A fistful of Christmas!

November’s pub-science will be held on the Thursday 26th.  Time and place as usual: Britons Protection from 5pm.  Since this is our last pub-science gathering before christmas feel free to bring cake, santa hats…and a moustache (well okay, you can leave the moustache out, but it’s your loss…remember, it is Movember).

This month we will be discussing Alan Turing. Here is some literature to get you started:

1. The Chemical Basis of Morphogenesis.
A. Turing (1953), Phil. Trans. R. Soc. Lond. B. vol. 237 no. 641 (37-72).
2. Alan Turing and Morphogenesis, by Jonathan Swinton (AZ)

We will be discussing the man himself as well as his scientific work, so feel free to read around and make other suggestions via our  mailing list or below.

Published in: on November 16, 2009 at 3:53 pm  Leave a Comment  

Sex & drugs & rock & roll are all my brain and body need

It’s my last journal club here in Manchester, so I’ve chosen three light-hearted papers which have been classified using the Ian Drury Ontology [1]. The first two come from NCBI ROFL (The National Center for Biotechnology Information: Rolling On The Floor Laughing) while the third comes from Natalie ROFL.


The first paper is titled “Male condoms that break in use do so mostly by a “blunt puncture” mechanism” [2]. As pointed out in  those are the [condom] breaks, of particular interest is the “laboratory coital model” used to test condom breakage. A question scientists (especially systems biologists) are always asking themselves is, how accurate is the model? Bear this in mind when you read the paper.


Talking of drugs, and since we’ll be in an ethanol dispensing pub, the next paper is titled “Endogenous ethanol ‘auto-brewery syndrome’ as a drunk-driving defence challenge” [3]. The main challenge here is to find the original paper, which looks interesting. As pointed out in I swear I haven’t been drinking, Officer. It was my gut flora! this is an interesting condition.

Rock ‘n’ Roll

Finally, the main paper of this week has been brought to our attention by the head-banging hard-rockin’ metal-head Natalie Stanford. Read this paper and wonder how they ever got funding to do the research… It’s just rock’n’roll.


  1. Ian Drury (1977) Sex & Drugs & Rock & Roll
  2. WHITE, N., HILL, D., & BODEMEIER, S. (2008). Male condoms that break in use do so mostly by a “blunt puncture” mechanism☆ Contraception, 77 (5), 360-365 DOI: 10.1016/j.contraception.2008.01.014
  3. Logan BK, & Jones AW (2000). Endogenous ethanol ‘auto-brewery syndrome’ as a drunk-driving defence challenge. Medicine, science, and the law, 40 (3), 206-15 PMID: 10976182
  4. Patton, D., & McIntosh, A. (2008). Head and neck injury risks in heavy metal: head bangers stuck between rock and a hard bass BMJ, 337 (dec17 2) DOI: 10.1136/bmj.a2825
Published in: on September 29, 2009 at 5:13 pm  Leave a Comment  
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The hypothesis is dead, long live the hypothesis!

Next journal club is Thursday 28th of May at 4 on the clock, in Kro. We’re going to be discussing the unreasonable effectiveness of data, since we don’t need a hypothesis any more. Or do we?

Three closely related papers, start by reading “The Unreasonable Effectiveness of Data” [1] from some top Googlers in the Googleplex. Move on to a short but provocative piece by Chris Anderson of Wired Magazine about “The End of Theory” [2]. Then finish with a piece by Doug and Steve “Here is the evidence, now what is the hypothesis?” [3], which was written a few years before Google Inc. and Wired magazine published theirs.

For discussion: Is the hypothesis dead now? [4]


  1. Alon Halevy, Peter Norvig and Fernando Pereira (2009) The Unreasonable Effectiveness of Data IEEE Intelligent Systems, Vol. 24, No. 2. (2009), pp. 8-12.
  2. Chris Anderson (2008) The End of Theory: The Data Deluge Makes the Scientific Method Obsolete (2008) Wired magazine 16.07
  3. Douglas Kell and Steve Oliver (2004) Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. Bioessays, Vol. 26, No. 1. (January 2004), pp. 99-105. DOI:10.1002/bies.10385
  4. The King is dead. Long live the King!

Physics, Computation, and Why Biology Looks so Different

Journal club details from Natalie:

We have set a date for the paper discussing this month, it will be Wednesday 29th April starting at 5.00pm.  We shall say provisionally occurring at the usual pub, but if the weather is exceptionally nice we may head to Kro instead…but that can be decided on the day!

A bit of change of schedule this month as we have only one paper [1], which has been chosen by Olu.  And after a recent geeking session with Mr Platt we decided to do some ‘back of the envelope’ science in place of a second paper.  This will be along the lines of ‘how many electrons in a swimming pool?’ (but perhaps a little more biology based).  The aim is to get some ‘back of the envelope’ numbers for things you wish you had a vague idea about when asked a stupid question.

Could be interesting, could be terrible…only one way to find out though!


  1. J.J. Hopfield (1994) Physics, Computation, and Why Biology Looks so Different Journal of Theoretical Biology, Vol. 171, No. 1., pp. 53-60. DOI:10.1006/jtbi.1994.1211
Published in: on April 27, 2009 at 10:26 am  Comments (2)  

It must be true, I read it on the Interweb

Pub science part three will be held at the same venue (Britons Protection)  at 5pm on Thursday 26th March.  The papers being discussed are as follows:


  1. Jens Nielsen (2007). Principles of optimal metabolic network operation Molecular Systems Biology, Vol. 3 DOI:10.1038/msb4100169 suggested by Robert Platt
  2. Robert Schuetz, Lars Kuepfer, Uwe Sauer (2007) Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
    Molecular Systems Biology, Vol. 3 (10 July 2007) doi:10.1038/msb4100162
  3. Linus Pauling (1968). Orthomolecular psychiatry. Varying the concentrations of substances normally present in the human body may control mental disease. Science (New York, N.Y.), Vol. 160, No. 825., pp. 265-271. suggested by Paul Dobson and Duncan Hull

The Fiction of Function

Round two of the pub science (aka a fistful of papers) is scheduled for Friday 27th February. Same place, Britons Protection, from 3.30pm onwards.

The papers up for discussion this time are:


  1. Jeff Shrager (2003). The fiction of function. Bioinformatics 19 (15), 1934-1936. DOI:10.1093/bioinformatics/btg277 (suggested by Paul Dobson)
  2. Matthew D Jankowski, Christopher S Henry, Linda J Broadbelt, Vassily Hatzimanikatis (2008). Group contribution method for thermodynamic analysis of complex metabolic networks. Biophysical Journal 95 (3), 1487-1499. DOI:10.1529/biophysj.107.124784 (suggested by Natalie Stanford)
Published in: on February 20, 2009 at 4:47 pm  Comments (1)  
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Can a Biologist Fix A Radio?

First meeting, The Britons Protection (M1 5LE), 29th January to discuss papers below.

Any suggestions for papers for the next meeting? Leave a comment below if you have any good ideas…


  1. Yuri Lazebnik (2002). Can a biologist fix a radio? or, what I learned while studying apoptosis. Cancer Cell 2 (3), 179-182. DOI:10.1016/S1535-6108(02)00133-2
  2. Monica Mo and Bernhard Palsson (2008). Understanding human metabolic physiology: a genome-to-systems approach. Trends in Biotechnology 7(1):37-44. Epub 2008 Nov 17. DOI:10.1016/j.tibtech.2008.09.007
Published in: on January 29, 2009 at 3:50 pm  Comments (1)  
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