Archive March 2010

Myriad Genetics patent of BRCA (breast cancer) genes denied Grant Jacobs Mar 30


Myriad Genetics face a judicial ruling against their patent of the BRAC1 and BRAC2 genes.

Solution structure ensemble of BRCA1/BARD1 RING domain heterodimer. Brzovic, Rajagopal, Hoyt, King and Klevit Nat. Struct. Biol. 8:833 (2001) (Source: PDB.)

Solution structure ensemble of BRCA1/BARD1 RING domain heterodimer. Brzovic, Rajagopal, Hoyt, King and Klevit Nat. Struct. Biol. 8:833 (2001) (Source: PDB.)

Judge Sweet presented this as to centre around the issue,

Are isolated human genes and the comparison of their sequences patentable?

(Isolated here means ‘extracted in pure form’.)

His ruling goes on to say,

It is concluded that DNA’s existence in an “isolated” form alters neither this fundamental quality of DNA as it exists in the body nor the information it encodes. Therefore, the patents at issues directed to “isolated DNA” containing sequences found in nature are unsustainable as a matter of law and are deemed unpatentable subject matter under 35 U.S.C. §101.

The full ruling is available on-line as a PDF file. (165 pages.)

To my hurried reading, the Judge Sweet has indicated, no, isolated DNA sequences may not be patented just because have been isolated. Read widely this may have implications, not just for Myriad’s patents on the BRAC1 and BRAC2 genes, but for many other applications.

Chromosomal location of BRCA1. (Source wikipedia.)

Chromosomal location of BRCA1. (Source wikipedia.)

I haven’t time to explore this in detail unfortunately–the ruling runs to 156 pages!–so I welcome comments elaborating on my rushed presentation of this news. The ruling mentions a “partial grant”, so I would guess there’s details to be considered too. (Interested readers find Google News a useful source for further stories on this.)

Patently of gene sequences has been deplored by biologists and many others. It would be excellent to think that this might be the beginning of the end of what many see as legal nonsense. (The judicial ruling outlines how the use of ’isolated’ is used in what others perceive as a ’lawyer’s trick’ to get around ’the prohibitions on DNA patenting of the DNA in our bodies’ in the introduction.)

An interesting take on the patent posted earlier this month, points to a paper by Kepler et al who point out that read literally this patent would cover most genes, never mind just the BRCA1 gene. (The patent claims for ’at least 15 nucleotides’ of the BRCA1 gene; most genes would contain 15 nucleotides that matched.)

HT: Many people via twitter.

LHC ready to rumble . . . Grant Jacobs Mar 30


How many computer screens does one physicist need? (Source: CERN)

How many computer screens does one physicist need? (Source: CERN)

News from CERN (European Organisation for Nuclear Research) is that the Large Hadron Collider, better known as the LHC, is to take is first attempts at it’s designed highest energy levels, 7 TeV, tomorrow (March 30th). Links to a press release, videos and a live webcast from 8:30 to 18:00 CEST (Central European Summer Time), are available the CERN’s public site. (There is also a page of photos of physicists in the control room. The photograph to the left is of only one part of the room.)

I’m too busy to write anything original, sorry. Hopefully I’ll be more active later in the week.

Aww, crap. Grant Jacobs Mar 28


D’em shrews have shat in me again.

(Souce: ; image credit: .)

(Souce: Clarke et al, 2009 ; image credit: Chien Lee.)

Botanist Dr. Charles Clarke (Monash University, based at Monash’s Selangor campus) has published two research papers showing that the pitchers of mature pitcher plant Nepenthes lowii are opportunistic toilets rather than predatory traps.

Carnivorous pitcher plants typically have waxy interiors and other devices in their pitchers and narrow entrances to traps ants or other insects.

Insects are rare in the mountainous habitat of some pitcher plants, like Nepenthes lowii from Borneo and Sarawak. The carnivorous features typical of other pitcher plants are absent in mature Nepenthes lowii and the entrances to the pitchers are broad and open. (Juvenile plants have pitchers growing from ground level that are more typical of the carnivorous species and trap insects. It is the mature plants with their aerial pitchers that were studied.)

While Dr. Clarke had previously reported not observing rodents or invertebrates (insects) trapped in these plants’ pitchers, but observing animal droppings, suggesting an association with animals rather than insects.

In addition to the pitchers, these plants grow a ’lid,’ with glands that exude nectar.

Dr. Clarke’s research showed that these lids where the right size and geometry so that if a shrew were feeding on the nectar, it’s butt would be appropriately placed to defecate into the pitcher.

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Congratulations C.K. Stead! Grant Jacobs Mar 27

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In writerly (and readerly) news, New Zealander and long-time author C.K. Stead has won the inaugural Sunday Times EPG Private Bank Short Story Prize, worth £25,000 (a little over $NZ50,000).

His winning entry was selected from six short-listed entries from a long-list of 20, from 1152 entries. The long-list includes several established writers, among them Rose Tremain. (The full long-list is available on the Times website.)

Looking at the age range of the long-listed candidates, 28 to 78, it is perhaps fitting that one of the oldest entrants is the winner.

Prior to his retirement, Christian Stead was a Professor of English at the University of Auckland. His former students and colleagues will no doubt be delighted.

It’s a fine achievement.

Bioinformatics S.O.C., Not Exactly Rocket Science moves, pop science book writing Grant Jacobs Mar 27


Ed Yong’s popular science blog, Not Exactly Rocket Science, has just moved to a new home at the Discover magazine blogs. Another newcomer there is Razib Khan’s Gene Expression, also formerly of

Do I perceive a perceived hierarchy of science blogs? Lone riders, smaller collectives (like sciblogs),, with the Discover blogs currently being perceived as the pinnacle by some bloggers?? (I emphasise perceived as I don’t really believe in this sort of thing, one of my favourites–Mystery Rays From Outer Space–stands on its own and I know it’s not alone in that.)

The Open Bioinformatics Foundation is participating the Google Summer of Code.

As Google’s Summer of Code page explains, the ’Google Summer of Code is a global program that offers student developers stipends to write code for various open source software projects.’ If this sounds like your thing, head over there to read more about it, and check out the project ideas on the OBF’s Google Summer of Code page.

Laelap’s (Brian Switek’s) popular science book writing series continues! I’ve previously written about the earlier instalments. The fourth–and final–instalment is So you want to write a pop-sci book, Part 4: Getting the word out. All products need marketing, books are no exception… Head on over to pick up the series if you haven’t already (see my earlier post for additional sources) and join in the discussions.

Other posts on Code for life:

Friday picture: molecular modelling of the cytoplasm

Prince or pauper? Tell Nature what you earn

International teamwork: Anthony Doesburg on collaborations

Developing bioinformatics methods: by who and how

Friday picture: molecular modelling of the cytoplasm Grant Jacobs Mar 26


A very striking image features on the cover of the March 2010 of PLoS Computational Biology (below), showing a molecular simulation of the interior of the cytoplasm of the bacterium Escherichia coli.

Source: PLoS Computational Biology; image credits: Elcock

Source: PLoS Computational Biology; image credits: Elcock, University of Iowa.

One of the things that has impressed me as important to understand molecular biology is a need to understand how molecules work within the very dense of the interior of a cell.

’Test tube’ studies of molecules–properly termed in vitro studies (literally, in glass) as opposed to in vivo studies (literally, in life)–are usually in very different conditions to the crowded conditions found in the interior of the cell the molecules being studied came from.

The research associated with this figure reports one of a small number of attempts to examine the impact of crowding effects inside the cells on the behaviour of proteins.

The authors based their model on the 50 most common molecules found in the cytoplasm of E. coli. The molecules in a mixture of green and yellow are RNAs (ribonucleic acid), the others are proteins.

They show that their model matches reasonably well with in vivo measurements of the diffusion rate of a fluorescent ’marker’ protein (the popular cell biologists‘ work horse GFP, green fluorescent protein, which won the 2008 Nobel Prize for Chemistry). Likewise, the thermodynamic stabilities of the protein studied are comparable.

This work points to a promising future of detailed molecular simulations of large collections of molecules aimed at understanding the behaviour of molecules in these conditions.


Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

McGuffee and Elcock, PLoS Computational Biology 6(3)694 (2010).


Other articles in Code for life:

Bioinformatics blog carnival

Prince or pauper? Tell Nature what you earn

Developing bioinformatics methods: by who and how

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

Retrospective–The mythology of bioinformatics

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

Bioinformatics — computing with biotechnology and molecular biology data.

Writing a popular science book; links and writers’ warnings Grant Jacobs Mar 25


I had been meaning to write about the series of articles in Nature on science writing for some time, hoping to tack Laelaps & colleagues series about popular science book writing on to this. Unfortunately just as I was to start it I was scooped! What I get for procrastinating…

In it’s place I will present a slightly longer list of popular science book writing links and some thoughts juggled into some sort of order.

(If you just want the main list of posts without the writers’s warnings pre-amble, skip down to Anyway, that list… There’s good links before then though…)

David Winter mentions Cornelia Dean’s advice not to write unless you can’t help yourself. I’ve seen that advice before. It seems it’s often repeated!

I had no luck relocating the source, but I first saw it an anthology of writers thoughts’ on writing. The guy’s piece started along the lines of asking if the reader wanted to write, then saying ’Don’t.’ It asked the same question again, with the same reply. And a third time, answering with words to the effect of ’well, go ahead, you’re beyond helping.’

Likewise, in October I quoted from the introduction to Best American Science Writing 2009. In it editor Natalie Angier offers a response to enquiries from inspiring science writers:

Dear Reader, you want to be a science writer? Have you lost you carbon-based buckeyballs? [...]

Although she is writing about science writing more in the sense of magazines and newspapers, and in the light of the rounds of redundancies, I imagine she’d be just as forceful if a correspondent mentioned book writing.

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You can change the ideas, but not the data Grant Jacobs Mar 24


Not too long ago I attended Lawrence Krauss speaking in Dunedin. Others here have written reviews of Lawrence Krauss’ talks in Dunedin (David Winter at The Atavism) and Auckland (Fabiana Kubke at Building Blogs of Science).

prof-lawrence-krauss-200pxAfter the talk, having not much else to do, I sat for for some time watching Lawrence respond to younger audience members who’d gathered around him. Many (most?) of these seemed to be religious people who choose not to speak up during the questions (too timid, perhaps?), but who wanted to argue with him afterwards.

He put a lot of effort into a good-humoured responses to these people and gave them a considerable amount of his time.

I was unable to follow the dialogue, as those asking questions had their backs to me, but one thing Lawrence said I thought was worth repeating here, something not said in his talk, words to the effect that:

You can change the ideas, but not the data

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Prince or pauper? Tell Nature what you earn Grant Jacobs Mar 23

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In a recent post about Google search suggestions for questions about scientists, I noted that one question that recurred as you tried different disciplines was how much people in that field earned.

Nature are now running the 2010 edition of their international survey on science-related jobs and incomes. Let ’em know if you’re prince or pauper…

It’ll be interesting to see what the numbers come to.

Other articles on Code for life:

New internet meme: google suggestions for scientists

137 years of Popular Science back issues, free

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

Developing bioinformatics methods: by who and how

Internet news: Google redirects Chinese users to Hong Kong site Grant Jacobs Mar 23

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This is all over the internet already, but just in case my readers haven’t heard the news (exceedingly unlikely I know…), Google has moved to close it’s China website, redirecting users to the ’open’ website based in Hong Kong, as reported in a post on their official blog. Google points out this will mean that China is open to blocking the new Hong Kong-based site. It sounds almost like ’dare you.’

Google have created a web page that presents a simplified summary of what internet services are currently available in China, which they say they will periodically update. You will notice that YouTube and Blogger are marked as blocked.

Other sources point to that in China Google faced strong competition from a local counterpart,, and that the China operation is a small part of Google’s total takings, balancing this against that Google risk losing a potentially large market in the longer term. (It would be interesting to understand the popularity of the Chinese competitor.)

Stories covering this can be found at Google’s blog, the New York Times, the BBC, and–according to Google news–at 1,111 other places. (Well, at the time I looked; it’s grown since. Good timing on my part to get the four ones lined up…)

On a side note, I wish newspapers would cite their internet sources. Provide links. This is the internet, right? It’s silly to have to track down a source through searching on the quoted passages.

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