Should Science be Open to the Public? Obama Wants to Know

This man loves science

So, I’m on a mailing list for the journal “Science”, and I got an email today about a new policy idea about open access science.  If you’ve been keeping up with my blog, you know that I’m a huge promoter of such science, and tend to limit my reviews of articles to ones that most readers would have easy access to.  But, this isn’t easy, since if the article didn’t appear on Biomed central, or pubmed, then getting your hands on it may be nearly impossible unless you have access to a University library like I do.

That is a major problem.  The email said:

The Obama Administration is seeking public input on policies concerning access to publicly-funded research results, such as those that appear in academic and scholarly journal articles. Currently, the National Institutes of Health require that research funded by its grants be made available to the public online at no charge within 12 months of publication. The Administration is seeking views as to whether this policy should be extended to other science agencies and, if so, how it should be implemented.

And then broke it down into two areas:

Features and Technology (Dec. 21 to Dec 31): In what format should the data be submitted in order to make it easy to search and retrieve information, and to make it easy for others to link to it? Are there existing digital standards for archiving and interoperability to maximize public benefit? How are these anticipated to change?

Management (Jan. 1 to Jan. 7): What are the best mechanisms to ensure compliance? What would be the best metrics of success? What are the best examples of usability in the private sector (both domestic and international)? Should those who access papers be given the opportunity to comment or provide feedback?

Each of these topics will form the basis of a blog posting that will appear at www.whitehouse.gov/open and will be open for comment on the OSTP blog at blog.ostp.gov.

If research is funded by the government, then by definition, it is funded by you (and me).  Therefore we have the right to access it right away after it is published … since we are part owners of it!  Unfortunately, it doesn’t currently work that way, which to my mind is a violation not only of our sovereign rights, but of the “code” of science.  Progress is never made when information is sequestered.

I think a simple change that would be great is simply allow the authors of the papers themselves be allowed to post the articles on their own websites or blogs.  Then, in addition to the traditional channels through which scientists can provide them with feedback, the public at large would have the ability to do so themselves.

Features and Technology (Dec. 21 to Dec 31): In what format should the data be submitted in order to make it easy to search and retrieve information, and to make it easy for others to link to it? Are there existing digital standards for archiving and interoperability to maximize public benefit? How are these anticipated to change?

* Management (Jan. 1 to Jan. 7): What are the best mechanisms to ensure compliance? What would be the best metrics of success? What are the best examples of usability in the private sector (both domestic and international)? Should those who access papers be given the opportunity to comment or provide feedback?

Is The Biggest Loser Bad for America?

Is the TV show The Biggest Loser bad for America?  Does it portray unrealistic results that are in fact going to discourage people from doing the hard work necessary if they’re going to lose weight?  Are the contestants put into life-threatening situations?  And what does all this have to do with Triple H?

I wrote up a full article on my fitness website here about it.  But, the connection to this site is that obesity  is fascinating from an evolutionary  and cultural standpoint.  We are the ONLY primate that has an obesity problem (when was the last time you saw a fat baboon?).  There are other fat animals on the planet, sure, but they are rather different  from us, and all of them have a good reason for their weight gain.  Some, like whales need it to stay warm in cold water.  Others, like hippos, use it for buoyancy.  We don’t have a good reason.  The only exceptions in the animal kingdom are domesticated pets–that WE feed too much.

They need a biggest loser for pets

For all the hype and craziness, the show makes it clear that losing massive amounts of fat is  possible.   It will be hard, very hard, but it is possible.

Before the recent past, the only overweight people on the planet were rich people.  Before civilization, when there were no rich people, there were no overweight people either.

The cat on the left has a similar history.   Felines are not fat by nature.   But, given enough food, and a sedentary lifestyle, anything is possible.

The real question for us as a species is, then, how do we alter our culture enough so that obesity ceases to be the norm.  That is, if we live in a cultural and physical environment now that increases (by a lot) the likelihood that you will get fatter as time goes on; then how do we change it.  And to what?

Self control is not enough of an answer, though, on the individual level, it is a good place to start.  I think we need to build better institutions–far better PE programs in school would be a huge start.

We went through nearly 20 years of people telling us that the problem is genetics.  If your parents were fat, then you’ll be fat too.  Not only is that bullshit, but it’s demotivating.  (Of course, genes for fat storage exist, but that doesn’t mean you were doomed from birth.)  How are you supposed to get motivated to get into the gym and to eat healthier if you’re told it is probably genetics, and therefore, there is nothing you can do about it.

The show makes it clear that you CAN lose the fat.  Even if they are doing some wacky stuff, huge people are losing a lot of weight.  And that is inspirational.  Hype or not.

Thexder on the Tandy

I almost forgot about how many hours my brother and I spent trying to beat this game. The levels just kept going and going.

Games have come a long way. But, there is something fun about these games that seems to have gotten lost in all the uber mega graphics we have now.

Here’s a Youtube vid of a dude playing it.

HIV and the T Cell Life Cycle

In an excellent review of a paper in the Journal of Biology (“Generalized immune activation as a direct result of activated CD4+ T cell killing“), Nienke Vrisekoop , Judith N Mandl, and Ronald N Germain discuss the life and death of the T lymphocyte.

T lymphocytes have a difficult existence. As mature cells, they are essential for immunity to infection, but in the early stages of their development in the thymus, more than 90% of them fail selection for the appropriate antigen receptors and die before export to the peripheral immune system. Those that achieve maturity spend weeks, months or even years circulating through the body, in constant search of a foreign antigen that their antigen-specific receptor can recognize, and needing continuously to compete for trophic signals necessary for their survival. Most fail to find an antigenic match and remain as small resting cells until death. A few encounter the right partner and undergo a transient bout of exponential clonal expansion, only for more than 90% of these progeny to be lost by apoptosis shortly after the antigen is cleared. The remaining 10% are maintained as memory cells (Figure 1), conferring lasting protection.

Understanding the mechanism of T cell death is a major concern when confronting HIV and its progression into full blown AIDS.

Although it is known that HIV kills activated CD4⁺ T cells, it is still a major unresolved question why these cells progressively decline after infection. It is clear that in infected individuals, the rate of loss of CD4⁺ T cells is greater than the rate of production so that the CD4⁺ T cell pool is gradually eroded over time, but it remains to be determined how the balance between these processes is impaired. It is unlikely that direct killing of infected target cells by HIV is sufficient to cause CD4⁺ T cell depletion. Natural hosts for simian immunodeficiency virus (SIV), such as sooty mangabeys, do not progress to AIDS and maintain near-normal levels of peripheral CD4⁺ T cell numbers despite high rates of viral replication [4]. In fact, the level of immune activation is a better predictor of disease progression than viral load. Consistent with this, HIV infection in humans leads to chronic generalized immune activation characterized by an increased rate of exit of CD4⁺ and CD8⁺ T cells and of natural killer (NK) cells from the resting state, increased T and NK cell turnover and death, polyclonal B cell activation with increased levels of gamma globulins, and elevated production of pro-inflammatory cytokines. Conversely, chronic immune activation is not seen following SIV infection in natural hosts that do not show progression to AIDS [4].

That is, there is a question as to what causes the autoimmune response that is so devastating to people with AIDS.  There are two proposed methods of activation.  The first is that chronic activation of the hosts immune system disrupts CD4+T cell homeostasis.  The second is the opposite, that HIV drops the CD4+T count out of homeostasis and the bodies over-active response is chronic immune activation.  The authors make the point that these two possibilities are not incompatible.

Clearly, the two possible causal relationships between chronic immune activation and CD4⁺ T cell loss are not mutually exclusive. In fact, chronic immune activation and the loss of CD4⁺ T cells may amplify each other in a loop that makes it difficult to establish which process underlies and drives the other.

The study in review attempted to induce this same response in mice.

Marques et al. [1] suggest that the OX40-DTA mouse is one approach to this issue and that the findings in these mice provide important insight into the control of lymphocyte dynamics in infected humans. Indeed, in the absence of exogenous infection, OX40-DTA mice do show features consistent with generalized immune activation (Table 1), including an expansion of effector CD8⁺ T cell numbers that inverts the usual CD4⁺:CD8⁺ T cell ratio, and increased serum levels of inflammatory cytokines. This generalized activation cannot be attributed to the release of microbial components into the circulation from the gut, because deletion of activated CD4⁺ T cells does not in itself lead to a breach in the gut epithelium. Notably, Marques et al. [1] show that the expansion of effector CD8⁺ T cells and increases in serum levels of inflammatory cytokines can be reversed following reintroduction of Tregs from normal mice, suggesting that the increased immune activation in OX40-DTA mice can in part be ascribed to a Treg insufficiency, which they propose is a key event in HIV-infected individuals leading to CD4⁺ T cell depletion.

There’s a lot more, and the review goes into much more detail.  But, I can see how this approach could be fruitful in illuminating the underlying causes of a disease that plagues such a large number of humans on the planet.

Astrobiology: Part of RNA Built in the Lab

Astrobiologists have built Uracil, a component in RNA, in space-like conditions in the lab.

“We have demonstrated for the first time that we can make uracil, a component of RNA, non-biologically in a laboratory under conditions found in space,” said Michel Nuevo, research scientist at NASA’s Ames Research Center. “We are showing that these laboratory processes, which simulate occurrences in outer space, can make a fundamental building block used by living organisms on Earth.”

Change Geeks Can Believe In: White House Goes Drupal

President Obama promised us change, and change we get.  The White House official website, whitehouse.gov, has changed its CMS (Content Management System) to the open source platform Drupal.

Drupal is, quite frankly, a pain in the butt if you don’t know any php, and aren’t comfortable learning the architecture of a site.  For most individuals who just want to blog, or have a small business website, I still think WordPress is king.  It’s easy as hell to understand and it’s quite flexible.  Nearly every site I’ve ever created I did with WordPress. I’m a mathematician, not a web developer.

But, for large websites needing lots of features or, in this case, for a large government, Drupal is well worth the learning curve.  It can do pretty well anything you want it to do.  It’s more secure than most CMS’s. And, it’s got a large community of developers backing it up.

WhiteHouse.gov’s switch is part of an effort on the part of the Obama Administration to make the white house a more interactive and “Web 2.0″ friendly place.  He is the first President to be addicted to his Blackberry after all.

House Passes Health Care Bill with Public Option

It looked dicey, but last night it happened.  The House passed the health care bill with a public option.  I’m not sure the Senate will keep the public option–regarless of 60% approval ratings for it in the public.  But, we’ll see.

According to the Huffington Post:

The Congressional Progressive Caucus had pushed hard for a “robust” public option that would have reimbursed providers using Medicare rates. Blue Dog Democrats beat back that effort, costing taxpayers $85 billion over ten years — money that will go to hospitals, doctors and drug makers, increasing the cost of health care.

The bill also prevents insurers from discriminating against people with preexisting conditions, caps the financial responsibility that insured individuals will face when medical emergencies strike, bans insurers for dropping folks because they get sick, and proposes a host of other insurance industry reforms.

It passed with only 220 to 215 votes.  All of them were Democrats except for one, Rep. Anh “Joseph” Cao, R-New Orleans.

“Twenty percent of the people in my district are uninsured and we have tremendous health care issues in the district, and I believe this is good for the people of my district,” Cao said minutes after the vote.

“I feel both courageous and lonely,” he said.

You can read the entire bill here.

Happy 40th Sesame Street: Let’s Count to 12!

This is how I learned how to count to 12.  Arguably the coolest counting song of all time (sung by the Pointer Sisters).  Thanks Sesame Street.

Ardipithecus, Poster Child for an Evolutionary Adaptive Plateau

“Ardi”, or Ardipithecus ramidus, has been much in the news lately.  Most of the reporting has been decent, but there are some clearly over hyped ones.  Thankfully, Paleoanthropologist John Hawks wrote an article for Seed magazine about Ardipithicus and its significance to the ongoing science of human origins.  He also wrote up a great FAQ page on his blog, where he goes into some real detail.

As paleoanthropologist C. Owen Lovejoy describes it, Ardi gives us a view of a previously unknown “adaptive plateau” among early hominins—a suite of anatomical and behavioral characteristics that lasted for a long, stable period in the early Pliocene environment. The Ardipithecus form might account for the bulk of the whole story of human evolution—a kind of hominin that was different from anything that came before or after.

New Paint Job

As you can see (unless you’re reading this via RSS or email), I’ve changed the look slightly of the blog.  It’s not a major shift, but I dropped one of the sidebars, and changed the decorations and fonts.  I’m still using Sandbox 0.6.1, but while the old theme was based on Biology by Ntuat, this new one is based on Blog.txt by Scott Allen Wallick.

The skeleton pic in the top right hand side of the blog is Ardipithicus, or “Ardi”, the new fossil that is getting so much press. It’s a bit large and creeps into the text, so I may need to alter it.  I’m planning on having the image change periodically, for fun.

I’ll be tweaking the CSS here a bit till I get it “dialed in”.  Hopefully that won’t seem to jarring to you.