Evolutionary mechanisms

overtone · November 14, 2012

There is no possible way phenotypic plasticity, niche construction, epigenetics, endosymbiosis etc etc can fit into the "neo-Darwinian" framework without atleast a serious expansion or major revisionism, these mechanisms are about as far away from "Darwinism" as you can get.

You are in error, there. Most people interested in the field have no trouble whatsoever fitting those concepts into standard Darwinian theory as it currently exists.

In addition to not recognizing such concepts as they are incorporated into our understanding of evolution (you don't, for example, recognize their employment in internet forums such as this one) -

based on standard Darwinian theory, generally -

you appear to be unfamiliar with neo-Darwinian theory itself. How else would you arrive at the bizarre conclusion that, say, endosymbiosis, is difficult to fit into modern standard Darwinian evolution?

Ringer · November 14, 2012

I honestly don't think he even reads the articles he cites because if he think this:

In GA, plasticity is of paramount importance because it allows the initial survival of the organism under novel environmental conditions. However, if the new conditions are the only ones being experienced by the population (i.e. the environment is not predictably variable), then standard evolutionary theory predicts the loss of plasticity and the evolution of a canalized phenotype: plasticity has led to assimilation. On the other hand, when both the old and new environments continue to be encountered, selection will favor the evolution of a reaction norm that is appropriately plastic.

from his last link calls for a paradigm shift I could say he is sadly mistaken. Especially when Figure 3 of that paper has Natural Selection directly in it, not much of Darwinian Theory being thrown out since that was his only thing. Let's look at the closing paragraph of this paper

. . . Fig. 3 shows how these are actually related: phenotypic plasticity is (in part) a developmental process, not an evolutionary one. As such, it can be the target of natural selection (an evolutionary mechanism, though of course not the only one), and yield – under certain conditions – the evolutionary outcome of genetic assimilation or phenotypic accommodation. Once one recognizes the clear hierarchical distinctions among these concepts, most fears about an imminent overthrow of the Modern Synthesis should dissipate.

It's neither a paradigm shift, an overthrow, or anything of the sort. It's just a bunch of different things that work together. You know, like what science does when new information comes out.

Edited November 14, 2012 by Ringer

darryl88 · November 14, 2012

Sorry but I have no reason to believe any of the opinions expressed by users on this forum because nothing you say is backed up via any scientific evidence whatsoever and you have ignored the scientific papers I have cited. Science is not about personal belief, if you want to make a case please cite scientific papers, but you never do.

Here are more papers proving my point.

All these papers either discuss the new synthesis, the paradigm shift in evolutionary biology, extension and revisionism etc etc. This is fascinating stuff which clearly users on this forum ignore and have no idea about.

Please read these papers, And you should then agree with me and actually be thanking me that this extension and new synthesis does indeed exist.

The next evolutionary synthesis: from Lamarck and Darwin to genomic variation and systems biology

http://www.ncbi.nlm....les/PMC3215633/

A New Evolutionary Synthesis in Developmental Biology. 6th edition.Gilbert SF

http://www.ncbi.nlm....books/NBK10128/

The molecular and mathematical basis of Waddington's epigenetic landscape: a framework for post-Darwinian biology?

http://www.ncbi.nlm....pubmed/22102361

Beyond Darwinism? The Challenge of Macroevolution to the Synthetic Theory of Evolution

http://www.jstor.org...=21101436771937

Post-modern synthesis?

http://www.nature.co...l/6800471a.html

Recent Developments in Evolutionary Biology

https://papers.econ....ers/2009-11.pdf

Towards A New Evolutionary Theory

http://www.intercien.../v35_11/862.pdf

Horizontal gene transfer in evolution: facts and challenges

http://www.ncbi.nlm....les/PMC2842723/

Evolution of microbes and viruses: a paradigm shift in evolutionary biology?

http://www.ncbi.nlm....les/PMC3440604/

Is evolution Darwinian or/and Lamarckian?

http://www.biology-d.../content/4/1/42

Evo-devo: extending the evolutionary synthesis

http://www.ncbi.nlm....pubmed/17984972

elements of an extended evolutionary synthesis

http://homepage.univ...%20Elements.pdf

Beyond DNA: integrating inclusive

inheritance into an extended theory

of evolution

http://champagnelab....ChampagneNR.pdf

Systems biology and the prospect of a Post‐modern Evolutionary Synthesis

http://www.asbmb.org...iles/Koonin.pdf

Towards a postmodern synthesis of evolutionary biology

http://www.ncbi.nlm....pubmed/19242109

THE EPIGENOME IN EVOLUTION: BEYOND THE MODERN

SYNTHESIS

http://www.bionet.nsc.ru/vogis/pict_pdf/2008/t12_1_2/vogis_12_1_2_21.pdf

The new biology: beyond the Modern Synthesis

http://www.biology-direct.com/content/2/1/30

As I said I have about 100 of these scientific papers proving my case about the paradigm shift in evolutionary biology yet users here will attack me, ignore every paper I cite and ignore all this scientific evidence. So I will not be posting anymore on this forum.

Anyone honest should read the above papers and then agree that I was correct. Thanks.

You have now been given this knowledge, hopefully you can learn about evolution instead of ignoring this evidence.

Darryl.

Edited November 14, 2012 by darryl88

jeskill · November 14, 2012

I wrote a whole bunch of stuff, and then lost it. So I'll just ask this:

On talkorigins, they say this about the Modern Synthesis:

In other words, the Modern Synthesis is a theory about how evolution works at the level of genes, phenotypes, and populations whereas Darwinism was concerned mainly with organisms, speciation and individuals. This is a major paradigm shift and those who fail to appreciate it find themselves out of step with the thinking of evolutionary biologists. Many instances of such confusion can be seen here in the newsgroups, in the popular press, and in the writings of anti-evolutionists.

My question to you: How do endosymbiosis, HGT, and phenotypic plasticity (to use a few examples) NOT fall into this definition of the Modern Synthesis?

As a suggestion, you may want to consider responding specifically to queries, and using your citations to BACK UP your arguments. Randomly posting a whole bunch of links that lack context is not useful on the internet, or when you hand in a scientific paper, for that matter.

Ophiolite · November 14, 2012

Sorry but I have no reason to believe any of the opinions expressed by users on this forum because nothing you say is backed up via any scientific evidence whatsoever and you have ignored the scientific papers I have cited.

In the immediately preceding post Ringer quoted from one of your cited papers and demonstrated that far from supporting your position it contradicted it. There are several hours between posts, so you have no excuse for not having read. Consequently your statement is a lie.

**CharonY** · November 14, 2012

I wonder how often this has to be discussed. Obviously, attempts to create a complete theoretical framework (note that such a thing has never truly existed) we have to integrate novel findings into existing systems. While the relative importance of certain aspects (say, importance of selection vs drift) or the realization that certain tenets are simply not easily applicable (e.g. species concepts in prokaryotes). But it is hardly a revolutionary process. Modern synthesis was established, what, around the 1940s? Of course new mechanisms have been detected since then and their relative relevance to evolutionary models have to be discussed.

Obviously a certain amount of change in certain aspects is necessary and has been under discussion for a long time. Obviously this is more of an advanced discussion and since no complete, simple teachable framework has been established to replace the existing models, it is obvious that in most high-school and undergrad classes it is not taught in-depth.

So what is actually the topic of this thread? Are these things wildly ignored within the scientific community? Of course not. Are they revolutionary? Not really. Are changes necessary? Obviously. As with basically (almost) any "fact" you learn in biology (just thing about the "dogma of molecular biology" and the holes in that commonly taught model).

One thing detrimental to the discussion is the overall tone of the OP that is accusatory and regularly falls back on appeal to authority (i.e. posting links to paper instead of bringing forth a complete argument) and finally shifts in goalposts (e.g. challenges of modern synthesis vs. people are ignorant of evolution).

For instance, what are the true limitations of the modern synthesis? From my point of view is the lack of integration of genomic plasticity, species definitions and their use as durable units and a focus on optimization of the organismal machinery and also a focus on hierarchical evolution.

However, for basically anyone working in the area is aware of the issues. In many cases there is still a struggle in integrating it in a meaningful way (often HGT cannot be accounted for easily, for example), though efforts are underway. It is typical academic handwaving to call these paradigm changes, but unless it is complete replaced it is not the case.

**Phi for All** · November 14, 2012

Sorry but I have no reason to believe any of the opinions expressed by users on this forum because nothing you say is backed up via any scientific evidence whatsoever and you have ignored the scientific papers I have cited.

[snip]

As I said I have about 100 of these scientific papers proving my case about the paradigm shift in evolutionary biology yet users here will attack me, ignore every paper I cite and ignore all this scientific evidence. So I will not be posting anymore on this forum.

!

Moderator Note

Since your assertions here do NOT reflect the reality of the situation, and numerous posters have cited plenty of evidence to refute your assertions, and since you are NOT addressing posts that clearly point to evidence, in your own links, that fails to support your stance, I can only conclude that you're choosing to troll this thread to evoke harsh and unproductive responses. This is against the rules you agreed to when you joined and if you continue you will be suspended or banned.

If you have a problem with this modnote, do not further derail the thread by responding to it here. PM another mod or report this post and other staff members will deal with it.

hypervalent_iodine · November 15, 2012

!

Moderator Note

darryl88,

I've merged all 5 of your threads on evolution as they are essentially repeats of the same thing. Please do yourself a favor and read over them and what others have said to you before posting in this thread and do not open any more on this topic, as they will be closed.

Ringer · November 16, 2012

Sorry but I have no reason to believe any of the opinions expressed by users on this forum because nothing you say is backed up via any scientific evidence whatsoever and you have ignored the scientific papers I have cited. Science is not about personal belief, if you want to make a case please cite scientific papers, but you never do.

Here are more papers proving my point.

All these papers either discuss the new synthesis, the paradigm shift in evolutionary biology, extension and revisionism etc etc. This is fascinating stuff which clearly users on this forum ignore and have no idea about.

Please read these papers, And you should then agree with me and actually be thanking me that this extension and new synthesis does indeed exist.

The next evolutionary synthesis: from Lamarck and Darwin to genomic variation and systems biology

http://www.ncbi.nlm....les/PMC3215633/

Since I said earlier that I do not believe that you read the papers you cite I will ask something simple and in return I will read every single link and explain, in detail, why it's not the huge thing you believe it to be. The link I left is one I read, please thoroughly explain what in this paper makes the accepted evolutionary void, and that there is a fight within the evolutionary biologists to try to keep the current models from changing. If you can successfully do this I will, point by point, go through the papers. The reason I ask this is what I said before about you reading the papers yourself as well as it seems like you don't understand the papers if you are reading them.

darryl88 · November 16, 2012

Since I said earlier that I do not believe that you
read the papers you cite

I have read all of the papers. Here is the one you mention:

1. The next evolutionary synthesis: from Lamarck and Darwin to genomic variation and systems biology

http://www.ncbi.nlm....les/PMC3215633/

In this paper it discusses the controversial views of the biologist James A. Shapiro and the neo-Lamarckian views of the biologist Eva Jablonka and her collegues (by neo-Lamarckian we are talking about epigenetic mechanisms). Both of these authors discuss how new discovery of evolutionary mechanisms has caused the emergence of a new evolutionary synthesis.

As the paper states:

In the latter half of the twentieth century, the view of the process by which new species originated was based on meshing Darwinian variation and selection with work on population genetics and mutation. This view, the evolutionary synthesis, suggested that mutation within individuals led to genetic variation within a population;

The old neo-Darwinian view of evolution is described above. You will all agree with this.

The enormous amount of molecular information that has emerged during the last couple of decades is making us review this synthesis, partly because we now know that the relationship between the phenotype and genotype is not as simple as previously assumed, partly because the genome is a richer, more complicated world than the scientists who put together the modern synthesis could ever have supposed and partly because there is data that does not fit comfortably within the synthesis.

As we can see above in the statement evolution is not simple like the neo-Darwinians would have us believe, things have been discovered in biology (genome research etc) which show evolution is far more complex, and note "there is data that does not fit comfortably within the synthesis" so there is evidence that certain mechanisms cannot possibility fit into the limited neo-Darwinian synthesis hence the purpose of this thread. Agree yes?

So to the next questions, what is this data that does not fit comfortably within the neo-Darwinian synthesis? What is it? Of course this is just one paper (a book review even) and it nowhere near goes into enough detail. But we will discuss it anyway.

Again for a quick summary of why a new synthesis is needed according to the paper:

1. Data has been found which cannot fit into the neo-Darwinian framework of evolution.

2. The simple view of evolution based on mendalian genetics is a minimalist view of genetics and does not match up to the evidence:

There is a serious underlying problem with the evolutionary synthesis: it is based on a minimalist Mendelian view of genetics which assumes that a very small number of genes underpin a trait and a mutant gene leads to an abnormal phenotype. While the advantage of the formulation is that it provides a model for evolutionary genetics, the disadvantage is that the approach assumes a naively simplistic view of how genes generate traits, as Waddington pointed out in the '50s. If more than about three genes (nature unspecified) underpin a phenotype, the mathematics of population genetics, while qualitatively analyzable, requires too many unknown parameters to make quantitatively testable predictions. The inadequacy of this approach is demonstrated by illustrations of the molecular pathways that generates traits the network underpinning something as simple as growth may have forty or fifty participating proteins whose production involves perhaps twice as many DNA sequences, if one includes enhancers, splice variants etc. Theoretical genetics simply cannot handle this level of complexity, let alone analyse the effects of mutation.

So the strict neo-Darwinian view of mendelian does not explain the entire picture of evolution, it only explains part of it.

The reality is that the evolutionary synthesis says nothing about any of this; for all its claim of being grounded in DNA and mutation, it is actually a theory based on phenotypic traits. This is not to say that the evolutionary synthesis is wrong, but that it is inadequate - it is really only half a theory!

So what neo-Darwinism is explaining is only half of evolution, if that!

And again from the paper:

evolutionary synthesis needs to incorporate a proper model of DNA variation and a more sophisticated means of linking phenotypes to genotypes than Mendelian genetics. A modern version of the evolutionary synthesis thus has to be based on the reality of the genome and how it works; in particular, it has to provide answers to three key questions about how organisms change.

The neo-Darwinian synthesis has never had a proper model of DNA variation. As explained there is much more to evolution than just mendelian genetics.

The paper then asks some questions

What controls the rate of evolution?

This area currently generates more heat than light! Selection pressure is part of the story but we do need some insight into why evolution sometimes seems to go very rapidly.

Neo-Darwinism has no answer on this question.

How is genetic variation manifested as phenotypic variation?

Neo-Darwinism has no answer. And the paper points out it is systems biology which is attempting to answer this question. Neo-Darwinism has rejected systems biology.

The next section is a review of two books - one by shapiro and one by jablonka.

I have to admit the book review of Shapiro is very poor and does not describe his views very well. But do check out the section on Lamarckian evolution:

data that fit more comfortably within a Lamarckian than a Darwinian framework

So is there data which fits within a Lamarckian framework?

Yes and this data is evidence for non-Mendelian inheritance. If non-mendelian inheritance is proven then neo-Darwinism is wrong, becuase it denies the role for any important action for non-mendelian inheritance in evolution.

As the paper summarises some of their ideas:

Of particular note are Markel & Trut's description of the Russian experiments on the domestication of wolves, Braun & David's extraordinary results on how Saccharomyces cerevisiae adapts to genomic rewiring, and the work on genetic assimilation in butterflies and in Arabidopsis thaliana that are brought up in the discussion.

The strongest reason for rejecting Lamarckian thinking or soft inheritance is the difficulty in providing a mechanism for genomic change that is a response to environmental pressure. The chapter and appendix by Jablonka summarises, within a historical context, much of the work now being done on the many known examples of epigenetic inheritance through methylation, chromatin-marking, RNA-mediated inheritance and structural templating. These ideas are discussed in detail in the following chapters and it is clear that plants are rather easier model systems to work with here than animals partly because of the speed of change [Feldman & Levy] and that there is a great deal more to be learnt from symbionts [Gilbert]. If there is a conclusion, it is that we cannot yet reject the idea that germline change can occur in ways other than through standard mutation.

Of course neo-Darwinism has denied germline change in anything apart from random mutation. Neo-Darwinians ignore all of the data for epigenetic inheritance or claim it is not important.

And neo-Darwinism is also dogmatically gradualistic denying any role for saltational evolution, but epigentic processes can be saltational as both books point out (there is lots of evidence for saltational evolution). So the fact that saltational evolution exists is just more evidence that evolution has moved beyond the neo-Darwinian synthesis? Why? Becuase neo-Darwinism denied that it can happen... but it does happen! Therefore neo-Darwinism was wrong.

The paper also mentions the views of conrad waddington on genetic assimilation this was a mechanism which was denied by the neo-darwinian synthesis as being "lamarckian" (even though waddington described the mechanism in "darwinian" terms.) It is usually described as a Lamarckian mechanism but this is not really true, it is actually a special case of phenotypic plasticity. There is evidence that this mechanism exists.

This was just one paper. Note the reviewer was actually critical of some of Shapiro's book but still agreed that a new synthesis is needed becuase the neo-Darwinian view does not match up to the evidence. Of course like I have said scientists in the field are saying these things, but you come to an internet forum with non-scientists and they have no clue about it and deny it.So you have been given evidence for scientists calling for a new synthesis Ringer, there is no reason do deny this new synthesis or claim it does not exist.

Edited November 16, 2012 by darryl88

overtone · November 17, 2012

As we can see above in the statement evolution is not simple like the neo-Darwinians would have us believe,

Nobody who is familiar with it thinks the modern Darwinian theory of evolution is "simple" in its real world application.

If non-mendelian inheritance is proven then neo-Darwinism is wrong, becuase it denies the role for any important action for non-mendelian inheritance in evolution.

Non-Mendelian inheritance has been incorporated into standard evolutionary theory for almost a century now. http://en.wikipedia.org/wiki/Non-Mendelian_inheritance.

Mendelian inheritance itself was not rediscovered and finally incorporated into applications of Darwinian theory until fifty years or more after Darwinian theory had become generally accepted. The early basic principles of Darwinian theory were developed without reference to it. The explanation of complex Mendelian inheritance patterns in complicated situations was one of the accomplishments of Darwinian theory - not a limitation of it.

And neo-Darwinism is also dogmatically gradualistic denying any role for saltational evolution,

Bullshit.

So you have been given evidence for scientists calling for a new synthesis Ringer, there is no reason do deny this new synthesis or claim it does not exist.

The claim is that the best name for this new synthesis will be "Darwinian Theory of Evolution", or "neo-Darwinian" if you prefer, since the basic principles of Darwinian theory will remain at its core - they seem to be unchallenged, and the recent elaborations of their mechanisms rather improve than replace them in application.

darryl88 · November 17, 2012

Once again overtone if you want to make a case can you please go further than just your personal opinion and please cite actual scientific references for your claims.

Bullshit.

No it is not "bullshit". And you are being very dishonest, since the neo-Darwinian synthesis formulated in the 1930's it was very critical of saltationism and it rejects that it can happen.

Here is a main tenent of neo-Darwinism:

Evolution is gradual: small genetic changes regulated by natural selection
accumulate over long periods. Discontinuities amongst species (or other taxa)

are explained as originating gradually through geographical separation and

extinction.

Please see Ernst Mayr's book describing the main points of neo-Darwinism such as The growth of biological thought: diversity, evolution & inheritance. He writes that saltational evolution is impossible.

Of course he was writing this back over 30-40 years ago and he was wrong.

Darwinian gradualism has been refuted. This is not to say that gradual evolution does not exist, but the strict gradualism of neo-Darwinism is wrong. As Prof Koonin summarised:

The discovery of pervasive HGT and the overall dynamics
of the genetic universe destroys not only the tree of life as we

knew it but also another central tenet of the modern synthesis

inherited from Darwin, namely gradualism. In a

world dominated by HGT, gene duplication, gene loss and

such momentous events as endosymbiosis, the idea of evolution

being driven primarily by infinitesimal heritable

changes in the Darwinian tradition has become untenable.

Below is a very aburd quote from you:

The claim is that the best name for this new synthesis will be "Darwinian Theory of Evolution", or "neo-Darwinian"

Saltationism and Lamarckian feedback have been observed as well as many other non-Darwinian mechanisms, evolution is evolution, it is made up of pluralistic mechanisms and processes, to conclude that the entire field of evolution is just "Darwinian" is ignorant of the evidence and pure denialism. Evolution is not limited and science is not static, you have been told this many times.

since the basic principles of Darwinian theory will remain at its core - they
seem to be unchallenged

Please see the table to see why many basic principles of the Darwinian theory have been replaced and challenged. It is the fourth time you have been given this, but you refuse to look at it.

http://www.ncbi.nlm....84144/table/T1/

Edited November 17, 2012 by darryl88

overtone · November 17, 2012

And you are being very dishonest, since the neo-Darwinian synthesis formulated in the 1930's it was very critical of saltationism and it rejects that it can happen.
- - - -

Here is a main tenent of neo-Darwinism: - - - - Evolution is gradual - - - -

As stated, that's not a main tenet of modern Darwinian theory. It's a consequence, and not an inevitable one - a probability. Much hinges on the meaning of the word "gradual" (see Dennett's critique of "punctuated equilibrium), for starters.

If you are going to argue against a school of thought last seen dominating evolutionary theory with its particulars decades before the structure and role of DNA was elucidated, then no problem - horizontal gene transfer would, as you claim, "challenge" that anachronistic framework.

But there's no sense in confusing it with what Darwinian evolutionary theory is now.

Please see the table to see why many basic principles of the Darwinian theory have been replaced and challenged

Playing whack-a-mole with your latest obtusity is not an indefinitely engaging game - the fate of your assertions regarding Mendelian genetics and horizontal gene transfer and so forth, above, is not interesting, for example. It's commonplace.

But this table of yours does have a source not obviously and immediately crackpot, so let's look at it: Yes means an agreement between the author's notion of "neo-Darwinian" theory and the author's notion of physical reality as recently established.

Random (undirected), heritable variation is the principal material for natural selection - - - Yes

Despite the immediate temptation to take that "Yes" and move on, we note that nothing in Darwinian theory requires the heritable (not "inherited", note) variation to be "random" in every strict sense imaginable. Bacteria are known to manage their mutation rates and locations, swap genetics wholesale, etc, for example, and Darwinian theory has no problem with that.

Fixation of beneficial changes by natural selection is the main driving force of evolution that tends to generate increasingly complex adaptations; hence progress as a general trend in evolution

Modern Darwinian theory is explicit in denying the inevitability of "progress", and has no problem with the many examples of degenerative evolution (flightless birds, blind cave dwellers, tapeworms and the like, etc). As far as "general trend", that is an observation of the real world which was explained by Darwinian theory only after some difficulty - a success of the theory in application, not a "basic principle".

Natural selection operates on ‘infinitesimally small’ variations, so evolution never makes leaps - the principle of gradualism

Nothing in Darwinian theory requires that the steps be "infinitesimally small". One of the strengths of the theory is that very small steps - which are much more probable - are all that is needed, but larger steps are not ruled out thereby. They are merely less common, on probabilistic grounds.

Evolutionary processes were, largely, the same throughout the evolution of life – the principle of uniformitarianism borrowed by Darwin from geology

The article seems a bit confused here - it seems to take endosymbiosis as a supposed counterexample to that, among other muddlings, and posits the necessity of unspecified evolutionary mechanisms other than the also unspecified "normal" ones before the advent of familiar cellular life, for some reason not clear. But overall we have agreement - Darwinian evolutionary processes such as we see now also proceeded in the distant past.

Species is a central unit of evolution, -

This is just wrong. Even in the early years, Darwin used the theory to explain the origin of species - as a consequence, not a prerequisite or necessary "unit". Famous explicators of the more modern theory have written entire books titled "The Selfish Gene". The unit of Darwinian evolution is not the species

and speciation a key evolutionary process

Well, yeah. Just because bacteria don't do it quite the same, it isn't important?

The entire evolution of life can be depicted as a single “big tree” that reflects the evolutionary relationships between organisms and species (species tree)

This is a nice idea for explicatory diagram, and very useful with large animals and such. But explanatory posters on school classroom walls are not the foundation of fundamental theory, of "basic principles".

likewise:

All existing life forms descend from a single ancestral form, the Last Universal Common Ancestor (LUCA)

This is even less a basic principle - Darwinian theory says almost nothing about how many separately originating lines of evolution there are (it says: you only need one. That doesn't mean there weren't more). The conclusion that there are very few, perhaps even only one, is a consequence of research and reasoning informed by Darwinian theory - again, a successful application, not a basic principle.

So the reward for yet again taking your posting much more seriously than would be indicated, is what?

Ringer · November 17, 2012

In this paper it discusses the controversial views of the biologist James A. Shapiro and the neo-Lamarckian views of the biologist Eva Jablonka and her collegues (by neo-Lamarckian we are talking about epigenetic mechanisms). Both of these authors discuss how new discovery of evolutionary mechanisms has caused the emergence of a new evolutionary synthesis.

Not really. The only mention of controversial is genetic assimilation, not epigenetics. Though they could be considered similar, as I understand them, they are not the same. More strictly, it's a review of two books that talks about what later editions should include, mention or change. You say the second part is about the books, but the only part that's not is the introduction. The introduction, in any paper, states what is already known. This goes against your entire idea that the ideas are unknown/ignored. In short, you have not at all shown how this paper supports your idea. Yes, they say it doesn't come to terms with specific mutation to phenotype relationship, but as far as I know the answer is not yet known. It does not at all support the assertion that these ideas are controversial, being fought, or discredit decades of evidence. The closest it gets is saying things are more complex than early models indicate.

As the paper states:

The old neo-Darwinian view of evolution is described above. You will all agree with this.

As you say yourself, this is an old way of thinking. Evolutionary biology has assimilated fairly well, though as with any science, it's still working out kinks.

As we can see above in the statement evolution is not simple like the neo-Darwinians would have us believe, things have been discovered in biology (genome research etc) which show evolution is far more complex, and note "there is data that does not fit comfortably within the synthesis" so there is evidence that certain mechanisms cannot possibility fit into the limited neo-Darwinian synthesis hence the purpose of this thread. Agree yes?

So to the next questions, what is this data that does not fit comfortably within the neo-Darwinian synthesis? What is it? Of course this is just one paper (a book review even) and it nowhere near goes into enough detail. But we will discuss it anyway.

All you are saying is that things are more complex than a simple explanation. Darwinian theory, neo or otherwise, is not simple, but it does take a simplistic view of certain things. It still works and is correct at various levels, but is less so in other areas. What you are stating is equivalent to me saying that Newtonian ideas are invalid because some things behave in a non-Newtonian manner.

Again for a quick summary of why a new synthesis is needed according to the paper:

1. Data has been found which cannot fit into the neo-Darwinian framework of evolution.

2. The simple view of evolution based on mendalian genetics is a minimalist view of genetics and does not match up to the evidence:

There is always new data, and frameworks are always being revised. This is not an overthrow by any stretch of the word.

So the strict neo-Darwinian view of mendelian does not explain the entire picture of evolution, it only explains part of it.

Again, this doesn't make it incorrect, not that it uses pure Mendelian genetics but that's beside the point. This is not an overthrow, it's an incorporation.

I'm not going through point by point because it's more of the same. The evidence you describe is being incorporated to evolutionary frameworks, not being ignored. You have not even begun to sufficiently show that any of these things are pointing towards an overthrow, not incorporation, or how they otherwise show Darwinian theory incorrect. Not explaining everything is part of science, but it does not mean the theory is incorrect. The ideas and views are still valid.

This was just one paper. Note the reviewer was actually critical of some of Shapiro's book but still agreed that a new synthesis is needed becuase the neo-Darwinian view does not match up to the evidence. Of course like I have said scientists in the field are saying these things, but you come to an internet forum with non-scientists and they have no clue about it and deny it.So you have been given evidence for scientists calling for a new synthesis Ringer, there is no reason do deny this new synthesis or claim it does not exist. <br style="font-size: 13px; line-height: 16px; background-color: rgb(248, 250, 252);">

Yes, there is new evidence that new-Darwinian theory does not fully explain. Again, this goes back to saying Newtonian mechanics is void because of things like Relativity. I don't see why it matters that some people on the internet are not up to date on scientific ideas. If this is your entire argument, it's a pointless argument. Some people are not up to date on evolution is like being upset that people on the internet don't understand Calculus. Many people are dumb and ignorant and trying to give them information is great, but acting like it's some huge deal that people are ignorant is kind of ignorant in itself. Again, you have been arguing for an overthrow of theories, not a merging. So no, you have still not argued the case that the new ideas overthrow the old one. You have supplied evidence that new data comes out and Biologists are working to incorporate the data in various ways to show which way is the best. This is, as I said before, what science does.

[edit]

I felt the last paragraph should be addressed and I skipped it before[/edit]

Edited November 17, 2012 by Ringer

darryl88 · November 18, 2012

Listen I respect your replies Ringer and especially your comments on the table overtone but the problem is you are offering me nothing more than opinion.

You have attempted to shoot down pretty much everything Prof Koonin has written in that table, but note how every point he makes is backed up via scientific sources. So when you have listed your criticisms you are not only rejecting Koonin's work but also the view of many other scientists on evolution. So what do we have? We have your personal criticism or the work of professional scientists in the field backed up with evidence. Who do you think I am going to choose to believe?

Now it is perfectly acceptable to give criticism if you think something is wrong, but personal opinion goes little far in scientific debates and discussion, especially if you are offering criticism of something without any evidence to back up your claims at all. So can you give me some scientific evidence to back up any of your criticism? If you can actually back up your criticisms, then perhaps you may actually have a case but at the moment you have not offered anything scientific.

Edited November 18, 2012 by darryl88

Ringer · November 18, 2012

Listen I respect your replies Ringer and especially your comments on the table overtone but the problem is you are offering me nothing more than opinion.

You have attempted to shoot down pretty much everything Prof Koonin has written in that table, but note how every point he makes is backed up via scientific sources. So when you have listed your criticisms you are not only rejecting Koonin's work but also the view of many other scientists on evolution. So what do we have? We have your personal criticism or the work of professional scientists in the field backed up with evidence. Who do you think I am going to choose to believe?

Now it is perfectly acceptable to give criticism if you think something is wrong, but personal opinion goes little far in scientific debates and discussion, especially if you are offering criticism of something without any evidence to back up your claims at all. So can you give me some scientific evidence to back up any of your criticism? If you can actually back up your criticisms, then perhaps you may actually have a case but at the moment you have not offered anything scientific.

First the reply you are referring to was not mine, it was overtone's. Second, I saw no sources cited in that table showing that those 'central tenets' are anything other than the author's view of neo Darwinian theory. So let's take a look at the paper that table is based on, more specifically this snippet:

The emerging landscape of genome evolution includes the classic, Darwinian natural selection as an important component but is by far more pluralistic and complex than entailed by Darwin's straightforward vision that was solidified in the Modern Synthesis (16,184). The majority of the sequences in all genomes evolve under the pressure of purifying selection or, in organisms with the largest genomes, neutrally, with only a small fraction of mutations actually being beneficial and fixed by natural selection as envisioned by Darwin. Furthermore, the relative contributions of different evolutionarily forces greatly vary between organismal lineages, primarily, owing to differences in population structure.

Again, not overthrown, just added to.

Arete · November 19, 2012

if you want to make a case can you please go further than just your personal opinion and please cite actual scientific references for your claims.

Now that the treads have been merged - see post #52.

I provided you with the contents page of a respected evolutionary journal, which showed, conclusively, that scientists in the field are happily publishing away on the topics you've listed in the profound absence of this new paradigm of evolution. This goes a considerable way in conclusively demonstrating that conceptual and empirical progress is being made, without the need to generate a magical new fantastic paradigm of evolutionary theory.

Your response was to inform me of the rather obvious fact that biological journals are in fact, written by multiple authors and a single, superhuman scientist doesn't conduct dozens of multiple lengthy and involved studies every month to produce an entire edition of a journal. This didn't substantiate the need for your new paradigm, nor counter the progress being made in its absence.

Next you told me that a "revolution" would be evident if I went to an evolutionary biology conference. I demonstrated that the issue was not discussed at the largest meeting of evolutionary biologists in the world - the fact that with over 1000 presenters and over 3000 attendees there was no session on a new paradigm - demonstrating, again conclusively, that any discussion of a new paradigm could hardly be described as a "revolution".

You then criticized the entertainment choice of the meeting and presented me a small list of 16 scientists who attended a meeting about an extended - note not new; evolutionary synthesis almost 5 years ago. 16 people is not a field-wide consensus, nor does an extension of existing theory really support your case, nor is 5 years ago particularly current. So, you neither addressed the fact that the "revolutuion" you claimed was not happening at this conference, nor really supported your assertion that it was at other meetings.

There is no evidence you have read any of the papers I have cited, you have not been able to comment on a single one of them. You are the reason evolution makes so little progress thesedays on the internet you are rejecting any evidence based on your personal beliefs, what you are doing is no different than what the creationists do. This is anti-scientific.

That's an out and out lie.

1) See post #21 for a comment by me on Koonin et al.

2) I don't reject the role of ANY of the processes described in evolution. To give you a short run down: I cut my teeth as a research scientist in landscape genetics - which inherently examines the role of population genetic dynamics in adaptation. I then moved to PhD studies in the role of discordance generated by horizontal gene transfer in gene tree estimation, and the role of phenotypic plasticity and adaptation in sympatric diversification. I currently work on gene flow and trait liability in parasites and adaptation to environmental fluctuation in RNA viruses. I actually work on the process you seem to be insisting that I don't accept - though I've mentioned that I accept and work on these aspects of evolution multiple times.

3) Given I've never, apart from a single outlier, encountered a biologist who doesn't acknowledge these mechanisms, I simply don't accept that there is widespread non-acknowledgement of them. The fact that we, as scientists in the field have been working on, publishing on, getting grants on and focusing our research on these topics for as long as I've been in research clearly demonstrates that the current, widely accepted way evolution works incorporates these processes.

Given 2) and 3), in order to argue for your paradigm shift, you need to present a view of evolution which is outdated by around 40-50 years and argue against it - this is a textbook example of a strawman argument. As was thoroughly demonstrated to you, this view is no longer held by the bulk of the scientific community.

At the moment it's like an argument that we need a new medical paradigm which explicitly states that MRI is a better detection tool for some things than ultrasound. If we can demonstrate that doctors regularly use MRI, doctors are taught MRI in med school, and that the majority of doctors are using MRI where appropriate, there would be a strong case AGAINST the need for a new paradigm. Here, we've shown that biologists widely accept the role of HGT etc, that these processes are taught to biologists as part of their training and that they apply the role of these processes to contemporary study of evolution - providing a strong case AGAINST the need for a new evolutionary paradigm.

Ergo, the contemporary validity of the review article by Koonin et al is questionable by the lack of scientific literature upholding a purely allopatric, gradualist evolution. If you could present current literature which upholds this viewpoint on evolution, you would have a case.The evidence opposing the need for a new paradigm is the scientific literature incorporating all of the "new" processes you mentioned which are evident with even a cursory glance at a current evolutionary journal contents page.

Rather than condescendingly and ignorantly telling me my research impedes scientific progress and telling me I am no different to a creationist; how about you tell us how your paradigm shift will aid scientific progress and accelerate scientific discovery beyond the current regime: how will the "new synthesis" bring about understanding and investigation which isn't currently being investigated? As (assumedly) a research student, how will your thesis add to scientific understanding? What hypotheses are to be tested?

Because, and I'm again repeating myself, it appears from the current publications coming from the field of evolutionary biology:

http://onlinelibrary...sue-11/issuetoc

http://www.sciencedi...ournal/10557903

http://onlinelibrary...sue-12/issuetoc

http://sysbio.oxford...content/current

etc.

That the study of all of the mechanisms you've listed is ubiquitous and unimpeded in its absence - and that the "new synthesis" is a self inflationary overstatement to try and sell one's review paper, or a strawman attack of a viewpoint which faded from mainstream science several decades ago.

Edited November 19, 2012 by Arete

darryl88 · November 20, 2012

Arete you have given me 5 links to three random scientific journals - but the links you have given are not to specific papers which can be read online, they are to a couple of book reviews that can not be clicked on without access or things which are not relevant to this topic. It seems you have just randomly tried to get hold of anything to try and back yourself up. I was thinking of calling you dishonest but it appears you are lazy as well. Why can you not cite one single paper to back up your claims. And no don't get angry or abuse me... I am really interested why.

Can you point to a single actual scientific paper to back up your claims that a paradigm shift/extended synthesis has not occured in evolution in the last 60 years?

WOW, what is this? I have just found another paper calling for an extended synthesis just published last month!

Epigenetic synthesis: a need for a new paradigm for evolution in a contaminated world

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3434969/

Evolutionary theory accounts for the process of change in life forms. It
has had two epochs, with a third emerging. The first, Darwinian evolution,

established the principle of change through selection. The second, the Modern

Synthesis, provided the units of heredity and their control, particularly change

in DNA by recombination and mutation. We are entering the third epoch, what we

might call the Epigenetic Synthesis, which combines elements of the previous

iterations and incorporates environmental modulation of temporal and spatial

control of gene expression without altering the underlying DNA

sequence.

Only when molecular biology and genetics incorporate the deep history and
perspective of other disciplines, such as evolutionary biology, evo-devo,

behavioral ecology, ethology and psychology, will the potential of epigenetics

be realized. We suggest that an Epigenetic Synthesis (E_g X E_c) combines elements

of classical Darwinian theory, together with the Modern Synthesis, and extends

it to understanding how the contaminated world has transformed the trajectory of

evolution. It is clear that environmental contaminants are already influencing

evolution on a global scale. What is not clear is what this means for our

future.

The list goes on and on, I could be citing these papers all day which are calling for an extended or new synthesis beyond just neo-Darwinism. Evolution has progressed beyond the modern synthesis of the 1940's, I have no idea why specific users online want to deny this. As I said knowledge about evolution progresses and this is what science is all about.

jeskill · November 20, 2012

Darryl8, instead of attacking with ad hominim fallacies, why not respond to Arete's question?

... [H]ow about you tell us how your paradigm shift will aid scientific progress and accelerate scientific discovery beyond the current regime: how will the "new synthesis" bring about understanding and investigation which isn't currently being investigated? As (assumedly) a research student, how will your thesis add to scientific understanding? What hypotheses are to be tested?

I think this is a great question, as it's the main reason why most people aren't agreeing with you here.

Arete · November 20, 2012

Arete you have given me 5 links to three random scientific journals - but the links you have given are not to specific papers which can be read online, they are to a couple of book reviews that can not be clicked on without access or things which are not relevant to this topic. It seems you have just randomly tried to get hold of anything to try and back yourself up. I was thinking of calling you dishonest but it appears you are lazy as well. Why can you not cite one single paper to back up your claims. And no don't get angry or abuse me... I am really interested why.

I linked you to the contents pages of four of the top journals in the field of evolutionary biology: Evolution (IF: 5.2), Journal of Evolutionary Biology (IF: 3.2) , Systematic Biology (IF: 8.8), Molecular Phylogenetics and Evolution (IF: 3.9). They are not links to book reviews, that is another out and out lie. Do you think other people are incapable of clicking the links? The reason you were linked to these journal contents pages was explained multiple times: a cursory glance over any of these contents pages will show you that people are happily publishing away on ALL of the mechanisms you have brought up.

Again, my point is that people are working on all of these mechanisms in the absence of your new synthesis. What exactly is it you want "backed up?" It is unclear which exact point you want evidenced. This is because you are not arguing with an actual representation of what has been said, but a caricature of what has been said which suits the argument you are making: i.e.

Can you point to a single actual scientific paper to back up your claims that a paradigm shift/extended synthesis has not occured in evolution in the last 60 years?

This is not what anyone in this thread has said or argued. IT IS A STRAWMAN ARGUMENT. ARGUING AGAINST THIS MISREPRESENTATION DOES NOT PROVE YOUR POINT IN ANY WAY SHAPE OR FORM. I can't prove a point with scientific evidence if it's a point I never argued in the first place.

If you're going to accuse people of being dishonest and lazy you might want to start by not misrepresenting people and actually reading other people's responses to you, instead of strawmanning them and slinging insults around.

I'm tired of being told that I don't believe in evolutionary mechanisms I actively study and am currently conducting experiments on. At best, it means you simply aren't reading my posts. At worst, you're persistently misrepresenting me and deliberately presenting a dishonest argument.

Edited November 20, 2012 by Arete

**Phi for All** · November 21, 2012

!

Moderator Note

This thread has failed to show any relevance to mainstream scientific knowledge and the OP continues to argue against a stance none of the replies seems to take. Since many students come to the main fora for help with school, I'm moving this to our Speculations section.

overtone · November 21, 2012

Uh, Darryl, If you keep listing commonplace stuff like symbiosis and hybridization as "non-Darwinian" and in need of a radical new theory, nobody is going to take you seriously around here. This is a science forum.

Ringer · November 21, 2012

So, I'm beginning to feel like this entire thread is just trying to get people on board to come up with a new name for evolutionary processes. In which case this entire thread is pure idiocy, not that much of it wouldn't be if this isn't the case. Honestly I don't even know what is being argued anymore. Is it semantics of names, that some ignorant people online spout non-sense, biologists don't believe in common evolutionary mechanisms, etc? Please let me know because this is getting so damn pointless.

proximity1 · November 21, 2012

To Arete, RE your : ..."3) Given I've never, apart from a single outlier, encountered a biologist who doesn't acknowledge these mechanisms"

I'm curious about and interested in knowing who you have in mind as this "single outlier". I might find that name interesting.

Here are a few other incidental thoughts about this thread, which until now I'd not noticed--

to me, it isn't surprising that a thread such as this should occur. I don't happen to agree--as far as I've read them--with the main tenets here or some of them, but I think that the apparent controversy on this topic ought to tell us something about the questionable character of certain standard views in this subject. But there's not much to indicate that it does tell us that if the annoyance of some critics in the thread is any indication.

In his post, N° 81, above, CharonY remarks, "I wonder how often this has to be discussed."

I think the answer is that it will be discussed again and again as more and more people come accidentally into acquaintance with the fact that there are a number of aspects of standard theory which deserve an attention and critical examination that they are not getting and, frankly, aren't allowed to get under present circumstances. So, there's no good reason to be surprised if some who have questions and doubts raise them in fora such as this. Again, I don't think the views being presented here by the thread(s)' author are the best or the correct ones to bring against this Modern Synthesis, but that there are objections, that "this has to be discussed (often)," that doesn't surprise me at all and I look forward to the time when that exasperated lament will not seem justified because no one will find it surprising that the doubts and questions persist.

Arete · November 21, 2012

I'm curious about and interested in knowing who you have in mind as this "single outlier". I might find that name interesting.

Jerry Coyne - who holds the view that allopatry is required for speciation - which is not representative of the majority of evolutionary biologists.

http://www.huffingtonpost.com/james-a-shapiro/jerry-coyne-fails-to-unde_b_1411144.html

http://www.the-scientist.com/?articles.view/articleNo/23704/title/Evidence-for-sympatric-speciation/

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