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Author Topic: Truth be Told about Human Chimp DNA  (Read 1327 times)
Reasoned Faith
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« on: October 21, 2007, 10:32:39 AM »


For years evolutionists have been making hay over the claim that Chimps and Humans are genetically similar to about 99%.  Well it seems that much of that was hype.  The similarities are less than thought and now it appears they are converging on a figure near 94%.  Well below the similarity for mice at nearly 98%.  This is significant because at the same time we have learned how evolution has not been able to produce even one new protein interaction in the billions and billions and billions of lab organisms observed and yet these genetic differences between humans and chimps include thousands of them. 

How can it be?  Evolutionists estimate that the population pool involved in the presumed evolution of humans from ancestral apes is less than 20 billion and in that pool thousands of significant protein structure differences must have occurred if evolution is correct.  Well if so, this completely contradicts experimental biology and molecular biology studies which show that known evolutionary processes don't generate these kinds of changes given the low population density and probability analysis provides the theoretical basis to demonstrate why this is the case.  In order to generate these changes given observed processes, the population pool must be increased billions and billions and billions and billions of time over.

The conclusion should be obvious.  Some process other than random mutation, and the other evolutionary processes along with natural selection had to be involved.

The article below describes how genetics researchers are backing away from the 1% difference claim but it does not discuss the implications directly.  I have added that here for additional possible discussion.

Truth be Told about Human Chimp DNA
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tejtej
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« Reply #1 on: October 21, 2007, 11:39:22 AM »

For years evolutionists have been making hay over the claim that Chimps and Humans are genetically similar to about 99%.  Well it seems that much of that was hype.  The similarities are less than thought and now it appears they are converging on a figure near 94%.  Well below the similarity for mice at nearly 98%.

Comparing genomes is difficult when there are large rearrangements or several small, such as a difference in gene copy number. The main difference between chimp and humans is that human have two chimp chromosomes spliced into one. The divergence rate is 1.23% when comparing orthologous sequences (source), coding regions produce almost identical proteins (from the same source)

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Orthologous proteins in human and chimpanzee are extremely similar, with approx 29% being identical and the typical orthologue differing by only two amino acids, one per lineage.

In the meantime, there has been more chromosomal rearrangements between mouse and human (as obvious already from the difference in chromosome number, chimp - 48, human -46, mouse - 40, there are a lot more of other inter and intra chromosomal rearrangements between mouse and human than between chimp and human, google "syntheny maps"). You can't directly compare sequences if portions of it were translocated or inverted. Or to be precise, you can, but you must use the same model for comparison. From your links, the choice of method is unclear, 30 years ago melting temperature of DNA heteroduplexes was used, you really can't compare that to methods based on nucleotide sequences.

As for comparing all three genomes, pick individual orthologous gene sequence or noncoding regions and compare them. Below is just an example, but if you increase the number of compared othologs, the human-mouse divergence rate will always be obviously larger than human-chimp.

Example, hemoglobin, alpha 1, first 60 nucleotides of coding region (from genebank, acession numbers NM_000558, NM_001042626, NM_008218)

human: atggtgctgt ctcctgccga caagaccaac gtcaaggccg cctggggtaa ggtcggcgcg
chimp:  atggtgctgt ctcctgccga caagaccaac gtcaaggccg cctggggtaa ggtcggcgcg
mouse: atggtgctct ctggggaaga caaaagcaac atcaaggctg cctgggggaa gattggtggc

pick a gene, any gene
« Last Edit: October 21, 2007, 11:41:51 AM by tejtej » Logged

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« Reply #2 on: October 21, 2007, 02:59:56 PM »

Similarities are interesting but they only tell part of the story.  It is the differences that reveal inherent weaknesses in the  evolutionary narrative.  How do you address them?
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« Reply #3 on: October 21, 2007, 09:07:24 PM »

Similarities are interesting but they only tell part of the story.  It is the differences that reveal inherent weaknesses in the  evolutionary narrative.  How do you address them?

It is difficult for me to explain details because I don't know your background. I will just focus on 2 things at the moment.

In order to generate these changes given observed processes, the population pool must be increased billions and billions and billions and billions of time over.

1. It does takes a lot of time for a large population to accumulate changes, but it is assumed that trough most time the population of human species or closely related species did not went over 100 000. Effective population size is usually 10% of that and bottleneck effect are common in evolutionary history. In such small populations mutations can fixate much faster. In addition, mutations are not generated every generation, but during every DNA replication. Gametes in male sperm undergo thousands and thousands of replications in individual's reproductive period.

2. Measuring difference between 2 organisms. OK, lets simplify this and instead of nucleotide strings take "reasoned faith"

- comparing "reasoned faith" and "reasoned faith" - 100% similarity = identical
- comparing "reasoned faith" and "reasones faith" - 1 difference =12/13 92% identity
- comparing "reasoned faith" and "faith reasoned" - hm... aligning these two strings as a whole would give 0 identity = 0%.

But in fact it is a result of a single mutation event, just like in "reasones faith". So should it be equivalent to the 92% ? Using some methods, it would be 100% identical, because only individual othologs would be directly compared "reasoned" with "reasoned" and "faith" with "faith". To include single changes and indels and translocations in a pack, a scoring system is usually used, but preferably all three are described separately.
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« Reply #4 on: October 22, 2007, 05:34:22 AM »

Well first off it isn't "The Truth Is Now Told About Chimp DNA"; this implies there was a lie, and there wasnt. They were simply incorrect, off by a bit. Could be they're still wrong. Could be we find out in 10 years it's 99% like ours, or more alike with 'more important' dna. This happens when you're actually looking for an answer rather than simply sitting back re-assured in any answer you come up with and prove with mere faith is the right one.

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The conclusion should be obvious.  Some process other than random mutation, and the other evolutionary processes along with natural selection had to be involved.

I don't see why that conclusion is obvious in the least. In fact I don't even see what it has to do with it. There is only one thing to conclude when faced with an unknown: that it is unknown. Blackness. A big question mark. Nothing 'obvious' about it. It's not a cue to insert any answer.



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« Last Edit: October 22, 2007, 05:43:14 AM by Ahkenaten » Logged
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« Reply #5 on: October 22, 2007, 04:54:52 PM »

Well first off it isn't "The Truth Is Now Told About Chimp DNA"; this implies there was a lie, and there wasnt. They were simply incorrect, off by a bit. Could be they're still wrong.

Fair enough Ahk, we embellished for dramatic effect.

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Could be we find out in 10 years it's 99% like ours, or more alike with 'more important' dna. This happens when you're actually looking for an answer rather than simply sitting back re-assured in any answer you come up with and prove with mere faith is the right one.

I suppose, one way that the results are confused is by how you score differences.   Some are scored by base pair differences while other disregard amino acid substitutions that are thought to be inconsequential.   I agree that the key is in the "important" differences.  These are the protein binding site and gene control sequences for example and it is these differences that I am attempting to discuss.  Since evolutionary processes are unable to account for these alterations, I wonder how the narrative will be adjusted as this reality becomes better realized.

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Quote
The conclusion should be obvious.  Some process other than random mutation, and the other evolutionary processes along with natural selection had to be involved.

I don't see why that conclusion is obvious in the least. In fact I don't even see what it has to do with it. There is only one thing to conclude when faced with an unknown: that it is unknown. Blackness. A big question mark. Nothing 'obvious' about it. It's not a cue to insert any answer.

It is interesting that you say this because this is not the way the scientific method is described.   The process is to form a hypothesis and then test it with observation and experiment.  If the observations and experiments don't match the hypothesis  then you conclude the hypothesis is incorrect and you move on to a new one.

In the case of evolution, experiments and observation over the past 50 years demonstrate clearly that known evolutionary processes don't form new protein-protein interactions.  Meanwhile probability analysis provides the explanation.   Studies of 3D shape space together with electro-chemical affinities show us that most interactions require six consecutive specific amino acid combinations to generate a new binding site.  For most proteins given the number of base pairs and the mutation rate, this would require a pool of 10^40 or more organisms just to create one new interaction by known processes.  Meanwhile biologists estimate there have only been 10^35 or so organisms in existence on earth in the entire time span.

So how do we resolve this?  Do we really leave this as an unknown or do we begin to look for a better hypothesis? 

Also where is the proper assignment of the unknown?  Is it that macro-evolution is correct, we just don't know how it happened and cannot demonstrate right now that it did happen?  Or is it that common descent is correct we just don't know what processes were involved?  Or is it that we don't know what is correct and what isn't correct?
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« Reply #6 on: October 22, 2007, 08:40:15 PM »

In the case of evolution, experiments and observation over the past 50 years demonstrate clearly that known evolutionary processes don't form new protein-protein interactions.

Thomas Hunt Morgan (Nobel prize in 1933). Almost all known mutant fruit flies with drastic phenotype changes (result of changed protein-protein interaction) were produced in the lab.
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« Reply #7 on: October 22, 2007, 10:22:05 PM »

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I suppose, one way that the results are confused is by how you score differences.   Some are scored by base pair differences while other disregard amino acid substitutions that are thought to be inconsequential.   I agree that the key is in the "important" differences.  These are the protein binding site and gene control sequences for example and it is these differences that I am attempting to discuss.  Since evolutionary processes are unable to account for these alterations, I wonder how the narrative will be adjusted as this reality becomes better realized.

What this always comes down to is that since science cannot explain everything it must be flawed. Of course it's 'flawed'. We can't even explain a circle. Not the point. An unknown is an unknown.

Quote
It is interesting that you say this because this is not the way the scientific method is described.   The process is to form a hypothesis and then test it with observation and experiment.  If the observations and experiments don't match the hypothesis  then you conclude the hypothesis is incorrect and you move on to a new one.

You put the cart before the horse. If there is an unknown all that can be done is further examination. The process you describe comes after an unknown is presented. A hypothesis is made which is basically a best guess, and even then this comes about with at least a scratch of evidence to support the reasoning in the first place. As I said, simply because you don't have an answer or a sufficient answer to unanswerable questions, like what is our purpose, this does not actually mean there is a god. An unknown is an unseen nothing more. You say 'some other process must be involved'. Okay, I agree. Sure. Does that mean it's "God" time? No offense, RF but no. Just because we can't see it doesn't make it something. It's null.

People have to do this though, including scientists/researchers. People must insert a best guess in place of any unknown. It is our flaw and our greatness. We are very very good at pattern-matching, but we also have to do it even when we 'cant' in order to understand our world. We look up at the sky at night and we do not know what we're looking at, but we must always put an answer there so the god's made it...a canvas of night with pin holes, or whatever. It is not enough to simply not wonder about it We can't do that. We can't not presuppose, then construct, and then think we know.  It always seems obvious too that the things we can't explain means there "must be more to it all". Well yeah. There is, so lets keep looking.


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« Reply #8 on: October 23, 2007, 06:29:40 PM »

It is interesting that RF is ignoring COS, who has responded with scientific, not scientistic, answers. Its a shame that Creationists simply refuse to see real science and focus on propaganda.
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« Reply #9 on: October 23, 2007, 06:47:29 PM »

In the case of evolution, experiments and observation over the past 50 years demonstrate clearly that known evolutionary processes don't form new protein-protein interactions.

Thomas Hunt Morgan (Nobel prize in 1933). Almost all known mutant fruit flies with drastic phenotype changes (result of changed protein-protein interaction) were produced in the lab.

I would urge you to recheck your information.  You are speaking no doubt of the work of Morgan to establish the chromosome theory of heredity.  However it was much later in the seventies that Edward Lewis showed how mutations in the developmental regulatory genes often had bizarre effects including flies with four wings or flies with legs sprouting from their heads where antennae should have been.  These "homeotic" mutations were formed by very minor mutations that caused big mix-ups in the body plans.  However these mutations do not involve new protein bindings they are a result of developmental control genes that coded for proteins that in turn switched other genes on and off.  These are now called the hox proteins.  Further work uncovered a large number of cascading control genes and proteins that when altered would cause no end of mix-ups.  But none of these changes address the kinds of difference observed between Chimps and humans and none of them explain alterations to body parts.  In fact substitution of the gene that controls eye development in a mouse when inserted into a fruit fly in the antennae control region causes a fly eye to grow on the antennae but not a mouse eye thus confirming that these are indeed control switches.
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« Reply #10 on: October 23, 2007, 08:51:13 PM »

You are speaking no doubt of the work of Morgan to establish the chromosome theory of heredity.  However it was much later in the seventies that Edward Lewis showed how mutations in the developmental regulatory genes often had bizarre effects including flies with four wings or flies with legs sprouting from their heads where antennae should have been.  These "homeotic" mutations were formed by very minor mutations that caused big mix-ups in the body plans.  However these mutations do not involve new protein bindings they are a result of developmental control genes that coded for proteins that in turn switched other genes on and off.

Morgan was working (among other things) on how fast do mutations develop, what are the consequences of mutations, where on the chromosome is the cause of mutation. The DNA and protein level of his experiments was explained later.

A typical gene regulatory protein has 2 domains. A DNA binding domain and kinase domain (that interact with protein). A gene is switched on/off either by mutation in DNA binding domain (won't go into details as you are interested in protein:protein) or by mutation in kinase domain. Now mutation in this region does not necessarily cause on/off. It can also result in changed affinity with binding protein (resulting in over expression or lower expression of gene regulated by this protein), or that it binds with a different protein altogether. So yes, there is a changed/new protein:protein interaction.

An even better example is sickle cell anemia in human medicine (but I left this one out, because the initial mutation was not observed in the laboratory, for obvious reasons). One single nucleotide mutation in one of the globin genes changes amino acid sequence in the protein, causing to fold differently, causing to interact with other protein components of hemoglobin in a different way, causing multiple haemoglobin to bind into a cristal structure, interacting with components in the cytoskeleton and on the cell surface to misshape the cell. A whole bunch of new protein:protein interaction from one single nucleotide change.

But none of these changes address the kinds of difference observed between Chimps and humans and none of them explain alterations to body parts.

In know people are often frustrated why fundamental genetics is done on flies, E.coli and mice. There is a very good reason... ethics.

It is interesting that RF is ignoring COS, who has responded with scientific, not scientistic, answers. Its a shame that Creationists simply refuse to see real science and focus on propaganda.

RF is not ignoring me, we have discussed this issues several times before. From my perspective, it is difficult to find simple examples to explain them to forum members. For RF, he tried to explained me in details about ID, but we ended that debate on weather a cloud in the shape of Austria is complex enough or not. It's the criteria of what is complex enough and what not that I don't accept from ID.

About real science vs propaganda vs religion, I am sick of that subject.
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« Reply #11 on: October 24, 2007, 06:49:27 PM »


RF is not ignoring me, we have discussed this issues several times before. From my perspective, it is difficult to find simple examples to explain them to forum members. For RF, he tried to explained me in details about ID, but we ended that debate on weather a cloud in the shape of Austria is complex enough or not. It's the criteria of what is complex enough and what not that I don't accept from ID.

About real science vs propaganda vs religion, I am sick of that subject.
Very good, then, I will take my leave. I am enjoying your explanations and find it frustrating that for all RF claims to have settled on ID as a better explnation, he seems to refuse or ignore the actual science and only takes the Discovery Institutes version of science.

Keep up the good work. I'd love to hear more.
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« Reply #12 on: October 24, 2007, 07:00:58 PM »

Keep up the good work. I'd love to hear more.
I second this COS, I am fascinated by your explanations.
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« Reply #13 on: October 24, 2007, 08:56:07 PM »

Yes, thank you tejtej.

Very informative.

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« Reply #14 on: October 25, 2007, 09:59:33 AM »

A typical gene regulatory protein has 2 domains. A DNA binding domain and kinase domain (that interact with protein). A gene is switched on/off either by mutation in DNA binding domain (won't go into details as you are interested in protein:protein) or by mutation in kinase domain. Now mutation in this region does not necessarily cause on/off. It can also result in changed affinity with binding protein (resulting in over expression or lower expression of gene regulated by this protein), or that it binds with a different protein altogether. So yes, there is a changed/new protein:protein interaction.

Again I would ask you to recheck your information.  Can you provide a specific example of a new binding site or are you only speaking of changes to existing binding sites resulting in changed binding affinities as you indicated?  Evolution has demonstrated that it can change and in the process break existing function including over and under expression of regulated genes and the out of order expressions I described earlier.  I have asked specifically about new binding sites and new interactions.

Quote
An even better example is sickle cell anemia in human medicine (but I left this one out, because the initial mutation was not observed in the laboratory, for obvious reasons). One single nucleotide mutation in one of the globin genes changes amino acid sequence in the protein, causing to fold differently, causing to interact with other protein components of hemoglobin in a different way, causing multiple haemoglobin to bind into a cristal structure, interacting with components in the cytoskeleton and on the cell surface to misshape the cell. A whole bunch of new protein:protein interaction from one single nucleotide change.

Actually this is another example of a change but not in a binding site but rather in a folded area that normally prevents the heme portion of the mutiprotein hemoglobin to contact other areas of the structure that have modest affinity to it and also to other heme structures that are otherwise also protected but only when the heme is not bound to Oxygen.  The result of the change is that existing (unitended)  binding sites are exposed, but these are not new binding sites.  More importantly is the impact of this change.  This change causes the hemoglobin to form up into a gelatinous mess and alters the entire shape of the blood cell causing it to clump in capillaries when the heme is not bound to oxygen and more importantly the spleen recognizes that these cells are deformed and destroys them leading of course to anemia.

The primary point is that this change in the fold only exposed otherwise protedted heme causing a major misfuntion.  These areas that are now exposed existed already.  They are not new.

So do those of you who see the kinds of examples offered as valid indicators of ability to generate the actual observed differences?  Do you believe these examples are "close enough"?

I ask this because if these examples did represent the mechanisms the generated new protein protein interactions and since these single step mutations are relatively frequent (1 per 100,000 base pairs) why is it that the examples are so sparce and why is it that we can't identify even one example of a mutation that exposes a previously concealed potential binding site that builds useful new function?  In other words, why does the narrative not match observation?  

But none of these changes address the kinds of difference observed between Chimps and humans and none of them explain alterations to body parts.

In know people are often frustrated why fundamental genetics is done on flies, E.coli and mice. There is a very good reason... ethics.

Did you misunderstand? The bizzare effects demonstrated with mutations to regulatory control genes in fruit flies are not in the same category of differences as those between apes and humans and therefore do not offer a solution to the issue I have raised.  They represent changes in control function that dramatically messes up normal developmental function.  They are not new proteins, new protein binding sites and new protein function that make up the differences in expressed genes that this article and this discussion focuses.

It is interesting that RF is ignoring COS, who has responded with scientific, not scientistic, answers. Its a shame that Creationists simply refuse to see real science and focus on propaganda.

RF is not ignoring me, we have discussed this issues several times before. From my perspective, it is difficult to find simple examples to explain them to forum members. For RF, he tried to explained me in details about ID, but we ended that debate on weather a cloud in the shape of Austria is complex enough or not. It's the criteria of what is complex enough and what not that I don't accept from ID.

Actually I agreed that a cloud shape is absolutely complex enough.  My point was that the shape could not be specified inependently from the event prior to the actual stipulated occurance.  It was not detatchable in that we cannot say that we regularly observe clouds in the shape of countries. The marker for design requires complexity and specification but the cloud represents only complexity.
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