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

Princeton University ^ | November 10, 2008 | Kitta MacPherson

[GodGunsGuts]

A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution.

The scientists do not know how the cellular machinery guiding this process may have originated, but they emphatically said it does not buttress the case for intelligent design, a controversial notion that posits the existence of a creator responsible for complexity in nature...

[allmendream]

OK, you are obviously too simple minded to understand that chimps ARE apes.

The authors included all possibilities and tallied them up quantitatively; this is often done in “the scientific method”, where alternate ideas are given a chance to see if the data conforms. The data that fit the assumption that humans and gorillas were more similar than human and chimp was a “significant fraction”, but obviously not a majority. The majority of the data fit the assumption that humans and chimps are more similar than either is to a gorilla.

Thus their conclusion was that time 1 from the chart your included was for the chimp human split and was about 4 million years ago. The arrow pointing to the gorilla split, you may notice, had time 1 plus time 2. Obviously time 1 plus time 2 gives a greater amount of time than just time 1; but maybe I need to point that out to you, as you seem completely oblivious to the data that you yourself posted.

Their conclusion, from a paper you sourced, was that what you called the “logical impossibility” of humans and chimps being closer in their DNA than either is to a gorilla is in fact the case.

Now you say that the authors you sourced are blinded by ideology. How did their ideology change either their summation of the DNA differences or the DNA data do you suppose?

[GodGunsGuts]

==OK, you are obviously too simple minded to understand that chimps ARE apes.

That is one distinct possibility. An even more distinct possibility is that you are too simple-minded to understand that I occasionally use ape in place of gorilla for the sake of brevity.

==Thus their conclusion was that time 1 from the chart your included was for the chimp human split and was about 4 million years ago. The arrow pointing to the gorilla split, you may notice, had time 1 plus time 2. Obviously time 1 plus time 2 gives a greater amount of time than just time 1; but maybe I need to point that out to you, as you seem completely oblivious to the data that you yourself posted.

I am quite aware of the data, that is why I posted it. Face it Allmendream, your “open-and-shut” case just went up in smoke. And pointing to the philogenetic tree (State HC1) that shows humans diverging from chimps gets you nowhere because the authors layout other philogenetic trees that show humans and chimps diverging from gorillas, but not from each other. And lest there be any doubt about what the authors are saying, they explicitly state that there are hidden philogenetic states that go beyond the sequence data that “can be decoded using the coal-HMM methodology.” And when this methodology is used, it opens up the possibility (again, from a brain-dead Evo point of view) that humans and chimps diverged from apes and not from each other.

PS You can have the last word on this one. Repeating the obvious over and over has become more than a little tiresome.

[allmendream]

Yes, they considered the possibility, and counted where it occurred, but the data conclusively showed that humans and chimps are closer than chimps and gorillas.

Your argument boils down to this..

I say that kid A and B have more classes together than either has with kid C. You point out that kid A and kid C take chemistry together while kid B is taking art class. This doesn't change the fact that kid A and kid B still share more classes with the other than either does with kid C.

Understand?

They dealt with EVERY grouping possibility and counted them up. The pattern of similarity was such that the inescapable conclusion was that chimps and humans are closer than either is to gorilla. THIS was their conclusion, despite your clumsy attempt to cloud the issue, that humans and chimps are more similar than either is to a gorilla, not that they were more similar over every sequence tested, but that they were more similar overall.

You have done NOTHING to show that what you claim is a “logical impossibility” is not in fact the case, as both I, and the authors you sourced maintain.

It must be tedious to keep repeating the same untruthful and made up statements.

Again I quote....

“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)”

Nowhere do they conclude that there is a shorter speciation time for chimps and gorillas. That is simply not true, no matter how many times you repeat it.

Once again, that which you claim is a “logical impossibility” is supported by the data. Obviously God knows more about what is logical and possible than you do; as it is obviously part of God's plan to have human and chimps be more similar in DNA than either is to a gorilla.

[allmendream]

Here is a popular press review of the same data. Your “logical impossibility” is clearly the reality that biologists must deal with. Humans and chimps are closer in DNA than either is to a gorilla.

http://www.iol.co.za/index.php?set_id=1&click_id=31&art_id=nw20070224080303465C200804

Experts agree that humans split off from a common ancestor with chimpanzees several million years ago and that gorillas and orangutans split off much earlier.

Experts have long known that humans and chimpanzees share much DNA, and are in fact 96 percent identical on the genetic level.

[GodGunsGuts]

If you are indeed a scientist, as you say you are, why do you need popular press reviews to interpret the data?

[allmendream]

I don’t, I am just pointing out to you that the scientists, myself, and the popular press article about the science all agree; chimps and humans are more similar in DNA than either is to a gorilla.

[GodGunsGuts]

==Experts agree that humans split off from a common ancestor with chimpanzees several million years ago and that gorillas and orangutans split off much earlier.

It would seem YOUR "experts" are starting to question the Temple of Darwin's Human-Chimp catechism:

Fig.1

"To understand why regions in the human genome can differ in their evolutionary history, it needs to be acknowledged that genetic lineages represented by DNA sequences in the extant species trace back to allelic variants in the shared ancestral species (Nei 1987) (fig. 1). In here, these variants persist until they join in their most recent common ancestor (MRCA). Some genetic lineages, however, do not coalesce in the progenitor exclusively shared by humans and chimpanzees. They enter, together with the lineage descending from the gorilla, the ancestral population of all 3 species, where any 2 of the 3 lineages can merge first. Thus, in two-thirds of the cases, a genealogy results in which humans and chimpanzees are not each other's closest genetic relatives. The corresponding genealogies are incongruent with the species tree. In concordance with the experimental evidences, this implies that there is no such thing as a unique evolutionary history of the human genome. Rather, it resembles a patchwork of individual regions following their own genealogy."

Mapping Human Genetic Ancestry. Molecular Biology and Evolution 2007 24(10):2266-2276; doi:10.1093/molbev/msm156

[allmendream]

You are still trying to argue that any overlap that puts humans closer to gorillas outweighs the overwhelming pattern of human and chimp’s greater similarity.

Once again your selective quotation of data does not reflect the authors conclusions.

http://mbe.oxfordjournals.org/cgi/content/full/24/10/2266

In summary, our study highlights the extent and implications of the intertwined genetic relationships between humans, chimpanzees, and gorillas. Clearly, a comprehensive understanding of how humans evolved their unique characteristics, which distinguishes them from all other extant species, depends essentially on our knowledge of the evolutionary history of our genes. From this perspective, an extensive sequencing of the gorilla genome will be required to make full use of the chimpanzee genome sequence on the way toward a map of our genetic ancestry.

[allmendream]

Here is their Fig 4. Notice their estimates of splitting time for the human chimp lineage and the gorilla lineage.

[GodGunsGuts]

Face it, dreamer, your so-called open-and-shut case just went up in smoke (again). And this is just the beginning. Just wait and see. Evolutionary biology is a subjective mess, and it will only get worse because God’s Creation resists evolutionary explanations (from the paper):

“Thus, in two-thirds of the cases, a genealogy results in which humans and chimpanzees are not each other’s closest genetic relatives.”

And then there is this...Take out the obligatory Darwiniac “closest living relative” faith statement, and I would say that 23% is creating splitting headaches all across the worldwide Temple of Darwin:

“For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee.”

[allmendream]

Their figure 4 still shows that humans and chimps diverged more recently than gorillas and humans or gorillas and chimps.

Your “logical impossibility” is the reality that Biologists must deal with. Humans and chimps are more closely related in DNA than either is to a gorilla.

You have yet to find a source that doesn’t end up concluding the exact same thing, as Figure 4 from your latest source shows.

[GodGunsGuts]

==Their figure 4 still shows that humans and chimps diverged more recently than gorillas and humans or gorillas and chimps.

That's the current evolutionary dogma. However, more and more Evo scientists are using the data to draw alternative evolutionary scenarios which show humans diverging from gorillas, and still others that have humans diverging further up with the common ancestor of both chimps and gorillas, with chimps not even being included in the same branch with humans. In other words, human evolution is a subjective mess that is getting worse by the day. And the reason is obvious...life resists evolutionary explanations because God created all life approx. 6,000 years ago, with each creature reproducing after its own kind, just as it is described in the Bible.

[allmendream]

Please provide a source for your contention. So far every source you have cited in an attempt to muddy the water has concluded that humans and chimps diverged more recently than any other two primate species; as Figure 4 does.

[GodGunsGuts]

Have you already forgotten about Figure 1 from the same paper?

[allmendream]

Can you not see that it, like the earlier paper you sourced, has “T1” (time one) as the branching of chimp and human, and has “T2” (time two) as a greater amount of time showing the branching off of the gorilla group.

You want to find one that branches off humans BEFORE the branching off of chimps and gorillas. One EXACTLY like the one shown, but with “human” and “gorilla” interposed.

Are you smart enough to understand that or should I explain it to you again?

[GodGunsGuts]

In scenario A, two genetic lineage possibilities are traced. One show humans and chimps diverging from an interspecie that diverged from the common ancestor with apes. Whereas the other shows humans diverging with the common ancestor of chimps and gorillas further up the tree. That means that the Evos are coming to the conclusion that there is more than way to read the data, and that more than one way includes chimps and gorillas diverging from each other, and humans diverging from the ancestor of all three further up the tree. I find it hard to believe you can't pick this up simply by looking at the species tree (and the genetic trees contained within it). But then again, this wouldn't be the first time you have surprised me in this way. d:op

[allmendream]

The figure clearly shows that humans and chimps are closer and diverged more recently than either did from gorilla. This is both what the figure shows and what the authors conclude.

You need one that goes like this.....

H***G ***C
\** \ ***/
\** \**/
\*** \/
\* /

Showing Gorillas and Chimps as more recently diverged from the other than either is from a human. So far you have yet to find a source for such a graph, because the data does not support it.

[GodGunsGuts]

==You need one that goes like this.....

H***G ***C

\** \ ***/

\** \**/

\*** \/

\* /

Are you blind? Take a look at the dashed Tree in A and Tree C. Just admit it, your supposedly water-tight case is leaking like a sieve (just like the rest of the HMS Beagle):

[allmendream]

Are you blind? Tree C has humans and gorillas together and the chimps as the odd man out. Only the dotted green line has humans as the odd man out.

If you look at their Figure 5 you will see the proportion of red, green and blue for the sequences they tested. Red is the color that you see, with a bit of green and blue.

Red = (H*C)G, Green = H(C*G), Blue = (H*G)C

http://mbe.oxfordjournals.org/cgi/content-nw/full/24/10/2266/FIG5

If you look at their Table 2 you will find that 76.58% of the sequence supported humans and chimps being closest (red), only 11.46% supported chimps and gorillas being closest (green), and 11.39% supported humans and gorillas being closest (blue).

http://mbe.oxfordjournals.org/cgi/content-nw/full/24/10/2266/TBL3

Also this places 98% of the DNA they tested supporting tree’s that put chimps humans and gorillas all closer to each other than any is to an orangutan or a monkey.

Clearly your ‘similar body plan = similar DNA” is what is not just sinking but sunk. It never did hold water.

[GodGunsGuts]

Do you really not see what is obvious to anyone who is not blinded by blind evolution?!?!

In the case of the dotted genetic tree in A, chimps and apes diverged from each other, whereas humans diverged from the common ancestor of all three. In Tree C, apes and humans should be closer to each other. Thus, the Evos cannot make up their mind who came from who, which means your open-and-shut case supposedly establishing a clear lineage from the great apes to humans is about as supportable as the cheerios man with no cheerios.