What I have noticed about these debates...

TB:
Demonstrate a non-allelic example of macroevolution.
M: You will have to be more specific...syncytin is one example, the RAG2 gene evolution is another. I will deal with your Hox gene fallacy below.[/qs]Care to give a one line sumamry of these examples?M: I'll do better, and will post more of the 100's of references I found on this subjecti.e.
Nucleic Acids Res 2002 Dec 1;30(23):5229-43 Related Articles, LinksDetection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily.Mazumder R, Iyer LM, Vasudevan S, Aravind L.National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.2',3' Cyclic nucleotide phosphodiesterases are enzymes that catalyze at least two distinct steps in the splicing of tRNA introns in eukaryotes. Recently, the biochemistry and structure of these enzymes, from yeast and the plant Arabidopsis thaliana, have been extensively studied. They were found to share a common active site, characterized by two conserved histidines, with the bacterial tRNA-ligating enzyme LigT and the vertebrate myelin-associated 2',3' phosphodiesterases. Using sensitive sequence profile analysis methods, we show that these enzymes define a large superfamily of predicted phosphoesterases with two conserved histidines (hence 2H phosphoesterase superfamily). We identify several new families of 2H phosphoesterases and present a complete evolutionary classification of this superfamily. We also carry out a structure- function analysis of these proteins and present evidence for diverse interactions for different families, within this superfamily, with RNA substrates and protein partners. In particular, we show that eukaryotes contain two ancient families of these proteins that might be involved in RNA processing, transcriptional co-activation and post-transcriptional gene silencing. Another eukaryotic family restricted to vertebrates and insects is combined with UBA and SH3 domains suggesting a role in signal transduction. We detect these phosphoesterase modules in polyproteins of certain retroviruses, rotaviruses and coronaviruses, where they could function in capping and processing of viral RNAs. Furthermore, we present evidence for multiple families of 2H phosphoesterases in bacteria, which might be involved in the processing of small molecules with the 2',3' cyclic phosphoester linkages. The evolutionary analysis suggests that the 2H domain emerged through a duplication of a simple structural unit containing a single catalytic histidine prior to the last common ancestor of all life forms. Initially, this domain appears to have been involved in RNA processing and it appears to have been recruited to perform various other functions in later stages of evolution.Here is anotherMol Biol Evol 2002 Dec;19(12):2118-30 Related Articles, LinksKRAB Zinc Finger Proteins: An Analysis of the Molecular Mechanisms Governing Their Increase in Numbers and Complexity During Evolution.Looman C, Abrink M, Mark C, Hellman L.The Department of Cell and Molecular Biology, Uppsala University. The Biomedical Center, Department of Veterinary Medical Chemistry, Swedish University of Agricultural Sciences. Medical Products Agency, Uppsala.Kruppel-related zinc finger proteins, with 564 members in the human genome, probably constitute the largest individual family of transcription factors in mammals. Approximately 30% of these proteins carry a potent repressor domain called the Kruppel associated box (KRAB). Depending on the structure of the KRAB domain, these proteins have been further divided into three subfamilies (A + B, A + b, and A only). In addition, some KRAB zinc finger proteins contain another conserved motif called SCAN. To study their molecular evolution, an extensive comparative analysis of a large panel of KRAB zinc finger genes was performed. The results show that both the KRAB A + b and the KRAB A subfamilies have their origin in a single member or a few closely related members of the KRAB A + B family. The KRAB A + B family is also the most prevalent among the KRAB zinc finger genes. Furthermore, we show that internal duplications of individual zinc finger motifs or blocks of several zinc finger motifs have occurred quite frequently within this gene family. However, zinc finger motifs are also frequently lost from the open reading frame, either by functional inactivation by point mutations or by the introduction of a stop codon. The introduction of a stop codon causes the exclusion of part of the zinc finger region from the coding region and the formation of graveyards of degenerate zinc finger motifs in the 3'-untranslated region of these genes. Earlier reports have shown that duplications of zinc finger genes commonly occur throughout evolution. We show that there is a relatively low degree of sequence conservation of the zinc finger motifs after these duplications. In many cases this may cause altered binding specificities of the transcription factors encoded by these genes. The repetitive nature of the zinc finger region and the structural flexibility within the zinc finger motif make these proteins highly adaptable. These factors may have been of major importance for their massive expansion in both number and complexity during metazoan evolution.Sycytin is a HERV-W envelope gene that causes syncitotrophoblast fusion critical in the formation of the placenta. It only does this in Old World Monkeys and the great apes as other primates do not contain this class of HERV. They also require syncitiotrophoblast fusion but it is carried out by an unrelated gene.For a description of RAG2 evolution..hereSchatz DG.
Transposition mediated by RAG1 and RAG2 and the evolution of the adaptive immune system.
Immunol Res. 1999;19(2-3):169-82. Review.Care to provide evidence that these are all wrong and that they just poofed banged into existence?TB:
Regardless of what crystal form is found, the eelctron density yields the same backbone fold for hemoglobin and it is differnt to that found for any other protein. NMR, a completely independent method finds eactly the same 3D structre from non-crystalized samples in solution.M: Funny, works that way for every life form ever studied to....molecular evidence, in many cases coroborating fossil evidence, biochemical evidence, behavioral all supporting evolution over poof bang individual independent creation of all organisms.TB:
What pop-genetisists do is very good science. But it is all allelic as you know. A genomics researcher does very good work too (I am one) but all it proves is that comparing any two genomes one finds reused genes and brand new taxa-specific genes. You can interperet that as macroevoltuion but the data is completely consistent with the creaiton of genomes followed by allelic plasticity and gene losses and duplicaitons.M: Pop gen and genomic demonstrates identity by descent..even your re-use mantra pre-supposes identity by descent. Thus, amphioxus and humans have hox genes due to a common ancestor i.e. we did not all just poof bang into existence. To show that would require that genes in different organisms were completely unrelated to each other i.e. not inherited traits.TB:
But you have simply assumed that these organisms have evolved! I don't believe those Hox genes evolved from each other. You have not shown that!M: Funny then that there are so many different species with hox genes and that hox genes (particularly in the promoters) vary and that the timing and level of expression varies among taxa....here is some lit on the topic:Larhammar D, Lundin LG, Hallbook F.
The Human Hox-bearing Chromosome Regions Did Arise by Block or Chromosome (or Even Genome) Duplications.
Genome Res. 2002 Dec;12(12):1910-20.Hinchliffe JR.
Developmental basis of limb evolution.
Int J Dev Biol. 2002;46(7):835-45.Mazet F, Shimeld SM.
The evolution of chordate neural segmentation.
Dev Biol. 2002 Nov 15;251(2):258-70.TB:
We have no probelm with horizontal transfer. But that does not mena that is how most funcitonal genes ended up in each organism.M: Um..how does this address my point? In any case, horizontal transfer is a very common event and is a rapid way of diseminating novel genetic information among distantly related taxa for example:Kondo N, Nikoh N, Ijichi N, Shimada M, Fukatsu T.
Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect.
Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14280-5.TB:
I'm sure you are aware that there are theories and theories.M: No, enlighten me.TB:
But all of your evidences are for allelic evolution. 99% of the human genome has appeared 'poof' from nowhere along your suppossed evolutionary tree. Simple bacteria only have about 100 gene families. The evidence very well supports the idea that funcitonal sub-networks of genes are conserved together. There is a logical reason for the reuse becasue they are parts of subsystems.M: Could you tabulate the 99% that has arisen poof out of nowhere please? Most is repetitive DNA where we know full well what the origins are i.e. LINEs, SINEs, HERVs, solo LTRs etc.TB:
What evidence can any of us provide but the genomes and today's processes? Together these support the idea of kinds that vary within allelic limits.M: Ignoring all the fossil evidence..or fossil DNA evidence for that matter, how does anything support allelic variation within a non-defined "kind"?TB:
Your idea that all of the gene families arose is the fairy tale Mammuthus. Our idea arises naturally, yours needs the shoe-horn.M: I will take my data supported "fairy tale" any day over a myth that is in direct contradiction to the physical evidence and science.TB:
We do plenty of 1-4, you just view the data with blinkers I'm afraid.M: Then kindly provide 1-4.
What is the testable hypothesis of creation? Just that would suffice TB. Which god created everything? Vishnu? Who created the creator? Lots of questions, no data, no testable hypothesis. And I am not wearing blinders. Again please supply:1) testable hypothesis
2) supporting data
3) predictions of this hypothesis
4) is the hypothesis falsifiable.Don't just wave it away as I am blind. You did not even attempt 1-4. That puts you arguemnt in the same camp as those who just claim everything they believe is self evident rather than actually supporting their assertions. I am asking you to do better.cheers,
M

Here is a new sequenced genome (tunicate) which does not suggest poof bang either. This paper should interest you. Read the commentary also by Pinisi in the same issue.Research ArticleThe Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate OriginsParamvir Dehal, Yutaka Satou, Robert K. Campbell, Jarrod Chapman, Bernard Degnan, Anthony De Tomaso, Brad Davidson, Anna Di Gregorio, Maarten Gelpke, David M. Goodstein, Naoe Harafuji, Kenneth E. M. Hastings, Isaac Ho, Kohji Hotta, Wayne Huang, Takeshi Kawashima, Patrick Lemaire, Diego Martinez, Ian A. Meinertzhagen, Simona Necula, Masaru Nonaka, Nik Putnam, Sam Rash, Hidetoshi Saiga, Masanobu Satake, Astrid Terry, Lixy Yamada, Hong-Gang Wang, Satoko Awazu, Kaoru Azumi, Jeffrey Boore, Margherita Branno, Stephen Chin-bow, Rosaria DeSantis, Sharon Doyle, Pilar Francino, David N. Keys, Shinobu Haga, Hiroko Hayashi, Kyosuke Hino, Kaoru S. Imai, Kazuo Inaba, Shungo Kano, Kenji Kobayashi, Mari Kobayashi, Byung-In Lee, Kazuhiro W. Makabe, Chitra Manohar, Giorgio Matassi, Monica Medina, Yasuaki Mochizuki, Steve Mount, Tomomi Morishita, Sachiko Miura, Akie Nakayama, Satoko Nishizaka, Hisayo Nomoto, Fumiko Ohta, Kazuko Oishi, Isidore Rigoutsos, Masako Sano, Akane Sasaki, Yasunori Sasakura, Eiichi Shoguchi, Tadasu Shin-i, Antoinetta Spagnuolo, Didier Stainier, Miho M. Suzuki, Olivier Tassy, Naohito Takatori, Miki Tokuoka, Kasumi Yagi, Fumiko Yoshizaki, Shuichi Wada, Cindy Zhang, P. Douglas Hyatt, Frank Larimer, Chris Detter, Norman Doggett, Tijana Glavina, Trevor Hawkins, Paul Richardson, Susan Lucas, Yuji Kohara, Michael Levine, Nori Satoh, and Daniel S. Rokhsar
Science Dec 13 2002: 2157-2167.

TB:
OK, let's look at these one at a time (I'm about to decorate our tree so I've only got a couple of minutes):M: Take your time...the threads are moving slowly these days.TB:
These proteins form a 'super family'. As such they share the same fold and the same chemical funciton. It wouldn't even surprise me for these proteins to have drifted away from a common anscestor if indeed (i) sufficent time had occurred or (ii) these organisms were related by evolution.M: That is a strange thing to say since immediately below you deny it.TB:
But you have simply assumed both (i) and (ii), not shown them. So your evidence is neither non-allelic (these could be heavily mutated alleles!) and only proves evolution if you already believe it.M: Not so. And this is why "proving" in science is not a valid concept. The data from this paper show an extremely well conserved functional domain that is part of a superfamily of proteins indicating that the family evolved from a common ancestor. The KRAB superfamily is the same concept. If you deny identity by descent you cannot believe in the concept of a protein superfamily. To be a "family" means that they have to show similarity by common ancestry.TB:
The data is perfectly compatible with separate creation.M: Then there should be no reason for KRAB memebers to show ANY sequence similarity. You could get the function multiple ways so why are KRAB proteins in one species more similar to KRAB proteins in the related species than in very distant relatives? Does not sound like INDEPENDENT creation.TB:
The distant 'profile similarity' (let me know if you want me to explain that bioinforamtics to you), even from an evolutionary point of view, could be physico-chemical (ie convergent or separately created) rather than divergent evolution.M: What a bunch of nonesense TB...so you god follows the rules of chemistry but then ditches the observable rules of transmission genetics? Your independent creation schtick is hardly parsimonious..it requires ignoring a huge amount of data to believe in.TB:
Two proteins with the same fold can have totoally different sequences but the same 'profile' and catalytic residues without being related by evolution. Go look up the definition of a superfamily to prove it to yourself.M: However, that is not what I posted..and neither are the KRAB family, HOX, HERVs etc.TB:
Mammuthus, unless I have missed something, this ref has zero relevance to proving that evolution is capable of generating gene types that are non-allelically related. It would help the discussion if you at least explained what you think its relevance is rather than simply pasting abstacts.M: I will point out TB, that you almost never post a single reference that supports you claim that I could read. I don't mean creationist literature. I mean, post a section of a genetics, genomics, zoological, or paleontological article or book that you think is a good example of creation and we can discuss it. As to my posting abstracts, I posted references that I felt dealt with the subject at hand. If you don't understand them or some part of them let me know. I thought the KRAB article and the tunicate genome sequencing article are pretty self explanatory.The phophodiesterase article was just to show that evolution works by exon shuffling, duplication, deletion, di-tri-tetra nucleotide expansion etc etc to generate novelty. Horizontal transfer is another mechanism. Syncytin was originally an envelope protein for a retrovirus...now it initiates syncytiotrophoblast fusion for Old World Monkey and Great Ape placental development. It is all consistent with the fact that in sexually reproducing animals you inherit you genes from your parents who inherited theirs from their parents all the way back to the common ancestor of all living things. Not a poof bang creation event at each step.Have fun decorating the tree. I myself will not be doing that this year as I will be travelling for a month leaving Xmas eve (and for all the lucky creationists, I will be offline cheers,
M

Hi TB:This is precisely where you do the jumping to conclusions. You simply have blinkers on. The data is equally conmpatible with God reusing a design.Correct. If I had my way I would call these protein supergroups or something lke that. Anything that categorizes could be either a 'family' or a 'group'. Semantics cannot help anyone here.M: So you do not believe that you pass on any genetic material to your offspring i.e. they are genetically no more related to you than to a housefly? That is what you have to accept in order for you to claim I have blinkers on and that the proteins are similar, can be grouped by related organisms, have conserved functions. You can change it to protein superman groups for all the difference it would make. There is no reason for there to be homology of systematic relevance if the proteins are not similar by descent.TB:
'Superfamily' is an evolutionary misnomer anyway. Members of a superfamily are not necessarily related via divergent evolution even by the evolutionary definiton of superfamily. The term 'family' here simply means 'group'.M: Why would you call it a group in any case if you don't believe the proteins are related? You are not being consistent.Why do you insist that God could not reuse designs just as a human engineer would?M: Then your god is a pathetically poor engineer? And what human engineer are you claiming built the genome? But you seem to indicate you accept the natural process as it is but then insert god as responsible without evidence. Those are the blinkers you are wearing.TB:
Could you explain what you're getting at here?M: You were stating that the rules of chemistry are inviolable and are followed for whatever reason by your god. But then against the rules governing inheritence and population genetics, you claim that there is no identity by descent but rather constant independent creation events that you have no evidence for. How is that a parsimonious or even a testable hypothesis? And why should god obey the rules of physics and chemistry but then ignore the observable rules of inheritence which is ultimately also chemistry?TB:
What's your point precisely? My point is simply that protein superfamilies have certain vauge 'profile' similarities that could be any of:(i) Convergent evolution
(ii) Divergent evolution
(iii) CreationM: Why 3? Convergent evolution (I am not sure what you mean by divergent evolution) but anyway, evolution predicts similarity by because of common ancestry. Why would creation? How would you test it? Created by who? If you answer that how do you know it was not created by something else? What created the creator?...TB:
I haveb't addressed your KRAB stuff. I'm talking it one abstract at a time and your first abstract was compeletley irrelevant. On the surface it kindo f sounds relevant, but in the end it has no relevance as I have explained.M: It did have relevance which I explained. However, handwaving away data that you do not like is hardly like you.TB:
Guess what, I agree! If genomes arrived by evoltuion then one mechanism is shuffling, duplication etc. But the evidence that exists only demonstrates allelic examples. No-one has shown where distinct protein families come from. All you guys ever whow is that if evoltuion aoccurred it must have had such and such features. We agree! What we point out is that your mistake is your initial assumption that macroevolution has occurred.M: Umm what exactly don't you get TB? If amphioxus has one hox cluster which developmentally restricts it to a very basic body plan and then you see Drosophila with a more complex body plan and more hox clusters and mammals with 4 hox clusters and yet more complicated body plans. The devo's have mapped out the transcription profiles particularly in drosophila for the significance in change in expression upon morphology even among fairly distant related species. How is this not macroevolution? If the duplicates, HERVs, shuffled exons are exclusive to a group and have some impact on the morphology, behavior etc on that group that makes it distinct, that is macroevolution. You are really not clear on what you want in terms of information. When you argued that bacteria have no evidence of hemoglobin I showed that they do and that it has a different function in bacteria. Hemoglobin evolution is macroevolution as well between bacteria and multicellular organisms.TB:
But that's simply your assumption. God could have inserted the gene in the genomes of all sorts of organisms of course as he could have for the entire proteomes. EDIT: see below, now that I have read the remainder of your post.M: We know the how and why HERVs transpose just like other proviruses. There have been direct observations as well as experimentall induced cases of retrotransposition. The HERV-W endogenous retroviruses are only known from Old World Monkeys and Great Apes from an infection of the last common ancestor of all. Given that we know how and why retrotranposons work, we know the systematics of primates and can perform tests of the relevant hypothesis involved, what compelling reason should I have for accepting your assertion that none of this occurred by the known natural mechanisms like other HERVs but is a case of "god did it"? I can test retrotranposition mechanisms..I can even find the most closesly related HERV envelope gene to syncytin (well I dont have to, it was alread published)...can you show any positive evidence that all of this entire field of inquiriy (which includes HIV research as it is a retrovirus to) is complete bullshit and that your god did it? Please provide some positive evidence for it.TB:
Yes it's consistent. It's also consistent with God creating kinds and then letting them go for it within allelic boundaries as one would expect from an engineering point of view.M: How so? Please detail how it is consisten with god creating kinds and what testable hypothesis there is that would support this view. Also list the kinds of experimental evidence you would gather for god creating kinds and the predictions you would make based on the testable hypothesis.cheers,
M

TB:
Much of this is again simply assumed.M: For example? What is assumed?TB:
On the other hand I agree that genes can duplicate and mutate. Some of the members of this family probably have their origin in duplicaiton. But they are all still transcription factors and the protein folds are still the same.M: I don't get you point. And didnt you just say in the last point that this was also consistent with your god individually creating each duplicate copy and in the process being so completely incompetent that he littered the genome with pseudogenes, recessive lethal mutations, etc etc.?TB:
I am quite prepared to agree with you that this sort of 'non-homologous replacement' as it is called has occurred in nature. It's clear that this is simply an example of horizontal transfer and that it does not explain how the gene itself arose.M: I dealt with that in the last post..HERV's are ancient proviruses..if you want to see a modern one look in the T cells of HIV infected patients and you will find modern versions of HERVs...if any of the HIV proviruses were to infect the germ line they would have a chance at becoming HERVs.TB:
Did it create a novel subsystem? No the system was working nicely.M: What are you talking about?TB:
Then the gene hoped into the genome from elswhere and was able to funciton in parallele with the existing gene yielding redundancy. Then one or other gene, in this case the one that had been arond longer, mutated and becomae non-funtional. I agree that that is what may have occurred in this case. But the funciton already pre-existed as did the non-homologous, but similarly functioning, genes.M: A completely unrelated gene took over a critical function in a specific group of organisms...and you don't consider this a radical difference? By the way, the envelope gene is not a similarly functioning gene...like hemoglobin in bacteria..it has drastically changed its function.TB:
So that is definitely non-allelic, I'll grant that. But it does not represent the origin of a new gene family or new subsytem. Both were pre-exisiting.M: I still get the impression you are looking for the first gene that ever existed i.e. abiogenesis...but in your debates you constantly shift your creation myth in time to it happened in the primate lineage..it happened after bacteria..it happened whenever it is convenient to the arguement. When exactly do YOU think the creation event occurred and what is your evidence for it? Since you on and off accept macroevolution, in some twisted way accept a very odd version of evolution within groups, it is not clear what your position is.I would like to point out one last thing...we are in amolecular evolution debate and this is the Faith and Belief thread..I have the distinct feeling that we are way off topic for this thread and should perhaps consider moving the entire topic over to the Evolution or Origin of Life thread...what say you Adminaquility ? I would guess we are boring the crap out of the people who are reading this for he "what I have noticed about these debates..."cheers,
M

TB
"There's nothing wrong with your POV except that it is only one interpretation, hence the blinkers."Question again, do you or do you not accept the proven facts of transmission genetics? If not, what is you counter evidence to the last 100 years of genetics research."If God created the genomes the sequence homology could be presnet due to creative reuse. And superfamily simlarity is not necessarily at the sequence level (see next)."Why? Why does god have to do anything? I thought this was the supreme being..but here he is limited to "creative reuse". What is the evidence for this?M: "Why would you call it a group in any case if you don't believe the proteins are related? You are not being consistent.[/qs]"TB:
The proteins are related by 3D structure, that's why they have the same seqweunce profile. A superfmaly is a structural family that does not need to be related deivergenetly. Trust me on this one will you. It's a mainstream definition! I teach it in my lectures."M: I don't doubt that you believe and don't doubt you teach it that way but this is not my question. Why if each and every protein is an independent creation of your god, should there be any similartiy between them? Especially like the KRAB family a phylogenetic signal? It only makes sense if they share a common ancestor."Nature does obey the rules of genetics. But if God created kinds the rules of genetics have been only in action since the gneomes were created. You see tantalizing evidence of common descent in the homologous genes but it never bnothers you that tens of thousands of new unrealted genes have appeared since the simplest bacteria."M: Now nature obeys the rules of genetics but a minute ago you basically denied transmission genetics??? Anyway, what are the tens of thousands of unrelated genes between humans and chimps? Or humans and gorillas ? Anyway, as with hemoglobin in bacteria, why should I be troubled by the development of new genes as organisms adapt to new environments or new resources become available? And I have yet to see tens of thousands of new genes that are unrelated to anything. You also make a false assumption about bacteria and that is that you imply they are the same now as they were billions of years ago...that is not true. Bacteria have also evolved and may share very little similarity with their distant ancestors. Look up any bacterial evolution paper and you will see how quickly and dramatically they can change genomically over short periods of time."All you are doing is putting a slant on reuse. I am putting the other slant on it. Over time one or other of our viewpoints may be ruled out or become hard to justify (as future genomes turn up). Currently both are compatible with the data."M: That assumes there are only two possible views on the subject which is not clear. And my slant follows from observations, experiments, and a testable hypothesis and your slant ignores all of these scientific criteria."Divergent evoltuion is evolution that leaves undoubted signatures of common descent. For us it is simply reuse of a gene. As you probably know, convergent evolution is a stumbling upon a similar feature without evidence of common descent (for that feature). For us it is resuse of a protein fold without the sme sequence."M: You might want to use more mainstream terms than divergent evolution. Divergent does not imply "undoubted signatures of common descent". And you are also mis-defining convergent evolution. A birds wing and a bats wing are convergent evolution. Or most of the physical characteristics of the Tasmanian wolf and eutherian canids are convergent evolution..not just protein folds as you state.
Since you are saying all similar sequences are re-use of genes, do you believe you passed on genes to your children? Or were they magically created and have nothing to with you but are genetically more similar to you than to any other male on the planet because of god re-using genes? This is starting to sound like Peter Borger's multipurpose genome ga ga."I get all of that. What you keep forgeting is that in additon to the generation of new paralogs new taxa systematically discover new protein families and systems that did not exist before."M: Except that they exist in all the relatives of the taxa or exceptions such as syncytin where it is known what happened, or inactivation of genes like several differences between humans and chimps etc....this is not a problem for genetics or evolution."I have no problem with horizontal transfer as I have said on many occasions. It does not account fo the origin of any gene family."M: Why not? And actually, HERVs and transposons do account for gene family evolution. They are a great mechanism for causing duplications of chromosomal regions and genes...and in most high copy number regions of the genome..you find retrotransposons i.e. HLA, globin cluster, etc etc.M: How so? Please detail how it is consisten with god creating kinds and what testable hypothesis there is that would support this view. Also list the kinds of experimental evidence you would gather for god creating kinds and the predictions you would make based on the testable hypothesis.[/qs]"The genomes are undoubtedly consistent wiht God creating x thousand gneomes and letting them evolve since then via all the mechanisms of plasticity that you believe in. God created fully working genomes that have evolved allelically and via horizontal transfer and via gene loss. It is perfectly conpatibel with thegenome projects. You just don't like it. You insist on reading the reuse as common descent over time. It could simply be reuse by God."M: If it were undoubtedly consistent then why do most scientists and a large number of non-scientists doubt it? Anyway, what is your evidence for god creating x genomes? If it is undboutebly consistent you should be able to provide the evidence that it was created and not due to natural processes. Your claim that I just don't like it is false. I see no evidence for it. You are claiming in this last paragraph that everything about genetics and evolution I said is correct but then that there is no such thing as common descent (so I guess I can never have kids) and that you have to insert a creator of each genome for which you have no evidence. I could do the same and claim that a big blue monkey with a banana in its nose and a bottle of gin in its hand created the genomes...what is your evidence that your god did it and not my monkey?"Experiments? The data comes from the genome projects. If the idea of kinds is true we should be able to catalog life into kinds from genomes. The members of each kind will be distinguished by allelic differences and relative losses. Kinds will be differentiable by relative gene family and paralog gains. Because gene losses vs gains aren't always distinguishable it may not always be possible to identify kinds in this way. Hence it may be difficult to objectively distinguish between the creation and evolution models, as we are finding, becasue the actions of history are not always carefully recoded for us in the genomes."M: Funny, then I see no reason to use a blanket term like "kind" when species, genus, family, order etc. are far more descriptive. How does a gene loss versus gains in any way make it difficult to distinguish evolution and creation? What evidence for creation is there in a HERV deletion or a partial deletion of a HERV in the salivary amylase cluster?

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I plan to read Charles Darwin's book for the express purpose of being able to know everything evolutionists think.

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Everything we think? You will be over 150 years behind the times...

deleted duplicated post[This message has been edited by Mammuthus, 08-26-2003]

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And evolution isn't about thinking at all, but agreeing. If it were
about thinking----creationism would not be considered a threat by the
ACLU...

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Says a guy who does not even know what the theory of evolution is much less spends time thinking about composing his own posts much less thinking about anything at all...but I am happy to know I don't have to think when I plan experiments and run projects...man, I must be smarter than I thought if I can do all this science without thinking

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ALL traces of DNA will disappear under adverse conditions or within
8 THOUSAND years (whatever comes 1st).

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Figures...he gives his first hard number to try to support his claim and it is wrong...Mol Biol Evol. 1999 Nov;16(11):1466-73. Related Articles, LinksNuclear DNA sequences from late Pleistocene megafauna.Greenwood AD, Capelli C, Possnert G, Paabo S.Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany. alexgr@amnh.org.We report the retrieval and characterization of multi- and single-copy nuclear DNA sequences from Alaskan and Siberian mammoths (Mammuthus primigenius). In addition, a nuclear copy of a mitochondrial gene was recovered. Furthermore, a 13,000-year-old ground sloth and a 33,000-year-old cave bear yielded multicopy nuclear DNA sequences. Thus, multicopy and single-copy genes can be analyzed from Pleistocene faunal remains. The results also show that under some circumstances, nucleotide sequence differences between alleles found within one individual can be distinguished from DNA sequence variation caused by postmortem DNA damage. The nuclear sequences retrieved from the mammoths suggest that mammoths were more similar to Asian elephants than to African elephants.Mol Ecol. 2002 May;11(5):913-24. Related Articles, LinksMolecular analysis of an 11,700-year-old rodent midden from the Atacama Desert, Chile.Kuch M, Rohland N, Betancourt JL, Latorre C, Steppan S, Poinar HN.Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22 04103 Leipzig, Germany.DNA was extracted from an 11,700-year-old rodent midden from the Atacama Desert, Chile and the chloroplast and animal mitochondrial DNA (mtDNA) gene sequences were analysed to investigate the floral environment surrounding the midden, and the identity of the midden agent. The plant sequences, together with the macroscopic identifications, suggest the presence of 13 plant families and three orders that no longer exist today at the midden locality, and thus point to a much more diverse and humid climate 11,700 years ago. The mtDNA sequences suggest the presence of at least four different vertebrates, which have been putatively identified as a camelid (vicuna), two rodents (Phyllotis and Abrocoma), and a cardinal bird (Passeriformes). To identify the midden agent, DNA was extracted from pooled faecal pellets, three small overlapping fragments of the mitochondrial cytochrome b gene were amplified and multiple clones were sequenced. These results were analysed along with complete cytochrome b sequences for several modern Phyllotis species to place the midden sequence phylogenetically. The results identified the midden agent as belonging to an ancestral P. limatus. Today, P. limatus is not found at the midden locality but it can be found 100 km to the north, indicating at least a small range shift. The more extensive sampling of modern Phyllotis reinforces the suggestion that P. limatus is recently derived from a peripheral isolate.Mol Phylogenet Evol. 2003 Sep;28(3):485-99. Related Articles, LinksAncient DNA analysis reveals woolly rhino evolutionary relationships.Orlando L, Leonard JA, Thenot A, Laudet V, Guerin C, Hanni C.CNRS UMR 5534, Centre de Genetique Moleculaire et Cellulaire, Universite Claude Bernard Lyon 1, 16 rue R. Dubois, Batiment G. Mendel, 69622, Villeurbanne Cedex, FranceWith ancient DNA technology, DNA sequences have been added to the list of characters available to infer the phyletic position of extinct species in evolutionary trees. We have sequenced the entire 12S rRNA and partial cytochrome b (cyt b) genes of one 60-70,000-year-old sample, and partial 12S rRNA and cyt b sequences of two 40-45,000-year-old samples of the extinct woolly rhinoceros (Coelodonta antiquitatis). Based on these two mitochondrial markers, phylogenetic analyses show that C. antiquitatis is most closely related to one of the three extant Asian rhinoceros species, Dicerorhinus sumatrensis. Calculations based on a molecular clock suggest that the lineage leading to C. antiquitatis and D. sumatrensis diverged in the Oligocene, 21-26 MYA. Both results agree with morphological models deduced from palaeontological data. Nuclear inserts of mitochondrial DNA were identified in the ancient specimens. These data should encourage the use of nuclear DNA in future ancient DNA studies. It also further establishes that the degraded nature of ancient DNA does not completely protect ancient DNA studies based on mitochondrial data from the problems associated with nuclear inserts.to name a few studies...

Sorry Percy....I will desist...but could you define replying in "kind"? what is a kind?

quote:

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I'm not impressed with
most of what evolutionists THINK they know. It is what they
want everyone else to accept is what bothers me.

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Hi AC,
I am not surprised that you are unimpressed. You have even indicated that you basically do not understand science at all so it is a trivial matter for you to dismiss the ACTUAL research on which scientific theories are based.You claimed it will take years of scientific work to prove creationism...how about giving it a start...1. propose a testable hypothesis of creation
2. demonstrate how it is falsifiable
3. indicate the supporting evidence
4. show how it better explains the accumulated data than the ToEIf you cannot do this then creationism will never be science...

quote:

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I enjoy the
way evolutionist belittle those that disagree with them. Don't
you know that only make you look vular and cheap.

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I enjoy when those who admit they do not know much about a subject equate their opinions with scientific theory and then get upset when scientists don't roll over and accept what they say...it those who make the assertions look ignorant and arrogant.

Ok..just scrolled back and saw that AC got himself suspended...so in case he does not come back...can any like minded individual please present or at least summarize the "data" presented during the James Kennedy program?

Thanks Macavity,AC was claiming that the data that supposedly refutes evolution is contained in this lecture...I will take a look at the program later though it will probably give me a headache.
cheers,
M