Evolution's new wrinkle: Proteins with cruise control provide new perspective (DIRECTED MUTATION!)

Sure, but one can just count the differences to figure out that humans and chimps are both closer to each other than either is to a gorilla.

Over a thousand bases of genetic DNA a human and chimp will differ by about 10-20 bases, while a chimp and gorilla or gorilla and human will differ by about 20-30 bases over the same stretch.

DNA annealing experiments indicated what the genome sequencing confirmed.

==Still nothing to contradict the clear and unambiguous DNA data that shows a chimp is closer to a human being than it is to a gorilla.

Just imagine all the logical impossibilities your materialist faith impels you to embrace. Compared to you, the Queen of Hearts is a cold, hard rationalist.

==The data says that your “logical impossibility” is the truth.

BS. The data suggests a common designer. It’s obvious—except to brain-dead Temple of Darwin fanatics.

Still nothing to contradict the data.

Over a thousand DNA bases a chimp will have more similarity to a human that it will to a gorilla.

What explains this data that is obvious to all except a brain-dead Temple of Luddite fanatic?

Do you invent a conspiracy theory to explain it? That is usually how you explain away contradictory data.

Why do DNA genome databases show that chimps are more similar to humans than they are to gorillas?

==Still nothing to contradict the data...Over a thousand DNA bases a chimp will have more similarity to a human that it will to a gorilla...Do you invent a conspiracy theory to explain it? That is usually how you explain away contradictory data.

I actually broke down and decided to look into the matter as it is obvious that your materialist faith prevents you from grasping the obvious. The first thing I noticed is that your sources, as per usual, have been rendered out-of-date by further research. If the human-chimp similarity is such an open and shut case, then why do the most recent papers on the subject allow for multiple geneological scenarios with respect to the relationship between human, chimp and gorilla? Does your materialist faith allow you to grasp the significance of State CG in the phylogenetic trees below? Does this mean your fellow Darwiniacs are in on the conspiracy too?:

Bottom: Each of the four hidden states in the coal-HMM corresponds to a particular phylogenetic tree. In state HC1, human and chimpanzee coalesce before speciation of human, chimpanzee, and gorilla, i.e., before τ1 + τ2. In states HC2, HG, and CG, human, chimpanzee, and gorilla coalesce after speciation of the three species, i.e., after τ1 + τ2. In HC2, the human and chimpanzee lineages coalesce first, and then the HC lineage coalesces with gorilla. In state HG, human and gorilla coalesce first, and in state CG, chimpanzee and gorilla coalesce first. The hidden phylogenetic states cannot be observed from present-day sequence data, but they can be decoded using the coal-HMM methodology.

Hobolth A, Christensen OF, Mailund T, Schierup MH 2007 Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model. PLoS Genetics 3(2): e7 doi:10.1371/journal.pgen.0030007

Amazing. All that data shows the branching of humans and chimps as being closer than the branching off of the gorilla line.

This is not a contradiction, and it does not render the data out of date. It confirms the closer evolutionary relationship of humans and chimps than either humans or chimps to gorilla.

Once again you show that you have no idea what the data shows. Once again this is not new, I have been telling you that ERV and genomic data shows this for over a year now GGG.

As the data you source concludes......

http://www.plosgenetics.org/article/info:doi%2F10.1371%2Fjournal.pgen.0030007

“Furthermore, we have applied this methodology to four long autosomal human–chimp–gorilla–orangutan alignments and estimated a very recent speciation time of human and chimp (around 4 million years)”

==but one can just count the differences to figure out that humans and chimps are both closer to each other than either is to a gorilla.

As usual, you are behind the times, Allmendream. Your neo-Darwinian attachment to DNA comparisons is quaint, but is already quite out of date with respect to the new biology. For someone who is such a recently minted scientist, I am shocked that your graduate school neglected to instruct you on the basics of non-genetic inheritance (and what that means for Darwin’s increasingly discredited creation myth).

State CG was the exception not the rule. They accounted for all possible states and used a model that showed that state CG was much less prevalent than the states that grouped humans and chimps. Their data unambiguously showed that humans and chimps split more recently than gorillas split from the human chimp line, as they concluded with their estimate of 4 million years for the human-chimp split.

Your selective quoting just shows your desperation. The scientists you are quoting clearly concludes that chimps and humans are closer to each other than either is to a gorilla. Are the scientists in error over their own data GGG?

"Analysis of such large fragments is challenging because different parts of the alignment will have different evolutionary histories (and thus different genealogies, see Figure 1) because of recombination [14,20]. Ideally, one would like to infer the genealogical changes directly from the data and then analyze each type of genealogy separately. A natural approach to this challenge is to move along the alignment, and simultaneously compute the probabilities of different relationships and speciation times. While recombination has been considered in previous likelihood models [14], the spatial information along the alignment has largely been ignored. In this paper we describe a hidden Markov model (HMM) that allows the presence of different genealogies along large multiple alignments. The hidden states are different possible genealogies (labeled HC1, HC2, HG, and CG in Figures 1 and 2). Parameters of the HMM include population genetics parameters such as the HC and human–chimp–gorilla (HCG) ancestral effective population sizes, NHC and NHCG, and speciation times τ1 and τ2 (see Figure 1). We therefore name our approach a coalescent HMM (coal-HMM)."

I am not “attached” to DNA.

You made two specific claims about DNA that I am showing are in error.

You claimed that DNA similarity could be explained by physical and lifestyle similarity. I showed you the data that chimps and humans are closer to each other than either is to a gorilla, although clearly the gorilla and chimp are more similar in lifestyle and physical form. Clearly your ‘similar DNA is explained by similar physical form and lifestyle’ construction breaks down once you actually look at the DNA data.

You also claimed that the DNA similarity observed between humans and chimps that is greater than either’s similarity to gorilla DNA was a “logical impossibility”. Now that I have shown you (and you have sourced yourself) numerous data that show this to be the case you claim I am ‘quaintly attached to DNA’.

I guess when you cannot deal with the error of your specific claims regarding DNA the only tact is to claim I am the one somehow obsessed with DNA.

Clearly God laughs at your “logical impossibility”. Do you often claim superior knowledge of God's will than what the data clearly shows? It is indeed part of God's plan to have human and chimp DNA more similar than chimp and gorilla DNA.

Yes, a “considerable fraction of single genes” are more similar between humans and gorillas than between humans and chimps. Not the majority.

This is predictable based upon the small amount of total difference in genetic DNA. Humans and chimps are about 1-2% different, and humans and gorillas are about 2-3% different, there is some overlap there making a “considerable fraction of single genes” more similar between humans and gorillas than humans and chimps; but obviously not the majority. The data clearly doesn’t show that chimps and gorillas are closer than chimps and humans, the data clearly shows a divergence time between chimps and humans as being less than the divergence time between gorillas and chimps.

==You claimed that DNA similarity could be explained by physical and lifestyle similarity.

Actually, a common designer explains DNA similarities. I was merely stating that organisms have been designed to have similar body plans and similar functional needs will quite naturally be similar in terms of their
genetic/epigenetic blueprint.

==You also claimed that the DNA similarity observed between humans and chimps that is greater than either’s similarity to gorilla DNA was a “logical impossibility”.

You are quite right. See above.

==Now that I have shown you (and you have sourced yourself) numerous data that show this to be the case you claim I am ‘quaintly attached to DNA’.

The most recent research demonstrates that even your fellow Temple of Darwin fanatics are being forced to insert question marks into their human-chimp catechism. You can't even get your own position right, let alone my position. But you are correct about one thing...you are indeed ‘quaintly attached to DNA.’

I have my position and it is clearly stated and agrees with the data both you and I have sourced.

You have your position and it is contradicted by the data both you and I have sourced.

Your two specific claims about DNA are contradicted by the data. More similar animals will not have more similar DNA in the case of chimps and gorillas, new world and old world vultures, and many other examples. And despite your attempt at selective quotation of a paper, both the paper you sourced and I clearly tell you that chimps and humans are more similar to each other in DNA than either is to a gorilla.

Obviously you are having problems reconciling the truth that God has put before us in terms of DNA sequence data, and your preposterous claims to know God's mind enough to declare reality to be a “logical impossibility”.

Thanks for the laughs. :)

Once again, you are trapped by your reductionist understanding of the role of DNA. Your sloven commitment to reductionist materialism has blinded you from the reality that DNA is but one component that determines our body plan and functional needs. And for some reason, you don't seem to realize that there is as of yet no whole genome sequence of the ape genome to compare with the whole genome sequences of humans and chimps. And finally, you also managed to miss the passage where the authors admit that the fact that humans and apes are more similar to each other than to chimps with respect to a considerable fraction of single genes creates a “conflict between species and gene genealogy” that cannot be explained by “instant speciation and a large ancestral effective population size.” This is what forces them (from a Darwiniac point of view) to conclude that State CG (where chimps and humans both diverge from the ape, but not from each other) is a distinct possibility.

Wrong again GGG. They included case CG because a fraction of genes did fit that pattern, not the majority. This overlap is more frequent in genetic DNA than genomic DNA because there is less difference in genetic DNA between species than genomic DNA, and in terms of absolute difference humans chimps and gorillas are all fairly similar in DNA. Analysis using ERV data, for example, has much less to no “overlap” as the differences are more pronounced (as predicted by Kamura’s neutral mutation theory).

The authors you source clearly show that the majority of the genetic data they worked with was more similar between humans and chimps than between chimps and gorillas.

Do you think the authors were similarly “trapped by (their) reductionist understanding of the role of DNA”. Were the authors the victim of a “slovenly commitment to reductionist materialism”? The inescapable conclusion of their data is that humans and chimps diverged more recently than gorillas. Do you see fit to correct them on their own data, and based upon what exactly?

==I have my position and it is clearly stated and agrees with the data both you and I have sourced.

Wrong.

==You have your position and it is contradicted by the data both you and I have sourced.

Wrong again.

==And despite your attempt at selective quotation of a paper, both the paper you sourced and I clearly tell you that chimps and humans are more similar to each other in DNA than either is to a gorilla.

Your inability to comprehend a straightforward reading of your fellow Temple of Darwin fanatics is almost as bad as your inability to comprehend a straightforward reading of Genesis. As I mention in my last reply, the authors admit that (A) apes are closer to humans than to chimps in a considerable fraction of single genes (B) that this is in conflict with the Evo human-chimp catechism and (C) that this leaves open the possibility (from a Darwiniac perspective) that humans and chimps diverged from apes, but not from each other. If you think this is not what the authors of this paper are saying, then may I suggest that the Darwiniac worms have ate too much of your brain.

Humans chimps and gorillas are all apes according to taxonomy classification. Even if you want to exclude humans from the ape clade, chimps are obviously still apes. So your sentence “apes are closer to humans than to chimps” shows your ignorance - chimps ARE apes.

When you say “ape” you mean gorilla?

The authors conclude that chimps and humans diverged some 4 million years ago. Their data indicates that chimps humans and gorillas diverged at greater than 4 million years ago.

If you cannot comprehend this you are clearly in need of remedial reading classes.

The authors conclusion is that...

“Our molecular dating estimates are generally in agreement with a large number of studies using different calibration points; Kumar et al. [26], Glazko and Nei [27], and even the classical study of Sarich and Wilson [28] found a molecular divergence of HC at 5–7 Myr, 6 Myr, and 5 Myr, respectively. Speciation, defined as the total cessation of gene flow, is necessarily more recent than these molecular dates, and our value of approximately 4 Myr agrees very well with the time suggested by Patterson et al. [2]”

==They included case CG because a fraction of genes did fit that pattern, not the majority.

Correction: a CONSIDERABLE fraction that cannot be explained by the current Darwiniac human-chimp catechism.

==This overlap is more frequent in genetic DNA than genomic DNA because there is less difference in genetic DNA between species than genomic DNA

I bet you haven’t the slightest clue how important the genomic DNA is in determining both similarities and differences between species. You are way behind the times my friend.

==Do you think the authors were similarly “trapped by (their) reductionist understanding of the role of DNA”.

Yes!

==Were the authors the victim of a “slovenly commitment to reductionist materialism”?

Yes, it’s obvious...except to Temple of Darwin fanatics.

==The inescapable conclusion of their data is that humans and chimps diverged more recently than gorillas.

How many times are you going to get this wrong before it finally dawns on you that your materialist brethren are now saying that it is possible that humans and chimps diverged from apes but not from each other? Good grief!

==Do you see fit to correct them on their own data, and based upon what exactly?

Yes, not even their data isn’t their own. It is on loan from God. And the data points to common design, not common descent. Don’t worry, I have a feeling you too will be able to see the obvious soon, because I’m praying for you. In fact, I’m thinking of tapping some people from my church to pray for you as well. “Wherever two or three are gathered together in my name...”

==When you say “ape” you mean gorilla?

I was using ape because it is shorter to type than gorilla, and I was distinguishing between ape and chimp. So from now on, when I use the word ape in the same sentence with chimp, I mean gorilla unless otherwise noted.

==The authors conclude that chimps and humans diverged some 4 million years ago. Their data indicates that chimps humans and gorillas diverged at greater than 4 million years ago.

But they also leave open the possiblity that humans and chimps diverged from apes, but not from each other. Thus, even from a Darwiniac point of view, your open and shut case is not an open and shut case any more.

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