Archive May 2010

Martin Raff on what is autism Grant Jacobs May 31

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The open-access scientific journal BMC Biology is currently hosting an interview with Martin Raff, presenting his responses to questions about autism. Prof. Raff gives the background in simple form well.

A neurobiologist with an excellent scientific pedigree Professor Raff did not study autism during his research career, but became interested in it after he retired when his grandson was found to be autistic.

BMC Biology has placed a copy of their interview in two parts on YouTubeâ„¢, which I have included below. A transcript of the interviews can be found on the BMC website for those that prefer to read it rather than listen. There are references to further reading at the end of the transcript.

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Sunday reading – mental time warps, treating OCD, bio banking, All Whites beat Serbia Grant Jacobs May 30

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Neurophilosophy sits in my blogroll for it’s constant supply of excellent stories about intriguing topics of the mind. Apparent motion steers the wandering mind tells of research indicating that motion, forward or backward, prompts the mind to think of the past or future. Perceived motion acting as a sort-of mental warping device? You be the judge.

Joseph Calamia gives an excellent summary of a research paper in Cell in his article Obsessive-Compulsive Mice Cured via Bone Marrow Transplant over at 80 beats. This isn’t a call for bone marrow transplants for those suffering OCD, but it is a wonderful example of thinking about the whole animal (mice in this case), molecular biology and intervention (treatment).

Sunday should be a time for long pieces on interesting topics, right? At Wired magazine, Libraries of the flesh, discusses storage of tissues samples similar to the national melanoma tissue bank planned in New Zealand to store surplus tissues from melanoma diagnostic samples as a base for research studies.

Well off the subject of science, I’d like to congratulate the All Whites football team for their victory over Serbia, ranked 15th in the world, in a World Cup friendly. Neither side was at full strength, with Serbia leaving some top players on bench and New Zealand with one injury and one with a prior engagement. (His wedding!)

I’m frustrated that there is no free-to-air television coverage of these warm-up matches. Written coverage is available in New Zealand and Serbia (the latter more balanced, and with a better understanding of the sport IMO). The game featured the on-field captain trying to calm fans as the Guardian report highlights. I don’t think I’ve ever seen that before.

Professors, lost souls with great oratory power? Grant Jacobs May 29


As I sit here, looking out into the damp grey twilight, a younger Leonard Cohen is lamenting that ’all the rain falls down on last year’s man.’

It’s been raining for five days now and it almost seems as if it will go on forever. The news is full of floods and slips in my area.

(Source: Open Library.)

Last night I started Kostova’s The Historian.

In it the protagonist’s father tells a story, in which he describes a lecture given by a Professor Rossi:

… This semester he was giving a course on the ancient Mediterranean, and I had caught the end of several lectures, each brilliant and dramatic, each imbued with his gift for great oratory. Now I crept to a seat at the back in time to hear him concluding a discussion of Sir Arthur Evan’s restoration of the Minoan palace in Crete. The hall was dim, a vast Gothic auditorium that held five hundred undergraduates. The hush, too, would have suited a cathedral. Not a soul stirred; all eyes were fixed on the trim figure at the front.

Rossi was alone on a lit stage. Sometimes he wandered back and forth, exploring ideas aloud as if ruminating to himself in the privacy of his study. Sometimes he stopped suddenly, fixing his students with an intense stare, an eloquence gesture, an astonishing declaration. He ignored the podium, scorned microphones, and never used notes, although occasionally he showed slides, rapping the huge screen with a pole to make his point.  Sometimes he got so excited that he raised both arms and ran partway across the stage. There was a legend that he’d once fallen off the front in his rapture over the flowering of Greek democracy and had scrambled up again without missing a beat of his lecture. I’d never dared to ask him if this were true.

The character is a historian, not a scientist, and from another age – it’s not stated (yet), as far as I recall, but somewhere in the 1930s perhaps – and this is fiction.

Several movies and books seem to use this motif, the lost obsessive soul with powerful oratory presence.

It makes me wonder what is the image of a professor to those who have never been near universities, who’ve never met a professor.

Is this depiction friend or foe? Or just accepted as fiction?

Other articles in Code for life:

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

Career pathways for NZ science Ph.D. students

Explore ancient science books on-line

Royal science

I remember because my DNA was methylated

I remember because my DNA was methylated Grant Jacobs May 29


Our memories keep our yesterdays, our friends’ faces, the distinctive smell of previous partners, if we’ve read that book before, what clothes you wore to the party.

in_search_of_memory_movie_posterMovies and books have been written about memories. Or the trials not being able to keep them.2

Poets and lyricists evoke them, talk about them and reminiscence over them: ’Preserve your memories, they’re all that’s left of you.’ (Paul Simon, Old friends/Bookends.)

Is DNA methylation what preserves your memories?

Among neurobiologists are some looking for the basis of memory, how is it that neurons (nerve cells) record an event, a smell, a sight? We know they do, but how?

DNA methylation is one of several ways to control the state of a gene, if it is able to be used or not. Regulation of the state of a gene might be used to define a pattern of responses to signals in a neuron, that can then represent part of a memory.

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Book sales, frumpy readers, and mental rotation of book titles Grant Jacobs May 27


Last Friday I attended the 30th annual 24-hour book sale at the Regent Theatre, Dunedin, held to raise funds to maintain that glorious old place, all red seating with the lolly-decorated proscenium arch and pillars of an older era. Books are donated, collected and sorted by volunteers and ’sold’ to the punters.


(Source: Wikimedia Commons. Slightly pixelated on reduction.)

It starts at noon Friday and proceeds through the night until noon Saturday with live entertainment on the stage.

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Vote for the Quarks (science blogging awards) Grant Jacobs May 26


Get your votes in for this year’s science blogging Quark awards.

three-quarks-prizeYes, there is cash on offer.

Yes, you can nominate your own blog post.

They only take the first 200 nominations accepted, so get moving.

Please read the rules carefully! No excessively long posts, only from the last year, nominate one post only (note: post, not blog), etc.

This is a two-step process. Nominations are collected until midnight (NYC time) May 31st. Public voting follows.

I’ve listed my own more substantial posts below horizontal rule if readers feel any I’ve written are up to it.

Also worth reading are the thoughts of Professor Steven Pinker, who judged this prize last year, on selecting winning essays:

The best science essays give readers the blissful click, the satisfying aha!, of seeing a puzzling phenomenon explained. When I was a graduate student the antiquated plumbing in my apartment sprang a leak, and an articulate plumber (perhaps an underemployed PhD) explained what caused it. When you shut off a tap, a large incompressible mass moving at high speed has to decelerate very quickly. This imparts a big force to the pipes, like a car slamming into a wall, which eventually damages the threads and causes a leak. To deal with this problem, plumbers used to install a a closed vertical section of pipe, a ’pipe riser,’ near each faucet, . When the faucet is shut, the water compresses the column of air in the riser, which acts like a shock absorber. Unfortunately, gas under pressure is absorbed by a liquid. Over time, the air in the column dissolves into the water, which fills the pipe riser, rendering it useless. So every now and again a plumber has to bleed the system and let air back into the risers, a bit of preventive maintenance the landlord had neglected. It may not be the harmony of the spheres, but the plumber’s disquisition captures what I treasure most in science writing: the ability to show how a seemingly capricious occurrence falls out of laws of greater generality.

Struggling in a typical moment of self-doubt (I seem to live permanently in these), I don’t think my work is up to the high standards Pinker is looking for but I’ll let others be the judge. It’s not as if I have much choice on that!

Please do nominate my fellow scibloggers, too. You know where to find them.

Below are some of the more substantial post on Code for life over the past year. Looks like I’ve been busy!

Monkey business, or is my uncle also my Dad?

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

Aww, crap.

Popularity does not mean effectiveness or sensibility

Deleting a gene can turn an ovary into a testis in adult mammals

GMOs and the plants we eat: neither are ’natural’

Testing common ancestry to all modern-day life

You can change the ideas, but not the data

Tracking disease and human migration through genetics

Rubella, not a benign disease if experienced during early pregnancy

All this talk about 3-D movies and TVs is depressing

Media thought: Ask what is known, not the expert’s opinion

Epigenetics, a confused muddle in the media

Retrospective–The mythology of bioinformatics

Science communication shorts Grant Jacobs May 25


For my science communication readers:

A collection of science communication articles are being shared on Mendeley. I need to look into this more (another post to write…), but this may be a good way to share science communication research. It’s a small start so far (only 36 articles as I write), but contribute and it may grow. (HT: @bengoldacre)

Jennifer Ouellette, Director of the Science and Entertainment Exchange set up by the US National Academy of Sciences to encourage interactions between Hollywood and scientists, has a video up about some thoughts on scientists criticising or advising on movies:

YouTube Preview Image

A Pew Research Centre survey of the blogosphere (New Media, Old Media) notes that science is the third most-frequent topic in blogs posts, representing of 10% of blogs posts, but makes up only 1% of traditional media stories. (HT: @BoraZ.) There are wide range of other statistics presented that may interest those wanting to understand the ’makeup’ of the blogosphere and traditional media.

Pharyngula has hit a million comments. Enough said. (Pun intended. Too good to resist…)


I do have a few substantive posts on the way. Some are held up waiting for permissions to clear, others for time to fill in the gaps. Now if only I could invent a ’more time’ device. Hermione had one, didn’t she?

Other articles on Code for life:

More science in literature done right

Scientists’ other lives

Replying to the editor, in sign

Synthetic genome in living cell round-up: the good, the bad and the ugly

Testing common ancestry to all modern-day life

Brevia – Wakefield saga continues… struck off Grant Jacobs May 24


Andrew Wakefield, the doctor behind the MMR-vaccine scare, has been struck off by the UK’s General Medical Council. While this forbids him from practicing in the UK, he has lived in the USA for the last several years. (Reports say that the ruling does not affect his ability to practice medicine outside the UK.) He previously resigned (or was removed) from his position in Thoughtful House in the USA and has had his controversial research paper retracted, with another withdrawn. The Times Online has a timeline of events spanning over the 12 years of this on-going story.

As others point out, this is unlikely to be the last we will hear from or of him. Latest reports include media interviews and him providing the ‘keynote’ speech for anti-vaccine rally.

Previous articles on Code for life on the Wakefield saga:

Has Andrew Wakefield resigned from Thoughtful House? (Updated)

Another Wakefield paper pulled?

Lancet formally retracts Wakesfield paper

eWeather in NZ Grant Jacobs May 24


Here in New Zealand we’re experiencing a bout of wet weather. MetService is NZ’s go-to place for weather information. It can show you the weather six ways before Sunday,* and a whole lot more.

rain-radar-2pm-mon-24-may-2010Some time ago I wrote about electronic warnings of geological events. GeoNet’s services are excellent, but MetService is no slouch in the e-services department either.

Those that haven’t explored the MetService website, do. It’s got a great range of weather maps, satellite images, forecasts, hourly rain radar images (like the one shown on the right), information on the national parks and ski fields, marine forecasts, … Go and get lost in it all.

Today it was pointed out to me that you can get email alerts to weather warnings via the NZ MetService. Registering for the email service is as easy as entering your name and email address, select the warnings you want from the long list on offer and you’re done.

They also offer mobile services, both for browsers and as texts. You  can also follow them on twitter.

Now you’ve got no excuse not to check the weather before heading out!

They even have a blog that features explanations of weather science, usually with a topical angle. One recent article explains how the MetService provides one of nine Volcanic Ash Advisory Centres (VAACs) world-wide; another covers thunderstorms, featuring their lightening strike recordings. Check it out.

HT: @five15design, for the tweet on the email feeds.

*It’s Monday as I write.

Other articles on Code for life:

Synthetic genome in living cell round-up: the good, the bad and the ugly

Testing common ancestry to all modern-day life

Career pathways for NZ science Ph.D. students

Career motivations (video)

A plastic ocean

Synthetic genome in living cell round-up: the good, the bad and the ugly Grant Jacobs May 24


As everyone will know by now, a team headed by Daniel Gibson from the J. Craig Ventor Institute have reported the ’Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome.’

In our little corner of the ’net, I’ve previously pointed to commentary by other scientists (as has Peter Griffin, using other sources) and the TED talk with Craig Ventor presenting the subject is up for your viewing.

Like Carl Zimmer–and countless others–I too feel it’s besides the point of

my doing a big post today, when you [Jerry Coyne] and so many others have laid out all the issues so clearly? Sometimes I feel like the blogosphere doesn’t need any of us in particular. There will always be so many bloggers to handle any subject…

A story this big has everything. The Good, the Bad and the Ugly, all in one tangled-up mess.

Worthwhile accounts. Before diving into the more dubious things, a few of the better accounts are worth pointing to (one by a synthetic biologist). Those wanting more depth might like Elizabeth Pennisi’s summary in Science or Jerry Coyne’s question and answer format.  There will be many, many more.

Direct communication efforts. At Reddit, you can ask questions of members of the research team.

Then there are…

Doomsday scenarios. Britain’s Daily Mail declared we’re all going to die. Actually the long headline ends ’but could it wipe out humanity?’ ’Michael Hanlon, Science Editor’ head written under the headline ’Has he created a monster?’ Sigh. But that is the Daily Mail for you…  (Hat tip to Richard Grant.)

Catholic remonstrations. The Vatican were quick in putting forth their views. This also featured on Yahoo! News, drawing, at the time of writing, over 1,700 comments.

Embargo breaks. The Embargo Watch blog has the story of an embargo breach on this news. (Note informative comment.)

White House ethics study commissioned. This isn’t bad per se but the speed at which it has been commissioned reads like a knee-jerk response. Perhaps the American public needs more pacifying than those of other nations? Read The White House Blog’s report ’Synthesized DNA and the Presidential Commission for the Study of Bioethical Issues.’ In a letter to Dr. Amy Gutmann (PDF file), the  Barack Obama reassures her that there will be a study commissioned into the ethical issues.

Other articles from Code for life:

Testing common ancestry to all modern-day life

Career pathways for NZ science Ph.D. students

Scientists’ other lives

Aww, crap.

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