Kinds and diversification through microevolution and hybridization

JoeThe point is that the current data doesn't distinguish between macroevotluion and design + microevolution. So, yes, we all need better data to distinguish between these scenarios. I am simply uncovering (as usual) the typical strawman of - ha, ha - look - frogs have hemoglobin too - so macroevoltuion is true! Not so.Darwin jumped from homology and microevotution to macroevoltuion. None of the data actually disagrees with creation of kinds followed by microevolution and hybridization. That is the point.

MammuthusI had a great sea-side break - how's the 'travelling'?1. Taxonomic ambiguity
Interesting about insectivores.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.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.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.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.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.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!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.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.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.
(ii) "Unlikelihood is not evidence". If we are talking about God vs nature then the unlikeliness of nature doinfg it is evidence of God. (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.Physical evidence of creation?
The organisms or their genomes.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.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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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?[This message has been edited by Tranquility Base, 09-30-2002] Adminnemooseus changed end "/unquote" to "/quote", and put a blank line in there, no extra charge

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[This message has been edited by Adminnemooseus, 09-30-2002]

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

What i think may be coming revealing is that unlike evolution by descent that necessarily concieves to a taxogeny from a common lineage it is the baraminologist who can relize a larger number of laws of growth (if these exist IN ADDTION TO SELECTIOn as Darwin thought "may be")per any orthoganal data base of the evidence.Let it be as it were.I have been able to clearly seperate (in my mind) growth and development which I had only been able in the past to so isolate from reference to acual herpetological examples. The seperation could be as false as for instance however : vicariance, displacement currents, electrotonic size. I do not know. But I thought therefore biologically I was.

Agreed Brad. Not every convergent genomic appearence is horizontal transfer. Just like not every out of sequence fossil is a wash in or a folding event.

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5.(ii) "Unlikelihood is not evidence".
If we are talking about God vs nature then the unlikeliness of nature doing it is evidence of God.

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Do you really want to say that?An argument from incredulity is evidence of God?Because something may seem unlikely in the current state of
knowledge means very little.150 years ago people most likely thought that it would be
impossible to travel from Europe to America in less than
a few months ... unliklihood just shows a lack of imagination

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?

quote:

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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

PeterIt is an issue of extent. I think our bodies, our eyesight, our consciousness is incrdible evidence that God created. How the sun works? You're right we understand that now - but I still think how we got here is qualitatively differnet.

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Originally posted by Tranquility Base:
Peter

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It is an issue of extent. I think our bodies, our eyesight, our consciousness is incrdible evidence that God created. How the sun works? You're right we understand that now - but I still think how we got here is qualitatively differnet.

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Oh brother...Life is soooo incredible, that it MUSTA been done by the God of the bible...Sorry TB, 'awe' and personal incredulity does not count as evidence of anything other than a lack of actuqal proof for one's position.Such appeals work on school children and the mentally challenged, but using it with educated adults is just insulting.

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'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.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. We know from he genomes that most have arisen after your supposed abiogenesis. 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).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! Duplications only link paralogs to each other. Shufflings swap domains. There are no systematic hints as to where most protein families came from.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. But creationist studies by PhDed molecular biologists have shown that random searches for folded enzymes take too long for macroevolution.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.Duplicaiton within protein families could have been evoltuion although I personally believe God created all HOX genes. HOX genes in fish are more similar to those in reptiles than those in birds. What you call phylogentics I call common designer.To be continued . . .[This message has been edited by Tranquility Base, 10-02-2002]

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.

^ Interesting Mammuthus.So I'll reconsider hemoglobin as a 'core-genome' protein in that case. But you can't argue that for all protein families. Mycoplasma Genitalium only has about 80 families and yet thousands exist in vertebrates!Thsands of new folds and families still had to originate somewhere post abiogenesis.[This message has been edited by Tranquility Base, 10-02-2002]

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Originally posted by Tranquility Base:
Peter

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It is an issue of extent. I think our bodies, our eyesight, our consciousness is incrdible evidence that God created. How the sun works? You're right we understand that now - but I still think how we got here is qualitatively differnet.

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In what way different, and why do you think that?A problem that I have come across once or twice (on various
issues not just CvsE) is that a certain portion of humanity
find it hard to take that mankind (forgive the un-pc expression)
is nothing special, just another animal doing what animals
do. Similarly life, fundamentally, is just an emergent property
of a chemical system.I know that causes problems for some people, but using that
'unbelievability' in a discussion should be discouraged.