Grant Jacobs

Dr Grant Jacobs is a computational biologist, a biologist who uses computers (algorithms, statistics, etc.) to explore biological systems, and who develops computer algorithms and tools for biologists to explore data from genes, genomes and proteins. He contracts to research groups and biotech companies through his Dunedin-based consultancy, BioinfoTools. He has an established interest in science communications and is open to science communication work as well as computational biology. Grant is on Twitter, @BioinfoTools.

TV psychics: not in the real world, please - Code for life

Oct 11, 2009

Before getting back to science pieces, I'd like to join fellow sciblings Petter Griffith and Mike Kilpatrick in expressing disappointment over TVNZ's encouragement of the services of their "TV psychic" for the family of missing toddler Aisling Symes. Entertainment often plays on fantasies, asking viewers to temporarily accept some clearly fictional plot devices. There's a place for "psychic abilities" as "super" powers to make a central character be more than a mere mortal for harmless fun. But encouraging the use of a "psychic" to assist in a serious, real-world, matter? Not in the real world, please. Read More

The 2009 Nobel Peace Prize - Code for life

Oct 11, 2009

Internationally there has been much fuss about Barack Obama being awarded the 2009 Nobel Peace Prize. Before passing your judgement, though, it may help to remember that the award committee aren't dumb and that it might be useful to first read what the Peace Prize is awarded for to try understand their thinking. My reading of many reactions is that many people are thinking in terms of the aims of the science prizes, which are strictly for past achievement. The aims for the Peace Prize, by contrast, are interpreted as including encouragement of efforts started that are on-going. Read More

Peter Lawrence's Kafka tale of research grant funding - Code for life

Sep 30, 2009

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. Read More

Major earthquake in Samoa, 8.3 - Code for life

Sep 30, 2009

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. Read More

Scientists can’t write? - Code for life

Sep 30, 2009

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. Read More

Introducing Code for Life - Code for life

Sep 24, 2009

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 … Read More