Friday, June 24, 2011
Long time no see. This blog has suffered from a phase of no posts due to several reasons, namely being a long period of laziness and then the stress of having to write my Masters thesis and defend it. So I hope you'll forgive me, because I would really like to get back into doing this. Even if few people read it, in the least it would be good writing practice.
What has shaken me from my blog post-less slumber? A number of months ago I heard somewhere that a new TE book was going to be coming out, which is a rare event and welcome since the number of TE-related books is quite small. I decided more or less on the spot that I would review it on the blog when I finished reading it.
The book in question, Mobile DNA Finding Treasure in Junk, was written by noted human L1 retrotransposon researcher Dr. Haig Kazazian Jr currently at Johns Hopkins University School of Medicine. The Kazazian Lab has been one of the premiere L1 research labs for the last 20 years and has made many great discoveries into the biology of L1 elements and non-LTR retrotransposons in general.
I more or less enjoyed the book, although for different reasons than I thought I would have originally, and it was a rather quick read, for me at least, clocking in at around 3 or 4 hours which I managed to do yesterday evening. I was expecting a broad overview of TE biology and perhaps the history of their discovery and characterization but it wasn't quite that. There were a few introductory chapters on basic TE biology, and a very brief summary of their discovery and some of the major researchers in the field. A lot of the opening chapters felt a little scattershot, with not a great deal connecting them besides they unifying fact they were all about TEs. I think they would have been fine there had been a little more depth in the chapters, but ah well. The next part of the book is essentially the history of L1 research in the Kazazian Lab, which is a bit jarring at first and quite a departure from the format at the start of the book but this is where the most interesting material lies. It's always nice to see the more human and nitty-gritty part of research that you never get reading the primary literature. Learning a bit more about the people behind the author lists on papers is always quite cool, I find. And although I never expressed interest in learning about the behind the scenes of L1 research before I found it hard to put the book down during this section. For example, I've been seeing the terms LINEs and SINEs for years, since undergrad, but never once wondered who actually coined the two terms. It actually turned out to be Maxine Singer, one of the pioneering L1 researchers and someone who was instrumental in introducing Kazazian to them. The personal touches reminded me a little of Esra Galuns book on TEs that I read a few years back which I enjoyed. So for those interested in the human side of research, and those who are dying to know about the history of L1 this book is not too shabby.
One of the things I found problematic with this book was it's treatment, or rather lack thereof, of the selfish DNA hypothesis. I find it hard to imagine writing a modern book about TEs without going into Selfish DNA at least a little bit but this book manages to do that. Although one of the selfish DNA papers is cited (Orgel and Crick but not Doolittle and Sapienza), it is cited as the source for the term 'junk DNA ', which was actually coined by Susumu Ohno. Not only this but in another paper several years later Doolittle (1982) responded to critics by arguing that junk and Selfish DNA are not synonyms and should not be used as such. I don't think I have ever seen this latter 1982 paper cited, and the confusion between junk and selfish DNA is a common one in the TE literature unfortunately.
Near the end of the book, Kazazian waxes about the prevalence of TEs in genomes and falls into that familiar trap of " if TEs are so prevalent, abundant and persistent in genomes it's hard to imagine they aren't performing some beneficial function". This is where I think it is so crucial, nay, essential, to come at transposon biology from a evolutionary perspective because to me it makes understanding and interpreting TEs so much more tractable. I don't argue that sometimes TE-derived sequence have provided benefit to host organisms, by this point it's a foregone conclusion (see Feschotte and Pritham, 2007; Feschotte, 2008 and Sinzelle et al., 2009 for numerous examples). What I do argue is that most TEs in genomes provide no benefit and persist due to a combination of intra-genomic selection, antagonistic co-evolution with their host and other TEs and genetic drift due to the low effective population sizes of many eukaryotic organisms.
In conclusion, not a great book if you want an overview of TE biology, for that I'd recommend picking up and reading some key papers, but if you are interested in some of the behind the scenes of the history of L1 research, than this book is for you.
Ohno, S. 1972. So much "junk" DNA in our genome. In Evolution of Genetic Systems (ed. H.H. Smith), pp. 366-370. Gordan and Breach, New York
Doolittle, W.F. and C. Sapienza. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601-603
Orgel, L.E. and F.H.C. Crick. 1980. Selfish DNA: the ultimate parasite. Nature 284: 604-607
Doolittle, W.F. 1982. Selfish DNA after Fourteen Months. In Genome Evolution (eds. G.A. Dover and R.B. Flavell), pp. 3-28. Academic Press, London
Feschotte, C. and E.J. Pritham. 2007. DNA transposons and the evolution of eukaryotic genomes. Annual Review of Genetics 41: 331-368
Feschotte, C. 2008. Transposable elements and the evolution of regulatory networks. Nature Reviews Genetics 9: 397-405
Sinzelle, L., Z. Izsvák, and Z. Ivics. 2009. Molecular domestication of transposable elements: From detrimental parasites to useful host genes. Cellular and Molecular Life Sciences 66: 1073-1093