UPDATE: As reader Michael found out and reveals in a comment below, Skinner is well funded by Templeton. It crossed my mind, but I thought, “naaaah. . .” and couldn’t be arsed to look it up. But yes, Skinner is eating well from the Templeton trough. It’s pretty clear that Templeton is deeply invested in showing that the “conventional” view of evolution and genetics is wrong, for they’ve also put millions into other researchers to that end. I’m not quite sure why they’re doing this, but the money would be more widely invested in other research not explictly designed to bust a paradigm.
__________
I’m not sure what’s with the website Aeon, as it seems to publish some good stuff, but their science sometimes seems wonky. Such is the case with an article published by Michael Skinner last November but just called to my attention by reader Rodney, “Unified theory of epigenetics“, which bears the subtitle “Darwin’s theory that natural selection drives evolution is incomplete without input from evolution’s anti-hero: Lamarck.” Lamarck, of course, was the French biologist and polymath who proposed that animals could stably inherit modifications of their body, behavior, and physiology that were imposed by the environment. The classic example is the giraffe’s long neck “evolving” over generations by giraffes stretching their necks ever further to reach leaves higher on the trees. Each stretch would somehow feed back into the DNA, so straining giraffes would have offspring with longer necks.
The problem with this idea, and why Lamarck hasn’t become any kind of evolutionary hero, is that it doesn’t work. While the environment can play a role in sorting out those genes that their carriers leave more offspring, there’s no good way for environmental information to somehow become directly encoded in the genome. For that would require a kind of reversal of the “central dogma” of biology, stated by Francis Crick like this:
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred back from protein to either protein or nucleic acid.
Now there are some exceptions to this, and we’ll mention one of them here, but by and large this is correct, especially in its implication that information from the environment cannot change the sequence of DNA or the proteins that DNA produces through RNA intermediates. If this were possible, and you lifted weights before your kid was born, that kid would either be born with bigger muscles or would be more prone to develop them than the children of non-lifters.
Of course the environment can act to turn genes on and off. The classic example is the presence of lactose in the environment, which activates genes in E. coli that can metabolize that sugar: that was the classic Nobel-winning work of Jacob and Monod on gene regulation. But lactose does not change the structure of DNA or protein, but rather acts, in an evolved system, to turn on genes helping the bacterium use a sugar not normally present in the environment.
One exception to the central dogma is “epigenetic” modification of DNA and the histone proteins used in packaging DNA. Some environmental factors can act to modify the DNA, usually by attaching methyl groups to its bases, and these modifications can not only change gene action, but can be inherited—but only for a couple of generations. The fact that these epigenetic markers are usually erased from the DNA during sperm and egg formation, and none have been found to be permanent, mean that environmentally-induced epigenetic change cannot be an important part of evolutionary change, which requires permanent alterations of genes (invariably by mutations). Some epigenetic modifications, however, can play a role in evolution: these are markers coded by the genes themselves, like gene X coding for instructions to “put a methyl group at position Y on gene Z”. These changes, however, are coded in the DNA, arose by mutation, and were not induced by the environment.
On this site I’ve repeatedly discussed the problem with seeing environmentally-induced epigenetic changes in DNA as a neglected and important aspect of evolutionary biology, and what I’ve written above is somewhat of a refresher. You can search on this site here for the many pieces I’ve written about it, including critiques of Siddhartha Mukherjee’s misleading article touting epigenetics in The New Yorker.
Skinner, a professor of biological science at Washington State University and somewhat of an epigenetic evangelist, ignores the many criticisms of epigenetics that have been made, still maintaining that it’s so important that it mandates a paradigm shift in evolution. He claims, for instance, that “regular” genetic variation in DNA caused by mutations is insufficient to fuel adaptation, and thus we need “something else”—that something else being epigenetic “mutations” caused by the environment. This claim has been refuted by, among others, Deborah Charlesworth and her coauthors in a paper I’ve highlighted before. (The pdf is here.)
In the rest of the essay, Skinner gives several examples of environmentally induced changes in the DNA that can be passed to offspring. The problem is that none of the changes are passed on for more than a few generations, and thus cannot be a meaningful scaffold for evolutionary change. (Skinner’s example of the environmentally-induced flowering trait found by Linnaeus and being transmitted for over 100 generations is wrong.) I’ll just give two of Skinner’s examples quoted from his Aeon piece:
One example that we studied in our lab involved the impact of environmental chemical exposure on trait variation and disease. In our study, we set out to investigate the ability of an environmental toxicant – vinclozolin, the most commonly used fungicide in agriculture today – to alter traits through epigenetic change. First, we briefly exposed a gestating female rat to the fungicide; then we bred her progeny for three generations, to great-grand-offspring, in the absence of any continued exposures. For nearly all males down through the lineage, we observed a decrease in the number and viability of sperm and an associated incidence of infertility with age. And we observed a variety of other disease conditions in both males and females three generations removed from the direct exposure, including abnormalities in the testis, ovaries, kidneys, prostate, mammary glands and brain. Corresponding epigenetic alterations in the sperm involve changes in DNA methylation and non-coding RNA expression.
What we see here is an epigenetic change that is not adaptive (it reduces fertility) induced by a toxin. The important thing is that it was observed to last for only three generations. This is not something that can support the possibility of adaptive evolutionary change—or any evolutionary change—and certainly doesn’t buttress the paper’s conclusion that the results “have significant implications for evolutionary biology.”
Here’s another example (there are several, but all suffer from the same problem of transitory change):
Our research showed that ancestral exposure to the toxicant vinclozolin also affected sexual selection in animals three generations down the lineage. Considered a major force in evolution since Darwin first posed his theory, sexual selection – also known as mate preference – was assessed by allowing females from other litters to choose between either descendants of exposed or unexposed males. Females overwhelmingly selected those who lacked the transgenerational epigenetic alterations and whose ancestors had not been exposed. In conclusion, exposure to the fungicide permanently altered the descendant’s sperm epigenetics; that, in turn, led to inheritance of sexual selection characteristics known to reduce the frequency with which their genes might propagate in the broader population and directly influence evolution on a micro-evolutionary scale.
Here we have exposure to another toxin, with the result that female rats preferentially chose males who hadn’t been exposed to the toxin (those males, being poisoned, may have lacked vigor). It is true that if there is genetic variation in female preference for males not exposed to the toxin, this could cause an increase in the frequency of genes for that preference—but for only three generations. There would be very short-term evolution, but it would be halted when the epigenetic markers disappeared, for then there would be no selective pressure on the females because there would no longer be epigenetic markers differentiating the males.
And so the long essay goes on, concluding, with the merest evidence, that neo-Darwinism needs a big reboot (my emphasis):
Despite the pushback [JAC: he means the arguments from people who have pointed out the weaknesses of the epigenetic model], I’m convinced that we have reached the point where a paradigm shift is due. Accepting that epigenetics plays a role in evolution does not topple the science of genetics; embracing neo-Lamarckian ideas does nothing to challenge classic neo-Darwinian theory. The accepted sciences are essential and accurate, but part of a bigger, more nuanced story that expands our understanding and integrates all our observations into a cohesive whole. The unified theory explains how the environment can both act to directly influence phenotypic variation and directly facilitate natural selection, as shown in the diagram above.
With a growing number of evolutionary biologists developing an interest in the role of epigenetics, there are now some mathematical models that integrate genetics and epigenetics into a system, and the work has paid off. Consideration of epigenetics as an additional molecular mechanism has assisted in understanding genetic drift; genetic assimilation (when a trait produced in response to the environment ultimately becomes encoded in the genes); and even the theory of neutral evolution, whereby most change happens not in response to natural selection, but by chance. By providing an expanded molecular mechanism for what biologists observe, the new models provide a deeper, more nuanced and more precise roadmap to evolution at large.
Taken together, these findings demand that we hold the old standard, genetic determinism, up to the light to find the gaps. It was Thomas Kuhn who in 1962 suggested that when a current paradigm reveals anomalies then new science needs to be considered – that is how scientific revolutions are born.
A unified theory of evolution should combine both neo-Lamarckian and neo-Darwinian aspects to expand our understanding of how environment impacts evolution. The contributions of Lamarck more than 200 years ago should not be discounted because of Darwin, but instead integrated to generate a more impactful and insightful theory. Likewise, genetics and epigenetics must not be seen as conflicting areas, but instead, integrated to provide a broader repertoire of molecular factors to explain how life is controlled.
This is a call to revolution that is way too early, for there are no good data calling for such a change, much less for even a minor evolutionary role of environmental epigenetic changes in DNA. I’m not sure why people drag in Kuhn when the current paradigm is still satisfactory (see the Charlesworth et al. paper), but of course one makes one’s name in science not by buttressing a well-established paradigm, but by overturning it. Neither Skinner nor anyone else has yet done that to the neo-Darwinian theory of evolution. Those of us who continue to adhere to it do so not out of loyalty or stubborness, but because there aren’t good data showing that the theory is wrong.
Epigenetic modification remains an important discovery, and has implications for gene regulation, cell differentiation, disease, and the evolution of genetic conflict between males and females, but the evolutionarily important modifications are those instilled into the genome by natural selection, not by abrupt intrusions from the environment.
Use of “paradigm” always sets a red flag off for me, for starts.
Man said he wanted to see a paradigm shift, so I took twenty cents and shook it real good!
Use of “genetic determinism” is what sets off mine.
Frequently a flag of either religious fundies, or SJWs committing the Moralistic Fallacy.
Are there any ways “environmental information [can] become directly encoded in the genome”?
Sort of, but not this way. It turns out that the genes in an organism’s genome may, by our figuring out what they do, give clues to past environmental factors involved in natural selection. This kind of reverse-engineering of DNA was suggested by Richard Dawkins in an essay about “The genetic book of the dead.” (I’m not sure where it is, but I’m sure some readers know.)
It is Chapter 10 of “Unweaving the Rainbow”.
It was a response to Edge’s 2017 question
https://www.edge.org/response-detail/27237
Kuhn was an enabler for postmodernism.
That’s about as fair a claim as when someone charges that Darwin was an enabler for racists. One should not be held responsible for what unhinged or stupid people do with their ideas.
Seconded. There’s nothing in The Structure of Scientific Revolutions endorsing epistemic relativism.
Postmodernists who recruit it are just trying to dress up an older, more petulant argument: “scientists have been wrong before, so there’s no reason to think they’re correct now. Nah nah nah.” Not at all the point Kuhn was making.
Or blaming Oasis on the Beatles.
Kuhn’s insistence that each paradigm overthrew its predecessor is an important basis for the postmodernist claim that there is no such thing as reality. Note that I carefully described him as an enabler, not an adherent.
If that’s true then Fox News needs to give back the term ‘optic’ to physicists. Kuhn is not an enabler of stupidity.
Yes, he undoubtedly was.
Kuhn held that paradigms are in-commensurable; cannot be translated to each other because the meaning of the words in one theory are incompatible with the meaning of the same words in another theory.
Paul Feyerabend used Kuhn’s and Quine’s work for his book “Anything goes”.
And as far as I can see it, he is probably right: from a philosophical point of view indeed anything goes.
Further we cannot deny that science is not immune for political, psychological and economic forces (f.i. Templeton).
The way I personally resolve my cognitive dissonance is to claim that the philosophical point of view is not important at all and that besides science there are no other ways of knowing.
Funny enough Paul Feyerabend used to think this himself before he came with his epistemic relativism about paradigms.
Kuhn was always a bit unclear about his relativism; sometimes he denied it, sometimes not. That didn’t help.
American Quarter Horse breeders betting big on epigenetics.
Anything in the pursuit of marketable coat color & patterns!
I’ve found the horse world highly gullible to not just shaky genetics (e.g., “dosage” is still revered in the racing industry), but also unadulterated woo.
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Lamarck did not so much propose that environmental modifications would be inherited, he simply invoked the widespread perception, the “common knowledge” of his day, that this would happen. What he proposed was that the strivings of the organism (say, to swim) would increase the size of the relevant parts, and that this modification would be passed on. This was an explanation of why change would preferentially be in an adaptive direction.
Epigenetic modifications don’t last long enough to be responsible for long-term or even moderate-term evolutionary change. In addition, they are not “Lamarckian” in that they do not preferentially cause an adaptive response to a need. If you have epigenetic changes owing to your parents experiencing a famine, the changes may cause you to be more susceptible to cancer or heart disease, but not on the whole better at surviving a famine. So Skinner is wrong to say that the effect of epigenetics is “Lamarckian”.
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Equally, Darwin, like virtually everyone else at the time, assumed that the effects of using an organ could be passed on to offspring – he used the allegedly well known example that a blacksmith’s offspring will have big arms. The difference with Lamarck was that Lamarck tended to invoke the ‘will’ of the organism, not the actual activity. As a consistent materialist, Darwin disagreed with this. The lesson of all this is that the epigenetic paradigm-busters are as poor in their grasp of history as they are in their grasp of genetics. – MC
You’re right about the “will”. Though it has also often been described as a theory of change due to “use and disuse”. I think Lamarck thought that, during use, the “will” was involved.
There is a sense in which “use and disuse” is valid. If an organ is not used, then natural selection cannot operate and deleterious mutations can accumulate. Then the organ will generally degenerate: human tails and cavefish eyes for example. On the other hand, for a heavily used organ like the human brain or the cheetah’s muscles, natural selection can provide progressive improvement.
I was recently re-reading the relevant bit of the Origin, and I started to wonder if this was where Darwin was heading. His endorsement (in the sixth edition) of the inheritance of acquired characteristics is hardly enthusiastic:
Nevertheless, I do regard Lamarck as an evolutionary hero. He was the first to propose a full-length evolutionary theory. He got important things right, such as the graduality of evolutionary change. Of course, he got other important things wrong. I think it was inevitable. The knowledge available at his age allowed that much. And his mistakes were honest, unlike those of today’s Templeton moochers. Therefore, I am not giving him to them; I am claiming him for our side.
Lamarck was also a pioneer of cell theory, but almost nobody gives him the credit.
I’d agree with that. And I think it likely that Lamarck’s theory – wrong though it was in some details – was plausible and comprehensible by the average person and so established ‘evolution’ as a concept and paved the way for Darwin.
cr
Unfortunately, claiming to be a ‘misunderstood genius’ will always attract adherents.
Environmental conditions causing heritable changes in DNA used to be called “mutagenic.” Now they’re all Lamarckian and shiny and wondrously “epigenetic.” Evolution does indeed work in mysterious ways!
Let’s hope this isn’t prelude to an outbreak of neo-Lysenkoism in Putin’s Russia.
I’m curious, Jerry, as to why various people who otherwise understand evolution are continually trying to make this ridiculous “paradigm shift” happen. Is it so they can be famous if it does? That doesn’t seem likely for most of them, as writing a couple of articles in support of it doesn’t seem likely to boost one’s career much if this shift occurs. What other reason could there be? Are they simply misguided? Has this become a sort of cult phenomenon within the scientific community surrounding evolution?
Regarding the example of giraffes or other possibilities of “proving” this theory, one would think these people could find demonstrative bones or fossils spanning a small time period to support their theory…if it was correct.
SJWs loathe the idea that some individuals have inherent (i.e., genetic) advantages over others. All inequality is the fault of ‘systemized’ cultural oppression. Or at least ‘toxic’ environments disproportionaly endured by the oppressed.
Massimo Piglucci is a prominent ‘new synthesis’ advocate whose politics dictates his science. There’s another guy who does this too, a school teacher in the midwest, whose name I can’t remember.
I really wonder how one would seriously think that SJWs are behind epigenetics…
The term “SJW” is like the term “postmodern”.
They are drawn to epigenetics, misinterpret and misapply it. Not unlike how new-agers glom onto QM.
In Michael Skinner’s case it’s influenced by Templeton Grants
Plus “paradigm shifters” = Stronger grip on the academic greasy pole
Ah, well there it is! There’s no shortage of people willing to sell their authoritative position for sweet, sweet cash.
Does anyone think that environmental conditions could exert these 2-3 generational effects consistently over a period of time thus altering phenotypes to correspond to transient, or not so transient, environmental conditions without affecting the underlying genetic material? It’s something I can imagine, but I have no idea, and certainly, no data, to suggest it’s a real thing. My problem with the idea is that I’m struggling for an environmental agent that could do this that’s not a man made toxicant/environmental estrogen.
Jerry: Damn, you’re good. Even I (a lawyer) appreciate the sense you make out of complexity — and, with a bad finger, no less.
A fat bank account, land holdings has or could have more of a role in genetic fitness and passing on traits… inheritance of another kind!
It can certainly outlast epigenetic three generational qualities if the receiver is prudent and disposed to a family life.
Actual Lamarckian evolution is a consequence of hypermutability. It’s how our B lymphocyte populations evolve. Although, obviously, those populations don’t continue in time after our demise, they do offer a mechanism. The role of hypermutable sites has also received attention in bacteriology. See, for example, thie (somewhat overwrought) 2000 review.
Well, Lamarckian evolution would be far more efficient, probably by orders of magnitude, than the extremely indirect, ‘noisy’ (in signal processing terms), interference-prone feedback mechanism that is Darwinian evolution.
Which raises an argument against the deistic (?) idea that ‘God set it up and just let it run’ – if God was that smart, he should surely have included a mechanism for Lamarckian feedback in His creation. Not to do so is a defect comparable with all the other bits of defective design that people have pointed out.
cr
JOHN TEMPLETON FOUNDATION: Grants to Michael Skinner as Project Leader, Washington State University, 2014
[1] Pilot Project: Role of Epigenetics in Evolutionary Biology: Darwin’s Finches Model
$215,870
[2] Molecular Etiology of Epigenetic Transgenerational Inheritance of Disease
$2,587,500
I would also like to point out that some of Aeon’s ‘partners’ are funded by Templeton. Thus an author can be funded indirectly via a partner.
An example of that is a recent crap ‘Cold Fusion’ article on Aeon that was funded by the Centre for the Study of Existential Risk @ Cambridge University. CSER was/is funded by Templeton. CSER are a partner of Aeon.
There are others I think…
https://aeon.co/partners
Any idea of Skinner’s position on unit(s) of selection? He talks a lot in terms of species and individuals.
Nice article. This site often posts articles and images about mimicry. That’s not only a captivating feature of evolution but also highly ubiquitous and I believe it quite valuable when it comes to help debunking Lamarckism. I would like Mr. Skinner to explain how the environment influences the DNA of an organism to achieve mimicry. What could the actual mechanism by which the environment (“presence of other organisms nearby”) alters an organism’s DNA to give it the trait of “looking like other organisms nearby” be? What chemical or physical effects could possibly “similarity with organisms” have on another organism for it to resemble them? And yet the results we see are so profound and tangible. I could grudgingly contemplate the idea of toxins or muscular use or nutrition be catalysts for some kind of physical DNA alteration, but “resemblance to other organisms” as a physical mechanism of the environment? I don’t think so.
@Eduardo There’s a flow chart in the Aeon article that includes the bit that Skinner is plugging
Anything not explainable by his ‘Paradigm Shift’… he’ll point you at the natural selection part of the chart I’m sure
Perhaps, but as I said, the case of mimicry shows such profound and tangible results as a mechanism for adaptive trait generation simply by Darwinian natural selection that in my view makes it a powerful argument against Lamarckism.
Well, in theory, both could operate. That is, even if Lamarckist inheritance was a fact, that wouldn’t preclude Darwinian natural selection from happening as well (in aspects where Lamarckism was neutral or inoperative).
cr
Nautilus Magazine, another Templeton-funded “science” project, recently launched a campaign to get into as many schools as possible.
Science wrapped around mushy piety.
Reblogged this on The Logical Place.
Likely a naive view due to recent study, but what Skinner describes is the transcriptome which is both a great complement to understand the genome and its evolution and a lot less well understood. There are red flags raised in analysis of sequencing data which speaks of minor but pervasive , not well understood bias. Which is in principle – but perhaps not in practice – problematic for an epigenetic biased Lamarckian interpretation. Skinner’s episodic epigenetics can perhaps best be interpreted as an amplified, prolonged environmental response.
I try to actively stay away from Aeon (and Nautilus and NASA’s astrobiology blog). Sooner or later my reading becomes too inundated by apologetics. I will just repeat my longstanding interpretation why that is:
“In this homework assignment written for a Social Science Research Council consultation, I reflect on recent digital work on religion.
I decided to ground my reflection on the frontiers of digital work on religion in a discussion of two publications that have emerged over the past year that both seek to bring science writing to new publics. I chose these two publications not because I think these publications are “the most exciting and productive” examples of such work — they may or may not be — but because they appear to make interesting case studies of work being done to bring together digital media and religion. The two publications, Aeon and Nautilus, are, as I mentioned, science publications, but both are set up in a way that ensures religion is among their chief areas of interest. …
[On Aeon:]The founders are Paul and Brigid Hains, an Australian couple. Paul is the son of one the richest people in Australia, the hedge fund manager David Hains, whose net worth according to Forbes is two billions dollars.
Commented Brigid Hains at the time of the launch,
We believe that there is a need to find new ways to talk about the ideas, values and beliefs that make us tick. Recruiting insightful writers, with a deep understanding of their subjects is the best way to get that started.
Not long before Aeon launched, the Hains set up a charity called “The Touchstone Trust for Education” in the UK. According to the deed, the charity makes grants to support, among other things, “artists and researchers who are working on projects exploring contemporary beliefs, values and rituals.” Given the close fit between the Trust’s mission and Aeon’s goals, it’s not a big leap to assume that the Trust funds the work of Aeon. (According to the site of a London freelancers association, writers for Aeon are paid by the Trust.)
Aeon publishes long-form articles in five thematic areas:
World Views
Nature & Cosmos
Being Human
Living Together
Altered States
The first articles published by Aeon include an article on the New Atheism by the philosopher Michael Ruseand an article on Western Buddhism by the British writer Tim Lott. Recently Aeon also published a widely-read article by philosopher Graham Priest discussing surprising parallels between ancient Buddhist philosophy and modern Western mathematical logic. …”
[ https://www.jboy.space/log/ssrc-digital-media-reflection.html ]
I am puzzled about the way epigenetic changes are lost. Is it a fixed probability of loss in each generation, similar to radioactive decay? It is difficult to think of a mechanism that would allow persistence of the changes for 3 generations, followed by loss.
Let me assume that everything Mr Skinner has written is correct.
Epigenetics and evolution are now equal partners.
What does Mr Skinner and the Templeton Foundation “get” out of this?
To me their reasons may be far more important than this hypothesis.
Errm, how about “So Darwin was NOT completely right, therefore Darwin was fallible, therefore Evolution is shaky, therefore God” ?
There seem to be two different issues at play here.
First, germline toxicology resulting in heritable pathogenesis, stemming from an adverse germ cell exposure triggering heritable molecular alterations short of an outright change of nucleotide sequence.
Second, the implications for evolution over the long term.
I’m wondering if Dr. Coyne accepts the possibility of the first, but just not the second, as he says, “What we see here is an epigenetic change that is not adaptive (it reduces fertility) induced by a toxin. The important thing is that it was observed to last for only three generations….”
Neither Aeon nor Nautilus seem to have any standards about what they publish other than “sensationalism.” Unless you know the author by reputation, suspicion is called for.
When I read this piece, I though the ‘central dogma’ and the Weismann barrier was the same thing. Even though they are related to this issue of Lamarck and epigenetics, wikipedia tell us they’re not the same thing.
Professor Coyne (or anyone with a better grasp than me 🙂 , could you clarify better than wikipedia the difference between the Weismann barrier and the central dogma of mol. biology?
Thanks in advance
The central dogma is about the direction of template synthesis (based on its mechanism): nucleic acids are both templates and products, proteins can be only products and never templates, therefore genetic information is transmitted from the nucleic acids to the proteins.
The Weismann barrier is about the separation between somatic and germline cells in the animal organism.