Teaching evolution in the context of science

Yes Jaako, even most scientists know very, very little about evolution. And they all equate the moths and finches as evidence that life on earth really could have evolved fom simpler forms.The most amazing thing is that most PhDed biologists also know almost nothing about macroevolution. In fact, the scientific literature has very little in it on genuinely macroevoltionary topics. I'm serious.The other point is that you of course are well read on the topic so your 10th grade class was too simplistic for you. It may not have been for the much of the rest of the class. But I agree that mainstream science rarely if ever gets to the crux of the matter and they never, ever point out that modern creationism is completely compatible with natural selection. Don't worry, just learn to live with it and take your opportunities when you can to correct these mistaken views.

Schraf, I work in a life sciences department (sorry Percy, but it's relevant to my pioint ) at a large mainstream Australian university. I know what I said is true. I lecture to 2nd and 3rd year students. I actaully teach evolution! (I qualify my statements with the phrase 'evoltuionary/taxonomic' relationships, I'm actaully very fair about it.) I know what our undergraduates are taught, I know what textbooks they read and I know what happens when they become graduate students (they specialise). The amount of macroevoltuion taught in uni courses/textbooks is near zero. It really is pepperred moths and finches. I am truly not kidding. I recently dropped in our uni bookshop and carefully went through a half dozen biology textbooks. Almost zero macroevoltuion evn in the non-Bible belt Australian texts.I would define genuinely macroevoltuionary topics as those that discuss the origin of genuinely novel features. This is best done at the molecular level where things are more unambiguous but there are very few well documented examples of the origin of novel anatomical features. The literature is almost empty of these discussions.I have searched in vain for a good discussion of the origin of protein families for example. I can not find it in Medline. I'm sure there are one or two but even if there are there are very, very few papers on this stuff. Behe points out that the 1000 papers published in the Journal of Molecualr Evoltuion over the last decade can be split into 3 catgories: (i) 5% mathematical, (ii) 15% chemical evoltuion and (iii) 80% sequence comparisons. In those 1000 papers he couldn't find a single paper which showed evidence or even simply proposed a step by step series of events whiich could have led to any molecualr system.The alternative of creation is dismissed with a single line in many biology texts without mentioning that it could be compatible with natural selection.

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[This message has been edited by Tranquility Base, 06-26-2002]

John99.5% (stat plucked out of the air) of PhDed biologists do not work on evoltuion John!I define macroevoltuion via studies on the origin of novelty and there is very, very little of this in the literature. I do not search for the word macroevoltuion (although when one does there are 61 hits in Medline - pretty amazing for a word that deosn't exist in the mainstream lit).Here's a paper which shows there is a clear micro/macro diff:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11258393&dopt=AbstractThe crux of the matter is the origin of novelty and evolutionists hardly address this issue. See Behe's study of 1000 papers in JME in my above post.

SchrafOf 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.Tell me about Doolittle's work on Blood clotting.I'm not faulting biologists for not having all the answers right away. But there are many systems which are almost completely understood at the molecualr level for a decade. Systems biology people are selling software that mimics many of the pathways of yeast! There are almost no papers attempting to explain the origin of tehse sytems. If you believe they will come, fine for you.Your question 'How do we tell the difference between an Intelligently Designed system and a natural system that we don't understand yet? ' is answerd by Behe via his elephant analogy which you wont like. He agrees that nothing is impossible but saying that biocehmistry is not designed is like a team of detectives studying the crushing murder of a man not noticing the elephant standing in the middle of the room. It is the creaitionist use of Occaam's razor.If life evovled it evovled novelty non-stop via an unkwon mechanism. If you want to call this a god of the gaps arguement then feel free but I'll continue to use Occaam's and Sherlock Holmes' style reasoning.Because you are so 'scientific' you feel that it is silly to examine the possibility that a religion explains the origin of life even in the midst of evidence of design. That seems quite fool hardy if you can let me say that as I would to a friend.I do not ask that the Judea-Christian religion be mentioned in the class room. I do personally feel that the data sceintifically justifies the discussion of the evidence for design of life and a rapid origin for the geological column. But I will not go and campaign for this.

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[This message has been edited by Tranquility Base, 06-27-2002]

JohnLots 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.

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[This message has been edited by Tranquility Base, 06-27-2002]

JohnYou 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.

ZhimboI'll have a close look at your examples.

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.

JohnThat'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:

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"These discontinuities impose a hierarchical structure to evolution and discredit any smooth extrapolation from allelic substitution to large-scale evolutionary patterns."

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As we go from genome to genome, there are introductions of cellular novelities which correlate with novel gene families. That is indispuitable.

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[This message has been edited by Tranquility Base, 07-02-2002]

JohnProtein 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.

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[This message has been edited by Tranquility Base, 07-03-2002]

PercyThe 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.

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[This message has been edited by Tranquility Base, 07-04-2002]

JohnProportional 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.

PercyI have ordered the Erwin paper and will carefully read it but you tell me exactly how I've misused it? I simply want to point out the distinctness of micro/macro and that's what both the abstract and it's title says.Erwin does use the term allele. Non-homologous genes have completely unique folds about 10% of the time, ie, thousands of genes have their own corresponding fold family. Whether Erwin knows it or not, what he is saying is essentially about protein fold families! We'll see when I get the paper.I stand by what I said in that post you cited - most of what we do is indistinguishable from what you would call science.

JohnI don't think mainstream evolution researchers would say that speciation had to be macroevoltuion. I think the Erwin ref supports my statement. Allelic variation can no doubt lead to speciation but Erwin wouldn't call that macroevoltuion.

PercyI quote Erwin from the abstract:

quote:

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"These discontinuities impose a hierarchical structure to evolution and discredit any smooth extrapolation from allelic substitution to large-scale evolutionary patterns."

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He says exactly the point I wanted to make. Allelic subsitution is microevolution. He is ultimately talking about the orign of new folds which are non-allelically derived.If you think an abstract entitled"Macroevolution is more than repeated rounds of microevoution"is irrelvant to our POV you are utterly deluded.PS - and an SNP is an allelic variation which is an allelic substitution. My use of these terms with reference to this abstract was entirely correct and it seems you are simply using a 'find' button. If you don't believe me about folds being non-allelically related then you go find another mainstream structural biologist and he/she will confirm it. I'm simply putting this abstract in the language of structural biology.

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[This message has been edited by Tranquility Base, 07-05-2002]