Evolutionary mechanisms

[Ophiolite]

A major revolution is occurring in evolutionary biology.

I found this was a little like a documentary on, for example, astronomy, that declared "Scientists now suspect the universe was once in a much denser state and has been expanding for the last 13 billion years." I exaggerate slightly, but not by much.

 

Unlike CharonY I am not immersed in the field, yet my sketchy amateur interest is sufficient to the point that none of the outline concepts strike me as novel. The field, at times, seems split between two extremes: those who think the Modern synthesis has just undergone some minor adjustments and those who think the world has been turned upside down. I believe those viewpoints have mroe to do with personality than science and ultimately don't do much for the field.

[Unity+]

I found this was a little like a documentary on, for example, astronomy, that declared "Scientists now suspect the universe was once in a much denser state and has been expanding for the last 13 billion years." I exaggerate slightly, but not by much.

 

Unlike CharonY I am not immersed in the field, yet my sketchy amateur interest is sufficient to the point that none of the outline concepts strike me as novel. The field, at times, seems split between two extremes: those who think the Modern synthesis has just undergone some minor adjustments and those who think the world has been turned upside down. I believe those viewpoints have mroe to do with personality than science and ultimately don't do much for the field.

The reason why it doesn't seem novel is the fact that ideas now days grow slowly instead of just instantly come out with all these new ideas and people are saying "Whoa, this is new." When information slowly comes out of the blue we are less excited about the new pieces of information. This presented only a stepping stone in the knowledge of evolution. Though, simply to say that this information isn't a novel is quite ignorant(not in an offensive way, but you get what I mean). If you don't get the meaning of the information of course it isn't novel. However, to some who understand the implications are flabbergasted by the information.

[Ophiolite]

Since the evidence I saw from palaeontology in the 1960s left, in my view, gaping gaps in the explanation of evolution - which clearly was reality - I turned to those life sciences that actually deal with living, rather than fossilised things. Again I felt there was a degree of complacency about the comprehensiveness of the explanations and proposed mechanisms. When hox genes were discovered and evo-devo gained some notoriety I thought "Now we are getting somewhere." So, all of this is, for me definitely not novel, just long overdue and the process is far from complete.

[Unity+]

Since the evidence I saw from palaeontology in the 1960s left, in my view, gaping gaps in the explanation of evolution - which clearly was reality - I turned to those life sciences that actually deal with living, rather than fossilised things. Again I felt there was a degree of complacency about the comprehensiveness of the explanations and proposed mechanisms. When hox genes were discovered and evo-devo gained some notoriety I thought "Now we are getting somewhere." So, all of this is, for me definitely not novel, just long overdue and the process is far from complete.

It still de[ends on your point of view.

[CharonY]

And as Ophiolite pointed out, from the viewpoint of anyone even tangentially involved, it is not new, but overdue. I have to add that the viewpoint presented in the paper is still insufficient. Essentially it argues against modern synthesis (which many did over the years) and promotes a different viewpoint. What is needed however, is an integrative view (a theory of everything, if you will) that, (and this is the critical part in my opinion) provides more quantitative information of the respective aspects. Yes, there are epigenetic factors involved in, but what is the quantitative contribution relative to the other factors. How does it shape rates, for example, how much do existing models have to be changed? Do they have to be changed at all?

Often times the molecular knowledge is not quantitative enough to assess that either, for that matter.

 

And going back to the novelty, as Ophiolite already mentioned a first big push (that I still remember) came from the evo-devo area and there quite some papers around the 90s for a new modern synthesis, quickly followed by a large number of publications from the area of microbiology (as they were more or less left out from the modern synthesis and just did their own stuff)/ So as it stands it falls into a long line of arguments which I hope will eventually be married to more integrative approaches. Interesting? Yes. Revolutionary? Probably not.

[overtone]

Am I the only person around who picked up this supposedly novel, new, earthshattering redefinition of the word "gradual" in the first place, many years ago, from reading children's books about the extinction of the dinosaurs and the rise of the mammals and the way babies grow according to the "instructions" from the genes (like a recipe rather than a blueprint)?

 

I thought this was what we'd been talking about all along, with fertile arguments regarding the relative importance of, say, symbiosis, or the Baldwin effect, taking place within the overall variation/selection framework.

 

I just don't see how the discovery of soap means you have to redefine the whole theory of the bath, and in particular throw the baby out.

[Darryl Forests]

 

Rocking the foundations of biology

A major revolution is occurring in evolutionary biology. In this video the President of the International Union of Physiological Sciences, Professor Denis Noble, explains what is happening and why it is set to change the nature of biology and the importance of physiology to that change. The lecture was given to a large general audience at a major international Congress in Suzhou, China. The implications of the change extend far beyond biology itself. This video will also interest economists, business leaders, politicians and others who deal with the important social questions that have been raised by ideas in evolutionary biology ever since Darwin wrote his Origin of Species. To share the excitement see reactions worldwide and the article.

A new version of the lecture will be given at the Opening of the IUPS 2013 Congress. Answers to questions frequently found on blogsites discussing the video and the article can be found here.

Key quotations from the article:

All the central assumptions of the Modern Synthesis (often also called Neo-Darwinism) have been disproven. Moreover, they have been disproven in ways that raise the tantalising prospect of a totally new synthesis: one that would allow a re-integration of physiological science with evolutionary biology. It is hard to think of a more fundamental change for physiology, and for the conceptual foundations of biology in general.

 

My article returns to a more nuanced, less dogmatic, view of evolutionary theory which is much more in keeping with the spirit of Darwin’s own ideas than is the Neo-Darwinist view.

 

To Maynard Smith’s comment (“it is hard to conceive of a mechanism whereby it [Lamarckism] could occur”) the reply must be that some of those mechanisms have now been found and they are robust.

 

The organism should never have been relegated to the role of mere carrier of its genes

 

I recommend visiting the website of Denis Noble:

 

link removed

[Arete]

Rocking the Foundations of biology

 

Not really.

 

The topic was thoroughly discussed in a previous thread.

 

As I posted there, the expansion of evolutionary theory to encompass novel mechanisms has been ongoing for decades. It should come as no surpise to anyone even tangentially involved in evolutionary biology that we've discovered that the mechanisms involved are more complicated than Mayr and Dobzhansky understood.

 

PZ Meyers comment on the Arlenberg 16 sums up the whole "new synthesis" hype succinctly:

 

"There are no grand reformulations of the neo-Darwinian synthesis in there, nor is anyone proposing to overturn our understanding of evolution — but that’s what I expected. It’s saying that there are a lot of exciting ideas and new observations that increase our understanding of the power of evolution, and promise to lead research in interesting new directions."

 

http://scienceblogs.com/pharyngula/2008/07/19/altenberg-2008-is-over/

[hypervalent_iodine]

 

I recommend visiting the website of Denis Noble:

 

link removed

 

!

Moderator Note

I recommend responding to some of the comments and criticisms in this thread instead of spamming websites, or this thread will be closed. I'm removing your link. Please make posts of more substance in future.

[Ophiolite]

I posted this on the forum during a similar discussion, but I'm not sure where. I think it is relevant to this thread.

 

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, as CharonY points out, 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.

 

 

[Unity+]

I posted this on the forum during a similar discussion, but I'm not sure where. I think it is relevant to this thread.

 

 

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, as CharonY points out, 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.

 

 

Well it isn't frustrating me at all...

 

Just as a suggestion, keep scientific discussions from swerving to a really bad direction of trying to disprove anything of the religious sense with science because it ain't going to work(that is just the way it is). Ultimately it will lead to a hole of insanity and evil(meaning the discussion won't end well).

[Arete]

Well it isn't frustrating me at all...

 

Just as a suggestion, keep scientific discussions from swerving to a really bad direction of trying to disprove anything of the religious sense with science because it ain't going to work(that is just the way it is). Ultimately it will lead to a hole of insanity and evil(meaning the discussion won't end well).

 

One of the dangers of presenting the discussion as "rocking the world of biology" or a "paradigm shift" or *insert hyper-exaggerated tagline here* is that, for those who want to hear it as such, it may sound like the theory of evolution is being ditched by science - when that is unequivocally NOT happening. This is exactly what happened after the "Alternberg 16" meeting in 2008.

http://pandasthumb.org/archives/2008/07/luskin-has-lost.html

 

There was some discussion of what the result of the whole debacle was 5 years on at this year's joint Evolution meetings. The resultant conclusion was that, as has been noted above and in the previous thread - evolutionary theory has been gradually accruing new information and mechanisms for decades. There hasn't been a "eureka" addition of game changing information - like for example, plate tectonics was to geology. Cynics/skeptics in the evolutionary biology community would even suggest that the whole "new synthesis" of evolutionary theory was a profile building exercise undertaken by a few scientists in the field looking to generate high impact review papers as their tenure clocks ran out.

[Darryl Forests]

 

One of the dangers of presenting the discussion as "rocking the world of biology" or a "paradigm shift" or *insert hyper-exaggerated tagline here* is that, for those who want to hear it as such, it may sound like the theory of evolution is being ditched by science - when that is unequivocally NOT happening. This is exactly what happened after the "Alternberg 16" meeting in 2008.

http://pandasthumb.org/archives/2008/07/luskin-has-lost.html

 

There was some discussion of what the result of the whole debacle was 5 years on at this year's joint Evolution meetings. The resultant conclusion was that, as has been noted above and in the previous thread - evolutionary theory has been gradually accruing new information and mechanisms for decades. There hasn't been a "eureka" addition of game changing information - like for example, plate tectonics was to geology. Cynics/skeptics in the evolutionary biology community would even suggest that the whole "new synthesis" of evolutionary theory was a profile building exercise undertaken by a few scientists in the field looking to generate high impact review papers as their tenure clocks ran out.

the neodarwinin synthesis was deeply flawed and has been disproven, it was a very restrictive view of evolution that is very outdated. science is not static.

 

 

 

You obviously didn't even listen to the lecture by Noble or read the paper.

 

Listen, the neo-Darwinian synthesis made a number of assumptions and they have been proven false. There is no way round it.

 

Firstly the neo-Darwinian synthesis denied that acquired charateristics can be inherited. As noble cited, we now have evidence that they can be and after many generations. See his references on epigenetic inheritance.

 

There next assumption of neo-Darwinian synthesis was that all evolution is gradual, well we now know that saltational mechanisms have exist in evolution. Both gradual and saltational evolutionary events have occurred in evolution. Neo-Darwinian synthesis has been proven wrong for denying saltational events could occur.

 

Next the neo-Darwinian synthesis said all mutations are random, well if you watched the video, you would see evidence for direct mutation. the other assumption of the neodarwinism was the dogma of molecular biology. it has been broken.

 

Eugene koonin also wrote on this.

 

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472225/

 

Does the central dogma still stand?

 

so the assumptions of neo-Darwinian have been disproven. there is no Neo-Darwinism. the next evolutionary synthesis is characterised for a plurality of evolutionary processes that defies any general categorization or generalization.

Edited July 24, 2013 by Darryl Forests

[Ringer]

You obviously didn't even listen to the lecture by Noble or read the paper.

 

Listen, the neo-Darwinian synthesis made a number of assumptions and they have been proven false. There is no way round it.

 

Firstly the neo-Darwinian synthesis denied that acquired charateristics can be inherited. As noble cited, we now have evidence that they can be and after many generations. See his references on epigenetic inheritance.

It's not that simple. Epigenetic factors such as those, IIRC, are genetic switches that may be turned on or off dependent on environmental factors. This is very different from changes in phenotype directly affecting genotype.

 

There next assumption of neo-Darwinian synthesis was that all evolution is gradual, well we now know that saltational mechanisms have exist in evolution. Both gradual and saltational evolutionary events have occurred in evolution. Neo-Darwinian synthesis has been proven wrong for denying saltational events could occur.

Yes, so? This has been known this for over a decade. Keep in mind saltational evolution is not a couple generations, it's still an extremely long time, there is just some stability thrown in there.

 

Next the neo-Darwinian synthesis said all mutations are random, well if you watched the video, you would see evidence for direct mutation. the other assumption of the neodarwinism was the dogma of molecular biology. it has been broken.

Again, things that have been known for decades, what's your point? Certain types of mutations are more common than others, but some mutations are, very nearly, completely random.

 

Even Crick said that he did not know the definition of dogma when he named that, so don't take the name at face value.

 

Eugene koonin also wrote on this.

 

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472225/

 

Does the central dogma still stand?

 

so the assumptions of neo-Darwinian have been disproven. there is no Neo-Darwinism. the next evolutionary synthesis is characterised for a plurality of evolutionary processes that defies any general categorization or generalization.

No, the central dogma was never dogma. There is no dogma in science, you have brought nothing to the discussion that hasn't been discussed in the previous threads that have been linked. You have brought nothing to the discussion that the people here do not know. In short you have brought nothing to the discussion.

 

What you seem to be arguing is a name change, if so get over it. There is no reason to change a name that works well enough, the modern synthesis is exactly what the name implies. It is a synthesis of Darwinian and other macroevolutionary factors as well as information from molecular biology and other areas of biology. A name change is unnecessary and arguing over a name is meaningless. If one wants to make a contribution, collect data. If you want to argue over what something's name should be have a child.

[Arete]

You obviously didn't even listen to the lecture by Noble or read the paper.

 

Having attended a seminar on the topic at a globally recognized meeting, I feel qualified to comment without sitting through a youtube video.

 

BTW Darryl88 - is that you?

 

Firstly the neo-Darwinian synthesis denied that acquired charateristics can be inherited. As noble cited, we now have evidence that they can be and after many generations. See his references on epigenetic inheritance.

 

Keyword - both. We gained additional information about epigenetically acquired, as well as inherited characteristics some time ago.

 

There next assumption of neo-Darwinian synthesis was that all evolution is gradual, well we now know that saltational mechanisms have exist in evolution. Both gradual and saltational evolutionary events have occurred in evolution.

 

Keyword - both. We gained additional information about variability in rates of evolutionary change some time ago. Sometimes the rate is slow, as previously thought, now we know that sometimes the rate of evolutionary change is fast.

 

Next the neo-Darwinian synthesis said all mutations are random, well if you watched the video, you would see evidence for direct mutation.

 

Keyword - both. We gained additional information about variability in stochasticity of mutations some time ago. Some mutations are relatively random, as we thought, some are less so.

 

so the assumptions of neo-Darwinian have been disproven. there is no Neo-Darwinism. the next evolutionary synthesis is characterised for a plurality of evolutionary processes that defies any general categorization or generalization.

 

Ringer said it perfectly. The information provided by these new discoveries is a) Additional to existing theory not contrary to. None of the processes discovered in the substantial period of time since the 1940's dramatically disproves previous theory. They happen IN ADDITION to previously known mechanisms. b) It isn't exactly new information - evolutionary biology has taken on board and incorporated many new aspects of evolutionary theory as they've been discovered. c) No one in the field is denying that any of these processes exist, or play a role in evolution.

 

As I've previously argued, as Ringer seems to argue and PZ Meyers argues the whole "synthesis" is a fluctuating beast. it's a synthesis of new, old and embryonic ideas as to how organisms evolve. You seem to be playing semantics with names.

Edited July 24, 2013 by Arete

[CharonY]

Me thinks that that OP has not read the posts that have been put forward. No one is contesting that new information came about and it has been known for a long time that many tenets of the modern synthesis simply never held universally.

Just try to apply the species concept to prokaryotes, for example. Nonetheless they were kept around because simplifications are common when you develop models. The big questions is always how much you can leave out and have it still being useful.

 

Looking at the body of publications coming out since the 40s in evolutionary sciences, I am pretty confident that it held out pretty well. Also note that specialists in their field do not simply follow a paradigm blindly but adjust things according to the subject of their study. No evolutionary microbiologist would even mention reproductive isolation, for example.

 

All these things mentioned in the paper/talk have been around for decades, and not something we just found out. But so far no one is able to integrate all the knowledge in a useful manner. And neither does the author. As everybody is pointing out, just renaming things does not revolutionize it. Improve it, then you get to talk. (As a side note the dogma of molecular biology already got long int he tooth when I studied, and as many things in biology, it is just a convenient convention, in this case a simple model to teach proteinbiosynthethis. And it is hard to argue that it has been very successful).

 

And as I said before if you look at the literature, pushes to have a new modern synthesis been made pretty much since we started with genomics (let us say, around the 90s) but there is no integrative model yet. And Ophiolite makes a a good point (again) that in some cases (and political climates) keeping well known names has its advantages.

 

I will repeat myself: due to their complexity biological (and other complex) models are never fully accurate. The real question is always whether they are useful. People preoccupied with naming conventions are IMO valuing style over substance.

[Delta1212]

The word dinosaur means "terrible lizard." We now know that they weren't lizards, may have been warm-blooded, mostly had feathers and were the ancestors of birds.

 

Please choose one of the following:

A) We now know more about dinosaurs.

B) We should come up with a different name because "dinosaur" was used to describe the animal when we thought it had some slightly different characteristics than we do now.

C) Dinosaurs didn't exist because dinosaurs are lizards. The bones instead belong to a different kind of animal more closely related to birds that isn't a dinosaur.

 

 

I'd go with A, myself, but maybe that's just me.

[Ophiolite]

Well it isn't frustrating me at all...

 

Just as a suggestion, keep scientific discussions from swerving to a really bad direction of trying to disprove anything of the religious sense with science because it ain't going to work(that is just the way it is). Ultimately it will lead to a hole of insanity and evil(meaning the discussion won't end well).

Hi Unity+, I am slightly puzzled by your post. Nowhere in the post do I suggest that you might be frustrated, so I don't understand why you mentioned it.

 

I am also puzzled by your reference to "trying to disprove anything of a religious sense". I suppose this is related to my remark favouring the use of the term Darwinism because it would 'piss off creationists'. That was a lighthearted jibe at the obssession some creationists have for bandying around the word Darwinist as a catch-all to describe 99.9% of biologists. I wasn't seeking to disprove anything religious - just indulging in some gentle mockery. I don't see the evil in that.

 

If I misunderstood your points, please clarify.

[overtone]

The characteristic provision of weak points or areas of greater/lesser vulnerability to mutation (during times of stress or otherwise) along the line of code is itself inherited through DNA (maybe RNA also) recombination and replication, mother to child, yes?

 

As is the code that produces the ability to respond "epigenetically" to environomental factors, code which is inherited by progeny and selected over generations by the fluctuating pressures commonly experienced in the big world.

 

After all, such "epigenetic" features as various mechanisms of repair, shielding, expression rate boosting, expression timing, and the like, are familiar by now, and not regarded as challenges to any "central dogma".

 

One of the difficult aspects of getting a mental grip on Darwinian theory, and the area of great discovery celebrated by the physiologists in the OP, is the nature of the "environment" that does the selection in the standard two-step formulation. Finding great complexity in this environment, with consequent complexity in the selection pressures, seems to confuse people. IIRC even basics such as cooperation benefits rather than competition advantages have been at times presented as if they were evidence against Darwinian theory.

Edited July 24, 2013 by overtone

[CharonY]

In cases of mobile genetic element the site-dependence is actually more on the side of the element (e,g. type of transposase) and is therefore in principle not that tightly coupled to the host line per se.

Also note that certain areas that have low mutation rates may not be mechanistically protected, but if they are negatively selected against, we won't find them easily (or not at all, if they are fatal).

[Delta1212]

Hi Unity+, I am slightly puzzled by your post. Nowhere in the post do I suggest that you might be frustrated, so I don't understand why you mentioned it.

 

I am also puzzled by your reference to "trying to disprove anything of a religious sense". I suppose this is related to my remark favouring the use of the term Darwinism because it would 'piss off creationists'. That was a lighthearted jibe at the obssession some creationists have for bandying around the word Darwinist as a catch-all to describe 99.9% of biologists. I wasn't seeking to disprove anything religious - just indulging in some gentle mockery. I don't see the evil in that.

 

If I misunderstood your points, please clarify.

I believe Unity+ considers himself a creationist.

[hypervalent_iodine]

!

Moderator Note

Well-spotted, Arete.

 

Since they are the same person, I have merged their identical threads, Furthermore, as Darryl has asked to have bans on both accounts, and as I see no reason to keep this nonsense open, I am locking the thread.