Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 78 (8896 total)
Current session began: 
Page Loaded: 03-22-2019 6:49 AM
43 online now:
(43 visitors)
Chatting now:  Chat room empty
Newest Member: WookieeB
Post Volume:
Total: 848,541 Year: 3,578/19,786 Month: 573/1,087 Week: 163/212 Day: 5/25 Hour: 0/0


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
1
23Next
Author Topic:   an example of ID research and paper
randman 
Suspended Member (Idle past 2975 days)
Posts: 6367
Joined: 05-26-2005


Message 1 of 35 (470643)
06-11-2008 4:39 PM


As the New Scientist acknowledged, funding for the research underlying these peer-reviewed articles was provided by Discovery Institute's research fellowship program—thus disproving the twin canards that Discovery Institute does not support scientific research, and that pro-ID scientists do not publish peer-reviewed research. Yet the New Scientist tried its best to downplay the relevance of the articles to the theory of intelligent design....

.......

Dr. Axe wrote back the following, which the New Scientist declined to quote:

I have in fact confirmed that these papers add to the evidence for ID. I concluded in the 2000 JMB paper that enzymatic catalysis entails "severe sequence constraints". The more severe these constraints are, the less likely it is that they can be met by chance. So, yes, that finding is very relevant to the question of the adequacy of chance, which is very relevant to the case for design. In the 2004 paper I reported experimental data used to put a number on the rarity of sequences expected to form working enzymes. The reported figure is less than one in a trillion trillion trillion trillion trillion trillion. Again, yes, this finding does seem to call into question the adequacy of chance, and that certainly adds to the case for intelligent design.

http://www.evolutionnews.org/2007/01/journal_of_molecular_biology_a.html

I really cannot debate the research itself and so am not proposing it for a thread topic except to mention it in the "In the News" section to show that as far as the author of the paper, right or wrong, he considers the paper and research to be evidence in favor of Intelligent Design. To simply claim no ID research or papers are done is false. Keep in mind I am not saying anything about the veracity of his paper except it was published, is in the news, and the author considers it ID research and publication.


Replies to this message:
 Message 2 by Deftil, posted 06-12-2008 11:12 PM randman has not yet responded
 Message 7 by Wounded King, posted 06-13-2008 6:46 AM randman has responded
 Message 27 by Dr Adequate, posted 06-17-2008 6:57 AM randman has responded

  
Deftil
Member (Idle past 2532 days)
Posts: 128
From: Virginia, USA
Joined: 04-19-2008


Message 2 of 35 (470844)
06-12-2008 11:12 PM
Reply to: Message 1 by randman
06-11-2008 4:39 PM


This is interesting. It's a shame I can't get access to the paper w/o paying for it, but that's how it goes.

I wouldn't get carried away with giving ID much credit for conducting scientific research though. I mean, presenting ONE research paper that possibly could lend some credence to ID isn't making much of a convincing case that ID proponents are conducting extensive scientific study.

I did some quick online investigating to see if I could find more papers of this type (along with the fact that I've been keeping my eyes open for this type of thing for awhile now) and I wasn't able to find anything else. I did come across a website called ResearchID.org, a pro ID site, though. I didn't find much there, however. Basically a bunch of articles with no actual results from scientific research, but simply a framework for how the articles should be set up, should anyone have any relevant info to go into the articles. Also, by the site's own admission:

quote:
As the foundations of ResearchID.org were being constructed, we realized there was no well-articulated general approach to undertaking research (theoretical or empirical) from an "intelligent design framework." In fact, to our knowledge there was not even a framework.
and also
quote:
Up to the present, theoretical research is by far the most commonly undertaken study of intelligent design, with empirical research trailing behind.
source for both quotes: http://www.researchintelligentdesign.org/wiki/Breaking the Mold I: Theoretical Research of Intelligent Design

When they say "empirical research" (ER), it is a clickable link with more info about ER as it relates to ID. For some reason "theoretical research" (TR) isn't a clickable link, so one is left to wonder how TR is usefully conducted in regards to ID.
TR can be useful in scientific studies, but w/o more info about it as it relates to ID, I get the impression that's it's code for "vague philosophizing".
Also, they don't say that "ER is trailing right behind" or "close behind" TR, just that it "trails behind". Taking that into consideration along with the fact that I can't seem to find any actual ER for ID on the site, it appears to be a meaningless claim. There could essentially be no ER for ID and they could still technically state that "ER research trails behind TR for ID".

I do bear in mind that my criticism here for ID scientific research is being primarily based off one website, but it's also worth noting that any other time I've tried to follow a trial of ER for ID I come to the same dead end.

I haven't read the following 2 blogs entries in their entirety, but they seem to provide interesting commentary on Axe's paper, including some excerpts.
http://idintheuk.blogspot.com/2007/01/very-controversial-paper.html

http://idintheuk.blogspot.com/2007/02/douglas-axe-jmolbiol2000-301-585-595.html

I'll ask the Mol Bio and Biochem people I know if they are aware of Axe and his research and what they think of it.

Also, I don't mean to jump to any definitive conclusions without being able to properly analyze the paper, but in theory, can ID ever be proved? Theoretically, Darwinian evolution could be falsified (as impossible as it seems, given the TONS of scientific evidence supporting it) but could we ever scientifically (naturally) prove that a supernatural designer is the reason behind the observable biodiverity on the Earth?

I apologize if my response has transcended the scope of what this thread was intended for. I'm not really familiar with the "In the News" forum and how it exactly differs from the other forums where threads go through the proposed threads process. I'll have to look into that.

Edited by Admin, : Shorten link.


This message is a reply to:
 Message 1 by randman, posted 06-11-2008 4:39 PM randman has not yet responded

    
BeagleBob
Member (Idle past 3753 days)
Posts: 81
Joined: 11-21-2007


Message 3 of 35 (470847)
06-13-2008 12:44 AM


If I remember I can dig it up in work tomorrow.

I do know of one paper that was published and presented in the Dover trial as evidence for Intelligent Design. Dembski had gushed over it, saying that "this may well be the nail in the coffin [and] the crumbling of the Berlin wall of Darwinian evolution."

Details here.

Yes, IDists do publish a few scant papers that they say supports Intelligent Design, but generally they aren't very good.


Replies to this message:
 Message 4 by Deftil, posted 06-13-2008 3:35 AM BeagleBob has not yet responded

  
Deftil
Member (Idle past 2532 days)
Posts: 128
From: Virginia, USA
Joined: 04-19-2008


Message 4 of 35 (470867)
06-13-2008 3:35 AM
Reply to: Message 3 by BeagleBob
06-13-2008 12:44 AM


If I remember I can dig it up in work tomorrow.

Cool. What do you do/ where do you work?

I do know of one paper that was published and presented in the Dover trial as evidence for Intelligent Design. Dembski had gushed over it, saying that "this may well be the nail in the coffin [and] the crumbling of the Berlin wall of Darwinian evolution."

Oh, yes. Thanks you for reminding me of that, BeagleBob. It's Simulating evolution by gene duplication of protein features that require multiple amino acid residues by Michael J. Behe and David W. Snoke
http://www.proteinscience.org/cgi/content/full/13/10/2651

And the claims of that paper seem amply refuted in Simple evolutionary pathways to complex proteins by Michael Lynch
http://www.proteinscience.org/cgi/content/full/14/9/2217
and other places by other people as well.


This message is a reply to:
 Message 3 by BeagleBob, posted 06-13-2008 12:44 AM BeagleBob has not yet responded

    
Minnemooseus
Member
Posts: 3708
From: Duluth, Minnesota, U.S. (West end of Lake Superior)
Joined: 11-11-2001
Member Rating: 3.9


Message 5 of 35 (470871)
06-13-2008 4:58 AM


The same, or a different Axe paper?
I happened upon Stylus: A System for Evolutionary Experimentation Based on a Protein/Proteome Model with Non-Arbitrary Functional Constraints -->Stylus: A System for Evolutionary Experimentation Based on a Protein/Proteome Model with Non-Arbitrary Functional Constraints< !--UE--> by Douglas D. Axe et all via one of PZ Meyers articles at Pharyngula, which in turn was via Panda's Thumb.

PZ's evaluation includes:

quote:
The paper is called Stylus: A System for Evolutionary Experimentation Based on a Protein/Proteome Model with Non-Arbitrary Functional Constraints. It's a description of a new software package written by the secret Biologic Institute, which they argue will have utility in modeling protein evolution. The paper says absolutely nothing about Intelligent Design, makes no arguments against evolution, and is utterly untroubling to evolutionary theory, and it's clear that the way they got it published was by studiously avoiding the kinds of stupid statements that are the hallmark of the Discovery Institute.

See the source for more.

Moose

Edited by Minnemooseus, : Added "Panda's Thumb" credit and link.

Edited by Minnemooseus, : Had to re-disable the smilies, which were mucking up one of the links.


Replies to this message:
 Message 6 by PaulK, posted 06-13-2008 5:19 AM Minnemooseus has not yet responded

    
PaulK
Member
Posts: 14749
Joined: 01-10-2003
Member Rating: 1.7


Message 6 of 35 (470872)
06-13-2008 5:19 AM
Reply to: Message 5 by Minnemooseus
06-13-2008 4:58 AM


Re: The same, or a different Axe paper?
The most significant paper seems to be the 2004 paper also discussed at The Panda's Thumb
This message is a reply to:
 Message 5 by Minnemooseus, posted 06-13-2008 4:58 AM Minnemooseus has not yet responded

    
Wounded King
Member (Idle past 2171 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 7 of 35 (470879)
06-13-2008 6:46 AM
Reply to: Message 1 by randman
06-11-2008 4:39 PM


Keep in mind I am not saying anything about the veracity of his paper except it was published, is in the news, and the author considers it ID research and publication.

I think this is the problematic point. Does the fact that the author considers this ID research actually make it in any way supportive of ID. The Behe and Snoke paper has already been mentioned and despite having been pushed as supportive of ID it still showed that irreducibly complex features could arise, and that was with some highly restrictive assumptions in the modeling.

Axe doesn't actually seem to be estimating the likelihood of anything by evolution,but rather that of any randomly generated protein domain having a specific function.

The actual linkage of this to problems with evolution or support with ID is tenuous. Axe writes ...

So, if re-creating a fold by ordered assembly of sections of sequences that already adopt that fold is not a simple matter, generating new folds from parts of old ones may be much less feasible than has been supposed.

This argument seems to be that since we can't necessarily recreate a functional ancestral protein just by cutting and pasting elements of homologous proteins together then domain shuffling and other common genetic mechanisms may not be sufficient to generate the diversity we see in protein structure. It has very little to do with the figure Axe estimates, since that figure was for the proportion of all possible sequences of a particular length which could adopt very specific stable conformation and confer function.

Axe himself writes ...

At first glance, it seems implausible that natural sequences could diverge through a space where function is represented so sparsely. How, for example, can we account for the substantial diversity among the large-domain homologues (Figure 5) if randomly altered sequences have such slim prospects of retaining function? The answer follows from the fact that functional sequences are not distributed uniformly through sequence space. A random change to a functional sequence actually has a good chance of leaving function undisturbed if very few positions are affected. As estimated above, the likelihood of a signature-compliant substitution in the large-domain reference sequence producing a comparably functional variant is about 38%. Since 70% of the ~1000 possible non-synonymous base changes to the reference coding sequence produce signature-compliant substitutions, about one in four random single-residue changes are functionally neutral. The proportion would be somewhat lower under conditions requiring a higher level of function (such as those under which neutral drift normally occurs) but not so low as to preclude progressive sequence divergence by gradual accumulation of point mutations.

So where is the support for ID? Axe generates a really big number but doesn't tie it in to evolution. His argument about domain shuffling seems almost entirely divorced from his calculations of the proportion of stable functional large domains in the whole set of possible sequences of large domain length.

I'm also not sure of his phrasing as being concerned with 'the rarity of sequences expected to form working enzymes' since the paper discusses 'the proportion of all sequences of large-domain length that perform the specified function by means of any tertiary fold'. There is a world of difference between forming a specific functional fold and forming any functional fold. The only reasoning I can see for this is that he may be shaving a few orders of magnitude off as a way of encompassing all 'working enzymes' and basing this reduction on the estimates of how many extant fold types are needed to cover all biological functions. This fails to take into account the fact that this does not represent all possible functional folds making the estimate omly about the probability of randomly coming up with a long domain sequence forming a stable fold which confers function and corresponds to one already extant.

Axe also gives only the highest range of the reported figure (one in 1077), using his lower estimate (one in 1053) you could knock a couple of trillion off it.

Doug Axe's papers always strike me as being pretty good science,although I'm not sure how useful Stylus will turn out to be it is certainly interesting, but the support for ID is only there if you squint and want really hard to see it.

TTFN,

WK

Edited by Wounded King, : No reason given.


This message is a reply to:
 Message 1 by randman, posted 06-11-2008 4:39 PM randman has responded

Replies to this message:
 Message 8 by randman, posted 06-13-2008 11:52 AM Wounded King has not yet responded

    
randman 
Suspended Member (Idle past 2975 days)
Posts: 6367
Joined: 05-26-2005


Message 8 of 35 (470909)
06-13-2008 11:52 AM
Reply to: Message 7 by Wounded King
06-13-2008 6:46 AM


well, beauty is the eye of the beholder
One thing is clear to me, what one considers factual or real science or logical is very subjective. I am not going to debate the paper's content except to say his comment seems correct and appropiate and not something you have to squint to see as you suggest. It's clear it was funded by the Discovery Institute and the author considers it supportive of ID. There are other ID papers out there as well, some more direct in their support of ID.

In fact, there are probably more ID papers than evo papers in the sense that at least there are some ID papers trying to establish ID related concepts whereas the fundamentals of Darwinism are merely asssumed.


This message is a reply to:
 Message 7 by Wounded King, posted 06-13-2008 6:46 AM Wounded King has not yet responded

Replies to this message:
 Message 9 by Deftil, posted 06-13-2008 10:15 PM randman has not yet responded

  
Deftil
Member (Idle past 2532 days)
Posts: 128
From: Virginia, USA
Joined: 04-19-2008


Message 9 of 35 (471001)
06-13-2008 10:15 PM
Reply to: Message 8 by randman
06-13-2008 11:52 AM


Re: well, beauty is the eye of the beholder
In fact, there are probably more ID papers than evo papers in the sense that at least there are some ID papers trying to establish ID related concepts whereas the fundamentals of Darwinism are merely asssumed.

Oh, no, that's not the case at all. The fundamentals of Darwinian evolution are in no way merely assumed as anyone who has looked into the matter extensively is certainly aware. Your assertion has no basis in reality. It would have been a good idea to do a little research before making such a bold claim.

What do you believe to be "the fundamentals of Darwinism"? I'd be glad to provide you with lines of research and observational evidence involving them. There's tons of research involving Darwinian evolution. In fact, nearly every legitmate paper from the subfields of Biology in some way supports it.

I'll briefly run through some things.

I think the existence of units of inheritance is a fundamental component of Darwinian Evolution. Gregor Mendel got the ball (peas) rolling in that department, back in 1856. Click on his name for more info about him and his experiments.

Here's a paper called Mendelian controversies: a botanical and historical review published in the American Journal of Botany that reviews Mendel's research efforts in detail.

Here's a work by Douglas L. Theobald, Ph.D., Department of Biochemistry, Brandeis University called 29+ Evidences for Macroevolution - The Scientific Case for Common Descent. It discusses lines of evidence in favor of macroevolution in depth, listing all the sources of that evidence. The paper has 5 basic sections, each with it's own list of references including books and scientific papers. I was going to list the references he used for the paper here for you to see, but then I realized it would make my post far too long. So I decided to just put the references for just 1 of the paper's 5 parts here, but even then my post would be too long. So I then decided to just count the number of references for part 1, but I gave up counting at 50. I had only made it to the G's. So its 50 plus all the H - Z references for part 1, then all the references for parts 2,3,4, and 5 in just that one work. That piece has more sources in the A - G references of 1 section than there are in the entire "study" of ID.

I'll also include a random sceintific paper from The Journal of Cell Biology called Evolution of a neuroprotective function of central nervous system myelin that addresses the evolution of a membrane that surrounds nerve cells.

In 1971 Theodosios Dobzhansky & Olga Pavlovsky published a paper in Nature called Experimentally Created Incipient Species of Drosophila.
They state:

quote:
By means of selection in many generations, ethological (sexual) isolation has been built between strains of Drosophila which were formerly not reproductively isolated.

They basically made new species of fruitflies in the lab. They were able to so do in as little as 10 fruitfly generations.

As you can see, there aren't more ID papers than evolution papers. It's not evenly vaguely, remotely close. Even to someone who has been drinking heavily. Just counting the 50 sources of A - G of 1 of the 5 sections of the above papers, plus that actual paper itself, plus the other 3 I listed, plus Mendel's paper makes 55 for evolution to the 3 or 4 I see listed in this thread for ID. And I could go on all day listing ones for evolution. And then come back tomorrow and keep doing it. and the next day as well. Who knows how long it could go on for. Look what I was able to find in about 10 minutes using the internet.

Edited by Deftil, : added a few words I left out at the end


This message is a reply to:
 Message 8 by randman, posted 06-13-2008 11:52 AM randman has not yet responded

Replies to this message:
 Message 10 by RAZD, posted 06-14-2008 4:44 AM Deftil has responded

    
RAZD
Member
Posts: 19756
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.5


Message 10 of 35 (471057)
06-14-2008 4:44 AM
Reply to: Message 9 by Deftil
06-13-2008 10:15 PM


The number of ID papers?
And I could go on all day listing ones for evolution. And then come back tomorrow and keep doing it. and the next day as well. Who knows how long it could go on for. Look what I was able to find in about 10 minutes using the internet.

And you could limit your search to papers done by people named Steve ... just to make it interesting:

Google

quote:
Scholar Recent articles: Results 1 - 10 of about 117,000 for steve.

And of course you have to include all journals that have (low) standards similar to where ID papers are published ...

Enjoy.

Edited by RAZD, : steve results

Edited by RAZD, : .


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 9 by Deftil, posted 06-13-2008 10:15 PM Deftil has responded

Replies to this message:
 Message 11 by Deftil, posted 06-15-2008 10:36 AM RAZD has responded

  
Deftil
Member (Idle past 2532 days)
Posts: 128
From: Virginia, USA
Joined: 04-19-2008


Message 11 of 35 (471174)
06-15-2008 10:36 AM
Reply to: Message 10 by RAZD
06-14-2008 4:44 AM


Re: The number of ID papers?
And you could limit your search to papers done by people named Steve ... just to make it interesting:

Google

quote:
Scholar Recent articles: Results 1 - 10 of about 117,000 for steve.

Which I find particularly fantastic, seeing as how my name is Steve and all. Go team Steve.


This message is a reply to:
 Message 10 by RAZD, posted 06-14-2008 4:44 AM RAZD has responded

Replies to this message:
 Message 12 by RAZD, posted 06-15-2008 12:29 PM Deftil has not yet responded

    
RAZD
Member
Posts: 19756
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.5


Message 12 of 35 (471190)
06-15-2008 12:29 PM
Reply to: Message 11 by Deftil
06-15-2008 10:36 AM


The Steve List
Which I find particularly fantastic, seeing as how my name is Steve and all. Go team Steve.

Have you heard about the Steve List?

http://www.ncseweb.org/article.asp?category=18
http://www.ncseweb.org/resources/articles/3697_the_list_2_16_2003.asp

Meant to be compared to the Discovery Institute list of evolution "skeptics" ...

One could use the list to search by author for articles only by the 889 (and counting) steves on the list if one really wanted to get anal about the numbers game ...

Enjoy

Edited by RAZD, : .


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 11 by Deftil, posted 06-15-2008 10:36 AM Deftil has not yet responded

Replies to this message:
 Message 13 by BeagleBob, posted 06-15-2008 2:52 PM RAZD has acknowledged this reply

  
BeagleBob
Member (Idle past 3753 days)
Posts: 81
Joined: 11-21-2007


Message 13 of 35 (471204)
06-15-2008 2:52 PM
Reply to: Message 12 by RAZD
06-15-2008 12:29 PM


Re: The Steve List
I downloaded the papers and am trying to find time to look through them. If anyone wants a copy, feel free to PM me or send me an email.
This message is a reply to:
 Message 12 by RAZD, posted 06-15-2008 12:29 PM RAZD has acknowledged this reply

  
randman 
Suspended Member (Idle past 2975 days)
Posts: 6367
Joined: 05-26-2005


Message 14 of 35 (471209)
06-15-2008 3:06 PM


So you guys are wrong?
Generally it is claimed there are no ID papers, and then when confronted with ID papers, what is your argument?

You try to say you don't consider them ID research and papers but the scientists conducting such research and publicizing them do. There is a nice list of some ID papers on the Discovery Institute's site. Imo, it is patently false to go about claiming no ID research and papers are done.

Are you guys going to continue to make that false claim now that you are aware such research and papers are done?


Replies to this message:
 Message 15 by BeagleBob, posted 06-15-2008 3:22 PM randman has not yet responded

  
BeagleBob
Member (Idle past 3753 days)
Posts: 81
Joined: 11-21-2007


Message 15 of 35 (471215)
06-15-2008 3:22 PM
Reply to: Message 14 by randman
06-15-2008 3:06 PM


Re: So you guys are wrong?
quote:
Generally it is claimed there are no ID papers, and then when confronted with ID papers, what is your argument?

You try to say you don't consider them ID research and papers but the scientists conducting such research and publicizing them do. There is a nice list of some ID papers on the Discovery Institute's site. Imo, it is patently false to go about claiming no ID research and papers are done.

Are you guys going to continue to make that false claim now that you are aware such research and papers are done?


It really depends on the content of the paper. If the conclusions of the paper match the claims of ID, then sure, you could say that ID papers are being published, albiet very few.

However, the problem with Intelligent Design isn't just a lack of evidence, it's an utter lack of a proper, well-formulated research paradigm. Michael Behe is just about the only biologist who tried to develop standards for data that would constitute evidence for ID (irreducible complexity), but the definition he first developed was proven to be unworkable by Miller. When he revised it to circumvent criticism, he redefined Irreducible Complexity so that it became totally divorced from biological reality.

If you can't formulate workable benchmarks for what would count as "evidence" for ID, you can't say that any particular research paper supports ID.

Edited by BeagleBob, : Added a "however" into the second paragraph for readability.


This message is a reply to:
 Message 14 by randman, posted 06-15-2008 3:06 PM randman has not yet responded

  
1
23Next
Newer Topic | Older Topic
Jump to:


Copyright 2001-2018 by EvC Forum, All Rights Reserved

™ Version 4.0 Beta
Innovative software from Qwixotic © 2019