Epigenetics: Human effects (Introduction)

by David Turell @, Wednesday, February 13, 2013, 17:49 (4302 days ago)

Fat fathers may influence chldren's development:-http://www.the-scientist.com//?articles.view/articleNo/34307/title/Fat-Dads--Epigenetic-Legacy/

Epigenetics: Plant adaptation

by David Turell @, Thursday, February 14, 2013, 18:36 (4301 days ago) @ David Turell

This mustard plant is shown to adapt to environmental changes by various genomic changes:-http://f1000research.com/articles/2-5/v1?emailType=Feb2013MonthlyUpdate&utm_source=Email_Monthly_Feb2013&utm_medium=Email&utm_content=Research_Article_1&utm_campaign=F1K_Monthly_Feb2013

Epigenetics: Plant adaptation

by David Turell @, Wednesday, March 27, 2013, 13:58 (4260 days ago) @ David Turell

Another study finding a controlling segment in 'junk' DNA in the modification of corn:-http://www.sciencedaily.com/releases/2013/03/130326112003.htm

Epigenetics: speedy changes

by David Turell @, Tuesday, April 09, 2013, 19:34 (4247 days ago) @ David Turell

Rediscovering what other species have already shown. Change environment and there is rapid change. Just like Reznick's guppies from 1990.-"Our study underlined that evolution can happen on a short timescale and even small 1 to 2 per cent evolutionary changes in the underlying biology caused by your harvesting strategy can have major consequences on population growth and yields."- Read more at: http://phys.org/news/2013-04-environmental-triggers-rapid-evolution.html#jCp

Epigenetics: speedy changes (guppies)

by David Turell @, Wednesday, September 02, 2015, 22:37 (3371 days ago) @ David Turell

With four generations a year, finding epigenetic changes in guppies is not a surprise:-http://www.sciencedaily.com/releases/2015/09/150902134937.htm-"FSU Professor of Biological Science Kimberly Hughes and a team of researchers set out to find how this tiny tropical fish would evolve if they transplanted wild Trinidadian guppy fish from a stream with predatory fish into two-predator-free streams. Because guppies reproduce multiple times in a year, they were able to track three to four generations of the fish living in a predator-free zone.-"By sequencing genetic material in the guppies' brains, researchers found that 135 genes evolved in response to the new environment. Most of the changes in the gene expression were internal and dealt with a fish's biological processes such as metabolism, immune function and development.-"But more importantly, the immediate response of genes to change in the environment did not reflect the eventual evolutionary change.-"Genes can change their activity levels in an immediate response to the environment -- what evolutionary biologists call plasticity -- or in an evolutionary response that occurs over many generations.-"What Hughes and her colleagues found was that the evolutionary change in gene activity was usually opposite in direction to the immediate plasticity of gene activity. A gene that had changed in response to drastic change in the environment would then evolve in the opposite direction after a few generations.-"'Some evolutionary theory suggests that plastic and evolutionary changes should be in the same direction," Hughes said. "But our results indicate that at least in the very early stages of evolution, genes that respond in the 'wrong' way to an environmental shift are those that will evolve most quickly.'"

Epigenetics: guppies' adaptations

by David Turell @, Monday, July 31, 2017, 18:15 (2673 days ago) @ David Turell

As described by Reznick guppy size changes quickly within a two year period, but new research finds other important changes depending upon predation:

https://phys.org/news/2017-07-competitive-world-guppies-born-bigger.html

"Essentially one of two fates confront the guppies who inhabit the South American island's mountain streams. Guppies who live lower down the mountain face a constant threat of predators. Fish higher up the slope live a relatively predator-free life, but it's no paradise because in waters teeming with fellow guppies, the competition for limited food is stiff. Up to now, what scientists had observed is that guppy moms in the high-predation (HP) waters produced scads of smaller young while guppies in the low-predation areas (LP) produced fewer but larger young.

"In the new study in Scientific Reports, Brown postdoctoral researcher Terry Dial and colleagues report that the size difference of a couple of millimeters of length may not be the most meaningful one. Instead, the larger guppies in the LP streams are born significantly more mature, at least where it counts for their way of eating. It's their internal anatomy that may promote their survival.

"LP guppy mouth joints swing twice as widely (22 degrees instead of 11), the researchers found. As a result their jaws open to a bigger gape. The heads of LP guppies are 90 percent hardened at birth, while HP guppies are only 20 percent hardened. Finally, the muscles controlling the jaws are bigger in LP guppies. Eventually, HP guppies will catch up - if they survive - but LP guppies are born better at scraping algae and diatoms off stream rocks for dinner.

"'There is more to it than just an investment in sheer size," Dial said. "This is the first time we'd really gone into the morphology and anatomy of these animals and tried to tease apart what is different about these fish other than just size."

"Dial found that not only were the HP and LP populations significantly different in this regard, but also the larger newborns within LP populations were significantly more mature than the smaller newborns in LP populations.

"Of course the guppies aren't consciously strategizing. Instead, Dial said, evolution in LP environments apparently selects for moms that produce more fully mature newborns, because those babies are better at competing for food and are therefore more likely to survive and carry on mom's lineage. On the other hand, in HP streams where the main danger is predators, evolution may favor moms who produce so many young, because surely some number will survive to grow up and reproduce without being eaten."

Comment: These guppies are amazingly adaptable, but they do not create a new species.

Epigenetics: DNA controls

by David Turell @, Tuesday, June 11, 2013, 02:33 (4185 days ago) @ David Turell

More and more complex:-http://www.licr.org/index.php/mapping_the_embryonic_epigenome/

Epigenetics: DNA controls

by David Turell @, Tuesday, June 11, 2013, 15:42 (4184 days ago) @ David Turell

And again complexity. In histones, the spools around which DNA is wound, there is a code to control methylation and other gene modifications. The code is not yet understood, but provides another layer of controls over gene expression. It shows why only roughly 22,000 genes control human biology.-http://medicalxpress.com/news/2013-06-piece-histone-code-puzzle.html

Epigenetics: Love among voles

by David Turell @, Wednesday, June 19, 2013, 18:08 (4176 days ago) @ David Turell

Epigenetics: In pathogenic bacteria

by David Turell @, Wednesday, June 19, 2013, 18:14 (4176 days ago) @ David Turell

"Upon revisiting the data—and applying the new software—Schadt and colleagues discovered that along with the Shiga toxin, this particular E. coli had also adopted a methylase from the same phage. This methylation-laying enzyme resulted in a complete epigenetic makeover, the team learned. The group is still working on characterizing the effects of these epigenetic modifications, but Schadt said that the various pathways that were upregulated and downregulated in the bacterium, including changes in swarming and growth patterns, could have contributed to making it more virulent.
 
"The technology is transforming the study of bacterial genome modification, said Richard Roberts, chief scientific officer at New England Biolabs, who started collaborating with PacBio to investigate bacterial epigenetics in 2010. In addition to simply mapping the epigenomes of hundreds of bacteria species, including emerging pathogens, Roberts is adding to his library of knowledge on how bacteria use methylation to protect their genomes from the restriction enzymes they release to cut up invading viral DNA. Other researchers are working on understanding the role of methylation in the cell cycle.
 
"It's like you've been in a closed room for a long time, and you open the window and look out," said Roberts. "And there's a whole lot of stuff out there, and you don't know where to look.' "-
http://www.the-scientist.com//?articles.view/articleNo/35581/title/Decoding-Bacterial-Methylomes/-The genome is layer upon layer of complexity even in simple folks like bacteria.

Epigenetics: Passing the effects

by David Turell @, Friday, June 21, 2013, 15:14 (4174 days ago) @ David Turell

What we do in our lives may be passed on as changes in children. How this might happen in the genome through modified histones, as managers of DNA:-"In a comprehensive study, scientists at the Friedrich Miescher Institute for Biomedical Research identified the molecular logic underlying the retention of histones and their marks during the development of the sperm. These findings set the stage to address a fundamental question in epigenetics: whether and how chromatin marks in sperm are passed on to the next generation and contribute the epigenetic inheritance of traits shaped by experience or the environment." -Read more at: http://phys.org/news/2013-06-stage-epigenetic.html#jCp

Epigenetics: exercise changes

by David Turell @, Thursday, August 08, 2013, 02:27 (4127 days ago) @ David Turell

Fat cell gene modificiation by six months of exercise with new methylation points in the DNA:-"Given the important role of epigenetics in gene regulation and disease development, we here present the genome-wide DNA methylation pattern of 476,753 CpG sites in adipose tissue obtained from healthy men. Since environmental factors potentially change metabolism through epigenetic modifications, we examined if a six months exercise intervention alters the DNA methylation pattern as well as gene expression in human adipose tissue. Our results show that global DNA methylation changes and 17,975 individual CpG sites alter the levels of DNA methylation in response to exercise. We also found differential DNA methylation of 39 candidate genes for obesity and type 2 diabetes in human adipose tissue after exercise. Additionally, we provide functional proof that genes, which exhibit both differential DNA methylation and gene expression in human adipose tissue in response to exercise, influence adipocyte metabolism. Together, this study provides the first detailed map of the genome-wide DNA methylation pattern in human adipose tissue and links exercise to altered adipose tissue DNA methylation, potentially affecting adipocyte metabolism."-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694844/

Epigenetics: changing \'eye\' spots

by David Turell @, Tuesday, August 20, 2013, 16:23 (4114 days ago) @ David Turell

Fools predators:-http://www.sciencedaily.com/releases/2013/08/130819102728.htm

Epigenetics: changing \'eye\' spots

by Balance_Maintained @, U.S.A., Tuesday, August 20, 2013, 21:49 (4114 days ago) @ David Turell

Would love to know how an evolutionary theorist would explain how this same mechanism arose in fish, moths, butterflies, Cervils, birds and more.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Epigenetics: changing \'eye\' spots

by dhw, Wednesday, August 21, 2013, 13:36 (4113 days ago) @ Balance_Maintained

TONY: Would love to know how an evolutionary theorist would explain how this same mechanism arose in fish, moths, butterflies, Cervils, birds and more.-Maybe the same way as lots of different species came up with real eyes, legs, teeth and waggly bottoms: through a mechanism that devises useful inventions to cope with the environment. David and I have called it "the intelligent cell/genome". And we would all love to know how THAT arose!

Epigenetics: induced fear

by David Turell @, Tuesday, December 03, 2013, 00:43 (4010 days ago) @ dhw

Carries down three generations in mice taught to fear an odor.:-http://www.nature.com/news/fearful-memories-haunt-mouse-descendants-1.14272

Epigenetics: how developed?

by David Turell @, Monday, December 23, 2013, 14:54 (3989 days ago) @ David Turell

Where did the gene modifications of the epigenetic mechanisms come from. They had to develop through evolution to accurately follow the theory. What Shapiro has done is push the debate back to a deeper level of development. We can now see how the genome might be changed enough for macroevolution and true innovaton, but we are not there yet:-
"There is another aspect of this issue that is worth mentioning. Imagine for a moment that Shapiro is on to something. Perhaps his natural genetic engineering toolkit can generate biology's many incredible designs. Even if that is true, it would not solve the problem of novelty, it would just push it back one step.
 
"For if those natural genetic engineering tools could create such complexities, it would raise the question of how evolution created such tools in the first place. You see those natural genetic engineering tools are, themselves, the result of complex structures and information. Adaptive mutations and horizontal gene transfer don't "just happen."- 
"Imagine a fully automated factory that builds automobiles. That would be amazing and the discovery of how the factory works wouldn't explain the origin of cars. Likewise, the discovery of genetic tools that created the species would be a tremendous advance, but it would hardly solve evolution's problem of novelty. For how did the novel genetic tools evolve?"-http://darwins-god.blogspot.com/2013/12/james-shapiro-cries-foul-i-was-outraged.html-This last brilliant paragraph is a perfect analogy for the problem. The car has to be planned by intelligence.

Epigenetics:Lamarkism revived

by David Turell @, Friday, March 07, 2014, 15:35 (3915 days ago) @ David Turell

Many experiments in plants and animals show environmental effects can be passed on in subsequent generations, but how is the current question. It is not accidental mutations, but a direct effect. Two examples:-"The public first started to take notice in the mid-2000s, after large epidemiological investigations in Europe began to show transgenerational effects in humans. One study of Swedish historical records showed that men who had experienced famine before puberty were less likely to have grandsons with heart disease or diabetes than men who had plenty to eat5. Similar work with children in Britain reported in 2005 that fathers who had started smoking before the age of 11 had an increased risk of having boys of above average weight."-http://www.nature.com/news/epigenetics-the-sins-of-the-father-1.14816

Epigenetics:Telomere length

by David Turell @, Monday, April 07, 2014, 16:13 (3884 days ago) @ David Turell

Telomeres are caps on the ends of chromosomes to protect them. Shortening means loss of protection. Stress affects telomere length:-http://www.nature.com/news/stress-alters-children-s-genomes-1.14997

Epigenetics: Dplicate gene controls

by David Turell @, Wednesday, April 09, 2014, 15:52 (3882 days ago) @ David Turell

Differential methylation is found to conrol duplicate gene actions:-http://www.pnas.org/content/early/2014/04/02/1321420111-"Duplicate genes are essential and ongoing sources of genetic material that evolution can act on, yet new duplicates are under constant risk of being inactivated by mutations and subsequently lost. We show that a common heritable epigenetic modifier, DNA methylation, plays an important role in duplicate gene evolution. DNA methylation clearly distinguishes young and old duplicates, and the differences in DNA methylation of duplicate genes are associated with functional differences in expression. Remarkably, for a majority of duplicate gene pairs, a specific duplicate partner is consistently hypo- or hypermethylated across highly divergent tissues. Our results indicate that epigenetic modifications are intimately involved in the regulation and maintenance of duplicate genes."

Epigenetics: innate language program

by David Turell @, Wednesday, April 09, 2014, 16:08 (3882 days ago) @ David Turell

More support for Chomsky's contention that we are born with the ability to have language:-http://www.sciencedaily.com/releases/2014/04/140408122316.htm-"Working with Italian newborn infants and their families, we observed that newborns react differently to good and bad word candidates, similar to what adults do. Young infants have not learned any words yet, they do not even babble yet, and still they share with us a sense of how words should sound. This finding shows that we are born with the basic, foundational knowledge about the sound pattern of human languages.
 
"It is hard to imagine how differently languages would sound if humans did not share such type of knowledge. We are fortunate that we do, and so our babies can come to the world with the certainty that they will readily recognize the sound patterns of words-no matter the language they will grow up with."

Epigenetics: quick worm changes

by David Turell @, Saturday, May 17, 2014, 15:48 (3844 days ago) @ David Turell

Study shifts worms on plants and sees how quickly DNA is changed in one year:-http://news.sciencemag.org/biology/2014/05/evolution-predictable-http://www.sciencedaily.com/releases/2014/05/140515163836.htm-Minor adaptations ain't slow

Epigenetics: quick worm changes

by David Turell @, Tuesday, May 27, 2014, 21:38 (3834 days ago) @ David Turell

Bacteria recode interpretations of DNA in nature quite often:-http://www.scientificamerican.com/article/microbes-defy-rules-of-dna-code/?&WT.mc_id=SA_DD_20140527

Epigenetics: silence of the crickets

by David Turell @, Monday, June 02, 2014, 15:14 (3828 days ago) @ David Turell

In 20 generations as a response to a parasite:-http://www.nature.com/news/evolution-sparks-silence-of-the-crickets-1.15323

Epigenetics: passing on fear

by David Turell @, Saturday, October 18, 2014, 01:54 (3691 days ago) @ David Turell

From one generation to the next epigenetically in mice:-http://www.the-scientist.com/?articles.view/articleNo/41239/title/Epigenetics-Paper-Raises-Questions/- "commentary published in GENETICS this week (October 15) questions the results of a December 2013 Nature Neuroscience paper about how mice, when conditioned to fear odors, pass on their fears to their pups, as well as to their pups' offspring, presumably by an epigenetic mechanism."

Epigenetics: through phenotype changes?

by David Turell @, Wednesday, January 14, 2015, 01:41 (3603 days ago) @ David Turell
edited by dhw, Wednesday, January 14, 2015, 08:22

Do animals have control over their evolution through choosing minor changes in habits that modify their bodies:-"What they are saying is something subtler. Over their lifetimes, living things make all sorts of adjustments to their physical being - what biologists call the phenotype, as opposed to the genetic make-up, or genotype - to get along better in the environment they find themselves in. They grow differently based on how they use their bodies, they turn certain genes on and others off, they learn new behaviours, and so on.-"None of these changes count as evolution, because they don't directly change the organism's genetic make-up. But they do shape the way natural selection acts on these genes, and in that way they push evolution in a different direction. In effect, the genes, which we have always thought of as occupying the driver's seat, have slid over to let the phenotype take the wheel. When the phenotype changes for some purpose, the genes that enhance that response might come along for the ride."-http://www.newscientist.com/article/mg22029380.700-lifes-purpose-can-animals-guide-their-own-evolution.html?full=true#.VLXI9mA5C1s

Epigenetics: through phenotype changes?

by dhw, Wednesday, January 14, 2015, 19:55 (3602 days ago) @ David Turell

DAVID: Do animals have control over their evolution through choosing minor changes in habits that modify their bodies:-"What they are saying is something subtler. Over their lifetimes, living things make all sorts of adjustments to their physical being - what biologists call the phenotype, as opposed to the genetic make-up, or genotype - to get along better in the environment they find themselves in. They grow differently based on how they use their bodies, they turn certain genes on and others off, they learn new behaviours, and so on.
"None of these changes count as evolution, because they don't directly change the organism's genetic make-up. But they do shape the way natural selection acts on these genes, and in that way they push evolution in a different direction. In effect, the genes, which we have always thought of as occupying the driver's seat, have slid over to let the phenotype take the wheel. When the phenotype changes for some purpose, the genes that enhance that response might come along for the ride."

http://www.newscientist.com/article/mg22029380.700-lifes-purpose-can-animals-guide-thei...

QUOTE: Jablonka thinks the evolution of associative learning may have been what sparked the Cambrian explosion, the relatively sudden burst of diversification that produced almost all of today's animal phyla about 550 million years ago. If she is right, then we owe almost everything - from the diversity of animal life to human culture - to the ability of organisms to direct evolution towards useful ends.-This article appeared in print under the headline "Life's purpose"-This and the quote below are worth noting for two reasons. 1) You think God's purpose was to create humans, though you refuse to speculate on why he would want to do such a thing. Here we have the proposal that the organisms themselves direct evolution towards useful ends - which I summarized earlier as survival and improvement. An end in itself.-QUOTE: 
Gambling on evolution
Might organisms be able to order up mutations, exactly when they need them? The idea is far from proven, but not as far-fetched as you might think.-2) Perhaps, then, I am not alone in thinking that organisms might possess an inventive mechanism which enables them to innovate. As your own quotes show, the article does not go that far, and still clings to random mutations as the main supplier of innovation. But the above is clearly heading in the direction of my hypothesis. We simply don't know the extent of control that cells/cell communities have over their own development.

Epigenetics: through phenotype changes?

by David Turell @, Thursday, January 15, 2015, 00:12 (3602 days ago) @ dhw


> dhw: 2) Perhaps, then, I am not alone in thinking that organisms might possess an inventive mechanism which enables them to innovate. As your own quotes show, the article does not go that far, and still clings to random mutations as the main supplier of innovation. But the above is clearly heading in the direction of my hypothesis. We simply don't know the extent of control that cells/cell communities have over their own development.-I presented this article to demonstrate how strongly the Lamarckian theory is raising its ugly head. (Ugly to strict Darwinists). We are still learning how strong this self-improvement mechanism may be. And you have admitted the mechanism may be God given. I think it is and you are still unconvinced, but we are not that far apart.

Epigenetics: through phenotype changes?

by dhw, Thursday, January 15, 2015, 16:39 (3601 days ago) @ David Turell

dhw: 2) Perhaps, then, I am not alone in thinking that organisms might possess an inventive mechanism which enables them to innovate. As your own quotes show, the article does not go that far, and still clings to random mutations as the main supplier of innovation. But the above is clearly heading in the direction of my hypothesis. We simply don't know the extent of control that cells/cell communities have over their own development.-DAVID: I presented this article to demonstrate how strongly the Lamarckian theory is raising its ugly head. (Ugly to strict Darwinists). We are still learning how strong this self-improvement mechanism may be. And you have admitted the mechanism may be God given. I think it is and you are still unconvinced, but we are not that far apart.-There are interesting developments here. I offered survival and improvement as purposes for life. You have now subtly changed my term “inventive mechanism” to “self-improvement mechanism”, and “how autonomous” has now become “how strong”. I have no objections if those are the terms you want to use. But we shall remain miles apart if you still insist that your God programmed the very first cells with all the inventions or improvements (from weavers' nests and monarchs' lifestyles to eyes, ears and penises) that have taken place in the history of evolution, just for the sake of producing humans.

Epigenetics: through phenotype changes?

by David Turell @, Thursday, January 15, 2015, 19:17 (3601 days ago) @ dhw

dhw: But we shall remain miles apart if you still insist that your God programmed the very first cells with all the inventions or improvements (from weavers' nests and monarchs' lifestyles to eyes, ears and penises) that have taken place in the history of evolution, just for the sake of producing humans.-Terms are not important. It is concepts that fit the known evidence. I repeat, Gould termed humans as a 'glorious accident'. We are here against enormous odds. My only answer to 'why' is that I think it was planned. You think 'lucky'. That is fine with me. I can't think of any other possibility than those two. Lucky implies chance. So we are back to square one.

Epigenetics: through phenotype changes?

by dhw, Friday, January 16, 2015, 19:43 (3600 days ago) @ David Turell

Dhw: There are interesting developments here. I offered survival and improvement as purposes for life. You have now subtly changed my term “inventive mechanism” to “self-improvement mechanism”, and “autonomous” has now become “how strong”. I have no objections if those are the terms you want to use. But we shall remain miles apart if you still insist that your God programmed the very first cells with all the inventions or improvements (from weavers' nests and monarchs' lifestyles to eyes, ears and penises) that have taken place in the history of evolution, just for the sake of producing humans-DAVID: Terms are not important. It is concepts that fit the known evidence. I repeat, Gould termed humans as a 'glorious accident'. We are here against enormous odds. My only answer to 'why' is that I think it was planned. You think 'lucky'. That is fine with me. I can't think of any other possibility than those two. Lucky implies chance. So we are back to square one.-As always you scurry back to chance v. design and gloss over the issue of the inventive mechanism, which is the point of this particular post on this particular thread. (It begins with the researchers' claim that organisms might have a degree of control over their evolution.) My fault for bringing in your anthropocentrism, which I'll tackle on the “Animal Language” thread. You seem to have accepted the idea of an inventive/self-improvement mechanism, but on the other hand we have the problem of the weaverbird, the monarch, the plover and billions of innovations and complex lifestyles. My point here, to put it as succinctly as possible, is that an inventive/self-improvement mechanism which doesn't invent/self-improve is not an inventive/self-improvement mechanism. So, to take just one example in conjunction with my post under “Animal Language”, do you still categorically exclude the possibility that the first generation(s) of weaverbirds designed their own nests?

Epigenetics: through phenotype changes?

by David Turell @, Saturday, January 17, 2015, 01:16 (3600 days ago) @ dhw


> dhw: As always you scurry back to chance v. design and gloss over the issue of the inventive mechanism, which is the point of this particular post on this particular thread. ... My point here, to put it as succinctly as possible, is that an inventive/self-improvement mechanism which doesn't invent/self-improve is not an inventive/self-improvement mechanism. So, to take just one example in conjunction with my post under “Animal Language”, do you still categorically exclude the possibility that the first generation(s) of weaverbirds designed their own nests?-As I have said before, we do not understand the origin of instinctual behavior. What the weaverbirds do now is instinct within their DNA. They didn't design the complex nest we see now all at once. Did they design it gradually over many generations? I don't know. I think they contributed but were helped by a design plan. For me this issue doesn't settle the major of chance or design.

Epigenetics: through phenotype changes?

by dhw, Saturday, January 17, 2015, 14:01 (3599 days ago) @ David Turell

dhw: As always you scurry back to chance v. design and gloss over the issue of the inventive mechanism, which is the point of this particular post on this particular thread. ... My point here, to put it as succinctly as possible, is that an inventive/self-improvement mechanism which doesn't invent/self-improve is not an inventive/self-improvement mechanism. So, to take just one example in conjunction with my post under “Animal Language”, do you still categorically exclude the possibility that the first generation(s) of weaverbirds designed their own nests?
-DAVID: As I have said before, we do not understand the origin of instinctual behavior. What the weaverbirds do now is instinct within their DNA. They didn't design the complex nest we see now all at once. Did they design it gradually over many generations? I don't know. I think they contributed but were helped by a design plan. For me this issue doesn't settle the major of chance or design.-It can't (nothing can), and it's not meant to do so. I'm trying to pin you down on the issue of how you think evolution works, and I'm using the weaverbird's nest as a test case. For the sake of argument, I continue to wear my theist hat, and offer these theistic choices: 1) God preprogrammed the first cells to pass on the design of the weaverbird's nest; 2) God dabbled to design the nest; 3) God provided the first cells with an inheritable, autonomous, intelligent, inventive mechanism which enabled the weaverbird to design its nest for itself. If you think any of these three hypotheses could be combined, please tell me how. If you can't, it's either 1, 2 or 3, so please tell me which you think is most likely.

Epigenetics: through phenotype changes?

by David Turell @, Saturday, January 17, 2015, 14:35 (3599 days ago) @ dhw


> dhw: I'm trying to pin you down on the issue of how you think evolution works, and I'm using the weaverbird's nest as a test case. For the sake of argument, I continue to wear my theist hat, and offer these theistic choices: 1) God preprogrammed the first cells to pass on the design of the weaverbird's nest; 2) God dabbled to design the nest; 3) God provided the first cells with an inheritable, autonomous, intelligent, inventive mechanism which enabled the weaverbird to design its nest for itself. If you think any of these three hypotheses could be combined, please tell me how. If you can't, it's either 1, 2 or 3, so please tell me which you think is most likely.-We are full circle back to my dilemma. I don't know. By a process of elimination, recognizing that chance mutations won't work, I'm left with the conclusion that God guided evolution, and you want me to tell you how, and I can't. Your three alternatives are correct considerations. The only other possibility is the concept (Sheldrake) of species consciousness combined with an IM (God-given) so that the whole flock of weaverbirds worked it out over a period of time as they evolved as a species of birds.

Epigenetics: through phenotype changes?

by dhw, Sunday, January 18, 2015, 13:12 (3598 days ago) @ David Turell

dhw: I'm trying to pin you down on the issue of how you think evolution works, and I'm using the weaverbird's nest as a test case. For the sake of argument, I continue to wear my theist hat, and offer these theistic choices: 1) God preprogrammed the first cells to pass on the design of the weaverbird's nest; 2) God dabbled to design the nest; 3) God provided the first cells with an inheritable, autonomous, intelligent, inventive mechanism which enabled the weaverbird to design its nest for itself. If you think any of these three hypotheses could be combined, please tell me how. If you can't, it's either 1, 2 or 3, so please tell me which you think is most likely.-DAVID: We are full circle back to my dilemma. I don't know. By a process of elimination, recognizing that chance mutations won't work, I'm left with the conclusion that God guided evolution, and you want me to tell you how, and I can't. Your three alternatives are correct considerations. The only other possibility is the concept (Sheldrake) of species consciousness combined with an IM (God-given) so that the whole flock of weaverbirds worked it out over a period of time as they evolved as a species of birds.-Whether they worked it out slowly, quickly, individually or flockily is not the point. The question is whether they did it themselves, or God did it for them. The extent to which information gets passed on from organism to organism or through some kind of species consciousness is also irrelevant to what you call your dilemma. You have agreed that either God did it all (preprogramming or dabbling), or he gave the weaverbirds (and millions of other organisms) the wherewithal to work it out for themselves. I know you don't know. You don't know whether God exists either, but you have very strong convictions. And you even have a strong belief that you know what God wanted to do when he started life. So I'm surprised you can't tell me which you find most likely out of these three possible roles for God in the design of the weaverbird's nest. (More pecking to be found on the "Animal Language" thread!)
.

Epigenetics: through phenotype changes?

by David Turell @, Sunday, January 18, 2015, 15:44 (3598 days ago) @ dhw


> dhw: You have agreed that either God did it all (preprogramming or dabbling), or he gave the weaverbirds (and millions of other organisms) the wherewithal to work it out for themselves. I know you don't know. You don't know whether God exists either, but you have very strong convictions. And you even have a strong belief that you know what God wanted to do when he started life. So I'm surprised you can't tell me which you find most likely out of these three possible roles for God in the design of the weaverbird's nest. -Yes I have strong convictions, because I look at the result of the evolutionary process, and humans are a totally unnecessary ending, based on the lesser animals and how they survive beautifully. I'm not looking at survival of the fittest, but appearance of the thinkers. So I've looked at the 'big picture' and I've concluded God did it, not on the basis of this one consideration but all the importance reasons listed in my books which express the totality of the evidence for God. I've used weaverbird nests as an example of complex instinct. But we don't know the full story on instinct. It exists, but just how is not explained. So to me it is a minor issue. It is enough for me to say, they have the nest-building instinct, God helped them, and I don't know how. That is all guess-work.

Telomere length protection

by David Turell @, Friday, November 13, 2015, 14:58 (3299 days ago) @ David Turell

Telomeres are caps that protect the ends of chromosomes, which tend to shorten with aging. A new use for a known enzyme is found: it protects:-http://www.the-scientist.com/?articles.view/articleNo/44464/title/Another-Telomere-Regulating-Enzyme-Found/-"ATM kinase, an enzyme known to be involved in DNA repair, is required for telomere elongation, according to a study published this week (November 12) in Cell Reports. The results could have implications for diverse diseases, from cancer, which is typically linked to overly long telomeres, to lung and bone marrow disorders that are associated with shortened telomeres.- “'We've known for a long time that telomerase doesn't tell the whole story of why chromosomes' telomeres are a given length, but with the tools we had, it was difficult to figure out which proteins were responsible for getting telomerase to do its work,” Carol Greider, a director at the Johns Hopkins Institute for Basic Biomedical Sciences and a corecipient of the 2009 Nobel Prize in Physiology or Medicine for the discovery of telomerase, said in a press release."-Comment: More and more complexity

Epigenetics: Passing the effects

by David Turell @, Monday, February 02, 2015, 23:06 (3583 days ago) @ David Turell

More research in C. elegans finds epigenetic effects can pass through 25 generations when double stranded RNA (dsRNA) acts on the germ cells:-http://phys.org/news/2015-02-mechanism-inheritance-advance-evolution-disease.html-"The team's biggest finding was that dsRNA can travel from body cells into germ cells and silence genes within the germ cells. Even more surprising, the silencing can stick around for more than 25 generations. If this same mechanism exists in other animals—possibly including humans—it could mean that there is a completely different way for a species to evolve in response to its environment.-"'This mechanism gives an animal a tool to evolve much faster," Jose said. "We still need to figure out whether this tool is actually used in this way, but it is at least possible. If animals use this RNA transport to adapt, it would mean a new understanding of how evolution happens.'"

Epigenetics: Passing the effects

by dhw, Tuesday, February 03, 2015, 21:13 (3582 days ago) @ David Turell

DAVID: More research in C. elegans finds epigenetic effects can pass through 25 generations when double stranded RNA (dsRNA) acts on the germ cells: -http://phys.org/news/2015-02-mechanism-inheritance-advance-evolution-disease.html
 
QUOTE: "'This mechanism gives an animal a tool to evolve much faster," Jose said. "We still need to figure out whether this tool is actually used in this way, but it is at least possible. If animals use this RNA transport to adapt, it would mean a new understanding of how evolution happens.'"-This would clearly bring us one step closer to the autonomous inventive mechanism which I have suggested drives evolution. Under “New ancient fossils” (many thanks again for all these highly educational articles) we learn about very early multicellular organisms big enough to be seen by the naked eye. The authors link this development with an increase in oxygen (a factor which some researchers also link to the Cambrian Explosion). No doubt you will see this as another piece of your God's preprogramming, passed on by the first cells, but I can't help feeling it fits in perfectly with the concept of cells themselves experimenting as the environment offers new opportunities.

Epigenetics: Passing the effects

by David Turell @, Wednesday, February 04, 2015, 15:13 (3581 days ago) @ dhw


> dhw: The authors link this development with an increase in oxygen (a factor which some researchers also link to the Cambrian Explosion). No doubt you will see this as another piece of your God's preprogramming, passed on by the first cells, but I can't help feeling it fits in perfectly with the concept of cells themselves experimenting as the environment offers new opportunities.-I have never denied that organisms have self-evolutionary abilities. I've discussed epigenetics endlessly here. It is the issue of how independent those abilities are that we are in disagreement about. I still think your Darwin roots from earlier in your life play a role. But I admit you seem to have accepted much of my anti-Darwin-theory proposals.

Epigenetics: Passing the effects

by dhw, Thursday, February 05, 2015, 19:26 (3580 days ago) @ David Turell

dhw: The authors link this development with an increase in oxygen (a factor which some researchers also link to the Cambrian Explosion). No doubt you will see this as another piece of your God's preprogramming, passed on by the first cells, but I can't help feeling it fits in perfectly with the concept of cells themselves experimenting as the environment offers new opportunities.-DAVID: I have never denied that organisms have self-evolutionary abilities. I've discussed epigenetics endlessly here. It is the issue of how independent those abilities are that we are in disagreement about. -Your argument has always been that cells / cell communities are automatons obeying instructions. You have, however, recently tried to introduce a concept of semi-autonomy. We have agreed that no organism can “self-evolve” beyond the limits imposed by its own nature and by the environment, but for you even the weaverbird cannot be granted a sufficient degree of autonomy to design its own nest. That is why I find your concept of semi-autonomy totally unsatisfactory, and have asked if you think the bird just designs half of its nest.
 
DAVID: I still think your Darwin roots from earlier in your life play a role. But I admit you seem to have accepted much of my anti-Darwin-theory proposals.-Yes, they play a significant role, because I believe that all living organisms except the first descended from earlier organisms. (Natural Selection seems to me self-evident, though in Darwin's time it wasn't.) I do accept your objections to random mutations and gradualism, and had already done so when I wrote the “brief guide”, but the breadth of your own scientific knowledge has been of huge benefit to me in understanding the problems associated with the theory of chance. When I opened this website seven years ago, I expressed the hope that by combining our discoveries, we might help one another to gain new insights. You have done this on a scale far beyond what I could have hoped for, and thanks to you, George, BBella, Tony, Matt and many others who have come and gone, even though I'm still on the fence, I have a much broader view!

Epigenetics: Passing the effects

by David Turell @, Thursday, February 05, 2015, 21:58 (3580 days ago) @ dhw


> DAVID: I have never denied that organisms have self-evolutionary abilities. I've discussed epigenetics endlessly here. It is the issue of how independent those abilities are that we are in disagreement about. 
> 
> Your argument has always been that cells / cell communities are automatons obeying instructions. You have, however, recently tried to introduce a concept of semi-autonomy. We have agreed that no organism can “self-evolve” beyond the limits imposed by its own nature and by the environment, but for you even the weaverbird cannot be granted a sufficient degree of autonomy to design its own nest.-Simply, the nest is too complex for the weaverbirds to have designed it. But they could have been helped in the design development, a cooperative effort, much like a parent teaching a child how to dress. View it like coaching cricket. Coach demonstrates, player learns and improves.-> 
> DAVID: I still think your Darwin roots from earlier in your life play a role. But I admit you seem to have accepted much of my anti-Darwin-theory proposals.
> 
> dhw:Yes, they play a significant role, because I believe that all living organisms except the first descended from earlier organisms. .... When I opened this website seven years ago, I expressed the hope that by combining our discoveries, we might help one another to gain new insights. You have done this on a scale far beyond what I could have hoped for, and thanks to you, George, BBella, Tony, Matt and many others who have come and gone, even though I'm still on the fence, I have a much broader view!-Thank you for all of us. I pity your rump.

Epigenetics: Passing the effects

by dhw, Friday, February 06, 2015, 18:28 (3579 days ago) @ David Turell

DAVID: I have never denied that organisms have self-evolutionary abilities. I've discussed epigenetics endlessly here. It is the issue of how independent those abilities are that we are in disagreement about. -Dhw: Your argument has always been that cells / cell communities are automatons obeying instructions. You have, however, recently tried to introduce a concept of semi-autonomy. We have agreed that no organism can “self-evolve” beyond the limits imposed by its own nature and by the environment, but for you even the weaverbird cannot be granted a sufficient degree of autonomy to design its own nest.-DAVID: Simply, the nest is too complex for the weaverbirds to have designed it. But they could have been helped in the design development, a cooperative effort, much like a parent teaching a child how to dress. View it like coaching cricket. Coach demonstrates, player learns and improves.-So God took time off from preparing the way for humans in order to coach the weaverbird, monarch, salmon, spider? That's the only way the process could have been divinely cooperative. And the reason? Let me guess. Because they were all essential for a balanced food supply? (And only God knows who eats the nest.) My alternative is that the birds themselves cooperated in pooling their (God-given?) intelligence to develop the design. No need for God to get involved at all.

Epigenetics: Passing the effects

by David Turell @, Friday, February 06, 2015, 18:45 (3579 days ago) @ dhw

dhw: My alternative is that the birds themselves cooperated in pooling their (God-given?) intelligence to develop the design. No need for God to get involved at all.-First you proposed committee meetings of single cells, now birds. Don't you think God chaired the meetings?

Epigenetics: Passing the effects

by dhw, Saturday, February 07, 2015, 19:32 (3578 days ago) @ David Turell

DAVID: Simply, the nest is too complex for the weaverbirds to have designed it. But they could have been helped in the design development, a cooperative effort, much like a parent teaching a child how to dress. View it like coaching cricket. Coach demonstrates, player learns and improves.-DHW: So God took time off from preparing the way for humans in order to coach the weaverbird, monarch, salmon, spider? That's the only way the process could have been cooperative. Of course my alternative is that the birds themselves cooperated in pooling their (God-given?) intelligence to develop the design. No need for God to get involved at all.-David: First you proposed committee meetings of single cells, now birds. Don't you think God chaired the meetings?-So you're saying that committee meetings are possible, but only if God chaired them. Are you suggesting, then, that at different times God summoned all the weaverbirds, monarchs, salmon, plovers, spiders etc. to give them a demonstration? “Committee meetings” was of course your term, in an attempt to ridicule the concept of cooperation by anthropomorphizing it. We KNOW that cells cooperate, that even different species cooperate, and that social organisms like ants cooperate, all of them producing something new (there must have been a first ants' nest, though it may well have become more complex through the work of subsequent generations). Many species of weaverbird are actually social - apparently African sparrow weavers build apartment houses! If only you could rid yourself of the prejudice that humans alone are possessed of any autonomous inventive intelligence (a prejudice that persists despite the many articles you have posted, demonstrating the reasoning powers of other species) you would see that there is no need for a 3.7-billion-year computer programme to cover every single innovation and lifestyle, or for your God to give personal demonstrations to all his creatures to show them how to build nests and webs and honeycombs and dams, and live wacky lifestyles.

Epigenetics: Passing the effects

by David Turell @, Sunday, February 08, 2015, 00:25 (3578 days ago) @ dhw

dhw: If only you could rid yourself of the prejudice that humans alone are possessed of any autonomous inventive intelligence (a prejudice that persists despite the many articles you have posted, demonstrating the reasoning powers of other species) you would see that there is no need for a 3.7-billion-year computer programme to cover every single innovation and lifestyle, or for your God to give personal demonstrations to all his creatures to show them how to build nests and webs and honeycombs and dams, and live wacky lifestyles.-We are covering old territory. I agree with Kauffman that life may contain a self-organizing mechanism. We see it in epigenetic changes that are heritable. I just don't see it as fully autonomous. Humans and other animals reason. I've never denied that. However you continue to fail to see the enormous difference in capacity humans have, and the fact that there was no necessity in evolution to automatically invent humans. Just as Hoyle commented about the resonances of carbon, 'it looks as if someone monkeyed with the works' (paraphrased), the appearance of humans gives the same impression to me.

Epigenetics: Passing the effects

by dhw, Sunday, February 08, 2015, 19:51 (3577 days ago) @ David Turell

dhw: If only you could rid yourself of the prejudice that humans alone are possessed of any autonomous inventive intelligence (a prejudice that persists despite the many articles you have posted, demonstrating the reasoning powers of other species) you would see that there is no need for a 3.7-billion-year computer programme to cover every single innovation and lifestyle, or for your God to give personal demonstrations to all his creatures to show them how to build nests and webs and honeycombs and dams, and live wacky lifestyles.-DAVID: We are covering old territory. I agree with Kauffman that life may contain a self-organizing mechanism. We see it in epigenetic changes that are heritable. I just don't see it as fully autonomous. -So what part is not autonomous (other than the obvious fact that organisms cannot do what organisms cannot do)? This is why I have challenged you on your insistence that your God must have given personal demonstrations to the weaverbird, salmon, monarch, plover, spider etc. on how to build their homes or organize their weird lifestyles. I notice you have skipped that passage.-DAVID: Humans and other animals reason. I've never denied that. However you continue to fail to see the enormous difference in capacity humans have, and the fact that there was no necessity in evolution to automatically invent humans. -I am fully aware of the enormous difference, but (a) I tend to see it as a natural development from our less able ancestors, and (b) that is not the point we are discussing here, which is the possible autonomy of the inventive mechanism, as opposed to your 3.7-billion-year programme or your divine interventions. (There was no necessity for evolution to have come up with the duck-billed platypus, so what does that prove?)

Epigenetics: Passing the effects

by David Turell @, Sunday, February 08, 2015, 20:30 (3577 days ago) @ dhw


> So what part is not autonomous (other than the obvious fact that organisms cannot do what organisms cannot do)? This is why I have challenged you on your insistence that your God must have given personal demonstrations.... I notice you have skipped that passage.-Just covered the issue of instinct in the balance of nature thread.
> 
> DAVID: Humans and other animals reason. I've never denied that. However you continue to fail to see the enormous difference in capacity humans have, and the fact that there was no necessity in evolution to automatically invent humans. 
> 
> dhw: I am fully aware of the enormous difference,... (There was no necessity for evolution to have come up with the duck-billed platypus, so what does that prove?)-They are part of the higgledy-piggledy bush. We are above it.

Epigenetics: DNA markers

by David Turell @, Tuesday, February 10, 2015, 19:34 (3575 days ago) @ David Turell

There are research systems for finding them:-"Researchers at the FMI in Basel have now investigated the mechanisms that underlie the epigenetic marking of the genome. Three enzymes, known as DNA methyltransferases (DNMTs), can tag DNA with methyl groups: in this process, DNMT3A and DNMT3B create new methylation patterns, while DNMT1 ensures that the pattern established is propagated through each cell division.-"The team of epigeneticists led by FMI Group Leader and University of Basel Professor Dirk Schübeler, demonstrated how these methylation patterns are established. Lead author Tuncay Baubec comments: "Our studies indicate that the placement of epigenetic modifications follows defined rules. Certain patterns in the DNA sequence together with genetic activity influence where the DNMTs can bind in the genome. This in turn explains the methylation patterns that arise. In this case, one can argue that genes can determine for themselves whether they become methylated or not."-"And what about the great potential of epigenetics? Schübeler explains: "The fact that methylation patterns are largely genetically determined does not surprise us. We're glad that we now have a better understanding of the interplay between DNA sequence and methylation. This allows us to recognize where these modifications actually play a role. In addition, methylation patterns are very valuable. For example, in identifying different cell conditions. They are excellent tools for distinguishing different stages of disease, or for monitoring the effectiveness of treatment. But it's time to forget the simple notion that these markings are independent of the underlying DNA sequence.'"-http://medicalxpress.com/news/2015-02-genetic-epigenetics.html-This may be a part of an inventive mechanism. Note the authors reference tight gene control of this mechanism.

Epigenetics: Father's diet affect offspring

by David Turell @, Monday, January 04, 2016, 15:08 (3247 days ago) @ David Turell

Mouse experiments show the effects on glucose tolerance:-http://medicalxpress.com/news/2016-01-father-diet-impact-offspring.html-"In the first study, the team fed one group of mice a high fat diet, while another group was fed a normal diet. Sperm was harvested from both groups and used to impregnate female mice. Offspring had their weight monitored along with their level of glucose intolerance and insulin resistance. The team repots that the offspring of the males fed the high fat diets did not gain more weight than those from the control group, but they did develop an impaired resistance to insulin and glucose intolerance—precursors to diabetes. To ensure that the change was due to tRNA fragments, the team ran the same experiment again, but the second time around they purified the RNA before injection into the eggs. The resulting offspring developed intolerance to glucose but did not develop insulin resistance.-"In the second study, the researchers conducted the same type of experiment but had the male study group eat a low-protein diet. The team reports they found no differences between the offspring except for changes to a group of genes that are responsible for the development of stem cells."-Comment: Our population is heavier. We see more diabetes. The study makes the point.

Epigenetics: Transgenerational effects questoned

by David Turell @, Sunday, May 22, 2016, 15:49 (3108 days ago) @ David Turell

The simple point is humans are not rodents, where most of the research has been done:-http://nautil.us/blog/epigenetics-has-become-dangerously-fashionable-"Social scientists' excitement surrounds what we can refer to broadly as transgenerational epigenetics. To understand why social scientists have become enamored with it, we must first consider basic genetics. Many metaphors exist for describing and understanding the genome; they all capture the reality that genes provide the information for building and running biological machinery like the human body. -***-“'Development of an organism from a fertilized egg is driven primarily by the actions of regulatory proteins called transcription factors. In sequential waves and combinations, these proteins bind to specific DNA sequences—called cis- regulatory sequences—associated with specific genes, and encourage (activate) or discourage (repress) transcription into mRNA of those genes.” -***-"What could this have to do with social science? Consider a landmark study, ... which practically started the conversation over transgenerational epigenetics. The authors analyzed whether different nurturing styles might influence stress responses in offspring. The findings suggested that different types of nurturing from participant moms impinged on how babies developed by directly tinkering with their gene expression. Let that sink in: Our experiences—such as how our parents treat us—may alter how our genes are expressed, thus impacting our physiological and psychological development. The weightier implication, though, was that these epigenetic “markers” in the genome might also be transmitted to future generations (thus, the “transgenerational” moniker).-***-"Harvard psychologist Steven Pinker reminds us why we shouldn't carelessly fling ourselves on the transgenerational epigenetics bandwagon:-“'Also inflating the epigenetics bubble is a set of findings that genuinely are surprising, namely that some epigenetic markers attached to the DNA strand as a result of environmental signals (generally stressors such as starvation or maternal neglect) can be passed from mother to offspring. These intergenerational effects on gene expression are sometimes misunderstood as Lamarckian, but they're not, because they don't change the DNA sequence, are reversed after one or two generations, are themselves under the control of the genes, and probably represent a Darwinian adaptation by which organisms prepare their offspring for stressful conditions that persist on the order of a generation. (It's also possible that they are merely a form of temporary damage.) Moreover, most of the transgenerational epigenetic effects have been demonstrated in rodents, who reproduce every few months; the extrapolations to long-lived humans are in most instances conjectural or based on unreliably small samples. -***-"That's right, the most compelling evidence for transgenerational epigenetics is in rodents, not humans. We are fans of animal research, but as Pinker noted, the strengths of it (fast reproductive cycles allowing for the study of numerous generations in a short window of time) may also curtail its applicability to humans in this particular case. Additionally, scientists can randomly manipulate a rodent pup's exposure to different parenting/rearing strategies. But doing this with human babies would never fly with a university ethics committee. -***-"Pinker reminded us of another key point. When social scientists say “environment” they mean something very different than when biologists say “environment.” To a geneticist, environment is anything that isn't DNA (in essence, the cellular environment of DNA). To a social scientist, though, the environment captures everything from the way your parents raised you to the international political climate. The cellular environment might be relevant for understanding environmental regulation of gene expression, but this does not necessarily mean that social environments (like neighborhoods) have a similar impact. More time and research is needed to unpack the latter possibility.-"Many of our expert epigenetics research colleagues are deeply embarrassed by the warm, uncritical response their work has attracted from the social sciences,” say Terrie Moffitt, a distinguished clinical psychologist at Duke University, and Amber Beckley, a criminologist also at Duke. “A biologist attendee at a July 2014 Washington, DC workshop on the social and behavioral implications of epigenetics gasped, ‘The biologists there were horrified at the thought . . . we really don't understand the basic biology well enough yet to do this!'”-Comment: A good cautionary article. Social science tends to have loose experimental controls and conclusions.

Epigenetics: Transgenerational effects shown

by David Turell @, Monday, August 21, 2017, 14:46 (2652 days ago) @ David Turell

In C. elegans, the simple tiny worm:

https://cosmosmagazine.com/biology/worms-inherit-epigenetic-traits

"Geneticists love the tiny worm Caenorhabditis elegans for its simplicity and the way it replicates the functions of more complex and intractable creatures. It has played a key role in much fundamental biological research in the last 50 years.

"It was the first multicellular organism to have its whole genome sequenced, the first to have the full wiring of its nervous system (or connectome) mapped, and the full developmental path of every cell in its body is known.

"Now researchers at the Centre for Genomic Regulation in Barcelona, Spain, and colleagues have used C. elegans to show that impairments to the DNA replication process can cause epigenetic changes – alterations in the way that certain genes are expressed in the body – that can be passed on to as many as five generations of descendants.

"Even when the descendants did not themselves carry the mutation that caused faulty DNA replication, they nonetheless carried the changes in gene expression.

"The research is an important new clue in the study of how epigenetic changes are inherited, an area which is still poorly understood."

Comment: Adaptations certainly occur through changes in gene expression, but we still have no evidence of the process of speciation, the real key to evolution. Most species appear to be the result of saltation.

Epigenetics: Dutch transgenerational effects

by David Turell @, Saturday, February 03, 2018, 23:51 (2486 days ago) @ David Turell

This has been mentioned before. but the Dutch famine in 1945 as the War ended left its marks and is now restudied:

https://www.nytimes.com/2018/01/31/science/dutch-famine-genes.html

"By the time the Netherlands was liberated in May 1945, more than 20,000 people had died of starvation.

"The Dutch Hunger Winter has proved unique in unexpected ways. Because it started and ended so abruptly, it has served as an unplanned experiment in human health. Pregnant women, it turns out, were uniquely vulnerable, and the children they gave birth to have been influenced by famine throughout their lives.

"When they became adults, they ended up a few pounds heavier than average. In middle age, they had higher levels of triglycerides and LDL cholesterol. They also experienced higher rates of such conditions as obesity, diabetes and schizophrenia.

"By the time they reached old age, those risks had taken a measurable toll, according to the research of L.H. Lumey, an epidemiologist at Columbia University. In 2013, he and his colleagues reviewed death records of hundreds of thousands of Dutch people born in the mid-1940s.

"They found that the people who had been in utero during the famine — known as the Dutch Winter Hunger cohort — died at a higher rate than people born before or afterward. “We found a 10 percent increase in mortality after 68 years,” said Dr. Lumey.

“'How on earth can your body remember the environment it was exposed to in the womb — and remember that decades later?” wondered Bas Heijmans, a geneticist at Leiden University Medical Center in the Netherlands.

"Dr. Heijmans, Dr. Lumey and their colleagues published a possible answer, or part of one, on Wednesday in the journal Science Advances. Their study suggests that the Dutch Hunger Winter silenced certain genes in unborn children — and that they’ve stayed quiet ever since.

"While all cells in a person’s body share the same genes, different ones are active or silent in different cells. That program largely is locked in place before birth.

***

"the researchers merged the results — and found a few methyl groups that were linked both to the famine and to health conditions later in life. “We were able to connect the three dots,” said Dr. Lumey.

"Dr. Lumey and his colleagues propose that these methyl groups disrupt how cells normally use genes. One methyl group that is linked to a higher body mass index may be able to quiet a gene called PIM3, which is involved in burning the body’s fuel.

"So here’s the theory: Perhaps the Dutch Hunger Winter added a methyl group to fetuses born to starving mothers, which made the PIM3 gene less active — and continued to do so for life.
The result? “Maybe your metabolism is in a lower gear,” Dr. Heijmans said.

***

"John M. Greally, the director of the Center for Epigenomics at Albert Einstein College of Medicine, noted that blood is made up of many different types of cells, each with its own epigenetic profile.

"Maybe the Dutch famine made some types of cells more common, he said, rather than altering the epigenetics.

"But Dr. Heijmans and his colleagues studied the same methyl groups in muscle cells, fat cells and other tissues they got from cadavers. In any given person, the pattern was roughly the same."

Comment: Lamarckism is alive and well through methylation of genes.

Epigenetics: Father's stress affects offspring' brain

by David Turell @, Saturday, February 17, 2018, 22:36 (2472 days ago) @ David Turell

The stress causes changes in sperm as described in this study in mice:

https://www.sciencedaily.com/releases/2018/02/180216110547.htm

"New research in mice has found that a father's stress affects the brain development of his offspring. This stress changes the father's sperm, which can then alter the brain development of the child. This new research provides a much better understanding of the key role that fathers play in the brain development of offspring.

"Scientists have known that a mother's environment during pregnancy, including factors such as poor diet, stress or infection, can cause damage negatively impact her offspring. This may be due in part to how this environment affects the expression of certain genes -- known as epigenetics.

***

"Previously, Bale had found that adult male mice experiencing chronic periods of mild stress have offspring with a reduced response to stress; changes in stress reactivity have been linked to some neuropsychiatric disorders, including depression and PTSD. She and her colleagues isolated the mechanism of the reduced response; they found that the father's sperm showed changes in genetic material known as microRNA. MicroRNA are important because they play a key role in which genes become functional proteins.

"Now, Bale and her colleagues have unraveled new details about these microRNA changes. In the male reproductive tract, the caput epididymis, the structure where sperm matures, releases tiny vesicles packed with microRNA that can fuse with sperm to change its cargo delivered to the egg. The caput epididymis responded to the father's stress by altering the content of these vesicles.

"This suggests that even mild environmental challenges can have a significant impact on the development and potentially the health of future offspring."

Comment: Lamarck is alive and well.

Epigenetics: transgenerational pregnancy effects

by David Turell @, Friday, May 25, 2018, 14:59 (2375 days ago) @ David Turell

DES in pregnancy is shown to affects future generations:

https://cosmosmagazine.com/biology/banned-pregnancy-med-still-affecting-daughters-grand...

"The grandchildren of women who used a drug called diethylstilbestrol, or DES, during pregnancy have a higher risk of attention deficit hyperactivity disorder (ADHD), new research shows.

"Endocrine-disruptors are chemicals that interfere with the body’s intricate hormone system, and have been associated with a number of neurological disorders, including ADHD. Increasing evidence suggests they can alter the epigenetic programming of reproductive cells. In other words, they can cause heritable changes in gene activity.

"Animal studies show that endocrine disruptors, such as di(2ethylhexyl)phthalate (DEHP) and bisphenol A (BPA), are indeed linked with negative neurological effects in subsequent generations, but it was unknown if this was also the case for humans.

***

"DES was prescribed to millions of women between 1938 and 1971, because it was thought to prevent miscarriage. However, a 1953 study showed it to be ineffective. Another study in 1971 revealed increased rates of vaginal cancer in the daughters of women who had taken it, and it was banned that same year.

"DES, it turned out, was a potent endocrine disruptor.

"The new research examined the self-reported health information of 47,540 participants enrolled in the ongoing study. Of these, nearly 2% had mothers who had used DES during pregnancy. Moreover, many of the nurses in the cohort had gone on to have children of their own.

“'Our aim was to explore the potential impact of DES use across generations, and specifically on third-generation neurodevelopment,” says the study’s first-author, Marianthi-Anna Kioumourtzoglou of the Columbia University Mailman Institute of Public Health.

***

"The findings revealed that grandchildren of the women who had used DES were 36% more likely to have ADHD than grandchildren of women who had not used the drug, regardless of whether those grandchildren were male or female.

"The findings provide evidence in humans that exposure to endocrine disruptors during pregnancy can alter neurodevelopment in later generations.

“'While DES is banned, pregnant women continue to be exposed to a large number of environmental endocrine disruptors,” says co-author Marc Weisskopf of Harvard.
“And although current exposures are at a lower level and potency than seen with DES, cumulative exposures to these chemicals may be cause for concern and is deserving of further study.'”

Comment: Autism was unknown when I was in Med school. Alzheimer very rare. we live in a chemical world and don't fully understand it. We are too smart for our own good.

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