Rankings of "Open Access"-journals: PLoS ONE rocks!

As several of you might know, I have been complaining about how conservative attitudes some of my colleagues have towards "Open Acess"-publishing in general, and towards PLoS ONE in particular. This is quite frustrating, as me and several of my colleagues in the Editorial Board are doing our best to promote this new "revolutionary" journal, with the hope that it will in the long run change the entire publication landscape - to the benefit of both scientists, readers, taxpayers and the general public.

There are two classical objections against PLoS ONE by ecologists and evolutionary biologists. First, some of them are afraid to publish in PLoS ONE since it is not yet listed in Thomson's databases (ISI), such as "Web of Science". This is the database from which Impact Factors (IF:s) are calculated, and Thomson actually has a monopoly (!) on how to calculate IF:s. Since Thomson has up until now refused to list PLoS ONE in their data-base, some of my scientific colleagues are afraid that work published in that journal will be "forgotten" or not appreciated by the scientific community.

This objection partly shows a lack of knowledge and the misunderstanding about citation data-bases as reflecting some kind of "objective truth". In reality these data-bases are run by commercial companies with their own agendas. ISI is certainly not the only data-base, and it is one of the slowest to list new publications and it does only cover a small minority of all scientific journals. Scopus, for instance, covers more journals and so does probably also Google Scholar and PubMed. Thus, there is luckily severe competition among different data-bases, and hopefully ISI will soon become outcompeted and run out of business by better and faster alternatives with better litterature coverage. ISI is for the scientific world what Microsoft is for the computer world: a mean big company that we should all hate!

The second objection is that PLoS ONE has a publication policy that aims for "technical quality", rather than arbitrary and subjective criteria for acceptance of papers, such as "novelty". In that respect, PLoS ONE differs significantly from all other journals, including Science, Nature, PNAS and PLoS Biology. The philosophy of PLoS ONE is that it is the future scientific readership that should judge whether a paper is "significant" or not, not a few subjective referees or journal editors. The scientific process does not end with the publication of a paper, it starts. This is when a paper is read, discussed and (hopefully) gets cited and thus "accepted" as being important by other scientists.

Some researchers consider this as a weakness of PLoS ONE, and fears that it will become a "dumping ground" for poor quality papers that have not been published elsewhere. I, and many others, on the contrary view this as as strength of PLoS ONE, and I can honestly not say that I think that PLoS ONE has become such a vehicle for bad papers that some feared that it would become. But I am of course biased in my views, since I am involved in the journal, and it is up to others to decide about this.

Given the inherent problems with impact factors and how they are increasingly becoming "corrupt" and the arbitrary parts of traditional publication (biased referees, commercial data-bases, unfair editors etc.), I think we probably all agree that there is a need for newer ranking criteria of journals. These criteria could be based on things like number of downloads of articles, number of citations, more or less informal "ranking lists" by the scientific community, blog coverage, coverage in media etc. None of these rankings are likely to be perfect or reflect the final "truth", but they would provide a nice complement to the traditional measures, such as impact factors of journals.

The blogger "The Open Source Paleontologist" have done some such ranking lists of OA-journals, and you can read about them here, here and here. Although these ranking lists have their limitations and only deal with the paleontological science community, they are nevertheless interesting and revealing. I predict that we will see many more of these lists in the future, and I bet that the traditional "impact factor" hysteria, will soon go away (to the benefit of all science).

Not surprisingly, and pleasingly to me, PLoS ONE does very well in these ranking lists: it is always in the top 15 list of journals, and often among the top 5. Way to go, PLoS ONE!!! I am delighted. And the young scientists among you who reads this should of course not be afraid of publishing in PLoS ONE in the future, it will benefit your careers.

Bill Maher on Evolution

OK, I've told some of you that Bill Maher is an often funny, politically oriented comedian. Here is a You Tube video of five minutes or so of his segment "New Rules", from last weeks show (when people were freaking about about swine flu). The last three minutes or so is a diatribe about evolution, so should be of some interest to our group.

Click here to see it.

PS: He's not exactly politically correct.

BBC - The Darwin Debate (48mins)

Just wanted to post a link to a televised debate that took place at the Linnean society a few years back.

It was not about evolutionary theory vs id or anything, but rather a debate about how our evolutionary history has shaped us.

It reminded me of a debate Erik, Fabrice and I had a few years back at a mongolian restaurant in Copenhagen. After a few glasses of wine we started debating the role of natural selection in modern society, and asked are we still evolving? The TV debate may appear slightly better structured, but I think we can all agree that 3 drunken men spitting half chewed chicken and beef at each other is a far classier arena than some stuffy room in London. 

Part 1

Part 2

Part 3

Part 4

Part 5

Melvyn Bragg and a panel of international experts debate what Darwin’s theory of evolution tells us about ourselves and human society. Filmed at the Linnean Society - the world’s oldest biological society - in Piccadilly, London.

Steven Pinker , professor of psychology Massachusetts Institute of Technology
A prominent Canadian-born American experimental psychologist, cognitive scientist, and popular science writer known for his spirited and wide-ranging advocacy of evolutionary psychology and the computational theory of mind.

Meredith Small , Cornell professor of anthropology
A primatologist by training and professor of anthropology by vocation, Small has spent untold hours watching monkeys interact in captivity and in the wild. So if you’re looking for a few clues about why people do some of the strange things we do, she’s happy to offer a few million years of evolutionary perspective

Steve Jones , biologist and a professor of genetics and head of the biology department at University College London
He is one of the best known contemporary popular writers on evolution. His popular writing shows a wry, sometimes rather dark, sense of humour. In 1996 his writing won him the Royal Society Michael Faraday prize “for his numerous, wide ranging contributions to the public understanding of science in areas such as human evolution and variation, race, sex, inherited disease and genetic manipulation through his many broadcasts on radio and television, his lectures, popular science books, and his regular science column in The Daily Telegraph and contributions to other newspaper media

Sir Jonathan Miller, CBE is a British theatre and opera director, neurologist, author, television presenter, humorist and sculptor
In 2004, he wrote and presented a series on atheism, Atheism: A Rough History of Disbelief (on-screen title; but more commonly referred to as Jonathan Miller’s Brief History of Disbelief) for BBC Four TV, exploring the roots of his own atheism and investigating the history of atheism in the world. Individual conversations, debates and discussions for the series that could not be included, due to time constraints, were individually aired in a six-part series entitled The Atheism Tapes.

Wednesday: Dragonfly excursion!

For those of you who are interested, there is a possibility to participate in a dragonfly excursion on Wednesday, instead of our regular lab-meeting. Because of nice weather, I think we should skip lab-meetings from now, and instead spend time in the field (or lab, if we need to).

However, those of you who can are welcome at Stensoffa Ecological Field Station at 09.00 on Wednesday. If you go by your own car, you can decide to go back when ever you want (e. g. after a few hours), but I will probably spend more or less the whole day in the field visiting my census plots for the Official Dragonfly Census in Skåne that has just taken off and will run for the next five years. This is an excellent opportunity for those of you who wish to learn how to identify dragonflies. Everybody are welcome to book one or several census plots (5 x 5 km), which can be done by contacting these persons, and no special expertise is needed.

In case you cannot arrange transportation, there is also the opportunity to take the bus to Dalby and go with me, or send me an e-mail (erik. svensson@zooekol.lu.se).

Quizz of the week: Which species of odonate is shown above?

More reflections about quantiative genetics from Norway

I am currently in Oslo (Norway) at "Centre for Ecological Synthesis and Evolutinary Synthesis" (CEES) where I have been visiting theoretical evolutionary biologist Thomas F. Hansen. Also visiting here are evolutionary geneticists David Houle and Gunter P. Wagner. So it has been an interesting group of people to discuss, as you understand.

I talked to David Houle about the paradox that the molecular markers explain only a tiny fraction of total genetic variation in human height (see my previous bloggpost), whereas classical quantitative genetic studies (based on covariances between relatives) indicate that the real amount of genetic variation is substantially higher (between 80 and 90 %). David Houle interpreted this discrepancy very much as I did: it provides support for the so-called "infinitisemal model" in quantitative genetics, as formulated (among others) by Russel Lande.

In other words, many loci, perhaps the vast majority of all coding genes, influence human height, but each has a very small contribution in terms of percentages. This is not surprising as many independent genetic factors are likely to influence "condition" or growth, each giving a very small contribution. This makes the prospects for molecular genetic association studies quite bleach, since this approach can only (because of statistical power issues) only detect those few factors that have a relatively large effect. We are left with a situation where quantitative genetic approaches "capture" more of the existing variation than do molecular association studies that fail to detect all these small genetic factors.

This also means that we should perhaps be aware of the fact that many beatiful genetic association studies and studies of candidate genes such as the melanocortin receptor (MC1R) studied by Hopi Hoekstra's laboratory might be untypical and not representative for the vast majority of quantitative traits governed by many different genes (height being one of them). This is not surprising to me, however, it also shows that there is a lot of interesting work remaining to be done and a lot of theoretical and empirical challenges ahead.

Why molecular genetics will not replace quantiative genetics

Today, at our lab-meeting, I briefly mentioned an interesting bloggpost by Juha Merilä at his research group's blogg, that I would like to discuss a bit. The reason is that it is not only interesting from the viewopoint of quantitative genetics vs. molecular genetics per se, but also of its wider implications in terms of the value of reductionism in science vs. emergent properties of biological systems. What do I mean by this?

Emergent properties of systems simply means that "the whole is more than the sum of the parts". This is nothing metaphysical, but it means that one might not fully understand a system simply by de-composing it in to separate parts, because the parts often interact with each other. One actually needs to understand how the parts work together, and it is here where I see the value of quantitative genetics. Quantitative genetics is focussed on the "units" (=traits) that we as evolutionary biologists are most interested in and which we would like to understand how they evolve. It focuses on these higher-level units, while at the same time ignoring the details (=the particular single genes governing the traits). This might be perceived as a weakness of quantiative genetics, but others would argue that it is a strength. I will not dwell in to this here.

Although none of us would deny that the traits are governed by many different genes, as well as the environment of course, we do still not fully understand the genetic basis of the vast majority of traits, in spite of the explosion of molecular information and the presence of fully-sequenced genomes. And if you ask me, I am not sure we will necessarily get the answers to these fundamental questions in biology simply by sequencing even more, or by hoping that new molecular techniques will solve all the remaining questions. In short: the whole will always be more than the sum of the parts, and quantitative genetics is still live and kicking. At least in some circles.

Back to Juha's bloggpost. An interesting "paradox" is that quantitative genetic studies of human height indicate that heritability of height is very high: between 80 and 90 %. In other words, height is a highly heritable trait that can rapidly evolve by natural or sexual selection. One would therefore think that height would be an excellent trait to focus on if we wish to find candidate genes or do genome-wide association studies to identify the precise genes. Such a study has indeed been performed, but as the blogg "Genetic Future" rather brutally points out, these studies have been "a resounding disappointment".

Some more specific examples of these disappointing results:

The first genome-wide association for height, published in September last year, examined 4,921 individuals and found a single significant and replicable variant associated with height (in the HMGA2 gene) that explained a meagre 0.3% of the variation in the general population. The second such scan, published in January this year, examined 6,669 individuals. This study confirmed the HMGA2 finding and identified one further significant signal, this time near the GDF5 and UQCC genes, which again explained less than 0.5% of the total variation. I saw an abstract at the American Society of Human Genetics meeting last year (as yet unpublished, as far as I can tell) in which a genome scan was reported for 10,737 individuals, which pulled out a total of 8 associated variants which together explain just 3% of the variance in height.

To summarise these results: to date genome-wide scans for height, even extremely well-powered ones with more than 10,000 participants, have identified variants responsible for less than 5% of the variation in this trait - despite height being a trait that is largely genetically determined and varies substantially between humans. What's going on?

Well, I certainly do not know the answer, and neither does Juha or the blogger "Genetic Future". But we can safely conclude that a major fraction of the genetic variation in height is "missing" and not picked up in these genome-wide association studies and by the molecular markers. Hopefully, future studies can improve resolution and increase these depressingly low percentages somewhat. However, these low percentages should be somewhat worrying, at least for those who thought that it would be easy to study the molecular basis of this trait. Especially given that we already know that there is ample genetic variation for human height from the quantitative genetic studies.

It seems to me that either the heritability estimates have been severely inflated (e. g. by maternal effects), or the molecular markers do not fully capture all the genetic variation in human height. Although it is definitely possible that heritability is somewhat overestimated, I doubt that heritability will only be a few percent, as the molecular marker studies indicate. Most morphological traits have heritabilities much higher than a few percent, so it seems a safe conclusion that the molecular markers miss a large amount of the genetic variation that is actually present. Therefore, it seems as if the association studies are missing the big picture. The results from these genome-wide association studies must in any case be a big dissappointment, given the large research resources that have been put in to them and the HUGE sample sizes in these studies.

The EGRU-blogg cites a recent update about this work in Nature, and (musingly?) concludes:

"Read the thought provoking ‘news feature’ from Nature by Brend Maher about the statue puzzle. It might even give some (quantum of?) solace for those sticking with their parent-offspring regressions and tedious experiments while the others in their spotless labcoats are drowning in their high throughput data."

Juha Merilä also comments on another interesting bloggpost with the title "Do we still need quantiative genetics in the 21st Century":

"It seems that people were a bit optimistic about the utility of the new technologies in solving old problems. This has also lead to situation where students have jumped into the fancy wagon of genomics, and left quantitative genetics with some interesting (and unfortunate) consequences of which you can read from here:

http://www3.interscience.wiley.com/cgi-bin/fulltext/119408495/HTMLSTART

Actually, all the 2008 volumes of the Journal of Animal Breeding and genetics feature nice Editorials each which touch some general issues interesting also for Evolutionary Biologists. Go and have a look:

http://www3.interscience.wiley.com/journal/118521919/issueyear?year=2008"

I, myself, is like Juha a big fan of quantitative genetics, and I do of course agree with him and his colleagues that this is a useful tool that is unlikely to be replaced by molecular genetics, neither in the short- nor in the long-term. As a matter of fact, molecular genetics might have its greatest utility as a complement to quantitative genetic approaches, e. g. in the combination of QTL-approaches and estimations of quantitative genetic parameters such as to understand the "anatomy" of genetic correlations. Are genetic correlations mainly a result of linkage disequilibrium or pleiotropy, is one such interesting question that can be adressed by the combination of quantitative genetics and QTL-approaches.

And it might of course always be good to keep in mind that one should be critical of scientific bandwagons and premature claims that new techniques will solve all problems. Finally, do not forget the emergent properties and that the whole is always more than the sum of the parts. Reductionism can be taken too far, particularly in biology.

Dragonfly season has started!

This weekend I spent a few hours in the field and the first odonates have already emerged! It appears as it will be an as early season this year as last year, and we probably need to start to catch Ischnura elegans soon. Hopefully, the Calopteryx-season will still not start until early June. This means that lab-meeting on Wednesday will be at the Ecology Building (as planned), when we will see the second part of "Life in Cold Blood", although the week after is an open issue (at least to me). Depending on weather, we might do a joint field trip, although I want to keep this day open for other possibilities, depending on weather.

For this week, I suggest that we skip the TREE-article I suggested last week, as I feel it will be a bit too much with both that article (a rather heavy one!) and the movie. I hope nobody objects to this. Time and place as usual: "Darwin" at 10.15 (Wednesday 6 May). Could Shawn bring popcorn or somebody else this week?

Quizz: Which species of dragonfly is depicted above? It is a very common species that is one of the earliest fliers in the season.