Peanut Gallery - AronRa/Enyart - Phylogeny

[Frenger]

I'm currently working on a response to his clock calibration claim for mitochondrial eve, just to give you a spoiler, he was wrong again.

 

[Inferno]

I'm currently working on a response to his clock calibration claim for mitochondrial eve, just to give you a spoiler, he was wrong again.

My, that sounds familiar.
Looking forward to that response.

 

[Visaki]

I'm currently working on a response to his clock calibration claim for mitochondrial eve, just to give you a spoiler, he was wrong again.

And this is why these kinds of seemingly pointless debates are actually worth it. It's not about who wins and who loses, though I think all honest people here know who "won", but about spreading information. I've learned many things from this and looking at what Frenger says, I'll learn even more.

 

[Entrak]

Hi there! First post of mine here and I'm somewhat dreary to have it be one where the point of it can be summarized to this:

My brain hurts from all the stupid.

I've been reading up on the debate and summarily, this thread to see what the responses and rebuttals were.
And I'm baffled.

Baffled on how the creationist side can be this.. Well, let's just call it deceitful in their responses.
Deliberate quote-mining, misinterpretations, dishonesty, logical fallacies (, not to mention illogical assertions) and blatant lying. And by ignoring any response and refusing to answer questions to clarify your own point-of-view, claiming that this is a victory?

Putting words in other peoples mouths does not make that persons opinion be what you claim it to be and on a WRITTEN medium, where ANYONE can go back and see what was actually written, this behavior is just, in lack of a better word, sad.

Although, I'll grant you this: It was fun to see the efforts of the wailing tantrums in an obvious attempt to be banned, just to have an excuse to end the debates with self-proclaimed martyrdom and claims of censorship.

I'm sorry that my first post on a board like this have to be one where I'm so blatantly whining about a party in a debate. But I do think it warranted to reply to the discussion that brought me here in the first place, a discussion I've enjoyed for the most part. But that being purely because of the factual and falsifiable documentation provided in the responses, causing me to expand my own knowledge by quite a bit.

So I'm going to thank both AronRa and Enyart for providing me with this debate, I have learned quite a lot by reading through all that's been provided, both in the main parties debate-thread and by the peanut gallery.

 

[Inferno]

Welcome to LoR, Entrak.
Glad you enjoyed yourself, that's basically the only reason anyone debates a creationist any more.

 

[Dragan Glas]

Greetings,

Greetings,

YesYouNeedJesus, just out of interest - since you've said you're a YEC - would you care to start a thread in the Creationism/ID forum regarding what you believe to be the age of the Earth and why?

I'd welcome a chat about that.

Kindest regards,

James

Yes, pretty soon.

Still waiting (since January).

Kindest regards,

James

 

[Inferno]

Just sent a message to both Bob Enyart and Will Duffy. Let's see if this does something... DraganGlas, do tell me if I was polite enough?

Mr. Enyart

Both before and during your debate with AronRa, Will Duffy appeared on the League Of Reason forum and engaged in a discussion with us. In this discussion, he failed to answer several questions that were of central importance to the topic. After eight months and several requests to Mr. Duffy, none of which have been acknowledged, I would like to ask you for a favour: Press him for an answer, preferably to all (a handful) questions left unanswered, but at the very least to this one question I asked him. (Details below)

After all... "...Always be prepared to give an answer to everyone who asks you to give the reason for the hope that you have." (1 Peter 3:15).

Reproduced below is the E-Mail I just sent to Mr. Duffy, in the hopes that he will respond.

Thank you for your time
Benedikt Lernhart aka Inferno

Mr. Duffy

After months and months of waiting, I still haven't had a response from you regarding this question I posed to you: http://bit.ly/P2h9GT

Given that I sent you the paper that was discussed and given that I clarified the issue for you, I thought it quite rude of you not to answer me.

I would therefore ask you to give me an answer now, be it by E-Mail, by PM on the forum or by posting in the above thread.

I shall also be forwarding this message to Bob Enyart, in the hopes of getting an answer from at least one of you.

Thank you for your time
Benedikt Lernhart aka Inferno

 

[Dragan Glas]

Greetings,

Seems quite reasonable requests to both of them, Inferno.

Kindest regards,

James

 

[he_who_is_nobody]

I just added your question to the list of unanswered questions to YesYouNeedJesus.

 

[Inferno]

I just added your question to the list of unanswered questions to YesYouNeedJesus.

That question was already on there, third question and now also last question.

 

[he_who_is_nobody]

I just added your question to the list of unanswered questions to YesYouNeedJesus.

That question was already on there, third question and now also last question.

Blast.

Oh well. Not like YesYouNeedJesus will ever see that thread anyways.

 

[Frenger]

In Ann Gibbon's Science article, "Calibrating the Mitochondrial Clock," rather than again using circular reasoning by assuming their conclusion (that humans evolved from ape-like creatures), they performed their calculations calculating with actual measured mutation rates on human DNA. This peer-reviewed report stated tha if these rates have been constant, "mitochondrial Eve"¦ would be a mere 6000 years old."

Sorry on my late reply on this, I have been moving house and have had no internet. But here is my brief response.

First I would like to thank Inferno for getting me the paper, I had a feeling this part was bollocks, not just because Enyart had stated it, but because it did sound intrinsically bollocks. Who'd a thunk it was eh?

Anyway, Enyart doubtless has not read the paper, or if he did he in no way understood it. For those that don't have access to it let me start by summarising it. The paper starts by outlining some of the troubles molecular biologists have had recently with trying to determine the identity of a recently exhumed body thought to be Russian Tsar, Nicholas II. The problem was this chap was carrying two mtDNA where as it was recently thought only one sequence was carried. The paper was published in 1996 in genetics when they found that the tsar's brother also had this condition, called heteroplasmy.

Now heteroplasmy is more common than previously thought, about 10-20% of people inherit the coding for two copies of mtDNA. Why is this a problem? Why is it a problem for the mitochondrial clock? Well, the paper states that because heteroplasmy is caused by mutations, this unexpectedly high incidence suggests that mtDNA mutates much more often than previously estimated

Before I continue (I want to be as thorough as possible) I would like to first outline why and how mitochondrial DNA (or mtDNA) is used for dating.

Unlike DNA which is a mix of both parents, mtDNA is passed down only through the mother; this means there is no complicated mixing of genes to sort out when looking for mutations. The way it works is two strands of mtDNA are put side by side and then the differences are counted. As mtDNA is thought to mutate at a steady rate (mutations every 6,000 to 12,000 years) we can make estimates on when we shared common ancestors for example our common ancestor with Chimpanzees is thought to be around 5 million years ago (give or take). This is of course calibrated with fossil and archaeological evidence. That's right, as with most areas of science there are areas of overlap where different areas are used to check others. So in the example of our common ancestry with Chimpanzees being around 5 million years ago, we can check the fossil record for examples of what we would imagine a common ancestor to look like, which would be a mammal sharing traits with both humans and chimpanzees. And would you know it, that's what we find. Back around 3-4 million years we find Ardipithicus Ramidus a mammal sharing more traits with chimpanzees although sporting a straight down spine which infers it was probably bipedal. Bipedalism of course being one of those traits we have which differs from those of the chimpanzees.

So there we have a brief outline of how mitochondrial DNA is used to trace ancestry back through maternal parents. Of course I don't think this needed to be outlined for anyone on this forum, this is more for our friend Will (Bob I think probably knows this although denies it).

So back to the paper, and back to where Bob went wrong. The easiest way to show Bob's "tricky" tactic of quote mining is usually to simply quote the next line of the paper"¦"¦..and today is no exception

For example, researchers have calculated that "mitochondrial Eve"-the woman whose mtDNA was ancestral to that in all living people-lived 100,000 to 200,000 years ago in Africa. Using the new clock, she would be a mere 6000 years old. No one thinks that's the case, but at what point should models switch from one mtDNA time zone to the other?

Emphasis mine

So, no one thinks that is the case, but why is that?

Well, the paper not only goes on to explain, but with a quick google search you can see why this method of dating is no good in this (and many other) circumstance.

Just to quote some other parts of the paper before I dig a bit deeper.

"This is all a fuss about nothing," says Oxford University geneticist Martin Richards, who thinks the fast rate reaches back hundreds of years at most"

"The easiest explanation is that these two rates are caused by hot spots"

"If so, these short-term rates need not perturb long-term studies. "It may be that the faster rate works on the short time scale and that you use the phylogenetic rate for long-term events," says Shoubridge"

So, the paper itself is not conclusive and along with that, few studies have been done;

"Because few studies have been done, the discrepancy in rates could simply be a statistical artifact, in which case it should vanish as sample sizes grow larger, notes Eric Shoubridge, a molecular geneticist at the Montreal Neurological Institute"

So Bob, as with the Dinosaur soft tissue, forces a paper to say something it doesn't based his desire to win points in a debate. So much for truth huh?

The paper concludes by saying fast-mutation rates are now taken into consideration in the short-term by labelling single mutations as "inconclusive" rather than "mismatch". This is also done in regards to some evolutionary rates.

The other thing to say is that this paper is dated 1998, so what has happened since then?

Well, a lot as it happens. (This is just for the benefit of showing that "mitochondrial eve" does in fact date back to between 150,000, 200,000 years ago) So;

Hasegawa, Cao and Yang, Preponderance of Slightly Deleterious Polymorphisms in Mitochondrial DNA: Nonsynonymous/Synonymous Rate Ratio is Much Higher within Species than Between Species, Mol Biol Evol 15, 1499 -1505

In this paper, Hasegawa and his team note that the rate ratio of non-synonymous to synonymous mutations is much higher in species than between. As synonymous mutations make no difference to the protein encoded their mutation is neutral and their incidence depends only on the dynamics of the lineage possessing them. Non-synonymous mutations however do cause changes in proteins so the probability of their survival over many generations depends on whether they are deleterious, neutral or beneficial. As most are deleterious, the ratio between non-synonymous and synonymous is less than one. The study shows that ratio within species (primates) is around 5 to 10 times that of between species. (Human ratio = 0.2, chimpanzee = 0.5, gorilla = 0.4, between species = 0.033 - 0.04). It was concluded that this was due to slightly deleterious mutations being eliminated from the population. As synonymous mutations have no effect on phenotype, they will probably remain the same across the different species. Therefore the differences are explained by the fixing of non-synonymous mutations over generations. It was also found that the D-loop was functional, so mutations found were a result of deleterious mutations being observed before there was chance for them to be eliminated, compared with long-term, phylogenetic studies.

Now taking the above into account, the following paper;

Max Ingman et al, Nature 408, 708 - 713, Mitochondrial genome variation and the origin of modern humans (published in 2000)

shows that there is big variation in the D-loop for different populations. Excluding this however, Ingman shows that mutation rates in mtDNA has remained constant in Human's and using data from other primate species, they see no significant difference in the evolutionary rate in any mtDNA.

Using a sample of 53 diverse individuals, Ingman then compares the variation within the human population along with the difference between Human and Chimpanzee DNA to obtain a mutational rate across the whole mtDNA genome (excluding the D-loop).

With a mutational rate of 1.7x10-8 mutations per site per year Ingman concludes that the most recent common ancestor shared by this diverse group of individuals is 175,000 years +/- 50,000 years.

So there we have it. The most recent studies show that our most recent common ancestor or "mitochondrial eve" lived between 100,000 and 200,000 years ago and not the 6,000 years ago that your man Enyart wants to put forward.

Sorry if this is a bit long and if anyone has any corrections please put them forward. Like I said this is brief and I'm sure I have missed some bits out but time has been short as of recent and this is the best I could do with the time I had.

Cheers.