The Next Hurrah

Freeing our genomes

by emptypockets

J. Craig Venter, one of the original competitors in the race to sequence the human genome, has sequenced and published his own DNA, the first time a single individual's genome has been sequenced.

In the New York Times, Nicholas Wade does a good job with the story, focusing on the original race between the academic consortium and Venter's then-company, Celera. The academic consortium won that race, and the first draft copy of the human genome sequence was public domain -- not privately owned, as Celera's version would have been. Venter left Celera and started a new institute (named for himself) and set out to sequence a single individual's DNA (his own). His success today is being portayed as a Return of the Jedi moment, with Venter in the hero's role. But to me, today's news is a big win for Venter, but an even bigger victory for public science.

Consider: Venter published the DNA sequence itself free, to the public, with no restrictions on its use. It's been deposited in the free, public DNA database at the government-funded National Center for Biotechnology Information, part of the NIH. He's going to publish, for free, his own medical records for researchers to compare his genetics and his health. And the paper itself was published in Public Library of Science (PLoS), an upstart journal begun a few years ago with the aim of overturning the subscription-only stranglehold of the Elsevier publishing empire, and hoping to become an Open Access journal of the same caliber as the subscription-only Science, Nature, and Cell.

As a result, you own his genome. You can read the original paper, free, the day it is published (today). If you're not in the field, you can read an editor's summary, written just for you, also free. There's a free interactive poster (PDF) for you to play with, and you can even access the raw data of the original shotgun sequencing reads, if you ever wanted to.

Venter gets the last word, but ultimately it's public science over privatized science that has won out. What's a real shame is that he had to raise money for this privately, because the NIH pocketbook is too tight to fund even a project of such monumental importance (and there were other issues too). Good for Venter for giving back to the public more than he was given.

Republican Senator violates Constitution, takes orders from Bush

by emptypockets

I know -- you're flabbergasted.

Referring to the establishment of Congress, the Constitution says, "no Person holding any Office under the United States, shall be a Member of either House during his Continuance in Office." Yet there was Sen. Lindsey Graham, in Iraq, pistol in a shoulder holster, serving an elective two weeks of reserve duty as an Air Force Reserve colonel.

He didn't even have to read the Constitution to know he was violating it. The highest military court read it to him a year ago, when it found that he had violated the Constitution by serving as a military court judge while a Senator.

Obviously, there is a separation of powers problem with having a Senator under command of the President. And it's a clear violation of Article I of the Constitution -- just ask any strict constructionist. Like Lindsey Graham.

Presidential Campaigns as Job Interviews

by emptypockets

There is a quote widely attributed to Al Gore, calling presidential debates "a job interview with the American people." Whether he actually said it, I don't know -- I can't find the original attribution, and it seems to be cited most widely by Bush and Cheney during the 2000 campaign -- but wherever it originated, I think the idea has stuck. For example, AFL-CIO President John Sweeney called the recent labor debate "the biggest interview in job history." And Bill Richardson has a (sorta) humorous ad in which he gets to talk about his bona fides by playing himself literally appearing at a job interview.

All of which led me to muse, when I saw a C-SPAN "Road to the White House" program tonight encapsulated as "Candidate Chris Dodd (D) talks about his family," what if the presidential campaign really was run as a job interview? Let me just go down a list of illegal job interview questions quickly, and consider what we know about the candidates

Marital status is off-limits. That does away with much of the coverage of the Giuliani campaign. Probably quite a bit of Clinton's as well, and a sizeable portion of Edwards's.

Age and Religion are not something you can ask about. Good news for McCain and Romney?

Race is not a legal topic. No more "Is Obama black enough, too black, or just right?" nonsense. What a loss.

Family life is right out. Is there anything left to talk about?

My impression is that, compared to past campaigns, Campaign 2008 has been fairly substantive. Maybe it's the wide field and the open seat, or maybe it's just that there are so many serious problems to solve. Maybe people have a new appreciation of the Presidency as an office that can make or break the future of America.

But, I'd love to see talk of family, religion, hometowns, and race eliminated completely from the campaign, and the focus kept 100% on issues related to job credentials. Because, if we don't allow discrimination in everyday job interviews, why should we tolerate it in "the biggest interview in job history"?

Bushwatch: Unbuilding America

by emptypockets

"Maybe I'm missing something here. I mean, we're going to have kind of a nation-building corps from America? Absolutely not."
George W. Bush, October 11 2000

Currently, the Department of Defense has budgeted over $140 billion in 2008 for Iraq and Afghanistan. Under President Bush, the U.S. has appropriated over $600 billion for activities relating to Iraq and Afghanistan.

Newt Gingrich Told Me To Blog This

by emptypockets

Somtimes, I question my own intentions. Do I really think it's in Americans' interest to pay me to do basic biology research, or do I just like getting paid? Is the NIH anything more than welfare for academics? When such moments strike, I like to turn for advice to a liberal luminary, an advocate of the power of Big Government doing big jobs for the common good. Someone like -- Newt Gingrich?

NIH funding has been flat since 2004, undermining the gains earned through the doubling of the budget and slowing the pace of progress in biomedical research. The Bush administration's proposed fiscal year 2008 budget would cut $329 million from last year's allocation of $28.6 billion. Biomedical inflation significantly compounds the impact of this reduction. This is exactly the wrong course for the country. Investment in the NIH should be expanded, not cut.

[...]

The National Institutes of Health Reform Act, approved by Congress in 2006, contained the authorization of an increase of 8 percent for the agency in 2008. The House Appropriations Committee vote on June 7 calling for a 2.6 percent increase for NIH does not go far enough. The House, Senate and the Bush administration should follow the 8 percent increase authorization, and make a choice now to secure longer, healthier lives for Americans with this as the benchmark for future years.

Those paragraphs, emphases mine, are from an op-ed Gingrich co-authored in the June 24 San Francisco Chronicle. As I recently posted, the current Senate and House plans increase the NIH budget by only 3.5%, compared to an inflation rate in the life sciences of 3.7% (detailed numbers here). The current plans also shift funding obligations around within NIH in a way that leaves most Institutes with increases of less than 2.5%, a stunning real dollar cut relative to inflation. At this point, let me stop and ask, what upside-down, ass-backwards planet am I living on when Gingrich advocates government spending on medical research while the Democratic Congress wants to starve it out?

Cheney Must Be a "Big Fan of Al's"

by emptywheel

As he said in yesterday's CBS interview.

Cheney, asked in an interview with CBS radio whether Gonzales should keep his job, replied: "I do. I'm a big fan of Al's."

Because he seems to have caught Al's "Cannot Recall Flu."

On Sunday, Josh Marshall pointed out that the New York Times editorial on the potential need to impeach Attorney General Alberto Gonzales said that “Vice President Dick Cheney sent Mr. Gonzales and another official to Mr. Ashcroft’s hospital room to get him to approve the wiretapping.” As Marshall noted, before the editorial, Cheney’s involvement in the incident had never been established.

Today on CNN, in a preview of his interview with the Vice President tonight, Larry King said he asked Cheney about the allegation. “I asked the Vice President about that and the story that he was the one that asked him to go,” said King. “And he said he had no recollection.”

“He did not want to deal with specifics, which tells me, they’re looking at trouble,” King added. “If you don’t want to deal with specifics…I think you’re looking at trouble and you’re looking the other way if you’re denying it.”

I seem to recall (see, I haven't been kissing either Cheney or Gonzales!) that I floated a $700 million bet that Cheney had sent Gonzales and Card. Anyone still want to take that bet?

Operation Secret Squirrel

by emptypockets

Iraqi and Iranian news media are proving that silly season is a cross-cultural phenomenon by giving wind to conspiracy theories about the British military depositing metazoan "bioweapons," including badgers, snakes, and rabid dogs, in the country as a Parthian gift. The New York Times derides the naivete of these nervous villagers:

The Iranian news media have gotten in on the act too, claiming that foreign forces have been fitting squirrels with miniaturized surveillance devices and sending them scurrying across the border to spy. Iranian news reports, monitored by the BBC, recently referred to 14 spy squirrels being captured by alert Iranian intelligence officials before the animals could take action against the nation.

It's a fun story. Now, if only the NYT had shown a similar skepticism five years ago when reporting the over-the-top bioweapon conspiracy theories that got us into this mess in the first place.

Healthcare research: Ask your Congresspeople where they stand

by emptypockets

This is a community action project:

1. Go to http://yourcongressyourhealth.org

2. Search for your Congresspeople and Senators

3. If they have not yet completed the 15 question survey about their views on health care research, then please use the form to ask them to put their views in writing.

The survey, which they received in May, asks their views about funding for NIH, CDC, and science education; American health care coverage and Medicare; and stem cell research. They can complete it by mail, fax, email, or on-line.

There is no excuse for any Congressperson to refuse to let their constituents know where they stand -- and to let us hold them accountable if their words are not backed up by actions.

Will Democrats help stem cell research?

by emptypockets

Are Congressional Democrats really going to support stem cell research, or were stem cells simply a political device for the campaign trail?

We have seen that stem cell research is a useful political wedge to separate fundamentalist candidates, beholden to the extreme religious right, from an electorate of mainstream Republican voters (who support stem cell research). Democrats have done a great job stumping on stem cells and using legislation sure to be vetoed as a means to get incumbent Republicans on record voting against the publicly popular research.

But their policy action so far is disappointingly mixed. Democrats have continued to champion federal funding of stem cell research as a legislative matter -- that is, they have passed legislation aimed at reversing Bush's directive to the NIH and thereby freeing up federal money for the research. (A similar bill was also passed by the Republican-controlled House in May 2005 and the Republican-controlled Senate in September 2006.) However, when it comes to appropriating funding that would pay for that research, the current budget bills show a meager allocation for NIH, on par with the 2004-2006 budgets set by Republicans.

Hillary Clinton et al.: Don't use diplomacy to save Libyan medics' lives

by emptypockets

New York and New Jersey's four Democratic Senators intend to block a diplomatic mission to Libya that would attempt to negotiate the freedom of five nurses and one doctor who have been sentenced to death for treating children who were later found to be infected with HIV. The Senators say that no diplomatic relations with Libya should be established until the country has coughed up the remaining cash it owes the families of Americans killed in bombings in 1986 and 1988.

It is unclear to me how letting six innocent medics be executed is going to help.