Creationism and Baraminology Research News

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An ongoing list of creationist research projects. This is not a creationism-verse-evolution site, but a site to publicize the research work done by members of the creationist community and the intelligent design community, or research work by the science community at large constructively relating to creation topics. Evolutionary critiques may be included on occasion but only under special consideration, and especially where the research pertains directly to developing a creationist model.

Monday, December 12, 2005

Two Must-Reads from Sternberg on Genome Reconfiguration

I just finished two great articles by Sternberg:

Both are excellent, but I recommend that every person go straight to their library, and do an Interlibrary-loan request for the latter. Take it home, read it with a dictionary, and re-read it until you understand every word. It is fabulous.

Both of these articles have a unifying purpose: clarifying the genotype/phenotype distinction, and how it occurs.

The first article is good. It contains a hypothesis that genomes are just as much a product of cell structure as cell structure is a product of the genome. The cell structure has intelligence (us creationists would say "designs" or "programming") to try out new genomic designs, a form of "research and development" carried out by the cell itself. It's main purpose is to show that phenotype can affect genotype just as much as the genotype affects phenotype. Traditional biology holds that this occurs in one direction alone, but recent advances show that this is actually co-recursive.

The second article is absolutely fabulous. He discusses in-depth the roles of repetitive elements and transposable elements. He notes many reasons that the idea of junk in the DNA is false. His main thesis is that repetitive and mobile elements are integral, functional parts of the genome software system.

Some interesting things he notes on the genome:

  • The "selfish DNA" hypothesis relies on genes being context-independent. However, we have found more and more that genes are actually highly context-dependent.

  • The fluidity of a thing does not imply the non-function of a thing. With respect to the genome, the fluidity of transposable and repetetive elements does not imply that they aren't functional, but in fact their fluidity is what makes them highly functional

  • Genomic change through transposable elements occurs in fairly large leaps, all of which maintain internal consistency, context, and cohesion. While being fluid, it maintains an internal consistency. (note that this gives credence to the idea that the change process is informationally directed, and operates according to a stable semantic).

  • While transposable elements can change the biochemical nature of the cell in many ways, they are not responsible for macro-evolution, because such elements are taxonomically restricted. Despite the fact that species can undergo massive configuration changes in a single generation, none of the changes would cause a taxonomic reclassification.

  • The genetic/epigenetic system is a continuous one

  • Transposable elements appear to be rapidly-deployable DNA units for the cell to reconfigure itself with in response to specific inputs, stresses, or events



There is a TON of stuff in the article, and I can't even begin to do it justice in a short post after a first reading. Also, for those of you who argue against neo-Darwinism, most of the article contains direct arguments against such thinking. However, those arguments are outside the scope of this blog, but they are _fabulous_.

Anyway, I might return to this article later. There's too much here to really absorb. But in reality, I'll probably be too busy to revisit it in any meaningful way. But, again, I suggest that you get it from interlibrary loan and read it through. Sternberg is absolutely great.

Comments:
Here is another post you ought to read on Sternberg.
 
I've read it. It's basically slandering Sternberg on his association with creationists. The underlying assumption of that post is that legitimate scientists cannot be creationists. Therefore, while legitimate scientists can disagree with each other, if the disagreement is over creationism, the creationist cannot be a legitimate scientist by definition.

Most of the numbered facts on that post are fairly irrelevant, and are not disputed by any post I've ever read on the Sternberg issue.

Why does fact 1 end with an exclamation point? Is there anything even remotely interesting in fact 1?

Why is fact 2 interesting?

What do you mean by the paper was "held" in fact 3? That's a pretty normal delay in peer review. It seems the evolutionists have gone from saying it was "rushed through" to it was "held" trying to find something that will stick.

Fact 4 only exists for the purpose of injecting speculation.

Fact 5 is simply a smear by association, pretending that associating with creationists is some sort of biological crime, and that you can't legitimately be a scientists and a creationist.

Is it really illegitimate to have Todd Wood review your paper? Fasting forward to fact 10, first of all, you should be more careful who you quote from. He did not talk about Wood et al on O'Reilly. That was in the acknowledgements of his paper. Second, it is not clear (though it is irrelevant), that these were his peer-reviewers. I don't know what the peer-review policies for tha Annals of the New York Academy of Sciences is (I have tried to look, but to no avail), but I would be highly surprised if you got to pick your own reviewers.

However, how does Todd Wood not qualify as a legitimate reviewer? He is actively published on various issues about the genome, was part of the team that sequenced the rice genome, and has written chapters in two different fairly standard textbooks on genetics. So what, other than labelling, disqualifies him as a legitimate scientist that should not be peer-reviewing?

Since we're on rule #10, there is no real contradiction. First of all, I've read the paper you were referring to, and he was _very_ careful to not criticize neo-Darwinism itself but only its relationship to transposable elements. Second, the existance of a journal or two that doesn't exhibit this problem does not mean that it doesn't exist. But Sternberg was quite careful to avoid criticizing Darwinism in its entirety. Even more so, Sternberg did not suggest a non-material explanation, which is a double-whammy.

Fact 6 is not in dispute. However, you left out two important facts:

1) Sternberg discussed the paper with a member of the council, who agreed it should be published.

2) After-the-fact, the President of the BSW examined the peer-review file, and agreed that, scientifically, the paper was good to publish, but was a bad move politically:

"Finally, I got the [peer] reviews and agree that they are in support of your decision [to publish the article]."

Also, according to Sternberg:

"At no time during my nearly three years as managing editor did I ever ask the Council as a body for its input on any editorial decision regarding any particular paper. Nor did the Council itself or anyone on the Council intimate to me that the Council ought to be in any way involved in editorial decision-making with regard to particular papers."

This "fact" also manages to leave out the important fact that Sternberg HAD IN FACT DONE THIS BEFORE:

"I had previously chosen on several occasions to handle certain papers directly and that was accepted as a normal practice by everyone involved with the Proceedings."

In fact, this fact is counter-factual, implying the opposite:

"he does not say is whether or not that gives the managing editor the right to solely review a paper, without involving the associate editors or anyone else in the journal's editorial board"

He DOES say that (the quote above) and on the SAME WEB PAGE! For "facts" these are getting awfully disingenuous.

Fact 7 is irrelevant. The ISCID is part of the ID movement, but is not solely about Intelligent Design.

Fact 8 simply is a restatement of the fact that the investigation was not allowed to be completed.

I find it interesting that in fact 9 you automatically choose the side of the smithsonian as "fact" over Sternberg's. How is this distinguished as fact, especially when the information from the OSC is considered with much questioning? I don't know the truth, but to say that FACT resides with one or the other indicates that the author has independent knowledge of the situation.

In addition, Fact 10 fails to address many of the accusations Sternberg himself made.

Anyway, the idea that this is a listing of "facts" is rediculous -- it is deceptive and manipulative treatment of the facts to smear Dr. Sternberg.

The truth is, I don't know for sure what the final truth is as far as Sternberg's beliefs or his persecution. But this list of "facts" does the word "facts" a disservice.
 
Crevo:It's basically slandering Sternberg on his association with creationists.
-D-draw your own conclusion about whether or not reporting an association automatically slanders

Crevo:Most of the numbered facts on that post are fairly irrelevant...anything even remotely interesting in fact 1?
-D-I have seen mistaken assumptions that Sternberg lost his editorial position as a result of the fallout.

Crevo:Why is fact 2 interesting?
-D-The timing of the publication gives pause for thought, considering RS was on his way out the door

Crevo:What do you mean by the paper was "held" in fact 3? That's a pretty normal delay in peer review. It seems the evolutionists have gone from saying it was "rushed through" to it was "held" trying to find something that will stick.
-D-I concede your point that "normal" here is subjective. Take what you will, leave what you won't.

Crevo:Fact 4 only exists for the purpose of injecting speculation.
-D-Clears up why there is no final/official investigation.

Crevo:Fact 5 is simply a smear by association
-D-See above, but I freely admit that "creation science" is IMO an oxymoron. You can "be" both a creo and scientist, so long as one clarifies the boundary between the two, just as you can be a Buddhist and scientist, etc. Helping your baraminology cause from the perspective he does is as odd as me helping alchemists become more respected scientifically.

Crevo:Is it really illegitimate to have Todd Wood review your paper?
-D-no, just revealing

Crevo:how does Todd Wood not qualify as a legitimate reviewer?
-D-never said that

Crevo: the existance of a journal or two that doesn't exhibit this problem does not mean that it doesn't exist
-D-unwritten rule?

Crevo: 1) Sternberg discussed the paper with a member of the council, who agreed it should be published.
-D-he said, quote, "Nevertheless, recognizing the potentially controversial nature of the paper, I consulted with a colleague about whether it should be published. This person is a scientist at the National Museum of Natural History, a member of the Council"
so who is lying? the statement by the PBWS or him? he offers no name to validate his claim. I simply repeated the statement by the PBWS. I even carefully documented how he defends his circumventing the associate editors and other journal staff.

Crevo:2) After-the-fact, the President of the BSW examined the peer-review file, and agreed that, scientifically, the paper was good to publish, but was a bad move politically:
-D-so the statement is false? "all of us"?

Crevo:"Finally, I got the [peer] reviews and agree that they are in support of your decision [to publish the article]."
-D-can you give me the link to this quote, i can't find it. plus, one is a source he provides, indirectly, to support himself, another is a direct source, I simply posted the available direct source

Crevo:Also, according to Sternberg:
-D-yes I posted this defense as it relates to the assoc eds, I don't think anyone believes he ought to have involved the whole d*mn council

Crevo:This "fact" also manages to leave out the important fact that Sternberg HAD IN FACT DONE THIS BEFORE:
-D-boy you didn't read carefully, did you?

Crevo:In fact, this fact is counter-factual, implying the opposite:
-D-NO, he only confirms that he had handled the review process, not that he had not even mentioned a paper to other eds.
quote,"critics of the Meyer paper have made the false claim that proper procedures were not followed by quoting out of context a sentence from the inside cover of the Proceedings which reads, "Manuscripts are reviewed by a board of Associate Editors." What the sentence means is that manuscripts are reviewed by some member of the group of associate editors. At no time in the past has the board as a whole (or even more than one associate editor) ever reviewed any paper, nor has that practice and policy changed as a result of the Meyer controversy."-end quote-
this still does not answer whether or not an assoc ed ought to have been involved, at some point, even tho he had the final authority

Crevo:For "facts" these are getting awfully disingenuous.
-D-no, you are getting awfully selective in your perception. there is a large difference between having the final authority, and having the prerogative to never involve another editor when it seems clear from the statement by the PBWS and from Sternberg's page that they ought to have been involved.

Sternberg doesn't clarify for us by posting the document he mentions here, "The Council asked me, moreover, to draft a formal process document describing the procedures of the Proceedings including their ruling on the role of the managing editor." --he could clear up the controversy entirely by posting this.

Sternberg even says, "[managing editors] can choose and supervise the associate editors at his or her discretion"; is this the same thing as choosing not to use/have/inform assoc eds??

Crevo: Fact 7 is irrelevant. The ISCID is part of the ID movement, but is not solely about Intelligent Design.
-D-Riiiiight...but for shi*s and giggles, let's so you're right. So what? I just posted a fact. Take/leave what you will.

Crevo: Fact 8 simply is a restatement of the fact that the investigation was not allowed to be completed.
-D-and illustrating that, THUS, given that the invest. was not completed, Sternberg's posting of the letter is a bit sketchy, and that the general reaction by those who read it as it being "official" is misconstrued.

Crevo: I find it interesting that in fact 9 you automatically choose the side of the smithsonian as "fact" over Sternberg's.
-D-there was no mention in the OSC letter or by Sternberg or anywhere I can find of any name of a supervisor other than Coddington. the "fact" is that Coddington was his only known/mentioned supervisor. JAC's response is not as important as the "fact" that one of Sternberg's claims (moved to a hostile supervisor-quote, "Supervisor replaced. I was transferred from the supervision of a friendly sponsor (supervisor) at the Museum to a hostile one.") is debunked

Crevo: How is this distinguished as fact
-D-no other supervisor is ever named or indicated anywhere I can find. if you find it, i'll gladly retract, promise

Crevo:In addition, Fact 10 fails to address many of the accusations Sternberg himself made.
-D-like? they are all plainly on his homepage

Crevo:this list of "facts" does the word "facts" a disservice.
-D-so publish a rebuttal list of "counterfacts". put up or shut up.
 
Crevo:It's basically slandering Sternberg on his association with creationists.
-D-draw your own conclusion about whether or not reporting an association automatically slanders
Daniel, you can disingenuously ask us to draw our own conclusions. To some audiences, it would be slander, and to others, not. Your intention was transparent, however.

Crevo:Why is fact 2 interesting?
-D-The timing of the publication gives pause for thought, considering RS was on his way out the door
"Pause for thought" is not a very serious charge.

Crevo:What do you mean by the paper was "held" in fact 3? That's a pretty normal delay in peer review. It seems the evolutionists have gone from saying it was "rushed through" to it was "held" trying to find something that will stick.
-D-I concede your point that "normal" here is subjective. Take what you will, leave what you won't.
What was that point again? Normal is normal. It can be quantified.

Crevo:Fact 4 only exists for the purpose of injecting speculation.
-D-Clears up why there is no final/official investigation.
OSC actually had a serious jurisdiction question not resolved until later.

Crevo:Fact 5 is simply a smear by association
-D-See above, but I freely admit that "creation science" is IMO an oxymoron
Now we're seeing what the real issue is. Your opinion happens to be philosophically naive regarding to the nature of science, by the way. I can't fully fault you for it, for it's a widely held view, but the view that ID (and even creation science) are necessarily excluded from the category of valid science is not supportable.

Crevo:Is it really illegitimate to have Todd Wood review your paper? 
-D-no, just revealing
Revealing of what? As you said further down, Wood is a legitimate reviewer.

Crevo: Fact 7 is irrelevant. The ISCID is part of the ID movement, but is not solely about Intelligent Design.
-D-Riiiiight...but for shi*s and giggles, let's so you're right. So what? I just posted a fact. Take/leave what you will.
More of the same, but with less politeness.

Crevo:this list of "facts" does the word "facts" a disservice.
-D-so publish a rebuttal list of "counterfacts". put up or shut up.
Not impressive for civil attitude.

BTW, fact 10 was later disavowed in part by Daniel, deep in the comments. As I've said elsewhere, blogs being what they are, it would be of value to note that correction near the place where the error was made.
 
One more point: The "correction" on Daniel's website is not correct:

In Sternberg's "Acknowledgements" section, he divulges the identities of the 3 reviewers for his paper I wanted to comment on:
I warmly thank Drs. Lien (Linda) Van Speybroeck, Gertrudis Van de Vijver, and Dani De Waele for their patience, encouragement, and comments and suggestions that greatly improved the manuscript. I also thank Drs. Paul Nelson, Stanley Salthe, Jonathan Wells, and Todd Wood (alphabetical order) for their very helpful criticisms of the manuscript.


The reviewers named here for Sternberg's paper are not, as implied "peer reviewers." They read the manuscript and offered ideas. The paper certainly went to anonymouse reviewers for its official looking-over.
 
"anonymouse" of course means "rodent with no name." oops :-)
 
Another point -- you will notice if you read Sternberg's list of complaints and the OSC's letter that nearly every one of Sternberg's complaints were validated, and none were invalidated. The only one that seemed questionable to me was that it appears that the reason he _lost_ his original supervisor was that he died. It appears from the memos that he was without a supervisor until after the incident. Whether or not the supervisor was "hostile" or not is subject to interpretation. The rest of the allegations appear to be fully corroborated. All of the emails speak of getting this Research Associate under control, limitting his access, etc.

Anyway, in case anyone missed this, this blog is not intended to be a bomb-throwing exercise, but just to talk about research. I hereby redirect all comments to my other blog where such conversation is ontopic. Any posts past this one talking anything other than research-oriented ideas will be deleted, be they for or against Sternberg.
 
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