Kinds and diversification through microevolution and hybridization

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]

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

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

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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quote:

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Originally posted by Tranquility Base:
Mammuthus

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I read it and never got back to it . . . OK, here we go . . .

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1) Defn of kind no use?
Becasue we can't prove the 'kind' concept exists, for now we define it seperately and see if it naturally aligns with some level of Linneanism. If it does, great. If not the Linnean system may be modified (if even mainstrreamers agree) or a parellel system may be developed. The point is inbetween we need to refer to the term 'kind' so that we do not pronounce something proven before it is. The term 'family', or any other Linnean term has no formal definiton genetically, let alone genomically and has not be shown by anyone to unambiguously agree with our/my definition of kind. It may, it may not.
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Perhaps there is not a quantitative genomic definition of a Family or Order but the differences are hardly spurious. Are you then going to call artiodactyls the artiodactyl kinds? or marsupial kinds? What advantage does that provide? Just lumping lots of things together randomly into a kind is not useful . Order, families, genera, species are all defined using morphological, physiological, and now genetic characteristics.
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You say there are "non-shared alleles even between populations of the same species". What I said was that kinds are distinguished within (ie species in a kind are characterizable) by differnt allele sets. Non-shared genes between closely related species can usually be shown to be due to loss or horizontal gain. I just read some genomics papers on multiple Bascilus (spelling?) species genomes and the proposal was that all distinct protein families are due to either of these mechanisms. Horizonal transfer is fairly easily proven. Genomic loss may be difficult to prove in some instances (eg if pseudo genes have drifted to complete unrecogizability).
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How is this different in cases of macroevolution i.e. differences between marsupials and eutherians for example? What works at the species level works at all other levels...there is no reason to suppose a sudden shift in the natural world for which there is no evidence merely to fit it to a religious belief.

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2) Mutations and macroevolution.
Of course I know you are not proposing we came directly from fish! I'm familiar with biomednet although this is one of the only sites my instituion doesn't have rights to non-free stuff on-line. I'll check out that article although horizontal transfer is not somehting that distinguishes our views. I can accept it as a means of diversification. It does not explain the original origin of any protein familiy. Fascinating that Aradopsis has that much horizontal transfer. I accept that genomes are very plastic.
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Biomednet should be free. I think you just have to provide your email address and make a password and you are automatically in. At least it used to be that way.

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Horizontal transfer of genes DOES explain the sudden appearance of genes or gene families within a lineage. It is not an exclusive explanation but it is one mechanism. When you say original origin it still sounds like you are mixing in abiogenesis.

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3) BLAST and HOX.
Yes, but you still wont find out where the first HOX came from. It's not as if protein families can be systematically traced to each other.
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That is called phylogenetics...and there is an entire discipline of trying to recreate the original or at least ancestral forms of various proteins and characterizing their functions.

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4) Evolution & proof?
Some theories do get 'proven' within reasonable doubt. It is semantics to debate this surely. You think (macro)evoltuion is more proven than I think it is. Multiple lines of eveidence - eg distinctness of protein families - suggest creation of kinds followed by evolution.
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Scientific principles are not semantics TB. The thoery of gravity is not "proven". I think macroevolution is fully supported by multiple distinct and reproducible areas of research.

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Please show the multiple lines of evidence for creation.

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I am not mixing evoltuion with abiogenesis although it may sound like it. I believe God created genomes at approximately the Linnean family level. But what I am saying is that I wont argue with you that paralog 1 could have come from paralog 2 (even though I don't believe it did typically). But I will argue that the distincness of protein families suggests creaiton of kinds and underlying protein families. I hope that clarifies my position.
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I understand your position but I am asking whether it is purely based on faith or whether you can provide testable hypothesis and experimental data to support the assertion.
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"Where do you draw the line where microevolution stopped and the "poof bang" creation started? Kinds with distinct genomes comprising the thousands of protein families that make up all of the genomes.

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This definition makes no sense I'm afraid. It does not establish a precise defnintion of kind nor the boarders of where you define evolution versus creation...between mouse species and mouse species? Between chimp and human?

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6) Phenotype/genotype?
Why do you say the stasis in phenotype isn't recorded in geneotype? Just becasue the genotype may look like it is changing to an untrained eye, a trained eye may see that it dicates an unchanged phenotype. A simple case proves the point: a base change does not necessarily change the amino-acid coded for as you know.
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I am saying you can have large scale genomic changes including speciation events while maintaining the gross morphology of an organism i.e. sharks...thus large amounts of genotypic change do not automatically imply gross phenotypic change.

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7) Epigenetics
Yes if there is a lot of imprinting going then there may be more epigenetics than we may think.

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More and more discovered but it is a relatively new field...and a bizarre one.

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8) Struc Biol/novel families in molecular evoltuion?
I do understand what you said about phylogentics. But it is also consistent with common design with genotype (mostly ) dictating phenotype. Would God make animals with placentas have genes more similar to snails than to placentals? Of course not.
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Why not? What is the evidence for this? Why couldnt an omnipotent being create an organism where genotype and phenotype are fully uncoupled?

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9) Thin air?
I believe God would say to you that your origin is inherently potentially different to snowflake ordering.

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I don't believe in god. But regardless, why should the principles of complexity be different for origins of non-biological and biological systems?

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Let me know if you still can't get into biomednet. If not I will post the article here in this thread.

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Cheers,
M

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[This message has been edited by Tranquility Base, 09-19-2002]

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Hi TB,I will go point by point again. If you get to my response today I can probably go one more round but then I am travelling for the next week and won't get to your post until I am back...but I will try to pick up wherever we leave off.Anatomical differnces are not spurious, sure, but, unless I am mistaken, it is not always clear what to call a genus vs a family. Whether there is also confusion at the order level I am unaware. The genomic kind concept of distinct genome may turn out to be a useful concept (even if only to molecular biologists) and may not perfectly align with a Linnean level. That sentence can not be debated surely?Genus vs family is not so controversial though there are problems placing insectivores. Species level designations are difficult. The closer you get to a speciation event the harder it is to separte out distinct species.You ask how what I said is differnet ot macroeovltuion? Horizontal transfer is somehting no one would deny. The gene already exists it just moved. That is very differnt from a new enzyme family evolving that bears no resemblance to any other family! I hope yo can see tha tjust becasue you see jumping genes this has almost nothing to do with the original orgin of each gene family. (And I am not implying abiogenesis here - the simplest organims do not (and did not) have anything like all of the protein families and you know that!).No, I don't know that simple organisms did not have more complex genomes at one time. Bacteria are "simple" but they to have been evolving and for much longer than multicellular organisms. I have no reason to suppose that they have not gained and lossed genetic information. In addition, in single cell organisms like bacteria, I would never expect then to have hemoglobin as they have no need to transport oxygen. If there is no selective advantage or pressure, there is no reason to expect an organism or group of organisms to develop the novelty. As to the ultimate origins of genes, this is still a part of abiogenesis I'm afraid.2) Mutations and macroevolution.Yes, horizontal transfer of genes DOES explain the sudden appearance of genes or gene families within a lineage. But I am talking about where ethe first member of each family came from - very, very different.It is partially an abiogenesis question. But it can also be studied looking at organisms with rudimentary functions related to a more complex function i.e. bacteria photosensitivty and development of photopigments. It could also be done experimentally by shuffling protein domains (or even DNA or RNA) and selecting for specific functions over multiple rounds until you have an extremely good molecule for the selected purpose. This is combinatorial chemistry which is a major part of biotech and pharmaceuticals where they use evolutionary principles to develop drugs. You can come up with completely novel functions with these systems.3) New protein families
There is not much work on the origin of new protein families because there is very little evidence for this.There is not evidence that the families are new or for there origins?4) Evolution & proof?
Science isn't semantics but your use of 'good support' vs 'proof' is semantics. I will say any day that gravity theory is proven whether Netwonian or Einsteinian. We are using differnt definitons of words.That is not semantics and what you said is patently false. If the theory of gravity is "proven" please state how it works. It is unknown how gravity works...there is a theory that is supportable but it is in no way proven. It could be overturned tomorrow.Creation evidence (note - not proof, just evidence): the distinctness of protein families, distinctness of Linnean families, irreducible complexity of cellular systems (as well as the unlikelihood of abiogenesis)1) irreducible complexity is not evidence...there is no evidence for irreducibilty and complexity is not defined.
2) unlikelihood is not evidence. It is unlikely that I would have stumbled into this website looking for something completely different but that is how I ended up here.
3) How does your problem with abiogenesis have any bearing on evolution?My position? Is based on considering the possibility that we are created. And the evidence is good that we were IMO (see above). Other evidence favours evoltuion.Please supply physical evidence for creation. How do you test such evidence?My definiton will work fine when we actaully have the chimp genomes with the proviso of horizontal gain/loss issue. Of course it is of not much practical use right now. The Bacillus genome analysis is an example of within kind study where even the evotutionists writing this 2002 paper chose themselves to accept that all gene family differences were expected to be due to horizontal transfer or loss.I'm not really sure what you are getting at here. If you find sequences very similar to cyanobacterial gene sequences in a plant what is wrong with horizontal transfer? I am also not clear as to what you are so sure will be supported when the chimp genome is sequenced? Thus far, the larger sequencing efforts from chimp have not yielded controversy surrounding our sharing a common ancestor with Pan troglodytes and Pan paniscus.6) Phenotype/genotype?
Sure - large amounts of genotype change don't have to lead to large pheotype changes. What I am saying is that if this is predictable from the genotype then it is not epigenitic or a suprise to anyone.However, it is often not predictable from the genotype...there are even diseases which exhibit a phenomenon known as phenocopy which is not predictable from the genotype.8) Restricting God?
Of course God gets 'restricted' by what he has left behind. If he exists and he created life as it is then that is how he did it! The pioint is that I am not eliminating he possibility that God created us as you do. You are the one restricing him. You are saying he couldn't create semi-monophyletically.That is a very strange position and would put you in conflict with a large number creationists.
So you are willing to limit your god and concede that he is a truly lousy engineer?9) Thin air?
If God doesn't exist then there is no dif between the origins of non-bio and bio. If God does exist then there potentially is a difference. God might have created just like described in the Bible - you can't rule it out!I am an atheist and see no evidence for god or the supernatural I have no reason to invoke a god at any point and I see it as no conflict for evolution. As to abiogenesis, since I do not have direct empirical evidence or a well formulated theory for abiogenesis I cannot obviously say I know how life began. On the other hand, as I see it, there are many things that seemed to be unanswerable in science even a few decades ago which are now accessible. So I have no reason to believe this will not be the case with the chemistry of life.I'll get around to biomednet today. I'm 99.99% sure that it wont give me access to all pdfs. Perhaps you are linking to a free review article.There are some articles that biomednet will link you to that are not free i.e. when a news item has a link to a Science paper for example. But Trends in Genetics for example should be free via biomednet. I was trying to refer you to a news piece biomednet did on horizontal transfer..that should be free to access.Cheers,
M[This message has been edited by Tranquility Base, 09-19-2002][/B][/QUOTE]

Hi TB,Had a great time travelling in Spain. Glad you enjoyed your time off. I am back with tons of results that just piled in that I was waiting for so I will be almost like my namesake for a bit i.e. extinct from posting But I will try to answer your post tomorrow if I get a bit of time to spare. I want to keep the conversation going on this topic.Best wishes,
Mammuthus

Hi TB,
Have a few minutes to respond so I will go point by point as usual. [QUOTE]Originally posted by Tranquility Base:
[B]MammuthusI had a great sea-side break - how's the 'travelling'?1. Taxonomic ambiguity
Interesting about insectivores.Go to medline and look up Stanhope MJ and you will find lots of papers on this subject.1.5 Simple organisms
Reghardsless of losses, evolutionary genomics researchers definitely propose that genomes have got more complex over time. The anti-progression idea (was it ever more than just PC gone mad?) has died over the last 20 years.Not true. Please name the evolutionary genomics researchers and their published papers where they claim that all genomes must become more complex over time. Many genomes show reduced complexity such as fugu.I only used hemoglobin as an example. Mammals have far more protein types overall than bacteria! Of course I can't prove that was the case in the past. But each protein family can be placed at a definite location on the standard evoltuionary tree of life! I really don't understand your resistance to standard concepts that transcend the C vs E debate.I was debating your use of the term complexity. I am not saying that we have less genes than bacteria. However, we don't have evidence that we have more genes than several other mammals that you would perhaps define as less complex.The ultimate origin of each gene type is NOT abiogenesis by any definition I have ever seen. I completely disagree with your statement that it is.How can the ultimate origin not be abiogenesis??? Your creation event that you believe in is an ultimate origin to. You claim beyond that, that at some unspecified time each gene family came poof bang into existence for which you have no evidence nor a testable hypothesis. I can easily look at Hox genes for precursors, duplications, horizontal transfer or even design experiments to see if any of those mechanisms are possible to support claims I make (note: I am not working on this but others are). That is one of the reasons why evolution and genetics are science and creationism is not.If you believe in macroevoltuion of life on earth then you believe that new protein families with distinct biochemical functions have been evolving non-stop throughout the last 500 million years.Yup....and they are still going like the energizer bunny 2) Mutations and macroevolution.OK - if you define the origin of new genes as abiogenesis then it is! So now I see what we are arguing. We agree! I agree with all of the evoltuion that is not abiogenesis (by your definition). That is the point - I agree with all of the plasticity of the genome you believe in except that I believe each gene family was created by God.No, see above why we don't agree. I am saying the first self reproducing organism origin and the contents of that organism are the subject of abiogenesis. Not that every gene we see suddenly appeared by some mythological being.I am fully aware of biotech artificial evoltuion and combibnatorial chemistry - I just sent of a combi-chem manuscript for review. The point is that there is still a big difference between mutating a gene and coming up with a totally new protein fold!Please elaborate TB. I saw a lecture by a guy who was able to make small fragments of DNA with unbelievably strong binding properties for just about any substrate using selective chemistry over successive rounds. This is not just mutating a gene or creating a new protein fold.3) New protein families
"There is not evidence that the families are new or for there origins?" There is little evidence that the families evolved from each other.Except that every protein family shows homology to either another gene in another related organism i.e. phylogenetics or part of the protein does. Or you have to say for example, that each Hox paralog had to be created de novo from amphioxus through vertebrates and your god was too stupid to make a new gene for each function and just by chance made it phylogenetically informative.4) Evolution & proof?
Neither Newton or Einstein make any attmept to state how gravity works. Their theories can simply be thought of as empiricism if you like. But you can't deny that within the scope of the theory (generaing forces from mass distributions) they work perfectly (Newton for v << c). So both Newton and Einsten are proved as far as I am concerned.That is cute but irrelevant. There is more supporting evidence for evolution than for the theory of gravity so your standards of proof are wildly variable.5) Creation evidence
(i) "There is no evidence for irreducibilty and complexity is not defined." Every biochemical pathway has IC components that need prior funcitons to explain their presence.List the components and the evidence that mandates that they are irreducibly complex. So far the only answer that I have ever seen provided for IC is that the proponent cannot imagine how it could have happened and therefore defines it as IC.(ii) "Unlikelihood is not evidence". If we are talking about God vs nature then the unlikeliness of nature doinfg it is evidence of God.That is sad that you study science and hold this view. This is the antithesis of science TB. Even if there were no supporting evidence for evolution, this would not be evidence of god. I could substitute Barney the ugly purple dinosaur in your sentence and it would make as much sense.(iii) "How does your problem with abiogenesis have any bearing on evolution?" I have shown you that the same problems that plague abiogenesis plauges macroevoltuion. New gene families aising non-stop. Abiogenesis itself is just much harder again.You have NOT shown me how exon shuffling, horizontal transfer, and the processes of microevolution over large time scales do not account for what we see in the genome.Physical evidence of creation?
The organisms or their genomes.LOL! This can be reduced to "it is because it is". This is not logical TB. I could be equally illogical and state that the existence of organisms and their genomes is evience against creation..nja nja...it does not work.6) Horizontal transfer?
I have no problem with horizontal transfer. What I am trying to point out is that evoltuioonists skirt around the original origin of each protein family! And it is not abiogenesis except for wghatever the simplest creature was.Um. Could you please define what abiogenesis means to you. We are still talking past each other.8) Restricting God?

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I said:
Of course God gets 'restricted' by what he has left behind. If he exists and he created life as it is then that is how he did it! The pioint is that I am not eliminating he possibility that God created us as you do. You are the one restricing him. You are saying he couldn't create semi-monophyletically.

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I say I do not believe in a god(s) and there is no evidence for it. So I am not restricting it. You do by saying it has to work in a specific way and is therefore not omnipotent...and actually a pretty crappy engineer.

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You said:
That is a very strange position and would put you in conflict with a large number creationists.
So you are willing to limit your god and concede that he is a truly lousy engineer?

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Now I say:
What conflict? What's wrong with semi-mono-phletics if designed well?How is semi-monophyletic design in any way a testable scientific hypothesis?
Cheers,
Mammuthus

Hi TB [QUOTE]Originally posted by Tranquility Base:
[B]Mammuthus1.5 Simple organisms
I do not claim that all genomes increase in complexity over time. However, the human genome is more complex than a fly's which is more complex than yeast's which is more complex than a prokaryote's. I'm talking big picture - I know that hundreds and thousadns of genes can be lost over time due to switching niches.
******************************+I am surprised you can acknowledge genetic change due to niche switching but then put the brakes on in considering how that is a component of macroevolution. Why do you think for example many cave dwelling specialists (I'm thinking of things like the albino salamanders that I don't know the name of) end up with vestigial eyes? No selective pressure to maintain eyes when there is no light.I'm reading the fugu paper on the train tonight.I wont argue with you about complexity within mammals - it's about equal by most objective measures. It's too hard to quantitate speaking and thinking.
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I would still argue that complexity is both hard to define and almost impossible to quantitate even at deeper taxanomic levels but I won't keep pushing the issue.You said: "How can the ultimate origin (of gene families) not be abiogenesis???" The reason is by definition - nobody believes that the 'first or simplest' organism had anything like all known protein families - it would have had only a small percentage.However, you have several times switched your definition of abiogenesis then from the first genes to genes seen among different families or orders of organisms. The first simplest organism would have merely had enough to be self replicating i.e. to propagate. The environment has not been stable over the billions of years of earth history. They would have been under intense selection to diversify and all you need is a non perfect replication mechanism, time, and selection and lots of interesting things can happen We know from he genomes that most have arisen after your supposed abiogenesis.
**********************No we don't. We don't know what has been gained or lost yet from specific genomes. We are diploid but there is evidence that we (meaning and ancestral mammal) may have been polyploid at one time.Do you disagree with this? So the 'first' organisms genes were abiogenesis, but the new gene families as we go from prokaryotes to eukaryotes to multiellualr to vertebrates to mammals are not called abiogenesis by anyone I've ever met (and not you by your next paragraph).
*************************************+I don't completely agree with this. I don't know that the first organism actually had what we would call genes by current definitions. If it had a non enzymatic self replicating RNA genome it would be hard to compare with most (but not all) living organisms today. However, as to the second part of your question, you have switched around your definitions a bit. When I pointed out syncytin as a way that a completely novel gene can arise in a few million years you say that you believe the data but then say where did the first hemoglobin come from without making the connection that it was probably a similar type of mechanism..or exon shuffling etc. I have not studied piece by piece the hemoglobin domain homologies among other non-related genes to see if one can trace the origin of this group to another class of genes of unrelated function. While it might be interesting to do, hemoglobin is old and those homologies could have been blurred by random mutation over millions of years. But one can still look at such things (which has been done in some cases) to try to trace the origin of a gene or gene family.
-----------------------You continue to talk of duplications and horizontal transfers etc. Please stop doing that - becasue I wont argue with that. But surely you know that that doesn't connect more than a handful of the known protein famiiles!
++++++++++++++++++++++No, I don't know that and niether do you. 18% of arabidopsis genome is cyanobacteria! 8% of ours is made of HERVs. Hervs can lead to novel genes i.e. syncytin. There is no reason to think that this is not a very common phenomenon or that it is not connected to the origin of gene families.
*********************************Duplications only link paralogs to each other. Shufflings swap domains. There are no systematic hints as to where most protein families came from.
++++++++++++++++++++++++++++++++++++Over time, the duplicated copy can radically diverge, take on new functions, or disappear by mutation i.e. pseudogenes. There are systematic studies to trace the origin of gene families.2) Lab evolution
Are you sure the lecture you went to wasn't a 'phage display' peptide lecture? That makes much more sense. I know all about phage display. Great technique. Allows one to try billions of sequences. These peptides do not form folded proteins - they are only ten or so amino-acids long.
************************No, it was using short oligonucleotides of random sequence and then using successive rounds of selection for a specific characteristic like the ability to bind to a specific protein.
******************************But creationist studies by PhDed molecular biologists have shown that random searches for folded enzymes take too long for macroevolution.
***************************If this is true please list the names, the papers, and the supporting data. I have never seen a creationist study that did not either a priori define their conclusions as true, fail to present a testable hypothesis, or argue merely from lack of understanding or disbelief.3) Protein families & BLAST
Most protein families only show homology within their family. The other hits will usually have high E values. Some families are huge. but many genes only give a handful of hits to paralogs and the equivilent homologs.
*****************I am not sure what you point is but if you were to look for exon shuffling etc., you would not do it using BLAST and you would not use the entire protein as your query. You have to see where each domain comes from.
**********************************Duplicaiton within protein families could have been evoltuion although I personally believe God created all HOX genes.
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This is a belief and has no bearing on science however.HOX genes in fish are more similar to those in reptiles than those in birds. What you call phylogentics I call common designer.
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How about Hox pseudogenes? If each animal was created separately why are there homologies? Why does phylogenetics work? Why can you polarize character states with outgroups from distant taxa? Go back far enough and you are at the beginning? Where did the creator create? Kindom? Phylum? Order? species? This morning and then implanted all your lifes experiences in your head 15 minutes ago?
All of these questions are not answerable because creationism is a BELIEF TB. NOT science.For my part I can understand at some level (though I don't share the belief as there is no evidence) that some people would turn to the idea of a creator beginning all life in the universe somehow...I would say probably most biologist hold a such a view since most are christians. But beyond that, it is really hard for me to understand that a molecular biologist would completely dump scientific thought in explaining the natural processes of transmission genetics and evolution and supplant it with a personal mythology
--------------------.To be continued . . .Look forward to it. Talk to you soon.Best wishes,
Mammuthus

Well what do you know...hemoglobin can be traced to bacteria...so, so much for sudden creation.
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J Exp Biol 1998 Apr;201 ( Pt 8):1099-117 Hemoglobins from bacteria to man: evolution of different patterns of gene expression.Hardison R.Department of Biochemistry, Pennsylvania State University, University Park, PA 16802, USA. rch8@psu.eduThe discovery of hemoglobins in virtually all kingdoms of organisms has shown (1) that the ancestral gene for hemoglobin is ancient, and (2) that hemoglobins can serve additional functions besides transport of oxygen between tissues, ranging from intracellular oxygen transport to catalysis of redox reactions. These different functions of the hemoglobins illustrate the acquisition of new roles by a pre-existing structural gene, which requires changes not only in the coding regions but also in the regulatory elements of the genes. The evolution of different regulated functions within an ancient gene family allows an examination of the types of biosequence data that are informative for various types of issues. Alignment of amino acid sequences is informative for the phylogenetic relationships among the hemoglobins in bacteria, fungi, protists, plants and animals. Although many of these diverse hemoglobins are induced by low oxygen concentrations, to date none of the molecular mechanisms for their hypoxic induction shows common regulatory proteins; hence, a search for matches in non-coding DNA sequences would not be expected to be fruitful. Indeed, alignments of non-coding DNA sequences do not reveal significant matches even between mammalian alpha- and beta-globin gene clusters, which diverged approximately 450 million years ago and are still expressed in a coordinated and balanced manner. They are in very different genomic contexts that show pronounced differences in regulatory mechanisms. The alpha-globin gene is in constitutively active chromatin and is encompassed by a CpG island, which is a dominant determinant of its regulation, whereas the beta-globin gene is in A+T-rich genomic DNA. Non-coding sequence matches are not seen between avian and mammalian beta-globin gene clusters, which diverged approximately 250 million years ago, despite the fact that regulation of both gene clusters requires tissue-specific activation of a chromatin domain regulated by a locus control region. The cis-regulatory sequences needed for domain opening and enhancement do show common binding sites for transcription factors. In contrast, alignments of non-coding sequences from species representing multiple eutherian mammalian orders, some of which diverged as long as 135 million years ago, are reliable predictors of novel cis-regulatory elements, both proximal and distal to the genes. Examples include a potential target for the hematopoietic transcription factor TAL1.