Tuesday, November 4, 2008

The DNA Network

The DNA Network

Election Day LIVE-BLOGGING [the skeptical alchemist]

Posted: 04 Nov 2008 08:48 PM CST

6:43 PM

Couldn't I have internet problems at some other times?? Crap!

Anyway, MSNBC just called Ohio for Obama. However, keep cool: this is only after 18% reporting. I think they are calling this wing state too early, to be honest.

The more I think about it, the more I think that McCain was the sacrificial animal for the Republican Party in this election campaign.

P.S. Skepchick is also live-blogging tonight.

5:49 PM

While we wait, I would like to give some link love to other bloggers I know who are live-blogging this election (whether they meant to do it or not!). Check out Greg Laden, Good Math Bad Math, Respectful Insolence, Built on Facts. There must be more of you... if you are live-blogging and I did not link to you, leave a comment on this post, and I will link you up!

5:37 PM

Pennsylvania keeps going Democrat, while you need to keep your eyes on Florida, as McCain is getting closer.

In the meantime, victory is being projected in North Carolina... for the Democratic Senate seat. A 60:40 majority for Democrats in the Senate is becoming more and more likely.

For now there isn't much more to say, apart form the fact that Pennsylvania is the big news for now. We are waiting for Colorado and New Mexico... it is going to take time.

Also, NBC just called Indiana for McCain.

5:14 PM

Virginia might just go to McCain: with 22% of reporting done, the Republican candidate leads by 56.6% to 42.5% for Obama. I say, watch Florida: with 20% reporting, Obama is leading there, 54.4% to 44.9%. Mississippi is too close to call according to MSNBC. The Democrats are trying to pick up the majority in the Senate, and they are also looking at New Mexico and Colorado -- so let's see what happens there later on. All these states are way West, so right now most of this is purely speculation.

MSNBC says that Obama's dead grandmother's absentee ballot will be counted. Well, as Messier De Lapalisse would say... she was alive right before she was dead (duh).

Stay tuned!

5:04 PM

Things are still very confusing. MSNBC reports that this still looks like the status quo from Bush-Kerry 2004. On the other hand, it has been reported that Pennsylvania and New Hampshire went to Obama. However...here is the most recent update for the Electoral College count: 103 to 34 for Obama.

4:23 PM

The first results are now in, although most of the places where the polls just closed are too close or too early to call. At this point in time, Vermont went to the Democrats and Kentucky to the Republicans, with the current partial Electoral College count at 8 to 3 for John McCain. There are partial results for Maine, New Hampshire, Indiana, Virginia, Georgia and Florida. North Carolina is too close to call, and it is the same for Ohio and West Virginia.

3:28 PM

I have been setting up my Twitter account, as you might have noticed. Now you can follow me there as well, although I will not be continuously updating today, as I am already blogging. I am still not very familiar with the whole Twitter platform, but I hope I will pick it up soon, it does look like a very neat tool.

In the meantime, while still waiting for the result for poll stations in the states mentioned above... I was looking at the distribution of campaign funding. This map is very useful to get an overview of that -- it is amazing to see how much Obama managed to raise over the course of the campaign. Possibly the very heated Democratic primaries gave him a head start with the fundraising in a way we haven't really seen before. Also, his focus on small individual donations gathered through the internet might have made a significant difference with past strategies.

2:32 PM

The first polls will start closing at around 7 PM EST. In the meantime, there isn't much to talk about... apart from more problems at the poll. So I would like to talk about something else which nobody has really been talking about.

I would just like you to stop for a moment, and wonder what the next President of the United States, no matter who he is, will have to face: two wars abroad, worsening relations with countries in the Middle East (excluding Israel), a bad rep abroad... and one of the biggest public debts I have ever seen -- about $10.5 trillion!

This means that the next President, if he wants to even stop the debt from growing at this exorbitant pace, will have to seriously tighten the US' belt in the very first months of his presidency. The Iraq War is unlikely to end, one way or another, before 2011; which means, public expenditure of other kinds will need to take a rough cut. I doubt that the new President will be able to work right away on health care and energy independence, although those are two big items on the bill.

So what I am observing is the Republican Party dumping all the mess created by the Bush administration on either a Democrat, or a relatively unknown Republican - in this way, the Republican establishment can start pointing fingers and whining very soon, and aim at winning the next election in 4 years, basically maintaining a solid control on Washington either way.

Call me pessimist, but no matter how good the intentions of the next President are, they will need to deal with those who will ultimately decide whether to pass their laws or not - the special-interest-funded Congress and Senate.

2:00 PM

Rupert Murdoch states he does not support Obama because, if he became US President, he would take the US in a "different direction". You can watch the interview here and listen for yourselves.

1:50 PM

People in America are coming out in record numbers -- 130 million people are expected to cast their ballots today. Of course, a higher turnout, and the huge variety of ballots being used, as well as the mix of paper and electronic voting techniques are creating a bit of a mess at some polling stations. This is adding to the backlog created by the high turnout, with some people reportedly lining up for up to 6 hours to cast their vote! I suggest the US get their act together and standardize their voting method, especially with propositions popping up together with federal elections at the same time and confusing people.

Moreover, the number of provisional ballots seems to be increasing as problems keep happening. It does look like things are not gonna get clear that soon, unless one of the sides wins by a landslide...

1:33 PM

Back to it -- even though my lunch isn't even fully cooked yet! Some of the polls are closing soon on the East Coast. Here are the polls that will be closing very soon: Kentucky, Georgia, South Carolina, West Virginia, North Carolina, Alabama, Connecticut, Washington DC... keep your eyes on West Virginia and North Carolina, they will be able to give us a sense of what is going on, and what could possibly happen later on. The BBC has also put up a map where they will keep count of Electoral College votes going to Obama and McCain. In the meantime, McCain is continuing his campaign in Colorado.

11:56 AM

I am going for lunch, I will be back soon! In the meantime, here is one more gadget for you -- and election result map, updated in real time, by the New York Times. You can find it here. Of course, it is not updated at this point, but you might find it useful later on.

11:54 AM

Voting "situation" in Ohio which could give trouble later on -- people who opt to vote using a paper ballot are being directed to give "provisional ballots". These ballots are not necessarily counted at the end of the election!!! Why is this being done?? And by the way, Ohio is one of the key swing states -- McCain needs to get this one, if he wants any hope of snatching the presidency.

11:43 AM

McCain in Colorado says "I will protect your Medicare", and "we will invest in any energy alternative", including "safe nuclear power, and off-shore drilling...when I am President, we will drill our shore, and we will drill now!" And of course, "drill baby drill... and we will, my friends". He is taking the old line of the maverick -- he has tried to change Washington, was not elected Miss Congeniality there for it, and he will not need to learn on the job. "I'd rather lose an election than lose a war... today [...] we are succeeding in Iraq, we will succeed in Afghanistan, and when I am president our troops will come home with honor and in victory, not in defeat".

McCain has been uninterruptedly talking for so much he is losing his voice. He says, "fight for what is right for America". Even his audience sounds tired -- the cheer him on, but they seem try to shout as much as he is. I give it to him, it is Election Day, and he is still going at it... together with his 96-year-old mother!

MSNBC calls him "vintage John McCain" and that they could "put this among one of the top speeches in his campaign" and that he should have done this a month ago. I have my doubts -- he sounds very tired of all this, and holding on to whatever strength he has left to keep going for another day.

11:36 AM

If you are voting today, make sure you check when your polling stations are going to close, because they are closing at different times across different states! You can find more info about when the polls are going to be closing in your state here -- and of course, if you are watching, you also want to know that!

11:28 AM

Some piece of news you might not get from the mainstream media... Twitter has put up a magical voter map. You can send in your vote report via Twitter, and also let people know if you had issues at the polling station. Do you want to see the map? Check it out! You can also use the site to get updated on the highest wait time reported across the country.

This is an interesting experiment not only for Americans, because it signals a fundamental shift in the use of "non-tradtional" media in spreading ideas usually relegated to the sphere of the traditional. YouTube, blogs, and now Twitter are playing a role that, although we have never seen so prominent in the past, we can expect to play an important role for such events in the future.

Some of the traditional media are adapting, of course, broadcasting for free on the internet, or running live blogs -- check out the BBC, they are also live-blogging the election, and including messages coming from their audience. In fact... talking about that, I just found out that the BBC is also following the election on Twitter !?!

11:25 AM

I am following MSNBC right now, and they are discussing the Bradley Effect, and supporting the view that race might, after all, be less important than expected, as the major problems that the future President will have to face, most importantly the economic crisis, is shifting people's attention towards these issues (and away from race).

It might be so... but from what I have heard, America still has a long way to go to reach full equality in terms of opportunity, socially and economically, between the white majority and all other racial minorities, but especially African Americans. But let's see, it might be revealing not just for America, but also for the rest of the Western world, to see Obama become president. After all, I can dream the day when a black man will be President in any of the Southern-European countries...

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I Voted . . . Blindly [evolgen]

Posted: 04 Nov 2008 07:45 PM CST

If you hold on until the end of the post, you'll see that it's got science content. But you'll have to wait until the end.

First, here's how it starts. I had an optometrist appointment at 8am this morning. I could have voted prior to the appointment, but the polling place is in between the optometrist's office and work, so I figured I'd vote after getting my eyes checked. Big mistake. The eye doctor dilated my pupils, which, much to my surprise, made me far-sighted (I'd never had both pupils dilated simultaneously before). I did not realize this until, when checking out of the office, I could not read the credit card receipt I signed. I thought, "Fuck, how the hell am I gonna vote if I can't read the ballot?"

An aside: the doctor had a picture of his daughter posing next to Dick Cheney with her violin. Doc said something about her being a musician, so I imagine she won some competition that earned her a trip to the White House.

So, I ride my bike to the polling place (don't worry, the pupil dilation didn't affect my distance vision). Thankfully, there was a short line. When I checked in, I asked the retired people how small the writing on the ballot is. They pointed me to a sample ballot across the room. I could not read it. Ever resourceful, I asked if anyone had reading glasses. I figured one of the five retirees staffing the place would be able to lend me a pair. They did not. Luckily, a nice lady waiting in line to vote let me borrow her specs, which, while not perfect, allowed me figure out which line on the ballot corresponded to each party.

Read the rest of this post... | Read the comments on this post...

Need something to distract you from the election? [adaptivecomplexity's blog]

Posted: 04 Nov 2008 03:48 PM CST

If you've already voted here in the US, or if you're not from the US and just burned out on US politics, here's a distraction:

Basic Books' Feynman extravaganza - all of their products (of course), but also some great reminiscences, interviews, videos, and links. If you can't get enough of Feynman, the scientist par excellence, this site is a good place to start.

read more

Teaching with wikis: navigation, student notes, and integrating Google forms [Discovering Biology in a Digital World]

Posted: 04 Nov 2008 03:00 PM CST

This quarter, I'm using a wiki with my bioinformatics class and posting sometimes about the things that I learn.

Two things I've been experimenting with are:

  1. Setting up pages for individual students so they can take notes while they're working.

  2. Embedding a Google form into one of my wiki pages for student assessment.

Read the rest of this post... | Read the comments on this post...

Two more “religious” videos… [Mailund on the Internet]

Posted: 04 Nov 2008 02:27 PM CST

Pam sees DNA test as a gift [deCODE You]

Posted: 04 Nov 2008 10:04 AM CST

genetic test customer Pamela Ayers and her grand-children, Spokane, WA

Genetic test customer Pamela Ayers and her grand-children, Spokane, WA

After watching her parents and brother suffer with diseases that might have been prevented with the right care, Pam Ayers has become vehemently proactive. She now believes that genetic health scans are the way of the future and early testing could help parents change their own and their children’s life-style for the better. This proud grandmother is taking care of her family.

Read the whole interview with Pamela Ayers in the Customer Stories section of deCODEme.

Phenotype of the Day [genomeboy.com]

Posted: 04 Nov 2008 09:56 AM CST

Sway: I know people have piercings, tattoos. Eric, in particular, is talking about a ban on sagging pants. Do [you] feel like people should be penalized?

Obama: Here is my attitude: I think people passing a law against people wearing sagging pants is a waste of time. We should be focused on creating jobs, improving our schools, health care, dealing with the war in Iraq, and anybody, any public official, that is worrying about sagging pants probably needs to spend some time focusing on real problems out there. Having said that, brothers should pull up their pants. You are walking by your mother, your grandmother, your underwear is showing. What’s wrong with that? Come on. There are some issues that we face, that you don’t have to pass a law, but that doesn’t mean folks can’t have some sense and some respect for other people and, you know, some people might not want to see your underwear — I’m one of them.

Via the immortal Balk

November is about elections and grants [FinchTalk]

Posted: 04 Nov 2008 08:45 AM CST

Halloween is over, and today is election day, go vote! Then, come back and read about what we planning for our next steps in Next Gen sequencing. This month we are preparing SBIR proposals to target...

Coffee and cancer [Bayblab]

Posted: 04 Nov 2008 08:43 AM CST

I recently had an armchair expert tell me that french press style coffee vs a filtered coffee preparation method increases your risk of cancer. [Don't confuse french press coffee for the biological apparatus]. This person was foggy on the details but indeed got rid of their Bodum(tm). Personally I find coffee from a french press tastes superior, but then again, I'd drink it off a dog some mornings. Some googling revealled one source of the idea that unfiltered coffee increases your risk of cancer the source they cite is an article that shows increased homocysteine levels in drinkers of unfiltered coffee vs NO COFFEE. (no coffee?!?!) Homocysteine itself is not directly derived from your diet, however, high levels in the blood are indicators for high risk of heart attack and stroke, and possibly cancer. The thought was that filtering coffee removed what the authors assumed was causing the rise in homocysteine levels. Turns out filtering coffee doesn't change the fact that drinking coffee raises homocysteine levels.
To me this is a good example of something I see often, that is, cancer research NOT serving the public who funds it. If this is the crappy way that the public is informed about cancer research I'm surprised it still is funded. Someone gets rid of their french press because their concerns for their health based on the mainstream medias reporting of an incorrect assumption in the literature. What is also strange is that the damage is done. I think I would have a hard time convincing this person that their french press coffee is no worse for them.
Also I think there is a leap of logic here that I have heard is similar to the leap in logic made for the statin class of drugs. That is that since higher homocysteine levels correlate with higher risk of cancer (let's assume the one article I found linking the two is correct), then homocysteine is a cause of cancer. An indicator is not necessarily the cause but is merely associated with increased risk.
Also it may be that coffee raises cancer causing homocysteine levels by an appriciable amount, however, other factors associated with coffee drinking may result in an overall reduction in cancer incidence. So again even if homocysteine causes cancer, coffee may not.
Of course, perhaps coffee has so taken over control of my thought processes that I am in denial.

Gamers will detect the problem in this study. [Genomicron]

Posted: 04 Nov 2008 07:45 AM CST

From New Scientist:

Video games don't train your brain

Does playing computer games boost your brainpower? Not necessarily, seems to be the answer.

Walter Boot and colleagues at the University of Illinois, Urbana-Champaign, found that non-gamers showed no improvement in memory skills or the ability to multitask after spending more than 20 hours on one of three video games. This appears to contradict previous studies which detected superior mental aptitudes among habitual gamers.

Any gamers care to discuss?

I'm not saying that video games do improve aptitude, but this seems like saying "Weight lifting does not increase muscle mass. Researchers showed no major increase in muscle mass among non-athletes who lifted weights for one week. This contradicts previous results which detected muscle increase in regular weight lifters."

Dear University of Melbourne... [Genomicron]

Posted: 04 Nov 2008 05:51 AM CST

... mites are not insects.


(Same goes for you PhysOrg, Science Alert, Biology News Net, and whoever else reprints press releases without reading them)

Gates Foundation Innovations on Funding Science [Bitesize Bio]

Posted: 04 Nov 2008 04:04 AM CST

All fields in Science thrive on fresh ideas that contest accepted theory.

Yet, researchers seeking funded face ever greater competition for limited funds - funds that are overly wedded to safe, unadventurous research. This, in effect, ostracizes off-the-wall ideas, which often cross disciplinary boundaries and would have potentially big payoffs should they work. Researchers long ago learned that the last people they should tell about their big ideas are their sources of financial support.

There are exceptions and a limited number of researchers succeed in injecting revolutionary ideas into mainstream science. And some degree of “safe, unadventurous research” is going on and is much needed. But in the face of calls to revise the NIH grant review process, perhaps one solution is to expand high risk efforts.

Efforts like the US National Institutes of Health (NIH), which has systematically promoted risky research through several initiatives. Or military imperatives for innovation through the US Defense Advanced Research Projects Agency (DARPA).

Or efforts like that of the Bill & Melinda Gates Foundation:

In a similar vein, frustrated with repeatedly encountering the same faces from the same countries, and a narrow range of ideas, the Bill & Melinda Gates Foundation decided to cast the net wider in the search for new people and ideas. Last week, it announced the 104 winners of the first round of its five-year, US$100-million ‘Grand Challenges Explorations’ programme. This solicited unconventional ideas for protecting against infectious diseases, limiting drug resistance and exploring latent tuberculosis. Future rounds will include ideas for vaccines for killer diseases and tools to help eradicate malaria.

It is the nature of the call for proposals, and their peer review, that is intriguing. The grant proposal is one that many researchers can only dream of — a two-page explanation of the idea, with no supporting data required. To emphasize that it’s the idea that matters, reviewers were blinded to the name, profession and nationality of the applicant.

The reviewers themselves were atypical. Instead of consensus review by experts in the field — as is the norm — the 4,000-odd proposals received were sent to individuals, not just in science but also in engineering, business and beyond — people the foundation considers to be ‘champions’ with strong track records in high-risk research.

[...]The first-round grants, at $100,000, are small. Dishing out large sums of money on far-fetched ideas would be foolhardy, given that as many as nine out of ten of these projects are expected to fail. But those that show signs of success will be eligible for further funds of $1 million, or much more.

Why wouldn’t this be a better model for the grant review process? Make small amounts of funding relatively easy to get for important ideas, streamline the evaluation of those grant applications, and provide large benefits to those few ideas that manage to succeed.

For another great article on research funding, check out Undergraduate Research: Genomics Education Partnership - an effort to promote undergraduate research experiences in genomics.

Election Special [Sciencebase Science Blog]

Posted: 04 Nov 2008 02:00 AM CST

obama-mccainNot really…I cannot imagine there is anyone in the world who is not fed up to the back teeth with the US election media saturation, debates and discussion about Obama and McCain and their irritating sidekicks. Of course, after today, one of those men will be called “Mr President” for the first time and a new finger will be on the red button of fate. In the meantime, some chemistry news:

In Issue 100 of the relaunched ChemWeb Alchemist, we report on energy is top of the agenda with a record-breaking solar cell material from Australia. New insights into the ripening of bananas reveals they get the blues while crystallography has been thrown a curveball as scientists discover the active sites in many models of protein receptors are not what they seemed to be. The chemistry of alternative medicine sits toxically under the glare of the Alchemist’s lamp and revelations about yet another small molecule with a crucial role to play in cellular control. Finally, a double ACS award for research on the structure and reactivity of molecular oxygen binding to copper and iron complexes, which could have future energy applications.

In SpectroscopyNOW this week, rather than designing and building new instrumentation from bespoke components, researchers in Canada have turned to the laser-based optical read-write technology of DVD and CD players to create a biomedical diagnostics system that requires no hardware modifications. Hua-Zhong “Hogan” Yu and his colleagues Yunchao Li, Lily M. L. Ou in the Department of Chemistry, at Simon Fraser University, in Burnaby, British Columbia, Canada, are all for recycling. They have now developed a digital signal readout protocol for screening disc-based bioassays that uses a standard optical drive (CD/DVD) from an ordinary desktop computer.

blue-bananasAlso, this week “Yes, we have blue bananas!” - Forget the so-called morning banana diet, blue is the new yellow and researchers in Europe and the US have no intention of slipping up when it comes to explaining why ripened bananas glow blue under ultraviolet light.

A gold star for SERS - Scientists at the National Institute of Standards and Technology (NIST) in Gaithersburg, Maryland, are using surface-enhanced Raman spectroscopy (SERS) to test the properties of star-shaped gold nanoparticles. They have found that these particles have optical qualities that outshine the competition and could make them useful in chemical and biological sensing and imaging.

Athletic support - Researchers have used NMR to show that endurance-trained athletes have a higher resting muscle metabolism than couch potatoes. The work suggests that the dissociation of oxidation and adenosine triphosphate (ATP) production could be another route by which exercise improves insulin sensitivity and burns excess energy and may have implications for understanding the development of type 2 diabetes.

Crystals foxed - Obtaining a high-resolution crystal structure of a protein, a receptor or an enzyme, for instance, has been at the forefront of the drug design field for many years. Finding small molecules that will dock with the active site of the protein and either stimulate it or inhibit it is the basis on which many pharmaceutical products were built and are thought to work. But, what if that fundamental concept were wrong? This is the sobering and at the same time very important conclusion made by researchers at Leiden University in The Netherlands and the Scripps Institute, La Jolla, California

Election Special

Pat Condell video [Mailund on the Internet]

Posted: 04 Nov 2008 01:15 AM CST

I always enjoy Pat Condell’s video rants.  Maybe because I agree with them so much…

If you haven’t seen them, start here.

Last Call for Cancer Posts! [Bayblab]

Posted: 04 Nov 2008 12:48 AM CST

The 15th edition of the Cancer Research Blog Carnival will be up on Friday at the carnival home page. For all you procrastinators/last second folks it's time to write or dig up something and submit it to the carnival.

New journal shows half-broken gene is enough to cause cancer [Think Gene]

Posted: 03 Nov 2008 07:17 PM CST

Josh: So while this research is very interesting, I would first like to call attention to biologists’ odd sense of humor. Apparently, SMAD4 stands for “Mothers against decapentaplegic homolog 4″. This is obviously some type of a joke made from MADD, but the bizarre sense of humor doesn’t stop here. Who can forget the signaling molecule Sonic Hedgehog (SHH), bride of sevenless (BOSS), frizzled, dishevelled, amongst many others that are escaping me at the moment.

Tumour suppressor genes do not necessarily require both alleles to be knocked out before disease phenotypes are expressed. Research published in BioMed Central’s new open access journal PathoGenetics reveals that only one allele of SMAD4 has to be damaged to put a person at risk of pancreatic and colorectal cancer.

Riccardo Fodde led a team of researchers from Erasmus MC, Rotterdam, who investigated SMAD4, a tumor suppressor gene implicated in pancreatic and colorectal cancer. They found that having one mutated SMAD4 allele was associated with the development of gastrointestinal polyps. This research is the first to address the molecular and cellular consequences of SMAD4 damage on a genome-wide scale.

This high quality research is typical of that which will be published in PathoGenetics, an open access journal created to meet the need for a resource focused solely on the pathogenesis of genetic diseases. The journal’s co-Editors in Chief are Professor Stylianos Antonarakis and Professor Andrea Ballabio. Ballabio said, “PathoGenetics will give scientists a unique opportunity to publish exciting research on the molecular mechanisms underlying the manifestations of disease phenotype”.

PathoGenetics will focus on both in vitro and in vivo studies on the cascade of events leading from gene mutations or genomic rearrangement to disease. The discovery of novel molecular and metabolic pathways relevant to disease pathogenesis will be given specific emphasis. The first issue includes a review by James Lupski and colleagues that deals with mechanisms for human genomic rearrangements and a groundbreaking piece on the methodology of knock-in vector construction by Nicholas Hastie and colleagues. According to Antonarakis, “Given its unique characteristics, PathoGenetics is likely to become the ideal journal for scientists from different backgrounds to publish and read exciting research on disease pathogenesis”.

Source: BioMed Central

Smad4 haploinsufficiency: a matter of dosage. Paola Alberici, Claudia Gaspar, Patrick Franken, Marcin M Gorski, Ingrid de Vries, Rodney J Scott, Ari Ristimäki, Lauri A Aaltonen, Riccardo Fodde. PathoGenetics 2008, 1:2 (3 November 2008)

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