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Author
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Topic: The primacy of nucleic acid
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Paul A. Nelson
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Member # 26
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posted 16. October 2002 10:45
In another thread (response to Howard Van Till), several writers have expressed disbelief or frank astonishment at the unwillingness of some ID theorists to grant a privileged status to DNA.
This is a topic worth kicking around. To start things off, here's a quiz. Is the author of the following passage an ID theorist?
quote:
The best evidence describes the basic nature of biological order as being distributed over several parallel and mutually dependent systems such that no one system, and certainly no one molecule, could reasonably be accorded the status of being a program, blueprint, set of instructions, etc., for the remainder....I offer a highly detailed, if somewhat technical, description of the membrane-based organization of the cell into structurally and functionally differentiated compartments. These highly specified membranous bodies constitute the necessary and irreplacable template of their own existence, must be passed along from one generation to the next, and provide the unavoidable context in which, in effect, DNA can be adequately intepreted, i.e., in which genes can be genes. (emphasis in original)
I'll post the answer later.
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brauer
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Member # 398
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posted 16. October 2002 11:36
Paul,
I'm not sure what you mean by "priveleged status". Genomic information certainly is getting a lot of attention, for several good reasons.
- It's easy to analyze. Sequencing, PCR and other techniques in molecular genetics have given us a very good way to study and manipulate this particular polymer.
- Its organization corresponds to that of other biochemically interesting molecules. The genetic code means that one need not sequence every protein one is interested in. Sequence motifs that signal post-translational modifications help in this regard. Expression patterns are increasingly understood to be correlated with specific regulatory sequences.
- DNA is the major mediator of inherited traits. If you're interested in how an organism works, you'd be best served by understanding the major effects first, and only then working to untangle the discrepancies.
In general I agree with you: there is an emphasis on DNA that perhaps discourages extensive investigation into other biochemical units of organization.
But this fact illustrates quite nicely the concept of methodological versus ontological assumptions. We work with DNA because right now it's easiest. We don't work with other cellular structures (membranes for example) that may contribute to inheritance because it's hard. It's a "more bang for the buck" kind of thing.
Most molecular biologists don't think about this much: they simply work in the realms in which they think they have a good handle. If questioned seriously, they'd admit that DNA is not necessarily the whole story. But from the perspective of a practitioner, it doesn't really matter: our technology makes it convenient to make the assumption that it is for methodological reasons.
Similarly for methodological naturalism (MN). MN allows us to be productive where we can. Many biologists believe in a supernatural or higher power, but either can't figure out how to incorporate these beliefs into their work, or don't trust that their incorporation will be sufficiently rigorous and objective. Assuming that these factors do not enter into the picture simply allows the work to proceed. (Quite successfully I might add, and as any student of science and technology could tell you).
If someone ever comes up with a technique for the study of membranes in the context of inheritance, then the molecular biology community (and the Nobel Prize Committee) will beat a path to his door. In the meantime, complaints that we overemphasize the roles of the structures that we can work with (without additional alternative insights) do not contribute an iota to the effort. Rather, they are simply the products of crank science.
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Paul A. Nelson
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Member # 26
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posted 16. October 2002 11:52
Hi Matt,
You wrote:
quote:
complaints that we overemphasize the roles of the structures that we can work with (without additional alternative insights) do not contribute an iota to the effort. Rather, they are simply the products of crank science.
Would you say, then, that the (unnamed) author of the passage I cited above is a crank?
I realize that's an unfair question. But there's a world of difference between "DNA is important because DNA is easy to manipulate" and "DNA really is the Helmsman of Life's Vessel." Calling someone a crank can be a facile way of dismissing significant open problems.
[ 16. October 2002, 11:54: Message edited by: Paul A. Nelson ]
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brauer
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Member # 398
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posted 16. October 2002 13:45
Paul,
I retract the "crank science" claim as unhelpful and provocative. And I agree that it really is important to question the concept that "DNA is life's helmsman" (to the extent that people truly believe it).
But this stuff is nothing new: my undergrad cohort was talking about it more than 10 years ago. (And, I might add, we were talking about it in the manner that is common among sophomores: as if we had discovered the Great Truth that had Eluded the Experts).
Sometimes the Great Truths really do elude the Experts. Quite often though, the Great Truths are not particularly productive of useful and applicable ideas. Sometimes the Great Truths have to be tabled because they are too vague.
The fact that our professors had tabled this particular truth in their own research was not an indication of their lack of imagination. Rather it was characteristic of disciplined and productive researchers who chose not to worry about questions they couldn't address, while a universe of questions they could address was clamoring for their attention.
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Daniel Edington
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Member # 421
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posted 16. October 2002 16:58
Paul,
Acctually I think I expressed disbelief (and frank astonishment) that "some ID theorists" failed to answer some important questions raised by Howard Van Till.
What exactly do you mean by privelidged status? Are we to take it that you are proposing that the transmission of traits from parent to offspring does not depend on transfer of DNA, because DNA doesn't code for cellular membranes?
As far a I know we were dicussing the bacterial flagellum, which is a complex assembly of proteins. Genes specify the structure of proteins and not the other way around as implied by "some ID theorists".
Dan
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Moderator
Administrator
Member # 1
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posted 16. October 2002 17:13
Dan,
I'll let Paul respond to you if he likes. However, please note that your question:
quote:
Are we to take it that you are proposing that the transmission of traits from parent to offspring does not depend on transfer of DNA, because DNA doesn't code for cellular membranes?
indicates that you do not fully understand the topic of the thread. As moderator, I'd like to just point out to you that the only claim being made by Paul here is that DNA isn't the "all in all" in the development and organization of biological systems.
It would be wise of you to clarify your misunderstandings before posting with dissapointment or dismay (notice the blue smiley face). Blue faces do make a difference to the tone of discussion ![[Wink]](wink.gif)
[ 16. October 2002, 17:58: Message edited by: Moderator ]
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Daniel Edington
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Member # 421
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posted 16. October 2002 18:47
Moderator,
When Paul refers to "several writers" I can only assume he means me and the couple of people who replied to my post. I can't speak for the others, but I believe it was Paul who misunderstood my post, hence my disappointment.
My post had nothing to do with granting "a priveledged status to DNA." nor did I suggest that DNA was the "the "all in all" in the development and organization of biological systems." I was only suggesting it is important in the development of the bacterial flagellum.
Dan
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rafe gutman
Member
Member # 134
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posted 16. October 2002 23:05
quote:
moderator:
I'd like to just point out to you that the only claim being made by Paul here is that DNA isn't the "all in all" in the development and organization of biological systems.
that's not entirely true. paul also seemed to be claiming that the ID critics from the other thread were denying that. that was not the case. the ID critics raised an objection to dembski's notion that "genes follow proteins". this does not require one to "grant a privileged status to DNA", whatever that means.
perhaps paul can address this issue by answering the following question: which came first, the flagellar genes, or the flagellar proteins?
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Paul A. Nelson
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Member # 26
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posted 17. October 2002 11:02
Rafe asked:
quote:
which came first, the flagellar genes, or the flagellar proteins?
Richard Dawkins: The genes came first.
Richard Lewontin: The genes and proteins evolved contemporaneously. Neither takes causal precedence over the other.
Design theorist: The function came first. The genes and proteins were actualized as an integrated system, to enable the function. While DNA makes RNA makes protein, this (the Central Dogma) is simply a description of information flow through cellular machinery. Using a photocopier does not explain the origin of a photocopier.
Daniel asked:
quote:
What exactly do you mean by privelidged status?
It was wrong of me to impute this "privileged status" view to folks in the other thread. But I saw it as implicit in certain remarks there (e.g., from David Mullenix). Here's a clear statement of the notion:
quote:
...we still find it difficult, indeed boringly pedantic, to refrain from teleological language when discussing adaptation. Birds' wings are obviously 'for' flying, spider webs are for catching insects, chlorophyll molecules are for photosynthesis, DNA molecules are for...What are DNA molecules for? The question takes us aback. In my case, it touches off an almost audible alarm siren in my mind. If we accept the view of life that I wish to espouse, it is the forbidden question. DNA is not 'for' anything. If we wish to speak teleologically, all adaptations are for the preservation of DNA; DNA itself just is.
(Richard Dawkins, "Replicators and vehicles," in Current Problems in Sociobiology [Cambridge University Press, 1982], p. 45; emphasis in original)
Given a "replicators first" view of the history of life, DNA (originally, RNA) does have a privileged status. But that's not a view that any design theorist is likely to find reasonable.
The author of the passage cited in the opening post of this thread is Lenny Moss, an assistant professor of the philosophy of science at Notre Dame. The passage is taken from Lenny's Northwestern University Ph.D. dissertation, "What Genes Can't Do: Prolegomena to a Philosophy Beyond the Modern Synthesis" (1998), recently published as What Genes Can't Do by MIT Press (2002) (I'm citing the dissertation itself). Lenny also has a Ph.D. in molecular biology from UC-Berkeley. He is not a design theorist.
[ 17. October 2002, 11:07: Message edited by: Paul A. Nelson ]
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charlie d.
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Member # 159
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posted 17. October 2002 13:43
quote:
Design theorist: The function came first. The genes and proteins were actualized as an integrated system, to enable the function. While DNA makes RNA makes protein, this (the Central Dogma) is simply a description of information flow through cellular machinery. Using a photocopier does not explain the origin of a photocopier.
I do not get this. Even assuming that bacterial motility was initially just a gleam in the designer's mind, so to speak, (I guess that what you mean by "function first", oherwise please explain) whenever it became actualized, the designer must have done one of the following:
1. Created the genes so that they would encode the proteins that then would form a flagellum;
2. Created the proteins that make a flagellum, checked out it was working as expected, then used some "retrograde" information transfer system to insert that information into the genome;
3. Created both at the same time (seems kind of redundant, but who am I to question the engineering here).
So, which one it is?
As for your Dawkins and Lewontin caricatures, I am sure both would in fact agree that the genes and proteins evolved together, with progressive genetic changes appearing in the gene first, then being subject to selection in their protein form. The "primacy" of DNA, if any, only concerns its stand as the fundamental replicator and main conveyor of heritable information in most living organisms.
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Paul A. Nelson
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Member # 26
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posted 17. October 2002 17:21
Charlie wrote:
quote:
As for your Dawkins and Lewontin caricatures, I am sure both would in fact agree that the genes and proteins evolved together, with progressive genetic changes appearing in the gene first, then being subject to selection in their protein form.
For Dawkins, the origin of proteins lies well downstream from that of “replicators” (nowadays, DNA and RNA – originally, probably some form of ribozyme [catalytic RNA]). He envisions this as the sequential crossing of key thresholds:
quote:
Threshold 1 is, of course, the Replicator Threshold itself: the arising of some kind of self-copying system in which there is at least a rudimentary form of hereditary variation, with occasional random mistakes in copying....To begin with, success among rival replicators will be judged purely on the direct properties of the replicators themselves – for example, how well their shape fits a template. But now, after many generations of evolution, we move on to Threshold 2, the Phenotype Threshold. Replicators survive not by virtue of their own properties but by virtue of causal effects on something else, which we call the phenotype.
(R. Dawkins, “The Replication Bomb,” in River Out of Eden, Basic Books, 1995, pp. 151-152)
The “phenotype” includes proteins, of course.
While Lewontin has written much less than Dawkins about the origin of life -- except to say that the problem is unsolved -- he leaves no doubt that he sees isolated nucleic acid as causally inert:
quote:
No living molecule is self-reproducing. Only whole cells may contain all the necessary machinery for “self”-reproduction....Not only is DNA incapable of making copies of itself, aided or unaided, but it is incapable of “making” anything else....The proteins of the cell are made by other proteins, and without that protein-forming machinery nothing can be made. There is an appearance here of infinite regress (What makes the proteins that are necessary to make the protein?), but this appearance is an artifact of another error of vulgar biology, that it is only the genes that are passed from parent to offspring. In fact, an egg, before fertilization, contains a complete apparatus of production deposited there in the course of its cellular development. We inherit not only genes made of DNA but an intricate structure of cellular machinery made up of proteins.
(R. Lewontin, “The Dream of the Human Genome,” NY Review of Books, 28 May 1992; p. 33.)
"Vulgar biology" here is a code phrase for Dawkins-style DNA-centrism. Lewontin has, over the years, taken pains to distinguish his own organismal-centered conception of biological function from that of Dawkins. In short, I don't think one can harmonize their respective viewpoints as readily as Charlie thinks.
Charlie also asked some tongue-in-cheek questions about what the designer did first. Speaking for myself, I think the designer first arranged a press conference to tout his cool new microscopic inventions.
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charlie d.
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posted 17. October 2002 17:44
I was unaware we were talking specifically about OoL. I thought this whole issue came out with regard to whether Dembski's calculation on flagellar origins, based on proteins, make any sense. From what we know about biology, it would seem the most obvious way to make new flagellar proteins is to make their genes, and have them transcribed and translated by the existing cellular machinery. Incidentally, this is the way any human bioengineer would do it.
It would seem counterintuitive therefore that Dembski, trying to tout design and engineering in biological systems, would ignore an obvious strategy, known to molecular biologists since the '70s, in exchange for a cumbersome process in which proteins are assembled first as individual entitities.
[ 17. October 2002, 17:45: Message edited by: charlie d. ]
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rafe gutman
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Member # 134
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posted 17. October 2002 21:06
paul, again you seem to be avoiding the issue. i did not ask "what came first, genes or proteins", but rather, "what came first, the flagellar genes or the flagellar proteins"? i'm not sure why you interpreted that as a question regarding the origin of all genes and proteins.
here's another question: if a designer wanted to give a flagella-less bacteria a flagella, would he inject flagellar genes into the bacterium, or flagellar proteins?
quote:
Design theorist: The function came first. The genes and proteins were actualized as an integrated system, to enable the function. While DNA makes RNA makes protein, this (the Central Dogma) is simply a description of information flow through cellular machinery.
i like this statement. it goes a long way toward explaining the logic dembski was using when he made his "genes follow proteins" statement. i have no problem with what you wrote above here, if i were a designer, i'd do it in that order as well. conceptually design a flagella, determine the amino acid sequence that would yield such a structure, then determine the DNA sequence to encode those proteins (then of course insert the DNA into the cell!) so in this "design" sense, the function comes first, followed by the proteins, then the genes (at least on paper; in reality, the actual products would appear in reverse order). i have only one problem with this, dembski's statement had nothing to do with design. he was saying it to justify his calculations for the evolution of the flagella. in an evolutionary context, the direction of information always follows the central dogma, as a bacteria does not "conceive" the notion of a flagella before making one.
so assuming my interpretation is correct, would you agree that dembski's analysis, which focuses on proteins, would be more relevant if it focused instead on genes?
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Paul A. Nelson
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Member # 26
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posted 20. October 2002 11:49
Hi Rafe,
I've been thinking for a few days about a model of evolutionary change where "function" is causally primary, but I'm not quite there yet. So I'll have to bracket your questions for a while. Also, I want to take another look at the relevant passages in No Free Lunch.
I'll be away from Brainstorms until 10/30, lecturing in Los Angeles (public event: "Darwinism in Crisis," Chase Gymnasium, Biola University, Thursday, October 24, 7:00 pm; speakers include Jed Macosko, Bill Dembski, Jonathan Wells, John Bloom, Fuz Rana, Hugh Ross, and Paul Nelson).
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