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Evolution driven by laws? Not random mutations?

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So claims a recent book, Arrival of the Fittest, by Andreas Wagner, professor of evolutionary biology at U Zurich in Switzerland (also associated with the Santa Fe Institute). He lectures worldwide and is a fellow of the American Association for the Advancement of Sciences.

From the book announcement:

Can random mutations over a mere 3.8 billion years solely be responsible for wings, eyeballs, knees, camouflage, lactose digestion, photosynthesis, and the rest of nature’s creative marvels? And if the answer is no, what is the mechanism that explains evolution’s speed and efficiency?

In Arrival of the Fittest, renowned evolutionary biologist Andreas Wagner draws on over fifteen years of research to present the missing piece in Darwin’s theory. Using experimental and computational technologies that were heretofore unimagined, he has found that adaptations are not just driven by chance, but by a set of laws that allow nature to discover new molecules and mechanisms in a fraction of the time that random variation would take.

From a review (which is careful to note that it is not a religious argument):

The question “how does nature innovate?” often elicits a succinct but unsatisfying response – random mutations. Andreas Wagner first illustrates why random mutations alone cannot be the cause of innovations – the search space for innovations, be it at the level of genes, protein, or metabolic reactions is too large that makes the probability of stumbling upon all the innovations needed to make a little fly (let alone humans) too low to have occurred within the time span the universe has been around.

He then shows some of the fundamental hidden principles that can actually make innovations possible for natural selection to then select and preserve those innovations.

Like interacting parallel worlds, this would be momentous news if it is true. But someone is going to have to read the book and assess the strength of the laws advanced.

One thing for sure, if an establishment figure can safely write this kind of thing, Darwin’s theory is coming under more serious fire than ever. But we knew, of course, when Nature published an article on the growing dissent within the ranks about Darwinism.

In origin of life research, there has long been a law vs. chance controversy. For example, Does nature just “naturally” produce life? vs. Maybe if we throw enough models at the origin of life… some of them will stick?

Note: You may have to apprise your old schoolmarm that Darwin’s theory* is “natural selection acting on random mutations,” not “evolution” in general. It is the only theory that claims sheer randomness can lead to creativity, in conflict with information theory. See also: Being as Communion.

*(or neo-Darwinism, or whatever you call what the Darwin-in-the-schools lobby is promoting or Evolution Sunday is celebrating).*

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Comments
#522 DNA_Jock
I see you opted for the buns.
Why did you write that? What did you mean by that statement you wrote?Dionisio
November 7, 2014
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One very interesting thing about questions like the ones posted on #512 is that their correct answers lead to deeper questions, which eventually point to an elaborate information-processing system that’s a real delight for any passionate computer scientist or engineer. Do you understand this?
Yes. One of the cool things Robert M. Pirsig points out in “Zen and the Art…” is that the more tests you do, the more hypotheses increase in number. Makes science a lot of fun, if rather poorly remunerated. I see you opted for the buns. :)DNA_Jock
November 7, 2014
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#517 DNA_Jock
I did once work on human actin genes, but that was over 30 years ago.
Definitely you have missed the best part of the ride so far. Are you aware of how much has been discovered in the last 30 years? But also, have you noticed how many new questions have been raised lately?Dionisio
November 7, 2014
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#517 DNA_Jock
You’ll have to forgive me for not participating in that thread, as I was banned at the time.
Participating in what thread? What are you talking about? Did anyone ask you to participate in any thread? Can you explain what you meant by that statement you wrote? Did you understand what I wrote? Apparently you didn't. Please, don't tell me your reading comprehension is as poor as mine. :)Dionisio
November 7, 2014
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#517 DNA_Jock
I used to be a molecular biologist.
Would a passionate molecular biology scientist ever leave such a fascinating profession? What could be more exciting than that? Can you elaborate on this? Thank you.Dionisio
November 7, 2014
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#517 DNA_Jock Did you read post #516? Did you understand it? Do you agree? No? Why not?Dionisio
November 7, 2014
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Dionisio -
Ok, let me see if I understand this: is “the Purpose” related to your work or profession?
Prior employment, yes.
Does that mean you’re a molecular biology scientist and you possess some breakthrough information but can’t reveal it here?
I used to be a molecular biologist. I would not characterize the information as “breakthrough”.
Obviously, my guessing was wrong, because a molecular biology scientist would be too busy working on serious research, hence no spare time to squander on the blogosphere.
Not necessarily. [beat] I could be arguing in my spare time. ;)
However, maybe there’s a possibility that you could help me to answer questions like these: [questions re cytokinesis] Would “the Purpose” allow you to answer questions like those, as long as you don’t reveal any confidential breakthrough information?
I did once work on human actin genes, but that was over 30 years ago. Your curiosity would be better served by someone a little bit more up to date – perhaps Dr. Bezanilla herself. And don’t worry, it’s only the technology described in Keefe & Szostak that’s an issue.
There are gazillion questions like those in over 550 posts in the “Third Way” thread in this same site.
You’ll have to forgive me for not participating in that thread, as I was banned at the time.
Did you read gpuccio’s post #501 carefully enough to comment on it so fast?
What can I say? I’m a quick study. :)
gpuccio I didn’t mean to interrupt your interesting discussion with DNA_Jock.
As far as I’m concerned, you are welcome to join in. Or throw buns. Your choice. :)DNA_Jock
November 7, 2014
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#502 DNA_Jock One very interesting thing about questions like the ones posted on #512 is that their correct answers lead to deeper questions, which eventually point to an elaborate information-processing system that's a real delight for any passionate computer scientist or engineer. Do you understand this? :)Dionisio
November 7, 2014
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gpuccio I didn't mean to interrupt your interesting discussion with DNA_Jock. :)Dionisio
November 7, 2014
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#502 DNA_Jock Let's see: gpuccio posted @501 a very informative 85-line comment for you, time-stamped 10:05am About 36 minutes later your 10-line reply appeared: 502 DNA_Jock November 7, 2014 at 10:41 am Did you read gpuccio's post #501 carefully enough to comment on it so fast? This confirms what I wrote in post #507. :(Dionisio
November 7, 2014
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Did I shutdown this discussion thread? Oops! Sorry. :(Dionisio
November 7, 2014
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#508 DNA_Jock #511 PS However, maybe there's a possibility that you could help me to answer questions like these:
What makes myosin VIII to become available right when it’s required for cytokinesis? Same question for actin. What genes are they associated with? What signals trigger those genes to express those proteins for the cytokinesis? BTW, how does the transcription and translation processes for those two proteins look like? Are they straightforward or convoluted through some splicing and stuff like that? Are there chaperones involved in the post-translational 3D folding? Where is it delivered to? How does that delivery occur? How does the myosin pull the microtubule along an actin filament? How many of each of those proteins should get produced for that particular process? Any known problems in the cases of deficit or excess?
Would "the Purpose" allow you to answer questions like those, as long as you don't reveal any confidential breakthrough information? There are gazillion questions like those in over 550 posts in the "Third Way" thread in this same site.Dionisio
November 7, 2014
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#508 DNA_Jock #510 correction Obviously, my guessing was wrong, because a molecular biology scientist would be too busy working on serious research, hence no spare time to squander on the blogosphere. :)Dionisio
November 7, 2014
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#508 DNA_Jock Does that mean you're a molecular biology scientist and you possess some breakthrough information but can't reveal it here? Is that right? Sorry if I got it wrong again. Please, refer to post #507 to understand my condition.Dionisio
November 7, 2014
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#508 DNA_Jock Ok, let me see if I understand this: is "the Purpose" related to your work or profession?Dionisio
November 7, 2014
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Dionisio, Confidentiality agreements define "the Purpose", such as "to assess whether the parties wish to enter into a collaboration". Confidential information that is disclosed is only allowed to be used for "the Purpose". That is, no stealing someone else's ideas and using them to further your own program. Likewise, if you have confidential information about a company's finances, it is illegal to use that information to enhance your returns in the stock market... Hope this helpsDNA_Jock
November 7, 2014
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#506 DNA_Jock
Contractually, I am only permitted to use these data for “the Purpose”.
Please, note that my reading comprehension is poor, English is not my first language, my IQ score is about the same as my age (but it changes in the opposite direction), when someone says a joke at a weekend social gathering, it takes me until Monday or Tuesday to get it, after my wife patiently explains it to me. All that said, can you tell me in easy terms, what is “the Purpose”? Thank you for your compassion. :)Dionisio
November 7, 2014
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Dionisio, I was hoping y'all would be able to read between the lines... Contractually, I am only permitted to use these data for "the Purpose". Sadly, "the Purpose" does not include proving some schmuck on an internet blog wrong. If I produced this excuse in the middle of an argument about the implications of Keefe & Szostak 2001, then I would fully sympathize with anyone who responded "Wow! That's the lamest excuse ever!" So I bring it up now, before gpuccio and I get into details.DNA_Jock
November 7, 2014
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Oops! I meant 'my pay grade'Dionisio
November 7, 2014
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gpuccio and KF Perhaps I have said this before, but I have no problem saying it again: If the Nobel prize included a category for 'patience' you two would have been nominated for it. I hope many lurkers are benefiting from reading what you are writing. However, it seems like some of your interlocutors aren't getting it. Some of the stuff you write is above my ay grade, but I enjoy reading it anyway. Thank you! :)Dionisio
November 7, 2014
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#502 DNA_Jock
our conversation might reach a point where I am reduced to saying “I know for a fact that you are wrong about X”, but I will be unable to provide supporting data for my position
[...] “I know for a fact [...]”, but I will be unable to provide supporting data for my position
Say what? Please, can you explain what you meant by that? Thank you. :)Dionisio
November 7, 2014
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No gpuccio, The wall was always there. The bullet-holes arose before humans existed (by three or more days). :) Biochemists arrive. They observe bullet holes, and paint circles around the bullet holes that they observe. They may debate how big a circle they should draw. That this is, in fact, the sequence of events is highlighted by your observation of the biochemist that discovers a new enzyme activity: "Look, a new bullet hole! Quick, pass me the paint!" I would be interested in hearing your complaints re Keefe and Szostak. One caveat with regard to this paper: our conversation might reach a point where I am reduced to saying "I know for a fact that you are wrong about X", but I will be unable to provide supporting data for my position. I know that this would be a deeply unsatisfying way to end the conversation, so I warn you ahead of time.DNA_Jock
November 7, 2014
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DNA_Jock: I always appreciate your comments. First of all, the Szostak paper I refer to is not that one, but the one about finding functional sequences in random peptides. It has been discussed many times here, and that's why I assumed you knew what I was talking about. It's this one: https://molbio.mgh.harvard.edu/szostakweb/publications/Szostak_pdfs/Keefe_Szostak_Nature_01.pdf The Hazen paper you reference seems interesting, I will study it carefully. I am interested in any approach to the concept of functional information, except the denial of it. I think that Durston's approach is valuable. I have never said it is perfect. The problem here is to recognize functional information and try to measure it. There can be many ways to model it or measure it, but for the design inference we are interested in an estimate of its orders of magnitude, rather than an exact measure. I don't agree with you that mathematical constants are so different from machines, both biological and not. The mathematical constant coveys a meaning. A machine implements a function. One is descriptive information, the other prescriptive information. But both meaning and function are pure conscious dimensions: they can only be recognized by a conscious witness, and they don't exist as purely objective things. I believe that you still miss an important aspect of the problem. The important point is that the conveyance of meaning, or the implementation of function, are conscious related events which can be simulated by non conscious events, but only in simple form. In that sense, an English sonnet and a functional machine, either biological or not, or just a piece of working software, are better than a "simple" mathematical constant in binary form. Indeed, if we can still imagine that our unawareness of some algorithm which can explain the sequence of pi digits could in principle be due to our lack of imagination, that is practically impossible for a Shakespeare sonnet. Do you really believe that some algorithmic, non conscious process could output the sonnet I have quoted? Do you really believe it? The same is true for function. A watch cannot be the result of a blind watchmaker, if it is complex enough. A watch expresses the desire to measure time. No blind process really desires to measure time. Function is the expression of desire. From desire, through understanding of meaning, comes planning, and therefore design. All that happens in consciousness, and only in consciousness. Now, non conscious processes may look designed and functional. That is true. But only simple ones. I maintain that any definable function which need more than 500 specific bits to be implemented will always be found to come from a design process, from a conscious planning. I maintain my challenge to anyone to offer a false positive to my dFSCI procedure. I maintain that ATP synthase has at least 1600 bits of functional information, and that there is no possible algorithmic explanation for that. I have not even used the Durston method here, I have just counted the conserved AA positions from bacteria and archaea to humans. I am not giving a precise number, but a relaible order of magnitude. It's enough. ATP synthase expresses the need to store energy in biochemical form, starting from a proton gradient across a membrane. That's an engineering problem, a very refined one, and very refined is the solution. These are not painted targets. They are objective targets, existing on their own. ATP synthase has accomplished its task for 4 billion years, well before our existence as possible "painters". Going back to Texas shooters, I would like to try to clarify why I think that you have mixed two different problems in one argument. Bear with me. First of all, let's say that our problem is a scenario where a shooter who is not sharp at all is erroneously considered sharp. OK? Now, I say that there are two different situations where that can happen. I will call them TS fallacy and TS error. a) TS fallacy. Very simply, a not so sharp shooter shoots to a distant wall. Then we go to the wall, ans we paint a target for each shot, and we say that the shooter is sharp. This is a logical fallacy: the targets were not there before, no shooter has aimed at them. We painted the targets after the shooting. The targets have not independent reality. Their position is fixed by the previous positions of the shots. b) TS error. Very simply, a not so sharp shooter shoots to a distant wall. Then we go to the wall, and we see that the wall was filled with targets, and that some shots have hit targets because it was really likely to hit some, even without any aiming. So, if we say that the shooter has hit the targets because he is sharp, we are making an error. This is not a logical fallacy. It is simply a wrong inference. We attribute the hits to a good aim because we don't evaluate correctly the probability of random hits, which is high because there are a lot of targets. Mow, my point is that a) cannot be used against ID and the dFSCI procedure. Functional specification is not a post-hoc painting. It is a post-hoc description of what exists independently. We are not inventing the functionality of ATP synthase because we have discovered it in our lab: it has always been there. We are inventing nothing, not any more than Newton was inventing the law of gravity when he discovered it. The molecule has always been able to do what it does. The law of gravity has always been there. We only recognize the meaning in what we observe. That is a conscious process. b), instead, can be used against ID, but only if you can demonstrate that the search space is really filled with targets which can be useful to explain what we see. IOWs, neo darwinists must demonstrate one of two things: b1) That the search space if filled with long and complex functional molecules like ATP synthase. I am not holding my breath. b2) That the search space is filled with simpler functional molecules which can be expanded by positive NS, so that they can serve as "bridges" to loner and more complex functional molecules like ATP synthase, and that the path to ATP synthase and all the other long and complex functional molecules can be deconstructed, as a general rule, into those naturally selectable steps, each of them in the range of a reasonable RV system. OK, demonstrate that. So, my point is that b (the TS error) is a valid argument, but is simply wrong: the search space is not filled with complex molecules, and complex molecule cannot be deconstructed into simpler, naturally selectable ones. Not as a rule, and not even as a single example. However, if that is your line, we can discuss. But a) is simply a wrong argument. It is completely false.gpuccio
November 7, 2014
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kf, Sadly, you provided no answers to my questions, viz: Are quite comfortable with Durston’s assumption that the exploration of insulin’s aa sequence has been a random walk, without any intervention? Every single one of your calculations of p(T|H) and related alphabet soup rely on the assumption of independence (as you have admitted) and that this assumption is false (as both you and Durston have admitted). You assert that the error is “not material”. How big is the error? How do you know? Your post 497 was relatively concise, but non-responsive. Please be as precise and concise as you can while answering these questions.DNA_Jock
November 7, 2014
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What do they do for insulin in parts of the world that have probs with pigs?
Recent advances in genetic engineering have led to the sale of recombinant human insulin. Since 1982, at least.DNA_Jock
November 7, 2014
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PS: What do they do for insulin in parts of the world that have probs with pigs?kairosfocus
November 7, 2014
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D-J: OOL is the heart of the matter, you were implying OOL as a one shot event. Sims that are reasonable do explore a stochastic pattern, but the problem is too many evo computing or genetic algorithm cases end up bringing in intelligently directed configuration by the back door or substitute hill climbing within a well behaved island of function for the real task of finding such islands. A grossly simplified, off track sim taken on "Pascal washes whiter" or the like is worse than no sim. I further suggest that Durston's summary shows the sort of range that is reasonable, compatible with retaining function on something important. Though of course pig insulin does not quite do the same as human. The fundamental thing is, we do not have a situation where for the typical 300 AA protein, say, any of 17 or so AAs of the 20 would do for any position. The constraints observed consistent with retained function are much tighter than that. As for the game on probabilities, the answer has long been, take the Dembski 2005 calc one step forward to see what it means. Immediately, it is an info beyond a threshold metric, and we have independent ways to get info values and to estimate thresholds of feasible complexity on any reasonable blind chance process. Where search of a set of possibilities W is selection from the set of subsets of cardinality 2^W. That is, the blind search for a golden search is strongly likely to be much worse than any reasonable blind chance search of the first order config space W, in which islands of function T1 . . . Tn are. Where per atomic resources the search cannot but be maximally sparse -- a needle in haystack challenge. As for assumptions of independence, you are not thinking physically. Any AA or any base can succeed any other and there is no mechanical constraint. For DNA the sequence used is tied through a translation process to fold-collaborate-function requisites that are remote, and come much after the fact. A change that happens somehow in a protein is not back-translated into a new DNA sequence; 2 bits per base is reasonable. Moving to looking at coded patterns is like looking at frequency patterns in English text and suggesting that that somehow constrains the bit positions in a memory register. The more complex metrics are on we are already in the genetic code and are already at a family of related proteins across the world of life. While that has its place and is perhaps more palatable to Darwinists (though even that is doubtful) we must not get the causal chain cart before the horse. And that is already leaving aside the Darwin's pond context of energetically uphill rxns, chirality and cross-interference. And there is more. I need to get back to the local issues already in progress and hotting up today with an announcement of Speaker. Then, there was the speech on history and the value of cultural, historical and natural heritage, yesterday afternoon and its aftermath. KFkairosfocus
November 7, 2014
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kf, We were not talking about OOL. As Pa Grape said “Why even bring it up?” You state:
When it comes to Monte Carlo runs, it seems to me that we do not invalidate such because the sims are programmed and set up then run by presumably intelligent programmers, once the dynamics are reasonable and appropriate randomness [or often pseudo- . . . ] is injected.
Personally, I accept that well-designed Monte Carlo’s are useful for modeling unintelligent processes. However, many IDists (including, to my disappointment, gpuccio) reject simulations for precisely the reasons you state. You should let them know they are wrong. On the other hand, if the programmer steps in during the run and replaces certain of the pseudo-random numbers with numbers designed to achieve a specific goal, we might question the validity of the analysis. Especially if n=1. We might say “Get you b|**&/y thumb off the scale!” Regarding the fact that n=1, you state:
“there have been many types of organisms and a lot more individuals, allowing chance driven random walks around the AA-sequence space”
So you are quite comfortable with Durston’s assumption that the exploration of insulin’s aa sequence has been a random walk, without any intervention? Careful, it’s a trap. But nowhere, nowhere do you even attempt to address the fact that every single one of your calculations of p(T|H) and related alphabet soup rely on the assumption of independence (as you have admitted) and that this assumption is false (as both you and Durston have admitted). You assert that the error is “not material”. How big is the error? How do you know? Please be as precise and concise as you can.DNA_Jock
November 7, 2014
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To further expand on the limited utility of Durston's results: He is taking the observed variation in the aa sequences of extant, optimized sequences and, assuming neutral variation, he then estimates the degree of substitution allowed. Thus what he measures is the degree of substitution allowed without any selectable degradation of function. This is analogous to Gibbs sampling. However, any sequences that have a slight degradation of function will be underestimated in his sample. Any sequence with a moderate degradation of function will be vanishingly unlikely to appear in his dataset. Hence the disconnect between his results and the more systematic approach of McLauglin 2012 (PMID:23041932). Both Durston and McLauglin suffer from the shortcoming that they are exploring functional constraint around an optimum. Therefore the approach of Hazen et al. 2007 (PMID:17494745) is preferable. Is this paper the "wrong Szostak paper" to which you refer? There are 220 Szostak papers in PubMed... You are going to have to explain to me why you think it is "wrong". And "not liking the results" is not a valid reason. Cognitive bias, indeed! Finding binaries on an alien planet: I like your hypothetical; it made me think. Before I address the Texas SS aspect, a word of caution re the design inference aspect: if I found pi and e in binary I would be drawn to conclude design because, as you so rightly put it "with all [y]our knowledge of physical laws in the universe, there is no natural process which can explain those specific sequences". If OTOH the binaries represented the Fibonacci sequence, I would continue looking for natural processes to explain the sequence. Thus my conclusion of design for pi and e may just be a failure of my imagination or the result of my ignorance. Wouldn't be the first time. For the following, I would like you to imagine that, like the Fibonacci sequence, there is some natural process that can produce square roots of smallish numbers in binary. I agree with your point that pi and e exist outside of any specification we might draw up, they existed before we saw these marks on the wall, so pi in binary and e in binary avoid the Texas SS issue. Unfortunately for your argument, there is a flaw in your analogy. Imagine that instead we had found (to 10^6 bits a piece) the square root of 3,001 and the square root of 500,001. This is what we are doing when we specify a functionality for a protein that we have already found. The specification "ATP synthase" did not exist before we found ATP in the same way that pi existed. The specification "ATP synthase" is like the specification "the square root of 3,001 in binary" and the specification "APP synthase is like "the square root of 500,001 in binary". The only reason were are not discussing the latter is because we haven't seen it yet.DNA_Jock
November 7, 2014
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DNA_Jock: About Durston again, obviously there are assumptions in his method. I don't agree with you that they are "terrible, completely unsupported". I find them very reasonable. The point is, he is measuring something. He measures differences in the functional density between proteins. So, while his values are obviously related to the total protein length, as shown in the regression, the variance in functional density is reasonably explained by different functional constraints for different functions. So, his results tell us two very important things: that functional complexity always increases with the length of the sequences, but that it also depends critically on the type of function. I am confident that the computation of functional complexity in proteins will become even more precise and reliable. But Durston has given us a very good approach. I have given one important reason to think that Durston's method really underestimates functional complexity, here: https://uncommondescent.com/junk-dna/junk-dna-only-20-all-but-8-2/ Posts #5, 11 and 12.gpuccio
November 7, 2014
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