SciBlogs

Archive September 2009

Peter Lawrence’s Kafka tale of research grant funding Grant Jacobs Sep 30

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Recently a very readable perspective article Real Lives and White Lies in the Funding of Scientific Research was published in the scientific journal, PLoS Biology (PLoS = Public Library of Science), by senior scientist Peter Lawrence FRS. (I mean senior in the sense of achievements, notwithstanding that his first publication was in 1965.) Peter’s concern at the state of the grant funding system no doubt stems from his move to Cambridge University’s Department of Zoology in 2006, after roughly 37 years working at the MRC LMB, based on the outskirts of Cambridge. (Disclosure: I was post-graduate student at the LMB.) As his article notes, he wrote his first grant application after 40 years as a scientist, which will startle many scientists on this forum!

Woven through this article is the story of a new principle investigator ‘K.’ who, like K. from Kafka’s The Castle, is eaten up by bureaucracy. For some (many?) scientists here, I am sure this story may have an all too familiar ring to it.

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Major earthquake in Samoa, 8.3 Grant Jacobs Sep 30

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Quick post: There has been an 8.3 earthquake near Samoa.

See: http://www.stuff.co.nz/world/south-pacific/2916140/Deaths-after-8-3-quake-tsunami-hit-Samoa

Best wishes to anyone in Samoa, or with family or friends there.

Scientists can’t write? Grant Jacobs Sep 30

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Currently I’m reading sections of Investigating science communication in the information age: implications for public engagement and popular media. In chapter 4.1, Making science newsworthy: exploring the conventions of science journalism, Stuart Allan cites journalist W. T. Stead who wrote in 1906 (see page  152):

In editing a newspaper, never employ an expert to write a popular article on his own subject, better employ someone who knows nothing about it to tap the expert’s brains, and write the article, sending the proof to the expert to correct. If the expert writes he will always forget that he is not writing for experts [b]ut for the public, and will assume that they need not be told things which, although familiar to him as ABC, are nevertheless totally unknown to the general reader.

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Introducing Code for Life Grant Jacobs Sep 24

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Welcome to Code for Life. I hope you get something out of my modest efforts to educate and entertain.

The material below can also be found in the ’About’ page. I’m popping it in here by way of introduction.

What’s with the name of the blog?

Code4Life was a name I considered for my consultancy, BioinfoTools. It plays on a number of things related to my work and what I write about:

  • My work involves programming (coding) for life sciences (molecular biology and genetics).
  • The data I examine and write algorithms for are the sequences of bases in DNA (genes, genomes), the amino acid sequences of proteins (enzymes, hormone receptors, etc.) and the three-dimensional atomic structures of proteins. These are the codes in life, the “information base” of biology and life. (If readers are interested in an introduction to this, let me know.)
  • It can mean moral codes and other “rules” people guide their lives with. I won’t be writing about this much about this in the sense of rules for life, but I may look at role of honest skepticism, logic and testing in science.
  • You can stretch it to be about writing about life sciences, writing being a code of sorts.
  • It has nothing to do with The Code for Life, an album by the heavy metal band Warrior. I am not a fan of heavy metal.

The banner photograph

My current banner may later be replaced with something reflecting the title of the blog… In the meantime it shows where I used to do my science. I work from a home office most of the time and until very recently I was based in a village in the Otago peninsula, near the Otago harbour. The village is near the right of the image. Science from a semi-rural, near maritime location! (The image is open source, obtained from wikimedia and edited using GraphicConverter v6.5.1.)

Topics

Most articles will target a general audience. I’ll try remember to let you know if I think an article is a bit geeky for general readers; once in a while I may write assuming a little basic background for those with deeper interests.

Likely topic areas include:

  • Genetics, genomics and evolution. Stunning new findings pour out each week…
  • Human biology, esp. cognitive neuroscience and rare diseases or disabilities. The workings of our minds is fascinating stuff and it’s intriguing to explore others’ lives.
  • “What science is”, what the basic terms mean, how to read a report on science, sorting out the good stuff from the bad.
  • Science and the media.
  • “Natural remedies” vs. science-based medicine. The naïve presentation of some of the “woo” out there by various people (including, sadly, a considerable number of media reports) is appalling.
  • Vaccinations. (No “flame wars”, please. Seriously.)
  • Issues within science, especially within New Zealand. Science is a great enterprise, but there’s always room for improvement.
  • Developments in computational biology (my profession).
  • Computing & computers (the tools of my trade).
  • Plain old ruminations. We all have our navel-gazing days…

Please feel free to ask questions and suggest topics you’d like covered. If possible, I’d like to try base a few posts every month on a subject that a reader has brought up.

I don’t claim to be some gifted philosopher or expert on matters far and wide, in fact I’m frequently embarrassed by my sheer stupidity… (Aren’t we all?) Some of my articles will be off my specialist expertise, in fact probably most will and I’ll let you know. Readers are most welcome to correct any errors but please substantiate your claims.

My background

By training I’m a computational biologist, a biologist who uses computers (algorithms, statistics, etc.) to explore biological problems, and who develops computer tools for biologists to explore data from genes, genomes and proteins. I work as an independent scientist through my consultancy, BioinfoTools, contracting to research groups and biotech companies.

A more commonly-known name for the field is ‘bioinformatics’ but ’strictly-speaking’ this originally referred to a subset of the field. Some of us who started before the “genome era” prefer the computational biology label, for reasons I’ll explain sometime… ‘BioinfoTools’ is a contraction of ‘bioinformatics tools’.

I have strong interests in science communication and am open to writing contracts or other work (e.g. editing) in this area.

Copyright

The material on my blog is copyright. Journalists, editors & publishers are welcome to contact me if you wish to use this material.

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