One day in 1835 Herschel got talking to Sir David Brewster (renowned in the field of optics; inventor of the kaleidoscope). Herschel had a problem with his telescope: at higher magnifications not enough light reached the viewer, leaving images indistinct. The two men were discussing how this situation might be improved.

Suddenly Sir John had a breakthrough. Might it be possible, he wondered, to use the same principle as Brewster’s new illuminated microscopes but on a larger scale?

Sir David sprung from his chair in ‘an ecstasy of conviction’. ‘Thou art the man!’ he exclaimed (no, really).

Within months the two men had acquired a £70,000 grant from the Royal Society and had completed a seven ton mega-telescope capable of clearly magnifying distant objects up to six thousand times. Naturally the first thing that they pointed it at was the moon.

The view was incredible. They recorded some interesting basaltic rock formations.

Then they noticed a patch of greenish-brown vegetation. And some lunar tree-melons. What looked like reindeer with a single horn and, um, beards gambolled in meadows. Winged humanoids flapped around a golden domed temple.

Panning left (possibly) they come across some moon beavers who walked on their hind legs and whose huts were ‘constructed better .. than those of many tribes of human savages’. The beavers had also discovered fire, the better to cook bearded unicorn steak with.

Not that’s a proper hoax. They knew how to do it properly, back in ‘35.

To be fair Sir John didn’t have a clue that he was being attributed with having discovered bipedal beavers – it was a stunt by the New York Sun to increase their circulation (it worked). Complete story here, a contemporary account and the complete text of the collected articles is in pamphlet form here .

(via Metafilter)

Groups do all have other alerting mechanisms, though, in the form of email and RSS.

Email alerts are just evil and subscribing to fifty different RSS feeds would be messy, so I hooked up a single, consolidated feed using Yahoo! Pipes:

Consolidated groups feed

Enter your username where it says ‘what’s your Nature Network username?’ and then click on ‘Run Pipe’ – it’ll fetch all your (public) group memberships then merge all of the RSS forum and noticeboard feeds into a single consolidated feed.

Once the pipe has run use the ‘more options’ menu to get the RSS feed.

Your username is the last bit of the web address of your profile page, e.g.

http://network.nature.com/profile/euan username is euan
http://network.nature.com/profile/UB614A588 username is UB614A588
http://network.nature.com/profile/henrygee you get the idea

If you join any new groups they’ll be added to your consolidated feed automagically.

post over, rambling nerdiness follows

The nice thing about Pipes is that if you really want you can get updates via SMS or Instant Messenger when somebody posts a new forum topic. JSON, too, if you fancy building a blog sidebar.

You can also build on existing Pipes, so it’d be good to extend this one to, for example, filter out everything that wasn’t authored by you. Then you’d have an RSS feed of your activity on Network – perfect for FriendFeed.

I’d like Network to have some sort of ‘follow’ mechanism – a little icon next to comment threads, blogs and groups which when clicked added any updates there to a single, personalized feed. There’d be a single page where you could uncheck items and set up filters like the one described above.

Chernoff Faces are a visualization technique developed in the 70s to take advantage of our innate ability to detect small differences in the size, shape and expressions of human faces. The idea is to take a dataset and then map each dimension to a different facial feature, be it the slant of the eyebrows, size of the nose or the chubbiness of cheek (Herman Chernoff, who came up with the idea, suggested ten different possibilities).

It’s an appealing concept. Sadly Chernoff Faces never really took off, possibly because existing implementations don’t produce anything that looks like a face. You’d have a hard time finding anybody who prefers the faces produced by R to the data table they were derived from.

Computer graphics have moved on a bit from 2D lines and circles, though. Photorealistic 3D facial models are de rigeur nowadays in everything from Second Life to video games. What if we took the technology from there and applied it to Chernoff Faces?

I gave it a go. Check out Pubmed Faceoff (and be gentle – it hooks into other webservices and can be quite slow).

Pubmed Faceoff is a mashup of Pubmed, Carl Bergstrom’s Eigenfactors dataset and Scopus, inspired by something that Pierre Lindenbaum mentioned on Twitter. It renders PubMed results as a set of photorealistic Chernoff Faces whose facial features are determined by the age, citation count and journal impact factor associated with each paper. The idea is that you can tell at a glance which papers are new, exciting and high impact and which are languishing, uncited and unread.

I’m quite pleased with how the system turned out although to be honest I still think the usefulness of Chernoff Faces is debatable. Does it actually work? Is the amount of time it takes you to adjust to scanning the faces more than the amount of time it’d take to simply scan a table of data? Or is it just cute?

The gender and ethnicity of each face are picked at random to add a bit of visual interest but personally I find it slightly easier to interpret the faces when they’re all male and European. That I’m rubbish at reading women comes as no surprise but the ethnicity thing is interesting as it fits with research into cross-race facial recognition that suggests we’re each better at recognizing the types of faces that we see every day.

While the photorealism helps it’s important with Chernoff Faces to map dimensions to the right features to aid comprehension. It definitely helps that it’s a short logical leap from ‘happy faces’ to ‘happy papers’ (in good journals that have been cited lots). The age feature for age of paper is also a no-brainer.

It’d be interesting to incorporate other dimensions into the faces, though. Perhaps the number of authors of a paper could determine how fat or thin a face is? A spotty complexion could indicate a first time author? Nature papers could be represented by Chuck Norris?

update: for more on the ‘sort by impact’ idea have a look at the commentary surrounding Pierre’s original tweet.

Almost all of the scientist-turned-editors straw polled inside Web Publishing said that they’ve read papers while on beach holidays before, but maybe they’re freaks that’s just selection bias – editors are paid to read papers, after all.

How about you? Do you take reviews to the tub? Scan papers in the pub? Click on the links below to participate in the public poll, we can analyze the results in a week or two.

On the beach: yes or no

On the bus: yes or no

In bed: yes or no

While bathing: yes or no

Did you know that you can pick up a homemade EEG kit and the open source software to run it for under fifty quid? I have been irrationally excited by this all week.

Admittedly it does ship from somewhere in Bulgaria as a bare PCB board and comes with documentation explaining that attaching it to humans or animals ‘may result in electric shock or seizure’ – you probably wouldn’t want to mention that to your initial test subjects.

The neuroscientists in Web Publishing have explained to me that EEG can’t actually read your mind as such since the electrical signal it detects isn’t localized. It’s only useful as a general measure of brain activity.

Still, I reckon it’s worth thinking about (or something?). Forget Singstar – at your next house party why not invite some rhesus macaques and hold a monkey vs human mental ping pong tournament? Totally doable with EEG.

We could put the personal touch back into email messages. As you write the EEG records your emotional state and then retroactively formats the message appropriately – so angry sentences are larger and in red, distracted, off the cuff missives are in a scribbly font, calm and collected messages are a cool blue.

From a work perspective you could harness the collective intelligence of entire departments without them actually having to do anything – except wear a silly hat with cables coming out of it that occasionally results in shocks or seizures, obviously. I suggest we hook up all of Nature’s editorial staff and record their brain activity while they are browsing scientific papers, then use the data to automate the ‘Editor’s Picks’ sections of journals, or perhaps create a sort of upmarket scientific Digg…?

Best news story ever?

Colonel John Blashford-Snell, 71 year old professional explorer, has found a living example of a rare breed of two nosed dogs while in Bolivia looking for a giant meteorite. Xingu, the dog in question, is ‘small but aggessive’ with a great sense of smell (naturally). His best friend in the village where he lives is a wild pig called Gregory (again, naturally).

Blashford-Snell, presumably wearing his patent, mosquito repelling refrigerated Explorer Hat, carried ‘a church organ from Dorset’ up the Andes as a gift to the locals to help him find where the meteorite landed.

The Colonel is no stranger to wild and wonderful beasties. He’s honourary life president of the Centre for Fortean Zoology. Two nosed dogs are nothing to him.

I don’t know if any of this is true and frankly I don’t care.

As part of the Women in Science thing L’Oréal and UNESCO run an online forum called Agora. A lot of the content there is from researchers in developing countries. It’s interesting to get an international perspective on the problem of how to get more women into science.

Apparently 55% of L’Oréal’s research staff are women. At first I didn’t think that this was particularly noteworthy. Scientists in all of the labs I knew back in the day (not many, I didn’t get out of the basement much) were predominantly female. Turns out that’s because clinical research – the area in which I worked – is the exception and every other field of scientific endeavour has a startling gender imbalance.

How systemic is the problem? Which is a bigger deal, old boy networks or not being able to balance research lab timetables and outdated working practices with raising a family?

For the record NPG is, again, predominantly female, even within Web Publishing.

On a less serious, more manly note – Gillette, the best Spectral Subtraction Using Fourier Transform Infrared Spectroscopy a Man can Get. You’ll have to imagine that last bit sung to the jingle. Who knew that the particle accelerator thing they have in the Fusion advert was actually real? Yes, the (potentially underground) Gillette Research Institute really is owned by Proctor & Gamble and they really do research there.

Shockingly it turns out that the Telegraph is exaggerating slightly (just like the Guardian last week), but it’s a really interesting area.

What the research in question actually shows is that giving propranolol – a betablocker aka Inderal – to people who have recently suffered or ‘reactivated the memory of’ a traumatic event reduces their physiologic response the next time they remember the event in question, implying that it has become less of a painful experience.

Preliminary work in humans and rats has been happening for years but I think this is the first trial with actual trauma sufferers (this isn’t my area of expertise, feel free to correct in the comments).

The idea of dampening or removing painful memories raises many interesting questions, some of which were tackled by The President’s Council on Bioethics in a meeting in 2003. They’re quite critical of memory altering drugs, mostly because of the huge potential for misuse.

All of us can think of traumatic events in our lives that were horrible at the time but made us who we are. I’m not sure we’d want to wipe those memories out. Rebecca Dresser, PCoB

Perhaps easier to agree with when you haven’t been a victim of horrific assault or abuse, but Dresser’s point is worth thinking about. Are your raw, emotional memories – however traumatic – valuable because they make you who you are now?

In a way we’ve already made this decision as a society. Inderal is already taken (sometimes prescribed, sometimes not) for stage fright and social anxiety . Does being frightened of performing a clarient solo or attending a job interview make you ‘who you are’? Do you just need to pull your socks up, hit all the bum notes and accept that it in the long run it’ll make you a better person? Apparently it doesn’t, necessarily, and you don’t. How then can we begrudge accident victims or veterans use of the same drug?

This involves being locked up in a special facility outside of Moscow for 520 days and generally pretending that you’re on the real mission – you’ll eat only astronaut food, perform whatever role has been assigned to you… apparently there’ll even be an exploration phase on a mocked up Martian surface.

At first I wondered how many people could possibly want to give up so much of their lives to be locked up in an isolated, closely monitored environment with a bunch of strangers picked on the basis of how ‘interesting’ they are, psychologically speaking. Then… yeah, you see where I’m going with this.

I checked out the application form (luckily physical fitness isn’t a dealbreaker) and was a bit disappointed – many years ago I filled out an application to work at KFC (it was, er, right after the dotcom bust) and the questions were pretty much exactly the same ones as the ESA are asking. Maybe there’s a secret space code hidden in the Word document – take the first letter of each question, it spells out a phone number, say the codeword and you’re in….

Snarky comments aside it’s a worthy experiment, of course, something that has to be done sooner or later. I’m interested to see who gets picked and why they do it – as a selfless act for the good of science or for personal reasons? How many more of the latter than the former are there?

Near mental breakdowns because you had to work sixty hour weeks and go in on Sundays to check on cell cultures don’t count – everybody does that nowadays. If you can’t hack it I suggest that you take up computational biology instead, then you can check on experiments from home, smoking a pipe while in your underwear.

Anyway: risking wellbeing. I can’t decide if it’s admirable or stupid. Barry Marshall got a Nobel for ingesting H. pylori. Isaac Newton famously poked himself in the eye with a needle to investigate colour perception. Both actions were admirable if slightly unsettling.

But what about what Brady Barr has been doing?

He’s a Texan whose research involves catching wild crocodiles. He also looks suspiciously like the late Steve Irwin and is followed everywhere by a film crew from National Geographic.

You can probably guess the rest of the press release. Get closer to the crocs, less stressful for them than being ‘wrestled and roped’ on cable TV, yadda yadda.

Publicity stunt or brilliant out-of-the-box thinking?

In Egan’s story science gets hijacked for marketing purposes and things end badly for all concerned.

Anyway, three years after Greg Egan’s story got published Bryan Sykes wrote The Seven Daughters of Eve. You may have heard of it:

The title of the book comes from one of the principal achievements of mitochondrial genetics, which is the classification of all modern humans into mitochondrial haplogroups. Each haplogroup is defined by set of characteristic mutations on the mitochondrial genome, and can be traced along a person’s maternal line to a specific prehistoric woman. Sykes refers to these women as “clan mothers”, though these women did not all live concurrently, and indeed some “clan mothers” are descended from others (although not maternally). All these women in turn shared a common maternal ancestor, the so-called Mitochondrial Eve.

The last third of the book is spent on a series of fictional narratives, written by Sykes, describing his creatives guesses about the lives of each of these seven “clan mothers”. This latter half generally met with mixed reviews in comparison with the first part.
(from Wikipedia)

Sykes owns Oxford Ancestors, who in return for £180 will test your DNA and tell you who your clan mother is.

The seven clan mothers (Xena, Starbucks, Zelda, Paris, Tara, Katrine and Lindsay Lohan) have now been painted by Danish artist Ulla Plougmand-Turner. Not with just paint, though! The relevant ancient DNA was also applied by brush to each canvas.

I took special care to use different brushes for the DNA of the seven individual women in order not to disturb and mix their ‘genetic fingerprints’ during this process.

[..]

My interpretation of the women is symbolical and an embodiment of beauty. My Tara is not just the original clan mother from 17,000 years ago. She is ALL the Taras that have ever lived, those alive now and those who have carried her DNA through the generations to the present day.
(from Ulla-art.com)

I have to say that I’m skeptical. I mean, Sykes is obviously a smart guy and Ulla is a good artist – but this is stupid, right? I don’t mean the painting with DNA thing, either, I mean the whole underlying concept. There weren’t really seven clan mothers who each represented some aspect of modern humanity. If my clan mother was Tara then that doesn’t mean I have any of her characteristics. I’m not linked to her spiritually in any way, at least not any more than I am to anybody else on earth.

I appreciate that the stories made Syke’s book a bit more interesting but perpetuating myths to sell more overpriced DNA kits just seems wrong.

An editorial assistant at the Journal of the Science of Food and Agriculture – where the paper was published – threatened her with legal action unless she removed the images immediately. You can see how the blogosphere reacted here.

Shelley’s post pointed out that much of the widespread MSM coverage that the paper received had overstated the results. She wasn’t toeing the line. Somebody at the journal threatened to sue her. To some this means that there’s an evil conspiracy at work:

But her article doesn’t fit the spin that the authors/publishers wanted to put on it. So they resorted to legal threats to try to shut her down – Good Math, Bad Math

This was nothing more than intentional intimidation by a large, wealthy corporation against a lone blogger who’s a graduate student and thus unlikely to have the resources to fight back – Orac Knows

I am appalled at the heavyhanded tactics Wiley has decided to use against fellow ScienceBlogger Shelley at Retrospectacle [..] what makes it particularly heinous is the fact that Wiley is in the business of spreading scientific knowledge. – Afarensis

If there’s one lesson to be learned from this debacle (which has aroused the ire of scientists around the world), it’s this: don’t submit your papers to the Journal of the Science of Food and Agriculture, because they will harass and intimidate people who try to do public scholarship with your work – Boing Boing

Whatever their motives, this is a thuggish, cowardly act. They’re supposed to be helping scientists disseminate their findings. They should have been happy about the small bit of publicity Shelley sent their way. – EvolutionBlog

Wiley come into it because they publish journals for SCI, who produce JSFA.

While I agree that the journal is in the wrong I think these comments are all a bit harsh. If it was a matter of policy at SCI or Wiley to crack down on mouthy bloggers then sure, a blog pile-on like this is appropriate.

The fact is, though, the whole thing is most probably down to an editorial assistant in London doing her job a bit too eagerly. Maybe it was six thirty, she’s had a tough day, figures that it’s better to err on the side of caution and send Shelly the stock ‘stop infringing our copyright’ email.

Her name and email address are out there now. She’s inevitably going to get reams of hate mail from freedom of information loving BoingBoingers who assume that there’s an evil corporate conspiracy at work. Imagine looking for a new job when anybody who searches for your name in Google sees pages calling you thuggish and cowardly.

This doesn’t seem like a fair and reasoned response. What happened to writing letters to the editor? Why the near instant transformation into braying mob?

Shame on the journal for sending bloggers threating letters, but shame on the science blogosphere for making it personal, too.

Update: as Sarah mentioned below the issue has now been resolved

Ostensibly this is because I don’t think there’s much interesting debate to be had about either of those subjects. ID is bunk and homeopathic treatments (as opposed to alternative medicine treatments in general) are no better than placebos. I think that most people who have thought about it scientifically are already agreed on those points so what’s left to talk about in a science blog entry? Not much.

(I suspect that the real reason I dislike posts discussing ID or homeopathy might be that the overwhelming weight of scientific evidence to the contrary makes me feel sorry for them. I can’t help it, I’m a sucker for the underdog. The same thing happens if I’m sat in the pub and somebody brings up George Bush (he’s an idiot, should be shot, needs hanging etc.). I start thinking: poor George Bush! Surely he can’t be that bad. Perhaps people hate him now just because it’s fashionable to do so? If you cut him, does he not bleed?)

Brief educational interlude… check out the origins of the word underdog:

The origin of the word “underdog” comes from naval shipbuilding when the planks of wood were sawn for their construction. The logs of wood were placed over a pit on planks of wood called “dogs” (a bit like fire dogs). The senior sawsman stood on top of the plank and he was the overdog. The junior had to go into the pit and saw and of course he got covered in saw dust. He was the “underdog”.

it’s from wikipedia so it must be true .

Anyway, my point is that I don’t like blog posts about homeopathy so it takes a lot to make me write one. Something like this article from last week’s Observer, in fact. I am outraged on many levels and no longer feel sorry for the homeopathic underdog.

”Britain’s leading homeopathic hospital, supported by the Queen and the Prince of Wales, is facing crisis because the medical establishment is turning against the remedies used by tens of thousands of people every year.”

[...]

”The Queen, an advocate of homeopathy, alongside Catherine Zeta Jones and Sir Paul McCartney, always has 60 vials of alternative remedies in a leather carrier when she travels abroad in case she falls ill.”

Firstly: what?! Prince Charles, sure. He talks to plants and makes organic biscuits – but the Queen? I thought that she was better than that. There was me thinking that we had an enlightened, rational monarchy.

Secondly: I think that the article is far too lenient – bloody hippies. Michael Hanlon at the Daily Mail would have written the story up right. I wish they’d stop doing the random word bolding, too.

The thing that really annoyed me, though, was the revelation that some PCTs were funding treatments at the Royal London Homeopathic Hospital to begin with. When I first moved to London I encountered the NHS postcode lottery: I had to stop taking a drug for my bad back because my PCT didn’t have the funds to pay for it (I got a letter explaining that they needed the money for cancer treatments instead – how do you argue with that? Maybe that’s their cunning strategy).

Was this because they were contributing to the homeopathic hospital’s £5.5m pound budget?

The Observer calls £5.5m a ‘a tiny sum by NHS standards’ but it would have done me and several thousand other patients nicely, thanks. Instead my quality of life suffered so that some homeopath could hand out 9,000 officially sanctioned glasses of water to Prince Charles and his ilk.

Bah. Make them go private.

• London Zombie Walk
• via Mind Hacks : the ethnobiology of Haitian zombies

drooling, braindead monsters in search of fresh meat, average Friday out in London, your research is boring in comparison to ethnobiology of zombies

• Miracle fruit makes sour foods taste sweet
• Fruit bats get hangovers, prefer fruit to fry-ups

”It was found that ethanol levels measured in fruit bat breath…”, “after consuming Synsepalum dulcificum, rhubarb tastes like a sugar stick and strawberries taste like candy”, your research is boring in comparison to breathalyzing fruit bats and checking to see if pints of bitter suddenly taste like a milkshake

• Unrealistic optimism is to blame for your credit card debt
• Panda porn encourages pandas to breed

”Before, he might have been clumsy and not known how to approach and react to a female panda. Now he will remember and imitate the video”, got your unrealistic optimism right there.

”Hi… I’m, um, here to, ah, fix your fridge?”

.. also, your research is boring in comparison to filming panda porn

Lewis Wolpert was the speaker in question. He’s an intriguing chap and gave an entertaining if rather short talk on the biology of belief.

The answer to the cats question, incidentally, is that they lack any concept of physical cause and effect (there’s the whole opposable thumbs thing too, of course).

The turnout was good, with some audience members left standing. A bit of added excitement was supplied by having a BBC camera crew present. I pouted, stroked my chin and nodded thoughtfully each time the camera swung past – ideal audience reaction material, if you ask me…

Lewis Wolpert

Anyway, the gist of Wolpert’s talk as I understood it – which may not have been very well – was that humans are the only animals to have causal beliefs, the aforementioned concept of physical cause and effect. We evolved a ‘belief engine’ because it helped us understand enough about the physical world to make tools; religion arose because once we started working out why simple things happened we wanted to understand the causes of other, more complex events and believing in supernatural powers made us feel less anxious about not having all the answers.

We’ve still got this drive to understand why things happen, a psychological urge to explain even those events that have no simple, common sense answer. Think about the family of an air crash victim who, ten years on, still want to know exactly why the plane went down.

Our beliefs are all brain chemistry: when depressed you believe that you’re alone, that you’re unlovable – even thought these things are untrue. Tripping on LSD the meaning of life suddenly becomes clear (if you’re Timothy Leary). Mental patients subconsciously maintain delusions in the face of contradictory evidence.

All very interesting. The point of Cafe Scientifique is for the public to engage the speaker so an hour of audience participation followed Wolpert’s talk: some people asked interesting questions or voiced thoughtful opinions and some people, um, talked to hear the sound of their own voice.

It was a worthwhile hour and a half, anyway. The next event was in May, I think, though I’m not sure exactly when – keeping an eye on the Nature Network events page is perhaps the best course of action if you’re interested in going along.

computational biologist, in a bath

You get home. You run a bath, light some scented candles. Put on some relaxing new age music. You step gently into the soothing bubbles then let the warm water envelop you. Mmmm, soothing bubbles. The sweet smell of frangipani fills your nostrils.

Still, something is missing. What you really need now, you think as you sip from your wine glass, is something to read. Something to stimulate you intellectually. Something covering the topics that you’re passionate about. Something like a freely available compilation of the best bioinformatics blogging from the past month in easy to print PDF format.

Fantastically enough such a thing exists in the form of Bio::Blogs, which gets published on the first day of every month. Bio::Blogs pulls together posts from all over the bioinformatics blogosphere and has a different guest editor each issue (the schedule is coordinated by Pedro Beltrao at EMBL). It’s a good read and a gentle introduction to scientific blogging in general. The PDF is a relatively recent development but a welcome one – it means that you can print out all of the posts at once to read at your leisure.

After downloading B::B you should check out Nodalpoint, the ‘by the people for the people’ bioinformatics group blog founded by Greg Tyrelle which has recently seen a resurgence of activity. Some of that activity has been focused on updating a list of blogs about computational biology which is worth going through to find good reads.

Eigenfactors are a novel alternative to journal impact factors. They’re calculated using random walks through a network of citations:

The Eigenfactor algorithm corresponds to a simple model of research in which readers follow chains of citations as they move from journal to journal. Imagine that a researcher goes to the library and selects a journal article at random. After reading the article, the researcher selects at random one of the citations from the article. She then proceeds to the journal that was cited, reads a random article there, and selects a citation to direct her to her next journal volume. The researcher does this ad infinitum.

The amount of time that the researcher spends with each journal gives us a measure of that journal’s importance within network of academic citations.

One advantage of this approach is that it can handle the fact that different disciplines have different citation patterns:

The average article in a leading cell biology journal might receive 10-30 citations within two years; the average article in leading mathematics journal would do very well to receive 2 citations over the same period.

The list of the top 10 journals by eigenfactor looks pretty much as you’d expect – Nature and Science are sitting pretty at the top, natch.

One issue: in an attempt to include more material from the social sciences the eigenfactor dataset includes articles from newspapers and popular magazines. As newspaper articles don’t typically have reference lists attached I’m not sure how they are incorporated into the network, but in any case don’t they skew eigenfactors towards those journals that have the best press releases? Could I start a Journal of Sensational Medicine and start publishing pseudo-scientific quackery, be spurned by academia but have a high eigenfactor simply because I feed the London Lite headlines?

(via Three Toed Sloth)