Data Not Shown

'Impact' crater

2009-12-01T01:01:00.001Z

Tonight I attended the twitter-inspired 'Blue skies ahead?' debate in which science minister Lord Paul Drayson gamely engaged a youthful panel (and audience) of scientists on 'the prospects for UK science'.

The first half of the debate was dominated by one word: 'impact'. It's an unfortunate word choice, really: it's vague, loaded and unidirectional, suggesting science impacts society but not the other way around. There was lively disagreement regarding the extent to which science funding should hinge on retrospective and/or predicted impact.

As evidenced by my flush of tweets during and after the event, I have a lot to say about 'impact', but in this post I'm going to set aside my opinions and instead tell a personal story of how 'impact' impacted me.

I wouldn't have thought to tell this story (it happened a while ago and as it has a happy ending I don't give it too much thought anymore), but after two respected tweeps, Ed Yong and Evidence Matters, specifically asked for it, I thought it might merit daylight.

In 2002, shiny new PhD in hand, I was looking for a job in the UK. I was casting a wide net, applying and interviewing for not only postdoctoral research positions but also assistant editorships at peer-reviewed journals and various jobs involving popular science communication. During my PhD years, I had enjoyed writing and communicating science to both expert and non-expert audiences, and moreover I think it is a scientist's civic duty to engage the broader public, to improve general science literacy but also to pave the way for future science funding.

One of the postdoc fellowships for which I interviewed seemed perfect; the project addressed some fascinating evolutionary developmental-genetic questions using a range of new and old techniques, the lab seemed like it was thriving, and the lab head had written books and popular science articles which I not only admired but which also suggested that he might be a good mentor for that element of my training.

My interview seemed to go very well: my CV was strong, I was happy with my presentation, I had good discussions with the lab head and the other members of the lab during which I asked questions, made suggestions and I even proposed an experiment that it turned out they hadn't thought of yet.

At one point during my interview, I mentioned how keen I was to stay active in public outreach, through writing and perhaps other forms of engagement, and that I admired his own accomplishments in that area.

And that's where it all went wrong. In a sudden change of tone, the lab head started asking me probing questions about my commitment to the project, suggesting that I might not be up to seeing it through. He said I might be more suited to a career as a journal editor or science communicator. I reiterated my commitment to the research project, and said that I thought that shouldn't preclude engagement with the wider public; indeed, his own success in both research and popular science writing showed that it was possible to do both, and to do them well.

But it was too late. He had made up his mind. He wanted the people in his lab to have their noses to the research grindstone; he saw public outreach as icing on the cake, something you did only once you'd achieved success in your research career and were running your own lab.

Sure enough, a few weeks later he emailed me to say he'd decided to give the job to someone else. He cited his concern about my 'level of interest and commitment to the project', repeating a phrase he had used the day of the interview after I'd divulged my sordid secret interest in improving public understanding of science.

For a while I had some regret, but then I came to realize that it was better this way. I'm glad I didn't go to his lab only to find out too late that my 'extra-curricular' interests wouldn't be looked upon favorably.

Ultimately I found a job at an institution with a genuine commitment to both scientific research and public engagement with science. There will always be a natural tension between the two - after all, there are only so many hours in the day and science is a demanding career - but I'm glad to be in a place where public outreach isn't considered a character flaw.

Coming back to the 'Blue skies ahead' debate, I hope my story illustrates what every research scientist already knows: career progression depends primarily on one's (peer-reviewed) publication record and, to a lesser extent, one's history of winning research grants. Anything that takes time away from these two activities is therefore by definition a drag on one's career. Many of us do it anyways, because we enjoy it and think it's important. But there will not be any significant increase in the number of scientists engaging in public outreach until recognition of these activities is incorporated into research career progression criteria.

My first mix on 8tracks

2009-09-06T15:49:00.002+01:00

8tracks is a simple way to share music mixes online. Here's my first attempt:

I love the NHS but not their Ramadan health FAQs

2009-08-28T19:40:00.004+01:00

The health care debate taking place in my homeland right now is immensely important. The outcome will affect all 300 million Americans, especially the 46 million that are uninsured, and if reform doesn't pass now, we probably won't get another shot at it for another decade or two.

It's also important to me, personally, as I do hope to repatriate one day. I am absolutely pro-reform and I find two aspects of the debate particularly infuriating:

the spread of outright lies about the proposed reforms by the small but very screechy anti-reform camp (debunked here), including the slinging of vast quantities of mud across the Atlantic at the UK's National Health Service
the sheer number of Americans--64%--who 'don't want to pay more taxes to expand health coverage to the uninsured'

As an American living in the UK, I feel it is my particular duty to counter the misinformation about the NHS that is circulating in the States right now. I've been counter-circulating as much information and testimonials by email and facebook as I can, and even have an 'I [heart] NHS' twibbon on my twitter avatar as a sign of my support.

I do, by the way. [Heart] the NHS, that is. It is difficult to overemphasize the peace of mind it gives me that those I love and I will never be unexpectedly refused coverage as a result of some policy small print about, for example, pre-existing conditions, nor financially ruined by a health problem. What a relief it is to be able to go to the doctor without having to fill out any forms or make any co-payments. Oh, and prescriptions are either free or £6.95 depending on whether you are capable of paying. I could go on but that's not what this post is about, and others have said it much better than me.

This post is about something the NHS did that has me pretty irked. I know, I know, given all of the above, maybe now isn't the best time to point out flaws in the NHS, but to that I say: a) this flaw has nothing to do with the general premise of the NHS or the health care they provide and b) I think it's right to be honest even when it's not politically expedient. Ahem.

So. The NHS has this website called 'Healthy Ramadan' which offers advice on staying healthy if you happen to have chosen to observe the daylight fasting that is part of the Muslim holy month of Ramadan. Of course, the word 'chosen' is tricky because it's difficult to quantify the extent to which religious indoctrination limits one's perceived if not real choices, but I digress.

The site seems like a pretty good idea: there are pages containing general advice on healthy fasting, suggestions on what to eat and what not to eat, and even a suggested meal plan. There's also an important section that lists the health risks that can be associated with fasting, and the site urges people to use Ramadan as an opportunity to quit smoking.

But then we get to the page, 'Ramadan health FAQs'. This page got my hackles up immediately with its introductory note that explains that 'the answers have been put together by medical experts and Islamic scholars and researchers'. I can see why Islamic scholars and researchers might help with devising the questions - after all, they are the experts on what the likely FAQs are going to be. But why should they be involved with putting together the answers? This is supposed to be health advice. It should come from the medical experts alone.

The first several Q&As about diabetes, migraines and blood pressure were okay, I suppose, though I was a little uncomfortable with how the questions were worded: each one was based around the question, 'should I fast?' when they really should have asked, 'is it alright to fast?' because then the answer would be less likely to be interpreted as prescriptive rather than permissive. But then I got to this one:

Is fasting harmful when a woman is expecting a baby? Must pregnant women fast?

There's medical evidence to show that fasting in pregnancy is not a good idea. If a pregnant woman feels strong and healthy enough to fast, especially during the early part of the pregnancy, she may do so. If she doesn't feel well enough to fast, Islamic law gives her clear permission not to fast, and to make up the missed fasts later. If she is unable to do this, she must perform fidyah (a method of compensation for a missed act of worship).

Let's just start with the question, shall we? 'Must' should never appear in front of or inside the phrase 'pregnant women fast', and certainly not on a national health service website. In fact the only time those two phrases should ever go together on any kind of government literature is if 'not' is inserted directly after 'must'.

The answer to the question starts out a bit better--using 'may' instead of 'must'--but then it all goes downhill. 'Islamic law gives her permission not to fast...' is useful information, as it may give uncertain women the religious argument they are looking for to give themselves permission not to fast (though of course that opens up a whole can of worms that I'm not going to go into today). But that last sentence is abhorrent. It's missing a big fat 'Islamic law says' before 'she must'. The way it is now, it looks like the NHS is the one telling her that she must perform fidyah!

I suppose one could argue that 'Islamic law' is mentioned in the penultimate sentence and therefore it is meant to indicate that Islamic law, and not the medical establishment, is the authority in both of the final two sentences. And I suppose that if this were the only problem with the website then I might have given them the benefit of the doubt. But two questions later it gets worse, and this time there's no qualifying 'Islamic law says' anywhere to be found:

From what age can children fast safely?

Children are required to fast from the age of puberty. It isn't harmful. Fasting before this age is tolerated differently depending on the child’s general health, nutrition and attitude. Fasting under the age of seven or eight isn't advisable. It is a good idea to make children aware of the practice of fasting and to practise fasting for a few hours at a time.

Look at that first sentence and tell me the NHS--the NHS!--didn't just say that children are required to fast during Ramadan!

The next few Q&As are okay, I suppose. They're about asthma, swimming and blood transfusions and there are occasional qualifiers like 'Muslim experts say...' and 'in their view...'. But I don't like how the answer to the asthma question contains an implication that it's somehow incumbent on Muslims to 'achieve good control' of their asthma ...as if it's some kind of personal failing if your asthma isn't under control. And I don't like that the answer to the transfusion question mandates fidyah with no qualifiers in sight. But I'm passing over these so that I can address this final doozie:

Does a breastfeeding woman have to fast?

No. Islamic law says a breastfeeding mother does not have to fast. Missed fasts must be compensated for by fasting or fidyah once breastfeeding has stopped.

As with the Q&A about pregnancy, the question itself contains an implication that the answer is mandataory rather than permissive. And again, missed fasts 'must' be compensated, no qualifiers, unless you count the one in the first sentence, but at this stage I'm not exactly inclined to give them a pass.

So, all you NHS web content editors out there, would you please do us all a favor and go in there with a red pen and change 'must' and 'should' to 'can' and 'could'? And while you're at it, add a liberal sprinkling of 'Muslim scholars say...' and 'Islamic law says...' before each sentence in which fasting is 'permitted' or fidyah 'suggested'? Oh, and could you please pay particular attention to those Q&As regarding women and children? Because I've noticed that those were most prescriptive and least qualified of all.

I'd do it myself, but I'm hungry.

Saved by Science (NHM) Photo Series

2009-08-27T18:41:00.008+01:00

I'm now six installments into a twitter photo series I've been calling "Saved by Science (NHM)" and I've decided I'm enjoying myself enough to warrant formalizing it a bit more.

It all started when I was browsing SEED magazine's special Darwin bicentenary collection (as a professional Darwin groupie is wont to do) and saw a link to an article by Carl Zimmer called 'The Awe of Natural History Collections'. I clicked it (as an Natural History Museum employee is wont to do) and was immediately enthralled, from the subtitle--'visiting the hidden side of natural history museums, where the vast collections of scientific specimens are kept'--through to the end. It's a real Zimmer gem, if you ask me.

Anyways, the article links to an audio slide show by Justine Cooper called "Saved by Science". It's not your average window-dressing to an article, it absolutely steals the show. And considering how good Carl Zimmer's writing is, that's really saying something. It's a brilliant piece of stand-alone journalism. Some of the slides are astonishingly intimate and poignant. Go there now and watch (and listen to) the whole thing.

I was immediately struck by the familiarity of the photographs. They were so similar to scenes I'd witnessed myself at the Natural History Museum in London, where I work. And then I realized that there was a communication void just waiting to be filled; I realized that I really should start taking candid behind-the-scenes photos at 'my' museum along the same lines as Justine Cooper's photos of AMNH.

And so began "Saved by Science (NHM)", a series of tweets (1, 2, 3, 4, 5, 6...) with my Cooperesque NHM photos attached as twitpics. Of course, my photos are usually taken with my iPhone, not a large-format camera, and of course they're not nearly as good as Cooper's, but the point is to reveal the hidden side of the Natural History Museum to a wider audience.

To keep up on my series you can follow me on twitter, but as twitter is a pretty ephemeral thing, and as not everyone tweets (I know--shocking), and as I'd hate for the series to get lost in that ever-growing graveyard of old, unarchived tweets, I've created a permanent archive on my website.

Gene angst: finding a DNA barcode for plants

2009-08-03T13:30:00.016+01:00

I've been incubating this post since September 2008, so it's kind of cathartic to finally be writing it. I think it will be a good representation of the title and purpose of this blog in the sense that it's a window to some of those things that go on in science - and in the lives of scientists - that don't make it into the peer-reviewed publications.

So why the wait? On top of that it's inappropriate to talk in public about a piece of research before it's published unless all your co-authors agree (and a quick peek at the number of co-authors on this paper will explain why that was a non-starter), this work involved a lot of personalities and politics - even more than the usual paper - and some rather sensitive discussions and debates were being had right up to the publication date.

Speaking of the publication date, you'd be forgiven for thinking this open access PNAS paper came out on Tuesday; there was, after all, a rash of online and print news items¹ and press releases² about the paper that day, even radio and television interviews. But the paper wasn't published in the Early Edition until Thursday. See, PNAS does this weird thing where they lift the press embargoes on all of the papers in each week's issue on Monday night, even though the papers themselves may come out any day that week. I'm not sure why they do this and I find it a little annoying, largely because though we see a flood of news about a paper on Tuesday, it isn't actually available to non-journalists - you know, like those scientist and taxpayer schmucks - until a few days later. The result is that by the time the paper is out it's too late to influence or even critically filter any of the media surrounding it.

But I digress.

'A DNA barcode for land plants' is the culmination of 4 years' ~~blood, sweat and tears~~ work by a global consortium of researchers called the Plant Working Group (PWG) of the Consortium for the Barcode of Life (CBOL).

The purpose of the PWG is to bring plants up to speed with animals in an international effort to build standardised reference libraries of DNA sequences from known and unknown species. These libraries of 'DNA barcodes' will ultimately enable the rapid identification of unknown specimens (or fragments of specimens) even by non-experts. In the meantime the collaborations and frameworks created to build the libraries will, in the words of John F. Kennedy from his famous "We choose to go to the Moon" speech, "serve to organize and measure the best of our energies and skills."

Because I've blogged about DNA barcoding several times before³, both here and on The Beagle Project Blog, I'm not going to give you a lengthy background on barcoding in this post. Rather, I'll explain briefly why plants needed bringing up to speed in the first place, but then move on quickly to how we did it, and what it was like to be involved.

Why have plants lagged behind animals in terms of amassing DNA barcode reference libraries? It's not that botanists aren't keen to participate. Rather, it's that the gene chosen (and officially endorsed by CBOL and therefore GenBank) to serve as the DNA barcode for animals, CO1, though present in plants, is not variable enough to use in species identification. So the search was on for a CO1 equivalent in plants: a region conserved enough through evolution to be found in and easily amplified from every plant's genome but carrying enough variation to distinguish species.

The approach CBOL took to finding such a region was to assemble a consortium of botanists actively working on DNA barcoding, and to pay for them to have meetings with each other in order to hash it out amongst themselves. As someone working on DNA barcoding plants at the Natural History Museum, I was invited - along with several others - to join in.

This was my first time as a direct participant in science-by-consortium and boy, was it an eye-opener. It turns out trying to get scientists - botanists no less (eek!) - to agree on something is not as easy as one might imagine. (There is a long and inglorious history of botanists disagreeing, but I've already indulged in one digression today...)

The PWG has met several times, most notably at a side meeting during the 2nd International Barcode of Life conference in Taipei in September 2007, and then again at the Royal Botanical Garden Edinburgh in September 2008.

The Taipei meeting was widely believed and reported to be something of a mess, with lots of claim-staking but not much progress towards the all-important Final Decision. I vividly remember one moment from the meeting in which we used a white board to list all of the candidate plant barcode regions (and combinations of regions). I photographed the white board (right). Looking back at it now, I think this picture speaks a thousand words with regard to the indecision that was left hanging in the air after Taipei.

The Edinburgh meeting, on the other hand, was more focused, with a mandate to have a decision made before everyone went home. Ably chaired by Pete Hollingsworth, head of the Genetics and Conservation section at the Garden, we spent two days (rather than two hours, as in Taipei) focused on the task.

I can't speak for anyone else, but I personally found the Edinburgh meeting to be a whole lot of fun. In essence, we - 15 plant DNA barcoding specialists from around the world - locked ourselves in a small room and agreed not to come out until we had made a decision. Coffee was administered by IV drip and snacks and sandwiches delivered to an adjacent room for when our brains ran out of ATP. Unlike the Taipei meeting, we had lots of data to hand in Edinburgh. Print-outs of spreadsheets and figures flew around the room like so much confetti and got annotated by hand as they were discussed.

Participants of the Plant Working Group meeting in Edinburgh emerged breifly from their self-confinement for a group photo.

I mentioned data. Our group from the Natural History Museum in London contributed amplification success rates and DNA sequences for six regions from 138 flowering-plant specimens. These specimens were collected during our project to repeat Darwin's botanical survey of Great Pucklands Meadow at Down House (pause for one of those 'oh if Darwin only knew about DNA' moments). This might seem like an impressive amount of data but in fact it was a modest contribution; some of the other groups contributed not hundreds but thousands of sequences. All in all the various research groups contributed data from 907 specimens from 550 species representing the major groups of land plants (including 670/445 angiosperm, 81/38 gymnosperm, and 156/67 cryptogam samples/species) for up to seven candidate regions that had been flagged in Taipei. These regions are, in no particular order, the genes rpoC1, rpoB, matK and rbcL and the inter-genic regions psbK-psbI, atpF-atpH and trnH-psbA.

Back to our little room in Edinburgh. In some cases we analyzed this mountain of data right then and there, and in other cases, as when there were gaps in our data set that still needed filling, we agreed to go back home and churn out those data pronto.

One of the more illuminating analyses we did was to compare how well all possible combinations of one, two, three and seven candidate regions performed in terms of discriminating species. We were (or at least I was) surprised to find that while increasing the number of regions used in combination from one to two improved the power of species discrimination, combinations of three or more weren't any better (right, Figure 1C from the paper).

In addition to discriminatory power, we also looked at practical issues like universality (i.e., the rate at which we were able to successfully amplify any given region from our collection of specimens) and sequence quality (e.g., the frequency of high-quality sequences obtained for each region, the amount of manual editing required and the concordence of bidirectional sequence reads).

Ultimately, after all of these analyses, there was no obvious winner, no gleaming silver bullet. And so began the war of attrition, during which we said our tearful goodbyes to certain regions that were okay in terms of universality and sequence quality, but pretty useless for species discrimination (as was the case for two regions, rpoC1 and rpoB), or good at species discrimination but with poor amplification success rates and sequence quality (as was the case for psbK-psbI).

After this weed-out process, we were left with three regions - two genes, matK and rbcL, and one intergenic spacer region, trnH-psbA. Though these three outperformed the rest none of them alone performed ideally for all three criteria.

At this stage there was an intense discussion about whether we should recommend all three as a combinatorial plant DNA barcode to CBOL, or just two of the three. Some in the group preferred the better-safe-than-sorry approach of a three-region barcode that could be pruned down to two at a later date if one of the three proved superfluous. The majority, however, thought a two-region barcode preferable because it would be both be less expensive in terms of sequencing costs and also because it was felt that we needed to be decisive; many would-be plant barcoding projects were being denied funding as a result of funding agencies fears that their money might be wasted if CBOL shifted the goalposts. Moreover, as I said above, though two regions are better than one at discriminating species, three are not better than two.

So of the three remaining regions, we tasked ourselves to decide which two in combination to recommend to CBOL as 'the' plant DNA barcode. It made sense to choose two regions which would complement each other: one with high universality and sequence quality and good, but not great discriminatory power (rbcL), the other with better discriminatory power but needing further technical work to improve universality (matK) or sequence quality (trnH-psbA). In the end, the group felt it was easier to overcome the universality difficulties posed by matK than the sequence quality difficulties posed by trnH-psbA.

And there we have it: the Plant Working Group recommends that CBOL adopt⁴ the combination of rbcL and matK as the official plant DNA barcode.

So that's the story of the scientific process that the Plant Working Group went through to select a DNA barcode for plants, but before I end I want to say a little bit more about the political and social process. If you read between the lines of my account here, you can probably guess that there were some intense disagreements between various members of the working group over how many, and which, regions to select. This begs the question, why would anyone care? It's supposed to be cold, hard, evidence-based science, right?

As PWG member Damon Little carefully said in his WNYC radio interview, '...when this started, a lot of people...[had] their favorite region for various reasons,...because they were the ones that discovered it or...because it was a region that had worked well for them in the past...' In other words, different research groups involved had to some extent pinned their reputations on certain candidate regions. As a result, they advocated those regions for a combination of political and historical reasons as well as scientific reasons.

But it wasn't all sorrow and strife. As you can imagine, after the workshop was over, there was a sense of relief and accomplishment - and for some, lingering frustration - and how better to mark the occasion than by refreshing ourselves at the Scotch Malt Whisky Society Vaults in Leith (right)?

And now we have finally come to my last bit of data in this blog post ...consider it supplementary data to Science Creative Quarterly's 'manuscript' entitled 'Scientists will geek out under any circumstances': at the Whisky Society, we were treated to PWG chariman Pete Hollingsworth's expert tutelage in whisky tasting. Here are some of the various drams we tried:

Whisky tasting with the Plant Working Group. Crop at right shows drams labeled by distillery (actually they don't tell you which distillery they're from, so these are actually Pete's guesses).

As is only natural, our conversation turned to DNA barcoding, and we noticed that, just as whiskies have thier own personalities, so do the plant barcode candidate regions. Moreover, we figured these personalities could be mapped onto one another...

rbcL=Highland Park, trnH-psbA=Longmorn, CO1=Laphroaig,
matK=Caol Ila and rpoC1=Glen something
...obviously.

...because that's what we humans do. We identify things, and we classify things. And I hope that the new plant DNA barcode helps us do that a wee dram better.

Reference:

CBOL Plant Working Group (2009). A DNA barcode for land plants Proceedings of the National Academy of Sciences of the United States of America, 106 (31), 12794-12797 : 10.1073/pnas.0905845106

Footnotes:

¹Notable press coverage (last updated Saturday, 1st August, 2009): BBC, CBC News (Canada), The Citizen (South Africa), Guelph Mercury, Science, Science Daily, Scientific American, The Scotsman, The Sydney Morning Herald, The Telegraph
²Press releases: Consortium for the Barcode of Life, Imperial College, Natural History Museum, Royal Botanical Gardens, Kew, University of Guelph
³Data Not Shown: Barcode of plants ~~mapped~~ ~~identified~~ tested; The Beagle Project Blog: Would that which we call a rose by a DNA barcode smell as sweet? and Arbor DNA
⁴Notice I wrote 'CBOL', not 'everyone'. This is because 1) the next step is for the PWG to submit a formal applicaiton to CBOL to have the two-region barcode approved (and this is important because CBOL alone can tell GenBank to rubber-stamp these two regions with the keyword 'BARCODE') but also 2) no matter what the PWG or CBOL says, individual researchers can always sequence whatever they want from whatever plant species they want, for whatever purposes they want. It's only if they want to participate in, and derive useful data from the international DNA barcoding effort, that this recommendation even matters.

'Man must explore'

2009-07-21T03:56:00.004+01:00

At this very moment, exactly forty years ago, two men set foot upon the surface of the Moon.

The Moon, people!

There are many celebrations taking place 'in real life' and online; some of the most compelling of these are the real-time-plus-40-years commemorations like the Apollo 11 Radiocast, We Choose the Moon and ApolloPlus40.

As with all anniversaries (and boy, do I speak from experience), this is a time to reflect on the past and contemplate the future - in this case, of space exploration.

Almost as if to emphasize this, a review of the US Human Space Flight program is taking place right now, and they want our feedback. That's right: they want us rabble to tell them what we think about the future of manned missions into orbit and beyond.

So, here's what I think:

I think Apollo 15 Commander Dave Scott knew exactly what he was talking about when, upon becoming the 7th man to walk on the Moon, he said, "As I stand out here in the wonders of the unknown at Hadley, I sort of realize there’s a fundamental truth to our nature: man must explore. And this is exploration at its greatest."

I think that John F. Kennedy was absolutely right when, in his famous "we choose to go to the moon" speech, he said that we should go to the moon "because that goal will serve to organize and measure the best of our energies and skills...".

And I think that science and exploration are not just icing on a cultural cake to be undertaken during economically flush times, not just things we do to reap cold, hard, profitable benefits, but a core part of who we are as human beings.

As Brian Greene wrote in his brilliant NY Times Op-Ed piece 'Put a Little Science in Your Life', "science is a language of hope and inspiration, providing discoveries that fire the imagination and instill a sense of connection to our lives and our world. [snip] We must embark on a cultural shift that places science in its rightful place alongside music, art and literature as an indispensable part of what makes life worth living."

Update (21st July 12:15pm): I also think that people are holding science in general and the space program in particular to a double standard when it comes to federal funding. Have a look at Death and Taxes, an excellent and intuitive visualization of the federal budget. Is the NASA circle bigger or smaller than you expected?

DNA-encrypted recipes

2009-06-19T08:47:00.006+01:00

This morning I woke up with an idea for a science education/outreach project in my head. The idea is borne out of a fun exchange on twitter yesterday which occurred at the tail end of a long series of frustrated tweets about some problems I'm having submitting DNA sequences to Genbank:

kejames: Perhaps I should just tweet the sequences to Genbank: ctagctgctgttgaagttccatctataaatggataagactttggtcttagtatatacgagttctt
gaaagtaaaggaacaata

TwistedBacteria: chloroplast Prunus laurocerasus (cherry laurel) RT @kejames: Perhaps I should just tweet the sequences to Genbank: ctagctgctgttgaagttccatcta

That's right, TwistedBacteria actually thought to take my DNA fragment - tweeted in a moment of pure, hands-thrown-in-air frustration - and see if he could identify what species the fragment came from. What he did is essentially DNA barcoding (but using Genbank instead of the voucher-specimen-linked BARCODE-tagged databases 'approved' by CBOL).

The really cool thing is that even though I tweeted such a short sequence (just 83bp), and even though I had copied that sequence from a randomly chosen place in my data set, TwistedBacteria's correctly identified the genus if not the species of my specimen; the fragment I tweeted is from blackthorn (Prunus spinosa), not cherry laurel (Prunus laurocerasus).

It was entirely by accident that I happened to choose a blackthorn sequence to tweet, but because I did, I was reminded of a little haiku I did for the Science Creative Quarterly a while back:

SLOE GIN INGREDIENTS
a haiku by Karen James

Prunus spinosa
Juniperus communis
Triticum sp.

And that's when the idea hit me: why not take this 'recipe' one step further and make a fun and educational puzzle out of it by leaving the title of the recipe blank and encrypting the ingredients as DNA sequences? And why not do this for a bunch of recipes and make a whole DNA-encrypted recipe book? Here's what my sloe gin recipe might look DNA-encrypted:

The following ingredients make up what alcoholic beverage?

gcacaggctgaaacaggtgaaatcaaagggcattacttgaacgctactgcaggtacatgcgaagagatgatgaa
aagagctgcatttgccagagaattgggggttcctatcgtaatgcatgattacttaacagggggattcactgcaaata
ctaccttggctcattattgccgagataatggtttacttcttcacatccaccgtgcaatgcatgcagttattgatagaca
gaagaatcatggtatgcactttcgtgtactagctaaagcgttacgtatgtctggtggagatcatatacacgctggtac

ggatgtactatcaaaccaaaattgggtctatctgccaagaattatggtagagcggtttatgaatgtctccgtggtgga
cttgattttaccaaggatgatgaaaacgtgaattcccaaccatttatgcgctggagagatcgtttctgcttttgtgcag
aagcactttataaagctcaggctgagacgggtgagattaagggacattacctgaatgcgactgcagggacatgtga
agaaatgatgaaaagagcagtattcgccagagaattgggagttcctatagtcatgcatgactatctgactggaggtt

aagaaatgattaagagagctgtatttgcaagagaattaggggttcctattgtaatgcatgactacttaactggggga
ttcaccgcaaatactactttggctcattattgccgcgacaatggcctacttcttcacattcaccgtgcaatgcatgcagt
tattgatagacagaaaaatcatggtatgcatttccgtgtattagctaaagcattgcgtatgtctgggggagatcatatc
cactccggtacagtagtaggtaagttagaaggggaacgcgaaatgactttaggttttgttgatttattgcgcgatgatt

One could mix it up a bit and use some amino acid sequences too, and for ingredients that are pure products of biochemical pathways (sugar, alcohol, etc.), one could use sequences of genes that function in those pathways.

Lessons would include:

our food is (or was, or was produced by) living organisms with DNA in them (this is an important lesson - I've heard that children are generally unaware that what they ate for breakfast consisted of plants and animals)
you can identify species by their DNA
genes encode proteins, which have functions in the cells of plants and animals
practice using Genbank and BOLD databases

So, what do you think?

I remember*

2009-06-06T19:46:00.008+01:00

Sixty-five years ago this morning, the 'largest single-day amphibious invasion of all time' commenced. It was the beginning of the end of Hitler. My heartfelt thanks to the men and women who, without the reassuring benefit of our victory-tinted hindsight, undertook the task.

Portsmouth, England: Veteran Leonard Hackett, 86, takes part in the commemoration services for the 65th anniversary of the D-Day landings. Photograph: Jonathan Brady/Epa.
Source: The Guardian.

*Of course, technically, I don't remember, since I wasn't born yet, and that's the reason it's all the more important that I do remember, and anyways, you know what I mean.

New Darwinius t-shirts

2009-05-28T22:00:00.001+01:00

Dear fellow Darwinius hype debunkers, I hope my newest wares will interest you:

Proceeds to The HMS Beagle Trust (UK Charity No. 1126192).

Why Darwinius is not our ancestor

2009-05-28T00:02:00.005+01:00

I have been blogging and tweeting the dead ~~horse~~ primate that is ~~Ida~~ Darwinius masillae for several days now, culminating in last night's twitter-fest during the BBC documentary Revealing Our Earliest Ancestor: The Link. During our lively little twitter event, which made the Times Online today, I was, apparently, pretty worked up: Andrew Maynard even wrote 'Warming my toes from the heat of your ire...'.

Of course, it's not only us twitterers bemoaning the Darwinius hype machine; there's going to be a special Darwinius blog carnival on Monday, and I'm pleased to see a growing number of mainstream outlets casting a critical eye over the story, or at least giving space to external critics. For example, today I found an excellent opinion piece by Chris Beard the NewScientist called Why Ida is not the missing link. In it, Beard dresses down not just the hype - "unbridled hoopla" as he called it - but also the science itself. His final paragraphs are particularly good:

'So, Ida is not a "missing link" – at least not between anthropoids and more primitive primates. Further study may reveal her to be a missing link between other species of Eocene adapiforms, but this hardly solidifies her status as the "eighth wonder of the world".
Instead, Ida is a remarkably complete specimen that promises to teach us a great deal about the biology of some of the earliest and least human-like of all known primates, the Eocene adapiforms. For this, we can all celebrate her discovery as a real advance for science.'

Great stuff. Great enough to make me shout "Yes!" out loud while alone in my flat. What Beard is saying here is that Darwinius is not the 'missing link' between anthropoid side of the primate family tree (including humans) and the lemur side because the authors of the paper in which Darwinius is described have not convincingly demonstrated that she belongs with the former and not the latter. Beard contends that the balance of evidence keeps Darwinius - and all the rest of the adapiforms by extention - anchored firmly on the lemur line. To explain this, he provides this useful diagram of primate evolutionary history:

Evolutionary tree diagram reproduced from NewScientist.

The diagram shows the two competing hypotheses: the red dot in the diagram indicates where Chris Beard contends Darwinius belongs, on an early branch in the lemur (brown) lineage. The paler spot with the "?" indicates where the paper's authors claim Darwnius belongs, as an early member of the (blue) anthropoid lineage and, specifically, as they have contended in interviews and on their website if not in their paper, ON the line. In other words, they claim she is our direct ancestor.

I don't have any professional background in primate anatomy but I find Beard's argument - especially in combination with Laelaps' analysis - pretty compelling, certainly compelling enough to remain very skeptical of the authors' conclusions. We will have to wait for further analyses of the Darwinius specimen, however, before this controversy can be more soundly resolved.

But here's the thing: even if upon further analysis Beard is shown to be mistaken and the authors are right about Darwinius and her fellow adapids being on the anthropoid lineage, she will still not necessarily be the 'missing link', nor - perhaps more importantly because it actually means something - 'our ancestor'. To explain my point, I re-drew Beard's diagram:

My re-drawing of Chris Beard's diagram in which I shift his representation of the paper's conclusion about Darwinius' systematic position from ON the anthropoid line to a BRANCH off the anthropoid line.

I re-drew it this way for the simple reason that, considering the abundance of species upon the Earth at any one time, it would be very unusual for us to find a fossil on our direct ancestral line, rather than on a branch off of that line. As John Wilkins put it, "There is no missing link. Rather, there are an indefinite number of missing branches. [snip] We might have a species that is an ancestor of some other species, and yet not know enough to say that they are indeed the ancestor in question."

Additionally, as Richard Carter notes, Ida herself can't be our direct ancestor because she died as a juvenile. But as I've just explained, even her whole species is very unlikely to include our ancestor.

Interestingly, as I mentioned in passing above, the hype machine (including the paper's authors themselves when interviewed) puts Darwinius directly on the line to us, while in Supplementary Figure 7 in the PLoS ONE paper, the authors put Darwinius on a early branch off the line. In other words, what they're saying in public isn't just hyped up, it's fundamentally different from what they're saying in the paper itself.

To summarize, if Darwinius is found, as the authors contend, to belong on 'our' side of the primate family tree (and even that conclusion is shaky) she is not a 'missing link' (because there's no such thing), and she is very unlikley to be our ancestor.

Darwinius has left the building

2009-05-26T20:08:00.004+01:00

So there I was earlier today, minding my own business at home (I attached a day of annual leave to the bank holiday weekend in order to take care of a few pressing things like, apparently, writing this blog post), and all the while, over at my workplace, the over-hyped but nevertheless stunningly complete and aesthetically beautiful fossil Darwinius messilae was on display for a few hours on its way from New York to Oslo.

The brief display was occasion for a press conference (or is it the other way around?), but there was also a short time during which staff were invited to view ~~Ida~~* the fossil. I found out at about 3pm when I stumbled across a BBC News story which led me to an NHM press release:

Visitors to the Natural History Museum in London will be able to see Ida, the fossil of the ancient lemur-like creature, when a cast goes on display from tomorrow.
[snip]
The Ida cast was donated to the Natural History Museum today by the University of Oslo Natural History Museum. Sir David Attenborough will be there to see the cast and is also narrating Uncovering Our Earliest Ancestor: The Link, a one-off documentary about Ida on BBC One at 21.00 tonight.
[snip]
Scientists at the Natural History Museum, London, will get a glimpse of the real specimen when it is brought to the Museum for just a few hours.
The lucky scientists will see the most complete fossil primate ever found. It is so well-preserved that the remains of its last meal are still in its stomach and you can see an outline of where the fur once was.

Upon realizing that "the lucky scientists" might in fact include me, I leapt towards the telephone to call a colleague in the NHM press office to find out how long it would be on display today. Annual leave or no, if there was a chance to see it, I was going to get onto my bicycle and get myself over there pronto!

You can imagine how I felt when my colleague told me that the staff viewing time had ended at 2pm and that the fossil was no longer in the building. Actually, you don't have to imagine how I felt because my disappointment is documented for posterity on twitter (thanks to Rowan and Mun-Keat for the consolatory tweets).

The wave of disappointment that washed over me, though, was quickly followed by introspection. Why was I so disappointed? Had I actually succumbed to the hype? I could tell you (and more importantly, myself) that I was just disappointed not to get to see a beautiful, complete 47-million-year-old primate fossil, but if I'm honest, I have to admit that I also wanted to see the the source of all the commotion and get to feel like an insider. So I did succumb, but more in the way gawkers slow down to look at traffic accidents than in an "OMG THE MISSING LINK" way. Following this analysis, I felt a little less disappointed. Hooray for analysis!

Of course, this doesn't mean that tomorrow morning on my way up to my newish digs in Phase II of the NHM's Darwin Centre I won't stop off and have a look at the cast of Darwinius, which, though not the real thing is still one of maybe only two casts in the world (the other at the AMNH in New York).

But seeing the cast won't quite make up for not seeing the real thing (Rowan Hooper tweets that the cast doesn't quite do the original justice), and I still will have missed the press conference, which would have been interesting because, judging by the BBC video coverage, Jørn Hurum (the most hyperbolic of the scientific authors) and David Attenborough seem to be toning down the hype a little:

Attenborough even says - tellingly - that Darwin "would have been absolutely riveted by it - I have no doubt about that, and he would - I am sure - have sat and looked at it and thought about it - probably for a decade - before he said anything about it. Maybe that's quite a wise thing to do." Might this final sentence signal that David Attenborough feels a twinge of regret about the way the project was handled?

Similarly, Rowan Hooper's blog and video coverage of the event shows Hurum apparently backpedaling a bit in the face of recent criticism that the paper was weak on evolutionary analysis - I can only imagine he's referring to Brian Switek's excellent critques of the scientific paper - by claiming that this only ever meant to be a descriptive paper and that a more rigorous phylogenetic analysis was still in the pipeline.

But there's a problem: as Rowan Hooper writes, "Phylogeny [evolutionary history], he says, is not the most important part of the paper, and is only mentioned in the discussion. But, of course, it is the phylogeny of Ida - and the claims that it is an ancient human ancestor - that have made it such a big news story."

*Like pretty much everyone else, I have been using the nickname "Ida" for Darwinius massilae, but I'm stopping today for three reasons: 1) the ICZN have - at short notice - worked their proverbial tails off to guarantee the nomenclature of this specimen, and calling it "Ida" seems to me to diminish their efforts specifically and the importance of nomenclature generally, 2) I feel a little queasy about how one of the paper's authors, Jørn Hurum, has been fanning the hype, saying things like "this is the first link to all humans" (whatever that means), and he's the one who named the fossil "Ida" so using it feels like an approbation 3) "Darwinius" has a nice ring to it.

Now that's what I'm talkin' about

2009-04-26T10:03:00.002+01:00

From the New York Times: Mrs. Obama helped plant a tree on April 21 as part of an event at the Kenilworth Aquatic Gardens in Washington. Photo by Martin H. Simon.

Live-blogging the Darwn-200 Anniversary Conference in Istanbul

2009-04-23T18:30:00.007+01:00

Update Saturday 25 April: The conference is now over, so I've removed the twitter widget below and replaced it with the twitter history of the event, that is, my tweets from the conference in order. In a second update I will thread them with replies and retweets from the twitter community. Thanks to everyone in twitterdom who followed and participated!

Background here. This live-blog session ~~will consist~~ consisted of a twitter feed ~~plus longer live (or at least live-ish) updates to this blog post below the twitter widget~~ and will be followed up with a separate post with my thoughts on the conference that I couldn't manipulate into 140 characters or less (which I'm starting to realize is probably the best way to cover a conference since it's too onerous to sit down and compose paragraphs with the conference still in progress).

Test tweet from Turkey!2:50 PM Apr 23rd from txt

Test text tweet two from Turkey!6:48 AM Apr 24th from txt

Okay everyone, the conference is starting now! Just joining in? Wondering what's goin' on in Istanbul? http://tr.im/jAcp http://tr.im/jAcs7:17 AM Apr 24th from Nambu

First talk of the day: Prof. Vidyanand Nanjundiah [Indian Institute of Sciences, Bangalore] ‘The Evolution of Cooperativity’7:18 AM Apr 24th from Nambu

Nanjundiah: "I hope you won't mind if I quote extensively from Darwin" - no, not at all! First quote = the 'problem' of the social insects7:20 AM Apr 24th from Nambu

Nanjundiah: Darwin's four solutions to the problem (to his theory) of the social insects. 4th solution: Descent of Man, Chapter V.7:22 AM Apr 24th from Nambu

@milagro88 It's the Darwin200 Anniversary Conference in Istanbul. Tweeting it now!7:24 AM Apr 24th from Nambu in reply to milagro88

Oh ffs. RT @edyong209 WSJ not accepting comments on blogging=opinions piece. Even after arcane registration process. Hmph. http://ow.ly/3yaO7:26 AM Apr 24th from Nambu

Yes, exactly, Grace! RT @grace_baynes @rpg7twit @kejames except if you want to bring said 120 ml home again and have hand luggage only :-/7:27 AM Apr 24th from Nambu

Nanjundiah: Haldane &'s Wright group selection vs. Williams who said group selection doesn't exist & when it does, it's just individual sel.7:29 AM Apr 24th from Nambu

Nanjundiah: Dictyostelium discoideum and D. giganteum as a model for group selection (if it exists, that is)7:32 AM Apr 24th from Nambu

Nanjundiah: Why do Dicty stalk cells behave altruistically? He's begging the question "what is an organism" & "what is a group"?7:36 AM Apr 24th from Nambu

Nanjundiah: even before the initiation of sociality in Dicty, there are tendencies that hint towards which cells will become sacrificial7:47 AM Apr 24th from Nambu

Nanjundiah: phenotypic plasticity (from stochastic gene expression) suggests 'sociology' > important than kinship in cooperative behaviour7:51 AM Apr 24th from Nambu

Q for Nanjundiah: this has become widely accepted among those who study social insects, so this talk very welcome; 'farewell kin selection'!7:52 AM Apr 24th from Nambu

Darwin200 Istanbul, next up: Prof. Hüseyin Atay [Faculty of Theology, Ankara University] ‘Science, Evolution & the Qu’ran’7:54 AM Apr 24th from Nambu

Atay: "I owe my practice to being non-dogmatic to the Qu'ran"7:56 AM Apr 24th from Nambu

Atay: 'the desire [for God] originates in infancy & continues to death' (I'd say ''from the point of indoctrination' instead of 'infancy')8:00 AM Apr 24th from Nambu

Atay: "from my study of the Qu'ran" & "according to the Qu'ran" but he assumes we think, like he does, that the Qu'ran is a source of truth8:06 AM Apr 24th from Nambu

Atay: "listen to every word" but I can't understand HIS every word (he's reading an English translation of his talk in Turkish)8:09 AM Apr 24th from Nambu

Atay: "whoever argues for his faith should be tested" ...oooh, it's getting good now (the bit I can understand)8:12 AM Apr 24th from Nambu

Atay: "the Qu'ran does not refer to the first creation of other beings" & on origin of man it describes man's origin in developmental terms8:14 AM Apr 24th from Nambu

Atay: "the Qu'ran speaks of science but is not a book of science"; it aims to draw man's attention to (not to instruct in) these things8:16 AM Apr 24th from Nambu

Atay: "the mind is not subject to the Qu'ran" and "reason does not produce knowledge, it makes use of knowledge produced by mind"8:17 AM Apr 24th from Nambu

From Atay's abstract: "Creationists have misunderstood God."8:21 AM Apr 24th from Nambu

Also from Atay's abstract: "Evolutionists attribute awe to evolution; in so doing, they ascribe divine provenance, just as creationists do."8:23 AM Apr 24th from Nambu

Atay: "The mind knows the unknown by using inference."8:24 AM Apr 24th from Nambu

If Dawkins, PZ et al are the "new atheists" then I think Atay is a "new moderate" for saying things like this: (...continued in next tweets)8:28 AM Apr 24th from Nambu

Atay: Creationists say God created everything; then he also created evolutionists, so to criticize evolutionists is to criticize the creator8:31 AM Apr 24th from Nambu

Atay: "Evolutionists say man evolved; since creationists are men, to criticize creationists is to criticize evolution." <--see what I mean?8:33 AM Apr 24th from Nambu

On this last point Atay assumes we are reluctant to criticize evolution. Does he think we adhere still to the great chain of being?8:38 AM Apr 24th from Nambu

Q from a self-professed "former religious fanatic" that I couldn't understand a word of. :(8:41 AM Apr 24th from Nambu

Atay's talk will be published on the conference website and/or in a newspaper, which is good b/c I only understood every 5th sentence or so.9:18 AM Apr 24th from Nambu

Darwin200 Istanbul: Next up: Prof. Francisco Ayala [University of California] ‘The Intelligent Design Movement – a Critique’9:19 AM Apr 24th from Nambu

Ayala: "Darwin's discovery of natural selection provided the main process which accounts for the design of organisms by natural processes"9:20 AM Apr 24th from Nambu

Ayala: "Intelligent design is not science. Even worse, it is bad religion"9:22 AM Apr 24th from Nambu

Ayala: the famous mosaic of images of butterfly wings that make all the letters of the alphabet; doesn't mean they were designed for wri ...9:26 AM Apr 24th from Nambu

Ayala: The Copernican revolution is really a commitment to the idea that laws that explain observable phenomena can be discovered & tested.9:27 AM Apr 24th from Nambu

Ayala: William Payley expressed idea of intelligent design better than modern talking heads, and with much better biological understanding.9:28 AM Apr 24th from Nambu

For anyone just joining - I'm tweeting live from the Darwin200 Anniversary Conference in Istanbul. Background here: http://tr.im/jAA99:31 AM Apr 24th from Nambu

Ayala reading now from The Origin of Species, Chapter IV, Natural Selection, "As more individuals are produced than can possibly survive..."9:32 AM Apr 24th from Nambu

A privilege to hear Ayala explain evolution, natural selection, intelligent design (which he is critiquing, in case that wasn't clear)9:33 AM Apr 24th from Nambu

@TEDchris Thanks for the mention!9:35 AM Apr 24th from Nambu in reply to TEDchris

@USelaine Thanks! FYI @nytimeskristof Tonight's public session is on Turkish TV & attended by journalists including, rumor has it, from NYT9:38 AM Apr 24th from Nambu in reply to USelaine

Ayala now using famous melanic moth example. Though correct, I think this story's effectiveness tainted by bad press (wrong but still bad)9:43 AM Apr 24th from Nambu

Ayala now hammering it home with a detailed explanation of the step-by-step evolution of molluscan and vertebrate eyes. Yesssss!9:46 AM Apr 24th from Nambu

@rpg7twit Unfortunately it's the size of the container, not the amount of liquid remaining.9:49 AM Apr 24th from Nambu in reply to rpg7twit

Ayala: "the vertebrate eye has an imperfection that the molluscan eye doesn't" namely, the blind spot. Heh. Man IS but a worm!9:50 AM Apr 24th from Nambu

Ayala: "I will now criticize the design movement in 2 ways: 1) my own criticisms & 2) those of John Jones (Dover judge)" *sits up straight*9:52 AM Apr 24th from Nambu

Ayala: Philip Johnson (ID proponent) claimed "Give us 5-10 years, and you'll see sci breakthroughs biologists hadn't dreamed of before I ...9:54 AM Apr 24th from Nambu

Ayala: ...well that was 1998!9:55 AM Apr 24th from Nambu

Ayala: "The ID proposal has several probs" (holy understatement, batman!) including "Imperfect Design" e.g. human jaw, human birth canal &c.9:59 AM Apr 24th from Nambu

Ayala! Snap! If God intelligently designed organisms then high rate of human miscarriages implies that "God is the greatest abortionist"10:04 AM Apr 24th from Nambu

Ayala: "Science is methodologically naturalistic not philosophically materialistic."10:05 AM Apr 24th from Nambu

Ayala's final slide: "Evolution: Darwin's gift to religion"10:06 AM Apr 24th from Nambu

Q to Ayala: "Sci & religion are 2 different approaches but are they really compatible?" Ayala: "yes, as it is w/ aesthetics, economics, &c."10:10 AM Apr 24th from Nambu

Ayala's book (for any tweeps interested) is "Darwin's Gift To Science And Religion" Joseph Henry Press, 200710:11 AM Apr 24th from Nambu

Next up: Prof. Aykut Kence [Middle East Technical University, Ankara] ‘Creationism – Historical and Contemporary Perspectives’10:13 AM Apr 24th from Nambu

Kence: "evolution is most controversial theory in history of science not b/c of 'drawbacks' but b/c so many non-scientists can't accept it"10:16 AM Apr 24th from Nambu

Kence now giving us a history of creationism in USA and Turkey (which are, as a poster reminded me, top 2 countries for evolution denial).10:17 AM Apr 24th from Nambu

Kence: "The 'problem' w/ evolution didn't exist at the founding of Republic of Turkey" ergo rejection of Darwinism a recent development.10:26 AM Apr 24th from Nambu

Kence: "In 1970s Fethullah Gulen started giving anti-Darwinism conferences. He said sci textbooks should be written by 'our religious men'"10:27 AM Apr 24th from Nambu

Kence: US creationist talking points were simply adopted and modified to Islam. Specific examples in textbooks show cut-and-paste approach.10:28 AM Apr 24th from Nambu

Now a romp through tragic Turkish textbook quotes e.g. "to give creation to Allah makes things easier/saves scientists from wasting energy"10:35 AM Apr 24th from Nambu

Turkish textbook: "contrary to what evo'ists claim, it was demo'd that frog, mouse & snake blood more similar to human blood than monkeys"10:35 AM Apr 24th from Nambu

Kence: huge amounts of money in Turkey going to defamation of Darwinism. One tactic is 'vilifying evolutionists as Marxists, communists'10:38 AM Apr 24th from Nambu

Kence: younger Turkish teachers less likely to 'believe' in scientific validity of evolution than older Turkish teachers. Awful.10:39 AM Apr 24th from Nambu

Quote from Mustafa Ataturk: "My moral legacy to Turkish people is Science and Reason. The only salvation for Turkey (& middle East!) is ...10:41 AM Apr 24th from Nambu

...to embrace that legacy again. Wow. Powerful.10:41 AM Apr 24th from Nambu

Turkish creos have branded science as "vulgar philosophy"; It appears the Discovery Institute's Wedge doc has been translated into Turkish.10:43 AM Apr 24th from Nambu

Beautifully put! RT @crc2008 faith is personal, all dogma is dogma, science is public acknowledgement of doubt and verification...10:44 AM Apr 24th from Nambu

Now for lunch.10:55 AM Apr 24th from Nambu

Just caught the end of 2pm talk ‘The Challenges of Science Education Today’ by Prof. Nidhal Gessoum [American University of Sharjah, UAE]about 22 hours ago from Nambu

Gessoum: More girls pursuing science in university in Middle East than boys; anecdotal evidence that boys want to go into the Army. Scary.about 22 hours ago from Nambu

Gessoum: What we need most: training and workshops for teachers, and more science endowments and patronage (two words: Beagle Project!)about 22 hours ago from Nambu

Up next: Prof. Sema Ergezen [Marmara University] ‘Teaching Evolution in Turkey: Present and Future’about 22 hours ago from Nambu

Good morning America! If you're just joining in, I am live-tweeting the Darwin200 Anniversary Conference in Istanbul http://tr.im/jBepabout 22 hours ago from Nambu

Ergezen exploring causes & consequences of systemic anti-evolutionism in Turkish teaching. Wow, & to think we thought it was bad in the US.about 22 hours ago from Nambu

Ergezen: Turkish teachers complain of not having had specific courses on evolution at University, or that those courses are superficial.about 22 hours ago from Nambu

Ergezen: Turkish teachers say they don't know how to teach evolution; others don't know how to defend evolution (against creat'ist students)about 22 hours ago from Nambu

62% of 1st year biology students in Ergezen's class "don't accept evolution" i.e. they arrive at school biased against evolution.about 22 hours ago from Nambu

Ergezen: we are failing to help teachers think evolutionarily, and to infuse evolution throughout all biologyabout 22 hours ago from Nambu

@imascientist Why thank you! *blushes* (or is that the Turkish coffee?)about 22 hours ago from Nambu in reply to imascientist

@flascience Thanks, we're hearing now about one of your fave topics: evolution education! Pro development for teachers an important theme..about 22 hours ago from Nambu in reply to flascience

Ergezen: we must 1) create collaborations between scientists and teachers, provide pro. development to teachers, promote evolution-thinkingabout 22 hours ago from Nambu

Ergezen: We must take action! We must start now! A passionate call not to be passive! (*cough* Beagle Project *cough*)about 22 hours ago from Nambu

Welcome to Twitter friend, wordsmith, Yorkshireman & Beagle Proj co-founder Peter McGrath! @pietromcg (a.k.a. the Ben Goldacre of the North)about 21 hours ago from web

THIS IS WHAT CENSORSHIP LOOKS LIKE http://pic.im/1Veabout 21 hours ago from Nambu

Up next: FInal Panel Discussion ‘A Better Vision - The Public Understanding of Evolution in Turkey and Beyond’about 21 hours ago from Nambu

Panel Discussion Chair Prof. Aslı Tolun giving us background on Turkish evolution education & outreach situation. To paraphrase: it's bad.about 21 hours ago from Nambu

Hearing inside scoop from Tolun on the (most recent) Darwin censorship incident http://tr.im/jBxs (aside: even Iran teaches evolution!)about 21 hours ago from Nambu

Tolun asks: why is evolution edu important; what are the major problems; what are the challenges; what are the means for effective teaching?about 21 hours ago from Nambu

Panelists' answers to "why is evolution important": 1) b/c scientists need frameworks to link their findings w/ a context...about 21 hours ago from Nambu

2) nothing in bio makes sense w/o it; 3) b/c it helps us take greater meaning fr. your interactions w/ nature (kids shouldn't be afraid ...about 21 hours ago from Nambu

...of insects!); 4) human health and disease prevention all founded on evolution (<--panelists' answers to 'why evolution important')about 21 hours ago from Nambu

I asked panel: is evolution denial demographically linked to climate change denial in Turkey as it is in USA? ...about 21 hours ago from Nambu

... answer is "No, it's a more general problem of apathy & ignorance. Even those who support evolution do so w/o knowing why; it's ideology"about 21 hours ago from Nambu

Good morning West Coast! If you're just joining in, I am live-tweeting the Darwin200 Anniversary Conference in Istanbul http://tr.im/jBepabout 21 hours ago from Nambu

First-year Turkish university students, presented with an 18-million-year-old fossil and asked to guess how old, will answer 50-200yrs.about 21 hours ago from Nambu

@CR_Fauchald Many at this conference would agree w/ you. Others wouldn't. Sadly all this 'haggling' is hurting our science & our society.about 21 hours ago from Nambu in reply to CR_Fauchald

Turkish panelist informs us that though Turkish academy founded to advise government, it doesn't work that way anymore.about 21 hours ago from Nambu

Another panelist says there is no professional community for science education scholarship in Turkey: there's a lack of associations & unityabout 21 hours ago from Nambu

Solution offered to panelists by audience member: need to boost cultural support for evo; to do this, must know history of their alienationabout 21 hours ago from Nambu

The quality of curricula on evolution is a big problem in Turkey, USA, UK, France; they put too much emphasis on particular bio processesabout 21 hours ago from Nambu

Juxtaposition giving me goosebumps: In session on evolution & religion & can hear the mosque next door to the hotel calling to prayerabout 20 hours ago from Nambu

Great comment from audience: consensus at this conference is that religion & evolution are compatible, but society at large it's 'either/or'about 20 hours ago from Nambu

Panelist: "evolution has been used as an ideological battleground; teaching evolution is not about converting people, it's about explaining"about 20 hours ago from Nambu

Comment: getting the mullahs to tell their followers to accept evolution is NOT the point; the point is to inspire critical thinking.about 20 hours ago from Nambu

@crc2008 First of all, I said "evolution and religion are compatible" is the consensus of this conference, not necessarily my own view!about 20 hours ago from Nambu in reply to crc2008

@crc2008 Second of all, I would have like to have said 'acceptance of evolution' not just 'evolution' but such is twitter ;-)about 20 hours ago from Nambu in reply to crc2008

Only when the religious stop meddling w/ sci edu! RT @tuibguy teach the biology let the religious worry about their part. Will it work?about 20 hours ago from Nambu

Commenter: better science education is needed in the seminaries. (Yep, that'd be good, I agree. Good luck though.)about 20 hours ago from Nambu

@mwinther @rdmpage @neuro100 Heh. Unfortunately all of the spokesmen for this view (Dawkins et al.) were specifically *not* invited here.about 20 hours ago from Nambu in reply to mwinther

OMG this is scary. Someone is standing up and saying 'the problem is democracy' because culture is king in democracy.about 20 hours ago from Nambu

Double OMG! He called Dawkins "an extreme vulgar ideologist"! ...then said people need to be persuaded not forced to accept evolution. Hmm.about 20 hours ago from Nambu

Me: In all our talk about the education-ignorance dichotomy & how to argue better, let's not forget about the apathy-inspiration dichotomyabout 20 hours ago from Nambu

Phew! My talk is over and now enjoying a production of Re-design, a dramatization of the Darwin-Gray correspondence.about 17 hours ago from txt

This is the public portion of the symposium w/ 300+ Turkish students in attendance. Next up a televised panel discussionabout 17 hours ago from txt

Still tweeting live from Darwin200 Istanbul though less frequently b/c by text. Televised panel discussion beginning!about 15 hours ago from txt

Audience questions!about 15 hours ago from txt

One questioner practically reading out of Hurun Yahya; he just won't accept the existence of transitional fossilsabout 15 hours ago from txt

Panelist: Science uses hypothesis & experiment to find out truth. Religion uses... uh... something else.about 14 hours ago from txt

@pseudonymTrevor Love that Thoreau is your avatar (*follows*). Glad you found DCP. Darwin-Online is also good resource http://tr.im/jG5Uabout 1 hour ago from Nambu in reply to pseudonymTrevor

Damn, missed my chance. RT @pietromcg Harun Yahya sounds like he's doing a pavement pizza in a shop door after 7 pints & a curry. Tell him.about 1 hour ago from Nambu

Thanks to all who replied to & RT'd my live tweets from Darwin200 Conference in Istanbul. Conf over now, but I'm in Istanbul through Monday.about 1 hour ago from Nambu

Plans to live-blog the Templeton-funded Darwin conference in Istanbul

2009-04-21T23:45:00.008+01:00

Do I win the award for most lightning rods in a blog post title yet?

I mean, there's Turkey's ...uh... ...how shall I say... delicate relationship to Darwin and evolution (and atheism, *cough* not that that has anything to do with Darwin and evolution *cough*), there's the general distaste evolution advocates have for the Templeton Foundation and then there's Turkey's recent censorship of Blogger and Wordpress blogging platforms. Thrrreeee lightening rods, Ah Ha Ha!

But before I explain about the conference, how I will be live-blogging it and what on Darwin's entangled bank I was thinking about when I agreed to accept the Templeton Foundation's support for my participation, let's all just get this out of our systems first shall we?

In case you're wondering, yes I do love the They Might Be Giants cover, but this original* is pretty swingin' and I figured its existence might be news to a certain percentage of my readers.

With that obligatory Obnoxious American^TM preface to all blog posts with 'Istanbul' in the title out of the way, let's get down to business:

Starting at an undisclosed time later this week, from an undisclosed location in Istanbul (undisclosed presumably to keep Oktar's ilk away), I will be participating in the Darwin-200 Anniversary Conference. I've been invited give a short talk about The HMS Beagle Project during the final, public session, which follows a more exclusive two-day scientific symposium on the scientific, historical, cultural and religious implications of evolution including a 'critique' of intelligent design by a famous person (*rubs hands*) and panel discussions on "Evolution and Purpose" and "Public Understanding of Evolution in Turkey and Beyond".

What, my evolution peeps might be wondering, 'possessed' me to accept an invitation to a Templeton conference? Don't I know that "Templeton funds stealth religion, and the good work they support is a façade to conceal their aims", paying "hefty bribes to get scientists to cross that line [between science and religion]"? Why yes, I do, but I figure if I can use up some of that money to get me to Turkey where I can do my fly-in-the-ointment thing, live-blog it and also proselytize a bit for the Beagle Project, a project that will promote science in general, evolution in particular, and a rational approach to solving our most pressing problems, well, then, that's a good appropriation of their money as far as I'm concerned.

Moreover, if Bernard d'Espagnat, who, on winning a Templeton Prize, didn't reject the prize but said:

I feel myself deeply in accordance with the Templeton Foundation's great, guiding idea that science does shed light [on spirituality]. In my view it does so mainly by rendering unbelievable an intellectual construction claiming to yield access to the ultimate ground of things with the sole use of the simple, somewhat trivial notions everybody has.

(via Darwin's Teapot)

...then I figure I'm in pretty good company.

Rationalizations safely behind me now, here are the details my impending coverage of the conference:

I've scheduled a post to go live here at approximately the same time I expect to start tweeting from Istanbul later this week. The post will consist mainly of an embedded twitter feed, but I will also try to update the post itself a few times during the conference with more substantive stuff.

I have to confess that - in a Rebel Girl kind of a way - I'm actually kind of excited to try my hand at tweeting and blogging from a place that has censored both evolution and blogging in the recent past. There are potential hazards. For example, if for some reason Blogger is still banned in Turkey (though Reporters Sans Frontieres says it was restored), this might not go as planned. I would think my tweets should still get through, though (unless Turkey suddenly bans twitter).

To stay in the loop, follow this blog's feed or follow me on twitter.

One last thing before I go, a little test of ye olde twitter widget:

Update Friday: Hmm, well it's working, but only if you have Flash (and not everyone does!) and formatting not great. Think I will use the html widget instead in the live-blog post.

*which itself is so similar to Irving Berlin's Puttin' on the Ritz (here's a classic performance by Fred Astaire), I'm not even sure 'original' is the right word

Proud to be one of thirteen twits

2009-04-16T14:51:00.001+01:00

Two days ago I found myself inundated with literally hundreds of new twitter followers (as of today, ~450 and counting). After sending a delighted if baffled tweet asking my new followers what the trigger might have been, I was kindly informed by quite a few that it was probably because I was featured on mashable in an article by Andrew Maynard:

13 "Twits" who will change your perspective on reality"

In his preamble to the list, Maynard writes, "Is there profundity to be found on Twitter? Indeed there is. The service plays host to some real gems; seemingly off-the wall users who get inside your head and challenge you to think differently. Some of them are big names like CTO of Cisco Padmasree Warrior and Web 2.0 guru Tim O’Reilly, with followings in the six digits. Many of the best tweets, however, come from regular folk who have something worthwhile to say. Here are just 13 with a penchant for science and technology that make me think in new ways."

And so, without further ado, here's the list of us "Twits":

Charles Darwin: tweeting from the Beagle, where else?
Chris Anderson: runs the TED conference
Laura S. Marshall: publishing editor
Marcus du Sautoy: the “Simonyi Professor for the Public Understanding of Science” at the University of Oxford in the UK (until recently held by Richard Dawkins)
Lord Drayson: British government Minister for Science and Innovation
Joerg Heber: senior editor for the scientific journal Nature Materials
Karen James: Maynard describes me thusly: "A self-confessed Darwin groupie, Karen works at the Natural History Museum and is heavily involved in attempting to rebuild the Beagle: The ship that carried Charles Darwin around the world. Her tweets will give you an unashamedly Darwinian view of life—entertaining and provocative."
Tim Harper: entrepreneur, investor and emerging tech adviser
Alexis Madrigal: Wired.com’s energy and science staff writer
Eric Berger: science reporter for the Houston Chronicle
David Bradley: writes the Sciencebase blog where he maintains a growing list of “scientific Twitter friends”
Arjun Basu: Maynard describes his tweets as "thought-provoking fiction, in bite-sized chunks"
Tim Jones: freelance science communicator

Holy good company, Batman. Do visit Maynard's mashable article for a lot more information about each Twit including 'sample tweets' and the specific reasons you should follow them. And I can't end without saying a huge "thank you" both to Andrew Maynard and all my new followers: I hope I live up to your expectations!

Why I love humans: extreme sheep LED art

2009-03-20T22:56:00.003Z

On the soon-to-be-formally-rebooted Data Not Shown, one of the things I intend to post on a regular basis is a category of items I like to call "why I love humans". These are examples of when we use our creativity to make good things out of bad, to amuse each other in unexpected places or ways, and generally to lift each other up using our higher social faculties.

Here is my first entry, from the Guardian's weekly Viral Video Chart:

Preboot

2009-03-08T17:02:00.007Z

Hello again, world! I'm just about to reboot this here sadly neglected blog, but before I write my big comeback post I thought I'd break the ice by posting this rather exciting little missive. Let's call it a 'preboot', shall we?

We might also call it "Karen's femtosecond of fame" though it's really more like a few flashes of curly hair on either side of a close-up of my hands preparing DNA samples using white Whatman FTA cards, spread across a three-minute segment squarely in the middle of the hour-long first episode of a three-part series. Under normal circumstances this might not even be noteworthy at all, except that IT'S THE BBC, BABY, and no matter how bit my part is, I will always be proud to be associated with the network of David Attenborough.

The series is called Darwin's Garden and this episode, Dangerous Ideas* , is available to watch until the 26th of March. The segment I'm in, about a project I'm involved with through my work at the Natural History Museum to resurvey Great Pucklands meadow at Down House, runs from 30:10 through 33:15:

That's me on the left, squishing bits of our voucher specimens onto FTA cards for DNA sequencing later.

*You'd think that someone, somewhere in Beebdom would have noticed and bothered to mention to the filmmakers that Andrew Marr was planning on using the same title for his three-part BBC series.

Reinvention

2008-12-06T13:38:00.005Z

It's going to be a little untidy here at DNS while I mess around with the layout, finally populate that scrawny sidebar over there and, most importantly, set a few rules about what this blog is and isn't going to be about. Yep, we're talkin' discipline. And it's not even New Year's Day yet.

Speaking of reinvention, don't miss Richard Grant's play-by-play account of transitioning from science to, well, not science. I'm not entirely clear yet what Richard's new gig is but whatever it is, if these posts are any indication, he's going to shine:

And in case you're wondering why he's talking about leaping out of a void, you might do well to take in Jennifer Rohn's April 2007 excellent post on leaping into one.

Five Things

2008-11-27T22:05:00.001Z

Michael Barton tagged me with the Five Things Meme. And so, without ~~further~~ any ado:

5 Things I Was Doing 10 Years Ago:

Mourning the loss of my father
Mourning the loss of my grandmother
Enduring the mid-PhD doldrums
Enjoying the company of my the fellow residents at 2333 N. 58th Street in Seattle (including Luna the malamute, may she rest in peace)
Starting my second season of telemark skiing

5 Things On My To-Do List Today:

Finish manuscript for submission to Molecular Ecology Resources (or Systematics and Biodiversity, haven't decided yet) and circulate to co-authors
Assemble, edit, align and export DNA sequence data for another paper I'm working on
Buy plane tickets to North Carolina for ScienceOnline'09
Try to forget that, back home, everyone is getting today off of work and gorging themselves on turkey and stuffing
Write this blog post (check!)

5 Snacks I Love:

Tortilla chips and homemade guacamole
Whole wheat toast with butter and raspberry jam
Green & Black's Milk Chocolate
Pretty much anything from the deli at Carluccio's
Innis and Gunn

5 Things I Would Do If I Were A Millionaire:

Give £60,000 to the Galapagos Conservation Trust for their Floreana mockingbird campaign
Give £5 million to to The HMS Beagle Project
Send anonymous money-grams to friends and family in financial stress
Donate to various environmental, humanitarian and progressive charities
Buy a small house with a big garden and then hire Ten21 Architecture to make it into the eco-home of my dreams

5 Places I've Lived:

Washington, D.C.
Colorado Springs
Fort Collins
Seattle
London

5 Jobs I've Had:

Veterinarian's assistant
Tour guide at the US Olympic Training Center in Colorado Springs
Research assistant
PhD student (yes, that most certainly does count as a job, thankyouverymuch - worked hard, got paid ...a little)
Research scientist

I'm not going to tag anyone right now. Too lazy. I might add some tags this weekend.

Shake your frozen assets

2008-11-16T12:55:00.005Z

I got hip to mobile clubbing when I read (and, I admit, wept over) a Guardian piece appropriately titled An Explosion of Delight, which describes the scene at London's Liverpool Street station on an October evening in 2006, just over a year after the horrific terrorist bombing there, when hundreds if not thousands of people who had moments before seemed to just be going about their daily commute, suddenly broke into dance at the appointed moment.

And so it was, that on that evening, by participating in a public expression of joy and solidarity with hundreds of perfect stangers, Londoners took back Liverpool Street Station from the terrorists:

There's another mobile clubbing event coming soon, this one timed to help us all shake off some of our financial frustrations by shaking our ~~booties~~ frozen assets this Tuesday, at 6:20pm, outside the Bank of England. For more info click the bank note:

Everything's gonna be okay: Obama is a Mac

2008-11-12T09:52:00.006Z

This is a new series in which I plan to highlight how everything's gonna be okay* now that we've elected the anti-matter opposite of George W. Bush to the highest office in our humble little land.

Part I: Obama is a Mac

Obama uses a Mac. I love the idea that there will be a Mac laptop on the desk in the Oval Office. I mean, how cool is that? And is that a photo of Martin Luther King Jr on the table next to the Mac? And is that a clever little Pac Man sticker on his Mac eating the Apple? Oh, I like what I see, Mr. Obama, I like.

...and so is Biden! Somebody pinch me.

*yes, I know that Obama's not a silver bullet (no such thing as a silver bullet in our complex world) but he's as damn-well close to it as I can possibly wish for at this stage in our history, and I intend to celebrate that, so there.

'Mama Afrika' dies at 76

2008-11-10T21:53:00.010Z

I first came across Miriam Makeba when my friend Jennie (Stella's mum) put me onto Makeba's mind-bending, world-expanding Qongoqothwane, (The Click Song). From there I ran out and bought the album Africa (back when we still physically ran out to buy albums).

I was blown away by the power of her voice and its comforting, encircling maternal resonance. Maybe that's what earned her the nickname 'Mama Afrika', though I suspect that was only a small part of it - she truly was an African icon - a exile of South Africa during apartheid. From the New York Times:

Widely known as “Mama Africa,” she had been a prominent exiled opponent of apartheid since the South African authorities revoked her passport in 1960 and refused to allow her to return after she traveled abroad. She was prevented from attending her mother’s funeral after touring in the United States.

Although Ms. Makeba had been weakened by osteoarthritis, her death stunned many in South Africa, where she stood as an enduring emblem of the travails of black people under the apartheid system of racial segregation that ended with the release from prison of Nelson Mandela in 1990 and the country’s first fully democratic elections in 1994.

In a statement on Monday, Mr. Mandela said the death “of our beloved Miriam has saddened us and our nation.”

He continued: “Her haunting melodies gave voice to the pain of exile and dislocation which she felt for 31 long years. At the same time, her music inspired a powerful sense of hope in all of us.”

“She was South Africa’s first lady of song and so richly deserved the title of Mama Afrika. She was a mother to our struggle and to the young nation of ours,” Mr. Mandela’s was one of many tributes from South African leaders.

“One of the greatest songstresses of our time has ceased to sing,” Foreign Minister Nkosazana Dlamini-Zuma said in a statement. “Throughout her life, Mama Makeba communicated a positive message to the world about the struggle of the people of South Africa and the certainty of victory over the dark forces of apartheid and colonialism through the art of song.”

For 31 years, Ms. Makeba lived in exile, variously in the United States, France, Guinea and Belgium. South Africa’s state broadcasters banned her music after she spoke out against apartheid at the United Nations. “I never understood why I couldn’t come home,” Ms. Makeba said upon her return at an emotional homecoming in Johannesburg in 1990 as the apartheid system began to crumble, according to The Associated Press. “I never committed any crime.”

Music was a central part of the struggle against apartheid. The South African authorities of the era exercised strict censorship of many forms of expression, while many foreign entertainers discouraged performances in South Africa in an attempt to isolate the white authorities and show their opposition to apartheid.

From exile she acted as a constant reminder of the events in her homeland as the white authorities struggled to contain or pre-empt unrest among the black majority.

Ms. Makeba wrote in 1987: “I kept my culture. I kept the music of my roots. Through my music I became this voice and image of Africa, and the people, without even realizing.”

Her path was marked by the stars of the southern hemisphere
and she walked the length of her days under African skies...

Goodbye, Mama Africa, and thank you.

Too bad the Obamas aren't a good-looking couple

2008-11-10T21:49:00.001Z

Warning: gratuitous cuteness

2008-11-09T18:38:00.002Z

Can't go wrong with baby hedgehogs:

Ratified

2008-11-07T18:33:00.002Z

h/t Nicole Maturen

I voted: can I have my free coffee and sex toys now?

2008-11-04T12:43:00.002Z

Vote, people!

2008-11-04T08:58:00.003Z

Black Bromptons bearing bounty

2008-11-04T00:02:00.007Z

pip-pip gives us this wonderful photo of a quintessentially English Brompton folding bicycle (be still my beating heart) with a lush harvest of leeks from the allotment. Two years ago last week I snapped this photo of our Brompton with a truly ginormous butternut squash from Wimbledon Farmers' Market:

Coincidence? Perhaps.

Stella by starlight

2008-11-02T21:32:00.003Z

Welcome to the world, Stella! Your mother has put out a request for lullabies but after having racked my brain for two weeks, I couldn't come up with anything, and though I do plan to ask my own mum, she is on an RV trip right now. However, a little searching yielded this, something that I know both of your parents will dig:

Languages from the Cradle is a European Union funded project to collect the lullabies of Europe. Learn more in this mp3 from United Nations Radio (did you know there was such a thing? neither did I) including a lovely Sudanese lullaby, and don't miss the Languages from the Cradle wiki.

I also offer two lullabies from my favorite British songstress, Kate Rusby. The first is a real lullaby and the second and third are two versions (second one is live and I love how the audience embraces it ...I even see some young heads nodding off) of a traditional song that works well as one:

Scientist Pin-Ups: Kitty Joyner

2008-11-01T20:55:00.007Z

Thanks to Darwin-dispersalist Michael Barton who suggested this pin-up, asking, "do engineers count?" I was pondering my response to the question as I clicked through to the link he sent me and as soon as I saw the oh-so-pinuppable-in-that-1950's-you-know-what-I'm-talkin'-'bout-way image I knew my answer had to be hell, yes.

Kitty Joyner, electrical engineer, at Langley in 1952 (NASA Images).

On top of being aesthetically beautiful, this pin-up is hot for the following reasons:

I have a soft spot for NASA
Kitty Joyner is not a household name and as such provides another much-needed example of a 'normal woman' in science
Even in 2008 a woman engineer is a relatively rare thing (in the US, only 12.4% of electrical engineering bachelor's degrees went to women last year); I can't imagine how rare it must have been in 1952 ...perhaps this is the tail-end of the of the Rosie the Riveter era?

Down syndrome research pop quiz: fruit flies 94, Sarah Palin zilch

2008-10-28T22:18:00.024Z

This story has already been covered to death (or at least I hope so) on teh interwebs, but I must have my say. You see, when Palin dissed fruit flies...

...she didn't just diss fruit flies and the general and specific importance of model organism research (for which she is rightly and expertly skewered by Christopher Hitchens, Kevin Berger and others). She also dissed me.

As mentioned previously here and here, I did my PhD research on the fruit fly* Drosophila melanogaster. Specifically, I worked my butt off for six years to understand some of the myriad and complex functions of a fruit fly gene called Ras (the human counterpart of which plays a role in the onset and/or development of almost every kind of cancer) on the ovarian and embryonic development of the fruit fly, and how this has been modulated during fruit fly evolution.

That's right, friends, I am officially (and, it must be said, very proudly) on Sarah Palin's shit list: not only did I do research on fruit flies (booooo!) but I also did research on evolution (hissssss!).

But enough about me.

Almost unbelievably, Palin's sneer came directly on the heels of her own call to help families with special needs kids like her nephew with autism and her son with Down syndrome. See, in Palin's (surprisingly young) universe, it cannot possibly be fathomed that something as obscure as a fruit fly could help special needs kids. But a quick search on PubMed for 'Drosophila and "Down syndrome"' yields 94 peer-reviewed research articles including this one [my emphases]:

Dscam guides embryonic axons by Netrin-dependent and -independent functions.

Andrews GL, Tanglao S, Farmer WT, Morin S, Brotman S, Berberoglu MA, Price H, Fernandez GC, Mastick GS, Charron F, Kidd T.

Development. 2008 Oct 23. [Epub ahead of print]

Developing axons are attracted to the CNS midline by Netrin proteins and other as yet unidentified signals. Netrin signals are transduced in part by Frazzled (Fra)/DCC receptors. Genetic analysis in Drosophila indicates that additional unidentified receptors are needed to mediate the attractive response to Netrin. Analysis of Bolwig's nerve reveals that Netrin mutants have a similar phenotype to Down Syndrome Cell Adhesion Molecule (Dscam) mutants. Netrin and Dscam mutants display dose sensitive interactions, suggesting that Dscam could act as a Netrin receptor. We show using cell overlay assays that Netrin binds to fly and vertebrate Dscam, and that Dscam binds Netrin with the same affinity as DCC. At the CNS midline, we find that Dscam and its paralog Dscam3 act redundantly to promote midline crossing. Simultaneous genetic knockout of the two Dscam genes and the Netrin receptor fra produces a midline crossing defect that is stronger than the removal of Netrin proteins, suggesting that Dscam proteins also function in a pathway parallel to Netrins. Additionally, overexpression of Dscam in axons that do not normally cross the midline is able to induce ectopic midline crossing, consistent with an attractive receptor function. Our results support the model that Dscam proteins function as attractive receptors for Netrin and also act in parallel to Frazzled/DCC. Furthermore, the results suggest that Dscam proteins have the ability to respond to multiple ligands and act as receptors for an unidentified midline attractive cue. These functions in axon guidance have implications for the pathogenesis of Down Syndrome.

In other words, research on fruit flies is helping us to understand Down Syndrome better. The same can be said for almost all human biology, both pathogenic and 'normal' (whatever that means).

And here's where Palin's mocking is even more resonant: the reason fruit fly biology illuminates human biology is because our genomes are so similar and the reason our genomes are so similar is because we inherited them from the last common ancestor of humans and fruit flies [cue Sarah Palin's head popping off and steam shooting out].

*Though not technically correct, 'fruit fly' is the colloquial name for the monumentally important model organism Drosophila melanogaster. True fruit flies belong to the insect family Tephritidae and it was in fact a research project on these Tephritid flies that Palin was so gleefully skewering as wasteful earmark spending. Some have argued that this fact exonerates Palin-- i.e. that she was not mocking D. melanogaster research because she knows how important that is (right, as if Palin knows the difference between true fruit flies and model organism 'fruit flies') but rather she was mocking Tephritid fruit fly research. Problem is that the project she mocked is more applied to human benefit (in this case agricultural productivity) than most D. melanogaster research, not less, so there's that argument out the window.

Mood blogging

2008-10-22T14:30:00.001+01:00

h/t Chris Coltraine via Matt Brown

Scientist Pin-Ups: Senta's sexy sextant

2008-10-18T00:10:00.005+01:00

Senta Osoling learns how to determine latitude by using a sextant in September 1942 at Polytechnic High School, Los Angeles (which is, coincidentally, where my father went to high school). Senta later became a chemist, and is now the Director of National Center for Improving Science Education. Profiled here.

h/t Michael Barton

"I'm a scientist, and I'm voting for Barack Obama"

2008-10-17T23:42:00.005+01:00

Scientists and Engineers for America Action Fund and ScienceBlogs have launched A Vote for Science, a collection of YouTube videos made by scientists explaining who they are voting for and why. So in addition to casting my absentee ballot, I think contributing something to A Vote for Science should be my other pre-election duty this weekend. I'm not sure I need a whole video, though, when one picture pretty much says it all:

A good friend's uterus, this week. I'm going to hazard a guess that this future heir of our environmental legacy is not going to look back kindly on the folks who chanted "drill, baby, drill! and pretended for way, way, way too long that climate change wasn't caused by human activity.

Scientist Pin-Ups: DNA's dark lady

2008-09-21T18:43:00.014+01:00

Update: Elke and Miriam have ~~accepted~~ embraced the challenge!

In this first installment of Scientist Pin-Ups, I have decided to feature an important (and lovely) figure in the history of science: Dr Rosalind Franklin. I have selected three imminently pin-uppable pictures of Franklin, but before you feast your eyes, please take a moment to read this short excerpt from the National Library of Medicine's excellent Rosalind Franklin Papers:

Rosalind Elsie Franklin (1920-1958) was a British chemist and crystallographer who is best known for her role in the discovery of the structure of DNA. It was her x-ray diffraction photos of DNA and her analysis of that data--provided to Francis Crick and James Watson without her knowledge--that gave them clues crucial to building their correct theoretical model of the molecule in 1953. While best known for this work, Franklin also did important research into the micro-structure and properties of coals and other carbons, and spent the last five years of her career elucidating the structure of plant viruses, notably tobacco mosaic virus.

There is also the brilliant BBC Four documentary, The Dark Lady of DNA (called Secret of Photo 51 in the US) both with associated online content. Now on to the pictures:

Rosalind Franklin, "seen here serving coffee in evaporating dishes at her Parisian laboratory in the late 1940s" (image from NOVA's Secret of Photo 51)

Rosalind Franklin on holiday in Tuscany in Spring, 1950.
Image from the National Library of Medicine's Rosalind Franklin Papers

Rosalind Franklin mountain climbing in Norway, ca. 1940s.
Image from the National Library of Medicine's Rosalind Franklin Papers

In my next post I will highlight one more historical (lovely) figure in science before moving on to caricatures of sciency sexiness (as I said in the grand challenge, the Scientist Pin-Up is ultimately what we're after here, the idealized sexiness of scientists). But I couldn't move on to that until I set the baseline with some big-name scientists with beautiful visages to match their profound intellects.

If you know of a good Scientist Pin-Up that you'd like to see featured in future posts, please post a link to the image(s) in comments.

Girlfight!

2008-09-16T18:48:00.008+01:00

*shakes off cobwebs and preoccupation with politics*

My friend M sent not one but two shots across my bow today. The first was her assertion on Facebook that the only sandal Birkenstock should bother producing is the Milano. Pfffft. Everyone (minus one) knows the Arizona is where it's at.

The second, and this is going to be the subject of this post, was her post on [name of blog removed], [name of post removed]. In the ~~challenge~~ post, M gives us a tantalizing spread of brainy-therefore-intimidating-and-inhibited-therefore-oh-so-debauchable-therefore-sexy pin-up girls.

Which is all well and good.

Except...

Why do the librarian types get to have a monopoly on brainy-sexiness? Where are the scientists? We're brainy, after all, and therefore I think we should bebetter represented in our cultural repertoire of brainy-sexy images.

And therein lies the challenge: go ye my ~~minions~~ readers and find me images of sexy scientists! Extra credit will be given for images which are caricatures of sciency sexiness. The Scientist Pin-Up is ultimately what we're after here, the idealized sexiness of scientists.

I will now gather a few starter images, and recruit a few allies, and will get back to you soon with my first salvo of sexy science images. In the meantime, please post links to your own submissions in comments. At some stage we'll do a poll or a vote or something. Winner to receive bragging rights and possibly a mention on the Cafe Press t-shirt that I plan to make from the winning image with the caption "science is sexy".

Why I'm a member of the Union of Concerned Scientists

2008-08-25T19:35:00.000+01:00

To-do:

*I took the photo at right while on a trip to Washington DC last November. If it's this stained and peeling on the outside, what's it like on the inside? If John McCain gets elected, we can hope for more of the same.

By the dawn's early light

2008-07-04T15:36:00.005+01:00

This is my fifth Independence Day as an American expat in the UK. Every year, I take a few minutes to read the Declaration of Independence, copied in its entirety below, and every year I am surprised afresh by feelings of homesickness and nostalgia that wash over me on this day to remember the high ideals to which we aspire.

Today is an especially good Independence Day for me, because for the first time in a long time, I have real hope that in November this year, we will "throw off" our current government and "provide new guards for our future security". Of course, I'm talking about the potential that we might signal, both to ourselves and the rest of the world, by the election of Barack Obama as our 44th President, that we as a nation are finally waking up and shaking off the last eight years of bafflingly woolly-headed nationalism in favour of a fresh new progressive, globally aware patriotism.

I look forward to the possibility that on Wednesday the 5th of November this year (which, coincidentally, is a big night for fireworks in the UK - how handy!), I might wake up and be able to hold my head up high again as an American abroad, proud of the corrective action that we have taken by electing Barack Obama and in so doing taking a first step towards healing the many wounds, both inside and outside of our country, that have been either inflicted or infected by the present administration, for which, I might add, I most certainly did not vote. Either time.

IN CONGRESS, JULY 4, 1776

The unanimous Declaration of the thirteen united States of America

When in the Course of human events it becomes necessary for one people to dissolve the political bands which have connected them with another and to assume among the powers of the earth, the separate and equal station to which the Laws of Nature and of Nature's God entitle them, a decent respect to the opinions of mankind requires that they should declare the causes which impel them to the separation.

We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness. — That to secure these rights, Governments are instituted among Men, deriving their just powers from the consent of the governed, — That whenever any Form of Government becomes destructive of these ends, it is the Right of the People to alter or to abolish it, and to institute new Government, laying its foundation on such principles and organizing its powers in such form, as to them shall seem most likely to effect their Safety and Happiness. Prudence, indeed, will dictate that Governments long established should not be changed for light and transient causes; and accordingly all experience hath shewn that mankind are more disposed to suffer, while evils are sufferable than to right themselves by abolishing the forms to which they are accustomed. But when a long train of abuses and usurpations, pursuing invariably the same Object evinces a design to reduce them under absolute Despotism, it is their right, it is their duty, to throw off such Government, and to provide new Guards for their future security. — Such has been the patient sufferance of these Colonies; and such is now the necessity which constrains them to alter their former Systems of Government. The history of the present King of Great Britain is a history of repeated injuries and usurpations, all having in direct object the establishment of an absolute Tyranny over these States. To prove this, let Facts be submitted to a candid world.

He has refused his Assent to Laws, the most wholesome and necessary for the public good.

He has forbidden his Governors to pass Laws of immediate and pressing importance, unless suspended in their operation till his Assent should be obtained; and when so suspended, he has utterly neglected to attend to them.

He has refused to pass other Laws for the accommodation of large districts of people, unless those people would relinquish the right of Representation in the Legislature, a right inestimable to them and formidable to tyrants only.

He has called together legislative bodies at places unusual, uncomfortable, and distant from the depository of their Public Records, for the sole purpose of fatiguing them into compliance with his measures.

He has dissolved Representative Houses repeatedly, for opposing with manly firmness his invasions on the rights of the people.

He has refused for a long time, after such dissolutions, to cause others to be elected, whereby the Legislative Powers, incapable of Annihilation, have returned to the People at large for their exercise; the State remaining in the mean time exposed to all the dangers of invasion from without, and convulsions within.

He has endeavoured to prevent the population of these States; for that purpose obstructing the Laws for Naturalization of Foreigners; refusing to pass others to encourage their migrations hither, and raising the conditions of new Appropriations of Lands.

He has obstructed the Administration of Justice by refusing his Assent to Laws for establishing Judiciary Powers.

He has made Judges dependent on his Will alone for the tenure of their offices, and the amount and payment of their salaries.

He has erected a multitude of New Offices, and sent hither swarms of Officers to harass our people and eat out their substance.

He has kept among us, in times of peace, Standing Armies without the Consent of our legislatures.

He has affected to render the Military independent of and superior to the Civil Power.

He has combined with others to subject us to a jurisdiction foreign to our constitution, and unacknowledged by our laws; giving his Assent to their Acts of pretended Legislation:

For quartering large bodies of armed troops among us:

For protecting them, by a mock Trial from punishment for any Murders which they should commit on the Inhabitants of these States:

For cutting off our Trade with all parts of the world:

For imposing Taxes on us without our Consent:

For depriving us in many cases, of the benefit of Trial by Jury:

For transporting us beyond Seas to be tried for pretended offences:

For abolishing the free System of English Laws in a neighbouring Province, establishing therein an Arbitrary government, and enlarging its Boundaries so as to render it at once an example and fit instrument for introducing the same absolute rule into these Colonies

For taking away our Charters, abolishing our most valuable Laws and altering fundamentally the Forms of our Governments:

For suspending our own Legislatures, and declaring themselves invested with power to legislate for us in all cases whatsoever.

He has abdicated Government here, by declaring us out of his Protection and waging War against us.

He has plundered our seas, ravaged our coasts, burnt our towns, and destroyed the lives of our people.

He is at this time transporting large Armies of foreign Mercenaries to compleat the works of death, desolation, and tyranny, already begun with circumstances of Cruelty & Perfidy scarcely paralleled in the most barbarous ages, and totally unworthy the Head of a civilized nation.

He has constrained our fellow Citizens taken Captive on the high Seas to bear Arms against their Country, to become the executioners of their friends and Brethren, or to fall themselves by their Hands.

He has excited domestic insurrections amongst us, and has endeavoured to bring on the inhabitants of our frontiers, the merciless Indian Savages whose known rule of warfare, is an undistinguished destruction of all ages, sexes and conditions.

In every stage of these Oppressions We have Petitioned for Redress in the most humble terms: Our repeated Petitions have been answered only by repeated injury. A Prince, whose character is thus marked by every act which may define a Tyrant, is unfit to be the ruler of a free people.

Nor have We been wanting in attentions to our British brethren. We have warned them from time to time of attempts by their legislature to extend an unwarrantable jurisdiction over us. We have reminded them of the circumstances of our emigration and settlement here. We have appealed to their native justice and magnanimity, and we have conjured them by the ties of our common kindred to disavow these usurpations, which would inevitably interrupt our connections and correspondence. They too have been deaf to the voice of justice and of consanguinity. We must, therefore, acquiesce in the necessity, which denounces our Separation, and hold them, as we hold the rest of mankind, Enemies in War, in Peace Friends.

We, therefore, the Representatives of the united States of America, in General Congress, Assembled, appealing to the Supreme Judge of the world for the rectitude of our intentions, do, in the Name, and by Authority of the good People of these Colonies, solemnly publish and declare, That these united Colonies are, and of Right ought to be Free and Independent States, that they are Absolved from all Allegiance to the British Crown, and that all political connection between them and the State of Great Britain, is and ought to be totally dissolved; and that as Free and Independent States, they have full Power to levy War, conclude Peace, contract Alliances, establish Commerce, and to do all other Acts and Things which Independent States may of right do. — And for the support of this Declaration, with a firm reliance on the protection of Divine Providence, we mutually pledge to each other our Lives, our Fortunes, and our sacred Honor.

—

John Hancock

New Hampshire:
Josiah Bartlett, William Whipple, Matthew Thornton

Massachusetts:
John Hancock, Samuel Adams, John Adams, Robert Treat Paine, Elbridge Gerry

Rhode Island:
Stephen Hopkins, William Ellery

Connecticut:
Roger Sherman, Samuel Huntington, William Williams, Oliver Wolcott

New York:
William Floyd, Philip Livingston, Francis Lewis, Lewis Morris

New Jersey:
Richard Stockton, John Witherspoon, Francis Hopkinson, John Hart, Abraham Clark

Pennsylvania:
Robert Morris, Benjamin Rush, Benjamin Franklin, John Morton, George Clymer, James Smith, George Taylor, James Wilson, George Ross

Delaware:
Caesar Rodney, George Read, Thomas McKean

Maryland:
Samuel Chase, William Paca, Thomas Stone, Charles Carroll of Carrollton

Virginia:
George Wythe, Richard Henry Lee, Thomas Jefferson, Benjamin Harrison, Thomas Nelson, Jr., Francis Lightfoot Lee, Carter Braxton

North Carolina:
William Hooper, Joseph Hewes, John Penn

South Carolina:
Edward Rutledge, Thomas Heyward, Jr., Thomas Lynch, Jr., Arthur Middleton

Georgia:
Button Gwinnett, Lyman Hall, George Walton

"Elections matter"

2008-06-18T09:33:00.003+01:00

What he said:

Saturdays are for catblogging

2008-05-31T20:44:00.004+01:00

...or so says Lunartalks. Excellent - this is just the trigger I've been waiting for to unleash these homemade LOLs:

In which I wake up to a sexist leaflet on my doorstep

2008-05-29T23:25:00.001+01:00

In case there is anyone out there laboring under the impression that it is 2008, prepare to be disabused:

Puh-leeeze.

Christmas in July, or, how to set a girl-scientist's heart a-flutter

2008-05-25T17:10:00.001+01:00

I organise. It's heritable, too; my mother is a world grand-master list-maker who taught me, among other things, how to use the backs of envelopes to survive paper shortages (which pose a serious psychological risk to list-makers) and save the planet at the same time (list-makers love killing two birds with one stone).

Through my life, I've met a few others like me, most notably my friend Jennie with whom I sat back to back during grad school. She and I fanned the flames of each other's list-mania and to this day we exchange new and improved ways of making, keeping and organising our lists.

And oh boy, do I need my lists. I've got ~~my country's~~ Charles Darwin's ~~five~~ two hundredth anniversary to plan, my ~~wedding~~ Beagle Project science programme to arrange, my ~~wife~~ research to ~~murder~~ publish, ~~and Guilder to frame for it~~. I'm swamped. (If you're really confused right now, stop reading this and go watch The Princess Bride.)

I've tried a few different organising systems, including but not limited to:

Ansel Adams Engagement Calendar
Uncalendar
A teacher's planner (courtesy Jennie's organised mother Ruth)
iCal (comes with Apple OS)
Microsoft Excel
Moleskine Weekly Notebook

This year, though, I think I've finally hit on a winner: a combination of iCal (especially using the File > New To Do function) and Moleskine's Weekly Notebook. Nearly halfway through 2008, it's working really well.

I really like how the calendar is on the left hand side of the opened diary, and on the right there is a simple ruled page to jot down notes (that way your notes are instantly traceable by date). I love my Moleskine, and I look forward (as all list-makers do) to the end of the year when I can start with a shiny new Moleskine with fresh, clean pages.

Problem is, I'm already starting to accumulate things for 2009 and my Moleskine ends in December. What to do? I turn to the last page and keep a list (I'm so predictable) of things that will have to go into my 2009 Moleskine. It's not very satisfying but at least I know I won't forget anything important.

You can imagine my delight then when I found in my in-box an email from UK online Moleskine dealer MojoLondon that Moleskine is now selling 18-month diaries that start in July and go through the end of the following year. That means I can start my clean and shiny new Moleskine this July ...a mere four weeks away. And here I thought I had to wait until Christmas.

The big decision is whether to get the Large Weekly Notebook Hard Cover or the Extra Large Weekly Notebook Soft Cover. What a lovely decision to have to make. I think I'll go put it on my to-do list for tomorrow.

Update, 2 June 08: Lacy has discovered an even better way to make sure you don't forget any of those important t0-dos.

Apparently, celebrity Nature editor Henry Gee and I both:

2008-05-15T00:27:00.000+01:00

work from home on Thursdays
suffer a gag reflex from the close proximity of over-perfumed/cologned train passengers
think 'presenteeism' is so not Web 2.0
advocate an expansion of London's new ban on alcohol on public transport to include talking, overt sexual display and smelly grooming products

Source: Dr Gee's amusing Nature Network blog post, Aboard the 06:55 from Much Twittering.

P.S. Please, dear reader, kindly vote for my new SciFri blog name, upper right.

Moving to Science Friday & vote for new blog name

2008-05-10T08:01:00.000+01:00

In January I met Talia Page and Ann Marie Cunningham of Talking Science at the Science Blogging Conference in North Carolina, and they invited me to write for Science Friday Blogs (the site is currently being re-vamped to be way more blogolicious).

I've always loved Science Friday--Ira Flatow's calming tones and fascinating guests used to help get me through Friday afternoon fruit fly ovary dissections in grad school--and I admire their ambitions, so I consider it a real honour to be asked to blog with them.

You can probably tell from my patchy posting here that Data Not Shown has been something of an experiment. I wasn't sure when I started it how many posts I'd end up wanting to write that weren't appropriate for The Beagle Project Blog, and I think the answer has turned out to be a resounding "not many".

So. I'm closing up shop here at Data Not Shown and re-inventing myself a little bit for the new Science Friday blog. I think part of the reason I didn't get really jazzed about Data Not Shown is that it didn't have a coherent and succinct theme. Thus my aims for the new blog are:

to post regularly if not as often as I do on the Beagle Project Blog, say, once a week to start.
to write themed series' of posts, for example a weekly biology and/or evolution glossary entry, a series of interviews with scientists I admire, or maybe even a series of video podcasts from the lab and other parts of the Natural History Museum.

I am also thinking of re-naming the blog. Please use the poll on the upper right side of this page to let me know what name you like best.

Thanks for reading and I look forward to seeing you over at SciFri blogs!

Plant genomes made easy

2008-04-25T11:00:00.000+01:00

Science has a new multimedia feature on plant genomes "From evolutionary insights to crop development" which does a pretty good job demystifying plant genomics in reasonably* plain language.

*If you've had a basic biology class and know the meaning of such words as "chromosome", "gene" and "DNA replication" you should be able to follow along.

When people do good

2008-04-12T02:15:00.000+01:00

Whether inspired by a religious mandate to love others or a humanist motivation to engage in acts of kindness towards one's fellow man, I am always heartened to hear stories about my fellow humans who do good.

Most of these stories don't make the headline news and so go largely unnoticed until they happen within our circles of acquaintance. Case in point: my friend Lacy Claeys, a dentist from Helena, Montana and her young dental assistant, Helena High School senior Luke Dutton, rode a bus for 22 hours south of their comfort zones to perform heroic acts of kindhearted dentistry on young orphans in Juarez, Mexico.

Some of their stories are so unfathomably heartbreaking--like the 12-year old prostitute with a herpes infection in the back of her throat--that it's no wonder Lacy and Luke are having trouble reintegrating back in Helena. To say I wish them well would be an understatement.

So here's to all the unsung heroes out there like Lacy and Luke, may they find the strength to do more good, and may we all--regardless of religious affiliation or lack thereof--be inspired by their acts of human kindness and willingness to expose themselves to soul-wrenching poverty despite the psychological consequences.

Read more about Lacy and Luke and their great big hearts at Helenair.com.

Radio Ga Ga

2008-04-06T20:20:00.001+01:00

I'm on the radio! Listen again (mp3) and/or visit Atheists Talk. It's a full hour of Peter McGrath and me stumping for The Beagle Project, so you might want to use the loo and get some popcorn before you click.

Squiddy tour for science bloggers and UK Pharyngulites

2008-04-01T17:23:00.000+01:00

Following on from the successful first meeting of the UK Pharyngulites in early March, I am pleased to announce another opportunity for sciencey bonding in Blighty ...this time over squid!

I'm organising it over at The Beagle Project Blog. Hope to see you there!

Photo by Peter McGrath, co-founder of The HMS Beagle Project.

Hide the children: creationist Ken Ham is coming to Blighty

2008-03-26T13:33:00.000Z

Ken Ham, founder of Answers in Genesis and the Creation Museum in Kentucky, will be delivering several talks in the UK over the next month. You know what to do, my freethinking friends:

28-30 March Vale of Glamorgan, South Wales (Firm Foundations Creation Conference, a "residential conference" *shudder*)

31 March Liverpool

1 April Grimsby

2 April Bedford

3 April Leicester

4-5 April London (Creation Conference)

9-10 May Belfast (this is an important one, methinks, because it seems likely to attract proponents of the notorious Giant's Causeway Creation Committee)

I am going to try and attend the London conference. It is a ticketed event and so I have emailed the organisers (yes, using my real name) and will post an update here as soon as I know any more.

Hat tip to Marc.

Update: Tickets to the London event cost £5 for Friday, £10 for Saturday and £15 for both days. So, is it worth a fiver to confront Ken Ham in person? Hmmm.

Here is a part of the PDF I received in response to my ticket enquiry:

Sheer comic genius from Rick MacPherson

2008-03-24T22:33:00.000Z

Click the crop to see the full comic strip...

On my honour, I will try (3/4)

2008-03-23T16:41:00.000Z

This is the third post in a four-part series, begun over on the Beagle Project Blog in Part 1 (which includes an introduction to The Science Scouts) and Part 2.

Here is the third batch of my Order of the Science Scouts of Exemplary Repute and Above Average Physique badges:

The "I've done science with no conceivable practical application" badge. Well, maybe I lack imagination but I simply cannot conceive of a practical application that might come from an understanding of the evolutionary mechanism of interspecific variation in fruit fly eggshell morphology. The whole point was to understand evolution just a little bit better, and to me that is enough to make it worthwhile. That said, science for curiosity's sake also sometimes leads to practical applications that are only as yet inconceivable but may very well become earth shatteringly important at some later stage. For example, there's the story of that guy who was fascinated by the mold spores that landed on his petri dish (inconceivable!) but then it turned out to be the source of Penicillin. 'Nough said.

The "science has forced me to seek medical attention" badge. More people can claim this badge than probably realise it, especially if we count mental health, which I think we should. I get the badge for a number of reasons: 1) repetitive strain injury, numbness in my right hand and a strained muscle in my neck, all from writing my thesis, 2) astigmatism partly due to looking through a microscope for too many hours per day in grad school and 3) Temperomandibular joint disorder (TMJ) from PhD related stress.

The "somewhat confused as to what scientific field I actually belong to" badge. This badge was made for me. During my PhD I moved from developmental genetics to evo-devo. Now it's even more pronounced; you see, sometimes a geneticist can feel rather alone in a natural history museum. For example, whenever I meet a new member of staff or visitor, the question always comes up, "so, what group of plants do you work on?" Me: "Uh, um, well, see, I work on genetics/genomics as they apply to just about any group of plants." Them: "oh" *walks away*. It turns out that when one's "specialty" is (or was) Drosophila melanogaster, that doesn't seem to count. Sometimes this transdisciplinary thing isn't all it's cracked up to be. Oh well, it seems to be working out okay.

The "works with acids" badge. Two words: deoxyribonucleic acid. Then there are all the other acids which come with working in any wet lab. I won't bore you with the details. They really are boring. Really.

One batch of badges to go! Sneak preview in the sidebar.

What are you doing here?

2008-03-21T18:11:00.000Z

...when you could be wetting yourself with laughter over what will likely be one of the biggest stories to hit the science blogosphere this year: the famous biologist-blogger PZ Myers (but inexplicably not the even more famous biologist-author Richard Dawkins) was expelled from a screening of creationist propaganda film Expelled! Many thanks to Greg Laden who has put together (and kept up to date) an impromptu blog carnival about it. Now get on over there for a dose of hand-rubbing glee!

Update 1: What Bad Astronomy said.

Update 2: Digital Cuttlefish has already set the saga to verse. Bravo!

Update 3: Thoughts from Kansas has a wonderfully concise analysis:

"If you make a movie that falsely claims there's a massive conspiracy to expel dissenting voices, it's probably unwise to then expel dissenting voices."

In which I recant my aversion to marriage

2008-03-20T13:07:00.000Z

As most of my friends and family know (and some lament), I am apathetic about and occasionally hostile towards the institution of marriage. But today, my armour has been chinked by the thought of a bridal registry that includes this:

"evo-cut" cutlery by Harry White

evo-cut is a one-off set of cutlery designed according to the principles of population genetics and natural variation. Rather than just having two sizes, this set or population of cutlery shows continuous variation in size and shape. Further, the set shows inheritance of several kinds of mutation, as explained by a family tree, that alter the cutlery functionality, sometimes in unexpected and useful ways. Because the cutlery pieces show natural variation in size, there is always a piece suitable for every age, appetite and ability. Through use and exploration, the true adaptive potential of different pieces will be discovered and the novel functionalities revealed when the situation demands it, just like evolution. evo-cut is now the property of Central Saint Martins School of Art and Design and is occasionally on display.

You can view close-ups of both the cutlery and its pedigree at Harry White Design. This is simply wonderful. Morning cereal would never be the same.

A Somewhat Old, But Capacious Accolade

2008-03-19T22:51:00.001Z

Many thanks to MissPrism at A Somewhat Old, But Capacious Handbag who has rated lil' ol' Data Not Shown "E for Excellent"!

Of course, the decks were stacked in my favor (just a little), because it was yours truly wearing my Beagle Project Blog hat who rated MissPrism "E" in the first place. But hey, I'll take it, because when one's blog is young and still a little wayward like Data Not Shown, one is obliged to enthusiastically trumpet any and all instances of link love that one can get.

And I now humbly bestow the "E for Excellent" upon the following blogs (yes, it's an entirely separate list from the Beagle bestowal):

Botany Photo of the Day was my very first regular blog read from way back in the day when I didn't even know what a blog was... you know, like two years ago.
Just today I discovered the Londonist, for Londoners in the know.
A Natural History of Runswick Bay, written by none other than fellow Beagle Blogger Peter McGrath, brings all manner of treasure from England's northeast coast direct to our desktops.
Oceanographic Research Vessel Alguita, a real-time blog by intrepid marine environmental scientists, on location from the place where plastic crawls away to ~~die~~ live forever.
The Oyster's Garter: smart and sassy, in a sciencey way. In other words, I love it.
Space Cadet is off to kind of a slow start but I really like what I see there and think it should be encouraged.
xkcd, "A webcomic of math, romance, sarcasm and language". Also has an utterly fabulous online shop.

Pharyngula readers: what a handsome bunch!

2008-03-16T11:49:00.000Z

While I was stuck at home coughing up greenish phlegm, a gaggle of previously unacquainted Pharyngula readers descended (as planned) on the Doric Arch near Euston Station in London. Malcolm FCD reports by email:

"We started at the Doric Arch, and went on for a pizza. We pretty well agreed we'd like to do something similar in 6 - 8 weeks... Starting with Debi on the left and going clockwise around the table, we were ___, ___, Malcolm, ___, ___, ___ and ___. Disclaimer - I don't know who wants their names published... Malcolm (posting as Malcolm, FCD)"

I'm really bent that I couldn't make it, but delighted to hear there will be a next time! I think you'll agree, this looks like an excellent bunch of people. If you were there and don't mind having your name attached with your face, please let me know in the comments and I'll fill in the blank that corresponds to you.

Giant's causeway digression

2008-03-15T15:17:00.000Z

I just can't hold it in any longer. I've been over at the Beagle Project Blog writing my counter-response to the Causeway Creation Committee's reply to my 2007 post "Not just an American Problem (Part II)". I was really trying to keep the whole science vs. religion thing out of it, focusing instead on science vs. young-earth creationism. But when I read this:

"the philosophical view of the atheistic naturalist scientist (as opposed to the observational scientist) is that human life is of no more worth or value than a dust cloud or a black hole"

...it got personal. Paul, I am getting really, really tired of the claim that the ability to value human life must necessarily stem directly from a belief that human life was purposefully created by a big guy in the sky. It mustn't. In fact, often religiosity correlates with bad behaviour. Get over it.

Science spam

2008-03-12T17:35:00.001Z

The daily barrage of Viagra, Microsoft software and Rolex rip-offs is bad enough, but recently I've noticed a category of specialised spam reserved just for us scientists. For example, today I received this:

Dear Dr. James,

Cloning is tedious and unpredictable. The process can get stuck anywhere. For example, the template may be hard to get or a restriction site may be not available. Sometimes ligation doesn’t work. All these problems may stop your great idea from becoming a high-impact publication. Our Gene Synthesis Service offers an easy and affordable alternative to solving all these problems by yourself.

http://www.biologyproject.net/gene_synthesis.html

And keep the rest of the matter in mind:

· De novo synthesis can start right after we receive your sequence
· Codon optimization is included, compliments of GenScript
· Unlimited mutations – at any position
· We deliver your gene in any vector, including those suitable for protein expression

Get a sense of how easy and comprehensive our service is – ask for quotation today

Our customer representatives are available 24 hours, Monday through Friday. You may contact us anytime for assistance. Please check our contact page http://www.biologyproject.net/contact.html for our local reginal numbers.

Gen Script Corporation - VWR Strategic Partner
120 Centennial Ave., Piscataway, NJ 08854
Tel: 1-732-885-9188 ext 128
Fax: 1-732-210-0262

Sadly, it appears that even science spam is rife with bad English ("And keep the rest of the matter in mind") and innuendo ("sometimes ligation doesn't work", "unlimited mutations - at any position"). What do they think, that I'll be titillated by their promise to "deliver your gene in any vector" and do some impulse shopping at VWR?

UK Pharyngulites unite!

2008-02-24T18:56:00.000Z

Confirmed! Come one, come all to the London Pharyngula readers' meet-up on Saturday, 15 March, 7pm at the Doric Arch near Euston Station. When you get there, look for the Pharyngula embryo sign, right. Also, I will wear my Beagle Project t-shirt.

PZ Myers noticed something of "a strange phenomenon" (if you can still call social networking on the internet a strange phenomenon...) that began when Pharyngula readers in Boston organised a local pow-wow marked, of course, by squid. He thought (and I think) this is something worth propagating and so suggested we all get into it and start forming satellite Pharyngulite clubs all over the world.

Turns out there are lots of us here in the UK. As of 19:14 GMT on Sunday, the following had identified themselves in PZ's comment thread as habitating here:

Mark UK (Edinburgh)
Jonathan (Sheffield)
Didi (Norwich)
Peter Mc (Whitby)
mmghosh (Bristol)
Don (Tynedale)
Miss Prism (London)
Marc (London)
Maureen (Hebden Bridge)
oh, and me, nunatak (London)
You?

So, I thought I'd create a post to help us organise ourselves without having to wade through the hundreds of comments over at PZ's place.

If you are in the UK and interested in meeting up please leave a comment here. If people want to spin off and form sub-groups that's fine by me, everyone's welcome to do their own thing of course!

So, I think all that's left to say is: go forth into the Comment thread, all ye UK Pharyngulites, and self-organise!

Total lunar eclipse begins in four hours

2008-02-20T22:48:00.000Z

At 1:43am GMT (8:43pm EST) the Moon will enter the blurry edge of the Earth's shadow, called the Penumbra. Then, at 3:01am GMT (10:01pm EST) the total eclipse (Moon in the darkest part of the Earth's shadow, the Umbra) will begin, and will last for 50 minutes before the Moon begins its slow exit from the Earth's shadow through the Penumbra on the other side.

So put on a pot of Rainforest Alliance Certified coffee and get ready for a lovely reminder of the orbital dance that takes our cold and lonely Moon about our precious Earth about our helium Sun. Me, I'll be reminiscing about my close encounter with Moon rocks back in November.

More info at NASA (naturally) including diagrams like the above for other time zones and an explanation for why the moon is depicted here moving from east to west.

Update 21 Feb.: Stayed up until 2am only to be thwarted by London fog. Damn. Others were more fortunate. My favorite picture at right, the eclipse as seen from Cape Town.

Curing the disease of human self-importance

2008-02-16T11:47:00.000Z

Michael Pollan's book The Botany of Desire* changed my life. More specifically, it changed my lazy, conceited assumptions about the primacy of human consciousness.

Sure, I'd known for a long time that the Great Chain of Being (and its counterpart in evolutionary language, the concept of "higher" species the highest being Homo sapiens) is a load of anthropocentric hogwash. And I've known for slightly less time that there are several simple but earth-shaking ways to visualise the specific truth and putridity of said hogwash.

One of these is this simple list of the number of genes in various genomes that have been sequenced:

Rice.............50,000
Mouse...........29,000
Thale cress.....25,500
Sea urchin......23,300
Human..........20,500
Nematode......19,000
Fruit fly........13,700
Baker's yeast....5,800
E. coli...........4,400

Then, for the more visual among us, there's also the lovely evolutionary tree of life, with its teeny tiny "you are here" annotation (high res pdf):

So, then, if we already know that humans are not at the top of some mistakenly conceived evolutionary escalator, what's so special about The Botany of Desire*?

The core concept of the book boils down to this question: what would happen if we looked at agriculture "not as an invention, not as a human technology, but as a co-evolutionary development in which a group of very clever species--mostly edible grasses--had exploited us/figured out how to get us to basically deforest the world" to benefit their genetic legacy?

It's a new way of thinking about agriculture, to be sure. But how is Pollan's idea any different or better than the list of gene numbers (in which the relative positions of rice and humans are already fairly suggestive of some kind of grassy overlordship), or the "you are here" tree of life?

Pollan's hook does go deeper than the list and the tree, by penetrating the skin of human physical form and getting down to the sinew of human intention. But is the botany of desire really anything more than a "literary conceit" as Pollan himself calls it? Does it actually benefit anyone or anything beyond giving us "some entertaining insights"?

In his Ted talk, below, Pollan argues, I think convincingly, that there are real tangible benefits to thinking about ourselves in this new way. For example, he cites its power to "really make us feel the Darwinian idea". It certainly did that for me. I had seen any number of "you are here" diagrams but it didn't really come home until I thought about how I was being expertly manipulated by the edible grasses.

But enough of my trying to explain it, why not hear it straight from the eloquent and impassioned Pollan himself:

H/t to Greg Laden.

*no Amazon link, support your independent bookstore

Vote!

2008-02-15T23:32:00.000Z

...in the Nature Conservancy 2007 Photo Contest. And while you're there, why not check out some ways you can help them with their noble causes, not least their Rescue the Reef campaign?

Polar Bears, Hinlopen Strait, Svalbard
Steve Price

Storm, Monument Valley, northern Arizona, USA
Sergej Bulychev

Giraffe and Yellow-billed Oxpecker, Ndutu Conservation Area, Tanzania
Billy Dodson

"Barcode of plants mapped" identified tested

2008-02-05T23:23:00.001Z

I just started a draft post (which I fully intend to decorate with ResearchBlogging's recently besmirched icon) on the new paper that my Google alert tells me is coming out on DNA barcoding in plants, my main area of research at the Natural History Museum.

The only thing missing is... well... um... the paper.

The Nature News article reporting the results of the (as yet nonexistent) paper even links to the paper's DOI, which looks promising until you click it and find out it doesn't actually lead anywhere. So, like any good Web 2.0 denizen, I left a comment there: "The DOI for the cited article does not appear to exist, nor can I find anything about this paper on the PNAS website. Any suggestions?" The response I got was, "Please note that PNAS releases the news of its upcoming papers on Mondays at 5pm Eastern time, but the papers themselves may go live at any time during that subsequent week. So this paper will appear eventually... check back on Friday and you should find it."

Well, okay, but then this has a disturbing (if not surprising) implication: none of the 10+ news reports announcing the findings could possibly be the result of a science journalist actually reading and understanding the paper (which is, I note with interest, one of the guidelines for using the ResearchBlogging icon). (The journalists would, in fact, have had a chance to see the paper before they wrote their news items - see koffeekat's very welcome comment below. -KJ 28/7/09)

So, I thought, what better to do while I'm waiting for the paper to be published than to pick apart some bad science writing? Oh, there's the usual assortment of inaccuracy and sensationalism, but my complaints here are going to be more focused on the specific content, that is, DNA barcoding.

Scalpel, please.

Here is my dart-board collage of the offending titles and sentences from a selection of three news pieces reporting the key findings of the mystery DNA barcoding paper. I gave up after three when it became clear they were all just copying and pasting from the same (lame) press release. In bold are the bits that need trouncing, followed immediately by the actual trounce.

"'Barcode' of plants mapped" (title, inthenews.co.uk). Mapped? What, with like a road atlas? I don't need to go into detail on why this is just so wrong, simply because Miss Prism has already done it with verve.

"Scientists have identified a 'barcode' gene that can be used to distinguish between the majority of plant species on Earth." (inthenews.co.uk). Well, actually, according to the news release they tested 1600 species of orchids in the study that is (supposedly) going to be published and yet there are nearly 300,000 recognised plant species. Now, unless you're the US Electoral College, 1600/300,000 does not a majority make.

"As such scientists can use the gene to distinguish between different plants, even closely related species." (inthenews.co.uk). How closely would that be? ...seems like an important question.

"matK Gene Is A "Barcode" DNA For Plants (title, ScientificBlogging)." These guys can't even get the word order right. It's a DNA barcode not a barcode DNA.

"They found that when one plant species was closely related to another, differences were usually detected in the matK DNA. (ScientificBlogging)". Is ScienceBlogging having a secret internal competition on who can be the most vague? "Usually" in this context could mean one of two things for a putative plant DNA barcode: 1) spectacular success, 2) cringe-worthy failure.

The matK gene may not, however, be able to be used to identify every plant species on Earth. In a few groups of species, additional genetic information may be required for species-level identification because hybridization - where species cross-breed and genetic material is rearranged - may confuse the information provided by matK. (ScientificBlogging). Okay, where to begin. First of all, hybridization is not just a minor problem in the plant kingdom, it's more the norm. Second, genetic material is rearranged as a normal result of the normal process of normal sexual reproduction, so hybridization doesn't have anything special going for it there. Third, hybridization does not "confuse the information" but rather the information is inadequate to tell when hybridization has occurred.

The team behind the discovery found that DNA sequences of the gene 'matK' differ among plant species, but are nearly identical in plants of the same species. (Bio-Medicine). Not so much a discovery as a trial of something that had already been proposed and partially tested.

Needless to say I am looking forward to the paper actually getting published so I can blog it using words a little more informative than "usually", "majority", "a few" and "closely related".

Evidence that Drosophila can, in fact, be cute

2008-01-17T18:56:00.001Z

I spent six years, nine months and twelve days doing my PhD on egg development in Drosophila melanogaster, and, though I did come across a few mutants like curly that I suppose in retrospect were passably cute in the loosest meaning of the word, I never did fall in love with my organism the way "they" say you do. Then, yesterday, out of the blue, I saw this at The Other 95%:

Click the undisputably cute Drosophila
to see the Joe Sayers comic strip in its entirety.

This is one cute fruit fly. The tiny eyes! The little wings! The itty bitty straight stick figure legs (the correct number no less!) supporting the featureless body like a grape on a comb!

And it's not just cute, it's useful, too: the next time you see maggots on a banana just take a deep breath (through your mouth) and think of this little guy. It will help you to not recoil in disgust. Trust me on this one.

Coming soon: data not shown

2008-01-06T18:38:00.000Z

If you're reading this you probably just clicked over from the Beagle Project Blog. Welcome to Data Not Shown, a new blog that I created because, much as I love blogging for the Beagle, I wanted a new outlet for posts that 1) have nothing to do with the Beagle and/or 2) contain personal opinion that I wouldn't want to foist onto the other Beagle Projecteers.

As is traditional in first posts, I am now going to explain the title of my blog. "Data not shown" is a commonly used parenthetical statement in scientific research papers. It means "we did the experiment but we're not showing you the data, so you'll simply have to take our word for it", and it is usually employed for one or more of the following reasons:

1. The data are reliable but so eyewateringly boring and predictable that they would just clutter an otherwise riveting manuscript.

2. The data are reliable but very, very unpretty.

3. The data are both interesting and pretty, but we just had so much of it (blush) that we had to make difficult decisions to meet the journal's word and/or page limit (this is less relevant now in the era of online supplementary material ...oh dear, am I showing my age?).

4. We didn't do the experiment, but are willing to stake our reputations on the outcome should someone actually "repeat" it.

Here's an example of "data not shown" in a paper that I wrote, used for a combination of reasons 1 and 3 above:

It is important not to confuse "data not shown" with other, related parentheticals such as "unpublished data" (we are going to milk another paper out of this baby) or "personal communication" (our collaborator/competitor let it slip at the conference mixer).

For this blog, "data not shown" should be interpreted in its broadest sense, to mean everything that goes on in science (and life) that doesn't get published (that is, except here). I hope this wider net will keep the blog from being eyewateringly boring. After all, who except the most die-hard masochist wants to read a bunch of posts that say things like "ventral Ras clones had no effect on pipe-lacZ expression"?

Oh, and I might occasionally show some data. Hopefully the universe won't implode when I do.

More soon, but for now best get back over to the Beagle Project Blog and while you're at it why not donate or buy something from one of our shops.