Boring blog overall, but I wanted to put a collection of links here for information about Open Access, especially as it regards to biomedical literature. I will add more links to this over time, and welcome suggestions.
The Lasker Award for Basic Medical Research was given a few days ago (see here). It went to Elizabeth Blackburn, Carol Greider, and Jack Szostak for work on telomerase, the enzyme that synthesizes the ends of linear chromosomes. The whole history of the discovery of telomeres and telomerase is fascinating and a good summary can be found at the Lasker site. The discoveries were made possible in a large part due to the unique and tractable biology of the single celled eukaryotes Tetrahymena thermophila, one of my favorite bugs. Perhpas most importantly, this species has a lot of telomeres and teomerase in each cell since it contains >200 linear chromosomes in the macronucleus and each are present in about 40-50 copies.
I of course have a vested interest in this since I have been in charge of the project to sequence the macronuclear genome of this species. We just published a summary of our findings in PLoS Biology (see the paper here). Research on this organism has led to some other fundamental discoveries in biology, including, for example, the discovery of catalytic RNA, which won the Nobel prize in chemistry in 1989.
Winning the Lasker award bodes well for Blackburn, Greider, and Szostak as many previous recipients have gone on to win a Nobel (the Lasker site has a good list of this connection here). However the Lasker listing includes people who won the Lasker AFTER they won a Nobel, which is a bit silly. I am sure they were happy to also get the Lasker Award, but that does not provide useful information for the Lasker as a predictor of the Nobel.
Anyway, a tip of my hat to team telomerase and Tetrahymena thermophila.
The Royal Society has announced that they are making their full archive, including papers going back hundreds of years, available online for the first time. I read this line and thought – “Finally, the Royal Society is moving towards Open Access”. After all, the US National Academy of Sciences provides full and free access to all articles 6 months after publication.
Then I read the next sentence, which says that the Royal Society wil provide this free access to their archive until December.:
And until December the archive is freely available to anyone on the internet to explore. ….
After December 2006 subscribers to our subscription packages (S, A and B) will enjoy privileged online access to the archives. Private researchers will also be able to access individual articles for a small fee per download.
The Royal Society appears to simly want to hold on to every little last shred of money they can get for things published originally hundreds of years ago. They could make a great contribution to the world by opening up their archive completely. But clearly, the Royal Society is not about making contributions to humanity. What they appear to be about is a scientific oligarchy that exists mostly to promote themselves and their freinds. I would like to point out again that of 1316 fellows, 62 are women.
So this group of scientists appears to be trying to continue the bad traditions started hundreds of years ago, like excluding women from science. I looked for but could not find information on minorities but can only assume that their record in this area is even worse, as they do not discuss it on their web site.
Perhaps some day the UK public will wisen up and stop giving money to this collection of Neanderthal wannabes.
Well, it appears that the anti bio-piracy movement continues to spread into the genome sequencing realm. Today, an article was published in the Australian suggesting that Australia in essence stop working with the scientific community and to not let anyone else sequence the genomes of organisms from that country. The basic argument is as follows:
My gut instinct is that this idea is absurd. But the more I think about it, the more I come to the conclusion that something needs to be done to encourage countries to share genomic information about their biological resources. I see two critical reasons this is needed. First, it will help encourage countries to protect their biodiversity in the hope that they will get something from it. Second, the more this information is shared and put in the public domain the more we will learn about life on this planet.
This is of course not the first time this issue has come up. Diversa, for example, which has sampled the world looking for novel enzymes, has been accused of biopiracy wherever it goes (e.g., see here). They have argued that what they are doing is bioprospecting, not biopiracy. However this argument did not always calm critics in various locations.
Diversa has been accused of biopiracy in part because they are a for profit company trying to benefit directly from other countries biological resources, much like those looking for new drugs in the tropics. Since Diversa did their work through molecular biology, they were viewed in many countries much like GMOs are. Many other companies doing “bioprospecting” have also been accused of biopiracy and I guess the truth of the accusations depend on the company involved.
However, what we have now is potentially much more damaging to scientific research. These people are in essence arguing against ANY release of genomic information regarding organisms native to other countries because once the information is out, the countries lose control over how it might be used. See for example
The critics in essence consider this analogous to someone stealing seeds for some plant. I think we run the risk of genome sequencing becoming labelled as horribly evil in much the same way GMOs and biopiracy is. I guess I do not completely disagree with the critics, but I see so many potential benefits to the world from sharing genomic information that I am hoping there is a way to do this without committing egregious acts of biopiracy.
One possible solution that has been suggested would be for DNA sequence databases to contain some reference to the country which “owns” the biological resources behind the sequence data. But this does not really protect any potential intellectual property in the data. Patenting DNA sequence has been frowned upon by courts and governments alike, as well as many policy folks. Thus this is probably not an option. As a supporter of open data release and open access to publications, I cannot believe I am about to write this but … maybe it would be worth considering the DNA patenting issue again if it allowed for release of sequence information and protection from biopiracy.
It seems that there may be a need for DNA sequence databases to record in some way that certain information was produced from a country’s biological resources.
There has been a growing trend in biological research, for scientists to release their data in some way or another prior to publication. This data release is meant to promote the advancement of science, and it frequently does. This is perhaps best seen with genome sequencing projects, such as the public version of the “Human Genome Project.” In many if not most cases, centers that do the bulk of the sequencing work release the sequence data for searching by others, even before publishing papers on their own data. In most cases, restrictions are placed on how the data can be used, but the data is still released for others to look at.
This is of course in contrast to how much of science works, with researchers keeping their data to themselves until they are ready to publish something. The genome centers who have made their data available prior to publication deserve some credit for this openness. Especially since the data release in general by genome centers has been so far and beyond what biology researchers do. In fact, many of these centers go out of their way to promote getting such credit (they even got Clinton and Blair to play along) The best example of this was the public human genome project, which made multiple claims about how great they were for humanity for releasing the data “within 24 hours of gathering it.” This data release policy was captured in something that became known as the Bermuda Principles, due to a meeting that took place in Bermuda (see a nice summary of this by John Sulston here).
What is appalling to me, however, is that these same centers that try to take credit for their openness, then turn around and usually publish their papers in non Open Access journals (for those who do not know, this means that then one has to pay money, frequently enormous sums of money, just to read the paper). I do not understand this. A paper about an analysis someone did on a data set may in fact be more valuable to the community than the data itself. If the genome centers like TIGR, JGI, Sanger, Whitehead, etc. really wanted to be on the side of openness, they should stop publishing their papers in non Open Access journals. Unfortunately these places publish very few of their papers in such journals.
For example, the Joint Genome Institute (JGI) which I am now affiliated with, is continually showing two faces on this issue. On the one hand, the issue press release after press release regarding their release of data on various genome projects (e.g., here). That is fine, although a little over the top sometimes. But then they almost never publish any of their work in Open Access journals (e.g., see their latest press release on a paper published about a genome in Science, a non Open Access journal). Any taxpayers out there should be disappointed with this as the genome centers get TONS of money to carry out this work for the public benefit. And then for the papers on the work to be hidden behind huge subscription fees is a waste of your money.
This is particuarly surprising coming from JGI since JGI is run directly by the Department of Energy (unlike most other centers which are either private or part of a university). Thus apparently DOE does not want to follow even the recommendations of congress and the senate regarding Open Access to publications. Nor does DOE apparently want to do the right thing by requiring their institutes for publish in Open Access journals. Too bad. Taxpayers hopefully will begin to get more and more upset about the waste of their money as these centers take enormous amounts of the federal science budget and convert it into documents that only a few can read.
OK
I just read about this new claim, made at a meeting, regarding “phone telepathy” in which some people claim to know that someone is about to call them, just before the phone rings. Now, a researcher is claiming to have conducted a controlled experiment that supports this. For the key details seee the Reuters news story or the link at CNN. But here is the key part of the article:
Each person in the trials was asked to give researchers names and phone numbers of four relatives or friends. These were then called at random and told to ring the subject who had to identify the caller before answering the phone.
“The hit rate was 45 percent, well above the 25 percent you would have expected,” he told the annual meeting of the British Association for the Advancement of Science.
“The odds against this being a chance effect are 1,000 billion to one.”
Now, it is entirely possible that the Rupert Sheldrake who conducted this research is on the up and up. However, every time I have seen claims that make me giggle like this one did, they have turned out to be wrong. But rather than claim that after the fact, I will put it out there in the blog world. I state, with complete confidence, that the conclusions of Sheldrake (that people use telepathy to sense when someone is going to call) will be shown to be wrong. Now – I do not know how it will be shown to be wrong. For example, his method theoretically should have controlled for the fact that when the phone rings sometimes you can guess who is calling by the hour of the day or by world events (e.g., my brother will call just after any major REDSOX event). Nevertheless, it will turn out that something is amiss.
Anyway, people can get a good giggle out of doing a google search (giggle from google) with his name and checking out some of his other work (like that Dogs That Know When Their Owners Are Coming Home). Now I am not saying that we know everything about human perception. Nor am I saying that there is no way that we know everything about all the means of animal communication. But do people know, even when all behavioral variables are removed, who is about to call them simply from telepathy? I predict, the answer, despite how much fun it would be to be true, will be, alas, no.
As I assume many people know, Steve Irwin (aka the Crocodile Hunter) died today. He has been lauded as an environmentalist, which he clearly was. However, he should also be praised as one of the more effective science educators of the last 20 years.
In this day and age, most of the TV shows are either 24 hour news, or some bizarre new reality show, or some crime drama. But Irwin managed to be successful with what could be called a animal-encounters reality show. Except that unlike some other such shows (e.g., “When Animals Attack“) his shows tended to be rich in moral lessons and education for the public about biology, life and animal behavior. We desperately need such little openings into the general public for education about science. Whether you liked his shows or not, whether you agreed with his methods for apporaching and protecting mean looking animals, I think everyone should say thanks today for Irwin’s dedication to educating the public about life on this planet.
Well, even though the traditional press did not pick up the story about the Tetrahymena genome paper, it seems that lots of blogs and online news sources picked it up.
Here are some:
Maybe the press release from TIGR did not excite the “real” press too much, I do not know. But nevertheless, it is good to see people discussing the article and even better to see that the article is currently the #1 viewed article for the week at PLoS Biology. I asumme that most of this comes from slashdot running an item about the article but I am not 100% sure.
I think the blogger world seems to run stories about Open Access publications much more than
about non Open Access publications since they can read them freely. It would seem that the blogger world is helping to promote Open Access papers and may explain why in the recent past I have gotten much more response to Open Access papers than even to papers in Nature or Science.
It is so important for scientific research to reach all people, not just scientists who can afford subscriptions to journals. Thus a partnership between bloggers and open access publications seems perfect for the new way of doing science.
Just thought I would put out a little self-promotional posting here on a paper we have published today on the genome of a very interesting organism called Tetrahymena thermophila. This organism is a single-celled eukaryote that lives in fresh water ponds.
This species has served as a powerful model organism for studies of the workings of eukaryotic cells. Studies of this species have led to some fundamental discoveries about how life works. For example, telomerase, the enzyme that helps keep the ends of linear chromsomes from degrading, was discovered in this species. This may not seem too important, but many folks think that degradation of chromosome ends in humans is involved in aging. Perhaps even more importantly, (to me at least) studies of this species were fundamental to the discovery that RNA can be an enzyme. This discovery of catalytic RNA revolutionized our understanding of how cells work and how life evolved. Tom Cech and Sidney Altman were given the Nobel Prize in 1989 for this discovery.
Many (including myself) believe that having the genome sequence of this species will further spur research and its use as a model organism. In addition, we believe that some of the findings we report in our paper will further cement the importace of this species. For example, this species, though single celed, encodes nearly as many proteins as humans and possesses many processes and pathways shared with animals but missing from other model single celled species.
The project that led to this publication was undertaken while I was at TIGR (The Institute for Genomic Research) and involved a collaboration among people at dozens of research institutions around the world. It all started in 2001 when Ed Orias and his colleagues sought to see if anyone at TIGR would be interested in putting in a grant to sequence this species’ genome. I responded to the email saying I was interested, especially since I had interacted with multiple people who used this species as a model system (e.g., Laura Landweber at Princeton and Laura Katz at Smith). So I went to a FASEB meeting where the Tetrahymena Genome Steering Committee was meeting and discussed with them how TIGR might help sequence the genome. And after talking to other genome centers, they selected TIGR to put in a grant proposal with them.
We ended up getting funding from two grant proposals – one from NIGMS and the other from the NSF Microbial Genome Sequencing Program. The sequencing was done in a rapid burst at the new Joint Technology Center which TIGR shares with the Venter Institute. And then we spent ~1.5 years analyzing the sequence data (and assemblies) that came out and in the end we fortunately were able to get our paper into PLoS Biology, in my opinion the best place available to publish biology research.
Importantly PLoS Biology is Open Access which allows anyone anywhere to read about our work. This goes well with the free and open release we made of the genome sequence data. In fact, many people published papers on the genome before we did (sometimes scooping us). In the end, I accepted the risks of releasing the genome data with no restrictions inexchange for advancing research on this organisms. I think this risk was well worth it as we still got our big paper published and the field has advanced more rapidly than if we had not released the data.
Other links that may be of interest to people:
Eisen, J., Coyne, R., Wu, M., Wu, D., Thiagarajan, M., Wortman, J., Badger, J., Ren, Q., Amedeo, P., Jones, K., Tallon, L., Delcher, A., Salzberg, S., Silva, J., Haas, B., Majoros, W., Farzad, M., Carlton, J., Smith, R., Garg, J., Pearlman, R., Karrer, K., Sun, L., Manning, G., Elde, N., Turkewitz, A., Asai, D., Wilkes, D., Wang, Y., Cai, H., Collins, K., Stewart, B., Lee, S., Wilamowska, K., Weinberg, Z., Ruzzo, W., Wloga, D., Gaertig, J., Frankel, J., Tsao, C., Gorovsky, M., Keeling, P., Waller, R., Patron, N., Cherry, J., Stover, N., Krieger, C., del Toro, C., Ryder, H., Williamson, S., Barbeau, R., Hamilton, E., & Orias, E. (2006). Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote PLoS Biology, 4 (9) DOI: 10.1371/journal.pbio.0040286
I am astonished at the behavior of the Royal Society regardling publication. As dozens of funding agencies and societies and individuals move towards Open Access for publications, the Royal Society crawls back into the medeivel hole from which it originated.
In article after article, the Royal Society’s publishing folks rant on and on about the evils of Open Access publishing. NOTE …. THANKS TO DBERGESSON FOR POINTING OUT THE MISTAKE IN THIS BLOG. I USED A QUOTE FROM THE WRONG ROYAL SOCIETY HERE. I AM LEAVING IT IN TO KEEP THE ORIGINAL POSTING. I STILL FIND THE REAL ROYAL SOCIETIES POSITION ON OPEN ACCESS TO BE ANNOYING. SEE COMMENTS FOR MORE DETAIL.
For example, in a recent article from RSC:
But the Royal Society of Chemistry’s director of publishing, Peter Gregory, disagrees. ‘We have absolutely no interest shown from our editorial board members, or our authors, for open access publishing,’ he said.
Gregory believes that the open access author-pays model is ‘ethically flawed’, because it raises the risk that substandard science could be widely circulated without being subjected to more rigorous peer review. This could be particularly problematic in chemistry, where rapid, open access publication could be used to establish priority ahead of more time-consuming patent applications from rival groups, he added.
What this basically means is that the Royal Society wants to continue to make money publishing the results of scientific research that is largely funded by the government and the public. And that they are willing to have people suffer (e.g., die unnecessarily because their doctors do not have a subscription to the Royal Societies journals) rather than use their supposedly brilliant minds to come up with a way to make money and simultaneously make the research freely available. The NIH, Wellcome Trust, and dozens of other groups are pushing for Open Access. Yet the Royal Society is sticking to their old boys club ways (to see how old boys clubbish they are go to here).
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If we actually go to the details of the Gregory quote above, I have a hard time knowing where to begin with the flawed logic here. For example, the idea that substandard science does not get published in non Open Access journals is just absurd. Consider the latest example of the Korean Cloning scam. Those articles were published in top non open access journals. Same thing with just about every other case of bad science or scientific fraud in the last twenty years. The claim by Gregory is simply unfounded. First, Open Access journals do not say there should be no peer review and they tend to be peer reviewed even more carefully than non-open access journals. Just try publishing a paper in PLoS Biology, which I have found to be more stringent than Science. Why is this? Becuase scientists are more willing to commit time to reviewing for such journals because their work benefits humanity rather than some publisher like Gregory.
Another reason Gregory’s claim is unfounded is evidenced by the physics community. They put preprints out for the world to see, which allows for global peer review, rather than peer review by a select list of people. The idea that peer review as it is in current non open access journals is perfect is completely ridiculous. Sometimes you get objective reviewers, but other times you get people that, even if they wished to be objective, would probably have a hard time doing so. This is unavoidable in any peer review system. The more open the publication system and the peer review system is, the more likely it is to avoid outrageous variation in quality.
The Royal Society should be ashamed. They are preventing the distribution of scientific findings and trying to maintain a publishing system that limits the speed of scientific advances and enriches the publishers at the expense of governments and the public.
So I suggest that anyone who knows someone harmed by a doctor who did not know what they were doing, or anyone who wishes for scientific advancement to proceed at a rapid pace, to consider writing to your favorite member of the Royal Society and asking how they feel about this.
To contact the Royal Society directly go here.
I have been unable to come up with email lists of society members but if anyone can find one I will post it.
Jonathan Eisen's Lab 