Do Chimps and Humans Share a Common Ancestor?

Helium can move in and out of zircons, especially at the depths these zircons were found.

Also, this paper would not pass peer review for one obvious reason: repeatability. What Gentry needs to do is show this same He retention in zircons that are old AND have been exposed to the surface for quite some time.

Not only that, but the RATE group fudged data from other zircon studies so that it would fit in their 6,000 YEC paradigm. From here:

Dr. Humphreys admits in Humphreys et al. (2003a, p. 6) and Humphreys (2005) that the Soviet data are ambiguous. So, if Dr. Humphreys recognizes that these data are ambiguous, why didn't he simply discard them? Instead of discussing the activation energy of the Magmedov data and adequately explaining his manipulation, Humphreys (2005) accuses me of just wanting to reject the Magmedov data because I find them "inconvenient." In reality, it was Humphreys et al. (2003a) that found the extremely fast helium diffusion results from Magomedov (1970) to be so inconvenient that they manipulated the units of measure to protect their "creation date" of 6,000 years. Without fudging the Soviet data, Dr. Humphreys is put into an extremely inconvenient position of trying to explain why these Soviet results are several orders of magnitude higher than his measurements (my Figure 2) and why his "dating" equations would probably indicate that these Soviet zircons were "created" in the 20th century.

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"Since YAC [Young-Age Creation] epistemology accepts Biblical claims over physical evidence and human reason, logical or evidential arguments for evolution and/or against YAC are likely to be ineffective in converting most YACists."--Kurt Wise

Yes I'm aware that the dates were ambiguous, but that doesn't mean that they should be ignored.

Where does the fudging take place? I shall now quote the data from Humphreys et al. (2003)



Table I: Observed helium retentions for zircons recovered from various depths in borehole GT-2 and others nearby, Fenton Hill, NM. Samples 2002 and 2003 were recovered for the RATE project and named for the years we analyzed them. Samples 1-6 are those reported by Gentry et al. (1982a). Column 4 is the total helium yield (1 ncc = 10-9cm3 at standard temperature and pressure) per microgram of zircon. Column 5 is the corresponding fraction of the estimated amount of helium deposited in the zircons by nuclear decay. Column 6 is the estimated error in the fraction. All zircons were of length 50-75 µm, except for those from sample 2002, which were not sorted into size groups.



Table II: Latest (2003) helium diffusion data for 5075 µm length zircons from borehole GT-2 at a depth of 1490 meters. Column 3 is the amount of helium released (ncc defined in Table I) at the given temperature step. Column 4 is the time at each step. Column 5 is the cumulative fraction of the total helium yield (at bottom of table). Column 6 is the value of D/a2 estimated by the experimenter according to standard formulas, where D is the diffusivity and a is the average effective radius. Column 7 is the value of D assuming a = 30 µm, and omitting steps 1-9 according to advice from the experimenter (see below).



Figure 6. Recent (2003) zircon diffusion rate data compared with the Creation and Uniformitarian models shown in Figure 4.

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You will do me the justice to remember, that I have always strenuously supported the Right of every Man to his own opinion, however different that opinion might be to mine. He who denies to another this right, makes a slave of himself to his present opinion, because he precludes himself the right of changing it.

-- Thomas Paine

No one is ignoring the data. What is being contested is the conclusion.



The data that the RATE group derived from the following source:

Magomedov, Sh. A., 1970, "Migration of Radiogenic Products in Zircon," Geokhimiya, v. 2, p. 263-267 (in Russian). English abstract: Geochemistry International, v. 7, n. 1, p. 203.

From the website linked above:

To be exact, when Humphreys (2000, p. 347) applied the natural log (unmanipulated) Magomedov diffusion results to Fenton Hill sample #1, he got a ridiculous "creation date" of 23 years!

The RATE group had to manipulate data in order to get a creation date of 6,000 years.

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"Since YAC [Young-Age Creation] epistemology accepts Biblical claims over physical evidence and human reason, logical or evidential arguments for evolution and/or against YAC are likely to be ineffective in converting most YACists."--Kurt Wise

Why?

Yes.

This might not be a surprise to you, but I don't take Talk.Origins to be a great primary source.

"Without fudging the Soviet data, Dr. Humphreys is put into an extremely inconvenient position of trying to explain why these Soviet results are several orders of magnitude higher than his measurements (my Figure 2) and why his "dating" equations would probably indicate that these Soviet zircons were "created" in the 20th century."

I would like to know HOW and WHERE Humphreys et al. fudged the Magomedov results. Please try to point it out from Humphreys et al. (2003).

"To be exact, when Humphreys (2000, p. 347) applied the natural log (unmanipulated) Magomedov diffusion results to Fenton Hill sample #1, he got a ridiculous "creation date" of 23 years!"

That's simply not true, the following is what Humphreys himself wrote in Humphreys (2000) about an experiment that he wanted to perform in the future, which actually took place in 2003, he wanted to create an experiment later where he could determine which model best described the Magomedov data. He never ever placed the Creation date at 23 years.

From Humphreys (2000) :






From Humphreys (2005) :

"Henke’s word “fudging” is a lie about what we did, as anyone who wants to read section 5 of ICC 2003 can find out. As Figures 5 and 6(a) of that paper show, interpreting the ambiguous label of the Soviet graph in a reasonable way makes its high-temperature zircon data line up with everybody else’s zircon data."

All portions of the Rate book available online are copyright :

Institute for Creation Research
PO Box 2667
El Cajon, California 92021

and

Creation Research Society
PO Box 8263
St. Joseph, Missouri 64508

__________________
You will do me the justice to remember, that I have always strenuously supported the Right of every Man to his own opinion, however different that opinion might be to mine. He who denies to another this right, makes a slave of himself to his present opinion, because he precludes himself the right of changing it.

-- Thomas Paine

Because it is not supported by the data.

The RATE paper is also not a primary source because it never went through peer review.

If Humphreys used the same methodology for dating the Magomedov zircons as he did for the Fenton Hill samples he would have dated those zircons to 23 years before present. That's seems to be a problem, does it not?

But since you linked to the RATE paper I thought I would bring your attention to one of the diagrams which better illustrates the problems with their experiment.



In this diagram they represent helium diffusion as a set rate. What they do not tell you is that helium diffusion is greatly affected by ambient temperature, ambient pressure, and ambient helium concentrations. They took a zircon from deep in the earth (hot and higher pressure) and then measured diffusion at room temperature under vacuum. Of course the He diffusion is going to increase. Only a dunce could not figure this out.

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"Since YAC [Young-Age Creation] epistemology accepts Biblical claims over physical evidence and human reason, logical or evidential arguments for evolution and/or against YAC are likely to be ineffective in converting most YACists."--Kurt Wise

Just two questions LM, respond as you see fit. Do you still believe that the divergence between chimps and humans on a nucleotide sequence level is less then 2% and do you believe that ERVs makeup 4% of the human genome?

I only ask because you have been soundly refuted on your position on both of those questions.

Have a nice day
Mark

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Of the DNA shared by common ancestry between humans and chimps there is a 2% difference. When indels are considered (i.e. new DNA that has been removed or added since common ancestry) the difference is 5% or so. The reason that the numbers are different is that indels can affect more than just one base where as substitutions only affect a single base.

As to ERV's, according to the 2000 human genome paper ERV classes I-III make up 4.54% of the human genome. When MaLTR's are added the number baloons to 8.29%. I have excluded MaLr's because they are a combination of a retrovirus and a retrotransposon. MaLr's are in effect an LTR that has hitched a ride on a transposon. I focused on ERV's because their primary source is exogenous.

From the infamous table 11:

ERV class I 2.89%
" class II 0.31%
" class III 1.44%
MaLr 3.65%

If you want we could also discuss all of the Alu and LINE elements that are also shared at orthologous positions, but I don't think that will help your case.

Where?

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"Since YAC [Young-Age Creation] epistemology accepts Biblical claims over physical evidence and human reason, logical or evidential arguments for evolution and/or against YAC are likely to be ineffective in converting most YACists."--Kurt Wise

Then the divergence is 5%.

From the often quoted, cited and linked, 'Retroelements and the human genome: New perspectives on an old relation':


All I want to do is to show you one last time that you have your facts wrong.

Recently these problems have been lessened both by the systematic isolation of endogenous retroviruses from many different vertebrate taxa and by the generation of large amounts of sequence data by the Human Genome Mapping Project (HGMP) (7, 16, 32). As of December 1998, sequence information was available for over 10,000 BACs, or cosmids, representing approximately 235,000,000 bp, or 7% of the human genome (5)...The above criteria suggested the presence of 22 endogenous retroviral families within the 7% of the human genome that has been sequenced to date (Identification and Characterization of Novel Human Endogenous Retrovirus Families by Phylogenetic Screening of the Human Genome Mapping Project Database. J Virol. 2000 )

Endogenous retroviruses (ERVs) represent the proviral phase of exogenous retroviruses that have integrated into the germ line of their host (1). They typically consist of an internal region with three genes (gag, pol, and env) plus two flanking, noncoding LTRs, which are identical at the time of integration. Human ERVs (HERVs) comprise ≈5–8% of the human genome (2), with 98,000 elements and fragments (3), but phylogenetic analysis of conserved regions within their pol and env genes indicates that they form only a small number of clades among nonhuman exogenous and endogenous retroviruses (Long-term reinfection of the human genome by endogenous retroviruses. Proc Natl Acad Sci U S A. 2004)

Approximately 8% of the human genome is derived from retrovirus-like elements termed endogenous retroviruses (ERV) (14). Most of them are likely remnants of exogenous retrovirus infection of the germ line which became fixed in the population millions of years ago. (Human Endogenous Retrovirus Family HERV-K(HML-5): Status, Evolution, and Reconstruction of an Ancient Betaretrovirus in the Human Genome J Virol. 2004)

The human genome is littered by endogenous retrovirus sequences (HERVs), which constitute up to 8% of the total genomic sequence. The sequencing of the human (Homo sapiens) and chimpanzee (Pan troglodytes) genomes has facilitated the evolutionary study of ERVs and related sequences. (Divergent Patterns of Recent Retroviral Integrations in the Human and Chimpanzee Genomes: Probable Transmissions between Other Primates and Chimpanzees. Journal of Virology, February 2006)

ENDOGENOUS retroviruses arise from retroviral infections of germ-line cells and subsequent incorporation into the host's genome. The human genome is estimated to contain tens of thousands of copies of human endogenous retroviruses (HERVs) and related sequences, accounting for ~8% of its sequence content (Human Endogenous Retroviral Elements as Indicators of Ectopic Recombination Events in the Primate Genome. Genetics, Vol. 171, 1183-1194, November 2005)

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I wish to comment on this one thing. I remember a while back that you guys (evolutionists) didn't include the indels in these discussions, and so did "Nature" I think it was. I see that as absolutely dishonest.

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You will do me the justice to remember, that I have always strenuously supported the Right of every Man to his own opinion, however different that opinion might be to mine. He who denies to another this right, makes a slave of himself to his present opinion, because he precludes himself the right of changing it.

-- Thomas Paine

*sigh*

When the DNA pol moves along a DNA strand and replicates it, it does so with an incredible efficiency, this despite the fact it incorporates 50 bases/second in eukaryotes and 1000 bases/second in prokaryotes. However, ever now and then, 1 in every billion bases, it makes a mistake. Due to the stochiochemistry of the DNA bases, the most likely mistake is a transition, from purine to purine or from pyrimidine to pyrimidine. About half as often, the mistake will be a transversion, exchanging a puring for a pyrimidine. The statistics of these events and nice parametric models for them exist, so it is relatively easy for us to talk about the mutation rate in a genome, by which we imply the point mutation rate.

This issue is clouded by DNA damage and repair, a process which can also introduce point mutations, especialy in the de-amination of methylated cytosine (which is one of the primary drivers of hypervariability of immunoglobulin gene rearrangements, as it turns out)

Indels, which is a contraction of insertion/deletion, are fare more problematic. Firstly, there are a number of mechanisms that can cause them which are independent of replication, such as transposons, and there are factors that are replication dependent, such as repeat-stutter. In either case, the probabilities of these events occurring are hard, if not impossible, to model with any kind of algorithm. In addition, a single indel event can result in the inclusion or occlusion of thousands, even tens of thousands, of base pairs.

So it is that when we talk about divergence rates, we talk about the well modelled nature of point mutation, and do not include other mutational events. This is not to say they are ignored, they simply cannot be included in the parametric model. To lump indels in with point mutations and use that as some mesure of a divergence ratio is entirely inappropriate, for the reasons set out above. Only someone with superficial knowledge of biology who skim reads papers and stops when he gets to a bit he likes would even suggest that it is a good idea. And whilst on the topic of that kind of foolishness, have a nice day mark

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I hear stories from the chamber / How Christ was born into a manger
And like some ragged stranger / Died upon the cross
And might I say it seems so fitting in its way
He was a carpenter by trade / Or at least that's what I'm told
--Mercy Seat, Nick Cave and the Bad Seeds