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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: The_Reader_David; VadeRetro
Oh, bother, more than the usual run of typos today: early in my long post regarding common descent it should read,
'. . .I regard as a sound. . .' rather than '. . .a regard as a sound. . .'
81 posted on 03/03/2004 11:43:55 AM PST by The_Reader_David
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To: The_Reader_David
Do try to continue a civil discussion and actually read my posts to address their content rather than some preconceived idea of what a critic of Darwinism would say.

I don't have to extrapolate a thing to be unimpressed with your arguments.

You seem to have overlooked the end of my post in which I promised a more thorough answer. It would have been courteous to wait, rather than 'giv[ing]. . .some more'.

So, long after this thread had been forgotten, here's the result of your labors. Sorry if it doesn't take as long to unravel the BS as it did to try to spin it.

Still, I will answer your 'more' first:

You miss the point of introducing the "curse of the gods 'theory'": it was not introduced as a serious attempt to explain biological diversity (hence your jibe about ring species is utterly irrelevant) but to clarify a point about the nature of falsifiable theories by illustrating how an unfalsifable theory can be appended onto a falsifiable one, the composite inheriting the falsifiability of the properly scientific subtheory, and then moreover dressed up with additional (readily modifiable) assumptions to 'make more predictions'. The point is that both Darwinism and the "curse of the gods 'theory'" inherit falsifiablity from their common element: the theory of common descent, which I have already told you a regard as a sound scientific theory which has survived many falsification tests.

Common descent alone does not explain the diversity of life. After all, as creationists like to point out, robins only produce robins and lions only produce lions. So you have to explain whence ariseth the diversity of life. Occam's Razor says that there may be an infinite number of ways to do that, but not all of them are reasonable.

In point of fact, the "curse of the gods" theory does not look far at all from where you're going with your non-random variation and non-natural selection. However, barring any direct evidence for gods running around cursing life forms, Occam's Razor cuts it right out. If that's where you're going, it's going to need some justification.

I am also puzzled why you insist that I must specify one thing which bothers me.

I'm teasing. You're looking for whatever objection you can muster.

For whatever reason, you've abandoned neutrality toward science and have decided you know where God fits in and science is refusing to see. You probably should have remained patient and let Him reveal in time where he fits in and let science do what it does.

I have made plain what my objections to Darwinism are: first that natural selection (or environmental pressure, if you prefer) is not a mechanism at all, but a tautological definition which can be given any non-tautological content a biologist sees fit to fill in to offer an explanation of any observed change;

Sometimes stronger is better, yes. Sometimes faster is better. Sometimes a better serration on the grasping surface of the claw is better. Sometimes armor is the answer. There can be more than one way to survive, or less than one. All of the individual instances that sculpt populations are non-tautological. Natural selection is a term invented to describe a pruning action of the enviroment, regardless of what exactly it's favoring at the moment. It's a shorthand. To pounce upon such as an excuse to throw away useful information is ridiculous.

... second that the one falsifiable element in the usual description of the theory--random variation--has not, in fact, been subjected to any serious falsification tests (something you seem to admit);

I simply don't know, and neither do you. OK, I've mentioned a few things I did know of and you didn't. If you're really interested in this area, you should be looking into it for yourself. It appears that you're simply continuing to chant mantras. The ethical thing to do would be to check and see if what you're saying is true.

I'm sure it's been looked at more than either of us is aware.

... and finally that a combination of cleverness in inventing 'selection pressures' to explain any observation together with sociological effects of defending Darwinism against religiously motivated obscurantists (which make the definition of theory itself maleable) has led to a situation in which Popper's original view that Darwinism is a 'metaphysical research programme' which can generate real, falsifiable scientific theories, but is not itself one, is in fact correct.

Funny that I gave you links to Popper's original statement and his retraction and you've already forgotten the latter.

Now as to the rest of the long post you faulted me for only beginning to critique:

First, I am puzzled why you assume cosmic ray strikes are the only issue.

It's the only thing I mentioned. Many mutagens are known. Probably many more are still unknown.

We are both aware that there are mutagenic chemical compounds. We are both aware that reverse-transciptase enzymes exist. You even point to strongly conserved portions of some genomes--an observation which I was hitherto unaware, and which plainly tells against the randomness of variations.

Science has known this for decades. If it were revolutionary, someone would have noticed. That should tell you something other than "It's all a conspiracy." In conserved regions, mutations still happen but are usually corrected before replication continues.

Of course, you explain this as an adaptation, just as you explained the reverse 'rolling the dice more often' as an adaptation.

Conserved regions are conserved because mutations within them are usually catastrophic. If you need it "explained" to you that a mechanism to protect sensitive parts of the code is adaptive then you're lawyerng too hard.

I've already told you that the falsifications are going to lie in other areas besides pointing to an adaptation and saying "I don't understand how that evolved, so it didn't evolve." Please do not make me repeat this any more.

And pushing selection pressure down to the cellular level doesn't really do anything but insist that I push my critique down to the cellular level, which I am glad to do.

Finally, as regards the tautological nature of selection pressure, your analogy with F = ma isn't really a good one.

Your demonstration here is just bogus. Bo-gus. The critique of Newton is not my invention. Better minds than either of ours made it. You might have realized up front that this is not a good area to try to blow smoke up people's butts. Then there's the matter of your actual argument...

The fact that force, which is also related to energy expenditure via W = Fd (for simplcity I remain in the 1-dimensional picture with forces constant over time), and then linearly to the second time derivative of a body's position is hardly tautologous, and subject to test (one could imagine a dynamics in which while W = Fd, there is a non-linear relation between force and acceleration, or a world where Aristotle's physic correctly predicted motion).

W = Fd looks like a non-mass definition of force only if you have a non-mass, non-force definition of "work." Work is not one of Newton's basic terms. It is essentially expended energy, which is why it has the units of energy. The nicest thing you can say about your attempted lawyerly nitpick is that the joule does have two parallel definitions:

1) the work done by a current of 1 amp traversing a resistance of 1 ohm for 1 second, and

2) the work done when the point of application of a force of 1 newton is displaced 1 meter in the direction of the force.

Newton could not have used the electrical definiton of work for the problems considered in the Principia as they concern mass, force, inertia, and gravity.

You're stuck with definition 2. What's a newton? Force. What definition of force? F=ma.

Natural selection (or environmental pressure), however, really comes down to 'survivors survive'.

It is possible in individual cases to identify just how they do that. It is not possible to make a sweeping statement describing who will live and who die. But that's just irrelevant.

The 'Humans allow to breed those which they allow to breed,' tautology likewise does not contribute to a scientific theory of the observed outcomes of animal husbandry, as without a theory about what humans want in their domesticated animals it provides no testable predictions (beyond those built in by common descent).

Just stay stupid. Obviously you can study the effects of human selection.

Replacing 'environmental pressure' with an actual testable theory of what is well-adapted for each ecological niche and a theory of what ecological niches will exist under what conditions would give a properly scientific theory of natural biological, just as replacing the 'humans allow to breed. . .' tautology with a testable theory of what humans want in their domesticated animals would yield a scientific theory of the outcomes of human animal husbandry.

When you have an example of what you're babbling about, publish. When you first started posting here, you seemed like one of the sane ones. Sad.

82 posted on 03/03/2004 11:50:36 AM PST by VadeRetro
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To: The_Reader_David
Do try to continue a civil discussion and actually read my posts to address their content rather than some preconceived idea of what a critic of Darwinism would say.

I don't have to extrapolate a thing to be unimpressed with your arguments.

You seem to have overlooked the end of my post in which I promised a more thorough answer. It would have been courteous to wait, rather than 'giv[ing]. . .some more'.

So, long after this thread had been forgotten, here's the result of your labors. Sorry if it doesn't take as long to unravel the BS as it did to try to spin it.

Still, I will answer your 'more' first:

You miss the point of introducing the "curse of the gods 'theory'": it was not introduced as a serious attempt to explain biological diversity (hence your jibe about ring species is utterly irrelevant) but to clarify a point about the nature of falsifiable theories by illustrating how an unfalsifable theory can be appended onto a falsifiable one, the composite inheriting the falsifiability of the properly scientific subtheory, and then moreover dressed up with additional (readily modifiable) assumptions to 'make more predictions'. The point is that both Darwinism and the "curse of the gods 'theory'" inherit falsifiablity from their common element: the theory of common descent, which I have already told you a regard as a sound scientific theory which has survived many falsification tests.

Common descent alone does not explain the diversity of life. After all, as creationists like to point out, robins only produce robins and lions only produce lions. So you have to explain whence ariseth the diversity of life. Occam's Razor says that there may be an infinite number of ways to do that, but not all of them are reasonable.

In point of fact, the "curse of the gods" theory does not look far at all from where you're going with your non-random variation and non-natural selection. However, barring any direct evidence for gods running around cursing life forms, Occam's Razor cuts it right out. If that's where you're going, it's going to need some justification.

I am also puzzled why you insist that I must specify one thing which bothers me.

I'm teasing. You're looking for whatever objection you can muster.

For whatever reason, you've abandoned neutrality toward science and have decided you know where God fits in and science is refusing to see. You probably should have remained patient and let Him reveal in time where he fits in and let science do what it does.

I have made plain what my objections to Darwinism are: first that natural selection (or environmental pressure, if you prefer) is not a mechanism at all, but a tautological definition which can be given any non-tautological content a biologist sees fit to fill in to offer an explanation of any observed change;

Sometimes stronger is better, yes. Sometimes faster is better. Sometimes a better serration on the grasping surface of the claw is better. Sometimes armor is the answer. There can be more than one way to survive, or less than one. All of the individual instances that sculpt populations are non-tautological. Natural selection is a term invented to describe a pruning action of the enviroment, regardless of what exactly it's favoring at the moment. It's a shorthand. To pounce upon such as an excuse to throw away useful information is ridiculous.

... second that the one falsifiable element in the usual description of the theory--random variation--has not, in fact, been subjected to any serious falsification tests (something you seem to admit);

I simply don't know, and neither do you. OK, I've mentioned a few things I did know of and you didn't. If you're really interested in this area, you should be looking into it for yourself. It appears that you're simply continuing to chant mantras. The ethical thing to do would be to check and see if what you're saying is true.

I'm sure it's been looked at more than either of us is aware.

... and finally that a combination of cleverness in inventing 'selection pressures' to explain any observation together with sociological effects of defending Darwinism against religiously motivated obscurantists (which make the definition of theory itself maleable) has led to a situation in which Popper's original view that Darwinism is a 'metaphysical research programme' which can generate real, falsifiable scientific theories, but is not itself one, is in fact correct.

Funny that I gave you links to Popper's original statement and his retraction and you've already forgotten the latter.

Now as to the rest of the long post you faulted me for only beginning to critique:

First, I am puzzled why you assume cosmic ray strikes are the only issue.

It's the only thing I mentioned. Many mutagens are known. Probably many more are still unknown.

We are both aware that there are mutagenic chemical compounds. We are both aware that reverse-transciptase enzymes exist. You even point to strongly conserved portions of some genomes--an observation which I was hitherto unaware, and which plainly tells against the randomness of variations.

Science has known this for decades. If it were revolutionary, someone would have noticed. That should tell you something other than "It's all a conspiracy." In conserved regions, mutations still happen but are usually corrected before replication continues.

Of course, you explain this as an adaptation, just as you explained the reverse 'rolling the dice more often' as an adaptation.

Conserved regions are conserved because mutations within them are usually catastrophic. If you need it "explained" to you that a mechanism to protect sensitive parts of the code is adaptive then you're lawyerng too hard.

I've already told you that the falsifications are going to lie in other areas besides pointing to an adaptation and saying "I don't understand how that evolved, so it didn't evolve." Please do not make me repeat this any more.

And pushing selection pressure down to the cellular level doesn't really do anything but insist that I push my critique down to the cellular level, which I am glad to do.

Finally, as regards the tautological nature of selection pressure, your analogy with F = ma isn't really a good one.

Your demonstration here is just bogus. Bo-gus. The critique of Newton is not my invention. Better minds than either of ours made it. You might have realized up front that this is not a good area to try to blow smoke up people's butts. Then there's the matter of your actual argument...

The fact that force, which is also related to energy expenditure via W = Fd (for simplcity I remain in the 1-dimensional picture with forces constant over time), and then linearly to the second time derivative of a body's position is hardly tautologous, and subject to test (one could imagine a dynamics in which while W = Fd, there is a non-linear relation between force and acceleration, or a world where Aristotle's physic correctly predicted motion).

W = Fd looks like a non-mass definition of force only if you have a non-mass, non-force definition of "work." Work is not one of Newton's basic terms. It is essentially expended energy, which is why it has the units of energy. The nicest thing you can say about your attempted lawyerly nitpick is that the joule does have two parallel definitions:

1) the work done by a current of 1 amp traversing a resistance of 1 ohm for 1 second, and

2) the work done when the point of application of a force of 1 newton is displaced 1 meter in the direction of the force.

Newton could not have used the electrical definiton of work for the problems considered in the Principia as they concern mass, force, inertia, and gravity.

You're stuck with definition 2. What's a newton? Force. What definition of force? F=ma.

Natural selection (or environmental pressure), however, really comes down to 'survivors survive'.

It is possible in individual cases to identify just how they do that. It is not possible to make a sweeping statement describing who will live and who die. But that's just irrelevant.

The 'Humans allow to breed those which they allow to breed,' tautology likewise does not contribute to a scientific theory of the observed outcomes of animal husbandry, as without a theory about what humans want in their domesticated animals it provides no testable predictions (beyond those built in by common descent).

Just stay stupid. Obviously you can study the effects of human selection.

Replacing 'environmental pressure' with an actual testable theory of what is well-adapted for each ecological niche and a theory of what ecological niches will exist under what conditions would give a properly scientific theory of natural biological, just as replacing the 'humans allow to breed. . .' tautology with a testable theory of what humans want in their domesticated animals would yield a scientific theory of the outcomes of human animal husbandry.

When you have an example of what you're babbling about, publish. When you first started posting here, you seemed like one of the sane ones. Sad.

83 posted on 03/03/2004 11:50:39 AM PST by VadeRetro
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To: The_Reader_David
Oh, bother, more than the usual run of typos today:

Hah! I double posted a huge one. (Don't know how I did it, either!)

84 posted on 03/03/2004 11:57:07 AM PST by VadeRetro
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To: VadeRetro
Curious. In your view, you are the one advocating science here (in mine, we are advocating different visions of what science is) and yet you are the one who runs to abuse and appeal to authority. (And yes, you do use appeal to authority--what else is the point of 'better minds than ours' or pointing again to a brief quotation of Popper's recantation of his original view? I do not appeal to Popper's authority for that view, I hold it myself, knowing full well Popper changed his mind.)

Is your purpose in replying to my posts to convince me of the validity of your position, or to drive me beyond my original critique to hold the view that there is in fact an epistomological symmetry between the sides of the creation/evolution debate? Certainly the brag and bravado you give me sound more like your characterizations of creationists than a serious attempt to discuss science or the philosophy of science.

Nor do I think that I need to supply a theory of the sort I am advocating for my criticism or my desire to have such a theory to have validity: one need produce neither a full-blown neurophysiological theory of personality nor even a single paper to contribute to such a theory to show that Freudianism is unfalsifiable and would be better replaced with such a theory.

In your eagerness to verbally abuse my position rather than engage it, you consistantly overlook the fact that I, like the earlier Popper, am happy to grant Darwinism the position of a framework from which to find proper, refutable, scientific theories.

I really think the shrill tone, and deliberate resort to insult in your last post show precisely how much the defense of Darwinism against religious obscurantism has distorted the thinking of its advocates.

85 posted on 03/03/2004 12:28:23 PM PST by The_Reader_David
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To: The_Reader_David
In your honor, a new tagline.
86 posted on 03/03/2004 1:46:50 PM PST by VadeRetro (Kinder and gentler than a junkyard dog.)
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To: VadeRetro; Doctor Stochastic
I'll grant you the content of your new tagline. ^_^

I think I might add some clarity to our discussion by observing that intellectual constructions which are not themselves falsifiable scientific theories can be of great use in furthering science. I am quite happy to admit this fact.

A perfect example is Hamiltonian mechanics. In itself it is not a falsifiable scientific theory, but a collection of mathematical definitions abstracted from physics, and rigorous theorems about them. Thus the entire thing is tautological. (The job of the mathematician is to discover and save up the non-obvious tautologies in case mankind needs them.)

This theory (in the mathematical, not scientific sense) can be used to construct models of many physical phenomena. Each model is a scientific theory in the sense of Popper.

Darwinism, I would contend, is rather like Hamiltonian mechanics: it provides a framework for constructing a large family of properly scientific, falsifable theories. However, there is a difference.

The rigorous mathematical form of Hamiltonian mechanics made it possible to identify physical systems to which its formalism would not apply (e.g. the two-slit experiment, the hydrogen atom, . . .). Darwinism's more amoprhous form--philosophical rather than mathematicsl--I contend, makes it impossible to identify the limits of its applicability, a view you and DoctorStochastic seem from some of your statemetns to also hold. (If you would like more evidence of this boundless applicability, look at the attempts of cosmologists to apply the Darwinian schema to universes as organisms to deal with the anthropic principle.)

Perhaps we just have differing views, tastes, even in falsifiablity. Perhaps you are content with every theory generated by a formalism being falsifiable, while I insist that the applicability of the formalism as a whole be falsifiable.

87 posted on 03/03/2004 3:57:31 PM PST by The_Reader_David
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To: VadeRetro
Having brought up Occam's razor, it seems to me that dropping the adjective 'random' from variation yields a simpler theory which accounts for all the facts equally well, in the absence of tests for statistical randomness of which neither of us are aware.

Any problems on that score? (And NO, I don't want to replace randomness with divine intervention by God or gods, I'd like a naturalistic law thank, you very much.)

88 posted on 03/03/2004 4:01:53 PM PST by The_Reader_David
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To: The_Reader_David
Didn't mean to be slow in getting back to you, but got very distracted on other threads. Looking at your latest post, I wonder if we aren't talking past most of biology.

"Random" as in "random up and down the entire genome" is indeed wrong. "Random" as in "varying in a mostly unpredictable manner simultaneously about different population means" is still true so far as I personally know. I say "mostly" because sexual recombination is a big source of variation but works with a fixed set of input genes. The initial occurrence of new mutations is so far as I know random. Some are edited out and some are not viable, so the visible output of the reproductive process is not random up and down the genome because selection starts immediately.

Anyway, the latter sense is what Darwin, who knew nothing of genomes, meant. For a given trait, you have a population distribution. It's almost always the expected symmetrical bell curve. An individual plots out on the curve somewhere. If he's in the fat middle, he's dirt common. If he's out on one of the skinny ends, he's rare. If he's so far out he looks unconnected from the rest, he's a freak.

89 posted on 03/05/2004 7:05:31 AM PST by VadeRetro
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To: VadeRetro; Doctor Stochastic
I really am content to leave random in the theory in the constrained sense you propose--I already told you very early in our discussion that the heat generated over randomness in the model (between atheists who like it due to their non-scientific philosophical commitments and theists who despise it due to theirs) is generated by jointly held misunderstandings about the philosophical implications of stochastic processes occuring in models of phenomena.

In a way I was just teasing with that post. I do, after all, know the difference between epistemological randomess and ontological randomness.

I'm more interested in you reaction to #87. I suspect we have been talking past each other (as well as perhaps past most of biology) because I have been insisting on falsifiablity for the entire Darwinian schema as a means of generating theories about biological diversity--and thus, have deliberately ignored parts of your posts (and those of the redoubtable DoctorStochatic) which pointed to correct predictions from theories created by filling in the schema (e.g. legged whale-ancestors).

I think the entire evolution/creation debate would be better served by defending my view that Darwinism is a very useful formal schema for producing testable, falsifiable scientific theories about biological diversity, rather than trying to defend the schema itself as a scientific theory in Popper's sense. I think the effort which goes into defending what I regard as an undefendable claim detracts both from trumpetting the successes of the theories the schema as produced and from getting beyond the schema to a better general theory (which I really would like to itself be globally falsifiable in the sense Hamiltonian mechanics is).

It really isn't like the defenders of evolutionary biology would loose anything by this: you would still be in a position to challenge the advocated of competing schemas on the creationist side, the block-headed six-day literalist schema, and the intelligent-design schema (and all positions in between) to come up with scientific theories on the basis of their philosophical positions. The former wouldn't be able to--well, other than the already falsified prediction of complete stasis in terms of the species observed--the latter, if they apply themselves should be. (Not they the have: I really should write to some of them sometime and point out that actual designed systems generally aren't very complex in the Kolomogorov sense--and certainly not irreducibly so, i.e. random--but somehow never get round to it.)

90 posted on 03/05/2004 9:41:21 AM PST by The_Reader_David
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To: VadeRetro
Oh, and I will be slow in getting back to you. I won't be on-line at all when I log off of this FR session until sometime on Monday.
91 posted on 03/05/2004 9:44:22 AM PST by The_Reader_David
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