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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
"Show actual chance variation plus actual differential reproductive success creating a new body plan or major body plan feature involving FSCO/I on our observation — the vera causa test. Not minor adaptations like oscillations in Finch beaks or loss of eyes in cave fish, actual addition of large scale functional organisation and info on realistic populations and time lines." kairosfocus's "challenge" is based on false and vague premises. FSCO/I is a term that he made up that has no credibility with evolutionary biologists and has nothing to do with evolutionary theory. His unreasonable expectations also include but don't define "realistic populations and time lines". He will apparently only accept what meets his YEC definition of "realistic populations and time lines". It is not the responsibility of evolutionary biologists or any other scientists to cater to kairosfocus's unreasonable, non-scientific expectations.Reality
November 9, 2014
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#641 Me_Think Hasn't your question been addressed by KF and gpuccio before? Can you just read what they wrote about it?Dionisio
November 9, 2014
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keith s you may want to attempt meeting this ‘easy’ challenge, courtesy of KF: Show actual chance variation plus actual differential reproductive success creating a new body plan or major body plan feature involving FSCO/I on our observation
Is FSCO/I = dFSCI = FSC = CSI ?Me_Think
November 9, 2014
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635 DNA_Jock
Sorry to disappoint, but I am not a Young Earth Creationist. They are the only people according to whose world view it should be possible to meet kf’s vera causa test.
Are you sure about what you wrote? I think that there are many folks in this UD blog who would agree with KF's challenge, but they are not YECs. I'm not a YEC myself (I don't even understand exactly what that acronym stands for). Actually, I don't even consider myself an ID proponent, though I agree with many of the central concepts associated with ID. My identity is not in any of those acronyms. Did you understand this now?Dionisio
November 9, 2014
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keith s you may want to attempt meeting this 'easy' challenge, courtesy of KF:
Show actual chance variation plus actual differential reproductive success creating a new body plan or major body plan feature involving FSCO/I on our observation — the vera causa test. Not minor adaptations like oscillations in Finch beaks or loss of eyes in cave fish, actual addition of large scale functional organisation and info on realistic populations and time lines.
Dionisio
November 9, 2014
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Learned Hand you may want to attempt meeting this 'easy' challenge, courtesy of KF:
Show actual chance variation plus actual differential reproductive success creating a new body plan or major body plan feature involving FSCO/I on our observation — the vera causa test. Not minor adaptations like oscillations in Finch beaks or loss of eyes in cave fish, actual addition of large scale functional organisation and info on realistic populations and time lines.
Dionisio
November 9, 2014
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#635 DNA_Jock As you should remember, I told you about my poor reading comprehension skills. :) I better let KF discuss that point with you directly. However, the last sentence can be removed without affecting the challenge. :)Dionisio
November 9, 2014
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DNA_Jock Would you treat me better if I tell you that my wife and I have a beautiful orange tabby cat and that we had a golden retriever for almost 16 years when our children were younger? I agree with you that canines and felines are quite different in certain aspects of their physiology and specially in their behaviors, but remember that they all, along with us humans, share a FUCA and a LUCA, and came to being by the power of the magic 'n-D e' formula RV+NS+T. Hey buddy, you're much better than I am. But you may want to try being more considerate to those who are not as good as you are. You may want to learn from gpuccio's example. He is very nice to everyone, including his interlocutors. :)Dionisio
November 9, 2014
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Dionisio, LMAO Sorry to disappoint, but I am not a Young Earth Creationist. They are the only people according to whose world view it should be possible to meet kf's vera causa test. It's "challenges" like this one that display the ignorance of most "IDiots" (that's kf's term, not mine). Here's a test of your comprehension skills: what is wrong with the final sentence of kf's challenge?DNA_Jock
November 9, 2014
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#629 DNA_Jock
I love a challenge.
Oh, really? do you? Then, can you meet this one, courtesy of KF?
Show actual chance variation plus actual differential reproductive success creating a new body plan or major body plan feature involving FSCO/I on our observation — the vera causa test. Not minor adaptations like oscillations in Finch beaks or loss of eyes in cave fish, actual addition of large scale functional organisation and info on realistic populations and time lines. Production of FSCO/I involving intelligently directed contingency is a routine matter, and thanks to Venter et al, engineering of genes is demonstrated fact.
Dionisio
November 9, 2014
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Learned Hand, We've tumbled into a world where Logic is not spoken. KF and gpuccio claim that FSCO/I are dFSCI are useful. Gpuccio suggested a test procedure to prove this. Yet both KF and gpuccio admit that you don't even need to do the calculation. It reveals absolutely nothing that you didn't already know. Why would anyone bother? Gpuccio, can you come up with a test procedure in which dFSCI actually does something useful, for a change? It's pretty clear why you and KF don't submit papers on this stuff. Even an ID-friendly journal would probably reject it, unless they were truly desperate.keith s
November 9, 2014
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LH, Let me first point out at the nubbin of the matter, as I noted at 589 on even going to one bit per AA:
From my lost draft, I add, take Cy-C and halve the info metric value from Yockey, 125 bits call it. Say, 100 proteins of similar avg value per AA as the halved Cy-C; we have 12,500 functionally specific bits to get dna for and to get support machinery for already such as Ribosomes [which use a lot of RNA]. Such is well past 500 or 1000 bit thresholds. The only empirically warranted, needle in haystack blind search plausible source for such is design. And, by starting from a simple approach then adjusting per factors, we can see how we get there, though there is a lot of underlying work by Yockey etc there. Durston et al 2007 did fairly similar work, which is unfortunately not easy to follow for those likely to be reading a blog. Those who need it know where to find it. The point is, even if, after going through various factors we set about one y/n choice per AA as the info content of a typical protein on average, once we set that in the context of hundreds of proteins, we are back to the same basic conclusion — if we are willing to allow the force of inductive patterns of reasoning that undergird science. And believe us, there have been objectors about who would burn down not only induction but logic.
That is, at OOL, we already have that if we take 1 bit per AA, just on a toy model of 100 proteins of scale comparable to Cy-C we are still at 10,000 + bits of FSCO/I to account for, not to mention origin of a code and support system. Where the RNA, the organisation of the cell to make the proteins work and much more, are still to be reckoned with. Where, every bit beyond 1,000 bits doubles the config space beyond 1.07 *10^301 possibilities. At 10,000 bits, we are dealing with a space of 2 *10^3010, to be searched by blind watchmaker processes that can account for 10^111 atomic scale events of 10^80 atoms at 10^14 events per s (fast chem rxn rate) and 10^17 s. Sparse search of a big haystack, without any reasonable way to bring self replication and hoped for powers of chance variation and differential reproductive success to bear, as that is also to be accounted for. As for isolation of proteins, it is generally acknowledged that there are thousands of fold domains, which are largely unrelated to one another in terms of sequence, leading to deeply isolated islands of function. Cf the current thread here on that, which BTW is from a professional literature source. Typical numbers cited run about 1 in 10^65 to 10^77, as I recall. So even if Bradley made an error of citation, he is in the general ballpark. As well, the matter is that his logic is generally right and obviously so to someone who knows a little of how info content of a string is assessed. Which is why I gave the summary. We start fromteh causal chain end and see that there is no physical or chemical barrier to sequence succession so there is good reason to take the number of y/n q's to specify state as a good index of the info content implied in what is used. After that one may look at the actual patterns and do a SUM pi log pi measure, and may adjust for flexibility of characters that does not affect functionality. Do that, work with half his result, and even at 1 bit per AA, we end up with the same material result. FSCO/I needs to be explained and there is no good blind watchmaker thesis account that is adequatele observationally backed. Intelligently directed configuration aka design, routinely creates FSCO/I as posts in this thread show. Dead links are a bane, and I don't have time to do a deep search. I need to get on the horn, back to duty calls. Later. KFkairosfocus
November 9, 2014
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D: That is the challenge. Maybe the most significant thing about the debate at and around UD since 2012 -- cf here a few days back -- is that there is a standing offer to host at UD a warranting case for the Darwinist blind watchmaker thesis origins narrative on chance and necessity from OOL up to us. After a full year I had to cobble together a composite response which basically conceded there is no OOL solid case, and was rather wobbly on origin of body plans. In the meanwhile I had taken up Wiki and Theobald as stand-ins, neither of which came across very well. Since then, there has been no interest whatsoever in a further more serious attempt. Much interest in attacking, dismissing ID thinking and supporters but little on laying out their own case. And yet, such a solidly, empirically grounded case would answer decisively. The dog that would not bark is telling. KFkairosfocus
November 9, 2014
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KF
Show actual chance variation plus actual differential reproductive success creating a new body plan or major body plan feature involving FSCO/I on our observation — the vera causa test. Not minor adaptations like oscillations in Finch beaks or loss of eyes in cave fish, actual addition of large scale functional organisation and info on realistic populations and time lines. Production of FSCO/I involving intelligently directed contingency is a routine matter, and thanks to Venter et al, engineering of genes is demonstrated fact.
Clear challenge. That's it. Just don't hold your breath waiting for anyone to meet it soon (or ever).Dionisio
November 9, 2014
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Gpuccio, Thank you for the kind words. You actually read, understand, and respond to what is addressed to you. I think this makes you unique amongst the regulars here. Even if it’s a “sidetrack”, having a discussion with you is enjoyable.
[ in reference to my having a dog] I have three cats. How could we ever expect to understand each other!
Actually, I too am a “cat person”, but in the interests of staying married, we have had two dogs. I think that dogs, even more so than non-human primates, offer a fascinating case-study in communication and empathy. Cats, on the other hand, are completely effing inscrutable; I love a challenge.
You will maybe admit that there is some pre-commitment to a specific worldview here. No problem in that. I respect pre-commitments. I have mine too. But they are different.
No argument here. EVERYONE has their pre-commitments. Sadly, many people are blissfully unaware of them. Exhibit 1: people who find ID (or MES) attractive for theological reasons. On a related topic, I find the interaction between (usually amateur) philosophers of science and people who have actually done basic research very entertaining. It may be my intellectual arrogance (not joking here), but I think the former are far, far more prone to confirmation bias. There’s a reason for that. ;)
I must say that I have great respect for Dionisio and for his contributions here.
I’m sorry to say I don’t see why.DNA_Jock
November 9, 2014
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Kairosfocus, Sorry for the delay replying. The analysis you offer (in #587) by Bradley is interesting. Unfortunately, your citation for this analysis, [http://www.oneplace.com/common/pdf/ministries/creation_update/who_is_the_designer/07OriginOfLifePRNT.pdf], is dead. Do you have another? Perhaps this analysis been published in a mainstream biology journal? But we can discuss what you quote him as saying. I hesitate to use the word, but starting off with “pi = 0.05 for all residues”, which yields 4.32 bits per amino acid is , ahem, a strawman . Taking into account the observed frequencies in extant proteins is somewhat more honest, but still ignores the effect of correlation. This brings bits/aa down slightly, to 4.139. Not much of a movement; one might argue that the change is “not material”. However, I was able to find (Strait and Dewey, 1996), Bradley’s source for the 1 in 10^75 number. Strangely, that value is not to be found in the cited paper. Nevermind. OTOH Strait and Dewey do offer up a number of ways of trying to estimate the information content in extant proteins, methods which do at least try to take into account the lack on independence between amino acids, if only partially: using Zipf or k-tuplet analysis they obtain values of between 2.4 and 2.6 bits/aa; using a Chou-Fasman algorithm (that attempts to capture the effect of proteins being three-dimensional) they obtain a value of 2.0 bits/aa. Dewey’s previous work suggests that Kolmogorov complexity (a different beast, I admit, but a rather interesting one) is only 1 bit/aa. So, even using the sequences of extant proteins as the source data (which is inappropriate if we wish to understand the early evolution of a protein) we find that the reduction-in-uncertainty per residue drops two-fold when any attempt is made to try to account for correlation. Therefore, blithely asserting that the lack of independence is ‘not material’ is going to require some real data to support it. Of course to address this issue properly, you are going to have to also deal with the subject of my discussion with gpuccio: selection. Until you have dealt with both, you have not calculated p(T|H) for any biological. Ever. “we are looking at the results of deeply entrenched, often indoctrinated in core assertions of a system of thought.” I’ll say. P.S. You did not answer my question “Are you quite comfortable with Durston’s assumption that the exploration of insulin’s aa sequence has been a random walk, without any intervention?”. I understand your reticence; as I noted when I first asked you, it is a trap. P.P.S. Do any of the regulars here know why Bob Sauer used lambda repressor, perhaps the most highly evolved protein on the planet, for his mutagenesis study? It seems a somewhat biased choice. I do think there is an innocent explanation.DNA_Jock
November 9, 2014
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Adapa
Now all you have to do is disprove the ability of genetic variation filtered by selection to produce new and often complex features. You only have about 70 years’ worth of empirical scientific data to overturn. Best of luck, let us know how it turns out.
Please define the terms "new and often complex features" and explain how their production supports the claim that Darwinian processes can produce macro-evolution.StephenB
November 9, 2014
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Adapa, actually, scientifically, it is you who need to show that power. Show actual chance variation plus actual differential reproductive success creating a new body plan or major body plan feature involving FSCO/I on our observation -- the vera causa test. Not minor adaptations like oscillations in Finch beaks or loss of eyes in cave fish, actual addition of large scale functional organisation and info on realistic populations and time lines. Production of FSCO/I involving intelligently directed contingency is a routine matter, and thanks to Venter et al, engineering of genes is demonstrated fact. KFkairosfocus
November 9, 2014
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StephenB It makes 1 a better explanation than 2. Now all you have to do is disprove the ability of genetic variation filtered by selection to produce new and often complex features. You only have about 70 years' worth of empirical scientific data to overturn. Best of luck, let us know how it turns out.Adapa
November 9, 2014
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Adapa
1. Design did it 2. RV + NS did it 3. A currently unknown natural process besides RV +NS did it.
Why would you choose an unknown cause over a cause already known to produce the effect.
Disproving 2. doesn’t make 1. right.
It makes 1 a better explanation than 2.
That’s why science requires positive evidence for claims,...
And yet you appeal to an unknown cause.StephenB
November 9, 2014
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gpuccio No dichotomies and no default. Just empirical science. Your whole ID argument rests on a false dichotomy and faulty logic. The scientific community recognizes it which is why the argument is rejected. Pity that your biases make you too blind to see it. Or perhaps at some level you do recognize the fatal flaws which is why you won't submit your ideas to any scientific journals. You gave it your best shot but you failed. It's not the end of the world. Props to you for trying.Adapa
November 9, 2014
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Adapa: I am tired to listen to your "arguments". OK. 1. is a good explanation, the best explanation. Indeed, the only one available. 2. is a bad explanation, which does not work. 3. is no explanation at all, just wishful thinking. No dichotomies and no default. Just empirical science.gpuccio
November 9, 2014
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gpuccio The simple point is: if I infer design for ATP synthase, it is because I am sure that nobody can offer an explicit algorithmic explanation for it. Blind faith in the undemonstrated powers of generic RV + NS is not a valid explanation. You couldn't make your basic logic failure any clearer. You are offering the classic false dichotomy. If RV + NS can't explain it then it must be Design by default. But you always forget the third option. 1. Design did it 2. RV + NS did it 3. A currently unknown natural process besides RV +NS did it. Disproving 2. doesn't make 1. right. That's why science requires positive evidence for claims, and why trying to support ID strictly by attempting to falsify ToE will never work.Adapa
November 9, 2014
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Adapa, are you familiar with inductive logic? In that logic, one validates a pattern or explanation as sufficiently reliable on known cases, to trust or take seriously on cases where one cannot cross check. dFSCI, and the broader FSCO/I are tested and reliable on billions of cases. We have a buttressing analysis on sparse search for needles in haystacks, relative to atomic resources of observed cosmos or solar system. The conclusion is that such are highly reliable signs of design as cause. So, we have an epistemic right to trust them on cases where we do not directly see the causal story. Think about signs of arson as cause for a fire. KFkairosfocus
November 9, 2014
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Adapa: Great. We really missed your contribution.gpuccio
November 9, 2014
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LH: Pardon a side note. The simplest way is to apply (b^n)^m = c, turned into a log expression, log_10 X/ log_10 2 = Log_2 x In short take ratio of log x to a standard base to log 2 to said base. That's log of x to base 2. - log_2 x is really log_2 (1/x) = 0 - log_2 x (And onwards that is about a posteriori accuracy of detection. What was sent in the comm sys is accurately detected.) KFkairosfocus
November 9, 2014
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gpuccio I have said that I will infer design for any string of more than 600 characters which has good meaning in English. Or for any software of more than 3000 bits which can receive lists of words and order them in Windows. Without knowing anything else of those sequences. I am not “starting from the conclusion that design happened”. I start form an observable property of the string itself. How useful is dFSCI? With dFSCI you can conclude design in strings you already know are designed. Good one. :)Adapa
November 9, 2014
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KF: Thank you for your comments. Sometimes it is difficult to answer in detail, but I always try to do it when the interlocutor is asking true questions and proposing real arguments, either right or wrong. The results are usually not encouraging, but it is worthwhile to discuss and defend what we believe to be true.gpuccio
November 9, 2014
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Learned Hand:
I don’t think that your procedure will ever generate a positive unless you start from the conclusion that design happened, or have some independent means of determining that design happened. Essentially, it only confirms that vastly unlikely events are vastly unlikely, and by ignoring known natural alternatives concludes that life is so unlikely it must have been designed.
This is simply false. I have said that I will infer design for any string of more than 600 characters which has good meaning in English. Or for any software of more than 3000 bits which can receive lists of words and order them in Windows. Without knowing anything else of those sequences. I am not "starting from the conclusion that design happened". I start form an observable property of the string itself. What you say is simply not true.
So I’m not sure I can give you a false positive, although I’ll put some thought into it.
I will wait.
In the meanwhile, why don’t you do the same? I’d be much more impressed with ID if its advocates took their own ideas more seriously.
Because I am sure that false positives don't exist. Because I take my ideas very seriously. And because I have not much time, and I don't want to waste it.gpuccio
November 9, 2014
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GP: The fixation on the believed powers of subtraction and culling through differential reproductive success is such that I find it very useful to start at the problem of Darwin's pond or the like, to understand the point of the challenge of getting TO islands of function in large config spaces from arbitrary initial points, on sol system or cosmic resources that only allow very sparse search for the needle in the haystack. Next, it will be helpful for objectors to recognise that the usual term, natural selection, misses the supposed generator of actual novel info, some form or other of chance variation. NS REMOVES failed or relatively failed varieties, it does not generate them. And the hoped for incrementally functional advance up a continent of possibilities not only lacks warrant on the fossils but runs into the issue that major body plan units require well matched, interacting, multiple, correctly arranged parts that yield specific function, which are also embryologically feasible and coded in the zygote or whatever. That is going to confine to narrow zones or islands in the space of configs, e.g. to account for flying wings, one way flow lungs or the like. But, we are looking at the results of deeply entrenched, often indoctrinated in core assertions of a system of thought. Generally, per Lakatos, Kuhn et al, that is going to take crisis and collapse of the system -- similar to Marxism. (I assure you, the deeply locked in Marxists were not open to external critique, only when all collapsed did they find themselves bewildered and forced to question.) KFkairosfocus
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