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Author Topic:   Recent paper with an ID spin? Abel and Trevors (2005).
Wounded King
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From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 1 of 85 (245947)
09-23-2005 11:28 AM


In a recent paper in Theoretical biology and medical modelling, a rether obscure member of the BioMed Central family of open access pulications, Abel and Trevors publish a paper on the nature of information and complexity in biopolymers(Abel and Trevors, 2005).
Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC). FSC alone provides algorithmic instruction. Random and Ordered Sequence Complexities lie at opposite ends of the same bi-directional sequence complexity vector. Randomness in sequence space is defined by a lack of Kolmogorov algorithmic compressibility. A sequence is compressible because it contains redundant order and patterns. Law-like cause-and-effect determinism produces highly compressible order. Such forced ordering precludes both information retention and freedom of selection so critical to algorithmic programming and control. Functional Sequence Complexity requires this added programming dimension of uncoerced selection at successive decision nodes in the string. Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).
There is a lot of highly jargonistic terminology in the paper, presumably the sort of things that information theorists are familiar with, which doesn't mean a whole lot to me.
Some of it sounds rathe IDist however, for example...
Naturalistic science has always sought to reduce chemistry to nothing more than dynamics. In such a context, chemistry cannot explain a sequencing phenomenon that is dynamically inert. If, on the other hand, chemistry possesses some metaphysical (beyond physical; beyond dynamics) transcendence over dynamics, then chemistry becomes philosophy/religion rather than naturalistic science.
One of the Authors works at the Origin-of-Life Foundation which, apart from having a pretty crappy website, seems to be an abiogenesis version of the JREF prize. I am slightly worried that they feel they have to state in their description of themselves ...
The Origin-of-Life Foundation should not be confused with "creation science" groups.
I'm not sure why they feel the need for this clarification unles sthey expect their line of enquiry to look suspiciously like those followed by 'creation science' and even more like those of ID proponents like Dembski.
Anyone care to comment on the information theory aspects of this? Pretty much all the actual biology simply seems to be linked to assertions that certain types of information cannot arise by particular mechanisms and I don't feel qualified to judge those claims.
Am I just being paranoid about the ID nature of this paper?
TTFN,
WK

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Message 2 of 85 (246072)
09-24-2005 8:26 AM


Thread moved here from the Proposed New Topics forum.

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Percy
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Message 3 of 85 (246084)
09-24-2005 8:51 AM
Reply to: Message 1 by Wounded King
09-23-2005 11:28 AM


After having read the abstract and the first two paragraphs of the paper, I guess I have two reactions:
  • My own opinion is that this is full-blown ID.
  • The peer-review process of Theoretical Biology and Medical Modelling is seriously broken.
The 2nd paragraph is instructive:
Abel and Trevors writes:
Little progress has been made, however, in measuring and explaining intuitive information. This is especially true regarding the derivation through natural process of semantic instruction. The purely syntactic approaches to sequence complexity of Shannon, Kolmogorov, and Hamming have little or no relevance to "meaning." Shannon acknowledged this in the 3rd paragraph of his first famous paper right from the beginning of his research.
I've quoted the 3rd paragraph of Shannon's paper to Creationists many times ("Frequently the messages have meaning; that is they refer to or are correlated according to some system with certain physical or conceptual entities. These semantic aspects of communication are irrelevant to the engineering problem."). Abel and Trevors avoid the mistake of confusing Shannon information with meaning, but they proceed on to concoct replacement principles of information theory out of thin air. They provide no underlying mathematical foundation, or any other kind of foundation. They simply make assertions.
Wounded King writes:
One of the Authors works at the Origin-of-Life Foundation which, apart from having a pretty crappy website, seems to be an abiogenesis version of the JREF prize. I am slightly worried that they feel they have to state in their description of themselves ...
The Origin-of-Life Foundation should not be confused with "creation science" groups.
I think they say this because they don't want Intelligent Design confused with Creation Science, which they view as a distinctly different discipline. It's become common for those in the ID movement to distance themselves from the largely unsuccessful Creation Science movement. My own view of this is that Creation Science and ID are in an uneasy and unacknowledged alliance based upon the "the enemy of my enemy is my friend" principle. Creation Science groups like ICR are quietly watching from the sidelines hoping that, even though skeptical of many ID positions, enough disruption is caused with science to provide them further openings.
--Percy

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Brad McFall
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Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 4 of 85 (246085)
09-24-2005 8:54 AM
Reply to: Message 1 by Wounded King
09-23-2005 11:28 AM


I would be surpised if ID gets a free pass, I could be wrong
I had noticed in Russell's “Principles of Mathematics” that whenever it comes to understanding how to apply a series (which might be subsumed ) there is a problem with use of the German word “strecke” compared to interval or strech. I suspect that this covers any fundamental points made logically that bear not on biology as it actually exists. The only way I found to resolve that linguistic issue in Russell’s history of logic (as to the tools necessary to separate the kinds of mechanisms”” in this paper) was to start from a volume of perceptible space. Papers like this do not seem to assume such except by implication. I am sorry I have not written yet on EVC on my view on computer science motivated recursion and biological tissue restruction as this bears on evaluating the truth claims in the paper,( I doubt I would hold to the concept of “functionality”(in any biological organon because the instruction sink would not be as wide as the possible imaginable sources whether in current program rules or not) if I made the recursion by object oriented classes).
It is clear enough to me that chemistry should be reworked. The kind of changes these kinds papers suggest however seems so broad that we would first hear of individual colleges and universities that teach it before the research starts to compete for changes in the structure of all departments of natural science. Pehaps I am too far out of the loop any more to know any better. The paper seems a priori interesting in that it attempted to separate where Shannon measures are not useful or appropriate. That does not appear to me to be particularly IDist. I need to think if that characterization will actually enable one to induce changes to biological deductions. Such a separation of kinematics could enable one to cut into the set theoretic (reverse lexicographic ordering approach etc) use of Shannon measures of Collot in Paris
see also etc.
The attempt at mathematization of F. Collot's concept of form
but I generally still agree somewhat with Mayr that Kitcher’s empirical math attempt to bring sets into theoretical biology was a backward not a forward step. I often wonder if math sets are the proper application of Cantorian diagonalization. Certainly if there was a Keynesianbiology the Cantor proof technique would have biological praxis with determinants. Whether the philosophy of functionalism remains I have not thought through as of yet.
This message has been edited by Brad McFall, 09-24-2005 09:14 AM
This message has been edited by Brad McFall, 09-24-2005 09:15 AM

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nwr
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Message 5 of 85 (246113)
09-24-2005 2:22 PM
Reply to: Message 1 by Wounded King
09-23-2005 11:28 AM


First a word of caution. I have a side interest in artificial intelligence (AI) and cognitive science. However, I have not spent much time studying genetic algorithms (GA). Thus you should assume that my knowledge of GA is amateurish at best. The main reason I have not spent much effort in studying GA, is that I see it as based on a misunderstanding of biological processes. My skepticism of GA might be apparent in my comments below.
Abel and Trevors appear to be basing their report on what has been learned through experimentation with GA (genetic algorithms) in AI.
On the use information theory, there is less there than meets the eye. The authors mention three kinds of sequence complexity, RSC, OSC and FSC. Most of their time is spent on FSC, which is the only one that they consider important. They clearly state that Shannon's measures of information content are mainly applicable to RSC and OSC, not to FSC. That greatly diminishes the relevance of information theory. They are left with making comments about information with respect to FSC, but admitting that this information is not easily quantified.
Percy (Message 3) seems to think that this is an ID article. That's possible, but it is hard to be sure of the intentions of the authors. I don't see anything that attacks ToE (theory of evolution). If it is an ID article, then it is abiogenesis that is in their targets. Their section headed "Testable hypotheses about FSC" presents 4 "null hypotheses", which they presumably believe can be established by a failure to falsify them. Those null hypotheses appear to be aimed at the idea that RNA might have arisen spontaneously, and thus have started off bioligical life. However, it doesn't necessarily follow that they are proposing ID. Their intention might be to have research on abiogenesis redirected elsewhere, rather than on spontaneous creation of RNA.
Speaking for myself, I think the spontaneous creation of RNA is an unlikely explanation of life on earth. Assuming life originated here (as opposed panspermia), I think it far more likely that some far simpler sort of pre-life developed first, and the use of a genetic code evolved later out of early pre-life processes.

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Percy
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Joined: 12-23-2000
Member Rating: 5.3


Message 6 of 85 (246149)
09-24-2005 5:24 PM
Reply to: Message 5 by nwr
09-24-2005 2:22 PM


nwr writes:
The main reason I have not spent much effort in studying GA, is that I see it as based on a misunderstanding of biological processes.
GA's received a lot of discussion a couple years ago (Information and Genetics is one of the threads), and I've written a couple simple GAs. What do you think is the misunderstanding?
Independent of that, I didn't see anything in the paper based upon GAs, which makes sense since successful GAs are strong evidence against ID, as if any were needed.
Percy (Message 3) seems to think that this is an ID article. That's possible, but it is hard to be sure of the intentions of the authors.
This quote from the article is pure ID:
We can hypothesize that metabolism "just happened," independent of directions, in a prebiotic environment billions of years ago. But we can hypothesize anything. The question is whether such hypotheses are plausible. Plausibility is often eliminated when probabilities exceed the "universal probability bound".
This, too, is pure ID, for it is one of the fundamental tenets of ID that random processes cannot create information:
Null hypothesis #1
Stochastic ensembles of physical units cannot program algorithmic/cybernetic function.
Here's another pure ID statement from the conclusion:
But under no known circumstances can self-ordering phenomena like hurricanes, sand piles, crystallization, or fractals produce algorithmic organization.
The paper is very similar to the Meyer paper that appeared in the BSOW last year both in its lack of scientific rigor and in its lack of evidence to support any of its arguments.
--Percy

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Message 7 of 85 (246161)
09-24-2005 7:15 PM
Reply to: Message 2 by Admin
09-24-2005 8:26 AM


I have a bone to pick with the Head Adminstrator

Off Topic. Do Not Respond to this message.

What's with you ?! It must be all or nothing (removing a part of a thread shouldn't be any trouble at all) I knew the Director was methodical but I didn't know he was also a control-nut as well.
I knew what we were : Removing obstacles to optimism, gratitude, and ... or just bugging the hell out of you
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Well Now That "makes you mad" doesn't it
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Percy
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From: New Hampshire
Joined: 12-23-2000
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Message 8 of 85 (246164)
09-24-2005 7:47 PM


This Paper is Very Suspect
I went back to the paper to check the citation used to support the "universal probability bound", because I couldn't believe that there could be a legitimate reference for it in the scientific literature, and what I found appeared suspicious. Here's the statement from Abel and Trevors paper:
Abel and Trevor writes:
The question is whether such hypotheses are plausible. Plausibility is often eliminated when probabilities exceed the "universal probability bound" [132].
Here's the reference:
132. Tuerk C, Gold L. Systematic evolution of ligands by exponential enrichment -- RNA ligands to bacteriophage - T4 DNA-polymerase. Science. 1990;249:505–510. [PubMed]
It doesn't sound like a paper that would ever mention the "universal probability bound." Unfortunately, PubMed has only the abstract, but the abstract reinforces the view that this paper has nothing to to with the "universal probability bound."
This wasn't conclusive of course, but my suspicions raised, I checked their next cited claim:
Certainly no prediction of biological self-organization has been realized apart from SELEX-like bioengineering. SELEX is a selection/amplification methodology used in the engineering of new ribozymes [133-135].
For the first paper cited I could find only an abstract:
Robertson DL, Joyce GF. Selection in virtro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature. 1990;344:467–468. doi: 10.1038/344467a0. [PubMed]
The words "organize", "organized", "organization", "SELEX", "selection" and "amplification" do not appear in the abstract. But that's only an abstract and proves nothing. But I found full text for the next reference:
Rhoades E, Gussakovsky E, Haran G. Watching proteins fold one molecule at a time. PNAS. 2003;100:3197–3202. doi: 10.1073/pnas.2628068100. [Free Full text in PMC]
The words "organize", "organized", "organization", "SELEX", "selection" and "amplification" do not appear anywhere in the entire paper. Checking the next reference:
Abel, DL.; Trevors, JT. More than metaphor: Genomes are objective sign systems. Journal of Biosemiotics. 2005. p. (In press).
This reference is by Trevors, one of the authors, but it is "in press", and so no text, not even an abstract, is available.
So I've checked out 4 references so far and haven't even found a single indication of a match with the text in the paper. So returning to the beginning of the paper I started checking the references one by one.
References 1-3 are to Shannon's papers, no problem there.
References 4-8 are supposed to be about linear complexity, and they do appear to be about that topic.
Reference 9 is correctly about redudancy coding.
Here's an interesting dismissal of 35 references:
The inadequacy of more recent attempts to define and measure functional complexity [10-45] will be addressed in a separate manuscript.
Moving on:
Nucleic acid instructions reside in linear, digital, resortable, and unidirectionally read sequences [46-49].
References 46-48 are to papers by Yockey. Yockey's a legitimate scientist, but he's hard to classify, and he's often cited by Creationists, for example, his paper A Calculation of the Probability of Spontaneous Biogenesis by Information Theory. Citing Yockey is not auspicious.
Reference 49 is to Maeshiro and Kimura. The papers title, The role of robustness and changeability on the origin and evolution of genetic codes, would not seem to have anything to do with the claims to which it is attached.
Replication is sufficiently mutable for evolution, yet conserved, competent, and repairable for heritability [50].
Reference 50 is Molecular Genetics of Bacteria, which seems a rather narrow title to support so broad a claim in the paper, though the claim itself is completely non-controversial. One wonders why they felt the need to footnote so general and non-controversial, indeed, foundational a statement. Could they [gasp!] be loading the paper up with extraneous footnotes to give it the appearance of greater scientific significance?
In life-origin science, attention usually focuses on a theorized pre-RNA World [52-55].
References 52-55 appear right on target.
As a result, many investigators suspect that some chemical RNA analog must have existed [56,57].
No problems here.
I'm not finding what I expected to find. While they do seem to be padding the footnote list, none of the citations is to papers having nothing to do with the claims to which it was attached. So I'm going to jump ahead to reference 132 and work backwards. Perhaps the problematic footnotes were just an anomolous part of the paper, and most of the rest are fine.
So starting at 131 and working backwards:
Semantic/semiotic/bioengineering function requires dynamically inert, resortable, physical symbol vehicles that represent time-independent, non-dynamic "meaning." (e.g., codons) [73,74,86,87,128-131].
These all look fine, except for 131, In vitro selection of RNA molecules that bind specific ligands. Like the references that follow it, I don't believe 131 has anothing to do with the claim to which it is attached. So let me continue going forward starting at 136:
In theory, the same protein can fold and unfold an infinite number of times via an ensemble of folding pathways [136].
Reference 136 is titled The accuracy of DNA replication. I don't believe this paper has anything to do with the claim to which it is attached. Once again, though the claim is uncontroversial. One wonders why they felt the need to footnote it.
Abel has termed this The GS Principle (Genetic Selection Principle) [137].
I think I'm going to stop checking now. Abel is one of the author's of this paper, yet reference 137 is by Liebovitch, Tao, Todorov and Levine. Something's wrong with their footnotes. Either they got confused in the numbering at some point, or after a certain point they began attaching citations to random papers at random points in their own paper.
Obviously, this journal's peer review doesn't include checking the citations.
--Percy

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nwr
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Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
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Message 9 of 85 (246168)
09-24-2005 8:08 PM
Reply to: Message 6 by Percy
09-24-2005 5:24 PM


quote:
nwr writes:
The main reason I have not spent much effort in studying GA, is that I see it as based on a misunderstanding of biological processes.
GA's received a lot of discussion a couple years ago (Information and Genetics is one of the threads), and I've written a couple simple GAs. What do you think is the misunderstanding?
Hmm. I misstated that. I should have said that the way GA is used in AI is based on a misunderstanding. The kind of problems that AI attempts to solve are very different from those solved by evolutionary processes.
Thanks for that reference to Information and Genetics. I'll take a look.
quote:
This quote from the article is pure ID:
We can hypothesize that metabolism "just happened," independent of directions, in a prebiotic environment billions of years ago. But we can hypothesize anything. The question is whether such hypotheses are plausible. Plausibility is often eliminated when probabilities exceed the "universal probability bound".

You have probably read more ID articles than I. Any discussion of what happened in a prebiotic world is necessarily speculative. The problem I see is that there are only hand waving assertions, and no actual attempt to calculate probabilities. There is no way of telling whether the authors were making realistic assumptions in coming to their conclusions.
quote:
The paper is very similar to the Meyer paper that appeared in the BSOW last year both in its lack of scientific rigor and in its lack of evidence to support any of its arguments.
I grant that it is a weak paper that provides very little support for its assertions.

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Funkaloyd
Inactive Member


Message 10 of 85 (246175)
09-24-2005 8:56 PM
Reply to: Message 8 by Percy
09-24-2005 7:47 PM


Re: This Paper is Very Suspect
You're right about reference 132, btw. I've got access to the full text, and not only does it not mention Dembski in the body or reference list, but it doesn't even contain the word "probability" (or probable, probably, etc.).

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Percy
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From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 11 of 85 (246221)
09-25-2005 3:36 AM
Reply to: Message 9 by nwr
09-24-2005 8:08 PM


nwr writes:
Hmm. I misstated that. I should have said that the way GA is used in AI is based on a misunderstanding. The kind of problems that AI attempts to solve are very different from those solved by evolutionary processes.
The purpose of GA is to apply the principles of descent with modification and natural selection to problems having nothing to do with biological evolution. I think if you look into it a bit more you'll find that it does not misinterpret or misapply any evolutionary principles.
The use of the term "genetic algorithms" in the paper is misleading, and it only appears twice, once in the abstract, and once in the body of the paper itself. They're not talking about the field of genetic algorithms, but merely drawing an analogy between the genetic instructions of DNA and computer programs. They claim algorithmic programming possesses FSC (Functional Sequence Complexity), then claim that DNA instructions have FSC, then assert that only an intelligence can create algorithms with FSC. It's the Dembski idea with different terminology and identical lack of support.
They would like people to think they've done the same for information with meaning as Shannon did for information without meaning. Shannon's paper is pretty heavy on math (and information theory hasn't gotten any simpler since Shannon), and any attempt to address the even more complex problem of semantic meaning in information would invariably contain even more math. The paper's nearly complete absence of math is telling. The paper is just a long rhetorically empty argument for ID.
The big question is how this paper ever passed peer review. I'm fearful that the the Meyer paper in BSOW is just the first trickle of what may well become a torrent of scientifically empty ID papers in the literature. I've sent PubMed an email inquiry.
--Percy
This message has been edited by Percy, 09-25-2005 04:03 AM

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nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 12 of 85 (246267)
09-25-2005 9:29 AM
Reply to: Message 11 by Percy
09-25-2005 3:36 AM


The big question is how this paper ever passed peer review.
That is a puzzle. My guess would be that a referee was confused by the references to information theory. I have never expected peer review to be perfect. However, I doubt that there will be a torrent of such papers, at least not in reputable journals.

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RAZD
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Posts: 20714
From: the other end of the sidewalk
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Message 13 of 85 (246268)
09-25-2005 9:32 AM
Reply to: Message 11 by Percy
09-25-2005 3:36 AM


I've sent PubMed an email inquiry.
I was going to ask. Thanks. Let us know the result?
My opinion of the paper was that it was intentionally obscuring its points with gargonisms, a problem that occurs in a lot of scientific papers (due to thought "in-breeding"?), but in this case not really saying anything in the process. Your points on "reference padding" only reinforced that opinion.
I would say they are studying the physical appearance of scientific papers and evolving their argument's camouflage to match.

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Wounded King
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Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 14 of 85 (246456)
09-26-2005 5:31 AM
Reply to: Message 11 by Percy
09-25-2005 3:36 AM


I'm not sure pubmed would be the right people to approach. Wouldn't you be better off contacting the publishers if you have a concern?
I've been a big fan of Open Access models of publishing journals but I'm not sure that BioMedCentral's new line of allowing interested groups of scientists to open up effectively their own journals may not be open to abuse, or at least likely to greatly increase the number of very low impact niche specific journals into which thinly disguised ID could be insinuated. I doubt that 'Theoretical Biology and Medical Modelling' really wants to become the open access equivalent of 'Rivista di Biologia' but for one out of the 3 reviews it has so far published to be this one I hope they were careful with the review process.
This inaugural editorial suhhests that the paper is looking for some more outre theoretical ideas, so maybe they consider shades of ID to be within that remit.
TTFN,
WK

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Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 15 of 85 (246498)
09-26-2005 9:34 AM
Reply to: Message 14 by Wounded King
09-26-2005 5:31 AM


Wounded King writes:
I'm not sure pubmed would be the right people to approach. Wouldn't you be better off contacting the publishers if you have a concern?
I clicked on the link provided at the website.
This inaugural editorial suhhests that the paper is looking for some more outre theoretical ideas, so maybe they consider shades of ID to be within that remit.
Their proof editing of their own prose is as weak as their peer-review process, e.g., "sort-after" instead of "sought-after". After reading this portion from their "The nature of the journal" section, I'm prepared to place their journal in the crank science category:
The new journal on the web will consider high quality, peer-reviewed theoretical papers. It will also seek to provide new ideas that may be quite off the main-stream of biomedicine; after all, today's "crazy" notion has a not so infrequently had the habit of becoming tomorrow's received wisdom.
It sounds like they're prepared to ignore the distinction between sound speculation and baseless speculation. If a paper as poor as this one can pass their peer review process, one can only feel dismay at how poor a paper would have to be to be rejected.
--Percy

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