Does evolutionary theory need a rethink?

[starlarvae]

http://www.nature.com/news/does-evolutionary-theory-need-a-rethink-1.16080 This link goes to a recent article in Nature magazine, in which a group of scientists working in various areas of evolutionary biology propose that evolution theory -- the Modern Synthesis -- needs to be reworked, because so many new discoveries don't fit neatly into the current model. What do you think? Are the authors on to something, or are they over-reacting? There's also a rebuttal from other researchers who think the current model is just fine.

[CharonY]

That is actually a discussion long in the making, and it boils down to usefulness for the respective sub-disciplines (IMO). The modern synthesis is, actually quite old and was developed before the rise of modern molecular biology. The biggest issue is that we have so many approaches and so much data that it has become problematic to unify all those into a nice cohesive model (again, to my knowledge, but maybe Arete could comment on this).

Instead, people tend to use the basic backbone and develop specialized models for the type of question they are looking at. So the overall conceptual narrative mostly remains the same, but the complexity has reached a point where one can look at evolution at various resolutions (ranging from molecule to complex organisms) and that the applied methodologies vary for each vantage point.

[Strange]

All science is about trying to break existing theories, producing new hypotheses and testing them against the evidence. Evolutionary theory has already changed a lot since Darwin's day and will continue to do so.

 

There's also a rebuttal from other researchers who think the current model is just fine.

 

And they are working on the very topics that the "yes" group say are important.

 

It seems more to be an argument about naming: as the theory evolves, should it still be called the "modern synthesis" or "extended evolutionary synthesis". I couldn't care less.

[starlarvae]

Evolution seems to work less by changes in gene sequence or mutation of genes and more by changes in regulation of existing genes than was suspected prior to its being discovered. Would you say that this Is a significant or a superficial modification of the Modern Synthesis?

[CharonY]

Superficial at best. Also changes of regulation are typically changes of sequences- either in non-coding regulatory sequences or the regulators themselves (or due to duplication events, etc.).

None of which is different from the canonical view.

[starlarvae]

I find it interesting that, as a result of developments in evo-devo, such as changes in regulation being granted considerable responsibility for the differentiation of species, evolution comes to look more like a process of development (phylogeny comes to look more like ontogeny). During the development of a complex organism, the genotype of the zygote gives rise to the variety of cell types that makes up the organism's body, by way of regulation of the cells' shared genotype. There's enough conservation of DNA during evolution, underlying the diversity of species, so that at least some commenters are willing to write about the "universal genome" (e.g., https://www.landesbioscience.com/journals/cc/shermanCC6-15.pdf ), which would correspond to the "universal" genotype shared by the cells in a body. Haekel came close with, "ontogeny recapitulates phylogeny" but not close enough. Maybe phylogeny just is an ontogeny.

[Arete]

Maybe phylogeny just is an ontogeny.

 

I don't think many biologists would agree. Instead it's long been known that ontogeny itself evolves - an embryo's early development is strongly shaped by phylogeny, rather than selection.

 

http://evolution.berkeley.edu/evosite/evo101/IIIC6aOntogeny.shtml

http://en.wikipedia.org/wiki/Recapitulation_theory#Modern_status

[starlarvae]

How about these guys? You think they're going down a wrong path? http://www.thethirdwayofevolution.com/

[overtone]

 

 

How about these guys? You think they're going down a wrong path?

Their implication of scientific or intellectual equivalence between creationism and evolutionary theory is misleading and irresponsible.

 

Aside from that, new and better theory is always welcome. I've got a hundred bucks says whatever they come up with will be classifiable as neo-Darwinian theory, but it might be interesting nevertheless.

[chadn737]

How about these guys? You think they're going down a wrong path? http://www.thethirdwayofevolution.com/

 

Eva Jablonka is part of that group, so it is guaranteed that they propose an overemphasis on epigenetics. However most epigenomic differences are not epigenetic, but due to genetic differences. Jablonka has long ignored the fact that there are just very few examples of true epigenetic phenomena with any long-term effects. In short term this may play a role, but in describing the breadth of evolution, it will not.

[starlarvae]

Would you agree that, in light of, say, evo-devo and niche construction theory, evolution theory increasingly downplays the effects of environment, via natural selection -- that is, the effects of exogenous factors -- and increasingly credits endogenous factors with shaping evolutionary outcomes? That seems to be the general drift of the "Extended Synthesis" in evolution theory.

[Arete]

Would you agree that, in light of, say, evo-devo and niche construction theory, evolution theory increasingly downplays the effects of environment, via natural selection -- that is, the effects of exogenous factors -- and increasingly credits endogenous factors with shaping evolutionary outcomes? That seems to be the general drift of the "Extended Synthesis" in evolution theory.

 

I think the main issue is that, at least in the scientific field of evolutionary biology, no one has shied away from studying or acknowledging mechanisms like plasticity, horizontal gene transfer, epigenetics, regulatory changes, transposition, methylation etc. They are all actively studied and accepted as playing a role in evolution. It's not as if there's a large degree of debate as to whether there's a role for such processes or that they need to be considered.

 

Given this, does there need to be a "paradigm shift" or "new synthesis"? As a scientist in the field I don't see a need - especially as none of the additional processes negate previous ideas, they are simply additions to the processes that were considered before. If anything the synthesis of evolutionary theory has simply been ongoing.

 

There's been groups like the Arlenberg 16 who have tried to re-brand evolutionary theory, but it's generally turned out to be hype and personal investment in tenure clocks etc that's motivated it. It's hard to decree a revolution in a scientific field which as been consistently "evolving" (no pun intended) for the last 50 years.

[CharonY]

I agree completely with that assessment. Also a new theory would, in my opinion, only be useful if it is able to synthesize all those directions in a cohesive way that allows quantitative predictions.

However, the analysis of these mechanisms is split between disciplines with a lot of unknown in each area. In fact, one could argue that the complexity of the processes and their implications need to be broken down into sub-research topics as there is not enough information available to research in a unified manner.

[starlarvae]

[N]o one has shied away from studying or acknowledging mechanisms like plasticity, horizontal gene transfer, epigenetics, regulatory changes, transposition, methylation etc. They are all actively studied and accepted as playing a role in evolution. It's not as if there's a large degree of debate as to whether there's a role for such processes or that they need to be considered.

 

Given the net effect of incorporating these mechanisms into evolution theory, would you agree that the theory has, to an appreciable degree, shifted its story away from exogenous causes and given greater agency to endogenous causes, when it comes to explaining how phenotypes get to be how they get to be?

[Essay]

Would you agree that, in light of, say, evo-devo and niche construction theory, evolution theory increasingly downplays the effects of environment, via natural selection -- that is, the effects of exogenous factors -- and increasingly credits endogenous factors with shaping evolutionary outcomes? That seems to be the general drift of the "Extended Synthesis" in evolution theory.

 

No, and that is why there is no need to wholly rethink the theory, except maybe to rename it, as others have pointed out. That's all this is about; definitions! Whatever we learn about it, and however we define it, shift happens.

 

 

Given the net effect of incorporating these mechanisms into evolution theory, would you agree that the theory has, to an appreciable degree, shifted its story away from exogenous causes and given greater agency to endogenous causes, when it comes to explaining how phenotypes get to be how they get to be?

 

No, not as some Lamarkian type of endogenous factor or driver. I think what you are seeing, in these new discoveries, are new and more broadly defined ways that 'natural selection' can operate.

 

~

[Ophiolite]

I posted this before, but it seems apt. (For the creationists among you it provides evidence of non-evolution........in my thinking.)

 

What we call something is, or at least should be, less important than what it is. Our understanding of evolutionary mechanisms is still far from complete and not fully integrated. Large steps have been taken over a century and a half. Is it important to mark those steps? Important, but not necessarily essential.

Darwin's idea was accepted with suprising alacrity by the scientific community, supporting the claim by some that it was an idea whose time had come. (And Wallace served to offer confirmation to that notion.) Yet by the turn of the century Darwinism was all but dead as people gravitated to mutation and the concepts of Mendel rediscovered by Bateman, de Vries and Corren. When the two were fused in the 1930s and 40s did the resultant concept merit a new name? One could hardly call it Haldane/Huxley/Dhobzhanksy/Fisher/Simpson/Stebbins/Wright/Mayrism, so the Modern Synthesis was born.

And now, more than half a century later, we've learnt even more about the mechanisms and processes, so much more that some people think a new name is in order. Is it?

I said at the outset that what we call something is, or at least should be, less important than what it is. But is this true? Darwin may have been the right man in the right place at the right time, but he ignited a revolution that is arguably of greater scientific importance than any other. His handful of principles still lie at the heart of evolutionary thought, so my view is simple. Let's just call the current hypothesis and those that will develop in future, Darwinism. Direct, concise, effective.

And it has the secondary advantage that it will piss off the creationists.

[sialic acid]

Yes, evolution and the way we understand life needs a complete overhaul. Genetics may be the blueprint of life, but it does not directly encode and contain information about how entire metabolic and proteomic networks interact together to regulate life. Genomics misses a higher level of systems biology that defines life.

 

Darwinian evolution and classic thoughts about genetics and evolution have some very, very profound questions that are difficult to answer. For example, if it takes a mutation and at least one generation for this mutation to be passed down, how then can humans defend themselves against most infections from bacteria and other pathogens if pathogens can replicate by the billions in only a matter of a few hours? Additionally, many mutations would lead to a loss of function for proteins which would often be deleterious, so evolution on the genetic level can not explain how we are still alive today even under the constant bombardment of pathogenic assaults. We'd be wiped out in a matter of no time because evolution from pathogenic stresses would cause many deleterious mutations over time and human genetic evolution is extraordinarily slow while pathogens can replicate orders of magnitude faster. There's obviously a higher level of control outside the realm of genetics that allows human to adapt to environmental stress that also regulates many aspects of life. Our view of life is overly reductionist and the reason why genetics has failed to produce the ground breaking cures promised is because we have long ignored those mechanisms outside of genetics which regulate life at the systems level. Forever now we've ignored many other -omics fields and one of the biggest ones we've ignored until about the end of the 20th century is the role that carbohydrates play as another essential macromolecule that truly defines life. Carbohydrates and glycomics are called now called the "3rd alphabet of life" after DNA and proteins. The DNA code and proteome is surprisingly quite small in contrast to the glycome--- the total sum of all carbohydrate structures that get added to proteins post translationally. The glycome is orders of magnitude more complex than the proteome or genome and is possibly one of the most complex entities in nature. The glycome takes proteins and completely alters their behavior ( even though the proteins have the same exact sequence) or can fine tune their activity. The same protein in different tissues or areas within the same tissue can behave differently-- and it is due to multiple glycoforms of the same protein. Carbohydrates can dominate biology, and its why glycobiology and glycomics are predicted to revolutionize medicine in the next 100 years. Almost every single aspect of the immune system is in some way regulated by carbohydrates and the glycome. Life requires fidelity AND flexibility. While DNA and proteins provide fidelity and make up the cornerstone of Darwinian evolution theories, classical evolution arguments based on DNA absolutely fail to explain many important phenomena regarding evolution, such as the example above, where we somehow have the bility to survive under constant assault from pathogens without the need for high speed genomic mutations and evolution. This is where flexibility of the human genome must come in, and this flexibility is controlled through both glycosylation and epigenetics. The glycome can be rapidly altered in response to environmental cues and stresses to significantly change the physiological function of the genome and proteome. Changes in glycosylation to modulate our immune system and fight infection allow us to survive while simulataneously allowing us to avoid mutations to our proteins that would often be deleterious and would probably cause important proteins to become inactive. DNA and proteins would be equivalent to Newtownian/classical physics while sugars and glycomics are now being viewed as basically the "quantum physics" of biology--there's simply no code to controlling the glycome, it responds in a stochastic manner, but it is significantly perturbed in many diseases and altered in ways we do understand to unlock different physiological functions of the same protein to ultimately produce a massively expanded landscape for the physiological possibilities of all proteins encoded by the genome. In much as the same way a ton of physics could not be explained until the advent of quantum/non-classical physics, tons and tons of biology can not be explained by the genetic code, classical views of Darwinism, and proteins. What lies outside of the realm of the genome and genes, such as the glycome (which is orders of magnitude more complex than the proteome), is a massive missing piece of the puzzle for understanding life and evolution at the systems level and alterations to the entire glycome, which can occur due to epigentics and metabolic abberrations, can profoundly alter the entire physiology of a cell through alteration of the glycome. Even more strikingly, new studies are beginning to show that sugar patterns from parent to offspring can even be passed down from generation to generation and gene expression alone isn't enough to explain how those sugar patterns can be passed down.

Edited November 19, 2014 by sialic acid

[CharonY]

Very long read but the first few sentences already highlight lack of understanding of basic biology:

 

 

For example, if it takes a mutation and at least one generation for this mutation to be passed down, how then can humans defend themselves against most infections from bacteria and other pathogens if pathogens can replicate by the billions in only a matter of a few hours?

 

The immune system adapts itself depending on what it is exposed to. Moreover there are variable regions in the recognition part of antibodies that get reshuffled so that mammals have a large variation of potential antigens they can potentially identify. None of them has anything to do with evolution as they happen in individuals (evolution is a population game) and on top within its life time.

 

 

 

Additionally, many mutations would lead to a loss of function for proteins which would often be deleterious, so evolution on the genetic level can not explain how we are still alive today even under the constant bombardment of pathogenic assaults. We'd be wiped out in a matter of no time because evolution from pathogenic stresses would cause many deleterious mutations over time and human genetic evolution is extraordinarily slow while pathogens can replicate orders of magnitude faster.

 

What do mutations have to do with pathogens? What are pathogenic stresses? Why would they increase mutation rates?

 

However, the single most important misunderstanding here is mixing up mechanisms that effect the physiology of a given individual and try to extrapolate evolutionary mechanisms from it.If an organisms reacts to a stress, we are talking physiology, not evolution. If we talk about mechanisms and their spread and prevalance in a given population, we are starting to touch upon evolution.

[chadn737]

What determines proteomic interactions? The specific domains of that protein and sequence of the proteins. Mutate an amino acid in a critical binding site and you eliminate.

 

What determines the lipids, the sugars, the other components of a cell? In order for a cell to have them, they have to be manufactured, moved, and combined. This is all done by the proteins present and what those proteins do.

 

What determines all of this? The DNA sequence. The DNA sequence encodes the proteins, it encodes their interaction, it encodes what products are ultimately made.

 

In the end, it ultimately reduces to the DNA sequence.

[starlarvae]

However, the single most important misunderstanding here is mixing up mechanisms that effect the physiology of a given individual and try to extrapolate evolutionary mechanisms from it.If an organisms reacts to a stress, we are talking physiology, not evolution. If we talk about mechanisms and their spread and prevalance in a given population, we are starting to touch upon evolution.

 

You are way off. You ever come across references to epigenetics? This is an growing field in molecular biology and evolutionary biology. Some stresses and other environmental effects produce epigenetic changes that regulate gene expression and are heritable and that therefore can participate in evolution.

 

Here is one of many papers on this topic:

http://onlinelibrary.wiley.com/store/10.1113/jphysiol.2014.272096/asset/tjp6184.pdf?v=1&t=i2qjfhim&s=03d1cc76a24527cb58bd2df8e3c7c34ea29b1b9a

 

If that link doesn't work, the paper is in

J Physiol 592.11 (2014) pp 2307–2317 2307

The Journal of Physiology

title : Inheritance is where physiology meets evolution

authors : Etienne Danchin and Arnaud Pocheville

the authors make their case that "non-genetic inheritance shatters the frontier between physiology

and evolution, and leads to the coupling of physiological and evolutionary processes to a point

where there exists a continuum between accommodation by phenotypic plasticity and adaptation

by natural selection."

Yes, evolution and the way we understand life needs a complete overhaul. [. . . .] What lies outside of the realm of the genome and genes, such as the glycome (which is orders of magnitude more complex than the proteome), is a massive missing piece of the puzzle for understanding life and evolution at the systems level and alterations to the entire glycome, which can occur due to epigentics and metabolic abberrations, can profoundly alter the entire physiology of a cell through alteration of the glycome. Even more strikingly, new studies are beginning to show that sugar patterns from parent to offspring can even be passed down from generation to generation and gene expression alone isn't enough to explain how those sugar patterns can be passed down.

 

Thanks for that contribution. Epigenetics is central to the new evolutionary paradigm, but as yet underappreciated by those members of the olde guard preoccupied with rooting out creationists.

[Arete]

You are way off. You ever come across references to epigenetics?

 

Epigenetics is a very loose term for a wider range of more specific processes which are heritable, but not directly attributable to non-synonymous changes in coding DNA . To infer that evolutionary biologists have not been considering regulatory functions, secondary RNA/DNA structure, methylation, etc. would simply be wrong - some of these have been studied for a long time, and their roles in evolution have been considered for just as long.

 

The reason that most scientists wouldn't consider their advent to herald a "new paradigm" is both due to their gradual inclusion in evolutionary study, and the fact that they don't overthrow the traditional model of expression, phenotype, selection - in fact the very word "epigenetics" implies that they overlay the existing genetic model. Additionally, epigenetic changes are subject to environmental selection themselves, so are consistent with existing evolutionary theory. In fact, there's a rapidly growing body of literature on the entwined roles of natural selection and epigenetic gene expression regulation in tumor growth.

 

As such, most people actively researching and thinking about contemporary evolutionary theory have long incorporated "epigenetic" changes in their interpretations.

[Endy0816]

Da, epigenetics has been talked about in the past here. From my own observations the essential workings are the same, only the means by which the information is encoded is different. Essentially the relatively set nature of DNA can work against it in shorter time frames. Makes a certain amount of logical sense, you don't update the blueprint if all you want to do is paint the house. Besides the encoding scheme everything is otherwise the same though.

 

Ideally we end up with something broader in scope we can apply to our understanding of both real and artificial evolution. Would take much of the guesswork out of existing approaches in both arenas. What factors are needed to create brittle or supple code as necessary to solve a given problem.

[chadn737]

 

You are way off. You ever come across references to epigenetics? This is an growing field in molecular biology and evolutionary biology. Some stresses and other environmental effects produce epigenetic changes that regulate gene expression and are heritable and that therefore can participate in evolution.

 

Here is one of many papers on this topic:

http://onlinelibrary.wiley.com/store/10.1113/jphysiol.2014.272096/asset/tjp6184.pdf?v=1&t=i2qjfhim&s=03d1cc76a24527cb58bd2df8e3c7c34ea29b1b9a

 

If that link doesn't work, the paper is in

J Physiol 592.11 (2014) pp 2307–2317 2307

The Journal of Physiology

title : Inheritance is where physiology meets evolution

authors : Etienne Danchin and Arnaud Pocheville

the authors make their case that "non-genetic inheritance shatters the frontier between physiology

and evolution, and leads to the coupling of physiological and evolutionary processes to a point

where there exists a continuum between accommodation by phenotypic plasticity and adaptation

by natural selection."

 

Thanks for that contribution. Epigenetics is central to the new evolutionary paradigm, but as yet underappreciated by those members of the olde guard preoccupied with rooting out creationists.

 

No, epigenetics is not central. This is my field. I work on DNA methylation and transgenerational inheritance of DNA methylation in both plants and animals.

 

The overwhelming evidence from both plants and animals is that heritable differences in either DNA methylation or Histone modifications is typically due to genetic variation. For instance, if you find a region of a genome that differs in DNA methylation between two individuals...often times there is some underlying or neighboring genetic variation that is causing this....like a new transposon insertion. In this case, what many people call "epigenetics" actually reduces down to genetics, since DNA methylation and gene expression are phenotypes of a genetic variant.

 

When the variation in DNA methylation or histone modifications are induced by environmental factors, almost never is this heritable, and even then, it is typically stable only for a generation or two. This is not enough time to have long term evolutionary consequences, at least not in anyway to require a rewrite of evolutionary theory.

 

In the field of epigenetics, we do not define it as the environment....gene x environment interactions were known prior to epigenetics and were never part of the original definition. We define it as heritable variation that is not due to underlying differences in the DNA. If that variation is caused by genetic differences...its not epigenetic. If its not heritable and stably inherited...its not really epigenetics.

 

The cases where it is what is called a "pure" epialle (not induced by genetic variation and stably inherited)...these are actually quite rare as a whole and so are the exception, not the rule. We also have little idea how stable they are in the long term. It is also far more likely that if that trait achieves stability, that it is because it becomes a "genetic" trait rather than an epigenetic trait.

 

With the exception of prions, epigenetics operates through the silencing or unsilencing of genes by DNA methylation or histone modifications. While these are common features of development, they are typically tissue specific and reset every generation.

 

Because they are silencing genes, they are actually operating on the DNA already and so ultimately epigenetics is still a function of the DNA. It is hypothesized, and there is some evidence that mutations can accumulate in methylated/silenced genes. Methylated cytosines sometimes become deaminated which can lead to mutation of the cytosine residue. In this way, the silencing of the gene can become encoded genetically through the mutation disrupting that gene function. At this point, the trait becomes genetic.

 

So epigenetics can serve as a transitory phase in evolution, but in the long term, there is no evidence from epigenetic that suggests evolution needs a rewrite. Those who argue that it does, do so not from a standpoint of evidence, but from a standpoint of untested hypothesis and often conviction.

Edited November 21, 2014 by chadn737

[CharonY]

 

So epigenetics can serve as a transitory phase in evolution, but in the long term, there is no evidence from epigenetic that suggests evolution needs a rewrite. Those who argue that it does, do so not from a standpoint of evidence, but from a standpoint of untested hypothesis and often conviction.

 

Well, conviction and/or the need to carve a niche for their career. Of course at the beginning there will always be a bit of overselling, before there is enough data to demonstrate the actual impact of new findings.

[chadn737]

 

Well, conviction and/or the need to carve a niche for their career. Of course at the beginning there will always be a bit of overselling, before there is enough data to demonstrate the actual impact of new findings.

 

Funny thing is that at least in the plant community, those that are considered leading the field of plant epigenetics (old and new scientists) are typically pretty adamant about how this ultimately ties back to genome evolution (in particular transposons) and is not really environmentally variable. I see a lot more of that come from certain people in the animal community and few of them experts in epigenetics.

 

For years there has been a problem (and continues to be a major problem) that studies looking at DNA methylation or histone modification differences between populations or generations fail to test or control for genetic variation. They make huge claims that they found a DNA methylation difference and therefore its epigenetic and yet not once did they look for any genetic variation that might be causing it. In the cases where genetic variation is also looked at...often its linked to the variation in DNA methylation or histone modification and likely causative.

Edited November 21, 2014 by chadn737