ago, 15 million years older than the oldest tetrapod body fossil," said Simões.
"The researchers also found that most of the close relatives to tetrapods had exceptionally slow rates of anatomical evolution, suggesting the fish relatives to tetrapods were quite well adapted to their aquatic lifestyle.
"'On the other hand, we discovered the evolutionary lineages leading to the first tetrapods broke away from that stable pattern, acquiring several of the major new adaptive traits at incredibly fast rates that were sustained for approximately 30 million years," said Simões.
***
"They found that all parts of the tetrapod skeleton were under strong directional selection to evolve new adaptive features, but that the skull and jaws were evolving faster than the rest of the body, including the limbs.
***
"'We see several anatomical innovations in their skull related to feeding and food procurement, enabling a transition from a fish-like suction-based mode of prey capture to tetrapod-like biting, and an increase in orbit size and location" said Simões. "These changes prepared tetrapods to look for food on land and to explore new food resources not available to their fish relatives." (my bold)
***
"'What we've been finding in the last couple of years is that you have lots of anatomical changes during the construction of new animal body plans at short periods of geological time, generating high rates of anatomical evolution, like we're seeing with the first tetrapods. But in terms of number of species, they remained constrained and at really low numbers for a really long time, and only after tens of millions of years do they actually diversify and become higher in number of species. There's definitely a decoupling there," said Simões."
Comment: There are two ways to view this study, especially using my bolded comments. The Darwinist view describes a speedier selection process with no explanation of how that happens. In their view it just 'is' naturally. But note the rapid jaw changes in advance of actually hunting on land. Doesn't that suggest purposeful planning from a theistic viewpoint?
Interpretation can certain be valid at the eye of the classification of the beholder
Evolution: speciation related to satellite (junk) DNA
by David Turell , Monday, August 23, 2021, 19:09 (1186 days ago) @ David Turell
Species within a family are designated by their differing Satellite (junk) DNA:
https://phys.org/news/2021-08-so-called-junk-dna-key-role.html
"More than 10 percent of our genome is made up of repetitive, seemingly nonsensical stretches of genetic material called satellite DNA that do not code for any proteins. In the past, some scientists have referred to this DNA as "genomic junk."
"Over a series of papers spanning several years, however, Whitehead Institute Member Yukiko Yamashita and colleagues have made the case that satellite DNA is not junk, but instead has an essential role in the cell: it works with cellular proteins to keep all of a cell's individual chromosomes together in a single nucleus.
***
[They] "take these studies a step further, proposing that the system of chromosomal organization made possible by satellite DNA is one reason that organisms from different species cannot produce viable offspring.
***
"Researchers have known for years that satellite DNA is highly variable between species. "If you look at the chimpanzee genome and the human genome, the protein coding regions are, like, 98 percent, 99 percent identical," she says. "But the junk DNA part is very, very different."
***
"When the researchers deleted a protein called Prod that binds to a specific satellite DNA sequence in the fruit fly Drosophila melanogaster, the flies' chromosomes scattered outside of the nucleus into tiny globs of cellular material called micronuclei, and the flies died. "But we realized at this point that this [piece of] satellite DNA that was bound by the Prod protein was completely missing in the nearest relatives of Drosophila melanogaster," Jagannathan said. "It completely doesn't exist. So that's an interesting little problem."
***
"Taken together, these findings suggest that because satellite DNA mutates relatively frequently, the proteins that bind the satellite DNA and keep chromosomes together must evolve to keep up, leading each species to develop their own "strategy" for working with the satellite DNA. When two organisms with different strategies interbreed, a clash occurs, leading the chromosomes to scatter outside of the nucleus."
Comment: Species differences are maintained by their differing satellite/junk DNA. Another clue as to how speciation happens by genome changes.
Evolution: can work at high speed
by David Turell , Monday, May 30, 2022, 14:57 (907 days ago) @ David Turell
Another study sells adaptation speed as evolution:
https://www.sciencealert.com/evolution-may-be-happening-up-to-four-times-faster-than-we...
"New research suggests that Darwinian evolution could be happening up to four times faster than previously thought, based on an analysis of genetic variation. (my bold)
"The more genetic differences there are in a species, the faster evolution can happen, as certain traits die off and stronger ones get established. The team behind this latest study calls it the "fuel of evolution", and they looked at data on 19 different wild animal groups around the world.
***
"'The method gives us a way to measure the potential speed of current evolution in response to natural selection across all traits in a population," says evolutionary ecologist Timothée Bonnet, from the Australian National University.
***
"The average length of each field study was an impressive 30 years, with details of births, deaths, mating and offspring all recorded. The shortest was 11 years and the longest a whopping 63 years. That gave the researchers a grand total of 2.6 million hours of field data to combine with genetic information on each animal.
***
"As there's no baseline to work from – this is the first study of its type – the researchers emphasize there's not yet enough evidence to show species are evolving faster than in the past. What is clear is that there's more of this "fuel of evolution" than we thought.
"With the world and its wildlife reeling from the ongoing effects of climate change, knowing more about how quickly animals can adapt will be helpful in modeling which species will be able to survive and which won't.
"The concern is that as shifts in the global climate continue to accelerate, species won't be able to adapt in time. Even more comprehensive and longer term studies are going to be important to figure out exactly how quickly evolution is taking place.
"'This research has shown us that evolution cannot be discounted as a process which allows species to persist in response to environmental change," says Bonnet.
"What we can say is that evolution is a much more significant driver than we previously thought in the adaptability of populations to current environmental changes.'"
Comment: pure Darwin propaganda. True evolution progresses by speciation. This is simply the speed of existing species adapting to changes in environment and other factors. It could well be called epigenetic variation. Darwin expected these variations would lead to new species, but this study is not that result.
Evolution: as immaterial information
by David Turell , Tuesday, May 31, 2022, 15:36 (906 days ago) @ David Turell
A new evolutionary theory basedvon transferred information:
https://www.sciencedirect.com/science/article/pii/S0303264721001544
"Abstract
Most biologists agree that evolution is contingent on inherited information shaped by natural selection. This apparent consensus could be taken to indicate agreement on the forces shaping evolution, but vivid discussions reveal divergences on how evolution is perceived. The predominant Modern Synthesis (MS) paradigm holds the position that evolution occurs through random changes acting on genomic inheritance. However, studies from recent decades have revealed that evolutionary inheritance also includes DNA-methylation, RNA, symbionts, and culture, among other factors. This has fueled a demand of a broader evolutionary perspective, for example from the proponents of the Extended Evolutionary Synthesis (EES). Despite fundamental disagreements the different views agree that natural selection happens through dissimilar perpetuation of inheritable information. Yet, neither the MS, nor the ESS dwell extensively on the nature of hereditary information. We do - and conclude that information in and of itself is immaterial. We then argue that the quality upon which natural selection acts henceforth is also immaterial. Based on these notions, we arrive at the information-centric Information Continuum Model (ICM) of evolution. The ICM asserts that hereditary information is embedded in diverse physical forms (DNA, RNA, symbionts etc.) representing a continuum of evolutionary qualities, and that information may migrate between these physical forms. The ICM leaves theoretical exploration of evolution unrestricted by the limitations imposed by the individual physical forms wherein the hereditary information is embedded (e.g. genomes). ICM bestows us with a simple heuristic model that adds explanatory dimensions to be considered in the evolution of biological systems."
***
"We contest that ICM also have countless philosophical implications and find that the most fundamental question the model rises is: what defines life? According to ICM, living systems are manifestations of immaterial information propagating through time, in essence, by reorganizing matter. Also, according to ICM, evolution of life happens through differential propagation of diversifying immaterial information. We argue that the implication of this is that information that propagates is life and that reserving the quality of life for a subset of information embedded in physical forms with certain arbitrary, anthropogenically-defined attributes is inconsistent. However, discussions regarding the definitions of the interconnected conceptions of life, free will, and the nature of the self, have always thrived within the branches of Philosophy. Accordingly, we recognize that one may disagree with our definition of life, but defend the view that the concept of life has connotations related to values and rights and that it should therefore at least be defined consistently."
***
Summary
{"1. Information is immaterial by nature but must have a physical form to exist.
2. Inherited information may be found in many forms.
3. The forms have divergent properties and information may over time change its physical form.
4. We suggest the term ‘hereditome’ to refer to the sum of inherited information and its forms.
5. The substrate of natural selection is immaterial information.
6. The Information Continuum Model is a simple heuristic model that allows evolution and natural selection to be investigated without conceptual restrictions imposed by the properties of individual hereditome components.
7. The conceptual nature of Information Continuum Model enables it to serve as an interdisciplinary platform for collaboration between natural and social sciences."
Comment: This is totally consistent with my view that the material genome delivers immaterial information taht forms lifev adn makes it exist.
Evolution: as immaterial information
DAVID: A new evolutionary theory based on transferred information:
https://www.sciencedirect.com/science/article/pii/S0303264721001544
I’m afraid I find such articles totally off-putting. We are swamped with language, terms are left undefined, and if there really is a new evolutionary theory, I have no idea what it is. But I am a layman, and you seem to understand all this stuff, so do please correct any misunderstandings in the following howls of frustration:
QUOTE: Most biologists agree that evolution is contingent on inherited information shaped by natural selection.
This makes no sense at all to me. Even if we accept the concept of “information” as being central, evolution is contingent on inherited information changing itself, and the changes are not shaped by natural selection, which only functions when the changes have been made, i.e. by “selecting” those which prove to be advantageous. So the crucial question is what changes inherited information and how does this change the genes? Answer: “The predominant Modern Synthesis (MS) paradigm holds the position that evolution occurs through random changes acting on genomic inheritance. However, studies from recent decades have revealed that evolutionary inheritance also includes DNA-methylation, RNA, symbionts, and culture, among other factors.” Random changes could only mean that the genes produce and change the immaterial information. Culture can only mean that immaterial information changes the genes. How? No hint. Instead the authors delve into the nature of “inherited information”.
Then they suddenly decide that the crucial question is: “what defines life? According to ICM, living systems are manifestations of immaterial information propagating through time, in essence, by reorganizing matter. Also, according to ICM, evolution of life happens through differential propagation of diversifying immaterial information. We argue that the implication of this is that information that propagates is life.”
The very first item in the summary is: “Information is immaterial by nature but must have a physical form to exist.” So how does immaterial information create (let alone diversify) life by “propagating”, if it doesn’t exist until the material form already exists? Besides, there are plenty of physical forms that are full of “information” and are not alive, so the authors might just as well define life as the product of “information” that makes materials live. Not exactly edifying.
DAVID: This is totally consistent with my view that the material genome delivers immaterial information that forms life and makes it exist.
At least you have materials producing information, which makes sense, but it still doesn’t explain anything. We still don’t have a clue WHAT “information” makes materials live or how it does so, and if it doesn’t exist until the materials exist, the implication would be that it actually comes from the materials, which means we have materials producing information which animates or changes materials. But I really don’t know why we have to be constantly bombarded with the term “information” anyway, as if the word (which has multiple applications in multiple contexts) somehow solves all the mysteries. Nobody knows how materials become alive, and evolution is the process whereby living organisms have complexified and diversified into different forms – nobody knows how. We don’t have enough information.
Evolution: as immaterial information
by David Turell , Wednesday, June 01, 2022, 15:31 (905 days ago) @ dhw
edited by David Turell, Wednesday, June 01, 2022, 15:45
DAVID: A new evolutionary theory based on transferred information:
https://www.sciencedirect.com/science/article/pii/S0303264721001544dhw: I’m afraid I find such articles totally off-putting. We are swamped with language, terms are left undefined, and if there really is a new evolutionary theory, I have no idea what it is. But I am a layman, and you seem to understand all this stuff, so do please correct any misunderstandings in the following howls of frustration:
QUOTE: Most biologists agree that evolution is contingent on inherited information shaped by natural selection.
dhw:This makes no sense at all to me. Even if we accept the concept of “information” as being central, evolution is contingent on inherited information changing itself, and the changes are not shaped by natural selection, which only functions when the changes have been made, i.e. by “selecting” those which prove to be advantageous. So the crucial question is what changes inherited information and how does this change the genes? Answer: “The predominant Modern Synthesis (MS) paradigm holds the position that evolution occurs through random changes acting on genomic inheritance. However, studies from recent decades have revealed that evolutionary inheritance also includes DNA-methylation, RNA, symbionts, and culture, among other factors.” Random changes could only mean that the genes produce and change the immaterial information. Culture can only mean that immaterial information changes the genes. How? No hint. Instead the authors delve into the nature of “inherited information”.
Then they suddenly decide that the crucial question is: “what defines life? According to ICM, living systems are manifestations of immaterial information propagating through time, in essence, by reorganizing matter. Also, according to ICM, evolution of life happens through differential propagation of diversifying immaterial information. We argue that the implication of this is that information that propagates is life.”
The very first item in the summary is: “Information is immaterial by nature but must have a physical form to exist.” So how does immaterial information create (let alone diversify) life by “propagating”, if it doesn’t exist until the material form already exists? Besides, there are plenty of physical forms that are full of “information” and are not alive, so the authors might just as well define life as the product of “information” that makes materials live. Not exactly edifying.
DAVID: This is totally consistent with my view that the material genome delivers immaterial information that forms life and makes it exist.
dhw: At least you have materials producing information, which makes sense, but it still doesn’t explain anything. We still don’t have a clue WHAT “information” makes materials live or how it does so, and if it doesn’t exist until the materials exist, the implication would be that it actually comes from the materials, which means we have materials producing information which animates or changes materials. But I really don’t know why we have to be constantly bombarded with the term “information” anyway, as if the word (which has multiple applications in multiple contexts) somehow solves all the mysteries. Nobody knows how materials become alive, and evolution is the process whereby living organisms have complexified and diversified into different forms – nobody knows how. We don’t have enough information.
I know the authors are simply trying to convey the concept that DNA is a code that delivers information which using biochemistry creates life, as I noted above. Information theory studies the complexity of information. Bolded above is your comment which means you do not understand the point of information theory. Most physical forms contain oodles of repetitive info, not much meaning as in DNA. Google Shannon information theory to get a sense of how information is viewed today and can be applied to genome studies in creating life through biochemistry which follows instructions.
Of course, ID touts this approach, because only a mind can create meaningful information as instructions to be followed. You have struggled with info every time I bring it in. Shannon developed his math approach to guide computerization of telephone transmission and it was then carried over into understanding DNA code as carrying info in life. I appreciate your digging into this article. It means you are trying to recognize why you resist accepting this subject's importance to current theories about life. You have resisted every time over the years. Dip a while foot, not just a toe
Evolution: the bush is different if genomes used
by David Turell , Wednesday, June 01, 2022, 18:33 (904 days ago) @ David Turell
Comparative anatomy does not give the same branches in the bush of life as genome-DNA studies reveal:
https://phys.org/news/2022-06-evolutionary-trees-wrong.html
"New research led by scientists at the Milner Centre for Evolution at the University of Bath suggests that determining evolutionary trees of organisms by comparing anatomy rather than gene sequences is misleading. The study, published in Communications Biology, shows that we often need to overturn centuries of scholarly work that classified living things according to how they look.
"Since Darwin and his contemporaries in the 19th Century, biologists have been trying to reconstruct the "family trees" of animals by carefully examining differences in their anatomy and structure (morphology).
"However, with the development of rapid genetic sequencing techniques, biologists are now able to use genetic (molecular) data to help piece together evolutionary relationships for species very quickly and cheaply, often proving that organisms we once thought were closely related actually belong in completely different branches of the tree.
"For the first time, scientists at Bath compared evolutionary trees based on morphology with those based on molecular data, and mapped them according to geographical location.
"They found that the animals grouped together by molecular trees lived more closely together geographically than the animals grouped using the morphological trees.
"Matthew Wills, Professor of Evolutionary Paleobiology at the Milner Centre for Evolution at the University of Bath, says that "it turns out that we've got lots of our evolutionary trees wrong.
"'For over a hundred years, we've been classifying organisms according to how they look and are put together anatomically, but molecular data often tells us a rather different story."
"'Our study proves statistically that if you build an evolutionary tree of animals based on their molecular data, it often fits much better with their geographical distribution."
"'Where things live—their biogeography—is an important source of evolutionary evidence that was familiar to Darwin and his contemporaries."
"'For example, tiny elephant shrews, aardvarks, elephants, golden moles and swimming manatees have all come from the same big branch of mammal evolution—despite the fact that they look completely different from one another (and live in very different ways)."
"'Molecular trees have put them all together in a group called Afrotheria, so-called because they all come from the African continent, so the group matches the biogeography."
"The study found that convergent evolution—when a characteristic evolves separately in two genetically unrelated groups of organisms—is much more common than biologists previously thought.
"Professor Wills says that "we already have lots of famous examples of convergent evolution, such as flight evolving separately in birds, bats and insects, or complex camera eyes evolving separately in squid and humans."
"'But now with molecular data, we can see that convergent evolution happens all the time—things we thought were closely related often turn out to be far apart on the tree of life."
***
"Dr. Jack Oyston, Research Associate and first author of the paper, says that "the idea that biogeography can reflect evolutionary history was a large part of what prompted Darwin to develop his theory of evolution through natural selection, so it's pretty surprising that it hadn't really been considered directly as a way of testing the accuracy of evolutionary trees in this way before now."
"'What's most exciting is that we find strong statistical proof of molecular trees fitting better not just in groups like Afrotheria, but across the tree of life in birds, reptiles, insects and plants too.'"
Comment: Darwin had a surface view of what was really happening underneath in the genome codes. It is obvious Darwinism theory has to give in to this new approach.
Evolution: convergence of eyes
by David Turell , Monday, April 01, 2024, 16:16 (234 days ago) @ David Turell
Adapted to lifestyle:
https://www.sciencealert.com/the-weirdest-eyes-in-the-animal-kingdom-see-a-world-we-can...
"... different organisms have evolved to view the world differently, with eye structures and configurations optimized for various kinds of existence.
"...the horizontal pupils of herbivores give them a panoramic view of their surroundings, which helps both to see predators coming, and to avoid obstacles as the animals make an escape. Meanwhile, nocturnal predators have vertical pupils to maximize their night vision.
"No other animal has a pupil quite like the cuttlefish. It's shaped like a W, a trait biologists have determined helps the animals balance a vertically uneven field of light, which is common in the watery depths they inhabit. But that's just the start.
"Cuttlefish only have one type of photoreceptor, which should mean they can only see in monochrome. Yet those strange, wide pupils of cuttlefish and other cephalopods could facilitate an entirely different way of seeing color – by using the way light passing through a prism splits into a rainbow.
***
"Unlike other cephalopods, though, cuttlefish eyes can swivel, allowing them to see the world in 3D as well; recently, scientists found these swivelly eyes result in stereoscopic vision, giving cuttlefish yet another advantage in their environment.
***
"Cephalopods only have one photoreceptor type, as we have established. Humans have four, three cones and a rod, which means we have color sensitivities at three peak wavelengths, what we call trichromatic vision. (The rod is for low-light vision.)
"Birds have six – four cones giving tetrachromatic vision, a rod, and an unusual double cone for non-colored motion perception.
"In addition, a protein in their eyes could allow them to see magnetic fields. Migratory birds can navigate extraordinarily well; scientists narrowed it down to a class of proteins called cryptochromes, which are sensitive to blue light.
"Birds' magnetoreception – that is, their ability to perceive magnetic fields – seems dependent on blue light, suggesting that the sense may be vision-based. There's the distinct possibility that this magnetic filter for the color blue is the result of a quantum quirk. More recent lab studies have shown how a magnetic field affects a quantum property of cryptochromes, governing their electrons.
"Behold the largescale four-eyes (Anableps anableps), of the four-eyed fish genus.
"This fascinating beastie doesn't actually have four eyes – but its two eyes have evolved an incredible adaptation. Their ecological niche is the surface of the water, where they spend the majority of their time, preying on insects that hover around aquatic ecosystems.
"Their eyes are situated on top of their heads, all the better to see the flying bugs in an aerial environment. But a portion of their optic organ sits below the surface of the water, and this is where things get interesting: each pupil is divided into two halves, one of which sits above the waterline (dorsal), while the other sits below (ventral), pointing downwards into the murky depths.
"In this way, the fish can simultaneously see above and below the water – environments through which light propagates differently – to watch for both predators and prey. The thickness of the lens varies too, to accommodate the different refractive indices of aerial and aquatic media, as does the thickness of the corneal epithelium.
"And the proteins in the retinal photoreceptor cells are slightly different as well – more sensitive to green light in the dorsal retina, and more sensitive to yellow light in the ventral retina. Since the fish often live in muddy environments, like mangroves, this is thought to improve vision in murky waters.
***
"Mantis shrimps of the order Stomatopoda, have 16 in their compound peepers. What do they do with these photoreceptors? They see. They see all of the things...They can see five different ultraviolet frequency bands.
"In addition, mantis shrimps can see polarized light; that is, the orientation of the oscillations of the wave of propagating light. Many animals can see linearly polarized light, including cuttlefish. Mantis shrimps are the only animals that can see circularly polarized light that we know of.
"Each eye is mounted on a stalk, and can be moved independently. And each eye has the ability to perceive depth. Humans rely on binocular vision for depth perception. Mantis shrimps only need one.
"Chitons have eyes, but they're embedded in their armor, and made of mineral; more specifically, a type of calcium carbonate known as aragonite.
"The simple eyes of chitons, which litter the surface of their shells alongside hundreds of sensory organs known as aesthetes, consist of an aragonite lens covered by a cornea, and some sort of retina; to the surprise of scientists, these tiny primitive organs can actually resolve images.
"Trilobites, for example, also had mineral eyes, with lenses made of calcite. These extinct creatures had the first truly complex eyes that we know of, so understanding them can tell us a lot about how vision evolved on Earth in all its dazzling complexity."
Comment: see the illustrations. Adaptations with a purpose. Designed.
Evolution: as immaterial information
DAVID: I know the authors are simply trying to convey the concept that DNA is a code that delivers information which using biochemistry creates life, as I noted above. Information theory studies the complexity of information. Bolded above is your comment which means you do not understand the point of information theory. Most physical forms contain oodles of repetitive info, not much meaning as in DNA. Google Shannon information theory to get a sense of how information is viewed today and can be applied to genome studies in creating life through biochemistry which follows instructions.
Of course, ID touts this approach, because only a mind can create meaningful information as instructions to be followed. You have struggled with info every time I bring it in. Shannon developed his math approach to guide computerization of telephone transmission and it was then carried over into understanding DNA code as carrying info in life. I appreciate your digging into this article. It means you are trying to recognize why you resist accepting this subject's importance to current theories about life. You have resisted every time over the years. Dip a while foot, not just a toe.
There is no point in my repeating the detailed problems I raised yesterday, since you have ignored them all with this collection of generalizations. The only direct reference you have made to my response is:
dhw: Besides, there are plenty of physical forms that are full of “information” and are not alive,so the authors might just as well define life as the product of “information” that makes materials live. Not exactly edifying.
You say I don’t understand the point, because “most physical forms contain oodles of repetitive info, not much meaning as in DNA”. How does this contradict my own comment? If you really want to help me, then please answer the question that preceded it: how does immaterial information create (let alone diversify) life by “propagating”, if it doesn’t exist until the material form already exists?
Evolution: as immaterial information
by David Turell , Thursday, June 02, 2022, 18:41 (903 days ago) @ dhw
DAVID: I know the authors are simply trying to convey the concept that DNA is a code that delivers information which using biochemistry creates life, as I noted above. Information theory studies the complexity of information. Bolded above is your comment which means you do not understand the point of information theory. Most physical forms contain oodles of repetitive info, not much meaning as in DNA. Google Shannon information theory to get a sense of how information is viewed today and can be applied to genome studies in creating life through biochemistry which follows instructions.
Of course, ID touts this approach, because only a mind can create meaningful information as instructions to be followed. You have struggled with info every time I bring it in. Shannon developed his math approach to guide computerization of telephone transmission and it was then carried over into understanding DNA code as carrying info in life. I appreciate your digging into this article. It means you are trying to recognize why you resist accepting this subject's importance to current theories about life. You have resisted every time over the years. Dip a while foot, not just a toe.dhw: There is no point in my repeating the detailed problems I raised yesterday, since you have ignored them all with this collection of generalizations. The only direct reference you have made to my response is:
dhw: Besides, there are plenty of physical forms that are full of “information” and are not alive,so the authors might just as well define life as the product of “information” that makes materials live. Not exactly edifying.You say I don’t understand the point, because “most physical forms contain oodles of repetitive info, not much meaning as in DNA”. How does this contradict my own comment? If you really want to help me, then please answer the question that preceded it: how does immaterial information create (let alone diversify) life by “propagating”, if it doesn’t exist until the material form already exists?
You have described the problem if evolution is viewed as a natural event. Which came first chicken or egg??? The answer is both must arrive together!!! The 'RNA first' theory makes the absurd approach that RNA is made naturally and suddenly the code has meaning!! That is why I follow the ID theorists. You are floundering because that means a mental agent did the creating. For me, all the deductive reasoning I use goes back to Sherlock, so if all else is impossible, the imporbable must exist. Like it or not, life runs on the information in the DNA of the genome and its other layers. The code contains the needed information which only living organisms can interpret.
Evolution: as immaterial information
dhw: You say I don’t understand the point, because “most physical forms contain oodles of repetitive info, not much meaning as in DNA”. How does this contradict my own comment? If you really want to help me, then please answer the question that preceded it: how does immaterial information create (let alone diversify) life by “propagating”, if it doesn’t exist until the material form already exists?
DAVID: You have described the problem if evolution is viewed as a natural event. Which came first chicken or egg??? The answer is both must arrive together!!! The 'RNA first' theory makes the absurd approach that RNA is made naturally and suddenly the code has meaning!! That is why I follow the ID theorists. You are floundering because that means a mental agent did the creating. For me, all the deductive reasoning I use goes back to Sherlock, so if all else is impossible, the imporbable must exist. Like it or not, life runs on the information in the DNA of the genome and its other layers. The code contains the needed information which only living organisms can interpret.
I am not floundering. Your response confirms most of the objections I raised in my original comments. Of course life depends on the workings of DNA, and of course only living organisms can “interpret” DNA. But you still have your DNA when you are dead, and no amount of blather about “information” can tell us what makes bodies live, or what makes bodies capable of evolving into different bodies. You can and do follow ID theorists without even mentioning the word “information”. The question I asked you typifies what to me is the sheer muddle that emerges from an article about "information" that is supposed to be explanatory. Once you yourself even provided us with a thread entitled “Information as the source of life”! Whereas what you really mean is that your God is the source of life. You might as well rename your God “Information” if the concept is so central to your thinking.
Transferred from “More miscellany”:
dhw: As a matter of interest, do all your information theorists believe in your God as the provider of all information?
DAVID: All ID folks who use information teory do believe in a designer.
All ID folks believe in a designer. I asked you if all information theorists believe in a designer!
Evolution: as immaterial information
by David Turell , Friday, June 03, 2022, 16:31 (902 days ago) @ dhw
dhw: You say I don’t understand the point, because “most physical forms contain oodles of repetitive info, not much meaning as in DNA”. How does this contradict my own comment? If you really want to help me, then please answer the question that preceded it: how does immaterial information create (let alone diversify) life by “propagating”, if it doesn’t exist until the material form already exists?
DAVID: You have described the problem if evolution is viewed as a natural event. Which came first chicken or egg??? The answer is both must arrive together!!! The 'RNA first' theory makes the absurd approach that RNA is made naturally and suddenly the code has meaning!! That is why I follow the ID theorists. You are floundering because that means a mental agent did the creating. For me, all the deductive reasoning I use goes back to Sherlock, so if all else is impossible, the imporbable must exist. Like it or not, life runs on the information in the DNA of the genome and its other layers. The code contains the needed information which only living organisms can interpret.
dhw: I am not floundering. Your response confirms most of the objections I raised in my original comments. Of course life depends on the workings of DNA, and of course only living organisms can “interpret” DNA. But you still have your DNA when you are dead, and no amount of blather about “information” can tell us what makes bodies live, or what makes bodies capable of evolving into different bodies. You can and do follow ID theorists without even mentioning the word “information”. The question I asked you typifies what to me is the sheer muddle that emerges from an article about "information" that is supposed to be explanatory. Once you yourself even provided us with a thread entitled “Information as the source of life”! Whereas what you really mean is that your God is the source of life. You might as well rename your God “Information” if the concept is so central to your thinking.
To clarify my belief: the information that makes life emerge through functional blichemistry comes from a designing mind, given the name God in Western religions.
Transferred from “More miscellany”:dhw: As a matter of interest, do all your information theorists believe in your God as the provider of all information?
DAVID: All ID folks who use information theory do believe in a designer.
dhw: All ID folks believe in a designer. I asked you if all information theorists believe in a designer!
I don't know.
Evolution: development of neuropeptides
by David Turell , Friday, June 03, 2022, 19:55 (902 days ago) @ David Turell
Appeared way before brains appeared:
https://www.quantamagazine.org/brain-signal-proteins-evolved-before-animals-did-20220603/
"Our human brains can seem like a crowning achievement of evolution, but the roots of that achievement run deep: The modern brain arose from hundreds of millions of years of incremental advances in complexity. Evolutionary biologists have traced that progress back through the branch of the animal family tree that includes all creatures with central nervous systems, the bilaterians, but it is clear that fundamental elements of the nervous system existed much earlier.
"How much earlier has now been made dramatically clear by a recent discovery by a team of researchers at the University of Exeter in the United Kingdom. They found that the chemical precursors of two important neurotransmitters, or signaling molecules used in nervous systems, appear in all the major animal groups that preceded creatures with central nervous systems.
"The big surprise, however, is that these molecules are also present in single-celled relatives of animals, called choanoflagellates. This finding shows that animal neuropeptides originated before the evolution of even the very first animals.
***
"A variety of molecules very similar to neuropeptides are made by nearly all the early animal groups, including the ctenophores (comb jellies) and the cnidaria (jellyfish, corals and sea anemones). Even the extremely simple animals called placozoans, which have no cells resembling neurons, make neuropeptides. Sponges seemed to be the only exception, which is why it was generally thought that animal neuropeptides originated in cnidarians or ctenophores, after sponges branched away from the rest of the animal tree.
***
"...as he [Yañez-Guerra] began looking for them farther down the animal tree, he stumbled on the realization that choanoflagellates made protein precursors of two mature neuropeptides, phoenixin and nesfatin.
"Their presence in choanoflagellates was a surprise because neuropeptides typically appear in the context of sender and receiver neurons. “In a unicellular organism, it’s more difficult to make sense of,” Yañez-Guerra said. “This shows that these neuronal molecules started evolving even before the need for this extensive communication between cell and cell. That’s why it was kind of shocking.” (my bold)
***
"A further search of the gene expression data confirmed Yañez-Guerra’s hunch that phoenixin and nesfatin might be the keys to understanding neuropeptide evolution. Not only were the precursor peptides present in the choanoflagellates, but they were also present in all the early animal groups — even the sponges, where they had been overlooked.
"Given that the precursor molecules in the choanoflagellates are so directly connected to these neuropeptides found in all animals, Burkhardt explained, “The last common ancestor of all animals likely had at least two neuropeptides.”
***
"The neuropeptides aren’t the only thing that’s unique about ctenophore nervous systems: The structures of their neural networks are so unusual that researchers suspect they evolved independently of those seen in humans and other animals. Why ctenophores do things differently is a mystery, but it’s clear that nervous systems went through a period of tremendous experimentation and innovation early in their evolution — and that at least some of that experimentation began before animals even existed."
Comment: this is a fantastic discovery. It shows that the evolutionary process depended upon precursors of biochemicals be developed long before needed in new applications (organ forms). The idea Darwin had to study evolution by following comparative anatomy has been discarded by biochemical studiesv and genomic trees being devoloped. dhw has persisted in sticking with the antiquated Darwinian approach of form development which is obviously very discontinuous as the Cabrian gap shows.
Evolution: as immaterial information
DAVID: You have described the problem if evolution is viewed as a natural event. Which came first chicken or egg??? The answer is both must arrive together!!! The 'RNA first' theory makes the absurd approach that RNA is made naturally and suddenly the code has meaning!! That is why I follow the ID theorists. You are floundering because that means a mental agent did the creating. For me, all the deductive reasoning I use goes back to Sherlock, so if all else is impossible, the imporbable must exist. Like it or not, life runs on the information in the DNA of the genome and its other layers. The code contains the needed information which only living organisms can interpret.
dhw: I am not floundering. Your response confirms most of the objections I raised in my original comments. Of course life depends on the workings of DNA, and of course only living organisms can “interpret” DNA. But you still have your DNA when you are dead, and no amount of blather about “information” can tell us what makes bodies live, or what makes bodies capable of evolving into different bodies. You can and do follow ID theorists without even mentioning the word “information”. The question I asked you typifies what to me is the sheer muddle that emerges from an article about "information" that is supposed to be explanatory. Once you yourself even provided us with a thread entitled “Information as the source of life”! Whereas what you really mean is that your God is the source of life. You might as well rename your God “Information” if the concept is so central to your thinking.
DAVID: To clarify my belief: the information that makes life emerge through functional biochemistry comes from a designing mind, given the name God in Western religions.
You didn’t need to clarify that. What needs clarifying is the muddle created by this article and others, which arises from placing “information” (undefined and undifferentiated) at the heart of still unsolved mysteries such as the origin of life and the means whereby organisms can change their structure in order to adapt and innovate, and so create new organs and new species. Among other questions, I asked: “How does immaterial information create (let alone diversify) life by “propagating” if it doesn’t exist until the material form already exists?” The authors offer no explanation. They simply conclude: “information that propagates is life”. Can you follow this argument? As far as you are concerned, your God creates the material form and somehow makes it live. Nobody knows how. The information contained in DNA is still present when the material form is dead. Similarly, nobody knows how bodies change into new bodies. But apparently it’s all done by information “propagating”. If you understand this, please tell me what it means. If you can’t, then please stop defending arguments you don’t understand.
Transferred from “More miscellany”:
dhw: As a matter of interest, do all your information theorists believe in your God as the provider of all information?
DAVID: All ID folks who use information theory do believe in a designer.
dhw: All ID folks believe in a designer. I asked you if all information theorists believe in a designer!
DAVID: I don't know.
Then there is no point in assuming that information theory favours theism.
Evolution: as immaterial information
by David Turell , Saturday, June 04, 2022, 15:32 (902 days ago) @ dhw
edited by David Turell, Saturday, June 04, 2022, 15:37
DAVID: To clarify my belief: the information that makes life emerge through functional biochemistry comes from a designing mind, given the name God in Western religions.
dhw: You didn’t need to clarify that. What needs clarifying is the muddle created by this article and others, which arises from placing “information” (undefined and undifferentiated) at the heart of still unsolved mysteries such as the origin of life and the means whereby organisms can change their structure in order to adapt and innovate, and so create new organs and new species. Among other questions, I asked: “How does immaterial information create (let alone diversify) life by “propagating” if it doesn’t exist until the material form already exists?” The authors offer no explanation. They simply conclude: “information that propagates is life”. Can you follow this argument? As far as you are concerned, your God creates the material form and somehow makes it live. Nobody knows how. The information contained in DNA is still present when the material form is dead. Similarly, nobody knows how bodies change into new bodies. But apparently it’s all done by information “propagating”. If you understand this, please tell me what it means. If you can’t, then please stop defending arguments you don’t understand.
The muddle is yours, since your questions are easily answered if you accept a designer in charge of putting evertything together. The question in red shows the impossibility of chance natural events. The next comment: "information that propagates is life" can be understood by recognizing that life obviously propogates using its onboard information/instructions. That is simply a direct observation of fact. The need for a source of that arrangement, you deny, by your set of puzlements. Next: "The information contained in DNA is still present when the material form is dead", is true. Only living material interprets DNA. Here we can agree. Then you end with: " please stop defending arguments you don’t understand". What a turnabout!!! I fully and logically recognize the need for a controlling operative mind, which you refuse to understand as you revert to natural chance as the driving mechnaism. Pure plea from Darwinism. No wonder you are muddled. God does it and doesn't tell us how, so we research to reach as much understanding as we can.
Transferred from “More miscellany”:dhw: As a matter of interest, do all your information theorists believe in your God as the provider of all information?
DAVID: All ID folks who use information theory do believe in a designer.
dhw: All ID folks believe in a designer. I asked you if all information theorists believe in a designer!
DAVID: I don't know.
dhw: Then there is no point in assuming that information theory favours theism.
I have no idea if Claude Shannon was a believer, but all ID folks use his theories, and all of them are theists. Your weird point is?
Evolution: pattern of stasis and sprint
by David Turell , Saturday, June 04, 2022, 21:02 (901 days ago) @ David Turell
All through the period of evolution from start to now, he uses Chixculub extinction as an example:
https://aeon.co/essays/catastrophe-drives-evolution-but-life-resides-in-the-pauses?utm_...
"While dinosaurs get most of the attention, they weren’t the only ones to disappear. More than half of all life on Earth – from plankton to pterosaurs – perished following the impact of the Chicxulub asteroid that created a 150 km-wide crater in the Yucatán peninsula. It took 30,000 years for life to re-emerge in the fossil record, and another 4 to 9 million years to return to pre-impact levels.
***
"This postapocalyptic period was characterised by novelty. New genetic combinations resulting from crossbreeding would have added to an array of anomalies caused by developing in a stressful environment. The first generation of the new world order wouldn’t copy the habits that had enabled their lineages’ survival for aeons; instead, they would copy habits their parents had improvised out of the necessity of the moment. Emerging from the ashes, the biotic world looked nothing like the one before the asteroid struck. It would take millions of years for pre-impact levels of species diversity to rebound and for ecosystems to stabilise.
"When things did settle back down, the pace of evolution would return to a virtual standstill. That’s the pattern we observe in the fossil record: disruption, change and then long periods of stasis.
***
"But this persistent focus on natural selection as the sole mechanism of adaptive evolution has always been a sticking point. It can’t properly explain how anything new arises. After all, natural selection is a process that eliminates unfit variants – it doesn’t create, but changes the prevalence of what’s already there. Instead, novelty must come from the purely random process of genetic mutation. The problem is that when new mutations appear, they’re usually not a good thing. They are more likely to disrupt well-adapted systems than to improve them, especially if they have a big effect. The upshot is that the evolution of something new, such as eyes or feathers, requires a heck of a long waiting time. Not only is there a long wait for a beneficial mutation to come along, but then there’s the long process of accumulating enough of them to build up, step by step, a complex new structure. (my bold)
***
"However, there’s been a growing acceptance of this pattern among evolutionary biologists and theorists over the years, as new studies and techniques reveal it again and again across diverse organisms. For example, Stevan J Arnold, an evolutionary biologist at Oregon State University, and his colleagues looked at patterns of body size evolution in vertebrates ...They found that bursts of body-size evolution occur only on the order of every million years or so.
***
"The pervasiveness of this pattern means that modern-day evolutionary biologists now have two enigmas to explain. First, what prevents species from changing for the majority of their existence? And second, when they do change, how does it happen so fast?
***
"At moderate scales, perhaps glacial cycles or other gradual environmental changes push populations back and forth around a mean, but over very long timescales, there is little net evolutionary change.
"Examples of such dynamic stability, where a system shows fluctuations around a mean but little net change over time, are everywhere...We see it in brain waves, or in ecological systems where the number of individuals in a population or species in a community fluctuates across years, but overall remains steady.
***
"Such events are rare and occur only every million years or more – but when they do, the system must either change or cease to function. In evolutionary terms, that means it must evolve or go extinct. This suggests that macroevolutionary patterns can’t be understood by simply adding up microevolutionary changes over a long period of time because catastrophic events, such as the Chicxulub meteor, don’t occur on a constant gradual basis. In fact, all the evidence suggests that major evolutionary changes can occur in a blink of a geological eye and persist only when systems suffer a major disruption and are forced to massively reorganise.
***
"The pattern of evolutionary stasis dominates the history of life on Earth.
***
"Most importantly, viewing evolution through a systems lens fundamentally changes how we view the story of life on Earth. It’s not a story of the constant struggle for existence. Rather, it’s a story that resides in the pauses – the uneventful interludes, where components of the systems maintain the status quo, and change necessarily comes with painful and extreme disruption."
Comment: of course, he mentioned Punc-inc from Gould as being widely accepted. Note my bold with the true view of Natural selection being passive, not inventive. The author doesn't solve the problem of speciation nor does he recognize the possibility of a desgner running the show. The main point is evolution is filled with gaps.
Evolution: as immaterial information
DAVID: To clarify my belief: the information that makes life emerge through functional biochemistry comes from a designing mind, given the name God in Western religions.
dhw: You didn’t need to clarify that. What needs clarifying is the muddle created by this article and others, which arises from placing “information” (undefined and undifferentiated) at the heart of still unsolved mysteries such as the origin of life and the means whereby organisms can change their structure in order to adapt and innovate, and so create new organs and new species. Among other questions, I asked: red“How does immaterial information create (let alone diversify) life by “propagating” if it doesn’t exist until the material form already exists?”red The authors offer no explanation. They simply conclude: “information that propagates is life”. Can you follow this argument? As far as you are concerned, your God creates the material form and somehow makes it live. Nobody knows how. The information contained in DNA is still present when the material form is dead. Similarly, nobody knows how bodies change into new bodies. But apparently it’s all done by information “propagating”. If you understand this, please tell me what it means. If you can’t, then please stop defending arguments you don’t understand.
DAVID: The muddle is yours, since your questions are easily answered if you accept a designer in charge of putting evertything together. The question in red shows the impossibility of chance natural events. The next comment: "information that propagates is life" can be understood by recognizing that life obviously propogates using its onboard information/instructions.
You have completely missed the point. I am attacking the vagueness of the article, and you are providing your own theory (which I already mentioned – now in bold) to make up for the muddle. Once more: If information doesn’t exist until it has a material form, how can it create life by “propagating”? The word means reproduce or spread, so information that reproduces and spreads itself is life, although it doesn’t exist until it has a material form. Why not cells or even materials that reproduce and spread themselves are life? The authors don’t explain anything. At least ID, like yourself, offers us a clear theory: living forms are so complex that they cannot be the product of chance, and therefore must be the product of an intelligent designer. You don’t even need to mess about with "information" and “propagating”. The terms need defining, and I cannot see how they explain the source of life or the mechanisms of evolution.
DAVID: I fully and logically recognize the need for a controlling operative mind, which you refuse to understand as you revert to natural chance as the driving mechnaism. Pure plea from Darwinism. No wonder you are muddled. God does it and doesn't tell us how, so we research to reach as much understanding as we can.
Nowhere have I reverted to “natural chance”, and nowhere do the authors mention chance or design or God. I have not offered any theory at all. I have simply criticized the article because I find it muddling.
Transferred from “More miscellany”:
dhw: As a matter of interest, do all your information theorists believe in your God as the provider of all information?
DAVID: All ID folks who use information theory do believe in a designer.
dhw: All ID folks believe in a designer. I asked you if all information theorists believe in a designer!
DAVID: I don't know.
dhw: Then there is no point in assuming that information theory favours theism.
DAVID: I have no idea if Claude Shannon was a believer, but all ID folks use his theories, and all of them are theists. Your weird point is?
That information theory as presented in this article and every other article you have reproduced on the subject leads to confusion and not clarification in its approach to the issues it is supposed to be explaining.
Evolution: as immaterial information
by David Turell , Sunday, June 05, 2022, 15:39 (901 days ago) @ dhw
dhw: You have completely missed the point. I am attacking the vagueness of the article, and you are providing your own theory (which I already mentioned – now in bold) to make up for the muddle. Once more: If information doesn’t exist until it has a material form, how can it create life by “propagating”? The word means reproduce or spread, so information that reproduces and spreads itself is life, although it doesn’t exist until it has a material form. Why not cells or even materials that reproduce and spread themselves are life?
You are fussing about their terminology. Their point is the only way life can work is that it must interpret the information that guides its processes. They are presenting it as it supportd the theory yhou commment on below from ID.
dhw: The authors don’t explain anything. At least ID, like yourself, offers us a clear theory: living forms are so complex that they cannot be the product of chance, and therefore must be the product of an intelligent designer. You don’t even need to mess about with "information" and “propagating”. The terms need defining, and I cannot see how they explain the source of life or the mechanisms of evolution.
DAVID: I fully and logically recognize the need for a controlling operative mind, which you refuse to understand as you revert to natural chance as the driving mechnaism. Pure plea from Darwinism. No wonder you are muddled. God does it and doesn't tell us how, so we research to reach as much understanding as we can.
dhw: Nowhere have I reverted to “natural chance”, and nowhere do the authors mention chance or design or God. I have not offered any theory at all. I have simply criticized the article because I find it muddling.
I think you find it muddling becasue you and I don't have the same background in information theory as prtesented by ID
Evolution: as immaterial information
dhw: You have completely missed the point. I am attacking the vagueness of the article, and you are providing your own theory (which I already mentioned – now in bold) to make up for the muddle. Once more: If information doesn’t exist until it has a material form, how can it create life by “propagating”? The word means reproduce or spread, so information that reproduces and spreads itself is life, although it doesn’t exist until it has a material form. Why not cells or even materials that reproduce and spread themselves are life?
DAVID: You are fussing about their terminology. Their point is the only way life can work is that it must interpret the information that guides its processes. They are presenting it as it supports the theory you commment on below from ID.
Of course I’m fussing about their terminology! We have obviously not been reading the same article. Here is the section preceding their attempt to define life, which I took as my example of sheer muddle.
QUOTE: Despite fundamental disagreements the different views agree that natural selection happens through dissimilar perpetuation of inheritable information. Yet, neither the MS, nor the ESS dwell extensively on the nature of hereditary information. We do - and conclude that information in and of itself is immaterial.
Surprise, surprise, information is immaterial. If information doesn’t exist until it has a material form, but life is “information that propagates”, what – according to you (or the authors) - interprets what? “Information that propagates” (= life) interprets information? Where have you found mention of chance v. design? How does this conclusion support ID?
QUOTE: “We then argue that the quality upon which natural selection acts henceforth is also immaterial. Based on these notions, we arrive at the information-centric Information Continuum Model (ICM) of evolution. The ICM asserts that hereditary information is embedded in diverse physical forms (DNA, RNA, symbionts etc.) representing a continuum of evolutionary qualities, and that information may migrate between these physical forms. The ICM leaves theoretical exploration of evolution unrestricted by the limitations imposed by the individual physical forms wherein the hereditary information is embedded (e.g. genomes). ICM bestows us with a simple heuristic model that adds explanatory dimensions to be considered in the evolution of biological systems."
So now we have information migrating independently of (unrestricted by) the materials without which it can’t exist. So hey ho, evolution takes place independently of the genome, and this offers us “explanatory dimensions”. Again: where have you found the dismissal of chance and the inevitability of a designer?
QUOTE: "We contest that ICM also have countless philosophical implications and find that the most fundamental question the model rises [sic] is: what defines life?"
That is the example I discussed earlier. Their answer: “information that propagates is life.” Yet again: where have you found the impossibility of chance and support for ID?
DAVID: I fully and logically recognize the need for a controlling operative mind, which you refuse to understand as you revert to natural chance as the driving mechnaism. Pure plea from Darwinism. No wonder you are muddled. God does it and doesn't tell us how, so we research to reach as much understanding as we can.
dhw: Nowhere have I reverted to “natural chance”, and nowhere do the authors mention chance or design or God. I have not offered any theory at all. I have simply criticized the article because I find it muddling.
DAVID: I think you find it muddling becasue you and I don't have the same background in information theory as presented by ID.
I can only discuss the article you have reproduced. It has nothing to do with ID. Please respond to the points I have raised instead of repeating your own beliefs and then attacking me for points I have never made (chance as the driving mechanism) – and in fact have constantly rejected since the very beginning of our discussions.
Evolution: as immaterial information
by David Turell , Monday, June 06, 2022, 15:13 (900 days ago) @ dhw
dhw: Surprise, surprise, information is immaterial. If information doesn’t exist until it has a material form, but life is “information that propagates”, what – according to you (or the authors) - interprets what? “Information that propagates” (= life) interprets information? Where have you found mention of chance v. design? How does this conclusion support ID?
Information can exist without interpretation: I look up a word in a thesaurus and interpret. Here immaterial information is in material form. This is what the genome is, immaterial informaton expressed in its coded (material) form, interpreteted by it living cell.
QUOTE: “We then argue that the quality upon which natural selection acts henceforth is also immaterial. Based on these notions, we arrive at the information-centric Information Continuum Model (ICM) of evolution. The ICM asserts that hereditary information is embedded in diverse physical forms (DNA, RNA, symbionts etc.) representing a continuum of evolutionary qualities, and that information may migrate between these physical forms. The ICM leaves theoretical exploration of evolution unrestricted by the limitations imposed by the individual physical forms wherein the hereditary information is embedded (e.g. genomes). ICM bestows us with a simple heuristic model that adds explanatory dimensions to be considered in the evolution of biological systems."dhw: So now we have information migrating independently of (unrestricted by) the materials without which it can’t exist. So hey ho, evolution takes place independently of the genome, and this offers us “explanatory dimensions”. Again: where have you found the dismissal of chance and the inevitability of a designer?
ID produces this to show only a designer can do this, must exist and not by chance. I am interpreting the article in an ID view.
QUOTE: "We contest that ICM also have countless philosophical implications and find that the most fundamental question the model rises [sic] is: what defines life?"dhw: That is the example I discussed earlier. Their answer: “information that propagates is life.” Yet again: where have you found the impossibility of chance and support for ID?
ID does not support chance. I know ID, do you?
DAVID: I fully and logically recognize the need for a controlling operative mind, which you refuse to understand as you revert to natural chance as the driving mechnaism. Pure plea from Darwinism. No wonder you are muddled. God does it and doesn't tell us how, so we research to reach as much understanding as we can.dhw: Nowhere have I reverted to “natural chance”, and nowhere do the authors mention chance or design or God. I have not offered any theory at all. I have simply criticized the article because I find it muddling.
DAVID: I think you find it muddling because you and I don't have the same background in information theory as presented by ID.
dhw: I can only discuss the article you have reproduced. It has nothing to do with ID. Please respond to the points I have raised instead of repeating your own beliefs and then attacking me for points I have never made (chance as the driving mechanism) – and in fact have constantly rejected since the very beginning of our discussions.
Come on, you consantly give credence to chance, and i give that absurdity (IMHO) a poke.
Evolution: as immaterial information
dhw: Surprise, surprise, information is immaterial. If information doesn’t exist until it has a material form, but life is “information that propagates”, what – according to you (or the authors) - interprets what? “Information that propagates” (= life) interprets information? Where have you found mention of chance v. design? How does this conclusion support ID?
DAVID:Information can exist without interpretation: I look up a word in a thesaurus and interpret. Here immaterial information is in material form. This is what the genome is, immaterial informaton expressed in its coded (material) form, interpreteted by it living cell.
Of course information exists without interpretation. I was replying to your own comment: “The only way life can work is that it must interpret the information that guides its processes.” But if life is “information that propagates”, you are telling us that the only way information that propagates can work, is that information that propagates must interpret the information that guides its processes. (And we mustn’t forget that information only exists when it has a material form.) Don’t you find all this a little confusing?
QUOTE: “We then argue that the quality upon which natural selection acts henceforth is also immaterial. Based on these notions, we arrive at the information-centric Information Continuum Model (ICM) of evolution. The ICM asserts that hereditary information is embedded in diverse physical forms (DNA, RNA, symbionts etc.) representing a continuum of evolutionary qualities, and that information may migrate between these physical forms. The ICM leaves theoretical exploration of evolution unrestricted by the limitations imposed by the individual physical forms wherein the hereditary information is embedded (e.g. genomes). ICM bestows us with a simple heuristic model that adds explanatory dimensions to be considered in the evolution of biological systems."
dhw: So now we have information migrating independently of (unrestricted by) the materials without which it can’t exist. So hey ho, evolution takes place independently of the genome, and this offers us “explanatory dimensions”. Again: where have you found the dismissal of chance and the inevitability of a designer?
DAVID: ID produces this to show only a designer can do this, must exist and not by chance. I am interpreting the article in an ID view.
And I am asking what the various statements about “information” and “propagation” are supposed to mean! There is nothing in the article about ID or chance, and you have not explained how evolution, which entails one form of life turning into another, can take place through immaterial information – which can only exist in material form - migrating independently of the materials in which it is embedded.
QUOTE: "We contest that ICM also have countless philosophical implications and find that the most fundamental question the model rises [sic] is: what defines life?"
dhw: That is the example I discussed earlier. Their answer: “information that propagates is life.” Yet again: where have you found the impossibility of chance and support for ID?
DAVID:ID does not support chance. I know ID, do you?
Of course it doesn’t! But the article is not about chance!!! It is about “Evolution as immaterial information”, and since you clearly can’t answer any of my precise objections to the authors’ theories, all you want to talk about is chance and ID, which are never even mentioned in the article!
DAVID: I fully and logically recognize the need for a controlling operative mind, which you refuse to understand as you revert to natural chance as the driving mechnaism. Pure plea from Darwinism. No wonder you are muddled. God does it and doesn't tell us how, so we research to reach as much understanding as we can.
dhw: Nowhere have I reverted to “natural chance”, and nowhere do the authors mention chance or design or God. I have not offered any theory at all. I have simply criticized the article because I find it muddling.[…]
DAVID: Come on, you consantly give credence to chance, and i give that absurdity (IMHO) a poke.
This discussion has become an "absurdity". Instead of dealing with my criticisms of an article about “information” which in my view creates confusion and explains nothing, you preach ID and twist my precise objections to the article’s equation of evolution with immaterial information into giving “credence to chance”. If I gave credence to chance, I would be an atheist, but that too is totally irrelevant. (As recently as yesterday I dismissed “chance mutations” as a “daft” explanation of the giraffe’s long neck with all the necessary adaptations made by the rest of its body.)
Evolution: as immaterial information
by David Turell , Tuesday, June 07, 2022, 17:48 (898 days ago) @ dhw
edited by David Turell, Tuesday, June 07, 2022, 17:55
dhw: Of course information exists without interpretation. I was replying to your own comment: “The only way life can work is that it must interpret the information that guides its processes.” But if life is “information that propagates”, you are telling us that the only way information that propagates can work, is that information that propagates must interpret the information that guides its processes. (And we mustn’t forget that information only exists when it has a material form.) Don’t you find all this a little confusing?
You are confused not me. If I have a newly developed concept in my brain, that is immaterial information that I can propagate. Why? I'm alive!! I can put it into sound or writing for others to interpret. That is all living cells do in their small way.
dhw: So now we have information migrating independently of (unrestricted by) the materials without which it can’t exist. So hey ho, evolution takes place independently of the genome, and this offers us “explanatory dimensions”. Again: where have you found the dismissal of chance and the inevitability of a designer?
This is from an ID propagated article: designer required as tranlated by me.
DAVID: I fully and logically recognize the need for a controlling operative mind, which you refuse to understand as you revert to natural chance as the driving mechanism. Pure plea from Darwinism. No wonder you are muddled. God does it and doesn't tell us how, so we research to reach as much understanding as we can.dhw: Nowhere have I reverted to “natural chance”, and nowhere do the authors mention chance or design or God. I have not offered any theory at all. I have simply criticized the article because I find it muddling.[…]
DAVID: Come on, you constantly give credence to chance, and I give that absurdity (IMHO) a poke.
dhw: This discussion has become an "absurdity". Instead of dealing with my criticisms of an article about “information” which in my view creates confusion and explains nothing, you preach ID and twist my precise objections to the article’s equation of evolution with immaterial information into giving “credence to chance”. If I gave credence to chance, I would be an atheist, but that too is totally irrelevant.
The absurdity is your misunderstanding of information and its use by living matter. DNA contains coded information. Acting upon it is what living things do. Speciation requires the deveopment of new infomation to form a new species. In design theory God adds new informtion to speciate. New informaatkon must be added!! Can your cell committees do that? Creating a new species requires a mental concept of what new form/s are desired. Where did the information come from to design and have formed all the new organ systems required? Especaily in the 410,000 time period shown in the new history I've presented. Darwin's worry, the Salurian gap throws his theory out the window.
Note, we have had this same information discussion for many years, simply because of your constant misuderstanding of the ID concept of how information theory impinges on evolutionary theory. Note all of the OOL reaseach I've shown, is based on intelligent design in the labratory. What is done is always following informative immaterial guesses in the scientists' brains.
Evolution: tracing the rise of the mammals
by David Turell , Tuesday, June 07, 2022, 21:31 (898 days ago) @ David Turell
A new book review reveals much interesting material:
https://www.sciencenews.org/article/mammal-world-evolution-innovation-dinosaurs-paleo
"Some of the moments of evolutionary invention that led to what we now think of as a mammal are remarkably subtle. There’s the hard roof of the mouth that created a dedicated airway to the lungs, allowing mammal ancestors to eat and breathe at the same time. There’s the change from a spine that bends from left to right (which produces the classically reptilian side-to-side gait) to one that enables bending up and down, which ultimately allowed mammals to take in more oxygen as they moved, helping them run faster. And there’s the variety of tooth shapes — incisors, canines, premolars and molars — that made it possible for mammals to eat many kinds of food. A reptile, by contrast, tends to have just one tooth type.
"Some mammalian characteristics are very familiar: milk production, warm-bloodedness, hair. But there’s one less–well-known evolutionary advance that was in its humble way quite profound, setting “us apart from amphibians, reptiles, and birds,” Brusatte writes. It’s a joint in the jaw that makes chewing possible. The ability to chew was “a major evolutionary turning point,” he writes. “It triggered a domino chain of changes to mammalian feeding, intelligence, and reproduction.”
"Brusatte also describes a second small, curious adaptation: the transformation of two bones in the reptile jaw, which migrated to the inner ear to become two members of a famous trio, the hammer and anvil (the third is the stirrup). These inner ear bones are the basis for yet another key mammalian feature: the ability to hear a wide range of frequencies, particularly in the upper register.
"The story of the Age of Mammals is often told as the flip side to the dinosaurs’ demise. But the fossil record reveals that mammals were hardly newcomers: They arose around the same time as the dinosaurs, over 200 million years ago. Even during the Age of Dinosaurs, “in the smaller and hidden niches, it was already the Age of Mammals,” Brusatte writes. “Mammals were better than the dinosaurs at being small.” (my bold)
"Within just a few hundred thousand years of the asteroid impact that wiped out all nonbird dinos some 66 million years ago, mammals moved in to fill the vacancy, rapidly getting a lot bigger, ballooning from, say, mouse-sized to beaver-sized. Pretty soon, they got a lot smarter too. In a geologic blink — a scant 10 million years — mammals’ brains caught up with their brawn, and then the Age of Mammals was off to the races."
Comment: from the standpoint of design, the story fits perfectly. Their waiting in the wings sounds exactlyliike pre-planning. What is the driving force that chance mutations could create? IT doen't exist. Only a desinging mind could direct mutations to produce a big-brained human
Evolution: maintaining mammalian body heat
by David Turell , Thursday, January 19, 2023, 15:36 (672 days ago) @ David Turell
The muscles do it:
https://www.sciencealert.com/our-muscles-evolved-a-clever-way-to-keep-us-warm-even-when...
"When the mercury drops, mammals like us have an advantage over so-called cold-blooded critters; our muscles can act as furnaces, generating the heat needed to keep our body temperature stable by turning fuel into movement.
"But even when relaxed, our muscles can continue to produce heat – a trick called muscle-based thermogenesis.
"As you sit quietly reading this article, appreciate that the development of muscle-based thermogenesis was a key step in your evolution, making it possible for your ancestors to spread into less tropical environments all over the globe. (my bold)
***
"'Cold-blooded animals, like frogs and toads, and warm-blooded mammals, such as humans, use the same basic muscle structures to generate force for posture and movement," said one of the authors, University of Queensland biomedical scientist Bradley Launikonis.
"But mammals have achieved their geographical freedom by changing the way the concentration of calcium ions is regulated in their resting muscles, setting them on a different course from our ectothermic relatives. This adaptation allows mammalian muscle cells to tolerate higher calcium concentrations in the surrounding fluid, requiring the muscle to expend energy in order to flush the calcium out.
"The calcium ion pumps in skeletal muscles work to keep the level of calcium ions steady. Previous research has shown the pump's activity also has an effect on how much heat skeletal muscle makes when it is at rest.
***
"Ryanodine receptors (RyR) are intracellular calcium channels in animal tissue like muscles and neurons, through which calcium ions flow. Calcium ion pumps work in the opposite direction, pumping calcium back the other way, to restore the balance inside cells.
"A type called RyR1 is expressed in skeletal muscle in mammals, whereas ectothermic animals express two types of the receptor in their skeletal muscle, αRyR and βRyR. (my bold)
"The results of this study showed that in mammals, abrupt increases in calcium in the fluid surrounding resting muscle fibers cause the ions to accumulate in a membrane-wrapped compartment inside cells called the sarcoplasmic reticulum, rather than be rapidly released.
"Usually, an influx of calcium ions into muscle cells triggers RyR channels to release more calcium into the cell's cytoplasm, setting off a cascade that leads to muscle contraction. However, mammals appear to have developed some resistance to rising calcium levels inside their muscle cells.
"This is important because it allows for a steady calcium ion leak from the sarcoplasmic reticulum, which forces the calcium ion pump to work harder, producing more heat.
"It seems that losing one form of RyR helped mammals' muscles become less sensitive to calcium ion triggers, which in addition to metabolism supports their endothermy."
Comment: Mammals are clearly very different than the rest of the cold-blooded animals. Why did a natural purposeless evolution produce body heat? The cold-blooded show us it is not necessary. Icefish can travel anywhere with antifreeze in their blood. But if evolution is viewed as purposefully directed toward humans, this course of mammalian evolution makes sense. As the first bold notes, we can travel anywhere on Earth.
Evolution: as immaterial information
dhw: Of course information exists without interpretation. I was replying to your own comment: “The only way life can work is that it must interpret the information that guides its processes.” But if life is “information that propagates”, you are telling us that the only way information that propagates can work, is that information that propagates must interpret the information that guides its processes. (And we mustn’t forget that information only exists when it has a material form.) Don’t you find all this a little confusing?
DAVID: You are confused not me. If I have a newly developed concept in my brain, that is immaterial information that I can propagate. Why? I'm alive!! I can put it into sound or writing for others to interpret. That is all living cells do in their small way.
The above makes perfect sense, but again you have ignored the article! Yes, you are you, and you are alive. But the authors define life as “information that propagates”. And so your bolded comment means information that propagates can only work if it interprets the information that guides its processes. Not confusing?
dhw: So now we have information migrating independently of (unrestricted by) the materials without which it can’t exist. So hey ho, evolution takes place independently of the genome, and this offers us “explanatory dimensions”. Again: where have you found the dismissal of chance and the inevitability of a designer?
DAVID: This is from an ID propagated article: designer required as tranlated by me.
Nothing whatsoever to do with the article.
dhw: This discussion has become an "absurdity". Instead of dealing with my criticisms of an article about “information” which in my view creates confusion and explains nothing, you preach ID [...]
DAVID: The absurdity is your misunderstanding of information and its use by living matter. DNA contains coded information. Acting upon it is what living things do.
Same problem as before. DNA in a dead body is still coded information. According to the article, life is information that propagates, and so you have information that propagates “acting upon” coded information. I find this confusing.
DAVID: Speciation requires the deveopment of new infomation to form a new species. In design theory God adds new informtion to speciate. New informaatkon must be added!! Can your cell committees do that? Creating a new species requires a mental concept of what new form/s are desired. Where did the information come from to design and have formed all the new organ systems required? Especaily in the 410,000 time period shown in the new history I've presented. Darwin's worry, the Salurian gap throws his theory out the window.
You have now abandoned the article completely! Cellular intelligence and the Cambrian are dealt with elsewhere. However, for the sake of clarity: information doesn’t design anything. New information (e.g. changing conditions) requires new responses from live organisms, and these responses will entail changes to the existing materials of which the organism is made. The responses are not made by information (which is passive), let alone by “migrating” or “propagating” information, but by intelligence, whether that of God or that of the cells. Intelligence is what perceives, interprets and uses information. But you won't find this even mentioned in the article, By all means, use it as evidence for ID if you like, but now please reread your bolded statement at the top of this post, in which you have life (= information that propagates) interpreting information that makes information work. Then perhaps you will recognize the confusion.
DAVID: Note, we have had this same information discussion for many years, simply because of your constant misuderstanding of the ID concept of how information theory impinges on evolutionary theory.
I see nothing in this article that supports ID or chance. What bothers me is the fact that here and elsewhere the arguments are unnecessarily confusing, often because of a failure to provide precise definitions of their terminology, and on each occasion I try to explain my objections. Instead of answering these, you simply repeat your ID theory, and shove in the word “information” wherever you think it makes sense.
DAVID: Note all of the OOL reaseach I've shown, is based on intelligent design in the labratory. What is done is always following informative immaterial guesses in the scientists' brains.
Since you are determined to digress from the article, note that in my balanced summary of different types of “madness” at the end of the brief guide, one example was the possible madness of humans worshipping something that might not even exist, and the other was a gibe at the Dawkins “species” of scientist:
2) the designer’s creations are just beginning to understand, after centuries of conscious endeavour, how life functions, but they are still unable to design an organism like themselves that can spring from inanimate matter into living existence, reproduce itself, adapt to a changing environment, invent new mechanisms, and pass on its adaptations and innovations to the organisms it engenders. They believe, however, that if they ever can consciously and deliberately design such an organism, it will prove that they themselves were not designed.
Evolution: as immaterial information
by David Turell , Wednesday, June 08, 2022, 17:16 (897 days ago) @ dhw
DAVID: The absurdity is your misunderstanding of information and its use by living matter. DNA contains coded information. Acting upon it is what living things do.
dhw: Same problem as before. DNA in a dead body is still coded information. According to the article, life is information that propagates, and so you have information that propagates “acting upon” coded information. I find this confusing.
They use inferences you refuse to follow. Life propagates information using information it has to translate.
DAVID: Speciation requires the development of new infomation to form a new species. In design theory God adds new informtion to speciate. New informaatkon must be added!! Can your cell committees do that? Creating a new species requires a mental concept of what new form/s are desired. Where did the information come from to design and have formed all the new organ systems required? Especaily in the 410,000 time period shown in the new history I've presented. Darwin's worry, the Salurian gap throws his theory out the window.dhw: You have now abandoned the article completely! Cellular intelligence and the Cambrian are dealt with elsewhere. However, for the sake of clarity: information doesn’t design anything. New information (e.g. changing conditions) requires new responses from live organisms, and these responses will entail changes to the existing materials of which the organism is made. The responses are not made by information (which is passive), let alone by “migrating” or “propagating” information, but by intelligence, whether that of God or that of the cells. Intelligence is what perceives, interprets and uses information. But you won't find this even mentioned in the article, By all means, use it as evidence for ID if you like, but now please reread your bolded statement at the top of this post, in which you have life (= information that propagates) interpreting information that makes information work. Then perhaps you will recognize the confusion.
I didn't abandon the article. The key to ID is understanding information theory as it is applied to living organisms. Of course intelligence translates code. But in a designer theory the translation mechanism is part of the instructions cells automatically follow.
DAVID: Note, we have had this same information discussion for many years, simply because of your constant misuderstanding of the ID concept of how information theory impinges on evolutionary theory.dhw: I see nothing in this article that supports ID or chance. What bothers me is the fact that here and elsewhere the arguments are unnecessarily confusing, often because of a failure to provide precise definitions of their terminology, and on each occasion I try to explain my objections. Instead of answering these, you simply repeat your ID theory, and shove in the word “information” wherever you think it makes sense.
I have explained ID information theory as best I can. See response above.
DAVID: Note all of the OOL reaseach I've shown, is based on intelligent design in the labratory. What is done is always following informative immaterial guesses in the scientists' brains.dhw: Since you are determined to digress from the article, note that in my balanced summary of different types of “madness” at the end of the brief guide, one example was the possible madness of humans worshipping something that might not even exist, and the other was a gibe at the Dawkins “species” of scientist:
2) the designer’s creations are just beginning to understand, after centuries of conscious endeavour, how life functions, but they are still unable to design an organism like themselves that can spring from inanimate matter into living existence, reproduce itself, adapt to a changing environment, invent new mechanisms, and pass on its adaptations and innovations to the organisms it engenders. They believe, however, that if they ever can consciously and deliberately design such an organism, it will prove that they themselves were not designed.
OOL will never be understood: all the foolishness in the lab is, as you note, intelligent designs.
Evolution: primate neurons are new
by David Turell , Wednesday, June 08, 2022, 17:34 (897 days ago) @ David Turell
Older forms are different:
https://www.sciencealert.com/study-shows-neuron-structure-is-different-between-primates...
"Scientists taking a very close look at the architecture of neuron cells in the brain have found a key structural difference between primates and non-primates in the cortical neurons – cells that are part of the cerebrum.
***
"Key to this difference in neurons is the axon fiber: a slender part of the neuron that carries electrical impulses. Before now, it was thought these axons almost always grow out of the cell body, but the new study shows they can also originate from dendrites – extensions that connect nerve cells together.
"These axon-carrying dendrites are a lot more common in non-primates like cats and pigs than they are in primates, the team discovered. The study was based on existing archived tissue and specimens, and included an analysis of more than 34,000 individual neurons.
***
"The researchers looked at samples covering mice, rats, pigs, cats, ferrets, macaque monkeys and humans. While axon-carrying dendrites were found in all species, there were significantly more of them in non-primates.
***
"Neurons usually act as gatekeepers when it comes to deciding which signals get passed on and which don't, according to other inputs they also receive. This is known as somatodendritic integration. One difference axon-carrying dendrites seem to have is the ability to bypass this gatekeeping and independently choose which messages make it around the brain network.
"As yet, we don't fully know what that means for brain processing, but we should get more clues over time. The researchers found that domestication in animals didn't seem to affect the number of these axon-carrying dendrites, with pigs and boars having similar proportions. Also, animals from various species seem to be born with them, rather than developing them as they get older.
***
"'Our findings expand the current knowledge regarding the distribution and proportion of axon-carrying dendrite cells in neocortex of non-primate taxa, which strikingly differ from primates where these cells are mainly found in deeper layers and white matter," write the researchers in their published paper."
Comment: nothing really new as we know primates are a big jump in complexity.
Evolution: most silent genetic mutations are harmful:
by David Turell , Wednesday, June 08, 2022, 22:32 (897 days ago) @ David Turell
Not good news in this new research:
https://phys.org/news/2022-06-silent-genetic-mutations-neutral-broad.html
"Occasionally, single-letter misspellings in the genetic code, known as point mutations, occur. Point mutations that alter the resulting protein sequences are called nonsynonymous mutations, while those that do not alter protein sequences are called silent or synonymous mutations.
"Between one-quarter and one-third of point mutations in protein-coding DNA sequences are synonymous. Ever since the genetic code was cracked, those mutations have generally been assumed to be neutral, or nearly so.
"But in a study scheduled for online publication June 8 in the journal Nature that involved the genetic manipulation of yeast cells in the laboratory, University of Michigan biologists show that most synonymous mutations are strongly harmful.
***
"To their surprise, the researchers found that 75.9% of synonymous mutations were significantly deleterious, while 1.3% were significantly beneficial.
***
"Zhang said the researchers knew beforehand, based on the anecdotal reports, that some synonymous mutations would likely turn out to be nonneutral.
"'But we were shocked by the large number of such mutations," he said. "Our results imply that synonymous mutations are nearly as important as nonsynonymous mutations in causing disease and call for strengthened effort in predicting and identifying pathogenic synonymous mutations.'"
Comment: dhw and I long ago threw out chance mutations as causes of evolution. That leaves us with not knowing how speciation occurs. I rely on God. dhw has his own veriouis theories.
Evolution: most silent genetic mutations are harmful:
by David Turell , Thursday, June 09, 2022, 17:57 (896 days ago) @ David Turell
Harmful mutations
DAVID: dhw and I long ago threw out chance mutations as causes of evolution. That leaves us with not knowing how speciation occurs. I rely on God. dhw has his own various theories.
dhw: I’ve only reproduced this because it marks one of the rare subjects on which we agree!
This issue creates another problem for neo-Darwinism. It attacks neutral theory:
https://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution
"The neutral theory assumes that most mutations that are not deleterious are neutral rather than beneficial. Because only a fraction of gametes are sampled in each generation of a species, the neutral theory suggests that a mutant allele can arise within a population and reach fixation by chance, rather than by selective advantage."
Here is ID commentary:
https://uncommondescent.com/evolution/the-death-of-neutral-theory/
"1 through 5 are citations. Who are they: Kimura, King and Jukes, Nei and Kumar, Li and Dan Graur. The heavyweights of neutral theory.
The abstract ends:
"The strong non-neutrality of most synonymous mutations, if it holds true for other genes and in other organisms, would require re-examination of numerous biological conclusions about mutation, selection, effective population size, divergence time and disease mechanisms that rely on the assumption that synonymous mutations are neutral. (my bold)
"In the Phys.Org press release, one of the authors is quoted saying:
“'Since the genetic code was solved in the 1960s, synonymous mutations have been generally thought to be benign. We now show that this belief is false,” said study senior author Jianzhi “George” Zhang, the Marshall W. Nirenberg Collegiate Professor in the U-M Department of Ecology and Evolutionary Biology.
“'Because many biological conclusions rely on the presumption that synonymous mutations are neutral, its invalidation has broad implications. For example, synonymous mutations are generally ignored in the study of disease-causing mutations, but they might be an underappreciated and common mechanism.”
***
"I have often made fun of those who hold to the Neutral Theory in the non–Kimuran sense. My problem with the idea of everything being ‘neutral’ was that, hypothetically, anything can become anything. There’s no start nor finish to this process. I thought it was extravagant; instead, it was just wrong. Modern techniques–the use of Crisper to make mutant genes, has now allowed us to see how NT is a ‘dead-end.’ We can only hope that evolutionary biologists can see this. But there’s really no reason for such hope, is there?"
Comment: I presented the article yesterday and did not note this viewpoint, as I am not as sharp as the ID folks, and I constantly learn viewpoints from them. I accept new peer-reviewed articles as accepted new knowledge as ID does. In the Ediacaran new time gap finding with Cambrain, dhw fights it with old quotes. Peer reeview means science has accepted the new finding. We have to use it!! dhw is hoping future research will overturn it to salvage his rigid theories about evolution.
Evolution: interaction of genes importance
by David Turell , Saturday, January 20, 2024, 18:23 (306 days ago) @ David Turell
edited by David Turell, Saturday, January 20, 2024, 18:32
Some control of mutations is present:
https://www.sciencealert.com/the-forces-that-drive-evolution-may-not-be-as-random-as-we...
"It's known that some areas of the genome are more likely to be mutable than others, but a new study now suggests a species' evolutionary history may play a role in making mutations more predictable too.
***
"University of Nottingham biologist Alan Beavan and colleagues harnessed the calculating power of AI to investigate more than 2,000 complete genomes of Escherichia coli bacteria.
"Bacteria are particularly tricksy when it comes to changing their DNA, being rather adept at stealing genes from their environment and incorporating them into their genome. Known as horizontal gene transfer, the process gives bacteria ready access to new traits, such as neatly sidestepping antibiotics – no pesky waiting around for selection to work across generations required.
"Curiously, horizontally transferred genes belonging to the same basic group can end up parking in different positions of the bacteria's genome. By investigating horizontal genes in different places, the researchers were able to see how the genes' immediate environment influenced them.
"They were able to test renowned evolutionary biologist Stephen J. Gould's thought experiment: replaying a tape of evolutionary history would result in a different, unpredictable outcome each time, since evolutionary paths depend on unpredictable events.
"If this is true, the bacteria's genome would keep evolving randomly after acquiring a new horizontal gene. But the AI found patterns of predictability across these thousands of "tape replays" after these gene acquisition events.
"'We found that some gene families never turned up in a genome when a particular other gene family was already there, and on other occasions, some genes were very much dependent on a different gene family being present," explains University of Nottingham microbiologist Maria Rosa Domingo-Sananes.
"So the history of the genome, amounting to which genes it has at the time, can determine which genes it will or won't have in the future. We've seen hints of this before through genes that are closely physically positioned on genetic molecules being lost or gained together – linked genes – but this was also happening with genes that had no close physical connection on the bacteria's genomes.
"'Some aspects of evolution are deterministic – i.e., they are likely to happen each time we replay the tape," confirm Beavan and team in their paper. "Gene presence or absence is predictable based only on other genes in the genome. For example, a hypothetical gene A may predict the presence of gene B only in the absence of gene C."
"This doesn't break the rule of random mutation; it's more that the forces of natural selection are working at a molecular level too, something we haven't had the computing power to fully see until recently. Essentially the genomes themselves are their own microscopic ecosystems, within which genes can help or hinder each other."
Comment: these genetic interactions are not a surprise. Years ago, I presented evidence of HAR regions in human genomes, areas of increased genetic activity. (Friday, August 14, 2020, 22:11) This work complements Shapiro's DNA studies in bacteria.
Evolution: females have bigger brains in animals
by David Turell , Saturday, January 20, 2024, 20:25 (306 days ago) @ David Turell
New study:
https://www.nationalgeographic.com/premium/article/female-male-animals-brain-brawn-evol...
"In fact, a study published today in the journal Behavioral Ecology and Sociobiology provides the first evidence that, as male mammals evolve larger weapons for combat and to signal their fitness, the females of those species develop larger brains than expected.
***
"However, while the focus has always been on what’s happening atop the heads of the males, there may be something just as remarkable taking place within the heads of the females. And it may upend what we thought about how much agency they have in choosing a mate.
***
Ummat Somjee, an evolutionary biologist at the University of Texas in Austin and the Smithsonian Tropical Research Institute in Panama, notes several limitations with the study. For instance, as the authors note, brain size does not necessarily translate to intelligence. For that conclusion, you would need behavioral data for every species involved, which is much harder to come by. (my bold)
"Similarlybrain size does not necessarily translate to intelligence. For that conclusion, , while he applauded the authors for examining as many specimens as they did, 29 species represents only a fraction of the weaponed ungulates on Earth. Who knows if the pattern might change when other antlered, horned, or tusked species are evaluated?
***
“'It’s amazing natural phenomena. It’s really weird, and strange,” says Somjee of rapid antler growth and loss. “But I think one thing that’s been left out is that what’s happening in females is also quite amazing.”
"For instance, females also divert vast amounts of calcium, phosphorus, and other nutrients from their own bodies to build entire offspring within their wombs. And of course, any tissues that go on to create antlers, horns, or tusks are first created by those females.
"For Lopez’s part, she points out that much of the scientific literature has focused on the battles between males to understand the sexual selection happening within these species. After all, the prevailing story has long been that the biggest, most heavily armed males get the females.
“'But it might just be that we’re not testing it in the right ways to show that [females] do have some type of decision in the males that they end up mating with,” says Lopez."
Comment: I guess the fairer sex has more to think about. I am not aware of a human difference in brain size, but then again we don't grow horns.
Evolution: Euglenids
by David Turell , Sunday, January 21, 2024, 16:07 (305 days ago) @ David Turell
Not plant nor animals:
https://www.sciencealert.com/bizarre-fossils-are-neither-plant-nor-animal-but-a-weird-f...
"It is neither animal, vegetable, nor mineral. It's not even a bacterium or fungi.
"It's called a Euglenid – and it's a weird fusion of a bunch of different living things.
Euglenids are a group of unicellular eukaryotes that gain energy through both photosynthesis, like a plant, and through consuming other beings, like an animal.
"These aquatic organisms split off from other eukaryotes roughly a billion years ago, and yet their fossil record for all that time on Earth is scarce.
***
"Their similarities over the years have stumped experts, as these fossils span immense timelines, from almost half a billion years ago to the present.
***
Using advanced microscopic techniques, they then established the structure of these cysts.
"'We were much surprised by the ultrastructure of the cysts," says paleontologist Wilson Taylor from the University of Wisconsin-Eau-Claire.
"'The structure of the wall does not resemble anything that is known. The ribs are not ornaments, like in pollen and spores, but part of the wall structure. The layered structure of the walls is also clearly different from many other fresh-water green algae."
"Researchers struggle to get living Euglenids to encyst in the lab, but a YouTube video by microscopy enthusiast Fabian Weston from Australia made for a perfect comparison.
""Unwittingly, Fabian provided a key piece of evidence. He is probably the only person on the planet to have witnessed Euglena encyst under a microscope," says Strother.
"Now that the researchers have established a possible deep timeline of Euglenid life, Strother hopes it will make it easier for scientists to recognize even older examples, possibly even ones that "go back to the very root of the eukaryotic tree of life."
""Perhaps related to their capabilities to encyst, these organisms have endured and survived every major extinction on the planet," suggests Van de Schootbrugge
"'Unlike the behemoths that were done in by volcanoes and asteroids, these tiny creatures have weathered it all.'"
Comment: a plant/animal type organism is a reasonable part of evolution.
Evolution: more evidence of early life
by David Turell , Monday, January 22, 2024, 18:10 (304 days ago) @ David Turell
In Africa:
https://www.newscientist.com/article/2413292-traces-of-ancient-life-reveal-a-3-4-billio...
"Manuel Reinhardt at the University of Göttingen in Germany and his colleagues studied rocks from the Buck Reef Chert, part of the Barberton Greenstone Belt in South Africa. The rocks are 3.42 billion years old and are thought to be the preserved remnants of the shallow seas around a chain of volcanic islands.
"The layers of rock contain microscopic blobs of carbon-based matter, believed to be the remains of microorganisms that lived in these seas. Reinhardt and his group subjected this matter to a battery of analyses to determine its chemical makeup, which they used to infer what sort of metabolism these microorganisms had.
"The team focused on the carbon itself. Carbon comes in several forms called isotopes, which are identical apart from the number of neutrons in the nucleus of the atom. The main two carbon isotopes are carbon-12 and carbon-13. Living things prefer to use carbon-12, so biological matter tends to have more carbon-12 and less carbon-13 than non-biological matter.
"However, not all living things are equally good at preferentially absorbing carbon-12. That means the ratio between the two forms can provide clues about an organism’s metabolism.
"Much of the material has a carbon signature that matches photosynthesis: the ability to use light energy to make sugar. This suggests there were enormous quantities of photosynthetic microbes living near the surface of the sea billions of years ago.
"However, some of the blobs had less carbon-12. Photosynthetic organisms can’t achieve this, so Reinhardt says those microbes must have been feeding on a chemical called acetyl coenzyme A.
"Other blobs had still lower levels of carbon-12, suggesting the microbes in them were making either methane or acetate as waste products, which other microbes were then feeding on.
***
"The study also adds to the evidence for an early origin of life on Earth, earlier than a crude reading of the fossil record might suggest.
The oldest widely accepted evidence for life is 3.5 billion years old, from Pilbara in Australia. Researchers have reported evidence of older fossils from 3.7 billion years ago or even earlier, but others say the evidence isn’t convincing in most of those cases.
***
"What does seem clear is that life is significantly older than 3.5 billion years. “Personally, I think life emerged on Earth during the Hadean [eon], probably about 4.2, 4.1 billion years [ago],” says Westall."
Comment: with the arrival of Earth 4.5 billon years ago such a quick appearance ofc life is surprising. Fits the theory of a designer, not a chance development..
Evolution: as immaterial information
DAVID: The absurdity is your misunderstanding of information and its use by living matter. DNA contains coded information. Acting upon it is what living things do.
dhw: Same problem as before. DNA in a dead body is still coded information. According to the article, life is information that propagates, and so you have information that propagates “acting upon” coded information. I find this confusing.
DAVID: They use inferences you refuse to follow. Life propagates information using information it has to translate.
They define life as “information that propagates”, and so now you are telling us that according to information theory, “information that propagates propagates information using information it has to translate.” If you think that clarifies how evolution is immaterial information, then good for you. (See my closing comment re the bolds.)
DAVID: Speciation requires the development of new infomation to form a new species. In design theory God adds new informtion to speciate. New informaatkon must be added!! Can your cell committees do that? Creating a new species requires a mental concept of what new form/s are desired. Where did the information come from to design and have formed all the new organ systems required? Especaily in the 410,000 time period shown in the new history I've presented. Darwin's worry, the Salurian gap throws his theory out the window.
dhw: You have now abandoned the article completely! Cellular intelligence and the Cambrian are dealt with elsewhere. However, for the sake of clarity: information doesn’t design anything. New information (e.g. changing conditions) requires new responses from live organisms, and these responses will entail changes to the existing materials of which the organism is made. The responses are not made by information (which is passive), let alone by “migrating” or “propagating” information, but by intelligence, whether that of God or that of the cells. Intelligence is what perceives, interprets and uses information. But you won't find this even mentioned in the article, By all means, use it as evidence for ID if you like, but now please reread your bolded statement at the top of this post, in which you have life (= information that propagates) interpreting information that makes information work. Then perhaps you will recognize the confusion.
DAVID: I didn't abandon the article. The key to ID is understanding information theory as it is applied to living organisms.
The article has nothing to do with cellular intelligence or the Cambrian, doesn’t mention chance or ID or the 410,000 years, or the Silurian gap. Nor does it set out to provide the key to ID, and I am simply analysing some of its statements to explain why I find them confusing. But you don’t even consider the way those statements turn your own into gibberish, even if I bold them. All you are interested in is ID!
DAVID: Of course intelligence translates code. But in a designer theory the translation mechanism is part of the instructions cells automatically follow.
I don't know why you introduced the term “translate” here and above. Translates what into what? Intelligence interprets and uses information. Do you or do you not agree? And the article is not about designer theory! It is about “Evolution; as immaterial information”, and I have explained why I find it confusing. It is clear from your various statements about life that you have not cottoned onto the authors’ definition of life, which turns your statements into nonsense, as bolded above.
Evolution: as immaterial information
by David Turell , Thursday, June 09, 2022, 16:46 (896 days ago) @ dhw
dhw: The article has nothing to do with cellular intelligence or the Cambrian, doesn’t mention chance or ID or the 410,000 years, or the Silurian gap. Nor does it set out to provide the key to ID, and I am simply analysing some of its statements to explain why I find them confusing. But you don’t even consider the way those statements turn your own into gibberish, even if I bold them. All you are interested in is ID!
DAVID: Of course intelligence translates code. But in a designer theory the translation mechanism is part of the instructions cells automatically follow.
dhw: I don't know why you introduced the term “translate” here and above. Translates what into what? Intelligence interprets and uses information. Do you or do you not agree? And the article is not about designer theory! It is about “Evolution; as immaterial information”, and I have explained why I find it confusing. It is clear from your various statements about life that you have not cottoned onto the authors’ definition of life, which turns your statements into nonsense, as bolded above.
I dumped all the discusson about the article. My intent in presenting it is/was to try and unscramble your brain's view of 'information' as a concept. We both know DNA is coded information. That code MUST be translated into active processes for life to appear. The translation method must exist and be provided for cells to use for life to appear. All the different layers of the genome are active and add contributikon to this process of translation and activation of living processes. None of this is disputable. For life to have started all of this had to be present and working. Design theory simply states the designer provided it.
So, once again, we see that immaterial information runs life. And as life propapgates, the information it carries propagates as life propagates. So the use of the word 'propagates' applies. The information is instructional since it creates living processes the cells produce. Design theory recognizes, as you do, that all of this, from the outside of the cell, looks like intelligent activity, and concludes an intelligetn designer produced it. The flip side is chance appearance of this arrangement is reasonably impossible.
Evolution: as immaterial information
dhw: I don't know why you introduced the term “translate” here and above. Translates what into what? Intelligence interprets and uses information. Do you or do you not agree? And the article is not about designer theory! It is about “Evolution; as immaterial information”, and I have explained why I find it confusing. It is clear from your various statements about life that you have not cottoned onto the authors’ definition of life, which turns your statements into nonsense, as bolded above.
DAVID: I dumped all the discusson about the article. My intent in presenting it is/was to try and unscramble your brain's view of 'information' as a concept.
There is no point in presenting an article which is so confusing that it even makes nonsense of your own statements about life and information. The fact that you have had to dump it shows that it had the opposite effect from that which you intended.
DAVID: We both know DNA is coded information. That code MUST be translated into active processes for life to appear. The translation method must exist and be provided for cells to use for life to appear. All the different layers of the genome are active and add contributikon to this process of translation and activation of living processes. None of this is disputable. For life to have started all of this had to be present and working. Design theory simply states the designer provided it.
This doesn’t make sense. How can all the different layers of the material genome be active in the “process of translation and activation of living processes” BEFORE life appears???
DAVID: So, once again, we see that immaterial information runs life.
No we don’t. Firstly, the genome cannot be “active” until the materials are already alive. (Dead people still have their DNA.) Secondly, what information are you talking about? The environment provides masses of information that has to be processed by what? Do you have immaterial information processing immaterial information?
DAVID: And as life propagates, the information it carries propagates as life propagates. So the use of the word 'propagates' applies.
The article, which you thought would unscramble my brain, defines life as "information that propagates". And so you are telling me that as information that propagates propagates, the information it carries propagates as information that propagates propagates. And this is supposed to unscramble my brain. But perhaps you have a different definition of life? Please let us have it.
DAVID: The information is instructional since it creates living processes the cells produce.
Information creates living processes which the cells produce? But the cells are material, and apparently they don’t come to life until information produces life, so now we have information producing life (= information that propagates) which is produced by materials which aren’t alive until information gives them life (= information that propagates). And this will unscramble my brain.
DAVID: Design theory recognizes, as you do, that all of this, from the outside of the cell, looks like intelligent activity, and concludes an intelligetn designer produced it. The flip side is chance appearance of this arrangement is reasonably impossible.
At last we have a clear statement, replacing all the gibberish about information with the fact that the activities of cells suggest that they are intelligent. Yes, it takes intelligence to perceive, process and use information. This may or may not have been designed by the supreme (but sourceless) intelligence we call God.
Evolution: as immaterial information
by David Turell , Friday, June 10, 2022, 16:35 (895 days ago) @ dhw
DAVID: We both know DNA is coded information. That code MUST be translated into active processes for life to appear. The translation method must exist and be provided for cells to use for life to appear. All the different layers of the genome are active and add contributikon to this process of translation and activation of living processes. None of this is disputable. For life to have started all of this had to be present and working. Design theory simply states the designer provided it.
dhw: This doesn’t make sense. How can all the different layers of the material genome be active in the “process of translation and activation of living processes” BEFORE life appears???
Perfect sense: all the information in a fertilized cell is alive, but must be translated for a living form to appear.
DAVID: The information is instructional since it creates living processes the cells produce.dhw: Information creates living processes which the cells produce? But the cells are material, and apparently they don’t come to life until information produces life, so now we have information producing life (= information that propagates) which is produced by materials which aren’t alive until information gives them life (= information that propagates). And this will unscramble my brain.
How obtuse can you be? We only get life from life, as we play with biochemistry. Only what is living can produce more of what is alive. All supported by the ability to translate information it contains. Life appeared and has never stopped producing more life.
DAVID: Design theory recognizes, as you do, that all of this, from the outside of the cell, looks like intelligent activity, and concludes an intelligetn designer produced it. The flip side is chance appearance of this arrangement is reasonably impossible.dhw: At last we have a clear statement, replacing all the gibberish about information with the fact that the activities of cells suggest that they are intelligent. Yes, it takes intelligence to perceive, process and use information. This may or may not have been designed by the supreme (but sourceless) intelligence we call God.
If not from God, how did the information appear, since it is immaterial to start with and MUST come from an active mind.
Evolution: as immaterial information
DAVID: We both know DNA is coded information. That code MUST be translated into active processes for life to appear. The translation method must exist and be provided for cells to use for life to appear. All the different layers of the genome are active and add contributikon to this process of translation and activation of living processes. None of this is disputable. For life to have started all of this had to be present and working. Design theory simply states the designer provided it. (Newly bolded by dhw)
dhw: This doesn’t make sense. How can all the different layers of the material genome be active in the “process of translation and activation of living processes” BEFORE life appears???
DAVID: Perfect sense: all the information in a fertilized cell is alive, but must be translated for a living form to appear.
Why have you jumped to a “fertilized” cell? Of course it’s alive. It’s been produced by living organisms! You might just as well tell me that life produces life (as in fact you do later!). Is there anyone who doesn’t know that? The mystery – as I have bolded in your statement above – is HOW LIFE STARTED!
DAVID: The information is instructional since it creates living processes the cells produce.
dhw: Information creates living processes which the cells produce? But the cells are material, and apparently they don’t come to life until information produces life, so now we have information producing life (= information that propagates) which is produced by materials which aren’t alive until information gives them life (= information that propagates). And this will unscramble my brain.
DAVID: How obtuse can you be? We only get life from life, as we play with biochemistry. Only what is living can produce more of what is alive All supported by the ability to translate information it contains. Life appeared and has never stopped producing more life.
Agreed. And that is the great mystery. HOW did life first appear? What is it that gives life to materials? Nobody knows. We don’t need to “define” life, though the authors tell us that defining life is the key, and their definition is “information that propagates”. Life is the state of being alive. And what you have written here is the only thing we know. Life comes from life. We don’t need any of these convoluted discussions of information that propagates (life propagates) or has to be “translated” (what has the ability to translate what?).
DAVID: Design theory recognizes, as you do, that all of this, from the outside of the cell, looks like intelligent activity, and concludes an intelligetn designer produced it. The flip side is chance appearance of this arrangement is reasonably impossible.
dhw: At last we have a clear statement, replacing all the gibberish about information with the fact that the activities of cells suggest that they are intelligent. Yes, it takes intelligence to perceive, process and use information. This may or may not have been designed by the supreme (but sourceless) intelligence we call God.
DAVID: If not from God, how did the information appear, since it is immaterial to start with and MUST come from an active mind.
Why do you need to bring in “information”? Nobody knows what brings materials to life. So why don’t you just ask: how did life appear? Clearly the complexities of the cell, which is the basis of all life, are such that they alone support the case for design. The unsolved mystery of what makes them live is NOT solved by all the blather about “information”! Hence these confusing and totally unproductive discussions – unless you really think “life comes from life” is too difficult for anyone to understand.
Evolution: as immaterial information
by David Turell , Saturday, June 11, 2022, 15:46 (894 days ago) @ dhw
DAVID: Perfect sense: all the information in a fertilized cell is alive, but must be translated for a living form to appear.
dhw: Why have you jumped to a “fertilized” cell? Of course it’s alive. It’s been produced by living organisms! You might just as well tell me that life produces life (as in fact you do later!). Is there anyone who doesn’t know that? The mystery – as I have bolded in your statement above – is HOW LIFE STARTED!
All of the processes in living cells we can see make life appear in cellular material. It is emergent. As you know I believe God started life.
DAVID: The information is instructional since it creates living processes the cells produce.dhw: Information creates living processes which the cells produce? But the cells are material, and apparently they don’t come to life until information produces life, so now we have information producing life (= information that propagates) which is produced by materials which aren’t alive until information gives them life (= information that propagates). And this will unscramble my brain.
DAVID: How obtuse can you be? We only get life from life, as we play with biochemistry. Only what is living can produce more of what is alive All supported by the ability to translate information it contains. Life appeared and has never stopped producing more life.
dhw: Agreed. And that is the great mystery. HOW did life first appear? What is it that gives life to materials? Nobody knows. We don’t need to “define” life, though the authors tell us that defining life is the key, and their definition is “information that propagates”. Life is the state of being alive. And what you have written here is the only thing we know. Life comes from life. We don’t need any of these convoluted discussions of information that propagates (life propagates) or has to be “translated” (what has the ability to translate what?).
Yes we do. Life runs by translating informational instructions it contains.
DAVID: Design theory recognizes, as you do, that all of this, from the outside of the cell, looks like intelligent activity, and concludes an intelligetn designer produced it. The flip side is chance appearance of this arrangement is reasonably impossible.dhw: At last we have a clear statement, replacing all the gibberish about information with the fact that the activities of cells suggest that they are intelligent. Yes, it takes intelligence to perceive, process and use information. This may or may not have been designed by the supreme (but sourceless) intelligence we call God.
DAVID: If not from God, how did the information appear, since it is immaterial to start with and MUST come from an active mind.
dhw: Why do you need to bring in “information”? Nobody knows what brings materials to life. So why don’t you just ask: how did life appear? Clearly the complexities of the cell, which is the basis of all life, are such that they alone support the case for design. The unsolved mystery of what makes them live is NOT solved by all the blather about “information”! Hence these confusing and totally unproductive discussions – unless you really think “life comes from life” is too difficult for anyone to understand.
The fact that life runs on immaterial information and operational information can only come from mental activity producing the informational concepts, a designer exists.
Evolution: as immaterial information
DAVID: Perfect sense: all the information in a fertilized cell is alive, but must be translated for a living form to appear.
dhw: Why have you jumped to a “fertilized” cell? Of course it’s alive. It’s been produced by living organisms! You might just as well tell me that life produces life (as in fact you do later!). Is there anyone who doesn’t know that? The mystery – as I have bolded in your statement above – is HOW LIFE STARTED!
DAVID: All of the processes in living cells we can see make life appear in cellular material. It is emergent. As you know I believe God started life.
The processes can’t even begin until the cells are alive! All parts of the cell are still present in a dead person. “God started life” is no more enlightening than “chance started life”, but at least in both cases we have now rid ourselves of “information” as the source of life.
DAVID: We only get life from life, as we play with biochemistry. Only what is living can produce more of what is alive All supported by the ability to translate information it contains. Life appeared and has never stopped producing more life.
dhw: […] what you have written here is the only thing we know. Life comes from life. We don’t need any of these convoluted discussions of information that propagates (life propagates) or has to be “translated” (what has the ability to translate what?).
DAVID: Yes we do. Life runs by translating informational instructions it contains.
So “information that propagates” runs by translating information that it contains. (Nothing to do with how life started, but we should abandon that question.) So into what does the information that propagates translate the information it contains? What sort of information is “propagating” information anyway? Once upon a time, I thought information was purely passive, and needed a mind to interpret and use it. But not now apparently: it can translate and reproduce itself and spread itself around.
DAVID: The fact that life runs on immaterial information and operational information can only come from mental activity producing the informational concepts, a designer exists.
Now we have propagating information, instructional information, operational information and informational concepts, and life runs on mental activity which proves that God exists. And all this is meant to “unscramble” my brain. I suggest the following: Life runs on mental activity perceiving, interpreting and using information. Life comes from life, and nobody knows how life and mental activity started.
Evolution: as immaterial information
by David Turell , Sunday, June 12, 2022, 16:34 (893 days ago) @ dhw
DAVID: All of the processes in living cells we can see make life appear in cellular material. It is emergent. As you know I believe God started life.
dhw:The processes can’t even begin until the cells are alive! All parts of the cell are still present in a dead person. “God started life” is no more enlightening than “chance started life”, but at least in both cases we have now rid ourselves of “information” as the source of life.
Information in cells can't be used by deadc cells, so chichen and egg problem. Information must be present for life to exist and run its information-dependent processes. The source of
life is either God or chance. The first appearance of life is withits informaton present.
DAVID: Life runs by translating informational instructions it contains.dhw: So “information that propagates” runs by translating information that it contains. (Nothing to do with how life started, but we should abandon that question.) So into what does the information that propagates translate the information it contains? What sort of information is “propagating” information anyway? Once upon a time, I thought information was purely passive, and needed a mind to interpret and use it. But not now apparently: it can translate and reproduce itself and spread itself around.
Life started with information on board!! Information in and of itself is passive, obviusly. Life interpreting information propogates and informaton is carried along with it. A new species has new information, source must be chance or God
DAVID: The fact that life runs on immaterial information and operational information can only come from mental activity producing the informational concepts, a designer exists.dhw: Now we have propagating information, instructional information, operational information and informational concepts, and life runs on mental activity which proves that God exists. And all this is meant to “unscramble” my brain. I suggest the following: Life runs on mental activity perceiving, interpreting and using information. Life comes from life, and nobody knows how life and mental activity started.
Still a constant scramble as I analyze the bold. Life runs on the informaton it contains, which is obvious.
Evolution: as immaterial information
DAVID: All of the processes in living cells we can see make life appear in cellular material. It is emergent. As you know I believe God started life.
dhw:The processes can’t even begin until the cells are alive! All parts of the cell are still present in a dead person. “God started life” is no more enlightening than “chance started life”, but at least in both cases we have now rid ourselves of “information” as the source of life.
DAVID: Information in cells can't be used by dead cells, so chichen and egg problem. Information must be present for life to exist and run its information-dependent processes. The source of life is either God or chance. The first appearance of life is with its informaton present.
All materials contain information. It takes intelligence to perceive, interpret and use the information. Your authors define life as “information that propagates”. Your second sentence therefore means: information must be present for information that propagates to exist and run its information-dependent processes. So information must exist for information to be present. Eureka! What is all this rigmarole meant to prove?
DAVID: Life runs by translating informational instructions it contains.
dhw: So “information that propagates” runs by translating information that it contains. (Nothing to do with how life started, but we should abandon that question.) So into what does the information that propagates translate the information it contains? What sort of information is “propagating” information anyway? Once upon a time, I thought information was purely passive, and needed a mind to interpret and use it. But not now apparently: it can translate and reproduce itself and spread itself around.
DAVID: Life started with information on board!! Information in and of itself is passive, obviusly. Life interpreting information propogates and informaton is carried along with it. A new species has new information, source must be chance or God.
Everything living and non-living starts with information on board! But it needs a mind to perceive, interpret and use it. Your authors say life is “information that propagates”, so now you have information that propagates interpreting information and propagating. Yes, a new species contains new information, but it is not information creating new information. The more you use the word, the more confusing it becomes. Of course the source of life and of intelligence must be chance or God, and if God created all the materials that contain all the information, then God is the source of all information and of the intelligence that perceives, interprets and uses it. If God exists, he is the source of everything. And if he doesn’t, he isn’t.
DAVID: The fact that life runs on immaterial information and operational information can only come from mental activity producing the informational concepts, a designer exists.
dhw: Now we have propagating information, instructional information, operational information and informational concepts, and life runs on mental activity which proves that God exists. And all this is meant to “unscramble” my brain. I suggest the following: Life runs on mental activity perceiving, interpreting and using information. Life comes from life, and nobody knows how life and mental activity started.
DAVID: Still a constant scramble as I analyze the bold. Life runs on the informaton it contains, which is obvious.
The bold shows what a confusing mess is created by indiscriminate use of the word “information”, which you agree is PASSIVE! Life itself is not information. What is your objection to my suggestion, now in red?
Evolution: as immaterial information
by David Turell , Monday, June 13, 2022, 16:33 (892 days ago) @ dhw
DAVID: Information in cells can't be used by dead cells, so chichen and egg problem. Information must be present for life to exist and run its information-dependent processes. The source of life is either God or chance. The first appearance of life is with its informaton present.
dhw: All materials contain information. It takes intelligence to perceive, interpret and use the information. Your authors define life as “information that propagates”. Your second sentence therefore means: information must be present for information that propagates to exist and run its information-dependent processes. So information must exist for information to be present. Eureka! What is all this rigmarole meant to prove?
All it means is for the start of life the cells had to contain information.
DAVID: Life started with information on board!! Information in and of itself is passive, obviusly. Life interpreting information propogates and informaton is carried along with it. A new species has new information, source must be chance or God.
dhw: Everything living and non-living starts with information on board! But it needs a mind to perceive, interpret and use it.
In cells, where is that 'mind'? What really exists is the cells ability to interpret the information code which also requires information.
dhw: Your authors say life is “information that propagates”, so now you have information that propagates interpreting information and propagating. Yes, a new species contains new information, but it is not information creating new information. The more you use the word, the more confusing it becomes.
The disucssion I am having with you does not revert back to the article. You are reverting for no good reason except to complain about it. I am attempting to show you how information is used in life and by life. Your wild discomfort about the information concept is showing.
dhw: Now we have propagating information, instructional information, operational information and informational concepts, and life runs on mental activity which proves that God exists. And all this is meant to “unscramble” my brain. I suggest the following: Life runs on mental activity perceiving, interpreting and using information. Life comes from life, and nobody knows how life and mental activity started.DAVID: Still a constant scramble as I analyze the bold. Life runs on the informaton it contains, which is obvious.
dhw:The bold shows what a confusing mess is created by indiscriminate use of the word “information”, which you agree is PASSIVE! Life itself is not information. What is your objection to my suggestion, now in red?
Life does not run on mental activity. Life runs by automatically interpreting the information it contains.
Evolution: as immaterial information
DAVID: Information in cells can't be used by dead cells, so chichen and egg problem. Information must be present for life to exist and run its information-dependent processes. The source of life is either God or chance. The first appearance of life is with its informaton present.
dhw: All materials contain information. It takes intelligence to perceive, interpret and use the information. Your authors define life as “information that propagates”. Your second sentence therefore means: information must be present for information that propagates to exist and run its information-dependent processes. So information must exist for information to be present. Eureka! What is all this rigmarole meant to prove?
DAVID: All it means is for the start of life the cells had to contain information.
All materials contain information, whether animate or inanimate, so this doesn’t get us anywhere. Once more: it needs a mind to perceive, interpret and use information.
DAVID: In cells, where is that 'mind'? What really exists is the cells ability to interpret the information code which also requires information.
We’re off again! Interpretation is a mental activity! What is the difference between a code and an information code, and what information does an information code require in addition to its information?
dhw: Your authors say life is “information that propagates”, so now you have information that propagates interpreting information and propagating. Yes, a new species contains new information, but it is not information creating new information. The more you use the word, the more confusing it becomes.
DAVID: The disucssion I am having with you does not revert back to the article. You are reverting for no good reason except to complain about it.
You have abandoned the article because clearly you cannot answer any of my criticisms. Now you are presenting your own muddled ideas instead.
DAVID: I am attempting to show you how information is used in life and by life. Your wild discomfort about the information concept is showing.
So far all you have told me is that for the start of life, cells had to contain information. We agree that cells spend their lives interpreting information, but that does not tell us how life started, or HOW they are able to interpret information. Information itself, we agree, is passive. It requires mental activity if it is to be interpreted. This leads you into a plethora of information types, as listed here:
dhw: Now we have propagating information, instructional information, operational information and informational concepts, and life runs on mental activity which proves that God exists. And all this is meant to “unscramble” my brain. I suggest the following: Life runs on mental activity perceiving, interpreting and using information. Life comes from life, and nobody knows how life and mental activity started.
DAVID: Still a constant scramble as I analyze the bold. Life runs on the informaton it contains, which is obvious.
dhw:The bold shows what a confusing mess is created by indiscriminate use of the word “information”, which you agree is PASSIVE! Life itself is not information. What is your objection to my suggestion, now in red?
DAVID: Life does not run on mental activity. Life runs by automatically interpreting the information it contains.
Living organisms respond to information both inside and outside themselves. I agree that many of these responses are automatic, when the information remains unchanged – e.g. no abnormality inside, and no environmental changes outside. But when conditions change, what you call the “information” changes, and that is when the mental activity of interpretation and decision-making is required. Your theory is that 3.8 billion years ago, your God compiled a book of instructions for each new problem, or alternatively he pops in to tell the cells what to do. I find this a little far-fetched, and suggest that instead he may have given cells the autonomous intelligence to work out their own solutions (adaptation) or even to design new ways of exploiting the changes. So we are back to the same straightforward discussion, and we don’t need any of the convoluted categories of information propagating, interpreting, instructing, operating, conceiving etc.
Missing a part doesn’t matter
QUOTE: "Study of EG has proceeded on the assumption that other regions of her brain had taken up the task of processing language. That’s not as unusual as it sounds; the brain is a living organ, not a machine. Given an opportunity, it can shift burdens around (neuroplasticity.)
Doesn’t this suggest to you that the cells of which the brain is composed are able to respond intelligently to new demands by taking on new functions? Or did your God include EG’s brain in his 3.8-billion-year old Book Of Instructions, or simply pop in to make the adjustments to her brain?
Entropy
dhw: […] Incidentally, the far-sighted Lynn Margulis was also a champion of the theory that cells are intelligent.
DAVID: Yes, they appear to be that way.
And what appears to be intelligent might actually be intelligent.
Evolution: as immaterial information
by David Turell , Tuesday, June 14, 2022, 16:55 (891 days ago) @ dhw
DAVID: In cells, where is that 'mind'? What really exists is the cells ability to interpret the information code which also requires information.
dhw: We’re off again! Interpretation is a mental activity! What is the difference between a code and an information code, and what information does an information code require in addition to its information?
All cells act as if they have mental activity. Cells use information they have to decode DNA and perform their procesees, all automatically.
DAVID: I am attempting to show you how information is used in life and by life. Your wild discomfort about the information concept is showing.dhw: So far all you have told me is that for the start of life, cells had to contain information. We agree that cells spend their lives interpreting information, but that does not tell us how life started, or HOW they are able to interpret information. Information itself, we agree, is passive. It requires mental activity if it is to be interpreted.
We are not discussing how life started but the fact that information had to be part of it.
DAVID: Life does not run on mental activity. Life runs by automatically interpreting the information it contains.
dhw: Living organisms respond to information both inside and outside themselves. I agree that many of these responses are automatic, when the information remains unchanged – e.g. no abnormality inside, and no environmental changes outside. But when conditions change, what you call the “information” changes, and that is when the mental activity of interpretation and decision-making is required.
Cells automatically respond various stimulations outside them.
dhw: Your theory is that 3.8 billion years ago, your God compiled a book of instructions for each new problem, or alternatively he pops in to tell the cells what to do. I find this a little far-fetched, and suggest that instead he may have given cells the autonomous intelligence to work out their own solutions (adaptation) or even to design new ways of exploiting the changes. So we are back to the same straightforward discussion, and we don’t need any of the convoluted categories of information propagating, interpreting, instructing, operating, conceiving etc.
You can't escape that without information life can't/doesn't exist
Missing a part doesn’t matterQUOTE: "Study of EG has proceeded on the assumption that other regions of her brain had taken up the task of processing language. That’s not as unusual as it sounds; the brain is a living organ, not a machine. Given an opportunity, it can shift burdens around (neuroplasticity.)
dhw: Doesn’t this suggest to you that the cells of which the brain is composed are able to respond intelligently to new demands by taking on new functions?
Yes, brain plasticity processes take on new tasks.
Entropydhw: […] Incidentally, the far-sighted Lynn Margulis was also a champion of the theory that cells are intelligent.
DAVID: Yes, they appear to be that way.
dhw: And what appears to be intelligent might actually be intelligent.
So tell how they developed that intelligence, by chance?
Evolution: as immaterial information
DAVID: In cells, where is that 'mind'? What really exists is the cells ability to interpret the information code which also requires information.
dhw: We’re off again! Interpretation is a mental activity! What is the difference between a code and an information code, and what information does an information code require in addition to its information?
DAVID: All cells act as if they have mental activity. Cells use information they have to decode DNA and perform their procesees, all automatically.
DNA carries “genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses.” (Wikipedia). Cells carry out these instructions. We don’t need all the blather about information code requiring information, not to mention propagating information, instructional information, operational information and informational concepts. The rest of your post is basically concerned with shoving in the word “automatically”, which leads to a discussion on cellular intelligence, and we don’t need to blather on about information in order to continue our endless discussion on that topic.
dhw: So far all you have told me is that for the start of life, cells had to contain information. We agree that cells spend their lives interpreting information, but that does not tell us how life started, or HOW they are able to interpret information. Information itself, we agree, is passive. It requires mental activity if it is to be interpreted.
DAVID: We are not discussing how life started but the fact that information had to be part of it.
In yesterday’s post, when I challenged the blather, you replied “All it means is bbbfor the start of lifebbb the cells had to contain information.” All materials, animate or inanimate, contain information, so of course information is “part of it”! I’m not denying the existence of information! I’m complaining about the way the term is used to confuse instead of clarify the issues we are discussing.
DAVID: Life does not run on mental activity. Life runs by automatically interpreting the information it contains.
dhw: Living organisms respond to information both inside and outside themselves. I agree that many of these responses are automatic, when the information remains unchanged – e.g. no abnormality inside, and no environmental changes outside. bbbBut when conditions change, what you call the “information” changes, and that is when the mental activity of interpretation and decision-making is required.bbb
DAVID: Cells automatically respond various stimulations outside them.
No need for informational blather. We are back to discussing the theory of cellular intelligence and your refusal to distinguish between automatic repetition when conditions remain normal, and the need for new interpretations and decisions when conditions change.
DAVID: You can't escape that without information life can't/doesn't exist.
All materials, whether animate or inanimate, contain information. That explains absolutely nothing.
Missing a part doesn’t matter
QUOTE: "Study of EG has proceeded on the assumption that other regions of her brain had taken up the task of processing language. That’s not as unusual as it sounds; the brain is a living organ, not a machine. Given an opportunity, it can shift burdens around (neuroplasticity.)
dhw: Doesn’t this suggest to you that the cells of which the brain is composed are able to respond intelligently to new demands by taking on new functions?
DAVID: Yes, brain plasticity processes take on new tasks.
The “plastic” cells of the brain make the necessary changes to conduct new processes to deal with new tasks. Why are you so reluctant to acknowledge that the brain is composed of cells?
Entropy
dhw: […] Incidentally, the far-sighted Lynn Margulis was also a champion of the theory that cells are intelligent.
DAVID: Yes, they appear to be that way.
dhw: And what appears to be intelligent might actually be intelligent.
DAVID: So tell how they developed that intelligence, by chance?
Do I have to keep repeating that your God may have been the designer?
Evolution: as immaterial information
by David Turell , Wednesday, June 15, 2022, 15:25 (891 days ago) @ dhw
dhw: So far all you have told me is that for the start of life, cells had to contain information. We agree that cells spend their lives interpreting information, but that does not tell us how life started, or HOW they are able to interpret information. Information itself, we agree, is passive. It requires mental activity if it is to be interpreted.
DAVID: We are not discussing how life started but the fact that information had to be part of it.
dhw: In yesterday’s post, when I challenged the blather, you replied “All it means is bbbfor the start of lifebbb the cells had to contain information.” All materials, animate or inanimate, contain information, so of course information is “part of it”! I’m not denying the existence of information! I’m complaining about the way the term is used to confuse instead of clarify the issues we are discussing.
I'm not confused by using the term as you just have.
dhw: No need for informational blather. We are back to discussing the theory of cellular intelligence and your refusal to distinguish between automatic repetition when conditions remain normal, and the need for new interpretations and decisions when conditions change.
Cells respond to new conditions with automatic answers following instructions they carry and by adding methylation for epigenetic responses.
DAVID: You can't escape that without information life can't/doesn't exist.dhw: All materials, whether animate or inanimate, contain information. That explains absolutely nothing.
Stones carry static descriptive information we assign to them. Cells operate by interpreting instructional information to make them alive.
Missing a part doesn’t matterQUOTE: "Study of EG has proceeded on the assumption that other regions of her brain had taken up the task of processing language. That’s not as unusual as it sounds; the brain is a living organ, not a machine. Given an opportunity, it can shift burdens around (neuroplasticity.)
dhw: Doesn’t this suggest to you that the cells of which the brain is composed are able to respond intelligently to new demands by taking on new functions?
DAVID: Yes, brain plasticity processes take on new tasks.
dhw: The “plastic” cells of the brain make the necessary changes to conduct new processes to deal with new tasks. Why are you so reluctant to acknowledge that the brain is composed of cells?
I never inferred the brain had no cells?
Entropy
dhw: […] Incidentally, the far-sighted Lynn Margulis was also a champion of the theory that cells are intelligent.DAVID: Yes, they appear to be that way.
dhw: And what appears to be intelligent might actually be intelligent.
DAVID: So tell how they developed that intelligence, by chance?
dhw: Do I have to keep repeating that your God may have been the designer?
I know that, but that doesn't tell me how it happens without God, which you seem to prefer..
Evolution: as immaterial information
dhw: So far all you have told me is that for the start of life, cells had to contain information. We agree that cells spend their lives interpreting information, but that does not tell us how life started, or HOW they are able to interpret information. Information itself, we agree, is passive. It requires mental activity if it is to be interpreted.
DAVID: We are not discussing how life started but the fact that information had to be part of it.
dhw: In yesterday’s post, when I challenged the blather, you replied “All it means is for the start of life the cells had to contain information.” All materials, animate or inanimate, contain information, so of course information is “part of it”! I’m not denying the existence of information! I’m complaining about the way the term is used to confuse instead of clarify the issues we are discussing.
DAVID: I'm not confused by using the term as you just have.
Of course you aren’t. And I suggest we go on using the term as I just have, instead of all the blather.
DAVID: You can't escape that without information life can't/doesn't exist.
dhw: All materials, whether animate or inanimate, contain information. That explains absolutely nothing.
DAVID: Stones carry static descriptive information we assign to them. Cells operate by interpreting instructional information to make them alive.
Why do you call it “instructional information” and not instructions? It is absurd to say they are “made alive” by interpreting instructions, since they cannot perform the mental activity of interpreting UNTIL they are alive!
dhw: No need for informational blather. We are back to discussing the theory of cellular intelligence and your refusal to distinguish between automatic repetition when conditions remain normal, and the need for new interpretations and decisions when conditions change.
DAVID: Cells respond to new conditions with automatic answers following instructions they carry and by adding methylation for epigenetic responses.
Exit information theory (thank heavens), and back we go to your definitive rejection of a 50/50 possibility of cellular intelligence. I find it hard to believe that 3.8 billion years ago your God provided cells with instructions on how to deal with every single new problem/condition/ opportunity that would arise for the rest of the future, or that he popped/pops in to issue instructions ad hoc.
Missing a part doesn’t matter
QUOTE: "Study of EG has proceeded on the assumption that other regions of her brain had taken up the task of processing language. That’s not as unusual as it sounds; the brain is a living organ, not a machine. Given an opportunity, it can shift burdens around (neuroplasticity.)
dhw: Doesn’t this suggest to you that the cells of which the brain is composed are able to respond intelligently to new demands by taking on new functions?
DAVID: Yes, brain plasticity processes take on new tasks.
dhw: The “plastic” cells of the brain make the necessary changes to conduct new processes to deal with new tasks. Why are you so reluctant to acknowledge that the brain is composed of cells?
DAVID: I never inferred the brain had no cells?
But you scrupulously avoid using the word, as you have done above: plasticity doesn’t take on new tasks. Plasticity is a quality of the cells. It is the cells that take on the tasks, i.e. I propose that they use their plasticity intelligently in order to initiate new processes in response to new requirements.
Entropy
dhw: […] Incidentally, the far-sighted Lynn Margulis was also a champion of the theory that cells are intelligent.
DAVID: Yes, they appear to be that way.
dhw: And what appears to be intelligent might actually be intelligent.
DAVID: So tell how they developed that intelligence, by chance?
dhw: Do I have to keep repeating that your God may have been the designer?
DAVID: I know that, but that doesn't tell me how it happens without God, which you seem to prefer.
How what happens without God? You claim that your God preprogrammed or dabbled every change in every organ and every organism, and I suggest he may have designed a mechanism which makes its own changes. I certainly find the latter more believable than the former, but I have also offered alternatives to explain how the former might be made to fit in with the history – unlike your own theory, which is so muddled that apparently only God can understand it. (See the thread on your theory.)
Evolution: as immaterial information
by David Turell , Thursday, June 16, 2022, 17:46 (889 days ago) @ dhw
edited by David Turell, Thursday, June 16, 2022, 18:26
dhw: All materials, whether animate or inanimate, contain information. That explains absolutely nothing.
DAVID: Stones carry static descriptive information we assign to them. Cells operate by interpreting instructional information to make them alive.
dhw: Why do you call it “instructional information” and not instructions? It is absurd to say they are “made alive” by interpreting instructions, since they cannot perform the mental activity of interpreting UNTIL they are alive!
They do become alive by interpreting their instructions they're are given. That had to happen when life was started. Just to emphasize it, insructions are always information.
dhw: No need for informational blather. We are back to discussing the theory of cellular intelligence and your refusal to distinguish between automatic repetition when conditions remain normal, and the need for new interpretations and decisions when conditions change.DAVID: Cells respond to new conditions with automatic answers following instructions they carry and by adding methylation for epigenetic responses.
dhw: Exit information theory (thank heavens), and back we go to your definitive rejection of a 50/50 possibility of cellular intelligence. I find it hard to believe that 3.8 billion years ago your God provided cells with instructions on how to deal with every single new problem/condition/ opportunity that would arise for the rest of the future, or that he popped/pops in to issue instructions ad hoc.
You find it hard to believe in God, so I'm not surprised at your view. Living one-celled Archaea started knowing exactly how to handle themselves or nothing would have evolved. Do you have any thoughts about first life's capabilities? I've given it lots of thought.
Missing a part doesn’t matterDAVID: Yes, brain plasticity processes take on new tasks.
dhw: The “plastic” cells of the brain make the necessary changes to conduct new processes to deal with new tasks. Why are you so reluctant to acknowledge that the brain is composed of cells?
DAVID: I never inferred the brain had no cells?
dhw: But you scrupulously avoid using the word, as you have done above: plasticity doesn’t take on new tasks. Plasticity is a quality of the cells. It is the cells that take on the tasks, i.e. I propose that they use their plasticity intelligently in order to initiate new processes in response to new requirements.
And I view the neurons as programmed to handle all new tasks given to them..
Entropy
dhw: […] Incidentally, the far-sighted Lynn Margulis was also a champion of the theory that cells are intelligent.DAVID: Yes, they appear to be that way.
dhw: And what appears to be intelligent might actually be intelligent.
DAVID: So tell how they developed that intelligence, by chance?
dhw: Do I have to keep repeating that your God may have been the designer?
DAVID: I know that, but that doesn't tell me how it happens without God, which you seem to prefer.
dhw: How what happens without God?
Cell intellence, which is the present subject. How do cells become intelligent without God's help?
dhw: You claim that your God preprogrammed or dabbled every change in every organ and every organism, and I suggest he may have designed a mechanism which makes its own changes. I certainly find the latter more believable than the former, but I have also offered alternatives to explain how the former might be made to fit in with the history – unlike your own theory, which is so muddled that apparently only God can understand it. (See the thread on your theory.)
God always does what He wihes for His own reasons, which you cannot know, as much as you analyze God's actions. I have asked you to explain the intelligence of cells without a God existing? You are either or. That is the other side of your agnosticism I'd like to hear about.
Evolution: what works at the genetic level
by David Turell , Thursday, June 16, 2022, 21:01 (889 days ago) @ David Turell
Mutations or diverse gene variations?:
https://www.sciencealert.com/breeding-2000-generations-of-bacteria-may-have-solved-this...
"Having a lot of genetic options to choose from might make natural selection move a lot faster at the start, but do the genetic mutations that happen over time contribute more to species survival in the end?
***
"Each population of bacteria was engineered to have different amounts of genetic diversity at the start of the experiment.
***
"Each population was fed glucose at the start of the experiment. To test adaptability, various sets of these bacteria populations were taken and propagated in a different growth environment, providing them with the amino acid D-serine instead of glucose for their energy needs.
***
"The E. coli samples were all derived from the Long-term Experimental Evolution Project, which was started in 1988 by one of the co-authors on the recent paper, evolutionary biologist Richard Lenski.
***
"At the early stages of the experiment (around 50 generations in), the wealth of genetic diversity in the initial population was important for adaptation.
"But, by the 500th generation, the diversity at the start of the experiment "no longer mattered" because the new mutations were "sufficiently large", the authors write in their preprint, which is available on BioRxiv ahead of peer review.
"By the 500th and 2,000th generation, there were "no differences in fitness" among all the different populations of bacteria, despite the variation in fitness at the start.
"'Any benefit of pre-existing variation in asexual populations may often be short-lived, as we saw in our experiment, because that variation will be purged when new beneficial mutations sweep to fixation," the researchers write.
"While it's yet to be vetted by others in the scientific community and published in a peer-reviewed journal, this result may close the book on the longest-running argument in evolutionary biology when it comes to bacteria.
"But there is no 'right' answer in terms of the relative importance of standing variation and new mutations for adaptation in nature, the researchers write.
***
"Those studying bacteria and viruses tend to look to mutations as the major source of evolution.
"But really, both forces – mutation and existing genetic diversity – "can contribute sequentially, simultaneously, and even synergistically to the process of adaptation by natural selection", the researchers say."
Comment: Lenski's E.coli are 34 years into evolving. Using bacteria gives evolution a real broad base of individuals evolving reproduction every 20 minutes. That mutation and diversity are equallly important seems a logical finding to me. This is a pure Darwinist study with no reference to intelligent design and I present it for general interest.
Evolution: as immaterial information
dhw: All materials, whether animate or inanimate, contain information. That explains absolutely nothing.
DAVID: Stones carry static descriptive information we assign to them. Cells operate by interpreting instructional information to make them alive.
dhw: Why do you call it “instructional information” and not instructions? It is absurd to say they are “made alive” by interpreting instructions, since they cannot perform the mental activity of interpreting UNTIL they are alive!
DAVID: They do become alive by interpreting their instructions they're are given. That had to happen when life was started.
How can they possibly interpret instructions before they are alive?
DAVID: Just to emphasize it, instructions are always information.
Yes, yes, you have instructional information, descriptive information, propagating information, operational information, static information…You have information in your ears, coming out of your ears, and appearing in articles that are so confusing that the only way you can explain them is by telling me not to take any notice of them.
dhw: No need for informational blather. We are back to discussing the theory of cellular intelligence and your refusal to distinguish between automatic repetition when conditions remain normal, and the need for new interpretations and decisions when conditions change.
DAVID: Cells respond to new conditions with automatic answers following instructions they carry and by adding methylation for epigenetic responses.
dhw: Exit information theory (thank heavens), and back we go to your definitive rejection of a 50/50 possibility of cellular intelligence. I find it hard to believe that 3.8 billion years ago your God provided cells with instructions on how to deal with every single new problem/condition/ opportunity that would arise for the rest of the future, or that he popped/pops in to issue instructions ad hoc.
DAVID: You find it hard to believe in God, so I'm not surprised at your view. Living one-celled Archaea started knowing exactly how to handle themselves or nothing would have evolved. Do you have any thoughts about first life's capabilities? I've given it lots of thought.
We keep dodging between bacteria and archaea in our discussions of first life. Your question relates to both, and in both cases I would suggest that they did indeed start by knowing how to handle themselves and, crucially, not only how to reproduce but also how to adapt and diversify, and ultimately – through cooperation and communication – to build increasingly complex organs and organisms in the process we call evolution. The mechanism I propose is - surprise, surprise - a form of intelligence which enabled them to do all these things. And - surprise, surprise - I regard it as possible that this mechanism was designed by an unknown intelligence we call God.
bacteria
QUOTES: "Those studying bacteria and viruses tend to look to mutations as the major source of evolution.
"But really, both forces – mutation and existing genetic diversity – "can contribute sequentially, simultaneously, and even synergistically to the process of adaptation by natural selection", the researchers say."
DAVID: That mutation and diversity are equallly important seems a logical finding to me. This is a pure Darwinist study with no reference to intelligent design and I present it for general interest.
“Mutations” are generally associated with randomness, which would indeed be Darwinist, so I’m surprised at your acceptance of the term, but if we take it as simply meaning “changes”, then I would say that changes arising from adaptation to or exploitation of new conditions cause diversity.
Missing a part doesn’t matter
dhw: […] plasticity doesn’t take on new tasks. Plasticity is a quality of the cells. It is the cells that take on the tasks, i.e. I propose that they use their plasticity intelligently in order to initiate new processes in response to new requirements.
DAVID: And I view the neurons as programmed to handle all new tasks given to them.
Yes, I know. And you know I suggest that they have the intelligence to handle new tasks.
DAVID: How do cells become intelligent without God's help?
And:
I have asked you to explain the intelligence of cells without a God existing? You are either or. That is the other side of your agnosticism I'd like to hear about.
Once again, a cheerful goodbye to blathering information, and so we’ll be able to close this thread, but I must answer your question (yet again) since you have never quite understood the nature of agnosticism. I find the argument for design (in this case, that of the intelligent cell) perfectly logical, and am therefore open to the possibility of there being a designer. However, while I find it difficult to believe that chance (the other option, given an eternity and infinity of possible combinations) could create such complexity, I find it equally difficult to believe that there is an eternal, immaterial mind that had no source, and has simply been “there” forever, somehow creating vast quantities of matter out of its own immateriality, and exercising its powers of psychokinesis to manipulate the materials into galaxies and solar systems, bacteria and dinosaurs, humans and the duckbilled platypus.
Evolution: as immaterial information
by David Turell , Friday, June 17, 2022, 16:24 (888 days ago) @ dhw
dhw: Exit information theory (thank heavens), and back we go to your definitive rejection of a 50/50 possibility of cellular intelligence. I find it hard to believe that 3.8 billion years ago your God provided cells with instructions on how to deal with every single new problem/condition/ opportunity that would arise for the rest of the future, or that he popped/pops in to issue instructions ad hoc.
DAVID: You find it hard to believe in God, so I'm not surprised at your view. Living one-celled Archaea started knowing exactly how to handle themselves or nothing would have evolved. Do you have any thoughts about first life's capabilities? I've given it lots of thought.
dhw: We keep dodging between bacteria and archaea in our discussions of first life. Your question relates to both, and in both cases I would suggest that they did indeed start by knowing how to handle themselves and, crucially, not only how to reproduce but also how to adapt and diversify, and ultimately – through cooperation and communication – to build increasingly complex organs and organisms in the process we call evolution. The mechanism I propose is - surprise, surprise - a form of intelligence which enabled them to do all these things. And - surprise, surprise - I regard it as possible that this mechanism was designed by an unknown intelligence we call God.
How else could intelligence have appeared besides your usual surry back to a possilbe God?
bacteria
QUOTES: "Those studying bacteria and viruses tend to look to mutations as the major source of evolution.
"But really, both forces – mutation and existing genetic diversity – "can contribute sequentially, simultaneously, and even synergistically to the process of adaptation by natural selection", the researchers say."DAVID: That mutation and diversity are equallly important seems a logical finding to me. This is a pure Darwinist study with no reference to intelligent design and I present it for general interest.
dhw: “Mutations” are generally associated with randomness, which would indeed be Darwinist, so I’m surprised at your acceptance of the term, but if we take it as simply meaning “changes”, then I would say that changes arising from adaptation to or exploitation of new conditions cause diversity.
Mutations are code change in DNA. Why do you question my acceptance of them?
Missing a part doesn’t matterdhw: […] plasticity doesn’t take on new tasks. Plasticity is a quality of the cells. It is the cells that take on the tasks, i.e. I propose that they use their plasticity intelligently in order to initiate new processes in response to new requirements.
DAVID: And I view the neurons as programmed to handle all new tasks given to them.
Yes, I know. And you know I suggest that they have the intelligence to handle new tasks.
DAVID: How do cells become intelligent without God's help?
And:
I have asked you to explain the intelligence of cells without a God existing? You are either or. That is the other side of your agnosticism I'd like to hear about.dhw: Once again, a cheerful goodbye to blathering information, and so we’ll be able to close this thread, but I must answer your question (yet again) since you have never quite understood the nature of agnosticism. I find the argument for design (in this case, that of the intelligent cell) perfectly logical, and am therefore open to the possibility of there being a designer. However, while I find it difficult to believe that chance (the other option, given an eternity and infinity of possible combinations) could create such complexity, I find it equally difficult to believe that there is an eternal, immaterial mind that had no source, and has simply been “there” forever, somehow creating vast quantities of matter out of its own immateriality, and exercising its powers of psychokinesis to manipulate the materials into galaxies and solar systems, bacteria and dinosaurs, humans and the duckbilled platypus.
How likely is chance vs an active mind? The picket fence as usual.
Evolution: life solves climate change worries
by David Turell , Friday, June 17, 2022, 17:24 (888 days ago) @ David Turell
Polar bears on glaciers don't need sea ice:
https://www.sciencealert.com/polar-bears-discovered-secretly-living-in-seemingly-inhosp...
"A secret population of polar bears in Greenland has been discovered in a seemingly impossible habitat – one that, for most of the year, lacks the floating platforms of sea ice the beasts use to hunt. The unusual group, which scientists previously thought was part of another nearby population, has been hiding in plain sight for hundreds of years.
"The bears live on the steep slopes around fjords – long and narrow coastal inlets, where glaciers meet the ocean – and hunt on a patchwork of glacial ice that breaks up in these inlets. The new discovery suggests that some polar bears, at least, may be able to adapt to sea ice disappearing as climate change worsens, the study suggests.
***
"Until recently, scientists had identified 19 known subpopulations of polar bears (Ursus maritimus) living in the Arctic Circle. One of those populations spans a 1,988-mile (3,200 kilometers) stretch of the eastern coast of Greenland. But when researchers took a detailed look at this group to monitor their numbers, they realized the bears actually comprised two completely separate populations.
"Researchers analyzed 36 years' worth of tracking data from bears tagged with GPS collars and found that bears from southeast Greenland did not pass above a latitude of 64 degrees north, and bears from the northeast did not pass the same line in the other direction. Genetic sampling from individual bears confirmed that the southeastern bears were distinct from their northeastern neighbors.
***
"The new southeastern population contains around 300 individuals, although determining an exact number is tricky, the researchers said. The newfound group is the most genetically diverse out of all 20 populations in the Arctic, and genetic comparisons suggest that they have been isolated from the northeastern population for around 200 years, the researchers said.
***
"These sea ice conditions mimic those predicted for the rest of the Arctic by the end of the 21st century, based on previous studies, which should make the fjords unlivable for polar bears, the researchers said.
"But the southeastern bears seem to be managing surprisingly well without the sea ice.
"The researchers think that the bears are taking advantage of glacial mélange, or the bits of ice that break off the fjords' glaciers and into the sea. The bears likely use these freshwater ice patches in the same way they use sea ice to hunt, which allows them to feed themselves during the long spells when sea ice is absent from the region.
"'This suggests that marine-terminating glaciers may serve as previously unrecognized climate refugia," the researchers wrote.
"The southeastern population also lives nowhere near any human populations, and the area is believed to be too hard to reach for most hunters, which adds an extra layer of security for the bears. However, the steep slopes of the fjords can also be quite tricky for the polar bears to traverse, which may limit their movements.
***
"Sea ice will continue to decline across the Arctic, which will decrease the survival odds for most polar bears, she added."
Comment: with lessening sea ice in Canada the polar population is actually increasing. The climatologist alarmists forget about the resilience of living organisms to find livable spots. The estimations of ice loss b y these folks is constantly overestimated when compared to satellite photos.
Evolution: life solves climate change worries
QUOTE: The newfound group is the most genetically diverse out of all 20 populations in the Arctic, and genetic comparisons suggest that they have been isolated from the northeastern population for around 200 years, the researchers said.
DAVID: The climatologist alarmists forget about the resilience of living organisms to find livable spots.
A useful reminder that local environments play an all-important role in diversity, and yes indeed, living organisms not only find new habitations, but they also adapt to new conditions, and it is possible that the mechanisms enabling them to do so may also have enabled them to design new ways of exploiting those conditions. (Hence evolution.)
I’m afraid I’m far from convinced that all living organisms, including human beings, are going to find “livable spots”. The current refugee crisis could prove to be a minor blip compared to future migrations.I have no idea to what extent we are responsible for the famines, floods, droughts, hurricanes etc. which are wiping out whole species and communities, but these “natural disasters”, allied to other appalling consequences of human greed, selfishness and lust for power, don’t exactly fill me with hope for our children’s and grandchildren’s future. Could these thoughts be the wisdom of old age or its ramblings? Whichever they are, I wish we could find some Great Leaders who would find ways of reversing the headlong rush to destruction.
Evolution: life solves climate change worries
by David Turell , Saturday, June 18, 2022, 16:09 (887 days ago) @ dhw
QUOTE: The newfound group is the most genetically diverse out of all 20 populations in the Arctic, and genetic comparisons suggest that they have been isolated from the northeastern population for around 200 years, the researchers said.
DAVID: The climatologist alarmists forget about the resilience of living organisms to find livable spots.
dhw: A useful reminder that local environments play an all-important role in diversity, and yes indeed, living organisms not only find new habitations, but they also adapt to new conditions, and it is possible that the mechanisms enabling them to do so may also have enabled them to design new ways of exploiting those conditions. (Hence evolution.)
I’m afraid I’m far from convinced that all living organisms, including human beings, are going to find “livable spots”. The current refugee crisis could prove to be a minor blip compared to future migrations.I have no idea to what extent we are responsible for the famines, floods, droughts, hurricanes etc. which are wiping out whole species and communities, but these “natural disasters”, allied to other appalling consequences of human greed, selfishness and lust for power, don’t exactly fill me with hope for our children’s and grandchildren’s future. Could these thoughts be the wisdom of old age or its ramblings? Whichever they are, I wish we could find some Great Leaders who would find ways of reversing the headlong rush to destruction.
The weakness of NATO and the EU is frightening. Merkel's toadying up tp Putin was a disaster, as we now see. You are so right about leaders.
Evolution: how country ants urbanize
by David Turell , Sunday, October 02, 2022, 18:31 (781 days ago) @ David Turell
In common country ants:
https://www.sciencedaily.com/releases/2022/09/220930133700.htm
"Research by Texas A&M AgriLife Research scientists in the Texas A&M Department of Entomology showed a common ant species undergoes physiological and behavioral changes in unnatural settings.
***
"The study focused on Tapinoma sessile, a relatively small ant species commonly known as the house ant or sugar ant. It is the most common house-invading ant across the U.S.
"In its native environment, the house ant creates small, single-queen colonies typically found under leaf litter, rocks and logs, Vargo said. But in suburban/urban settings, these house ants build ever-expanding multi-queen colonies around human-made structures such as sidewalks, plant containers and landscape mulching.
***
"Odorous house ants were observed and analyzed in natural and disturbed locations around the country including Indiana, Arkansas, Colorado and California.
"The team analyzed the ant's chemistry, such as hydrocarbons, genetic makeups of colonies and behaviors, such as aggression toward familial and outsider ants, and found stark differences based on the environment, Vargo said.
"The study found that house ants in urban and natural areas showed adaptations that resulted in genetic concentration. Vargo said house ant queens in their natural habitat typically leave the colony they were born in, fly to another suitable location and attempt to establish a new colony. Queens in urban colonies stay in the nest and expand the colony rather than leave.
"As a result, urban queens were closely related and less aggressive toward ants with genetic relation. Behavioral analyses showed ants in super-colonies were aggressive toward ants with outside genetics.
"Additionally, polydomous colonies, which are ant colonies that are spatially separate but socially connected, were only present in urban habitats, Vargo said. This suggests house ants only create super-colonies in developed areas. Ants from different urban areas shared some genetic similarities, suggesting they are adapting to features that are common in the urban environment.
"As a next step, researchers plan to compare stable isotopes in the ants to look at dietary changes and how they might relate to natural vs. urban environments and possible contributing factors like temperature and the urban heat island effect."
Comment: so far it is a descriptive study showing how ants adapt easily to city life.
Evolution: stromatolites early appearance
by David Turell , Thursday, March 16, 2023, 19:38 (616 days ago) @ David Turell
Masses of cyanobacteria making oxygen:
https://www.discovermagazine.com/planet-earth/we-owe-our-lives-to-3-billion-year-old-st...
"Stromatolites weren’t one distinct creature, but many — they’re formed by colonies of cyanobacteria, microscopic organisms that use photosynthesis to sustain themselves. Living mostly in water, the colonies that made stromatolites were somewhat sticky, thanks to a compound they secreted, which caused sediment to build up around the cyanobacteria.
"Long before any kind of creatures walked the Earth, in a time that predates even the existence of marine or plant life, stromatolites were already here. Billions of years ago, our young planet, once too hot and its surface too molten to harbor life, had begun to cool. This allowed the first oceans to form.
"Earth was still not a hospitable place, but simple bacteria could survive and form colonies that would become stromatolites. For at least two billion years, these sticky little cyanobacteria stromatolites were the dominant life form on Earth.
"Stromatolites predate the dinosaurs by a wide margin. Not only were they once the primary form of life here, as bacteria they are also the oldest known life on Earth and are found in the oldest fossils ever discovered. Evidence of their existence stretches back as much as 3.5 billion years, to an almost unimaginably remote time known as the Archean Eon.
"Back then, Earth was nothing like it is now. Were you to visit it during Archean times, you wouldn’t last long: The atmosphere of the planet then was a mix of gasses like carbon dioxide, methane and ammonia, among others, that would have been toxic to Earth’s current inhabitants. But that wasn’t the case for stromatolites, of course. They thrived in this environment, even as they were slowly changing it.
"In fact, most of life as we know it would never have developed on earth without those tireless little cyanobacteria colonies. Thanks to the wonders of photosynthesis, stromatolites in their billions were busily absorbing sunlight, water and carbon dioxide while pumping out tiny bubbles of oxygen into the world’s oceans.
"That doesn’t sound like much of a task, but the stromatolites of early Earth kept at it long enough that, over the eons, the oceans became saturated with oxygen. Eventually, this critical gas began to be released into the atmosphere, creating an environment that would support more complex forms of life, including the dinosaurs and, eventually, us.
***
"To date, scientists know of a few locations around the world where stromatolites can still live — generally, they require very salty and sheltered water environments. One of the most famous destinations — famous among stromatolite fans, anyway — is Western Australia’s Hamelin Pool Marine Nature Reserve. Australia is also home to an even rarer form of cave-dwelling stromatolite.
"Other living stromatolites have also been found in the Bahamas and Mexico, among a few other places. The ecosystems that stromatolites require to thrive are delicate and most of these rare enclaves of living fossils are under threat."
Comment: This shows how carefully God planned evolution. He had things worked out all in order of a necessary progression. Just as the survival rate of 0.01%b was necessary.
Evolution: air-filled bones strong but lightweight
by David Turell , Saturday, March 18, 2023, 15:17 (614 days ago) @ David Turell
Helped dinosaurs to reach giant size:
https://www.sciencealert.com/this-adaptation-allowed-dinosaurs-to-not-only-survive-but-...
"It's sometimes difficult to imagine how the planet we call home, with its megalopolis cities and serene farmlands, was once dominated by dinosaurs as big as buses and five-story buildings.
"But recent research has helped deepen our understanding of why dinosaurs prevailed: the answer may lie in their special bones, structured like Aero chocolate.
"Brazilian paleontologist Tito Aureliano found that hollow bones filled with little air sacs were so important to dinosaur survival, they evolved independently several times in different lineages.
"According to the study, aerated bones evolved in three separate lineages: pterosaurs, technically flying reptiles, and two dinosaur lineages, theropods (ranging from the crow-sized Microraptor to the huge Tyrannosaurus rex) and sauropodomorphs (long-necked herbivores including Brachiosaurus).
***
"The variant the Brazilian team studied was aerated vertebrae bones, which would have enhanced the dinosaurs' strength and reduced their body weight.
***
"The study found no common ancestor had this trait. All three groups must have developed air sacs independently, and each time in slightly different ways. (my bold)
***
"Echoes of this dinosaur legacy lie in many animals alive today. It is not only long-dead animals which found this type of adaptation useful. Many bird species living today rely on hollow bones to fly.
"Others animals use the air sacs to buttress and strengthen their large bones and skulls, without weighing them down.
"An excellent example of this is the elephant skull. Inside elephant skulls are large air sacs which allow the animal to move its massive head and heavy tusks without straining the neck muscles.
"The human brain is also protected by two layers of hard, compact, bone (inner and outer tables) which sandwich a layer of softer, spongey, and aerated bone in between, known as the diploe. This allows our skulls to be light, but strong and able to absorb shocks to cranium."
Comment: note my bold, no precursors!!! This gives us another design gap along with the Cambrian, etc.
Evolution: gut biome influences health and longevity
by David Turell , Sunday, June 04, 2023, 01:16 (537 days ago) @ David Turell
Japanese study of centenarians:
https://www.sciencedaily.com/releases/2023/05/230531150147.htm
"Studying 176 healthy Japanese centenarians, the researchers learned that the combination of intestinal bacteria and bacterial viruses of these people is quite unique.
***
"Previous research has shown that the intestinal bacteria of old Japanese citizens produce brand new molecules that make them resistant to pathogenic -- that is, disease-promoting -- microorganisms. And if their intestines are better protected against infection, well, then that is probably one of the things that cause them to live longer than others," says Postdoc Joachim Johansen, who is first author of the new study.
"Among other things, the new study shows that specific viruses in the intestines can have a beneficial effect on the intestinal flora and thus on our health.
***
"'We found great biological diversity in both bacteria and bacterial viruses in the centenarians. High microbial diversity is usually associated with a healthy gut microbiome. And we expect people with a healthy gut microbiome to be better protected against aging related diseases," says Joachim Johansen.
"Once we know what the intestinal flora of centenarians looks like, we can get closer to understanding how we can increase the life expectancy of other people. Using an algorithm designed by the researchers, they managed to map the intestinal bacteria and bacterial viruses of the centenarians.
***
"'We have learned that if a virus pays a bacterium a visit, it may actually strengthen the bacterium. The viruses we found in the healthy Japanese centenarians contained extra genes that could boost the bacteria. We learned that they were able to boost the transformation of specific molecules in the intestines, which might serve to stabilise the intestinal flora and counteract inflammation," says Joachim Johansen, and Simon Rasmussen adds:
"'If you discover bacteria and viruses that have a positive effect on the human intestinal flora, the obvious next step is to find out whether only some or all of us have them. If we are able to get these bacteria and their viruses to move in with the people who do not have them, more people could benefit from them."
"Even though this requires more research, the new insight is significant, because we are able to modify the intestinal flora.
"'Intestinal bacteria are a natural part of the human body and of our natural environment. And the crazy thing is that we can actually change the composition of intestinal bacteria. We cannot change the genes -- at least not for a long time to come. If we know why viruses and intestinal bacteria are a good match, it will be a lot easier for us to change something that actually affects our health," says Simon Rasmussen."
Comment: The problems faced by theodicy is to have folks blame God for the bad things bacteria and viruses create. But this shows all the good things they can do. So the result of having bacteria and viruses is a mixed bag of results. That we must have exposure to bacteria and viruses for their good results. It is when bacteria and viruses end up in the wrong places they can cause much trouble. But on balance the good side wins with increasing human longevity. Critics of God (note dhw)see Him as cruel and sadistic. God cannot create a perfect form of life where there is no illness or cancer or other health disasters. What He has created works as well as it can. Be thankful for all the good God created. Dayenu! An old Hebrew word meaning it is enough.
Evolution: bacteria's' role in animal biomes
by David Turell , Tuesday, August 22, 2023, 17:09 (457 days ago) @ David Turell
A study of whale shark skin microbiome:
https://phys.org/news/2023-08-whale-shark-health-habitat-dietand.html
"Loss of habitat and human activities such as fishing and shipping pose a grave threat to wildlife but diseases driven by the smallest organisms in the ocean are a less understood side of marine conservation.
"These diverse and abundant microbiome communities perform complex processes on skin and tissue of marine wildlife—and Flinders University scientists are breaking ground by understanding their role in an endangered shark species and to describe new marine microbes for the first time.
"In a new article, scientists from around the world have collaborated to sample microbes on the skin surface of the world's largest fish—the whale shark (Rhincodon typus)—at five of the most famous diving sites around the world,
***
"'While microbial species differ across the world, they work together to form a balanced network that contributes to the health of the sharks.
"'It is important to measure and analyze the distinct and diverse epidermal microbiome of the global whale shark populations to work towards understanding how the microbes affect the well-being and survival of this amazing animal.
"'The characteristics of a balanced microbial community are not well described for any species, but especially for sharks, which form a vital link in ocean food chains and ecosystems.
"'The microbes form a complex network pattern on the skin surface, which is consistent across sharks from each location, revealing characteristics of what comprises a balanced or unbalanced microbiome."
***
"Professor Dinsdale says the right balance of microbes are critical to the well-being and survival of the host with which they live.
"'In humans, for example, skin microbes are always present, and when these communities are 'healthy,' they go unnoticed; however, when they are unbalanced, they cause skin conditions such as dermatitis, or skin infections," she says.
"'As microbes are too small to see, it is important to gain an understanding of how these complex network patterns fit together for a healthy microbiome balance. Unbalanced interactions can lead to a loss of benefits for the host and can result in disease.
***
"Microscopic organisms conduct important processes including nitrogen and oxygen production in oceans, consuming organic matter and metabolizing carbohydrates."
Comment: more evidence of the important work microbiomes do. Only a tiny percentage of bacteria act badly.
Evolution: timing the Triassic extinction
by David Turell , Monday, November 16, 2020, 22:26 (1466 days ago) @ David Turell
200 million years ago with volcanic activity:
https://cosmosmagazine.com/history/palaeontology/volcano-link-to-end-of-triassic-extinc...
"Two hundred million years ago, the Triassic period was brought to a devastating end by extensive volcanic eruptions from the Central Atlantic magmatic province (CAMP), which formed as Pangea broke apart. As carbon dioxide spewed into the atmosphere, the Earth’s carbon cycle was disrupted, and the oceans became acidified.
"Delicate marine ecosystems collapsed, and a sweep of prehistoric creatures such as conodonts and phytosaurs went extinct – though somehow, plants, dinosaurs, pterosaurs and mammals scraped through. This new world allowed dinosaurs to expand their ecological niche and reign supreme for the next 135 million years.
"Evidence for this end-Triassic extinction event comes from two major compositional shifts observed in the carbon isotope record 200 million years ago, as extensive volcanism could have released isotopically light methane into the atmosphere.
***
“'Through our analysis of the chemical signature of these microbial mats, in addition to seeing sea-level change and water column freshening, we discovered the end-Triassic mass extinction occurred later than previously thought.”
"A drop in sea level in European basins – which may have been indirectly driven by volcanic activity on CAMP – caused localised environmental changes. The marine ecosystem became a brackish, shallow-water environment where microbial mats thrived.
***
"It is currently unclear exactly how much later the extinction event occurred. Grice says their new interpretation requires further reanalysis of the carbon isotope record, in order to gain a better understanding of the regional versus global effects of the CAMP.
"This research may also reshape our understanding of other mass extinction events – particularly those linked to volcanic activity – and could alert us to future potential mass extinctions on modern Earth."
Comment: The big extinctions certainly allowed marked shifts in the course of evolution. It is obvious that tectonic plate activity played a major role and is a requirement for a planet to host life.
Evolution: sudden flowering plant appearance
by David Turell , Thursday, January 28, 2021, 20:01 (1393 days ago) @ David Turell
It bothered Darwin and the issue may now be solved:
https://phys.org/news/2021-01-unravels-darwin-abominable-mystery.html
"The origin of flowering plants famously puzzled Charles Darwin, who described their sudden appearance in the fossil record from relatively recent geological times as an "abominable mystery". This mystery has further deepened with an inexplicable discrepancy between the relatively recent fossil record and a much older time of origin of flowering plants estimated using genome data.
"Now a team of scientists from Switzerland, Sweden, the UK, and China may have solved the puzzle. Their results show flowering plants indeed originated in the Jurassic or earlier, that is millions of years earlier than their oldest undisputed fossil evidence, according to a new study published in the scientific journal Nature Ecology & Evolution. The lack of older fossils, according to their results, might instead be the product of low probability of fossilization and the rarity of early flowering plants.
"'A diverse group of flowering plants had been living for a very long time shadowed by ferns and gymnosperms, which were dominating ancient ecosystems. This reminds me of how modern mammals lived for a long time laying low in the age of dinosaurs, before becoming a dominant component of modern faunas," said lead author Dr. Daniele Silvestro, from the University of Fribourg in Switzerland.
"Flowering plants are by far the most abundant and diverse group of plants globally in modern ecosystems, far outnumbering ferns and gymnosperms, and including almost all crops sustaining human livelihood. The fossil record shows this pattern was established over the past 80-100 million years, while earlier flowering plants are thought to have been small and rare. The new results show that flowering plants have been around for as many as 100 million years before they finally came to dominance.
***
"The new study, which was based exclusively on fossils and did not include genome data or evolutionary trees, shows an earlier age of flowering plants is not an artifact of phylogenetic analyses, but is in fact supported by palaeontological data as well."
Comment: We still don't know if the flowering plants appeared suddenly even if longer ago.
Evolution: cause of End-Ordovician
by David Turell , Thursday, July 14, 2022, 16:36 (861 days ago) @ David Turell
An ice age plus:
https://www.discovermagazine.com/the-sciences/the-first-mass-extinction-event-explained...
"Long before the dawn of humans, dinosaurs, insects or even trees, a cascade of unfortunate events threatened to end life on earth.
"During the Ordovician Period, around 485 to 444 million years ago, the diversity of marine life exploded. Trilobites and mollusks crawled on the ocean floor, plankton-like filter-feeders floated at all depths and coral and algae bloomed. Jawless fish, perhaps our oldest ancestors, drifted in shallow lagoons and deltas. Life may have also taken its first steps onto land during this period. Some researchers have speculated that Ordovician green algae may have migrated onto the shore with assistance from mycorrhizal fungi.
"However, sometime around 445 million years ago, 85 percent of species went extinct over the relatively short interval of 1.4 million years. This unprecedented die-off is now known as the earth’s first mass extinction, the Late Ordovician mass extinction or simply LOME. Many researchers have devoted time, or even careers, to uncovering the underlying forces of extinction. But pieces of the puzzle are still missing.
“'As you might imagine, trying to infer what exactly happened in the environment 445 million years ago is a fairly inexact process,” paleobiologist Charles Mitchell says. “But we can discern some things quite clearly.”
"What Caused the Ordovician Extinction
Around the time of the extinction, the earth’s climate underwent a series of significant changes. A period of warming and sea level rise was followed by an ice age. Glaciers encapsulated much of the ancient supercontinent Gondwana, a landmass that gave rise to parts of every major modern continent. Eventually the ice age gave way to warming once again.
"These climatic changes disrupted the ways in which nutrients like oxygen, carbon and nitrogen, cycled through the ocean at the time.
“'When you shift from greenhouse conditions to ice house conditions, there are going to be major changes in ocean circulation patterns,” Mitchell says.
"One prominent theory posits that an initial wave of extinction occurred when the ice age began. The organisms at the bottom of the food chain, algae and cyanobacteria, may have been slow to adjust to a colder climate. The same theory aligns the second wave of extinction with the end of the ice age. Warming temperatures may have caused a global “algal bloom,” much like the blooms caused by nutrient-rich wastewater in lakes and rivers today.
***
"While scientists will hotly debate the causes for decades to come, the outcomes of the extinction are clearer. All major groups of Ordovician organisms were affected — trilobites, brachiopods and bryozoans died off in large proportions. But, while subsequent mass extinctions selected broad categories of winners or losers, some species, from nearly every major group or organisms, survived the LOME. During the Silurian period, which succeeded the Ordovician, these survivors repopulated the oceans.
***
"By looking through thousands of graptolite fossils, Mitchell and his colleagues noticed something curious. The creatures were dying off, slowly, for long before the sharp decline associated with the mass extinction event.
“'Graptolites started going extinct considerably before the big pulse,” Mitchell says. “That means that whatever caused the turnover had to have been a longer-term event.”
"In other words, slow and incremental change eventually gave way to rapid decline."
Comment: all extinctions changed the course of evolution, but life never was destroyed and new forms charged on as if nothing every happened.
Evolution: a mass extinction in the Ediacaran
by David Turell , Thursday, November 10, 2022, 18:32 (742 days ago) @ David Turell
Just discovered:
https://www.sciencealert.com/scientists-uncover-evidence-of-what-may-be-earths-first-ma...
"Researchers from the US have uncovered evidence of one occurring earlier, around 550 million years ago during a period known as the Ediacaran.
***
"Because softer body parts typically don't fossilize as readily as harder, more mineralized bits of anatomy, researchers have typically suspected a relative absence of soft-bodied animals in the Ediacaran's later stages are simply the result of a failure to be preserved.
"But the global fossil record indicates otherwise.
"The team found that there was an overall increase in biodiversity between the earlier and middle stages of the Ediacaran, known as the Avalon (575 to 560 million years ago) and White Sea stages (560 to 550 million years ago).
"'We find significant differences in the feeding mode, life habit, ecological tier, and maximum body size between the Avalon and White Sea assemblages," the team writes in their paper.
***
"All types of feeding modes and life habits experienced similar losses, with only 14 genera still seen in the Nama out of 70 known groups from the earlier White Sea stage. If more newly evolved species had taken over, there also would have been temporal overlap between the new and the old species. This wasn't observed, the team argue, ruling out biotic replacement.
"'The decline in diversity between these assemblages is indicative of an extinction event, with the percentage of genera lost comparable to that experienced by marine invertebrates during the 'Big 5' mass extinctions," Evans and colleagues write.
"Many of the White Sea animals that survived the extinction event and remained in the Nama period were large, frond-like organisms with a high surface area to volume ratio. This could be a sign these animals were adapting to deal with a reduction in oceanic oxygen.
"'By maximizing the relative proportions of cells in direct contact with seawater, high surface-area taxa would have been comparatively better adapted to survive in low-oxygen environments," the team explains.
"There is also recent geochemical evidence to support this idea, with a 2018 study finding signs of extensive ocean anoxia that covered more than 20 percent of the seafloor at the end of the Ediacaran.
"'Thus, our data support a link between Ediacaran biotic turnover and environmental change, similar to other major mass extinctions in the geologic record," the team concludes."
Comment: not a surprising finding considering the other major events. Note the new ease of finding 'soft body' forms
Evolution: not always simple to complex
by David Turell , Thursday, November 10, 2022, 20:20 (742 days ago) @ David Turell
One animal proves the point:
https://phys.org/news/2022-11-ancient-simple.html
"Researchers at the University of Nottingham have solved an important piece of the animal evolution puzzle as their new study reveals that our ancient ancestors were more complex than originally thought.
"Way back in our distant evolutionary history, animals underwent a major innovation. They evolved to have a left and right side, and two gut openings. This brought about a plethora of significant advantages in terms of propelling themselves directly forward at increased speed through the early seas, finding food, extracting nutrients, and/or avoiding being eaten.
"It was such a successful strategy that, today, we share our planet with a huge diversity of other animals with bilateral symmetry and two gut openings just like us. They include animals as diverse as starfish, sea cucumbers, elephants, humans, crickets, and snails. They also include an enigmatic group of very simple marine worms called Xenacoelomorphs, who lack many of the complex features of their fancier looking cousins.
***
"For years, scientists have debated who is more closely related to who in this diverse collection of bilaterally symmetrical animals. Some experts argue that Xenacoelomorphs mark the first group to branch in that major jump in innovation from animals with circular body plans (e.g. jelly fish and corals) to bilateral symmetry. If this was the case, then the first bilaterian itself was also a very simple animal. Others argued for different placements of Xenacoelomorphs on the family tree.
"However, a research team, led by Dr. Mary O'Connell at the University of Nottingham has found that Xenacoelomorphs branch much later in time, they are not the earliest branch on the bilaterian family tree, and their closest relatives are far more complex animals like star fish. This means that Xenacoelomorphs have lost many of the complex features of their closest relatives, challenging the idea that evolution leads to ever more complex and intricate forms. Instead, the new study shows that loss of features is an important factor in driving evolution."
Comment: if a designer is involved, He can take any direction He wishes, just like the jump in Cambrian forms. And yes, to forestall the obvious, this jumping around suggests free-for-all if your thinking is skewed toward a human-like God.
Evolution: a mass extinction in the late Devonian
by David Turell , Wednesday, March 15, 2023, 18:55 (617 days ago) @ David Turell
Studies in 350 million year-old shale:
https://www.livescience.com/one-of-earths-biggest-mass-extinctions-caused-by-rising-sea...
"Depleting oxygen and rising hydrogen sulfide levels in the oceans may have been responsible for one of Earth's most significant mass extinctions more than 350 million years ago, a new study finds.
***
"Researchers studied samples of black shale from the Bakken Formation, a 200,000-square-mile (518,000 square kilometers) region partly laid down during the late Devonian that encompasses parts of North Dakota and Canada and is one of the largest contiguous deposits of natural gas and oil(opens in new tab) in the United States. The team found evidence that Earth experienced periods of oxygen depletion and hydrogen sulfide expansion, which likely contributed to the sweeping extinction events that ravaged Earth during the Devonian period (419.2 and 358.9 million years ago), or the "Age of Fishes."
"Hydrogen sulfide forms when algae decomposes on the ocean floor. The decomposition process also depletes the area of oxygen.
***
"To better the Devonian extinctions, the research team analyzed more than 100 core samples drilled from black shale deposits in the Bakken Formation. This organic-rich sediment accumulated near the end of the Devonian period, recording the environment within its chemical makeup.
"The team found evidence of "anoxic events," where waters were completely depleted of oxygen, they reported in the study, published March 8 in the journal Nature(opens in new tab).
These sharp drops "are likely linked to a series of rapid rises in sea level" due to the melting of South Pole ice sheets during the preceding Silurian period (443.8 million to 419 million years ago), Kaufman said in the statement.
***
"Simultaneously, plants transformed rocky land into soil, which would have released nutrients to flow into those rising oceans. The influx of nutrients into the oceans would have triggered massive algal blooms, which died, decomposed and soaked up oxygen. As they decomposed, the dead algae released hydrogen sulfide, increasing levels of the toxic chemical.
"The oxygen-depleted seas were too much for Devonian marine life. Researchers estimate that 75% of all life went extinct by the end of the Devonian.
***
"The team found evidence of "anoxic events," where waters were completely depleted of oxygen, they reported in the study, published March 8 in the journal Nature(opens in new tab).
"These sharp drops "are likely linked to a series of rapid rises in sea level" due to the melting of South Pole ice sheets during the preceding Silurian period (443.8 million to 419 million years ago), Kaufman said in the statement.
"Simultaneously, plants transformed rocky land into soil, which would have released nutrients to flow into those rising oceans. The influx of nutrients into the oceans would have triggered massive algal blooms, which died, decomposed and soaked up oxygen. As they decomposed, the dead algae released hydrogen sulfide, increasing levels of the toxic chemical.
"The oxygen-depleted seas were too much for Devonian marine life. Researchers estimate that 75% of all life went extinct by the end of the Devonian."
Comment: I do not think God controlled this event but it allowed Him to bring new organisms on the scene.
Evolution: one size does not fit various microbiomes
by David Turell , Tuesday, April 14, 2020, 21:14 (1682 days ago) @ David Turell
Human microbiome research findings do not fit lots of other species:
https://www.quantamagazine.org/why-is-the-microbiome-important-in-some-animals-but-not-...
"But the human example is not a good model for what’s going on in a diverse range of species, from caterpillars and butterflies to sawflies and shrimp, to some birds and bats (and perhaps even some pandas). In these animals, the microbes are sparser, more transient or unpredictable — and they don’t necessarily contribute much, if anything, to their host. “The story is more complex,” said Sarah Hird, an evolutionary biologist and microbial ecologist at the University of Connecticut, “more fuzzy.”
***
"So it’s not such a leap to think there could be animals that don’t have such relationships at all, or that have relationships that play by different rules. “I think there’s now an increasing realization that there’s this whole spectrum of kinds of associations that you might find,” Agashe said.
***
“'There’s a whole range of different kinds of lifestyles that are going to be really complicated.” Perhaps the transient, low-abundance microbes are doing something more nuanced, or perhaps they represent an early step in the formation of a more stable evolutionary relationship. Maybe they remain neutral most of the time and only become functional in certain contexts. Some researchers, for instance, posit that these microbes could protect a host from infections simply by taking up space in the gut and blocking out pathogens. Furthermore, bacteria that have adapted to a toxic plant or other hazard might be helpful even if they’re acquired just temporarily, without ever engaging in a formal symbiosis.
***
“'If you think about it, there’s lots of reasons not to have an established microbiome,” Agashe said. “It’s actually not surprising that there are animals that have gone a different route. … But the key thing is, we don’t know why” — what factors lead to and enable the formation and maintenance of a microbiome, and conversely, what factors might prevent those relationships.
"Caterpillars, dragonflies, certain ants and other animals provide a way to investigate the potential disadvantages of long-lasting symbiotic relationships with live-in microbes; such disadvantages tend to be difficult to measure and test. Researchers suspect that these animals might be selectively avoiding certain potential penalties of symbiosis: Bacteria might compete with their host for nutrients, for instance, or aggravate the immune system.
For some animals, those risks might outweigh the potential benefits. If they have already evolved whatever enzymes or behaviors they need to live on their own, they’re no longer bound by selective pressures to acquire a microbiome.
***
"...the findings illustrate that there’s much to learn by comparing species — and that there’s much to lose by making premature assumptions about what their relationships with bacteria might look like. At the very least, this means proceeding with greater caution when translating studies done in flies, mice and other model organisms to humans. (Already, significant differences have been found in the gut microbiomes that develop in wild mice versus lab-bred mice — and the former have often proved to be a more accurate model of how certain experimental drugs might function in humans.)
***
"Scientists’ emerging awareness of the diverse relationships that animals share with microbes “should make us really cautious about drawing inferences using fruit flies as models for gut microbiome importance or interactions, because fruit flies might be operating from a very different fundamental starting point compared to humans. It’s the same thing with mice.'”
Comment: Bacteria are still here to be helpful in certain microbiomes, where ever they are needed. They are not needed everywhere is the point of this paper. The answer to why or why not needs much more major research.
evolution: earliest land fungi
by David Turell , Wednesday, January 22, 2020, 19:42 (1765 days ago) @ David Turell
Found in the Congo dated between 715 and 810 million years ago:
https://phys.org/news/2020-01-mushrooms-earlier-previously-thought.html
"The origin and evolution of the kingdom Fungi—more commonly known as mushrooms—are still very mysterious. Only 2 percent of species have been identified, and their delicate nature means fossils are extremely rare and difficult to discern from other microorganisms. Until now, the oldest confirmed mushroom fossil was 460 million years old.
***
"The fossilized remains of mycelium (a network of interconnected microscopic strands) were discovered in rocks between 715 and 810 million years old—during a time in Earth's history when life on the continents' surface was in its infancy. These ancient rocks, found in the Democratic Republic of the Congo and part of the collection of the Africa Museum on Tervuren, formed in a lagoon or coastal lake environment. "The presence of fungi in this transitional area between water and land leads us to believe that these microscopic mushrooms were important partners of the first plants that colonized the Earth's surface around 500 million years ago," explains Steeve Bonneville, professor at the Université libre de Bruxelles and coordinator of the study.
"Previous mushroom fossils had been identified only based on the morphology of organic remains extracted from rocks using corrosive acid compounds. "This method damages the chemistry of organic fossils and only allows morphological analysis, which can lead to incorrect interpretations because certain morphological characteristics are common to different branches of living organisms," Bonneville says.
***
"'This is a major discovery, and one that prompts us to reconsider our timeline of the evolution of organisms on Earth," says Bonneville. "The next step will be to look further back in time, in even more ancient rocks, for evidence of those microorganisms that are truly at the origins of the animal kingdom.'"
Comment: As we know, the advance of evolution from bacteria takes lots of time
evolution: biological design
by David Turell , Monday, September 28, 2020, 15:07 (1516 days ago) @ David Turell
All the necessary layers:
https://uncommondescent.com/intelligent-design/jonathan-bartlett-elon-musk-inadvertentl...
"When referring to the process of building a manufacturing plant, he said, “The extreme difficulty of scaling production of new technology is not well understood. It’s 1000% to 10,000% harder than making a few prototypes. The machine that makes the machine is vastly harder than the machine itself.” — Elon Musk (@elonmusk) September 22, 2020
"Indeed, whatever the difficulty of creating life in the lab, making individual prototypes is not nearly as problematic as making “the machine that makes the machine,” which all reproducing living cells can do. That is, the ability of an organism to reproduce is at least an order of magnitude harder that the ability of an organism to just live.
"A comment: "What most people don’t realize, is, that when you look at any species, there are always multiple layers of design
"for example – a hummingbird
"Layer #1: the design of the humming itself – the shape of the body, the shape / geometry of the wings, its weight, the frequency of its wing-flaps … in other words, lots of sophisticated design features need to be met so the hummingbird flies as it flies including the hovering-ability.
"Layer #2: the design of hummingbird step-by-step self-assembly (biologists call it – the development). Because, as you may know, there are no workers, no parts / materials suppliers. There is nobody who assembles a hummingbird together. This self-assembly is an fully automated process, even in 21st century – an engineering SCIFI.
(Layer #2 – This is what Elon Musk was referring to)
"Layer #3: the materials the hummingbird’s body is made of. All sophisticated materials, perfectly developed and adjusted to fulfill its function. What is remarkable, all these sophisticated materials, some very lightweight and strong, are developed at species’s body temperature, no fire of thousands of degrees is needed. Material-engineers can only wonder…
"Layer #4: the design of automated maintenance / repair processes. Almost everything gets repaired. Broken bones, eye’s cornea, the skin,, even DNA molecule gets repaired… I am sure that a biologist could provide a very long list of what gets repaired.
"I never understood how Darwinists imagine the evolution of any repair-process. How an unguided natural process with no foresight can ever recognize a problem (e.g. broken leg). How does unguided natural process know, that this leg needs to be repaired, when, and in what way. Any repair process is an undeniable proof of design."
Comment: These comments make it easy to note that obvious design is a proof of a designer, God. Put another way from the same article:
"Indeed, whatever the difficulty of creating life in the lab, making individual prototypes is not nearly as problematic as making “the machine that makes the machine,” which all reproducing living cells can do. That is, the ability of an organism to reproduce is at least an order of magnitude harder that the ability of an organism to just live."
evolution: finding useful proteins
DAVID: Folded proteins of large size are necessary because they have specific functions in the biochemistry of life and are absolutely vital for life to exist. they are why the Darwin theory does not work:
https://www.asiatimes.com/2019/09/opinion/pseudo-science-the-bible-and-human-freedom/
QUOTE: The new science of DNA proves mathematically that the odds of a random mutation leading to an improvement in the adaptability of a living organism are effectively zero,
QUOTE: In short, the evolutionary biologists can’t explain how animal life made the great leap from protozoans to arthropods in the Cambrian Explosion, let alone how natural selection through random mutation might have shaped the human mind.
DAVID: the bolded paragraph shows why Darwin's materialistic chance mutation type evolution cannot work.
Yes, from the very beginning of this website, we have rejected Darwin’s theory that random mutations are the driving force of evolution. That is one part of Darwin’s theory. He himself recognized the problem of the Cambrian, and if only he had known about the astonishing complexities of the cell, one can imagine that he might well have embraced the concept of the intelligent cell and “natural genetic engineering”, which offers a credible alternative to randomness and yet still allows for the input of what he calls the “Creator”, who may have designed the intelligent cell in the first place.
DAVID: (under “FINDING TINY PROTEINS”): short modifications of large proteins, by having the small proteins inserted into larger ones is a neatly designed way to alter function on the fly. Further note these are the result of DNA and RNA work considered to come from 'junk' DNA, again reducing the amount of so-called junk DNA. Discoveries like this are pointing to the necessary conclusion that it is all designed.
Indeed, the case for design is the strongest possible case for the existence of your God, and thank you for this vast accumulation of evidence. If only the very concept of a God without origin who created life was not every bit as complex and mysterious as the origin of life itself, I would come down off my agnostic fence!
evolution: finding useful proteins
by David Turell , Tuesday, October 22, 2019, 14:53 (1858 days ago) @ dhw
DAVID: Folded proteins of large size are necessary because they have specific functions in the biochemistry of life and are absolutely vital for life to exist. they are why the Darwin theory does not work:
https://www.asiatimes.com/2019/09/opinion/pseudo-science-the-bible-and-human-freedom/QUOTE: The new science of DNA proves mathematically that the odds of a random mutation leading to an improvement in the adaptability of a living organism are effectively zero,
QUOTE: In short, the evolutionary biologists can’t explain how animal life made the great leap from protozoans to arthropods in the Cambrian Explosion, let alone how natural selection through random mutation might have shaped the human mind.DAVID: the bolded paragraph shows why Darwin's materialistic chance mutation type evolution cannot work.
dhw: Yes, from the very beginning of this website, we have rejected Darwin’s theory that random mutations are the driving force of evolution. That is one part of Darwin’s theory. He himself recognized the problem of the Cambrian, and if only he had known about the astonishing complexities of the cell, one can imagine that he might well have embraced the concept of the intelligent cell and “natural genetic engineering”, which offers a credible alternative to randomness and yet still allows for the input of what he calls the “Creator”, who may have designed the intelligent cell in the first place.
DAVID: (under “FINDING TINY PROTEINS”): short modifications of large proteins, by having the small proteins inserted into larger ones is a neatly designed way to alter function on the fly. Further note these are the result of DNA and RNA work considered to come from 'junk' DNA, again reducing the amount of so-called junk DNA. Discoveries like this are pointing to the necessary conclusion that it is all designed.
dhw: Indeed, the case for design is the strongest possible case for the existence of your God, and thank you for this vast accumulation of evidence. If only the very concept of a God without origin who created life was not every bit as complex and mysterious as the origin of life itself, I would come down off my agnostic fence!
Design is the key to the discussion. It requires a designer.
evolution: finding useful proteins ; enormous odds
by David Turell , Sunday, July 05, 2020, 20:56 (1600 days ago) @ David Turell
An entry from an IDer:
https://evolutionnews.org/2020/07/mistakes-our-critics-make-protein-rarity/
"...our immunity system can manufacture at least a trillion unique antibodies, and at least one will typically bind to any invading germ. This achievement is possible since the probability is relatively high for a random search to locate an amino acid sequence that sticks to some molecule, so the required amount of new information is relatively small. For instance, only a few billion trials are needed to find an antibody that can bind to an antibiotic molecule and break it apart. The problem is that this task is much easier than randomly generating an entirely new amino acid sequence that folds into an enzyme’s three-dimensional structure and performs the required complex structural (conformational) changes. Highly specified dynamic structures are required to support an enzyme’s often very complex chemical activities.
"In contrast, antibodies are comprised of unchanging constant regions that already provide the needed structural support, so only generating functional variable regions is required. The difference between a random search finding an operative variable region and a random search stumbling upon a novel functional enzyme is comparable to the difference in difficulty of pushing a loaded wheelbarrow across a flat driveway and pushing it across a tightrope suspended across Niagara Falls.
***
"In the past, the general public lacked the technical knowledge to decipher the science underlying the evidence for protein rarity, so they were powerless to see past the critics’ smoke and mirrors (see here, here, and here). Fortunately, a straightforward analysis of the research by protein expert Dan Tawfik (see here, here, and here) not only confirms and generalizes Axe’s results, but is much more accessible to the public. Tawfik’s research on β-lactamase yielded results that almost perfectly confirm Axe’s rarity estimate. In addition, the former’s research and research on the HisA enzyme demonstrate that randomly altering less than 2 percent of the enzymes’ amino acids disables them over half of the time. And, altering 10 percent will disable them nearly 100 percent of the time. In contrast, altering 2 percent of a paragraph written in English is usually barely noticeable, and altering 10 percent still leaves a paragraph largely readable. Therefore, protein sequences are often far rarer than readable English sentences, so they are even more difficult to generate by chance."
Comment: There are two parts to this discussion. First our amazing immune system which is designed to add a specific addition to an existing functional base molecule. The system looks at the invader, isolates an attack point and creates an answering protein segment copied to destroy the invader. That system finds answers rather easily. What the discussion compares it to is findings a functional enzyme to do a precise job in a specific molecular process. Enzymes are enormous protein molecules with specific configurations. They must be designed to fit the need. That is not easy, which strongly suggests they must be designed by a designer as the odds of it happening by chance are vanishingly small.
evolution: a transitioning form out from the Cambrian
by David Turell , Wednesday, November 04, 2020, 23:03 (1478 days ago) @ David Turell
An arthropod with five eye stalks and visible soft parts:
https://cosmosmagazine.com/nature/evolution/five-eyes-and-quite-a-story-to-tell/?utm_so...
"The fossilised 520-million-year-old creature shown above had five eyes on stalks, but that’s only part of its attraction.
"Its body structure combines features from different groups of arthropods, researchers have discovered, providing new insights into the early evolutionary history of the most successful animals on Earth.
***
"The previously undescribed species Kylinxia zhangi is named after a chimeric creature in Chinese mythology called Kylin and the Chinese word for shrimp. Six specimens were discovered in the Chengjiang Biota in Yunnan, which offers the most complete early animal fossils of the Cambrian era.
“'Owing to very special taphonomic conditions, the Kylinxia fossils exhibit exquisite anatomical structures,” says co-author Zhao Fangchen. “For example, nervous tissue, eyes and digestive system: these are soft body parts we usually cannot see in conventional fossils”
"Detailed anatomical examination shows that Kylinxia has distinctive features of true arthropods, including a hardened cuticle, a segmented trunk and jointed legs.
"However, it also has characteristics present in very ancestral forms, including the five eyes of Opabinia, known as the Cambrian “weird wonder”, and the raptorial appendages of Anomalocaris, the giant apex predator in the Cambrian ocean.
***
“'Our results indicate that the evolutionary placement of Kylinxia is right between Anomalocaris and the true arthropods,” says co-author Zhu Maoyan. “Therefore, our finding reached the evolutionary root of the true arthropods.”
"As such, adds Zheng, it contributes “strong fossil evidence for the evolutionary theory of life'”.
Comment: This doesn't close the Ediacaran/Cambrian enormous morphological gap, but it begins to fill in the transitional gaps to more modern forms from Cambrian animals.
evolution: first amphibian with slingshot tongue
by David Turell , Friday, November 06, 2020, 19:50 (1476 days ago) @ David Turell
99 million years ago:
https://www.sciencenews.org/article/ancient-amphibian-oldest-known-animal-slingshot-tongue
"A tiny amphibian that lived 99 million years ago had a secret weapon: A tongue that shot out of its mouth like a bullet to snatch its prey. It’s the earliest known example of this “ballistic tongue” style of predation, researchers say.
"The amphibian is a new species, represented by a few tiny bits of skeleton and soft tissue discovered in chunks of Myanmar amber. The centerpiece of these finds is a newly discovered complete skull, exquisitely preserved in 3-D, that includes a long thin bone connected to the creature’s neck, with some remnants of tongue attached to the end.
"The creature, which measured just 52 millimeters long from snout to pelvis (not including a tail), used this bone to shoot its tongue out of its mouth and catch prey. This “sit-and-wait” style of predation is similar to that of a modern chameleon, researchers report in the Nov. 6 Science.
***
'These amphibians were widespread — scientists have dug up thousands of albanerpetontid fossils in locations from Spain to Canada to Japan. These fossils built a picture of a wacky, salamander-like creature with pointy claws, an unusual jaw structure and a four-legged body covered in scales. Based on their scaly heads and claws, scientists thought that the creatures were probably burrowers, like some modern salamanders. But that didn’t explain some of the features.
***
“'These specimens completely change our understanding about albanerpetonids,” DeMar says.
***
"The skull fossil clears up a lot of confusion about this amphibian group’s lifestyle, Gardner says, but in other ways, albanerpetontids remain as enigmatic as ever. That’s because they’re so unusual, with so many odd features, that it’s difficult to sort out where they belong on the evolutionary tree of life, and how they’re related to other amphibians, living and extinct.
"Still, this find just goes to show that “one or two fossils can really upset the apple cart,” says Gardner, who admits that he, like many paleontologists, previously thought that this group were burrowers. “It’s very exciting. And I’m quite happy to be wrong.'”
Comment: this requires complex new designs with a brain that can handle the calculus calculations to aim the tongue accurately toward a rapidly flying insect. Design required.
evolution: playing possum
by David Turell , Wednesday, March 03, 2021, 20:11 (1359 days ago) @ David Turell
How is this developed?:
https://www.sciencedaily.com/releases/2021/03/210302212004.htm
"Many animals feign death to try to escape their predators, with some individuals in prey species remaining motionless, if in danger, for extended lengths of time.
"Charles Darwin recorded a beetle that remained stationary for 23 minutes -- however the University of Bristol has documented an individual antlion larvae pretending to be dead for an astonishing 61 minutes. Of equal importance, the amount of time that an individual remains motionless is not only long but unpredictable. This means that a predator will be unable to predict when a potential prey item will move again, attract attention, and become a meal.
"Predators are hungry and cannot wait indefinitely. Similarly, prey may be losing opportunities to get on with their lives if they remain motionless for too long. Thus, death-feigning might best be thought of as part of a deadly game of hide and seek in which prey might gain most by feigning death if alternative victims are readily available.
***
"'We use this approach to consider a small bird visiting patches of conspicuous antlion pits and show that antlion larvae that waste some of the predator's time, by 'playing dead' if they are dropped, change the game significantly. In a sense, they encourage the predator to search elsewhere."
"The modelling suggests that antlion larvae would not gain significantly if they remained motionless for even longer than they actually do. This suggests that in this arms race between predators and prey, death-feigning has been prolonged to such an extent that it can hardly be bettered.
"Professor Franks added: "Thus, playing dead is rather like a conjuring trick. Magicians distract an audience from seeing their sleights of hand by encouraging them to look elsewhere. Just so with the antlion larvae playing dead -- the predator looks elsewhere. Playing dead seems to be a very good way to stay alive.'"
Comment: How is this learned, since it implies conceptual thinking? How is the length of time that one plays possum determined? Perhaps God designed this mechanism.
evolution: when nothing happens; living fossil
by David Turell , Monday, March 07, 2022, 16:04 (990 days ago) @ David Turell
Tuataras are weird and basically unchanged for 190 million years:
https://www.tasnimnews.com/en/news/2022/03/07/2678410/fossil-reveals-secrets-of-one-of-...
"New Zealand’s tuatara look like somber iguanas. But these spiny reptiles are not actually lizards. Instead, they are the last remnant of a mysterious and ancient order of reptiles known as the Rhynchocephalians that mostly vanished after their heyday in the Jurassic period.
"And they truly are the oddballs of the reptile family. Tuatara can live for more than a century, inhabit chilly climates and are able to slide their jaws back and forth to shear through insects, seabirds and each other. They even possess a rudimentary third eye below the scales on the top of their heads that may help them track the sun.
"These bizarre traits make tuatara an evolutionary enigma, and a spotty fossil record of its long-lost kin has confounded paleontologists. Likely outcompeted by lizards and snakes, virtually all Rhynchocephalians went extinct at the close of the Mesozoic Era. Many left little more than dusty tooth and jaw fragments behind.
***
"The remarkable fossil was discovered in 1982 during an expedition to the Kayenta Formation, a fossil-rich outcrop in northern Arizona. This band of red rock was deposited during the early Jurassic period when the dinosaur reign was in its infancy. Around this primeval floodplain, early dinosaurs like the crested Dilophosaurus mingled with burly, crocodile-like creatures encased in armor. Underfoot scurried primitive, shrew-like mammals and this strange new reptile.
***
"The fossil illustrates that the bodies of modern tuatara emerged in the Jurassic era and have changed little in 190 million years. This supports the popular distinction that these remnant reptiles are “living fossils.” But Dr. Simões emphasized the differences: For instance, modern tuatara jaws end in a set of beaklike fused teeth that are absent in Navajosphenodon. (my bold)
"According to Kelsey Jenkins, a doctoral student at Yale who specializes in early reptile evolution, many lineages of Rhynchocephalians exhibited little change throughout their history. However, 200 million years is extreme. “The only things that are that highly conserved are things like horseshoe crabs and cockroaches — not a decent-sized reptile,” said Ms. Jenkins, who was not involved with the new study.
Researchers argue this lack of change may represent natural selection on overdrive. “Slow rates of evolution don’t necessarily mean absence of evolution,” Dr. Simões said. Basically, it’s the evolutionary equivalent of the adage: “If it ain’t broke, don’t fix it.” (my bold)
"While the discovery of Navajosphenodon helps flesh out a crucial chapter in tuatara evolution, much of this reptile’s back story remains hazy. Without more fossil discoveries, it will be difficult for scientists to determine exactly why these lone survivors appear to possess evolutionary cheat codes. (my bold)
“'Why the modern tuatara and their lineages have evolved so slowly for such a long period of time is a bigger question and a bit harder to get at,” Dr. Pierce said. “We need more fossils.'”
Comment: Note the bolds. They raise interesting questions. Darwinists wonder why no evolution. They expect responses to changing conditions. The tiny changes noted in Tuataras are just minor adaptations, not real advancing evolution. Why should there have to be 'cheat codes'? And 'natural selection in overdrive' implies 'where is the expected advance'? As if natural selection is a magical driving force that didn't have to work here. This is a distorted view purely based on an unthinking acceptance of pure old Darwin evolution theory. For my standpoint it all makes sense with God running the show. The Tuataras are in a minor ecosystem that needed no tweaking to maintain the supply of food need that is required since everyone has to eat.
evolution: symbiosis and metabolism swapping
by David Turell , Tuesday, May 03, 2022, 23:36 (933 days ago) @ David Turell
Not strictly Darwin mutation processes:
https://phys.org/news/2022-05-biologists-traits-tree-life.html
modern research suggests that the game of life is far more complicated than we had anticipated. There are opportunities to swap cards and even steal other players' hands.
Researchers at UC Santa Barbara have been investigating the effects of this strategy, particularly the ability to acquire metabolic pathways. The scientists found that adopting another metabolism can have major competitive consequences, with ramifications to a species' evolution and ecology.
***
Examples of acquired metabolisms abound in nature. Some are familiar, like the microbes in a cow's gut that enable it to digest cellulose. Others are more common but less well-known. For instance, consider the symbiotic fungi that help plants source minerals from the soil. And then there are truly unusual acquired metabolisms, like sea slugs that steal chloroplasts from their food so they can photosynthesize.
***
The authors considered two single-celled eukaryotes (organisms whose cells contain a nucleus). The first, a species in the genus Colpidium, subsists on a diet of smaller microbes. The second, Paramecium bursaria, shares its counterpart's diet, but had also acquired the ability to photosynthesize at some point in the past.
The researchers analyzed the two microbes under four different light conditions. Colpidium got along fine no matter the setting; however, P. bursaria fared much better under brighter conditions, where it could take advantage of its unique ability.
Then the scientists pitted the microbes against each other. They observed a gradient of competitive advantage across different light levels. In the dark, Colpidium outcompeted P. bursaria. Meanwhile, under bright conditions, P. bursaria dominated.
"I think it gets to this idea that you can't be good at everything," said co-author Holly Moeller, an assistant professor in the Department of Ecology, Evolution and Marine Biology. Adapting to an acquired metabolism might have come at the expense of P. bursaria's hunting prowess. But at high light levels, the boost from photosynthesis more than offsets this handicap.
Remarkably, the two microbes were able to coexist under intermediate light conditions. P. bursaria's acquired phototrophy enabled it to avoid direct competition with Colpidium in what scientists call "niche partitioning."
"The results demonstrate that symbiosis and acquired metabolism can drastically affect community dynamics. "Expanding on your metabolic repertoire has cascading implications on how you can make a living, and the extent to which you're going to shove other organisms out of the way," Moeller said.
***
"It's important to study how acquired metabolisms influence evolution and ecology because they're a fundamental part of life on Earth. For instance, we generally think of photosynthesis as a characteristic of plants. "But that's an ancient acquisition, too," said Moeller. "They inherited their chloroplasts from a eukaryotic ancestor that domesticated a cyanobacterium."
"'Mitochondria are also acquired from bacteria," added Hsu. In fact, both of these organelles have their own DNA, separate from a cell's nuclear genome.
"'This is how eukaryotes have been playing the game for some 2 billion years," Moeller remarked. And our simpler counterparts, prokaryotes, arguably engage in even more biological card-swapping. Many are able to directly share DNA in a process known as "horizontal gene transfer.'"
Comment: it is not just developing chance mutations. These combinations have purpose and easily can be seen as due to God's designing work.
evolution: symbiosis and reproduction
by David Turell , Wednesday, May 18, 2022, 15:58 (918 days ago) @ David Turell
In certain seafloor organisms:
https://www.sciencedaily.com/releases/2022/05/220517210412.htm
"Most bottom-dwelling marine invertebrate animals, such as sponges, corals, worms and oysters, produce tiny larvae that swim in the ocean prior to attaching to the seafloor and transforming into juveniles. A new study published in the Proceedings of the National Academy of Sciences (PNAS) and led by University of Hawai'i (UH) at Mānoa researchers revealed that a large, complex molecule, called lipopolysaccharide, produced by bacteria is responsible for inducing larval marine tubeworms, Hydroides elegans, to settle to the seafloor and begin the complex processes of metamorphosis.
***
"Most invertebrate larvae are capable of staying in the larval stage for extended periods of time until they find a right spot. In the study, led by Marnie Freckelton, a postdoctoral researcher at the Kewalo Marine Lab, a unit of the Pacific Biosciences Research Center (PBRC) in SOEST, the research team asked the question: how do 'right spots' cue larvae to settle and metamorphose?
"Metamorphosis is a profound change in the animal's form -- from a small swimming larva to an animal with a very different anatomy anchored to the seafloor. Although researchers have known that biofilms, thin layers comprised of bacteria, diatoms and small algae that blanket submerged surfaces, induce metamorphosis of a wide range of marine invertebrate larvae, the mechanism of induction remained poorly understood.
"In laboratory experiments with larval tubeworms, the team found that they would not settle on clean surfaces. They required a cue from a surface biofilm.
"The team isolated a single bacterial species, Cellulophaga lytica, that could, when formed into surface biofilm, induce the worm larvae to settle, and then we asked: what is it about that particular bacterium that causes the larvae to settle and metamorphose?" said Freckelton.
***
"'In fact, we have different strains of the same bacterial species obtained from Kaneʻohe Bay and Pearl Harbor, and the Hydroides larvae settle only in response to the one from Pearl Harbor," said Hadfield, who has been a researcher at the Kewalo Marine Lab in PBRC since 1968. "Furthermore, we found in our lab that larvae of the coral Pocillopora damicornis, which is abundant in Kaneʻohe Bay, will settle only in response to the Kaneʻohe Bay strain of the bacterium. This is a breakthrough, because it tells us about the specificity of certain bacteria that guide and maintain a community of animals where they occur.'"
Comment: not only is metamorphosis itself unexplained by Darwinism, but this also apparently necessary triggering mechanism is not explained either. The specificity of the trigger, a complex molecule, must be designed to work as it does.
evolution: gene continuity
by David Turell , Wednesday, May 18, 2022, 18:25 (918 days ago) @ David Turell
Evolution is not chopped up as dhw imagines:
https://phys.org/news/2022-05-important-genetic.html
"Having a head is quite an advantage. Although this may sound banal, it had to be tested in a long evolutionary process: As animal life developed, invertebrates initially dominated the oceans. These had already developed head structures, but the development of a novel, improved head led to the success of vertebrates. This "new head" allowed a wide spatial distribution and multiplication of sensory cells, and thus a much better perception of the environment. This was also essential for the development of a predatory lifestyle.
"When external stimuli are transmitted to the vertebrate brain, cranial sensory ganglia play an important role. These can be thought of as nerve nodes distributed throughout the head that receive information from the sensory organs. Until now, scientists did not know how exactly these ganglia were formed. A study which was published in Nature now reports answers.
***
"'Tunicates are like an evolutionary prototype for vertebrates," Rothbächer explains. "There is a large anatomical gap between the adults of these subphyla, as they are adapted to ecological niches. This complicates research on their evolution. Common structures and mechanisms can only be identified at the embryonic stage—our common ancestor was probably very similar to a tunicate larva."
"The study's model organisms were the lamprey, a primitive fish that resembles an eel and is often referred to as a "living fossil," and the tunicate Ciona intestinalis, which is surrounded by a yellowish, tubular mantle that protects the animal and filters food.
***
"The researchers found that Hmx controls the development of bipolar tail neurons in tunicates, whereas in vertebrates, it does so for cranial sensory ganglia. Surprisingly, lamprey Hmx gene segments inserted into Ciona DNA were similarly active as Ciona's own Hmx.
"'Hmx has been shown to be a central gene that has been conserved across evolution. It has retained its original function and structure and was probably found in this form in the common ancestor of vertebrates and tunicates," Pennati explains. Cranial sensory ganglia and bipolar tail neurons thus have the same evolutionary origin; Hmx was probably crucially involved in the formation of highly specialized head sensory organs in vertebrates."
Comment: There is full evidence in evolutionary continuity, both in conserved genes and in comparable biochemistry. dhw's blinkered view of phenotypical gaps causing discontinuity is strangely lacking in understanding how evolution works continuously beneath organismal forms.
evolution: symbiosis review
by David Turell , Tuesday, October 04, 2022, 16:09 (779 days ago) @ David Turell
A huge review article covering current research:
https://www.the-scientist.com/features/symbiotic-organs-extreme-intimacy-with-the-micro...
"All multicellular creatures interact with bacteria, but some have taken the relationship to another level with highly specialized structures that house, feed, and exploit the tiny organisms.
***
"While many of these symbiotic organs have traditionally been studied as peculiarities of particular species, some researchers are now pushing to consider them collectively, as extreme examples of what happens when multicellular organisms develop intricate relationships with the microbes around them. In all of these cases, “you create this emergent organ that would only exist in the context of the interaction,” says Joel Sachs, an evolutionary biologist at the University of California, Riverside (UCR) who studies bacteria-housing root nodules that endow many plant species with the ability to fix nitrogen. “Once that occurs, it reshapes the evolution of both the host and the symbiont. And that’s the commonality where I think it makes sense to join these crazy, diverse systems and start to compare them side by side to see these similar dynamics.”
***
"Despite the obvious differences across scales and phyla, there are important similarities in how these organs establish their symbioses, Sachs and UCR postdoc David Fronk argue in a recent paper. For a start, symbiotic organs are well equipped to control where a symbiont can and can’t settle. Nutrient-filled crypts, for example, appear in symbiotic organs across the animal kingdom, suggesting that there are benefits to confining bacteria in this way. Restricting interactions to these specific areas stops a symbiont from taking over other host tissues while letting the host focus its energy expenditure on feeding and housing the microbes in that space, Sachs says.
***
"Symbiotic organs also employ common mechanisms for ensuring that they only welcome desired guests. In beewolves and attine ants, for example, symbionts are transmitted directly among individuals in a population, eliminating some of the risk of environmental contamination. (While the beewolves have their brood cell secretions, the ants propagate microbes largely through physical contact between adult ants.) This sort of inheritance can have important consequences for bacterial evolution, notes Kaltenpoth. His group showed recently that beewolf symbionts are undergoing a reduction in genome size and complexity, consistent with their protected existence and reliance on hosts for transmission.
***
"However hard a host tries to attract the symbiont it wants, there’s always a risk that the microbes won’t hold up their side of the bargain. Bacteria reproduce much faster than the host they live in, and any strain that manages to hold onto its house without doing the costly work the host wants is likely to gain an advantage over its hardworking peers. Consequently, many multicellular organisms with symbiotic organs have evolved mechanisms to monitor and punish microbial cheaters.
***
"Despite such advances in understanding the biology of symbiotic organs, much about the intricacies of host-symbiont communication have yet to be worked out. Some symbionts, such as the bacteria living in tubeworms, are still impossible to culture in the lab, notes Cavanaugh, who also studies symbioses in bivalve mollusks and anemones. Other microbes are being sequenced and scanned for clues as to how they find their hosts, signal to those hosts that they’re performing their work, or interact with the host immune system to maintain their unusual relationship. Such studies could shine a light on microbial interactions across multicellular organisms, not just those that have developed separate organs for the purpose, Nyholm says.
"For example, “by understanding how the innate immune system is used to tell the difference between symbiotic and pathogenic or not-symbiotic bacteria, we can really discover some evolutionarily conserved mechanisms by which all animals detect bacteria,” he explains. “This is an open question still in symbiosis, whether you’re talking about the human microbiome, or a mouse, or a squid, or a zebrafish, or a plant: How do the partners find each other, and what’s the language they use to talk to each other?”
***
"It can be just as useful to study collapse in symbiosis as it is to study how it arises, notes Sachs, adding that while many plant species produce nodules, others seem to have lost the trait. Studying symbiont loss can help researchers understand not only the costs and benefits of symbiotic relationships, but also the long-term effects of the relationship on a species’ physiology and genetics. It’s a reminder, too, that even when you evolve an entire organ to host your microbes of choice, “symbiosis is this knife-edge,” Sachs says. “It’s beneficial for the host under a certain set of scenarios. But you alter the ecology, and suddenly it becomes neutral or even harmful.'”
Comment: I've only reproduced the commentary. Read to see the amazing symbiotic arrangements.
evolution: symbiosis with dolphin and man
by David Turell , Monday, June 12, 2023, 21:14 (528 days ago) @ David Turell
Fishing together they both benefit:
https://today.oregonstate.edu/news/fishing-synchrony-brings-mutual-benefits-dolphins-an...
"By working together, dolphins and net-casting fishers in Brazil each catch more fish, a rare example of an interaction by two top predators that is beneficial to both parties, researchers have concluded following 15 years of study of the practice.
***
“Using drones and underwater imaging, we could observe the behaviors of fishers and dolphins with unprecedented detail and found that they catch more fish by working in synchrony,” said Cantor, an assistant professor in OSU’s College of Agricultural Sciences. “This shows that this is a mutually beneficial interaction between the humans and the dolphins.”
***
"The practice is considered a cultural tradition in the city of Laguna on Brazil’s southern coast, where it occurred for more than 140 years and has been passed down through generations of fishers and dolphins. The cooperative fishing relationship is specific to this population of dolphins and is not a genetic trait in the animals, Cantor said.
***
“'From the fishers’ perspective, this practice is part of the culture of the community in all kinds of ways,” Cantor said. “They acquire skills passed down from other fishers and knowledge is spread through social learning. They also feel connected to this place and have a sense of belonging to the community.”
"Predictive models run as part of the study show that the future of the practice could be threatened if populations of mullet – the type of fish both dolphins and people are seeking – continue to decline, or future generations of fishers lose interest in learning the art of this unique fishing practice.
“'The practice is unlikely to continue if either the dolphins or the fishers no longer benefit from it,” said Farine.
***
"To better understand this cultural tradition and measure its short- and long-term consequences for both fishers and dolphins, the researchers combined drones, hydrophones and underwater cameras to capture the mechanics of the partnership, conducted long-term demographic surveys for dolphins and interviewed and observed the fishers.
"They found that foraging synchrony between dolphins and fishers substantially increases the probability of catching fish and the number of fish caught. This benefit then supports the dolphins’ survival – dolphins who engage in cooperative fishing in this area have a 13% increase in survival rates – and the socioeconomic wellbeing of the fishers. They also found that the fishers’ understanding of the fishing tradition matched the evidence produced through scientific tools and methods.
***
“'We don’t know what is going to happen in the future, but our best guess, using our best data and best models, is that if things keep going the way they are right now, there will be a time when the interaction will no longer be of interest by at least one of the predators – the dolphins or the fishers,” Daura-Jorge said.
Comment: this is a learned activity for both species, which means the last paragraph is prophetic. How does it start? The fisherman is attracting fish and that gets the dolphin's attention. The rest is obvious
evolution: symbiosis with corals and algae
by David Turell , Wednesday, August 16, 2023, 19:30 (463 days ago) @ David Turell
A great help to both:
https://phys.org/news/2023-08-corals-anemones-engage-symbiotic-relationships.html
"'Eat or be eaten" is not always the way things are in nature. It can be beneficial for different species to team up and pool their capabilities. Cnidarians such as corals and anemones were already committing to this kind of biological joint venture with algae from the dinoflagellate group 250 million years ago.
"Thanks to these symbioses, both sides are able to flourish in nutrient-poor waters where, in isolation, neither would stand a chance of surviving. Corals can thus lay the structural foundation for the most biodiverse of all marine ecosystems. They protect their dinoflagellate symbionts from predators and supply them with inorganic nutrients such as nitrogen and phosphorus. Conversely, the algae provide the coral with the products of their photosynthesis: carbohydrates, protein and fat.
"Yet this happy marriage can only work if the 'barter' arrangement is precisely regulated. And although a successful exchange of nutrients is critical to the health of the corals and, hence, to the whole of the coral reef ecosystem, the molecular mechanisms that regulate communication within this partnership are still largely unknown. A new study in Current Biology now shows that a signal path from way back in the evolutionary process plays a crucial role in the 'trade' that takes place between algae and coral.
"'Most types of coral have to absorb new dinoflagellate symbionts from their environment in each new generation," explains LMU biologist Professor Annika Guse, lead author of the new study. The symbionts are initially absorbed like food into the coral's digestive cavity and from there into the host's cells. During this process, a kind of bubble known as the symbiosome forms around the algae.
"The symbiosome is chemically similar to a lysosome—another cell organelle that plays a pivotal role in digestion. "The difference to the lysosome is that, in the symbiosome, the dinoflagellates remain intact," Guse notes. In effect, the host eats its symbionts without digesting them. "We do not yet know exactly how the algae survive this process."
"Inside the symbiosome, the algae then continue to photosynthesize and produce nutrients that they share with their host. All nutrients and communication processes between the partners must therefore penetrate the shell of the symbiosome, which is made up of membranes from both host and symbiont.
"To do all this, the symbiotic partners evidently use a signal path known as the mechanistic target of rapamycin (mTOR), which regulates cellular metabolism in all eukaryotes as a function of environmental factors such as the availability of nutrients. It has already been proven for other species that mTOR is also used for nutritional symbioses: "Various insect hosts use mTOR signal transmission for their bacterial endosymbionts," Guse says. "Evidence of the same path has also been found for legumes and their fungal partners."
***
"'Our findings show that mTOR signal transmission is activated by the symbiosis, and that disruptions to the signal path impair symbiosis at both the cellular and the organismic level," Guse explains. "With the aid of a specific antibody, we were also able to show that mTOR is localized on the membranes of the symbiosome."
"Accordingly, Guse and her team propose a model in which the nutrients released by the algae activate mTOR signal transmission in the symbiosome and in the host tissue—similar to the sensing of nutrients from external sources.
"The activation of mTOR signal transmission was probably also an important step in the evolution of this symbiosis, allowing the algae to survive within the host cells. "The mTOR activity controls what is called autophagy, a very ancient immune reaction on the evolutionary scale that is triggered when pathogens penetrate the host and that leads to the destruction of the intruder," the biologist explains.
"This, she believes, is the reason why some pathogens—and the bacterial endosymbionts of some insects, too—have developed mechanisms to bypass autophagic elimination. Early symbionts could have been ingested by a cnidarian and absorbed into its cells. Instead of being ejected or destroyed, however, they were retained as they supplied the host cell with nutrients, activating the mTOR signals and thereby stopping the process of autophagy."
Comment: it is not hard to imagine free-floating algae landing on coral or into anemones. What is the problem is then inventing mTOR. Do the organisms in this example edit their own DNA like bacteria, or does God design it?
evolution: early eukaryote molecular evidence
by David Turell , Monday, October 23, 2023, 22:22 (395 days ago) @ David Turell
Finding ancient sterols in rocks:
https://www.quantamagazine.org/fossilized-molecules-reveal-a-lost-world-of-ancient-life...
"Limited fossil data shows that their first ancestor appeared at least 1.6 billion years ago. Yet other telltale proofs of their existence are missing. Eukaryotes should produce and leave behind certain distinctive molecules, but fossilized versions of those molecules don’t show up in the rock record until 800 million years ago. This unexplained 800-million-year gap in early eukaryotic history, a crucial period when the last common ancestor of all of today’s complex life first arose, has shrouded the story of early life in mystery.
***
"A recent study published in Nature offers an alternative explanation: Scientists may have been searching for the wrong fossilized molecules this entire time. When the study authors looked for more primitive versions of the chemicals others had been searching for, they discovered them in abundance — revealing what they described as “a lost world” of eukaryotes that lived 800 million to at least 1.6 billion years ago.
***
"When the fossil record is underwhelming, scientists have other ways to estimate when different species branched off from one another in the evolutionary tree. Primary among those tools are molecular clocks: stretches of DNA that mutate at a constant rate, allowing scientists to estimate the passage of time. According to molecular clocks, the last common ancestor of modern eukaryotes, which belonged to a diverse collection of organisms known as the crown group, first emerged at least 1.2 billion years ago.
***
"Organic material decays at different rates, and some parts of eukaryotes preserve in rock better than others. Tissues dissolve first. DNA might stick around for longer, but not too long: The oldest DNA ever found is around 2 million years old. Fat molecules, however, can potentially survive for billions of years.
***
"Eukaryotes create vast quantities of fat molecules known as sterols, a type of steroid that’s a critical component of cell membranes. Since the presence of a cell membrane is indicative of eukaryotes, and fat molecules tend to persist in rock, sterols have become the go-to molecular fossil for the group.
"Modern eukaryotes run on three major sterol families: cholesterol in animals, phytosterols in plants and ergosterol in fungi and some protists. Their synthesis starts with a linear molecule, which the cell molds into four rings so that the resulting shape fits perfectly into a membrane, Brocks said. That process has many stages: It takes another eight enzymatic steps for animal cells to make cholesterol, while plant cells require another 11 enzymatic steps to make a phytosterol.
***
"Some samples were filled to the brim with protosteroids. They found the molecules in rocks dating from 800 million to 1.6 billion years ago. It seemed that not only were ancient eukaryotes present for some 800 million years before modern eukaryotes took off, but they were abundant.
"The researchers could even recognize the eukaryotes’ evolutionary process as their steroids became more complex. In 1.3-billion-year-old rocks, for example, they found an intermediate molecule that was more advanced than the 1.6-billion-year-old protosteroids, but not as advanced as modern steroids.
***
"The molecular findings, put together with genetic and fossil data, reveal the clearest picture yet of early eukaryotic dynamics from around 1 billion years ago during the mysterious mid-Proterozoic era, experts said. Based on Brocks and Nettersheim’s evidence, stem- and crown-group eukaryotes likely lived together for hundreds of millions of years and probably competed with each other during a period that geologists call the Boring Billion for its slow biological evolution.
***
"Cohen, the Williams College paleontologist, agrees. The interpretation that these molecules were made by eukaryotes “is consistent with every other line of evidence,” she said — from the fossil record to molecular clock analyses. “I’m not as worried” about that possibility, she said."
Comment: much of evolution involves molecular transformations which then translates into morphologic changes and new biochemical processes. dhw wonders why God used this slow, laborious process. I don't know why. but God obviously knew what He was doing.
evolution: three inner ear bones
by David Turell , Wednesday, November 01, 2023, 19:01 (386 days ago) @ David Turell
In reptiles and early mammals:
https://ecoevocommunity.nature.com/posts/hearing-from-our-cretaceous-ancestors-a-remark...
"The evolution of the middle ear in early therians remains enigmatic. Our recent discovery of a detached, microtype ear in a newly uncovered Early Cretaceous eutherian mammal not only addresses this mystery, but also suggests independent decoupling of hearing and chewing apparatuses.
"At the heart of this story lies a pivotal question: where did the tiny but crucial bones of the middle ear, the malleus, incus, and stapes, originate? Contrasting with reptiles, which possess a single ear bone known as the columella, we explore the remarkable transformation of the mammalian middle ear, a subject that has been a textbook example of evolution and fascinated evolutionary biologists since the 19th century. Early embryologists made pioneering contributions by examining the intricate embryonic structures of vertebrates, establishing the homology of middle ear bones between mammals and reptiles.
***
"Within mammaliaforms, which include crown mammals and stem clades, there are three pivotal evolutionary and phylogenetic stages in the development of the mammalian middle ear: Mandibular middle ear (MME) (or Postdentary-attached ear), Meckelian-attached middle ear (MaME), and Detached middle ear (DME).
***
"The MaME is characterized by the absence of the postdentary trough and the shrinking postdentary bones connected to the mandible through the Meckel’s cartilage. The DME emerges as the Meckelian cartilage and sulcus diminish, leading to the detachment of middle ear from the mandible.
***
"Our discovery was triggered by a nearly complete fossil skeleton of a small mammal preserved in counterpart slabs. This fossil, likely representing a therian mammal, was a rare find in the Early Cretaceous terrestrial Lagerstätte Jehol Biota. The excitement of the discovery was followed by meticulous preparation and high-resolution micro-CT scan. After an in-depth comparative morphological analysis, we named it as a new genus and species, Microtherulum oneirodes. The specific name, "oneirodes", pays tribute to the dreamlike nature of this fossil's discovery, which fills a critical gap in our understanding of the middle ear evolution in mammals. Our comprehensive phylogenetic analyses revealed that Microtherulum stands as one of the earliest branching eutherians at the dawn of eutherian evolution.
***
"The most exciting discovery was the saddle-shaped articulation of two incomplete elements, identical to the malleus-incus articulation in modern therians. This discovery marks the earliest known record of the saddle-like incudomallear joint in any known Mesozoic mammaliaforms. It also confirms the presence of the typical saddle-shaped incudomallear joint in Early Cretaceous eutherians, representing a significant innovation in the mammalian middle ear. We offer a partial glimpse into the appearance of the middle ear in early therians together with the identification of the C-shaped ectotympanic and the stapes with an oval-shaped footplate in the specimens.
***
"...the new described middle ear is most similar to the microtype ear. Notably, this marks the first identification of the "microtype ear" in Mesozoic mammaliaforms. The discovery aligns with observations that microtype species are small mammals (e.g., bats, shrews and mice), not vice versa. The detachment of the ear, along with its functional characteristics (microtype), suggests that Microtherulum probably developed an enhanced capacity for high-frequency hearing.
***
"The detached middle ear in Microtherulum adds a layer of complexity to our understanding of middle ear variation in early therians. Notably, another Jehol eutherian, Cokotherium, discovered from the same geological formation, retained an ossified Meckelian cartilage (Wang et al., 2022). Our discovery of the microtype ear in early eutherians challenges Fleischer's hypothesis that the ancestral type ear preceded the true mammalian ear and evolved into other functional types. The ancestral states of therian ears remain an open question, raising further inquiries about how the evolutionary transformation occurred among different types of middle ears in early therians. These questions underscore the need for additional specimens to provide a comprehensive picture of the middle ear and morphological variation across various clades."
Comment: see the article, filled with marvelous illustrations and photos, to better follow the evolutionary road to our three ear bones, which very sensitively carry high- and low-pitched sound waves to the drum. Irreducible complexity is obvious.
evolution: starfish are all head, no trunk
by David Turell , Wednesday, November 01, 2023, 20:25 (386 days ago) @ David Turell
Most of the rest of us are bilaterians:
https://www.newscientist.com/article/2400256-starfish-dont-have-a-body-theyre-just-a-bi...
"Scientists trying to work out where a starfish’s head is have come to a startling conclusion: it is effectively the whole animal. As well as solving this longstanding mystery, the finding will help us understand how evolution generates the dramatic diversity of animal forms on Earth.
"Starfish, also known as sea stars, belong to a group of animals called echinoderms, which includes sea urchins and sea cucumbers. Their strange body plans have long puzzled biologists. Most animals, including humans, have a distinct head end and tail end, with a line of symmetry running down the middle of their body dividing it into two mirror-image halves. Animals with this two-sided symmetry are called bilaterians.
"Echinoderms, on the other hand, have five lines of symmetry radiating from a central point and no physically obvious head or tail. Yet they are closely related to animals like us and evolved from a bilaterian ancestor. Even their larvae are bilaterally symmetrical, later radically re-organising their bodies as they metamorphose into adults.
***
"To the team’s surprise, the genes that determine the head end in bilaterians were expressed in a line running down the middle of each arm on the underside of the starfish. The next head-most genes were expressed on either side of this line, and so on.
"Even more strangely, the genes normally expressed in the trunk of bilaterians were missing in the outer layer of the animal. This suggests that starfish have jettisoned their trunk regions and freed up the outer layer to evolve in new directions, says Formery.
"The findings show that “the body of an echinoderm, at least in terms of the external body surface, is essentially a head walking about the seafloor on its lips”, says Thurston Lacalli at the University of Victoria in Canada, who wasn’t involved in the study. Animals like us may have kept their trunks to escape predation by swimming away. “Echinoderms hunkered down and armoured themselves, so they didn’t need a trunk,” says Lacalli.
"The idea that echinoderms are “head-like” animals is “interesting and powerful”, says Andreas Heyland at the University of Guelph in Ontario, Canada. It raises some very important and fundamental questions about how ecological factors shape the evolution of anatomy, he says. “Finding underlying conserved patterns really provides critical insights into how development evolves.'”
Comment: perhaps the way they fit into their ecosystem dictates their shape.
evolution: symbiosis with Cycads
by David Turell , Tuesday, November 21, 2023, 15:59 (366 days ago) @ David Turell
New research:
https://www.nature.com/articles/s41559-023-02251-1?et_rid=825383635&et_cid=4994162
"Cycads are ancient seed plants (gymnosperms) that emerged by the early Permian. Although they were common understory flora and food for dinosaurs in the Mesozoic, their abundance declined markedly in the Cenozoic. Extant cycads persist in restricted populations in tropical and subtropical habitats and, with their conserved morphology, are often called ‘living fossils.’ All surviving taxa receive nitrogen from symbiotic N2-fixing cyanobacteria living in modified roots, suggesting an ancestral origin of this symbiosis. However, such an ancient acquisition is discordant with the abundance of cycads in Mesozoic fossil assemblages, as modern N2-fixing symbioses typically occur only in nutrient-poor habitats where advantageous for survival. Here, we use foliar nitrogen isotope ratios—a proxy for N2 fixation in modern plants—to probe the antiquity of the cycad–cyanobacterial symbiosis. We find that fossilized cycad leaves from two Cenozoic representatives of extant genera have nitrogen isotopic compositions consistent with microbial N2 fixation. In contrast, all extinct cycad genera have nitrogen isotope ratios that are indistinguishable from co-existing non-cycad plants and generally inconsistent with microbial N2 fixation, pointing to nitrogen assimilation from soils and not through symbiosis. This pattern indicates that, rather than being ancestral within cycads, N2-fixing symbiosis arose independently in the lineages leading to living cycads during or after the Jurassic. The preferential survival of these lineages may therefore reflect the effects of competition with angiosperms and Cenozoic climatic change."
***
https://mail.google.com/mail/u/0/#inbox/FMfcgzGwHpPGcvZrwjwFXZNBKjFQQMxG
"Modern cycads live in partnership with bacteria: The cycads share the sugars they make, and in exchange, the microbes convert nitrogen from the air into a form that the plants can use. This means that the nitrogen in cycad tissues comes more directly from the atmosphere than it does in other plants—and, therefore, examining it can tell researchers about that air. Kipp had already demonstrated this with living cycads , so he started applying methods to examine nitrogen in ancient foliage samples to cycad fossils. But his analysis didn’t tell him about the Mesozoic air. Instead, it revealed that the ancient cycads didn’t have microbial partners.
“'Instead of being a story about the atmosphere, we realized this was a story about the ecology of these plants that changed through time,” Kipp says.
"How nitrogen-fixing bacteria helped cycads survive the mass extinction isn’t clear. Maybe the nitro-boost helped them stay competitive in the face of rapidly diversifying flowering plants, Kipp suggests. The methods he helped develop should let researchers dig deeper. And hopefully, they’ll prove useful for studying ancient atmospheres, too."
Comment: we can't live without good bacteria. A major defense in theodicy essays.
evolution: symbiosis with many good bacteria
by David Turell , Wednesday, November 22, 2023, 18:59 (365 days ago) @ David Turell
Can influence animal behavior:
https://phys.org/news/2023-11-bacteria-contribute-modulation-animal-behavior.html
In recent years, researchers have gathered growing evidence that the composition and balance of the microbiome plays a decisive role in the function and health of the organism as a whole.
They have identified a fundamentally important aspect of these functional relationships in the communication between nerve cells of the host and its microbiome, which was first established very early in evolution. The significance of this cooperation and how these interactions affect behavior is still largely unknown.
a research team from the Collaborative Research Center (CRC) 1182 "Origin and Function of Metaorganisms" at Kiel University has gained new insights into the cooperation between the nervous system and the microbiome. Using the freshwater polyp Hydra as an example, the Kiel researchers investigated the neuronal basis of their feeding behavior and whether and in what way the microbiome intervenes in this behavior.
In doing so, they were able to prove mechanistically for the first time that a microbiome with reduced diversity affects the function of certain nerve cells and thus alters the feeding behavior. They published their research results today in the journal Current Biology.
***
"Underlying the feeding behavior is a neuronal control that is significantly more complex than was previously assumed from the simple nerve network of Hydra," Giez continues. Using a calcium-based visualization method, the research team was able to observe the nerve populations involved in feeding behavior in real-time in the living animal and thus identify the neuronal circuit involved.
***
In order to find out which bacteria have a particularly significant influence, the Kiel researchers first colonized germ-free animals with one defined bacterial species each in the next step. "A particularly interesting effect was seen when colonizing with the bacterium Curvibacter. The feeding behavior of animals colonized only with Curvibacter is very strongly impaired: These animals can only open their mouths to a very limited extent," Giez continues.
In further studies, Curvibacter was found to produce the amino acid glutamate, which also plays an important role in human metabolism. When the microbiome is greatly reduced in composition and only Curvibacter is present, glutamate accumulates, binds to neurons, and leads to a blockage of the mouth opening. The inhibitory effect of the Curvibacter bacteria is reversed as soon as the remaining members of the microbiome are also reintroduced to the tissue.
"Overall, we were able to prove that even in phylogenetically ancient animals, a diverse microbiome is necessary for normal feeding behavior. If the composition of this microbiome is severely disturbed, significant changes in behavior occur," says Professor Thomas Bosch, head of the Cell and Developmental Biology group.
The researchers have gathered evidence that this is due to interactions between the different members of the microbiome. If there is a species-rich, "normal" microbiome, the glutamate produced is taken up and utilized by other bacterial species, and the neuronal circuit responsible for feeding behavior is not disturbed.
***
"Our study opens the door for further research into the effects of the interplay between the microbiome and the nervous system on the functions of the whole organism. Among other things, we want to find out in the future whether and how microorganisms are already involved in the formation of the nervous system during embryonic development and what part the microbiome plays in the production of neurotransmitters," Bosch says.
Comment: constant contact with bacteria is part of life on Earth. Most of the contact is important to all living functions.
evolution: bird origin questionable
by David Turell , Sunday, December 31, 2023, 16:40 (326 days ago) @ David Turell
From dinosaurs, but when?:
https://evolutionnews.org/2023/12/fossil-friday-fossil-bird-tracks-expand-the-temporal-...
"The origin of birds involves a severe problem for Darwinists, which paleo-ornithologist Alan Feduccia has called a temporal paradox (1994, 1996). The paradox lies in the fact that primitive fossil birds are contemporaneous with or even appear earlier in the fossil record than their assumed theropod dinosaur ancestors. This is the opposite of the natural expectations from a Darwinian point of view, and therefore has to be explained away with ad hoc hypotheses such as ghost lineages, which are long spans of existence of groups that leave no fossil record.
***
"Now, a new discovery published in the journal PLOS ONE may have made the notorious temporal paradox of birds even worse — much worse — because it extends the existence of bird-like forms many million years further into the past, preceding any of the less bird-like theropods.
"Earlier this month, a team of scientists from the University of Cape Town (Abrahams & Bordy 2023) reported the identification of bird-like footprints from the Upper Triassic of Lesotho in southern Africa, which are at least 210 million years old. Actually, the fossil tracks were already discovered and described by paleontologist Paul Ellenberger in the mid 20th century and classified as ichnogenus Trisauropodiscus. The validity of this ichnogenus was later questioned by other scientists, and an avian affinity has been hotly debated. Abrahams and Bordy re-examined original field material, casts, historical photographs, and interpretative sketches in previous publications. Based on this revision they could identify “two distinct Trisauropodiscus morphotypes, one of which resembles footprints made by birds.”
***
"Consequently, the press release of the discovery says that “unknown animals were leaving bird-like footprints in Late Triassic Southern Africa” (PLOS 2023), and Smithsonian Magazine commented that “mysterious creatures with bird-like feet made these tracks long before birds evolved” (Kuta 2023). In the same spirit, another commenter (Yazgin 2023) asked “who made the footprints if the earliest known birds didn’t emerge until at least 50 million years later?” and answered: “Until the fossil of an animal that lived at the right time, in the right place, and with the right proportions is found, the mystery of who created the Trisauropodiscus tracks remains.”
"To be clear: nothing in these fossil footprints themselves suggests that they are anything but bird tracks, but they have to reinterpreted as something else to protect the evolutionary narrative from inconvenient conflicting evidence and unsolved mysteries. Theory trumps data in evolutionary biology."
Comment: hopefully the fossil gap will be explained by new discoveries. Whatever made the tracks was large enough to make the impressions.
evolution: the speed of evolution
by David Turell , Tuesday, January 02, 2024, 18:16 (324 days ago) @ David Turell
Seen in adaptability:
https://www.quantamagazine.org/evolution-fast-or-slow-lizards-help-resolve-a-paradox-20...
"These Anolis lizards had looked the same for millennia; they had apparently evolved very little in all that time. Logic told Stroud that if evolution had favored the same traits over millions of years, then he should expect to see little to no change over a single generation.
"Except that’s not what he found. Instead of stability, Stroud saw variability. One season, shorter-legged anoles survived better than the others. The next season, those with larger heads might have an advantage.
***
"His data reflected a paradox that had stymied biologists for years. In the long term, the anoles had traits that appeared to stay the same, a phenomenon called stasis — presumably caused by stabilizing selection, a process which favors moderate traits. However, over the short term, the lizards showed variation, with fluctuating traits. Stroud’s data was better explained by directional selection, which sometimes favors extreme traits that lead evolution in a new direction, and other times doesn’t appear to favor anything in particular.
"Because he had followed four species for three generations, he was able to show that a long-term pattern of stasis could emerge from such short-term fluctuating selection.
“'There’s lots of noise, but overall, it leads to fairly stable patterns,” said Stroud, who now runs his own lab at the Georgia Institute of Technology.
***
"Evolutionary biologists rapidly adopted the approach. Princeton University’s Rosemary and Peter Grant used the method in their celebrated studies of Darwin’s finches on the island of Daphne Major in the Galápagos. Their study, which began in 1973 and continues to this day, followed a population of the medium ground finch (Geospiza fortis) through a severe drought that began in 1977. That’s when the plants of Daphne Major stopped producing the small seeds on which the birds relied; only thick seeds remained.
"With little food, the finch population plummeted from 1,400 individuals to a few hundred in only two years. Then the Grants watched the population recover while taking careful measurements of the birds’ traits. The birds that survived, they found, had larger beaks suited to the larger seeds: The average beak depth had increased from 9.2 mm to 9.9 mm — a change of more than 7%.
"All told, a shift in annual rainfall had rapidly resulted in a change in the birds’ beaks. The Grants’ work became a classic example of evolution in action. They had identified marked, if often subtle, evidence of the directional push and pull of evolution acting on traits.
***
"Over and over again, on island after island, the anoles evolved to fill different niches, gaining characteristic sets of traits to help their survival in their preferred habitat. One species kept long legs — ideal for sprinting — and small, sticky toe pads more often planted on terra firma. Three others scampered up tree trunks: a small-bodied species that preferred the lower half of the trunk, one that ventured into the low canopy on large toe pads, and one that favored the high canopy, evolving short limbs to expertly navigate thin branches.
"After that initial burst of evolution, the lizards remained virtually identical over millions of years. And that’s how Losos found them when he began studying the reptiles in the 1980s.
***
"However, his years of data didn’t show stability at all. Instead, he saw evolution constantly shifting the traits that were best adapted to the environment. “If we look at any one period on its own, we very rarely see stabilizing selection,” Stroud said.
***
"Over time, however, that variability averaged out into stasis. Even if traits wobbled off their optimal, moderate peak from one generation to the next, there was a net effect of stabilization — ultimately leading to little change over the multiple generations.
***
"recent research from other labs also helps to support Stroud’s results. A study published in Evolution in September 2023 from the lab of Andrew Hendry, an eco-evolutionary biologist at McGill University, studied evolutionary changes in a community of finches on the Galápagos island of Santa Cruz over 17 years. There, too, Hendry found evidence of natural selection’s regular tug of war on traits that was embedded within a “remarkable stability,” he said, of the finches over evolutionary time."
Comment: These studies of minor adaptations to changing conditions do not tell us about the speed of past evolution when new species appeared. What we see now is a stasis of the evolutionary process that has obviously ended.
evolution: gut nerve controls
by David Turell , Wednesday, May 15, 2024, 17:53 (190 days ago) @ David Turell
Glial cells in the gut:
https://www.quantamagazine.org/in-the-guts-second-brain-key-agents-of-health-emerge-202...
"Breaking down food requires coordination across dozens of cell types and many tissues — from muscle cells and immune cells to blood and lymphatic vessels. Heading this effort is the gut’s very own network of nerve cells, known as the enteric nervous system, which weaves through the intestinal walls from the esophagus down to the rectum. This network can function nearly independently from the brain; indeed, its complexity has earned it the nickname “the second brain.” And just like the brain, it’s made up of two kinds of nervous system cells: neurons and glia.
***
"...Neuroscientists have increasingly discovered that glia play physiological roles in the brain and nervous system that once seemed reserved for neurons.
"A similar glial reckoning is now happening in the gut. A number of studies have pointed to the varied active roles that enteric glia play in digestion, nutrient absorption, blood flow and immune responses. Others reveal the diversity of glial cells that exist in the gut, and how each type may fine-tune the system in previously unknown ways. One recent study, not yet peer-reviewed, has identified a new subset of glial cells that senses food as it moves through the digestive tract, signaling to the gut tissue to contract and move it along its way.
***
"Thanks to some of these newer technologies, scientists now know that enteric glia are among the first responders to injury or inflammation in gut tissue. They help maintain the gut’s barrier to keep toxins out. They mediate the contractions of the gut that allow food to flow through the digestive tract. Glia regulate stem cells in the gut’s outer layer, and are critical for tissue regeneration. They chat with the microbiome, neurons and immune-system cells, managing and coordinating their functions.
***
"Those methods allowed her to get the “first glimpse into the diversity of these glial cells” across all tissues of the duodenum, Scavuzzo said. In June, in a paper published on the biorxiv.org preprint server that has not yet been peer-reviewed, she reported her team’s discovery of six subtypes of glial cells, including one that they named “hub cells.”
"Hub cells express genes for a mechanosensory channel called PIEZO2 — a membrane protein that can sense force and is typically found in tissues that respond to physical touch. Other researchers recently found PIEZO2 present in some gut neurons; the channel allows neurons to sense food in the intestines and move it along. Scavuzzo hypothesized that glial hub cells can also sense force and instruct other gut cells to contract. She found evidence that these hub cells existed not only in the duodenum, but also in the ileum and colon, which suggests they’re likely regulating motility throughout the digestive tract.
***
"Glia are likely involved because of their central role in communicating between the microbiome, immune cells and other gut cells. Healthy glia strengthen the intestines’ epithelial barrier, a layer of cells that keeps out toxins and pathogens and absorbs nutrients. But in patients with Crohn’s disease, glial cells don’t function properly, resulting in a weaker barrier and inappropriate immune response.
“Different subtypes of glia can be functioning differently or dysfunctioning in a wide range of diseases and disorders where motility is impacted,” Scavuzzo said. They have also been linked to neural inflammation, hypersensitivity in the organs and even neuron death.
"For instance, Gulbransen and his team recently discovered that glia contribute to gut pain by secreting molecules that sensitize neurons. This is likely an adaptive response intended to draw the gut’s attention to damaging substances to dispose of them, Gulbransen said, which as a side effect causes pain."
Comment: glia were ignored for a long time. It just shows everything is there for a reason.
evolution: sessile Ediacarans stirred water flow
by David Turell , Sunday, May 19, 2024, 19:11 (186 days ago) @ David Turell
An obvious event:
https://phys.org/news/2024-05-earth-earliest-sea-creatures-drove.html
"Using state-of-the-art computer simulations of fossils from the Ediacaran time period—approximately 565 million years ago—scientists discovered how these animals mixed the surrounding seawater. This may have affected the distribution of important resources such as food particles and could have increased local oxygen levels.
"Through this process, the scientists think these early communities could have played a crucial role in shaping the initial emergence of large and complex organisms prior to a major evolutionary radiation of different forms of animal life, the so-called Cambrian "explosion."
***
"Dr. Emily Mitchell at the University of Cambridge's Department of Zoology, a co-author of the report, said, "It's exciting to learn that the very first animals from 580 million years ago had a significant impact on their environment, despite not being able to move or swim. We've found they mixed up the water and enabled resources to spread more widely—potentially encouraging more evolution."
***
"First author Dr. Susana Gutarra, a Scientific Associate at the Natural History Museum, said, "We used ecological modeling and computer simulations to investigate how 3D virtual assemblages of Ediacaran life forms affected water flow. Our results showed that these communities were capable of ecological functions similar to those seen in present-day marine ecosystems."
"The study showed that one of the most important Ediacaran organisms for disrupting the flow of water was the cabbage-shaped animal Bradgatia, named after Bradgate Park in England. The Bradgatia from Mistaken Point are among some of the largest fossils known from this site, reaching diameters of over 50 centimeters.
"Through their influence on the water around them, the scientists believe these Ediacaran organisms might have been capable of enhancing local oxygen concentrations. This biological mixing might also have had repercussions for the wider environment, possibly making other areas of the sea floor more habitable and perhaps even driving evolutionary innovation.
"Dr. Imran Rahman, lead author and Principal Researcher at the Natural History Museum, said, "The approach we've developed to study Ediacaran fossil communities is entirely new in paleontology, providing us with a powerful tool for studying how past and present marine ecosystems might shape and influence their environment.'"
Common: anyone who has seen a stream knows standing objects will stir up flow. As A grantor of study funds. I would not have funded this one with such obvious results.
evolution: how bacteria protect Antarctic worms
by David Turell , Friday, June 21, 2024, 21:12 (153 days ago) @ David Turell
By producing anti-freeze:
https://www.sciencenews.org/article/bacteria-marine-worms-survive-cold
"Specialized bacteria living inside three different species of Antarctic polychaetes make proteins that help the worms not freeze to death, Corinaldesi and colleagues report June 21 in Science Advances.
"The finding illustrates how important microbes can be for their hosts, says Amy Apprill, a microbial ecologist at Woods Hole Oceanographic Institution in Massachusetts who wasn’t involved with the study. “Our knowledge of host-microbe interactions in the ocean is still incredibly limited.”
***
"The most common bacteria found in the worms were Meiothermus silvanus and two types of Anoxybacillus, which were not found in a separate analysis of the sediment itself or within DNA collected from other related worms.
"Bacterial proteins extracted from the polychaetes are known to be involved in cold tolerance. Two enzymatic proteins, for example, produce glycerol and proline, which are thought to protect against extreme cold “due to their ability to reduce the freezing point of internal liquids,” Corinaldesi says.
"Though missing from today’s Antarctic ocean floor, Meiothermus bacteria have previously been found in frozen sediment from underneath the nearby Ross Ice Shelf, which “suggests a long-term connection between polychaetes and these bacteria,” Corinaldesi says. She and colleagues think that the bacteria are passed down from parent worms to their offspring.
***
"The bacteria benefit from their partnership with the worms too, Corinaldesi says, as they receive a safe home in exchange for making protective proteins."
Comment: it is a perfect arrangement. If both species migrated from warmer areas into colder climates, it could explain the relationship. But that raises the issue of why the bacteria were producing antifreeze in a warm climate, and why they would get together with mutual benefits, if not needed. Worms crawl in seabed's so picking up the bacteria poses no problem. The most likely origin is they adapted together somehow.
evolution: new Archaea found
by David Turell , Tuesday, August 06, 2024, 16:21 (107 days ago) @ David Turell
In a California pool:
https://www.nature.com/articles/s41467-024-49872-z?utm_campaign=related_content&utm...
"Abstract
The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions in soil ecosystems remain unknown. Of particular interest are Asgard archaeal contributions to methane cycling in wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new Asgard lineage, and a complete genome of Freyarchaeia, and predicted their metabolism in situ. Metatranscriptomics reveals expression of genes for [NiFe]-hydrogenases, pyruvate oxidation and carbon fixation via the Wood-Ljungdahl pathway. Also expressed are genes encoding enzymes for amino acid metabolism, anaerobic aldehyde oxidation, hydrogen peroxide detoxification and carbohydrate breakdown to acetate and formate. Overall, soil-associated Asgard archaea are predicted to include non-methanogenic acetogens, highlighting their potential role in carbon cycling in terrestrial environments.
***
"Atabeyarchaeia and Freyarchaeia use different enzymes to produce pyruvate. Atabeyarchaeia encodes the oxygen-sensitive reversible enzyme, pyruvate:phosphate dikinase (PpdK), whereas Freyarchaeia encodes unidirectional pyruvate water dikinase/phosphoenolpyruvate synthase (PpS) and pyruvate kinase (Pk), producing phosphoenolpyruvate and pyruvate52, respectively. Pyruvate generated via the EMP pathway can then be converted to acetyl-CoA by pyruvate:ferredoxin oxidoreductase (PorABCDG) complex using a low-potential electron acceptor such as a ferredoxin. Alternatively, acetyl-CoA can also be generated via pyruvate formate-lyase (pflD) generating formate as a byproduct. The final step involves the conversion of acetyl-CoA to acetate via acetate-CoA ligase (ADP-forming), producing ATP via substrate-level phosphorylation, in a crucial energy-conserving step during the fermentation of carbon compounds in both lineages.
***
"We manually curated three complete genomes for Asgard archaea from wetland soils, uncovering bidirectional replication and an unexpected abundance of introns in tRNA genes. These features suggest another facet of the evolutionary relationship between archaea and eukaryotes. Metabolic reconstruction and metatranscriptomic measurements of in situ activity revealed a non-methanogenic, acetogenic lifestyle and a diverse array of proteins likely involved in energy conservation. The genome analysis uncovered some metabolic similarities between soil and sediment-associated Asgard archaea. In addition, the unusual genomic features, such as high intron prevalence and the presence of ESPs call for deeper investigations into their biological significance and contribution to the adaptability and evolution of Asgard archaea. Overall, the findings point to metabolic flexibility and adaptation to soil conditions of wetlands. Finally, they contribute to the cycling of carbon compounds that are relevant for methane production by coexisting methanogenic archaea. Future studies should aim to explore the functional roles of the identified genes and pathways in situ, which will further elucidate the ecological impacts and evolutionary history of these enigmatic microorganisms." (my bold)
Comment: it is amazing to find how chemically active are these newly found Archaea. They hold a unique position as very ancient forms yet closely related to Eukaryotes. Their chemical activities helped transform the Earth soils into useful substrates for life to use.
evolution: another asteroid may have helped kill dinosaurs
by David Turell , Wednesday, October 16, 2024, 22:07 (36 days ago) @ David Turell
Off West Africa:
https://www.nature.com/articles/s43247-024-01700-4
"The Nadir Crater offshore West Africa is a recently proposed near K-Pg impact structure identified on 2D seismic. Here we present 3D seismic data that image this crater in exceptional detail, unique for any such structure, which demonstrates beyond reasonable doubt that the crater-forming mechanism was a hypervelocity impact. Seismic mapping reveals a near-circular crater rim of 9.2 km and an outer brim of ~23 km diameter defined by concentric normal faults. An extended damage zone is evident across the region, well beyond the perceived limit of subsurface deformation for impact craters, except in a ‘sheltered zone’ to the east. The paleo-seabed shows evidence for widespread liquefaction because of seismic shaking, and scars and gullies formed by tsunami wave propagation and resurge. Deformation within the ~425 m high stratigraphic uplift and annular moat allows us to reconstruct the evolution of the crater, with radial thrusts at the periphery of the uplift suggesting a low-angle impact from the east. Structural relationships are used to reconstruct the deformation processes during the crater modification stage, with the central uplift forming first, followed by centripetal flow of surrounding sediments into the evacuated crater floor in the seconds to minutes after impact."
Here is another report on the paper:
https://mail.google.com/mail/u/0/#inbox/FMfcgzQXJkQwcBGpvjXhJPqXVSxsqrpr
"Geologists from the University of Edinburgh, U.K., report that a second large asteroid impacted Earth at around the same time as the large one that has been held responsible for the extinction of dinosaurs. The dinosaurs are believed to have fallen victim to the aftermath of the impact of an asteroid with a diameter of about 10 kilometres that left a crater in Middle America about 66 million years ago. The new crater is just off the West Coast of Africa, stems from an asteroid with approximately half a kilometre in diameter, and has been dated to around the same time. It’s unclear how much this made things worse for dinosaurs, but it probably didn’t help."
Comment: looks like Chixculub had help.
evolution: another eukaryote article
by David Turell , Monday, October 28, 2024, 19:01 (24 days ago) @ David Turell
Today:
https://www.quantamagazine.org/meet-the-eukaryote-the-first-cell-to-get-organized-20241...
"The eukaryotes invented organization, if we use the literal definition of “organize”: to be furnished with organs. Inside a eukaryotic cell are self-contained, membrane-bound bundles that perform special functions, called organelles. All eukaryotic cells — animal, plant, fungus or protist — have a nucleus that encloses and protects DNA. Nearly all of them have mitochondria, which produce energy to fuel biochemical reactions. (Any eukaryotic lineages that lack mitochondria used to have them and then lost them sometime in evolutionary history.) And across the evolutionary tree, different eukaryotes have evolved or procured additional organelles that assemble proteins, store water, turn sunlight into energy, digest biomolecules, get rid of waste, and more. If prokaryotes are a loose pile of papers on the floor, eukaryotes are a sophisticated filing system that binds pages into packets and labels them.
“'They’ve got the endoplasmic reticulum, Golgi apparatus, peroxisomes, lysosomes, vacuoles — all this machinery not present in bacteria or archaea cells,” said Thijs Ettema(opens a new tab), an evolutionary microbiologist at Wageningen University in the Netherlands.
"How this all happened isn’t entirely clear, but today, most experts agree that 2 billion or 3 billion years ago, an archaean cell engulfed a bacterial cell, which somehow escaped digestion and adapted to life inside its host. That bacterium evolved to become the organelle we now know as the mitochondrion.
"Since that original act, the eukaryote has transformed again and again. It first evolved into a smattering of unique unicellular creatures, such as the ancestors of modern diplomonads(opens a new tab), which swim with dual tail clusters, and the parasitic microsporidians(opens a new tab), which shoot out coiled tubes to infect victim cells.
***
"At some point, in a sequel to mitochondrial capture, a eukaryote engulfed a cyanobacterium capable of photosynthesis — the process of using sunlight to harvest carbon from the air and spin it into energy. That branch of the eukaryotic family, freshly equipped with green organelles called chloroplasts, evolved into plants and other photosynthesizers.
"Then, within the last billion years, some individual eukaryotes began working together. Collectives became colonies, and they further organized when entire cells began to specialize, or perform unique functions within a complex multicellular body. Multicellularity unlocked even higher levels of sophistication, resulting in mushrooms, trees, hippos and humans.
***
"Ettema and his team were surprised to find genes that looked suspiciously eukaryotic among the expected traces of archaea and bacteria. Upon further investigation, they found what might very well be the missing link in our understanding of eukaryotic evolution: a prokaryote(opens a new tab) with hallmark eukaryotic complexity in its genome. They named the microbe Lokiarchaea(opens a new tab) after its home vent.
"Ettema suspected that a cell from this family, later dubbed “Asgards,” might make a convincing candidate for that first hungry host that engulfed a bacterium that became a mitochondrion. If so, he proposed, that ancient Asgard archaean might have evolved into the eukaryotic branch while the rest of its family forged on as prokaryotes. (my bold)
***
"Researchers have since dug up Asgard DNA all over the world, including in North Carolina and Yellowstone National Park. But only two labs have successfully cultured Asgard cells. Those cells reveal some eukaryote-like features(opens a new tab), such as a cytoskeleton built with the protein actin. The rest are still under investigation, and their cellular structures are unknown.
"Today, most researchers agree(opens a new tab) that Asgards are the closest known prokaryotic relatives of eukaryotes. Modern Asgards aren’t our ancestors, but we likely share an ancestor somewhere in deep time. “You could argue that eukaryotes are Asgards in the same way that birds are dinosaurs,” said Itay Budin(opens a new tab), a biochemist at the University of California, San Diego. “They’re kind of our cousins.”
"The process by which an archaean cell turned a free-living bacterium into its own cellular machinery — called endosymbiosis — remains largely obscured by evolutionary history. Most biologists believe that one prokaryote “swallowed” another in a process called phagocytosis. However, phagocytosis takes a lot of energy. In fact, it is so energy-expensive that some believe it would have been impossible without the first host cell already having energy-generating mitochondria — opening a tricky, microbial chicken-and-egg debate.
"Modern Asgards offer a clue that could get us around this mind bender: Their cytoskeleton suggests that they might use tiny, armlike projections called blebs to entrap prokaryotic food, without needing mitochondria. Maybe the first eukaryotic ancestor did, too."
Comment: to followers of this website, this is all old news. Somehow all of this got cobbled together or evolved. Perhaps all designed. Note the bold. Asgards are the best clue we have
evolution: the effect of pressure and heat
by David Turell , Monday, October 28, 2024, 19:44 (24 days ago) @ David Turell
Creates unexpected events:
https://www.newscientist.com/article/2453548-weird-microbes-could-help-rewrite-the-orig...
"Compressing a type of single-celled microorganism makes it develop into a multicellular tissue-like structure with different cell types. This suggests that pressure can help drive key evolutionary leaps, such as the emergence of multicellularity.
"he organism is a type of archaea, one of the three domains of life, along with bacteria and eukaryotes. The eukaryotes are organisms with cells containing a nucleus and include animals and plants. Archaea lack a nucleus, so were originally mistaken for bacteria, but are now thought to share a common ancestor with eukaryotes.
"Unlike most organisms, archaea also lack a stiff cell wall, a trait they share with animal cells. Lacking a cell wall gives animal cells flexibility and allows them to develop markedly different shapes. They can also change cell type in response to mechanical forces. Archaea are also able to form complex shapes and interact with each other, but little is known about how they react to such forces.
"To find out more, Alex Bisson at Brandeis University in Massachusetts and his team squashed a salt-loving archaea called Haloferax volcanii under jelly pads, mimicking the forces they experience in their natural habitats – and saw something completely unexpected.
"The cells grew and started making multiple copies of their genomes. When the tension in the cells’ membranes reached a critical point, new membranes grew between these genomes to create individual cells that were genetic clones of the original cell, forming a mound-shaped multicellular tissue.
"The team tested 52 other similar species and found that more than 60 per cent of them formed tissues. This kind of cell division is also seen in a wide range of multicellular eukaryotes, such as during chick embryo development.
"Next, the team zapped individual cells in the tissues with a laser to test whether they were connected to each other. When a cell was killed by the laser, neighbouring cells moved towards the wound, as cells in animal tissues called epithelium do.
"This suggests that cells in the archaeal tissues are tethered together, just as they are in animal or plant tissues. Archaea lack the genes that animal and plant cells use for these tethers, so they have probably evolved their own method of doing this, says Bisson.
"The cells in the tissues also developed into two distinct types. Those around the edge – where less pressure was applied – were flat, while those in the middle formed an angular structure resembling a scutoid, a shape first identified in animal epithelial cells in 2018.
"This shows the advantages of exploring the biomechanical properties of cells across domains of life – rather than just genetic information – when studying evolution, says Bisson.
“'The idea that gene novelty alone governs evolutionary leaps now seems insufficient,” says Omaya Dudin at the University of Geneva in Switzerland. “Physical and mechanical factors are emerging as key players in orchestrating complex biological innovations in single-celled creatures.'”
Comment: an exciting finding that physical forces can play such a role, which means their DNA is coded for the proper responses. Of course, this means they could have been designed.
evolution: the effects of a theory without natural selection
by David Turell , Wednesday, October 30, 2024, 19:10 (22 days ago) @ David Turell
From Neil Thomas:
https://evolutionnews.org/2024/10/the-fate-of-evolution-without-natural-selection/
"The last four decades have produced numerous independent studies which have all found Darwin wanting on purely scientific grounds. This, as intimated above, has clear implications for materialist philosophy since, if the only materialist theory accounting for the nature of things is discredited, this in good logic leaves only supra-natural causation on the table. (my bold)
***
"...Jerry Fodor and Massimo Piattelli-Palmarini mounted an uncompromising critique of Darwin’s notion of natural selection, pointing out its fundamental misconception in devastatingly simple terms:
"Darwin was inadequately impressed by the fact that breeders have minds — they act out of their beliefs, desires and intentions and so on — whereas of course, nothing of that sort is true in the case of natural selection.
"Darwin’s impermissibly anthropomorphic and perhaps unwittingly vitalist comparison of stock-rearing with the purely inanimate tendencies of “natural selection” had already been pointed out to him by Alfred Russel Wallace and by Sir Charles Lyell who both objected that the analogy between resourceful nurture and dumb nature was untenable. Most gravely for Darwin, Lyell also pointed out that there could be no such thing in nature as natural selection (a process which would require cognitive abilities). What Darwin had meant to say, Lyell proposed, was natural preservation (which is wholly unpremeditated and in essence merely a statistic without creative power). (my bold)
"It was a criticism that Darwin rather grudgingly consented to accept but, despite his nominal concession, failed to explain how mere preservation could lead to the kind of new biological pathways which would be necessary to “evolve” different kinds of limbs, physical frames, or superior brains. As Richard Milner has commented, “Natural selection is an eliminative process that does not explain the generation, proliferation and direction of varieties.
(my bold)
***
"I find equivocation about the matter of evolution without natural selection puzzling. The briefest account of the historical sequence of the ideas of, first evolution, then natural selection, will explain my sense of disquiet.
***
"With reference to that brief chronological reprise, my point is: If some leading 21st-century scientists and philosophers are now picking (rather large) holes in the idea of natural selection, what price evolution itself? There is surely no logical necessity to accept the truth-status of evolution without natural selection, is there? Ideally, I would like to hear an answer to that question from a competent authority since I have a nagging feeling that I, a non-specialist, might be missing something here. At any rate it does not seem reasonable to accept the veridical status of evolution on the basis of what an increasing number of scientists are beginning to perceive as a “dodgy dossier” which nevertheless furnished the essential precondition for people’s acceptance of evolution in the first place."
Comment: the second and third bolds above is the position we have established here. Natural selection has no design capacity. It is a result of the struggle to survive. The first bold is my position. Why not design and its designer?
evolution of consciousness: a new comment
by David Turell , Friday, May 04, 2018, 22:54 (2393 days ago) @ dhw
A new book makes an attempt, looking at emergence, quantum theory and the amazing complexity of the brain:
https://www.wsj.com/articles/the-consciousness-instinct-review-how-our-minds-are-made-u...
"Mr. Gazzaniga’s approach echoes those of the American pragmatists of the late 19th and early 20th centuries, who believed that most philosophical problems needed not solving but dissolving. “Intellectual progress usually occurs through sheer abandonment of questions together with both of the alternatives they assume,” wrote John Dewey. Mr. Gazzaniga is not the first to suggest that the consciousness debate is hampered by just such a set of false alternatives: matter or mind, body or spirit. The dualist assumption that these are two mutually exclusive categories inevitably makes their reconciliation impossible, leading otherwise brilliant thinkers since Plato to abandon “their fierce reasoning skills and, deus ex machina,” throw in “a spook at the end of their analysis.”
"To escape the dualist trap, Mr. Gazzaniga takes as his unlikely inspiration Aristotle’s ancient distinction between four different kinds of causes. This review, for example, has a material cause (paper and ink), a formal cause (the shape of the letters on the page), an efficient cause (me writing it) and a final cause (to inform people about the book). Whether or not this taxonomy is entirely correct, it illustrates how “no one mode of explanation” suffices to understand anything, because the causal categories do not entail each other.”
"Mr. Gazzaniga updates this basic insight with the quantum-physical concept of complementarity, that “a single thing can have two kinds of description and reality.” We can think of matter as waves or particles, but not both at the same time. Similarly, the micro world of quantum physics follows different laws than the macro world of classical physics. “They inhabit different layers of description,” Mr. Gazzaniga writes, “and one is not reducible to the other.”
"The author’s point can also be made by thinking about the relationship between fundamental physics and biology. Both are hard sciences, but you simply cannot do the work of one with the other. Everything is made up of matter, but at different layers of organization different ways are needed to understand and describe it. This simple point cuts to the essence of Mr. Gazzaniga’s dissolution of the puzzle of consciousness. Once we accept that humans contain layers of physical organization, none of which can be wholly reduced to another, it is no longer puzzling that what goes on in the brain can have an objective, physical description and a subjective, mental one.
"Crucially, Mr. Gazzaniga also argues that it is wrong to attribute causal potency to only one layer—for instance, to suggest that neuronal firings can cause actions but decisions cannot. Heretical though this is to hard-nosed reductionists, Mr. Gazzaniga agrees with his mentor, Sperry, that “consciousness may have real operational value, that it is more than merely an overtone, a by-product, epiphenomenon, or a metaphysical parallel of the objective process.”
"Mr. Gazzaniga is very good at looking under the hood of consciousness to explain how its workings naturally follow from the ways in which the brain is organized. It is a hugely complex system with a layered, modular architecture, which enables it to “efficiently process multiple types of information concurrently.”
***
"Consciousness is not therefore a property of a central, single executive controller. What we perceive as consciousness is simply whichever module is most active, meaning that “its processing becomes the life experience, the ‘state’ of the individual at a particular moment in time.”
"Mr. Gazzaniga might be mistaken to nail his flag so firmly to the mast of the physicist-cum-theoretical biologist Howard Pattee. And he is almost certainly wrong in some details. But on all the main points, his instincts on consciousness are sound. Awareness is not the “special sauce” that brings dumb biological processes to subjective life but an emergent property of immensely complex neurological processes. This does not so much eliminate the mystery of consciousness as make it no more or less mysterious than the ultimately inexplicable existence of the universe itself."
Comment: This book is a materialist view which invokes the uncertainty of of quantum uncertainty and completely ignores the evidence from NDE's. But he certainly emphasizes the enormous complexity of the brain.
evolution of consciousness: another view
by David Turell , Monday, May 14, 2018, 20:46 (2383 days ago) @ David Turell
Another discussion of the problem of understanding consciousness:
https://theconversation.com/why-we-need-to-figure-out-a-theory-of-consciousness-93146
"there remains disagreement about whether or not we have a theory that actually explains what is special about the brain activity which produces our miraculous inner worlds.
"Recently, “Integrated Information Theory” has been gaining attention – and the backing of some eminent neuroscientists. It says that absolutely every physical object has some (even if extremely low) level of consciousness. Some backers of the theory claim to have a mathematical formula that can measure the consciousness of anything – even your iPhone.
"These big claims are controversial and are (unfortunately) undermining the great potential for progress that could come from following some of the ideas behind the theory.
"Integrated Information Theory starts from two basic observations about the nature of our conscious experiences as humans. First, that each experience we have is just one of a vast number of possible experiences we could have. Second, that multiple different components (colours, textures, foreground, background) are all experienced together, simultaneously.
"Given these two observations, the theory says that brain activity associated with consciousness must therefore be ever-changing, consist of lots of different patterns, and involve a great deal of communication between different brain regions.
"This is a really solid starting point for a theory, and to some extent, we have been able to test it. In one experiment, for example, researchers looked at brain responses to a short pulse of “transcranial magnetic stimulation”, in which a magnetic coil is placed on top of the scalp, and a very brief pulse of magnetic field emitted.
"The response was recorded from electrodes at locations all over the rest of the scalp. When fully awake, the response to the little burst of magnetic field would spread far and wide, in complex patterns of ripples.
"But when participants were in deep sleep, or under general anaesthesia, the response did not spread very far from the magnet, and the shapes of the ripples were much more simple. These results support the theory. They demonstrate that when we’re conscious, each region of the brain is doing something different, but are all managing to communicate.
"So far so good. But it would be great to go further than this. Hence the attempt to find a formula that can give us a precise “level of consciousness” from detailed data. It is here that the serious controversy begins.
"The theory claims that the ultimate formula will somehow quantify the information something contains. In this context, “information” means how much you can find out about the past and future of the object in question by looking in detail at the present.
"For example, you record voltages from a bunch of neurons in the brain, and see how well you can use one result to predict earlier and later results. If you can make good predictions from using the readings from all neurons, but only poor predictions if you use just some neurons, then you score high.
***
"Some people think perhaps this theoretical mathematical endeavour should be shelved for now. Experimental research on consciousness is going well, so maybe we should all just focus on that. But we can’t just do fact gathering experiments – we need a theory to understand what we’ve seen, and the basics of Integrated Information Theory do hold promise.
"What about the theory’s “panpsychist” position – the idea that everything is conscious? Can this be taken seriously? We need to be careful how to express this – talk of conscious spoons is unhelpful.
"If there were already many competing plausible mathematical descriptions of consciousness, none of which could be tested, then there would be no value in creating another. But so far there are zero, and only a handful of researchers have been working on this.
"Einstein’s theory of gravity was utterly compelling, even before it could be tested. Integrated Information Theory is not yet compelling to the informed mathematician. But it is by far the most promising foundation from which to tackle the very roots of consciousness.And progress on this ultimate frontier is worth some more conscious effort."
Comment: see the accompanying video:
It raises more questions than answers. An interesting point is made that the newborn brain is very inactive except for the amygdala, which is generally a fear center. It fits my view of starting as a blank slate with a suck and a grasp reflex as the only responses, as well as reacting to bowel and bladder needs.
evolution of consciousness: a new comment
by David Turell , Friday, December 10, 2021, 19:28 (1077 days ago) @ David Turell
A new book makes an attempt, looking at the amazing complexity of the brain:
https://www.wsj.com/articles/being-you-review-why-we-have-a-sense-of-self-11639093233?p...
"Mr. Seth argues that if we are to understand consciousness better, we would do well to stop going after the easy or hard problem. Instead he poses the “real problem” of consciousness. It requires that we explain “why a particular pattern of brain activity—or other physical process—maps to a particular kind of conscious experience, not merely establishing that it does.” His general answer to the “why” question is that our minds are prediction machines, making informed guesses not only about the world but about what is going on in our own bodies. As he puts it: “The entirety of perceptual experience is a neuronal fantasy that remains yoked to the world through a continuous making and remaking of perceptual best guesses.”
***
"Mr. Seth’s understanding of the mind as a prediction machine entails the idea that we don’t perceive the world as it is. Rather our perceptions are “controlled hallucinations,” designed by evolution to “enhance our survival prospects, not to be a transparent window onto an external reality.”
"The same is true of our sense of self. “The self is not an immutable entity that lurks behind the windows of the eyes, looking out into the world and controlling the body as a pilot controls a plane,” he says. It is rather a hodgepodge of functions that give us the abilities to perceive the world from a point of view, to make decisions, to possess a narrative sense of autobiography and to locate ourselves in society. The feeling that we have that this is all the work of a singular subject is just another controlled hallucination.
"Mr. Seth is meticulously precise in his use of language, for the purposes of clarity and rigor. But I’m not so sure that he was wise to use words like “hallucination” and “fantasy.” As he says, there is a big difference between normal perceptions when “what we perceive is tied to—controlled by—causes in the world” and what we normally call hallucinations, when our perceptions have “lost their grip on these causes.” Of course, how the world is in itself and how it seems to us must be different: All perception has to be mediated through the senses. But to call these representations “hallucinations” invites the misunderstanding that we never have a grip on reality at all.
***
"...his chapter on artificial intelligence cuts through the froth and hype, arguing that fears that conscious AI is just around the corner are based on the false assumption that consciousness and intelligence are intimately linked: “that consciousness will just come along for the ride.” It ignores the fact that consciousness is “a deeply embodied biological process.”
Comment: Pure materialism telling us that consciousness is simply an illusion the brain creates. We know from rabbit-duck illusions the brain presents us with patterns automatically in a helpful manner, but we cannot extrapolate from that observation. Consciousness in NDE's with no functioning brain tell us that. I'm currently reading Bruce Greyson's book 'After', about NDE's, and will discuss it when I'm finished.
evolution of consciousness: a new comment
by David Turell , Tuesday, March 08, 2022, 21:38 (989 days ago) @ David Turell
A book review:
https://www.nature.com/articles/d41586-022-00652-z?utm_source=Nature+Briefing&utm_c...
"A tour of the evolution of minds
"An informative guide takes in archaea, birds, primates and more — overconfidently.
"Look through a microscope at a macrophage cell pursuing, engulfing and consuming a bacterium, and it is hard not to impose a narrative: one is trying to catch the other, which is in turn trying to escape. In Journey of the Mind, neuroscientists Ogi Ogas and Sai Gaddam imply that this interpretation is not fanciful. They argue that minds of a sort have existed since the first archaea colonized the planet, billions of years ago.
***
"The narrative is enjoyable and illuminating, but it is flawed by a failure to separate fact from speculation. (my bold)
***
"Ogas and Gaddam take a very broad view of mind as “a physical system that converts sensations into action”. At face value, this grants a mind to thermostats and robots as much as to living entities. “A mind responds. A mind transforms. A mind acts,” they write. But the same is true of many machines. What, then, distinguishes a mind? If it’s sentience or awareness, the authors give a confusing picture. They say the “self-awareness” of an amoeba is “piddling” — and later seem to deny this quality to all organisms except vertebrates. (my bold)
"Many assertions go beyond the facts. The discussion of consciousness rests on the belief that the problem has been solved by cognitive scientist Stephen Grossberg (whom the authors thank for “guidance and support”). Since the late 1960s, Grossberg has developed the idea that consciousness arises from ‘resonance’ between specific modules of the brain. Ogas and Gaddam are vague about what resonance means here, beyond saying that the modules amplify and prolong each other’s outputs, and they give the reader little indication of what empirical evidence exists to support the idea. Grossberg’s theory is provocative and stimulating, but, couched in the abstract mathematical framework of dynamical systems theory, it remains contingent on his supposition that “all conscious states are resonant states”. I’m not convinced it amounts to the revolution that the authors assert.
***
"Ogas and Gaddam jump the gun, in my view, when they suggest that Grossberg has all the answers.
"There are other instances in which they present contentious ideas with certainty. For all of the minds they discuss, much remains open. They write that birds didn’t develop language “because they don’t have hands”, but in fact it’s still debated whether gestures helped lead to the origin of language. They state that insects have no consciousness, when there is good reason to suppose that bees, at least, have many of the mental attributes associated with consciousness, such as foresight and the ability to imagine. Even bacteria are not the simple automata portrayed here; other researchers describe bacterial behaviours in the language of cognition.
***
"There is more than a hint that evolution is striving to a particular end in Ogas and Gaddam’s suggestion that, once early single-celled organisms acquired the ability to sense and move, “the royal road to consciousness beckoned”.
***
"There is plenty to like in Journey of the Mind. It is so often informative and entertaining that it feels mean to cavil. But the book exemplifies a persistent problem in popular science, in which pet theories are presented with too much confidence and too little context. Readers deserve the full picture — less definitive and satisfying, perhaps, but ultimately more honest and illuminating." (my bold)
Comment: the reviewer's don't surprise me. Seeing something that seems to act intelligently doesn't mean it is intrinsically intelligent in and of itself. It may dimply be following instructions it has been given. Thermostats and robots are just that, looking as if they take intelligent actions and we understand how they do it by following built-in designed algorithms. So can cells and simple one-celled animals. To assume actual intelligence exists is a very thin analysis.
evolution of consciousness: a new view
by David Turell , Sunday, March 12, 2023, 20:03 (620 days ago) @ David Turell
Temporal view of consciousness:
https://inference-review.com/letter/on-the-temporal-structure-of-consciousness
"We usually believe, for example, that consciousness is continuous. We perceive the trajectory of a diver on her way down in the ocean seemingly at each moment of time. However, simple considerations and experiments show that perception is discrete rather than continuous—that is, consciousness occurs only at certain moments of time.
"How can discrete perception be explained? The classic idea is that there are moments of time during which perception is constant, similar to the frames in a movie where each frame shows only a snapshot of the world. In this scenario, motion is detected by comparing the differences between frames. There is no motion, no change, no processing within a single frame. It is often proposed that perception is not only discrete, but also rhythmic. Perception occurs with a fixed sampling rate of, for example, 10Hz, meaning that there is a new frame every 100ms. Staying with the movie metaphor: think of a surveillance camera that takes snapshots at a fixed rate. What happens in between the snapshots is lost, except for parts that may be carried over as artifacts on the camera’s sensors—so-called neural persistence—and bleed into the next frame.
***
"We propose that only consciousness is discrete. Unconscious processing, to the contrary, is continuous, sophisticated, and has high spatiotemporal resolution. This is very different from simplistic neural persistence—which would add up all information during a perceptual moment into a useless superimposed image, similar to when the shutter of a camera opens for too long. In our model, motion is processed unconsciously by motion detectors, of which only the output is consciously perceived at the end of an unconscious processing period. Thus, we do not perceive motion while it happens in the world, nor while it is computed by motion detectors. Instead, we perceive the output of the motion detectors much later...we do not perceive the motion exactly when it happens in the world, which is obvious, since neural processing takes time. We do not perceive motion exactly when neurons are reflecting the diver’s position. Rather, information about the diver’s trajectory is integrated over a substantial period of time, and we perceive the resulting motion after these computations are completed.
***
"We propose that entire events—e.g., a diver who jumped from a high cliff following a parabolic trajectory in the blue sky, are processed unconsciously, and rendered conscious at one discrete moment of time. Thus, there is no comparison across frames. In addition, unconscious processing does not stop at the end of a moment, it goes on continuously without breaks. Only the conscious “readouts” occur at certain moments of time. Importantly, our model is not rhythmic. We have shown that the duration of a conscious percept depends on the processing load: the higher, the longer.
***
"... our model implies that most of actions are executed unconsciously. We do not see any problem here concerning free will, which we argue operates on much longer time scales. For example, we want to engage in a soccer game. This is free will. We chose to start running upfield. This is also free will. In contrast, fast reactive actions during the game are usually executed unconsciously—in accordance with our will. If the unconsciously triggered action goes against our will, we consciously perceive the mistaken action and that it was against our will—at the next conscious update. In general, we propose that actions become part of the following conscious percept. Actions are part of the event that we perceive. As another example, when we catch a falling plate before it hits the ground, and in other situations where we make ultra-quick decisions, we cannot usually tell why, when, or how the action was triggered. This is because processing was unconscious.
"To reconcile our findings of long discrete unconscious periods with the shorter periods he and others have found, VanRullen proposes a 3-stage model: stage 1 corresponds to unconscious processing, stage 2 to classic discrete snapshots of 100ms corresponding to short instable conscious percepts, and stage 3 is a consolidated percept that comes several hundreds of milliseconds later. The instable percept of stage 2 can be overwritten and may be lost in the consolidated memory of stage 3. VanRullen identifies stage 2 with phenomenological consciousness, and stage 3 with access consciousness. Although we cannot rule out such a model, and are even partly sympathetic to it, we propose that there are no snapshots, but ongoing unconscious processing instead.
***
"Phenomenal consciousness, for example, may simply reflect the unconscious processing of objects, which are not (yet) conscious, but can strongly influence actions. Whatever the final answer is, a conceptual distinction between short term processing in the range of 100ms and longer discrete updates occurring every few hundred ms seems necessary to account for current empirical evidence regarding the temporal structure of consciousness.
Comment: Yes we see a motion picture in temporal or phenomenological consciousness. This only points out again my point that the brain is evolved to give us a desired continuous picture of reality, while the brain itself is stringing together unconsciously a series of electronic signals."