Kinds and diversification through microevolution and hybridization

Continuation of KINDS discussion from other thread (http://EvC Forum: My overall view from this boards. -->EvC Forum: My overall view from this boards.).Mammuthus1) Why kinds if families = kinds? Becasue kinds may not exactly be families. Why should they? Science is full of definitions that come from multiple angles and end up converged but different to both starting points. Genomics and microevolution has and will modify creationist conceptions of kinds. I personally doubt that sheep and cows are the same kinds but I could imagine that sheep and goats are. Are you saying that sheep and cows are in the same Linnean family? If that's the case that's one reason why creationiost say the kind is approximately at the family level. As you know, completely independently of my creationist interest, I am suggesting the redefinition of taxonomy using genomics. I am not alone on that.2) Mutations in promotor regions lead to macro. If that really is the case I believe in macroevoltuion. You tell me the pair of organisms where that is known? My point is that macroevoltuion requires new gene families becasue we can see them in the genomes!! I do not deny that point mutations also distinguish genomes. But that is the part we agree with! We are just saying that the changes that we think only God could do are the new protein families. I can agree with you that nature could switch on/off existing genes using promoter mutations. Note the Varki paper title - mutation generated the loss of the N-glycolylneuraminic acid pathway. Do you really think that is the only difference between man and apes? Most estimates suspect multiple new protein famiiles which is not discovered through the '98% similar' experiments. We'll see when the Pan genome comes in.3) BLAST? The good hits are proteins in the same families!4) Introns? I believe that introns were in us from day one of course. They serve a purpose as gene partioning for multiple splicing.5) Retroviruses? I can 100% agree we are gentically polluted and that the genome is extremely plastic.6) Finches? The finch issue is no differnt than any organism. We believe the genomes will be distinct at some level we call kinds. It is exactly the same issue as caused Gould to initiate PE. We just come from differnt angles.7) Broccoli, mustard etc genomically the same? They are the same but have differnet alleles. Just like dogs or humans. So genotypes do dictate phenotype to a 99.99% type level. Tell me about genomic imprinting? Is that the methylation issue? Yes I agree with epigentics but 99.99% of the story comes from genotype. I am interested in epigenetics, don't get me wrong.8) Molecular evoltuion? I am coming at it from a protein family/struc biol angle. This has less noise in it than just looking at sequences. This will/already is adding something to mol-evol. Comparative genomics already does look at presence/absence of protein families and that is the type of work I am doing on it. I read old mol-evol stuff, yes, but I'm not going to sit there pronouncing things about evolution from lists of homologous sequences! We have full genomes and can know look at the coming and going of new protein families - that is far, far more exciting whether one is a creationist or an evolutionist. There is no creaitonist agenda in this approach - it is basically the state of the art of mol-evol.9) Thin air? The data says that the genes 'came out of thin air' whether that is evoltuion from random or creation by God. The data does not particularly support your theory. You just have a religious dislike for our interpretaiton.[This message has been edited by Tranquility Base, 09-12-2002]

Hi TB
Thanks for starting the new thread.Mammuthus1) Why kinds if families = kinds? Becasue kinds may not exactly be families. Why should they? Science is full of definitions that come from multiple angles and end up converged but different to both starting points. Genomics and microevolution has and will modify creationist conceptions of kinds. I personally doubt that sheep and cows are the same kinds but I could imagine that sheep and goats are. Are you saying that sheep and cows are in the same Linnean family? If that's the case that's one reason why creationiost say the kind is approximately at the family level. As you know, completely independently of my creationist interest, I am suggesting the redefinition of taxonomy using genomics. I am not alone on that."Why kinds if families = kinds? Becasue kinds may not exactly be families. Why should they? Science is full of definitions that come from multiple angles and end up converged but different to both starting points." But science is not full of frivilous definitions that provide no information. What if a few people decided to call DNA...slimy stuff...that provides about as much information as "kinds".You personally doubt sheep and cows are the same "kinds"? That does not matter as they are both in the same Order and both are artiodactyls...plenty of morpho and molecular evidence to support it...since you cannot even define a "kind" then I could say the stuff in belly button lint and a tree are the same kind.So far genomics has not contradicted phylogenetics but has been answering questions that were inaccessible via morphology alone. And Linnean taxonomy has been undergoing revision since...well since Linneaus.....2) Mutations in promotor regions lead to macro. If that really is the case I believe in macroevoltuion. You tell me the pair of organisms where that is known? My point is that macroevoltuion requires new gene families becasue we can see them in the genomes!! I do not deny that point mutations also distinguish genomes. But that is the part we agree with! We are just saying that the changes that we think only God could do are the new protein families. I can agree with you that nature could switch on/off existing genes using promoter mutations. Note the Varki paper title - mutation generated the loss of the N-glycolylneuraminic acid pathway. Do you really think that is the only difference between man and apes? Most estimates suspect multiple new protein famiiles which is not discovered through the '98% similar' experiments. We'll see when the Pan genome comes in.Did you bother to read the Enard paper?
"My point is that macroevoltuion requires new gene families becasue we can see them in the genomes!!" What the hell kind of logic is this...do you see what nonesense this sentence is?"We are just saying that the changes that we think only God could do are the new protein families. " Nope, "we" don not think only god could do this...you do...there is no evidence for god."Do you really think that is the only difference between man and apes?"
Where did I say that this is the only difference? I was giving you a specific example and a reference....both of which are things you have never done for me regarding any points you have made."Most estimates suspect multiple new protein famiiles which is not discovered through the '98% similar' experiments. We'll see when the Pan genome comes in." Please povide a citation for these estimates. Nobody has proposed that chimps have less "protein families" than humans. And I gave you an example where humans have one less than chimps.By the way...why do you call them protein families and not "protein kinds"...that would be more consistent with your personal lexicon.3) BLAST? The good hits are proteins in the same families!If I search the complete human genome with a human sequence why would I not get a human sequence? If I search with an Alu element I will get millions of hits...what's the point?4) Introns? I believe that introns were in us from day one of course. They serve a purpose as gene partioning for multiple splicing.Aha...then provide evidence that they are all in the same place in closely related species! If not, they were not in us from day one (whatever that is). Pubmed search intron early intron late theories and you will see that introns have been moving around a lot.5) Retroviruses? I can 100% agree we are gentically polluted and that the genome is extremely plastic.But that does not fit with your increasing complexity argument.6) Finches? The finch issue is no differnt than any organism. We believe the genomes will be distinct at some level we call kinds. It is exactly the same issue as caused Gould to initiate PE. We just come from differnt angles.Actually, Niles Eldredge came up with the idea and co-authored it with SJ Gould. No mention in the theory about genomes so please elaborate how you connect finches, PE, and genomes?7) Broccoli, mustard etc genomically the same? They are the same but have differnet alleles. Just like dogs or humans. So genotypes do dictate phenotype to a 99.99% type level. Tell me about genomic imprinting? Is that the methylation issue? Yes I agree with epigentics but 99.99% of the story comes from genotype. I am interested in epigenetics, don't get me wrong.Where did you get 99.99%? Please cite a specific reference or show the data. Since you called it the "methylation issue" it shows you don't know the subject in detail yet make the pronouncment that it has little influence on "the story". Not to single you out specifically but this is a common creationist problem and is one reason of many that they have no credibility.Epigenetics has to do with methylation in part and with acetylation of histones as well i.e. dosage compensation of the X chromosome in females in mammals.8) Molecular evoltuion? I am coming at it from a protein family/struc biol angle. This has less noise in it than just looking at sequences. This will/already is adding something to mol-evol. Comparative genomics already does look at presence/absence of protein families and that is the type of work I am doing on it. I read old mol-evol stuff, yes, but I'm not going to sit there pronouncing things about evolution from lists of homologous sequences! We have full genomes and can know look at the coming and going of new protein families - that is far, far more exciting whether one is a creationist or an evolutionist. There is no creaitonist agenda in this approach - it is basically the state of the art of mol-evol."Molecular evoltuion? I am coming at it from a protein family/struc biol angle. This has less noise in it than just looking at sequences."Please provide supporting evidence that protein family (why not kinds again?) has less noise than looking at sequences? Protein phylogenies have all the same noise as DNA based...or morphology for that matter."I read old mol-evol stuff, yes, but I'm not going to sit there pronouncing things about evolution from lists of homologous sequences!
How about reading some new mol evol stuff? Your post suggests you do not have a firm grasp of the fundamentals and just saying you refuse to learn something because you a priori don't believe it is no way to do science."it is basically the state of the art of mol-evol."
As you claim to refuse to learn about molecular evolution..how do you know what the state of the art is?9) Thin air? The data says that the genes 'came out of thin air' whether that is evoltuion from random or creation by God. The data does not particularly support your theory. You just have a religious dislike for our interpretaiton.The theory of evolution does not state that genes came out of thin air. Only creationism proposes this...or are you confused with abiogenesis and evolution?I have no religion...and that makes me a minority among scientists. Most of my colleagues are christian, jewish, hindu, or buddhist. Only a couple are atheists. That you assume otherwise is your fundie dislike of anybody who does not subscribe to your worldview.cheers,
Mammuthus[This message has been edited by Tranquility Base, 09-12-2002][/B][/QUOTE]

Yes, I like the new thread, too.Please go here, TB:http://www2.norwich.edu/spage/alignmentgam.htmand, using this objective data, tell us how we are to determine where 'microevolution within kinds' ends.Thanks.Oh - also, some evidence that introns were created by God, as per the other thread.Thanks.

Hi TB: I agree with my colleagues here that starting a new "kinds" thread was a great idea.

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Originally posted by TB:

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There are creationists who have been thinking about this - see their barimin stuff. But I prefer the genomics angle and when we've got more genomes we'll have a better idea.

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I have read some of the baramin stuff. It appears very loooong on sheer out-of-thin-air speculation and really really short (microscopic ) on actual data. Perhaps you might point me to a reference you feel provides compelling evidence that any of the so-called baraminologists have the first clue what they're talking about?

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What gene families distinguish? To a large extent I'm saying any gene families will. But if you have two identical genomes apart from one gene family it is certainly possible that the 'new' gene is one that became a pseudo-gene in the other so that should be considered. So I would suggest studying large numbers of genomes and see if there is an abrupt jump where suddenly a whole swag of genes comes in. If this occurs across life we would identify that with kinds. The data does approximately fit this scenario already but we need more genomes to really see.

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So you're saying (if I understand you) that each kind will have a completely unique genome? That no genes from the same family will be shared across kinds? I think you just shot yourself in the foot. No one doubts there are genetic differences between organisms - the more distantly related, the more differences appear. However, this doesn't translate to novel protein families. Unless you can show which ones actually delimit organisms (good luck), you have no argument.There's a lot of mainstream interest in this subject. The Promise of Comparative Genomics in Mammals. And another, Phylogenetic Origin of Human Chromosomes 7, 16, and 19 and their Homologs in Placental Mammals, which although dealing with chromosome homologs, talks quite a bit about the evolutionary development and divergeance of various proteins.

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I do plan (in my own mainstream research) to get into the sorts of questions you have asked (eg cat vs dog families). But, as you know, we only have two mammalian genomes and the other genomes we have are very differnet. But I am interested in catching up on the comaprative genomics of fly vs. mosquito for example.

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We may not have the complete genomes of many animals yet, but there is nothing indicated to date in those parts of the genomes that HAVE been sequenced that show the existence of whole unique families rather than individual genes.

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I agree this needs to go beyond hand waving. But at this point it is without doubt that there are core genomes, there are sub-genomes for each novelty (like the immune system) and these sub-genomes are characterizable by unique protein families. That is undeniable. I have started a new project in this area and I will report here even before I publish, OK!

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Sure - if all you're saying is that data at some unspecified point "in the future" may lend some evidence to your contention about protein families, that's fine. However, the problem has been here that you continually assert the existence of these families as one of your key arguments against so-called macroevolution. The truth is that nothing in any comparative genomics study to date shows even the inkling that there might be protein families that are unique to even taxonomic classes, let alone family or genus.Could there be? Of course. Is there ANYTHING ANYWHERE in the literature that even hints at it to date? Nope. IOW, you're using a pure "god-of-the-gaps" argument. Here's the catch: until and unless such data is produced, you cannot use the hypothetical existence as proof that your putative kinds exist. It's pure 18th Century taxic discontinuity - which is no more scientifically valid today than it was 200+ years ago.

MammuthusI'l respond point by point when I've got time but for now . . .I have defined kinds genomically - they are organisms with genomes characterised by distinct new sets of protein families. They are distinct clusters of protein famiiles - not distinct from all of life but life lower in the tree than themselves.You see, we agree with the standard tree of life as a way of organising life. The biochemsitry of life is made up of sub-systems. Simpler organisms have fewer of these sub-systems. You interperet this as common descent, we interperet it as the engineering of God.That is the key point in the whole homology arguement. We agree with the homologies! We agree that we are more like moneys. We agree that mammals are more related to reptiles than fish. But that is only an arguement against creation if you don't allow God to build organisms using common sub-systems.

Mammuthus - here's my point by point response:1) Defn of kind (See my first post today)
+ Pointless definitions? Our definition of kinds as being distinguishable from simpler kinds by unique clusters of genes is a completely sensible testable definition.2) Mutations and macroevolution.
I said that "My point is that macroevoltuion requires new gene families becasue we can see them in the genomes!!" and you call it nonsense. It makes complete sense. Macroevoltuion brings in genuinely new genes! You can pussy-foot around with mutations evident from alignements of homologous genes. I am taking you to the hard ask. I could define you as a different species from me on the basis of SNPs too but that would be ridiculous. It is many evoltuiuonists that misunderstand the differnece between mutaitons leading to variation vs novel protein families.I have seen a ref (and posted it here) that people expect novel protein families in humans. We expect it becasue we ahve always got it before. We have about 300 (?) novel proteins compared to mice I beleive.I use the term protien families becasue the mainstream term fits exactly with what I want to say.3) BLAST and human hits.
The point isn't that you get human hits to your query sequence it's that you get hits which have almost identical sequence. These clusters of genes are called protein families. There is nothing controversial here. The point is that one can't use this to work out where the first hemoglobin came from.4) Introns?
I have no problems with individual introns coming and going. I have no problem with any of the mechanisms of evolution!! I am simply making the point that these mechanisms have not been proven to lead to the evoltuion of anything genuinely new. You guys have simply assumed that the known plasticity of genomes etc can lead to the evoltuion of a heart from a system that didn't have one. You assume it simply becasue you see organims with increasingly complicated hearts. It is all one big assumption. We don't actually dispute your data one bit.5) Retroviruses argue against increased complexity?
Who says that life is now getting more complex? We beleive it is in a state of decay!6) Finches & PE? Every single anatomical paleotologist knows that ultimately things happen at the genomic level. The Gould/Dawkins arguements were not debating this. I am simply saying that genomic clustering into distinct groups would generate anatomical clusterings.7) Epigenetics
I am a genuine fan of epigentics. I just dpon't like peiople going overboard on it. A simple look at twins (sperated at birth if you require) shows intuitively that 99.99% of development is primarily genetic. I need no further proof than intuition here.I'd love to hear about the dosage compensation if you can do it in a non-condesecnding way. I can imagine it accounts for the fact that women have two Xs corrected for by epigenetic processes? All fascinating but what relevance does it have to C vs E?8) Struc Biol/novel families in molecular evoltuion?
Struc Biol and concentrating on clearly defined families has less noise for one basic reason: protein folds in 3D are more conserved than sequences. I agree at the plain seq alignemnt level protein is not much diff than DNA.Fundamentally why does comparative genomics concentrate on presence/absence of genes and not homolgous sequence aligenments? Becasue the former is far more interesting and enlightening!The researcher who says that humans have 15 base changes in hemoglobin relative to rat is going to end up in FEBS Lett. The researcher that shows that man has four brain proteins that rats don't have at all will end up in Nature. It is as simple as that. The gneomic era has made molecualr evolution a far more robust field.9) Thin air?
The data, not any theory, says that the genes 'came out of thin air'.[This message has been edited by Tranquility Base, 09-15-2002]

SLPxIn general:We believe that seqeunces were created (in each kind) and have since drifted by microevoltuion. Almost any sequence alignment will have clusters of more closely realted sequences and we could identify those as kinds perhpas. But, now that we have genomes, it is far more enlightening to identify kinds based on presence/absence of protein families! There is much less noise in doing this.There is no agenda here, it is simply a matter of what is easier to reconstruct. If there are underlying kinds then genomes are far more informative than homologous sequences.Your sequecne alignment?Why don't you first tell us what organisms these sequences are from? I seem to recall they are primate seqeunces(?). We aren't all primate experts - especially biophysicists.[This message has been edited by Tranquility Base, 09-16-2002]

Thanks for the response TB,
I will also go point by point.1) Defn of kind (See my first post today)
+ Pointless definitions? Our definition of kinds as being distinguishable from simpler kinds by unique clusters of genes is a completely sensible testable definition.Here is an example of why it is not so useful. Mus musculus domesticus is a separate species from Mus spretus (a european wild strain often used in mouse genetics). They can interbreed and produce F1 hybrids but the males are sterile. You would lump both into mouse kinds. I call them species. Rats share more genetic and morphological similarties with mice than they do with dogs. Carnivores share more in common with one another than they do with ungulates. The Linnean system and taxonomy were not frivilous efforts at classification of organisms. Kinds does not provide me with any information.2) Mutations and macroevolution.
I said that "My point is that macroevoltuion requires new gene families becasue we can see them in the genomes!!" and you call it nonsense. It makes complete sense. Macroevoltuion brings in genuinely new genes! You can pussy-foot around with mutations evident from alignements of homologous genes. I am taking you to the hard ask. I could define you as a different species from me on the basis of SNPs too but that would be ridiculous. It is many evoltuiuonists that misunderstand the differnece between mutaitons leading to variation vs novel protein families.I have seen a ref (and posted it here) that people expect novel protein families in humans. We expect it becasue we ahve always got it before. We have about 300 (?) novel proteins compared to mice I beleive.I use the term protien families becasue the mainstream term fits exactly with what I want to say.However, changes in gene expression of hox genes can also cause dramatic changes in phenotype...beneficial changes provide an advantage to those that carry it and becomes fixed.Here is an example of a new protein in humans that is completely explainable in evolutionary terms. SyncitinMi S, Lee X, Li X, Veldman GM, Finnerty H, Racie L, LaVallie E, Tang XY, Edouard P, Howes S, Keith JC Jr, McCoy JM.
Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis.
Nature. 2000 Feb 17;403(6771):785-9.this is an endogenous retroviral gene that has taken over a critical role in placental development in humans that is performed by other genes in other organisms.this is perfectly consistent with evolutionary theory and is an example of sudden appearance of a new gene. Exon shuffling can also lead to completey new genes.There is no real expectation that an organism has "more gene families" than another unless it is adapted to a specific environment that the others are not. Why would bacteria for example be expected to maintain hemoglobin or what selective pressure would cause bacteria to evolve an oxygen transport mechanism? Without variation and selection, there is no expectation of poof bang a heart suddenly appears.3) BLAST and human hits.
The point isn't that you get human hits to your query sequence it's that you get hits which have almost identical sequence. These clusters of genes are called protein families. There is nothing controversial here. The point is that one can't use this to work out where the first hemoglobin came from.I am still missing your point here. If I enter the sequence for a hox gene into the BLAST query field I will get back hits for the specific hox gene followed by other hox genes followed by hox genes of the most closely related organisms to humans i.e. chimp.4) Introns?
I have no problems with individual introns coming and going. I have no problem with any of the mechanisms of evolution!! I am simply making the point that these mechanisms have not been proven to lead to the evoltuion of anything genuinely new. You guys have simply assumed that the known plasticity of genomes etc can lead to the evoltuion of a heart from a system that didn't have one. You assume it simply becasue you see organims with increasingly complicated hearts. It is all one big assumption. We don't actually dispute your data one bit.I never said that introns lead to the development of the heart. But this sentence of yours "I have no problem with any of the mechanisms of evolution!! I am simply making the point that these mechanisms have not been proven to lead to the evoltuion of anything genuinely new." suggests you both have a problem with evolution and that you think that science "proves" things suggests you have a problem with the scientific method.5) Retroviruses argue against increased complexity?
Who says that life is now getting more complex? We beleive it is in a state of decay!Bacterial genomes argue against this. Puffer fish to...they are very streamlined. Our own mitochondrial genome argues against it to..
What would be the evidence of a "state of decay"? That implies that the system works less well now than previously...considering our incredible population explosion..seems like the human genome is doing very well for itself.6) Finches & PE? Every single anatomical paleotologist knows that ultimately things happen at the genomic level. The Gould/Dawkins arguements were not debating this. I am simply saying that genomic clustering into distinct groups would generate anatomical clusterings.They also know that the genome would be irrelevant unless there were selective pressures on the phenotype. Your last sentence implies that you actually do support phylogenetics then 7) Epigenetics
I am a genuine fan of epigentics. I just dpon't like peiople going overboard on it. A simple look at twins (sperated at birth if you require) shows intuitively that 99.99% of development is primarily genetic. I need no further proof than intuition here.Actually twin studies demonstrate that enormous numbers of characters are mainly environment determined. Cloning shows that slight mistakes in imprinting can have severe consequences..even later in developmentI'd love to hear about the dosage compensation if you can do it in a non-condesecnding way. I can imagine it accounts for the fact that women have two Xs corrected for by epigenetic processes? All fascinating but what relevance does it have to C vs E?Not necessarily trying to be condescending to you..but when you state something that is wrong or I disagree with I am here on this forum to argue about it.dosage compensation is important to evolution as the mechansim is varied and complex and it is an important evolutionary question as to why you have imprinting or need to compensate for the extra copies of the X linked genes in females. However, if you don't mind, I think I will start a separate thread for that topic so we don't drag this thread off topic. I may not get to it today though since I have a lot to do in lab.8) Struc Biol/novel families in molecular evoltuion?
Struc Biol and concentrating on clearly defined families has less noise for one basic reason: protein folds in 3D are more conserved than sequences. I agree at the plain seq alignemnt level protein is not much diff than DNA.I am not sure that I totally agree here. By that logic, morphology should be the clear winner as phenotype is more conserved than individual protein folds. And for many evolutionary questions, one needs less conserved sequences as opposed to more for analysis...Fundamentally why does comparative genomics concentrate on presence/absence of genes and not homolgous sequence aligenments? Becasue the former is far more interesting and enlightening!Sorry to disappoint you, but the majority of phylogenetic comparisons are done with sequence alignments. Presence/absence mutations (like variation in SINE integrations) are usefull because they make for extremely statisticall robust phylogenetic markers.The researcher who says that humans have 15 base changes in hemoglobin relative to rat is going to end up in FEBS Lett. The researcher that shows that man has four brain proteins that rats don't have at all will end up in Nature. It is as simple as that. The gneomic era has made molecualr evolution a far more robust field.I don't think I suggested that genomics are unimportant. But the researcher who shows that the same genes in rats and humans are completely differently regulated will also get a Nature paper i.e. Enard et al which I cited for you in post 2.9) Thin air?
The data, not any theory, says that the genes 'came out of thin air'.By that logic, you walk into your office and a colleague is sitting there, he or she must have appeared out of thin air.cheers,
Mammuthus

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Originally posted by Tranquility Base:
SLPx

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In general:

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We believe that seqeunces were created (in each kind) and have since drifted by microevoltuion.

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You BELIEVE that, sure. There are folks that believe that if you go to the south pole you will fall off the earth, too.

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Almost any sequence alignment will have clusters of more closely realted sequences and we could identify those as kinds perhpas. But, now that we have genomes, it is far more enlightening to identify kinds based on presence/absence of protein families! There is much less noise in doing this.

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Good thing that the 'protein families' - which are of course encoded by gene families - show good support for evolutionary hypotheses.[/quote]There is no agenda here, it is simply a matter of what is easier to reconstruct. If there are underlying kinds then genomes are far more informative than homologous sequences.[/quote]Funny, too, that the homologous sequences - which are, amazingly, found within the 'underlying genome' - are so clearly pattern-containing.

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Your sequecne alignment?

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Why don't you first tell us what organisms these sequences are from? I seem to recall they are primate seqeunces(?). We aren't all primate experts - especially biophysicists.

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[This message has been edited by Tranquility Base, 09-16-2002]

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What difference does that make? One need not be an expert on anything to see the distinct patterns of shared mutation.But I forgot about that ever-prsent "tack on criteria" schtick from the creationist crowd...

Mammuthus1) Defn of kind no use?
I want to keep Linneus - I just suggest that genomics may yield a more objective taxonomy that ultimately may prove useful. I respect standard anatomical taxonomy.So I still have your two mouse species within a kind. What is there to disagree about if we put 'kind' at approximately the family level?I don't see how anything you said after your mouse example has anything to do with the issue. You seem to forget that I am making a testable prediction! I am predicting that a close study of hundreds of genomes over the next 10 years will demonstrate that there is a natural 'kind' concept that is distinguished by the presence of distinct genomes. To go to the next kind you will have to add X number of protein families. Within the kinds the differences will be allelic or pseudo-genes. This is a perfectly sensible prediciton of our model and so far does fit with the data.We had a big discussion before here about alleles vs new genes. I'm pretty sure you understand the difference but I'll explain it if you don't.My summary is that kinds are distinguished by alleles within and novel protein families without.2) Mutations and macroevolution.
I 100% agree that simple changes in HOX genes can yield dramitic changes that could even be beneficial. There you go - if that is macroevoltuion then we both believe in macroevolution. I'm simply trying to tell you the part of macroevoltuion that I don't beleive in! And I'll even agree 100% with your syncitin example although I still reserve the possibility that both the virus and humans were given this protein separately although I'll admitt the evidence probably suggests otherwise. It is highly likely, as the paper itself sugested, that humans used to have the non-viral gene. I agree with the plasticity of the genome but that does not mean that we evolved from fish.I don't expect new banks of genes naturalistically either - we can agree. But the genomes tell us that new banks of genes systematically appeared! We don't have to talk theoretically - we can talk empirically. We have the genomes laid out before us.3) BLAST and human hits.
Yes, so my point is that you wont systematically find what the first HOX gene evolved from.4) Evolution & proof?
What problem with the scientific method do I have? I am simply challenging a notion that you think is proved and I'm saying it isn't! You tell me what my problem spoecifically is if you like. All I'm saying is that you guys assume evoltuion is responsible for homologous proteins. We say microevoltuion diversified each kind but that the original proteins were created. What we are saying is completely consistent with the data - you just don't like it. We say you jumped the gun from microevoltuion and homology to macroevolution.5) Decay?
My claim of decay is essentially a Biblical proclamation - I don't have empirical data to prove it becasue I'm sure you don't believe the ages in the Genesis genealogies.6) Evoltuion at genome level?
We can completely agree that selective pressure occurs at the phenotype. This is recorded for the next generation in the genotype. I think we both know how it works. PS - Do you know what the Dawkins/Gould debate was really about?7) Epigenetics
We're talking extents. The point is that 99.99% of the features of the body of an organism develops essentially determinstically due to the genotype. The faces of genotypically identical twins look essentially identical.8) Struc Biol/novel families in molecular evoltuion?
The question still is if a phenotype is due to the same underlying molecular mechanism. If it is the protein folds will definitely be the same.I know phylogentics is done via homolgous seqeucnes but it doesn't prove anything but similarity. We don't have enough distinct genomes to systematically use protein family appearence yet. Most are bactrial. But comparative genomics is the way of the future. From a CvsE point of view we will always agree with everything you say about sequence alignements except that it proves macroevolution. Your alignements just prove similarity!I agree with your regulation comment.9) Thin air?
Collegues in offices and the origin of life are two very differnt things. The way you and I practise sceince would be exactly the same on almost anything we could talk about. But the origin of life is something inherently potentially miraculous.[This message has been edited by Tranquility Base, 09-16-2002]

Hi TB,
Thanks for your response.
I'll go point by point again. [QUOTE]Originally posted by Tranquility Base:
[B]Mammuthus1) Defn of kind no use?
I want to keep Linneus - I just suggest that genomics may yield a more objective taxonomy that ultimately may prove useful. I respect standard anatomical taxonomy.So I still have your two mouse species within a kind. What is there to disagree about if we put 'kind' at approximately the family level?Again, if you agree with standard taxonomy, there is no reason to replace family with "kind". There is already a term in place.
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I don't see how anything you said after your mouse example has anything to do with the issue. You seem to forget that I am making a testable prediction! I am predicting that a close study of hundreds of genomes over the next 10 years will demonstrate that there is a natural 'kind' concept that is distinguished by the presence of distinct genomes. To go to the next kind you will have to add X number of protein families. Within the kinds the differences will be allelic or pseudo-genes. This is a perfectly sensible prediciton of our model and so far does fit with the data.Unfortunatly, this is already covered by standard taxanomic nomenclature and introducing the word "kind" provides no benefit. Again, I am not going to publish my next paper by replacing DNA with "funny curly chemical structure".
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We had a big discussion before here about alleles vs new genes. I'm pretty sure you understand the difference but I'll explain it if you don't.My summary is that kinds are distinguished by alleles within and novel protein families without.
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Then your definition of "kind = family" is flawed. There are non-shared alleles even between populations of the same species. and there are non-shared genes between cloesely related species i.e. syncytin.2) Mutations and macroevolution.
I 100% agree that simple changes in HOX genes can yield dramitic changes that could even be beneficial. There you go - if that is macroevoltuion then we both believe in macroevolution. I'm simply trying to tell you the part of macroevoltuion that I don't beleive in! And I'll even agree 100% with your syncitin example although I still reserve the possibility that both the virus and humans were given this protein separately although I'll admitt the evidence probably suggests otherwise. It is highly likely, as the paper itself sugested, that humans used to have the non-viral gene. I agree with the plasticity of the genome but that does not mean that we evolved from fish.
------------------------------------------Nobody suggested we evolved from fish. However tetrapods shared a common ancestor with fish. It is a misconception that we evolve from one thing to another as if a species suddenly wakes up and looks different.
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I don't expect new banks of genes naturalistically either - we can agree. But the genomes tell us that new banks of genes systematically appeared! We don't have to talk theoretically - we can talk empirically. We have the genomes laid out before us.
------------------------------------------------We don't have all the genomes yet but this site might be of interest to you. http://www.bmn.com. There is an entire new article on a newly discovered horizontal transfer of genes and how the system works. In addition, they refer to the evidence that 18% of the genome of Arabidopsis is a result of horizontal gene transfer....new genes can "pop up" all the time very easily with naturalistic explanations.3) BLAST and human hits.
Yes, so my point is that you wont systematically find what the first HOX gene evolved from.Certainly not by searching the human genome with human hox gene sequences. However, database search amphioxus..it has one of the most primitive hox clusters and a lot of information has been gained about simple body plan regulation from this organism.4) Evolution & proof?
What problem with the scientific method do I have? I am simply challenging a notion that you think is proved and I'm saying it isn't!
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that is problem number one. You don't "prove" theories in science. You do understand this don't you?You tell me what my problem spoecifically is if you like. All I'm saying is that you guys assume evoltuion is responsible for homologous proteins. We say microevoltuion diversified each kind but that the original proteins were created. What we are saying is completely consistent with the data - you just don't like it. We say you jumped the gun from microevoltuion and homology to macroevolution.
_____________________________________________________________Multiple lines of evidence support macroevolution...but I am getting the strong impression that you are mixing up abiogenesis and evolution because of this sentence. "We say microevoltuion diversified each kind but that the original proteins were created."
Origin of life and evolution are two different theories and I am not going to comment on abiogenesis in this thread as there is a forum dedicated to this subject. However, where do you draw the line (testably with data) where microevolution stopped and the "poof bang" creation started? It seems like an artificial construct of your mind.5) Decay?
My claim of decay is essentially a Biblical proclamation - I don't have empirical data to prove it becasue I'm sure you don't believe the ages in the Genesis genealogies.I don't so I won't comment futher on this.6) Evoltuion at genome level?
We can completely agree that selective pressure occurs at the phenotype. This is recorded for the next generation in the genotype. I think we both know how it works. PS - Do you know what the Dawkins/Gould debate was really about?
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However, when there is stasis of phenotype you can still have massive changes in genotype so the correlation is not really recorded from generation to generation.7) Epigenetics
We're talking extents. The point is that 99.99% of the features of the body of an organism develops essentially determinstically due to the genotype. The faces of genotypically identical twins look essentially identical.
---------------------------------------I am not sure this is completely known yet. There are lots of imprinted genes and there can be preferences for maternal or paternal imprinting which can have dramatic effects on phenotype. This is true for ALL X linked genes that do not escape inactivation...however, I will start a different thread for this...I got distracted yesterday and forgot...nag me if I forget again TB..it is an interesting subject.8) Struc Biol/novel families in molecular evoltuion?
The question still is if a phenotype is due to the same underlying molecular mechanism. If it is the protein folds will definitely be the same.I know phylogentics is done via homolgous seqeucnes but it doesn't prove anything but similarity.
-------------------------------------------But then you do not understand phylogenetics. That is the point! groups of organisms that share a common ancestor are expected to be more similar. If chimps were as similar to us as land snails at the genomic level, then evolutionary theory would have a real problem...however, this is not the case.We don't have enough distinct genomes to systematically use protein family appearence yet.
----------------------------------Not true necessarily, hox gene duplications, SINE, LINE, and HERV presence/absence are all used to study phylogenetics.Most are bactrial. But comparative genomics is the way of the future.
------------------------------I don't think I have argued against this point.From a CvsE point of view we will always agree with everything you say about sequence alignements except that it proves macroevolution. Your alignements just prove similarity!
____________________________Which therefore supports evolution..but again, it is important to distinguish that you do not "prove" science.I agree with your regulation comment.9) Thin air?
Collegues in offices and the origin of life are two very differnt things. The way you and I practise sceince would be exactly the same on almost anything we could talk about. But the origin of life is something inherently potentially miraculous.Two things, 1) I don't believe there is evidence that it is inherently miraculous because then everything is inherently miraculous i.e. snow flake stucture 2)We should be arguing evolution and not abiogenesis here. The two issues are separate.I noticed that others are addressing these issues in other threads and that you have directed them here. I will try to do the same when I catch it so we don't have to run around chasing down comments on this thread topic.Cheers,
Mammuthus

Oh yeah, sorry TB
The site I directed you to http://www.bmn.com
is the biomednet network. You may know of it already. They publish Trends in Genetics etc online and have a daily science news synopsis.
You have to register to use it but it is free.Cheers,
Mammuthus

TB:{quoteSLPx
OK, can you explain what the precise significance of those sequences is again in your opinion (for poor old TB) - and what organisms they came from, and what they code for and . . . ?[/quote]Primates, from several families, both Old and New world Primates. The loci are both coding and noncoding/nonregulatory (as I already explained).The precise significance, as per this discussion, is that it is quite easy to see the patterns of shared synapomorphy, in both coding and noncoding regions. There is no big 'jump' in the amount of change between families (calling into question the creationist claims that "kind" is roughly equivalent to 'family'), indeed, the patterns are relatively 'smooth' across taxa.

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Synapomorphic seqeunces?

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No, sequences that contain synapomorphies.

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Sure, but let's clearly define what we are trying to achieve. Are we trying to figure out what are the key differences between significantly different taxa? Or what? What are you trying to achieve?

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I thought you knew all about this stuff such that you can say your preferred criteria are more meritous? Guess not...We are looking at the patterns of shared mutation among taxa, and since we know that 1.mutations occur, and 2.they can be passed on, the logical deduction is that the obsevred patterns are the result of descent.
The goal of phylogenetics is not, nor do I think it has ever been, to 'discover' the molecular mechanisms of speciation and such, rather, it is to provide an objective mechanism for determining biological relationships between taxa. While it is true that such knowledge (mechanisms of speciation) can in principle be examined using phylogentic methods, again, it is not a goal of the field to do so.

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I am trying to find out what the key differences are between taxa. To a large extent I see hemoglobin in man and rat as being almost exactly the same thing. I want to see what really new things came up.

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Good for you. So basically, you are willing to thumb your nose at tested methodologies because it isn't exactly what you are interested in...

SLPxThe point is that although your molecular phylogeny work very clearly deomnstrates the plausibility of common descent it does not prove it. Mol-phylo is completely compatible with creaiton of kinds and diversification via mutations and natural selection. If all you want to do is demonstrate which species are more closely related then what you are doing is fine.For some reason you simply do not allow the possibility that God could have sat there and chosen initial seqeunces for each organism. The more physiologically similar the more similar the sequences.Becasue sequences can drift so far without changing function I do not expect to see the kind conept from homolgous sequences. But I do expect to see the kind concept from the complement of genes in the genome.The true quesitons of what genes originated when can be studied via comparative genomics where we find out what new genes are responsible for what new physiological features. And of course the new genes at each stage of complexity are a complete mystery.You are locked in a faith trap just as we are. The part of evolution which generates real novelty, that we say never happened naturalistically, is the part you have no evidence for. So you believe it happened.[This message has been edited by Tranquility Base, 09-18-2002]

Hi TB,
You going to address my last post to you...and did you look at the biomednet page...and update...the horizontal transfer of genes generating new families of proteins in Arabidopsis is out now here.Just a moment...

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Originally posted by Tranquility Base:
SLPx

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The point is that although your molecular phylogeny work very clearly deomnstrates the plausibility of common descent it does not prove it. Mol-phylo is completely compatible with creaiton of kinds and diversification via mutations and natural selection. If all you want to do is demonstrate which species are more closely related then what you are doing is fine.
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This is rather the point of phylogenetics...but at what point were the "kinds" created? Was the common ancestor of Mus musculus and Mus spretus created or are they the result of mutation and natural selection? Or was it back at the mouse rat split?..or was it back at the marsupial eutherian split? At what point were they created and at what point did they evolve? Phylogenetics is able to show relationships among extremely different organisms?...in fact it goes all the way back to the common ancestor of life...there is no reason to suppose a novel creation event for each node in a phylogenetic tree.

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For some reason you simply do not allow the possibility that God could have sat there and chosen initial seqeunces for each organism. The more physiologically similar the more similar the sequences.
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1) there is no evidence of god sitting there and doing any such thing
2) There are morphologically similar organisms that do not share similar sequences i.e. convergent evolution i.e. wolves and the marsupial thylacine.

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Becasue sequences can drift so far without changing function I do not expect to see the kind conept from homolgous sequences. But I do expect to see the kind concept from the complement of genes in the genome.
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Please read the PNAS paper I cited as it explains one way in which huge numbers of novel genes can appear in organisms without invoking god.

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The true quesitons of what genes originated when can be studied via comparative genomics where we find out what new genes are responsible for what new physiological features. And of course the new genes at each stage of complexity are a complete mystery.
++++++++++++++++++++++++++++++++++++++++++

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I agree with the first sentence mostly but in the second sentence you have to define complexity.

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You are locked in a faith trap just as we are. The part of evolution which generates real novelty, that we say never happened naturalistically, is the part you have no evidence for. So you believe it happened.
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How so? I am providing a citation on the generation of novelty and I referred you to syncytin a gene which is not even an intrinsic part fo the human genome originally as it is viral in origin. Science does not work on faith...that is the purview of religion.

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Cheers,
M

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[This message has been edited by Tranquility Base, 09-18-2002]

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