Genetic basis for human evolution

[shernren]

There is even a unit of evolution called, appropriately, a “darwin” which refers to how much divergence occurs within a set time frame. (100,000 years, I think, but it could be more.)

Just been reading Kenneth Miller's Finding Darwin's God (the book version! ) and he says the divergence in darwins is calculated as:

[ln(x2) - ln(x1)] / 10^6 yrs

where x2 is the mean measurement of a quantitative feature after evolution over one population and x1 is the mean measurement before. Or something such. He says observed evolutionary rates are somewhere along the line of at least 400 darwins, whereas the evolutionary rates required to explain the fossil record are something like 0.04 and 0.06 for two particular sequences. Looks like observation is far outrunning prediction here.

Is mark comming back to this thread? He got hot under the collar a few weeks ago when I told him he was intellectually dishonest for just dropping threads where his points were solidly refuted (thats just about all threads like this).

I don't know. But I'd say mark shouldn't be the center of attention in this thread, the facts should be.

 

[kenneth558]

.... But even more important, this second nested hierarchy, which has not taken physical similarities into account at all, turns out to match the one that is based on physical similarities....

gluadys, the above statement you made struck me. Could you direct me to the scientific support for it, please?

Please know that the type of evidence that I value is chromosome base sequencing that human geneology testing relies on. I am not impressed by so-called "molecular" genetics that nonchalantly bypasses the chromosome level sequences when the chromosome level doesn't fit their theory. My reasoning for staying with the chromosome level because the chromosome level is the most accurate level to compare organism lineages for numerous reasons. Higher levels of comparison are merely comparing the products of the chromosomes - products like hair color, eye color, etc. - which are of no value in conclusively determining lineage, be they at the molecular protein level or not. They are the physical similarities you mention.

 

[rmwilliamsll]

gluadys, the above statement you made struck me. Could you direct me to the scientific support for it, please?

Please know that the type of evidence that I value is chromosome base sequencing that human geneology testing relies on. I am not impressed by so-called "molecular" genetics that nonchalantly bypasses the chromosome level sequences when the chromosome level doesn't fit their theory. My reasoning for staying with the chromosome level because the chromosome level is the most accurate level to compare organism lineages for numerous reasons. Higher levels of comparison are merely comparing the products of the chromosomes - products like hair color, eye color, etc. - which are of no value in conclusively determining lineage, be they at the molecular protein level or not. They are the physical similarities you mention.

she is referring first to the protein homologies as in protein sequence in cytochrome C. i remember seeing whole books of amino acids sequences from different creatures.
secondly she is referring to the underlying DNA, where we are now, since it is easier to sequence DNA than protein.

the nested hierarchies are:
taxonomic-physical appearance
includes fossils, basis of our species-genus trees. this is the whole idea of figuring out what really separates creature Y from X and build it into a taxonomic flowchart. i did this with insects for a summer, neat stuff.

protein sequences then DNA sequencing
duplicate the taxonomic trees with some surprises. these use computer based algorithms that track the minimal number of changes to create clades.

and now ERV insertations which essentially build another set of clades which duplicate the two others. these use position of insertation and changes in the ERV's to map.

the point is that these are linked nested hierarchies in a few ways but separate in others, yielding a consilence or the idea the evidence is best spread out and from different directions.

try googling

taxonomic structural hierarchies
protein sequence homology
erv clades

looks like these might get you into the literature ok.

 

[kenneth558]

she is referring first to the protein homologies as in protein sequence in cytochrome C. i remember seeing whole books of amino acids sequences from different creatures.
secondly she is referring to the underlying DNA, where we are now, since it is easier to sequence DNA than protein.

Its too bad they are in that order. Precisely my point, BTW. The first is as irrelevant to me as the color of hair - both are PRODUCTS of chromosome sequences. Then you seem to base the second on the first. Like I tried to say, I am interested in evidence for her claim based on the chromosome sequencing, not its products. I endured my Organic Evolution, Molecular Biology, Cellular Biology classes, etc. NEVER being given this vital information. gluadys seems to have found what all my evolutionist instructors never did.

 

[rmwilliamsll]

Its too bad they are in that order. Precisely my point, BTW. The first is as irrelevant to me as the color of hair - both are PRODUCTS of chromosome sequences. Then you seem to base the second on the first. Like I tried to say, I am interested in evidence for her claim based on the chromosome sequencing, not its products. I endured my Organic Evolution, Molecular Biology, Cellular Biology classes, etc. NEVER being given this vital information. gluadys seems to have found what all my evolutionist instructors never did.

a couple of observations on the issues:

first, natural selection is on proteins and through them on the dna (some scientific controversy over this)
so looking at the protein is closer to the scene, so to speak.

second, DNA is messy. exons, introns, pre and post processing on transcription, control regions, histone binding regions, etc etc.
this really complicates the comparison of DNA sequences.


lastly, maybe you should describe a little bit more of what you are looking for. maybe it is something we all missed....

i'm not sure what the term "chromosome sequencing" means, perhaps i need more information!?

 

[kenneth558]

a couple of observations on the issues:

first, natural selection is on proteins and through them on the dna (some scientific controversy over this)
so looking at the protein is closer to the scene, so to speak.

second, DNA is messy. exons, introns, pre and post processing on transcription, control regions, histone binding regions, etc etc.
this really complicates the comparison of DNA sequences.


lastly, maybe you should describe a little bit more of what you are looking for. maybe it is something we all missed....

i'm not sure what the term "chromosome sequencing" means, perhaps i need more information!?

You're mixing up evolution with genetics. Let's stick with genetics. There is ABSOLUTELY no need whatsoever to talk about evolution in connection with geneology as you do in your first point.

Yes, dna is messy but it is the definitive word on geneology, as you know. Comparison of such is not too difficult for FamilyTreeDNA. They do a fine job. I say that this type of DNA sequencing is perfectly valid and DOES NOT support a common lineage between chimps/humans, okapi/giraffes, elephants/mastadons, etc. gluadys implies differently, and I am asking for her sources.

 

[random_guy]

You're mixing up evolution with genetics. Let's stick with genetics. There is ABSOLUTELY no need whatsoever to talk about evolution in connection with geneology as you do in your first point.

Yes, dna is messy but it is the definitive word on geneology, as you know. Comparison of such is not too difficult for FamilyTreeDNA. They do a fine job. I say that this type of DNA sequencing is perfectly valid and DOES NOT support a common lineage between chimps/humans, okapi/giraffes, elephants/mastadons, etc. gluadys implies differently, and I am asking for her sources.

There's a great reason to talk about evolution and genetics when talking about chromosomes. Let me repeat my post:

I do not know very much genetics, I just begun studying the subject, but isn't the human chromosome #2 huge evidence of ape human common ancestory? This chromosome contains telomeres in the middle and on the end. In chromosomes, they are usually only found at the end. This is evidence that two chromosomes fused together to become human chromosome #2.

Sequencing the chromosome, we find that it is extremely similar to chimp chromosome 2p and 2q. This is exactly what evolution predicts to explain the difference between human and chimp chromosome count.

 

[kenneth558]

There's a great reason to talk about evolution and genetics when talking about chromosomes. Let me repeat my post:

I do not know very much genetics, I just begun studying the subject, but isn't the human chromosome #2 huge evidence of ape human common ancestory? This chromosome contains telomeres in the middle and on the end. In chromosomes, they are usually only found at the end. This is evidence that two chromosomes fused together to become human chromosome #2.

Sequencing the chromosome, we find that it is extremely similar to chimp chromosome 2p and 2q. This is exactly what evolution predicts to explain the difference between human and chimp chromosome count.

This type of info would have credibility only when it is comprehensive. IOW, a lichen chromosome may be even more similar to one of the human's if everything is laid out for us. What evolution+genetics predicts is that the DNA sequencing ought to be the most authoritative in determining ancestry. But if that prediction held true, we would have no need to rely TOTALLY on chromosome products to support common ancestry between species like we do.

 

[rmwilliamsll]

You're mixing up evolution with genetics. Let's stick with genetics. There is ABSOLUTELY no need whatsoever to talk about evolution in connection with geneology as you do in your first point.

Yes, dna is messy but it is the definitive word on geneology, as you know. Comparison of such is not too difficult for FamilyTreeDNA. They do a fine job. I say that this type of DNA sequencing is perfectly valid and DOES NOT support a common lineage between chimps/humans, okapi/giraffes, elephants/mastadons, etc. gluadys implies differently, and I am asking for her sources.

first, i don't believe you mean to use the word geneology

second, i am unable to talk about genetics and DNA sequencing data without evolutionary theory, for TofE really forms the framework for putting things together in genetics, likewise developmental biology, and bioenergetics and any other 'ology' related to biology.

Biology is not this long list of descriptions, rather it is a serious attempt by people to systematize, to theorize, to unify these descriptions into coherent and understandable systems. i am simply unable to separate the systematics from the descriptions. sorry, it is probably a result of too many hours spent in class and reading, but the TofE is thorough part and parcel of how i see biology.

maybe a discussion of first principles is in order?

does homology of DNA, does the creation of sequence clades imply common descent?

i googled FamilyTreeDNA, it is website dedicated to selling genetic tests to build family trees.


how is this different than clades of the great apes? how can you understand that you, your parents, your siblings share certain relationships in genetic terms and not understand that this is based on:

homology is used to determine common descent.

 

[random_guy]

This type of info would have credibility only when it is comprehensive. IOW, a lichen chromosome may be even more similar to one of the human's if everything is laid out for us. What evolution+genetics predicts is that the DNA sequencing ought to be the most authoritative in determining ancestry. But if that prediction held true, we would have no need to rely TOTALLY on chromosome products to support common ancestry between species like we do.

Wait a minute, can you clarify what you're saying?

Yes, a lot of chromosomes are similiar in other species (due to UCA), but I'm looking at a specific example. You haven't even touched on the telomeres. We know that usually telomeres occur only at the end of chromosomes. We know that human chromosome 2 has telomeres in the middle. We know that apes have 24 pairs of chromosomes and humans have 23 pairs. Ignoring all other chromosomes for now, why would it seem that human chromosome 2 is a fusion of ape chromosome 2p and 2q?

 

[kenneth558]

Wait a minute, can you clarify what you're saying?

Yes, a lot of chromosomes are similiar in other species (due to UCA), but I'm looking at a specific example. You haven't even touched on the telomeres. We know that usually telomeres occur only at the end of chromosomes. We know that human chromosome 2 has telomeres in the middle. We know that apes have 24 pairs of chromosomes and humans have 23 pairs. Ignoring all other chromosomes for now, why would it seem that human chromosome 2 is a fusion of ape chromosome 2p and 2q?

Let's look at your specific example. If this mutation happened in a single generation, a male and a female would have had to acquire it, not detrimental to their survival, during the same generation, in the same physical vicinity of each other, then have offspring by each other. Somewhere in this scenario, they are separated from their population of origin so they can begin a new species. Or would you say that such a mutation might still allow the organism to mate within its population of origin? So first, convince me that an ape with such a mutation could start a new population before I even begin to think this is a viable postulation. Its like the old "what if" question about something impossible in the first place.

 

[kenneth558]

homology is used to determine common descent.

It won't hold up in court, my friend. They need DNA. Why do you suppose that is?

 

[rmwilliamsll]

Let's look at your specific example. If this mutation happened in a single generation, a male and a female would have had to acquire it, not detrimental to their survival, during the same generation, in the same physical vicinity of each other, then have offspring by each other.
snip to address just a single point

not true.
see a current thread at:
http://www.christianforums.com/t2785547-chromosomes.html

the process is called fixation of a mutation in a population. the alignment of the chromosomes appear to be a function of homology sites as well as centrosome spindles. something which can happen with the two 2p, 2q lining up with the new 2 combined one.

the issue is not completely clear to me after a few hours of googling and reading yesterday.
but the fixation of combined chromosomes and even polyploidy esp. in plants is certainly happening and has happened.

 

[kenneth558]

not true.
see a current thread at:
http://www.christianforums.com/t2785547-chromosomes.html

the process is called fixation of a mutation in a population. the alignment of the chromosomes appear to be a function of homology sites as well as centrosome spindles. something which can happen with the two 2p, 2q lining up with the new 2 combined one.

the issue is not completely clear to me after a few hours of googling and reading yesterday.
but the fixation of combined chromosomes and even polyploidy esp. in plants is certainly happening and has happened.

He was being specific about THAT mutation. The link you provide is not. Try again?

 

[random_guy]

He was being specific about THAT mutation. The link you provide is not. Try again?

No, you said that both a male and a female would require that specific mutation in order to be able to have fertile offspring. This is because you believe that species with different chromosome counts can not have viable offspring.

That thread gives examples of species with different number of chromosome counts that can still reproduce. The wild/native horse is a great example of something extremely similiar. Heck, there's even an example from some random poster about humans with different number of sex chromosomes that can still have viable offspring with other humans.

 

[Dannager]

It won't hold up in court, my friend. They need DNA. Why do you suppose that is?

What, for proving paternity cases? I imagine that's because the plaintiff wouldn't be very satisfied by the answer "We can conclusively state that the father is a member of the species homo sapiens sapiens."

 

[kenneth558]

I asked for something that should readily exist with our technology - DNA sequence evidence for gluadys' statement

.... But even more important, this second nested hierarchy, which has not taken physical similarities into account at all, turns out to match the one that is based on physical similarities....

Notice her use of the phrase "at all". She obviously wasn't paying attention in Cellular Biology and Organic Evolution classes. I DID pay attention and saw that physical similarities are VERY MUCH taken into account in both hierarchies, and that the "molecular" evidence simply ignored DNA sequencing most of the time because it didn't give them the evidence they hoped it would. I don't expect you to believe me because you probably weren't attentive to those facts when you all took those courses. So be it.

 

[rmwilliamsll]

I asked for something that should readily exist with our technology - DNA sequence evidence for gluadys' statementNotice her use of the phrase "at all". She obviously wasn't paying attention in Cellular Biology and Organic Evolution classes. I DID pay attention and saw that physical similarities are VERY MUCH taken into account in both hierarchies, and that the "molecular" evidence simply ignored DNA sequencing most of the time because it didn't give them the evidence they hoped it would. I don't expect you to believe me because you probably weren't attentive to those facts when you all took those courses. So be it.

i think gluadys is right and you don't understand what she said.


1. the linneaus taxonomy similiarities and differences create the trees we use to classify creatures by ....genus, species.
the basis is their morphological physical structures.

2. the second set of nested hierarchies are those, for example, created by

cytochromic C
list the sequence for a bunch of species then use a computer algorithm to determine the clades based on the simplest number of changes it takes to create each protein.

note: the second clade says nothing about physical anything. you can use any sets of proteins you want.
see: http://www.people.virginia.edu/~wrp/papers/ismb2000.pdf
use blood globulins. use a dozen unrelated proteins etc. etc. you create these clades completely independent of whatever information you may have access too from trees created in step 1.

note: protein sequencing has given way to DNA sequencing for a number of reasons. the same kind of clades are derived in much the same matter. so the 2nd kind of clades are from both protein and DNA sequencing now.

likewise the 3rd one is independent of the first 2.
take the ERV's and create a clade based on where they are inserted and how much the ERV's themselves have mutated.

again, you use no data from step 1 or step 2 to create these clades.


are the clades independent?
your idea is that 1 and 2 are not independent since they are both based on the functions of the proteins in some ways. ok. as far as it goes*, but that doesn't change the independence of either the method or the data.


*if for example, you get to a taxonomic flowchart that asks you
"it is yellow or is it red?"
and in step 2, you are comparing the proteins responsible for red color and yellow color then there is a relationship between the clades derived from 1 and 2. however this is not what is generally either sequenced nor used for taxonomic differentiation. it is an insignificant problem, however, if you present evidence to the contrary, i'll read it.

however you will have to refer to the data not to generalities in your argument.

I DID pay attention and saw that physical similarities are VERY MUCH taken into account in both hierarchies,
so, show how this physical similarities are used to create type 2 clades, from protein and dna sequences.

and that the "molecular" evidence simply ignored DNA sequencing most of the time because it didn't give them the evidence they hoped it would.
specify the molecular evidence ignored. which sequences, which creatures, where we can go to follow your argument. that ought to be easy enough for it is most of the time, however one example will suffice for our purposes of following your argument.

...

 

[kenneth558]

.... I DID pay attention and saw that physical similarities are VERY MUCH taken into account in both hierarchies,
so, show how this physical similarities are used to create type 2 clades, from protein and dna sequences.

and that the "molecular" evidence simply ignored DNA sequencing most of the time because it didn't give them the evidence they hoped it would.
specify the molecular evidence ignored. which sequences, which creatures, where we can go to follow your argument. that ought to be easy enough for it is most of the time, however one example will suffice for our purposes of following your argument.

...

You do seem to understand my point, but you haven't satisfied my concern...you're just trying to get me to think my concern is irrelevant. But as long as geneology labs such as FamilyTreeDNA feel the DNA sequencing is most reliable, so will I.

You want to challenge my statements. Why? So gluadys won't have to produce? I'll just be honest with you that I did not keep detailed notes of all the info from those two classes two years ago if and since it wasn't going to show up on the tests. But if you will accept current internet-available statements from molecular biologist sources of the same vein, I wouldn't mind digging up something similar to what I heard in class for you. Deal?

 

[mark kennedy]

What you stated was wrong about calculating the data content. I aven't read the paper yet but I know how to calculate bits and bytes - you did not.

I also remember your brain size comments in the past were erroneous with regard to time scales and sizes.

You may have read it but you are contradicting the content. From the paper:

"Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements."

Now, why don't you actually read what they wrote. Clearly, the bytes are nucleotides and it is blantant misinformation to suggest otherwise. My remarks concerning the size and timeline of human evolution as pontificated by evolutionists are that Homo habilis was well under the cerebral rubicon. Homo erectus on the other hand was above 1,000cc while Homo habilis was under 600cc. Don't take my word for it, L.S.B. Leaky said it not me.

"Until now, the definition of Homo has usually centered about a 'cerbral Rubicon' variably set at 700cc (Weidreich). 750cc (Keither) and 800cc (Vallois)."

(A New Species of the Genus Homo from Olduvai Gorge)

Now why don't you get your facts straight and try to understand. There are 125 million nucleotides that diverge between humans and chimpanzees and another 20 million nucleotides that are inverted.