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.

Teams, collaborations, lone wolves, and cranks - Code for life

Oct 01, 2017

Jeremy Farrar, the director of the London-based biomedical research charity the Wellcome Trust, has written an opinion piece in the Guardian newspaper espousing the value of (international) collaborations in the face of Brexit, Britain proposed exit from the European Union. Farrar rightfully highlights the importance of collaborations. Collaboration can be essential for many types of work, and direct interactions with other scientists are invariably valuable. His points made about Brexit are sound, too: the impact of Brexit on science in Europe—for both sides of channel—could be devastating for many. Let me take his piece as an opportunity to diverge using his brief mention of the lone genius portrayal of science. Many criticise the portrayal “lone wolves” as heroes, as how great science is done. The ‘lone genius’ portrayal is wrong-headed, but objections to that portrayal often miss or misplace … Read More

Avery, a little bird helping children talk about their genetic disease - Code for life

Sep 04, 2017

Science communication takes many forms, even when we limit it to written work. Here University of Cambridge professor Lucy Raymond has worked with children’s illustrator Marta Altes at the Cambridge School of Art at Anglia Ruskin University to make an illustrated book for young children with rare genetic conditions. Part of Professor Raymond’s aim is to give the book to the children and parents that are part of her research in the hope it might help the children talk with their parents and doctors. You can read about their story in Medium. The book is written and illustrated by Marta Altes, and copies can be ordered at the University of Cambridge online store. Professor Raymond heads the IMAGINE ID project. Some areas of science make terrible acronyms for their projects, processes, molecules, computer programs and algorithms.* This one … Read More

From here to there: Installing a 16kb computer to modern tape media - Code for life

Aug 07, 2017

While travelling I’ve visited some science-related locations and seen the odd bit of science-related trivia. On a wall of the ferry I took between Swedish the port town Oskarshamm and the walled city of Visby at the Baltic sea island of Gotland was a collection of photographs offering a pictorial history of the shipping company. One delightful photograph highlighted that they adopted modern computing devices early, their offices acquiring their first computer in 1976. As you can see from the photograph above, they got a crane in for the installation job, fitting it in through a window with the panes removed and planks for skids to get it into the room. Next time you get your computer delivered you won’t think that big box that the courier dropped off at the door is such a pain in the neck, … Read More

USA team editing embryos, early thoughts on alternatives and limitations - Code for life

Aug 03, 2017

Widely reported today is the research paper by an USA team who edited a gene that causes sudden heart failure in young adults. I’d like to take a different approach, briefly raising just two things that nagged at me while reading this work. Before I do be clear there are real technical advances reported.* I’m not denying or opposing them. It’s just that when I step back a little I have some questions. These questions include the sort of questions that a discussion about the use of embryo editing might want to have. There are methods to screen embryos before they are implanted, to try eliminate ‘defective’ embryos. (Similarly, there are some ways to try increase the number of ‘good’ embryos.) Without any gene editing about 50% of the fertilised embryos used in the study would not have the mutation, … Read More

Fixing our genes - Code for life

Jul 30, 2017

Gene editing could be a big deal. It offers some great stuff. For a few applications it also raises some interesting ethical questions. We might be able to treat some genetic disorders by convert a “broken” gene associated back to the working version of the gene, potentially providing a one-time, life-long fix for the patient. Gene therapy has a surprisingly long history and several cases of ‘gene therapy’ has been done. Some medical conditions have genes being used when they ought not to be. Gene editing could shut off meddlesome genes that aren’t supposed to be active. We might also develop ways to target cells with the re-arranged genes associated with some types of cancer. Edited butterfly wing patterns, from Barrangou & Doudna, Nature Biotechnology 34, 933–941 (2016). The list goes on with many other applications, including in agriculture … Read More

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