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Author Topic:   Recent paper with an ID spin? Abel and Trevors (2005).
RAZD
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Posts: 19757
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.8


Message 16 of 85 (246652)
09-26-2005 7:46 PM
Reply to: Message 15 by Percy
09-26-2005 9:34 AM


any link between the "publishers" and ID? the paper?
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Carson O'Genic
Junior Member (Idle past 4190 days)
Posts: 20
From: San Francisco, CA
Joined: 08-15-2005


Message 17 of 85 (246667)
09-26-2005 9:07 PM
Reply to: Message 15 by Percy
09-26-2005 9:34 AM


I'm a big fan of what the BMC series of journals and PubMed Central are trying to do. Nonethless, I'm not surprised if a few poor journals and/or articles in these journals show up. It is hard, if not impossible, to start a new journal and get only top notch science submitted to your journal. Bottom line is that these new electronic journals are probably hungry for submissions.

One good thing is that the online format allows for comments to be posted. I haven't seen much use of this; I think scientists aren't much into the idea of blogging or discussing papers in a public forum. Nonetheless, if anyone feels that they have legitimate problems with a paper, such as improper use of references, go ahead and post a question. I can't think of a more appropriate question to post to the authors.


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Wounded King
Member (Idle past 2172 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 18 of 85 (360734)
11-02-2006 9:50 AM


Abel and Trevors at it again
This time it is in that auspicious publication 'PHYSICS OF LIFE REVIEWS'.

Once again I can't tell if this paper is brilliant or some sort of post-modern Sokalian hoax. They go as far this time as to reference Dembski's 'No free lunch' as one source of an estimate of a universal probability bound.

Self-organization vs. self-ordering events in life-origin models

David L. Abel, and Jack T. Trevors

Self-ordering phenomena should not be confused with self-organization. Self-ordering events occur spontaneously according to natural “law” propensities and are purely physicodynamic. Crystallization and the spontaneously forming dissipative structures of Prigogine are examples of self-ordering. Self-ordering phenomena involve no decision nodes, no dynamically-inert configurable switches, no logic gates, no steering toward algorithmic success or “computational halting”. Hypercycles, genetic and evolutionary algorithms, neural nets, and cellular automata have not been shown to self-organize spontaneously into nontrivial functions. Laws and fractals are both compression algorithms containing minimal complexity and information. Organization typically contains large quantities of prescriptive information. Prescriptive information either instructs or directly produces nontrivial optimized algorithmic function at its destination. Prescription requires choice contingency rather than chance contingency or necessity. Organization requires prescription, and is abstract, conceptual, formal, and algorithmic. Organization utilizes a sign/symbol/token system to represent many configurable switch settings. Physical switch settings allow instantiation of nonphysical selections for function into physicality. Switch settings represent choices at successive decision nodes that integrate circuits and instantiate cooperative management into conceptual physical systems. Switch positions must be freely selectable to function as logic gates. Switches must be set according to rules, not laws. Inanimacy cannot “organize” itself. Inanimacy can only self-order. “Self-organization” is without empirical and prediction-fulfilling support. No falsifiable theory of self-organization exists. “Self-organization” provides no mechanism and offers no detailed verifiable explanatory power. Care should be taken not to use the term “self-organization” erroneously to refer to low-informational, natural-process, self-ordering events, especially when discussing genetic information.

I think I need to relax my brain after just reading through the abstract.

TTFN,

WK

Edited by Wounded King, : Added link to article abstract on journal site, may not work without subscription.


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nwr
Member
Posts: 5585
From: Geneva, Illinois
Joined: 08-08-2005


Message 19 of 85 (360749)
11-02-2006 10:29 AM
Reply to: Message 18 by Wounded King
11-02-2006 9:50 AM


Re: Abel and Trevors at it again
I found the abstract easy enough to read. That probably is a question of background.

It does assert assumptions as fact. But then, it's only an abstract. Maybe the full article provides better support. I disagree with the stated conclusions. But they might not be too far from current thinking in some parts of the AI community.


Compassionate conservatism - bringing you a kinder, gentler torture chamber
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Archer Opteryx
Member (Idle past 1675 days)
Posts: 1811
From: East Asia
Joined: 08-16-2006


Message 20 of 85 (360755)
11-02-2006 10:35 AM
Reply to: Message 1 by Wounded King
09-23-2005 11:28 AM


Origin-of-Life Prize®
Wounded King:

Am I just being paranoid about the ID nature of this paper?

For what context it may provide, The Origin-of-Life Foundation, Inc.®, where one of the authors works, says this about its Origin-of-Life Prize®:

quote:

Clarification of what the Foundation is looking for

We are primarily interested in how certain linear digital sequences of monomers acquired three-dimensional dynamic function. The Prize offer is designed to stimulate focused research on the origin of initial genetic instructions themselves.[....] How does an algorithmically complex sequence of codons arise in nature which finds phenotypic usefulness only after translation into a completely different language (AA sequence)? How did natural process produce so indirectly the hundreds of needed three-dimensional protein catalysts for life to begin?

Mathematically, it is impossible to go backwards from 20 AA to 64 codons. [....] Various models of code origin often pursue primordial codon systems of only two nitrogen bases rather than three. At some point, such a two-base codon system must evolve into a three-base codon system. But catastrophic problems such as global frame shifts would have resulted from such a change midstream in the evolution of genetic code.

[....]How did initial genetic code-certain sequences of codons-come to specify only certain three-dimensional sequences of amino acid strings that "work"?

The winning submission will likely provide both a novel and cardinal conceptual contribution to current biological science and information theory.

The Foundation welcomes theoretical models of a more direct primordial instruction system (one that might have preceded codon transcription and translation) provided the model provides explanation of continuous transition (abiding by the "continuity principle") to current prokaryotic and eukaryotic empirical life.

Inanimate stepping stones of abiotic evolution are essential components to any natural process theory of the molecular evolution of life. Full reign must be given to the exploration of spontaneously forming complexity and to self-ordering inanimate systems. But reductionistic attempts to provide models of life development must not sacrifice the very property of "life" that biology seeks to explain.[...]

http://www.us.net/life/



Archer

All species are transitional.


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Silent H
Member (Idle past 3897 days)
Posts: 7405
From: satellite of love
Joined: 12-11-2002


Message 21 of 85 (360766)
11-02-2006 11:06 AM
Reply to: Message 18 by Wounded King
11-02-2006 9:50 AM


Re: Abel and Trevors at it again
The fact that they quote Dembski, and the "universal probability bound", is not a good sign.

The abstract does not read as inherently ID supporting or evo breaking. In fact I'm sort of wondering what science or discovery is supposed to be going on here. It appears to me like the authors are simply creating definitions for terms, based on relatively arbitrary criteria, and concluding people should use those terms based on their criteria.

The only thing I'd note (and again just from the abstract) is that their terminology might be convenient for ID. The distinction between "ordering" and "organization", with crystalization in the former and some unnamed process involving "choice contingency" in the latter, sound similar to the claims/distinctions Dembski makes in his writings.

This would allow them to say, see this crystal is result of a natural chemical "ordering" process, but this over here (organic feature) must be from something else (nudge nudge wink wink) as it involves "organization". Then force opponents to argue about the chemical reactions involved using two different terms, one sounding loaded with "intelligence" behind it.


holmes
"What a fool believes he sees, no wise man has the power to reason away." (D.Bros)
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Brad McFall
Member (Idle past 3110 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 22 of 85 (360890)
11-02-2006 5:16 PM
Reply to: Message 20 by Archer Opteryx
11-02-2006 10:35 AM


Re: Origin-of-Life Prize®
It is possible that the abstract confuses semblance and description thus making it a prize to obtain the resemblance of motion outside a plane within a transferred one-dimensional encoding. It is true that it is a curious thing that the DNA is changed into proteins' structure via a triplet code but it may also be that attempts to expand one’s horizon by rewarding a description is short of what is needed. I have always felt that the 3-D nature of cells themselves suffices.
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RAZD
Member
Posts: 19757
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.8


Message 23 of 85 (360918)
11-02-2006 6:41 PM
Reply to: Message 21 by Silent H
11-02-2006 11:06 AM


Re: Abel and Trevors at it again
The distinction between "ordering" and "organization", with crystalization in the former and some unnamed process involving "choice contingency" in the latter, sound similar to the claims/distinctions Dembski makes in his writings.

Yeah, that struck me as the redefinition sidestep. Seems to me the criteria they set for not being "ordering" means the organisms need to have a brain, and that's pretty far into what I would consider "organization".

Looks like the old "we'll call it something else so we can pretend" that organization in simple systems does not occur.

Enjoy.


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pink sasquatch
Member (Idle past 4100 days)
Posts: 1567
Joined: 06-10-2004


Message 24 of 85 (360921)
11-02-2006 6:51 PM
Reply to: Message 8 by Percy
09-24-2005 7:47 PM


they're not padding - they just don't know how to use endnote...
Obviously, this journal's peer review doesn't include checking the citations.

Obviously not - their in-text references go up to 164, while the end list of references only goes up to 162. I checked the problem references in the range of 130-135, and if you substract two from the in-text references it solves the apparent disconnect between claims and citations.


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Silent H
Member (Idle past 3897 days)
Posts: 7405
From: satellite of love
Joined: 12-11-2002


Message 25 of 85 (361073)
11-03-2006 9:11 AM
Reply to: Message 23 by RAZD
11-02-2006 6:41 PM


Re: Abel and Trevors at it again
Looks like the old "we'll call it something else so we can pretend" that organization in simple systems does not occur.

Exactly, maybe this is the new line of attack, they will redefine everything so that (if adopted) everyone will talk as if they actually made their case.


holmes
"What a fool believes he sees, no wise man has the power to reason away." (D.Bros)
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Brad McFall
Member (Idle past 3110 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 26 of 85 (361207)
11-03-2006 6:06 PM
Reply to: Message 25 by Silent H
11-03-2006 9:11 AM


Re: Abel and Trevors at it again
Well, I dont actually read it as a dodge over the very specific declaimation contrary to simple systems as NOT being organized.

I think they just carry out the use of language a bit too far.

Try thinking of the difference of self-organization, self-regulation, and self-ordering. With choice one can have organizations at least partially ordered but without a contigent choice the regulation of any series so ordered would not occur by the same but from above or without. I do not have a problem seperating ordering and organization but there seems something suspect to me in the notion of prescribed information.

So then if my use language is just an attempt to get people to speak like me so that I can say that it was just a misunderstanding of my own views then I guess I fall out of agreement with you and Razd here. I do however feel that in the direct application to living things that Abel and Trevors have tried to use lingusitic insights out of the context that they extisted in. I do not suspect that deep structure can be allowed to cut language in any which way but loose.

I HAVE encounterd the emphasis towards prexistence of logic gates in somatic tissue functioning and I think THIS is what the redefintions are directed towards. There is nothing wrong with that, in my perspective. Sure one should not be held back from trying to construct universality in cellular automata etc but untill they have been demonstrated irrespective of the media the same kind of restraint towards these positions ought be the same for irreducible complexity in ID etc.


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Silent H
Member (Idle past 3897 days)
Posts: 7405
From: satellite of love
Joined: 12-11-2002


Message 27 of 85 (361424)
11-04-2006 9:23 AM
Reply to: Message 26 by Brad McFall
11-03-2006 6:06 PM


Re: Abel and Trevors at it again
So then if my use language is just an attempt to get people to speak like me so that I can say that it was just a misunderstanding of my own views then I guess I fall out of agreement with you and Razd here

If I am understanding this sentence correctly then I need to clarify. I was not saying that they were trying to adjust language in order to then claim this is all they meant all along and we misunderstood them.

I was suggesting that it (pure speculation) could be used to create definitions such that people would speak in ways that would sound like they agreed with ID claims... as if ID had been supported and accepted.

Scientists discussing ordered v organized systems, particularly with their prescribed info concept, would allow ID to continue their semantic claims by noting how scientists recognize the difference between types of processes based on how "information" is handled.

Of course people can define things any way they want, and if people accept the language so be it. It may not even be intended to help ID. Only the question was raised, and given one of their sources, the stated examples, and the obscure critera involved, I theorized on that possible connection... then jiggled the knife a bit.


holmes
"What a fool believes he sees, no wise man has the power to reason away." (D.Bros)
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Brad McFall
Member (Idle past 3110 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 28 of 85 (361582)
11-04-2006 5:06 PM
Reply to: Message 27 by Silent H
11-04-2006 9:23 AM


Re: Abel and Trevors at it again
Ok, I understand now. It happens for me that some kind of language "extension" is needed.

Yes, if one was only trying to jiggle lingo so that it aligns with belief ordained or conferred on/for some other and/or prior basis then yes, this would be bad news no matter how sharp a knife one owns ..."as if ID had been...". OK I get that.

I do myself have an issue with the notion of "denaturation" and I think that some attempts to expand acceptable scientific language towards differentiating more than simply clumped vs loose "strands" would be helpful regardless of one's personal biases chemically or otherwise.

Thanks for making your point clear. It helps. Thanks, Brad.


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Halbwertszeit
Inactive Member


Message 29 of 85 (371042)
12-19-2006 11:11 PM
Reply to: Message 18 by Wounded King
11-02-2006 9:50 AM


Re: Abel and Trevors at it again
I have seen a citation of that paper on the website of a German ID proponent. I have seen him citing papers immediately after Dembski cited them. And after googeling the title of the paper I found it: http://www.uncommondescent.com/archives/1749
So the paper is an ID paper. Can anybody say something about the journal?

According to the Dembski blog the paper gives a reference to Dawkins:
[38] Dawkins R. Climbing mount impossible. 1996
Well Dawkins did not write this book, did he?

Also it seems that it is quite improbable that a 'real' scientific article cites so many popular science books.
And the article criticises Prigogine by saying:

The title of Nicolis and Prigogine’s earlier book [86] was incorrect in the title, “Self-Organization in Nonequilibrium Systems”: and correct in the subtitle, “From Dissipative Structures to Order Through Fluctuations”.

And on Dembskis blog they also quote the article saying

'Anti-informationists often appeal to epigenetic factors, prions, self-replicating peptides, regulatory proteins and small RNAs to argue life is merely physical without need of formal genetic algorithmic control mechanisms.'

Anti-informationists ??

And the list of keywords for that article seems like a collection of fancy buzzwords. As if someone who does not really understand the issue want to impress some other people. Reminds me of Sokal.

But it seems that ID has achieved to get a propaganda article through the peer review. Or at least some form of peer review.


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Wounded King
Member (Idle past 2172 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 30 of 85 (371065)
12-20-2006 2:09 AM
Reply to: Message 29 by Halbwertszeit
12-19-2006 11:11 PM


Re: Abel and Trevors at it again
According to the Dembski blog the paper gives a reference to Dawkins:
[38] Dawkins R. Climbing mount impossible. 1996
Well Dawkins did not write this book, did he?

No, but he did write 'Climbing Mount improbable'.

TTFN,

WK


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