Into the Great Wide Open

My mother has spent the past 25 years working in the field of association management. What's that, you might ask? Well, if you're a scientist you probably belong to one or more associations such as the American Society for Microbiology (ASM). And it isn't just science; most professional fields have such organizations. There's even the American Society of Association Executives (ASAE), to which the people (such as my mom) who run the other associations belong. Associations, regardless of their topic, tend to fulfill the same functions, one of which is publishing journals. And that leads me into the topic of this posting.

My mother recently sent me a hardcopy of an article from ASAE's "Associations Now" magazine. It's entitled "Into the Great Wide Open" and it consists of an interview of Patrick Brown, one of the co-founders of PLOS. It is really significant that a publication of the ASAE would run such an article, because traditionally, the enemies of open access have not just been commercial publishers like Springer and Elsevier, but also many non-profit associations with publishing divisions. So I was expecting a hostile attack on open access, but actually it's quite a fair interview. In fact, they even printed the following exchange:

One thing that you've mentioned several times and I think is a big concern for the society publishers—especially societies that use income from their journal to subsidize other aspects of what they do for their members—is financial sustainability. What can you tell association publishers to show them that this transition can be sustainable?

There's a bunch of issues there. Number one, a lot of societies that make that claim—I would encourage people to look at their Form 990s. I get great enjoyment out of reading the Form 990s of scientific societies that talk about how important it is to preserve the income from their journals to do all these wonderful things they do, when, very often, the wonderful things they do, taken in aggregate, don't add up to the cost of their chief executive officer.

But let's just take that at face value—that their only motivation is to do good for the world and for science and for their community. One of the questions is, how important are those things that you're trying to fund with profits in your journal, compared to the good that you do for your mission through publishing itself and making access as freely available as possible?

The whole interview is interesting reading. And don't miss the informative sidebar containing a glossary of various Open Access terms. I have to admit I have a hard time remembering what the Berlin Declaration, etc. are, and I imagine most people who aren't professionally involved in the Open Access movement do too.

ISMB 2007 Vienna -- Part II Interesting Talks

I'd just like to comment on some talks that I also found particularly noteworthy or interesting.

Atul Butte gave an interesting talk on nosology. No, that's not the study of noses, but rather the classification of diseases. What Butte has done is cluster gene expression patterns from various diseases. And the results were surprising. For example, he discovered that cervical cancer expression clustered with that of an autoimmune disease andmuscular dystrophy clustered with some forms of heart disease. These connections were unexpected and may lead to better understanding of these diseases. I liked the idea (even though I am not normally a disease person) because I found the idea analogous to the way unexpected phylogenetic relationships can be informative.

Christian von Mering talked about phylogenetic analysis of samples from metagenomics projects. He is interested in this problem because contrary to what was generally believed prior to environmental sequencing, specific microbial species (& higher taxonomic levels) are not found everywhere it would be possible for them to live -- in other words, microbes have meaningful biogeography, just like plants and animals. Von Mering and colleagues have created an interesting pipeline for the interpretation of metagenomic data. Rather than try to analyze each of the millions of reads in detail, his method first identifies standard phylogenetically informative marker genes, then adds them to existing high quality alignments, and uses a custom phylogenetic program to test all possible phylogenetic positions on a reference tree. Both the limitation to markers and the custom phylogenetic component make this pipeline much more efficient than the typical phylogeny based methods.

Haipeng Li talked about a new maximum likelihood method for inferring positive selection and demographic history from chromosome-wide SNP data. His test case was Drosophila melanogaster and according to his model, the European population split off from the African lineage 16,000 years ago and underwent some sort of bottleneck. Current low levels of X-linked diversity (as opposed to the autosome) in the European population suggests a large excess of males in this population. This latter assertion was questioned by several members of the audience as it doesn't seem to be congruent with empirically measured numbers of males in the wild. Still, I find such studies fascinating. I would love to do a similar demographic study using bacteria, but I doubt we have enough data, even for things like E. coli or Bacillus anthracis.

And Alissa Resch, who works at the NCBI (just down the road from JCVI), also gave an interesting talk about positive selection. Odd that I'd have to travel thousands of miles to hear it though. Resch developed a new statistical test for positive selection that uses the rates of synonymous substitution in nearby intronic regions as a background. This allows detection of positive selection even at synonymous sites. She then applied it to orthologous gene pairs in mouse and rat.

ISMB 2007 Vienna, Part I - Keynotes

I realize that I'm a bit late in covering a conference that occurred July 21-25, but I combined the conference with post-conference trips to Prague, Leipzig, and Berlin and have been busy at work since returning to Washington earlier this week.

There doesn't seem to have been much coverage of ISMB 2007 in the blogosphere (I've only found the coverage at Suicyte Notes,
and Fungal Genomes -- a few others had humorous posts about misadventures getting to Vienna, etc., but didn't cover any of the talks -- let me know if I missed any science-related postings).

In this first posting, I'll talk about my impressions of several of the keynote talks that made the most impression on me.

First of all, there was Michael Eisen's talk. Having worked with his brother, Jonathan, for some years, it was fun to finally see (and after the talk, briefly meet) the "other" Eisen. As would be expected from Mike's papers, his keynote largely dealt with the evolution of regulatory sequences in Drosophila. In the midst of this he made an offhand comment which generated both cheers and boos from the audience to the effect that bioinformaticians should stop working on microarray analysis methods "as nobody will be using microarrays in a couple of years". Well, we'll see.

Then, there was John Mattick's talk, which made me angry. Not because I disagree with his assertion that our traditional picture of gene regulation is incomplete, and that non-coding RNA-mediated gene regulation is going to be an important part of our revised picture, but I found his attitude towards non-eukaryotes (and even just non-mammals) annoying. According to John, the reason why "prokaryotes" are "simple" is that their gene regulation is just protein-based, while "higher organisms" require the use RNA as well. He even had graphs where "complexity" (how exactly is that defined objectively, now?) was the y-axis -- humans at the top, of course -- just like the medieval "Great Chain of Being" (minus the superhuman levels). The simple fact is that RNA based regulation isn't just limited to eukaryotes - non-coding RNA has been shown to be important in bacteria and archaea as well. Our picture of gene regulation in all domains of life is changing. Those on the quixotic quest to show that the evolutionary branch leading to humans is somehow "special" will have to look elsewhere.

And then there was Terry Speed's talk, which was one of those "historical" talks that some people see as a waste of time. Maybe it's because I once seriously considered becoming a historian of science, or perhaps it's just that I'm getting old, but I like such talks. And I learned a lot from it. For example, I always assumed that HMMs first entered biology from computer science in the context of sequence analysis/gene finding in the early 1990s, but Terry showed how people in pedigree analysis (including, if I recall from the talk, Eric Lander in his pre-genomics career) brought them into biology earlier.

I will write further on ISMB in subsequent posts.

British accused of releasing badgers in Iraq

This article was from the BBC, and not the Weekly World News, I swear! The article (with the catchy, alliterative title British blamed for Basra badgers) claims, "British forces have denied rumours that they released a plague of ferocious badgers into the Iraqi city of Basra.". Of course, at first glance, this denial seems implausible -- what better way to solve the insane quagmire of Iraq than releasing badgers with the idea that chaos counteracts chaos? On the other hand, apparently the supposed badgers are not the noble Taxidea taxus, but apparently mere "honey badgers" (Mellivora capensis).

Anyone attending ISMB 2007 in Vienna?

Anyone atttending the bioinformatics conference ISMB 2007 (held in Vienna, Austria this year)? I'll be there, along with several fellow alumni of the bioinformatics group from Waterloo -- John Tsang, Tomas Vinar, and Broňa Brejová. Perhaps we could organize a bloggers' dinner or something there if we get a critical mass.

Tagged!

Well, just a few days after I did a "Friday Cat Blogging" (sort of), I find that there's another blogging tradition that I need to follow -- that of a "tagged post". I've been tagged by John Logsdon to follow up on his "eight random facts about yourself" posting and tag eight other bloggers with the same meme.

The rules are:

1. We have to post these rules before we give you the facts.
2. Players start with eight random facts/habits about themselves.
3. People who are tagged need to write their own blog about their eight things and post these rules.
4. At the end of your blog, you need to choose eight people to get tagged and list their names.
5. Don't forget to leave them a comment telling them they're tagged, and to read your blog.

1. I am a native Wisconsinite and my last name is indeed "Badger" (as Wisconsin is known as the 'Badger State', the sports teams of the University of Wisconsin are the 'Badgers' and so many businesses there are named Badger this and Badger that, this was the source of many jokes growing up). Apparently my name has no linguistic connection to the animal or state, though -- 'Badger' is a Scots name and my father's ancestors were Scots-Irish.


2. I don't drive. In the Midwest this fact generally generates gasps of incredulity, here on the East Coast it often generates compliments on the assumption that I've done it out of some noble principle, protesting urban sprawl or pollution or something. But really, given my poor eyesight, reflexes, and sense of direction, it's just better for everyone (including myself) that I stay off the road.


3. My scientific genealogy includes two Nobel Laureates (Rutherford and Chadwick) and well as a winner (Woese) of the Nobel-ish award for evolutionary biologists/ecologists, the Crafoord Prize in Bioscience. Not that that necessarily means anything for my own career -- as stock brokers say, "past performance is no guarantee of future returns".


4. I like languages. Both computer and human. The computer languages I know are Basic, Pascal, C, C++, Smalltalk, Forth, dBASE, Actor, Perl, and Ruby. The human languages I know are English, Esperanto, French, and German, although to be honest, I'm far better at reading than speaking the last two.

5. As if it wasn't obvious from my "Friday Cat Blogging", I'm a cat person. I don't much care for dogs. I find the large ones vaguely threatening, and the small yippy ones are just plain annoying. Plus, they neither clean themselves nor use a litter box. Human infants have similar defects, but I guess inclusive fitness must play some role because all the people I know with infants seem to overlook this.


6. I seem to have an obsession about the former East Germany. I own 27 books about East Germany and listen to albums like "Die Partei hat immer recht" and collections of Oktoberklub songs.



7. My favorite authors are John Crowley and A.S. Byatt. Besides the fact that they both write well, they both seem to be attracted to the Elizabethan and Victorian eras. These eras also attract me because they were also transitional times in the history of science -- the dawn of modern science in the early 1600s and the transition of science from hobby of the independently wealthy to practical career choice in the late 1800s.



8. I like my coffee black, and my art nerdy (Escher) or atmospheric (Hopper).






I tag:
Jacques Ravel
Neil Saunders
Eva
Steve Salzberg
Mike Hu
Naomi Ward (yes, your blog has to rise again!)
John Tsang (You need a blog!)
Marei Dose (ditto)

My 15 minutes (or 30 seconds) of fame

I've worked with people like Carl Woese and Jonathan Eisen who routinely get interviewed by the media, but this is the first time that I've been in the spotlight. In May, Chris Condayan interviewed me along with several other bloggers attending the ASM 2007 meeting in Toronto, and he's edited them into an edition of his MicrobeWorld series dealing with microbiologists who blog.

Besides me, the featured bloggers are John Logsdon, "Yersinia", Tara Smith, Elio Schaechter, and Larry Moran.

Tara seems to think that she is too "animated", but I think she is undervaluing the value of animation. After all, this week, the animated Ratatouille beat out the latest "Die Hard" movie....

I could complain about my segment too, but it's probably pretty representative of me (not that I tend to talk into phones without calling someone first...)