Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 78 (8960 total)
147 online now:
PaulK (1 member, 146 visitors)
Newest Member: Mikee
Upcoming Birthdays: AlexCaledin
Post Volume: Total: 869,795 Year: 1,543/23,288 Month: 1,543/1,851 Week: 183/484 Day: 1/105 Hour: 0/0


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   Recent paper with an ID spin? Abel and Trevors (2005).
Percy
Member
Posts: 19319
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


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


This message is a reply to:
 Message 1 by Wounded King, posted 09-23-2005 11:28 AM Wounded King has not yet responded

Replies to this message:
 Message 33 by Smooth Operator, posted 07-24-2009 12:54 PM Percy has acknowledged this reply

  
Percy
Member
Posts: 19319
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


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


This message is a reply to:
 Message 5 by nwr, posted 09-24-2005 2:22 PM nwr has responded

Replies to this message:
 Message 9 by nwr, posted 09-24-2005 8:08 PM Percy has responded

  
Percy
Member
Posts: 19319
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


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


Replies to this message:
 Message 10 by Funkaloyd, posted 09-24-2005 8:56 PM Percy has acknowledged this reply
 Message 24 by pink sasquatch, posted 11-02-2006 6:51 PM Percy has acknowledged this reply

  
Percy
Member
Posts: 19319
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


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


This message is a reply to:
 Message 9 by nwr, posted 09-24-2005 8:08 PM nwr has responded

Replies to this message:
 Message 12 by nwr, posted 09-25-2005 9:29 AM Percy has acknowledged this reply
 Message 13 by RAZD, posted 09-25-2005 9:32 AM Percy has acknowledged this reply
 Message 14 by Wounded King, posted 09-26-2005 5:31 AM Percy has responded

  
Percy
Member
Posts: 19319
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


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


This message is a reply to:
 Message 14 by Wounded King, posted 09-26-2005 5:31 AM Wounded King has not yet responded

Replies to this message:
 Message 16 by RAZD, posted 09-26-2005 7:46 PM Percy has acknowledged this reply
 Message 17 by Carson O'Genic, posted 09-26-2005 9:07 PM Percy has acknowledged this reply

  
Percy
Member
Posts: 19319
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


Message 40 of 85 (518490)
08-06-2009 10:16 AM
Reply to: Message 39 by Wounded King
08-06-2009 9:36 AM


Re: For those interested in bioinformatics
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:

Wounded King writes:

No I'm saying that different levels of understanding of the functioning of the heart can give rise to subjectivity in discussion of it, and that the same is true of functions at the molecular level.

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:

Durston writes:

As Abel and Trevors have pointed out, neither RSC nor OSC, or any combination of the two, is sufficient to describe the functional complexity observed in living organisms, for neither includes the additional dimension of functionality, which is essential for life [5]. FSC includes the dimension of functionality [2,3]. Szostak [6] argued that neither Shannon's original measure of uncertainty [7] nor the measure of algorithmic complexity [8] are sufficient. Shannon's classical information theory does not consider the meaning, or function, of a message. Algorithmic complexity fails to account for the observation that 'different molecular structures may be functionally equivalent'.

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.

--Percy

Edited by Percy, : Fix format.


This message is a reply to:
 Message 39 by Wounded King, posted 08-06-2009 9:36 AM Wounded King has responded

Replies to this message:
 Message 42 by Wounded King, posted 08-06-2009 10:55 AM Percy has acknowledged this reply

  
Percy
Member
Posts: 19319
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


Message 57 of 85 (521385)
08-27-2009 9:52 AM
Reply to: Message 56 by Wounded King
08-26-2009 5:06 PM


Re: Durston et al . program
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


This message is a reply to:
 Message 56 by Wounded King, posted 08-26-2009 5:06 PM Wounded King has responded

Replies to this message:
 Message 58 by Wounded King, posted 08-27-2009 10:20 AM Percy has responded

  
Percy
Member
Posts: 19319
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


Message 59 of 85 (521400)
08-27-2009 11:05 AM
Reply to: Message 58 by Wounded King
08-27-2009 10:20 AM


Re: Durston et al . program
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


This message is a reply to:
 Message 58 by Wounded King, posted 08-27-2009 10:20 AM Wounded King has responded

Replies to this message:
 Message 60 by Wounded King, posted 08-27-2009 11:36 AM Percy has responded

  
Percy
Member
Posts: 19319
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


Message 61 of 85 (521459)
08-27-2009 2:20 PM
Reply to: Message 60 by Wounded King
08-27-2009 11:36 AM


Re: Durston et al . program
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


This message is a reply to:
 Message 60 by Wounded King, posted 08-27-2009 11:36 AM Wounded King has responded

Replies to this message:
 Message 62 by Wounded King, posted 08-28-2009 4:52 AM Percy has responded

  
Percy
Member
Posts: 19319
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


Message 63 of 85 (521590)
08-28-2009 6:59 AM
Reply to: Message 62 by Wounded King
08-28-2009 4:52 AM


Re: Durston et al . program
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


This message is a reply to:
 Message 62 by Wounded King, posted 08-28-2009 4:52 AM Wounded King has not yet responded

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2018 by EvC Forum, All Rights Reserved

™ Version 4.0 Beta
Innovative software from Qwixotic © 2020