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Author Topic:   ID/Creationism - Comparison of Human and Chimp Genomes
Meddle
Member (Idle past 1270 days)
Posts: 179
From: Scotland
Joined: 05-08-2006


Message 31 of 83 (359127)
10-26-2006 7:06 PM
Reply to: Message 10 by eggasai
10-22-2006 5:22 PM


Re: Pause for effect
The problem with the 98.5% similarity between humans and chimp was that it was based on DNA hybridisation, since that was the only method available at the time. Identical sequences will anneal, no matter where they are found, so indels can't be identified with this method. To do that you need an accurate genetic sequence to compare.
Your second article is an abstract from the original 2003 article which used a direct comparison of human and chimp genetic sequences. Of course this value of 95% could change, since the comparison was performed on a 779kb sequence.
As for your first article it's from Time magazine, not exactly a primary science journal.
Edited by Evil Homer, : No reason given.

This message is a reply to:
 Message 10 by eggasai, posted 10-22-2006 5:22 PM eggasai has not replied

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Meddle
Member (Idle past 1270 days)
Posts: 179
From: Scotland
Joined: 05-08-2006


Message 32 of 83 (359129)
10-26-2006 7:07 PM
Reply to: Message 12 by eggasai
10-22-2006 7:05 PM


Re: number of point mutations is not equal to number of nucleotide differences
For instance, the PtERV1 gene is present in Chimpanzees and OWM but is absent in Asian Great Apes and humans.
For the PtERV1 sequences (not a gene, rather a collection of genes following the basic retroviral structure of ltr-gag-pol-env-ltr) it has been found there is virtually no overlap of insertion locations between species. This suggests it is not the result of vertical transmission from a common ancestor, but instead originated from horizontal transmission (infection after the species had diverged).
http://biology.plosjournals.org/perlserv?request=get-docu...
1) 35 million base pairs (Mb) due to single nucleotide substitutions.
2) 5 million indels, coming to 90 Mb in the respective genomes or 3%-4%.
3) 9 pericentric inversions from 2 Mb to 4 Mb in lenght, totally 20 Mb.
And just to add to those numbers, the human genome is 3 billion base pairs long, and only about 1.5% of this represents protein-coding genes.
With a population of over 6 billion the human genome diverges by 1/10 of 1%, but you know what, we can get back to that one. Let's say that these are permenantly fixed, this would account for the 35 Mb worth of single nucleotide substitutions. What about the indels?
Where did you get this value for the genomic divergence within the human population? Not that I doubt it, it would just be interesting to see what this was based on.

This message is a reply to:
 Message 12 by eggasai, posted 10-22-2006 7:05 PM eggasai has replied

Replies to this message:
 Message 34 by eggasai, posted 10-26-2006 7:53 PM Meddle has replied

  
eggasai
Inactive Member


Message 33 of 83 (359138)
10-26-2006 7:27 PM
Reply to: Message 26 by mick
10-26-2006 5:34 AM


Re: Where are the ID hypotheses?
quote:
This is certainly the standard approach of creationists, but it is not actually the first step in effecting a paradigm shift in science.
It most certainly is because natural selection is the default explanation for absolutly everything in evolution as natural history. God is excluded a priori and the evidence becomes secondary to that.
quote:
One would really want to forge a superior theory that can explain everything explained by evolutionary theory, plus some other things that evolutionary theory cannot explain. If all you want to do is "deconstruct Darwinism" but have not a single theory with which to replace it, that is hardly a constructive enterprise.
Deconstructing Darwinism might well be all that is required here. Did I say that creationism was going to propel science into the 21st century and Darwinism was all that was holding them back? I don't think so, I said that deconstructing Darwinism was the first step. Then instead of a default explanation that infers either God or exclusivly naturalistic causation you simply look at what happens in living systems. Projecting into the prehistoric and primordial past is well beyond the purview of science, science is nessacarily focused on what is observed and demonstrated.
quote:
Why not give us the Intelligent Design explanation for the origin of characteristics unique to the human brain, and let us see how it stands up against the evolutionary explanation?
Intelligent design is simply a group of intellectuals and scientists that has said science is taking this theory beyond it's range of inquiry. It wouldn't have happened if the Darwinian didn't claim the answer for every adaptation is natural selection. It is also an a priori assumption that offers no objective standard for falsification. Show me one creationist that has a problem with Mendelian genetics, or better yet. The Human Genome Project has a website with educational material on DNA and how it works. Not once is evolution even mentioned. Biology could go on ad infinitum and never once postulate an ape man transitional and genetic researchers have yet to find a genetic basis for the evolution of the humans brain. All creationism and ID really needs is the a priori assumption removed and let the evidence do what it is supposed to, show us how living systems work.
quote:
This thread is about the ID response to the human/chimp genome comparison, but we have heard not a single non-Darwinian hypothesis explaining the observed genome data. All we get is the standard creationist bluster, which is to claim that evolutionary theory is collapsing (just that no scientists have noticed, yet). If you have your way, and "Darwinism" is one day tossed into the grime at the back of history's fume cupboard, how are we going to explain the similarites and dissimilarities of the human and chimp genomes?
You want to hear something ironic? If Darwinism as natural history is discarded it will be because of natural selection and how it acts on deleterious effects. I know we haven't gotten aquinted but believe me when I tell you I'm not your run of the mill creationist. In fact, I think evolution as defined scientifically is the very antithesis of the Darwinian single common ancestor model.
As far as ID I think it makes some great insights into irreducible complexity. Everything in science seems to be boiling things down to an irreducible minimum, that's what is going on here. The problem is that they go the next step and say, therefore 'intellient design'. I've read Paley and I really like his analogy of a watch and a stone. it is natural theology though, that does not make it untrue or an illogical conclusion from the evidence. What it does is take the evidence outside the purview of science, into the intellectual and philosphical realms where scientists are illequiped to make an honest judgment.
You want to see creationism/ID go away tommorow, drop the presumption of exclusivly naturalistic forces. Then quit pretending you know what was going on in prehistoric and primordial ages past because you don't.

This message is a reply to:
 Message 26 by mick, posted 10-26-2006 5:34 AM mick has replied

Replies to this message:
 Message 36 by mick, posted 10-26-2006 11:33 PM eggasai has replied

  
eggasai
Inactive Member


Message 34 of 83 (359144)
10-26-2006 7:53 PM
Reply to: Message 32 by Meddle
10-26-2006 7:07 PM


Re: number of point mutations is not equal to number of nucleotide differences
quote:
For the PtERV1 sequences (not a gene, rather a collection of genes following the basic retroviral structure of ltr-gag-pol-env-ltr) it has been found there is virtually no overlap of insertion locations between species. This suggests it is not the result of vertical transmission from a common ancestor, but instead originated from horizontal transmission (infection after the species had diverged).
Shortened link

Wait a second here, if the homology arguement works in favor of common ancestor then why does the inverse logic not work. You want to focus on anecdotal evidence that favors one small segment of on ERV mutation. It's the progressive nature of the mutation that makes it so appealing a proof of common ancestry but when it is in OWM and not in humans at all you just want to dismiss it.
You might want to reconsider a simple assumption. What rational reason to you have to assume that 8% of the genome is made up of the fossilized remains of viruses. These germline invasions are rare at best, the idea that hundreds of millions of base pairs of DNA are permenantly fixed in genomes by viruses is absured.
quote:
And just to add to those numbers, the human genome is 3 billion base pairs long, and only about 1.5% of this represents protein-coding genes.
Let me ask you this, the gorilla split with both the human and chimpanzee lineage well before the austropithicene/homo split. Would you expect that 83% of the protein coding genes would show differences at an amino acid seqeunce level? You guys like to make a priori assumptions and use anecdotal evidence but you don't like making predictions. How about the spit between western and eastern gorillas, how much would you expect two seperate species to diverge within the same genus? The gorilla/chimpanzee split goes back further then the austropithecene/homo one, how would you expect the genes to line up?
Edited to add:
quote:
Where did you get this value for the genomic divergence within the human population? Not that I doubt it, it would just be interesting to see what this was based on.
Human Genome Projects website. It's a wonderfull place to go and look at genomics without all of this creation/evolution bluster muddying up the waters.
Edited by eggasai, : No reason given.
Edited by AdminJar, : No reason given.

This message is a reply to:
 Message 32 by Meddle, posted 10-26-2006 7:07 PM Meddle has replied

Replies to this message:
 Message 44 by Meddle, posted 10-28-2006 9:03 PM eggasai has not replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 35 of 83 (359145)
10-26-2006 7:55 PM
Reply to: Message 28 by eggasai
10-26-2006 6:33 PM


Sure, 40,000 amino acids don't seem like a whole lot until you take into consideration that this is 120,000 nucleotides at the very least.
No, no, no. You don't need three nucleotide changes to change one amino acid. Learn a little genetics before you start lecturing us on it.
Turkana Boys cranium has been compared to modern Chinese and it is only slightly smaller and as far as then can tell to internal proportions are pretty close.
Turkana boy had a cranial capacity of 880 cc; it is estimated that it would have been 910 cc at adulthood.
Average modern human cranial capacity is 1350 cc.
The point being the space between Homo habilis and Tukana Boy is simply not measured in millions of years but hundreds of thousands.
What of it? There is no reason, indeed, why you shouldn't find a habilis LATER than Turkana boy. Oh yes, and there are still monkeys.
* sigh *
You do need hundreds, if not thousands of mutations in hundreds if not thousands of genes for this to happen. Like the Cambrian Explosion and every major epoch in evolution as natural history this is invariably the case. Major mophological adaptations in a relativly brief period of time. This is exactly what a creationist would expect, a sharp line of demarkation between originally created kinds.
But this is a complete non sequitur. If there are major morphological adaptions in a relatively brief period of time, then there are not sharp lines of demarkation between kinds. Au contraire if there are major morphological adaptions in a relatively brief period of time, then there are major morphological adaptions in a relatively brief period of time.
Such as wolf ---> chihuahua.
I mean, this is weird. It's as though you'd got hold of historical documents proving that the Egyptians built the pyramids very quickly, and then concluded from this evidence that aliens must have built the pyramids, because Egyptians couldn't have built them that quickly.
Don't take my word for genes involved with neural functions, look up mutations affecting neural functions in the human brain. There is nothing indicating beneficial affects and yet it is here that the burden of proof weighs heaviest upon the evolutionist.
Again, could I point out that the differences between our brains and those of apes are in fact beneficial to us.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 28 by eggasai, posted 10-26-2006 6:33 PM eggasai has not replied

  
mick
Member (Idle past 4986 days)
Posts: 913
Joined: 02-17-2005


Message 36 of 83 (359202)
10-26-2006 11:33 PM
Reply to: Message 33 by eggasai
10-26-2006 7:27 PM


Re: Where are the ID hypotheses?
Hello again eggasai,
eggasai writes:
. I know we haven't gotten aquinted but believe me when I tell you I'm not your run of the mill creationist
Well, that remains to be seen . Really, I do appreciate your contributions and I do not wish to typecast you. I am debating with you on quite similar material on two separate threads, so I just want to make it clear at the outset that I do not want to give the impression that I am hounding you or anything like that.
eggasai writes:
It most certainly is because natural selection is the default explanation for absolutly everything in evolution as natural history. God is excluded a priori and the evidence becomes secondary to that.
This is a bit of a red herring. First, natural selection is not the "default explanation for absolutely everything in evolution". In reality, neutral models of evolution are often considered to be the null hypothesis and the existence of natural selection must be inferred by departures from the predictions of that null model. Second, because the exclusion of God does not make the evidence "secondary" in any way; scientists also exclude fairies, unicorns and Satan from their causal models for the simple reason that their existence cannot be empirically falsified and therefore cannot offer much in terms of material causation. So please don't feel that (the Christian?) God is being excluded because evolutionary biologists have some sort of religious axe to grind; at least, to no more an extent than all scientists have a methodological prejudice against pixies, fairies, Valhalla and elephant-headed gods playing a role in causal explanation.
eggasai writes:
Projecting into the prehistoric and primordial past is well beyond the purview of science, science is nessacarily focused on what is observed and demonstrated.
I have serious reservations about your statement, mainly because you don't reallly define what you mean by "observed". Prehistoric events can be directly observed in the sense that they leave behind physical traces of their existence (fossils, geological formations, corpses, written documents, radiation, etc). But I assume you have a problem more generally with the concept of inference used by evolutionary biologists. It is my opinion that inference is the cornerstone of science. Astronomers infer the existence of stars which they cannot directly observe, based on electron degeneracy; oil engineers infer the existence of oil fields which they cannot observe based on geology; chemists infer the strength and existence of chemical bonds based on the temperature required to effect a change in state of a substance; etc. etc. Evolutionary biology is no different in inferring the existence of an evolutionary process from existing observable data. However that process can also be directly observed in the laboratory, as you may know.
If you really want to get rid of inference in biology, I'm not sure what we would be left with other than a collection of statistical descriptions of the patterns evident in nature. There would certainly be no possible causal explanation of anything. But this really does appear to be what you are suggesting:
egassai writes:
econstructing Darwinism was the first step. Then instead of a default explanation that infers either God or exclusivly naturalistic causation you simply look at what happens in living systems...All creationism and ID really needs is the a priori assumption removed and let the evidence do what it is supposed to, show us how living systems work.
First, it is a bit rich to claim that creationists or ID proponents are in some way hindered by the a priori assumptions of evolutionary biology. There is nobody stopping them from abandoning such assumptions, "simply looking at what happens in living systems" and reporting what they find. Indeed I have specifically invited you to do precisely this! hence my request for an ID explanation of the genome data.
You want to see creationism/ID go away tommorow, drop the presumption of exclusivly naturalistic forces
I am perfectly happy to concede arguendo that evolutionary biology is a load of bunkum that cannot explain the first thing about chimpanzee genomes; that God or the divinity or intelligent agent of your choice has been monitoring and modifying the universe since its creation; and that exclusively naturalistic forces cannot explain the patterns we see in nature.
So, let us look together at the patterns you have described:
1. human and chimp DNA is extremely similar
2. human DNA contains a large number of repeated units of great similarity to viral DNA
3. the number of nonsynonymous nucleotide differences beween chimp and human DNA is smaller than the number of synonymous differences
When I look at these facts without any inferential framework I have a great deal of difficulty working out what they signify. How many identical aligned nucleotides should we expect to find between human and chimp? Is 8% a high proportion or a low proportion of apparently viral DNA in the human genome? Why does it look like viral DNA?
Since I have dropped what you define as the a priori assumptions of biology, could you explain to me what is supposed to have become clear?
Mick

This message is a reply to:
 Message 33 by eggasai, posted 10-26-2006 7:27 PM eggasai has replied

Replies to this message:
 Message 37 by Hyroglyphx, posted 10-27-2006 12:17 PM mick has not replied
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Hyroglyphx
Inactive Member


Message 37 of 83 (359311)
10-27-2006 12:17 PM
Reply to: Message 36 by mick
10-26-2006 11:33 PM


Re: Where are the ID hypotheses?
This is a bit of a red herring. First, natural selection is not the "default explanation for absolutely everything in evolution". In reality, neutral models of evolution are often considered to be the null hypothesis and the existence of natural selection must be inferred by departures from the predictions of that null model.
Natural Selection is not the only hypothesis within the theory of evolution, but it certainly plays a huge part. Taking primacy would likely be mutations and trailing in second would be gene selection. Unfortunately, mutations tend to be so injurious to an organism that one may draw a logical conclusion that mutations directly affect the organism as it relates to natural selection in the negative-- i.e., the organisms greatly affected by mutation are eliminated. There is no demonstrable evidence to suggest that either natural selection or mutations have the capacity to lead to higher taxon.
Second, because the exclusion of God does not make the evidence "secondary" in any way; scientists also exclude fairies, unicorns and Satan from their causal models for the simple reason that their existence cannot be empirically falsified and therefore cannot offer much in terms of material causation.
There is nothing in science, that draws inferences from the material universe, that could directly prove the existence of God. Granted. But that doesn't mean that one could not logically draw upon some conclusions that things just happening for fortuitous reasons are few and far between. Eggastai is simply saying that Darwinism and its uncle, 'Strict Naturalism,' has put science in a chokehold and refuses to accept any alternative hypotheses.
1. human and chimp DNA is extremely similar
Don't you see the presumption in the whole thing? Humans and chimps just happen to share anatomical similarities. Instead of simply assuming that because they share a similar genetic sequence they must be somehow related, why not simply consider that if there were an Intelligent Designer, that at some point, some organisms are going to resemble one another more closely than others.
2. human DNA contains a large number of repeated units of great similarity to viral DNA
Right, but humans share 97% similarity with a field mouse and 52% similarity with a banana. Does that mean we evolved from fruit or could it mean that we know much about the structure of DNA but almost nothing about what that means from an evolutionary standpoint? I mean, all this is still loads of conjecture that rests its case on circumstantial evidence. We're still looking for the smoking gun with some actual evidence either found in stratum or walking amongst us today.
3. the number of nonsynonymous nucleotide differences beween chimp and human DNA is smaller than the number of synonymous differences
Yes, we hear much about the synonymous sequences but almost nothing about non-analogous sequences.
When I look at these facts without any inferential framework I have a great deal of difficulty working out what they signify. How many identical aligned nucleotides should we expect to find between human and chimp? Is 8% a high proportion or a low proportion of apparently viral DNA in the human genome? Why does it look like viral DNA?
Because perhaps DNA is DNA. That might be as asinine as asking why the atoms that comprise a turtle are so similar to the atoms that comprise a rock. Could one be related to other or do we just know what atoms are? I mean, DNA is a very complicated molecule that is still in its infancy as far as it relates to our total grasp of unraveling all its mysteries.

"There is not in all America a more dangerous trait than the deification of mere smartness unaccompanied by any sense of moral responsibility." -Theodore Roosevelt

This message is a reply to:
 Message 36 by mick, posted 10-26-2006 11:33 PM mick has not replied

Replies to this message:
 Message 38 by Modulous, posted 10-27-2006 12:53 PM Hyroglyphx has replied

  
Modulous
Member
Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


Message 38 of 83 (359316)
10-27-2006 12:53 PM
Reply to: Message 37 by Hyroglyphx
10-27-2006 12:17 PM


Comparisons
There is no demonstrable evidence to suggest that either natural selection or mutations have the capacity to lead to higher taxon.
That's because evolution doesn't propose that new taxa will be arrived at, but instead only lower taxa. As things grow more and more different, new taxa are classified. Remember, a scientific theory can't predict the existence of subjective concepts such as the boundaries of a classification system.
The evidence is overwhelming that the vast majority of species are in some way related to each other - how species can be related is the question the Theory of Evolution seeks to answer with its myriad of mechanisms such as natural selection and variation.
Don't you see the presumption in the whole thing? Humans and chimps just happen to share anatomical similarities.
Yes they do. But they could have massively different genomes and still be anatomically similar. There is no reason why their cytochrome c protein is coded for in an identical manner other than heredity. A cytochrome c protein can be coded for in an astronomical number of ways - most of which we don't see in nature...they seem to be clustered around a sequence of very similar coding patterns (the closer related the organisms are hypothesized to be from other methods, the more similar).
What your explanation dramatically fails to take into account is that the genome comparison doesn't just discuss genes that control anatomy, and there are many many parts of the genome that do not control anatomy and they can be coded for in a very different way .
Instead of simply assuming that because they share a similar genetic sequence they must be somehow related, why not simply consider that if there were an Intelligent Designer, that at some point, some organisms are going to resemble one another more closely than others.
You have to explain why the assumption that close genetic sequences yields accurate predictions on what we should find in the fossil record and where. You'll also have to explain things like marsupials. The marsupial mouse and the marsupial mole are more genetically similar to a kangaroo than they are to their placental equivalents which are more closely related to humans. Two things which are anatomically close but which are genetically less like things which are anatomically different.
Here's the kicker - the differences are in line with the predictions that can be made from ToE. Creationism and/or ID have failed to take account of all this evidence and merely say 'similar designer' when they see similar genes and 'creativity' when they see dissimilar ones. Their response is not as a result of any predictive power of their concept, but an ad hoc explanation. Its possible that that whoever designed us designed us in a way to make it look like what we see - but that is why creationism has been called unfalsifiable - whatever we see is fine with creationism.
Right, but humans share 97% similarity with a field mouse and 52% similarity with a banana.
97% do you have a source for that? I can't find anything off the top of my head except a BBC article which states a figure closer to 80%
Does that mean we evolved from fruit or could it mean that we know much about the structure of DNA but almost nothing about what that means from an evolutionary standpoint?
No - it means that the mouse and human share a more recent common ancestor with each other (a mammal in the past 100 million years ago or so), than they do with a banana (a single celled entity closer to 3 billion years ago).
Edited by Modulous, : No reason given.

This message is a reply to:
 Message 37 by Hyroglyphx, posted 10-27-2006 12:17 PM Hyroglyphx has replied

Replies to this message:
 Message 39 by Hyroglyphx, posted 10-27-2006 3:27 PM Modulous has replied

  
Hyroglyphx
Inactive Member


Message 39 of 83 (359340)
10-27-2006 3:27 PM
Reply to: Message 38 by Modulous
10-27-2006 12:53 PM


Re: Comparisons
That's because evolution doesn't propose that new taxa will be arrived at, but instead only lower taxa... The evidence is overwhelming that the vast majority of species are in some way related to each other - how species can be related is the question the Theory of Evolution seeks to answer with its myriad of mechanisms such as natural selection and variation.
Well, of course lower taxa as subspecies are formed all the time within a host species, but then how is it that higher taxon exist? We know that horses and dogs have different breeds, which we should expect, but where is the smoking gun that shows any sort of macroevoultionary development? Darwin sought to answer this question in his day and hoped that an answer would eventually be uncovered. Here we are over 150 years after the fact and we are still asking the exact same questions. Don't you find that odd if the theory is presumed to be so solid?
But they could have massively different genomes and still be anatomically similar. There is no reason why their cytochrome c protein is coded for in an identical manner other than heredity. A cytochrome c protein can be coded for in an astronomical number of ways - most of which we don't see in nature...they seem to be clustered around a sequence of very similar coding patterns (the closer related the organisms are hypothesized to be from other methods, the more similar).
An interesting notion has that is often overlooked is that there is no tangible evidence that all things are related by a common ancestor since we don't have the progenitors sequence on file. And if you think about it logically, DNA comparisons are just a subset of the homology argument, which makes just as much sense as a common Designer argument. An engineer uses the same type of materials and conforms to the same laws of physics in most cases, so why should we expect something different in the engineering of a cell or a molecule?
As for cytochrome c, a common argument in defense of evolution, I have only made cursory glances at the argument and have not reviewed it in plenary. This article makes a persuasive argument from the viewpoint that I shared above.
Here's the kicker - the differences are in line with the predictions that can be made from ToE.
No, the real kicker is a case of garbage in, garbage out. No predictions were made, those were postdictions. They simply look at organisms that share the most similarity and tailor their argument according to that. That isn't a prediction at all.
97% do you have a source for that? I can't find anything off the top of my head except a BBC article which states a figure closer to 80%
This article posits that mice share 97.5% biochemical similarity with that of the common field mouse.

"There is not in all America a more dangerous trait than the deification of mere smartness unaccompanied by any sense of moral responsibility." -Theodore Roosevelt

This message is a reply to:
 Message 38 by Modulous, posted 10-27-2006 12:53 PM Modulous has replied

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eggasai
Inactive Member


Message 40 of 83 (359384)
10-27-2006 7:24 PM
Reply to: Message 36 by mick
10-26-2006 11:33 PM


Re: Where are the ID hypotheses?
quote:
This is a bit of a red herring. First, natural selection is not the "default explanation for absolutely everything in evolution". In reality, neutral models of evolution are often considered to be the null hypothesis and the existence of natural selection must be inferred by departures from the predictions of that null model.
That's not true, natural selection is not a big contributor to human evolution, it would have to be a spike in the mutation rate. They understate it but that's what the translation is, I don't think anyone is ready to explain the level of divergance.
"There is tentative evidence from in-depth analysis of divergence and diversity that natural selection is not the major contributor to the large-scale patterns of genetic variability in humans45, 46, 47. For these reasons, we suggest that the large-scale variation in the human-chimpanzee divergence rate primarily reflects regional variation in mutation rate."
Initial sequence of the chimpanzee genome and comparison with the human genome (see genome evolution)
quote:
If you really want to get rid of inference in biology, I'm not sure what we would be left with other than a collection of statistical descriptions of the patterns evident in nature. There would certainly be no possible causal explanation of anything. But this really does appear to be what you are suggesting
The only inferance I want to get rid of is the a priori assumption of a single common ancestor. It has very little to do with natural selection and less then nothing to do with genomics. Evolution as scientifically defined is the change of alleles in populations over time. This need not 'infer' anything about our primordial or prehistoric past.
quote:
First, it is a bit rich to claim that creationists or ID proponents are in some way hindered by the a priori assumptions of evolutionary biology. There is nobody stopping them from abandoning such assumptions, "simply looking at what happens in living systems" and reporting what they find. Indeed I have specifically invited you to do precisely this! hence my request for an ID explanation of the genome data.
I have a better idea, why don't you try to elaborate on a genetic basis for the divergance between chimpanzees and humans? If there is anything more irreducibly complex it's the human brain. To date I have yet to see any of the reseach determine a viable genetic mechanism capable of pulling this off.
quote:
I am perfectly happy to concede arguendo that evolutionary biology is a load of bunkum that cannot explain the first thing about chimpanzee genomes; that God or the divinity or intelligent agent of your choice has been monitoring and modifying the universe since its creation; and that exclusively naturalistic forces cannot explain the patterns we see in nature.
That's how you guys get by with this, you convince creationists that they are opposed to the genuine article of science. What you really are trying to hide is the fact that your presumption of a single common ancestor has nothing to do with the actual science. Biology does not need the single common ancestor model. Mind you, I'm not saying that there are no common ancestors (plural), just that your insistance on a single common ancestor is pure undiluted mythology.
quote:
So, let us look together at the patterns you have described:
1. human and chimp DNA is extremely similar
Diverging by 35 Mb of single nucleotide substitutions, 5 million indels of 90 Mb and 9 pericentric inversions from 2 Mb to 4 Mb adding up to 145 Mb. The level of divergance is simply not accounted for by the mutation rate observed in hominids. If you have a genetic mechanism for pulling this off I would love to hear about it.
quote:
2. human DNA contains a large number of repeated units of great similarity to viral DNA
Your talking about ERVs right? They make up 8% of the human genome and this makes for one of the all time sweeping assumptions of all time. You expect people to believe without qualification that 8% of the human genome is the fossilized remains of viruses from rare germline invasions? Your really going to have your work cut out for you on this one.
quote:
3. the number of nonsynonymous nucleotide differences beween chimp and human DNA is smaller than the number of synonymous differences
"The KA/KS ratio is a classical measure of the overall evolutionary constraint on a gene, where KA/KS1 indicates that a substantial proportion of amino acid changes must have been eliminated by purifying selection. Under the assumption that synonymous substitutions are neutral, KA/KS > 1 implies, but is not a necessary condition for, adaptive or positive selection. The KA/KI ratio has the same interpretation. The ratios will sometimes be denoted below by with an appropriate subscript (for example, human) to indicate the branch of the evolutionary tree under study...
Given the low rate of recombination in hominid genomes (a 1 kb region experiences only 1 crossover per 100,000 generations or 2 million years), such background selection should extend beyond exons to include nearby intronic sites94. However, when the divergence rate is plotted relative to exon-intron boundaries, we find that the rate jumps sharply within a short region of 7 bp at the boundary " (Chimpanzee Genome, Nature 2005)
quote:
Since I have dropped what you define as the a priori assumptions of biology, could you explain to me what is supposed to have become clear?
The level of divergance, the time it had to happen in and the mutation rate. Once these are established in your mind I can explain to you what is supposed to have become clear.
quote:
A total of 585 of the 13,454 human-chimpanzee orthologues (4.4%) have observed KA/KI > 1

This message is a reply to:
 Message 36 by mick, posted 10-26-2006 11:33 PM mick has replied

Replies to this message:
 Message 41 by crashfrog, posted 10-27-2006 10:16 PM eggasai has not replied
 Message 43 by mick, posted 10-28-2006 7:13 AM eggasai has not replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 41 of 83 (359408)
10-27-2006 10:16 PM
Reply to: Message 40 by eggasai
10-27-2006 7:24 PM


Re: Where are the ID hypotheses?
If there is anything more irreducibly complex it's the human brain.
I appreciate that "irreducable complexity" is a trait in want of a definition, but surely even you can't believe this.
Anybody who's suffered any sort of brain damage or stroke can testify how reducably complex the brain really is. The brain can suffer the removal of all kinds of parts and still continue to function.
No biggie, though. I'm sure you'll impugne my understanding of biology (and possibly the legitimacy of my parentage) without making any sort of correction to your argument. Have fun!

This message is a reply to:
 Message 40 by eggasai, posted 10-27-2006 7:24 PM eggasai has not replied

  
Modulous
Member
Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


Message 42 of 83 (359428)
10-28-2006 1:02 AM
Reply to: Message 39 by Hyroglyphx
10-27-2006 3:27 PM


Re: Comparisons
Well, of course lower taxa as subspecies are formed all the time within a host species, but then how is it that higher taxon exist?
The first life was in the ultimate highest taxon: life. This life developed along a number of paths. Paths we now call Domains. These Domains then had lower taxa which we call Kingdoms. The higher taxa are merely created by definition of lower taxa. So, evolution doesn't propose that new higher taxa will form, only more and more lower taxa.
We know that horses and dogs have different breeds, which we should expect, but where is the smoking gun that shows any sort of macroevoultionary development?
Probably more appropriate to discuss chimps and humans rather than dogs and horses. The evidence that the two have diverged from a common ancestor has been addressed already.
Darwin sought to answer this question in his day and hoped that an answer would eventually be uncovered. Here we are over 150 years after the fact and we are still asking the exact same questions. Don't you find that odd if the theory is presumed to be so solid?
We aren't asking the same questions as Darwin. Many of the concepts that Darwin proposed have been ultimately discarded and many of his questions have been answered. We are still asking very similar questions because science always asks questions. Nowadays scientists are rarely asking the kinds of questions you claim 'we' are asking. It is only 'we' when defined in terms of creationists.
An interesting notion has that is often overlooked is that there is no tangible evidence that all things are related by a common ancestor since we don't have the progenitors sequence on file.
There is evidence. First, the fossil record gives as an idea that life has existed in many varying forms which over time have changed in a variety of ways. Next, the genetic evidence is massive evidence that current species are related to one another by more distant common ancestors. The fact that the genetic evidence has successfully been used to predict where in the fossil record we'd expect to find certain organisms also indicates that the evidence is very strong.
And if you think about it logically, DNA comparisons are just a subset of the homology argument, which makes just as much sense as a common Designer argument.
Of course they are similar to the homology argument. It is a homology argument. The point is not that they are similar though - that could easily be the result of common design. I discussed this in the post you are replying to. The point is the specific patterns with the similarities. The fact that the morphological comparisons produce extremely similar conclusions to genetic comparisons. That is what must be explained, and that is what the common designer argument is currently unable to explain in terms not related to heredity.
I went into this very rebuttal in the post you replied to, so if you want to discuss it any more, simply refer back to that and respond to that.
No, the real kicker is a case of garbage in, garbage out. No predictions were made, those were postdictions.
Quite the contrary. Darwin himself stated that the marsupials and the placentals must have split from one another a long long time ago. If we don't know what the fossil date is, we can still calculate it using the genetic clock. That is a predictive power. It doesn't matter that we know the conclusion from other sources - since that fact does not enter the maths.
They simply look at organisms that share the most similarity and tailor their argument according to that.
I could share with you a paper, and you show where they did that some time. Indeed, if you have time you can quickly read some of my posts this related thread, you will see me discuss this issue step by step with Ray Martinez.
The methodology is to take a date from the fossil record of a probable common ancestor with two extant organisms. They then use that date to calibrate a clock. From that date they can work out the dates which other fossils will be calculated at. If the date they got from the fossil record was wrong, then the clock would be incorrectly calibrated and the calculated dates of common ancestors would be wildly incorrect. It could only give accurate results if the assumptions plugged into it are right or a gigantic coincidence has happened. The other alternative is that some agent deliberately placed the evidence there like that without leaving any evidence of them having done so. You should try that defense in court one day - see if they think that's enough to cause reasonable doubt.
So: if a person who was ignorant of the fossil record was told the date of one common ancestor, could take genetic samples from two or more descendants of that ancestor and tell you where the common ancestor for birds and crocodiles would be in the fossil record. Being able to tell somebody the date of a possible fossil, without even knowing if a fossil matching the description has ever been found is what we refer to as predictive power.
This article posits that mice [sic] share 97.5% biochemical similarity with that of the common field mouse.
I see it, I think that is using a similar method that gives us 98.5% for chimps, but I'm more used to seeing the currently more discussed figure of 96% for chimps.

This message is a reply to:
 Message 39 by Hyroglyphx, posted 10-27-2006 3:27 PM Hyroglyphx has not replied

  
mick
Member (Idle past 4986 days)
Posts: 913
Joined: 02-17-2005


Message 43 of 83 (359450)
10-28-2006 7:13 AM
Reply to: Message 40 by eggasai
10-27-2006 7:24 PM


Re: Where are the ID hypotheses?
Hi eggassai,
In post number 26 you said deconstructing darwinism is the necessary first step for its opponents because "natural selection is the default explanation for absolutly everything in evolution".
I replied that "In reality, neutral models of evolution are often considered to be the null hypothesis and the existence of natural selection must be inferred by departures from the predictions of that null model"
You replied as follows:
egassai writes:
natural selection is not a big contributor to human evolution, it would have to be a spike in the mutation rate. They understate it but that's what the translation is, I don't think anyone is ready to explain the level of divergance.
"There is tentative evidence from in-depth analysis of divergence and diversity that natural selection is not the major contributor to the large-scale patterns of genetic variability in humans45, 46, 47. For these reasons, we suggest that the large-scale variation in the human-chimpanzee divergence rate primarily reflects regional variation in mutation rate
Initial sequence of the chimpanzee genome and comparison with the human genome (see genome evolution)

Your quote supports MY position that natural selection is not the "default explanation" or null hypothesis for biologists. The example you give clearly shows biologists NOT inferring the importance of natural selection. You appear to be arguing against yourself.
You are arguing against the evolutionary explanation of human/chimp genome similarities and dissimilarities. I have asked you repeatedly to provide an alternative explanation. Your response to my request is:
eggasai writes:
I have a better idea, why don't you try to elaborate on a genetic basis for the divergance between chimpanzees and humans?
My proposed mechanism would consist of mutation, selection and drift. The parameters involved in these processes are described in the nature paper you keep citing.
Now perhaps it is your turn to describe an alternative mechanism? Last time I asked you, I got the following:
The level of divergance is simply not accounted for by the mutation rate observed in hominids. If you have a genetic mechanism for pulling this off I would love to hear about it...You expect people to believe without qualification that 8% of the human genome is the fossilized remains of viruses from rare germline invasions? Your really going to have your work cut out for you on this one...
That is not an alternative explanation, it is a critique of the existing one.
Please permit me to repeat myself. I will save you the trouble of debunking evolutionary theory. I am perfectly happy to concede arguendo that evolutionary biology is a load of bunkum that cannot explain the first thing about chimpanzee genomes; that God or the divinity or intelligent agent of your choice has been monitoring and modifying the universe since its creation; or that no such intelligent agency was involved.
You don't need to convince me that evolutionary theory can't explain the observed patterns. I am saving you the trouble! This is your chance to present an alternative hypothesis explaining the patterns of similarity and dissimilarity in the chimp and human genomes. I would be very interested to hear it.

This message is a reply to:
 Message 40 by eggasai, posted 10-27-2006 7:24 PM eggasai has not replied

  
Meddle
Member (Idle past 1270 days)
Posts: 179
From: Scotland
Joined: 05-08-2006


Message 44 of 83 (359558)
10-28-2006 9:03 PM
Reply to: Message 34 by eggasai
10-26-2006 7:53 PM


Re: number of point mutations is not equal to number of nucleotide differences
Wait a second here, if the homology arguement works in favor of common ancestor then why does the inverse logic not work. You want to focus on anecdotal evidence that favors one small segment of on ERV mutation. It's the progressive nature of the mutation that makes it so appealing a proof of common ancestry but when it is in OWM and not in humans at all you just want to dismiss it.
You might want to reconsider a simple assumption. What rational reason to you have to assume that 8% of the genome is made up of the fossilized remains of viruses. These germline invasions are rare at best, the idea that hundreds of millions of base pairs of DNA are permenantly fixed in genomes by viruses is absured.
The importance of ERV sequences as supporting evidence for common ancestry is that these sequences have been found at the same locations in the genomes of different species. The most likely explanation is that the retroviral DNA integrated itself into the genome of a common ancestor.
By comparison, PtERV sequences are not found in the same locations in the genomes of different species. This is what you would expect of retroviruses randomly inserting themselves into the genomes of separate species.
And as I already said, after integrating into the genome, ERV's are able to copy themselves elsewhere in the host genome. You do not need to rely on germline invasion to account for all the ERV sequences present in our genome. But as I asked in my OP, and as mick reiterated, what is the creationist explanation for ERV sequences?
And just to add to those numbers, the human genome is 3 billion base pairs long, and only about 1.5% of this represents protein-coding genes.
Let me ask you this, the gorilla split with both the human and chimpanzee lineage well before the austropithicene/homo split. Would you expect that 83% of the protein coding genes would show differences at an amino acid seqeunce level? You guys like to make a priori assumptions and use anecdotal evidence but you don't like making predictions. How about the spit between western and eastern gorillas, how much would you expect two seperate species to diverge within the same genus? The gorilla/chimpanzee split goes back further then the austropithecene/homo one, how would you expect the genes to line up?
Firstly I don't see how your questions relate to my quoted remarks. My point was that mutations and rearrangements affect a small proportion of the genome, and protein coding genes only take up a small proportion of the overall genome, so there is room for manoeuvre.
As to your questions, I don't think you can predict an accurate percentage for the divergence of amino acid sequence between species. With the chimp and human genomes we compared the sequences, identifying the mutations and various transposable elements, to get an accurate view of how much they diverge. The same process can be used for gorillas or any other species.
And just what would anecdotal evidence be in this context?
Human Genome Projects website. It's a wonderfull place to go and look at genomics without all of this creation/evolution bluster muddying up the waters.
Do you have a link to where on the HGP website you got that information from?
Edited by Evil Homer, : No reason given.

This message is a reply to:
 Message 34 by eggasai, posted 10-26-2006 7:53 PM eggasai has not replied

  
Lithodid-Man
Member (Idle past 2931 days)
Posts: 504
From: Juneau, Alaska, USA
Joined: 03-22-2004


Message 45 of 83 (359577)
10-29-2006 12:33 AM
Reply to: Message 39 by Hyroglyphx
10-27-2006 3:27 PM


Re: Comparisons
Nemesis_juggernaut writes:
This article posits that mice share 97.5% biochemical similarity with that of the common field mouse.
Sorry, but this is nowhere in the article. The article does compare human and mouse working DNA from one chromosome. The purpose is to illustrate how conservative the genome is in regards to functional proteins.

Wanda: To call you stupid would be an insult to stupid people. I've known sheep who could outwit you. I've worn dresses with higher IQs, but you think you're an intellectual, don't you, ape?
Otto: Apes don't read philosophy.
Wanda: Yes they do, Otto, they just don't understand it.
"A Fish Called Wanda"

This message is a reply to:
 Message 39 by Hyroglyphx, posted 10-27-2006 3:27 PM Hyroglyphx has not replied

  
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