Uncommon Descent Serving The Intelligent Design Community

The Elephant in the Room

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We are regularly told by proponents of evolutionary theory, from Darwin right up to the present day, that purely natural processes, such as random mutations and natural selection, have the ability to build, construct, fashion, purpose and create remarkable machines. Machines that rival, and in many cases surpass, our most advanced technologies.

We are assured in no uncertain terms that such natural processes have this great creative power. Yet when examples are sought, we are invariably given examples that either did not come about through purely natural processes (see Berra’s Blunder), or examples that are trivial in scope. But nothing that even comes close to verifying the grand claims of the evolutionary creation story.

There is a huge elephant in the room.

Why, if evolutionary processes are so incredibly adept at producing remarkable technologies that surpass our capabilities, do we not see such evolutionary processes being put to good use on a regular basis?

All around the world, every day, millions upon millions of new inventions, designs, projects, programs, and other creations are being pursued. Yet the most awesome creative force of all, so we are assured, is for some reason notably absent. Occasionally someone will claim that evolutionary processes were responsible for creating this or that product (the NASA antenna being the example most often trotted out, even though it is not a proper example of purely natural evolutionary processes). Sometimes someone will assert that an “evolutionary algorithm” has produced something mildly interesting (like the questionable and potentially flawed Avida results touted several years ago in Nature). But by and large, this alleged remarkable creative force is absent, irrelevant, a “no show,” when it comes to actually creating things in the real world.

Now the evolutionary proponent will no doubt argue that the reason is simple: not enough time. Easily impressed with all the zeroes in a number like the billions of years of Earth’s history, the evolutionist reposes faith in the power of deep time to take what is clearly an impotent process in the short term and turn it into the most potent creative force in the long term. But when the actual numbers are reviewed and the actual requirements for construction of functional creations assessed, it becomes clear that those zeroes in the age of the Earth or even the age of the universe are but a rounding error and are unhelpful in addressing the larger issue.

To be sure, a trial-and-error process like random mutations and natural selection can occasionally do something interesting – if there is a large enough population and a strong enough selective pressure. Behe has spent time searching for this “edge of evolution,” while in stark contrast most evolutionists never even bother thinking about what evolutionary processes can actually accomplish in the real world, simply taking it as an article of faith that “with evolution nothing is impossible.”

More to the point, such minor changes even when they do show up do not constitute evidence for the larger evolutionary claims. Particularly when many of the alleged examples of evolution’s power turn out to be, on closer examination, examples of breaking a machine, rather than building it.

So the elephant in the room remains. Design is a critical aspect of our modern lives. Design occurs across the spectrum of disciplines and across the globe on a near constant basis. Yet the most potent creative force that allegedly ever existed, that of evolutionary mechanisms, is noticeable in its near complete absence – dabbling at the fringes, only occasionally participating, rarely influencing, never doing much of any real consequence.

We might be forgiven for wondering if perhaps this is all the evolutionary mechanisms have to contribute.

Or all that they ever did.

Comments
gpuccio:
They are the peaks of so many rugged landscapes, exactly as the wild type domain of the protein is the peak of this rugged landscape.
The wild type is the product of vast populations, millions of generations, and a greater variety of mutation types (ignored in the study for simplicity, as the authors say). It can certainly achieve much more fine-tuning than in-vitro experiments. Relative fitness lower than that of the wild type does not mean "no infectivity"; it means lower infectivity. The mutants would be outcompeted in the wild, which is hardly surprising. The descendants of the successful survivors of innumerable rounds of selection must be tough.Piotr
March 3, 2015
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I plotted 3,933 twelve letter words and created a communality graph here As you can see the words form disjointed island and search would be difficult if this is represented in 2 dimensional landscape search. The graph has vertex count = 586, so it can be represented on 9 dimensional Hypercube 586=2^d. Solving for d, we get d=9.19 so the graph can be represented on 9 dimensional Hypercube. which brings even the distance 'functions' near each other. Landscape is 1930s concept. The 2 dimensional representation was for simplicity and even Wright acknowledged true landscape can be represented at higher dimensions only. With today's computational power, there is no need to confine our self to 2 dimensional landscapes.Me_Think
March 3, 2015
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Language evolution is another example of evolution via intelligent design. Why do evos think that everything "evolution" is automatically blind watchmaker evolution?Joe
March 3, 2015
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In any case, experiments demonstrate that natural selection, drift and all other blind watchmaker-type processes are impotent and incapable of producing anything of note.Joe
March 3, 2015
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gpuccio: Why?. Because the rugged landscape cannot be traversed. Why? Because they only used point mutation. Recombination can allow the search to move between local maxima. In any case, the experiment shows that a random sequence can have function, and that the degree of function can be substantially increased through natural selection.Zachriel
March 3, 2015
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Piotr: From the paper:
In practice, the maximum library size that can be prepared is about 10^13 [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.
You say: "What they found is not an ocean of dysfuctionality in which you drown as you try to move away from a fitness peak. The landscape is smooth and traversible by (nearly) neutral evolution, while adaptive walks can easily ascend its slopes up to a certain level." OK, but from that level on, the landscape is extremely rugged. The problem is, the whole experiment is of the kind "function retrieval". They produced a defective phage my substituting a random sequence in a domain, in a protein involved in the infectivity process. This kind of scenario is very good to test the ability of variation and NS to "optimize" a defective function, which however must be present even at the initial low level. So, what we see is that variation and NS can "optimize" the defective situation up to a certain level. At the same time, they cannot realistically optimize it even near the wildtype level. Why?. Because the rugged landscape cannot be traversed. You need an extremely big starting library (10^70, according to the estimate of the authors) to have a chance of finding the optimal level, even with all the process of variation and NS taking place. You say: "Improving the functionality a protein’s sequence further gets difficult because the landscape becomes rugged when the fitness factor is already pretty high. Who cares? Fitness is relative. As long as the organism is viable, it doesn’t have to be perfect in every respect." Wrong. First of all, the fitness factor is not high at all, in that experiment. Remember, we are only retrieving an existing function. We are optimizing a single damaged domain of a single protein. The infectivity is made possible by the whole protein, and by all the rest which acts in the infective process. We have just damaged a bit of the machinery, and still we cannot retrieve the function, even with all the focused power of variation and NS. The simple point is, the biochemical and biological functions that we see in living beings are extremely optimal. They are the peaks of so many rugged landscapes, exactly as the wild type domain of the protein is the peak of this rugged landscape. Those local optima could never be found by random search and NS, because the connectivity you dream of is not real.gpuccio
March 3, 2015
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Zachriel: Sure, but simple mutation will always be limited. Eric Anderson: Based on what? Simple inspection. For instance, "quixotic" is aloof. There are no single step mutations (point change, insertion, or deletion) which yield another word. By the way, this answers gpuccio's question above. However, if there is a population of words, and snippets and recombination are included, then "quixotic" can evolve. A simple snippet is "tic" (twitch) then mutation "tick" (insect) then mutation "tock" (bird) then concatenation "ticktock" (sound). Another example, not requiring snippets is "ticktock". "Ticktock" is aloof. (* According to our dictionary and search, it's a small island with the verbal forms of "ticktock" as well as the nounal forms of "ticktack".) That means it can't evolve from any other word, given only single mutation. However, if the population includes "tick" and "tock", then it can evolve by concatenation. In other words, recombination provides access to areas of the word-space that simple mutation cannot.Zachriel
March 2, 2015
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Zachriel @317:
Sure, but simple mutation will always be limited.
Based on what? It is supposed to have given rise to all manner of wonderful creations, certainly before all of the population-based swaps and sexual recombinations arose. Again, it is just a question of probabilities. Simple mutation has less likelihood of causing a change than a larger genetic change. Sure. Also less likelihood of catastrophic failure. Pick your poison. The fact is that swapping large amounts of genetic material is not some panacea for the limited powers of "simple mutations."
That is incorrect. Assuming only single-point mutation, there are many structures that are out of reach that are available to mutation plus recombination.
Why would we assume only single-point mutation within a single reproducing organism?* Surely the organism could also have, if not recombination from parents, then larger changes in genetic blocks during its lifetime or during the reproduction process. Further, how did those additional pieces of recombining parental DNA come about, if not, at some point in deep time, through "simple mutations"? And what it is it about a particular structure that puts it out of reach of point mutations? Either you are claiming that point mutations cannot produce X because it is: (i) not possible due to general lack of probabilistic resources, or (ii) not possible due to the irreducible complexity issue (i.e., cannot be built from slight, successive changes, so some larger, sudden change is required). Slightly different angles. But both are still subsets of the probabilistic resources issue. ---- * For wd400's benefit: again, talking about a single organism that reproduces asexually once and then dies; no large population ever exists; no outside swapping; no parental recombination; just the same genetic material from generation to generation (with whatever point mutations, copying errors, splicing errors, etc. may arise).Eric Anderson
March 2, 2015
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To claim that life is just lots of DNA is at least as reductionist as to claim that literature is just lots of letters.
Perhaps. It doesn't worry me because I've never claimed life is just lots of DNA.Piotr
March 2, 2015
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Piotr:
Phin: Can you go from Hamlet to A Tale of Two Cities with your additions, deletions, recombinations, etc.? Piotr: Why should I?
If you hadn't clipped the next few sentences, you'd already have my answer. To claim that life is just lots of DNA is at least as reductionist as to claim that literature is just lots of letters. There are layers of complexity to both life and literature. I also note that you avoided this:
Phin: But your analogy has additional arbitrary constraints (like the length of the word) that, when removed, tend to lead us right back to a rugged landscape with towering lonely peaks. It certainly doesn’t demonstrate that it is the external constraint and not the simplicity that is leading to an interconnected web, since with the same external constraint, but the addition of complexity, the connectivity disappears.
One explanation might be that you have nearly as little confidence in the fitness of your analogy as I do.Phinehas
March 2, 2015
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Phinehas
Can you go from Hamlet to A Tale of Two Cities with your additions, deletions, recombinations, etc.?
Why should I? The real linguistic replicators (more or less analogous to DNA sequences) are words, not sentences (except fixed phrases, which behave like vocabulary units), let alone literary texts. A word can be used millions of times by the same person, and is handed down from generation to generation (slowly changing its form over centuries and millennia). A sentence of ordinary spoken language (not to mention longer utterances) is meant for one-time use and and is rarely repeated in the same form ever again. We do design sentences and texts, but we inherit or borrow the building blocks (words, set phrases). You may try to "design" a word de novo from time to time, but unless you manage to make other people use it, it won't become part of language evolution.Piotr
March 2, 2015
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gpuccio, From the article you have linked:
The landscape structure has a number of implications for initial functional evolution of proteins and for molecular evolutionary engineering. First, the smooth surface of the mountainous structure from the foot to at least a relative fitness of 0.4 means that it is possible for most random or primordial sequences to evolve with relative ease up to the middle region of the fitness landscape by adaptive walking with only single substitutions. In fact, in addition to infectivity, we have succeeded in evolving esterase activity from ten arbitrarily chosen initial random sequences [17]. Thus, the primordial functional evolution of proteins may have proceeded from a population with only a small degree of sequence diversity.
What they found is not an ocean of dysfuctionality in which you drown as you try to move away from a fitness peak. The landscape is smooth and traversible by (nearly) neutral evolution, while adaptive walks can easily ascend its slopes up to a certain level. Improving the functionality a protein's sequence further gets difficult because the landscape becomes rugged when the fitness factor is already pretty high. Who cares? Fitness is relative. As long as the organism is viable, it doesn't have to be perfect in every respect.Piotr
March 2, 2015
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Piotr:
I just wanted to highlight one point: if functionality obeys some external constraints (here, the “Englishness” of words), functional structures are not randomly dispersed in the sequence space. They tend to cluster together and to form an interconnected web, rather than a rugged landscape with towering lonely peaks.
But your analogy has additional arbitrary constraints (like the length of the word) that, when removed, tend to lead us right back to a rugged landscape with towering lonely peaks. It certainly doesn't demonstrate that it is the external constraint and not the simplicity that is leading to an interconnected web, since with the same external constraint, but the addition of complexity, the connectivity disappears. I actually think that language is a very interesting and appropriate analogy. We are just talking about spelling at this point in the thread, but when you extend the analogy to the evolution of sentences, then you have to layer in things like grammar in addition to spelling. And when we expand it to literature, you need to layer in things like foreshadowing, allusions, irony, etc. Again, all in addition to grammar and spelling. Can you go from Hamlet to A Tale of Two Cities with your additions, deletions, recombinations, etc.? For me, this is a much closer analogy to what we actually see with life. Layers of information and coordination and regulation. Complex interrelatedness that boggles the mind.Phinehas
March 2, 2015
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P.S. Common origin does not imply "design factors". SING and SONG are related, but it's merely a statement about their (rather remote) history. An average language user with no linguistic expertise is vaguely aware of the relationship but can't even explain how and why they are related, let alone "design" such pairs.Piotr
March 2, 2015
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That kind of connectivity is based on design factors, and has nothing to do with natural functional constraints. And it is certainly responsible for much of the “connectivity” you observe in words.
Not quite. Connectivity via point mutation is almost never due to etymology, but mostly to so-called phonotactic constraints, defining the characteristic pronunciation patterns of a given language. Two adjacent words in a word ladder are rarely related: from LORD you can get LARD, WORD, FORD, LOAD, LORE, etc., none of which is related to LORD. Interestingly, in the chain LORD > LOAD > LOAF the first and last words do have a remote historical relationship (check up the etymologies of LORD and LADY), but this fact doesn't explain their being connectible. One possible counterexample is words formed by vowel alternation (MAN > MEN, SING > SANG, WRITE > WROTE), but here again the relatedness of connectible words is accidental rather than typical, at least in English. Likewise if you allow letter insertions. WRITER is morphologically derived from WRITE, but in a chain like ATE > RATE > IRATE > PIRATE no two words are related. Origin may play play a role if you allow concatenation (TOOTH + BRUSH > TOOTHBRUSH). But the fact that a combination of two functional elements may be functional too is hardly a matter of design. We can quite mechanically try out all sorts of combibnations and check if they are correct English words: thus, TOOTHBRUSH, TOOTHACHE, TOOTHPICK, TOOTHLESS and a few others happen to be lexicalised, but TOOTHROOM or TOOTHPAIN aren't. Note, however, that compounding is a productive process in English, and neologisms of this type are often co-opted as real words before they get recognised by dictionary editors.Piotr
March 2, 2015
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Piotr: "I just wanted to highlight one point: if functionality obeys some external constraints (here, the “Englishness” of words), functional structures are not randomly dispersed in the sequence space. They tend to cluster together and to form an interconnected web, rather than a rugged landscape with towering lonely peaks. That’s also part of Andreas Wagner’s message." And I disagree. You are completely ignoring the basic importance of the search space size. Which was the essential point in my arguments. As the search space becomes huge, the functional states do become dispersed in it. For proteins, we can check that simple fact by comparing the sequences of basic superfamilies, which are not related. And I am really surprised that you think that the functional landscape of proteins is not a rugged landscape, because that is exactly the model that what we know about it definitely favors. See this paper, for example: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0000096&representation=PDF I understand that your example with words is not an exact analogy. But, as an analogy, it supports exactly my point: as the search space grows, the connectivity (if ever there was one) fades. Dramatically.gpuccio
March 2, 2015
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Piotr: By the way, your statement that: "As for your concrete examples, QUIXOTICALLY is based on a foreign proper name, and so is likely to turn out to be “aloof” word (to use Lewis Carroll’s terminology). So is even the shorter adjective QUIXOTIC." allows me to anticipate a comment which I had thought of, but not expressed for the moment. You same statement shows that words are not only connected because of "natural" constraints (like the pronunciation patterns shaped by some natural restrictions on preferred sound combinations, or the anatomy of the vocal tract and the aerodynamics of sound production). They are also connected because of their origin and cultural context. That kind of connectivity is based on design factors, and has nothing to do with natural functional constraints. And it is certainly responsible for much of the "connectivity" you observe in words.gpuccio
March 2, 2015
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The single organism reproducing asexually can certainly evolve.
Nah, a single organism reproducing asexually makes a population.
. The only difference is that it gives more probabilistic resources.
Is there a process that does more than this? Something like Mt Rushmore might arise by erosion, having someone plan and sculpt a mountain merely increases the probability that it will do so.wd400
March 2, 2015
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gpuccio:
Before I comment on the other points, are you saying that you cannot do with 12 letter words what you did with 5 letter words? Because, you know, that was exactly my point! :)
I can't. There isn't much I can do with ANTIDISESTABLISHMENTARIANISM either, and I can't do anything with 47-letter words, because there are none in English. Moreover, QUIXOTE is only seven letters long and still "aloof" -- among other things because it's a word borrowed from a different language, with no detectable historical connection with anything in English, and so its structure stands out as somewhat exotic. Its "aloofness" is inherited by its derivatives. This, however, has to do more with the structural limitations of the English lexicon and the distribution of possible word lengths than with the nature of the search. The word-ladder thought-experiment wasn't supposed to be an exact analogy of evolutionary "searches" (for one thing, "functional" DNA sequences are of neither fixed nor limited length; for another, there are many possible types of mutations beside single point substitutions). I just wanted to highlight one point: if functionality obeys some external constraints (here, the "Englishness" of words), functional structures are not randomly dispersed in the sequence space. They tend to cluster together and to form an interconnected web, rather than a rugged landscape with towering lonely peaks. That's also part of Andreas Wagner's message.Piotr
March 2, 2015
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Eric Anderson: The single organism reproducing asexually can certainly evolve. Sure, but simple mutation will always be limited. Eric Anderson: The only difference is that it gives more probabilistic resources. That is incorrect. Assuming only single-point mutation, there are many structures that are out of reach that are available to mutation plus recombination.Zachriel
March 2, 2015
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gpuccio: You have still not answered my question about the two words. {SUBJECTIVISM to EXTEMPORIZER} Don't know. It's doubtful. However, many 12-letter words are easily available with populations and recombination. gpuccio: And we don’t know the details of your algorithm, and how it works. Sure you do. We already explained it. We have a population of words. They are subjected to either random mutation or random "addition or deletion, recombination, concatenation". If the result forms a new word, it can enter the population, otherwise, it's stillborn. Most are stillborn. But over time, longer and longer words evolve. gpuccio: And your algorithm has not brought us from SUBJECTIVISM to EXTEMPORIZER, showing that connectivity has been restored, whatever that means. Some words will be out of reach. Evolution is opportunistic, and it's easy to show that 12- or even 14-letter words quickly evolve.Zachriel
March 2, 2015
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Zachriel:
Individual don’t evolve.
This is far from certain, but let's leave that question for another post another time. We've been talking about the difference between a single-celled organism that reproduces itself asexually, versus a large population with sexual reproduction. The single organism reproducing asexually can certainly evolve.
Nor is it certain that a particular trait will evolve in a lineage.
Of course it isn't certain. And it isn't certain that a particular trait will arise with recombination either. The only difference is that it gives more probabilistic resources. Any way you cut it, we are dealing with more probabilistic resources. That is it.Eric Anderson
March 2, 2015
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Eric: "The only place the transition from minor adaptive change to large-scale organismal change ever takes place is in the minds of the faithful." Perfectly correct! And, I would say, in the discussions of the tricky...gpuccio
March 2, 2015
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Zachriel: You have still not answered my question about the two words. And we don't know the details of your algorithm, and how it works. And your algorithm has not brought us from SUBJECTIVISM to EXTEMPORIZER, showing that connectivity has been restored, whatever that means. I have a lot of other comments to do about Piotr's statements and yours, but I prefer to wait to see if Piotr concludes his reasoning, and how it relates to Wagner's ideas. So, I will take a little rest.gpuccio
March 2, 2015
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gpuccio @307:
. . . the origin of nylonase is perfectly compatible with ID theory as a form of non designed, maybe adaptational, microevolutionary transition.
Exactly. As is every real-world example of "evolution" that has ever been offered. The elephant in the room is that no observable evidence beyond that ever seems to be offered. The only place the transition from minor adaptive change to large-scale organismal change ever takes place is in the minds of the faithful.Eric Anderson
March 2, 2015
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Eric Anderson: Why would they be otherwise unavailable? I could have the father’s nose and evolve the mother’s eyes on my own later. Individual don't evolve. Nor is it certain that a particular trait will evolve in a lineage. Recombination allows for these combinations to be tested in each generation. Some combinations will provide benefits that are not available to the individual traits.Zachriel
March 2, 2015
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gpuccio: And neo darwinist theorists (including you) have considered it some incredible feat of random frameshift variation for a very long time. Frameshifts are just another type of mutation. gpuccio: the origin of nylonase is perfectly compatible with ID theory as a form of non designed, maybe adaptational, microevolutionary transition. Mutation and selection. That’s evolution for ya!Zachriel
March 2, 2015
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gpuccio: What algorithm? The algorithm we have been discussing when you said "And I don’t believe at all that if you add 'letter addition or deletion, recombination, concatenation' connectivity is restored." That statement was demonstrably incorrect.Zachriel
March 2, 2015
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Zachriel @293:
Somewhat more than that. It’s not just sharing of traits, but the many unique combinations of traits that would otherwise be unavailable. “Your father’s nose. Your mother’s eyes.”
Why would they be otherwise unavailable? I could have the father's nose and evolve the mother's eyes on my own later. It might just take longer and be less probable. Again, all we are bringing to the table with recombination is more probabilistic resources -- we're just tweaking the numerator. It doesn't substantively change what can appear through the evolutionary process.Eric Anderson
March 2, 2015
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Zachriel: "If you didn’t know the origin of nylonase, the ID theorist might consider it some incredible feat of engineering!" And neo darwinist theorists (including you) have considered it some incredible feat of random frameshift variation for a very long time. "But we ‘saw’ the origin of nylonase, and we do know its origin" Luckily. We can still believe that, in time, truth emerges. "It’s within a few steps of a known biological structure. That’s the whole point!" Indeed! The whole point is that neo darwinists were wrong, that their propaganda against ID based on the Ohno conjecture was, indeed, propaganda and nothing else, and that the origin of nylonase is perfectly compatible with ID theory as a form of non designed, maybe adaptational, microevolutionary transition.gpuccio
March 2, 2015
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