Doubts about blogging for scientists.

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It has been about 5 weeks now since I began this experiment to use a blog as a mechanism for public outreach. I have had some good experiences — seeing some excellent posts, learning a lot, making new friends and joining networks. There have also been some lively debates that I think showcase the utility of the medium for what really are high level scientific conversations.

There has also been a dark side, unfortunately. Sadly, I am not describing spam or anti-science, but how I have been treated by some of my fellow science blog participants. In particular, I point to the recent discussion about the Liu and Ochman flagellum article. A brief recount — the paper was published in the journal PNAS, several bloggers commented on it, and then Nick Matzke came down hard on it. I am glad he used his expert knowledge to point out potential flaws in the study, but I was very put off by the polemical manner in which this was accomplished. And I said so. I have been calling for more respectful discussions, and have been critical of the way this particular case was conducted.

Most recently, there have been discussions on T. taxus (very interesting and scholarly) and Panda’s Thumb, the latter of which has been staggering in its vitriol. I encourage you to have a quick read of the comment section to see what I am referring to. This episode really makes me question whether blogging is appropriate for scientists. I hope that the positive will outweigh the negative in the end, but being personally attacked for voicing an opinion (ironically, about elevating the discourse on blogs) by science bloggers is not something I will have much desire to endure.

Let us hope that this is not the true nature of blogs, but simply an anomalous occurrence.


Journal list.

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The following is not a complete list, and I freely admit to an evolutionary, genetic, and zoological bias in my research interests, but perhaps someone else will find these bookmarks useful too.
American Naturalist
Annual Review of Ecology, Evolution, and Systematics
Annual Review of Genetics
Annual Review of Genomics and Human Genetics
BioEssays
Biological Journal of the Linnean Society
Biological Reviews
Biology Letters
BioScience
BMC Bioinformatics
BMC Evolutionary Biology
Canadian Journal of Zoology
Cell
Chromosoma
Current Biology
Current Genomics
Current Opinion in Cell Biology
Current Opinion in Genetics & Development
Cytometry
Development Genes and Evolution
Evolution
Evolutionary Bioinformatics
Gene
Genetica
Genetical Research
Genetics
Genetics and Molecular Biology
Genetics Selection Evolution
Genome
Genome Biology
Genome Research
Hereditas
Heredity
Insect Molecular Biology
Journal of Evolutionary Biology
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution
Journal of Heredity
Journal of Molecular Biology
Journal of Molecular Evolution
Molecular Biology and Evolution
Molecular Ecology
Nature
Nature Genetics
Nature Reviews Genetics
Naturwissenschaften
Nucleic Acids Research
Philosophical Transactions of the Royal Society B: Biological Sciences
PLoS Biology
PLoS Genetics
PLoS ONE
Proceedings of the National Academy of Sciences
Proceedings of the Royal Society B: Biological Sciences
Science
Trends in Ecology & Evolution
Trends in Genetics
Zoological Journal of the Linnean Society


Blogs as a medium for scientific discussion.

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By way of follow up to my last post, and as a means of keeping things positive and forward-looking, here are some recommendations that come to mind regarding how the credibility of blogs as a medium for scientific commentary and discussion could be advanced. I hope this doesn’t come across as preachy. My intention is simply to share what I think would make me as a scientist more inclined to take blogs seriously as a venue for communicating in (versus about) science.

1) Stick to the science.

When discussing anti-evolutionism or culture or politics, obviously this would not apply. However, in commentaries that are intended to be about the merits of a scientific study, the focus should be on the science. Anti-evolutionism is a real concern, but it does not drive how science is conducted.

2) Avoid unnecessary rhetoric, polemics, or emotionally charged language.

We have all read papers that have raised our blood pressure. But if one wants his or her arguments to be taken seriously, then cooler heads must prevail. Throw the paper across the room if you must, but when you write out your critique, keep it scholarly.

3) Make it clear to non-scientists that this is a discussion, not peer review.

Blog comments, though potentially very effective in disseminating and evaluating scientific information, are not peer review. We do not want to give the wrong impression that what happens on blogs is on the same level of how most scientific papers are evaluated.

4) Eschew arguments from authority.

Arguments from authority are not acceptable in science. If you reject them when anti-evolutionists use them, avoid them in your own posts.

5) Other bloggers: don’t pass judgment without all the information.

The blogosphere is useful as a dissemination tool in large part because of its interconnected nature, with a large percentage of posts being links to other posts. When linking to another post, bloggers should avoid making strong statements about the paper or the commentary until the details are available. If you haven’t read the paper, or if the blogger to whom you are providing a link has not spelled out his or her arguments in detail, then scientifically you have no basis for drawing any conclusions either way about the article.

6) Commenters: avoid jumping on a bandwagon.

Everyone’s comments can be important, regardless of expertise. However, if you have not read or understood the paper in question, you may want to avoid calling for it to be retracted or speculating about the failure of peer review.

7) Contact the authors if appropriate.

There is no rule that says bloggers must not contact the authors of scientific papers. Most scientists are happy to discuss their work; they are generally very busy, however, so it is best to ask specific questions. If you are going to be critical, please bear in mind that in peer review, in print, or at meetings, authors typically have the opportunity to reply and the debate is not one-sided.

8) Provide references.

Scientific papers must reference pretty much everything they state that is not original to the authors. Blogs do not need to be this rigorous in referencing, but it does help to show that you have read something else besides other blogs. (And science writers: please tell us the title of the paper you are discussing; don’t just say “in an upcoming issue of X”!).

9) Choose the right blog*.

If a blog has a reputation for aggressive or even offensive comments, then it may not be appropriate as a place to start a serious discussion about scientific papers. At least, scientists are unlikely to participate if there is a high probability that they will come under personal attack or will be treated with disrespect.

I make these suggestions not to be critical, but because I remain optimistic about the potential of blogs to be employed in high level scientific discourse. As the medium matures, I hope that more scientists will take part, and thereby open more lines of communication to non-scientists. If anyone has additional recommendations or ideas of their own, please share them, be you scientist or non.

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* This is an updated entry added in light of my recent experience on a specific blog.


Peer review or peanut gallery?

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The flagellum paper saga continues, most recently with an interesting post and especially the ensuing discussion at T. taxus (also linked to from PT). Unfortunately, many people are still focusing on whether the Liu and Ochman article is scientifically valid, which is not something any scientist is going to take someone’s word for. We need to see the arguments formally presented and reviewed by other experts. Maybe that sounds too restrictive — well, you can’t have it both ways. To be frank, I find the notion that people consider this spectacle an example of the self-correcting nature of science (e.g., 1, 2) very alarming. It suggests either an only passing familiarity with the actual peer review system, or a willingness to let it slide while simultaneously holding it up as a primary argument against anti-evolutionists.

Here is Matzke’s explanation for his actions:

As one additional consideration, add the fact that the L&O paper was clearly aimed to get public attention, media attention, and to serve as a confident rebuttal to ID. It had the authority (PNAS) and rhetoric (We have debunked ID! Never mind that it has already been debunked!) to go far. I found out about the paper from a science journalist looking for an assessment, and it was already getting picked up on the blogs (and, we later found out, Science magazine). So I only had two real choices: (a) stay quiet and let a large number of pro-evolution people shoot themselves in the foot by triumphantly citing this paper as the latest and greatest anti-ID publication, only to have it collapse (as it would inevitably) later on, to the embarrassment of everyone and providing a permanent talking point to the ID guys about how evolutionists will uncritically accept any old thing that supports their position, or (b) do what I did and be frank about it. As I expressed in my initial blogpost, I didn’t like doing what I did, but it wasn’t really much of a choice.

Reality check. I saw a grand total of three blog posts about the paper from pro-evolutionists. Mine, which gave equal time to Nick’s model. Dennehy’s, which, like mine, was tentative in its acceptance of the paper, and Harrison’s, which also mentions Matzke’s model and mostly just summarizes the paper. The first two bloggers are professional scientists, the third is a freshman student. There was also a story in Science, which I agree was not particularly well done. Readers of this blog will be aware of my complaints about scientific reporting and the all too common trend toward sensationalism at the expense of accuracy. That’s about it. None of the blog posts claimed that this study refuted ID (whatever it means to refute an untestable idea), they merely described it as further evidence that an evolutionary approach is applicable to the question of flagellar origins, and that genome data will prove useful in this endeavor.

On the anti-evolution side, I saw a similar number of posts. These said little about the science (no surprise), and focused mainly on Matzke’s rhetoric. I see nothing to be embarrassed about in the three evolutionists’ blog posts above, and lots to be concerned about in terms of arming the anti-evolutionists with sound bites that excuse them from even having to read the paper under discussion. I therefore reject the rationale of needing to protect evolutionists from shooting themselves in the foot. As to whether the Liu and Ochman paper was intended to be an anti-ID PR piece as Matzke has suggested, I invite everyone to read the article. It is open access, as are about half a dozen other papers in every issue of the journal. From my reading, their focus is entirely on the science, and any comments about the evolution of complex structures being subject to confusion or speculation can be interpreted in a variety of ways, including as a statement about previous evolutionary discussion. Then read Pallen and Matzke (2006) for comparison (the latter is a nice paper, but note its explicitly stated message).

I am finding it hard to be any clearer about this. I have no problem with the paper being refuted, if that is what happens. But if so, it will occur through peer review, not by trying to convince non-experts online. Let me also point out that it is not a problem that Matzke is not a practicing scientist (I referenced his model very favorably in my post, and I respect his expertise in this area) nor that the discussion took place on blogs. My big problem, as I have stated again and again, relates to the way this was handled by Matzke, other bloggers, and blog commenters. More specifically, I am referring to 1) Matzke’s unnecessary polemics, 2) the immediate and unquestioning acceptance of Matzke’s claims by commenters and other bloggers without having read the paper or having been presented with any detailed analysis (a trend which, one would hope, is usually only observed among anti-evolutionists), 3) the misleading impression that this is even remotely similar to how peer review operates (namely, make a conclusion first, then gradually add more evidence as necessary to convince non-experts), and 4) letting fear of anti-evolutionism drive the way science is discussed.

I believe Matzke owes Renyi Liu and Howard Ochman a public apology, regardless of whether the paper was bunk or not. Until then, I maintain the hypothesis that this episode has alienated practicing scientists and has rendered them less likely to engage on blogs or to consider this a reasonable medium for serious scholarly discussion. So far, n = 1 for sure.

Update: I am rescinding my call for a public apology. I think it would be a good move, but I can’t argue that it is required. I have been in discussion with Nick and others and I think that in light of the context it makes the most sense to let Nick communicate with Liu and Ochman (or not) as colleagues in whatever way he thinks appropriate. I should also like to clarify that it is not just Nick’s approach that could alienate scientists, but the environment that it engendered.

On the flipside, I am still hopeful that blogs could be a venue for scholarly discussion, and I would like to see it appeal to and be accessible by non-experts while preserving a strong sense of academic rigor.


Effect versus function.

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There has been quite a bit of discussion in the media recently about discoveries of [indirect evidence for] functions in [small portions of] non-coding DNA. Unfortunately, the parts in square brackets are often omitted. It is also the case that many reports overlook the important distinction between effect and function, leaving readers with the impression that non-coding DNA can only be either totally insignificant or vitally important.

Here is the relevant part of the Merriam-Webster Dictionary entry on function:

“The action for which a person or thing is specially fitted, used, or responsible or for which a thing exists.”

And on effect:

“Something that is produced by an agent or cause; something that follows immediately from an antecedent; a resultant condition.”

In other words, a function fulfills a specific role to produce a positive result, with a close fit between cause and outcome shaped by either design (in human technology) or natural selection (in biological systems). Effects are also the outcome of identifiable causes, but they can be positive, neutral, or negative and may be generated directly or indirectly by the causal mechanism. Thus, it is not possible to have a function without any effects, but something can exert an effect — perhaps a very important one — without this constituting a function.

Consider an example. The immune system of the body has a clear function: to defend against pathogens. Viruses likewise have functions, but this only makes sense if one considers the issue from the perspective of the viruses themselves and not of their hosts. Specifically, parts of the virus function in allowing them to circumvent the host’s immunity and to usurp its replication machinery. Viruses do, however, have effects on hosts — usually negative, but apparently sometimes indirectly positive.

The genomes of eukaryotes consist of many types of DNA sequences. The exons that encode proteins make up a small percentage (less than 2% in humans), and the rest is non-coding DNA of various sorts: introns, pseudogenes, satellite DNA, and especially transposable elements (also called TEs, transposons, or mobile elements). The latter represent a diverse set of sequences that are capable of moving about and duplicating in the genome independently of the normal replication process. In this sense, they are often considered “parasites” of the “host” genome. Overall, TEs also make up the largest portion of non-coding DNA in the genomes analyzed so far (at least 45% in humans), although the particular types, abundances, and levels of activity of TEs vary among species.

Some TEs have evidently been co-opted (exapted) to perform functions at the host level, meaning that they have moved from being parasites to integrated participants in the functioning of the genome. This includes regulating genes, involvement in the genetic cutting-and-splicing mechanism of the vertebrate immune system, and perhaps cellular stress response. On the other hand, many diseases can result from mutations caused by the insertion of a TE into an existing gene. From the perspective of the host, TEs can have different effects depending on the context: some TEs are functional but some are detrimental. The large majority, however, have not been shown to fall into either category.

Nevertheless, a lack of evidence for either function or harm does not mean that TEs are without effects. It is well known that the total amount of DNA (genome size) is linked to cell size, cell division rate, metabolic rate, and developmental rate. In other words, a large genome is typically found in large, slowly dividing cells within an organism displaying a low metabolic rate and sluggish development. Conversely, organisms with high metabolic rate or rapid development tend to have small genomes. To the extent that total DNA content directly affects cell size and division, these can be considered effects — by their presence in the aggregate — of non-coding DNA elements.

Is slowing down metabolism or delaying development a function? Some authors think so, but most would argue that these are effects that are tolerated by the organism because they are not overly detrimental. That is, parasites spread within the genome and individually may have little or no effect (and no function), but in sum may have substantial effects on the cell and organism. The amount of accumulation would depend on the tolerance of the organism based on its biology. For example, it is unlikely that a mammal with a high metabolic rate could have a genome the size of a salamander’s.

The point of this discussion is to note that seeking functions for non-coding DNA is an interesting area of research, but that even if most sequences are not functional, they can still be important from a biological perspective. Similarly, one would not invoke function for hosts to explain the existence of viruses, nor would one dismiss viruses as unimportant if functions were never found at the host level. One would, however, focus considerable attention on explaining how viruses spread, why some are more virulent than others, and how they exert their effects.


Welcome new iSpiders blog.

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This is just a quick post to welcome University of Alberta PhD candidate David Shorthouse to the blogosphere with the launch of his new blog, iSpiders.

David edits the Canadian Arachnologist newsletter and developed the Nearctic Spider Database. He and I published a paper on spider genomes a few years ago that made the cover of Journal of Heredity.

David is interested in making biodiversity information open to everyone (as am I), so it’s worth checking out.

(Hat tip: iPhylo)


Introducing two new journals in evolution.

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Two new journals are set to launch in 2008 that deal with the teaching and application of evolution. The first, to be published by Springer, is Evolution: Education and Outreach. The editors are Niles Eldredge and his son Greg. I am privileged to be serving on the editorial board along with some very important people in the evolutionary research, education, and outreach communities. The official launch of the journal will occur at the National Association of Biology Teachers annual meeting in November. The second, to be published by Blackwell, is Evolutionary Applications. It is edited by my colleague Louis Bernatchez of Université Laval in Québec.

Here are the publishers’ journal descriptions:

Evolution: Education and Outreach

Darwin’s Theory of Evolution revolutionized scientific thinking. Since the publication of The Origin of Species 147 years ago, this theory has been extensively and rigorously tested. Overwhelming scientific evidence from many disciplines exists to support this theory. From the vast body of scientific evidence that has accumulated, we have come to an understanding of all areas of the biological world – from our cells and DNA to our lakes and forests. Evolutionary principles are the foundation of all modern biology and have led to major advances in fields as diverse as molecular biology, developmental biology, genetics, behavior, and paleontology. As such, evolutionary theory is a fundamental and necessary component of modern science education.

Evolution: Education and Outreach will promote accurate understanding and comprehensive teaching of evolutionary theory for a wide audience. Targeting K-16 students, teachers and scientists alike, the journal will publish articles to aid members of these communities in the teaching of evolutionary theory.

Evolutionary Applications

Evolutionary Applications publishes papers that utilize concepts from evolutionary biology to address biological questions of health, social and economic relevance. Papers are expected to employ evolutionary concepts or methods to make contributions to areas such as (but not limited to): agriculture, aquaculture, biomedicine, biotechnology, conservation biology, disease biology, fisheries and wildlife management and invasion biology. Theoretical, empirical, synthesis or perspective papers are welcome.


Signs of selfish DNA.

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Some people have trouble understanding the fact that eukaryotic genomes are made up primarily of transposable elements — genetic parasites that are there (at least initially) because they are good at being there. Some take on functions, but others remain causes of disease or simply become inactivated and remain as molecular fossils.

Here is one of those pictures that circulates around in emails that I find amusing, but which also conveys something about the concept of transposable elements in the genome (click for larger image):


Basically, the sign appears to exist largely for the sake of existing. But note that a small portion of it at the bottom has a critical function (“Also, the bridge is out ahead”).

It’s a weak analogy, maybe, but that is a pretty funny sign.


Suggestions for science writers.

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In an earlier post, I expressed some frustration at the way discoveries about non-coding DNA are reported. I noted in particular ScienceDaily‘s description of the recent publication of the opossum genome sequence. In case you missed it, here it is again:

Opossum Genome Shows ‘Junk’ DNA Source Of Genetic Innovation

(…)

The research, released Wednesday (May 9) also illustrated a mechanism for those regulatory changes. It showed that an important source of genetic innovation comes from bits of DNA, called transposons, that make up roughly half of our genome and that were previously thought to be genetic “junk.”

The research shows that this so-called junk DNA is anything but, and that it instead can help drive evolution by moving between chromosomes, turning genes on and off in new ways.

(…)

It had been initially thought that most of a creature’s DNA was made up of protein-coding genes and that a relatively small part of the DNA was made up of regulatory portions that tell the rest when to turn on and off.

As studies of mammalian genomes advanced, however, it became apparent that that view was incorrect. The regulatory part of the genome was two to three times larger than the portion that actually held the instructions for individual proteins.

Since my post, National Geographic has gotten in on the act as well:

First Decoded Marsupial Genome Reveals “Junk DNA” Surprise

(…)

The study reveals a surprising role in human evolution for “jumping genes”—parasitic bits of “junk DNA” that until now were thought to be nothing more than a nuisance—and may also lead to a number of medical breakthroughs.

(…)

The scientists were also surprised to find that these regulatory sequences have in large part been distributed across the human genome by so-called jumping genes.

These genes have hopped through chromosomes for more than a billion years, leaving behind many copies of themselves. So until now the genes had been widely regarded by scientists as parasites, or “junk DNA,” that played no creative role in evolution.

You can consult my earlier posts for specific complaints on this. More generally, I have the following suggestions for science writers who are reporting on interesting findings about non-coding DNA.

1) Don’t assume that every new discovery is overthrowing some recalcitrant conventional wisdom.

If you want to claim that all scientists have long believed that all non-coding DNA is totally functionless, kindly point to a few examples. Here are a few cases that suggest that you may have a bit of trouble with this.

When Barbara McClintock first characterized transposable elements in 1950, she called them “controlling elements”. Comings (1972), who gave the first detailed discussion of “junk DNA” (his paper, unlike Ohno’s, was an explicit discussion of the topic of “junk DNA” and appeared in print before Ohno [1972], which he cites as “in press”), stated that “being junk doesn’t mean it is entirely useless.”

Orgel and Crick (1980), in their paper introducing the concept of “selfish DNA”, noted very clearly that:

It would be surprising if the host organism did not occasionally find some use for particular selfish DNA sequences, especially if there were many different sequences widely distributed over the chromosomes. One obvious use … would be for control purposes at one level or another. This seems more than plausible.

Doolittle and Sapienza (1980), whose paper appeared along with that of Orgel and Crick (1980), were equally unambiguous on the issue:

We do not deny that prokaryotic transposable elements or repetitive and unique-sequence DNAs not coding for proteins in eukaryotes may have roles of immediate phenotypic benefit to the organism. Nor do we deny roles for these elements in the evolutionary process. We do question the almost automatic invocation of such roles for DNAs whose function is not obvious, when another and perhaps simpler explanation for their origin and maintenance is possible.

2) Don’t imply, intimate, or suggest, directly or indirectly, that the discovery of function in some non-coding DNA sequences means that all non-coding DNA is functional.

Remember to implement the onion test if you are tempted to argue otherwise. Note that simply having “junk DNA found to be functional” as a headline with no qualification or clarification commits the fallacy as well. The last two examples of poor reporting (see here and here) have neglected to mention that the amount of non-coding DNA that was shown to be conserved and presumably functional is less than 5% of the genome. I imagine that a reader’s interpretation may change somewhat when this important detail is made clear.

I am as excited as anyone about new discoveries in genome biology. I have also been critical of the tendency to focus too much on protein-coding genes or simple allele frequency changes in evolutionary science (Gregory 2005). But it does not follow that every new finding is revolutionary in and of itself, nor is it the case that non-coding DNA has been dismissed as unimportant for decades and that its relevance is only now being admitted by stubborn academics. The commentaries of people like Comings, Ohno, Orgel and Crick, and Doolittle and Sapienza were made in response to an overemphasis on functional explanations for all non-coding DNA, but even they did not reject the potential importance of some non-coding elements.

There is a growing frustration among scientists relating to the unnecessary search for “balance“ in journalists’ reporting. What I see happening with non-coding DNA is the opposite of this, though equally problematic. To wit, many writers are painting a monochromatic picture of genome biologists when in fact there has always been a full spectrum of opinions regarding the importance of non-coding sequences. The material is exciting; it doesn’t need to be embellished with exaggerated controversy to be worth reading about.

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References

Comings, D.E. 1972. The structure and function of chromatin. Advances in Human Genetics 3: 237-431.

Doolittle, W.F. and C. Sapienza. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601-603.

Gregory, T.R. 2005. Macroevolution and the genome. In The Evolution of the Genome (ed. T.R. Gregory), pp. 679-729. Elsevier, San Diego.

McClintock, B. 1950. The origin and behavior of mutable loci in maize. Proceedings of the National Academy of Sciences of the USA 36: 344-355.

Ohno, S. 1972. So much “junk” DNA in our genome. In Evolution of Genetic Systems (ed. H.H. Smith), pp. 366-370. Gordon and Breach, New York.

Orgel, L.E. and F.H.C. Crick. 1980. Selfish DNA: the ultimate parasite. Nature 284: 604-607.