The Human Genome and Evolution

Dear TB: Well I followed it alright. Apparently you are a dogmatic creationist who borrows all the terminology, methodology, and data of evolutionary biology and warps it to fit your predetermined, religiously motivated interpretation of reality. Shame on you. Your kind is the absolute worst, and the exact reason I started posting on sites like this one. I would say you are a pseudoscientific charleton hijacking the real data of real scientists and disingenuously re-interpreting it to selectively fit your world view without coming up with any valid data or testable theory of your own.Why aren't you and the rest of your ilk formulating your own hypotheses, generating your own evidence, and performing your own experiments to test and prove your world view? Why? Because your theories are NOT scientific in the slightest, you have no testable hypotheses, no experimental protocols, no basis for proving or disproving anything you say. Received any research funding lately? I thought not. No serious scientific entity would ever fund your endeavors to demonstrate the literal accuracy of biblical accounts. Perhaps then, you would be so generous as to describe just what process(es) gave rise to them WITHOUT resorting to terms 'borrowed' from evolutionary theory, which you apparently dismiss.You YEC types have yet to come up with a single objective definition of what a 'kind' is. It is NOWHERE adequately defined. Can you provide a defintion? It would be a 'YEC first'.I would not even be bothered by your facade of scientific 'understanding' if you were not trying to mislead people like GDR who are genuinely interested in advancing their understanding of evolutionary theory. Shame on you and all you hypocritical, religiously-motivated disseminators of falsehoods in the name of 'science'.Edited to correct an error and remove one or two overly irate adjectives.
This message has been edited by EZscience, 06-29-2005 05:50 AMThis message has been edited by EZscience, 06-29-2005 05:54 AM

Hi TB,
First, sorry I unloaded on you so vociferously from out of left field (late in the day for me and probably one beer too many) and thank you for your measured response. Let's see if we can't resolve some issues here. I am very curious as to what creation science is actually 'practising'.
I see nothing so far but criticisms of evolutionary interpretations - interpretations that I would argue only evolutionary biologists are qualified to make, given they have been responsible for all the underlying concepts of modern biology, the experimental design, data collection, and analysis.What data have been collected by creation scientists?
What experiments performed?
What practical problems in applied science solved by their insights? The methodologies of evolutionary biology do not address questions of 'final orgins'. Period. The overwhelming preponderance of evidence supporting commonality of descent has nothing to do with whether or not the first spark of life was ignited by some creator or not. Creationists are forced to borrow all the nomenclature from true biological sciences because they have produced no rigorous classification schemes or methodologies of their own. That creationsits borrow all the terminology and data produced by evolutionary biologists and try to warp it to fit their completely unsupported world view? YES. I don't like it one bit. Please produce one. We are all on the edge of our seats. Absolutely. But you guys have yet to bring anything remotely 'datalike' to the table. And I mean data that is reliable, authenticated, adn actually useful for infering a 'big picture'. Again, where are these data sets? I did not accuse you of laziness. I would just like to see your theoretical diligence directed to more profitable pursuits. And let's not forget that theory is only as good as the empirical observations it is based on. This brings us back again to your missing data sets. But I thought you didn't believe in common descent? And if you do accept speciation within 'kinds', then what is it that sets the upper limit one how different organisms can become without crossing over to become some other 'kind' ? And what branching rules are used to determine degrees of relatedness within kinds ? Possibly. You seem very rational on the surface. But once you started defending YEC I would have some serious reservations.How about this.Since you consider yourself both a philosopher and a professional scientist, I challenge you to a Great Debate on these specific contentions of yours:Creation science is not pseudoscience.
Creationists are generating new data sets.
The biblical concept of 'kind' has a valid scientific definition.We can title it "Validity of Creation Science Methodology" or something else of your choosing.
If you accept, I will solicit administration to set everything up.

Hi Randman - we meet again. That's exactly what we do.
Try and publish a paper in a biology journal and you'll learn exactly just how much criticism you have to face to publish ANYTHING remotely involving evolutionary inferences. You have to deal with multiple reviewers and a referee, and not all the criticisms are justified either - you often have to challenge these with the referee.You creationsists seem to think evolutionary biologists are all in this great conspiracy to deny creation interpretations and support each other. Nothing could be further from the truth.
Mostly, we ignore creationists because they have virtually nothing constructive to offer the discussion. On the other hand, debates and arguments about interpretation of real data sets are a constant reality. Evolutionary biology is a cut-throat business. Just ask Mick or Wounded King or Mammuthus or PaulK or any of the other actual scientists in this forum.But its difficult to address criticisms that are either not properly grounded in fact or are based on fundamental misunderstandings of scientific principles. People who insistently repeat such unfounded criticisms without realizing why they are unfounded are going to end up being ignored by scientists, and rightfully so.This message has been edited by EZscience, 06-30-2005 02:18 PM

It's a cop-out in the face of undeniable evidence of speciation. Only a few years ago creationsists denied speciation. Now they have tentatively retreated to higher taxa. Give it a break. You have had a whole other thread on Haekel's drawings to learn about why these archaic ideas have little relevance to modern evolutionary biology.

You need to give this whole Haekel thing a break.
You have flogged it to death elsewhere and it's off-topic in this thread.Also, it would be nice if you could consolidate your responses to one post into a single message so we could actually respond in one message.Got to go - maybe more later.

That, in my view, is a pre-determined bias that is incompatible with a truly objective scientific approach. No argument there. But a lot of mainstream science does get accomplished without direct funding. Even as a post-doc, most of my best work was never directly funded - I accomplished it on the side with leftover funds from other work that was funded - what we called 'bootleg' projects. I repeat, theory, however elegant, is only as good as the empirical observations on which it is premised. That is only one possible inference and definitely a debatable topic. Again, here is a topic that is definitely contestable, but first I would like to see it phrased in *specific terms* as a falsifiable hypothesis. Fine. But doesn't HG transfer decrease, rather than increase, the chance that there might be definitive and immutable 'kinds' of organisms? It would seem to be yet one more line of evidence against the creationist view. Absolutely. You still haven't come up with a rigorous definition, and I would contend that it is not possible. Sounds like you are trying to be as slippery as possible on this one, but I aim to pin you down. Yes, it is. And we don't need to sequence every single genome to debate the concept of a 'kind'. It is merely a biblical abstraction and completely unscientific. You bear the burden of demonstrating that it is. As I understand it, the moderators oversee the debate and make a decision at some point. It would not be endless, and certainly I don't have time for that either. No, that one is the least specific and the hardest to demonstrate incontrovertably. I would say the existence of a biological 'kind' is perhaps the best of the 3 to debate. Let me research your references - I am away from my fast connection but I want to verify if these authors have published anything credible outside of ICR. I already see the first three articles are by the same author, Andrew Snelling, and none of your references are published in accredited geology journals. Also, I am not a geologist, so I am not qualified to critique radio-dating of volcanic rock and such. I would be seeking a debate on issues relating specifically to evolutionary *biology*. I will respond further in a day or two.

But you use it selectively. You guys sift through mountains of data, seemingly ignoring the implications of 98 % of it, looking for tiny shreds that you can hold up and say "Look - this is consistent with the biblical account!". So how many did he create and how can this be objectively quantified at all? We can't debate final origins - only the process of evolutionary change and its boundaries. Are you not suggesting that such a boundary exists with your concept of 'kind'? There are no boundary conditions defined. If things can evolve and change with families (the taxonomic level you mentioned) but no further, what mechanism prevents higher level divergence? I see no basis for recognizing a 'kind' as a valid taxonomic distinction whatsoever. And even if it does correspond approximately to 'family', why not just use 'family'? What scientific understanding is to be gained by introducing this nebulous, biblically-derived concept? And you are trying to make it as cloudy and indefinable as possible. So you can only trace evolution back so far and then it magically breaks down at some imaginary, undetermined point corresponding to the 'poof' of creation? Why 'of course'? Surely independent peer-review is the litmus test of the scientific validity of these ideas? So you're saying that these guys have managed to achieve some credentials by publishing some 'conventional' research in their discipline, only to turn around and use those credentials to flog other stuff that could never pass peer review anywhere outside the ICR ? Seems a little disingenous to me.
That would be like me taking a big crappy data set from an entomological study with all kinds of methodological flaws and saying, hmmmm... this will never fly in a good journal, but look - it makes this new pesticide look like it works really well. I bet Monsanto would like to publish it as a promotional flyer...

Or Neanderthals , for that matter?I guess maybe we'll find out when old TB gets his posting privilidges restored. He's been suspended (again).

OK. But what is this invisible boundary that delimits the human 'kind'.
For example, to persue your argument from an evolutionary perspective, we might use chimps as an outgroup and test sequence homology between humans chimps and Neanderthals and find the latter closer to humans than the former. So we have:Humans __________________________(common ancestor)
Neanderthals_______/..................../
Chimps______________________/Presumably, you deny common ancestry between humans and ANY other animal, so the human lineage has to be essentially unbranched beyond the level of human 'kind'. And yet the existence of Neanderthals shows that it HAS branched *below* the level of kind.So I ask, yet again, what is it that somehow prevents branching *above* the level of 'kind' ?Further, what sort of criteria are used to determine the boundary of a kind?For example, the boundary of a species is defined according to isolation of a gene pool. If you can't come up with a single objective criterium for determining the boundary of a kind, then it is simply an arbitrary designation without any real biological significance.Now, most biologists would accept that all taxonomic designations above species level are also essentially arbitrary because they are not based on a clear biological criterium as is the species. However, in evolution we assume they represent important branch points in common ancestry because they are associated with major morphological differences, regardless of our inability sometimes to infer their exact location, since this inference is supported by many independent lines of evidence. There is no evidence to suggest that any arbitrary taxonomic designation (e.g. a 'kind') should remain immutable indefinitely, nor that it does not converge back to some common ancestor with another 'kind', regardless of how you see fit to define one, even though you haven't yet.

Well I just assumed that at some point the 3 must have shared as common ancestor. Starting with the lineage that ultimately led to humans, I am simply assuming that Neanderthals diverged from this lineage later than chimps did, given they are obviously closer to humans. I am not an expert on hominid phylogeny either, I was just trying to make the point that once you accept branching lineages, you may as well accept that more and more branches occur all the way back. There is no known mechanism that could ensure the eternal integrity of a 'kind', however defined, because this would imply no branching had ever occurred above this level.

Hi Mick,Yes, this is a truly curious situation. There are other known examples of zygotes that, once formed, discard the male genome and then develop normally. This is gynogenesis and it yields exclusively maternal inheritance. (I am not in my office or I would dig out some additional examples from my library). However, in this case what you have is essentially the phenomenon occurring in parallel in both sexes, something I had certainly never heard of before. I am not sure it undermines the general usefulness of the biological species concept (it is a very anomalous situation), but it does sort of create a gray area. Note that the two sexes are still 'linked' biologically, if not genetically, by virtue of ttwo factors: the requirement for 'fertilization' of the egg to trigger its development with the male genome, and the requirement of both genomes to produce viable workers, without which neither genetic lineage could survive.Another interesting example that comes to mind is certain species of gynogenetic fish. In these fish there is sort of 'genetic parasitism' of one species by another that is actually parthenogenetic. The parthenogenetic eggs still require the stimulation of sperm to begin development, but the enitre male genome is discarded. Females of the gynogenetic species must therefore court and seduce males of the truly sexual species and induce them to 'waste' their sperm in spawning with them. This would seem to comprise a very unstable ecological relationship given that one would expect strong selection for males to discriminate and avoid these females. Again, I am away from my university access point, but I did find one article on a genetic analysis of some of these fish. You can view the entire article here, but it seems to be an interesting example of duplication of an entire genome leading to speciation via triploidy.Mode of origin and sources of genotypic diversity in triploid gynogenetic fish clones (Poeciliopsis: Poeciliidae).Quattro JM, Avise JC, Vrijenhoek RC.Center for Theoretical and Applied Genetics, Rutgers University, New Brunswick, New Jersey 08903-0231.Most tributaries of the Rio Fuerte in northwestern Mexico contain one or more clones of allotriploid fish of the genus Poeciliopsis. We used multilocus allozyme genotypes and mitochondrial DNA (mtDNA) haplotypes to examine several potential modes of origin of these gynogenetic all-female fish. The allozyme studies corroborated earlier morphological work revealing the hybrid constitution of two triploid biotypes, Poeciliopsis 2 monacha-lucida and Poeciliopsis monacha-2 lucida. Each biotype carries one or two whole genomes from the each of the sexual species P. monacha and P. lucida. Restriction site analysis of mtDNA revealed that P. monacha was the maternal ancestor of five electrophoretically distinguishable triploid clones. Four of five clones were marked by closely related, composite, allozyme/mtDNA genotypes, suggesting they had common origins from an allodiploid clone of the P. monacha-lucida biotype. Genotypic analysis revealed that all five clones arose via the "genome addition" pathway. Fertilization of unreduced ova in P. monacha-lucida females by sperm from P. monacha and P. lucida males, respectively, gave rise to both biotypes.

Then there is no point in arguing for retention of the term or discussing the matter further.
It is just providing you biblical gratification without providing us with any scientific utility. So what happened to your precious human ‘kind’ created in God’s image ? But there is plenty of evidence for information *gain* in genomes, like for example in the article I cited back in message 56 of this thread. Plenty of other examples too. If divergence occurs primarily due to loss of information (genes), then why is it that we see organisms becoming more complex over time in the fossil record, rather than less? There is simply no evidence that some hypothetical initial ‘set’ of genomes were created. How, in your slippery view of the world, would we distinguish a ‘created’ genome from one that evolved ?When I asked if you deny branching of the human lineage, you said: Sorry, that’s not good enough. Without some sort of testability, postulates are just pipe dreams. The preponderance of the evidence points in the other direction, namely that the human lineage is one branch of the primate branch of the mammal branch which, itself, is only one branch of many others on a much larger tree. The idea of a 'kind' has absolutely no utility in this conceptualization. Fine. But the basic morphological differences between Neanderthals and modern humans (and other lines of evidence, I suspect) strongly suggest they would have been genetically incompatible. But I guess this distinction doesn’t matter to your definition of ‘kind’. Speciation is of no real consequence to your view of evolution because your imaginary immutable 'kinds' continue their evolution in parallel and can never be traced back to a common ancestor. So I ask you, yet again, once you have separate gene pools what can possibly limit the degree of divergence of one organism from another ? Answer: nothing. So there is nothing that can possibly maintain the integrity of your 'kind' within any of the implied limits. I meant that if the human lineage branched into Neanderthals 'below' the point where it became recognizably 'human' (which it did, despite your insistence in considering them the same ‘kind’), then what prevents the human lineage from being one branch diverging from another lineage (above the level of human ‘kind’)? But now, from the above quotes, it seems you have conceded (1) you cannot provide a functional definition of how a ‘kind’ is delineated and held immutable and (2) you accept that you cannot disprove genetic evolution of humans from primates. So what earthly (scientific) use is your nebulous, biblically-derived concept of 'human kind'?
I think I can rest my entire case at this point.

I agree that generation time is the meaningful unit of time to be considered when thinking about relative rates of evolutionary change in various species, but surely if you accept the basic fossil record with its time line of geological stratification then this means that all the most complex organisms appeared relatively late, while simple ones were around the longest (e.g. the Archaebacteria). Despite their shorter generation times and consequently ample opportunity to evolve complexity, they have not. They simply happen to occupy niches that favor simple body plans and select against increases in complexity. I doubt you would be willing to argue that simple organisms have frequently evolved from more complex ones, which is the essence of what we would expect if god created a fixed number of 'kinds' which then diversified through speciation in parallel, but with an overall trend toward loss of genetic information, albeit occurring at different rates in different lineages. So Mick's point about gene density being greater in the more complex organisms does have an implicit time component when viewed in the context of other evidence that most of us, and I suspect you also, accept.

Point well taken. Some primitive Archaebacteria obviously did evolve complexity, while those remaining in the ancestral niches did not. (I should have stated that better). So you get some lineages evolving complexity while others do not, but you don't usually see decreasing complexity as an overall trend in any lineage. But exactly how would he hide there and what on earth could possibly constitute evidence of 'genomic creation' as opposed to evolved sequences, whether they are coding or non-coding ? I argue against the concept of created kinds because there is no way to objectively distinguish one kind from another and no imaginable, let alone demonstrable, mechanism for preserving the boundaries. The same applies to created genomes, that are now apparently allowed to diversify and speciate within invisible boundaries that only god can recognize. So it falls upon creationists to come up with some kind of evidence for this apparent 'devolution' of living things they seem to be postulating. I have given up trying to 'convince' creationists. They will see god in a genome as fast as a Latin American will see the virgin Mary in a taco. I will settle for demonstrating they have no workable scientific mechanisms or testable theories, nor can any functional insights be derived from their musings.

True enough. Science does not address final origins. But it works very well to explain the 'how' without the need to invoke any metaphyscial intervention, so why postulate what isn't needed? Sorry, I'm not buying that. That's like saying "You can't proved there *isn't* a God, so its equally likely that there may be one". Science only requires 'faith' in the methods of data collection and analysis which have proven eminently reliable. Yes. and I am perfectly OK with that, provided that these philosophies and theologies do not try to encroach on the domain of science and color its interpretation to fit a predetermined world view. That is what 'creation science' does.