Archive July 2011

Appeals court concludes that Myriad can patent BRCA genes Grant Jacobs Jul 30


Friday saw the US Court of Appeals for the Federal Circuit (which we’re told by the New York Times told specialises in patent cases) rule that Myriad can patent the isolated BRCA1 and BRCA2 genes, mutations in which are diagnostic for (some) cases of breast and ovarian cancers.

The three judges didn’t rule unanimously, with the ruling based on a majority. Most sources are citing a 2:1 ruling. My reading of it is that all three judges differed in reasoning.

While the ruling has sided with patenting of the genes, the judges ruled against Myriad’s method of diagnosing the patients.

Below I’ve offered a few links for those interested in this decision.

  • New York Times (brief but good; includes brief takes on the Judge’s reasoning)
  • The CAFC ruling (PDF file; this is the actual legal ruling – while long it is for the most part quite readable; I’d encourage reading Judge Bryson’s dissenting views, some of which I have excerpted below.)
  • Genome Web News (or this article; free registration required)
  • ArsTechnica (good discussion and more depth; recommended)

My thoughts? I’m not a lawyer, and this will come down to understanding how their actions sit compared to current law in the USA (something I know nothing about), but colour me surprised. Regardless of the details, I would like to think I’m not a long in thinking that the Judges not putting forward a unified front suggests a need for clarity.

The argument that genes are chemically different through being extracted seems at first blush–to paraphrase Judge Sweet’s earlier remark–’a lawyer’s trick’. It reads to me to be a shifting of the target from sequences (which are information and–surely–what is sought) to ‘chemicals’ (the DNA) in order to try win favour in court.

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Google personalised searches and the ‘echo chamber’ effect? Grant Jacobs Jul 30


(Ruminating in the wee hours on google searches and echo chambers.)

The echo chamber effect describes where a person or group who repeatedly (mainly) only hears their own views echoed back to them.

My experience of this effect at work is what I have seen from groups touting anti-vaccine views, religious ideology, or supporting particular ‘alternative’ remedies, but it applies more widely.

One effect of repeating variants on the same answer can be re-enforcing of more extreme versions of the original information, which can then be taken as the accepted view by the group.

Echo chambers and advocacy groups

Advocacy groups of all kinds encourage their followers to favour their views over the views of others. They’re advocating a particular position, after all.

The better groups engage fairly with other views, particularly if they might learn something new from them.

Some groups, however, favour excluding alternative views entirely so that their group only ’hear’ what the group’s organiser wants the group to hear.

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Science advisor position Grant Jacobs Jul 29

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The newly-formed Ministry of Science and Innovation (MSI) has advertised for a Science Advisor, who

will be a unique position in that 50% of the role will report to and work closely with the MSI Chief Science Advisor [Dr. Prue Williams] and be responsible for contributing expert independent advice on the science system to MSI including analysing information, preparing documents and liaising with others on issues of priority. The remaining 50% will be responsible for providing direct support services to the Prime Minister’s Chief Science Advisor. This will include attending meetings, liaising with other departments and preparing written material.

It seems to me that this is an interesting and possibly influential role for someone. (Of course, the Minister of Science and Innovation will have a whole other level of clout, but there is something for this being more hands-on.)

If you know someone that might serve New Zealand’s science community well, I’d be letting them know and perhaps encouraging them a little. It’d be nice to see good people in these positions.

Other articles on Code for life:

Haemophilia — towards a cure using genetic engineering

External (bioinformatics) specialists: best on the grant from the onset

Take a summer studentship in Dunedin, New Zealand

Your thoughts on the future of bioinformatics in New Zealand

Who has the most bioinformatics scientists?

Should we teach examples of scientists falling for unscientific practices? Grant Jacobs Jul 28


Not long ago I learnt of another former scientist I know of who has, apparently, fallen for pseudoscience or ‘woo’. It was a bit distressing. A lovely person, but you had to think ’good grief, why?’

With that in the back of mind my while reading blog posts and writing about this to others I got to wondering if that when teaching ‘how science works’ as part of senior high school and first-year undergraduate courses if ordinary, approachable, examples of scientists who’ve strayed, and how they strayed, should be taught too.

Perhaps it’s just my dismay speaking unreasonably and too loudly at this moment. Nevertheless, let me continue with this line of thinking as something to mull over. My thought, or I guess wistful hope, was maybe these ‘ordinary examples’ might serve to alert students to where they don’t want to end up, to where lack of introspection, critical thinking and scientific integrity can lead.

I’ve highlighted those phrases, as they’re what I want to focus on.

You might think of it this as self-reflecting on your reasoning, having the skills to think soundly and the integrity to hold up to what your criticism of your own thinking found.

Before I expand on this, I’d like to ask those who think this suggestion ‘odd’ to hold off a bit. I’m well aware this will seem a strange suggestion to some, particularly those focused on the use of the science to the exclusion of it’s lack of use or misuse. I’m not suggesting science courses or degrees need radical reworking; I’ve outlined this more in an extended footnote.[1]

It asks (first-year) university and high school science courses to face a wider brief than generating more scientists. It also asks for a full appreciation of–let’s be frank–how wide-spread non-scientific nonsense is. I don’t know about others, but I find the extent of nonsensical belief expressed in the community is overwhelming sometimes, and when I see the occasional former scientist (or even, rarely, current scientists) fall for it’s a little disturbing.

How do you enable students to recognise themselves as straying into pseudoscience, non-scientific practices, or just ordinarily sloppy thinking?

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Haemophilia – towards a cure using genetic engineering Grant Jacobs Jul 28


Science fiction has humans cured of genetic diseases by tailored re-engineering of their genes.

It’s coming closer to a reality, with a recent report on treating mice with haemophilia B by re-engineering the ‘broken’ gene in mice.

Haemophilia B

Haemophilia is an inherited genetic disorder that disrupts blood clotting.

Prince Leopold, son of Queen Victoria and Prince Albert.

Prince Leopold, son of Queen Victoria and Prince Albert.

There are two main forms of haemophilia, imaginatively called A and B, although to be fair haemophilia B is also known as Christmas’ disease after Stephen Christmas, the first patient formally identified with it.

Among the most famous patients with haemophilia B would be the male descendants of Queen Victoria, the last Russian royal family, the Romanovs. (An article from Science tells part of the story of extending the genetic analysis of identifying the remains of the murdered Romanov royal children of Russia to testing if they had haemophilia.)

Both haemophilia A and haemophilia B are genetic disorders caused by variations of blood clotting (coagulation) factor genes that result in less of the protein that the gene codes for, or a defective protein that it doesn’t do it’s job well.

The more common form is haemophilia A, caused by a deficiency in clotting factor VIII. Rarer is haemophilia B, which arises from a deficiency in clotting factor IX. (Taking the imaginative route to naming again, the genes coding for these proteins are named F8 and F9, respectively.)

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Research project coding v. end-user application coding Grant Jacobs Jul 27


Hurtling around around the tubes have been links to John Cook’s excellent short article Software exoskeletons. Relayed on some with legions of followers, it will have been widely read.

John contrasts the programming styles and objectives of two camps: ’There’s a major divide between the way scientists and programmers view the software they write.’ I encourage readers to read his piece; it’s short and well worth the thoughts it raises.

I’d like to offer a few thoughts on what he’s written.

In particular, I’m left thinking that this comes back to talking with others and thinking ahead as you design a project, before you get into the meat of it.

If an aim is to spin off an end-user application ideally this wants to be recognised and built into the project from the onset, so that the coding approach used reflects that the code later intends to be part of an application.

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Structured procrastination (#2) Grant Jacobs Jul 24


My structured procrastinations[1] consist of rummaging through the contents my web browser, relocating tabs of mostly lighter material I’ve left open that I thought that might interest my readers. It’s a potpourri, so you should find something to suit your tastes. I’ve enboldened phrases that capture each topic.

To start off on a startling note, there is this tweet from Deborah Blum who adds to a tweet that attempts to graft monkey testes onto men, to say that it didn’t work:


OK… I’m not sure I really want to know more, but a brief google gives me an on-line discussion between Deborah Blum and Professor Anne Fausto-Sterling. While talking about AndroGel and other attempts to boost–how can we put it delicately?–‘masculine performance’ (and related topics) Deborah writes:

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What genetic changes make us human? Grant Jacobs Jul 22

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Katherine Pollard sets her aim at about 2:05 into the presentation: ’we want to pinpoint the parts of the human genome that are most different [...] between humans and chimps, or other primates, and try to link these to human-specific biology.’

She talks about work by her research group finding the portions of the human genome that make us human, compared to extant species closely related to us.

Her talk has excellent slides and interesting tidbits, introducing, for example, some specific difference between humans and chimpanzees. The talk is directed at a general audience, although it will be harder going for many in the second half.

One reason it appeals to me is that it introduces a simplified version of some of the thinking that people in my field–bioinformatics, or computational biology–use in comparing genes or genomes from different organisms.

I’ve added a few words below the video that some might want to read before viewing the video; those that just want to plunge on in, here it is:

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Before installing Mac OS X Lion Grant Jacobs Jul 21


…make a copy of the installer first.

Once you download Mac OS X Lion, if you press ‘Continue’ and charge on, the installation process will remove the installer once it’s done. (This may not happen until after restarting, but I haven’t details on this.)

If you’re anything like me, you’ll want to make a copy of the installer as a backup, if nothing else to save downloading the whole thing again. You can make installation DVDs or thumb drives.

One good take on this can be found on David Alison’s blog. (Read the comments, too.)


I haven’t tried this, I’m just relaying it on in case it benefits others. I’m likely to hold off upgrading for a while as I invariably do.

For regular readers: I have longer posts in the works, but I’m waiting on tech support to put right an issue with the blog before putting them out. In the meantime all I can do is ask for your patience! I’m very sorry about this, but it’s a little out of my hands. Hopefully this will be put right sooner rather than later.

Bioinformatics: ISMB on-line Grant Jacobs Jul 19

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Over the past few days–when I’ve had time–I’ve been catching a little of the on-line feeds coming from the ISMB (the International Society of Computational Biology annual Intelligent Systems for Molecular Biology meeting).[1]

Perhaps the easiest is to scan the FriendFeed for the meeting and see what talks have generated comments. You’ll have to scan several pages back to get to the first talks–there’s an awful lot of them! The help page for blogging indicates that you can–supposedly–access the FriendFeed (FF) via the meeting schedule, but I’m having no luck trying that, so I suggest just going straight to the FF page.

You can also trying following the #ismb twitter hashtag. Of course, you’ll end up with all the different parallel sessions merged into one stream, but it still has some gems that are worth the effort. Don’t forget to select ‘All’ (to the right of ‘Tweets’ immediately above the tweet stream) if you want to see all the tweets, not just the top ones.


Please excuse the hiccup earlier tonight; with any luck normal service will have resumed…

I’ve no idea if the talks are being recording to be presented later as on-line videos.

1. I’m not keen on the name of the meeting – it feels like a flashback to meetings focused on the AI approach; the current meetings have a far wider brief.

Other articles on Code for life:

(The links below have been lost, presumably as a consequence of tech support’s effort to correct an unrelated problem. I’ll try restore this soon.)

Retrospective–The mythology of bioinformatics

Developing bioinformatics methods: by who and how

Who has the most bioinformatics scientists?

The Roots of Bioinformatics in Theoretical Biology

On alternatives to academic careers and ’letting go’

Reproducible research and computational biology

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