Sep 292011

I just noticed that an old publication of mine has a typo in the title on the Nature website “Animal mitochondrial DMA recombination”, anyone want to guess what the error is? Web of Science has the correct title, Pubmed has the correct title, and it used to be correct on the Nature website, but somehow they have gone there and broken it. It’s an easy typo to make, M and N are adjacent keys. Easy if you are retyping stuff- but who on earth retypes journal article titles? You are professionals, copy and paste it from a reliable source. Jesus.

What makes it worse is that when this paper (the paper that got me a job) first came out early on the Nature website they had spelled my name wrong! Adjacent keys typo again. They fixed it eventually, but it took a while. When you are a postdoc applying for jobs it only adds to the stress.

So I decided to email them to let them know. After about 10 minutes looking for an appropriate way to contact them on the website I’ve just given up. Hey, I’ve got a job now, and it makes Nature look stupid not me.

Lunt, D. H., and B. C. Hyman (1997) Nature 387:247-247. PDF Animal mitochondrial DNA recombination (no doi in my citations anymore as it points to a webpage with a stupid unprofessional typo).

Jul 192011

Bill Jordan was an evolutionary biologist at the Institute of Zoology in London who tragically passed away in May this year. He worked in many areas of evolutionary genetics but particularly in those relating to adaptation. He was a first-rate scientist, very sharp, very practical. He was also one of the nicest, most entertaining, most genuine people I’ve met. Bill was great fun, had a sharp wit that only seemed to get better after a few drinks, and used to stay up drinking with me at conferences- talking interesting science and interesting rubbish. When I got a call in May to say he had just passed away I was quite shocked.

There is a nice piece about him on the IoZ website

  • 2001-present: Senior Research Fellow and Head of Research Theme: Genetic variation, fitness and adaptability, Institute of Zoology, Zoological Society of London.
  • 1995-2001: Research Fellow, Institute of Zoology, Zoological Society of London.
  • 1994-1995: Research Fellow, Insect Molecular Genetics Group, Institute of Molecular Biology and Biotechnology, Heraklion, Crete.
  • 1992-1994: Research Fellow, Department of Biology, University of Louisiana, Lafayette, Louisiana.
  • 1991-1992: Research Fellow, Division of Environmental and Evolutionary Biology, School of Biology and Biochemistry, Queen’s University, Belfast.
  • 1990-1991: Research Fellow, Department of Molecular and Cell Biology and Department of Zoology, University of Aberdeen.

I also thought I’d post some of his publications

Lopez-Vaamonde, C. et al. Lifetime reproductive success and longevity of queens in an annual social insect. JOURNAL OF EVOLUTIONARY BIOLOGY 22, 983-996 (2009).

Gardiner, A., Butlin, R.K., Jordan, W.C. & Ritchie, M.G. Sites of evolutionary divergence differ between olfactory and gustatory receptors of Drosophila. BIOLOGY LETTERS 5, 244-247 (2009).

Zaki, S.A.H., Jordan, W.C., Reichard, M., Przybylski, M. & Smith, C. A morphological and genetic analysis of the European bitterling species complex. BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 95, 337-347 (2008).

Gardiner, A., Barker, D., Butlin, R.K., Jordan, W.C. & Ritchie, M.G. Drosophila chemoreceptor gene evolution: selection, specialization and genome size. MOLECULAR ECOLOGY 17, 1648-1657 (2008).

Paulo, O.S. et al. The role of vicariance vs. dispersal in shaping genetic patterns in ocellated lizard species in the western Mediterranean. MOLECULAR ECOLOGY 17, 1535-1551 (2008).

Gardiner, A., Barker, D., Butlin, R.K., Jordan, W.C. & Ritchie, M.G. Evolution of a Complex Locus: Exon Gain, Loss and Divergence at the Gr39a Locus in Drosophila. PLOS ONE 3, (2008).

Ciborowski, K.L. et al. Stocking may increase mitochondrial DNA diversity but fails to halt the decline of endangered Atlantic salmon populations. CONSERVATION GENETICS 8, 1355-1367 (2007).

Clark, A.G. et al. Evolution of genes and genomes on the Drosophila phylogeny. NATURE 450, 203-218 (2007).

Ciborowski, K.L. et al. Rare and fleeting: an example of interspecific recombination in animal mitochondrial DNA. BIOLOGY LETTERS 3, 554-557 (2007).

Garcia de Leaniz, C.G. et al. A critical review of adaptive genetic variation in Atlantic salmon: implications for conservation. BIOLOGICAL REVIEWS 82, 173-211 (2007).

Lopez-Vaamonde, C. et al. Effect of the queen on worker reproduction and new queen production in the bumble bee Bombus terrestris. APIDOLOGIE 38, 171-180 (2007).

de Eyto, E. et al. Natural selection acts on Atlantic salmon major histocompatibility (MH) variability in the wild. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 274, 861-869 (2007).

Dukes, J.P. et al. Isolation and characterisation of main olfactory and vomeronasal receptor gene families from the Atlantic salmon (Salmo salar). GENE 371, 257-267 (2006).

Sumner, S., Pereboom, J.J.M. & Jordan, W.C. Differential gene expression and phenotypic plasticity in behavioural castes of the primitively eusocial wasp, Polistes canadensis. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 273, 19-26 (2006).

Verspoor, E. et al. Population structure in the Atlantic salmon: insights from 40 years of research into genetic protein variation. JOURNAL OF FISH BIOLOGY 67, 3-54 (2005).

Jordan, W.C. et al. Allozyme variation in Atlantic salmon from the British Isles: associations with geography and the environment. JOURNAL OF FISH BIOLOGY 67, 146-168 (2005).

Pereboom, J.J.M., Jordan, W.C., Sumner, S., Hammond, R.L. & Bourke, A.F.G. Differential gene expression in queen-worker caste determination in bumble-bees. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 272, 1145-1152 (2005).

Consuegra, S. et al. Rapid evolution of the MH class I locus results in different allelic compositions in recently diverged populations of Atlantic salmon. MOLECULAR BIOLOGY AND EVOLUTION 22, 1095-1106 (2005).

Consuegra, S., Megens, H.J., Leon, K., Stet, R.J.M. & Jordan, W.C. Patterns of variability at the major histocompatibility class II alpha locus in Atlantic salmon contrast with those at the class I locus. IMMUNOGENETICS 57, 16-24 (2005).

Lopez-Vaamonde, C., Koning, J.W., Jordan, W.C. & Bourke, A.F.G. A test of information use by reproductive bumblebee workers. ANIMAL BEHAVIOUR 68, 811-818 (2004).

Dukes, J.P., Deaville, R., Bruford, M.W., Youngson, A.F. & Jordan, W.C. Odorant receptor gene expression changes during the parr-smolt transformation in Atlantic salmon. MOLECULAR ECOLOGY 13, 2851-2857 (2004).

Lopez-Vaamonde, C., Koning, J.W., Brown, R.M., Jordan, W.C. & Bourke, A.F.G. Social parasitism by male-producing reproductive workers in a eusocial insect. NATURE 430, 557-560 (2004).

Lopez-Vaamonde, C., Koning, J.W., Jordan, W.C. & Bourke, A.F.G. No evidence that reproductive bumblebee workers reduce the production of new queens. ANIMAL BEHAVIOUR 66, 577-584 (2003).

Youngson, A.F. et al. Management of salmonid fisheries in the British Isles: towards a practical approach based on population genetics. FISHERIES RESEARCH 62, 193-209 (2003).

Paulo, O.S., Jordan, W.C., Bruford, M.W. & Nichols, R.A. Using nested clade analysis to assess the history of colonization and the persistence of populations of an Iberian Lizard. MOLECULAR ECOLOGY 11, 809-819 (2002).

Paulo, O.S., Pinto, I., Bruford, M.W., Jordan, W.C. & Nichols, R.A. The double origin of Iberian peninsular chameleons. BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 75, 1-7 (2002).

Paulo, O.S., Dias, C., Bruford, M.W., Jordan, W.C. & Nichols, R.A. The persistence of Pliocene populations through the Pleistocene climatic cycles: evidence from the phylogeography of an Iberian lizard. PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES 268, 1625-1630 (2001).

Youngson, A.F., Dosdat, A., Saroglia, M. & Jordan, W.C. Genetic interactions between marine finfish species in European aquaculture and wild conspecifics. JOURNAL OF APPLIED ICHTHYOLOGY 17, 153-162 (2001).

Jordan, W.C. & Bruford, M.W. New perspectives on mate choice and the MHC. HEREDITY 81, 127-133 (1998).

Jordan, W.C., Verspoor, E. & Youngson, A.F. The effect of natural selection on estimates of genetic divergence among populations of the Atlantic salmon. JOURNAL OF FISH BIOLOGY 51, 546-560 (1997).

Jun 202011

I hope I’m going to submit my PhD student’s first comparative genomics paper very soon. Three of us have written the manuscript collaboratively using Google Docs. GDocs is an online word processor and although I’ve used it quite a bit before, this is the first time I’ve used it to write a manuscript with colleagues. Its been (almost) excellent, here’s the review.

I’ve had a number of manuscript experiences where I’ve spent long hours trying to collate different authors’ contributions into the same Word document. The idea of using GDocs is that multiple authors can have the same document open at the same time making changes without any conflicts or the whole thing crashing. You never have to ask “which is the live copy?” since there is only one copy.

Good parts

  • Nobody has had to collate mutually incompatible versions into one document and circulate (again) for people to check.
  • It is a clean GUI and a pleasure to use.
  • There is a good comment system and these are supplemented with a realtime discussion panel, just like Skype or other IM client.

Less good parts

  • It doesn’t work well in some older browsers. Tell collaborators to use Chrome, otherwise they may complain that its a bit rubbish and doesn’t work properly. Using Chrome there are few to no problems (ie better than Word).
  • You cannot use any sensible reference software. Mendeley, Zotero or any of the other reference managers you know will not allow you to insert references and format a bibliography the way you would in Word.
  • Track changes is not as good as in Word.

Google Docs revision history

Overall its been great I think. There are a few things I really wish were different. Track changes could be easily improved to identify who has done what. Yes versions of the document can be compared, and rolled back to previous versions, both of which are useful but none of it is quite as obvious and easy to use as in Word. More than anything I really wish that reference management was better. We have been typing in place holders (Smith 2000) and then exporting the document as a Word file and introducing the citations using a reference manager before submission. This sounds bad. Why not just do everything in Word? Well, even today, two of us were making some last minute changes on the Word version, each copy with someone’s initials appended and somebody tomorrow has to reconcile it all.

I think Google Docs if adopted widely would have a great impact on writing multi-authored manuscripts. I don’t think it will be very widely used in science though unless reference managers can integrate with it properly. Despite this I have really enjoyed writing a manuscript with it, and, even though it has to be passed through MS Word at the end, on the whole I’ve much preferred it.

Jun 142011

I’ve just finished marking a lot of different exam scripts for a several courses. I thought it would be fun to post some of the best quotes from student’s answers that have amused/appalled me over the last couple of years. These answers are from Molecular Genetics, and Evolutionary Biology exams mostly. Hull students are not well represented by this list, most do have really good answers.

Although the desert living sticklebacks, and the dangerous rock pocket mice hunting snakes and owls come close, my personal favourite is the effect of public health measures on Indian morality.

“Alternative splicing is hybridising two different gentetic sets such as a snake and a monkey”

“introns are removed by using exons which occurs using protein synthesis”

“most of this work is done on mices”

“DNA is made up of proteins which are made up of amino acids. Each protein has a series of codons which are 3 amino acids that code for different things that each protein does in order to synthesis the DNA, such as Stop and Start codons.”

“Both species of chimpanzee are omnivores, having being observed feeding both on vegetation, such as shoots and leaves as well as animals, such as termites or small vertebrae.”

“Although there isn’t much difference between some of the A. fulgerator’s colour patterns or adult faeces, which would normally be assumed meant they were the same species”

“All the rest of the population may fall victim to the new virus, meaning extreme death of all the organisms… “

“The saltwater sticklebacks have hard bony scales which help protect it from an attack by predators in the water such as sharks… “

“The semi conservative and dispersive where then tested again with the use of testing the density gradient. 14N + 15N. This is used to see the effect of the weight of density”

“Rock pocket mice… It’s main prey are snakes and owls”

“The Pleistocene glacial cycles caused much of northern and central europe to be pushed south to refugia in Iberia, Italy and the Balkans.”

“The genetic change do not have polytechnic effect”

“SOX genes are intronless, which means they do not contain an intron”

“By 1903, just in India the plague was killing a million a year. However, the morality rate was overall much decreased in this plague due to the increased public health measures, and eventually, antibiotics.”

“Wild sticklebacks have had to adapt to thier surrounding. Their wild and dry surroundings….. to help them to conserve water and live through desert conditions”

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 182010

Last January I made a list of (science) new year resolutions and made some predictions for the coming year. Thought I’d have a look back…

2009 Resolutions
* Read more. I used to read at least a paper a day during my PhD. Some PDF counting last year showed me I had averaged 3 per week over the last 10 years. I think I could get back to 1 per day with a bit of determination. I must concentrate the effort a little bit more though, no more reading up on snail biogeography just because I’ve found a cool one at the beach.
I’ve read slightly less papers, but many more academic blogs. Not yet sure what I think to this strategy, it may fall into the “snail biogeography” category (above), but on the other hand I have learned a lot, some of it even related to my research areas.

* Sort out my electronic lab book system
Success I think. My ELN is running very well. I have implemented it with students, mostly successful. I’m very pleased with the whole ELN thing.

* Add more to Wikipedia, especially species, and get into the habit of taking and posting images to Wikimedia.
I’m starting to get addicted to Wikipedia, and I’ve even suggested starting a Biology Reviews course for undergrads based on writing a Wikipedia page.

* Reread the Origin of Species (its been too many years)
Fail. I read about half of it over Christmas but then holiday ended and I stopped having any book time. Really enjoyed the first half though.

* Celebrate Darwin year!
Yes indeed

Resolutions for 2010

  1. Take 1 day per week purely for science (rather than bureaucracy)
  2. Teach myself some Second Generation Sequencing informatics
  3. Sequence my first genome
  4. Blog more (I have moved all the small “posts” to FriendFeed this year, but that is still no excuse)

2009 Predictions
Stuff that didn’t happen
* Creationists will exploit PR better than scientists to get their stories into mainstream newspapers and onto TV and we will see a new telegenic and ‘reasonable’ face of evolution-bashing.
I am very glad to say that this was wrong. A good year for evolution on TV.

Stuff that I didn’t notice happen and thankfully probably didn’t
* Some apparently maladaptive (to the casual public observer) part of the human body or disease susceptibility will be touted as a demonstration that evolution does not work.
* A famous, possibly well-meaning, UK politician will advocate ‘teaching the controversy’ (i.e. creationism alongside evolution in science lessons).
* Some evolutionary biologist you have actually heard of with a new paper disagreeing with some minutiae of evolutionary biology (maybe in some aspect of population genetics) will be put forward as a critic of evolution on a really slow news day.
* Steve Jones ‘evolution has stopped’ will resurface yet again and get more air time and column inches than all evolutionary biology research published in 2009 put together

Stuff that was almost right
* The Pope will give a speech extolling the power and vision of God in bringing his laws of evolution by natural selection into Darwin’s stubborn mind. I hope he remembers to mention Wallace too!
Close. “The Vatican has admitted that Charles Darwin was on the right track when he claimed that Man descended from apes. A leading official declared yesterday that Darwin’s theory of evolution was compatible with Christian faith, and could even be traced to St Augustine and St Thomas Aquinas. “In fact, what we mean by evolution is the world as created by God,” said Archbishop Gianfranco Ravasi, head of the Pontifical Council for Culture.” The Times, Feb 11 2009

Predictions for 2010

  1. New sequencing technologies will launch and emphasize why we should be calling 454/Illumina second (not ‘next’) generation sequencing.
  2. BBC reporters will continue to call DNA sequencing “mapping” in all possible situations until, finally, biologists agree to change their terms and alter all the textbooks
  3. Large scale sequencing and evolutionary analysis of flu will (continue to) make a really powerful case for evolution to the public, and there will be an evolution-centric TV documentary on flu
Aug 152009

In Britain Top Trumps cards have been favourite games of 5 to 11 year olds for at least 30 years (one of my most traumatic childhood memories is dropping my entire collection while crossing a main road and seeing it become Top Trumps roadkill). I recently bought my son the Dinosaurs set as in-flight entertainment when going on holiday. The cards describe lots of dinosaurs, and have good pictures and descriptions, but I’m really annoyed with the Stenonychosaurus (also called Troodon) card. They are perpetuating the very problematic interpretation of paleontologist Dale Russell which moves from the large brain to body mass ratio of Stenonychosaurus to conclude that they were very intelligent and then that this dinosaur would have evolved into a humanoid dino-man if only they hadn’t gone extinct at the K-T boundary. This has been criticized many times previously. This quote comes from a blog by Darren Naish

“Furthermore, the humanoid body shape is not a prerequisite for the evolution of big brains given that brains proportionally as big as, or bigger than, those of hominids are found in some birds and fish (that’s right: humans do NOT have the proportionally biggest brains)”

Although the dinoman is often labeled as a “thought experiment” it is thought but no discernible experiment. The idea of human(oids) as the pinnacle of evolution is quite pervasive and is an easy thing to pitch at kids. No wonder teaching evolution is so difficult. This is especially bad as the real Stenonychosaurus is really cool.

May 032009

I’ve moved out of my office while falling plaster and cracks in the wall (last years earthquake damage!) are repaired. While packing up I made a decision to see if I could get rid of most of the paper in my office (and not replace it). This is both for environmental reasons and also because I can never find anything when its a paper copy but a search through my hard drive is almost instantaneous.

The first thing I’ve done is get rid of almost all journal articles in paper form. I knew there would be a few exceptions to this where I have rare articles, but I intended that everything else would be kept as PDFs or not at all. I use the excellent Papers software for my literature.
This recycling worked quite well. I got rid of almost two filing cabinets, but I was expecting more. It turned out that some collections of papers, particularly those I use with students, just work better as physical copies. This is partly because some classic papers we need to go through together. I also found that some papers I am working with a lot (either because I need to read them 10 times to understand them or because they are important sources for something I’m writing) I find more comfortable as paper copies. In the end I kept more than I thought I would, but maybe this will change when I start the unpacking cull.

In all I estimate that I recycled about 600kg of paper (about the same as a large cow!). This truly amazing amount wasn’t mostly journal articles, but catalogs, old teaching material, all my back issues of Nature, Evolution, Molecular Phylogenetics and Evolution, Systematic Biology, TIG, manuals for old equipment, files full of old grant applications and folders of old data printouts.

I now need to buy a decent scanner and make sure I don’t start to restock my herd.

Feb 122009

Today is the 200th anniversary of Charles Darwin’s birth. But hey, you already knew that. All the images going around seem to have Darwin with a big white beard. But lets not forget that his Beagle voyage and much of his scientific work was completed when he was a young man. So this is really just an excuse to post an image of Darwin without a beard, this is a portrait from 1816 when he was 7 years old. I got it from the excellent Wikimedia Commons, and I really encourage you to post lots of evolutionary biology images there as free use content. There are many fewer images of Darwin, his work and other Darwin-related things than I thought there would be. I keep intending to take photos of some of his other books and post them, but last time I was struggling to get good shots- must try again.

A hat-tip to Google also for posting an excellent logo today.

Jan 302009

I started this blog one year ago. Its been a lot of fun and gone really fast. I’ve done approx 1 post per week on average, which is about as many as I anticipated.

I intended I would blog mostly on research:- phylogenetics, bioinformatics etc but I’ve not done as much of that as I thought. I’ve had less and less time available for research at work. I have to think about how to change that, but I’m still optimistic I’ll get to blog more research in the coming months.
I never got any time to finish creating, and blog about, enormous trees. I really need to get some clear time to make progress with this. I’ve also posted a bit on Darwin-related stuff, and even managed to get a creationist comment (a badge of honour think). I guess there will be more Darwin stuff during 2009.

I’ve used the excellent StatCounter to check out blog traffic. The vast majority of all traffic coming in after searches are googling for some variant of “electronic lab book”. I wasn’t expecting that, especially as I have only one post on the topic. Other searches are as varied as you would imagine. At least that was true until this week when Google searches for “Mike Majerus” and “What Darwin Didn’t Know” have, in just 3 days, swamped everything else from the last 12 months. That tells me that if I want this to be a well read blog I should post more on popular topics, especially BBC TV programs. But, to be honest, I really don’t care about that at all and I doubt I will change the mix very much.

This year my posting plans include-

  • Handling next-gen 454 sequence data from environmental surveys
  • Large 18s trees again from SILVA
  • Some visualisation stuff (I hope)
  • Genome-wide orthology detection
  • My electronic lab book experiences

Thanks for reading.