Darwin Unhinged: The Bugs in Evolution

An interesting new article lays out how new advances in biology have now discredited the common Darwinian argument that attempts to debunk Michael Behe and claim that "cooption" can explain irreducible complexity, in particular the bacterial flagellum. The new research undermines virtually all possibility for neo-Darwinian RM + NS evolution to generate complex adaptations.

Some excerpts:

"Some of the most relevant research related to evolutionary timescales was conducted through Harvard’s Program for Evolutionary Dynamics and IST Austria. They published a key article (The Time Scale of Evolutionary Innovation, at https://journals.plos.org/ploscompbiol/a...bi.1003818 ) which lays out two crucial findings:

(1) The expected time required for a random search to find one member of a set of target sequences (e.g., nucleotide sequences corresponding to a functional gene) of length L increases exponentially with L. 
(2) The expected time required to find a target from a starting sequence that is only a “few steps away from the target set” is the same as from a starting sequence that is randomly chosen. 

(Analyzing the results of this study) the chances of any organism evolving a new protein of comparable length (500 amino acids) (that is, comparable to just one of the unique structural or assembly proteins of the flagellum rod or filament or other parts) in all of Earth’s history is much less than 1 chance in a trillion trillion. In addition, the numerical data on the exponential growth of the timescales can be interpolated to demonstrate that the chance of any novel protein much longer than 250 amino acids appearing would be miniscule. 

....the single evolutionary step of building just one part of the flagellum - the flagellar filament - requires the creation of the genes for the filament (FliC), the assembly cap (FliD), and the two joint-proteins (FlgK and FlgL) along with the genes’ regulatory regions. ...The number of amino acids associated with each protein are as follows: FliC — 498, FliD — 468, FlgK — 547, FlgL — 317. Their lengths all exceed the limit for a target that could ever be found in the entire history of the Earth, and most exceed the limit significantly. Compounding the challenge, all of the proteins are required before the filament can properly assemble, which dramatically increases the disparity between the available and the required waiting time.

The challenges for evolving the flagellar filament are actually far greater than described. The addition of any combination of the needed proteins to the genome results in a selective disadvantage until all four arrive with properly coordinated regulatory control regions. For instance, if the filament, joint, or assembly cap proteins were not all available precisely when needed, the filament structure would fail to assemble. Moreover, any protein not manufactured at the correct time would either fail to enter the transport gate, or it would enter at the wrong time and interfere with the assembly of other parts.

All evidence points to the conclusion that the formation of the flagellum requires vast quantities of new genetic information (e.g., new functional genes) to appear in a geological instant while the time required for any undirected process to generate the needed amount would exceed the age of the universe by hundreds of orders of magnitude. Similar insurmountable hurdles face the vast majority of attempts to invoke cooption to explain other irreducibly complex innovations. As biology research advances, the challenges faced by the cooption explanation appear increasingly intractable."

An interesting new article lays out how new advances in biology have now discredited the common Darwinian argument that attempts to debunk Michael Behe and claim that "cooption" can explain irreducible complexity, in particular the bacterial flagellum. The new research undermines virtually all possibility for neo-Darwinian RM + NS evolution to generate complex adaptations.

Some excerpts:

Did you look at the research article which is quoted? It explored a way to estimate exponential time scales for evolution, and it showed how a regeneration process enables evolution to work in polynomial time. Rather than discrediting the idea that evolution can generate complex adaptations, it showed a reasonable process whereby complex adaptations can be produced in reasonable time scales. Also, if Evolution News was jumping on this as proof that evolution follows exponential time scales, it wasn't a "finding" of the research that evolution does this, but rather a starting assumption built into their models. That claim is questionable, rather a given.

Linda

Did you look at the research article which is quoted? It explored a way to estimate exponential time scales for evolution, and it showed how a regeneration process enables evolution to work in polynomial time. Rather than discrediting the idea that evolution can generate complex adaptations, it showed a reasonable process whereby complex adaptations can be produced in reasonable time scales. Also, if Evolution News was jumping on this as proof that evolution follows exponential time scales, it wasn't a "finding" of the research that evolution does this, but rather a starting assumption built into their models. That claim is questionable, rather a given.

Linda

It depends on what you mean by "reasonable" and by "complex adaptations". 

The research paper is theoretical - and it comes up with very unrealistic estimates of the probability of a random search finding in any realistic time period an actual real-world amino acid target sequence for a target protein, as explained by Brian Miller in his Evolution News article. As he explains, the new study is unrealistic for several reasons, for instance because its assumptions disagree with experimental studies with mutating bacterial strains and Drosophila mutation studies. And most critically, the theoretical claims of the research study to have found a mechanism for evolution of new function in realistic time scales completely ignore the actual (non-theoretical) problem of target complexity in an actual real-world example such as the bacterial flagellum. 

As Miller explains, 

"As alluded to already, the single evolutionary step of adding the flagellar filament requires the creation of the genes for the filament (FliC), the assembly cap (FliD), and the two joint-proteins (FlgK and FlgL) along with the genes’ regulatory regions. The cap is not essential in one special group of bacteria, but it is believed to have been essential in the hypothetical common ancestor to all flagella. Each of these proteins is so highly specialized for its role in filament construction that it could not possibly serve any other cellular purpose. 

One can now assess for the addition of the filament a minimum required timescale. The number of amino acids associated with each protein are as follows: FliC — 498, FliD — 468, FlgK — 547, FlgL — 317. Their lengths all exceed the limit for a target that could ever be found in the entire history of the Earth, and most exceed the limit significantly. Compounding the challenge, all of the proteins are required before the filament can properly assemble, which dramatically increases the disparity between the available and the required waiting time. 

Conversely, one might start by assuming that all four proteins could form within a few billion years. The fact that timescales grow exponentially with the number of coordinated proteins would then constrain the average time for the appearance of an individual protein in standard laboratory studies of microorganisms to less than a decade and in nature to less than a day. This result clearly does not match reality since no evidence exists that any new protein has recently appeared in any species."   

 
Of course, you could claim that for this real-world example the target sequences were actually much more achievable. That somehow for each of these four or more long target flagellar proteins there exists a long developmental chain of similar intermediate amino acid sequences, where the protein of each had some other function or enough of the target flagellar function to make it advantageous or selectable over drift, and also which didn't significantly interfere with cellular function, and didn't interfere with each other especially if they came in out of the needed flagellar sequence. This is the assumption of a "fitness seascape" consisting of an expanse of closely-spaced little islands, completely contrary to actual research results. Then there is also the crucial time factor on getting all of this done in a long series of little steps. A lot of assumptions, that would have to be backed up by verifiable specifics. I don't think that is going to happen any time soon. Of course, the good Darwinian absolutely must make this assumption (the usual "just-so" story), since to him his belief system is the absolute truth.

It depends on what you mean by "reasonable" and by "complex adaptations". 

The research paper is theoretical - and it comes up with very unrealistic estimates of the probability of a random search finding in any realistic time period an actual real-world amino acid target sequence for a target protein, as explained by Brian Miller in his Evolution News article. As he explains, the new study is unrealistic for several reasons, for instance because its assumptions disagree with experimental studies with mutating bacterial strains and Drosophila mutation studies. And most critically, the theoretical claims of the research study to have found a mechanism for evolution of new function in realistic time scales completely ignore the actual (non-theoretical) problem of target complexity in an actual real-world example such as the bacterial flagellum. 

As Miller explains, 

 
Of course, you could claim that for this real-world example the target sequences were actually much more achievable. That somehow for each of these four or more long target flagellar proteins there exists a long developmental chain of similar intermediate amino acid sequences, where the protein of each had some other function or enough of the target flagellar function to make it advantageous or selectable over drift, and also which didn't significantly interfere with cellular function, and with each other especially if they came in out of the needed flagellar sequence. This is the assumption of a "fitness seascape" consisting of an expanse of closely-spaced little islands, completely contrary to actual research results. Then there is also the crucial time factor on getting all of this done in a long series of little steps. A lot of assumptions, that would have to be backed up by verifiable specifics. I don't think that is going to happen any time soon. Of course, the good Darwinian absolutely must make this assumption (the usual "just-so" story), since to him his belief system is the absolute truth.

I don't see that there is anything new here. The paper is almost 5 years old. It starts by making assumptions which are already considered highly debatable among scientists working in the field (that time scales are exponential). And uses that as an excuse to support their particular regeneration model which does allow for reasonable time scales. 

The IDers seem to jump on this only because the authors made an assumption they also like to make - the time scales are exponential. The authors of the paper certainly didn't conclude that this meant Evolutionary Theory is all wrong, and God is necessary. The rest of the Evolution News article seemed to just be a reiteration of their assumptions about time scales - assumptions which are far from certain and have been contradicted by the empirical findings in the field of evolution.

"Cooption is implausible if you use assumptions which would make it implausible."

I don't see that there is anything new here. The paper is almost 5 years old. It starts by making assumptions which are already considered highly debatable among scientists working in the field (that time scales are exponential). And uses that as an excuse to support their particular regeneration model which does allow for reasonable time scales. 

The IDers seem to jump on this only because the authors made an assumption they also like to make - the time scales are exponential. The authors of the paper certainly didn't conclude that this meant Evolutionary Theory is all wrong, and God is necessary. The rest of the Evolution News article seemed to just be a reiteration of their assumptions about time scales - assumptions which are far from certain and have been contradicted by the empirical findings in the field of evolution.

"Cooption is implausible if you use assumptions which would make it implausible."

I notice that as usual with Darwinists you don't actually address the technical issues brought up by the article such as the specific flagellar filament proteins and how they could have been originated by RM + NS and cooption. You're right - nothing new here.

Did you look at the research article which is quoted? It explored a way to estimate exponential time scales for evolution, and it showed how a regeneration process enables evolution to work in polynomial time.

Are we talking about a way to find (in the evolutionary sense) proteins in a time polynomial in N, the number of amino acid residues in the protein?

Other than maybe using a quantum computer, I can't imagine any way to do this.

It has always seemed to me that as soon as science knew about the structure of proteins and the way this structure is encoded in DNA/RNA, this is the key question.

I can't see where you linked to this article - can you post the link here please?

I notice that as usual with Darwinists you don't actually address the technical issues brought up by the article such as the specific flagellar filament proteins and how they could have been originated by RM + NS and cooption.

Right, because the assumptions, on which the "technical issues" are based, don't seem to be valid. This would make any "technical issues" moot.
Linda

Are we talking about a way to find (in the evolutionary sense) proteins in a time polynomial in N, the number of amino acid residues in the protein?

Other than maybe using a quantum computer, I can't imagine any way to do this.

It has always seemed to me that as soon as science knew about the structure of proteins and the way this structure is encoded in DNA/RNA, this is the key question.

I can't see where you linked to this article - can you post the link here please?

The article was linked, by nbtruthman, in the post I was responding to. It didn't occur to me to link to it, yet again, in my response, given it was right there. Live and learn, I guess.

Here it is again:

https://journals.plos.org/ploscompbiol/a...bi.1003818

Linda

As Miller explains, 

 
Of course, you could claim that for this real-world example the target sequences were actually much more achievable. That somehow for each of these four or more long target flagellar proteins there exists a long developmental chain of similar intermediate amino acid sequences, where the protein of each had some other function or enough of the target flagellar function to make it advantageous or selectable over drift, and also which didn't significantly interfere with cellular function, and with each other especially if they came in out of the needed flagellar sequence. This is the assumption of a "fitness seascape" consisting of an expanse of closely-spaced little islands, completely contrary to actual research results. Then there is also the crucial time factor on getting all of this done in a long series of little steps. A lot of assumptions, that would have to be backed up by verifiable specifics. I don't think that is going to happen any time soon. Of course, the good Darwinian absolutely must make this assumption (the usual "just-so" story), since to him his belief system is the absolute truth.

I found that paper hard to read - is it your understanding that the paper is postulating that each of those proteins needed to construct the flagellum can evolve down a sequence of stages, each of which is useful (and so selectable by Natural selection)?

If this is the case, that seems to be a pretty unlikely hypothesis - at least someone would have to demonstrate what that sequence is!

I found that paper hard to read - is it your understanding that the paper is postulating that each of those proteins needed to construct the flagellum can evolve down a sequence of stages, each of which is useful (and so selectable by Natural selection)?

If this is the case, that seems to be a pretty unlikely hypothesis - at least someone would have to demonstrate what that sequence is!

I also found it hard to read. It is entirely theoretical and doesn't tie its analysis and results to any particular real-world example like the bacterial flagellum. As I have said earlier, the authors implicitly assume that there always must be some sort of achievable closely spaced sequence of stages, where each must be useful or at least non-deleterious. As you mention, for this to be believable it would need to be demonstrated. Brian Miller in his Evolution News article points out how the flagellar filament proteins example can't remotely plausibly fit this assumption. Anyway, the authors of this paper try to find a way this can happen in some sort of realistic evolutionary time, rather than the intractably greater time shown by many analyses. They come up with the "regeneration" hypothesis:

"What are then adaptive problems that can be solved by evolution in polynomial time? We propose a “regeneration process”. The basic idea is that evolution can solve a new problem efficiently, if it is has solved a similar problem already. Suppose gene duplication or genome rearrangement can give rise to starting sequences that are at most k  point mutations away from the target set, where k is a (small) number that is independent of the length L (of the protein's amino acid sequence). It is important that starting sequences can be regenerated again and again. We prove that L^k+1 many searches are sufficient in order to find the target in polynomial time with high probability.... There are two key aspects to the “regeneration process”: (a) the starting sequence is only a small number of steps away from the target; and (b) the starting sequence can be generated repeatedly. This process enables evolution to overcome the exponential barrier. The upper bound, , may possibly be further reduced, if selection and/or recombination are included." 

As the bolded passage shows, in order to try to make their scheme work they make some very unrealistic assumptions right at the start - that there are very many peaks in the fitness landscape and that they are closely spaced, that each of the many stages is providentially only a few mutations away from the adjacent ones. And they also assume that the regions in between are only neutral, not deleterious to fitness. Earlier in the article they say, "We approximate the fitness landscape by broad peaks and neutral regions...".