Eisen Lab Blog

SciFoo Camp, the prequel

Just got back from a mind and life altering experience. I was a participant in the first scifoo camp, a shindig put together by O’Reilly and Nature and held at the mythological Googleplex campus in Mountain View. I was first invited to this scifoo camp in an email in June from Tim O’Reilly himself and Timo Hannay the director of Web publishing for Nature.

John,

We’d like to invite you to join us the weekend of August 11-13 for
Science Foo* Camp, a free, invitation-only gathering produced by
Nature and O’Reilly Media, and hosted by Google at the Googleplex in
Mountain View, CA. (See the end of this message for more about Nature
and O’Reilly). ……

I confess, I thought this was a mistake or some spoof by a friend since they addresed the email “Dear John” I never use John, always Jonathan. The thing was, the letter seemed so realistic, with details on the hotel and other people who were involved, etc. So I did what any respectible other person would have done. I googled the crap out of all of the people’s names and other details in the letter.

For example I had no frigging idea what this “foo camp” concept was. So I found some old stories about a foo camp last year, where the people actually camped at the O’Reilly headquarters in N. California. This sounded cool to me but also a little wacky since it seemed from reading the few blogs and stories about this that the event had no real schedule and that people sort of showed up and just gave presentations without a detailed plan. Of course, most conferences I go to have detailed schedules and I hate them since the best part about conferences is the talking at the coffee breaks or hanging out in pubs or doing something other than going to canned talks. In particular, the quotes they had at the end of the invitation email made me interested in going:

“The controlled chaos and the random encounters with very interesting people is just what I needed. I learned more than I expected, and got infected with new ideas. Who can ask for more?”

“Big kudos for having the courage to try a self-organizing event and for having succeeded WAY beyond belief!…Foo Camp was truly epic.”

Though I was still not sure if this whole foo camp thing was real or not (more elaborate scams have been pulled on me before) the upside was clearly high – a geek gathering at Google headquarters, just a 1.5 hour drive from Davis where I now live. So I wrote back saying I would come and then waited to learn more …

Human Evolution and Neanderthals

Well, I suppose everyone should have seen this coming. An announcement has been made of plans to sequence the genome of a Neanderthal. The plan is to take DNA extracted from a Neanderthal fossil, and sequence it using a relatively new method from a company known as 454 Life Sciences.

I am torn about this project. Yes, it is cool to read DNA sequence from an extinct species, especially one that has not been around for some time and one of direct relevance to understanding human evolution. On the other hand, I would personally find it much more interesting to try and sequence an ancient Homo sapiens first. This is because the comparison of the Neanderthal to modern humans may not be the right comparison. It would be better to first compare an ancient Homo sapiens sample to modern humans, maybe with both being done with the same methods to be used in the Neanderthal study. This would be for two reasons. First, we do not really know how well the method(s) they are using work. And second, if the methods work well, it is possible that some of the differences they observe would actually be due to degradation or damage to the DNA sample. Therefore, if they simultaneously did work on an ancient Homo sapiens they might better be able to calculate which differences are do to real differences in the Neanderthal DNA and which are due to damage to the sample.

Assuming they do something like this and they are able to detect differences in the Neanderthal genome. What then? In the end, the major area of interest will be population genetic analyses trying to figure out how long Homo sapiens and Neanderthals were separated for and whether there was any interbreeding. To figure this out, they will need more Neanderthal samples and ancient human samples. Nevertheless, it is always good to do something that brings attention to the public for scientific research.

Open Access Rant: How Does Your Doctor Learn About the Newest Medical Findings??

Everybody would like to find a doctor who is knowledgable about the latest developments in medicine. Whether these developments relate to new treatments, or new methods of diagnosis, or treatments that are dangerous or do not work, we want our doctors to know this information. How do doctors find out about these things?

Well, there are many sources of this information, but one we hear a lot about these days is a little disconcerting. It turns out that a lot of doctors get the latest information from drug company reps who stop by the office and leave imformation pamphlets or who talk up their companies latest products. This could be OK, except for the fact that many of the drug company reps either purposefully provide misleading information, or in fact do not actually know what is good or bad information.

One reason this is such a big problem is that, like everyone else these days, doctors are really busy and overwhelmed. So they sometimes do not have any time to read the actual medical studies that might be relevant to what the drug company reps are saying. But that is a bit lame of an excuse, since it is their job to know these things. Thus I really think they should read more of the medical literature and not just drug company propaganda.

But herein is one of the biggest problems in modern medicine. Even if you have a really hard working doctor who is willing to read the latest papers, they may not be able to. This is because even though most of the medical studies were paid for by the government in some way, they are not freely available for the doctors to read, because they are published in journals that charge exceptionally high prices for subscriptions. Doctors in large institutions probably have good access to this information. But doctors in small groups may not. Imagine if congress passed laws but lawyers were not allowed to read them without paying a fee to someone. The system for medical literature is really absurd.

I got thinking about this when re-reading Lance Armstrong’s autobiography “It’s Not about the Bike.” In the book, Armstrong describes how when he had testicular cancer he had a friend who was a doctor bring him the latest studies on this type of cancer and he read all of them. Well, this only was possible because his friend must have had access to all the publications through a university or very large medical group. Wouldn’t it have been better if Armstrong could have just gotten the studies himself, given that most were paid for by the US Government in the first place? Well, if people doing medical research published their finding in Open Access journals, then anyone could read the articles, from doctors, to patients, to family members, to journalists. We would all benefit if this was done.

Ancient DNA

Studies of “ancient DNA” are becoming all the rage these days in various circles. The term “ancient DNA” refers to DNA isolated from very old samples, lets say at least 1000 years old.

Many years ago, it was considered almost taboo among biologists to say you worked on ancient DNA. It was the cold fusion of biology. This was becuase a variety of esteemed scientists basically said it was impossible for one to study ancient DNA since DNA was not stable enough to survive for so long a period of time. It is clear now that these people were pontificating without any real evidence, but at the time, they carried a lot of weight.

At first, the papers published on ancient DNA seemed to support the naysayers. Many many early claims were found to be flawed. But as researchers learned the problems, they also learned how to circumvent them. They learned how to keep samples very clean and avoid the possibility of contamintions. And they learned how to help deal with fragile DNA (it is sort of the chemical equivalent of dealing with a crumbling manuscript of days past).

And most recently, ancient DNA has gotten a new kick in the pants. This comes from applications of methods originally designed for genome sequencing projects (like the human genome project) to the field of ancient DNA. The genome sequencing methods allow researchers to characterize in more depth samples that supposedly contain ancient DNA. The deeper sampling allows more statistical approaches to analyzing the data and this in turn allows one to test a variety of possible explanations for what one observed (e.g., one can do a test that distinguiushes contamination from other possibilities).

And one can tell that ancient DNA is really a hot topic again as it is getting covered in all sorts of popular mags (see the recent article in Wired magazine for example here).

What can one do by studying ancient DNA? Well, basically the same things that anthropologists and paleontologists and archaeologists and evolutionary biologists have been trying to do by examining fossils. Only now, by looking at the DNA contained within fossils, one can both test (i.e., confirm, deny) inferences made from other information OR one can frequently make inferences that were impossible previously (the article in Wired is about Eddy Rubin’s studies of Neanderthal DNA that to them suggests that many anthropology-based claims about human-Neanderthal interbreeeding are wrong). Note – for full disclosure (which someone nagged on my previously for not doing), I am just starting to work with Eddy Rubin on some ancient DNA analyses, but I had nothing to do with the Neanderthal work described in the article.

The real question I think for ancient DNA studies is now no longer can they work. The question is – how far back can they go? Most likely, as one goes further and further back in time, the DNA will be in worse and worse shape. And thus what one can learn from looking at it will decrease significantly. But here is where the genome sequencing methods come into play. If one can get a large enough sample size, it may not matter so much that the DNA is in bad shape. For example, if one had one blurry picture of someones face, you would not know what they looked like. But if you had 10000 blurry pictures of the same face, you could reconstruct it with high accuracy by combining the information from the different pictures.

So – stay tuned – ancient DNA studies may be turning up some interesting tidbits in the near future. We are not likely to get to Jurassic Park territory soon – but it is not longer as absurd as it once seemed to many.

John McCain on Evolution

Just got very interested in reports of a Q&A session John McCain had a the Aspen Music Festival, as reported in the Aspen Times here. He was apparently, his normal self. Most interesting to me is his quote in response to a question about evolution

“I think Americans should be exposed to every point of view,” he said. “I happen to believe in evolution. … I respect those who think the world was created in seven days. Should it be taught as a science class? Probably not.”

It’s too bad more of the Republican party is not like him on this issue. I would bet he really cannot stand Bush but he has been trying to be a little more policial recently and thus has not said anything too critical. But it is good to know that at least one (and maybe only one) of the possible Republican candidates for president is not as anti-science as the core of the party seems to be these days.

Interesting interview with David Botstein

There is an interesting interview of David Botstein in PLoS Genetics here.

Botstein has been at the heart of many key discoveries and innovations in genetics and genomics and he discusses some of these in this interview. In addition he discusses his initiative at Princeton to try a new way of teaching science to undergraduates. It is not the most comprehensive interview, but it still has some juicy tidbits. In particular, the discussion of his 1980 paper on genetic mapping has some things I have not read elsewhere.

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.

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.