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Friday links Grant Jacobs Sep 03

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Time to clear out those tabs! Lurking on my web browser are some great reads… for those that have more time than I do!*

First up is the excellent visual tale, The Illustrated Guide to a Ph.D. Don’t forget to read right to the bottom: there is a “bonus” graphic and story tucked away at the bottom of the page.

(Source: xkcd.com)

(Source: xkcd.com)

The New Yorker has an abstract for a longer piece on local murderer, and former head of psychiatry at the University of Otago Medical School, Colin Bouwer. (The full article requires subscription, but the abstract is entertaining in it’s own right.)

I have a hearing loss, so I have a tendency to pick up on stories with hearing themes. This blog post describes research indicating that those with Williams Syndrome have something resembling synaesthesia.

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Welcome PLoGs Grant Jacobs Sep 02

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All this introducing new blogging networks is keeping me from writing about science. It has to end, I tell you, it has to end! (Either that, or I’m going to start ignoring you lot. Seriously.)

Hot on the heals of the Guardian newspaper science blogs is the announcement of an excellent science blog network at PLoS. (For non-biologists, PLoS = Public Library of Science, is an open-access publisher of a range of biology-related research journals.)

plos-blogs-banner

The in-jokes are abounding. They’re not blogs, they’re PLoGs. Jason Goldman thinks that PLoS blogs sciblings should be called PLoGsters. Sounds faintly criminal to me. (Others say plogger. I prefer PLoGster: plogging scans much too close to plodding, and these writers aren’t dull.)

The initial cast, as you might expect, is excellent.

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GoPubMed – PubMed browsing using ontologies Grant Jacobs Sep 01

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A brief look at GoPubMed, an ontology-based browser for PubMed. (Intended for those who use the biological research literature.)

While reading an article at Nature Network, a commenter (David Crotty) pointed to GoPubMed, a service I have heard of but not tried before, built on a commercial knowledge-base server. This short post is to introduce this to my readers, and hear your thoughts on it. (Plug them in the comment box below this article.)

Basically, GOPubMed is PubMed sorted using the GO and MeSH ontologies (explained below) so that you browse the contents based on these ontologies, rather than just rely on search strings.

GoPubMed is mostly self-explanatory: I suggest people just wander over and try it out. Nevertheless, I’ve jotted down a few tips from my few minutes of exploration, for whatever they’re worth.

GoPubMed-home-page

First, what’s an ontology? it’s a hierarchal collection of terms describing a domain of knowledge (biology, medicine, whatever). The ontologies GoPubMed uses should already be familiar to most biologists. GO is Gene Ontology and MeSH the Medical Subject Headings, a vocabulary thesaurus from the National Library of Medicine (USA). MeSH is now 50 years old! GO terms are shown with blue icons, MeSH terms using green icons. Read the rest of this entry »

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Major newspaper opts for science blogging Grant Jacobs Sep 01

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British newspaper, the Guardian, already home to the column of Bad Science writer Ben Goldacre, has gathered a small but very good collection of science bloggers to present as Guardian Science Blogs.

Stromatolites from Bolivia (Source: Wikimedia Commons.)

Stromatolites from Bolivia (Source: Wikimedia Commons.)

The science-writing internet has seen a lot of developments this year. It’s promising to see a major newspaper like the Guardian take this on.

Initially the Guardian have four blogs:

  • Punctuated equilibrium, by GrrlScientist (who also writes at several locations elsewhere). Her introductory post features her parrot, Orpheus reading, no make that eating, the Guardian. Good recycling, I suppose. (Great photo, too, well worth checking out.)
  • Political science, by Evan Harris (a former British MP), who has started out with some pretty hard-hitting stuff on MMR and religion v. science in teaching in schools. Interesting — and good! — to see a politician in the science-writing fray.
  • The Lay Scientist, by Martin Robbins, who might be familiar from those who followed Simon Singh’s case, who writes with skepticism about pretty whatever is the latest issue. (Sadly, there is always more to put right… On the bright side, this makes for more entertainment, too.)
  • Particle Physics, by Jon Butterworth, Professor of Physics at UCL who will no doubt bring some professorial clout to physics blogging, entertainingly too.

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Who blogs on what, and why Grant Jacobs Sep 01

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Floating around the science blogosphere for the last few days has been an informal survey of top 100 science blogs (according to wikio) by Vivienne Raper and her take on what these blogs cover.

It’s fun and gives an idea of what there is out there, at least for those at the wildly popular end of the scale. If you blog on science, or just follow them, read her survey, and ruminate over her data. I am!

Vivienne originally started this wondering if there was a bias towards biology, but concluded that’s not the case, particularly bearing in mind that there are more biologists that scientists in other disciplines.

Vivienne has commented in reply to Razib Khan pondering other issues, in particular “why there are no ‘popular’ blogs in certain subjects”. Razib Khan, in turn, has replied suggesting that it may be a case of not having ‘soul’. What do you think?

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Dictionaries, the OED, and what do you use? Grant Jacobs Aug 31

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As claims that the OED is looking towards ceasing print publication of the ‘complete’ edition circulate (and are countered), I ruminate on the OED and dictionaries.

OED-cover

Anyone involved in writing by now will know by now there are claims that the next edition of the OED — The Oxford English Dictionary — may not appear in print form. Other reports suggest this is not a done deal as initial accounts in newspapers around the world say. Nevertheless, it’s a nice excuse to ponder on the OED and dictionaries.

It’s a colossus of the English language, with the second edition running to 20 weighty volumes. There’s even a guide to it and a word of the day RSS feed, which you can also view as a webpage. (‘to cross or pass the Rubicon’ is up today. Given how many words they have to chosen from it’ll be a long time before they double up…)

Surgeon-of-Crowthorne-cover

On my shelves is a copy of Simon Winchester’s The Surgeon of Crowthorne. (I believe this now goes under the title The Professor and the Madman.) In it Winchester recounts how (paraphasing from the blurb on the rear cover) “Dr. W. C. Minor, lascivious, charismatic, a millionaire American Civil War surgeon and homicidal lunatic, confined to Broadmoor Asylum, pursued his passion for words and and became one of the OED’s most valued contributors.” It’s a short book (207 pages), but a great read. I have to admit I still haven’t gotten the account of this gentleman’s self-surgery out of my head. (I would give the spoiler, but it’s stunning.)

A later book, The Meaning of Everything, looks further into the history of the dictionary. (See the cover for a beard you’d rarely see today! The gentleman could step right into Lord of the Rings as a wizard.)

I have faint memories of an older edition of the “full thing” arrayed on the shelves of my college at Cambridge. While impressive, the volumes were so big and the writing so small as to make it unwieldy to use so rarely I did, preferring for most uses the more compact (and current) shorter versions.

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How does science work? Grant Jacobs Aug 26

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Regular readers will know that recently I posted a three part series of videos authored by SisyphusRedeemed, who lays out a (very!) brief history of science.

He has followed this up with a video, How Does Science Work? Three Views. At just under 15 minutes this is slightly longer, but packs a lot in there!

YouTube Preview Image
Other articles in Code for life:

What is your relationship with your research notebook?

I remember because my DNA was methylated

Book sales, frumpy readers, and mental rotation of book titles

The inheritance of face recognition (should you blame your parents if you can’t recognise faces?)

GMOs and the plants we eat: neither are “natural”

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Quotable lines Grant Jacobs Aug 26

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A short selection of quotable lines from or about science and medicine

Perhaps relevant to Kubke Fabiana’s recent post:

Sit down before fact as a little child, be prepared to give up every preconceived notion, follow humbly wherever and to whatever abysses nature leads, or you shall learn nothing. I have only begun to learn content and peace of mind since I have resolved at all risks to do this.

(Thomas Henry Huxley, in a letter to Charles Kingsley, 23 September 1860. Do note that this is an earlier Huxley than in Fabiana’s post. This family has several generations of renown scientists.)

Just for a bit of a laugh:

It is a good thing for a physician to have prematurely grey hair and itching piles. The first makes him appear to know more than he does, and the second gives him an expression of concern which the patient interprets as being on his behalf.

(A. Benson Cannon)

Not from a scientist, nor strictly a science quote, but one science bloggers will empathise with:

The whole problem with the world is that fools and fanatics are always so certain of themselves, and wiser people so full of doubts.

(Bertrand Russell)

A well-known classic, but too good resist repeating here:

Not only is the universe stranger than we imagine, it is stranger than we can imagine.

(Arthur Eddington)

Possibly my all-time favourite:

The most exciting phrase to hear in science, the one that heralds new discoveries, is not Eureka! (I found it!) but rather, “hmm…. that’s funny….”

(Isaac Asimov)

Offer your own favourites in the comments.

Other articles on Code for life:

Coiling bacterial DNA

Vitamin C, swine flu, media, lawyers

Friday’s Factoids and Quirky Quotes

Preserving endangered species – of gut microbes

I remember because my DNA was methylated

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Halt to funding new stem cell research in the USA Grant Jacobs Aug 25

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Judge rules a stay on federal funding for embryonic stem cell research in the USA.

Previously I wrote about a new twist in a law suit involving Christian groups and two scientists suing US government departments over embryonic stem cell research (ESC), based on their having to compete for funding.

Recent reports say that the judge has now issued an injunction putting a temporary stay on federal funding of human ESC research, resulting in NIH director Francis Collins freezing funding on up-coming grants. (Private funding is apparently unaffected.)

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Coiling bacterial DNA Grant Jacobs Aug 24

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A chain of proteins hold bacterial DNA in a compacted spiral.

You and I are eukaryotes. Our cells have nuclei, repositories that contain our DNA and the proteins that read them to produce an RNA copy of them.

HeLa cells*** stained for DNA (Source: Wikimedia Commons.)

HeLa cells* stained for DNA (Source: Wikimedia Commons.)

In earlier articles, I’ve mentioned in passing how the enormous length of DNA in our cells is fitted into a nucleus. Our DNA, all 2 metres of it, were you to stretch it out end-to-end — is fitted within a nucleus with a diameter of roughly 6-10 micrometres, about one-millionth of a metre.

The trick is that a DNA molecule is very skinny — it’s only about 2 nanometers wide (2 billionths of a metre wide). Wrap that up around a something handy and it’ll be quite compact.

The ‘something handy’ in eukaryotes are histone proteins. Eight histone proteins associate to form a disk-shaped octamer, wrap DNA almost twice around it and you have a structure called a nucleosome. Read the rest of this entry »

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