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.

Getting scientific research papers without paying - Code for life

May 02, 2017

Or, as it’s informally known: getting past the paywall. Occasionally I write about stuff that might be useful to other researchers, but also lets non-researchers see a little of what bugs some of us researchers! All but a relatively few (biological) science research journals require you to subscribe before you can get the research papers. Subscription fees can be hefty. I simply can’t afford to subscribe to more than a couple of journals, and then only those that ask very modest fees for personal subscriptions.[1] Scientists in poorer countries and institutions will have similar limitations, as will teachers, retired scientists, and others who have moved outside of the larger academic research institutions that carry access to large numbers of research publications. It’s also quite a challenge for anyone trying to … Read More

Please don’t share vaccine “concern” posts - Code for life

Apr 12, 2017

I’m losing far too much of my writing time to people with misbegotten ideas about vaccines.* I know people are very keen to make their own decisions. It’s understandable, but I wish if they insist on making their own decisions that they’d take equally as much care about the information they’re using to make their decisions — and in recognising if they are genuinely able to sort out good medical information from bad. I’ve been doing biological science for decades, and it takes me time to check things, lots of it. It’s much more sensible to make use of the people who know this stuff. It’s the same reason we call up plumbers, electricians, and other skilled people. They know their patch. You know what a DIY disaster looks like? That’s what popular opposition to vaccines looks like … Read More

A few vaccine resources - Code for life

Apr 08, 2017

Below are a few links to resources that people might find useful to share – or read if you want a quick introduction to vaccines for kids. Short takes For really short takes, these brochures—all in PDF format—might be useful. They make key points in few words: Immunization: Get the facts – a Canadian brochure covering 5 key concerns Top Ten Reasons to Protect Your Child by Vaccinating Questions Parents Ask About Vaccinations for Babies (a few of the questions are specific to the USA) What If You Don’t Vaccinate Your Child? (From the USA, but quite relevant) A bit longer on a few key topics Some what longer reading are these. They give more background and are well-written. Try them out! Clear Answers and Smart Advice About Your Baby’s Shots (PDF). Written by a doctor … Read More

Vaxxed at University of Otago: venues should be able to decline - Code for life

Apr 07, 2017

The University of Otago has allowed an anti-vaccine lobby group[1] to screen former-doctor Andrew Wakefield’s advocacy piece, ‘Vaxxed’ on campus. (Wakefield was struck off for research misconduct.) Vaxxed has attracted a number of comments in the media, such as Alison Mau’s If you watch Vaxxed, know you’re buying into the manipulation of a disgraced fraud. I was surprised to learn the university have allowed it to go ahead given the approach the organisers are taking. You get the impression they feel their hand is forced, that they are obliged to host essentially anything (because of current political thinking on freedom of speech). I think venues should be able to decline. Just my humble opinion, but I feel the organisers should have been asked to choose between a private screening for their members only at a private venue (i.e. not the university), or an open public event, … Read More

Human gene editing recommendations from USA science panel - Code for life

Feb 15, 2017

Just out today are the recommendations of a joint science advisory group of the USA National Academy of Science and the USA Academy of Medicine on gene editing. As an alert to any that might be interested I’ve copied their summary of their recommendations below.This post is meant as a simple heads-up, rather than an analysis of this report, as I’ve yet to read the full report, but their summary recommends (very) cautious movement forward. As expected, their summary of recommendations treat two different circumstances separately: where the gene editing only applies to the lifetime of the patient, it is not carried on to their children. where the edited genes are passed on to the children of those treated, so that the edit is inherited in the next generation(s). For the first they recommend work proceed, but initially … Read More

A Science and Technology advisory body for New Zealand? - Code for life

Feb 02, 2017

Over the last six months of or so a number of New Zealanders involved in science have suggested a body represent science and technology be formed, with the aim that government policy and lawmakers be better informed. What I would like to do to add to this mix is to very briefly introduce two organisations in the UK involved in offering recommendations to governments, the Government Office for Science and the UK House of Commons Science and Technology Committee, and offered a few informal comments. Professor Shaun Hendy, who has written about the issues surrounding scientists discussing work in public in New Zealand, has commented in the media and elsewhere (e.g. The NZ Herald, New Zealand Science Teacher) and offered a case for a Commission for Science in Science for … Read More

Excellent reading from the Wellcome Book Prize long-list - Code for life

Feb 01, 2017

These should all be excellent reading. You can think of this long-list as a list of excellent reads related to “medicine, health or illness” from many types of writing, fiction or non-fiction.* The 2017 long-list has five fiction titles and twelve non-fiction titles. The shortlist will be the exceptional reads, and the winner the pick of the bunch given the criteria and the current thinking of the judges. (Judges are only human!) The shortlist will be announced on the 14th of March, and the winner on the 24th of April. Below I’ve listed each long-listed book, and their rating on GoodReads. GoodReads reader ratings are out of five. In my experience, anything over somewhere in 3.8 – 4.0 on GoodReads is a very high rating. As you can see, there isn’t a lot in these books; they’re all well regarded by readers. You can … Read More

The mutant PRICKLE and the split brain - Code for life

Jan 31, 2017

We rarely hear of scientific work making positive use of otherwise unhappy situations, perhaps because writers feel they don’t “sell” well. But they can be a good thing to do. We also don’t often hear about smaller projects. Here a couple’s unfortunate luck with their child is put to learning more about brain development. We all have a brain, in a very real sense two half-brains joined. The two hemispheres of our brains are connected by a sheet of neurons called the corpus callosum. Some people have two independent, unconnected hemispheres.[1] They have what is known as agenesis[2] of the corpus callosum. Basically, their corpus callosum—the sheet of neutrons connecting their two hemispheres—isn’t there.[3] We’re often told we get half or our genes from each of our parents, and that it’s the mixing … Read More

Censoring US science, the backlash, and why - Code for life

Jan 26, 2017

[A follow-up of sorts is given in the Footnotes.] Better people offer to do better, not remove or block what they can’t compete against. Yesterday the Trump administration gagged several scientific institutes from communicating with the public. Grants were frozen to the EPA. And more. Are these Republications so frightened that their ideas can’t stand up against evidence that they need to gag and remove sources? It would seem so. Science works on the basis of better evidence bringing better explanations. It does not work by blocking what you don’t like. Many of these actions by the Trump administration looks to be focused on climate change data. Whatever the target, if these actions are to be on-going, the Republicans have essentially admitted that their ideas are so much weaker that that they can only try enforce their weaker ideas on others by brute force. The locations of 15 … Read More

Towards tackling milk allergy - Code for life

Jan 25, 2017

New Zealand agricultural scientists have learnt that the calves of a cow modified to have less allergenic milk also have less allergenic milk, raising hopes of developing a variety of cattle that those will one type of milk allergy can drink. Jamie Morton writing in the New Zealand Herald has the story, GE cow’s offspring show ‘super-milk’ potential. For those reading Jamie’s piece, ‘hypo-allergenic’ simply mean less allergenic. Hypo- is a Greek prefix scientists use to mean under or less. Hyper- is the enlarging counterpart. Milk allergy is not lactose tolerance. Apparently confusing the two is a fairly common mistake. A number of us are allergic to milk, in a similar way that a number of us are allergic to other types of foods. β-lactoglobulin is regarded as the main allergen in milk.* (β is the Greek letter, beta; you’ll … Read More