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Author Topic:   Teaching evolution in the context of science
Tranquility Base
Inactive Member


Message 16 of 76 (12307)
06-27-2002 9:34 PM
Reply to: Message 14 by John
06-27-2002 10:26 AM


John
Lots of areas of biology have to do with evolution but almost none of them are dependent on aspects of it which aren't compatible with creation. Very few researchers actually work on evoltuion itself. Most work on this or that gene, very few set out to study evoltuion. That is a fact. My 0.5% might even be an exageration in your favour.
Try looking at Medline (it's Googles first hit if you use that word) to study novelty. Behe already studied the Journal of Mol Evol - there's almost nothing in it on the origin of novelty!
The title of tha tabstract (that macro is not lots of micro) is very clear in my area of biology. Mutations of proteins cannot gradually go from one protein fold to another systematically whilst maintinaing some sort of function all the way. Micro/macro can be nicely differntiated at the gene family level.
Go read some of your Google hits and summarize.
[This message has been edited by Tranquility Base, 06-27-2002]

This message is a reply to:
 Message 14 by John, posted 06-27-2002 10:26 AM John has replied

Replies to this message:
 Message 17 by John, posted 06-28-2002 1:25 AM Tranquility Base has replied

  
John
Inactive Member


Message 17 of 76 (12320)
06-28-2002 1:25 AM
Reply to: Message 16 by Tranquility Base
06-27-2002 9:34 PM


quote:
Originally posted by Tranquility Base:
Lots of areas of biology have to do with evolution but almost none of them are dependent on aspects of it which aren't compatible with creation.
Well that's a wee bit more specific than 'even most scientists know very, very little about evolution' or 'most biologists don't work on evolution' Now it has become 'most biologists don't work on parts of evolution that are incompatible with creation'
quote:
Very few researchers actually work on evoltuion itself. Most work on this or that gene, very few set out to study evoltuion.
But many work with the concept and that requires some understanding of it.
quote:
Mutations of proteins cannot gradually go from one protein fold to another systematically whilst maintinaing some sort of function all the way.
I never said that protein folds change in this manner. Why should I? Protein folds don't evolve, the organisms carring the genes for those proteins do. That is, bad protein==dead organism... this would be natural selection. Good protein== reproductive organism. How is this different from textbook evolution? And how does it make micro and macro fundamentaly different?
I think that you have so completely equated protein folding and macroevolution that you can't see past yourself.
oh... all I ever do is read Google results. That's what I do.
Take care.
------------------
www.hells-handmaiden.com

This message is a reply to:
 Message 16 by Tranquility Base, posted 06-27-2002 9:34 PM Tranquility Base has replied

Replies to this message:
 Message 19 by Tranquility Base, posted 06-30-2002 9:52 PM John has replied
 Message 22 by Tranquility Base, posted 07-01-2002 1:56 AM John has replied

  
Zhimbo
Member (Idle past 6011 days)
Posts: 571
From: New Hampshire, USA
Joined: 07-28-2001


Message 18 of 76 (12349)
06-28-2002 2:43 PM
Reply to: Message 15 by Tranquility Base
06-27-2002 9:21 PM


quote:
Originally posted by Tranquility Base:
Schraf
Of course PhDed biologists know a lot about evolution - the fossil record, natural selection etc. But they are unaware of the near zero extent to which macroevoltuion is studied.
I would define the origin of the immune system or multicellularity as examples of novel systems. But it works for almost any cellular system - as I have referenced elsewhere, mnay cellular systems are characterised by the presence of new gene families which bare no resemblances to any other gene in the genome.

Evolution of immune system:
http://www.talkorigins.org/faqs/behe/icsic.html
(Includes relevant citations...)
Evolution of multicellularity:
http://www.talkorigins.org/origins/postmonth/jul00.html
(this post is very interesting as a counterexample for you. But I'm not really sure why you chose multicellularity as an example n the first place...the change from colonial to "truly" multicellular organisms is pretty darn subtle, and I don't see how multicellularity hinges upon any particularly "difficult" evolutionary change.)
I haven't talked about these in great detail. your argument is that such research doesn't exist, so I don't feel I need to do more than point out some existing examples.
------------------
"Colorless green ideas sleep furiously." - Chomsky

This message is a reply to:
 Message 15 by Tranquility Base, posted 06-27-2002 9:21 PM Tranquility Base has replied

Replies to this message:
 Message 20 by Tranquility Base, posted 06-30-2002 11:09 PM Zhimbo has not replied

  
Tranquility Base
Inactive Member


Message 19 of 76 (12418)
06-30-2002 9:52 PM
Reply to: Message 17 by John
06-28-2002 1:25 AM


John
You sound like a black box person from that post- you believe evoltuion in faith. Molecular evolutionists propose that proteins originated via duplicaiton and drift. Our point is, becasue of the folding problem, that you may as well start from random to get each fold. Although I can't find a mainstream article in Medline on the issue, a creationist paper estimates that there was far far too litle time for this to be the origin of protein families (let alone tie these together into pathways, let alone bridge gaps of irreducible complexity).
I suggesested that you read the links to your Google hits and not just complile word usage statistics.

This message is a reply to:
 Message 17 by John, posted 06-28-2002 1:25 AM John has replied

Replies to this message:
 Message 21 by John, posted 07-01-2002 1:42 AM Tranquility Base has not replied

  
Tranquility Base
Inactive Member


Message 20 of 76 (12429)
06-30-2002 11:09 PM
Reply to: Message 18 by Zhimbo
06-28-2002 2:43 PM


Zhimbo
I'll have a close look at your examples.

This message is a reply to:
 Message 18 by Zhimbo, posted 06-28-2002 2:43 PM Zhimbo has not replied

  
John
Inactive Member


Message 21 of 76 (12452)
07-01-2002 1:42 AM
Reply to: Message 19 by Tranquility Base
06-30-2002 9:52 PM


[QUOTE]Originally posted by Tranquility Base:
[b]John
You sound like a black box person from that post- you believe evoltuion in faith.[/QUOTE]
[/b]
Potent retort TB. You sound like someone who can't answer a straight question.
[QUOTE][b]Molecular evolutionists propose that proteins originated via duplicaiton and drift. Our point is, becasue of the folding problem, that you may as well start from random to get each fold.[/QUOTE]
[/b]
Fine. You still haven't answered the questions I asked. And how about some citations?
Something like this Molecular Biology Citation
Weird, all about protein evolution. Who knew?
Appeal to authority is still appeal to authority even if that authority is you.
quote:
I suggesested that you read the links to your Google hits and not just complile word usage statistics.
I suggest that you say something substantial. This could be interesting but I can barely hear you yelling down from that pedestal.
I suggest that you stop implying that I don't research my subject matter. I do.
------------------
www.hells-handmaiden.com
[This message has been edited by Admin, 07-02-2002]

This message is a reply to:
 Message 19 by Tranquility Base, posted 06-30-2002 9:52 PM Tranquility Base has not replied

  
Tranquility Base
Inactive Member


Message 22 of 76 (12457)
07-01-2002 1:56 AM
Reply to: Message 17 by John
06-28-2002 1:25 AM


John, I'm sorry I was abrupt with you.
The difference from textbook evolution is the following. Textbook evolution has Nature selecting from natural varieties for the best function. A protein can't typically change from one fold to another without being non-functional for most of the transtion time. Regardles, fold families contain no hints of their anscestral protein familes. Hence protein fold evolution brings one back to randomness.
So, microevoltuion is the optimization of an alrady functional gene (we see this all the time in mol biol). Macroevolution reuqires the origin of new genes and systems that in many cases we know generated novel fold families that bear no similarity at all to other genes in the genome. That is the difference between micro/macro from a genomics POV whether one is creationist or evolutionist.

This message is a reply to:
 Message 17 by John, posted 06-28-2002 1:25 AM John has replied

Replies to this message:
 Message 23 by John, posted 07-02-2002 1:29 PM Tranquility Base has replied

  
John
Inactive Member


Message 23 of 76 (12568)
07-02-2002 1:29 PM
Reply to: Message 22 by Tranquility Base
07-01-2002 1:56 AM


quote:
Originally posted by Tranquility Base:
Textbook evolution has Nature selecting from natural varieties for the best function.
'k
[QUOTE][b]A protein can't typically change from one fold to another without being non-functional for most of the transtion time.[/QUOTE]
[/b]
I think you may be overemphasizing protein folding as this article suggests to me.
Secondly, a protein doesn't evolve. The organism carring that protein survives or doesn't, and the population evolves. I can't shake the feeling that you are treating proteins as if they are directly evolving, or directly selected selected for and against independent of the rest of the organis and the poulation.
Evolution doesn't require the typical case. 1 in several thousand or ten-thousand is adequate.
quote:
Regardles, fold families contain no hints of their anscestral protein familes. Hence protein fold evolution brings one back to randomness.
"This is consistent with the view that the two proteins arose from a common ancestor protein (say CRP) via a gene duplication event ... and that they have been evolving and diverging since." http://www.keele.ac.uk/depts/ma/esgi2001/probs5.html
quote:
So, microevoltuion is the optimization of an alrady functional gene (we see this all the time in mol biol). Macroevolution reuqires the origin of new genes....
Change a gene and it becomes a new gene. I don't know how you can defend the distiction.
quote:
.... and systems that in many cases we know generated novel fold families that bear no similarity at all to other genes in the genome.
I can't make out what you mean.
Genes bear no resemblance to other genes?
Systems bear no resemblance to genes?
Fold families bear no resemblance to genes?
Fold families bear no resemblance to systems?
quote:
That is the difference between micro/macro from a genomics POV whether one is creationist or evolutionist.
I'm not buying it. Can you cite something supporting this assertation?
Proteins and protein folds are ancient in many cases. 403: Access Method Forbidden - Alert: Error - Stanford University School of Medicine">www.hells-handmaiden.com
[This message has been edited by Admin, 07-02-2002]

This message is a reply to:
 Message 22 by Tranquility Base, posted 07-01-2002 1:56 AM Tranquility Base has replied

Replies to this message:
 Message 24 by Tranquility Base, posted 07-02-2002 9:17 PM John has replied

  
Tranquility Base
Inactive Member


Message 24 of 76 (12608)
07-02-2002 9:17 PM
Reply to: Message 23 by John
07-02-2002 1:29 PM


John
That's a nice lab web site. Very little on that page is relevant to how we go from one fold to another. The one line saying 'evoltuonary links' are found between folds could mean nothing more than some a hint of sequence similarity or that they fulfil corresponding roles in a otherwise homologous pathway. The issue of how one would go from fold A to B is not addresed at all. I am actively searching for literature on this and I'll check out some of his papers.
Darwin's Black Box has been opened. All evolution happens at the molecular level as I will now prove. Variation clearly happens at the molecular level via recombinaiton and mutations of one sort or another. Selection occurs at the organism level via surival to reproducability but what is it that is passed on? The gene of course. The only reason we have variation in populations is becasue of genetic variation. We shouldn't be overly reductionist but the idea that selection can't be understood at the moelcualr level is a mistake. If you have a big nose it is becasue you have a gene that is different to the typical gene in the population.
The link to the keele paper doesn't work for me. If there is an unmistakable sequence similarity then these proteins are almost definitely of the same fold.
The distinction I make is that it is easy to mutate a gene into a gene that codes for a protein with the same fold. It is not easy to do otherwise.
I didn't say that 'Systems bear no resemblance to genes'? It is clear that cellualr systems have associated unique gene families, in addition to paralogs!
My micro/macro differentiation is completely suported by this mainstream paper "Macroevotution is more than repeated rounds of microevolution". Microevoltuion is identified with allelic variation = same fold but with SNP(s):
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list _uids=11258393&dopt=Abstract
quote:
"These discontinuities impose a hierarchical structure to evolution and discredit any smooth extrapolation from allelic substitution to large-scale evolutionary patterns."
As we go from genome to genome, there are introductions of cellular novelities which correlate with novel gene families. That is indispuitable.
[This message has been edited by Tranquility Base, 07-02-2002]

This message is a reply to:
 Message 23 by John, posted 07-02-2002 1:29 PM John has replied

Replies to this message:
 Message 25 by John, posted 07-03-2002 11:26 AM Tranquility Base has replied
 Message 28 by Percy, posted 07-04-2002 6:09 PM Tranquility Base has replied

  
John
Inactive Member


Message 25 of 76 (12678)
07-03-2002 11:26 AM
Reply to: Message 24 by Tranquility Base
07-02-2002 9:17 PM


quote:
Originally posted by Tranquility Base:
Very little on that page is relevant to how we go from one fold to another.
I know that. The point was to suggest that you over-emphasize the protein folding. But I wonder if you pay attention....
quote:
Variation clearly happens at the molecular level via recombinaiton and mutations of one sort or another. Selection occurs at the organism level via surival to reproducability but what is it that is passed on? The gene of course. The only reason we have variation in populations is becasue of genetic variation. We shouldn't be overly reductionist but the idea that selection can't be understood at the moelcualr level is a mistake.
Thanks for the biology lesson. I missed that in high school, and of course, I was drunk and tripping all through college.
I'm getting the feeling that you are being reductionistic, or myopic with reguard to protein folding.
quote:
The distinction I make is that it is easy to mutate a gene into a gene that codes for a protein with the same fold. It is not easy to do otherwise.
Sure, but not impossible.
Minor Shuffle Makes Protein Fold
U. of Arizona
Boston U.
And this sometimes is all it takes.
quote:
I didn't say that 'Systems bear no resemblance to genes'? It is clear that cellualr systems have associated unique gene families, in addition to paralogs!
This was a question, TB. Calm down.
quote:
My micro/macro differentiation is completely suported by this mainstream paper "Macroevotution is more than repeated rounds of microevolution".
I can't tell what this paper concludes since I only have the abstract. I wish you wouldn't post links to things that require memberships.
But I can't find anything making a similar claim online, except for creationist sites.
If you can't trust Cecil.....
quote:
As we go from genome to genome, there are introductions of cellular novelities which correlate with novel gene families.
Big deal!
You need to link protein folding inexorably with speciation. This is your micro/macro diff, yes? If you can't do so, then what you are arguing collapses. Correct me, please, if I've got your argument wrong. From what I've read, this can't be done, or at least hasn't been done.
------------------
www.hells-handmaiden.com

This message is a reply to:
 Message 24 by Tranquility Base, posted 07-02-2002 9:17 PM Tranquility Base has replied

Replies to this message:
 Message 26 by Tranquility Base, posted 07-03-2002 11:12 PM John has replied

  
Tranquility Base
Inactive Member


Message 26 of 76 (12716)
07-03-2002 11:12 PM
Reply to: Message 25 by John
07-03-2002 11:26 AM


John
Protein fold evoltuion is virtually untouched in the literature becasue it is both a difficult problem and a prohibative barrier to macroevoltuion.
I read that Nat Struc Biol paper last month (I'm a structural biologist). The protein fold is actually the same fold by many researchers definition! All fold families have extra strands and helices that come and go between members. It is interesting work but utterly expected. If they can argue that the SCOP or CATH databases of folds can be arrived at by these means then that will be meaningful.
I don't have access to that particular jounral I linked to either but abstracts themselves are a valuable resource. It is clear from the abstract that this mainstream author argues that macro is not just lots of micro and that micro = allelic mutaitons whereas macro equals novel features. I'll order this paper today, I've been meaning to get around to it.
I don't link micro/macro to speciation per se - we believe in rapid speciation. It's organisms with genuinely novel genomes (eg with new gene families) and organs we don't believe ever occurred naturalistically.
[This message has been edited by Tranquility Base, 07-03-2002]

This message is a reply to:
 Message 25 by John, posted 07-03-2002 11:26 AM John has replied

Replies to this message:
 Message 27 by John, posted 07-04-2002 11:50 AM Tranquility Base has replied

  
John
Inactive Member


Message 27 of 76 (12756)
07-04-2002 11:50 AM
Reply to: Message 26 by Tranquility Base
07-03-2002 11:12 PM


quote:
Originally posted by Tranquility Base:
Protein fold evoltuion is virtually untouched in the literature becasue it is both a difficult problem and a prohibative barrier to macroevoltuion.
TB: This is just silly in light of what I have been able to find on the subject.
quote:
The protein fold is actually the same fold by many researchers definition!
Does this make sense to you?
quote:
I don't have access to that particular jounral I linked to either but abstracts themselves are a valuable resource.
You're joking!!!! Ever heard of, 'a little knowledge is a dangerous thing'? Abstracts may be useful for browsing, but not for constructing arguments.
quote:
It is clear from the abstract that this mainstream author argues that macro is not just lots of micro and that micro = allelic mutaitons whereas macro equals novel features.
Clear that that is what the author argues, but not how it is argued. The later is the important bit. I remember seeing something like this once before. It turned out to be nothing it claimed to be.
quote:
I don't link micro/macro to speciation per se - we believe in rapid speciation. It's organisms with genuinely novel genomes (eg with new gene families) and organs we don't believe ever occurred naturalistically.
Huh?
------------------
www.hells-handmaiden.com

This message is a reply to:
 Message 26 by Tranquility Base, posted 07-03-2002 11:12 PM Tranquility Base has replied

Replies to this message:
 Message 30 by Tranquility Base, posted 07-04-2002 9:19 PM John has replied

  
Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 28 of 76 (12779)
07-04-2002 6:09 PM
Reply to: Message 24 by Tranquility Base
07-02-2002 9:17 PM


Tranquility Base writes:

My micro/macro differentiation is completely suported by this mainstream paper "Macroevotution is more than repeated rounds of microevolution". Microevoltuion is identified with allelic variation = same fold but with SNP(s):
Abstract for Macroevolution is more than repeated rounds of microevolution

There's a couple problems with this claim. First, your conclusion seems to be drawn more from the paper's title, which states things in an unequivocal manner perhaps to draw attention, and the abstract, which states:
"Recent developments in comparative developmental biology suggest a need to reconsider the possibility that some macroevolutionary discontinuities may be associated with the origination of evolutionary innovation."
Second, there's nothing in the abstract that endorses equating allelic variation with same fold but with SNP(s).
Third, Doug Erwin is aware of various misuses of this particular paper. About one such instance he says, "While the article considers the relationship between micro - and macro- evolution, the Discovery Institute is inaccurate in saying that I am challenging the standard view of evolution. The treatment of macroevolution in that paper is an extension, but by no means a challenge. Further, although more work may be needed to fully understand macroevolutionary events, there is no evidence that requires, or even suggests, a role for so-called ‘intelligent design’. ( National Center for Science Education Article)
Other Erwin papers have also become targets for Creationist misuse. About one such case he says, ""Of course not [intelligent design] is a non sequitur, nothing but a fundamentally flawed attempt to promote creationism under a different guise. Nothing in this paper or any of my other work provides the slightest scintilla of support for 'intelligent design'. To argue that it does requires a deliberate and pernicious misreading of the papers."
Found another interesting quote from Dr. Erwin, this one about Creationist citations of the scientific literature in the field of comparative developmental biology: Citing a paper from 1994 is decidedly poor scholarship, however, given how fast this field has moved. The rapid advances in comparative developmental biology have rendered much of this pretty outdated. We now have a very well substantiated metazoan phylogeny, at least in general outline, allowing some of the tests suggested at the end of the cited passage. Moreover, comparative developmental studies have only served to emphasize the fundamental unity of bilaterian animals.
--Percy

This message is a reply to:
 Message 24 by Tranquility Base, posted 07-02-2002 9:17 PM Tranquility Base has replied

Replies to this message:
 Message 29 by Tranquility Base, posted 07-04-2002 9:07 PM Percy has replied

  
Tranquility Base
Inactive Member


Message 29 of 76 (12790)
07-04-2002 9:07 PM
Reply to: Message 28 by Percy
07-04-2002 6:09 PM


Percy
The gist of the abstract itself is that there is a discontinuity.
Allelic variation in every known case in the moelcualr medicine literature would be due to SNPs or a gross chromosomal rearrangement resulting in a missing or misfolded gene. Structural studies of misfolding demonstrate gross lack of globular structure and association into fibrils typically (Alzhemers, prions etc).
I'm not one bit surprised Erwin said what he did. But I look at the genomic data and see distinct creation. He and I are both interpreting the data! But it is very clear that 'macro is not just lots of micro'. Erwin beleives there is a naturalistic reason for this, we believe it is God. We are both potentially correct but it is bizaree to say that it is not an interesting paper for us.
Your attmepts to a priori pronounce everything we say as silly, naive, pseudo-science or misleading is doomed to utter failure. The devil is in the details but what we have to say is, at least a priori, very sensible.
[This message has been edited by Tranquility Base, 07-04-2002]

This message is a reply to:
 Message 28 by Percy, posted 07-04-2002 6:09 PM Percy has replied

Replies to this message:
 Message 31 by Percy, posted 07-04-2002 10:55 PM Tranquility Base has replied

  
Tranquility Base
Inactive Member


Message 30 of 76 (12791)
07-04-2002 9:19 PM
Reply to: Message 27 by John
07-04-2002 11:50 AM


John
Proportional to the size of the problem there is very little research on the origin of folds. I just came across 3 or 4 more papers yesterday - I'l post link to them if you like.
The two structures in that Nat Struc Biol paper wold normally be classified as the same fold. As I mentioned every fold is an idealised object and the members of the family will have extra/missing/modified segments.
I read hundreds of abstracts and only dozens of papers a month I'm afraid. I don't think that is unusual. A good abbstract should give one the gist of the result and it is clear in this instance although I'm as interested as you in getting this paper into my hands.
My statement about speciaiton is what I meant to say. We beleive in speciation! I don't believe God created hundreds of species of finch! But I do beleive he created horses and giraffes seperately. Very, very different.

This message is a reply to:
 Message 27 by John, posted 07-04-2002 11:50 AM John has replied

Replies to this message:
 Message 33 by John, posted 07-05-2002 12:26 AM Tranquility Base has replied

  
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