Darwin lobby: Don’t teach epigenetics, kids won’t understand

'Experimental results in epigenetics and related fields of biological research show that the Modern Synthesis (neo-Darwinist) theory of evolution requires either extension or replacement.' 'This paper explains why replacement rather than extension is called for. The reason is that the existence of robust mechanisms of trans-generational inheritance independent of DNA sequences runs strongly counter to the spirit of the Modern Synthesis. In fact, several new features of experimental results on inheritance and mechanisms of evolutionary variation are incompatible with the Modern Synthesis'. https://jeb.biologists.org/content/218/1/7 Truthfreedom

wd400:

Doesn’t the title of that book suggest the new stuff extends rather than supplants the modern synthesis?

Sure it does! But why extended the modern synthesis if it's not necessary?

More than half a century has passed since the integration of several strands of evolutionary thought that came to to be called the Modern Synthesis (MS), the conceptual framework that has defined evolutionary theory since the 1940s. Despite significant advances since then in all methodological and disciplinary domains of biology, including molecular genetics, developmental biology, and the "-omics" fields, the Modern Synthesis framework has remained surprisingly unchanged.

You're mot surprised. Neither am I. So who is surprised? Mung

It was both factually and theoretically WRONG. How? What was WRONG about it? Doesn't the title of that book suggest the new stuff extends rather than supplants the modern synthesis? wd400

IOW, Darwinism, aka neo-Darwinism, aka The Modern Synthesis, has been supplanted. It was both factually and theoretically WRONG. Now, what was the role of evo-devo and epigenetics in the displacement of neo-Darwinism? Sure, let's talk about it. But let's not pretend that it posed no challenge to Darwinism. Mung

In the six decades since the publication of Julian Huxley's Evolution: The Modern Synthesis, spectacular empirical advances in the biological sciences have been accompanied by equally significant developments within the core theoretical framework of the discipline. As a result, evolutionary theory today includes concepts and even entire new fields that were not part of the foundational structure of the Modern Synthesis. - Evolution: The Extended Synthesis (back cover)

Mung

In this book we propose a major new scientific theory: facilitated variation that deals with the means of producing useful variations. - The Plausibility of Life: Resolving Darwin's Dilemma

Mung

wd400:

The modern synthesis didn’t include development, which is to say it doesn’t include how genetic variants give rise to morphological variants.

Development was not included for a reason, it was not by accident. The how was considered unimportant. Unnecessary to the theory. Irrelevant. Prior to "the modern synthesis," developmental biology was thought to be important to evolutionary theory. Amundson's book is worth reading, even if you disagree. If the how is important, then it follows that this is a problem for Darwinism (neo-Darwinism, aka "the modern synthesis"), since it was excluded from the theory. wd400:

You are now talking about epigenetics meaning all of development, which is not what most people mean by the term these day.

Right. But it seems to have become a subject of focus by both you and Elizabeth. Where and when are the primary effects of "epegenetics" relevant? During development? Then I think I am on point. Mung

The evolutionary synthesis was not so much a synthesis as it was a cut-down of variables considered important in the evolutionary process ... What was new in this conception of evolution was not the individual variables, most of which had long been recognized, but the idea that evolution depended on so few of them ... This I will now call the "evolutionary constriction," which seems to me to be a more accurate description of what actually happened to evolutionary biology. - William Provine

Mung

Mung, You are now talking about epigenetics meaning all of development, which is not what most people mean by the term these day. The modern synthesis didn't include development, which is to say it doesn't include how genetic variants give rise to morphological variants. Now we know a lot more about how genetic variants give rise to morphological variants, and thus we understand evolution much better. That doesn't mean population and quantative genetic don't work any more. The alleles involved in development are subject to mutation selection and drift, after all. So it's not at all clear to me that developmental biology is a problem, even for new synthesis. wd400

...for population genetics to be the foundation of an evolutionary theory, it must be able to take account of the two general factors involved in evolutionary change: heredity and adaptation. The MCTH concept of narrow heredity allowed this to happen. Narrow heredity divorced ontogenetic development from heredity itself. - The Changing Role of the Embryo in Evolutionary Thought

But now we're asked to ignore the divorce. Heredity is what takes place during development. No challenge to Darwinism here. Move along. Mung

EL:

Mung, you are incorrect.

At least I understand the distinction between what needs to be explained and what the explanation is. And if I'm incorrect, so is William Provine. Mung

wd400:

It’s not a shell game, I don’t usually use the term Darwinism because if it means anything (and I’m not sure it does) it’s a restricted part of evolutionary biology.

It's also known as "the modern synthesis" (aka neo-Darwinism) and it is the dominant version of evolutionary theory sold to the public at large and has been for decades now. An it is a shell game because when someone addresses one aspect of the theory and shows why it is inconsistent with emerging facts it all of a sudden becomes "that's not what I was talking about." Elizabeth has already been kind enough to explain the core aspects of "the modern synthesis" and even agrees that it is deficient. The only question that remains is whether once all is said and done there will be anything recognizable left of the original theory. "Modern Evolutionary Theory" is remarkably plastic. What is the role of developmental biology in "the modern synthesis" (aka neo-Darwinism)? None? So yeah, it's a challenge to "Darwinism." Mung

Lifespy, What are you talking about? There are tonnes and tonnes of studies associating observed phenotypic variation with specfic genetic variants? How are these studies going to vanish now we can measure DNA methylation? wd400

Mung, It's not a shell game, I don't usually use the term Darwinism because if it means anything (and I'm not sure it does) it's a restricted part of evolutionary biology. Evo devo is different to the 1960s versino of the modern synthesis, but the two fields attempt to understand evolution through complimenting frames rather than offering competing explanations for biology. For a population geneticists it's not usually important to know if an allele has its phenotypic effect via a change in protein sequence or a change in some regulatory element. Evo devo lets us understand the molecular and development basis of phenotypic variablity. That's cool. Why it's a problem for evolution or "Darwinism" I can't imagine. wd400

lifepsy: Because eventually people are going to learn that most of the phenotypic changes you guys have been bullhorning as the result of neo-darwinian processes are actually epigenetically induced by the environment. Elizabeth,

Oh, right. Well, if there was evidence that phenotypic variation is “most[ly]” caused by epigenetics not genetics, you might have a point. But there isn’t.

I'm not talking about the fairytales you guys tell about where existing phenotypes came from. I'm talking about *observed* phenotypic variations in living populations. These changes have been bullhorned far and wide as neo-darwinian evolution, or selection of genetic variants, but they aren't. That's why Darwinian-mystics don't like Epigenetics. It shows how much imaginary storytelling you guys have been publishing over the years. lifepsy

Mung, you are incorrect. Elizabeth B Liddle

Jerry, This is really typical of what happens when people are pushed to explain why epigentics is such a big deal. Most of you comment has nothing at all to do with epigenetics, and what does is a collosal extrapolation from a twig of evidence. First, I have mentioned the concept of gene expression and that it may be what is thought to have been evolution may be just changes in gene expression. Why "just". Lots of change is brought about by changes in gene expression, which in turn are brought about my mutation and selection. That's evolution, I don't know why anyone who deny that. Some of these methylation changes are brought on by the environment and some can be passed on to offspring through germ cells. There is no given that if passed on by inheritance that the changes will stay. Is this evolution? Very few cases of direct environmental impact methylation leading to a stably inherited trait are known, and none of them are beneficial changes in expression. So it's very hard to see how this how apparent-adaptation could be explained by this sort of mechanism. And some of these gene expressions may be just changes to control mechanisms But the control mechanisms, epigenetic or not, are ultimately encoded by genes which are subject to mutation and selection and drift and all the evolutionary mechanisms we already understand. So why "just" changes to control mechanisms? An interesting question is since these are just one species how did the changes to the control mechanisms arise? Was it through mutation or did the environment create the changes? I am certainly not an expert but this is an interesting question. You don't have to be an expert to read the Grants' papers and see the traits are heritable, no matter what the environment that have thrown at them, so it'c can't be simply the environment creating changes (they also aren't one species). Second, I also mentioned the new level of complexity coding for functionality of the organism... To convince someone else you will have to establish more than your own incredulity Third, I mentioned the problem of body plans and that the information for this is not in the genome. Not methylation but it is epigenetic. It is here that very severe challenges to Darwinian evolution are apparent. Well, you'd first need to establish such a thing exists. I'm not aware of any evidence for this idea. So, we are left with your own misunderstandings of how gene expression is controlled, some speculative ideas about direct environmental impacts of methylation being benifical, personal incredulity and an evidnce-free idea about development. I'm not sure evolutionary biology is in as bad a shape as you think it is. wd400

Elizabeth Liddle:

Natural selection results in adaptation: tick

No, Elizabeth, adaptation results in natural selection. You have it backwards. That's why it should not be taught to children. Even grown adults who "know a lot" about it can't get it straight. Mung

Elizabeth:

Can you explain why epigenetics is evidence against Darwinian evolution

wd400:

why is epigentics a problem for evolutionary biology?

Do you folks really think we don't notice the shell game? I respond to the question posed by Elizabeth and wd400 claims I haven't addressed it because he's asking a different question. Now if epigenetics is what happens during development, then the reason it's a problem for Darwinian theory is because Darwinian theory is explicitly not evo-devo. Again, Ron Amundson has written an entire book on the subject and the subject is also treated in What Darwin Got Wrong, and Part Two of Meyer's latest is "How to Build an Animal so no doubt it's covered there as well." Elizabeth says she's read Darwin's Doubt, so surely none of this is "News" to her. Mung

Jerry:

Never said that. Said that a lot of phenotype change could be epigenetic and should be investigated. There are several places in all my comments where I give natural selection its due. But it is all trivial. That is the word I frequently use and will use it below a few times. I don’t do off the charts. My Navy experience taught me that.

That was lifepsy at 73. By "off the charts" I mean the probability, based on current evidence, that transgenerational epigenetics will turn out to have a greater effect on the phenotype than genetics is infinitessimal. We have copious examples of the second, and a few interesting examples of the first.

BTW, re teaching evolutionary biology: Universal common descent: untick – no clear proof – suggest one produces evidence of such that is not begging the question

As I said, jerry, there's no proof in science. But a vast amount of evidence.

Natural selection results in adaptation: tick – yes but trivial

No reason to think it is trivial.

Phenotypic variation reflects genotypic variation: tick – but not an issue for anyone on the planet

Quite. Apart, possibly from lifepsy.

Phenotypic variation in multicellular organisms is largely due to differences in regulatory genes affecting the developmental timetable of gene expression: untick – I haven’t a clue what this means so I may agree or disagree.

OK. This is from the evo-devo literature. And just devo.

There is phenotype variation without regulatory causes. There is phenotype variation due to regulatory causes. Have to define regulatory and what constitutes it to have a clear dissuasion. Speciation results when a population splits into two, and the two subpopulations evolve down separate lineages: tick – yes it probably happened but it is trivial unless you have some specific examples

Every single bifurcation in the phylogenetic tree.

Evolution results from drift as well as adaptation: tick – yes but trivial

Not at all. Hugely important.

The species most closely related to humans are the great apes: tick – but what this means, I haven’t a clue. How does this relate to Darwinian evolution

It places us on the next branch in the tree of life. Elizabeth B Liddle

I don’t think “kiddies” or anyone, should be told that any scientific model is sufficient.

Rather than repeat all your points. They are all trivial except UCD for which there is no proof and symbiosis which is all speculation above the prokaryote level. So welcome to the ID side. jerry

And the idea that most phenotypic variation is epigenetic rather than genetic really is off the charts.

Never said that. Said that a lot of phenotype change could be epigenetic and should be investigated. There are several places in all my comments where I give natural selection its due. But it is all trivial. That is the word I frequently use and will use it below a few times. I don't do off the charts. My Navy experience taught me that.

BTW, re teaching evolutionary biology:

Universal common descent: untick - no clear proof - suggest one produces evidence of such that is not begging the question Natural selection results in adaptation: tick - yes but trivial Phenotypic variation reflects genotypic variation: tick - but not an issue for anyone on the planet Phenotypic variation in multicellular organisms is largely due to differences in regulatory genes affecting the developmental timetable of gene expression: untick - I haven't a clue what this means so I may agree or disagree. There is phenotype variation without regulatory causes. There is phenotype variation due to regulatory causes. Have to define regulatory and what constitutes it to have a clear dissuasion. Speciation results when a population splits into two, and the two subpopulations evolve down separate lineages: tick - yes it probably happened but it is trivial unless you have some specific examples Evolution results from drift as well as adaptation: tick - yes but trivial The species most closely related to humans are the great apes: tick - but what this means, I haven't a clue. How does this relate to Darwinian evolution jerry

Actually, yes, I do agree, CS. I don't think "kiddies" or anyone, should be told that any scientific model is sufficient. Nor do I think "kiddies" or anyone should be told it is not "sufficient". Neither is knowable. What I do think is that Common Descent should be taught as the best explanation for the nested hierchical distribution of morphological features of living things, and about the statistical methods that test for these hierarchies in the science of phylogenetics. I think they should also be taught that the best accounts we have to date for how living things might have diversified and adapted is heritable variance in reproductive success plus drift and speciation events (when a population subdivides and two subpopulations continue to evolve down largely and increasingly separate lineages). In addition they should be taught that adaptation by means of heritable variance in reproductive success has been observed in real time, in the lab and in the field, including the evolution of novel adaptive features not present in the ancestral population. They should be taught that variance arises from a number of mechanisms that result in changes to DNA sequences between generations of cells and of whole organisms, and that some of these mechanisms themselves may be the result of population-level adaptation, but that a great deal of research remains to be done in this area. They should also be taught that one of the most important vectors for phenotypic variation in multicellular organisms is changes to regulatory genes that affect the timetable of gene expression in the developing organism, as well as changes to regulatory genes that affect how the organism functions in daily life. But that it is possible that other sources of heritable variation are possible, including symbiosis, and this may account for certain step-changes in the lineage. As for OoL, they should be taught that although there are a number of promising leads, but as yet we do not know how the first life-forms, or proto-life forms emerged from non-life. Also, some more stuff. But as I said in another thread, and was puzzled to be disagreed with - I don't think science should be taught as a body of facts. I think it should be taught as what it is - a body of models of reality, many of which are extremely well-supported but all of which have some fuzzy stuff around the edges that further hypothesis testing may elucidate. Elizabeth B Liddle

EL:But at least we agree that we shouldn’t be teaching stuff to kids that has no evidential support.

So you agree that random variation + natural selection is responsible for all the cell types, tissue types, organs and body plans found among Earth's biosphere should not be taught to the kiddies? Well, brava, Dr Liddle, brava! Welcome to "our side." CentralScrutinizer

Well, you are just wrong about that Jerry :) But at least we agree that we shouldn't be teaching stuff to kids that has no evidential support. And the idea that most phenotypic variation is epigenetic rather than genetic really is off the charts. BTW, re teaching evolutionary biology: Universal common descent: tick Natural selection results in adaptation: tick Phenotypic variation reflects genotypic variation: tick Phenotypic variation in multicellular organisms is largely due to differences in regulatory genes affecting the developmental timetable of gene expression: tick Speciation results when a population splits into two, and the two subpopulations evolve down separate lineages: tick Evolution results from drift as well as adaptation: tick The species most closely related to humans are the great apes: tick. That seems to be a fairly substantial amount of evolutionary theory that is very well supported by evidence. Elizabeth B Liddle

You surely don’t want kids to learn something in science class that no scientist has actually discovered?

The best rationale for deleting Darwinian evolution from the curriculum (except for minor changes in genome) I have seen. Thank you for agreeing with the pro-ID people on the elimination of Darwin's ideas from biology textbooks. Bravo on your road to Damascus moment!!! jerry

So far, in 72 comments, Jerry has offered some ideas about gene expression generally, but noone, as far as I can tell has been able to answer this simple question: why is epigentics a problem for evolutionary biology?

No true. First, I have mentioned the concept of gene expression and that it may be what is thought to have been evolution may be just changes in gene expression. Some of the phenotype changes that are held up as evolution may be just changes in gene expression. Some of these methylation changes are brought on by the environment and some can be passed on to offspring through germ cells. There is no given that if passed on by inheritance that the changes will stay. Is this evolution? And some of these gene expressions may be just changes to control mechanisms which have not usually been thought as the source of these changes. As an example I mentioned the Darwinian Finches which are essentially all one species with no genetic reasons to prevent inner breeding. So are these finches an example of Darwinian evolution even though they have been held up as such by evolutionary biologists. An interesting question is since these are just one species how did the changes to the control mechanisms arise? Was it through mutation or did the environment create the changes? I am certainly not an expert but this is an interesting question. Second, I also mentioned the new level of complexity coding for functionality of the organism. A code on top of the code that must be coordinated with these exquisitely fine tuned entities. If one does not admit that is a problem for Darwinian evolution, they are being dishonest. Maybe it was somehow accomplished by a small change here, a small change there but it just got extremely more complicated. How does all these methylation changes come and go in the history of an organism. Or should we say how does the gene pool expand to include an ever changing methylation pool. One that is constantly varying to ensure the organism is viable. Third, I mentioned the problem of body plans and that the information for this is not in the genome. Not methylation but it is epigenetic. It is here that very severe challenges to Darwinian evolution are apparent. So, yes epigenetic poses a problem for simple story telling of Darwinian evolution. The off hand remark used constantly, "that this or that was selected for", is really a non scientific way of say we haven't any WAGs as to how it happened. jerry

lifepsy:

Because eventually people are going to learn that most of the phenotypic changes you guys have been bullhorning as the result of neo-darwinian processes are actually epigenetically induced by the environment.

Oh, right. Well, if there was evidence that phenotypic variation is "most[ly]" caused by epigenetics not genetics, you might have a point. But there isn't. The evidence of links between genetic variation and phenotypic variation completely dwarfs the albeit interesting links between trans-generational epigenetic variation and phenotypic variation. You surely don't want kids to learn something in science class that no scientist has actually discovered? Elizabeth B Liddle

That's a nice story Gensci but, and we are now 72 comments into this thread, why is epigenetics bad for "Darwinists" even in this new definition of the word you are offering us? If folks are repressing epigenetics to protect Darwinism, what threat does epigentics hold for that idea? So far, in 72 comments, Jerry has offered some ideas about gene expression generally, but noone, as far as I can tell has been able to answer this simple question: why is epigentics a problem for evolutionary biology? wd400

Elizabeth,

Can you explain why epigenetics is evidence against Darwinian evolution?

Because eventually people are going to learn that most of the phenotypic changes you guys have been bullhorning as the result of neo-darwinian processes are actually epigenetically induced by the environment. lifepsy

Hi Wd400, in an earlier post I mentioned this article in Science: http://m.sciencemag.org/content/341/6150/1055.full As it mentions, epigenetics "raises hackles" for some evolutionary biologists, but not all. The "some" I think the article is referring to are those like Eugenie Scott who have made an idol out of Darwinism. Darwinism requires that cells be as simple as possible, which means challenges to teach students more than a 20th Century understanding of DNA are unacceptable, and/or brushed aside as "too difficult". Eugenie Scott is a Darwinist, not a scientist, and she will convince a lot of gullible people to suppress 21st Century science in an effort to protect her sacred cow. gensci

Second it may be a problem for Darwinian thinking by showing that many of the examples of so called evolution may be just gene expression and not changes to the genome. You;re still not understanfing the Grants' studies. The traits they looked at where heritable - it's just a gene expression program that is flipping based on the environment. They didn't need to know anything about epigenetics to prove that, just the quantatative genetics developed in the 1920s. It's imaginable that the beak traits are transgenerationally inherited epigenetic tags, but there is no evidence for that idea and hardly any studies that show transgenerational inheritence at all (at none in brids, so far as I know). Even if they were, the finch studies would be an example of selection: differential survival of heritable variation leading to a change in the population. Then you start on teh regulatrory sequences attached to genes, seemingly as if they aren't themselves part of the genome presentation of the Galapagos finches by the Grants in which they said the difference between the various forms of the birds was not in the coding part of the genome but in the regulators of the various genes such as those responsible for beak size. How much of the genes get expressed is due to regulators not the genes themselves. These non coding regions could be selected for so in the future we have to consider that it may not be alleles that are changing but their control areas. If there are two different versions of the same regulatory sequence floating around in a population then those are alleles which are subject to selection. The idea that much evolutionary change is the result of differences in gene expression (themselves coded by changes in transcription factors and regulatory sequences) is not new, nor is it a problem for evolutionary biology. wd400

Thank you for your views Jerry. "I am just trying to lay out the issues. I could certainly be off because this is a very new area and it may take time to think it all the way through especially with new research appearing all the time." I applaud your approach Jerry. No dogmatism and a willingness to inquire. Your opinion definitely has a lot going for it. As for the neurons...well what can one say! "Gosh!" I suppose says it best. 'Blueprint' certainly seems the mot juste from my perspective. 'Recipe' I'm not so sure of. One an throw a recipe in a cement mixer and just let it churn itself together, but 100,000,000,000 neurons forming a cohesive network, does seem to be asking for something a little more rigorous in description. Thank s for book recommendations. I have not yet had the pleasure of sampling Dr Meyer's latest efforts. It is on my list now though. As for Dr Dawkins, one cannot deny that he can whittle a good sentence and spin a good yarn. Most adroit with the pencil. Although, whilst I find his jottings enjoyable for their lyrical lilt, they always leave me with the sense of 'I shot an arrow in the air, it fell to earth I know not where.' if you follow my meaning. Not that I have anything against the man (as some people do, for understandable reasons), he just isn't my cup of tea in the thinking department. Once again, thank you for sharing, Jerry. Ho-De-Ho

There is no blueprint. The genome is more akin to a a recipe

I am afraid some people disagree with this. I once saw a lecture on the brain that talked about the origin of neurons in a human brain during gestation. The body produces 85-100 billion neuron during a 24 month period starting shortly after conception. That is about 13-14 thousand every second for a two year period. And all these billions of neurons knows exactly where to go and end up forming one of the most complex configurations on the earth. Absolutely amazing without any blueprint or direction.

Dr Dawkins’ book The Greatest Show on Earth

I read this book by Dawkins. What is amazing about the book is what is not there. There is no explanation for the origin of complex novelties except deep time. Otherwise he just present trivial examples some of which may have epigenetic explanations and may not be Darwinian. jerry

You are not saying that epigenetics is completely against any form of evolution, and specifically not neo-darwinian evolution.

I reworded your comment a little. Some aspects of epigenetics are certainly compatible with the Darwinian paradigm but others are very problematic.

Plus we have been told that random mutations were the cause of changes, and now we know they are not.

I personally do not believe that random mutations can explain evolution, in the sense of providing the richness of information that is necessary for everything to happen. But you will get a lot of dissenters to this from those who visit here. I am just trying to lay out the issues. I could certainly be off because this is a very new area and it may take time to think it all the way through especially with new research appearing all the time. Two books to read are Meyer's "Darwin's doubt" and Eva Jablonka, "Evolution in Four Dimensions." Meyer references Stuart Newman who is an expert in developmental biology, specifically "Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology." Available via Amazon: http://www.amazon.com/Origination-Organismal-Form-Developmental-Evolutionary/dp/0262134195 And some of it can be found on the internet. jerry

Jerry, I don't think I've said hello before, so 'How do you do?' Jerry, I really liked your explanation and take on the epigenetic issue. And the problem it poses for evolution, as you have elucidated quite masterfully, is a bit of sticky one. I will chew over your comments during my evening stroll. May I ensure that I have your viewpoint clear. You are not saying that epigenetics is completely against any form of evolution, but specifically neo-darwinian evolution. One step at a time mutation and selection sure seemed to have its work cut out in creating sensible code in the first place and now this! We have a tagging code (like bar-codes I've heard some say) and lots of other stuff above the DNA, chivvying it about as it were. How in blazes can an organism randomly generate a code to operate another code without having the faintest idea what it is doing? Plus we have been told that random mutations were the cause of changes, and now we know they are not. Have I grasped it correctly Jerry? Excuse my colloquial interpretation, it is my scourge. On the flip side, Jerry, is there any means of evolution that you would think epigenetics lends itself too? Not saying you believe it, but just your thoughts. Thanks. Ho-De-Ho

One of the most interesting concepts in Meyer’s book, which I bet will be a major focus of discussion in the future is just where is the blue print for the organism in the zygote. It is seems certain that it is not in the genome but someplace else.

There is no blueprint. The genome is more akin to a a recipe. Certain instructions are turned off and on depending on what stage of the process has been reached. The is a very good and accessible discussion of this in Dr Dawkins' book The Greatest Show on Earth. I'm sure there are other places where it's explained but that's the one that came to my mind. Jerad

I will repeat my comment about the definition of epigenetics.

I don’t think there is a specific definition for epigenetic except that it is anything not in the genome that affects gene expression. A lot of what is called epigenetics is methylation which is a major factor that affects gene expression. Other non-genetic factors during gestation are in the embryo which also affects body layout and gene expression. Little is known about this except it is most likely in the egg cytoplasm or cell wall.

I suggest that those interested go to Wikipedia and look at the discussion of methylation. But this is only a start. http://en.wikipedia.org/wiki/Methylation In Meyers book he devotes 3 chapters to epigenetics. So anyone commenting should read this to get one perspective on the term. One of the most interesting concepts in Meyer's book, which I bet will be a major focus of discussion in the future is just where is the blue print for the organism in the zygote. It is seems certain that it is not in the genome but someplace else. One of the main points of Meyer's book is just how do these blueprints arise and how are they potentially modified. It is here that the discussions of body plans will most likely center. It is there that real evolution has to take place, not just in modification of certain parts of the genome.

How does epigenetics pose a problem for Darwinian thinking?

One it indicates that the process is much more complicated that originally thought by many levels of intricacy of precisely interacting parts. How does such an incredibly complex system arise? Could the nickel and dime accumulation ascribed to Darwinian processes really add up to all the major innovations in life? It just got incredibly more complicated. Second it may be a problem for Darwinian thinking by showing that many of the examples of so called evolution may be just gene expression and not changes to the genome. So in this case is there any evolution going on? A related example. There was a presentation of the Galapagos finches by the Grants in which they said the difference between the various forms of the birds was not in the coding part of the genome but in the regulators of the various genes such as those responsible for beak size. How much of the genes get expressed is due to regulators not the genes themselves. These non coding regions could be selected for so in the future we have to consider that it may not be alleles that are changing but their control areas. After 2-3 million years on the Galapagos, all the finch varieties could still inner breed. There was no genetic barriers. So was there any evolution going on in this example? We are only just beginning to get beneath the surface of adaptation and biological change. But everyone knows how it happened. Right. jerry

Oh, and Mung, thank you for your response at post 32, very courteous of you. I am chewing it over. You make a lot of sense and I enjoy your comments. Ho-De-Ho

This has been most entertaining and interesting to read. Thank you everybody. It seems that epigenetics has potential to be a thorny issue. There was something about this thread that sounded a tad familiar but I couldn't put my finger on it. A slumber on the straw mattress has served to bring it back to me though. There is a short ditty, or anecdote if you prefer, recorded about the artist Amedeo Modigliani that puts me in mind of the back and forth of this splendid discussion. Here it is. Modigliani had an admiration of Maurice Utrillo, another artist. He thought his work was the cat's pajamas. As luck would have it, Utrillo didn't think Modigliani was all that bad either. One evening, they began to get complimentary. Modigliani said "Utrillo, you are the best painter in the world." "No, you are the world's greatest painter." said Utrillo. "I forbid you to contradict me." "I forbid you to forbid me." Naturally the argument escalated with one of them saying "If you say that again then i'll biff you on the nose." "You are the greatest painter." said the other and a brawl ensued all over the carpet. Later on they made friends again over a few bottles down the local establishment. Then, as they walked down the street together, one of them said "You are the world's greatest painter." Lo and behold! the next morning they were found sleeping in the gutter covered in mysterious whelps and bruises. What has always caused me to scratch the old bean about this tale, is that the two artists sketched such different things. Modigliani liked painting people, Utrillo's forte was in city-scapes. They didn't have - and now I come to my point - a common platform on which to base their assertions. Do we think that this is what needs to be addressed here perhaps? What is the commonly agreed upon definition of epigenetics in this debate? Perhaps not all the T's can be crossed and one or two I's may end up dotless, but wouldn't a mutually agreed upon definition of epigenetics prove rather valuable here. Otherwise, all arguments might end up in the gutter with Modigliani and his chum Utrillo. Maybe the great minds of both sides could thrash out a mutually agreed upon platform and then discuss the implications of such to both world views. Just a thought. Thank you for bearing with me on my little ramble. Ho-De-Ho

Mung:

Which version is true? Which version ought to be taught?

Your question reminds me of a class I once had to run, to prepare students for an exam. The exam required essays to be written in response to questions, and as the students were science students, some were worried about essay questions, hence the class. The questions generally took the form: "discuss the hypotheses X and Y for Z, and present evidence for and against the two hypotheses". I started off with a general pep-talk about hypothesis testing and the nature of scientific models. Then I went through some specific hypotheses, and the evidence for and against. Then one student raised her hand and asked "so which hypothesis is right?" This is why, on another thread, I tried to put forward the idea that science isn't about a body of facts, but about iteratively improving the fit of our models to data. Sadly, many teachers, and students, still think that science is a body of facts, and that the job of science teachers is to teach the right facts not the wrong ones. I'd rather see poor models taught along with a good method for testing them, than good models taught with a poor or no method for testing them. So to me, it doesn't matter "which version" of a very new model is taught. What matters is that students learn that all "versions" of scientific models, are provisional, including extremely well-established models, and all are subject to update in the light of new evidence. But of course they do also need to learn a vast amount about extremely well supported models, in which differences between "versions" are small print details. They should not be given the erroneous idea that because a model needs an update (e.g. the model that DNA is the answer to how we inherit traits from our parents) that the entire model is thrown into doubt. There isn't a very great difference between "We inherit features from our parents because we inherit their DNA" and "we inherit features from our parents because we inherit their DNA, and also possibly sometimes a few features, some of which are pathological, and some of which might be beneficial, via epigenetic marking on the DNA". But if there is time for the longer version, sure, teach it. Elizabeth B Liddle

Mung:

Now, if in fact I do not understand or I am confused, then I’d surely like to rectify that deficiency.

I think I can explain, Mung, but as you seem so determined not to understand, this may not work. But, hey ho: Cells reproduce themselves. If a cell has a particular variant in its DNA sequence, or if it is methylated in some way, or has certain other novel features, the resulting reproduced cells will inherit that variant. Multicellular organisms develop - grow from a single cell to an adult with differentiated organs and tisses - because that first cell reproduces itself billions of times. During that process, some cells are altered in such ways that affect gene expression, and some of these changes are inherited by subsequent generations of that cell. Where those heritable changes are not genetic (i.e. changes to the DNA sequence) they are called "epigenetic". And the consequences of such heritable changes to a particular population of cells is that those cells become a specific tissue. They cease to be "totipotential" as the original single cell was, and as stem cells are, and become largely incapable of forming any kind of tissue other than that of the parental cell. So a liver cell cannot become anything but a liver cell, although a bone marrow cell can become a number of things including more stem cells, which is why they are useful for general repair jobs in the body. Cancer cells often have genetic (DNA) changes that their offspring inherit, but some cancers are due to epigenetic changes. Any heritable change in a cell can potentially give rise to a tumour. However, epigenetic changes can also happen in gametes, i.e. germline cells. This means that in sexually reproducing species, those changes affect the zygote, a new organism completely and thus passed on not only to cells within the same organism, but cells in the offspring organism. The key concept to grasp in this context is that "heritable" refers to both within-organism inheritance (e.g. the inheritance down generations of liver cell, or indeed a cancer cell) and between-organism inheritance (down the lineage of the whole organism. For some reason, I gather from the enthusiasm for "epigenetics" among anti-Darwinians, the idea has got about that because epigenetic changes can affect the germline, giving us an additional vector for between-organism inheritance of phenotypic variation, that this presents some kind of problem for evolutionary theory that "evolutionists" want to keep high schoolers from discovering. Which is rather ironic, seeing as Darwin did not now how phenotypic variation was inherited, and considered acquired characteristics (Lamarckian variation) a possible candidate. The mechanism he proposed does not, obviously, require that heritable variance in reproductive success is passed on via DNA, because he didn't even know about DNA. And while germline epigenetic marking is very interesting, it remains a tiny subset of the topic of epigenetics, and a small-print footnote to the general principle that DNA is the vector of heritable phenotypic features. What is of possible interest to those who are obsessed with "neo-Darwinism" is that it extends the synthesis of genetics and Darwinian principles to include epigenetics. It is also, in my view, exciting from an evolutionary theory point of view, because of possible implications for natural selection (i.e. heritable variance in reproductive success) above the level of the individual within a population, to population within populations, and thus the evolution of mechanisms by which populations can more readily adapt to environmental changes. But HS students have a lot to learn, and while I'm all for presenting cutting edge research to HS students, the sad truth is that a lot of science education does consist in learning extremely well understood and well-supported phenomena, and it is far too early to include epigenetics in that body of phenomena. So by all means teach HS students about epigenetics. But don't expect them to mug up on the details of how it works just yet, because by the time they reach college the details may well have changed. Elizabeth B Liddle

I just noticed how desperate News is to spin Dr Scott's statement:

In short, the best-known Darwin lobbyist thinks the evidence for evolution in general is so weak that doubts about the power of natural selection to randomly produce intricate new equipment must mean that evolution never happens. Good thing she said it herself.

That's so pathetic it's not even funny. Jerad

That's certainly something someone that is advocating the teaching epigenetica should be asking... For me, high school biology students should learn that the control of gene expression is a central topic in molecular biology, that gene expression both controls development and allows organisms to react to environmental cues, and that DNA methylation is important mechanism for this in mammals (but entirely absent from many other creatures that nevertheless get through life fine). I don't think trans-generational epigenetics deserves more than a mention at high school level. wd400

wd400:

What version of epigenetics is “now common knowledge to biologists”?

Which version is true? Which version ought to be taught? Mung

What version of epigenetics is "now common knowledge to biologists"? wd400

Still want to teach epigenetics in HS? Definitely! What about you wd400? Give students what is now common knowledge to biologists, or handicap them for a decade? gensci

... still want to teach epigenetics in HS? The very old definition of epigenisis (not epigenetics...) that Dawkins is talking about is the idea that organisms develop from undifferentiated forms (as opossed to simply scaling up from miniature pre-formed versions of themselves). The debate between those schools was more nuanced than that, but that's the central point. Then Waddington gave us the term epigenetics to describe the genetic basis of that unfolding process - which is more or developmental biology. Somewhere along they way epigenetics also came to mean stable changes in gene expression that could be heritable across cell divisions. Or even between generations, although there is still little evidence for that process. Even more lately, people think epigenetics as any chemical modification to DNA that changes it's expression, or in fact any modification to DNA expression (which Wikipedia seems to suggest). So, if you are using term only to describe trans-generation epigenetics inheritance then you shuold explain that. You should also be aware that most epigenetic research doesn't relate to that idea. wd400

wd400:

Epigenetic is, traditionally, the inheritance of gene expression traits from one cell division to the next.

IOW, epigenetics has nothing to do with heredity? Epigenetics is what takes place during development? So is epigenetics simply a misnomer? Dawkins writes:

The early history of embryology was riven between two opposing doctrines called preformationism and epegenesis.

You agree with Dawkins? wd400:

Epigenetic is, traditionally, the inheritance of gene expression traits from one cell division to the next.

Is that what you mean when you speak of heredity? Because if it is, I can understand why you don't understand what I am talking about. Wikipedia:

In biology, and specifically genetics, epigenetics is the study of changes in gene expression or cellular phenotype, caused by mechanisms other than changes in the underlying DNA sequence—hence the name epi- (Greek: ???- over, above, outer) -genetics. Some of these changes have been shown to be heritable.

Now, if in fact I do not understand or I am confused, then I'd surely like to rectify that deficiency. Mung

The short version: Epigenetic is, traditionally, the inheritance of gene expression traits from one cell division to the next. These patterns have been known about since at leas the 1970s, and there are many ways to achieve them. For instance, some genes set up "feed back" loops where the presence of their gene's product in the cytosol is enough to ensure their continued production. Recently, people have got excited about another method of epigenetic inheritance called DNA-methylation. Basically, some "C"s in the DNA are tagged with a chemical group, which results in gene silencing. This is important in mammalian development and plants (less so is most other well-studied organisms). They tagging and maintanance of methy- groups is controlled by proteins in the genome, and target to specific regions in the cells based on DNA-sequence. Other modifiers (histone modifications, miRNAs etc) are sometimes called epigenetic but it's not clear that many of them are. There is also trans-generational epigenetics (which I think Elizabeth has called "germiline" epigenesis) in which altered states of gene expression can make it through no just normal (mitotic) cell division but through meosis and into the next generation. It's not at all clear how wide-spread this process is in nature, but there are a few example that suggest it's possible. How do you model it? Well... just the same way as normal. For population genetics you can just add "epi-alleles" with a very high (epi)-mutation rate to the model. In terms of teasing out environmental and genetic effects of gene expression and how they interact with selection, well, that's what quantative genetics was invented for. So. You can see I'm a little bit lost as to why this is a big problem. It's interesting for sure, and amazing that we can directly measure the methylation state of whole genomes. But it seems to me like the me that the anti-evolution team is just grasping at anything "new" and hoping it fits their case. (Which is how lots of folks have reacted to modern epigenetics, I should say) wd400

wd400:

I agree entirely with those statements Mung. I think you might be confused about what epigenetics is, and how it works

Well, first, I appreciate that you still post here at UD. But does any one really understand yet "how it works"? Now I'm always willing to learn. So what is epigenetics and how does it work? How do you model epigenetics in Darwinian theory? Mung

Mung: in future I will try to remember to use the locution "I don't know what you mean by that term" in future. Thank you for the hot tip. Elizabeth B Liddle

Mung:

What do you think epigenetics means, Elizabeth?

Well, there are a number of definitions in use, but broadly, the term refers to heritable changes in a cell that do not involve changes to the DNA sequence. Specifically, this means that if a gene is "switched off" in a DNA sequence in one cell, the daughter cell inherits not only the DNA sequence but the "switched off" state of that gene as well. The most well-known mechanism is methylation of cytosine, which is a chemical alteration to one of the bases in the DNA, so the methylated cytosine is inherited along with the rest of the DNA. Regulatory sequences (sequences that control the switching on or off of coding genes) can be "silenced" by methylation. This is extremely important for multicellular development, as it means that once a cell has been differentiated to produce a particular set of proteins, all daughter cells will do the same thing, allowing tissues of a particular type to form in a particular place. This is called "somatic" epigenetics as it affects the cells within a single multicellular organism. However, epigenetic changes can also affect germline DNA, so that those changes are inherited by the organisms offspring. So environmental factors that cause methylation in the germline can cause phenotypic effects in the offspring, which in turn may be passed on to the next generation. Many of these effects are problematic, as gensci says, so that an environmental change that affects the parent can result in germline epigenetic changes that cause pathology, e.g. diabetes, in the offspring, and possibly the offspring's offspring. However, there are a few examples of where environmental changes in the parent environment can result in germline epigenetic changes that are beneficial for the offspring in that environment. That is what I mean when I said that the overwhelmingly great proportion of heritable phenotypic traits passed on via genetics, but there are a few that may be passed on via epigenetic marking, and of these, a few may be beneficial to the offspring in the current environment. I have no idea why this is perceived to be problematic for Darwinian evolution. It is certainly a source of heritable phenotypic variance, and therefore subject to natural selection (i.e. heritable variance in reproductive success), and more interestingly, it offers the prospect of natural selection operating at a higher level than that of the individual. But clearly the anti-Darwinian community have got excited about it. I have yet to discover why. Elizabeth B Liddle

Mung, you are using "Darwinian" in a way that exludes Darwin's own theory. And you're surprised that Liz doesn't know what people hear mean by "Darwinism"? wd400

(I should say, there is yet a fourth definition of epigenetics that limits itself to direct-environmental effects of methylation etc. That would be interesting if it was big player in biology, but there is little evidence that it is, and ti would not be very relevant to evolution since the tags would presumably switch back and forth over generational time scales) wd400

I don’t think there is a specific definition for epigenetic except that it is anything not in the genome that affects gene expression. A lot of what is called epigenetics is methylation which is a major factor that affects gene expression. OK. But for the most part methyl- tags are placed on genes by proteins which are "in the genome" and specific regulatory elements are targeted for methylation in different cells based on those sequences which are "in the genome". So it's not as if something "other" than what's in our genomes and subject to the usual evolutionary forces is what's contributing to these epigenetic patterns... wd400

wd400:

Mung, how does epigenetics challenge the Darwinian model of HEREDITY?

The Changing Role of the Embryo in Evolutionary Thought: Roots of Evo-Devo What Darwin Got Wrong Mung

Mung: "Because it’s not Darwinian" wd400:

I find that very hard to understand, since Darwin himself believed in epigenetic inheritance.

Then you also probably know that there's very little of Darwin left in "the modern synthesis." Mung

Hi WD400, I think everyone here understands epigenetics, so no need to define it, correct? Have you read this thread! There are least 3 definitions of epigenetics that go around, and people seem to chop and change among them as suits. That's why it's important for people to actually clearly define what they mean when they use the word. As I say. I've asked several times in each of several threads for someone to simply state who epigenetics, as they define the term, is a problem for evolutionary biology. The fact I'm yet to get answer seems pretty telling... wd400

Elizabeth:

I know a lot about Darwinian evolution, Mung, as you well know.

Yes, you often speak as though you do. So pardon those of us who are confused when you say you don't know what you are talking about. If you "know a lot" about "Darwinian evolution" then if quite logically follows that you know "a lot about" what is included and what is excluded. So when you say, "'Darwinism' is a mystery to me" it really is a mystery to many of us here at UD how and why that could be the case. In fact, Darwinism is not a mystery to you at all, you have simply mis-identified what it is that you are confused about: Elizabeth Liddle:

It seems to mean whatever the writer using it wants it to mean.

So your confusion is about what a specific person means when they use the term. So why don't you say, "I don't know what you mean when you use that term," instead of saying, I don't know what that term means? Have you ever paused to think about why none of us here at UD are confused about what you mean when you say you know a lot about "Darwinian evolution"? We are not confused when you use the term "Darwinian evolution" but you are confused when people here use the term "Darwinism." How so? Seriously, I'd really like to know, as would many others here. Mung

gensci, I don't at all share your view that "everyone here understands epigenetics". I see a lot of evidence of a great deal of confusion. And to be referred to a children's video series costing rather a lot of dollars as a source, is not helpful. You said it was very simple, and therefore suitable to be taught to children. Please provide a short simple summary of what you think are the key concepts. If they are suitable to be taught to children, this should not be difficult. Elizabeth B Liddle

@Mung You may be interested in Wetware: A Computer in Every Living Cell Thanks. After a quick skim through the TOC and couple dozen pages on Amazon, it is precisely the position on the origin of biological novelty and evolution I have had for some time. That kind of computational perspective will eventually prevail. The sad part is that ID could have naturally taken that entire terrain as its own, but listening to Meyer and others, it doesn't seem it can change its language from the nature spirits talk (aka 'consciousness' talk) to the computational and algorithmic language which is the only way ID can evolve into natural science. Instead, the neo-Darwinists will morph their stories first into it and pretend to have been 'computationalists' all along. nightlight

even define epigenetics

I don't think there is a specific definition for epigenetic except that it is anything not in the genome that affects gene expression. A lot of what is called epigenetics is methylation which is a major factor that affects gene expression. Other non-genetic factors during gestation are in the embryo which also affects body layout and gene expression. Little is known about this except it is most likely in the egg cytoplasm or cell wall. jerry

Hi WD400, I think everyone here understands epigenetics, so no need to define it, correct? If you need a definition, you can purchase and listen to the Jonathan Park audio series for children I linked to earlier. Also, do a search for "Pennisi Evolutionary Heresy Science 2013" and you should come across her article where I got the "raising hackles" quote from, plus a definition of epigenetics. gensci

This is getting tiring. EL:

Germline epigenetic marking (which I gather is the “epigenetics” in question here) is not the same thing as targeted (or non-random) genetic changes.

EL:

And are you talking about somatic or germline epigenetics?

Mung

I agree entirely with those statements Mung. I think you might be confused about what epigenetics is, and how it works... wd400

Elizabeth Liddle:

Genetics is a far greater determiner of the phenotype than germline epigenetics. On the other hand, somatic epigenetics is vital to development, as it is key to tissue differentiation.

Just freaking wow. Elizabeth Liddle:

Nobody here, surely, of all places, disputes that DNA sequences are overwhelmingly responsible for the phenotype...

Elizabeth Liddle:

On the other hand, somatic epigenetics is vital to development...

Mung

What I’m finding is it raises hackles for almost every single evolutionary biologist I talk to, and that’s just weird. That's probably because folks keep saying epigenetics is a problem for evolutionary biology but no one (32 comments into yet another thread on the topic) and say why that's the case... or even define epigenetics. wd400

Elizabeth Liddle:

Nobody here, surely, of all places, disputes that DNA sequences are overwhelmingly responsible for the phenotype...

Really? What do you think epigenetics means, Elizabeth? Mung

The JP message is that God is an awesome creator, and that evoltion"ism" paints a false picture of reality. But hey, it's awesome that you think epigenetics should be included in government school texts, good for you! As a recent article in science said, epigenetics "raises hackles" for some biologists, but you don't seem to be one of those kind so much. What I'm finding is it raises hackles for almost every single evolutionary biologist I talk to, and that's just weird. gensci

Ho-De-Ho:

Is it because we have all been told for many a moon, that Natural Selection working on Random Mutation is responsible for all of the diversity of life around about?

That's a large part of it, I'm sure. But let's keep in mind that the epigenetic (and other related) challenges to neo-Darwinism are not of creationist manufacture. (Not that you've even hinted that they are.) The basic model of neo-Darwinism as that of population genetics. What would "the modern synthesis" be without it? And even our dear Lizzie can see that it wears thin:

But the idea that it might be suppressed because it undermines evolutionary theory really is very strange. It does mean we have to move beyond classical neo-Darwinism, which is a good thing, because I think (being Noble fan) that it is time we moved on from an exclusively gene-centred model.

Has she erected a straw-man? Does she really understand at least this much about neo-Darwinism? It is an exclusively gene-centered model. Then our dear Elizabeth, who doesn't know what 'Darwinism' is, states:

We also need to consider natural selection at between-population level as well as within-population (as Noble, and Shapiro) have argued, rightly in my view.

She knows about the gene-centric nature, and about natural selection at the level of the population, and disagrees with both, but stands in wonder at anyone who would question 'Darwinism.' Not a convincing act by any stretch. Mung

Elizabeth Liddle:

What is interesting about germline epigenetics is that it does potentially provide an additional adaptive mechanism to that of natural selection (although by no means all epigenetic changes are adaptive – some, I don’t know what proportion – are actually maladaptive).

Germline epigenetics? That comes awfully close to being an oxymoron, imo. But please do tell how it helps Darwinism at all? Epigenetics and the germline. Fine-tuning evolution: germ-line epigenetics and inheritance. Mung

nightlight:

The actual process producing evolutionary novelties is increasingly looking like computation by the biochemical networks running anticipatory algorithms, i.e. there is intelligent source of novelties, which is a position well within the ID perspective (minus the gratuitous, sterile “consciousness” mystification by Stephen Meyer and few others).

You may be interested in Wetware: A Computer in Every Living Cell Mung

Because it’s not Darwinian I find that very hard to understand, since Darwin himself believed in epigenetic inheritance wd400

I know a lot about Darwinian evolution, Mung, as you well know. "Darwinism" is a mystery to me. It seems to mean whatever the writer using it wants it to mean. Elizabeth B Liddle

Mung, how does epigenetics challenge the Darwinian model of HEREDITY? Or how much would evolutionary biology have to change in trans-generational epigenetic inheritance was found to be common-place in biology (it certainly hasn't been yet). wd400

For the simple reason, gensci, that there is a limit to how much can be taught at HS, and right now, germline epigenetic effects are small print, stuff, very much under active research, with lots of unknowns. Which is exactly why it is worth a mention - I think it is very important to teach about topics that are under active investigation as well as well-established mechanisms, like somatic epigenetics and their role in development, and the genetic vector for inheritance. I'd like to know, though, what you think that children's series you linked to, presents. Just a brief simple summary - what is the message? Elizabeth B Liddle

Elizabeth Liddle:

Can you explain why epigenetics is evidence against Darwinian evolution, news?

Because it's not Darwinian. But then, you wouldn't know about that, because you don't even know what Darwinism entails, do you. "I don’t know what 'Darwinism' is, and I am not a “Darwinist” - Elizabeth Liddle Mung

Hi Elizabeth, no confusion here. Glad you think somatic epigenetics should be taught. But germline epigenetics are only "worth a mention?" Are you kidding me?! Surely you know we basically have a diabetes epidemic in this country, and epigenetic studies by Randy Jirtle and many others are revealing the huge connections between diet and germline epigenetics. This is more than just "worth a mention." gensci

It was almost a relief when an antievolutionist contended that the books should be rejected because they don’t include epigenetics. At least the epigenetics argument is relatively recent (perhaps only 5-8 years old). In creation-think, including epigenetics in biology textbooks will weaken evolution because epigenetics is evidence against evolution. Yeah, I know it isn’t, but to creationists, any process that isn’t natural selection weakens natural selection as an evolutionary mechanism...

More Darwinist dissembling. Oh, look over here and ignore the real issue.

Ideas about heredity and evolution are undergoing a revolutionary change. New findings in molecular biology challenge the gene-centered version of Darwinism ... In Evolution in Four Dimensions Eva Jablonka and Marion Lamb argue that there is more to heredity than genes.

Epigenetics challenges the Darwinian model of HEREDITY. Eugenie Scott is either ignorant or willfully misleading people. Mung

Gensci, You'd have to explain what "ideology" is at stake when it comes to teaching epigenetics. As yet no one has given a clear argument as to why epigenteics (however they define it) is a problem for evolutionary biology... wd400

gensci, I'm asking you to explain it. Because I think you are confused. I'd like to know what you mean by "the epigenome directs the genome". I've already said that somatic epigenetics should be taught, and that germline epigenetics are worth a mention. Elizabeth B Liddle

Hi Elizabeth, here's a link to an audio series for elementary-aged kids that teaches them epigenetics. If they can explain it to little kids, don't you think HS students could understand it? Seems to me the only reason folks are saying "no" is they are clinging to tightly to their ideology: http://www.visionforum.com/browse/product/jonathan-park-the-voyage-beyond/default.aspx gensci

Hi Elizabeth, everywhere I read, scientists are talking about epigenetics. It is basic biology now to know that the epigenome directs the genome, yet there is zero mention of epigenetics in current government school texts. If mention of epigenetics doesn’t get into Texas textbooks now, it won’t be in for another 10 years, handicapping Texans, plus students in other states who purchase the same books. Do you think it should go in now, later, never?

Could you explain, in HS terms, how you think "the epigenome directs the genome"? And are you talking about somatic or germline epigenetics? Elizabeth B Liddle

No, I did not misread you. Germline epigenetic marking (which I gather is the "epigenetics" in question here) is not the same thing as targeted (or non-random) genetic changes. If the latter is what you are talking about, then you might have a point. Indeed Shapiro has raised this possibility - that mutations may not be orthogonal to fitness, and that mutational processes may preferentially result in fitter genomes in the current environment. This is an intriguing possibility, however, the evidence for it is extremely week. The vast majority of novel genetic sequences are neutral in the current environment. In a well-adapted population, evolutionary theory predicts that beneficial mutations will tend to be rarer than deleterious ones. The balance will tend to move towards beneficial mutations when the environment changes. And indeed, this is what we observe - optimisation is non-linear, proceeding more slowly as optimisation is reached. But it is certainly possible that there some additional factor actually promotes adaptive mutations. There would be population-level reasons to predict this, as Shapiro has suggested (and Noble). But, of course, there could be something even more interesting going on! Certainly, if I were an ID proponent, this is an area of research I would be focussing on. Elizabeth B Liddle

Jerard These change in gene expression is not Darwinian Why do you think that? As Elizabeth has said, the differences the Grant's measured in the Galapagos are heritable, so it's the direct effect of environment. We don't need "epigenetics" (a word that is fast loosing any meaning it once had) to understand that, just turn of the 20th Century quantative genetics. It's seems very unlikely that the traits would be inherited by stable trans-generational epigenetic modifications, but if they were, it would still be selection determining which "epi-allele" goes up or down in frequency. wd400

Hi Elizabeth, everywhere I read, scientists are talking about epigenetics. It is basic biology now to know that the epigenome directs the genome, yet there is zero mention of epigenetics in current government school texts. If mention of epigenetics doesn't get into Texas textbooks now, it won't be in for another 10 years, handicapping Texans, plus students in other states who purchase the same books. Do you think it should go in now, later, never? gensci

@8 Elisabeth B Liddle

No, really, it is not. Nobody here, surely, of all places, disputes that DNA sequences are overwhelmingly responsible for the phenotype, or that polymorphisms have phenotypic effects. You are not seriously suggesting that germline epigenetic marking is what primarily makes us different from each other, rather than the alleles we inherit?

You misread my objection to the neo-Darwinism: its fundamental problem is the random attribute of the mutation as the source of evolutionary novelty. The emphasis is on gratuitous attribute "random" (aimless, 'orthogonal' as you labeled it), not on the mutation (i.e. DNA transformation) or phenotypic role of DNA or evolution. The last three elements are not problematic for ID at all since they have close analogues in other well known instances of intelligently guided evolution, such as those of technologies, sciences, arts, fashions, etc. Systems that evolve and improve require greater intelligence to design and construct than the static, unchanging ones anyway, hence the phenomenon of biological evolution is the friend of ID, not the enemy. The actual novelty generator is a far smarter class of algorithms than the random trial and error of neo-Darwinism. These algorithms computed by the cellular biochemical networks (which run these algorithms) aim the genetic and epigenetic changes toward the phenotypic objectives that yield the most favorable outcomes for the present or anticipated environments. These networks with adaptable links are the same general kind of distributed self-programming computers as the more familiar networks such as those of neurons forming the human brains. They are all mathematically modeled by neural networks which are general computers (they can compute anything that is mathematically computable). Their links adapt locally without need for supervision by an external oracle (to guide them to some higher level objectives), merely seeking to optimize their local net {rewards - punishments} signals. Such systems spontaneously develop (see an earlier post on how they do that and its followup) and run a common type of anticipatory algorithm for such optimization, consisting of internal model of their environment, which includes the self-actor (the system itself) as well as the model-actors of other networks in the environment as the components of the internal model. Then they run this internal model with all its actors forward in model time, play out different admissible moves by the self-actor and evaluate the resulting future net {rewards-punishments} on the network, then select the highest scoring actions by the self-actor as the one to execute in the actual environment (that implements the so-called "free will" endowed by the creator to its creatures). Hence, this common algorithm works like a chess player thinking ahead about the next move, by playing out different legal moves in the mental model of the current position, then possible opponent's responses to each, then own responses to those,... several moves ahead (even dozen or more by stronger players), evaluating each final ('terminal') position and choosing the best one to make on the real chess board. In the above context, the rising appreciation and understanding of the role of epigenetic mechanisms in the operation of the biochemical networks merely adds another computational layer, rendering the neo-Darwinian "random" trial and error algorithm seem ever more naive and archaic, an irrelevant relic of the 19th century. Unfortunately, the loudest ID advocates are presently either from the softer disciplines (lawyers, philosophers of science, theologians, etc) or those from hard science but religiously overecommitted to certain ancient scriptures, who are doing disservice to the ID perspective by needlessly shifting the debate to the nebulous "conscious" intelligence (a bottomless tarpit that has drowned countless philosophers over the last 2-3 millennia). What they need to do to make their valuable observations and insights gain the traction as the seed for genuine natural science is to rephrase the "conscious" intelligence talk into the computational and algorithmic language which is what it comes down to when logically followed through. For this reason, the most effective ID proponents, unwitting and unwilling allies as they may be, are actually James Shapiro and the folks at Santa Fe Institute developing "Complexity Science" last couple decades. What is already happening (and what your own posts reflect) is that neo-Darwinists are hurriedly morphing their story toward the latter developments, adopting them as their own (even though they dismissed and fought them as conjectures throughout decades) and are just about ready to declare, yeah, that's what we were always saying, while quietly dethroning the "random" attribute of the mutation as the source of evolutionary novelty, eventually dropping it altogether. In the meantime, the present style ID will likely continue drowning in its own self-inflicted 'consciousness talk' tarpit for another few millennia. nightlight

Jerry

My guess is that some or a lot of examples of evolution have not been evolution but examples of change in gene expression. Darwin’s finches being probably one. These change in gene expression is not Darwinian and should not be considered as evolution. The end result may be that Darwin’s ideas would be trivialized even more than they have been in recent years. Maybe that is what they are afraid of.

Actually my "I agree" was only to your first sentence. Certainly the changes in Darwin's finches were changes to gene expression, and expression of at least one gene governing beak length has been identified (BMP4). But it is far more likely that the difference in gene expression was due to alleles in regulatory sequences than germline epigenetic marking, although that is of course possible. However, it is contra-indicated by the Grants' work on the family trees of the finches. Beak size in chicks was strongly determined by beak-size in parents, even though the environment was common to all finches. An epigenetic explanation would be much less parsimonious than a genetic one, expecially given that we know that alleles of regulatory genes do produce marked phenotypic effects. Elizabeth B Liddle

...Sorry. I forgot to comment on the 'kids won't understand' epigenetics - humm., It is pretty mind blowing when you really sit down and think about it all. But, that's because we are stuck in the old paradigm. Personally, I think kids will absolutely get it and be saying - 'sure that's obvious - how else would a caterpillar change into a beautiful butterfly?' It's just another excuse to try and save face, because epigenetics alone blows Darwinian evolution right out of the water. cosmicrabbit

I agree, jerry. But there is certainly an argument for teaching the biggest effects first, and leaving the small print for later. Although I'd be all for mentioning it germline epigenetic effects in passing. Genetics is a far greater determiner of the phenotype than germline epigenetics. On the other hand, somatic epigenetics is vital to development, as it is key to tissue differentiation. Elizabeth B Liddle

teaching it in schools

There should never be any problem teaching what is known and not known in the schools. Unfortunately a lot of the text books over sell what is known. My guess is that some or a lot of examples of evolution have not been evolution but examples of change in gene expression. Darwin's finches being probably one. These change in gene expression is not Darwinian and should not be considered as evolution. The end result may be that Darwin's ideas would be trivialized even more than they have been in recent years. Maybe that is what they are afraid of. jerry

Oh dear. Whoops. When I started writing my last post, only Elizabeth had left any comments. Now I just appear inattentive. Apologies. That will teach me not to go and prepare tea whilst mid-flow in writing a comment. Ho-De-Ho

nighlight:

It is evidence against gratuitous, algorithmically primitive and empirically unsupported neo-Darwinian mechanism for generating novelty: random, aimless mutation (serving as the main bludgeon of the militant atheists).

No, really, it is not. Nobody here, surely, of all places, disputes that DNA sequences are overwhelmingly responsible for the phenotype, or that polymorphisms have phenotypic effects. You are not seriously suggesting that germline epigenetic marking is what primarily makes us different from each other, rather than the alleles we inherit? If you are, this is simply, and demonstrably, untrue. Germline epigenetic marking is certainly interesting, but not even the most ardent enthusiast for the adaptive effects of germline epigenetic marking would claim that the effect is anything but marginal! If you want something to challenge the idea that variation is not orthogonal to reproductive success, you'd be better looking at at the mechanisms of DNA rearrangement in the germline (for instance, recombination) than epigenetics. Although that doesn't take you all that far, because, as Shapiro and Noble note, Darwin's principle can be applied to any reproducing level, including population level, and we know that the vast majority of populations go extinct. Therefore any population that has a reproductive system that renders the population more robust to environmental change, including the capacity for adaptive evolution, or, for that matter, epigenetic blunting of adaptive evolution (i.e. epigenetics doing some of the adapting, thus keeping the gene-pool rich), is likely to contribute to that populations chances of not going extinct. Not that I expect this to go down to a standing ovation here, so I'll just reiterate my first point: nobody is suggesting that epigenetics will replace genetics as the primary vector of inheritance! Lamarck wasn't as wrong as was once thought, but he was a lot wronger than Mendel, nonetheless! Elizabeth B Liddle

Greetings greetings one and all. Good evening, or day, Elizabeth B Liddle? Nice to see you about on the boards again with your usual polite discussion. Whatho News. Thank you for the post. Epigenetics eh? Exciting stuff! News, would you mind if I to chime in alongside Elizabeth? In what way is the epigentics revolution (as I believe Nessa Carey dubbed it) a threat to the Evolution status quo? In some respects, one would imagine that it would really give it quite a fistful more oomph in its ability to produce lots of novelty items. In your opinion, News, how has epigenetics thrust an unwanted wrench in Darwin's motor? Is it because we have all been told for many a moon, that Natural Selection working on Random Mutation is responsible for all of the diversity of life around about? It is a fact as well understood as Gravity and that the Earth orbits the Sun...except that now it evidently is not quite as factual. I am genuinely interested on your take and anybody else's. Of course, there are likely to be snags or perforations in most arguments, but let us be generous towards others opinions. Like a fine pair of scales purchased from Harrods maybe we can weigh the merits of each others opinions and try to see from where they approach the matter. I look forward to all you topping ladies and gents putting forth on this topic. I will read with bated breath, although my remarks will be limited due to my lack of expertise. Hope you don't mind my throwing in a question or two though. Ho-De-Ho

Try thinking of epigenetics at the early stages of evolution. Epigenetics control/trigger/regulate jumping genes (transposible elements. Now think of metamorphosis as in a caterpillar to a butterfly. There, the code is less defined (like stem cells in an embryo - not fully programmed until signals are given from the environment). It is really hard for us to get our heads around all this because we are so indoctrinated about Common Descent. I am working on a book about it all as we speak. Good discussion. cosmicrabbit

That's an interesting point, Jerry. What is interesting about germline epigenetics is that it does potentially provide an additional adaptive mechanism to that of natural selection (although by no means all epigenetic changes are adaptive - some, I don't know what proportion - are actually maladaptive). You could argue, that epigenetic effects might blunt the effects of natural selection. That might itself be adaptive at population level, of course, in that it might help maintain robustness in the face of environmental change. So yes, it is an interesting line of research. My own take on teaching it in schools, is that it would be worth teaching, as it is extremely important in understanding the development of multicellular organisms. Its role in gene expression during function is less clear, and, as yet, the size of the effect on germline cells, and to what extend these effects tend to be adaptive, is not clear, and so probably not ready for HS. But the idea that it might be suppressed because it undermines evolutionary theory really is very strange. It does mean we have to move beyond classical neo-Darwinism, which is a good thing, because I think (being Noble fan) that it is time we moved on from an exclusively gene-centred model. We also need to consider natural selection at between-population level as well as within-population (as Noble, and Shapiro) have argued, rightly in my view. But, as Noble himself says (and, interestingly, Margulis), that's not a problem for Darwin's theory - it does however lead us beyond neo-Darwinian models. Elizabeth B Liddle

Ask Eugenie Scott, I guess. She seems to think including epigenetics in text books will lead the children astray. C'mon this sounds a little "1984"-ish, Dr. Liddle. Whether the concern has merit or not, this instance makes it appear as though Eugenie Scott wants to wait until minds of students are indoctrinated before anything that can be deemed as counter to Darwinism is introduced to them. It's not exactly a great PR move. TSErik

nightlight, interesting all, but wouldn't call James Shapiro "conventional biochemist." He's sort of like not having to open the window. News

Can you explain why epigenetics is evidence against Darwinian evolution, news? It is evidence against gratuitous, algorithmically primitive and empirically unsupported neo-Darwinian mechanism for generating novelty: random, aimless mutation (serving as the main bludgeon of the militant atheists). The actual process producing evolutionary novelties is increasingly looking like computation by the biochemical networks running anticipatory algorithms, i.e. there is intelligent source of novelties, which is a position well within the ID perspective (minus the gratuitous, sterile "consciousness" mystification by Stephen Meyer and few others). Even the conventional biochemist James Shapiro has arrived to similar conclusions, that the evolutionary novelties are result of sophisticated molecular engineering, not the aimless random mutations of the "modern" synthesis. Despite his denials that is in the ID camp, he is being shunned by the neo-Darwinians and praised by the ID folk. nightlight

Selection based on epigenetics may not be evolution. Then again it depends on how one defines evolution. If morphological changes over time are just changes in gene expression while not changing the gene pool, is that evolution? If this is true then the morphology may revert back when the environment changes and we are back to square 1. This may be the case in Darwin's finches and cichlids. Are there other cases of so called evolution that may be just epigenetic changes. Should be a ripe area for research. What causes the methylation changes to change the gene expression? Why might it change back. Was most of what Darwin thought was changes in species just differences in gene expre ssion? Interesting questions which we will find out in the coming years. jerry

Can you explain why epigenetics is evidence against Darwinian evolution, news? I am still mystified. As I said in the other thread, without epigenetic marking, multicellular development wouldn't work. Why should that be a problem for Darwinian evolution? Why is it a problem for natural selection? It seems to me that there is powerful selective pressure for it. Or are you thinking of germline epigenetics? Again, why is this a problem for natural selection? Natural selection is heritable variance in reproductive success. It doesn't matter whether the heritable variance is genetic or epigenetic as long as it is heritable and has phenotypic effects. Darwin didn't even know what caused heritable variance, and at one point favored the Lamarckian model. Which is essentially what this is. I really don't understand why you think this is such a big deal. Elizabeth B Liddle