Quick note: if you’re interested in science communication you can right now follow Science Online London via twitter. (10:50pm NZ time.)

It’s a confusing but wonderful mess of short notes on the events as they happen. Lots of sound bites that trigger food for thought. There is a live video stream, too. (I find the video stream a bit hard to follow, but those with better hearing should be fine – ?)

The programme is also on-line.

Better move fast… there have been 50+ tweets has I’ve written these few words!

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)

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.

As if you could miss it, this week has seen the announcement of two different excellent science blogging groups. I’m told there is more coming, too.

One of the opening articles at PLoGs is an interview from Steve Silberman with Oliver Sacks, featuring a new book he has out, The Mind’s Eye. Deborah Blum opens with Tarantula Tales. (Her father was an entomologist who liked to bring his work home with him…)

(This one  for skeptics.) Fairly recently I wrote about vitalism in a local chiropractor’s advertising. While waiting for scientopia’s server to be upgraded, The White Coat Underground has re-posted an old article on vitalism.

Also from scientopia I like MarkCC’s post on three-valued logic, but I suspect my taste for this is too geeky for most of my readers… (Part of my interest is that I implemented code for three-value logic, following a trend I noticed in my coding. Geeky coding stuff!)

Vivienne Raper rounds out her analysis of what science bloggers blog about. (I wrote a little about this earlier in the week.)

Quite a while ago I wrote about reproducible research and bioinformatics. This article from the OpenHelix blog looks at how the Galaxy genome browser can assist reproducible bioinformatics research. Readers may also like this paper, presenting the recommendations that followed from a roundtable meeting at Yale Law School as food for thought.

Oh, one more! Brian Switek’s The Mosasaur’s kinky tail over at the new Guardian science blogs.

Footnotes

I may bring a list of more research-oriented reading out later. May. If I have time. (You get it.)

* I have a growing list of half-written articles to complete and get to you. Owing to demands on my time I can’t start on these until at least Saturday week.

Other articles on Code for life:

Welcome PLoGs

GoPubMed – PubMed browsing using ontologies

Looking for a book to read?

Loops to tie a knot in proteins?

Consumer brain-computer interface

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.)

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.

Scientists who blog (with snippets nicked from their on-line bios*):

• GenomeBoy, who says his genome has been sequenced
• Gobbledygook - Martin Fenner, a medical doctor and cancer researcher
• Neuroanthropology from a two-person tag team
• Obesity Panacea from, erm, another two-person tag team. (Is there a theme here?)
• Take As Directed David Kroll, who may be better known as AbelPharmaboy to those who visited his previous digs (Terra Sigillata) at scienceblogs
• The Language of Bad Physics from Sarah Kavassalis

The scientists are matched with a cast of science journalists:

• Body Politic – Melinda Moyer, who has a long list of top magazine publications to her name
• NeuroTribes – Steve Silverman, who also writes at Wired
• Speakeasy Science from Pulitzer-prize winning science writer and a professor of journalism, Deborah Blum. (Also author of The Poisoner’s Handbook and other books.)
• The Gleaming Retort – John Rennie, former editor-in-chief of Scientific American
• Wonderland – Emily Anthes, ditto as for Moyer!

Not to leave out the older blogs at PLoS, now in their new setting: PLoS.org, everyONE and Speaking of Medicine.

They’re on twitter, too: tweet to @plosblogs or use the #plogs hashtag. Like scientopia, there is no advertising on their site. (I like the clean design of their site, too.)

Now I’m going to have to update my Other science blogs page again. But Razib Khan, who must have inside news, says there are more to come…

Footnotes

* Excuse my not naming everyone. This is a rush job: one-liners rule…

Other articles on Code for life:

Major newspaper opts for science blogging

Who blogs on what, and why

GoPubMed – PubMed browsing using ontologies

Looking for a book to read?

Coiling bacterial DNA

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.

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.

To the left of the page is a familiarly-styled list of items, initially displaying from all of the contents in PubMed. Clicking on the arrows to the left will cause the topics to be expanded as you’d expect. If you’re looking for a very popular topic, you could just browse that way, although you’ll run into the usual problem on PubMed of there being just too much to read!

If you enter a search string (textbox in main pane), it’ll give you a description if it is able t0 (so if you give a gene name, you’ll get a brief description of the gene). Pressing on ‘search’ to the right of the textbox will update the browser to the left, so that it’s hierarchy is restricted by that term.

If you click on a subtopic itself, you’ll be presented with a floating menubar of options: Actions (with, without, and favourites; see below), Description (a short description of the ontology term), Tree (the part of the ontology tree the term falls within), and Wikipedia (a link to the Wikipedia entry for the term selected). You’ll sometimes also get synonyms where appropriate.

Actions are self-explanatory: they allow to add the term to your query (with), exclude it (without) or add it to your favourites. You’ll see as you add things, that the search string gets updated and new items appear in ‘my search’ section (top, left).

Results can be exported in RDF, EndNote, BibTex (Yay!) and text formats. (Nice to see the latter too: useful for those handy with programming tools and as a fall-back.) You’re limited to exporting 100 results at a time. To export, press ‘find it’ to bring up your results, then click on the icon with the arrow pointing to a computer (shown to right). Exports go straight to “standard” filename on some browsers, something I don’t like.

The service is English-only at present.

If you are using the clipboard (to the left, top), bear in mind it’s contents only last as long as your current session: save anything you want before you move on to the next thing!

If you know them, you can use the Search Field Descriptions and Tags from PubMed.

To the top you will see links to other services I haven’t looked at here: Go3R, GoGene, and GoWeb. GoWeb is like GoPubMed, but searches the internet. Go3R apparently provides alternatives to animal experiments. GoGene, as you might expect, searches gene annotation.

Other articles at Code for life:

Preserving endangered species – of gut microbes

Who blogs on what, and why

The roots of bioinformatics

What is your relationship with your research notebook?

Professors, lost souls with great oratory power?

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.)

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.

The Guardian are also offering a very promising line-up of guest articles, in a fifth blog that draws on from science bloggers around the world. Their initial line-up for this looks exciting. I spot at least one Pulitzer Prize winner in there; all of the people they list write very well, as you might expect. In some ways I’m looking forward to these more than the regular bloggers. Is that weird of me? You can read about these in Alok Jha’s article introducing the Guardian science blogs. His article closes quoting Guardian editor Alan Rusbridger, which I’d like to repeat here:

We are edging away from the binary sterility of the debate between mainstream media and new forms which were supposed to replace us. We feel as if we are edging towards a new world in which we bring important things to the table – editing; reporting; areas of expertise; access; a title, or brand, that people trust; ethical professional standards and an extremely large community of readers. The members of that community could not hope to aspire to anything like that audience or reach on their own; they bring us a rich diversity, specialist expertise and on the ground reporting that we couldn’t possibly hope to achieve without including them in what we do.

Other major newspaper and magazines do have science sections, but few have a dedicated science blogging initiative, and the philosophy behind this is interesting. (My initial impression is that they are not editing these blog posts, however. It’s possible that might change?)

Locally, The Listener magazine has recently added a fortnightly science section, and we have our own much more modest newspaper development of a guest post in the Herald Online, where selected articles (up to one per day) are reposted on their site.

Who blogs on what, and why

Aww, crap.

Friday picture: molecular modelling of the cytoplasm

Molecular biology in museums

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?

More recently Vivienne has put up an internet poll, hoping to probe this further.

Dave Munger, who runs ResearchBlogging.org, suggested categorising the contributions there. Doing a very hasty count* of the number of pages in each main category, the forerunners are distinctly bio- or homocentric: the top five are biology (284 pages), psychology (128), health (108), clinical research (90) and neuroscience (78), dropping to 50 (social sciences) then 33 (anthropology). “Last” (this isn’t a race!) is mathematics (6 pages), narrowly having fewer pages than engineering (7) and philosophy (7), with astronomy and computer science having 12 and 13 pages of articles, respectively.

(To consider which field blogs the most, these would need to be corrected by the number of people in each of these fields. I suspect once this is done the skew won’t be as dramatic. However, with chemistry and physics having only 23 and 19 pages of articles, respectfully, I imagine the bias toward biology and homocentric topics will remain.)

I wonder if self-reinforcement is at work here: biology research blogging may be encouraging more biology blogging in self-reinforcing fashion. As Munger pointed out, some probably don’t blog on peer-reviewed papers much: computer science may be an example. (Bear in mind that computing, a very popular topic on-line, isn’t necessarily the same as computer science.) Tricky stuff to account for.

My own anecdotal thoughts on what’s popular? (Help me out with your thoughts in the comments!)

Well, this is at least vaguely related to explaining and what people identify with… (Source: xkcd.com)

I suspect readers like things that they can grapple with reasonably easily, and ideally that they can directly relate to. By ‘direct’ don’t I mean something readers can physically touch, but something they can understand or visualise without a lot of indirect reasoning.

My suspicion is that topics that are abstract are harder to engage readers with. It’s simpler if you’re talking about an animal, a plant, a planet, something made of stuff we can all identify with. Or write about things that affect people, their moods, addictions, relationships.

So, one bias in topics might be towards the low-hanging fruit and the current topical interests (disease of the month, the latest astronomy buzz, etc.)**

That would be unfortunate, as it would leave readers with a skewed view of science, and furthermore one that doesn’t represent the day-to-day reality of working in science well either.

On that note, I like the biographical angle a few like Jennifer Rohn take. Let’s face it, if I wrote about the reality of writing a large bioinformatics application, it’d be tedious: day-to-day science work in any field is persistent stuff. That’s not to say it doesn’t have it’s daily moments, just that day-to-day you’re working to a longer-term plan.

Alternatively, another bias — more positively this time, have to end on a good note! — might be an appreciation that these writers can explain complex ideas to readers simply (and presumably accurately!) Many of the more popular writers in wikio’s top 100 have that skill.

With the balance of these two things in mind, I’d be curious to see what a survey of the specific topics showed, would it favour one over the other? The latter would be consistent with the oft-repeated statistic that the most emailed New York Times articles were “long articles on intellectually challenging topics”, including those on science.

It’ll be interesting to see where these surveys lead.

Footnotes

* Here‘s the full counts from ResearchBlogging in lazy fashion. I haven’t time to make a tidy table or pretty graph. Did I say I was being lazy? There are 20 pages per full page of articles, with up to 20 on the last page, so this rounds upward.

1. 284, Biology
2. 128, Psychology
3. 108, Health
4. 90, Clinical research
5. 73, Neuroscience
6. 50, Social science
7. 33, Anthropology
8. 27, Geo-sciences
9. 23, Chemistry
10. 21, Research/”school” (college, university)
11. 21, “Other”
12. 19, Physics
13. 13, Computer science
14. 12, Astronomy
15. 7, Engineering
16. 7, Philosophy
17. 6, Mathematics

How does science work?

Coiling bacterial DNA

Preserving endangered species – of gut microbes

Temperature-induced hearing loss

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

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.

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…)

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.

What do you use for a dictionary?

I rarely use on-line dictionaries, or dictionary aggregator sites. I almost only ever turn to these when wanting a translation of foreign-language words.

I’ll confess I occasionally exploit google’s alternative spellings as a spelling aid, when in-line dictionary look-up fails. (On Mac OS X, if you control-click a word in any text box, you get a list of actions you take on the word. If the word is incorrectly spelt, at the top alternative spellings are listed. If this can’t offer anything, sometimes I type the incorrectly spelt word into google and let it suggest alternative spellings instead. More often than not it does well.)

In place of on-line dictionaries, I use a mix of the dictionary available on my computer and the Shorter Oxford, the OED’s smaller cousin.

In my case my dictionary application is Apple’s Dictionary, a nice example of a small, focused application that does what it does well. Every complete word in the descriptions are themselves links to dictionary entries of the word. There’s a thesaurus and direct access to wikipedia. (If you leave the word selected and click on ‘Wikipedia’, the entry for that word appears.) Most times it’s enough.

For trickier words — the New Oxford American Dictionary that this is based on doesn’t have everything — I have my Shorter Oxford Dictionary to call on, a two-volume thing running to ~3800 large (~29×22cm) pages of small type. While it’s ‘Shorter’, it’s not short. Technical words, from scientific words for example, can still be a problem as even the Shorter lacks entries for many of these.

Other articles on Code for life:

To link or not to link: is that the question?

Looking for a book to read?

Coiling bacterial DNA

What is your relationship with your research notebook?

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!

Click here to view the embedded video.

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”

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.)

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)

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)

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

(Arthur Eddington)

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.

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

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.)

It seems that the judge has concluded that if embryos are “destroyed”* to make an embryonic stem cell line,** subsequent research that uses these embryonic stem cell lines, but that is not itself “destroying” embryos, cannot be funded, arguing the the sourcing of the research material and the research cannot be separated:

ESC research is clearly research in which an embryo is destroyed. To conduct ESC research, ESCs must be derived from an embryo. The process of deriving ESCs from an embryo results in the destruction of the embryo. Thus, ESC research necessarily depends upon the destruction of a human embryo.

Despite defendants’ attempt to separate the derivation of ESCs from research on the ESCs, the two cannot be separated. Derivation of ESCs from an embryo is an integral step in conducting ESC research. Indeed, it is just one of many steps in the “systematic investigation” of stem cell research. 45 C.F.R. § 46.102(d). Simply because ESC research involves multiple steps does not mean that each step is a separate “piece of research” that may be federally funded, provided the step does not result in the destruction of an embryo. If one step or “piece of research” of an ESC research project results in the destruction of an embryo, the entire project is precluded from receiving federal funding by the Dickey-Wicker Amendment. Because ESC research requires the derivation of ESCs, ESC research is research in which an embryo is destroyed. Accordingly, the Court concludes that, by allowing federal funding of ESC research, the Guidelines are in violation of the Dickey-Wicker Amendment.

This summary (I’m assuming it is accurate) lays out a brief history of events, pointing out that

Essentially, the NIH/Obama position banks on the interpretation that research done on ESC lines is fundamentally separated from the derivation of those lines.  In other words, that the Dickey-Wicker amendment does not pertain to the actual research done on derived cell lines because they define it as a separate “piece of research”.

and that it is this that the plaintiffs seek to overturn, going on to say that the court presents

[...] a crystal-clear equation of downstream research to upstream sourcing of research materials, and possibly brings up ethical dilemmas in other fields.

Either way, it is already disrupting research.

The memorandum opinion says, and as far as I understand rests upon, that the two scientists meet the “high standard for irreparable injury” if this injunction is not ruled, in this case because this “increased competition for limited funds is an actual, imminent injury” that I previously wrote about. It seems a nonsense to me, or perhaps more accurately a disingenuous excuse. (On a related note, it also says it doesn’t block ESC research groups from getting alternative funding. Wouldn’t the same logic apply to these scientists, too?)

There’s more, but you can read the full document on-line and decide for yourself.

A recent update is that the Justice department have said they intend to appeal.

For recent further reading, the New York Times features an editorial Wrong Direction on Stem Cells, as well as some words about the scientist plaintiffs.

Footnotes

* I write ‘destroyed’ in double inverted commas as my understanding is that these are derived from ‘surplus’ embryos from intro fertilisation that would otherwise be discarded. If so, they aren’t being “destroyed” in the sense that this word might imply. Others say that the definition of research used is suspect, too. (I’d go into that, but haven’t time.)

** An excellent concise description, with graphics, of how the different types of stem cells are created can be found on the University of Utah Genetic Learning Center website page Creating stems cells for research.

Other articles on Code for life:

Scientists can sue if not happy with funding priorities??

Coiling bacterial DNA

Vitamin C, swine flu, media, lawyers

Vitalism ideology in chiropractic advertising