As promised, here is my first response to a blog meme, namely the “evolution” meme with which I was tagged some time ago by Larry Moran of Sandwalk. I probably won’t make a habit of responding to these, but this one seems particularly appropriate given the content of the blog. I’m also not going to play by the rules, in which one is supposed to list five posts and tag others — I am listing a whole bunch of posts by genre and not tagging anybody else. Please bear in mind that evolution is not a progressive process, and that the particular path followed by a given lineage is not necessarily adaptive. So, that said, here is a brief history of the Genomicron blog…
Origins: I started the blog more or less as a lark. I had a new grad student who was an avid blogger, and through conversations with him I began reading some of the bigger science blogs. When I noticed that my work was being discussed on some of them, I obviously became more interested. However, it struck me that most of the big blogs were chimaeras of politics, religion, and science, and that few were dedicated to genome biology of the sort that I am interested in (The Tree of Life notwithstanding!). It seemed there was an available niche for a (mostly) science-only, genomes-plus-evolution blog, and so I decided to launch one. The first post was just a “well, here I am” sort of announcement [My grad student made me do it], and the second was a hat-tip to Larry for mentioning my lab [A nod to (and from) the Sandwalk]. At the time, I said that “Due to time constraints I expect to only post semi-regularly for the foreseeable future”. So much for that prediction.
Exaptation: Several of the early posts on Genomicron were recycled from things I had written for other reasons. I wanted to get some content up, so I modified existing texts or simply wrote about very basic topics in my field. Specifically, I posted some historical information about “junk DNA”, and some general information about genome size. I also began discussing new reports in genomics, such as the sequencing of the macaque genome and some studies that made reference to genome size.
Here are some examples from this phase:
Flagellum flap: My first foray into the wild world of blog debates came when I posted a brief summary of a PNAS paper by Liu and Ochman on the evolution of bacterial flagella [Genome sequences reduce the complexity of bacterial flagella]. I mostly commented on how this shows that so-called “irreducibly complex” structures can be and are studied from an evolutionary perspective, in particular using genomic data. I also gave roughly equal time to Nick Matzke’s excellent model. Little did I know that this paper would be highly controversial, and that I would be sucked into a vortex of bandwagon-jumping and ad hominem attacks that almost turned me off blogging [Doubts about blogging for scientists] and solidified my view that blogs are fine for commentary but that one must never give the false impression that this represents scientific peer review [Peer review or peanut gallery?]. I also tried to provide some comments on how one could conduct scientific discussions on blogs that were, most likely, rather unrealistic given the nature of teh interweb [Blogs as a medium for scientific discussion]. Incidentally, as far as I know, everyone involved in this dust up is getting along just fine now.
Junk, junk, everywhere: Meanwhile, I continued discussing “junk DNA” and the various misconceptions and intentional misrepresentations about it. I was not aware that this was such a hot issue, in particular with regard to the creationism/ID-evolution “debate”. To paraphrase Alvar Ellegard, junk DNA is one of those focal points of debate on which practically everybody is compelled to have some sort of opinion, though it cannot in most cases be called an informed one. This is especially true of anti-evolutionists, who really don’t get it at all. By way of example, I point to the short piece in Wired in which I was interviewed along with Francis Collins and some IDers that set off a firestorm of criticism in the science blogosphere [Junk DNA gets Wired].
Here are some posts on the topic:
- The onion test
- Function, non-function, some function: a brief history of junk DNA
- An opportunity for ID to be scientific
- Junk DNA: let me say it one more time
The media and me: When I started this blog, I really did not have any intention of commenting regularly on the quality of media reports. Honestly. However, it became clear that the state of science reporting is, shall we say, problematic. The first post about this that I wrote was about a common misconception regarding some living species being “more evolved” than others [Chimps are not more evolved than humans or anyone else]. Since then, I have become increasingly frustrated with media reports on science, as reflected by a growing list of posts on the subject, which extends up to the present:
- Non-coding DNA and the opossum genome
- Suggestions for science writers
- Cracking the code?
- Two-for-one misconceptions about genomes from the New York Times
- Decoding the blueprint. Sigh.
- Junk and genomes in The Scientist
- Should scientists nit-pick?
- Press offices may be the problem
- T. rex could outrun humans?
- The press going ape again.
- Another deep sigh courtesy of LiveScience
- Discovery wants to “demote” fungi
- The story that caused me to stop reading LiveScience
- Just when I thought it couldn’t get any stupider, along comes the BBC
- Et tu, Daily Mail?
Interestingly, one of the most widely read posts I have written was on this topic, in which I vented some frustration with a snarky, sarcastic list entitled Anatomy of a bad science story. This was picked up by various blogs, and was even printed in an issue of The Skeptic magazine published by Australian Skeptics [Terrible science writing in The Skeptic magazine].
To be fair, I have also regularly complimented good science writing:
- More about ENCODE from Scientific American
- New Scientist gets it right
- Why are there transitional animals?
- Another good science story
- Global warming: how do scientists know they’re not wrong?
DAPs: More recently, I have turned some attention to bad science in addition to bad science reporting. In particular, I have noted a few examples of biased data used to support hypotheses regarding genome size and noncoding DNA. I haven’t discussed this kind of thing much on the blog up to this point because I prefer to deal with it in the peer-reviewed literature, but since most people would not encounter those discussions, it seems useful to present it à la blogue as well. Examples of this include:
- What’s wrong with this figure?
- Worst figure of all
- Dog’s Ass Plots (DAPs)
- Genome size and gene number.
- Proof that introns are functional… come again?
- This just in: DNA barcoding is not the be all and end all of the universe
And there you have it. What does the future hold? Given the role of contingency in evolution, I’m as curious to find out as you are.