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.

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

Filing research papers and web browsing: Zotero, Zotfile and Vivaldi - Code for life

Jan 18, 2017

Three free tools for filing research papers and browsing the web. If you’re in research—be it scientific work, writing a book, or similar—you’ll be spending a lot of time gathering material on-line and filing it. There are a lot of tools out there, and everyone has their favourites. Let me introduce three I use (along with others*). I collect and read a lot of research papers. I also like to track other’s writing on science. It’s nice to be able to file both research papers and websites under the same tool and filing scheme. Zotero Zotero will file research papers and web pages direct from the web browser. In their blurb they say, “You can add PDFs, images, audio and video files, snapshots of web pages, and really anything else.” In that way Zotero … Read More

Is GM corn really different to non-GM corn? - Code for life

Dec 31, 2016

‘Substantially equivalent’ is the term used by regulatory bodies as part of confirming a GM crop is safe for consumption. Earlier work claims GM corn is ‘substantially equivalent’ to non-GM corn. Earlier this month a study was published in Scientific Reports claiming genetically modified corn is not substantially equivalent to non-GM corn, “Our molecular profiling results show that NK603 and its isogenic control are not substantially equivalent.” Plant biologists have said this research doesn’t show what it claims to. Rather than repeat what others have already said, I’m going to offer a brief explanation of what they have said. For those in a hurry the main point that has been made is that they haven’t found what the typical range of amounts of each protein* is first, and without that you can’t tell if the differences they found are unexpected or not—the … Read More

In a demon-haunted world - Code for life

Dec 22, 2016

20 years ago today a brilliant science communicator died. Over the last few months I’ve been seeing Carl Sagan’s words in my tiny corner of the internet, particularly his warnings of where we’d go if we ignorance and pseudo-science reigns. Sagan was a scientist, an author and a presenter. He was a huge figure in science communication, perhaps best known for the documentary Cosmos based on his book of the same title. He was a great advocate of skepticism. True skepticism, that is. The term has been pirated by so-called ‘denialists’ — people opposing one or other well-established scientific result or science-based practice, such as anthropocentric* climate change or vaccination. The quotes I’m seeing in my Facebook stream and on Twitter are from his writing encouraging strong skepticism. Not unexpectedly sharing them … Read More

Book review: Adventures in the Anthropocene - Code for life

Jul 06, 2016

Adventures in the Anthropocene Gaia Vince Vintage 2014. ISBN 9780099572497. 390 pages of body text, excluding illustrations, end notes and index. Adventures in the Anthropocene is an investigative travelogue of responses to the challenges posed by human alterations to our plant, including climate change. Her book offers a broad-ranging perspective of the impacts of the Anthropocene prefacing her visits to those working at the coal-face in many remote locations around the planet. The title in part springs from the idea that we have entered a new geological age, the Anthropocene. Geological ages are long spans of time characterised by particular changes on a planetary scale. The Holocene is the present geological age that is coming to an end. The … Read More