(2018-12-21, 07:09 PM)nbtruthman Wrote: [ -> ]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."
(2018-12-22, 03:07 AM)fls Wrote: [ -> ]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.
(2018-12-21, 11:38 AM)fls Wrote: [ -> ]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?
(2018-12-22, 09:17 AM)nbtruthman Wrote: [ -> ]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
(2018-12-22, 12:30 PM)David001 Wrote: [ -> ]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
(2018-12-21, 07:09 PM)nbtruthman Wrote: [ -> ]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!
(2018-12-22, 08:49 PM)David001 Wrote: [ -> ]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:
Quote:"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...".
New research keeps making the simultaneous Cambrian Explosion appearance of many complex new body plans harder and harder for Darwinian explanations. Now it appears that complicated exoskeletons, nervous systems, brains, eyes, other body systems, etc. including the vertebrate plan all appeared in less than half a million years. Good luck to the evolutionary biologists in trying to explain all this by RM + NS.
At
https://phys.org/news/2018-12-uranium-le...unger.html:
Quote:"The international research team dated suitable minerals from several volcanic ash layers in Southern Namibia by means of the uranium-lead method. This uses the radioactive decay chain of uranium in the mineral zircon to determine the exact time of the rock's origin. "We took the samples at the boundary between the Precambrian and Cambrian – the two geological eras can easily be distinguished by their respective fossils," explains Linnemann. "Our highly precise dating shows that the "Cambrian explosion" occurred approximately 2 million years later than we had previously assumed.""
Note the predictable exercise in presumptuous hand-waving:
Quote:"Moreover, the scientists' data series reveal that the development of the fauna took place within a very short period. The transition from the "Ediacara biota" – multi-celled but very simply organisms – to the diverse Cambrian life forms occurred over less than 410,000 years. "From a geological point of view, this represents a veritable sprint," according to the research team. Based on the current study, this rapid faunal change may be best explained as a kind of "biological arms race": New fundamental traits accelerated the subsequent evolution and fueled the next "adaptive breakthrough." "For example, if an organisms became increasingly mobile and fed on prey, previously even less mobile animals had to come up with new ways to protect themselves – which may have led to the rapid development of shells or skeletons. One achievement thus engendered the next – and, by necessity, within a shortened period of time," says Linnemann in summary."
(2018-12-24, 08:01 PM)nbtruthman Wrote: [ -> ]Note the predictable exercise in presumptuous hand-waving:
Lol. Because Goddidit isn't at all presumptuous hand-waving.
Linda
(2018-12-25, 11:23 AM)fls Wrote: [ -> ]Lol. Because Goddidit isn't at all presumptuous hand-waving.
Linda
Is that the best you can do? Instead of addressing the research news item you bring up the old "God Did It" myth about ID. Instead of addressing the evidence that Darwinian evolution is incapable of explaining the Cambrian event, how all the new genetic information came about that was required for the almost 20 new body plans that appeared suddenly in Cambrian layers, you bring out the old "God Did It" canard.
To claim that ID is an appeal to "God Did It" thinking is deliberately misguided. For most ID advocates, God has little to do with the field of Intelligent Design. ID merely observes that mindless, materialistic processes simply fail to explain or adequately describe many aspects of living things, in particular their origin. It is recognizing the clear design inference based on the data. Meyer describes the foundation of ID quite clearly, “the theory of intelligent design holds that there are tell-tale features of living systems and the universe that are best explained by an intelligent cause — that is, by the conscious choice of a rational agent — rather than by an undirected process”.
This is merely an attempt to distract from the scientific debate that the Darwinists can't win on the merits.