Another review of his book, The Strange Case of the Rickety Cossack, discussing the bushiness of the path of human evolution, and how the paleontologists have been too limited in their thinking:-http://www.wsj.com/articles/a-bone-to-pick-1434667925-"One of paleoanthropology's problems, as Mr. Tattersall sees it, has been professional isolation from other sciences. From its beginnings in the 19th century, the subject was dominated by anatomists who paid minute attention to bone shapes and little to taxonomy or other relevant biological disciplines. These anatomists would make oracular pronouncements, which were basically intuitions beyond the reach of scientific analysis. One advised the young Mr. Tattersall that if he stared at the fossils for long enough, the bones would speak to him. 
 
"A further source of disorder has been that those lucky enough to find new skulls get to speak the loudest. The importance of acquiring human fossils makes paleoanthropology sound, in Mr. Tattersall's telling, more like a contact sport than a science. There are few good locales for human fossil hunting, and many of them are in Ethiopia. Denouncing your competitors to the Ethiopian government can be an expedient route to opening up claims and making big fossil finds. With a new skull in hand, you declare it to be a missing link that lies on the main branch of human evolution, while claiming those of your rivals belong to side branches. You then lock up your skull on the pretense that you need to study it further, while denying competitors the chance to challenge your assertions.-****
"Mr. Tattersall is unsparingly critical of the mental habits of his fellow paleoanthropologists. He describes the profession as one “whose practitioners are often slow to change their minds, even in the face of compelling evidence.” For years they resisted the assertions of molecular biologists that hominid fossils must be far younger than assumed. Until the arrival of cladistics, a more rigorous form of biological classification, debates among paleoanthropologists about how one hominid species was related to another were far from scientific, and “salesmanship was at a greater premium than rigorous reasoning was.” -"Bad scientific habits, Mr. Tattersall believes, have been so pervasive that to the present day they distort knowledge of the human past. “If the entire hominid fossil record were to be rediscovered tomorrow and analyzed by paleontologists with no horses already in the race, it is pretty certain that we would emerge with a picture of human evolution very different from the one we have inherited,” he writes. -"The author concedes that not all his colleagues will agree with everything he says. Still, he has presented a scalding indictment of a scholarly community and shown how easily nonscientific motives can influence supposedly scientific conclusions. Fraud in science is all too common, but failings in objectivity, especially when part of a community groupthink, are harder to detect and far more corrosive."

http://nautil.us/issue/20/creativity/the-strange-inevitability-of-evolution - QUOTES: "You don't have to be a benighted creationist, nor even a believer in divine providence, to argue that Darwin's astonishing theory doesn't fully explain why nature is so marvelously, endlessly inventive.
But the biggest mystery about evolution eluded his theory. And he couldn't even get close to solving it.”
"What Wagner is talking about is how evolution innovates: as he puts it, “how the living world creates.”
"These ideas suggest that evolvability and openness to innovation are features not just of life but of information itself....Manfred Eigen, who insists that Darwinian evolution is not merely the organizing principle of biology but a “law of physics,” an inevitable result of how information is organized in complex systems. And if that's right, it would seem that the appearance of life was not a fantastic fluke but almost a mathematical inevitability." - David's comment: Huge essay. I covered only a little. Why inevitability? - Thank you for giving us this taster. We have been arguing the toss over the problem of innovation for the last eight years! I just don't have time to read the whole essay now, so what I am about to say may be unfair, in which case I apologize in advance. Firstly, there are two mysteries here, and they seem to have been telescoped: innovation is one, and the appearance of life is another. I can think of no reason why life should not appear without evolving, as it apparently did for millions of years here on Earth. Evolution requires favourable, changing conditions and a mechanism that enables an inventive response to those conditions. Secondly, the suggestion that the mechanisms for life and evolution were the inevitable result of a “law of physics” seems to me to be a cop-out on a par with “God did it”. If Wagner can tell us exactly how life began, and exactly how a law of physics can “inevitably” transform comparatively primitive, single-celled organisms into dinosaurs, dogs, humming birds and humans, he might have a case. But I repeat my apologies, as these comments are only based on the quotes.

One paragraph of what has been presented needed a correction: - "In the 1990s Schuster and his colleagues devised a computer program that could predict the simplest features of an RNA's shape (its secondary structure, which is how parts of the chain stick to other parts by pairing-up of bases) from its sequence. For an RNA of 100 bases, there are around 10^23 possible shapes of this sort. But what was remarkable was the way these shapes and their sequences were related. - Note the change in the number from 1023 to exponential 10^23. It becomes an enormous number and yet the author thinks that gives the evolutionary search for useful molecules an easier path! Coordinated patterns do simply, but the numbers are still huge.

Another essay from Andreas Wagner which explains the enormous protein landscape and how evolution seems to navigate it through large relationship networks. One should read the whole essay, as it is very informative and very large, and I can present only a small portion: - https://aeon.co/essays/without-a-library-of-platonic-forms-evolution-couldn-t-work?utm_... - "The glass lizard itself comprises billions of cells. Each cell contains thousands of different kinds of proteins - long string-like molecules made of 20 different kinds of amino acid. And each of these proteins has a unique ability. It might catalyse a chemical reaction, or prevent a cell from collapsing, or sense nutrients, or receive signals from other cells, and so on. Each of these abilities was an innovation - a qualitatively new and useful feature that can make the difference between life and death - when it first arose, millions of years ago. - "How do random DNA changes lead to innovation? Darwin's concept of natural selection, although crucial to understand evolution, doesn't help much. The thing is, selection can only spread innovations that already exist. The botanist Hugo de Vries said it best in 1905: ‘Natural selection can explain the survival of the fittest, but it cannot explain the arrival of the fittest.' (Half a century earlier, Darwin had already admitted that calling variations random is just another way of admitting that we don't know their origins.) - *** - "A protein is a volume in a library just like this, written in a 20-letter alphabet of amino acids. And while protein texts might not be as long as Tolstoy's War and Peace, their total number is still astonishing. For example, a library of every possible amino acid string that is 500 letters long would contain more than 10600 texts - a one with 600 trailing zeros. That vastly outnumbers the atoms in the visible universe. - *** - "..evolution can't simply look up the chemicals it needs in a giant catalogue. No, it has to inch its way painstakingly along the stacks. Imagine a crowd of browsers - each one representing an entire familial line - who must blindly explore the library, step by random step. This sounds like a party game, but there's a grisly twist. A mutation that compromises an essential protein such as haemoglobin is punishable by death. On that ill-fated volume, the bloodline ends. - *** - "And imagine that you could start this journey in not just one but 100 different ways, each one tracing one of a myriad alternative paths through the library, each encoding only synonymous texts that differ in most letters. Nature's libraries are just like that, permeated with sprawling networks of synonymous texts - I call them genotype networks - each encoding a molecule and its biochemical function. - *** - "But when you cannot make a beeline, because each step takes you in a random direction prescribed by a DNA mutation, it turns out that sprawling genotype networks are just what you need to survive. - "Random DNA changes in some members of a population could disable an essential protein such as haemoglobin and lead to death, but because genotype networks exist, other mutations can create a synonymous text that preserves the protein's function and saves the organism. This cycle of mutation and natural selection repeats in the survivors' descendants. Some of them die, but others live and get to take one step further. Step by step, the population of survivors spreads out through the library in a process that unfolds over many generations. - "Relatives of the lizard's oxygen transport protein illustrate how far this exploration can go. They are all descendants of a single long-forgotten ancestral protein that existed more than a billion years ago. By now, they occur not only all over the animal kingdom but even in plants. They have travelled far and wide throughout the library. And still they express the same chemical function. They all bind oxygen. - "Their amino acid text, however, has diverged beyond recognition. Today's haemoglobin proteins share as little as four per cent of the letters among their roughly 100 amino acids. - *** - "The remarkable thing is, having so many different ways to say the same thing means that there are many more possible slips of the tongue. And with each slip of the tongue comes the possibility of saying something different. Just as the word GOLD emerges from a single letter change in MOLD, some neighbours of a text express new meanings. And as the browsers work their way through each synonym for some original text, different innovations become accessible. By creating safe paths through the library, genotype networks create the very possibility of innovation. - *** - "So nature's libraries and their sprawling networks go a long way towards explaining life's capacity to evolve.....They exist in a world of concepts, the kind of abstract concepts that mathematicians explore." - Comment: He is suggesting chance mutation drives evolution because slightly changed molecules have similar function. He is ignoring the necessity of planning the coordinating of the millions of molecules that make up a single cell. He is also ignoring the highly complex world of giant enzymes in using, as an example, hemoglobin with only 100 amino acids.

dhw: ...and an experiment proving that organisms might be able to eat foods never before encountered - an ability which you say is “existing, but not used at all until a need arose”. In this case, the organism's existing digestive mechanism could clearly adapt, so are you saying it never used its digestive system before?-DAVID: Of course it had a digestive system, just using different enzymes in a different way than it now needed and adapted. -And this is the point I am trying to make. All the examples you have mentioned are of features which were already in use but changed their function, in contrast to your claim that they hung around for (hundreds of) thousands of years doing nothing.-dhw: It seems to me that there is enormous confusion, your two types involve innovation and adaptation, and both fit in just as well with an autonomous inventive mechanism as they do with pre-planning. 
DAVID: You are right about confusion. There are articles which are currently trying to explain the differences in types of exaptation. Some of them afraid of the pre-planning aspect.-Can you please point me to just one writer who interprets exaptations in terms of God's pre-planning?
 
DAVID: There is no logical reason for the change in larynx, palate and uvula requiring an epiglottis to protect from aspiration. A lot of mechanical change but no intelligible speech it is thought until the last 100,000 years. Lucy at 2.3 million years ago didn't have these changes. They all happened well before speech.
-What is “intelligible speech”? Intelligible to whom? If you define language in terms of English, French and German, with complex syntax and a vast variety of structures, then of course it's a modern phenomenon. But if you define language as signs, sounds, movements etc. used as means of communication, your whole theory becomes highly problematical. All living creatures have language, right down to bacteria, and you have no idea what sort of sounds were used for communication when the changes took place in the larynx, palate and uvula. But I'll bet you the organisms that experienced those changes continued to communicate, using new sounds, and didn't go dumb for (hundreds of) thousands of years.-In your first book, you wrote: “The human larynx is lower than the Neanderthals' was, allowing humans a much better articulation of speech.....language is not thought to have appeared based on “the behavioural record” until one of our most recent ancestors arrived on the scene.” Since you wrote that book, you have alerted us to many recent discoveries of evidence that Neanderthals used relatively sophisticated tools, buried their dead, built dwellings and boats, cooked their food, hunted, and may well have had their own form of speech. You are, of course, covered by “much better articulation”, but "is not thought to have appeared" raises plenty of questions. My point here is that whenever the changes took place, we simply have no idea whether they were or were not used to create more complex sounds to allow greater breadth of communication. Once again, I don't see how you can asssume they hung around doing nothing for (hundreds of) thousands of years.-You have quoted Gould, who sums up the problem: “I cannot present a ‘review article' of empirical cases of exaptation, for the defining notion of quirky functional shift might almost be equated with evolutionary change itself, or at least with the broad and venerable subject of, in textbook parlance, ‘the origin of evolutionary novelties'” (Gould, 2002, p. 1234).-Just where do you draw the line between adaptation, exaptation, and innovation? In fact, is there a line? Once again, I would suggest that they all come under the umbrella of an autonomous inventive mechanism, which enables organisms to adjust themselves in order to cope with new conditions (adaptation), to use existing organisms for new functions (exaptation), and to create new organs in order to exploit new opportunities offered by new conditions (innovation). The borderlines between these three categories must inevitably remain blurred.

The females make lots of testosterone:

https://phys.org/news/2020-10-duplications-inversions-dna-segments-masculinization.html

"Moles roam in an extreme habitat. As mammals that burrow deep into the earth, they have forepaws with an extra finger and exceptionally strong muscles. What's more, female moles are intersexual while retaining their fertility. Typical for mammals, they are equipped with two X chromosomes, but they simultaneously develop functional ovarian and testicular tissues. In female moles, both tissue types are united in one organ, the ovotestis—a feature unique among mammals.

"The testicular tissue of the female mole does not produce sperm, but large amounts of the sex hormone testosterone, meaning the females have similarly high levels as the males. Presumably, this natural "doping" makes the female moles aggressive and muscular, an advantage for life underground, where they have to dig burrows and fight for resources.

***

"According to the study, it is primarily changes in the structure of the genome that lead to altered control of genetic activity. In addition to the genetic program for testicular development, this also stimulates enzymes for male hormone production in the females.

***

"'We hypothesized that in moles, there are not only changes in the genes themselves, but particularly in the regulatory regions belonging to these genes," says Mundlos.

"In the course of the moles' evolution, then not only would individual letters of the DNA have changed, also larger pieces of the genome would have shifted, says the researcher. If segments of DNA move from one location to another, completely new or reorganized regulatory domains can emerge and thus activate new genes and enhance or attenuate their expression.

***

"...when comparing the genome to that of other animals and humans, the team discovered an inversion—i.e., an inverted genomic segment—in a region known to be involved in testicular development. The inversion causes additional DNA segments to get included in the regulatory domain of the gene FGF9, which reorganizes the control and regulation of the gene. "This change is associated with the development of testicular tissue in addition to ovarian tissue in female moles," explains Dr. Francisca Martinez Real, lead author of the study and scientist at the MPIMG as well as the Institute for Medical Genetics and Human Genetics at Charité.

"The team also discovered a triplication of a genomic region responsible for the production of male sex hormones (androgens), more specifically the androgen production gene CYP17A1. "The triplication appends additional regulatory sequences to the gene—which ultimately leads to an increased production of male sex hormones in the ovotestes of female moles, especially more testosterone," says Real.

***

"'Our findings are a good example of how important the three-dimensional organization of the genome is for evolution," says Lupiáñez. "Nature makes use of the existing toolbox of developmental genes and merely rearranges them to create a characteristic such as intersexuality. In the process, other organ systems and development are not affected.'"

Comment: This shows how God might dabble a genome. We do not know how is is driven naturally.

At the molecular level:

https://medicalxpress.com/news/2022-02-molecular-culprit-caught-cell-death.html

"Cell death is an important part of the body's immune response to infection. When uncontrolled, however, it can cause harmful amounts of inflammation in otherwise healthy organs and tissue. The research team uncovered how an overproduction of the molecule nitric oxide, which the protein caspase-8 helps to produce, caused dangerous levels of cell death. They showed that arresting the function of caspase-8 could prevent unregulated cell death and inflammation.

***

"While nitric oxide is critical to the body's circulatory and nervous systems, the recent findings link an overproduction of the molecule with excessive levels of cell death and inflammation. Cell death is critical for a healthy immune response, however, too much of it can send the immune system into overdrive and trigger inflammatory disease."

Comment: worn out cells have one process of apoptosis to produce new cells, separate from the destruction of cells required in immune defense reactions. Over=reactions are mistakes in molecular reactions, which it seems we can learn to correct with further research.

DAVID: Our presence has made enormous changes:
https://aeon.co/essays/revolutionary-archaeology-reveals-the-deepest-possible-anthropoc...

QUOTE: "...beginning in the Near East some 11,000 years ago, humans discovered how to control the reproduction of wheat and barley, which precipitated a rapid switch to farming. Within 500 to 1,000 years, a scattering of small farming villages sprang up, each with several hundred inhabitants eating bread, chickpeas and lentils, soon also herding sheep and goats in the hills, some keeping cattle.”

There is no question that the human species has had enormous influence on the planet. As an addition to this observation, I would like to mention a remarkable book, first published in 1988 by Yale University Press and still available: Peter J. Wilson, The Domestication of the Human Species, in which he argues that these discoveries were the root of our modern world – social, cultural, psychological, political etc.….The book is still available and highly recommended. The late author (who died in 2005) was Professor of Anthropology at the University of Otago, New Zealand, and he was my brother.

DAVID’s comment: This research supports Behe's theory about loss of DNA driving evolution. Note the comment about small population size. There were never very many hominins, yet major changes occurred. Deletion appears to be a major concept, supporting the idea that original DNA had all the information needed for evolution. Note the DNA of an amoeba is larger than a human DNA but with just a few functional genes. Note my bold about bacteria.

dhw: Evolution is an ongoing process! You seem to have forgotten that the migratory ocean sticklebacks had already evolved their spines, but when they entered new environments, they needed different structures, which in some cases meant jettisoning structures which had evolved earlier. (Like pre-baleen whales' teeth.) I propose that the original DNA contained the ability to make these changes (the ability is the “information”, not the changes themselves, which = your 3.8 byo computer programme for every change). And yes indeed, small individual groups in different environments would explain why different structures evolved in order to cope with different environments. This is why I have proposed that a particular group of apes in a particular location may have decided (and most likely needed) to descend from the trees, whereas elsewhere their brothers had no problem. [I should have said brothers and sisters.]

DAVID: Of course evolution is ongoing. You totally miss the point of small groups and large changes in form. To repeat, a small group of hominins evolved very advanced changes in the human form and brain.

dhw: How have I missed the point? That IS the point of my last example!

Yes you have. A tiny number of existent hominins made enormous changes to advance the human form and brain in short geologic time. Where did the large number of mutations come from your small group of apes on the ground? At one point it is thought there were only 10,000 pre-sapiens living! As for 3.8 byo pre-programming, it must an included a system for necessary minor adaptations within a species as I've described.

DAVID: Not millions of sticklebacks with new mutations and some changes. The issue is still chance vs. design.

dhw: No it isn’t. You claimed that the sticklebacks supported Behe’s theory that loss of DNA drives evolution. I have explained that in some cases evolution will require the jettisoning of previously evolved structures that are no longer suited to the new environment.

Same point as Behe. Jettisoning advances evolution.

DAVID: More to the point why do amoeba have more DNA bases the we do? All the evidenced points to the 3.8 byo DNA being ready for evolution with information supplied by God.

dhw: I don’t know enough about the subject to discuss amoeba, but of course DNA must have been ready for evolution from the start, or evolution would never have happened. That does not mean that your God provided the first cells with detailed programmes to be passed down through billions of years and organisms and environments for every single innovation, econiche, lifestyle and natural wonder in the history of life! The “information” – as you agreed earlier – could have been in the form of a mechanism capable of autonomous design, which would make its own changes according to the requirements and/or opportunities offered by changing conditions.

I never agreed to autonomous design, and you know it. Design with guidelines, in existing DNA.

A new fossil shows us:

https://www.newscientist.com/article/2313779-armless-fossil-sheds-light-on-how-animals-...

"Less than 100 million years after vertebrates first grew legs, some of their descendants had evolved to lose them again, fossils reveal. The discovery shows that land vertebrates first began to evolve a snake-like form at least 308 million years ago.

***

"The animal has been dubbed Nagini mazonense, representing a new genus and species, and it belongs to a group called the molgophids. It may have grown to be about 10 centimetres long, and had a snake-like body with no forelimbs. It also lacked the bony structures that support the attachment of forelimbs to the body, known as the pectoral girdle.

"However, N. mazonense did have a pair of small but fully formed back legs, with four toes on each foot.

"Along with the nearly complete skeletons, which are around 308 million years old, there were also impressions of soft tissue, revealing that N. mazonense had a round snout and a long body with about 85 vertebrae and ribs. There were no signs of soft tissue in the area where forelimbs might be expected, says Mann.

“'They’re relying on body-based locomotion like sidewinding and not really relying on limb-propelled locomotion anymore,” says Mann.

"It is a fascinating discovery, says Rolf Zeller at the University of Basel in Switzerland. “Snake embryos, such as pythons, still form hindlimb buds that disappear during development,” he says. “The discovery of an ancient snake-like fossil lacking forelimbs but retaining hindlimbs is a fantastic find, because it reveals the existence of transitional forms before complete limb loss during evolution.”

"Modern snakes also lost their upper limbs and pectoral girdle first, about 170 million years ago, he adds. But N. mazonense and other molgophids aren’t direct ancestors of modern snakes, says Mann. “They’re sort of an early experimental lineage of reptiles.'”

Comment: based on our 'loss of genes to advance evolution' discussion loss of limbs could simply be gene deletion

QUOTE: One of the lost genes, KLK8, is interesting because it is involved in the development both of sweat glands in the skin and of the hippocampus in the brain; cetaceans lost it during their transition from land back to water. The loss of this gene is linked to the development of a thicker epidermis and the loss of hair (hair is not adaptive in aquatic environments, where it creates drag and does not preserve body heat as it does in terrestrial animals).

dhw: I think this quote provides the clearest possible explanation of the whole process. Loss of genes does not mean that every single organism was planned in advance with its code implanted in the very first living cells. It simply means that as evolution progressed, and more and more species evolved, each new species would have jettisoned those inherited genes which were no longer needed. Hair genes evolved as protection against the climate, but what would be the point of your ancestors’ hair genes if you lived in the water and no longer needed hair? Just like organisms themselves, genes are subject to the process of natural selection - the same principle as shrinkage of the modern brain: cells that were no longer needed were discarded.

DAVID: Neat sidesteps. The big issue is if advances always result from the loss of genes the info was available and revealed in the smaller DNA with each step. Natural selection could only study what it received in each new advance, which it obviously did not control.

dhw: It is not a sidestep, and I challenge the view that advances ALWAYS result from loss of genes! I suggest that the process is on-going, with a constant acquisition of new genes (or new functions for old genes) and loss of unwanted genes. Natural selection merely decides which genes are necessary and which are not.

DAVID: Natural selection has nothing to do with genes directly!!! You are challenging two sources of advances in form and function through the gene loss concept: Behe's book, filled with examples and an article that lists many studies but never mentions Behe's ideas. How can you challenge it? From previous bias is obvious.

dhw: What do you mean by “directly”? If certain genes are no longer required, it is perfectly “natural” that they should disappear. I am puzzled by the theory you have presented, so instead of asking why I challenge it, perhaps you would enlighten me by explaining why my bolded proposal above is impossible.

Your proposal is wishful, but not supported by anything in the article I presented or by Behe's book. Facts are facts. DNA Loss is now known and supported by a source (quoting multiple studies other than Behe). The last of Darwin worship is dying.