Dec 042012

 I have in front of me a copy of the book “Nucleotide sequences 1984 Part 1 A compilation from the GenBankTM and EMBL data libraries” published by IRL Press. Wow, what a surreal book for anyone used to dealing with sequence databases today. The idea that DNA sequences would be printed out, in an actual book made of paper, and put on a shelf for people to consult, takes some getting used to. To say that it is an idea that has passed is something of an understatement. I bought it for almost nothing as a curio, and it is going to sit proudly on my office shelves. I might even buy Part 2 to go with it.

The sequences range from 1967 to late 1983. The paper is not very white and slightly absorbant, not due to age I just think it was just published that way. It weighs 1.55kg and isn’t a large book. I’ve put a gallery of images below with the book next to a DNA double helix for scale! OK there is a baseball too, a strange collection of things just came to hand, apparently. Quite a number of sequences are very short (<100bp) and remind me of second gen sequence reads! Despite my incredulity at the start of this post, some of the ideas concerning open access to data, which are referred to in this book’s Introduction are very contemporary. The international sequence databases really have been important torch bearers for open access to research data for the last few decades.

There are some nice quotes in the Introduction

While computerized management of the data is needed to provide accuracy, easy maintenance, and electronic access, it is also important to publish the complete database in printed form. This first annual printed compendium effectively makes the entire collection of information available to every member of the scientific community who wishes to use it, including investigators without access to computers.

One of the goals of the collaboration between GenBank and EMBL is continued movement toward common standards and conventions for the two databases.

This compendium, drawn from the American and European databases, is the first printed compilation of substantially all nucleic acid sequences reported between 1967 and late 1983.

As combined in this compendium, the two databases contain a total of nearly three million bases from over 4000 reported sequences.

Yeast and fungal sequences are in the Plant Sequences section

The individual entries within each section are arranged alphabetically by entry name.

The records seem to be closer to EMBL format than GenBank, although Appendix E (which is in part 2) “illustrates how the format used in the compendium relates to the formats used in the two databases“. The sequences are grouped into mammalian, other vertebrate, invertebrate, plant, and organelle sequence lists. There is also a table of contents, one record per line, giving the length of the sequence and what page it is on.

The first sequence in the entire book is “APE (CHIMPANZEE) ALU TYPE DNA ACCESSION NUMBERS: J00322″ and the last is “YEAST (S. CEREVISIAE) MITOCHONDRIAL VAR1 GENE 3′ FLANK . ACCESION NUMBERS: K00385″

Google books seems to have scanned in the entirety of both volumes, but I couldn’t get it to work for me. What a fantastic book.

Jul 182011

There have been several obituaries for Horace Judson recently [1][2], and today Larry Moran in an excellent Sandwalk blog post talked about the lack of knowledge of the history of their field by molecular biologists

modern researchers are completely unaware of the history of their field. That’s partly because the work on bacteria and bacteriophage—where the basic concepts were often discovered—is no longer taught in biochemistry and molecular biology courses. This leads to the false idea, as expressed in the press release, that all new discoveries in eukaryotes are truly new concepts that nobody ever thought of before. The solution to this problem is to make all students read The Eighth Day of Creation.

I liked the quote from John Hawks too

I suppose we could rephrase Santayana: Those who ignore history feel privileged to reinvent it.

Judon wrote the truly epic book “The Eighth Day of Creation: Makers of the Revolution in Biology” which describes in detail the development of molecular biology from extensive interviews with its early pioneers. It’s a great read, his writing style is easy and absorbing, and the content fascinating. Despite not having yet finished the book, I can recommend it very highly indeed. What? Wait, you haven’t finished the book yet? How good can it really be? It’s a great book, but one that suffers from poor publishing by Cold Spring Harbor Press. Let me get my excuses out of the way now; I’m really busy, have little time for reading things that aren’t journal articles, and have a big backlog of other books to read. Yet these aren’t the real reasons. The real reasons are that it is enormous and only comes as a paper copy. The book, at 714 pages, is very weighty and thick even as a paperback. It is about as thick as a single volume of this size can be, and of course the pages themselves don’t open out very flat. It is pretty heavy and I have decided not to take it on holiday with me based on this alone. That is a shame, as holidays are when I catch up on reading.

There is a simple solution however – release it as an eBook. I would love to read this as a Kindle book on my iPad and be able to take it anywhere and just dip into it. It wouldn’t matter then how long it was. What is more I would be able to look stuff up when sitting in seminars and journal clubs, just quickly checking the history of a topic. Lastly I would like to be able to highlight and comment on sections. I have an absolute phobia of writing in books, I just can’t do it. Somehow (almost religiously) I know it is just plain wrong, even though I can’t think of a single reason why. I have no such qualms about marking up an eBook however, highlighting sections and adding notes. These notes and highlighted sections are searchable and easily found again- very useful indeed.

Although I really agree with Larry Moran’s concluding sentence “The solution to this problem is to make all students read The Eighth Day of Creation” I think that the chances are remote without good modern publishers helping the process along. Do something useful today, go to the Amazon webpage of Eighth Day of Creation and click on the link (usually just under the picture) to request a Kindle version from the publisher.

Oct 112010

I just received promotional information about a new book from Garland Science publishers. “Genome Duplication; concepts, mechanisms, evolution and disease” By Melvin L DePamphilis and Stephen D Bell. Garland Science Oct 2010 ISBN: 978-0-415-44206. It sounds like a great title, especially for someone like me who thinks genome and gene duplication are among the most important processes in the whole of evolutionary biology.

Unfortunately, on the cover of the book it looks like they have drawn a tree of some model organisms and placed Drosophila melanogaster in a monophyletic group with Arabidopsis thalianato the exclusion of all other animals. Ooops.

You would have thought that a big publisher would have checked more carefully before creating a book cover image so obviously wrong, but I guess we all have bad days. Interesting to see what happens next.
Jan 252009

The other book I read over Christmas was “Dry Store Room No. 1: The Secret Life of the Natural History Museum” by Richard Fortey. This is an interesting tour of some of the past and present personalities behind the Natural History Museum, London. I found it a really interesting light read.

A good motto put forward in the book is “never throw anything away”, I was thinking that has some relevance for my recent experiences of computer files.

At times I thought Fortey’s views on museums a little old-fashioned, but then the very next sentence would launch into the importance of DNA sequencing in a modern museum and I would be slightly embarrassed to have doubted him. On the whole I was convinced by his views. He is very keen on the importance of naming species in the modern world, which although I don’t entirely disagree with think may ultimately be a bit of a distraction from the most important work of describing the big picture of diversity and the processes generating it. But he would probably agree with this too (he writes that we need to name things to understand their stories), its just that he talks about naming a lot and the importance of the processes generating biodiversity much less.

In previous eras he describes how keen amateurs became world experts by collecting all the relevant taxonomic literature on a group. In the recent past however, because of the amount of publications needed, amateurs could not hope to have access to enough literature to become experts on the taxonomy of any group. Now, he suggests, the internet may be reversing this trend as much more of the relevant literature is easily available. A great argument for open access publishing.

When discussing species status and hybridisation (pg 315-316) he has a quote that I like

“Since evolution is still happening all around us it would actually be rather surprising if there were not such difficulties of definition in nature.”

A light and entertaining read, worth the effort.

“Dry Store Room No. 1: The Secret Life of the Natural History Museum” Richard Fortey
Harper Press, 2008
ISBN: 978-0007209880

Jan 252009

Ben Goldacre is one of my favourite writers, I turn to his column in the Guardian each Saturday before anything else. I read his excellent book “Bad Science” over Christmas, and I really recommend it. He looks primarily at the reporting of science in the media but also about the science (lack of) in everyday life. He discusses for example homeopathy, the placebo effect and the MMR vaccine “hoax”. He writes really well, the book is funny (while at the same time being a bit scary) and its actually an important book. Important? Well, its more likely than anything I have seen to get people thinking about how we know what we know. That leads to a consideration of evidence, the scientific method and reduces the likelihood of been taken in by trendy but vacuous rubbish that can actually (as he discusses) be very dangerous.

It isn’t an academic text its a general book, but Bad Science is informative and interesting (and fun) even if you are a “proper” scientist who already knows about the scientific method, statistics and evidence.

One of his themes is that while science journalists are usually OK, when ridiculous “science” headlines appear in newspapers they are usually determined by an editor with a background in humanities who steers the story away from the trained science journalist to a general newspaper hack.

He is critical of humanities graduates who are journalists and know nothing of evidence and the scientific method. But I really wonder if modern biology graduates are so different, do they really learn this stuff on modern degree programs, or are they just sort of expected to assimilate it independently somehow? I have a colleague who was suggesting that we entirely abandon the first semester curriculum of the usual first year courses (diversity of life, ecology and evolution etc) and just teach the scientific method and experimental design. A very interesting idea.

Ben Goldacre’s blog

“Bad Science”
Ben Goldacre
Fourth Estate, London, 2008
ISBN: 978-0-00-724019-7

Sep 052008

I just received a copy of “Reading the story in DNA; a beginner’s guide to molecular evolution” by Lindell Bromham, OUP 2008, ISBN: 978-0-19-929091-8
I have only looked at it quickly but it is very impressive. I like the writing style. It is well produced. Figures are excellent. The parts I have read are full of common sense. It has a good mix of simplicity and depth. It seems at a good level for undergraduate students and some postgrads. It feels modern- a very very rare thing indeed for evolution books, as I often complain. It has “Techbox” sections describing such things as Genbank records, primer design, maximum likelihood methods. It has case studies- solving the mystery of the Chilean blob, using bioinformatics to describe endogenous retroviruses, horizontal gene transfer between parasitic plants and their hosts. Interestingly it also has “Heroes of the Genetic Revolution” boxes detailing the careers of some of the greats. Who would be your heroes?
OK so as I type this skimming through the book saying how much I like it I come across a nice picture and section on some work I contributed to on cryptic speciation in Brachionus rotifers[1]. So now it just looks like I’m sucking up, but I didn’t even know that was there when I started this post.

Anyway, it looks a great book.

1.Gómez A, Serra M, Carvalho GR & Lunt DH (2002) Speciation in ancient species complexes: evidence from the molecular phylogeny of Brachionus plicatilis (Rotifera). Evolution, 56(7):1431-1444, doi:1431-1444. 10.1111/j.0014-3820.2002.tb01455.x

Feb 032008

So I don’t hate all books. Over Christmas I read Michael Lynch’s new book “The Origins of Genome Architecture”. One of the best books I have read in a long time. Well-written, clearly argued, well referenced and important. If you like molecular evolution, genomics or related topics you should definitely read this. I learned a lot about topics I already thought I understood well. The book is in some ways similar to his 2007 PNAS paper “The frailty of adaptive hypotheses for the origins of organismal complexity” but much more extensive in both depth and breadth. I have been very frustrated by comparative genomics and some of molecular evolution for a very long time. This book made me feel I wasn’t alone. The logic is simple, clear and devastating, providing an intellectual framework that will be useful to many wanting to look at genomic data.
If you are annoyed by the ease with which adaptationist explanations for pretty much anything in genomics are published you might also like to check out Jonathan Eisen’s “Adaptationomics awards“.

[Michael Lynch “The Origins of Genome Architecture”, 2007, Sinauer Associates, ISBN 9780878934843]
Strangely the UK Amazon site lists this book as authored by Michael Lynch and Bruce Walsh, although there is no mention of Walsh on my actual copy of the book. The US Amazon site lists only Lynch.