Posted 1:03 PM by Paul

Chimps and Humans
"Robert Musil" asks the burning question on everyone's mind;

Where prior studies suggest that 98.5% of the human genetic code can also be found in the chimp, a new study published in Proceedings of the National Academy of Sciences says the true overlap may be only 95%.
(snip)
My confusion arises because I have never been able to determine from the popular media coverage (such as this linked article) if the "overlap" studies include comparisions of inactive genetic material. If the studies do include such comparisions, then why is it not possible that much of the active human code only overlaps with the inactive chimp code - and vice versa. Wouldn't that mean that a 95% (or 98.5%) "overlap" could be all but meaningless?

This opens the door to a couple of interesting issues. How do we determine how closely related two different organisms or species are, and how do we determine how much of the genome is "used"? Neither is a completely simple question to answer, but I will give it a shot. First, to the matter that Mr. Musil brings up. There are historical reasons for the 98.5% figure that has been commonly been used, but it has borne up under fairly intense scrutiny up till now. The initial studies used a technical analysis called a "CoT curve" (stands for concentration over time). This is also used to define the "complexity" of a genome, in a relative way. The method uses the biochemical tendency of DNA to reassociate after "melting" (heating to separate the two strands from one another), measuring the time it takes for double stranded DNA to re-form. Measuring the tendency of identical strands to reassociate gives a method for determining the amount of "junk DNA" in the chromosome. This is where the early understanding that most of the human genome was "junk" came from. As an aside, it may well turn out that that DNA is actually important, for some structural and regulatory reasons. The classic rehybridization experiment uses a method to tag the genomic DNA from one of the two organisms (say, a radioactive label), and then measures how much of the radiolabel sticks to an immobilized population of unlabelled DNA. There are lots of ways to think about doing this, and I am only giving you one. The point is that you can determine how strongly two pieces of DNA stick together, and this is a chemical way to determine how closely related they are.



In any event, the answer to Musil's query is "No, the comparison is not meaningless". That is, both the repeat DNA and the "useful" DNA seem to be very closely related. (there have been reports of even more closely related genome segments). The initial evidence for this very close relationship was based on DNA hybridization, as outlined above. Later studies, however, based on sequence analysis, bore out the hyb data. So what happened with this newest experiment?

(Incidentally, it is now thought that chimps are not our closest great ape relatives, that we are as closely related to bonobos)



Basically, the experimenter (on the faculty at Caltech, where I work), suggests that previous experimenters have underestimated the importance and prevalence of certain types of genetic change. We tend to think of mutation as being changes in the sequence at a single point (imaginatively called a point mutation), but there are other, perhaps more important ways to change the genetic code. Here are some examples:

Initial sequence: AGCTAGCTAGCT

Point mutant: AGCTAGGTAGCT

Deletion mutant: AGCTAG_TAGCT

Insertion mutant: AGCTAGCCTAGCT



The important thing to not in the latter two cases is that the insertion or deletion can be as long or short as you wish. It could be one base, 1000, up to an empirical limit on the order of a few hundred thousand bases (further investigations may turn up larger insertions). The insertion or deletion may be a result of recombination during DNA replication (someday, if you are very bad, I will explain this in excruciating detail), or as a result of insertion of foreign DNA such as a virus or transposon. Regardless, the end result is a serious disparity between the genomes being compared. So, Dr. Britten suggests, based on his analysis of a few million base pairs of the genomes of chimps and humans (about 0.1%), that we may be off in our estimate, and that it is probably closer to 95%. As far as Mr. Musil's concern goes, this study does not distinguish between "useful" DNA and "junk". The best guess, however, is that there isn't going to be a difference, but that, if anything, the functional genes are probably more similar, because they are constrained by their function. That is, the gene that encodes for hemoglobin is more restricted than an equal sized region that does not encode a gene, because what ever changes that hemoglobin gene, its essential function must be preserved. So, it is most likely that the "junk" DNA is not identical, with all the functional genes varying, but rather the other way around. In this sense, the very close similarity between our "junk" and chimp "junk" is further evidence of our close evolutionary pairing.

Posted 12:55 PM by Paul

War and Gore (Al, not the other kind)
So, Al Gore gives a speech, and as Bob Somerby notes, all the cool kids want to know is, "Did he do this to gain a political advantage?" Aside from the insipid "mind reading" of the various pundits (Noonan and Kelly in particular), there has been a great deal of blogorrhea about whether or not he "lied", as many are so fond of saying (I am sure you can see where I am going here). Tim Noah has a pretty sharp rebuttal of the claim that Gore has changed his tune on "regime change", noting that he seems mostly concerned with whether attacking Saddam will disrupt the war on terror by alienating our Arab "allies", as well as Germany and France, who have been helping us capture Al Qaeda members around the world. This seems like a pretty good argument, if a bit complicated for our sound-bite infested news cycle. The "Crooowing" started relatively quickly, attempting to find some bit of "lying". The final result was this passage (via Jay Caruso)

Henry Hanks rules. He found the information I was looking for. Here again, is what Gore said the other day:


Now, back in 1991, I was one of a handful of Democrats in the United States Senate to vote in favor of the resolution endorsing the Persian Gulf War, and I felt betrayed by the first Bush administration's hasty departure from the battlefield even as Saddam began to renew his persecution of the Kurds in the north and the Shiites in the south, groups that we had, after all, encouraged to rise up against Saddam.

And here is what he said in 1991:


"I want to state this clearly, President Bush should not be blamed for Saddam Hussein's survival to this point. There was throughout the war a clear consensus that the United States should not include the conquest of Iraq among its objectives. On the contrary, it was universally accepted that our objective was to push Iraq out of Kuwait, and it was further understood that when this was accomplished, combat should stop."

He can't even tell the truth about something like this, and we're supposed to take seriously the criticism he has leveled at the President?

Pretty damning, right? He clearly was not that upset in 1991, and now he is claiming that he was. Leaving aside the equally poor memories of Bush (Harken, Rangers) and Cheney (Halliburton selling to Iraq), is this pair of quotations fair? Fortunately for Gore's supporters, Hesiod is on the case. A full reading of Gore's April 1991speech, from which the above quote was ripped, brings some context.

"In my opinion, Madam President, and...

I want to state this clearly, President Bush should not be blamed for Saddam Hussein's survival to this point. There was throughout the war a clear consensus that the United States should not include the conquest of Iraq among its objectives. On the contrary, it was universally accepted that our objective was to push Iraq out of Kuwait, and it was further understood that when this was accomplished, combat should stop.

That is also why, after it became apparent that Iraqi forces were being routed, pressure mounted rapidly here and abroad to proclaim a cease-fire.

If it was a mistake to believe that Saddam Hussein would be a prompt political casualty of the war, as the debacle it turned out to be for Iraq, that his rule would end shortly after the defeat of his armies, then that was a mistake widely shared throughout our country.

But only the President could speak on behalf of the United States to suggest that Saddam Hussein ought to be overthrown, and only the President could decide on behalf of the United States to permit the use of Iraqi combat helicopters to suppress rebellion, in clear violation of the understanding of the conditions agreed to at Safwan. The President's appeal was, therefore, arguably a factor in stirring up rebellion.

The President's decision not to ground the Iraqi combat helicopters conferred an important, perhaps decisive, advantage to Saddam Hussein in overcoming rebellion and then in generating the mass, panicked flight with which we are now confronted.

There have been published reports that the United States took other steps to encourage rebellion. I do not know whether that is the case or not. We should know.

Certainly, I am prepared to accept that the President, as an individual, is as shocked and angered at what is happening before our eyes as any American. I believe, however, his initial refusal to act was the result of a conviction he has held and continues to hold about basic American interests in this situation."

This sort of makes it sound like Gore was pretty upset at GHWB, dontcha think? Like maybe that we should have supported the rebellion in Iraq by the Kurds and Shiites that we instigated to some degree, instead of allowing Saddam to put that rebellion down. We had, at that time, total control of the airspace over Iraq. If we had said "No helicopters", that probably would have been it. Now, I wouldn't be surprised if there were good reasons for GHWB's decision, such as pressure from neighboring Arab states, and possibly even Israel, to keep from falling to pieces. Just as an example, it was surmised that the Shiite population of Iraq (~60%, mostly in the south, I believe), might wish to join Iran's theocracy, destabilizing the political balance between Egypt, Saudi Arabia, Syria, and Iran (I am probably oversimplifying). Also, the Turkish opposition to a Kurdish separatist movement may have (almost certainly did) play a role. Nevertheless, it seems to me that Gore can hardly be called a "liar" in this context. He certainly does seem to have been upset that Saddam was not removed from power.