Author: froggywomp

William Fallon, the commander responsible for the Middle East region, announced his resignation. He had recently been profiled by Esquire as an independent voice in the military and notably told Egyptian President Hosni Mubarak that the US would not attack Iran, presumably upsetting Cheney et al. back home.
The take at TPM:

The resignation of a CINC is a big deal, under almost any circumstance. But considering the Bush Administration’s seven-year effort to put the Pentagon under its thumb, the resignation of a commander like Fallon, who by most accounts was willing to exercise his independent military judgment, is another setback for the professional officer corps as an institution.

Make no mistake. None of the Bush Administration’s efforts in this regard has been about re-asserting civilian control over the military in some constitutional sense. The effort has been focused on degrading the autonomy, independence, and institutional authority of the Pentagon in order to further the narrow ideological and partisan aims of this particular White House.

Fallon was considered by many to be the one man standing between Dick Cheney and bombing Iran.

According to the 9/11 report, I believe it was Cheney who authorized shootdown authority while Bush was either airborne or in a bunker–at any rate, he was not incapacitated or out of contact. I cite this not as a perfect analogy but as a case where perhaps true colors came out in a pinch–Cheney briefly took control directly, even though normally he acts through Bush.

And if there have been many situations where Cheney didn’t get his way when in conflict with another administration official (e.g. Powell or Rice), it hasn’t really come out; he has a widespread image as the power behind the throne, if not something even bigger.

If Cheney agitates strongly for military action against Iran after a replacement general has been installed who agrees with him, do you think that Bush will resist him? I don’t.

I think that perhaps the wording of the TPM piece is overdone regarding the degree to which the Pentagon should be independent of the President. However, the Pentagon is supposed to be independent of politics, and the record of this administration is very poor when it comes to respecting branches of government that are supposed to be nonpartisan (Alberto Gonzales and the DOJ, for example). That said, Fallon had to realize he was whacking the hornet’s nest when he told Mubarak that there would be no attack on Iran, and if he didn’t, it’s kind of a wonder that he rose as high as he did.

I think that an attack is significantly more likely now. Cheney’s rhetoric has been very aggressive and perhaps what this is is the removal of a squeaky wheel before letting things roll. I don’t think Cheney previously ordered an attack on Iran, but I would not be surprised if he’s been agitating for one, and this may be a sign that he will soon get his way. It could also be that they decided this guy was a loose cannon and had to go, but in that case I have trouble understanding how he got to this high a position in the first place.

Pending Fallon’s replacement, it may also be that this is an attempt to replace an independent thinker with a yes-man. If there is a suggestion that Fallon committed insubordination, I haven’t seen it; being willing to express an independent opinion should be a useful trait in a top-level commander, as he is supposed to bring up considerations that the president, a man with limited military experience, may not have thought of. This does not impinge on civilian control of the military, but rather the likelihood of the US armed forces going off on another poorly planned, half-baked misadventure.

On the lighter side of things, the Boston Red Sox have apparently come to an agreement  with Daisuke Matsuzaka, arguably the #1 pitcher in Nippon Professional Baseball.  This was apparently of such importance that it came up during the State Dept briefing on Six-Party talks regarding North Korea, at which Asst. SecState Christopher Hill started asking reporters what they knew once one of them gave him a tidbit of info (excerpt below the fold).

H/T SOSH Red Sox discussion board (registration required during high traffic periods).

After some fairly bland stuff such as “the purpose is not to talk, the purpose is to come to an agreement and have some effect on the ground,” Hill suddenly turns to the question of Matsuzaka:

ASSISTANT SECRETARY HILL: How’s the Matsuzaka afternoon going today? Do we know?

QUESTION: Not very well.

QUESTION: Are you going to —

ASSISTANT SECRETARY HILL: It’s going well today?

QUESTION: I heard they’re flying to Boston.

ASSISTANT SECRETARY HILL: Matsuzaka is coming to Boston?

QUESTION: Apparently.

QUESTION: He says there’s a lot of —

QUESTION: No, no, no, no.

QUESTION: No, I thought it fell through with the Red Sox.

QUESTION: No, no. He’s holding out for a six-party agreement. (Laughter.)

QUESTION: Really?

ASSISTANT SECRETARY HILL: I’m really sorry about doing this, but it’s very important. He’s going to Boston?

QUESTION: Apparently.

QUESTION: He’s only got a wire report.

QUESTION: Which is important.

QUESTION: Every time you go to these parties, you —

ASSISTANT SECRETARY HILL: Parties — it’s not a party. (Laughter.)

QUESTION: It’s going to be a big party for you.

ASSISTANT SECRETARY HILL: You’ve been going to parties; I’ve been going to six-party talks. (Laughter.)

The briefing then returned to the topic of the North Korean nuclear issue, just as abruptly as it left.

The reason Hill and lots of other people care about Matsuzaka is that he appears to be one of the best pitchers of his generation; if the preliminary reports are true, the Red Sox are spending at least $103 million to acquire him, an unheard of sum for a pitcher yet to face MLB hitters.  Many video clips of Matsuzaka performances can be found on Youtube.  He was the MVP of the first World Baseball Classic (sort of a world cup for baseball), held earlier this year.

A post of Josh Marshall’s crystallized an idea in my head today–the media, or large segments thereof, really has gotten pretty conservative.  Marshall wrote about Mort Kondrake’s column in Roll Call that included this bit of Bushery:

President Bush bet his presidency — and America’s world leadership — on the war in Iraq. Tragically, it looks as though he bit off more than the American people were willing to chew.

He assumes that it’s the people’s fault that Bush’s “bet” is going to fail.  Incompetence?  No, couldn’t be that.  But I digress.

There’s a lot of this crap floating around–how about how conservative the dems are and how much that had to do with congressional gains?  I suspect I am somewhat late to the party in this realization, but what I want to do here is make the point that the Republicans have been successful in sowing the idea that the media has a liberal bias, and the media themselves bought into this enough to move rightward.  

One way to combat this in a grass/netroots way is to challenge this assertion and make the contrary one–the media has become conservative, to the ruin of all.  They need to be skeptical, objective, and not allow themselves the sort of spoonfeeding by the administration that is all too common.

It will not be easy or quick to reverse the unfortunate rightward list of the media, but with time, I hope that at the very least our side can generate enough tension to cancel out that of the rightwing crybabies.  If we can pull them back to true objectivity, I’d count that as a victory, inasmuch as the facts have a liberal bias.

Time reports that unnamed Senators are considering a constitutional amendment to limit presidential powers:

Bush’s claims of wartime license are so great–the White House and Justice Department have argued that the Commander in Chief’s pursuit of national security cannot be constrained by any laws passed by Congress, even when he is acting against U.S. citizens–that some Senators are considering a constitutional amendment to limit his powers.
….
A source familiar with the nascent constitutional amendment says one version would make clear that any actions by the President as Commander in Chief that affect domestic policies or U.S. citizens are subject to the exclusive control of Congress.

The vagueness of this report makes it clear that, if there’s anything to this at all, it’s in the very early stages, and I think there must be a long way to go before 2/3 of each house of congress and 3/4 of the states would agree.  Even so, based on my understanding of the Constitution, I find it hard to believe that something like this amendment would even be necessary, but these are strange times.  However, as long as we still have some semblance of a constitutional government, an amendment is effectively Congress’ ultimate weapon against the other branches, as long as the states are with them.

Crossposted from dKos

Today’s White House Briefing is a doozy–don’t miss it.  Dan Froomkin goes in depth on the parallels between what is sure to be one of the biggest movies of the summer–Star Wars III, Revenge of the Sith–and our favorite chimp.  

The basic idea is that a major element of the movie’s plot, the transformation of the Galactic Republic into the evil Empire, parallels the loss of freedom that has occurred during Bush’s presidency.  One of the most glaring similarities is when the character soon to become Darth Vader tells Obi-Wan that he is either with him or against him.

Froomkin notes that Lucas claims believably that the story was written well before current events, and much of it was originally based on Vietnam, the rise of Napoleon, and the rise of the Roman Empire out of its predecessor republic.  Lucas does say that the degree of repetition in history, particularly between Vietnam and Iraq is “unbelievable.”

Could this movie be the one to get through to the masses?  Let’s hope for the power of parables…

I know, it’s supposed to be a Friday thing to post stuff about science, but I’m disorganized and busy enough that you’ll just have to bear with me.  Today’s topic: Why don’t red blood cells have nuclei?  

As an extra bonus, there’s a tangential philosophical digression…  see you on the flip.
There are two ways to answer such a “Why…?” question–in terms of procedural reasons and in terms of motivation.  Aristotle actually described four types of causes, and I’ll come to this below in the philosophical digression I promised.  Anyway, the procedural reason is often called mechanistic or proximate, and the motivational reason is often called ultimate or teleological.

The proximate (mechanistic) answer to this question is that during the cellular differentiation process, the pre-red blood cell developmental program induces the enzymatic degradation of the nucleus.  Simple enough.  That explains why red blood cells don’t have a nucleus, but why do they destroy a perfectly good set of chromosomes?  The ultimate (teleological) reason is that red blood cells have one purpose, which is to ferry hemoglobin (the protein that carries oxygen) out from the lungs to muscles and other tissue, and then to ferry the depleted oxygen-less hemoglobin back to the lungs to get more.  Red blood cells do not reproduce–stem cells in the marrow divide asymmetrically and one progeny of each division becomes a red blood cell, in part by getting rid of its nucleus.  They do not express genes once differentiated (all their hemoglobin mRNA is made before they get rid of their nucleus, of course).  So there is no need for the nucleus–it would just be taking up space that is better used for additional
hemoglobin, which makes them more efficient at transporting oxygen.  

Notably, this is an innovation that is not present in all animals; birds for example have red blood cells with nuclei.  It is therefore likely that enucleation evolved after the mammalian line diverged from reptiles, and presumably was related to the appearance of endothermy since this results in a significantly higher metabolic rate and consequently a greater need for oxygen throughout the body.

Now, that digression–what were Aristotle’s other two kinds of causes?

It turns out that most modern folk don’t really think of these as causes at all.  They are usually labeled as the formal cause and the material cause.  Stealing from this web page, I think this makes things relatively clear:

If we ask “what makes something so-and-so?” we can give four very different sorts of answer – each appropriate to a different sense of “makes.” Consider the following sentences:

   1. The table is made of wood. (material)
   2. Having four legs and a flat top makes this a table. (formal)
   3. A carpenter makes a table. (efficient, or proximate)
   4. Having a surface suitable for eating or writing makes this a table. (final, or ultimate)

So, there you have it–four causes.  Sort of.

Have a nice Saturday, and go Red Sox!!!

Natural selection is often described as “survival of the fittest.”  But fittest is an adjective–what are the fittest things that are doing the surviving?  The knee-jerk answer most of the time will be individual organisms, and this is true, but perhaps not the complete truth.  More on the flip.
I should mention at this point that much of this post is based on the writings of Richard Dawkins; the books of his I’ve read are all good, including the most recent one, the Ancestor’s Tale, and should be accessible to anyone with basic knowledge (undergrad or good high school level) of biology.  

So, what does natural selection operate on, if not organisms?  One possibility is genes.  To see what I am talking about, consider a thought experiment.  Suppose that genes could be copied and distributed to others at will, perhaps for a price, perhaps out of the goodness of your heart.  In this exchangeable situation, the best genes would become very common very quickly; in other words, they would undergo positive selection, and multiply.  Defective mutant genes would go away–who would want the gene for hemophilia?  Or colon cancer?  Not I.  

Now, in reality, you can’t replace your genes with other ones, but you have some choice as to which genes your children get through your choice of mate.  Of course, genes are generally only revealed through phenotype (outwardly observable characteristics) unless you happen to have a DNA sequencer handy and your potential mates submit to screening.  So, to some extent, you select the genes, or the set of genes, that gets passed on to part of the next generation.

What about organisms that reproduce asexually, in which each offspring is essentially a clone of its parent?  Here, there isn’t as much choice involved, but to some extent gene selection is still occurring in that it is the combination of genes and environment that determines whether an organism is successful/fit.  Gene redistribution just will not occur as quickly in this situation most of the time.

These ideas have been around for a while–I first heard of them in high school back in the early 90s.  What I just became aware of (in the Ancestor’s Tale) is something called clade selection, which is likely related to the evolution of evolvability–the ability of a lineage to change (adapt) more rapidly over time.  This is clearly a kind of selection that cannot operate on a single organism.

I may have lost some of you in that last paragraph, so let me go through it a little more slowly.  A clade is a group of all the species descended from a common ancestor.  Mammals are a clade, as are insects.  Animals are a clade too, that contains many smaller clades (however, reptiles are not a clade, but reptiles plus birds plus mammals are; mammals and birds descend from reptiles).  The idea is that the clades most able to adapt to changing situations (usually on geological time, but sometimes there are earth-shattering events like the one that wiped out the dinosaurs) will expand, or radiate, out and become more common.  So, you see lots of different mammals, because mammals were well-positioned to fill the niches made available when the dinosaurs vanished.  The ability of mammals to change rapidly under appropriate selection can be seen with dogs, who admittedly have undergone intense artificial selection, but show an absolutely amazing range of diversity that appeared in a matter of a few centuries–from ratlike chihuahuas to big great danes, which in the absence of humans could reasonably be expected to diverge into different species if given enough time (assuming they survived).  

What makes a clade more or less adaptable?  I think a lot of the answer to this is the absence of limitations at near-fundamental levels.  Compare mammals and insects.  Mammals are warm blooded (endothermic) with internal skeletons, while insects have exoskeletons and are exothermic.  Neither one of these is easy to change, although obviously it may have happened in the past.  (With endo/exothermy, it must have; the skeletons may have evolved separately from an original wormlike ancestor.)  However, endothermy gives a lower limit to size–if you’re too small, the rate of heat loss becomes unsustainable.  Exoskeletons have the opposite effect–it’s hard to grow because you’re stuck inside this case of armor, and if you want to get bigger, you have to get rid of it and make a new one, which is costly.  So, mammals smaller than mice presumably don’t do well, but insects don’t get as large as mice, perhaps with a very few exceptions (I hear there are some big cockroaches in Hawaii).  Reptiles have neither limitation, and so you see lizards smaller than mice, and also big things like crocodiles.  However, it looks like at the ant-size range, there are no reptiles, and perhaps this is because insects are too effective and would outcompete any newcomers, or perhaps there are other aspects of reptile physiology or anatomy that become problematic.  I believe exoskeletons are more efficient in terms of promoting muscle strength, so that may be part of it.

One of the things Dawkins says about the historical trajectory by which animals became more evolvable is that the appearance of segmentation was likely a watershed.  If the number of segments is expanded, they can then be diversified; a simple example is the difference between various segments of the human vertebral column.  This also has a pleasing analogy to conventional evolution, in which new genes often arise through accidental duplication, leading to specialized variants; there are multiple hemoglobin genes in our genomes, some of which are expressed only in the embryo and designed to outcompete maternal (adult) hemoglobin for oxygen, hence allowing “breathing” through the placenta.  Similarly, muscle myoglobin is more distantly related to hemoglobin but is also able to grab oxygen from the blood.  

One last example which may surprise you is DNA.  It is now thought that the original life forms that arose billions of years ago did not use DNA as their genetic material; one leading theory is that RNA was the original molecule, which is attractive because RNA also can catalyze chemical reactions, including potentially its own replication.  So, the first life may have been RNA-based, but when DNA came on the scene (or more generally, the genetic material was separated from the bulk of cellular metabolism) this was a huge deal–DNA is a better genetic molecule than RNA because it forms a much more regular structure (conversely, the lack of that regularity is why RNA can be a catalyst for multiple different reactions) and the regularity of DNA means that mutations can occur that do not adversely affect its structure.  In essence, DNA opened up a much broader range of possible diversifications, meaning the organisms that used it were much more adaptable.

So, in conclusion, it now appears that natural selection operates on multiple levels: genes, organisms, and clades.  I’m sure more ways in which evolvability has been improved will be brought to our attention in the near future.

If you are so inclined, I would be interested to hear if anyone has ideas about what other features of <insert organism here> make it particularly evolvable/adaptable.

Hi folks…  I answer questions for the Howard Hughes Medical Institute Ask a Scientist program, and it occurred to me that perhaps people here, who tend to be pretty well educated, would be interested in reading and discussing some of the questions.  So, in a pilot sort of way, I thought I’d try an experimental post along these lines.  (Quick disclaimer: This is not for the purpose of giving medical advice.)  Today’s topic is about the aging of cloned animals.

Some cloned animals seem to age faster than normal.  If the clone cells “remember” the age of the mother, the process of DNA replication through mitosis is less and less efficient (my limited understanding.)  She wanted to know why single-celled organisms do not eventually produce less perfect copies, as differentiated body cells would, because they are also reproducing by mitosis.

“Answer” on the flip…
For some background information, I recommend the web page http://senescence.info/causes.html particularly the third section, animal cloning and aging.  The results summarized there seem somewhat inconsistent, such that in some but not all cases of cloning has accelerated aging been observed, and the initial hypothesis for the cause of accelerated aging–telomere shortening–does not appear correct.

Baker’s yeast is the single-celled organism most intensively studied on topics of aging.  There is a significant difference between a multicellular organism and a culture of unicellular organisms.  The effects of aging on single cells seem to be sporadic or statistical to some degree–if you were to follow a lineage as time goes on, the number of age-related problems increase, but in a unicellular population, the phenotypically ‘aged’ cells are selected against and gradually disappear from the population (whereas in a multicellular body, the aged cells hang around for a while, and sometimes are not easily replaced when they die).  

With unicellular organisms, the cells that are lucky and remain healthy reproduce the most, and this leads to a steady-state situation where some fraction of cells are constantly becoming old and being outcompeted and outbred by cells that stay young.  This is particularly true in yeast because cell division/mitosis is asymmetric; one cell, called the bud cell, gets mostly newly synthesized proteins, whereas older proteins stay in the other cell. Painstaking experiments in which a scientist repeatedly separated the mother and bud after each division for many generations have shown that a mother begins to show signs of aging after about 25 divisions and usually becomes senescent (stops dividing) around 40, although there are mutations that can alter these numbers (interestingly, some mutations actually extend the ‘reproductive lifespan,’ as does caloric restriction, meaning that the food source is relatively meager–this is also true in mice).  Each newly produced bud cell then becomes a first-generation mother, which will eventually become old, but not before it has produced very many brand-new bud cells itself.  

So, aging does occur in this single-celled organism, but it is not readily apparent because the population is always a mix of young and old cells; the young cells reproduce, and the old cells slowly fade away.  A key idea is that cell division can be asymmetric–the two cells resulting from the division are not both ‘newborn.’  I suspect that this will be a common thing in many species.

Other single celled organisms have more apparently symmetric divisions than S. cerevisiae, but recent results indicate that in the bacterium E. coli, there is more underlying asymmetry than meets the eye, and the ‘new cell’ is more reproductively successful than the old cell; the reference is PLoS Biol. 3, e45 (2005).  So, there is aging, but not in a way that endangers the long-term viability of the population. This is somewhat analogous to populations of multicellular organisms, including humans–parents go to a lot of trouble to produce offspring that are brand spanking new (pun intended), and of course the offspring will outlive their parents all else being equal.

Any thoughts?  Questions?  Suggestions?  I’d like for this to be somewhat interesting, so if this is too much above/below your level, feedback would be useful.  Also, I hate to sound like I’m begging for attention, but I will be much more likely to continue this if I know there are people who are reading, so just saying that you like it would be appreciated.