Evolutionary biologist sees mutation driving evolution and thinks natural selection is of secondary importance

_{Denyse O'Leary

January 9, 2014

Evolution, Intelligent Design}

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The author is Matastoshi Nei, Evan Pugh Professor of Biology and Director of the Institute of Molecular Evolutionary Genetics, who seems well-connected in the science world :

The purpose of this book is to present a new mechanistic theory of mutation-driven evolution based on recent advances in genomics and evolutionary developmental biology. The theory asserts, perhaps somewhat controversially, that the driving force behind evolution is mutation, with natural selection being of only secondary importance. The word ‘mutation’ is used to describe any kind of change in DNA such as nucleotide substitution, gene duplication/deletion, chromosomal change, and genome duplication. A brief history of the principal evolutionary theories (Darwinism, mutationism, neo-Darwinism, and neo-mutationism) that preceded the theory of mutation-driven evolution is also presented in the context of the last 150 years of research. However, the core of the book is concerned with recent studies of genomics and the molecular basis of phenotypic evolution, and their relevance to mutation-driven evolution. In contrast to neo-Darwinism, mutation-driven evolution is capable of explaining real examples of evolution such as the evolution of olfactory receptors, sex-determination in animals, and the general scheme of hybrid sterility. In this sense the theory proposed is more realistic than its predecessors, and gives a more logical explanation of various evolutionary events.

Nicolas Galtier, introducing the book at Systematic Biology, offers a psychological explanation for the current obsession with Darwin’s natural selection:

There must be reasons for this, of which one is perhaps historical. To convince people that biological entities were not god-made creatures, Darwin and its followers had to simultaneously argue 1) that living forms change in time and 2) that their adaptations are sufficiently well explained by the process of natural selection. So, the two concepts have been and still are tightly associated in the context of anticreationist arguments. There might also be psychological reasons. Natural selection, unlike divine creation, is not an intuitive idea. Those who adopt it typically like it very much, and can hardly resist coming back to it again and again, finding the living world even more marvelous knowing that it was not generated by a creator. In a way, natural selection has somewhat replaced divine creation in many people’s minds as the process responsible for the beauty of nature.

The new book Mutation-Driven Evolution firmly opposes this view of natural selection as the unique biological creative force. …

You’d have to pay or sign in to read more. Even the review at Trends in Ecology & Evolution is paywalled.

Comments

Sebestyen, It's useless to argue with wd400 regarding "junk" DNA. Despite amazing recent discoveries, wd400 is still grimly clinging on to the sinking ship of "junk" DNA, and no amount of evidence will change that. The proportion of "junk" DNA has been revised from an estimate of 96% (as quoted by Dr. Ohno's 1972 paper about junk DNA), to about 99%, and now down to about 20% and shrinking. Statements such as this
Recent advances have established that the DNA of a pseudogene, the RNA transcribed from a pseudogene, or the protein translated from a pseudogene can have multiple, diverse functions and that these functions can affect not only their parental genes but also unrelated genes. Therefore, pseudogenes have emerged as a previously unappreciated class of sophisticated modulators of gene expression, with a multifaceted involvement in the pathogenesis of human cancer. (Laura Poliseno, "Pseudogenes: Newly Discovered Players in Human Cancer," Science Signaling, 5 (242) (September 18, 2012).
are apparently interpreted by wd400 as "most DNA is junk anyway," demonstrating his acquired immunity to both information and logic. In the January 11, 2014 issue of Medical News, we read
The term (junk DNA) is currently, however, a somewhat outdated concept, being used mainly in popular science and in a colloquial way in scientific publications, and may have slowed research into the biological functions of noncoding DNA.
Yes, most certainly slowed research! In a paper mentioned in UD http://www.nature.com/ncomms/2014/140107/ncomms3914/full/ncomms3914.html we read the following:
Various non-coding regions of the genome, once presumed to be ‘junk’ DNA, have recently been found to be transcriptionally active. In particular, pseudogenes are now known to have important biological roles.
Nevertheless, wd400 remains unconvinced, so Sebestyen, I would not waste any more time to try to enlighten someone who refuses to be enlightened. -QQuerius_{January 11, 2014
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PS: On what ID is, I suggest to you that you read the 101 survey here, and understand that Design thinkers recognise themselves in that mirror, but instantly spot the Wikipedia piece as a hatchet job based on loaded strawman caricatures and red herring distractors. KFkairosfocus_{January 10, 2014
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LP: I think regarding OOL, you should pause and view the video here, just as a start. KFkairosfocus_{January 10, 2014
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LP: Actually, irreducible complexity is a commonplace in complex organised systems [think of what happens to the engine in your car when just one core component fails), and it is unsurprising that such also occurs in living systems in several contexts and scales. To see what is going on, check out how without each and all of heat, fuel, oxidiser and an uninterfered with heat generating chain reaction, a fire will not start or if started will go out: four critical enabling causes, each necessary and in that case together jointly sufficient. Indeed, a concept very much like IC underlies how gene knockout (and restoration) studies work. KFkairosfocus_{January 10, 2014
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LP, re:
RV + NS can generate “complex functional information” as good as any designer (excluding obviously Gods or other supernaturals)
We know that a priori materialism demands that this be so, however the first problem is that the vera causa principle of explanation demands that you show this to occur within our observation or you do not have an actual known cause. And, we freely state that you cannot give us a good example of 500 - 1,000+ bits of functionally specific complex organisation and associated information originating within our observation by blind chance and/or mechanical necessity alone. We confidently say that, after years of seeing tries and seeing dozens of failed attempts. These observations, being backed up by needle in haystack analysis that shows that:
a: the 10^57 atoms of the Sol system -- our effective universe for chemical level interactions -- acting as observers of 500 fair coins each, b: flipped for each such set every 10^-14 s [as fast as ionic chem rxns] for 10^17 s, c: will give us a sample of the config space for 500 bits from 000 . . . 0 to 111 . . . 1 that stands as one straw to a cubical haystack 1,000 light years across. d: That's about as thick as our galaxy at its central bulge. In short, e: there is very good reason to conclude that if such a search were undertaken, in such a haystack superposed on our galactic neighbourhood, we would with all but absolute certainty only find straw on any reasonable blind search. Where also f: the set-up would essentially take up the 10^80 atoms of our observed cosmos for the observers, coins and tables as well as tossing mechanisms. If you want to be more stringent g: 1,000 coins would by far more intensely overwhelm the atoms of the observed cosmos acting as observers of 1,0000 coin sets. ____________ So, h: the abstract logical possibility of FSCO/I by chance is not an empirically plausible assertion.
The only plausible explanation of FSCO/I is design, and that is in fact backed up by billions of directly observed cases all around us, including posts in this thread. When you turned up at UD recently, we did not assign your posts to noise on the Internet, but accepted that here is an intelligent entity using this handle. Though, it probably is a sock puppet for someone or a group of persons with different identities. In short, you need to look back at your assumptions and confident manner assertions, to see where you have gone wrong. KFkairosfocus_{January 10, 2014
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To date no one has shown irreducible complexity in living things.
This is absolutely not true.Upright BiPed_{January 10, 2014
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Lincoln Phipps: 1) You say:
but it does not follow that “the same cannot be said of the mix RV + NS, because the possibilities of NS are extremely limited, if compared to those of IS.
Maybe it does "not follows", but it is true. Obviously, my brief statement did not go into the details of why it is true. Essentially, there are many reasons why IS is extremely more powerful than NS: a) NS can act only if the new information confers a reproductive advantage. IS can define in advance any function, and select for it. b) For NS to happen, the reproductive advantage (and therefore the local function or functions that confer that advantage) must be strong enough to ensure an expansion of the mutated clone in the population. IS can measure the desired function at any desired level, even when it is still very weak, and not likely to give any immediate advantage. c) IS can profit from the understanding of natural laws by the designer. For example, the context where random variation is applied can be more or less controlled, the type of variation can be selected, even if the variation itself is random, and the target of the variation can be delimited. We see these principles at work even in cases of protein engineering already embedded in the genome, such as antibody maturation after the first immune response. 2) You say:
RV + NS can generate the complex functional information we see in life. To date no one has shown irreducible complexity in living things. Ignorance rules here and the gaps in our knowledge are seen as impassible for no good reason that for ID supporters to claim it can’t be crossed.
My only comment: I have rarely read a more nonsensical statement. 3) You say:
You ask “So, how do you think that RV + NS build a new enzyme?” and the answer is through mutations of genomes. The gaps here are understanding the pathway from simple polypeptides to larger proteins. The ID claim is that this gap can’t be traversed through small steps. As we do know that there are miniproteins then that’s a ID bluff.
You seem to forget two very important points: a) The mini proteins you refer to have no function. b) The miniproteins you refer to are not selectable stepts to a bigger functional protein. Why are you so excited that miniproteins exist? You cited (in another thread) a couple of designed, artificial ones, but obviously there are natural peptides that have some function. In no way that means that they are selectable steps to longer functional proteins. You may keep your dogmatic faith in pathways that do not exist, that have no logical reason to exist, and that have never been observed, or simply reasonably hypothesized. I am interested in facts, not dogmatic fantasies. 4) You say:
The “mechanism to protect information” will have evolved over the multi-billion years from the first genome. The first genome that did this would be selected for (in that it would persist longer than those that did not have such mechanisms (that’s for Joe). The mechanisms will not have all burst into life at once but will slowly grow in complexity. I don’t know if it is over 1 year or 1 billion years. The ID dogma is simple; the cell is too complex and therefore it was designed. You can’t ask what did the designing or how it was done or where this was done, or when it was done or what about the design of the designers or the purpose of the design. The reply from science is that the evidence suggests life formed from a pre-biotic Earth around 3.5 billion years ago and that all life can be traced back to a single common ancestor and that as our knowledge increases then only natural mechanisms are ever needed to explain what is seen.
No comment. I don't like to offend people.gpuccio_{January 10, 2014
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Lincoln Phipps:
The ID dogma is simple; the cell is too complex and therefore it was designed.
That is the cartoon version of ID.
You can’t ask what did the designing or how it was done or where this was done, or when it was done or what about the design of the designers or the purpose of the design.
Of course you can ask those questions. They are just separate from the question "is it designed or not?" Lincoln, reality dictates that in the absence of direct observation or designer input, the only way to make any scientific determiantion to the designer(s), specific process(es) used and all the other questions, we study the deisgn and all relevant evidence. That is how it is done in forensic science, archaeology and SETI.Joe_{January 10, 2014
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GAs are designed to solve problems- they are a design tool. The selection coefficient is artificial and that is what makes it intelligent selection. The goal is to meet the spec of that selection coefficient. GAs employ a goal-oriented targeted search. OTOH NS isn't a search...Joe_{January 10, 2014
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Sixbooth, Selection isn't a requirement for change. Change is the groundstate, selection is required for directional change (positive selection) or status (negative selection). PeterJ, It's hard to talk about a general case, as many variables go into how a particlar adaptive response arises (or doesn't) in a population. But one important consequence of the fact most mutations are harmless in a given environment is that genetic diversity can build up. Alleles that are roughly equivalent in environment A might have quite different fitnesses in environment B. But adaptation doesn't have to be in the context of a degrading environment - it can also be a bonus. Look at lactase persistance in humans as an example - a mutation that was probably always arising in human populations became useful with the advent of farming and took off (multiple times in fact).wd400_{January 10, 2014
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Lincoln, I know NS is a result. Some evolutionists think NS is actual selection. And again I ask for evidence of NS actually doing something.Joe_{January 10, 2014
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Lincoln Phipps:
when someone uses a GA then they do not design the “genome” but pre-define what is fit.
The pre-define what they are looking for- ie an antenna that can do X. GAs employ goal-oriented targeted searches as the mechanism for solving their problem.Joe_{January 10, 2014
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Mapou, I'm not insulting your intelligence. I'm not playing a game or trying to win debating points. I think that one of the reasons we know most mutations are harmless is the relatively high per-indivdual mutation rate. Proofreading enzymes and the like don't come into it, since they prevent mutations from happening rather than removing mutations that have entered a gene pool. It's OK to have been wrong about something. But if there is any point to having discussions like this both party's need to be willing to modify their views. If all you can do is hurl invective at someone I don't see much point in engaging with you.wd400_{January 10, 2014
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gpuccio, 1) RV + NS can generate "complex functional information" as good as any designer (excluding obviously Gods or other supernaturals). You rightly state that "is well known that a mix of RV + Intelligent selection can be extremely more efficient than RV alone, and many examples of that are known, including bottom up protein engineering." but it does not follow that "the same cannot be said of the mix RV + NS, because the possibilities of NS are extremely limited, if compared to those of IS." No matter how smart the designer in an IS is, if the organism cannot survive in the ecological niche then the ID was wasting its time. NS is the ultimate trump card. Be it top-down or bottom - up, the ultimate fitness is defined by the niche and the designer must be present accurately mimic the natural world. 2) RV + NS can generate the complex functional information we see in life. To date no one has shown irreducible complexity in living things. Ignorance rules here and the gaps in our knowledge are seen as impassible for no good reason that for ID supporters to claim it can't be crossed. 3) You ask "So, how do you think that RV + NS build a new enzyme?" and the answer is through mutations of genomes. The gaps here are understanding the pathway from simple polypeptides to larger proteins. The ID claim is that this gap can't be traversed through small steps. As we do know that there are miniproteins then that's a ID bluff. 4) The “mechanism to protect information” will have evolved over the multi-billion years from the first genome. The first genome that did this would be selected for (in that it would persist longer than those that did not have such mechanisms (that's for Joe). The mechanisms will not have all burst into life at once but will slowly grow in complexity. I don't know if it is over 1 year or 1 billion years. The ID dogma is simple; the cell is too complex and therefore it was designed. You can't ask what did the designing or how it was done or where this was done, or when it was done or what about the design of the designers or the purpose of the design. The reply from science is that the evidence suggests life formed from a pre-biotic Earth around 3.5 billion years ago and that all life can be traced back to a single common ancestor and that as our knowledge increases then only natural mechanisms are ever needed to explain what is seen.Lincoln Phipps_{January 10, 2014
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Joe, anything unexpected is intrinsically "information". Mutations are unexpected and so they are always "information".Lincoln Phipps_{January 10, 2014
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Joe, when someone uses a GA then they do not design the "genome" but pre-define what is fit. Such a designer has no clue as to what genome is fit. They are ignorant of genomes. That is not "intelligent design" any more than a race driver can be called a designer of ECU curves for an engine because he can compare the engine performances.Lincoln Phipps_{January 10, 2014
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Joe, why don't you read how I have already said that NS doesn't select ? If it selected then it would have to search a vast problem landscape and that's pretty well impossible. NS is the end result that we see when some things live and some things die before they can reproduce. It is you that seems to be seeking something.It should be you that needs to read your own book recommendations.Lincoln Phipps_{January 10, 2014
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Alan Fox doesn't seem tp realize that genetic algorithms are am example of RV and intelligent selection.Joe_{January 10, 2014
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Lincoln Phipps- Why isa it that you cannot present any evidence for natural seelction av=ctually doing something? BTW NS does NOT select- Read Mayr "What Evolution Is"Joe_{January 10, 2014
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LP:
I said “Mutations do provide information but it is natural selection that makes this specific to the niche that the organism resides.” and you asked for evidence.
Do you have any that supports your claim?
Mutations are information. Anything unexpected is information by definition. As for the differences in niche, it would be possible to show the difference between two niches e.g. take a fish and stick it into a forest environment and then measure the population of fish after a few generations. Equally take say a hedgehog and stick in into a sea vent environment and observe how it develops.
Umm that isn't evidence for natural selection.Joe_{January 10, 2014
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Lincoln Phipps: Counter-thoughts: 1) What contradiction are you seeing? RV is random by definition. And so? NS is not random. I have just stated that RV cannot certainly generate complex functional information, because of the known probabilistic barriers. Where is the contradiction? Please, explain. Probabilistic barriers certainly apply also to ID if the designer uses RV as part of his strategy. But it is well known that a mix of RV + Intelligent selection can be extremely more efficient than RV alone, and many examples of that are known, including bottom up protein engineering. Unfortunately, the same cannot be said of the mix RV + NS, because the possibilities of NS are extremely limited, if compared to those of IS. Finally, it is not necessary, a priori, that the designer use RV as part of his strategy. Design can be top down as well as bottom up. 2) RV + NS cannot generate complex functional information (dFSCI) any more than RV alone, for the reasons I have debated many times here, and that I am ready to debate again anytime. The main reason is that complex functional information cannot be deconstructed into simpler, naturally selectable steps. Please, show even one case of new original dFSCI generated in a non design system. 3) I often give the example of enzymes. An enzyme is a functional protein with a well defined "local" function: it can accelerate a given biochemical reaction. That function is independent from the environment. It can be more or less useful for the fitness, but unless the local function (the biochemical activity) is present, the protein cannot be useful. And enzymes are frequent and complex. So, how do you think that RV + NS build a new enzyme? 4) The "mechanism to protect information" (DNA repair, checkpoints during the cell cycle, and so on) is itself extremely complex. It could never "evolve" by neo darwinisn mechanisms, like any other instance of dFSCI.gpuccio_{January 10, 2014
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I don’t have long on here today but would like to ask a question on a matter that has been bugging me for quite some time. WD400 makes the claim: “Natural selection is a requirement for stasis. THanks to mutation and finite population sizes, change is the gound state for any evolutionary process. To prevent change form happening you need some non-random force, and that force is “balancing selection” keeping creatures similar and well-adapted to their niche.” What I can’t get my head around is this; the length of time it would take a certain organism to adapt to a certain change in the environment (by means of random mutations), before the actual mutations themselves had accumulated enough (or had manufactured the necessary physiological changes) that would enable the said organism to survive? This to me is a real conundrum, which unfortunately is made all the more confusing by WD’s statement. They can’t both be right, surely? Either an organism changes by small steps over vast amounts of time to adapt to whatever environmental change it has been challenged by (preferably before said species goes extinct), or, it simply stays the same, but survives anyway. Evolution?PeterJ_{January 10, 2014
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PeterJ, I was replying to Joe so lets see if he notices that there are differences between these example niches. I hope he sees it as a thought exercise and doesn't demand evidence of the survival of hedgehogs in sea vents as I have not actually seen how well hedgehogs survive in that environment. I suspect he'll see that as another example of the indoctrination of Evolutionists and the bluff of Darwinism.Lincoln Phipps_{January 10, 2014
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LP@30 "Equally take say a hedgehog and stick in into a sea vent environment and observe how it develops." Seriously? :)PeterJ_{January 10, 2014
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gpuccio, also just a couple of thoughts... 1) You present a contradiction. Either something is random or it is not. RV on its own provides information which is why NS is important as that filters. The probabilistic barriers also apply to an ID too unless it is outside of nature if the ID is using any kind of RV. 2) RV+NS gives the same as a complex specified information i.e. they work together. NS selects candidate variations and over time the complexity increases as variation is added to what was already selected. 3) The wording of "defend what is already there" in the last sentence is nuanced; the process of adaptation is a balance and it is based on fitness. If the environmental niche of the organism does not change then there is no obvious change in the results but if the niche changes then the genome changes after the fact. ID-centric view is that the genome is changed in anticipation of the niche change but the naturalism view is that all genomes have variation and so what fitness a genotype has is with respect to the niche and if a genotype is placed in a different niche then it has a different fitness. There is no defence of the genotype by NS nor is there any prescience in the genotype for unexpected future niche changes. 4) As life has been on this planet for a few billion years then it is expected that mechanisms to protect information would have evolved. Why ? Well if we assume mutations have always existed then those phenotypes that have a genotype that can persist with the mutation load will be naturally selected (i.e. more fit) compared to those organisms that fail with a mutation load. What we end up seeing after this 3.5 billion year war with entropy are only those organisms that have information protection mechanisms. And equally that means that early life forms will not have these mechanisms.Lincoln Phipps_{January 10, 2014
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Just a couple of thoughts: 1) Of course a theory based mainly on random variation can be compatible only with an ID scenario. RV is completely incapable of building new complex functional information, for the probabilistic barriers we all well know. If variation is all that is there, then it has to be guided variation. 2) It is rather obvious, also, that NS has almost no role in selecting positive variation by its reproductive advantage, except for very simple adaptations. The reason is extremely simple: as new complex functional information cannot be the result of RV, as already said, there is not opportunity for NS to select what cannot appear. 3) However, there is no doubt, IMO, that NS has an important role as negative selection, that is by eliminating at least part of negative variation. There can be no doubt that living beings who undergo random mutations that are incompatible with life simply die. We have many examples of that even in humans. So, the so called "purifying" role of NS can scarcely be denied. But, as said by many here, its only result is to favor stasis, to defend what is already there. 4) Finally, even that "purifying", protecting role of negative NS has many limits. Only severe mutations are really eliminated. As we all know, even from human genetic pathologies, most deleterious mutations can and do survive in the population. Moreover, living organism have in themselves very complex, intelligent systems of preservations of their genomic integrity, which are much more powerful than simple negative NS. And still, negative mutations continue to exist and survive.gpuccio_{January 9, 2014
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wd400, I insult you because you insult my intelligence. You can go fly a kite, for all I care.Mapou_{January 9, 2014
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So, apart from your overwhelming need to insult me, I dint see an answer here. If mutations, being those copying errors that escape proofreading and enter the next generation, are soverwhelmingly deleterious why aren't you dead?wd400_{January 9, 2014
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Joe, I said "Mutations do provide information but it is natural selection that makes this specific to the niche that the organism resides." and you asked for evidence. Mutations are information. Anything unexpected is information by definition. As for the differences in niche, it would be possible to show the difference between two niches e.g. take a fish and stick it into a forest environment and then measure the population of fish after a few generations. Equally take say a hedgehog and stick in into a sea vent environment and observe how it develops.Lincoln Phipps_{January 9, 2014
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I simply find it amazing that evolution evolved a mechanism to slow down evolution. All without any intelligence. That's just amazing!sixthbook_{January 9, 2014
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