Counter Minds


The Rough Guide to Evolution


Professor in Training


Stimulating Aliquot

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Joan Walsh wonders: "Are Kaine and Bayh the best Obama can do?"

No. Conventional wisdom has narrowed the Democratic veepstakes to those two and Kathleen Sebelius. Kaine gets a lot of the DC attention, since he's right there in Virginia, but there's no reason Walsh should blow off Sebelius.

Bayh would be a stupid choice. Obama's strength against McCain is that he was right about Iraq, so his VP shouldn't be one of the war's congressional cheerleaders. The speculation (from Walsh if no one else) that Bayh would be some sort of sop to disappointed Clinton fans doesn't hold up, since there's no evidence in the polling of any substantial residue anti-Obama Clinton voters. Obama has to be thinking about the undecided voters, not folks who were passionate enough about the Democratic party to get into its primary fight. And he also has to think about governing with someone.

Bayh brings a good visual, the all-American white boy from Indiana, but ultimately that doesn't help Obama. Racists won't ignore his skin color and vote for his VP, so the Hoosier in the wings won't win him many votes from that bloc. Obama is a change agent, and the campaign will be stronger with a VP nominee who represents change. Bayh has been in the Senate forever, and comes from a long line of Indiana politicos. That ain't change, nor are Bayh's mushiness on a woman's basic right to choose nor his wrongheadedness on the war. Throw in that nominating Bayh lets Mitch Daniels (R) select a new Senator, and I don't see why Bayh is even in the running.

Kaine is fine, but has a weak environmental record, and not a lot of political seasoning. Plus he's got a Republican Lieutenant Governor, and there's no reason to give Republicans that power, especially heading into redistricting in a battleground state. That said, I don't think there's any compelling argument against him. Virginia's a battleground state, and Kaine could tip it Obama's way. Worry about Kaine's lack of foreign policy experience misses the point. A foreign policy whiz could make Obama look like he's compensating, or would be ceding his foreign policy agenda (the easiest place for a president to make a mark) to someone else.

Kathleen Sebelius, however, has a Democratic LG, has spoken out forcefully about the resources trapped in Iraq, and has a record of defending strong Democratic values in a red state. I'm a bit peeved that she hasn't done more to share her popularity (re-elected with 58% of the vote, but didn't even put the word "Democrat" on her yard signs and bumper stickers). I'd also like to see her run for the Senate seat Sam Brownback is abandoning in 2010. Of course, Jim Slattery is running a great campaign against Pat Roberts this year, and if he doesn't pull it off, he could come back in two years and take the open seat handily. Or Dennis Moore may decide to look at the Senate seat. Sebelius, however, would take it easily, and once there, she could stay for decades, not just for 8 years.

Still, I think Obama could do worse. She's got a great record of standing up for the environment, first denying permission to build massive coal plants (citing global warming as the basis for the denial), then vetoing three separate bills which would have overruled that decision. She brought the Kansas budget out of the fiscal hole dug by her Republican predecessor, and did it without cutting essential services or raising taxes. She wasn't afraid to call out George Bush for deploying National Guard troops and equipment overseas when they were needed in the aftermath of tornadoes in Kansas. As chair of the Democratic Governors' Association, she's got a national profile and useful allies in swing states. She's also got family ties in Ohio, where her father served as governor.

Time named her among the top 5 governors, and she was among four governors given the top rating in Inc. magazine's election-year survey in 2006. I've been consistently impressed with her ability to work with the legislature, including the ultra-conservatives who tend to run the show. Despite their disagreements, I've never gotten a sense of deep-seated hatred from the folks who work with her (and her staff) on a regular basis. That says a lot, and it goes to the heart of Obama's message about working across the aisle. She hasn't given away the store, and hasn't assumed everyone can be swayed. She has, however, treated people with dignity, and found ways to craft compromises that are fair to all, but that preserve core values. That's what we want from our President, and it's what we want from a Vice President.

Walsh objects that Sebelius is:

another appealing red-state moderate with no foreign policy credentials or national profile.

I don't consider foreign policy experience terribly critical in this election, and I don't think the VP needs to be the locus of that experience in an administration. That's what a Secretary of State and a UN Ambassador (as well as National Security Advisor, etc.) are for. And saying she's got no national profile is simply silly. She gave the response to the State of the Union this year (not her best performance, granted) and her service as chair of the DGA gives her as much national profile as President Clinton had before his successful bid for the presidency. Sebelius has gotten plaudits from national media for her excellent administration, and has gotten lots of attention for standing firm against new coal plants. The political media tends to focus on Congress, and then on neighboring states or those readily accessible from DC. But I'd wager that just as many swing voters need an introduction to Bayh, or perhaps even Biden, as need one for Sebelius.

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You can't have it until December, but you can pre-order it now (in case they run out!). Click the picture. Maybe. Probably, this is more properly thought of as the Zeroth Harry Potter Book.

Do you know about the Tales of Beedle the Bard? According to Julia (I didn't know) it has to do with these three brothers who encounter a river previously uncrossed by mortal men. They fool death or build a bridge or something and survive and get wishes. One asks for a powerful wand, one wants to bring back the dead, and one asks that Death not be able to follow him.

This results in the existence of the famous wand, the stone of Ingreness ... no wait, the Resurrection Stone, and the Invisibility Cloak. This is an oversimplification.

The stone actually turns dead people into zombies, the wand creates deadly hubris, and the invisibility cloak was not so dangerous, and that brother lived to an old age until he finally got tired of that gig, passed the cloak on to his offspring, and walked away from life arm and arm with death.

Harry Potter, it turns out, is related to these brothers, and the various objects ultimately would end up in his possession. This is an oversimplification. The night before Harry got his scar -- the night his parents were killed by he who shall not be named --- Dumbledore absconded with the invisibility cloak to study it.

Anyway, this fictional book turns out to really exist. JK Rowlings has written it, apparently, and it will be on sale in early December. You can preorder your copy by clicking on the book above.

Or, if you are a total Harry Potter Nut you can order the special collectors edition for a mere one hundred bucks, by pointing at your computer with your magic wand and issuing the following spell:

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I am a little shocked that none of my Sciblings has mentioned this. The Department of Health and Human Services is currently considering rule changes that would, in effect, define contraception as abortion. You can find a text of this proposal here. RH Reality Check has a thorough discussion of the issue. More recently, 28 Democratic senators lead by Patty Murray (D-Wash.) and Hillary Rodham Clinton (D-N.Y), have written to HHS Secretary Mike Leavitt condemning the action. A complete text of the letter is below the fold. Conspicuously absent was any member of the Republican Party - yet another reason why one should never vote Republican.

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So, let's see what's new in PLoS Genetics, PLoS Computational Biology, PLoS Pathogens and PLoS Neglected Tropical Diseases this week. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. Here are my own picks for the week - you go and look for your own favourites:

Patterns of Positive Selection in Six Mammalian Genomes:

Populations evolve as mutations arise in individual organisms and, through hereditary transmission, gradually become "fixed" (shared by all individuals) in the population. Many mutations have essentially no effect on organismal fitness and can become fixed only by the stochastic process of neutral drift. However, some mutations produce a selective advantage that boosts their chances of reaching fixation. Genes in which new mutations tend to be beneficial, rather than neutral or deleterious, tend to evolve rapidly and are said to be under positive selection. Genes involved in immunity and defense are a well-known example; rapid evolution in these genes presumably occurs because new mutations help organisms to prevail in evolutionary "arms races" with pathogens. Many mammalian genes show evidence of positive selection, but open questions remain about the overall impact of positive selection in mammals. For example, which key differences between species can be attributed to positive selection? How have patterns of selection changed across the mammalian phylogeny? What are the effects of population size and gene expression patterns on positive selection? Here we attempt to shed light on these and other questions in a comprehensive study of ~16,500 genes in six mammalian genomes.

Engaging the Community: An Interview with Uche Amazigo:

Walking purposefully towards the shabby grey concrete structure that functions as the main health centre of Kyenjojo district in western Uganda, public health doctor Andrew Byamungu makes a trip he has done many times before since joining the vector control department of the Ugandan Ministry of Health. Fighting his way through the crowds of waiting patients and relatives, he greets the tired-looking health staff who, among their many other duties, are responsible for education and drug distribution in the country's onchocerciasis control programme, which is one of the most advanced of the 19 country projects of the African Programme for Onchocerciasis Control (APOC).

H5N1 and 1918 Pandemic Influenza Virus Infection Results in Early and Excessive Infiltration of Macrophages and Neutrophils in the Lungs of Mice:

Patients who succumbed to influenza during the pandemic from 1918 to 1919 had severe lung pathology marked by extensive inflammatory infiltrate, indicating a robust immune response in the lung. Similar findings have been reported from H5N1-infected patients, raising the question as to why people expire in the presence of a strong immune response. We addressed this question by characterizing the immune cell populations in the mouse lung following infection with the 1918 pandemic virus and two H5N1 viruses isolated from fatal cases. We found that certain cells of the innate immune system, specifically macrophages and neutrophils, increase significantly early during infection but that the cells responsible for bridging the innate and adaptive immune responses, dendritic cells and the orchestrators of viral clearance, T cells, did not differ significantly between infection groups. Dendritic cells and mouse lung macrophages were shown to be susceptible to 1918 and H5N1 virus infection in vitro, suggesting a possible mechanism of pathogenesis. Our data shows excessive immune cell infiltration in the lungs contributing to severe consolidation and tissue architecture destruction in mice infected with highly pathogenic influenza viruses, supporting the histopathological observations of lung tissue from 1918 and H5N1 fatalities. Identification of the precise inflammatory cells associated with lung inflammation will be important for the development of treatments that could potentially enhance or modulate host innate immune responses.

Rise of the Machines:

Until recently, sequencing the entire genome of an organism was a major endeavor. New technologies are transforming this task into routine practice and launching a new assault on whole-genome sequencing.

It is more than 30 years since Sir Fred Sanger and colleagues published their method for sequencing DNA [1]. This Nobel Prize-winning work formed the basis of the vast majority of subsequent sequencing methodologies, albeit with some crucial technical innovations. Despite the great utility of Sanger sequencing, its scalability is inherently limited, and therefore the creation of warehouse-sized facilities was required to accomplish whole-genome sequencing projects. As a result, sequencing more than a few kilobases of DNA--a requirement for all but the simplest genomes--has long remained the province of a few dedicated sequencing centers. Within the last year, however, things have begun to change in dramatic ways. New sequencing technologies are emerging, announced in an assortment of reports, conference presentations, and press releases. In this issue of PLoS Genetics, Srivatsan et al. [2] report the resequencing of several genomes of the bacterium Bacillus subtilis using one of these new technologies. A new battle at the frontier of DNA sequencing has commenced.

A Model of Stimulus-Specific Neural Assemblies in the Insect Antennal Lobe:

It has been proposed that synchronized neural assemblies in the antennal lobe of insects encode the identity of olfactory stimuli. In response to an odor, some projection neurons exhibit synchronous firing, phase-locked to the oscillations of the field potential, whereas others do not. Experimental data indicate that neural synchronization and field oscillations are induced by fast GABAA-type inhibition, but it remains unclear how desynchronization occurs. We hypothesize that slow inhibition plays a key role in desynchronizing projection neurons. Because synaptic noise is believed to be the dominant factor that limits neuronal reliability, we consider a computational model of the antennal lobe in which a population of oscillatory neurons interact through unreliable GABAA and GABAB inhibitory synapses. From theoretical analysis and extensive computer simulations, we show that transmission failures at slow GABAB synapses make the neural response unpredictable. Depending on the balance between GABAA and GABAB inputs, particular neurons may either synchronize or desynchronize. These findings suggest a wiring scheme that triggers stimulus-specific synchronized assemblies. Inhibitory connections are set by Hebbian learning and selectively activated by stimulus patterns to form a spiking associative memory whose storage capacity is comparable to that of classical binary-coded models. We conclude that fast inhibition acts in concert with slow inhibition to reformat the glomerular input into odor-specific synchronized neural assemblies.

High-Precision, Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies:

In this manuscript, we describe novel applications of the newly developed Solexa sequencing technology. We aim to provide insights into the following questions: (1) Can whole-genome sequencing, while rapidly surveying mega-bases of genome information, also reliably identify variations at the base-pair resolution? (2) Can it be used to identify the differences between isolates of the same laboratory strain and between different laboratory strains? (3) Can it be used as a genetic tool to predict phenotypes and identify suppressors? To this end, we performed whole-genome shotgun sequencing of several related strains of the widely studied model bacterium Bacillus subtilis, we identified genomic variations that potentially underlie strain-specific phenotypes, which occur frequently in biological studies, and we found multiple suppressor mutations within a single strain that are difficult to discern through traditional methods. We conclude that whole-genome sequencing can be directly used to guide genetic studies.

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Two words:

New T-shirt.

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