How Darwinian Logic Works

_{Gil Dodgen

October 12, 2011

Intelligent Design}

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In this post we discover: According to Darwinian theory, new species emerge when mutations produce individuals who can outperform the stock they came from…

This statement, and so many like them, reveal how Darwinian “logic” is based primarily upon hyper-imaginative speculation, and not anything that could be described as science. Here’s how Darwinian logic works:

Given #1: A certain feature of a living system exists. (Let’s try a trivial example, like Mozart’s ability to write symphonies.)
Given #2: Since this feature exists, it must have a survival advantage.
Given #3: Since it is known (scientifically) that Darwinian mechanisms can explain everything about the history of life, there must have been a gradual pathway such that random mutations and natural selection could turn a microbe into Mozart. How could this not be obvious?

The ID proponent challenges the Darwinist with some obvious questions:

Which random mutations would be required to turn a microbe into Mozart? How long would this take? What is the probability that these beneficial mutations could take place, and what is the probability that they could be fixed in the population with the available reproductive and probabilistic resources? What about the fact that the simplest living cell is the most sophisticated and functionally-integrated information-processing system ever discovered?

The universal and entirely predictable Darwinist response to such challenges:

Are you a religious fanatic who wants to destroy science?

Comments

Well, if a feature exists, the likelihood is strong that at some point it provided survival, or rather reproductive, value. But we don't always know how, or even at what stages, it did. For example a peacock would probably survive better without that cumbersome tail, if all that mattered was survival. Similarly, peahens would probably have more successful offspring if they chose peacocks with nice trim tails than big cumbersome tails. But things don't always pan out that way, and nowadays, peacocks have to breed in an environment populated by peahens who will only mate with you if you have a cool tail, and peahens have to breed in an environment where only the healthiest individuals have the kind of tails that tickle their fancy. So feedback loops seem to have conspired to endow the peacock with a tail that is only of use in attracting peahens, and peahens with a fancy only for peacocks with beautiful tails. It is difficult to demonstrate a clear selective advantage of any one allele in any lineage, because a) we don't know what the environment was at the time or since it appeared, and b) because we don't necessarily know what other alleles (or environmental factors) it needs to interact with to confer selective advantage. What we can do, easily, is demonstrate that these processes can, and do, result in the kind of feedback loops of advantage that generate complexity, function, and, indeed, beauty. Which is what makes the ID inference untenable. We know there is a mechanism that can produce the kinds of phenomena we observe that does not involve an ID. Whether it did or not in any given case is another question.Elizabeth Liddle_{October 13, 2011
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Well, that is a nice idealistic thought. Perhaps when pressed and when being careful they would not say that a feature has survival value just because it exists. Personally, however, I have seen many interviews, press releases and the like with biologists who make precisely that kind of statement. I'd invite everyone to just keep a watch when you see articles/stories about particular features of life. The kind of circular statements Gil is referring to come up quite often.Eric Anderson_{October 13, 2011
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What I asked was:
Do you consider domain shuffling to be the creation of new information? How about incremental changes in gene expression?
I asked if they qualify as new information. It's asking for a definition of terms.Petrushka_{October 13, 2011
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Petrushka: My answer is simple. To establish life in the beginning, a lot of basic protein information was necessary. About half of basic protein domains were implemented at that level. That information has remained available for higher taxa. New information is inputted only whne it is really necessary to implement some completely new function. For instance, the hundreds of proteins, very complex proteins, that are necessary for basic processes like transcription and translation were alreadythere, in LUCA, and are still working in pretty much the same way in us humans. It is also true that, with the development of evolution, new information is inputted much more at the regulatory level (a level we still poorly understand). New information at protein level is less necessary.gpuccio_{October 13, 2011
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Umm if you have genes then you are starting with that which needs explaining in the first place.Joseph_{October 13, 2011
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The concept of most proteins as systems of domains exemplifies the new combinatorial thinking frequently emphasized in this book. It makes good sense a priori to expect that a protein will make a successful functional change by acquiring an existing intact binding or catalytic capability. Intuitively, this has a far higher probability of proving effective than does a random process of changing one amino acid at a time and gradually selecting modest improvements in catalysis or binding specificity. In many cases, existing sequences do not provide suitable starting material for evolving new functions one amino acid at a time, because those novel functions require entirely different polypeptide structures. But this restriction does not apply to the process of acquiring an entire new domain, which already comes appropriately configured. The fact that artificial protein evolution in the laboratory often works far better by domain-swapping methods than by localized mutagenesis is yet another indication that the former is a more effective protein innovation strategy than individual or multiple independent amino acid changes [746]. The systems view of proteins implies that they evolve by natural genetic engineering rather than by localized mutation. Is there experimental evidence that the requisite processes for swapping domain-coding sequences actually occur in living cells? Some of the earliest molecular genetics experiments in bacteria involved the formation of hybrid proteins by deletion events that eliminated termination signals and joined two coding sequences into one (for example, [747]). My late colleague Malcolm Casadaban developed a generalized in vivo technique using a DNA transposon that could fuse any E. coli protein coding sequence to the enzymatically active domains of LacZ beta-galactosidase [748]. Mammalian tissue culture experiments have demonstrated the domain-swapping capabilities of non-LTR retrotransposons through retrotransduction, either of upstream sequences (SVA elements) or downstream sequences (LINE elements) [522, 749, 750]. In addition to domain swapping by retrotransduction, genome sequences in plants and animals have begun to document protein-coding regions where new exons have been incorporated by different classes of DNA transposons (so-called “Pack-MULEs” in rice and helitrons in maize [213, 751–754]). So the capacity of living cells to carry out the requisite natural genetic engineering operations for protein evolution by domain swapping is unequivocally established. Shapiro, James A. (2011-06-08). Evolution: A View from the 21st Century (FT Press Science) (Kindle Locations 1771-1784). FT Press. Kindle Edition.
Petrushka_{October 13, 2011
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Petrushka: Domain shuffling, like any other form of variation, must be quantitatively analyzed. In principle, it could be explained by RV and NS, or by design. Again the problem is: how likely is it that existing protein domains are subkect to casual shuffling that produces a functional result? We should apply here the same methodology as for protein sequences, but it can be more difficult. That's why I rarely discuss this aspect. Anyway, we should know the combinatorial search space, and the target space of functional shufflings, and the probabilistic resources. And, if we want to invoke NS, we must provide some evidence that the results for which we compute probabilities are naturally selectable. My opinion is that domain shuffling can be bets explained as a form of modular programming. It is object oriented programming at its best. IOWs, it is a form of highest design. But at present I have not the resources to give a detailed analysis of that scenario, and I prefer to stick to basic protein domains as a model for ID. On the other hand, I doubt that there is any credible quantitative darwinist analysis of the domain shuffling model from a darwinian point of view.gpuccio_{October 13, 2011
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But are you saying that evolutionary biologists would generally disagree that particular features have a survival advantage?
They would not say that just because a feature exists, therefore it has a survival value. Rather, they would make judgments about survival value based on actual evidence.Neil Rickert_{October 13, 2011
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Eugene: I have discussed those points many times, but it is difficult for me to find where. There is something recent here: https://uncommondescent.com/intelligent-design/science-and-freethinking/comment-page-3/#comment-402266 and here: https://uncommondescent.com/intelligent-design/science-and-freethinking/comment-page-3/#comment-402272 My idea is: whatever the designer is, its interaction with physical reality must be explorable, to a point, in a bottom up way, starting from physical reality. Natural history, as it can be inferred form the traces we have now, is fundamental both to infer design and to reason on the modalities of implementation of the design. At the origin of design is always a conscious representation. That's what makes design design. But the process of design is an implementation of that representation on a physical plane. The designer does specific things to implement his representation. He has to "configure switches", to give them the desired form. The configuration of material switches must be explorable. ID gives us a powerful tool the computation of dFSCI (or any equivalent metrics). Applied to natural history, that can tell us when important informational outputs were realized. We must narrow our time windows. The big bang theory of protein evolution, to which I have often given reference, is IMO an important tool to understand what really happens in the proteome in the course of natural history. Darwinists continuoslu boast their "theories", but the truth is that they are blinded by the necessity of justifying a wrong theory. That's why they cannot see the obvious. The obvious is that new protein information emerges suddenly in the course of natural history, after having emerged much more suddenly and in huige quantities at OOL. The obvious is that such information changes gradually in the course of natural history, probably because of neutral evolution, while retaining the same function. The obvious is that in other cases the same basci information is tweaked and adapted to generate families of slightly different functions. We have to keep those facts well separated. The emergence of new basic information cannot be explained by darwinist theory. There can be no possible doubt about that. It is the best tool to trace important design events, and to investigate their modalities: time distribution, and possibly ways of implementation (guided mutations, or intelligent selection, or both), the existence of intermediaries, and so on. We must try to understand if the differences between the same functional proteins in far species are due only to neutral evolution in the island of functionality, or if they have a functional value. We have to better define the informational thrsholds of minor protein evolution within families, which is potentially in an intermediate range, and could be explained in principle by both RV and NS and design. And so on. A lot of good questions. But until research will be interpreted only in the light of darwinism, answers will be difficult to be found.gpuccio_{October 13, 2011
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Do you consider domain shuffling to be the creation of new information? How about incremental changes in gene expression?Petrushka_{October 13, 2011
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I find it interesting that domain invention seems to be mostly the work of microbes, and seems to have slowed down over time. Whatever the actual history of new domains, it seems associated with very high numbers of organisms. Can you offer an ID explanation for this trend?Petrushka_{October 13, 2011
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According to Darwinian theory, new species emerge when mutations produce individuals who can outperform the stock they came from wd400
Nope. (That’s actually adaptation)
Nope, adaptation is when they are (best) suited to their environment.Joseph_{October 13, 2011
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Mark: I would really like to see the "detailed hypotheses" you speak of. Most evolutionary hypotheses are just about lines of descent, without any trace of causal explanation. Those hypotheses are an attempt at reconstructing natural history, not explaining it, and they are as good for design research as they are for darwinism. Reconstructing natural history as precisely as possible is the basis for any attempt at explaining it, be it from a design poiny of view or from a darwinist point of view. But darwinists have never explained the emergence of even a single protein. They explain nothing. They can't, because their theory is wrong, and will never find support in natural hystory. What ID demands is an explanatory model, not just smoke and mirrors. ID has an explanatory model, and facts about natural history can and must be viewed in the light of that model. We have to answer to specific and important questions: a) How and when do new proteins emerge? b) Is the pattern gradual or discontinuous? c) How much new information seems to appear without any trace of step by step paths? d) Can we reconstruct a more or less detaile map of the emergence of new information in natural history? e) What can we really say about LUCA? When did it live? How old are the proteins which were already present in it? f) Can we define more in detail the fundamental transitions in natural history? OOL, emergence of eukaryotes, emergence of multicellular phyla? And try to objectively chracterize them in terms of time, space and information? Science must try to give objective amswers to these and other questions, getting rid of the delusion that darwinist theory is the only possible answer. Existing data must be viewed also from a design point of view, with open mind and sincere desire for truth.gpuccio_{October 13, 2011
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We now know that drift is responsible for many "particular features" and selection may play a less critical role. More to the point, the ability to write Mozart symphonies is not highly heritable, and, to the extent that it is, there are extremely important gene-environment interactions. What is heritable, of course, are many of the component abilities, many of which may well have had a survival advantage. But these are likely to be polygeneic.Elizabeth Liddle_{October 13, 2011
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Gil, You appear to provide three premises (indicated by the term 'Given') but you dont lay out any logic operations on those premises to arrive at a conclusion with a truth value. Is this really your idea of 'Darwinian Logic'?paragwinn_{October 13, 2011
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Gpuccio You are one of the few IDists that has openly discussed possible mechanisms but these are only a few informal conjectures at very high level. I don't think you mention any specific transition - not even at the phylum level (most IDists would refuse to go even that far). Contrast that with the detailed hypotheses that are proposed (and sometimes disproved) by biologists about the evolution of specific proteins, species, and higher taxons. And the even more detailed proof that the ID community demand of biologists - lack of which is taken as evidence for ID.markf_{October 13, 2011
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Is it possible to get it right even between two evolutionary biologists?Eugene S_{October 13, 2011
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GPuccio, "I have openly discussed possible mechanisms that can in principle be recognized from observed facts in natural history". Could you point me to the discussion. I have been wondering about the question of ID entailments lately. So that discussion would be of help. Thanks.Eugene S_{October 13, 2011
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Mark: No. I have discussed those things openly and in detail, even with you, I believe. There is often this misunderstanding. a) It is true that the details about inplementation of design are not required for the procedure of design detection, as it is outlined in ID. b) It is perfectly true, however, that details of design implementation can certainly be the object of scientific research, once ID is accepted as best explanation, or at least as possible explanation. Maybe some IDists prefer not to deal with the second point. I have no problems about that, and I have openly discussed possible mechanisms that can in principle be recognized from observed facts in natural history. I maintain, however, like all IDists, that the design inference needs not the details about design implementation.gpuccio_{October 13, 2011
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I didn't think of Mozart's genius as a feature as it would be the result of combination of nature and nuture. But let is put it this way - I doubt there is much disagreement in practice between IDists and biologists over whether a particular feature has a survival advantage (not that #2 does not say whether a particular feature arose because it had a survival advantage). Is it not true that IDists do not attempt to provide any detail whatsoever about how features evolved? And indeed resist any such attempt as being beyond the scope of ID?markf_{October 13, 2011
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wd400: Could you please, being probably a moderate adaptationist, explain what is in your opinion the general mechanism by which new complex information (such as a new basic protein domain) emerges, according to darwinian theory? You see, I am taking your counsel. I am trying to get my darwinian nonsense directly from a darwinist...gpuccio_{October 12, 2011
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Mark: #2 could be re-written, for all darwinists to accept it, this way: Given #2: Since this feature exists, it must have originated thorugh ramdom events plus natural selection of a survival advantage. I would definitely say that I don't agree with #2, however stated. Mozart's genius exists bevause it was intentionally designed, not because it gives a survival advantage, not because it is neutral. It is an intelligent feature whose purpose is to express some potentialities of consciousness. But you are right, the main dispute is about #3. And obviously, I absolutely dispute the way you represent the dispute :)gpuccio_{October 12, 2011
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err.. "Probably not a good idea to get your..."wd400_{October 12, 2011
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Probably a good to not get your evolutionary biology from people that oppose evolution According to Darwinian theory, new species emerge when mutations produce individuals who can outperform the stock they came from Nope. (That's actually adaptation) Since this feature exists, it must have a survival advantage. Nope. That's the kind of hyper-adaptationism that hyper-adaptationists laught at.wd400_{October 12, 2011
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I think most biologists would say that #2 is not always true. Some features may be neutral or mildly disadvantageous. Nevertheless it is clearly true that it makes sense in biology to ask of any feature “what does it do for the this organism?” – bearing in mind the answer might be “nothing much”. But surely even the most ardent IDist agrees with #1 and probably agrees with #2 even more than a biologist. So the dispute is about #3 – what is the best explanation. The biologist is challenged to give detail about an evolutionary explanation and does so to greater or less extent depending on the data available (and often changes the detail in the light of data). The IDist says “you can’t challenge me to provide detail because ID is not about how it happened”.markf_{October 12, 2011
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Neil, I think you're correct that the wildest stories come from the evolutionary psychologists. But are you saying that evolutionary biologists would generally disagree that particular features have a survival advantage? So would they say, for example, that wings, hearts, lungs, eyes, brains, didn't arise because they conferred a survival advantage?Eric Anderson_{October 12, 2011
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I can't think of a movie that got anything about evolution right. Certainly not the X-Men.Petrushka_{October 12, 2011
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Given #2: Since this feature exists, it must have a survival advantage.
I sometimes wonder whether some evolutionary psychologists think that. As far as I know, most evolutionary biologists would disagree.Neil Rickert_{October 12, 2011
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