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A Darwinist responds to KF’s challenge

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It has been more than a year since kairosfocus posted his now-famous challenge on Uncommon Descent, inviting Darwinists to submit an essay defending their views. A Darwinist named Petrushka has recently responded, over at The Skeptical Zone. (Petrushka describes himself as a Darwinist in a fairly broad sense of the term: he accepts common descent as a result of gradual, unguided change, which includes not only changes occurring as a result of natural selection but also neutral change.)

The terms of the original challenge issued by kairosfocus were as follows:

Compose your summary case for darwinism (or any preferred variant that has at least some significant support in the professional literature, such as punctuated equilibria etc) in a fashion that is accessible to the non-technical reader — based on empirical evidence that warrants the inference to body plan level macroevolution — in up to say 6,000 words [a chapter in a serious paper is often about that long]. Outgoing links are welcome so long as they do not become the main point. That is, there must be a coherent essay, with

(i) an intro,
(ii) a thesis,
(iii) a structure of exposition,
(iv) presentation of empirical warrant that meets the inference to best current empirically grounded explanation [–> IBCE] test for scientific reconstructions of the remote past,
(v) a discussion and from that
(vi) a warranted conclusion.

Your primary objective should be to show in this way, per IBCE, why there is no need to infer to design from the root of the Darwinian tree of life — cf. Smithsonian discussion here – on up (BTW, it will help to find a way to resolve the various divergent trees), on grounds that the Darwinist explanation, as extended to include OOL, is adequate to explain origin and diversification of the tree of life. A second objective of like level is to show how your thesis is further supported by such evidence as suffices to warrant the onward claim that is is credibly the true or approximately true explanation of origin and body-plan level diversification of life; on blind watchmaker style chance variation plus differential reproductive success, starting with some plausible pre-life circumstance.

It would be helpful if in that essay you would outline why alternatives such as design, are inferior on the evidence we face.

Here is Petrushka’s reply:

Evolution is the better model because it can be right or wrong, and its rightness or wrongness can be tested by observation and experiment.

For evolution to be true, molecular evolution must be possible. The islands of function must not be separated by gaps greater than what we observe in the various kinds of mutation. This is a testable proposition.

For evolution to be true, the fossil record must reflect sequential change. This is a testable proposition.

For evolution to be true, the earth must be old enough to have allowed time for these sequential changes. This is a testable proposition.

Evolution has entailments. It is the only model that has entailments. It is either right or wrong, and that is a necessary attribute of any theory or hypothesis.

Evolution is a better model for a second reason. It seeks regularities.

Regularity is the set of physical causes that includes uniform processes, chaos, complexity, stochastic events, and contingency. Regularity can include physical laws, mathematical expressions that predict relationships among phenomena. Regularity can include unpredictable phenomena, such as earthquakes, volcanoes, turbulence, and the single toss of dice.

Regularity can include unknown causes, as it did when the effects of radiation were first observed. It includes currently mysterious phenomena such as dark matter and energy. The principle has been applied to the study of psychic phenomena.

Regularity can include design, so long as one can talk about the methods and capabilities of the designer. One can study spider webs and bird nests and crime scenes and ancient pottery, because one can observe the agents producing the designed objects.

The common threads in all of science are the search for regularities and the insistence that models must have entailments, testable implications. Evolution is the only theory meeting these criteria.

One could assert that evolution is true, but it is more important to say it is a testable model. That is the minimum requirement to be science.

PS:

My references are the peer-reviewed literature. We can take them one by one, if kairosfocus deems it necessary to claim the publishing journals have overlooked errors of fact or interpretation.

PPS:

To make Dembski’s explanatory filter relevant, one must demonstrate that natural history is insufficient. So I will entertain ID arguments that can cite the actual history of the origin of life and point out the place where intervention was required or where some deviation from regular process occurred.

Same for complex structures such as flagella. Cite the actual history and point out where a saltation event occurred.

Or cite any specific reproductive event in the history of life and point out the discontinuity between generations.

PPPS:

If CSI or any of its variants are to be cited, please discuss whether different living things have different quantities of CSI. For example, does a human have more CSI than a mouse? Than an insect? Than an onion? Please show your calculation.

Alternatively, discuss whether a variant within a species can be shown to have more or less CSI than another variant. Perhaps a calculation of the CSI in Lenski’s bacteria before and after adaptation.

These are just proposed examples. Any specific calculation would be acceptable, provided it can provide a direct demonstration of different quantities of CSI in different organisms.

In his original challenge, kairosfocus promised:

I will give you two full days of comments before I post any full post level response; though others at UD will be free to respond in their own right.

So let’s hear it from viewers. What do readers think?

Comments
Eric Anderson @100, replying to scordova:
Other questions, what you referred to on the previous thread as “theories of intelligence” (identity, timeframe, how acted, personality, and so on of the designer), are interesting second-order questions, but not part of the design inference.* That these questions can, and indeed must, be kept separate from the design inference itself has been very clearly stated by the major ID proponents from day one. That is why I can’t understand this insistence on claiming otherwise. If your goal is to be provocative in a pro-ID forum, you have certainly accomplished that, but at the expense of clarity and sound reasoning.
I think I understand where Cordova is coming from and I sympathize with his concerns. ID is a misnomer. It should be renamed DI (design inference) instead. And this forum is more than being only about the design inference. I see all sorts of POVs being promoted here, some good and others not so good, IMO. There is lot that can be said about the intelligence aspect of design that would be very useful in the fight against materialism and Darwinism. For example, we know from observing design among humans that designs evolve over time and can be classified hierarchically like a tree. We know that intelligent human designers do not restrict themselves to a strictly nested evolutionary tree of designs. We know that various branches of the tree can be horizontally grafted to distant branches of the same tree, if desired. Indeed, this is what is observed in nature. This kind of thinking is extremely useful and should not be downplayed just because it does not fit the design inference.Mapou
March 14, 2014
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UD administrators: I believe that GPuccio, Eric Anderson, and Timaeus should be given posting privileges. Can there be any doubt that these three individuals grasp ID principles in detail and also from a big-picture perspective? Do they not always communicate in a spirit of friendliness and mutual respect even as they take their adversaries' arguments apart?StephenB
March 14, 2014
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RB, understood. KFkairosfocus
March 14, 2014
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Joe: Please tone down the verbal voltage, I don't think it is helpful, thanks. KFkairosfocus
March 14, 2014
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GP: I thought you had made original posts? KFkairosfocus
March 14, 2014
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petrushka most likely believes that all books arose from one original book via slight changes when the original was being manually copied:
I imagine this story being told to me by Jorge Luis Borges one evening in a Buenos Aires cafe. His voice dry and infinitely ironic, the aging, nearly blind literary master observes that "the Ulysses," mistakenly attributed to the Irishman James Joyce, is in fact derived from "the Quixote." I raise my eyebrows. Borges pauses to sip discreetly at the bitter coffee our waiter has placed in front of him, guiding his hands to the saucer. "The details of the remarkable series of events in question may be found at the University of Leiden," he says. "They were conveyed to me by the Freemason Alejandro Ferri in Montevideo." Borges wipes his thin lips with a linen handkerchief that he has withdrawn from his breast pocket. "As you know," he continues, "the original handwritten text of the Quixote was given to an order of French Cistercians in the autumn of 1576." I hold up my hand to signify to our waiter that no further service is needed. "Curiously enough, for none of the brothers could read Spanish, the Order was charged by the Papal Nuncio, Hoyo dos Monterrey (a man of great refinement and implacable will), with the responsibility for copying the Quixote, the printing press having then gained no currency in the wilderness of what is now known as the department of Auvergne. Unable to speak or read Spanish, a language they not unreasonably detested, the brothers copied the Quixote over and over again, re-creating the text but, of course, compromising it as well, and so inadvertently discovering the true nature of authorship. Thus they created Fernando Lor's Los Hombres d'Estado in 1585 by means of a singular series of copying errors, and then in 1654 Juan Luis Samorza's remarkable epistolary novel Por Favor by the same means, and then in 1685, the errors having accumulated sufficiently to change Spanish into French, Moliere's Le Bourgeois Gentilhomme, their copying continuous and indefatigable, the work handed down from generation to generation as a sacred but secret trust, so that in time the brothers of the monastery, known only to members of the Bourbon house and, rumor has it, the Englishman and psychic Conan Doyle, copied into creation Stendhal's The Red and the Black and Flaubert's Madame Bovary, and then as a result of a particularly significant series of errors, in which French changed into Russian, Tolstoy's The Death of Ivan Ilyich and Anna Karenina. Late in the last decade of the 19th century there suddenly emerged, in English, Oscar Wilde's The Importance of Being Earnest, and then the brothers, their numbers reduced by an infectious disease of mysterious origin, finally copied the Ulysses into creation in 1902, the manuscript lying neglected for almost thirteen years and then mysteriously making its way to Paris in 1915, just months before the British attack on the Somme, a circumstance whose significance remains to be determined." I sit there, amazed at what Borges has recounted. "Is it your understanding, then," I ask, "that every novel in the West was created in this way?" "Of course," replies Borges imperturbably. Then he adds: "Although every novel is derived directly from another novel, there is really only one novel, the Quixote." - David Berlinski "The Denial Darwin"
Joe
March 14, 2014
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Again petrushka demonstrates equivocation and ignorance. Some dialog this is. Please tell us how it was determined gene duplication is a blind watchmaker process (see "Not By Chance" by Dr Spetner). Then please tell us how you determined Axe didn't take gene duplication into account. Onto natural selection which has never been demonstrated to do anything vs goal-oriented searches which have been proven very powerful. Enough said. Then we have the bloviating about language.Joe
March 14, 2014
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Petrushka responds to Gpuccio (responses offered in three consecutive posts are here posted as one): gpuccio:
The opposite is not true. Neutral mutations cannot help in traversing the space between islands of functionality, for two important reasons: a) They can go in any possible direction, because they are random. Even considering the allelic effect of genetic drift, the result remains completely random. Therefore, neutral mutations in no way help in overcoming the probabilistic barriers: the number of possible states to be tested remains the same. b) Negative NS definitely acts against the traversing. When you argue about “lose money and argue that because he lost, it is impossible to win”, you are forgetting the exacting role of negative NS.
The number of states being tested is always limited to those in the immediate vicinity. That is not an astronomical number. Once a duplication occurs — as in the Lensky experiment — negative selection is pretty much irrelevant. Most mutations in the duplicate are going to be neutral. Again, Lensky. Until Axe accounts for the combined possibilities of duplication and drift, his work is not probative. ----- Regarding your “Experimental Rugged Fitness Landscape in Protein? Sequence Space” You are the proponent of intelligent selection. You have argued it is more powerful than natural selection, and I have argued the opposite. You present evidence that goal directed design is hard. Your conceptual problem is assuming there is a goal. You ignore sideways meandering. ----- gpuccio:
6) Regarding languages, I don’t think I understand your point. Languages are structures which are formed and evolve in conscious intelligent beings. Why do you use them as models for non designed evolution?
Because languages evolve. They are not designed. Designed languages like Esperanto do not survive in the wild. I do not know for certain your native language, but you are familiar with English. Despite centuries of effort by designers, no one is in charge of English spelling and grammar. Efforts to rationalize and standardize language fail over time. Usage and spelling change. ID proponents like the analogy with computer code and like to point out that a single bit error in a computer program will crash the system. But language is a much better analogy. Errors occur all the time and do not crash the system. Some of them get incorporated into the language. Over time, languages change to the extent that speakers of a language can’t read or speak the earlier version. Now about Basque. Unless you believe that the Basque language was poofed into existence by a designer, it evolved by incremental change. But it has no apparent continuity with any other extant language. It has no living cousins. It is a demonstration that a system of coding sequences can change incrementally over time, to the point that cousinship cannot be determined.Reciprocating Bill
March 14, 2014
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petrushka on language:
Because languages evolve. They are not designed.
I would love to see any language "evolve" without the help of intelligent agencies. As I said there isn't any debating people like petrushka.Joe
March 14, 2014
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Sal:
Fine, then we just say I theory and D theory, and never use the term ID theory again.
Sal, I didn't mean to be hurtful. I just can't understand where the disconnect is. The only thing that necessarily follows from the design inference is the existence of a designer -- one that can, by the very etymology of the word "intelligence", choose between contingent possibilities. That is all. So we don't throw out the concept of "intelligent" in ID; we just need to understand what it refers to and its limitations. Other questions, what you referred to on the previous thread as "theories of intelligence" (identity, timeframe, how acted, personality, and so on of the designer), are interesting second-order questions, but not part of the design inference.* That these questions can, and indeed must, be kept separate from the design inference itself has been very clearly stated by the major ID proponents from day one. That is why I can't understand this insistence on claiming otherwise. If your goal is to be provocative in a pro-ID forum, you have certainly accomplished that, but at the expense of clarity and sound reasoning. I don't have any problem with someone wanting to investigate the second-order questions. I'm not even particularly exercised about someone claiming, as you have done, that they aren't "science" (though good arguments can be made that some of those second-order questions should reasonably be treated as "science"). What I am concerned with is the conflation of the two, the suggestion that ID "merges" the design inference with second-order questions about the designing intelligence. Such talk muddies the waters, confuses sincere students who are interested in learning about ID, and gives unnecessary ammunition to critics who themselves love to conflate the concepts. It is both inaccurate from a logical and theoretical point of view and harmful from a practical and political point of view. Let's stop suggesting that ID has "merged" the two. It hasn't. The design inference is extremely simple -- and limited. That is the benefit and the usefulness of the concept. Let's keep it that way. If someone wants to investigate second-order questions, fine. But when we talk about ID let's be clear that if we start delving into second-order questions that we are doing so and that ID neither requires nor depends upon such an inquiry. ----- See in particular my comments #22 and #25 on the this thread: https://uncommondescent.com/philosophy/the-d-of-id-is-science-lessons-from-our-dealings-with-nick-matzke/Eric Anderson
March 14, 2014
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And to prove petrushka is clueless (discussing Lenski and citrate):
The key element of this discussion is the one or two enabling mutations. Unless Axe can bridge this gap, his work is not relevant to supporting or undermining evolution.
1- Axe isn't trying to undermine mere evolution 2- Lenski's citrate digesting bacteria didn't involve any new proteins 3- It didn't involve any new protein folds 4- No one can say if it had anything to do with blind watchmaker evolution. All that happened was an existing gene that encoded for a protein that aids in getting the citrate into the cell when O2 is not present, ie an anaerobic environement, was duplicated and put under control of a promoter that was active in the prsence of O2. petrushka is happily clueless wrt what is being debated. Pathetic.Joe
March 14, 2014
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And this should answer OMagain's question:
First, as observed in Table ?Table1,1, although we might expect larger proteins to have a higher FSC, that is not always the case. For example, 342-residue SecY has a FSC of 688 Fits, but the smaller 240-residue RecA actually has a larger FSC of 832 Fits. The Fit density (Fits/amino acid) is, therefore, lower in SecY than in RecA. This indicates that RecA is likely more functionally complex than SecY.
From Measuring the functional sequence complexity of proteins (see results and discussion) Specified information has been measured and CSI has been detected wrt biology. So please stop lying and saying that it hasn't been done.Joe
March 14, 2014
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Here are two of those papers again, complete with math: Is Intelligent Design Required for Life? Functional information and the emergence of biocomplexityJoe
March 14, 2014
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Sal:
Fine, then we just say I theory and D theory, and never use the term ID theory again.
No Sal, you are the problem, not ID. The I and D go together for the many reasons already provided. Don't tell me that you are turning into an evo-type and are going to ignore the reasoning presented. The Intellignet" in Intelligent Design is just describing the type of design.Joe
March 14, 2014
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And as predicted the TSZ ilk stuill refuse to read the references I provided that demonstrate how to measuree biological information. They are a pathetic little people. Heck Mike Elzinga thinks that all we are is condensed matter. And he complains that we don't have a testable methodology- LoL! no one can test the claims of materialism.Joe
March 14, 2014
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I liken petrushka and all evolutionists to losers to whine and cry about their opposition all the while unable to do anything to support the claims of their own position.Joe
March 14, 2014
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LoL! DR Axe knows more about molecular biology than all the TSZ ilk put together. And only incompotent morons think that calling the genetic code an actual code would think that is a metop[hor or analogy. And RB is one of the fools who denies the genetic code is an actual code.Joe
March 14, 2014
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KF:
RB: I will make a few comments...In short, by failing to actually tackle the challenge head on with empirically well founded responses, P created an impression of greater plausibility than is warranted.
Just to clarify, those responses (in 82, above) are wholly Petrushka's.Reciprocating Bill
March 14, 2014
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KF: The link was right, but there was an "http" too much! (just a typo). Here is the corrected link: http://www.tbiomed.com/content/4/1/47 By the way, I have not OP posting privileges. The only problem here is that it would be interesting to discuss with Petrushka or with other reasonable opponents, but I have neither the time nor the will to go on with discussions at TSZ, or with parallel discussions, as I have already done in the past. I believe that the level of discussion here has become lower, because of the absence of gifted opponents. Just my humble opinion.gpuccio
March 14, 2014
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PPPS: Googled the URL, saw the 2007 pdf here: http://www.tbiomed.com/content/pdf/1742-4682-4-47.pdf Maybe we need to update links? Wayback Machine, final pull as at Sept 2013: http://web.archive.org/web/20130927111508/http://www.tbiomed.com/content/4/1/47kairosfocus
March 14, 2014
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PPS: The Durston paper link seems dead, which one are you linking?kairosfocus
March 14, 2014
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PS: Oddly, that sounds a lot like the gap between immediate and long term functional advantage that underlies ever so much of the exchanges and debates about design. Foresight allows long distance purposeful action that passes on immediate advantage to gain in the long term. AKA the problem of sub-optimisation.kairosfocus
March 14, 2014
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GP: You too hold OP posting privileges, so you will easily be able to see that VJT, you and I do not have moderator powers in general; to test, go to your admin page and see if you can call up the full list of most popular posts beyond the first tier. (We do have power to release comments in moderation in our own threads.) The decision to restore commenting privileges -- not a right -- lies in other hands and if P was banned for cause or put on mod, there is going to have to be a balance of considerations. And if there is such a cause, maybe the point that posting privilege is valuable for the future will help restrain from heckler type behaviour in the present. Which, would contribute materially to improving the tone of discussion on these matters. KFkairosfocus
March 14, 2014
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RB: I will make a few comments. First, pardon, but most of the above is tangential to the main matter on the table even as can be seen from the agenda of points by P as cited by VJT, and even to the focal issues in Axe and Gauger's work . . . in a lab BTW that seems to have been developed through the despised DI CSC. So, it runs the risk of being a red herring led away to a strawman, already 2/3 of the notorious trifecta fallacy pattern. Whereupon, hostility easily supplies the ad hominem part. As for the hostility issue, I suggest you take a serious look at how the RTH thread looks. Now, I suggest a glance at Axe, Gauger & Luskin, Sci and Human Origins (DI Press, 2012) and onward links, to answer some of your technical questions, from p. 32 on, on some recent protein studies that started with single mutation studies of shifting from one function to another with similar protein structures. In summary, if a single mutation between two similar proteins leads to a valley of inferior function with many local peaks and valleys that may frustrate moving from A to B problem, multiple muts are likely to face more of the same, cf. Figs 2.2 and 2.3 pp. 37 & 38. We already know from Behe's work, that multiple muts for evolutionary steps becomes ever more implausible, especially in light of fixing under pop genetics conditions that are realistic. Recall, too the problem of fixing a pair of co-ordinated muts in a pop leading to enormous times to take small steps. I cite Axe, p. 40:
Darwin's engine often moves away from invention in its short-sighted pursuit of immediate fitness gains [--> as in Behe's first rule of evo] . . . . [it] can't climb a peak corresponding to a new invention unless that peak happens to be remarkably close to its current location -- closer that the peak-to-peak distance between any pair of proteins that we know of [--> he makes a remark on provisionality of such empirical knowledge in context] with distinct functions. Even if such an extraordinary case were to be found, it would be just that -- an extraordinary case. Traversing long distances would still depend on a very long and well coordinated succession of extraordinary cases, which amounts to nothing short of a miracle.
In short, the single mut case studied here has much to say to the hoped for multiple co-ordinated mut case. Such is a hoped for mini hopeful monster. Next, language evolution, of course, is an intelligent process, and so is irrelevant to a blind watchmaker process. It does not proceed by small, blind changes in phonemes that perchance happen to make better sense. A closer "analogy" would be trying to move from a hello world program to a complex control system by incremental single ofr several chance changes, hoping for progress at each stage, so that culling out processes will favour the intermediates. One favourable change is hard to find per needles in haystacks, several together that happen to be neatly co-ordinated, or that get commented off for a time then voila without step by step culling for success find themselves in a functional increment and get turned on back together, will be of much lower odds, and the process becomes indistinguishable from a materialist miracle in a quasi infinite multiverse. P's analogy of an investor unwilling to accept temporary losses again becomes irrelevant. As an MBA I can assure you that (as common sense will tell) investment is not a blind watchmaker process. Indeed, one of the principles is that expertise and associated inside knowledge and skill . . . valuable ideas, skills and synergy . . . creates value that is not readily perceptible to outsiders. So, cash burn to create the platform for takeoff is a risky investment, but sharp venture capitalists have made 20% ROI from hanging around watering holes and buying rounds for engineers crying in their cups; by judging the quality of the men and their determination to succeed against all odds -- a process that is intensely dependent on quality of long-term insight and foresight and sufficient familiarity to spot something that will credibly succeed. The notion that such is analogous to blind incremental survival of the fittest and/or luckiest leading to allele frequency shifts accumulating incrementally into body plan transformation in plausible timespans on reasonable mut rates, breeding pop sizes and gen spans, is simply not plausible. But then, all the way back to Darwin's analogies on breeding, that sort of argument by analogy has been used by advocates of evolution. As to the slipping in of that subtly dismissive term, "analogy," that too is to be corrected. Genetic information is coded, functionally specific info instantiated, not a mere analogy to it. Indeed, it is object code in a cluster of machine languages for protein building, ribosome and RNA building, regulation etc. Object code supported by and processed in clever molecular nanotech implementing machines that make Tour's nanocar look simplistic. To view and treat it and its protein derivatives in that light using tools of info theory is not argument by analogy, but analysis of a naturally occurring instance that on the usual timelines is what, maybe 3.5+ billion years old. Yes, codes, algorithms, co-ordinated support and execution machinery have been on the table since the origin of carbon chemistry, aqueous medium, cell based life in a cosmos fine tuned for that in dozens of ways. Why else do you think that ducking the OOL challenge is so significant as a factor in how P et al have gone off-course in their arguments? Do you think I went to the trouble of finding the Smithsonian modern tree of life with OOL as its root just on a whim? OOL is the root of the matter, and OOL has to come to grips with the known molecular nanotech of the cell and the sorts of precursors, contingencies and config spaces that are relevant to warm little soupy ponds or volcano vents or comets or gas giant moons etc. The undoing of diffusion multiplied by the minimum threshold to achieve encapsulated metabolism (with smart gating) joined to a code using vNSR already tell us the only credible, vera causa plausible source of such FSCO/I is design. Design sits at the table as a serious candidate best explanation for OOL. And once it is at the table, it is there for OOBPs too up to our own. A pint reinforced by the pop genetics challenge of single or multi-step cumulative muts. In short, by failing to actually tackle the challenge head on with empirically well founded responses, P created an impression of greater plausibility than is warranted. Incomplete, more work needed. KFkairosfocus
March 14, 2014
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To Petrushka: Well, I was right in missing you! Very interesting questions indeed. First of all, let's talk of the protein space and Axe's work. I understand your point, and it is a well known point. The proteins space is very complex, and very different sequences can generate very similar structure and function, as we see in protein families where distant members of the family can retain the function and structure, while having only partial homology (only 30-40%, or even less). By the way, that is my favorite observation in favor of common descent. So, as I think I understand well your point, I will try to answer it directly with a few brief comments. We can obviously deepen the discussion on each of them. 1) The fact that compensatory multiple mutations can give a different result than single mutations is exactly the reason why the functional protein space is so complex, huge, and difficult to explore. That is, however, no reason not to try. 2) Axe's approach is a top down approach. It is interesting and meaningful, but you are right in saying that it cannot entirely solve the problem of multiple compensatory mutations. That is a limit, but in no way it reduces the importance and value of Axe's results. 3) There are, however, bottom up approaches which give even more significant results. I will quote here the two works which are most important, IMO. 4) The first is, obviously, Durston's paper: http://http://www.tbiomed.com/content/4/1/47 5) The second is the famous rugged landscape paper: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000096 I quote here what I wrote to Elizabeth in the past: "Just consider the rugged landscape paper: “Experimental Rugged Fitness Landscape in Protein Sequence Space” “Although each sequence at the foot has the potential for evolution, adaptive walking may cease above a relative fitness of 0.4 due to mutation-selection-drift balance or trapping by local optima. It should be noted that the stationary fitness determined by the mutation-selection-drift balance with a library size of N(d)all is always lower than the fitness at which local optima with a basin size of d reach their peak frequencies (Figure 4). This implies that at a given mutation rate of d, most adaptive walks will stagnate due to the mutation-selection-drift balance but will hardly be trapped by local optima. Although adaptive walking in our experiment must have encountered local optima with basin sizes of 1, 2, and probably 3, the observed stagnations are likely due only to the mutation-selection-drift balance. Therefore, stagnation was overcome by increasing the library size. In molecular evolutionary engineering, larger library size is generally favorable for reaching higher stationary fitness, while the mutation rate, d, may be adjusted to maintain a higher degree of diversity but should not exceed the limit given by N=N(d) all to keep the stationary fitness as high as possible. In practice, the maximum library size that can be prepared is about 1013 [28,29]. Even with a huge library size, adaptive walking could increase the fitness, ~W , up to only 0.55. The question remains regarding how large a population is required to reach the fitness of the wild-type phage. The relative fitness of the wild-type phage, or rather the native D2 domain, is almost equivalent to the global peak of the fitness landscape. By extrapolation, we estimated that adaptive walking requires a library size of 10^70 with 35 substitutions to reach comparable fitness.” Emphasis mine. Don’t you think that “a library size of 10^70? (strangely similar as a number to some Axe’s estimate) for “35 substitutions to reach comparable fitness” (strangely similar to my threshold for biological dFSCI) means something, in a lab experiment based on retrtiving an existing function in a set where NS is strongly working?" I would appreciate your thoughts on that. 6) Regarding languages, I don't think I understand your point. Languages are structures which are formed and evolve in conscious intelligent beings. Why do you use them as models for non designed evolution? 7) Finally, a comment about the role of neutral mutations, which I believe are important to your views. I have always been very clear about that. Neutral mutations do exist, and they allow the "drift" which causes the differences in similar proteins in the course of natural history (the proteins with similar structure and function and different sequence). That is the "big bang theory of protein evolution", which I accept, and which is the strongest point in favor of common descent, as I have already said. That mean that neutral mutations can well change the sequence inside the island of functionality, because negative NS allows that. The opposite is not true. Neutral mutations cannot help in traversing the space between islands of functionality, for two important reasons: a) They can go in any possible direction, because they are random. Even considering the allelic effect of genetic drift, the result remains completely random. Therefore, neutral mutations in no way help in overcoming the probabilistic barriers: the number of possible states to be tested remains the same. b) Negative NS definitely acts against the traversing. When you argue about "lose money and argue that because he lost, it is impossible to win", you are forgetting the exacting role of negative NS. I am looking forward to your answers. I would really like that you could post here directly (VJ, can you do that, at least for this post?), or that someone goes on posting your answers here for you.gpuccio
March 14, 2014
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Dionisio @ 60: well said. KFkairosfocus
March 14, 2014
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Sal, I sure wish you would stop beating this drum. The idea that ID “merges” design theories and theories of intelligence is not helpful. Particularly not when the quote from Dembski that you provided a while back to support your assertion says precisely the opposite — namely, that they can, and should, be kept carefully separate.
Fine, then we just say I theory and D theory, and never use the term ID theory again. :roll:scordova
March 13, 2014
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Petrushka asked that I relay the following responses: I addressed a couple of questions specifically to VJT and gpuccio. I think there’s less animosity in that direction and it might be more productive. 1. Douglas Axe appears to be a competent lab technician. My question is, would his protocol have found the citrate metabolism sequence found by Lensky’s population? I’m interested in whether Axe has experimentally considered multiple enabling mutations. If not, of what probative value is his work? 2. As long as they are arguing from analogy and metaphor, I’d like to ask gpuccio what language is spoken in Italy, and what language was spoken in Italy 2000 years ago, and whether the transition was a saltation. And while on the subject of language evolution, I’d like to ask him whether Basque was created by the designer to have nothing in common with any other known language. 3. Another analogy: I would liken Axe to an investor who is unwilling to accept any temporary losses. What Axe does with protein evolution is argue that an investor cannot make money unless the value his portfolio increases with every trade and with every change in the market. No sideways trades allowed, and no temporary losses. What Axe does with his experimental work is lose money and argue that because he lost, it is impossible to win. If VJT or gpuccio would respond, I’d appreciate it.Reciprocating Bill
March 13, 2014
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Eric, Until petrushka stops equivocating and puts together a model that actually addresses the entailments of evolutionism, and thus addresses kairosfocus's challenge, he shouldn't get a forum here. petrushka won't even admit that ID is not anti-evolution. keiths at least acknowledged unguided evolution was the position that required defending. He just totally blew it by relying on Theobald's evidences for macroevolution which even Theobald says do not support any mechanism. So let petrushka back to defend his diatribe. It will just be more of the same. He definitely won't post a way to model unguided, ie blind watchmaker, evolution. It will all be an equivocation. And all attempts to correct him will be ignored, just as he has been ignoring them for years. The point is there is nothing new coming from petrushka. And he definitely isn't going to grasp what we say just because he is allowed back. Just sayin'...Joe
March 13, 2014
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EA: I of course cannot speak for UD's mods. However, when I issued the challenge, P had comment privileges here. I doubt that loss of such privileges -- if that is so (is it, UD mods?) -- would have been without fairly serious cause. On correction, the response was not actually posted here but at TSZ; VJT who seems to monitor there picked it up and reposted here. There is a parallel discussion, linked from here. Having been there to see how the challenge was made, I found the general context so nastily personal and willfully misleading that I posted some correctives above. I will not try to comment at TSZ so long as it drifts into the heckler's convention mentality I saw; life is too short for me to waste time and energy dealing with behaviour like that; other than to set the record straight. That said, if you or any other person see responses or remarks there that need a FTR or FYI or point-by-point response on merits or even know where any earlier actual overall response by P or another person is, why not clip-link such here? For that matter, if you have your own thoughts, those too would be welcome. KFkairosfocus
March 13, 2014
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