PolITiGenomics

Nearly two weeks after moving to a new URL, there are still more hits on this old address than the new one. Check out all my recent posts at the new location. Thanks.

I'm moving. Well, at least my blog is moving. PolITiGenomics is moving to its own domain. Check out the new home, www.politigenomics.com. The RSS feed URL should be unaffected, but you may see a deluge of "new" posts since the URLs of all the posts have changed.

Bill Moyers was on The Daily Show last night to talk about his new book, Moyers on Democracy. The wide-ranging interview covers a lot of interesting topics.


The Colbert Report also had a funny bit on some recent footage that surfaced of Bill O'Reilly. Be sure to keep watching through the "old footage" of Colbert.

Earlier this week there were several meetings about the 1000 Genomes Project at Cold Spring Harbor Labs. The first meeting Monday morning was about data flow and data repositories. NCBI's Short Read Archive (SRA) and the equivalent at EBI (which should be ready in a month or two) will house all the data. The pilot projects for the 1000 Genomes Project just started less than two months ago and have already generated as much sequence data as half of the entire trace archive (which contains the sequence data for all publicly funded genome projects over the last 10 years). In other words, this project is going to generate a lot of sequence data (not to mention all the data generated by analysis of the sequence). Paul Flicek from EBI estimates the pilot projects alone will generate about 1 PT (1,000,000 GB) of sequence data. Moving that much data from site to site will be a challenge. Normal solutions, e.g., FTP, rsync, and shipping hard drives, can't seem to keep up with the data generation rates. NCBI, EBI, and the sequencing centers are testing a high-speed data transfer solution called Aspera scp. It has impressive transfer rates, but seems to stall after a while for no discernible reason. We'll see if we can get it to work reliably over the coming weeks.

After the data flow meeting was a meeting of the 1000 Genomes Steering Committee. The day and a half that ensued was filled with a lot of lively discussion. When all was said and done, one thing was clear: there are a lot of questions that need to be answered. The analysis group presented convincing results from simulations that indicated 2× coverage in a large number of individual genomes (Pilot 1) is probably not sufficient to detect the rare variants the project is going after (present in 1-2% of the population). The simulations indicated that the power of the study to detect such variants (at a constant cost, i.e., constant total amount of sequence generated) would be greatly enhanced by sequencing half as many people at 4× coverage. There was no firm decision on how to change the pilot (if at all), but going forward it is likely that some of the individuals in Pilot 1 will be sequenced up to 4× or even 8×. Thus, while the project may be named 1000 Genomes, exactly how many genomes we are going to sequence is yet to be determined.

Another issue that arose was the rapid development of the massively parallel sequencing technologies. These platforms (454 FLX, Illumina Genome Analyzer, and AB SOLiD) increase their throughput, improve their data quality, improve analysis software, etc. several times each year. Such dynamic platforms make the development of tools to analyze their data, e.g., align the data to a reference genome and detect variants, very difficult. The right platforms and tools today may not be the best next month or next year when the main project gets underway. This causes two major needs to come to the fore. First, experimental design will not end when the project starts. The experiment will need to be adjusted as capabilities and capacities change. Second, we will not only have to continually develop and refine tools throughout the project, we will need to develop frameworks to continually test and compare the tools that are available. It's always fun to hit a moving target.

The meeting also discussed the ethical, legal, and social implications (ELSI) of the project. This discussion largely focused on which populations to sample for the project. Should we deepen our knowledge of individuals of Central European, African, and East Asian ancestry to aid in methodology development? Or should we broaden our knowledge of overall human variation by including fewer individuals from a larger number of populations? To be determined…

In the twisted logic of the Democratic Party you have Sen. Clinton arguing that the delegations from Michigan and Florida must be seated. Sen. Obama is arguing that they broke the rules and should not be seated (at least according to the voting in January). Sen. Clinton is arguing that the so-called superdelegates should vote their conscience. Sen. Obama says they should respect the will of the people. Anyone else see an inconsistency here? Sen. Clinton says that the people's votes must be counted. That is, unless they are in small states. Oh, and the superdelegates need not pay any mind to those votes. And no one should pay any attention to how people are voting with their money either (Sen. Obama has more than 1.5 million donors, she has loaned her campaign more than $11 million). Sen. Obama says the superdelegates must respect the will of the people. Unless of course those people are in Michigan or Florida. Oh, the insanity.

…and a little bit rock'n'roll. On Thursday, the paper describing the platypus genome will be published in Nature. From an evolutionary standpoint, the platypus is quite an interesting species. It is a mammal, but it has traits of birds (lays eggs, has a bill) and reptiles (lays eggs, produces venom). Oh, and did I mention you can literally scare a platypus to death? You can learn more from NPR's coverage, Platypus Is Even More Strange Than It Looks, including quotes from Rick Wilson, head of The Genome Center at Washington University.

Update: this story has been picked up by Slashdot and many other places (including the WU Record).

It seems something has happened on the way to the coronation. What happened to Obama mania? It seems the cult is falling apart. Could these pundits have been wrong about Sen. Obama's followers? In short, yes. Completely wrong. The truth of the situation is that Sen. Obama's base were always the most fragile and, in many ways, the most easily ignored. First to the fragility. Breaking down Sen. Obama's core supporters you have white, highly-educated voters, African-American voters, and young voters. White, highly-educated voters are drawn to Sen. Obama's message of post-partisanship/post-racism/post-Iraq. Thus, as the race drags on and Sen. Obama tacks more to the left to gain Democratic-primary voter support; as his business dealings and campaign tactics show him to be more of a politician and less a savior; as his race becomes more front and center in the campaign; as it becomes clear that none of the candidates can get us out of Iraq any time soon (despite their promises to the contrary), his support in this group wanes. Currently, African-American voters are assumed to have always been overwhelming in their support for Sen. Obama. This is just not true. As recently as late last year, Sen. Clinton led among African Americans in national polls. It was only after Sen. Obama won Iowa, proving he could win white votes, that African Americans began to support him in large numbers. As for young voters, they tend to be more idealistic about the political process. Therefore, Sen. Obama's post-partisan/above-the-fray approach to the campaign is highly attractive to them. However, as the campaign wears on, their idealism gets trampled by the negative campaigning and they turn away. All of this is why (all along) Sen. Obama's supporters have had more doubts about their candidate than do either of Sen. Clinton's or Sen. McCain's supporters. So, all in all, not very cult like. Thus, Sen. Obama's coalition is fragile. Why can it be ignored? The first two groups, highly-educated whites and African Americans, are very unlikely to vote Republican. They may stay home, the whites may vote for Nader, but they are not going to vote for Sen. McCain. The last group, young voters, are just not likely to vote at all. Remember, young voters were supposed to carry Sen. Kerry to victory in 2004. There is an old adage in politics, "What do you call a candidate that is relying on first-time voters? The loser." This is not a reliable voting block. They tend to lose interest over time, and this primary season has been a long time. Many more could fall off before the general election in November.

Now, Sen. Obama's coalition has proved reliable over the past months, but Sen. Clinton's have been even more reliable; even in the face of overwhelming odds against her victory. In 2004, the Democratic Party quickly coalesced (collapsed?) around Sen. Kerry after he won Iowa and New Hampshire. Sen. Obama won 11 contests in a row and there was no such mass migration. In fact, quite the opposite happened. Each candidates' supporters became more entrenched and the battle for the nomination became more embittered. Sen. Clinton's supporters are the old-time, Democratic party faithful. They relish this type of fight. They have been waging it for decades against the Republicans. Sen. Obama's supporters want to rise above all this petty bickering. The Clinton campaign won't let them (and neither will the Republicans in the fall).

What about the independents and moderate Republicans that have been voting for Sen. Obama? As discussed in a recent post, studies have shown that the more partisan someone is in their politics, the less they use the rational parts of their brain when thinking about political issues. It would be expected, then, that independents and moderate Republicans would be more rational in their political thinking. They also tend to pay less attention to politics. This works against Sen. Obama in two ways. First, when they see negative things about Sen. Obama, the negativity plants a seed of doubt in their minds. When they see Sen. Obama going negative, on the other hand, it makes him seem like a typical politician. Both of these things erode their support for him. The former because the seed of doubt gets planted and they are not naturally motivated to attempt to debunk it (whereas hardcore Sen. Obama supporters refuse to believe anything negative about him). The latter because when Sen. Obama behaves like "just another politician", it undercuts one of the major rationales for his support: the promise of change. Ultimately, these supporters are less likely to support their candidate if he or she were to behave in a way inconsistent with the reasons they supported him in the first place than the diehards in their coalition (which is what is happening to a greater and greater degree as the primary contest rages on).

The result of all this is that there is little chance that Sen. Obama can chip away at Sens. Clinton or McCain's core supporters. Conversely, there is little risk Sen. Clinton will lose her core supporters. Therefore, she is more free to attack. She has taken advantage of this by attacking Sen. Obama on issues where she is vulnerable: public financing of elections, shady business dealings, political doublespeak, taking a page out of Karl Rove's playbook, endorsements from questionable characters, etc. Conversely, when Sen. Obama responds in kind, he loses support because he has promised to run a positive, post-partisan campaign. When he goes negative, many supporters feel he has broken a promise, and rightly so.

The Senate has passed the Genetic Information Nondiscrimination Act (GINA). You can hear NPR's take in their story Senate OKs Bill Outlawing Genetic Discrimination. It seems Sen. Tom Coburn (R-OK) was satisfied with recent changes and therefore no longer felt the need to single-handedly hold up the passage of the bill which had overwhelming bipartisan support. The House is expected to take up and pass the bill next week. President Bush has said he will sign it into law.

This bill, when it becomes law, will prevent insurance companies from denying coverage to individuals based on the results of genetic tests or because of a family history of genetic disease (it also prevents employers from discriminating based on genetic information). This will greatly improve the current climate for genetic testing and genomic research as individuals will no longer need to fear that if they have a genetic test performed or participate in DNA sequencing research that the findings will prevent them from getting insurance in the future. The New York Times has a story about GINA written before the measure passed: Congress Near Deal on Genetic Test Bias Bill.

The Slashdot story has an interesting comment, "If I know I'm likely to get a certain condition, I'll stock up on 'insurance' for it." I am not sure how the submitter obtains his insurance, but health insurance is not really an a la carte system. You don't buy insurance for specific maladies. You get health insurance or you don't. You don't get separate insurance policies to cover cancer, Parkinson's disease, heart disease, etc. The submitter uses his flawed logic to predict the fall of private insurance. Apparently the purchase of health insurance is not the only thing he does not really understand. The health insurance companies in the U.S. are very entrenched and this bill does not really affect them much. Genetic testing has not been widely applied in diagnostic medicine (in part because this bill did not exist) so the insurance companies did not really use it when assessing policy risk. If anything, this bill might be a net plus for the health insurance industry: if people are free to have genetic testing done without fear of losing insurance, potential health risks can more readily be assessed and early treatment/lifestyle changes can be started to mitigate the increased risks. Let the age of personalized medicine begin.

Update: here is a story featuring geneticists' reactions to the bill's passage.

Happy DNA Day. Julie Bierach of KWMU (St. Louis' NPR station) has a story about The Genome Center's DNA Day outreach efforts entitled Young scientists learn about DNA. One of the main things we do is visit area schools and perform a DNA extraction experiment on strawberries. If you would like to try the experiment yourself, here is the lab protocol to extract DNA from strawberries or bananas.

The Rev. Jeremiah Wright will be on Bill Moyers Journal tonight. Check your local listings.

16"Tell this to the nations,
proclaim it to Jerusalem:
'A besieging army is coming from a distant land,
raising a war cry against the cities of Judah.

17They surround her like men guarding a field,
because she has rebelled against me,' "
declares the LORD.

18"Your own conduct and actions
have brought this upon you.
This is your punishment.
How bitter it is!
How it pierces to the heart!"

Jeremiah 4:16-18 (NIV)