Archive March 2010

International teamwork: Anthony Doesburg on collaborations Grant Jacobs Mar 22


I’d like to point readers to Anthony Doesburg’s article in the NZ Herald on international collaborations in science. This article introduces a local perspective to the Royal Society of London’s recently announced initiative to ’map and analyse where, why and by whom science is being carried out around the world, and how this is changing’. The results to be released in November this year.

Doesburg writes:

The modern collaboration tool is the data network, the most common of which is the internet. Smith thinks the web is lifting the standard of science by increasing international collaboration,

I agree, but I’d add that collaborations also rely on trust and people who have the wherewithal to make collaborations happen. I believe that despite this face-to-face meetings help. Video conferences can offer this, as his article says, but I’d be interested to hear if readers consider this a true replacement for, say, meeting through an arranged lab visit or day to one side of conference.

As an aside an interesting claim in the article is that each dollar invested in KAREN yields four in return. (It makes you wonder if the local plan by a group of businessmen to establish a direct fibre link to the USA and Australia read that!)

Readers are welcome to share their thoughts on international collaborations, networking (both computer and social) and ’all the rest of it.’ It’s an open-house in the comments!

HT: @KARENnews. (@KARENnews is the twitter newsfeed for the KAREN network; KAREN=Kiwi Advanced Research and Education Network).


Another form of networking that blends both the use of the internet (or WWW) and social networking are the science-oriented networking software or websites. It would be interesting to hear of people’s experiences in using these for generating or maintaining collaborations.

Epigenetics, a confused muddle in the media Grant Jacobs Mar 22


Guardian features writer Oliver Burkeman leads the on-line science section with a piece titled ’Why everything you’ve been told about evolution is wrong.’


DNA (unmethylated). Source: wikipedia.

It’s caused something of a fuss amongst some in science writing circles, with replies by Adam Rutherford and Jerry Coyne.

Reading these replies and the comments below them you’d be forgiven for thinking that some think it ought to be titled Why everything you’ve been told about evolution by Oliver Burkeman is wrong.

Personally I find his article well meant, but muddled and approached the wrong way.

There’s the title, which is not ’provocative’, but wrong. At the time of NewScientist’s ’Why Darwin was wrong about the tree of life’ cover title debacle, I ruminated that titles that seek attention through stating falsehoods, are best immediately corrected in the initial portion of the article. If they are not corrected immediately and firmly, they mislead.

In Burkeman’s case, I feel the title rather than serving as a teaser has readers falling back to it thinking ’that must be want he means’ when confused. Burkeman didn’t write the title, but it sets a position for unclear statements that don’t do him any favours.

His article draws from several popular science books, in particular Fodor and Piattelli-Palmarini’s What Darwin Got Wrong.

Burkeman’s biggest mistake, I think, is that he speaks for himself rather than representing the views of others, as it more usually the case in newspaper articles.

He indicates that he lacks scientific background on this topic and I think he would have been wiser to acknowledge this to himself better and not present his reading of what these authors mean but instead interviewed accepted specialists in evolutionary theory and epigenetics and present what they say.

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Bioinformatics blog carnival Grant Jacobs Mar 21

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I have been belatedly alerted to the first edition of the bioinformatics blog carnival.

"Code Monkey" (Source: wikipedia)

"Code Monkey" by Jawbone Len (Source: wikipedia)

For the uninitiated, blog carnivals are efforts to promote interest in a particular area through publishing a monthly (fortnightly, weekly) ’carnival’ collecting the better works from a call for submissions by bloggers in that area. Broad areas like science as a whole are well represented, specialist areas less so. This is the first carnival I’ve run into specifically for bioinformatics (but then I haven’t tried hard…)

The permanent home page for the bioinformatics blog carnival provides a form to offer submissions and contact form to reach the organiser, Iddo Friedberg. (Don’t you just hate the background pattern for blog hosting page!) More detailed instructions can be found on the call for submissions to the first carnival.

Sections included are Programming, Databases, Genomics and Structural Biology.

I’m particularly pleased to see the Structural Biology section, as this is ’home turf’ for me, one that to my huge frustration I don’t get to use enough.

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New internet meme: google suggestions for scientists Grant Jacobs Mar 19


I’m sure this will become a new internet or blog meme.

Bioemphemera (aka Jessica Palmer) has a post describing the top google suggestions for ‘are scientists’ and ‘do scientists’, shown using a lovely infographic. Do check it out.

When you type in a phrase, google offers the most frequent completions for the phrase. I get slightly different results to Jessica. Atheism ranks higher in ‘are’, but like her, global warming tops evolution in ‘do’. Being lazy, I’m just going to just use cut’npaste from my screen (shame on me…):


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Sources for medical information for non-medics and non-scientists Grant Jacobs Mar 18


A recent up-swing locally in credulous claims about vaccines and the diseases they address has prompted me to list a small number of resources that I have found to have readable explanations of medical information for non-medics and non-scientists.

My lists are not complete or ’definitive’, nor do I claim to be some authority on things medical. I’m just sharing a few sites I have used in the hope that they are useful for others who want find medical information. I have not listed sites that deal with medicines per se; these sites are focused on diseases.

Don’t forget that your best source of information is your registered medical practitioner.

(I emphasise registered medical practitioner to distinguish them from those offering ’natural remedies’ and those whose style themselves as doctors but are not in fact registered practitioners.)

Useful medical information websites

Others are welcome to recommend other sites in the comments below. The links are on the title of the sources.

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Medical DIY… Grant Jacobs Mar 18


You know how the classic scene goes. Naïve ambitious husband describes his Do-It-Yourself plans… and ‘skills.’ Wife stands there, wordless, with ever-widening eyes forecasting a disaster.

(Source: Wikipedia.)

(Source: Wikipedia.)

That’s how precisely researchers and medics feel watching non-medics and non-scientists determined to ’do it their way’ on things that affect others’ lives.

Sure, a few will genuinely do well. A rare few.

Most really should be honest and admit they haven’t the skills, or, realistically, the time to learn to become good at it.

Civilisations are built on an acceptance of division of labour. Builders know how to build sound structures so that your house doesn’t crash around your ears in a storm. Electricians know how to wire things up without zapping everyone to kingdom come. Plumbers know how to fit pipes that don’t create a lake in your living room. (Well, most of the time!) GPs know how to diagnose and treat the more frequent disorders, and a few besides (but they refer to specialists to for things out of the ordinary; they know when to pass the buck onto the better (wo)man).

Don’t fight it. Division of labour is there to get the best out of each area of knowledge.

Fighting it and trying to ‘do it yourself’ without the training and experience is like the household DIY thing: maybe OK for very minor things; dodgy for even modest things; and downright silly for everything else.

You or your family’s health is worth a bit more than DIY set of shelves or light fitting, right?

Anyone who claims that in a few hours or weeks or even months of study they are able to speak more authoritatively than someone who has spent years (or decades) of full-time study on a subject has got to be kidding themselves.

This isn’t just about medical research. It applies to everything. Building, electronics, cooking fine cuisine, motor mechanic, competitive sport, whatever.

Don’t be a DIY idiot.


Just in case anyone gets the wrong idea, this is not trying ‘bash’ anyone! I’m just trying to express the feeling of watching people try their hand at something they haven’t the background to do.

This was written thinking of those people trying to ‘out research’ the medical and medical research community. It’s good to see people trying to learn, but until they are at comparable level and have gotten past the ‘goofy error’ stage (let’s admit it, we all made goofy errors early on in whatever we’re now good at!) it’d be wiser to rely on those with experience and training.

Other recent articles on Code for life:

Simon Singh, leaving job to deal with chiropractic legal case

Molecular biology in museums

An horrific case of natural health treatment of cancer

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

Homeopathy check-up: Not in the health system, disclaimers on labels

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

Too much attentiveness leads to inattentiveness Grant Jacobs Mar 17

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Some time ago I presented a video illustrating change blindness (see Visual illusions, change blindness and autism). A related effect is inattentiveness, as featured in this short (1:22 min) video:

YouTube Preview Image

Then watch this for an explanation:

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Simon Singh, leaving job to deal with chiropractic legal case Grant Jacobs Mar 13


Science writer and journalist Simon Singh, who faces a libel suit from the British Chiropractic Association (BCA) for writing that a number of chiropractic claims of treatment of disorders unrelated to the spinal cord such as asthma were ’bogus’ has written in his column that it will be the last. He is resigning his job in order to give the libel suit the BCA has served on him full attention.

Simon Singh (Source: wikipedia)

Simon Singh (Source: wikipedia)

I recently pointed out an extensive review of the evidence for and against chiropractic treatment that showed that the claims that Singh objected as unsupported, are unsupported.

Another survey of the research literature for chiropractic treatments, that of Ernst (available free from the British Medical Journal), has an extensive collection of follow-on letters. The author, replying to the early letters, points out that neither his article nor the libel case are about safety; in moving onto safety in his reply, he concludes: ’Applying the precautionary principle, one should therefore not recommend chiropractic but warn patients not to use this form of therapy.’

Surely any sincere business would respond by simply pointing to evidence backing their original claims. Not so the BCA. The BCA was offered an opportunity to write a rebuttal in the Guardian (the newspaper that published Singh’s original article), but declined, seemingly preferring to legally bludgeon the writer, rather than reaffirm readers of the accuracy of their claims and the validity of the particular chiropractic practices referred to. (Or withdraw them.)

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High speed international connection? Yes, please Grant Jacobs Mar 11


Announced just a few hours ago, for me via KAREN on twitter, is an initiative to build a high-speed direct internet connection linking New Zealand, Australian and the U.S.A.

pacific-fibre-mapAlthough the Pacific Fibre website is short on technical details, it does a great job of conveying the essence of the idea simply. Some details are available on their news blog, e.g.

The current proposed cable configuration would be 13,000 km long, and have two fibre pairs with 64 wavelengths (lambdas) each at 40 Gigabits/sec per lambda. The maximum lit capacity initially would be 5.12 Terabits/sec, but would be upgradeable to over 12 Terabits/sec as the emerging 100 Gbit/sec per lambda technology becomes reality. The newer cable and repeater technology that Pacific Fibre proposes to use will be substantially more easily upgradeable than that of existing cables.

pacific-fibre-model-2010They say they aim to have this ready for 2013 and that it is expected to cost around $NZ900M. Whatever the details, I am sure this will have internet users in NZ talking for some time and hatching new business plans. (For example, it would be interesting to learn if this would affect the idea that NZ can act to exploit that it is ~12 hours out of cycle of most of the bigger Western nations to deliver overnight service efficiently.)

pacific-fibre_model-2011It has been noted that those academic researchers whose data transport problems are solved by KAREN, a new network may not be needed. (From what I understand KAREN still has plenty of capacity: anecdotally I’ve heard figures of 5-10% of capacity being used. Viewing their excellent near-live ’weather map’ is worthwhile, try it.)

For those who need fast networking outside of this high-speed academic network, which is most of us, I’m sure this initiative will be widely viewed very positively. It is great to see people taking the lead on these things and pushing for it to get done.

pacific-fibre-model-2012For my personal situation, I need to learn more about it first: my position is more complex as in principle I can gain access to the large databases I use through other means, but being able to deliver large volumes of data may open up new opportunities for me.

Interested readers can follow the Pacific Fibre twitter discussion. Here are a few replies that might be worth others’ reading (comments in square brackets are mine):

  • @kuahyeow Current estimate is under $900m [I presume this is in response to an estimate for the costs.]
  • RT @ronanq: Best of luck. Great fibre connections is one of the reasons Google, Amazon, Paypal, Microsoft, Facebook and IBM are in Ireland
  • @sam_DPS we will sell to ISPs and major corporates. We are aiming for prices which will let them fulfll the uncapped high speed mandate
  • @samfarrow just international – we are focussing on just that one part of the problem. Others are working on the rest.
  • RT @Pete_Robson:As a former “Senior Product Manager” of the current SouthernCross Cable, I can safely say that there’s $ in that Awesome job

Peter Griffin, writing at idealog, has more detailed coverage.

Upcoming popular lectures by Professor Lawrence Krauss Grant Jacobs Mar 10


The Psychology Department of the University of Otago is sponsoring two talks by leading physicist Professor Lawrence Krauss next week. If you’re in town, be there!

prof-lawrence-krauss-200pxAmong his popular science books are Hiding in the Mirror (2005) and The Physics of Star Trek (1995). Hiding in the Mirror is subtitled: The Quest for Alternate Realities, from Plato to String Theory (by way of Alice in Wonderland, Einstein, and The Twilight Zone), which will give readers a better idea of what it’s about!

Don’t be mislead by this to thinking he is a lightweight populist, he’s a serious physicist who has received many awards. According to wikipedia and his on-line biography he is ’the only physicist ever to have been awarded the highest awards of all three major US Physics Societies’.

He is also a recognised science publicist, with his awards noting this in alongside his physics contributions. With the credentials he has in science communication, I have no doubt that he will be an excellent speaker.

Below are the blurbs for the two lectures cut’n’pasted from the advertising poster (with permission):

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