on science and science fiction

There’s an engaging conversation in Nature this week with four science-fiction writers who concentrate on the life-sciences in their writing:

The biologists strike back.

I have this tremendous block about sci-fi. I have dabbled on the fringes and read Neal Stephenson and Iain Banks like everyone else, but virtually no classic sci-fi. Genre fiction intimidates me, I think, because it has its own rules and hierarchies. The other part of my block is self-preservation in the face of gateway drugs: because I’m fascinated by the communication of scientific ideas, I feel like indulging in a sci-fi reading habit would just be the end of it all and I’d never read anything else.

But perhaps that’s a cop-out? I’ve got a whole list of recommendations from various sources. I just need to start, I guess.

the need for science

The piece by Harry Kroto is actually entitled “The wrecking of British Science“, but it contains positive messages as well as cautions.

In the Guardian:

Many think of the sciences as merely a fund of knowledge. Journalists never ask scientists anything other than what the applications are of scientific breakthroughs. Interestingly, I doubt they ever ask a musician, writer or actor the same question. I wonder why.

The scientific method is based on what I prefer to call the inquiring mindset. It includes all areas of human thoughtful activity that categorically eschew “belief”, the enemy of rationality. This mindset is a nebulous mixture of doubt, questioning, observation, experiment and, above all, curiosity, which small children possess in spades. I would argue that it is the most important, intrinsically human quality we possess, and it is responsible for the creation of the modern, enlightened portion of the world that some of us are fortunate to inhabit.

Coming after the appalling set-piece of science “journalism” concerning an entirely groundless “electrosmog scare” on Panorama this week, such sentiments are timely.


Apparently so, because there are a number of bug posts on this blog.

Via Grow-A-Brain, a video of the amazing Megalopyge opercularis, a moth so fuzzy and furry I squealed a little at how cute it was. Of course, that fuzz is out to get you, as the “fur” is actually venom-carrying prickles that’ll have you scratchiing at best and in palpitations at worst should you try and touch it. Big fluffy spiders like Avicularia versicolor (11th down) also induce my “oh, FUZZY” reaction and irritate the skin similarly.

I am a huge fan of lepidoptera, especially moths. Here’s some good photos of the big New Zealand Puriri Moth, including one getting nabbed by a morepork. Ah, the food chain.

a vagary of links

A “vagary”, according to The Source, is the collective noun for ‘impediments’. More pages that collect collective nouns are here and here. I am amused that a group of submarines is called a wolfpack, and that a group of sheldrakes is a doading (shoutout to my friend Duckie!).

Henceforth a group of links to things almost, but not quite entirely like tea relevant to The Thesis shall be known as a Vagary.

First, the Guardian reports on what most menstruating women know: that your hot water bottle really does relieve internal pain. A couple months back I read about a study that demonstrated that heat was as effective as ibuprofen in relieving menstrual pain. This is good news for our livers, no doubt, but carrying around a hot water bottle is impractical for about 99% of women. Those stick-on heat things with the iron filings in them seem to do a good job though!

Chocolate, it seems, is really not anti-depressant: “any mood benefits of chocolate consumption are ephemeral.” It’s just cos you’re stuffing your gob, not the magical woo-woo power of cacao.

Some gems from Medical Hypotheses, which I might unfairly characterise as a place where MDs who still yearn for the third-year undergraduate speculative essays they never got to write because they were too busy memorising the major craniofacial nerves get to, um, write those essays. Hey, it’s called Hypotheses for a reason. I kinda love this. I wish *I* had left-field theory to write up. Hours of fun.

Ecstacy makes you feel good and want to touch people and rub up against them and slide your–sorry. Ecstacy makes you feel saucy ‘cos of vasopressin and oxytocin. Man, that oxytocin stuff is awesome. It makes women forget the trauma and pain of childbirth, stimulates breastfeeding, makes you trust people more, increases your pain tolerance… why can’t I buy *that* from those guys at Camden Market instead of the magic mushrooms?

This one argues that there might be adaptive reasons behind our pervasive use of alcohol and caffeine. That is, caffeine makes us SMRT in an environment where competition is social/intellectual rather than physical, and alcohol dampens down the stress response in environments that lack social networks and cause a greater fear response. Oh, and apparently, if you’re drunk and in some sort of traumatic injury situation you heal better or something. This article is so unnecessarily convoluted in its prose I could only skim it, and it seems to be the kind of evolutionary psychology armchair handwaving that could be problematised pretty quickly; they don’t seem to have a grasp on their timelines (like, WHEN are these environments) or their cross-cultural caff/booze frequencies. But, you know, some testable hypotheses.

Cultural evolution causing baldness. I dunno in what sense cultural evolution is being used here, but possibly the loosest type, i.e. cultural change. Anyhow, apparently wearing headdresses and having close-cropped hair means sebum builds up on the hair shaft, and that’s bad and causes baldness. This is my favourite bit:

“Many people affected by common baldness have noted that they started to suffer from it during military service. This theory could explain this fact. The difference in hair length is the key. Military people, skinheads and others wear their hair short and therefore they can induce problems with the sebum flow. On the contrary, hippies, Hindus, etc. wear long hair.”

Dude. Good luck with that one.

Finally, the piece de resistance: defecating at night-time (only) may help you lose weight. Because you’re carrying your shit around with you all day, and that takes energy.

This gets the special face: o.O

bayesian madness

A non-biologist friend of mine, on proofreading bits of the thesis-in-progress, got terribly excited about the program Mr Bayes.

"Mr Bayes!" she exclaimed. "That's the perfect name for a tabby cat!"

Her comments on the section where I actually described Bayesian methods in phylogenetics consisted mainly of 🙁 and >.< faces. "The words seem to be in the right order for the English language?" was her concession.

Don't blame her, obviously. I periodically beat myself over the head with my notes about Bayesian & likelihood methods; this appears to be an effective means toward keeping the information in my head. Today I found a couple more implements of self-harm at Paul Agapow's site, the first his own primer, the second a link to Peter Foster's The Idiot's Guide to the Zen of Likelihood in a Nutshell in Seven Days for Dummies. Tee hee.

So browsing the talk titles for the Evolution 2006 meeting, I came to the conclusion that biologists, especially those who dabble in phylogenetics, tend to have a very specific sense of humour. By specific, I mean "take any opportunity to make a pun, an allusion, or maximise alliteration to the point of tongue-twisting" and dude, there's nothing wrong with that. You wrap your brain around priors and posteriors and your brain wants to crack a funny. It's just the way it is.

molecule jewellery

Continuing my trend of providing free advertising to people who make science cool and accessible: Made With Molecules. ThinkGeek already did the t-shirt thing with their caffeine molecules, but the jewellery is very lovely, especially the earrings and simple necklaces (I loathe charm bracelets).  Putting on my once-was-jewellery-designer hat, I'm all for putting a premium on design work and charging people accordingly, but I think the prices are just out of reach for those (grad students/postdocs) who might want this sort of thing the most. I mean, I know precious metal prices have risen ridiculously in the last 2 years, but I wouldn't stretch to $85 for a simple silver necklace.

I know, what a killjoy, right? 

more chaucerian phylogenetics

Eagleton, C. & Spencer, M. 2006.

Copying and conflation in Geoffrey Chaucer’s Treatise on the astrolabe : a stemmatic analysis using phylogenetic software. Studies In History and Philosophy of Science Part A [link]

Chaucer’s works seem to be the focus of what one might call literary phylogenetics. This new paper uses network methods to try and unravel the lineages and relationships amongst multiple copies of his “Treatise on the Astrolabe”, a work that was copied at least 30-odd times, some in fragmentary pieces. Using NeighbourNet, the  authors construct diagrams of interelatedness, showing areas of “hybridisation” between manuscripts. They find that the scribes were diligent about creating a complete copy, and would consult other versions to fill in the gaps or verify uncertainties contained in a single exemplar. 

Other cool things in my inbox today included the ToC for PLoS Biology, which contains an article about Siphs, a community expertise-sharing forum for the life sciences. The article discusses the benefits of online databases for journal articles (less arduous time in the library) but the highlights that things like PubMed and WoS don’t actually tell you what is important, or answer your question. We have an information overload without access to expertise, and the Siphs project looks to be set up to counter that. Of course it will only succeed if individuals participate, but announcing it in PLoS is a good idea.

This information age is an exciting time in that knowledge is at our fingertips. But if we fail to innovate upon our means of accessing information, the Internet’s promise of providing us what we want will be lost as knowledge is drowned in a sea of facts. These new tools are founded upon the belief that we’re better off working together, but they work only if you think so too.

The article also linked to Connotea, which I’ve known about for a while but haven’t set up. Given how much I love the social bookmarking available at del.icio.us, I really have no excuse.