EvoPhylo

The monophyly of plants and insects

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.

Resolutions and Predictions

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

Take 1 day per week purely for science (rather than bureaucracy)
Teach myself some Second Generation Sequencing informatics
Sequence my first genome
Blog more (I have moved all the small “posts” to FriendFeed http://friendfeed.com/davelunt 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

New sequencing technologies will launch and emphasize why we should be calling 454/Illumina second (not ‘next’) generation sequencing.
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
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

From White to Meselson

Jan 162010

One of the most talked about ideas in genetic studies of asexual reproduction has been that of extreme Allelic Sequence Divergence (ASD), often called the “Meselson effect” after Matthew Meselson who is usually credited with this idea. In obligatory asexuals (apomicts), which never have the opportunity to recombine during meiosis, the once homologous chromosome pairs are now independent of each other. Their gene copies (previously normal alleles) can accumulate independent mutations, be subject to different types and intensities of selection, and diverge in structure and function without recombination bringing them back together again. Since homologous chromosomes contain the maternal and paternal alleles in meiotic (sexual) species these will in effect become independent genetic loci when meiosis is abandoned, much like gene duplicates elsewhere in the genome. Although they will start out as very similar, once meiosis stops they will start to diverge along independent trajectories and the prediction is that in ancient asexuals they will become very divergent indeed. There are some unusual phylogenetic relationships between apomict “alleles” too.Just like with gene duplicates there will be three broad classes of outcome.

One copy may accumulate debilitating mutations and become a pseudogene
Purifying selection may prevent the accumulation of many non-synonymous substitutions and the copies may continue to fulfill the same functional role.
They may diverge in function and become members of a gene family.

An interesting question is whether these apomicts can suffer from haploinsufficiency effects. Polyploid apomicts are more common, probably due to hybridization being a common way to originate apomixis, but do diploids apomicts suffer when option 1 or 3 (above) occur? Is 2 just a method of maintaining the di-allelic buffer that normal sexual diploids have?

I was reading MJD White (1945) “Animal Cytology and Evolution” last year and was struck by the similarity there to current ideas of extreme ASD.

“If we suppose an ameiotic form evolving for a very long period of time we might imagine its two chromosome sets becoming completely unlike, so that it could no longer be considered as a diploid either in a genetical or cytological sense.” (p283)

The divergence of chromosomes as described by White 65 years ago is, just like gene sequence divergence, continuous. I like this quote as a different perspective on modern ideas of extreme ASD in ameiotic species (Meselson effect). Did these ideas originate with White? Some of them it seems, but as always, its probably more complex than that. I would like to see a real review of the history of studies of asexual reproduction. I sometimes joke that if there is any doubt evolutionary ideas should just be assumed to originate with Haldane until there is evidence to the contrary.

The figure is taken from: Lunt, D.H. (2008) BMC Evolutionary Biology 2008, 8:194

Why kids don’t understand evolution

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.

Wolfram Alpha and Taxonomy

May 162009

I’ve been exploring Wolfram alpha the new “computational knowledge engine”. If you want to see what it can do have a look at the introductory screencast. It looks really interesting. Taxonomy and information about species is not what it does, its designed I guess to summarize and display primarily numerical data “GDP France / UK” will provide an answer (0.9197) and a chart of relative GDP of the two countries through time.

I tried it with a few species names. It couldn’t understand Meloidogyne incognita or Brachionus plicatilis and showed no signs that it recognized them as species names. Pan troglodytes, Turdus turdus, and Tyto alba however were recognized immediately and information displayed. I’ve displayed what you get below.

I quite like it in some ways. I like that they attempt to display species authority. I also like that it cites sources for the data.

I think its a bit prettier than Rod Page’s iSpecies.org, but I’m not sure the information is really as useful. Wolfram alpha results in general don’t seem to like linking out to other sites, maybe its an early marketing thing.

I then tried a few comparisons to see what it could calculate. I completely failed in all attemts to find a syntax that would produce the relative sizes of mice and elephants. “Compare mouse elephant” produced the taxonomy of the two and a branching network to show where they diverged, but it was really poor quality telling me that rodentia gave rise to mice without mentioning any other divisions (Sciurognathi; Muroidea; Muridae; Murinae) whereas elephants at least had Proboscidae and Elephantidae mentioned in their path.

After a bit of investigation it seems that when I type “size elephant kg” it returns an answer of 44,000 kg. Wow, big elephant. Wikipedia tells me

“The largest elephant ever recorded was shot in Angola in 1956. This male weighed about 12,000 kilograms (26,000 lb),with a shoulder height of 4.2 metres (14 ft), a metre (yard) taller than the average male African elephant.”

Hmmm, some investigation reveals Wolfram may be talking about the Elephant yoga publishing not the animal. I’m a little confused now what is being referred to, cumulative weight of their magazines I think.

I still think Wolfram looks interesting, and powerful on some topics, but taxonomy and species info isn’t where its strengths lie at the moment. Instead I cheered myself up by discovering that I may not die quite yet “life expectancy male UK”.

Paperless Office

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.

WordPress ELN and data files

Mar 072009

In my previous post I said that I needed to find out about associating data files with electronic lab book entries. I think I’ve got it sorted out now. Imagine you are recording an experiment and want to associate the actual data files with the post of your ELN blog. I don’t mean put the actual text there, rather a link to the file of whatever format.

In the post toolbar Upload/Insert area click on the last icon “Add Media”. You should then be in the “Add files from your computer” area. This doesn’t work for me and I have to click on the link that says “browser uploader” instead. Select the file from your computer and upload it. When it has uploaded you will see the details screen. Give the file an informative name as this will be the link text inserted into your blog post by default. If nothing much happens when you click “insert” then make sure you have clicked on the “File URL” button. This will add a link to download the file into your post. The actual files themselves are held in

domainname/wp-content/uploads (then year and month folders).

These data files are not backed up if you ‘export posts as xml’ as your backup strategy, but its easy enough to ftp a copy weekly, or even get a script to do it.

I normally fill my ELN with methods and conclusions and things to do next. I keep the data files and results archived locally and try to include the file name and location in the notebook (if I remember). Now I’ll move to keep both together in WordPress. It feels a much better arrangement, and I hope I will spend less time looking for the exact input file that generated a specific tree.

WordPress as ELN

Mar 032009

In my previous post I said that I had been testing software and decided that the new version of WordPress would be my electronic laboratory notebook (ELN). This post details some of the reasons.

WordPress is open software under a GPL license, allowing it to be distributed and modified. I really like this. There is a very large and active community of people supporting it. This means that even if WordPress HQ was hit by a meteorite tomorrow the software would be unlikely to die. Like Evernote (that I mentioned previously) WordPress exports as xml, but in a standard format that can be easily imported into Blogger or other software. It can also be made to export posts as PDF and MSWord via plugins. I can’t think of anything more important than having my data in easily interchangeable formats, I have changed my mind about ELNs before and I don’t want to be locked in.

Syncing: Since blogs are ‘on the web’ they are accessible from anywhere and cannot be out of sync.
Style: WordPress2.7 is very slick and attractive software indeed. More importantly since content and style are separate entities you can swap between >600 free themes. Yes, I know it still sounds superficial to be so worried about how it looks, but you will have to live with your ELN for years! I need flexibility to control appearance and layout. Beyond appearance WordPress2.7 has a lot of flexibility to control different aspects of your environment.

Other aspects of WordPress
Plugins: There are over 4000 community developed plugins to extend functionality. If its not there you could write it yourself. These include several functions I’ve become interested in using:- exporting posts as PDFs for archiving the last few months activity, automatically colouring code snippets, posting from pre-prepared templates.
Comments: I’m thinking primarily about my own use at the moment, but would like to use this with students and postdocs too. Sharing and commenting is very valuable.
Versioning: WordPress2.7 has a good, wiki-like versioning system. This is useful if you update an experiment and need to see exactly what changes you, or a lab-member, has made. Here are a couple of screenshots.

Privacy: This system allows you to implement your own level of privacy, from completely open, to selected users, to complete privacy according to your preference. I have thought about this issue quite a bit and implemented a private ELN for myself. If you come to different conclusions it is possible to allow selected users to subscribe, edit, author or administer as required.
Tags and Categories: The combination of categories (“selection”), subcategories (“hemagglutinin”) and tags (“dN/dS”) works better for me than just tags or just hierarchical folders.
“Press This”: the (strangely named) javascript button can be dragged into your browser and can be used to add selected text or the page as a blog post whenever you come across something. It isn’t as good as Evernote’s capture tool, but it captures text fine.
On the move: There is a WordPress application for iPhone/iTouch and other mobile devices. Posts can be emailed in too.

Something I’m not sure about yet is associating (non image) data. If I have an excel spreadsheet that is part of an experiment I believe I can upload it and then link to it from within the blog text. If I’m right that would be useful as it would permanently keep data and description together. The data files would then just be in an ftp-accessible folder on the server which I suppose could be backed up with a script. I’ll have to investigate more and see if this really is the case.

I tried WordPress out with a free blog hosted at wordpress.org. I used this for a while, but wasn’t entirely happy with the flexibility. The themes I wanted weren’t among those available and it isn’t possible to install plugins there. So although it was quite functional I decided to rent my own domain hosted at DreamHost. That is what I’m working with now, and in a post soon I’ll sum up my experiences both good and bad. Overall I’m quite happy with it though.

Electronic Lab Books 2

Mar 032009

Last year I posted about my search for an electronic laboratory notebook (eln). Since then I’ve had experience of several systems, and my ideas have changed quite a bit, so I thought it was time for another post.

I listed a number of criteria that I thought were important for my eln. I got it wrong however, it turned out that two of the things I valued most weren’t even on my list- synchronization and style.

Synchronization
I was at that time using journaling software, and syncing using either their internal capabilities to link to my .mac account, or later on using the excellent Dropbox to sync. This worked well 99% of the time, but 99% isn’t enough. I wanted my eln to be in perfect sync between work and home and NEVER get corrupted by conflicting changes. So I abandoned these journaling software elns despite the nice software.

Style
This sounds superficial, but I realized that using attractive software is very important to me. I spend most of the day working with my lab book, and I just can’t commit to using something spartan and ugly. I want to use a modern software environment that is attractive and well laid out. I was initially put off blogs and wikis not just because they are generally short of features but because most are really ugly to work with.

(Its not all about sync and style, I want many other things too, but I’ll discuss those specifically in a follow-up posting)

I’m impressed with Evernote, and seriously considered this as my eln. It works very well in fact, yet I have decided not to go this route. Evernote is proprietary software, which isn’t a deal breaker for me, but compared to many it has very poor export. It will export your data as an xml file, but as far as I can determine this xml file cannot be opened by any other application. If Evernote went out of business tomorrow could I get at my information? Well, the local copy would still work with the application but I would not be in a good situation at all.

So, having researched this quite a lot, I have decided that my eln will be WordPress. Not any blog, but specifically the new WordPress 2.7. I’ve been using it for 2-3 months now and I’m going to write why I’ve chosen it, and how I’m using it, in a following post.

Blogs have been discussed and used for eln before. I’m not suggesting a whole new approach here, just recording my personal experiences in finding an eln solution that works for me.

The Origins of Phylogeny

Feb 122009

I just saw a very interesting piece by Ben Zimmer, whose post details 144 words for which Darwin has the earliest recorded use in English (and he compares to Lincoln, who has one). One of these words is “phylogeny”. I was a little surprised because surely Haeckel invented the term phylogeny. Indeed he did, but on reflection he obviously didn’t write in english. The 6th edition of the Origin of Species (1872) includes this paragraph

“Professor Haeckel in his “Generelle Morphologie” and in another works, has recently brought his great knowledge and abilities to bear on what he calls phylogeny, or the lines of descent of all organic beings. In drawing up the several series he trusts chiefly to embryological characters, but receives aid from homologous and rudimentary organs, as well as from the successive periods at which the various forms of life are believed to have first appeared in our geological formations. He has thus boldly made a great beginning, and shows us how classification will in the future be treated.”

It seems that Haeckel first used the phrase in 1866 in “Generelle Morphologie der Organismen” as cited by Darwin above. Is the 6th edition the first one to include this quote? I’m not sure.

I think that 144 novel words indicates that, yes Darwin was inventive, but more than that he was also very well read, and did not confine himself to english sources.

Older Entries Newer Entries

The monophyly of plants and insects

Resolutions and Predictions

From White to Meselson

Why kids don’t understand evolution

Wolfram Alpha and Taxonomy

Paperless Office

WordPress ELN and data files

WordPress as ELN

Electronic Lab Books 2

The Origins of Phylogeny

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