27 February 2008

Blogrolling.

Coffee and Sci(ence). Compulsive reader and caffeine addicted, science blogger what's not to like? Bilingual, too. Allez!

And for those who like framing, go see some evo-inspired art: The Flying Trilobite. It's ace.

26 February 2008

Cue chorus of angels

Bora is angling for a berth on the new Beagle

How else can you explain the fact that he has singled out our very own Beagle Project Blog as one of ten "Excellent" blogs out of some 1500 blogs on which he keeps regular tabs (a fact divulged only after consuming at least two exceptionally large glasses of beer at the Radisson after the SciBlogCon in January)?

And as if that weren't good enough, it comes with a shiny new badge for our sidebar! Okay, so what if it looks like an eye exam for drunkards?

Sure, some people have actually had their work published in the Science Blogging anthology, but there are over fifty of them, and yet only ten of us! And sure, because this E-thing is a meme, probably the whole blogosphere will have one of these in their sidebar by the end of the week, but only ten of us can claim that we got ours directly from Bora.

Though no official rules appear to have come along with this thing, it seems that we're supposed to pick ten recipients on whom to bestow the badge. So without further ado, here are ten blogs, in no particular alphabetical order, that I deem Excellent (though like the others I am avoiding blogs from the Borg):
A Somewhat Old, But Capacious Handbag
Cephalopodcast
Charles Darwin's Beagle Diary
Free Range Academy
Inky Circus
The Barcode of Life Blog
The Dispersal of Darwin
The Other 95%
The Red Notebook
The Tiny Aviary

The 39 steps.

The Friends of Charles Darwin has 1961 members. We're not a confessional bunch.

FOCD was championing Charles Darwin (and evolution) long before it was as fashionable as it is in the run up to 2009, and got the great man on the UK £10 note. 39 more people are needed to join to hit the 2000.

Go find 'em and sign 'em up.

25 February 2008

Blogrolling...

A word of thanks to recently discovered bloggers for their Beagle Project support:

Hi to Sorting out Science for this splendid plug: The Beagle, Redux (ta, Dispersal of Darwin for the catch)

Also thanks for the blogroll to Amila at Gallicissa. A naturalist and birder in Sri Lanka he has make-you-weep-with-envy-rainforests to go at, so pop over for his terrific pics (not just birds, reptiles, insects and the occasional pic of his dinner...) and accounts of his days naturalizing in Sri Lanka.

If you've mentioned us and aren't on our blogroll, please let us know.

24 February 2008

'We'll need more sailing vessels'

as Nunatak wrote over at our old gaff. Well there's one more we definitely need. The French agree: they have started shipping Bordeaux wine using Belem, a 170 ft brig (left, or to port, as we sailors say when looking at a bottle of fortified wine). Using wind power to deliver 60,000 bottles of Bordeaux to Dublin will save 18,375 lbs of carbon, or 4.9 grammes per bottle. The bottles will be labelled 'Carried by sailing ship, a better deal for the planet.' Mais oui! We look forward to science being published similarly labelled.

In what has been a rather miserable week's news, read the whole charming Observer story here.

23 February 2008

Science in the media in the media.

The Archive Hour on BBC Radio 4 (Saturday, 8pm GMT) promises to be a good listen for those of us interested in communicating science and the media's mediating role.

In 'Putting it Simply'
Kathy Sykes charts the way that science has been seen and heard on radio and television, from the postwar lectures on the Third Programme to the animation of Walking with Dinosaurs.
The Archive Hour is usually Finest Kind Broadcasting, and I hope this lives up to the strand's high standards.

Should the programme provoke any debate about science communication in comments, please don't let it be dominated by the F word (framing). Listen live from the BBC Radio 4 website or if you're otherwise engaged you can listen at you leisure by going to Archive Hour homepage and use the archive to listen again.

Beagle shop traffic challenge: the results are in!

Alert readers will remember that about a month ago we revealed our top ten senders of traffic, which sparked an unexpected but highly enjoyable spate of rampant blogger posturing in comments.

One thing led to another, and, in the heat of the moment, I impulsively dangled a $25 Beagle Project shop gift certificate in front of the two most rampant of the posturers (posers?).

And so, with that, the battle was on between Kevin Z of The Other 95% and Michael Barton of The Dispersal of Darwin to see who could send the most traffic to the shop between January 22 and February 22. To prevent cheating, I made them give me their IP addresses so that I could exclude their own computers from the MyBlogLog tally.

At the fortnight mark the two were in a dead heat. Each of our earnest bloggers had sent exactly 31 hits to the shop. It really could go either way, folks...

Envelope, please.

Wow, it's a photo finish! Just a single shop hit separates the two contestants!

And the winner is... with 64 shop hits, The Dispersal of Darwin!

Let's all congratulate Michael Barton, who will be shortly receiving his very own CafePress gift certificate for $25 worth of Beagle swag. And to cheer up our Kevin Z, why not head over and pump up his ego by leaving a (nice) comment or two on his Beagliciouis Beagle swag promo post.

Of course, in the end, the real winner is the Beagle Project, which gets commissions on all shop purchases. In fact, just this week, we passed the $350 mark in shop commissions, a small but very meaningful boost in the right direction! So thanks to Michael, Kevin, and everyone, for buying our swag and helping to build the new Beagle!

22 February 2008

Darwin caught crabs

while on HMS Beagle. According to the BBC these specimens 'faded into obscurity' (did that make them hermit crabs?) before being rescued by the Oxford University Museum of Natural History. Darwin's Beagle crabs are now available on O.U.M.N.H. Darwin database.

The whole tale is best told (with pics) in an Oxford Science Blog post by Pete Wilson.

21 February 2008

Daydream plagiarists

It seems those crafty cartoonists at xkcd have gone and stolen my very own personal daydream complete with real life context, below. I demand royalties ...which will of course be put immediately towards building the new Beagle.

Note: these three panels are part of a 10-panel comic called "To Be Wanted". Click it to see the rest.

20 February 2008

Mr February

Whose tat is that?

Click it.

You know you want to.

Let's walk sail around the world

This xkcd comic goes out to my Real-Time Blogging in the Marine Sciences peeps:

Click the panel to see the whole comic strip, then substitute "cruise" or "sail" for "walk" and there you have it.

19 February 2008

"Charles Darwin and I first met under a rock"

Michael Barton's review of The Voyage of the Beetle by Anne Weaver and George Lawrence makes me desperate to be 9 years old again.

The subtitle is charming (A Journey around the World with Charles Darwin and the Search for the Solution to the Mystery of Mysteries, as Narrated by Rosie, an Articulate Beetle) and smacks of Darwin's own long-winded subtitle.

After you're done reading Michael's review, don't miss the book's companion site.

Now I know exactly what to buy for all of the children in my life on their 9th birthdays!

Making young people study science.

The title of a Daily Telegraph business blog post which reports that Prime Minister Gordon Brown's Business Council is mulling whether to lower university fees on science and engineering courses compared to the fashionable (and easier) humanities, arts and media studies courses which are attracting rakes of students and therefore lots of cash.

According to the author Mr Tyler:
The business bigwigs, who include among their number Mervyn Davies, chairman of Standard Chartered; Sir John Rose of Rolls Royce and Sir Terry Leahy of Tesco, all apparently agree that if Britain is to remain competitive something radical must be done to encourage young people into science and engineering.
Well I can think of one thing, and it's to build and launch a replica HMS Beagle for 2009. I feel three letters coming on. Standard Chartered, Tesco and Rolls Royce could dob in £1 million each and we'd be flying. I mean sailing.

Check out the comment, too. The commentator makes the point that even well-qualified scientists are poorly paid. Others lament the lack of career path or security in many sectors of UK science. You might be able to 'make' young people study science by compelling them to sit in the lab, as many of my classmates were. But the point, surely, is to inspire them. And that takes more than just chopping university tuition fees.

18 February 2008

Natura non facit saltum...umm?

The following is a guest post from Nicole Maturen, a PhD student in evolutionary developmental biology (evo-devo), who had to write a blog post as part of an application for an internship at an eminent open-access journal. Though publication of the post on an actual blog was not a requirement of the application, I thought it would be a real shame for such a gem to moulder away on a single lonesome hard drive. So, without further ado, over to Nicole! - nunatak

As noted on this blog earlier, this year’s celebrations of Darwin’s birthday were preceded by a bit of blog fanfare. I am happy to report that the goods were delivered during his Party at the Natural History Museum, London and that the warm-up toward 200 is going well.

Brian Charlesworth for PopGen opened the party-gritty with an overview of his field’s approach to the question of whether or not evolution makes jumps. The closest thing that he gave to an answer was the story of the Fisher --> Fisher + Kimura --> Fisher + Kimura + Orr geometric model of adaptation. QTL mapping data and this current model are in fairly close accord that the genetic change between (presumably closely-related) species comprises a small number of significant ‘hops’ followed by generous fine-tuning. So perhaps we can answer yes – or at least say that some steps that evolution takes are larger than others.

Brian also left us with two gems: 1) a careful disclosure of the assumptions behind the models that mold the way we think about these questions and 2) a handy review in case any of us had gotten a bit lost.

Next, David Stern for EvoDevo told several exciting stories (with data and pretty pictures). First, the story of Shavenbaby, a locus privileged among many in the genetic network of Drosophila by it’s switch-like position. It appears that Shavenbaby, which codes for a transcription factor controlling trichome development, has been turned on and off in the genus in a specific and reversible way multiple times. Upon closer inspection, we see that it actually consists of several switches; different parts of the gene which control distinct zones of its expression have been switched on and off separately. Thus, what appears from one vantage point to be a ‘monster’ mutation is actually the composite effect of several changes. It’s a question of scale, as we’ve heard twice before at Darwin’s birthday party, and as we read in this year’s assigned pre-party reading on the meaning of punctuated equilibria.

The mutated parts of the Shavenbaby gene are bits of sequence in the promoter region; it’s not the product of the gene, the protein molecule, which is different among these species, but rather the regulation of when and where the molecule is active. David also spoke about The Database of Evolutionarily Relevant Mutations (and welcomed any suggestions for a pithier name). One goal of assembling such a database was to address the question of how genes usually evolve new expression patterns – through mutations in regulatory elements, the favored hypothesis, or through mutations in the structure of a protein. One of the most interesting patterns to emerge from the data is a much higher incidence of regulation-type changes between species than within a species, as also found in this study.

In his rebuttal to Olivia Judson, Jerry Coyne argues that a jump, or macromutation, almost always produces a sickly organism (who is unlikely to pave the way for a new species) because of the multiple and necessarily deleterious side-effects of such a big-impact mutation. David Stern would agree, but he points out that all loci are not created equal, that is, they don’t occupy equivalent positions in the genetic network of an organism, nor do all mutations occur in equivalent positions in the genetic structure of a locus. Some changes, e.g. regulatory, in some types of genes, e.g. switches, produce clean(er), (more) functional mutants than average. David suggested that the mutations that lead to (macro)evolution might be those rare, non-pleiotropic ones, simply because they are non-pleiotropic (see this paper).

To conclude, David left us with a plea for MORE DATA about both the genetic architecture and the population dynamics of a range of organisms, to which everyone, even the spirit of Darwin himself, could happily raise a toast.

17 February 2008

Would that which we call a rose, by a DNA barcode, smell as sweet?

ResearchBlogging.orgFor my second post on peer-reviewed research (I suppose I'll have to stop introducing it like that after three or four), I've chosen a paper that gets right to the beating heart of my own tiny little corner of science geek-dom: DNA barcoding in plants.

To make things more interesting, the science press worked themselves into a premature and, as I will argue here, seriously specious frenzy last week when they collectively oohed and ahhed about the paper in terms that were well, let's just say, um, how do I put this delicately ...flat wrong.

So first, as is right (though apparently not at all customary) to do before trumpeting a paper's "conclusions" far and wide, why don't we have a look at the paper itself?

In the article (open access in PNAS), Renaud Lahaye and colleagues of the University of Johannesburg, with co-authors from Lankester Botanical Garden in Costa Rica and Imperial College London, and senior (and corresponding) author Vincent Savolainen at Royal Botanic Gardens, Kew, report the results of their significant new evaluation of eight proposed DNA barcodes in plants.

A DNA barcode is a short snippet (less than 600 base pairs) of a organism's native genome (billions of base pairs) that should contain enough unique information to accurately identify an unknown specimen (for example, a piece of mystery meat in a Japanese whale fish market) to the species level. This is to be done by comparing the sequence of the query snippet against a comprehensive database of sequences from specimens that have been identified and vouchered by expert taxonomists.

Importantly, a DNA barcode is not just any unique snippet of an organism's DNA, but the same snippet in all organisms, slight variations within which provide the sought-after species-specific signal. In other words, all DNA barcodes are ultimately descended from the same gene that was present in the common ancestor of all living organisms. Uh oh, creationists aren't going to like that, are they? They're especially not going to like the fact that it works.

Well, to be more accurate, it works for animals. See, the first big question that has had to be addressed to implement DNA barcoding as a common procedure for identificaiton is: which snippet? Finding a good DNA barcode is more difficult than it sounds. It has to have undergone just the right amount of mutation during its long evolutionary journey such that the differences between species (interspecific variation) are not swamped out by the differences within species (intraspecific variation). Unfortunately, finding a gene that harbours this sweet spot of variation, called the "barcoding gap", is like finding a needle in a haystack.

It was with great excitement, then, that in 2003 a group of Canadian scientists reported that a gene called cytochrome oxidase 1 (CO1) seemed to have just the right amount of variation. They showed that just about every species of animal has a unique CO1 sequence, and that the "barcoding gap" was nice and big (though serious doubt was later cast on this claim when Chris Meyer and Gustav Pauley showed that in three groups of marine gastropods the "barcoding gap" was an artifact of insufficient sampling). This meant that by comparing the sequence of an unknown animal’s CO1 gene back to a reference database of CO1 sequences built up from all known animals (which, as Meyer and Pauley argued, had better be extensively sampled and taxonomically sound), we would have an excellent chance of working out the species identity of the unknown animal.

Well that's just dandy for all those zoocentrics out there, who have already databased barcodes from hundreds of thousands of vouchered specimens, but what about plants? I mean, wouldn't it be great to be able to validate the identity of herbal extracts or rapidly survey the diversity of dormant seeds in the soil in a proposed conservation area? Well, unfortunately, CO1, though present in plants, is not variable enough in land plants to use in species identification (though it does seem to work for some marine algae). Land plants also pose other problems, like hybridisation, duplicated genomes and asexual reproduction, which may mean it’s not even possible to find an ideal DNA barcode in plants. In other words, the search is on.

Though there's a Science News Focus on this quest for the holy grail? a universal land plant barcode, it's subscriber-only (boo), so here's a quick list of the plant barcode candidates floated by various teams of investigators over the last three years:
As you can plainly see, plant barcoding is, as a discipline, one big ol' entangled bank. So what's a wannabe botanical barcoder to do?

Lahaye et al seem to have opted for the bigger is better approach: they tested all of the above (with the exceptions of the trnL intron and atpF-atpH) on a more challenging set of plant specimens than had yet been tested (previous barcode trials have necessarily had to examine a very broad taxonomic range with minimal in-depth sampling within species, and have not attempted to discriminate specimens from particularly species-rich areas that are likely to cause the most difficulty). As the authors put it, “the critical test of evaluating the applicability of DNA barcoding for biodiversity inventories in species-rich geographic areas has been lacking.”

Lahaye et al test the eight barcodes from specimens from not one but two of these "species-rich" areas: Costa Rica, where they focus on orchids, and Kruger National Park in southern Africa, where they focus on trees and shrubs.

On first glance, it seems that they have collected and tested a truly eye-popping number of specimens (1,667!) but as you read the paper more carefully you see that 1,495 of these were orchid matK sequences "collected" from GenBank (which, it must be said, is notorious for its bad taxonomy), and only the remaining 172 specimens (101 southern African trees and shrubs and 71 Costa Rican orchids) were tested against all eight candidate barcodes. Nevertheless, it's still a (slightly) more comprehensive effort than has previously been carried out, and the increased "sampling" provided by the GenBank accessions does seem to enable a robust examination of the "barcoding gap" for matK.

So, here is a rapid-fire summary of the main results:

1. With the exception of ndhJ an ycf5 in orchids, PCR amplification reactions were successful. This is not just a methodological afterthought, but rather an important result considering the fact that finding good, universal primer pairs (especially for matK) has been a real problem for the plant barcoding community.

2. Inter- and intraspecific genetic divergences were calculated, and the size of the "barcoding gap" assessed for each candidate barcode (I was very pleased to see that they used the Meyer and Pauley metrics for this). Both matK and trnH-psbA performed fairly well here (i.e. of the eight barcode candidates they had the highest inter- and lowest intraspecific divergences), though, as Meyer and Pauley would have predicted, no large barcoding gap was found. That said, analysis of the large matrix of (mostly GenBank) orchid matK sequences revealed a pretty darn good barcoding gap if you ask me:


Figure 1I from Lahaye et al shows the "barcoding gap" between interspecific divergence (yellow) and intraspecific distances (red) in the matK gene among Costa Rican orchids.

3. matK sequences were able to detect "cryptic species" (real species boundaries masked by physical similarity) in the orchid data set, certainly a good sign, since that is one of the eventual utilities of a DNA barcoding system. For example, one of their four samples of Lycaste tricolor did not cluster with the other three as expected and thus it may be another, separate species. To find out if it actually is another species, some real taxonomy will need to be done.

matK sequence data pointed to a potential "cryptic species" hiding amongst four samples of Lycaste tricolor.

So, in conclusion, Lahaye et al argue for the adoption of the matK gene as the universal DNA barcode for land plants (with an option for use of trnH-psbA as an alternative or complement to matK). matK had been previously tut-tutted because it was difficult to amplify from many different groups of plants, but this seems to have been overcome here by a particular set of primer pairs (390F and 1326R from Cuenoud et al., 2002) which amplified with "100% success".

However, and this I think is one of the key take-home messages here, Lahaye et al found that the power of matK and/or trnH-psbA to correctly identify species was only approximately 90% and that therefore "we may need to accept that no more than ~90% of species will be identified with universal plastid barcodes and that those difficult lineages will need 'case-by-case' analyses, using, for example, nuclear population genetic markers and taking advantage of recent developments in DNA sequencing technology."

Hmm, very provocative. *smiles knowingly*

To wrap things up here, I'd like to end where I began, with the premature media hype that preceded the publication of this paper. Various sources claimed that in this paper, a DNA barcode for plants has been "mapped", "revealed", "finally revealed", "found" "identified", "determined", "decided", or even just simply "is". Based on what you've read here, do any of these sound even remotely accurate?

Don't get me wrong, this paper is an important contribution to plant DNA barcoding, which is why I have chosen to blog about it in some detail here, but it is, in essence, just another proposal in a long string of proposals. To the authors' credit, they did not claim to have made The Final Decision on the identity of the plant DNA barcode(s), but the press sure did.

So, to get the bad taste of sensationalist hyperbole out of our mouths, I thought I'd leave you with some nice minty-fresh alternative headlines. How about:
"Candidate DNA barcodes for plants tested in largest study thus-far."
Or, if it must be short and sweet:
"DNA barcodes for plants tested" or "Plant DNA barcode proposed".
Now, how hard was that?

---------------------------------------

Lahaye, R., van der Bank, M., Bogarin, D., Warner, J., Pupulin, F., Gigot, G., Maurin, O., Duthoit, S., Barraclough, T.G., Savolainen, V. (2008). DNA barcoding the floras of biodiversity hotspots. Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0709936105

Hebert, P.D., Cywinska, A., Ball, S.L., deWaard, J.R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences, 270(1512), 313-321. DOI: 10.1098/rspb.2002.2218

Meyer, C.P., Paulay, G. (2005). DNA Barcoding: Error Rates Based on Comprehensive Sampling. PLoS Biology, 3(12), e422. DOI: 10.1371/journal.pbio.0030422

14 February 2008

Real time blogging from the North Pacific Gyre

Well, it doesn't get much more timely than this: in January I helped herd cats co-moderate a session at the SciBlogCon called Real-Time Blogging in the Marine Sciences (watch the session video). Then, early this month there was a spike of blog posts about the plastic mire in the North Pacific Gyre.

So, you can imagine my delight when Bora sent me a link to a real-time blog in the marine sciences, posted daily from none other than a research expedition to collect the plasticky plankton in the Gyre! It's the blog of the Research Vessel Alguita and here's their gig:
On January 2oth, 2008 ORV Alguita set out on a winter expedition through the North Pacific Gyre, sailing from Hilo, HI to Los Angeles, CA to conduct further research on oceanic plastic debris. The crew of 6 will collect samples for lab analysis, as well as for future Algalita Marine Research Foundation education projects.

Analysis from Algalita's September 2007 expedition shows a five fold increase in plastic quantities in the Gyre since Captain Charles Moore began his research in 1997. This next Algalita Expedition will build upon earlier data, and gather new information to provide a more complete, scientifically accurate picture of the issue's scope.
What a project! And what a blog, too, all full of day-to-day science-ey seafaring adventure!

Okay, okay, so both Oyster's Garter and Deep Sea News got there first but who's competing? This is a very worthy project that should be blogged again and again. Who's next?

Update (17 Feb): My significant other just reminded me of this priceless scene from The Graduate that simply can't not be included in this post...

13 February 2008

Dispersal of Darwin

...relays a very (very!) exciting announcement from Cambridge University Press all about Darwin, evolution and the Beagle. For more info you will have to click on over there.

Beagle victorious!

Uno the beagle wins Westminster! I don't believe in "signs" but if I did, I'd say this is a good one: read my 11 Feb post for more about the many links between dog and ship.

12 February 2008

Been a pretty good Darwin Day so far...

firstly Nunatak and I get the Darwin Day, the Beagle Project and some science on BBC Radio (see below), then, popping over to Pharyngula's Darwin Day post to share the joy and thank the scibloggers for their support, I was tempted into a comment by someone raining on our parade. PZ then awards us the Internet.

OK, the Internet is up for sale for $3 million to fund the Beagle and for that you get to helm the rebuilt Beagle into the Galapagos.

Beagle bloggers on BBC Radio!

It is 7pm now in the UK and I am delighted to announce that it has been a truly banner Darwin Day for your humble Beagle bloggers!

We were on BBC Radio for a solid five minutes, complete with ocean sound effects and audio clips from the BBC's much loved 1978 documentary about the voyage.

Listen again here. If you are listening before Wednesday 6pm GMT, simply click the "Listen to the latest edition" button. If it's after Wednesday 6pm you'll have to click "Tuesday edition" in the right sidebar. The interview starts at minute 22:58.

Peter steals the day with his gripping reading of Fitzroy's "sorely tried" passage and a hilarious comment about how if he'd been there he'd have wet himself.

There is also a blog post associated with the airing, written by BBC's Chris Vallance, who interviewed us. The post has an excellent supplementary interview with Darwin's great great grandson and author of Annie's Box Randal Keynes, who very kindly sings our praises (unprompted!).

Happy Darwin Day from all at the Beagle Project.

11 February 2008

Best in show

We spend a lot of time filtering dogs out of our news alerts. We even get the occasional email from a baffled breeder wanting to know what sort of kibble will bring out the best shine in his dog's coat.

Normally these items are instantly consigned to the electronic rubbish heap, but today seems like as good a day as any to give a shout out to the HMS Beagle's namesake.

According to Yahoo News, Uno, left, is best of the beagles at the 2008 Westminster dog show. With any luck, he'll go all the way and win Best in Show tomorrow, which also happens to be Darwin's birthday. Coincidence? Perhaps, but it's not the only one. You see, reading the Yahoo piece, I couldn't help noticing the parallels between beagle the breed and Beagle the ship.

For example, Ben Walker quotes Westminster host David Frei as saying, "Great show dogs often have an air about them. It's like this is their world and we're just living in it, but beagles want to be in our world." I can think of another Beagle that wants to be in our world.

Then Walker quotes Eddie Dzuik, one of Uno's co-owners, who said, "To have the general public see an average dog going and competing and actually winning would send a signal that everyone can do it." Everyone can do it: that is also the message of The HMS Beagle Project, except we're talking about science not the Platonic result of an intensive breeding programme.

"A beagle winning would bring down the house," Frei continues. You might say that the new Beagle will bring down a few ivory towers, too, by promoting participation in and understanding of science in all social quarters.

But the parallels don't end with the article. After all, an important part of Darwin's formulation and explanation of the theory of natural selection came from contemplating the results of artificial selection. Sure he focused primarily on pigeons in his masterful exposition, but he also pays quite a lot of attention to dogs. Just as Uno is the result of artificial selection for all the traits deemed essential to beagleness, so is the wolf the result of natural selection for traits that imparted enhanced survival and reproduction.

Maybe in 2009 Uno will agree to pose for the carving of the new Beagle's figurehead. I can think of no better emblem. Go Uno!

Update (12 Feb): Uno wins best in group!

Update (13 Feb): Uno wins best in show!

Beagle Projecteers go live on Darwin Day

Tomorrow is Darwin Day and it is chockablock with Beagle Project online goodies and other London events:

Tuesday 12 Feb 12:30 GMT
I (nunatak) will be speaking on "Darwin the young explorer" at the Natural History Museum in the Nature Live venue (live stream here). And no, I don't want to hear anything about how they chose an image of old Darwin to advertise the talk. Not my doing, nosiree. If it had been up to me, they'd have used the image at right, or something like it.

Tuesday 12 Feb 17:00 GMT
Peter Mc and I will be interviewed on BBC Radio 4's PM programme. You will have one week to listen again here.

Tuesday 12 Feb 18:30 GMT

Annual Darwin Day lecture at University College, London. This year, Tim Lewens of University of Cambridge will be lecturing on "Charles Darwin: a philosophical naturalist", and the session will be chaired by Professor Richard Dawkins. More info at the New Humanist blog.

Wednesday 13 Feb 16:00 GMT
If you are in London be sure to attend the now storied "Charles Darwin's Birthday Party" also at the Natural History Museum (event pdf). The title, "Nature does not make leaps ...or does it?" is oh-so-topical considering the latest brouhaha about hopeful monsters/saltation, punctuated equilibria and the like.

Image of Darwin the young explorer from Dispersal of Darwin.

10 February 2008

DSN Just One Thing Challenge #3 (UK Version)

Deep Sea News has just announced the third installment of their very important and worthy Just One Thing Challenge, a call for readers to pledge to do "just one thing" every week to help save the deep sea.

Now, being an American expat, I am fortunate (very fortunate) to know what "Trader Joe's" is but I'm guessing most of DSN's readers outside the US will have no idea what they are talking about. So, here I provide the information necessary to propagate DSN's Just One Thing Challenge #3 to a European audience.

For a long while, the Monterey Bay Aquarium's Seafood Watch was the only sustainable fish list in town. This was fine for North Americans but over here in the UK the list didn't make much sense. Only about half the species on the list were even sold over here, and there were a whole bunch of new ones that I'm sure hadn't been rated at all by MBA. Fortunately, the idea has caught on and now there are guides springing up all over the place. The MBA's Seafood Resources page is awesome. Click it. It lists all guides available by country. In the UK, we have the Marine Conservation Society's Good Fish Guide (pdf) and the FishOnline database with lists of fish to eat and fish to avoid.

To take that final step for DSN's Just One Thing Challenge, though, you need to write a letter to a supermarket (or better yet your local fish and chip shop!) to encourage them to source their seafood more sustainably. Fortunately, FishOnline tells me that British supermarkets, especially Waitrose, Marks and Spencer and Morrisons, are actually doing pretty well on the fish sourcing front. Fish and chip shops, though? ...them's a whole 'nother kettle of overfished cod.

9 February 2008

Down at the corner shop this morning

Health and safety disclaimer for readers outside the UK: News of a Darwinny treasure trove that you can't get your hands on might induce an envious green lather, with possible health consequences to those faint of heart. So, before you read on, please be reassured that every iota of content both pictured and not pictured here is available online.




8 February 2008

Dawkins on Darwin: free in the Guardian tomorrow

Saturday morning checklist: Coffee? Check. Toast and jam? Check. Pajamas and a nice comfy spot on the couch? Check. 34-page booklet by Richard Dawkins on "Why Darwin matters?" available for free in this Saturday's Guardian? You better believe it!

7 February 2008

The Beagle Project on the BBC and cut dead by creationists on a train.

Just returned from being interviewed for BBC Radio 4's PM programme for Darwin Day (Nunatak is next on his interview list). On the train on the way home I ended up sitting next to the journalist who'd interviewed me for a couple of stops. We yarned on about science, Darwin, Beagle etc.

He beetled off. A station or two later an elderly gentleman was getting ready to disembark, and was in something of a pother. Parkinson's, he explained as I helped him into his coat, put his bag around his neck (according to his precise instructions) and handed him his hat and stick. He'd been earwigging on our conversation and asked me what it was all about. I gave him the Beagle Project in a couple of lines.

'Well I'm a creationist and I hope you fail,' he said with some vehemence and doddered off without a word of thanks. Kindnesses from an evilutionist just ain't worth a civil word.

The interview will also be used on the BBC Radio 5 Live 'Pods and Blogs' (their blog here) section. I mentioned as many of you as I could fit in.

5 February 2008

Survival suit oneupmanship: a photo call

Competition has been in the air these last few weeks on the Beagle Project Blog, and it sure hasn't done any harm to our traffic. So, to keep the profitable tooth and claw theme going...

Just in case Kevin Z thinks he's the only one with a goofy photo of himself in a survival suit, here's yours truly volunteering for disaster drill duty on a ferry between Norway's Lofoten Islands and Bodø on the mainland.

Come to think of it, this could be the start of a great photoblog featuring scientists (that includes all those wonderful amateurs out there without whom the science of natural history would be in the gutter) in fantastical and/or embarrassing fieldwork gear. Please paste links to your photo submissions in the comments below.

(Confession at the outset: my photo here should probably be disqualified from appearing in the proposed photoblog because I'm not donning the suit for science, I'm just being silly while on holiday. However, I hope you'll agree, it does get the ball rolling nicely.)

Attenborough does it again

The newest David Attenborough Life series began airing last night on BBC One. This one is called "Life in Cold Blood", about amphibians and reptiles. Here's a video clip:


Sigh, every time an Attenborough special comes out (and, it must be said, at almost no other time) I curse myself for not having a TV. I'll get the DVD soon enough I suppose, but it's not quite the same as witnessing it simultaneously with millions of rapt British viewers.

The Life series began in 1979 with Life on Earth (I'm sure I'm not the only one with vivid memories of this), then The Living Planet (1984), The Trials of Life (1990, in which an orca tosses a seal out to sea and plays with it like so much bouncy play-doh), Life in the Freezer (1993), The Private Life of Plants (1995, one of his most popular and certainly my favorite), The Life of Birds (1998, in which a lyrebird memorably mimics the sound of a chainsaw), The Life of Mammals (2002, one word: pikas), Life in the Undergrowth (2005, in which super high-speed film reveals all sorts of invertebrate acrobatics) and now Life in Cold Blood (2008).

Rumour has it that Attenborough's next special is on Darwin, which gets us Beagle Projecteers all giggly. It is my fantasy that he'll agree to narrate or even write a series about the voyage of the new Beagle. He would most certainly be welcome aboard at any and all stages of the journey, not least so that I can shine his deck shoes (though I'll bet he wouldn't let me). How 'bout it Sir David?

3 February 2008

Detecting natural selection: a pika's tale

ResearchBlogging.orgChoosing a paper for my inaugural "blogging on peer-reviewed research" post was a real no-brainer. Anything that has both my favorite theory (natural selection) and my favorite animal (pika) in the title, and is published in my favourite journal (PLoS ONE), is the peer-reviewed equivalent of a flashing neon arrow.

Equally alluring is that the paper (Yang et al, 2008) offers me the chance to do battle with the the popular misconception that all evolutionary change is brought about by natural selection.

At this point I expect that some of you are scratching your heads and thinking "but isn't Darwin famous for evolution by natural selection?" and a smaller number of you are nodding your heads knowingly.

This post is aimed more towards the head scratchers than the head nodders (though far be it from me to discourage my fellow nodders from reading on and enjoying the sheer scientific pleasure of it all).

So, back to natural selection and why it's not all she wrote. Even the head scratchers will remember that natural selection is the mechanism proposed by Charles Darwin and Alfred Russel Wallace to explain the observable fact that organisms change through time.

Evolution by natural selection as they conceived it, and as we still know it today, is an adaptive process. Adaptive evolution is when 1) a new trait arises in a population because of a random, heritable change (which we now know is caused by a genetic mutation) and 2) the trait confers a non-random reproductive advantage or disadvantage. The end result is that the new trait will be preserved or discarded respectively by the process of natural selection.

For roughly sixty years after the publication of Darwin's On the Origin of Species by Means of Natural Selection in 1859, the scientific (if not wider) community was fairly content with the idea that natural selection was the sole agent of evolutionary change. In the meantime new areas of research bubbled up, not least genetics, and started making people itch for some way to integrate their new understandings in an evolutionary framework. Then, in the 1920's, along came Ronald Fisher, Jack Haldane, Sewall Wright et. al. and their brainchild, the modern evolutionary synthesis. Not only did it unite evolution with genetics but it also introduced a new competitor to natural selection called "genetic drift".

Genetic drift starts out in the same way as natural selection, with a random genetic change occurring in a population of organisms. With genetic drift, though, the change doesn't bestow any particular advantage or disadvantage on the organisms that carry it. Nevertheless, by pure chance (described mathematically in terms of probability), some genetic variants are carried forward (fixed) in the population while others simply fade away. This can cause evolutionary change without having to invoke natural selection.

So, to summarise so far:
Natural selection = random change + non-random (adaptive) selection
Genetic drift = random change + random (neutral) selection

Phew, after that bit of mental exercise, I'm ready for some light entertainment: cue tablas, enter pikas, stage right.

Pikas are...
  1. energetic little denizens of the alpine realm who collect wildflowers and belt out high-pitched warning calls from their prominent perches in the talus.
  2. members of the order Lagomorpha, which also contains rabbits and hares.
  3. indisputably cute.
  4. both harbingers and victims of climate change5.
  5. useful for studying the mechanisms of evolution, in particular detecting adaptive evolution and exploring its genetic and physiological mechanisms (keep reading).
  6. Did I mention cute?
So, pikas are not only cute (did I mention that?) but have also recently made an appearance in PLoS ONE precisely due to their generous participation (it must be acknowledged) in an evolutionary biological study that addresses point 5 above.

Let us all now put ourselves into the shoes of the pika researchers (sigh). Pikas, unlike other lagomorphs, live exclusively in cold, usually high alpine, environments. It seems an obvious thing to immediately start asking questions like "what selective advantage over the other lagomorphs do these animals have that has enabled them to colonise these cold, high places? Is it some kind of cold-tolerance? A dietary adaptation? Resistance to the effects of high altitude?"

In Darwin's day, it would have been just fine to mentally browse this set of questions, but since the modern synthesis, we know we have to be a little bit more careful. The first question we must ask is: do pikas differ (e.g. in appearance, behaviour, habitat) from other lagomorphs because of natural selection, or because of genetic drift? Most of us, of course, are rooting for natural selection so that we can have fun investigating our more advanced questions such as those mentioned above.

But how on earth does one go about separating the natural selection wheat from the genetic drift chaff?

Fortunately for us, some very clever people (Kimura M, 1983; Ohta T, 1992; Yang ZH et al, 2000) figured out that they could do it by taking advantage of a quirk of the genetic code (for an informative and humorous refresher course on the genetic code, I recommend A Somewhat Old, But Capacious Handbag).

Here's how it works: the genetic code translates the four-letter alphabet of nucleotides (the A's T's G's and C's of DNA) into the twenty-letter alphabet of amino acids (the lysines and arginines etc. of protein). Just as our English alphabet of just 26 letters can, by being combined into multi-letter words, encode millions of unique meanings, so can different combinations of the four nucleotide "letters" encode 20 unique amino acid "words".

As it turns out, the dictionary of amino acids is made up entirely of three-letter words, called codons. There are more possible three-letter "spellings" than there are possible amino acid "meanings", though, so most amino acids are encoded by more than one codon.

A happy implication of this for our natural selection vs. genetic drift question is that sometimes when a mutation (spelling error) occurs, the protein (meaning) is changed (a "nonsynonymous substitution"), and sometimes it isn't (a "synonymous substitution"). This means that if a gene is experiencing positive natural selection towards a particular amino acid outcome (a more cold-tolerant version of a protein for example), the ratio (ω) of non-synonymous to synonymous substitutions should be greater than one. Specifically, if...
  • ω = 1, the new mutation is neutral (ho-hum).
  • ω less than 1, the new mutation is deleterious; in other words, there is selection against it (not quite so ho-hum because, though it does not necessarily signal adaptive evolution, it does indicate functional importance of the protein).
  • ω greater than 1, the new mutation is advantageous; in other words, there is selection for it (yippee! adaptive evolution! natural selection!)
Now, back to our pikas (did I mention how cute they are?). In their PLoS ONE paper, Yang and colleagues ask whether the fact that pikas have been able to colonise cold places might be due to positive selection on a gene that regulates energy metabolism, specifically the leptin gene, famous for its role in obesity (Shimizu H et al, 2007). In their words, "Due to the extraordinary environment in which pikas live, and their apparent changes in energy metabolism under cold conditions, we hypothesized that leptin, acting as a cold stress-response protein, plays an important role in the pikas' ecological adaptation to the harsh plateau environment."

To test this hypothesis, they first measured the level of variation in the leptin gene among pikas (cold-adapted) and found that pika leptin had much higher levels of variation than the leptin gene among other lagormorphs (not cold-adapted). But while this result was consistent with adaptive evolution of pika leptin, it did not conclusively rule out neutral evolution (genetic drift).

To take that next step and ask whether the observed high level of variation in pika leptin was due to neutral evolution (genetic drift) or natural selection, they measured the ω ratio in pikas vs. other lagomorphs and found that the increase in leptin variation in pikas was in fact due to differences is non-synonymous, not synonymous, change (P less than 0.05). As Yang et al. put it, "Our study confirmed the previous hypothesis that leptin is a cold stress-response protein and that cold probably is the primary environmental factor for driving the adaptive functional evolution of leptin within the native cold-adapted Ochotona family, contributing to fitness enhancement for the pikas' survival in a stressful environment."

But the last word in this story really has to go to the pika (listen). Translation: let's hear it for leptin!

This post is dedicated to Kimiora Ward, fellow head nodding pika appreciator, whose thesis defense was the single most eloquent and succinct explanation I've ever heard of selection vs. drift.

References:

Yang, J., Wang, Z.L., Zhao, X.Q., Wang, D.P., Qi, D.L., Xu, B.H., Ren, Y.H., Tian, H.F., Bromage, T. (2008). Natural Selection and Adaptive Evolution of Leptin in the Ochotona Family Driven by the Cold Environmental Stress. PLoS ONE, 3(1), e1472. DOI: 10.1371/journal.pone.0001472

Kimura M (1983) The Neutral Theory of Molecular Evolution.; New York: Cambridge University Press. 367 p.

Ohta T
(1992) The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst 23: 263–286.

Yang ZH, Nielsen R, Goldman N, Pedersen AM
(2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431–449.

Grayson, D. 2005. A brief history of Great Basin pikas. Journal of Biogeography. Volume 32, Number 12, pp. 2103-2111(9)


Shimizu H, Oh-I S, Okada S, et al. 2007. Leptin resistance and obesity. Endocrine Journal 54 (1): 17-26. (pdf)

2 February 2008

Young Darwins in February: Bora 1, Greg 0

Unless you've been living in a hole in the ground (or Florida), you can't have failed to notice that Darwin's 199th birthday is coming up quick. Yes, Darwin Day will be marked worldwide on the 12th of February. I'm planning to celebrate on two consecutive days in February, and some have decided that it's impossible to pack all of their festivities into one or even two days and have thus deemed February "Darwin Month".

Both A Blog Around the Clock and Greg Laden's Blog are out of the gates early, each with a post to mark the first day of Darwin month. As an advocate of celebrating Darwin as a young man on a physical and intellectual adventure, I am delighted to see Bora using the painting of the 31-year old Darwin for his post, but somewhat disappointed that Greg chose an image of the rather inaccessible bearded septuagenarian.

So, I urge you, my fellow science bloggers, Darwin's bulldogs/flying lemurs, Wallace's rottweilers and other champions of science and reason to please use this Darwin Day as an opportunity to pour on more images of Darwin the young man. After all, it is the stories of Darwin's youth that enthuse young people today. Unfortunately, there aren't that many pictures available (if you know of more please do let us know!) but there are a few to be had...




Clockwise from top left: Darwin at 45 51 years old, 31 years old, 25 years old as drawn by Conrad Martens during the Beagle voyage (this is, I admit, an egregiously poor quality digital photo that I took of the colour plate in my own copy of Fossils, Finches and Fuegians by Richard Keynes; the original is supposedly at the National Maritime Museum but unfortunately the image is not available on their website) and 9 years old (clutching plants no less!).

Update! Michael Barton has answered the call by linking to two more pictures in comments:


...plus some fantastically manly line-drawings of Darwin the Beagle voyager on his blog Dispersal of Darwin: