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51x-WwY-sAL._SX387_BO1,204,203,200_ Periodically I get frankly stupid comments that seem to imply that the incredible swell of results coming out of molecuar genetics and genomics are revolutionizing our understanding of evolutionary and population genetics. Over the past generation it’s been alternative splicing, then gene regulation and evo-devo, and now epigenetics is all the rage. The results are interesting, fascinating, and warrant deeper inquiry (I happen to see graduate school admission applications for genetics, and I can tell you that conservatively one out of three applicants mention an interest in epigenetics; the hype is grounded in reality, as epigenetics may be a pretty big deal in human health that we can effect).

But these fields don’t tear down the bigger picture of evolutionary and population genetics in terms of what they teach us. It is not a revolution (see Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life for a dissenting take, but note that the authors are minority voices). Unfortunately the belief that everything has changed is widely held. I can understand why and how social scientists who wish to downplay classical heritability of traits would latch upon epigenetics (it’s this decades’s gene-environment interaction), but even biologists outside of genetics have told me in conversation that they assumed that the fields of evolutionary and population genetics has been “revolutionized” and the textbooks had to be “rewritten” (these are real words/phrases). Now mostly it’s because of epigenetics.

My patience with this sort of thing is minimal at this point. I’ve had to deal with it so much that I’ve written several “why genetics has not been revolutionized” posts. And here’s another. The media certainly isn’t helping by hyping so much. Rather soon we’ll see someone writing about how epigenetics is “disrupting” evolutionary biology like Uber is disrupting transportation! About ten years ago I remember trying hard to convince a producer on a public radio show out of doing a segment about how epigenetics was changing everything we knew about evolution. I just didn’t believe it was the case. He was frustrated, but thankfully he didn’t just go and just find people who wanted to say what he would have preferred to have been said on air. (and I’m sure he checked in with several people and they all came back with the same feedback)

The most recent edition of the closest thing that I know of to a Bible of population genetics, the venerable Hartl and Clark text, is nearly ten years old. In the last edition there was a chapter on “population genomics,” a field which really didn’t exist for the earlier editions. But I doubt that “population epigenomics” will be added for the next edition. Not because it isn’t potentially something important or research-worthy, I just don’t think that it will be a necessary part of every population geneticist’s toolkit (in contrast, pretty much all population geneticists who work with empirical data are going to become genomicists, if they aren’t already).

41PHSZN6AEL In science the word “revolutionary” is a big deal. Genomics has not revolutionized evolutionary and population genetics, so I definitely don’t think epigenetics has revolutionized these fields. There’s a reason that The Genetical Theory of Natural Selection, written by R. A. Fisher in the 1920s, is still useful reading for someone interested in evolutionary and population genetics. Fisher’s fusion of Mendelian genetics with evolutionary theory (along with the efforts of Sewall Wright and J.B.S. Haldane) allowed for the development of a formal field which could extend beyond verbal logic and empirical description. Perhaps the second major revolution to identify in the 20th century would be the emergence of molecular methods in assaying genetic variation after the work of Lewontin and Hubby. Though genomics has resulted in a quantitative increase of data on the orders of magnitude beyond what was available with allozymes in the 1960s, my own judgment is that the top-level inferences from the earliest results using coarse molecular markers have not been overturned as much as refined and specified. Genomics allows for a scaling up of the empirical possibilities, but it is a matter of extension more than doing something new under the sun.

5190MX7FYQL._SY344_BO1,204,203,200_ As with many things much of the confusion has to do with semantics. In his book The Darwin Wars Andrew Brown makes a distinction between thinkers who conceive of an ‘analytic gene’, as opposed to the more concrete sort favored by molecular geneticists today. By the latter, I mean a specific sequence mechanistically bound together in what we would today term a ‘genic region,’ transcribed and (a subset in many cases) translated into proteins. Though those with a fidelity toward the latter definitions often imply that their views are more concrete and adhere more to reality, it is important to note that the foundations of Mendelian thought are fundamentally about analysis as opposed to mechanism. There is a reason that a core textbook for introductory genetics is titled Genetic Analysis. Genetics began as inferences about the nature and character of inheritance from observed patterns, not by understanding molecular biological mechanisms. Mendelian genetics flourished 50 years before the final understanding of its molecular basis in DNA. Evolutionary biology emerged as a field 50 years before genetics as we understand it emerged.

Why? Let me quote two passages. First, from Dan Dennett in Darwin’s Dangerous Idea:

 

Darwin’s ideas about the powers of natural selection can be lifted out of their home base in biology. Indeed, as we have already noted, Darwin himself had few inklings (and what inklings he had turned out to be wrong) about how the microscopic processes of genetic inheritance were accomplished. Not knowing any of the details about the physical substrate, he could nevertheless discern what if certain conditions were somehow met, certain effects would be wrought. This substrate neutrality has been crucial in permitting the basic Darwinian insights to float like a cork on the waves of subsequent research and controversy, for what has happened since Darwin has a curious flip-flop on it. Darwin, as we noted in the preceding chapter, never hit upon the utterly necessary idea of a gene, but along came Mendel’s concept to provide just the right structure for making mathematical sense out of heredity (and solving Darwin’s nasty problem of blending inheritance). And then, when DNA was identified as the actual physical vehicle of the genes, it looked at first (and still looks to many participants) as if Mendel’s genes could be simply identified as particular hunks of DNA. But then complexities began to emerge; the more scientists have learned about the actual molecular biology of DNA and its role in reproduction, the clearer it becomes that the Mendelian story is at best a vast oversimplification. Some would go so far as to say that we have recently learned that there really aren’t any Mendelian genes. Having climbed up Mendel’s ladder, we must now throw it away. But of course no one wants to throw away such a valuable tool, sill proving itself daily in hundreds of scientific and medical contexts. The solution is to bump Mendel up a level and declare that he, like Darwin, captured an abstract truth about inheritance. We may, if we like, talk of virtual genes, considering them to have the reality distributed around in concrete materials of the DNA)….

51k+5+6j9OL._SY344_BO1,204,203,200_The Origin of Species is a rich and worthwhile read even today 150 years after its publication. Evolutionary ideas are as old as Western philosophy, and they were in the air during Darwin’s time. The reason we remember his theory is that it had a precise rigor and mechanism attached to its explanations of the empirical reality around us. In particular, the concept of natural selection driving adaptation upon heritable variation. A major lacunae, as noted above, was that Charles Darwin did not posit any plausible mechanism of maintaining variation. The attempts in The Origin of Species were reaches, and from what I recall there were multiple shifts in emphasis across the editions of this book. Without discrete particulate Mendelian inheritance the variation that was the raw material for natural selection disappeared. But observe that all that was necesssary was a system of inheritance where variation was maintained. If on an alien planet the substrate of inheritance was different in fundamental molecular configuration from DNA one would still be able to posit a theory of evolution in whose general outlines are Darwinian, because the ultimate input of heritable phenotypic variation would remain the same.

Second, W. D. Hamilton in Narrow Roads of Gene Land: Volume 1:

…I had made the decision that I would not even try to come abreast of the important work that was being done around me on the molecular side of genetics. This might well be marvelous in itself: I admitted the DNA story to concern life’s most fundamental executive code. But, to me, this wasn’t the same as reading life’s real plan. I was convinced that none of the DNA stuff was going to help me understand the puzzles raised by my reading of Fisher and Haldane or to fill in the gaps they had left. Their Mendelian approach had certainly not be outdated by any of the new findings.

51XHYubQzNL._SY344_BO1,204,203,200_ In case you are not aware of who W. D. Hamilton was, he was arguably he most influential evolutionary biologist of the second half of the 20th century (there are other contenders, but Hamilton’s name has to be in the mix). The idea of inclusive fitness was the fruit of his inquiry into the “problem of altruism” (a problem that the famed medical geneticist Lionel Penrose summarily dismissed as worthy of financial support according to Hamilton, who had a project relating to chromosome biology lined up for his potential mentee). As it happens molecular genetics, or more precisely its descendant, genomics, has taken some interest in Hamilton’s ideas even if he didn’t take quite an interest in it. The ubiquity of selfish genetic elements may be understood as an extension of Hamiltonian inclusive fitness dynamics at the intra-genomic level (there are other arguments, see Michael Lynch’s Origins of Genome Architecture). And many of the predictions that Hamilton’s formalism made in regards to the nature of the origins of sociality and sex are best explored with molecular genetic assays.

51zeajUmWhL._SX316_BO1,204,203,200_ Finally, I want to bring to your attention R. A. Fisher’s 1941 paper Average Excess and Average Effect of a Gene Substitution (the link is not gated). Fisher was writing before DNA. His conception of a gene was analytic by necessity (though by his period it was understood that genes were resident on chromosomes). That is, he was imagining a unit of inheritance characterized by alleles. Today we often think of a defined genetic sequence as this unit of inheritance, and alleles are usually assumed to be changes on a single base pair of DNA, a single nucleotide polymorphism (though there are other types of genetic variants, such as copy number variants). But these are not necessary to work out the basics of evolutionary genetics, as is clear from the fact that Fisher, Haldane and Wright managed to do so before comprehension of mechanistic details (though as a physiological geneticist Wright thought more mechanistically, and that might explain why he was right and Fisher was wrong in regards to the reason for the existence of genetic dominance). Fisher used terms like “allelomorphs”, and many of the characters he was familiar with would have been tracked through correlations of phenotypes. In an abstract and fundamental sense an allele is just a variant segregating in the population. It could be a SNP, or a CNV, a microsatellite, or an indel. Or it might also be a regulatory element. Fisher and many of his colleagues only postulated the allele after seeing the association between phenotypic marker and the novel trait (known markers had positions on the genetic map); they were often ignorant of the detailed biophysical basis for the variation.

41ZhyEU5lGL._SY344_BO1,204,203,200_Average effects and average excesses, keys to quantitative genetics, and underlying Fisher’s model of evolutionary change over time, have within them the richness to absorb the myriad mechanistic details cascading out of modern molecular genetics and genomics. If you read him closely it is clear that Fisher did not assume the sort of deterministic relationship that some of his critics impute to him. He understood penetrance, as did all geneticists long before the vagaries of gene expression and epistatic interaction were elucidated in their mechanistic details. But over the long haul the average effect of a substitution in the population is critical. Understanding the nature of the average effect gets you much of the way in this game, if not all the way.

There are some Christians who assert that their religion is the natural completion of Judaism and Greek philosophy.* There are others who rather argue that Christianity was a radical revolution against all that came before. Historically the latter has been a minority view. The Marcionites failed, and the Jewish origins of Christianity were sewn into the fabric of its foundational scripture in the form of the Old Testament. And despite periodic revolts, the reality is that intellectual Christianity speaks with a Greek philosophical voice. Ultimately this debate is of purely academic interest for me. But it exhibits a similarity with academic arguments and debates. In Endless Forms Most Beautiful: The New Science of Evo Devo Sean B. Carroll takes a traditionalist approach which suggests that novel 61DFNJkqyGL._SX331_BO1,204,203,200_ results from the new field of evolutionary developmental biology firmly supports and extends the Neo-Darwinian Synthesis. Carroll’s book is under 400 pages. It is elegantly written and economical of prose, and it proposes an evolution in our thinking about the nature of the variation which serves as the raw material for natural selection. Contrast that with the late Stephen Jay Gould’s The Structure of Evolutionary Theory, which came in at nearly 1,500 pages. Published in the early 2000s, much of it was written earlier. There are only two references to epigenetics within it. If Gould had not died in 2002 he would probably have come out with a new revised edition by now, and I’m rather confident that epigenetics would loom very large indeed. Though Sean B. Carroll is a very eminent scientist, he remains a bit player on the public intellectual scene. That’s because he does not promise revolution, he comes bearing a twist on the orthodoxy. In contrast, Gould’s prolix prose was rich with the promise of paradigms shattered and lost, and grand visions of heretics risen up to prophetic status, as the statues of the grand old men of the Neo-Darwinian orthodoxy were torn down to make way for the new idols (this old Paul Krugman slap at Gould is pretty on point about why he was so popular in the 1990s). Reality is more prosaic than intellectual revolts plotted in used bookstores!

Carroll’s ended with a quotation from Charles Darwin because his espousal of a particular theory in regards to evolution was in no way contradictory to the spirit of The Origin of Species. Endless Forms Most Beautiful was a paean to Darwinism, properly conceived. Charles Darwin was no dogmatist in regards to the origin of variation, though he was blind to the possibility that Mendel’s experiments provided. I doubt he would have taken much umbrage at Sean B. Carroll’s update to the canon, as its genetic nature postdated him by decades. Some of the original Mendelians had arrayed themselves against the biometrical school, which considered itself a custodian of Charles Darwin’s thought during the period when classical evolutionary theory was somewhat in decline (see The Eclipse of Darwinism: Anti-Darwinian Evolution Theories in the Decades around 1900). But as told in Will Provine’s The Origins of Theoretical Population Genetics the conflict was short lived, and the synthesis which emerged from the debates of that period laid the basis for modern evolutionary biology, a field far richer and more robust than during Darwin’s own time.

And I may be wrong here as I’m no historian of Watson and Crick’s discovery, but I don’t see that they thought of themselves as overthrowing Mendelianism, as opposed to putting it on a firmer molecular and biophysical basis. A comprehension of the biological machinery within the synaptonemal complex only enriches and extends our understanding of the nature of Mendelian process.

Quantum mechanics was a revolution in physics because it introduced a whole domain of understanding which operates outside of the purview of classical physics, parallel to it to this day. The modern project of unification and reconciliation continues and is unfinished. In contrast Darwinian evolution, Mendelian genetics, and molecular genetics extend and complement each other. If quasi-Lamarckian heritable epigenetic patterns within the genome were so powerful and ubiquitous as to overturn a Mendelian understanding of heritability, then the Mendelian model of inheritance would not have been so persuasive and crystal clear in the first place in the analyses of the Fly Room. If our understanding of evolution and genetics was contingent on perfect understanding of the molecular mechanisms and machinery by which evolutionary processes occur, then we’d have been at a loss before 1952 (in actually, 1952 was only the start in any case). We weren’t in the wilderness, because understanding can manifest itself at multiple layers of abstraction and complexity. Just as a deeper understanding of neuroscience can only benefit psychology, so a deeper understanding of biophysical phenomena such as epigenetics will only enrich our understanding of evolutionary and population level dynamics. There is no revolution in evolution. At least until we get better with CRISPR….

* This is a general trend. Some Chinese Christians have argued that the religion completes and complements Confucianism, while Karen Christians point to similarities between Christianity and indigenous religious beliefs.

 
• Category: Science • Tags: Epigenetics, Genetics 
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Epigenetics is real. But it doesn’t change everything. That needs to be said, because people seem to get the impression that everything is changed. In Trends in Genetics, Serving Epigenetics Before Its Time:

Society prizes the rapid translation of basic biological science into ways to prevent human illness. However, the premature rush to take murine epigenetic findings in these directions makes impossible demands on prospective parents and triggers serious social and ethical questions.

In their efforts to anticipate the eventual human applications of emerging areas of science, scholars of the ethical, legal, and social implications of genetics and genomics sometimes become too speculative to engage the immediate concerns of active scientists and policymakers. However, although evidence-based applications of human epigenetics may emerge in the future, premature epigenetic risk messaging is already here and its content and impact must be understood. The messages in circulation raise ethical and social concerns regardless of whether human epigenetic studies eventually confirm the murine results. Because the prospect for any successful human translation of epigenetic research depends as much on the management of these issues as on further human studies, they deserve close attention by all involved in their design, dissemination, and public consumption.

(the link is ungated)

 
• Category: Science • Tags: Epigenetics 
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Epigenetics is making it “big time,” Slate has a review up of the new book Epigenetics: The Ultimate Mystery of Inheritance. In case you don’t know epigenetics in terms of “what it means/why it matters” holds out the promise to break out of the genes → trait conveyor belt. Instead positing genes → trait → experience → genes, and so forth. Or perhaps more accurately genes → trait × experience → genes. Epigenetics has obviously long been overlooked as a biological phenomenon. But, I think the same could be said for the ubiquity of asexual reproduction and unicellularity! Life science exhibits anthropocentrism. That’s why there’s human genetics, and biological anthropology. My own concern is that epigenetics will give some a license to posit that the old models have been overthrown, when in fact in many cases they have been modified on the margin. Especially at the level of organisms which we’re concerned about; human-scaled eukaryotes. Humans most of all.

The last paragraph in the review highlights the hope, promise, and perils of epigenetics in regards to social relevance:

It’s almost enough to make one nostalgic for the simplicity of old-style genetic determinism, which at least offered the sense that the genetic hand you were dealt at birth was the same one you would play your whole life—except that epigeneticists hold out the promise that the blessings of a single life, too, can be passed on. Disease researchers, Francis reports, have hopes that the effects of abnormal epigenesis may be reversed. For example, it’s possible that the damage caused by many cancers is epigenetic. If those epigenetic attachments can be altered, then it’s possible the cancer can be stopped. Still, even if we are discovering that an extraordinary range of conditions may be epigenetic, not all of them are. There are still specific diseases that follow a deterministic path. If you are unlucky enough to draw the Huntington’s mutation in the genetic shuffle, you will develop the disease. Francis rightly emphasizes the wonder of epigenetics and the molecular rigor it brings to the idea that life is a creative process not preordained by our genome any more than it is preordained by God. Yet even as epigenetic research invites dreams of mastery—self-creation through environmental manipulation—it also underscores our malleability. There is no easy metaphor for this combination. But if we must have one, we should at least start with the cell, not the gene. The genome is no blueprint, but maybe the cell is a construction site, dynamic, changeable, and complicated. Genes are building materials that are shaped by the cell, and they in turn create materials used in the cell. Because the action at the site is ongoing, a small aberration can have a small effect, or it can cascade through the system, which may get stuck. Recall that your body is a moving collection of these building sites, piled in a relatively orderly way on top of another. Malleability? It’s an ongoing dance with chaos, but, incredibly, it works.

If people have a hard enough time with the concept of heritability, I have no idea how they’ll deal with heritability of epigenetic modifications! In science itself epigenetics has really come to the fore over the last 10 years. Here’s a plot which shows the change over time in the scientific literature:

And here’s the Google Trends results:

Either the media only discovered epigenetics in 2008, or Google’s index wasn’t very good. I suspect the former, as I started being asked about the term by intellectual non-science types circa 2008. For Google Correlate “epigenetic” and “subjective” have a correlation of 0.91, and “epigenetics” and “we create” have a correlation of 0.89. These are a little disturbing, and I hope epigenetics doesn’t go the way of quantum theory and general relativity and become abused in other disciplines. For example, “epigenetics means that genetic inheritance is a subjective fiction!”

(Republished from Discover/GNXP by permission of author or representative)
 
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A reader who goes by the handle “biologist,” and happens to be a molecular geneticist by training, states more clearly what is probably close to my own position (though he is far more well informed) in the comments below. I think it’s worth promoting:

As far as I can tell, the existence of epigenetic mechanisms doesn’t change anything that we *should* have already known about the social implications of genetics (i.e. what people care about).

Quantitative genetic methods that estimate a substantial contribution of genetic variation to phenotypic variation do not now and has never told us anything about actual or counterfactual causal mechanisms involved. They have also never told us much about development other than what we already knew must be true — there will be genes involved in some way.

Nothing we’ve learned in the last 30 years about molecular biology makes any difference at a general level to those conclusions. What it mostly does is make clearer that the causal mechanisms behind phenotypic variation in complex traits are probably themselves really really complex.

As soon as you realize that complex traits have non-Mendelian inheritance patterns — something that’s been abundantly clear for many many decades — everything else follows and epigenetics only adds new dimensions to the causal mechanisms that might be involved.

Whether a trait is amenable to manipulation (and at what stages of development) is an interesting and very challenging question, but there’s no revolution in our understanding of biology involved in asking it. The only way to see a revolution is to ignore all of the incremental changes in understanding that have happened between decades.

Just to be clear, this is not a very mature sounding 12 year old. The commenter above is a biologist with whom I am personally familiar and whose opinion on this topic I value because not only do they grasp molecular biology in its fine-grained details, but they are very familiar with quantitative and behavior genetics (a rare combination). I can probably transfer some of the same general cautions about epigenetics that I brought up with Jim Manzi in relation to epistasis several years back.

The great thing about science is that this likely won’t be a debate 10-20 years from now. If you have an equation of the form:

A[genetics] + B[epigenetics] + C[environment] → Outcome

The scalars A, B, and C will be known with more precision as science progresses. Or more accurately, their values will be known for the range of outcomes which we find of interest. Our current surfeit of commentary is a function of mystery and uncertainty.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Epigenetics, Genetics, Genomics 
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A quick follow up to my post Epigenetics arise! Adam Keiper, the editor of The New Atlantis, has graciously sent me a copy of the article, Getting Over the Code Delusion. I’ve also been told that the piece will be free to all on the website at any moment, so I invite readers to check it out when that occurs [it's online].

First, I want to add that Mr. Keiper doesn’t believe that the Wikipedia entry for The New Atlantis is particularly accurate. William Kristol for example has never been published in The New Atlantis, while the Wikipedia entry says he has. I would add though that many of the people associated with the magazine may broadly be considered “conservative.” Not that there’s anything wrong with that, I too may broadly be considered “conservative”! Others associated with the publication, such as Robert Zubrin, are not known for their politics from what I know.


As for Steve Talbott’s essay, it’s a peculiar beast. It weighs in at 25 pages, but it’s only the first of a series. Getting Over the Code Delusion is to a large extent a primer on molecular genetics, cytology, and genomics for the uninitiated. That’s a tall order. It’s really hard to avoid pitfalls of oversimplification in the space provided, so I’ll let readers judge where Talbott misleads or misunderstands in the details. Another definite aspect of the piece which is a bit out of the ordinary is its literary quality, which one does not usually find in primers of this sort. Consider:

…Noncoding DNA could provide the complex regulatory functions that direct genes toward service of the organism’s needs, including its developmental needs.

That suspicion has now become standard doctrine….

I think coventional technical writing would have avoided a word like “doctrine” (and I think it also misleads as to the disputes around issues such as the importance of cis-regulatory elements, which are not quite settled). But Talbott’s audience does not necessarily consist of individuals who get Science and Nature in the mail every month (or have academic access). So a more thorough judgement probably will have to await the whole series.

But I think I can already glean the gist of where Talbott is going: he wants to dethrone the centrality of the genetic sequence in our understanding of how life emerges and is specified. He is right to point out that debates about the importance of gene regulation, higher order genomic structures, and epigenetics, throw a monkey-wrench into a cool reductionist system where the mapping between genotype and phenotype is going to be easy to unravel. In this Steve Talbott is following many others who have objected to the image of genes as “puppet masters” which control our destinies. Included in this set is Richard Dawkins, who felt that the publicity materials around The Selfish Gene, and misunderstandings by other academics, resulted in a distortion of his underlying message. But in any case the science is still very much in flux. The old order may have fallen, but nothing has risen to replace it. Talbott nicely reminds us that 20 years ago mainstream scientists were engaging in genetic triumphalism with the success of family based linkage studies in adducing variants associated with recessive diseases such as cystic fibrosis. But my main worry is that the triumphalists of our age are again speaking too soon. Science is always full of surprises.

Addendum: One impression I get from Getting Over the Code Delusion is that the author is eliding the distinction between deterministic processes understood on a molecular genetic scale, and statistical associations on the scale of populations and the level of genomics. Prediction need not be conditional on perfection, and clearly systematic patterns and processes can emerge from a seemingly chaotic welter. That’s what developmental genetics certainly teaches. Also, early in the piece Talbot seems to be diminishing the importance of the sequence identity between the chimpanzee and the human, asking that “…we could have done the obvious and direct and scientifically respectable thing: we could have observed ourselves and chimps, noting the similarities and differences.” I think this sort of common sense objective phenetics when it comes to humankind’s closest relatives is not so easy to come by. A history of the taxonomic and evolutionary confusions as to the nature of relations among the homonid lineage are such that this was one area where phylogenetics informed at the sequence level was very useful. Perhaps it’s been overplayed, but it was, and is, a very significant finding, and the perceptions of broad phenotypic differences don’t refute that reality.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Epigenetics, Genetics, Genomics 
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