Friday, June 30, 2006

Science, Innocence and the Tour de France

This years Tour is turning out to be a total mess - due the what is being called the latest doping scandal. For some good coverage of this see Velonews. In summary, a whole bunch of riders names have been associated with a Spanish doctor who himself is implicated in doping. Apparently, the evidence is strong that these riders did something untoward. But from my reading of the news stories I am not so sure. What they are reporting on is finding log books with various riders names (or, actually, their names in some code) and notes as to what illegal doping activities they were doing.

And this has led to these riders basically being kicked out of the Tour. The list includes many of the top current riders, including Ullrich, Basso, Mancebo and others. Yes, I am sure a lot of professional cyclist dope. What I do not get is the almost depserate rush to kick these guys out when all that is being publicized is a bunch of innuendo. Apparently, the concept of innocent until provde guilty does not apply here. In the Olympics, they do not kick someone out for this type of thing - they kick you out if you fail a test. In other sports, testing is also the key. Yes, testing is imperfect. But you know a few years ago it was reported that Hitler's diary was found. And then Jesus' brother's grave. And so on. If you accept that people are willing to inject someone else's blood into themselves to gain a few seconds in a race, why would you not believe that someone might falsify some doping recrods just to screw with the Tour. I think they should be a litle more cautious in responding to the latest doping accusations in order to avoid sweeping up the innocent along with the cheaters.

Powerpoint slides from Nature and others do not give full credit to the sources of images

Well, I browsed around the Nature web site and did some searches for terms like "Reprinted with permission" and then looked at how they handled Figures that were reprinted from other places. I found some additional examples where the Figure image did not seem to do a complete job of crediting the source of the material. But without a doubt the most disturbing thing I found is that you can download powerpoint slides of the figures and all the ones I looked at only had "Copyright Nature" or something like that and no information crediting the actual source of the material. This is basically because they do not include the Figure legends on the ppt slides. I am not sure if technically they are allowed to do this in some cases (my gut feeling is there is something wrong with what they are doing) but it could not be that hard to include the Figure legend on the ppt slides, even in small font. They certainly are able to inlcude their "Copyright Nature" in large font. But even if technically they are allowed to do this, they should not.

Some examples:
  • Download the powerpoint slide of Figure 1 or Figure 4 from a paper on Listeria in Nature Reviews Microbiology if you have access to it here.
  • Or look at Figure 1 of a paper in Nature Reviews Genetics here.
I guess I could load up here on other examples, but it might be more interesting for people to find their own.

Here is how I found these.
  1. Go to the Nature Advanced Search page here
  2. Search for terms like "Reproduced with permission" --- I used the "The exact phrase" option.
  3. Browse away
I assume that this is not a purposeful thing they do, but it certainly seems pervasive there.
Unfortunately, it seems common in other places. For example, PNAS provides powerpoint slides but does not include Figure legends with them either. Look here. So - not trying to single out Nature here but that was where I looked first. It seems that many publishers are trying to hard to provide material (e.g., powerpoint slides) without being careful enough attributing the original sources.

Fruit flies going into space

The plan is to send some fruit flies into space on the next shuttle mission and to compare them to some flies at home in terms of how their immune systems respond to the trip into space.
Not sure whether this is completely novel or not, but good to see that NASA is at least trying to still support scientific research. See the press release here.

There have been some serious controversies as of late at NASA about whether it truly is suportive of scientific research or whether it (like many other agencies) is succumbing to the anti-science rhetoric and attitude of some of the higher ups in the Bush administration.

For example, see the NYTime Article from February about how the NASA admiistrator had to make an announcment calling for scientific openness in the agency.

Wednesday, June 28, 2006

Nature Journal Misappropriates Copyright of Open Access Material - though see comments ...

Recently, Nature (a science journal) ran a so-called news article presenting their analysis of the finances of one of their competitors. Already I am sure one can imagine some conflicts of interest that might lead them to be really careful with such a publication. But apparently they are not as it seems to contain many flaws (see here).

Nature in this instance appears more desperate than objective, since the competitor they are criticizing is a start up society that published "Open Access" journals. Open Access means many things but one of them is that the articles are free to all. This is bad for journals like Nature that make a killing by charging people to read the results of research funded primarily by the government.

Interestingly, a little browsing around Nature's web sites shows that not only are they apparently in a tizzy about Open Access publications, but they even have the gall to try and pretend that material published by others was generated by them.

For example, we recently published a paper on analysis of the genomes of some interesting bacteria. We published this in a PLoS Journal here.

Now take a look at this figure from the paper here.

Nature then published an article in Nature Reviews Microbiology (see here). The article is fine and even includes the figure linked above taken directly from our paper. This is OK in the world of Open Access if they attribute the origin of the figure correctly. In the article they sort of attribute it but do not do a robust job. And even more deceptively, they put "Copyright Nature" onto the Figure even though this is completely invalid. I have downloaded the figure and provide it here for those who do not have access to Nature.


I do this with no fear of the copyright gods since after all, they do not in fact have Copyrights to it.

Even worse, I saw that one can download a powerpoint slide of this figure. I did this and found that they kept the Copyright Nature part but left out the attribution so it looks like the figure is from Nature.

To me, this is plagiarism, plain and simple. And lame too.

Monday, June 26, 2006

Open Access Journals Allow one to Publish Complete Scientific Stories

I am positing here some of my opinions about Open Access journals.

One reason to publish in Open Access journals is that they generally allow one to publish complete scientific stories, rather than restricting the length of articles simply to make the publishers more money. For example, here are some comments I made in a online discussion about a lame article in the journal Nature that basically invented problems occurring with some Open Access journals:

As a follow up to Deltef's comments. PLoS journals and many other Open Access journals allow you to publish complete stories because most do not have arbitrary restrictions on the lengths of papers. I have been involved in dozens of publications associated with genome sequences, many in Nature and Science and now many in PLoS journals. For papers in Nature or Science we almost always had to make the stories incomplete because of page restrictions. For PLoS journals, we could tell the whole story. Note - PLoS does not encourage run on papers - they just allow one to include the material that is scientifically relevant.
Compare and contrast our genome papers in PLoS journals:
Sharpshooter symbionts
Life in hot carbon monoxide
Wolbachia
With those published in Science or Nature (I only publish in Open Access journals if I have a choice but for these I was a middle middle author):
Dehalococcoides
Geobacter
Silicibacter
Based on this difference alone I prefer to publish in PLoS journals every time. Note that this may in fact make it more expensive for PLoS to publish those papers and thus I am more than willing to pay for that cost.

Monday, June 12, 2006

PLoS One

Well, PLoS (The Public Library of Science) has announced a new publishing venture called PLoS One.

For those who do not know, PLoS was started a few years ago by a group of scientists (incuding my brother) with the goal of opening up access to scientific literature. For non scientists it may be surprising to find out that scientific and medical research is usually published in journals which are very expensive to purchase. Thus though the research is supposed to be for the benefit of humaninty, it turns out that one of the primary benefits goes to a few companies and societies that publish the journals. Amazingly, even though the journals frequently do little other than repackage papers written by scientists, they not only make enormous amounts of money off of this, they somehow get the copyright to the papers. In general, these journals are a massive roadblock to scientific and medical discovery.

PLoS started a few journals a few years ago to try and provide alternatives to the standard model. These journals are "Open Access" and thus much better for the world. What PLoS has done better than others attempting to make scientific literature open acces is to show that one can publish a very high quality journal that is still free to all (e.g., PLoS Biology).

Now PLoS has announced a completely new way to publish scientific literature. Called PLoS One this seems like a strong attemp to bring scientific publishing into the 21st century. Among the "features" they say will be there are much more rapid publication, publication of all science (with the only criteria being that it is validated by peer review - no restrictions will be made to force the publication to be radically novel) and development of an online community around the publications.

Stay tuned --- we will have to see how it works out but the initial impression I have is that it sounds quite nice.

Sunday, June 11, 2006

God, Evolution, and Science

Apparently Francis Collins has a new book coming out on how he balances his religious beliefs with his work as a scientist.

Well, that is all fine and dandy and I personally view science and religion as separately areas for the most part. However, if you look at some of Collins' interviews you realize that in fact his science appears to be compromised by his strict (i.e., fundamentalist) interpretation of certain aspects of religious belief.

For example see his PBS interview. In this he says that "Moral Law" comes from some higher power and gives the following example:

"If I'm walking down the riverbank, and a man is drowning, even if I don't know how to swim very well, I feel this urge that the right thing to do is to try to save that person. Evolution would tell me exactly the opposite: preserve your DNA. Who cares about the guy who's drowning? He's one of the weaker ones, let him go. It's your DNA that needs to survive. And yet that's not what's written within me."

What an absolute load of crap. What he is saying here is that since someone might do something that is not in their own direct self interest it cannot therefore have evolved. Apparently, Collins has either never taken an evolution course or did not pay attention in one if he did. Does he suggest that soldier ants are following some moral code to sacrifice themselves for the colony? What about skin cells? Or birds that warn of coming predators? Basically, Collins is using his position as the head of NHGRI to foment anti-evolutionary points of view. It is one thing to express an opinion that one has faith and that one follows ones faith rather than following science. But instead Collins repeatedly says things that are hostile to the field of evolutionary biology. He may not intend it, but that is the way it is. It is a shame too as NHGRI (the intitute he is the head of) has done some good things for the world. His blather about evolution however, is not one of them.

This is not to say the evolution and religion are not compatible, but the way to make them compatible is NOT to mislead people about what the science of evolutionary biology reveals. It's funny in a way - Collins claims he believes in "theistic evolution" or the idea that God created the natural laws, including those of evolutionary biology, and that those laws are how the hand of God works. But then I do not understand why it is OK to ignore those laws when convenient.

Saturday, June 10, 2006

Glassy winged sharpshooter symbionts

ResearchBlogging.org

For those interested in wine production, or symbioses, you maybe interested in a paper we published a few days ago. It was on a study we did of bacterial symbionts of an insect known as the glassy winged sharpshooter. This insect is a vector for Pierce's Disease in grapes - a nasty disease that if it is found in a vineyard might lead to the vineyard being sacrificed for the greater good.

Anyway - we did a study of bacteria that live inside the insect that make nutrients for their insect host and without whcih the insect will die. An understanding of these symbionts will hopefully lead to better methods to control the spread of this invasive insect.

Our paper can be found in PLoS Biology here.
A synopsis of our article is here.
An article in Science Now about our study is here
An article in the Central Valley Business Times is here.
Nature highlighted it in their "Research highlights" section
And ASM article about this here
Link to our collaborator's lab (Nancy Moran)

Some new links about our paper

For more information about the sharpshooter and Pierce's Disease seee the following links
  • Pierce's Disease Control Program for State of California: here
  • Glassy winged sharpshooter media information here
  • Introduction to Pierce's Disease here



Wu, D., Daugherty, S., Van Aken, S., Pai, G., Watkins, K., Khouri, H., Tallon, L., Zaborsky, J., Dunbar, H., Tran, P., Moran, N., & Eisen, J. (2006). Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters PLoS Biology, 4 (6) DOI: 10.1371/journal.pbio.0040188

Moving to Davis

Well, it has been a while. Things got a little out of hand in life. I am now a Professor at U. C. Davis, in their new Genome Center.

Prior to Davis, I was at The Institute for Genomic Research (TIGR), an incredible place that pioneered genome squencing and analysis. I was a faculty there from 1998-2006 and felt like a kid in a candy shop pretty much the whole time there.