An open reply to Mark Kennedy

Pedantic overemphasis of esoteric rhetoric chanted in the absence of an explanation for Class 1 ERVS that were neither predicted nor explained.

History tells me otherwise, especially when you STILL refuse to acknowledge that overall mutation rates do not and should not be required to accommodate indels..
Whatever...

Which is altogether typical. The mutation rate was considered close to the upper edge when it was 1% and some change and now it's like 5%. Nothing creates a problem for evolution because the a priori assumptions is never question and alternatives are never explored.

" esoteric rhetoric "?

What, the word "orthologous"?

But at any rate, you still haven't explained patterns of orthologous ERVs in primates. You keep trying to deflect the issue by bringing up non-orthologous ERVs. A red herring, as it were.

Incredible....

You simply REFUSE to learn a thing.

Let me explain it AGAIN - what is this, the 25th time over the last 5 years? Maybe one of your YEC pals can comprehend this and explain it to you - maybe you will listen to one of your own.

An indel is a one-time event. Regardless of the size of the event. Some indels can be 10s of thousands of bases in length, but it is inserted or deleted all at once.

At any rate, we'll see what the Professor has to say for himself when he gets here since he apparently wants to defend the statement as 'correct in certain context', whatever that means.

Yeah - just like old times. In fact, it is EXACTLY like old times - I see the exact same claims, even the exact same data being used (inappropriately, in most cases)

Yep, most of it is rehash since I long ago abandoned the hope that evolutionists would debate the topic on the evidence. It never ceases to amaze me that you scoff and mock at every statement and yet manage to find the time to have a discussion with someone who hold a view you deeply and venomously hate. I sometimes wonder what you get out of these discussions because you obviously could care less about persuasion.

My mistake - I thought you were referring to your same-old, same-old quotes of yore and I did not read this entire thread.

We have been through this, the Chimpanzee Genome project found that we are something like 95% the same in our DNA. It wouldn't be such a big deal if people like you were not pushing the myth that we are so alike physically and genetically we must be related by lineage and belong in the same genus.

I'm not sure what she is talking about.
Reading the actual paper, I think LifeToTheFullest is onto something - the paper is referring to a collection HARs and it seems to be in reference just to those when compared to chimp, but it is not clear and the SciAm article is clearly either a mistatement or an error.

It's just plain wrong.

quote]So I guess all evolutionary biologists mjust be dishonest conspirators...

So you want to condemn all evolutionary biologists on the basis of what one person said in one article?

This woman is someone I respect and admire, I'm saying the statement is bogus, nothing more. This is not about her, it's about the likes of you pretending to care about science when all you really want to do is mock a religion you know nothing about.

Can I use that criterion to condemn all Christians because I've seen a few celebrating the assassination of George Tiller?

I've seen creationists claim that no speciation has ever occurred. Does that mean that all creationists believe that ALL extant species were on the ark that didn't really exist anyway?

I do hope you realize that most creationists would have nothing to do with these discussions.

I also know that the number of bases in an indel has nothing to do with the overall mutation rate. What of it?

The web focus article announcing the publication of the Initial Sequence of the Chimpanzee Genome said:

What makes us human? We share more than 98% of our DNA and almost all of our genes with our closest living relative, the chimpanzee Chimpanzee Genome

This will be at the top of the list when you type Chimpanzee Genome into the Google search engine.

The paper says something like 1.4% from single base substitutions but indels are:

On the basis of this analysis, we estimate that the human and chimpanzee genomes each contain 40–45 Mb of species-specific euchromatic sequence, and the indel differences between the genomes thus total 90 Mb. This difference corresponds to 3% of both genomes and dwarfs the 1.23% difference resulting from nucleotide substitutions; this confirms and extends several recent studies (Initial sequence of the chimpanzee genome and comparison with the human genome)

How do you explain that Professor?

Time magazine did the exact same thing, they expressly cite the Chimpanzee Genome paper saying that it says we are 99% the same as Chimpanzees.

[ I wrote Time and of course they ignored it.

What do you mean, 'let it stand'? What would you have me do? Write SciAm and complain that someone said something wrong in an article and that the erroneous statement is really irrelevant to the overall gist fo the article?

The precise number is really not that important, frankly. You are just hung up on it as a means of making what you think is a good argument. It isn't

.

That statement is typical of the propaganda evolutionists are putting out. When I keep seeing the same half backed statistics and generalities knowing what the actual facts are it makes them (including you) look increasingly desperate.

Put the facts on the table and let the truth stand or fall on it's own merit. A year or so after the Chimpanzee article I started seeing research into human DNA comparisons. Guess what, we can diverge by more then 1% but that does not get to be a point when you let a statement like this stand. Then you either have to back peddle and explain the errors or suffer the loss of confidence and credibility.

And creationist detractors are not honest - or very well informed - when it comes to technical issues like this.

That is why I like to stay on the simplest, most obvious and undeniable point I know of. We are not 99% the same as Chimpanzees in our DNA but you guys have no problem with Pollard, Time or Nature Web Focus saying we are.

You will exaggerate and magnify any error creationists make but not this one, you will pretend I'm not as enlightened as you.

It has been explained to you proably a hundred times that the size of an indel is IRRELEVANT because it is a one-time mutational event. It counts as ONE, even if the indel is 10,000 bp long. It all gets inserted or removed in one shot. Therefore, they do not need to be included in the overall mutation rate, which is a measure of the OCCURRENCE of mutation. In fact, doing so would be an exercise in incompetence, sort of like claiming that if we launch a new rocket and it travels 1000 miles, we have to count it as 1000 individual launches because the old rocket could only go 1 mile.

You keep explaining that as if I didn't understand that in the first place.

You like to break it down to kindergarden level but the fact is that the differences between 99% and 95% involves hundreds of millions of base pairs. Let's do this again just for fun:

5 million years ago lived the common ancestor
35 million single base substitutions
5 million indels adding up to about 90 million base pairs

Thats one indel, permanently fixed per year for 5 million years and 7 single base substitutions. Given a generation of 20 years you have 20 indels and 140 single base substitutions. Mind you these do not include the 9 major chromosomal rearrangements that range from 2 Mb to 10 Mb.

Your right though, it really doesn't matter so why not use the right numbers instead of exaggerating the similarity? Could it be because you like these homology arguments so much you just can't help but hoard them even when they are obviously false.

As indicated, the actual divergence is largely irrelevant since it would be comparing apples and oranges

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Nonsense, it would be comparing two species thought to be related by lineage.

The further apart they are genetically the less likely they are to be related. What's the matter Professor, can't handle the inverse logic when it contradicts you forgone conclusions?

But it doesn't necessarily, as has also been explained to you repeatedly. And even if it did, what of it?

That regulatory gene HAR1f was virtually unchanged for over 300 million years allowing only 2 substitutions. Then for the human lineage to emerge there had to be 18 substitutions about 2 million years ago when the expansion of the cerebral cortex began to grow exponentially.

Add to that the fact that every ape fossil they dig up in Africa is automatically classified as hominid which is why there are hundreds of hominid fossils and none of them are classified as chimpanzee ancestors.

It is pure, undiluted duplicity.

Sometimes this happens. Sometimes it doesn't. You seem to require a uniform distribution of mutations at all loci for all time. Nature doesn't work that way, and I've seen your recycled quotes before. Not interested. Did you read the actual scientific pub, or just the SciAm bit? The actual article contains interesting information - such as most of the HARs are found close to the ends of chromosomal arms, indicating a positional effect. Hmmm....

Yes the article does touch on that and she has a couple of other papers that discuss brain related gene comparisons. The point is that this kind of homology argument is just plain wrong.

Why don't you write SciAm or Pollard why she said 99% when all the latest research is indicating no more then 96% the same in our DNA?

My guess its because you already know.

Sure, asking questions is fine. But presenting questions as if they are evidence for something is quite another thing

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The problem is that you guys like to exaggerate errors and beat creationists over the head with them. Why is it so hard to admit this one?

There are an abundance of genes that show accelerated evolution but the mention of actual mechanisms for making an adaptive evolutionary change never seems to enter the conversation. The problem is that it's assumed rather then proven and the evidence is organized around the assumption.

You keep tossing the term 'honest' around - do you think it is honest to repeat the same claims year after year when you have had your errors explained to you repeatedly?

It's not honest

and the error of the statement in SciAm is obvious and yet you do not explain it, correct it or have the slightest problem with it simply because it was not made by a creationist.

We talked about the three-fold expansion of the human brain from that of apes and the requisite genes involved and you guys derailed the discussion.[ I have discussed these bogus homology arguments from things like ERVs and watch them crumble into dust and ashes.

Why don't you address this error? Which is it Professor, 99% or 96% the same in our DNA?

You did not understand my statement - your desire to use total raw sequence differences as the yardstick by which to judge hypotheses of descent runs into trouble if we apply the same criteria to other inter- and intraspecies comparisons. So, if we say that we must include all the nucleotides in indels in the raw count, and the human-chimp divergence goes up to 5%, then we have to use the same criterion when comparing dogs to foxes and loggerhead turtles to leatherbacks and even when comparing two individuals of the same species and guess what - the divergence goes up in ALL those cases.

No sir, what I really want is a directly observed or demonstrated mechanism for the three-fold expansion of the human brain from that of apes.

Random mutations with some serendipitous beneficial effects simply have no way of accomplishing this.

I honestly would have to difficulty reconciling my religious convictions to a totally naturalistic evolutionary pathway except that I will not have this a priori assumption forced upon me by the Scientific or Academic elitists.

Whatever that means?

Not so hard, really.

If you are looking at the nucleotide sequence identity between chimps and humans in their shared coding genes, it is in the 99% range.

If you are looking at the raw, overall nucleotide identity between the genomes of chimps and humans, it isn't.

Pretty simple.


Say you are 5'8".

In a crowd of midgets, you are tall.

In a crowd of basketball players, you are short.

Different contexts.

History tells me otherwise, especially when you STILL refuse to acknowledge that overall mutation rates do not and should not be required to accommodate indels..
Whatever...

Which is altogether typical. The mutation rate was considered close to the upper edge when it was 1% and some change and now it's like 5%. Nothing creates a problem for evolution because the a priori assumptions is never question and alternatives are never explored.

There is no amino acid sequence in a gene, protein coding or otherwise.

[/quote[I don't know what kind of semantical word play your into here but I'm sure it's circular and empty rhetoric.

If I had written something as laughably ignorant as this:

"I know the difference between an amino acid sequence in a protein coding gene and other segments."

I'd probably try to weasel out of it, too.

The genetic code is the set of rules by which a gene is translated into a functional protein. *snip plagiarized Wiki entry*


That's what I'm talking about, the protein coding sequences as opposed to the regulatory genes like the HAR1f that are not in triplet codons. I don't know what you are tripping on.

This is so cute - it reminds of how you responded after you finaklly figured out what 'mutation' really meant 5 or 6 years ago.

And nobody would disagree. If adaptive evolution were easy, we'd all be supermen.First, we like to make sure that the claimed errors really were. Second, correcting a claim made by someone on a discussion forum is easy, it can be done in almost real time. Correcting an error made by someone in a national publication is a bit different. Considering the fact that those in the know, know that science is a tentative buisiness, especially on the details, that one researcher claims a 99% identity and another claims 98% and another claims 95%, I don't think it really matters. The fact is that humans and chimps share a greater identity in the overall genomic as well as the genic level than chimps share with the other apes. If we want to make the divergence dependant upon the raw nucleotide difference, then the divergence between chimps and gorillas increases probably by just as much as the human-chimp divergence does.

The statement is in error and current estimates are right around 96% and have been for some time.

What part of the above statement is in error?
I note that you ignored context again.

If you are so all fired zealous about correcting errors then correct this one and move on. If it's not that important then why do you dwell on the subject shoring up the homology argument as you go. I think it's because you got a lot of milage out of the homology argument and you really don't want to admit the inverse logic.

Correct what?

Funny how you talk about correcting erros and moving on - you've been making the EXACT SAME erroneous arguments for 5+ years despite multiple corrections, and you just keep spewing the same errors.
Had you ever, in your Christian humility, even considered the mere possibility that it might actually be YOU that is in error? Like, say, you were on mutations?

IOW, your argument is irrelevant

It's not an argument Professor, it's a fact

No, I'm sorry it is not.

You simply do not grasp the very simple fact that each individual nucleotide in an indel is NOT added one at a time.

[qu8ote]

See the above quote, it's whole genome comparisons. Other such comparions do not bear it out. No biggie. Hard to tell what Pollard meant. If she DID indeed mean whole genomoe comparisons, then she is wrong. If she was referring to HAR regions, then the statement was clearly either terribly edited or was simply misstated

The woman is a brilliant research scientist, right or wrong?

You cannot tell me that she was unaware that the current comparisons since at least 2005 were showing 5 times the divergence she claimed existed.

You guys can get away with that in pop press which is why I go to the peer reviewed source source material, they'll get it right there.

I learned the Bible and Christian doctrine like this, you would be amazed how much scientists and theologians have in common.

That was not what she said. That is what I said.

Then what is it? Incompetence? Perhaps an error of perspective? You are very quick to ascribe dishonesty when the answer is quite likley something else altogether. I've not read the article - I don't read popular press science magazines for a number of reasons - and I don't really care to. That one person's statement in one article seems incorrect is really quite irrelevant in the broader scheme of things.
Good.

I'm not following your reasoning here,

Funny then that the only people that do not seem to accept it are religious.

So what?

That is my principle objection, not to your conclusion but to the leap in logic that presupposes naturalistic causes and that anyone who concludes God as a cause as ignorant. Both assumptions are fallacious.

And therefore.... what? I shan't get my panties in a bunch over what someone wrote in a popular press magazine.

No but you get an atomic wedgy about what a creationist has to say abou it.

Real debate is fine. Manefactured, recycled nonsense for the purposes of ego stroking is not. The last time I was in an 'official' debate on a discussion forum, my opponant ran away from the agreed upon topic in his first response, and insisted that he won because I would not diverge from the agreed upon topic.
I have no cherished assumptions to reconcile, whatever that is supposed to mean. You cannot simply ignore evidence because a person makes an error in a popular press article.

No real debate is not fine, not when you are into Darwinian theatrics. You do have cherished assumptions that you guard jealously, that is evident and obvious.

I am not surprised or impressed by the fact that you are fixating on something as irrelevant as this. Nor am I impressed or surprised that despite 5 years of having your erroneous genetics claims explained to you, you are still proudly making them.
The fact of the matter is that Pollard's claim is really irrelevant in the overall scheme of things. That your are fixated on it is demonstrative of the minutiae with which anti-evolutionists confine themselves, for the big issues are too much for them to handle.
Pollard's error has no bearing whatsoever on the evidence for descent, and a person that thinks it does is living in a fantasy land.

Pollard made a bogus claim, plain and simple. You have admitted it is in error but you are not so quick to explain why she made it.

It's because evolution gets a free ride and homology arguments are the ticket. We are not so close to chimpanzees anatomically or genetically as we have been led to believe for the last half a century and now that this homology argument is proving itself to be false, it continues unchallenged.

I don't know what you want from me Professor but I expect I'm just a little duck in your intellectual shooting gallery.

None of this is for my benefit and your going to treat one argument just like the other. I cannot understand why you persist because I have been convinced that TOE as you are propagating it is mythical and deeply fallacious.

I have to wonder, if I am so much in error and it's not even possible that a creationist view of the origin of life is possible why do you bother having these exchanges.

I think you are addicted to the drama and secretly suspect there is merit in our claims. You'll never admit it, even to yourself but it's the only explanation that makes any sense.

Still 5'8. Nothing changes about you.