Recent paper with an ID spin? Abel and Trevors (2005).

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: 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. 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

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. This quote from the article is pure ID: This, too, is pure ID, for it is one of the fundamental tenets of ID that random processes cannot create information: Here's another pure ID statement from the conclusion: 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

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: Here's the reference: 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:

​

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:

​

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

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.--PercyThis message has been edited by Percy, 09-25-2005 04:03 AM

I clicked on the link provided at the website. 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: 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

I am fascinated, I would like to download the program and get into it, but I'm spreading myself a bit too thin these days.But I do have a question. You said this in Message 38: So given all we don't know about any particular protein's function, how can there realistically be any objective measure of FSC? Possibly I don't understand the proper definition of functional. Maybe it's a bit like information where the definition within information theory is much more constrained than in general usage. But the Abel/Trevors paper just jumped right in as if we all know what FSC is, and Durston's paper wasn't any better, e.g., this from the "Background" section: Not very helpful.I'm reminded of the mousetrap argument by Ken Miller. The function of a mouse trap is to catch mice. But you can also use it as a tie tack. When a window's open in the office you could use one as a paper weight. And how do you quantify these functions?This is the way it feels to me, and that's why I've paid little attention to Abel and Trevors et. al., but if you're looking into this then it tells me you must think there's something to it.--PercyEdited by Percy, : Fix format.

Isn't the ultimate goal of Durston and company to draw a connection between functional specificity and conscious intent or meaning? And don't they claim that they can detect functional specificity? And wouldn't their measurement technique show high functional specificity for both a real-life protein and an equally long but artificial protein constructed from a random sequence of codons?In other words, aren't they just making an unsupported claim that complexity is synonymous with meaning?--Percy

I guess I'm looking for the connection to ID. Don't they need to compare the FSC of random proteins with real-world proteins of comparable size?--Percy

Something's not right. If their measures were fundamentally still just Shannon information, then the greatest measures of information or complexity should have corresponded to the random proteins. I must not understand what Fit is actually measuring, but if it isn't somehow a function of information then I don't see the relevance to any ID claims.Let me know if I'm just not doing enough homework and I'll try to find some time to dig into the details of the Durston paper.--Percy

Thanks for the information. I have a minor release to get out today and then we've got to prepare to leave for vacation beginning tomorrow, but we often just wind down in the room at the end of the day, so let me plan to see what I can figure out regarding the variable they derive for their functions.--Percy