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Enzymes stitch together non-natural DNA [Getting closer to lab-made life]
Nature Magazine ^ | 24 February 2004 | PHILIP BALL

Posted on 02/24/2004 3:55:22 AM PST by PatrickHenry

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To: Sloth
So far as I am aware, 'intelligent design' is not focused on the identity of the designer.

Well, which designer decided to run a sewer through a recreational area?

41 posted on 02/24/2004 8:22:39 PM PST by Doctor Stochastic (Vegetabilisch = chaotisch is der Charakter der Modernen. - Friedrich Schlegel)
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To: PatrickHenry
Floyd Romesberg and co-workers at the Scripps Research Institute in La Jolla, California, have harnessed the principles of evolution to find an enzyme capable of assembling non-standard DNA1.

Typical question begging. And I speak as someone doing a post-doc in molecular neurobiology at a top U.S. university.
42 posted on 02/24/2004 8:26:21 PM PST by aruanan
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To: PatrickHenry
That's incredible bookmark. Non-natural base pairs. In a way it does make sense. Why reinvent the wheel (though some may claim that never happened) It would be difficult to get nano processors so small so quickly!

43 posted on 02/24/2004 8:57:22 PM PST by BiffWondercat
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To: adakota
These scientists have used their intelligence to manipulate a piece of machinery. And a very small one at that. Someday a teeny,tiny self-replicating weapon in some researchers eye?
44 posted on 02/24/2004 9:13:29 PM PST by BiffWondercat
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To: RightWingNilla
"Planet of the Apes VI" copyright.....
45 posted on 02/24/2004 9:20:14 PM PST by BiffWondercat
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To: PatrickHenry
Way cool! Thanks for the ping. Will read this evening. :-)
46 posted on 02/25/2004 7:42:38 AM PST by RadioAstronomer
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To: VadeRetro
Interesting, you assume I am criticizing common descent. I am not. I am criticizing the tautological nature of "selection" which inherently makes the concept unfalsifiable, and the polemical stance publicly taken by Darwinians which would produce exactly the reaction I suggested should the one plausible candidate for a Lamarkian (and non-random) source of genetic change be found to actually be active.

Of course, if you insist that 'common descent' is all that 'evolution' means, then you are adopting a rhetorical stance of agnosticism between stochatic-driven Darwinism and some other mechanism to account for biological variation. Is this in fact your position? If so, we really have nothing to argue about, as I was not criticizing such a stance.

Generally people use 'evolution' to mean more than common descent: they mean common descent with differences arising only by stochastic variation and 'natural selection'. Boysenberries, Himalyan cats, and the genetically modified soybeans which resist Round-up brand herbicide are not examples of 'evolution' in the sense the polemical advocates of Darwinism use the word, even though they evince the evidence of common descent. Indeed all are manifestly products of intelligent design.

I really do think you're arguing with one of the short-canon-Bible-as-axiom-system protestants who posts on the evolution threads, not with me.

47 posted on 02/25/2004 9:47:34 AM PST by The_Reader_David
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To: aruanan
[Floyd Romesberg and co-workers at the Scripps Research Institute in La Jolla, California, have harnessed the principles of evolution to find an enzyme capable of assembling non-standard DNA1.]

Typical question begging. And I speak as someone doing a post-doc in molecular neurobiology at a top U.S. university.

Oh? Where's the question-begging? The article says:

Romesberg and his co-workers tried a different approach called 'directed evolution'. They made millions of mutant polymerases by randomly scrambling part of the natural enzyme's chemical structure. Most of the mutants were useless, but some were quite good at stitching together non-standard bases. They plucked these useful mutants out of the crowd, and repeated the mutation and selection process to fine-tune their abilities.

After four rounds of selection, they found several mutants capable of doing the job. One was particularly good: it was able to copy the sequence of a template molecule into the modified form of DNA as efficiently and faithfully as DNA polymerase working with natural bases.

That sounds like a laboratory re-enactment of the kind of thing believed to happen naturally in the wild.
48 posted on 02/25/2004 10:10:08 AM PST by PatrickHenry (A compassionate evolutionist.)
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To: The_Reader_David
I am not. I am criticizing the tautological nature of "selection" which inherently makes the concept unfalsifiable...

One prong of what is often a two-pronged attack.

  1. "Variation is random and randomness doesn't go anywhere!"
  2. "Natural selection means 'The survivors survive' and is thus a tautology."
Tortured lawyerng! Evolution is the joint operation of variation and natural selection to create a convergence over time upon adaptation to current conditions. Evolution, the joint operation of these factors, is not random and not a tautology. The elucidation of this mechanism was a meaningful insight on Darwin's part.

Generally people use 'evolution' to mean more than common descent: they mean common descent with differences arising only by stochastic variation and 'natural selection'.

The obvious effects of human selection on domesticated animals helped Darwin to realize that animals in the wild were under similar 'natural' pressures. It's called "evolution" no matter whence the pressures arise. Thus we say the techniques used to produce a new enzyme in this article demonstrates evolution although neither the variations nor the pressures are 'natural' in origin. The final refinements employed 'rational design' and were not evolution. (Presumably this was because the goal was to polymerize unnatural DNA, not to demonstrate evolution.)

49 posted on 02/25/2004 10:47:23 AM PST by VadeRetro
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To: VadeRetro
Evolution, the joint operation of these factors, is not random and not a tautology.

Especially when the best strategy for survival changes over time with changes in the environment.

50 posted on 02/25/2004 5:20:03 PM PST by VadeRetro
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To: VadeRetro
Popper felt the same way I do about the issue of Darwinism's falsifiability. He relented, thought I am not sure whether he changed his judgement of the version of Darwinism he first citicized or whether it was a particular instantitiation of Darwin's program he later admitted was falsifiable.

I, too am quite happy to admit that a particular, say, game-theoretic model of a specific competition between traits in an ecosystem is science: it is most assuredly falsfifable. A particular account of genetic changes underlying a phenotype change, likewise is falsifiable in principle.

My point, which you continually refuse to address, perhaps because you are drawing only on a stock bag of tricks for arguing with ham-handed creationists, was made in my comparison between Darwinism's 'mechanism' of natural selection and classical Hamiltonian mechanics. Each is a way of generating specific falsifiable 'small theories' to account for the behavior of specific systems. The 'small theories' are all scientific theories. Lots of 'small theories' in evolutionary biology have been falsified. The difference is, the 'big theory' of natural selection is unfalsifiable, while the 'big theory' of Hamiltonian mechanics not only is falsifiable, but has been falsified for certain systems (cf. quantum mechanics).

It is particularly disturbing that the polemical defense of Darwinism against creationists may actually impede progress in producing a really scientific theory of natural selection.

I really have no quarrel with the notion of random variation (other than the fact that I have not heard of any statistical tests for randomness ever having been actually applied to DNA transcription errors), and the fact that the existence of reverse-transcriptase leaves open the possibility of a non-random source of variation in response to the environment. Are you aware of any work testing whether genetic mutations are in fact random? I'd really like to see the papers.

Two examples show that having a stochastic element in a model does not imply purposelessness in the system modeled (as the most hot-blooded polemicists on both sides--whether atheists who really want us to be a product of randomness so that Man can replace God as the source of purpose and the measure of all things, or theistic creationists--seem to think). The behavior of financial markets, arguably the result of purposeful action by investors and traders, is best modeled by stochastic differential equations. Likewise, the hardening of metal, is at an atomic level is the result of thermal, and thus random processes. Nonethless, upon finding a shard of hardened metal, the presumption among archeologists is that it is a work of craft, a purposeful creation.

Kindly respond to what I've actually said rather than just trotting out stock responses to creationists.

51 posted on 02/26/2004 8:54:11 AM PST by The_Reader_David
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To: The_Reader_David
I, too am quite happy to admit that a particular, say, game-theoretic model of a specific competition between traits in an ecosystem is science: it is most assuredly falsfifable. A particular account of genetic changes underlying a phenotype change, likewise is falsifiable in principle.

I gave you a lot more than this back in #32.

The difference is, the 'big theory' of natural selection is unfalsifiable...

You keep saying that. I can't imagine what you're talking about. Perhaps you need to look into why Popper recanted. I gave you a lot of material back in 32. There do remain minor questions of how much is natural selection, how much is neutral drift. That is, questions of precise mechanism. Yes, there have been ideas on the fringe of science concerning non-random ("self-directed") mutation. A somewhat former freeper (who keeps popping back in) was big on the ideas of one Shapiro who IIRC among other things claims that 21st century biology will uncover that organisms increase their mutation rates under stress. Most of us would respond that such a thing, if it exists, no doubt evolved. (Actually, some protists seem to prefer asexual reproduction in good times, sexual reproduction under stress. That seems to be a strategy to avoid extinction by increasing genetic variation, but not all the biologists on FR like that interpretation.)

52 posted on 02/26/2004 9:54:00 AM PST by VadeRetro
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To: VadeRetro
No you didn't: in #32 you gave me a link to a huge website. If we are having a discussion, make your points, don't refer me to something I haven't the time to read in its entirity.

Is there a page in the site linked in #32 which addresses my specific questions and objections? Is there a page which has citations for work on statistical properties of DNA transcription errors? If you won't argue the point yourself, at least give a link to the specific page which makes the specific point in the site which addresses them, rather than just pointing to a whole website. I scanned the website and saw that it was arguing very eloquently that 'common descent' is a falsifiable scientific theory which has survived falsification attempts. You point to it again by way of responding to a small fragment of a long post, even after I had made it clear that the theory of common descent was not what I am objecting to, but the notion of natural selection.

I would be glad to have a discussion, but you won't. You haven't addressed my analogy between Darwinism and classical Hamiltonian mechanics, despite two attempts to get you to do so. Repeatedly choose to address only the tiny fragments of my posts which seem most like typical creationist posts rather than engage what I am actually saying.

In point of fact your statement "Most of us would respond that such a thing, if it exists, no doubt evolved," seems to almost prove the stronger assertion that Darwinism itself is unfalsifiable: even the discovery of variation as a response to the environment wouldn't be seen as falsifying the theory. (Another point I already made in my prediction of the response should reverse-transciptase prove able to make inheritable changes.)

"No doubt it evolved" is no more scientific that "God made it that way."

53 posted on 02/26/2004 11:32:37 AM PST by The_Reader_David
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To: The_Reader_David
Is there a page in the site linked in #32 which addresses my specific questions and objections?

Speaking of not mentioning or not dealing with things, perhaps the second link is a little more accessible. As for the first link, it is made of sections, each of which contains a sub-section on "Potential Falsifications." For the purposes offered, a rapid skim can be done by reading the topic paragraph of each section and the "Potential Falsifications" within. Even if a rapid skim were not possible, your lack of time to discover the falsehood of your claims does not pluck my heartstrings terribly.

You haven't addressed my analogy between Darwinism and classical Hamiltonian mechanics, despite two attempts to get you to do so.

My point is that you do not support your assertions. I do not believe that evolution is unfalsifiable. The existence of counterexamples should be sufficient rebuttal unless you have a note from your mother excusing you from dealing with reality. I really don't care about an analogy which only provides an instance of something else being falsifiable.

54 posted on 02/26/2004 11:49:01 AM PST by VadeRetro
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To: The_Reader_David
In point of fact your statement "Most of us would respond that such a thing, if it exists, no doubt evolved," seems to almost prove the stronger assertion that Darwinism itself is unfalsifiable: even the discovery of variation as a response to the environment wouldn't be seen as falsifying the theory. (Another point I already made in my prediction of the response should reverse-transciptase prove able to make inheritable changes.)

Potential falsifications exist. The problem is that the most obvious of them should have turned up by now and are not coming. The theory will accomodate many ingenious modes of adaptation, yes. It is hard to put limits upon what might have evolved. As Dawkins put it, "Evolution is smarter than you are." That not anything someone desires to construe as a falsification passes muster as one is no more than tough cookies.

55 posted on 02/26/2004 11:55:58 AM PST by VadeRetro
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To: VadeRetro
It really seems I don't need to make my point. You are doing a magnificent job of doing it for me. If the theory can twist to absorb phenomena in such a way that even directional, non-random production of biological variation in response to environmental stress is 'explained' by claiming that this new source of non-stochastic variation is itself a product of evolution, then we are very close to establishing beyond doubt that evolutionary biologists can make up a 'just so' story to explain anything observed as a result of variation (note, not 'random variation' any more, the theory using random variation was just falsified in the hypothetical) and natural selection.

If that can be done, the theory isn't falsifiable, and Popper's original assessment was correct. My experience in discussing the matter with folks like you, shows that even though the exact phrasing of Popper's recantation may be true, in practice natural selection is never reformulated in a non-tautological way, since any observation not accounted for by previously thought of accounts of adaption is met with 'no doubt evolved that way', or 'must have some as-yet-unknown adaptive function.'

56 posted on 02/26/2004 3:47:35 PM PST by The_Reader_David
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To: VadeRetro
...organisms increase their mutation rates under stress...

Which would not preclude the mutations from being random. It would only mean casting the dice more quickly.

57 posted on 02/26/2004 3:54:48 PM PST by Doctor Stochastic (Vegetabilisch = chaotisch is der Charakter der Modernen. - Friedrich Schlegel)
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To: VadeRetro
Your sentiment "That not anything someone desires to construe as a falsification passes muster as one is no more than tough cookies." Is again quite telling.

First, you resort to abusive phrasing. I thought it was always the creationists who resorted to irrational abuse. Second, and more importantly, since I am the one insisting that Popper was correct in his original assessment, it is you who had better hope lots of things 'pass muster' as falsfications. My point was precisely that the 'theory' is so constructed in practice that nothing 'passes muster' as a falsification.

Now, let's see if you can answer a few questions:

1. Can you provide a gedankenexperiment an outcome to which would falsify natural selection? Can you provide a hypothetical finding in the fossil record which would falsify it? A hypothetical finding in molecular biology?

2. If those the gedankenexperiment were performed and the outcome found, or the finding in the fossil record discovered, or the finding in molecular biology from question 1., do you really believe that Darwinism would be abandoned?

3. Could you please give a citation to any work examining the statistical randomness of DNA mutations? (If it's a website, please link the specific page, not the index.html page.)

58 posted on 02/26/2004 4:26:04 PM PST by The_Reader_David
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To: The_Reader_David
1. Can you provide a gedankenexperiment an outcome to which would falsify natural selection? Can you provide a hypothetical finding in the fossil record which would falsify it? A hypothetical finding in molecular biology?

Falsify natural selection? Why not falsify that the joint operation of random variation and natural selection will change a population over time?

Yes, "natural selection" would be a "the survivors survive" tautology, if the environment were always the same. But in fact the pressures change and so does the species in response. Is there some lawyer's gaming point in requiring one particular phrase inside the hypothesis to be separately and independently falsifiable? This is not ordinarily done. "Natural selection" is not a hypothesis. That "isolated populations will change and diverge from each other due to the combination of variation and natural election" is a hypothesis.

2. If those the gedankenexperiment were performed and the outcome found, or the finding in the fossil record discovered, or the finding in molecular biology from question 1., do you really believe that Darwinism would be abandoned?

There are things that might have happened before Darwin's time, or between 1859 and now, which would have led to an abandonment of evolution. There is such a crushing preponderance of evidence now for the hypothesis--and such a lack of credible alternatives--that its abandonment is virtually unthinkable. Again, the most obvious falsifications are things that should have turned up by now if they were going to.

3. Could you please give a citation to any work examining the statistical randomness of DNA mutations? (If it's a website, please link the specific page, not the index.html page.)

Here's where you have to do your own work if you have a point to make. Perhaps you need to decide whether you're going to go after "random variation," "natural selection," or both. It's not my fault if you can't formulate what your objection is.

59 posted on 02/26/2004 5:42:16 PM PST by VadeRetro
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To: The_Reader_David
It really seems I don't need to make my point. You are doing a magnificent job of doing it for me. If the theory can twist to absorb phenomena in such a way that even directional, non-random production of biological variation in response to environmental stress is 'explained' by claiming that this new source of non-stochastic variation is itself a product of evolution, then we are very close to establishing beyond doubt that evolutionary biologists can make up a 'just so' story to explain anything observed as a result of variation (note, not 'random variation' any more, the theory using random variation was just falsified in the hypothetical) and natural selection.

Evolution tends to produce adaptation. Tuning the genetic variability of your population is potentially adaptive. When your species is superbly adaptive, variation can cost more than it's worth. When your species is threatened with extinction, variation gives natural selection more from which to select. This should be a "no brainer," but it's easier to snort "How convenient!" It is not easy to look at a useful adaptation and state with certainty that it could not have evolved. That's just not a good area to seek falsifications, as it involves conclusively proving a negative.

If that can be done, the theory isn't falsifiable, and Popper's original assessment was correct.

... then we are very close to establishing beyond doubt that evolutionary biologists can make up a 'just so' story to explain anything observed as a result of variation (note, not 'random variation' any more, the theory using random variation was just falsified in the hypothetical) and natural selection.

Are you claiming that the hypothesis is falsified if no one has proved to you that all variations are "random?" It doesn't work that way. If you want to claim something else is going on, you need to get off your butt and provide some evidence for what you claim is going on. Sniveling about "just so" stories is a signature of those blockhead creationists you don't want to be confused with.

60 posted on 02/26/2004 5:54:25 PM PST by VadeRetro
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