Necessary follow-up on the “Missing Link”

Ars Technica did a fantastic follow-up on the discovery of the “missing link”, which I posted about last week. As Ars points out, it’s looking like Ida was way more hype than anything, which could end up being extremely detrimental to science. Despite being a very well-preserved and valuable fossil, she does not appear to be a “missing link” in any way. If you were interested in the Ida news, this article is a must read. Score -1 for science and the media. :-/

Score 2 for Science

Just popping back in to tell you about a really cool scientific discovery. Some paleontologists discovered a new genus and species in Germany that is described as the “missing link” between humans and early mammals. The skeleton, dubbed Ida (or Darwinius masillae if you prefer), is an early mammal similar to a lemur that has opposable thumbs and forward-facing eyes. Score 1 for science and Darwin! Even better, their work was published in PLoS ONE, an open-access journal. Therefore, despite the fact that this revolutionary article was just published two days ago, anyone in the world can view the full text and high resolution images for free. Plus, you can print, reuse, redistribute, or even modify the images and text as long as you give the original authors credit. Score 2 for science! (hat tip: Jamey)

Taking Back The Power of Science

I read an article on Ars Technica [via /.]the other day that made me very worried about the future of scientific discovery in the US. With our currently failing economy, I don’t understand how we can still be making such idiotic decisions about the future of some of our most innovative industries.

The scientific research industry is fueled by governmentally funded programs like the NIH and NSF. As a taxpayer and citizen, I cannot believe the idiocy of some of statments against open access in Congress. There is a particularly poignant response on the /. article demonstrating how the greed of publishing companies in a dying industry are attempting to use their financial power and influence over government to squelch dissenters that oppose their bottom line. Let’s face it. With electronic distribution of written material available, the publishing industry as we know it is dying. There’s no way to stop it aside from them increasing their hold of copyrights and copyright law. There is no reason that publishing companies should be taking any sort of “ownership” of research that they publish. With the minuscule cost of publishing something online today, the publishers truly have almost no overhead to publish a scientific article. This was not the case 20 years ago when they had to print and ship their journals across the globe, but today they simply have to put it online. Their work is practically done for them by PubMed, the Google of biomedical science research. Sure, they need to find peer reviewers (one of the cornerstones of research), but do you think that publishing companies actually pay these reviewers? (No.) If that’s the case, why are they still charging thousands of dollars to researchers in order to publish an article? I think it’s because they used to have a reason to, and now that they don’t, it just means bigger profit margins. People don’t like it? They’ll pay the government to make them like it.

This article and the /. post made me start to wonder if an open access journal had already been started. A quick Google search showed me that it had: the Public Library of Science (PLoS). The PLoS is an open access journal published in the United States that guarantees that all of it’s material is available free of charge online. Not only that, but everything is released under a liberal Creative Commons Attribution license, the researchers retain their own copyright, and most importantly, the article is fully available on the day of publication. People don’t have to wait until tomorrow to learn about the discoveries of today. They can just dive right in. This is in stark contrast to the practices of current publishing conglomerates, who take over copyright and make non-subscribers wait a year or more (if at all) to access the material. Now, surely this is good for the publisher’s bottom-line, but you have to stop an ask yourself: Is this good for science?

Since most government-funded scientific research is done at large institutions with many faculty researchers, the scientists might not fully understand the problem. Their institutional affiliation gives them the ability to join together and pay the large fees for a subscription to the most popular journals. But some smaller institutions do not enjoy the luxury of being able to subscribe to anything. And even the largest institutions can’t subscribe to everything. There are simply too many journals. There are also many individuals, like students, and private researchers who wish to learn about what innovations our tax dollars are leading to and where these innovations might lead. Open access would likely generate a renewed interest in basic science and discovery, helping to fuel growth of the field. So should this even be an issue in today’s society? I mean scientists are generally trying to help us better understand the world we live in, the diseases we fight, and the things that affect us. The fact that a project has received a sliver of the ever dwindling government funding demonstrates that it’s a worthwhile project that will very likely yield extraordinary results for the world. Shouldn’t those results be available to anyone?

The PLoS has grown stronger since its inception, but it’s still generally small potatoes compared to the likes of Nature Publishing Group and even JACS. The PLoS now has separate journals in many of the biomedical sciences like biology, genetics, and medicine, and they even have a fast-track publication called PLoS ONE for those high priority articles.

So how is it that this journal, with its inherent ability to accelerate scientific discovery, has managed to stay beneath so many radars? The answer to that is two-fold. The scientific community does not currently seem to recognize both the underlying problem with current publishing companies and the innate ability of a publisher like PLoS to solve this problem once and for all. At the heart of this issue is the notoriety of publication. In order to be successful as a researcher, scientists want to be published in big name journals. Every one of them would love to have a publication in Nature or the NEJM. It’s extraordinarily competitive, and thus only the best of the best research makes it there. But scientists have lost sight of the fact that this notoriety is man-made. Nature is only as famous as it is because everyone wants to publish there. They get the best articles because of it. So if they want to break free of the hold that publishers have over their research, they need to set their own standards. If they want PLoS or any open access journal to be able to defeat the giants, or even get them to start listening, they have to remind the publishers that without their research, the publishers have no industry. Scientists do the work, and they should get to say what happens to it. In all likelihood, any attempt to dictate terms to a publisher is going to fail (at least at this point). But the scientific community needs to remember that they hold the power. They are the ones doing the research, and they are the ones volunteering to peer review. If the publishers won’t meet their demands, they need to meet their own demands. So listen up scientists: In this age of the Internet, you do not need them anymore. Take your research and your peer reviewers and make your own, new notoriety. Once they see you doing that, they’ll either follow suit or not. At that point, it won’t really matter.

But the reason that this has not happened and probably will not happen in near future is that scientists don’t see the dire need for open access because most of them are given most of the access they need. The sooner they realize that they need to demand open access to their work so that other scientists and the public can benefit from it, the better. Once they get past the encumbrance of permissions and red tape laid out by the publishers, they can get on with their life’s work in a much more open, collaborative environment. Otherwise, the publishing industry is going to keep tying researchers’ hands behind their backs, making it harder for them to exchange ideas, just so that they can continue to squeeze every possible dollar out of this industry. This is not good for the scientists, and it’s especially not good for science.

Summer Research

science-xkcdI’ve started a new research project this summer in Marcello Del Carlo‘s lab. Dr. Del Carlo is a new faculty member at Rush in the Department of Biochemistry. Our lab is affiliated with a clinical urologist faculty and we’re researching a urological disease called Peyronie’s Disease (PD) [Warning: male nudity]. From a biochemical perspective, we’re studying the process of growth and formation of a fibrous plaque underneath the skin of the male penis in a layer of connective tissue called the tunica albuginea. Currently, we’re analyzing both diseased and non-diseased tissue samples that have been surgically removed from patients with PD. In the future, we’ll also be working with a cultured fibroblast cell line doing similar work. So far we’re using Western Blots to identify and characterize proteins that are up- or down-regulated in diseased tissue compared to that of non-diseased. Our hope is that the studies will lead to a better understanding of PD and how the plaques form to aid in treatment.

In addition to research, Dr. Del Carlo is very interested in using FOSS as it relates to scientific research. By the time I met with him, he had already set up a database using PASSIM in order to keep track of tissue samples from patients. He also had the idea of using a WordPress blog as a sort of “online laboratory notebook”. I thought this seemed very in line with the Science Commons project, a derivative of Creative Commons. Science Commons is attempting to lower the barriers of scientific research, which is currently not nearly as “open” as it should be, considering almost all of it is funded by the U.S. Government. Most people believe that the fruits of governmentally funded projects should be available to the general public. In many cases, however, scientific research is locked down (for varying periods of time) due to copyright after being published in scientific journals. Since a scientist’s credibility is often judged by previous publications in journals, Science Commons is working to reduce the hold of copyright on this process, so that labs can publish data immediately to the web, allowing it to be indexed, freely searchable, and available immediately to anyone wanting to read it. This will continue to be an uphill battle since journals make a large amount of their money by licensing access to large academic institutions for their faculty. The idea that labs can make their data freely available on their own personal websites is being met with resistance. Still, I feel as a society we must push forward, despite the corporate interests, in order to do what’s best for the public. Plus, my thought is that journals will not suffer any major economic hardship. Their “seal of approval” by publishing the content will continue to be the scale by which research is judged. They would also continue to act as a collecting ground so that researchers looking for the latest data don’t need to worry about sorting through Google search results to find the latest findings in a field. Instead, some publishing groups have the gall to say that in order to publish in their journal you must leave the rights to your work on their doorstep, no matter who did the experiments. This will continue to be a very important issue in the scientific community in the future, and I’m hoping to gain a keener understanding of it over the next few weeks and months.

At least for now, I am the only one updating the Peyronie’s Disease Information Repository and it contains all of our experiments and results to date. Feel free to check it out, but unless it’s scientifically relevant, keep personal comments to my site.

Large Hadron Collider

Will the Large Hadron Collider bring about a cosmic Doomsday event, be used to shoot pidgeons, or just create the Higgs Boson and discover the meaning of life? Only the next few months will tell…

Note to dyslexics: Don’t transpose the “d” and “r” in that second word, or you’ll get an entirely different set of Google search results 😛

Pieter didn’t lie

Apparently Pieter wasn’t lying to me when he said my undergraduate thesis was on a really important topic. In yesterday’s Tribune, they dug up an apparently old piece of news that I hadn’t heard. The folks at UIUC‘s new IGB received a $7 million grant from the NIH back in April. For what? Apparently to use the technique Pieter and I (mainly Pieter, mind you) helped design for understanding and developing antibiotics.

“The genetic screening method they are using has been available to the scientific community for about three years. Metcalf considers it a powerful aid in his search because it replaces a hit-or-miss screening system in which scientists had to grow the bacteria under a variety of conditions to find out what antibiotics they could produce.”
-Chicago Tribune

Of course, this is only getting covered in the Tribune now (7 months after the grant was awarded) because of all the hype about MRSA in the high schools. Considering we specifically designed our method to promote development of new antibiotics that could kill MRSA (and do many other things), it’s no wonder someone decided it might be important around now. I just hope in a few years we hear that their work (and our technique) has paid off and that they’ve got a prospective drug candidate or two. For further reading, see my undergrad thesis below.

One problem I have with the Tribune newspaper article is that it didn’t mention the other 4 researchers. Now Prof. Metcalf may be the lead investigator, but let’s face it, mass spec is the backbone of the technique. A hat-tip to Neil or the Kelleher Group would have been nice, guys. But I guess the public really doesn’t care about the “how”, they just want to know that someone’s on the case. Well folks, the scientists are on it.

Jonathan Blackhall’s UIUC Undergraduate Thesis

Quantum Suicide?

I was checking my Google Homepage a few weeks ago and I noticed an article under How Stuff Works entitled “How Quantum Suicide Works.” The concepts in the article were a little complicated at times (well the background physics might be considered complicated), but overall I thought it was a pretty interesting and worthwhile read. It provides a couple of different perspectives to our universe that I hadn’t considered.