don’t judge a thesis by its title

I hate the academic colon. I think it is a specious piece of punctuation that, when applied to the title of a work, cries out for abuse via the lame pun.

I am the first to admit gratuitous cringe-worthy use of the colon and its licensing of the pop-culture reference/foreign phrase/alliterative list, but I want to stand up and be counted among those who wish to use a strong, active statement as the title for a work.

It’s just the colon is so tempting. So easy. A temptress of multiple keywords and simple specificity.

Yes, I have to finalise my thesis title today. WOEZ.

I used logistic regression vs logistic regression was used

Today I am pondering the use of the passive and active in scientific writing. I’ve seen the first person being used more frequently in journals–mainly in method sections–and the collegial “we” has become much less passive and directly related to hypotheses.

Personally I approve. I see the need for the science to stand separate from the author(s)’ editorial voice. But I think it is beneficial to the comprehension of (a) the prose, and (b) the scientific process, if the author(s)’ procedural voice is immediate and active.

Found a link to these three letters on the topic which appeared in Nature about ten years ago. The first and third articulate pretty much what I think. The second is so bafflingly offended I have to laugh. I’m also confused by the thought that we scientists are so easily swayed by a few pronouns that we mistakenly over-invest ourselves into the work. Um, what?

A more technical and high-level examination of writing scientifically: tailoring what you say and how you say it to the readers’ expectations.

Quis custodiet ipsos custodes?

(Pretentious latin post title for the win!)

The tension in academia–especially science–between communication and discretion fascinates me. On the one hand, you want to be able to discuss your ideas with as many people as possible; on the other, those ideas are your intellectual currency and you don't want them stolen or misappropriated.

The publishing process also intrigues me. It appears to be undergoing a sort of quiet revolution at present, with open access journals becoming more common, and with the review process itself being opened up by journals like Biology Direct. Nature has a commentary on that journal's review/editorial process and how it is faring here.

I'm all for this. I know the arguments about what the anonymous process allows/preserves, but I think that on balance science would be greater served by open peer review. Perhaps it's a naivete to assume that the majority of reviewers play the game correctly–review a paper irrespective of their personal feelings on the authors and their particular theoretical biases. Sure, there are always going to be vindictive wankers. But it's actually very easy to tell a vindictive wanker from someone making justified criticisms. Open peer review means that the wider science community can review the reviewers.

It's also a means to what I see as a desirable end: chopping up undeserved status hierarchies and allowing smaller voices to be heard without fear of career-hurting reprimand. People already mostly find out–through the grapevine or guesswork–who reviewed their paper. And so any wankery that goes on does so anyway, but with the protection of psuedo-anonymity for those playing pay-back games, and without recourse for anyone who has had a grant rejected or employment opportunity stifled. OPR leaves a public trail of cause and effect.

Of course, this means that one has to overcome one's need for approval, be it social or professional, in order to write that justifiably-critical review of someone with more status/funding/publications/associates than you. But science needs brave Gryffindors.

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, I really have no excuse.

students: self-important and indifferent

Regarding the general student reaction to the recent industrial action by the University and College Union (which I wholeheartedly endorse and therefore exempt myself from the classification in this post's title, heh) Edward Hall writes in sp!ked

This lack of solidarity within higher education was detrimental to the UCU’s quest for higher pay. The media and public seemed more concerned with the effect the action would have on graduates in the short term than with the decline in wages that has been occurring for nearly 30 years. A mix of self-importance and indifference characterised the student response to the strikes.

Article [here

perceptual thresholds in culture

Today at Culture Club [1] we discussed a recent paper by Eerkens & Lipo [link], where they present a null model of copying errors in cultural transmission. One of the notions they discuss is something I learnt a million years ago in Stage 1 Experimental Psychology: Weber's Fraction, or the Just Noticeable Difference. Interestingly, they reference the exact textbook from which I learnt psychophysics (wow, textbooks are expensive, I had forgotten!).

This made me think about what sort of "perceptual limits" there might be for complex social phenomena like kinship organisation, and where the JND might lie in scales of difference in (for example) inheritance. What would be the so-called "tipping point" for a formerly matrilineal system to start adopting as a norm a system of bilateral inheritance? What might the units to examine be? It struck me that this is possibly a way to get at some thorny "units of culture" questions, although it is beyond the scope of what I'm doing at present. But it would be so very nice to have some sort of null model that might group perceptually-bounded culture concepts together.

[1] Our weekly journal club/discussion meeting for the Centre for the Evolution of Cultural Diversity

encyclopaedia britannica V nature: ultimate showdown

(Everything is funnier when you reference the Ultimate Showdown)
The Guardian technology blog links to EB’s response to the claims by that journal that EB was no more accurate than Wikipedia.

The 20-page EB response is an exercise in the most miffed sort of quibbling, especially the appendix where they address the reviewers point by point. Good on them for taking on Nature; good on Nature for starting the comparison in the first place. Can’t wait to see round three.

ETA 24 March: Nature’s response. Very terse and unapologetic. They say they provided EB with the requested information, which was a major point of criticism.

scientific presentations

Garr Reynolds, at Presentation Zen (a moment for fangirling, please), has a post linking to resources for scientific presentations. Often presentation advice is geared towards commercial or creative models, and while it’s helpful to extract what works/what sucks from those sorts of domains, a Zen-approach to scientific/academic presentation couldn’t come soon enough. From the editorial “Let There Be Stoning” by J. H. Lehr, which Garr links to (available in entirety here and well worth the read) I snuck this gem:

Without exception a presentation … can and should be made extemporaneously. A scientist who cannot retain in his head the essence of his latest work can hardly be said to be enraptured by his subject. If a speaker is not excited enough by his area of expertise to weave it comfortably into the fabric of his cognitive thought processes, then how can he hope to excite an audience to an acceptable level of appreciation?

Presenting scientific work we’re constrained by the need to provide a certain base level of technical information or background, and results are generally graphical or in tables–not leaving much room to get crazy with the style. But 90% of academic talks err on the TMI (too much information) side, and by doing this, often they preclude people asking questions. I attended a talk yesterday and made a conscious effort to not look at the slides unless they had a picture, table or graph, and you know what? I didn’t miss anything important at all. Sadly, the speaker relied on looking at her laptop or reading off the screen in many cases, which is just as irritating as the philosophy-model of literally “reading a paper”.

I’m determined that the next talk I give will be pared down to the bare essentials, and that the focus will be on me and my information.

Teaching presentations are of course a different kettle of fish, but I’ll re-visit those issues when they’re pressing.

wear it, do it, teach it

Grrlscientist links to Yellow Ibis, which have the coolest science t-shirts. The Darwin phylogeny sketch ones are my favourite, but I’m also fond of “this is what a scientist looks like”.

Inside HigherEd offer columns and articles, including Academic AWOL by Mary McKinney, which I found to be a good kick-in-the-pants about Just Getting On With It.

A marvellous explication of the cognitive barriers to taking on-board evolutionary thinking, from Chris at Mixing Memory.