Genetic basis for human evolution

[mark kennedy]

take a minute and look at a blog entry from yesterday at: http://community.livejournal.com/useless_facts/634329.html#cutid1

I gave it a look and it seemed meaningless.

i responded to what appears to be a simple math error, not because it was a big deal but because it was simply wrong, completely wrong. the person posting it did NOT UNDERSTAND what they were doing. it is not insignificant to enter into a semi-technical discussion and mishandle the math.

Theres a simple solution to that, just tell me the number of nucleotides that diverge. It's right there in black and white. The SNPs are 35 million and the indels total around 90 million and the chromosomal rearrangements are over 20 million. You want to refute something then get the facts straight.

it is not discrediting any one. it is handling rightfully the data we have at hand in the best possible manner that we can consistent with the level of the discussion. megabits and megabytes differ by a factor of 8. this is very significance given that the argument is basically about DIFFERENCES between the chimp and human genome. it is fundamental to quantitizing the argument to get the math right.

You are still not quantifying the divergance, the chimpanzee genome project did.

but read the watch blog entry referred to above. the author wrote and explained what happened. now isn't that refreshing, both s/he learned something and so did we. that is what ought to happen here. education. learning. correcting mistakes, on all sides.

I am still waiting for you to tell me what the divergance is at a nucleotide sequence level.

 

[mark kennedy]

How can you understand something when it is stated WRONG - there is nothing to understand. And it is germane. Mark tries to come off as scientifically capable and having an ability to read technical info and somehow to be better informed than a team of 30 top university molecular biologists. But that he cannot get something as basic as this correct tells me he is incapable of even understanding the basics let alone figuring out the team analysing the Chimp genome are incompetent.

I have never said anything of the sort, I never called the authors incompetant. I do however have my doubts about you. Now why don't you show me from the paper where I fudged the math because it is nothing more then basic application. How much is 35 million plus 90 million?

What findings to attack. If he cannot get something that trivial correct I doubt he has stated the facts in the paper correct either. I haven't had time to read it yet. I just know from this, and past posts, if Mark states it then it is likely an incorrect summary based upon a poor understanding.

I did not attack anything, I simply quoted their findings. You want this to be a conflict between religion and science, this is completly absurd. I have had a number of exchanges with one of the authors who never once denied the facts as presented in the OP. In our discussions on the deleterious effects of mutations he admitted that 98% of mutations are neutral with the vast majority of the remainder being deleterious. What would be the mutation rate for 125 million nucleotides to diverge?

He didn't have a real answer for that and neither do you.

 

[Athene]

Why do you keep adding the number of SNPs, to the total number of bases involved in the indel events? It's not the amount of bases in indels which is relevant, but the total number of indels themselves. Indels can involve whopping chunks of DNA, I believe page 5 of the article states that 70,000 of the indels account for 73% of the bases.

 

[mark kennedy]

The point of course is that "brotherhood" (and sisterhood, btw...) is for the fellowship posts. Here we debate... we're all brothers and sister in Christ here, but that earns no free passes, changes no facts, and overlooks no errors.

I am quite happy to admit errors, I know I make them and I readily admit them when pointed out. So far not one substantive error has been noted. Now if there is an error in the OP then it has yet to be proven.

Now, my scientific knowledge is nowhere near up to par to actually follow the technical details of this thread, but what I have been able to glean goes something like this:

Mark Kennedy: "Here's my refutation of an evolutionist article."

Kerrimetric: "Your 'refutation' is based on a stunningly obvious error in calculation which, when corrected, shoots down your entire argument....which has happened before."

He says it, you agree with it and I quess that is supposed to settle it. There is no error there, he is trying to make a semantical point that is baseless. It's as simple as that.

Vossler: "hey, cut the guy some slack! He's a fellow Chistian!"

Kerrimetric: "That doesn't make him any less mistaken... and this isn't the first time."

So... have I got the gist of it?

There was no error in the OP, it was not even addressed. He does not want to admit that there is no way for evolutionary biology to explain the divergance. 125 million nucleotides diverged in about 5 million years. The question is how.

 

[mark kennedy]

Why do you keep adding the number of SNPs, to the total number of bases involved in the indel events? It's not the amount of bases in indels which is relevant, but the total number of indels themselves. Indels can involve whopping chunks of DNA, I believe page 5 of the article states that 70,000 of the indels account for 73% of the bases.

From the article:

"...the largest few contain most of the sequence (with ~70,000 indels bp comprising 73% of the affected base pairs). The latter indels > 80 bp fall into three catagories: (1) about one-quarter are newly inserted transposable elements: (2) more than one-third are due to micorsatelite and satelite sequences; (3) and the remainder are assumed to be mostly deletions in the other genome."

Is that the section that you are refering to?

 

[rmwilliamsll]

I am quite happy to admit errors, I know I make them and I readily admit them when pointed out. So far not one substantive error has been noted. Now if there is an error in the OP then it has yet to be proven.


i'm not out to prove anything.
i am here to understand things.

your statement:
Evolutionists go on ad infinitum about the Endogenus Retroviruses (ERVs). They seem to think this is something we inherited from a common ancestor. This is absurd as well. The ERVs are all but extinct in human lineage with only a single retrovirus human endogenous retrovirus K (HERV-K)
italitics are quoted from the article.

yes, everyone i read on the topic believes HERV's are evidence of common descent, a common ancestor. You call this absurd, yet as now 7 pages of the thread evidence, you have not offered a reason for us to think otherwise.

as i wrote in #6:
I've been watching your postings elsewhere about HERV's and in reading the OP here, it becomes obvious that you simply do not understand what HERV's are, nor are you handling the scientific information carefully. Often making serious mistakes in fundamental principles.

as to your challenge in #62, i have no reason to doubt the article's authors contention that about 3% of each genome is species-specific euchromatic sequence. i am not interested in the math, if you look, i responded consistently to the ERV part of your OP.

HERV's are important and interesting. It is to those issues i am willing to speak. i don't intend to get involved in the math of the article. if you wish to address your contention that HERV's are not evidence of common descent with the great apes, i will be glad to do the research to hold up my end of the conversation.

i tried to address these issues in #39.

 

[mark kennedy]

I am quite happy to admit errors, I know I make them and I readily admit them when pointed out. So far not one substantive error has been noted. Now if there is an error in the OP then it has yet to be proven.


i'm not out to prove anything.
i am here to understand things.

your statement:
Evolutionists go on ad infinitum about the Endogenus Retroviruses (ERVs). They seem to think this is something we inherited from a common ancestor. This is absurd as well. The ERVs are all but extinct in human lineage with only a single retrovirus human endogenous retrovirus K (HERV-K)
italitics are quoted from the article.

yes, everyone i read on the topic believes HERV's are evidence of common descent, a common ancestor. You call this absurd, yet as now 7 pages of the thread evidence, you have not offered a reason for us to think otherwise.

as i wrote in #6:
I've been watching your postings elsewhere about HERV's and in reading the OP here, it becomes obvious that you simply do not understand what HERV's are, nor are you handling the scientific information carefully. Often making serious mistakes in fundamental principles.

as to your challenge in #62, i have no reason to doubt the article's authors contention that about 3% of each genome is species-specific euchromatic sequence. i am not interested in the math, if you look, i responded consistently to the ERV part of your OP.

HERV's are important and interesting. It is to those issues i am willing to speak. i don't intend to get involved in the math of the article. if you wish to address your contention that HERV's are not evidence of common descent with the great apes, i will be glad to do the research to hold up my end of the conversation.

i tried to address these issues in #39.

Fair enough, I was making a point about this statement in the article:

"Where as older ERVs, like HERV-K, are primarily represented by solo LTRs resulting from LTR-LTR recombination, more than half of the PtERV1-like elements are present in the rhesus monkey, live baboon and African great apes but not in human, orang-utan or gibbon, suggesting separate germline inversions of these species."

Here is my point, we need not have inherited this distinction from a common ancestor. These are the result of seperate germline invasions, not a common ancestor. How this has any signifigance for human descent from ape anceostors remains a mystery to me.

 

[Athene]

From the article:

"...the largest few contain most of the sequence (with ~70,000 indels bp comprising 73% of the affected base pairs). The latter indels > 80 bp fall into three catagories: (1) about one-quarter are newly inserted transposable elements: (2) more than one-third are due to micorsatelite and satelite sequences; (3) and the remainder are assumed to be mostly deletions in the other genome."

Is that the section that you are refering to?

Yep that's the one.

 

[Athene]

Mark, bytes are a measure of the information capacity of a nucleotide sequence, this is related to the number of nucleotides but the two aren't the same. For example, the genome of E. coli has 4.6 million base pairs, and an information carrying capacity of 1.15 MB.

And that leads me to my next point, the article refers to Mb (megabases) not MB (megabytes), I made the same mistake myself.

 

[mark kennedy]

You guys do know that there are 35 million nucleotides that diverge right? The indels represent 3% while the SNPs represent 1.23% of the respective genomes. Now, tell me how 90Mb of divergance got in the respective genomes. By the way, if you want to tell me how many nucleotides that translates into I am all ears.

 

[mark kennedy]

Mark, bytes are a measure of the information capacity of a nucleotide sequence, this is related to the number of nucleotides but the two aren't the same. For example, the genome of E. coli has 4.6 million base pairs, and an information carrying capacity of 1.15 MB.

And that leads me to my next point, the article refers to Mb (megabases) not MB (megabytes), I made the same mistake myself.

I honestly never gave it a single thought. I thought they were refering to megabases. I don't know what the point is here but I assume it's basically a diversionary tactic.

 

[rmwilliamsll]

Fair enough, I was making a point about this statement in the article:

"Where as older ERVs, like HERV-K, are primarily represented by solo LTRs resulting from LTR-LTR recombination, more than half of the PtERV1-like elements are present in the rhesus monkey, live baboon and African great apes but not in human, orang-utan or gibbon, suggesting separate germline inversions of these species."

Here is my point, we need not have inherited this distinction from a common ancestor. These are the result of seperate germline invasions, not a common ancestor. How this has any signifigance for human descent from ape anceostors remains a mystery to me.

maybe switching fields for an example will help. chinese whispers.

say someone writes a blog entry on monday.
I really think that Genesis is about the Sabbath.

now 5 different people read his blog and think it so interesting that they add it to their blog. now i'm lazy i cut and paste so my blog entry is an exact copy of the original. Now joe, he is more daring and quotes the blog entry from memory, and Paul is a creative poet that modifies everything he reads to fit his personality.

me: I really think that Genesis is about the Sabbath.
joe: I really believe that Genesis is about the Sabath.
paul: we ought to think that Genesis is all about the Sabbath.

now, you google "genesis sabbath" for blog entries made this week.
you don't pick up joe's because he misspelled sabbath. you get mine, and pauls and peters

peter: we ought to think that Genesis is all about the Sabath. from: paul

can you construct a geneological relationship between these blog entries?

you know peter is quoting paul, he told you so.
what about the spelling error? did he copy it from joe? no reason to believe so, it is a common error.

------
we do this kind of reasoning all the time when we need to reconstruct historical type of hierarchical structures. that is why the plagarism analogy to pseudogenes is such an understandable argument. Dictionaries and encyclopedias insert false entries to catch copyright violaters.

it is the same with ERV's.

it is your contention that all ERV's are like the Sabbath spelling error, independent from all the rest. the problem is that they group, into distinct nested hierarchies. the only simple answer is clades.

just as you can track blog entries, who is reading whom, how they copy,whether from memory, cut and paste, paraphrase etc.

just as textual criticism of the Bible forms families of texts, like alexandrian, palestinain, armenian etc clades represent minimizing the number of changes to tie the various families together.

if everything in textual criticism was random scribal errors then the families of texts would not emerge as they have done. this is solely a result of copying, like my blog entry example.

copying is vertical transmission of genetic material. it is common descent. it is the fact that i share mutations with my ancestors and not with my wife's family tree mutations and our kids can have a mixture of the two trees.


i hope that helps a little bit.
start by distinguishing random errors from copying errors. it is both unreasonable and not parsimonious to declare that all ERV's are random insertation when they so easily fall into families, just like geneologies, and textual criticism both do.

 

[mark kennedy]

The back handed questioning my faith which I found ironic coming from someone carrying the icon of a denomination that should be sensitive to such comments hurled in their direction.

There was nothing backhanded about it, it was straightforward and to the point. Do you believe in the Nicean Creed or not? It was your statement that you would not be found in a Sunday School class that promted it and I am actually curious.

I personally have no problem with people asking me about my religious convictions. I am an evangelical and something of a Calvanist. I have some reservations about predestination but other then that I am pretty much a Calvinist five pointer. I have attended many different churches and found very few denomoninational distinctives to be a bar for fellowship.

My biggest concern on here as a moderator and now simply as a member is that Origins Theology is a discussion between Christians. The Nicean Creed is non-negotiable and every Christian denomination agrees with it or they are considered non-christian. Were someone to ask me if I believe it the answer would be automatic and unambiguise. Yes I believe the Nicean Creed, would be my answer, without hesitation.

Now I ask again, do you believe the Nicean Creed? You do know what I am talking about right?

 

[KerrMetric]

There was nothing backhanded about it, it was straightforward and to the point. Do you believe in the Nicean Creed or not?

The answer is Yes but this highlights why you should never have been a Mod.

And questioning the faith of others is against the rules, right?

 

[mark kennedy]

maybe switching fields for an example will help. chinese whispers.

say someone writes a blog entry on monday.
I really think that Genesis is about the Sabbath.

now 5 different people read his blog and think it so interesting that they add it to their blog. now i'm lazy i cut and paste so my blog entry is an exact copy of the original. Now joe, he is more daring and quotes the blog entry from memory, and Paul is a creative poet that modifies everything he reads to fit his personality.

me: I really think that Genesis is about the Sabbath.
joe: I really believe that Genesis is about the Sabath.
paul: we ought to think that Genesis is all about the Sabbath.

now, you google "genesis sabbath" for blog entries made this week.
you don't pick up joe's because he misspelled sabbath. you get mine, and pauls and peters

peter: we ought to think that Genesis is all about the Sabath. from: paul

can you construct a geneological relationship between these blog entries?

you know peter is quoting paul, he told you so.
what about the spelling error? did he copy it from joe? no reason to believe so, it is a common error.

------
we do this kind of reasoning all the time when we need to reconstruct historical type of hierarchical structures. that is why the plagarism analogy to pseudogenes is such an understandable argument. Dictionaries and encyclopedias insert false entries to catch copyright violaters.

it is the same with ERV's.

it is your contention that all ERV's are like the Sabbath spelling error, independent from all the rest. the problem is that they group, into distinct nested hierarchies. the only simple answer is clades.

just as you can track blog entries, who is reading whom, how they copy,whether from memory, cut and paste, paraphrase etc.

just as textual criticism of the Bible forms families of texts, like alexandrian, palestinain, armenian etc clades represent minimizing the number of changes to tie the various families together.

if everything in textual criticism was random scribal errors then the families of texts would not emerge as they have done. this is solely a result of copying, like my blog entry example.

copying is vertical transmission of genetic material. it is common descent. it is the fact that i share mutations with my ancestors and not with my wife's family tree mutations and our kids can have a mixture of the two trees.


i hope that helps a little bit.
start by distinguishing random errors from copying errors. it is both unreasonable and not parsimonious to declare that all ERV's are random insertation when they so easily fall into families, just like geneologies, and textual criticism both do.

I honestly did not follow your analogy, sorry about that. I do however, believe that the HERV strain found in the human genome was caused by a germline invasion of the human genome, not some ancestoral ape. What is more this retrovirus is not identical to the one found in apes, in fact, in human lineage it is nearly extinct.

This germline invasion tells us less then nothing about ancestory. I don't know how this is such a huge selling point for Darwinians, I mean to tell you I have no clue what signifigance they see in it.

 

[Mallon]

I have at least a dozen books by Intelligent Design scientists, philosophers and mathematitians on my bookshelf.

Might I also suggest you read some books about evolution so you have some clue as to what you're talking about? The more you talk, the more you reveal your ignorance on the subject. I'm sorry, but I don't know how to say it in a more Christian way.
And yes, I subscribe to the Nicene Creed.

 

[gluadys]

Who would you have me read? Richard Dawkins, Charles Darwin, Ernst Mayr, Richard Leaky? I have their books and or papers and I am not impressed in the slightest. I also have a college biology textbook that tells me what mutations are and how they effect living systems. I suggest you pick one up and learn the meaning of the expression 'deleterious effect'.

Of course, one thing you have never dealt with in any of your postings is the question: what effect do mutations that are deleterious have on the evolution of a species?

Note: on the species. I know you are very well acquainted with the effects on individual organisms.

 

[gluadys]

Who would you have me read? Richard Dawkins, Charles Darwin, Ernst Mayr, Richard Leaky? I have their books and or papers and I am not impressed in the slightest. I also have a college biology textbook that tells me what mutations are and how they effect living systems. I suggest you pick one up and learn the meaning of the expression 'deleterious effect'.

Of course, one thing you have never dealt with in any of your postings is the question: what effect do mutations that are deleterious have on the evolution of a species?

Note: on the species. I know you are very well acquainted with the effects on individual organisms.

 

[mark kennedy]

Of course, one thing you have never dealt with in any of your postings is the question: what effect do mutations that are deleterious have on the evolution of a species?

Note: on the species. I know you are very well acquainted with the effects on individual organisms.

gluadys, I don't want you to take this wrong but I would like to make a statement if you don't mind.

Attention, here is a theisitic evolutionists I am firmly convinced embraces Christian theism.

I'm sorry but I really wanted to get that off my chest. Ok, you made a point about mutations. You do realize that most mutations do nothing at all and the vast majority of the balance are deleterious right? Natural selection must have a beneficial effect in order to preserve a change in the nucleotide sequence right? Since the neutral and deleterious effects far outweigh the beneficial effects isn't it prudent to be skeptical of common ancectory when faced with this level of divergance?

Grace and peace,
Mark

 

[gluadys]

gluadys, I don't want you to take this wrong but I would like to make a statement if you don't mind.

Attention, here is a theisitic evolutionists I am firmly convinced embraces Christian theism.

Now I really don't know how to take that. It is not as if I am unique you know.

I'm sorry but I really wanted to get that off my chest. Ok, you made a point about mutations. You do realize that most mutations do nothing at all and the vast majority of the balance are deleterious right?

Right.

Natural selection must have a beneficial effect in order to preserve a change in the nucleotide sequence right? Since the neutral and deleterious effects far outweigh the beneficial effects isn't it prudent to be skeptical of common ancectory when faced with this level of divergance?

No. It just shows you do not understand natural selection. That has been the key missing element in all your presentations.

So let's try again. A mutation always occurs in a single cell (which may be a cell in a complex body).

It is a deleterious mutation. It has a deleterious effect on its carrier.

What effect will it have on the species that organism belongs to? Why?