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.

Glyphosate is to go back to trial - Code for life

Oct 13, 2018

Superior Court Judge Suzanne Bolanos[1] has written a Tentative Ruling that glyphosate is to go back to trial. I’m not a lawyer, but her ruling looks pretty damning. Let’s have a look at what it says. What’s a Tentative Ruling? Tentative rulings are preliminary indications of rulings ahead of the final ruling. (Lawyers indicate these tentative rulings rarely differ substantially from the final rulings.) As described in wikipedia, judgement not withstanding the verdict (JNOV) is, the practice in American courts whereby the presiding judge in a civil jury trial may overrule the decision of a jury and reverse or amend their verdict. This wikipedia entry is brief, clear and worth reading. Towards the end it notes, Reversal of a jury’s verdict by a judge occurs when the judge believes that there were insufficient facts on which to base the … Read More

Vaccines and risk on Auckland motorway billboard - Code for life

Oct 02, 2018

There’s a new billboard on South Auckland motorway near the exit to Middlemore hospital encouraging drivers to question the safety of vaccines, Short answer: yes. But what’s in vaccines is not really the issue, it’s a way to distract people from the real question: are you better off with the vaccine than without it? You could turn this around and ask: if you knew the harms causes by vaccine-preventable illnesses, would you risk not vaccinating? (Hell, no.) What you need to know are the risks from the vaccines compared to the risks from the illness the vaccine prevents. It’s the balance of risks that matters The Western Australian Dept. of Health has a useful side-by-side list comparing the risks of the illness and the vaccine for most of the common vaccines. In all of them you’re … Read More

A foil to the populist scourge: towards a Science Commission for New Zealand? - Code for life

Sep 24, 2018

While writing about the demise of Jacqueline Rowarth’s role as head of the New Zealand Environment Protection Agency (NZ EPA), Peter Griffin (former head of the Science Media Centre) also covers progress towards a NZ Science Commission. His piece provides an useful opportunity to revisit this initiative, raised during the election, and how it seems to be going sideways since. Is an opportunity to lift and safeguard New Zealand’s decision making at a time policies worldwide are on rough ground being missed? Could a skeleton Science Commission be set up to establish the concept as a new feature of the political and policy landscape, and flesh it out later? A foil to the populist scourge I won’t be alone in pointing out the usefulness of an established, independent source of policy evidence. It would be great to see New Zealand … Read More

Sticky thoughts on where research can most effectively influence policy - Code for life

Aug 30, 2018

New Zealand’s Chief Science Advisor (CSA), Professor Juliet Gerrard, has been asking where research can most effectively influence policy – one post-it note at a time, (Posted 21st August ~10:45pm, NZST; click on image to open tweet.) The comments after this piece are open for readers to offer their thoughts on where science should best influence policy. Please do! As I’m currently off-shore so I can’t attend these meetings. Besides, I always have too much to say… I’ll add my contribution below and hope readers will join in. Sticky-sticky-sticky She posted a photo to give me (and others) some idea of what’s happening – (Taken from the PMCSA website twitter feed, 21st August. Click on image to see tweet.) Some people have written 3 or 4 words. Others have crammed a mini essay onto a post-it. These must … Read More

Food Evolution – screening at Queenstown August 31st - Code for life

Aug 27, 2018

Food Evolution, the movie, is screening at Queenstown at the end of the month. If you’re in the area, check it out. It’s free: you just have to register at EventBrite. The screening and panel discussion is in the Clancy’s Meeting Room, Level 5, Rydges Lakeland Resort, from 7pm on Fri. 31 August. The film is narrated by well-known science communicator Neil deGrasse Tyson, Amidst a brutally polarizing debate marked by passion, suspicion and confusion the FOOD EVOLUTION movie expolores the controversy surrounding GMOs and food. Traveling from Hawaiian papaya groves to banana farms in Uganda to the cornfields of Iowa, the film, narrated by esteemed science communicator Neil deGrasse Tyson, wrestles with the emotions and the science driving one of the most heated arguments of our time. In the GMO debate, both pro- and anti- camps claim science is on … Read More

Newspaper warns of human-induced climate change in 1912 - Code for life

Aug 17, 2018

We’ve had more than 100 years of warnings of human-induced climate change now. It’s nearer 200 years, really. Before records were taken they would be extrapolations rather than observations. Extrapolations are harder for those outside of science to trust, but extrapolations are part of what science does. Looking to where things might go is useful. This pithy, insightful newspaper article is doing the rounds of social media again: Credit: Sustainable Business Network The basic idea was in fact well established by then. Alexander von Humboldt is a legendary figure.* In his day he was the equal of Darwin or Goethe. He theorised about human-induced climate change from 1799 onwards. He was one of the first, if not the first, to raise it. His ideas came from observing the effects of deforestation, from seeing changes in flora at different … Read More

USA Court ruling on glyphosate— the role of IARC and Eugenie Sage’s call - Code for life

Aug 13, 2018

A lot has been said about a recent court case ruling about Monsanto’s Roundup. Let’s look just at the role of IARC and Eugenie Sage’s call for the New Zealand Environment Protection Agency (NZ EPA) review their stance on Roundup. The role IARC seems to be very little understood. Many media reports (worldwide) on this court case offer a throw-away statement that the IARC report and regulatory rulings conflict. They are not in competition. The regulatory bodies have not “set aside” or “overlooked” the IARC findings. (That’s a lobby-group line.) In practice, regulatory bodies are using the IARC reports as they are meant to. This seems to have confused by objections to IARC’s findings, a parallel issue. Adding to the mix, in New Zealand the Associate Environment Minister, Eugenie Sage, has said she will ask the NZ EPA to … Read More

The ‘Impossible Burger’ is not genetically modified - Code for life

Jul 06, 2018

In the New Zealand media and social media people are talking about this genetically modified ‘Impossible Burger’. Except it’s not. Sorry everyone, but it really isn’t genetically modified. What was genetic engineered is a yeast that makes one of the ingredients used in the ‘Impossible Burger’. It’s just a different way of making that ingredient. The ingredient is the same as in soy plants. All the ingredients in the burgers are the same as in ‘natural’ plants.* A noisy few rush to declaim loudly everytime someone mentions genetic engineering or GMOs, calling to banish the use of a technique, rather than look at each application. Let’s look at this one. A key part of what gives the burger it’s ‘meaty’ taste is a “blood” protein, leghaemoglobin. The one used is actually from soy plants, not animals. Like the similarly-named haemoglobin … Read More

‘Fake author’ papers opposing HPV vaccine retracted, editor’s defence - Code for life

May 28, 2018

‘Fake author’ papers opposing HPV vaccine by ‘Lars Andersson’ are being retracted. The editor of one of the papers has offered an extraordinary defence, railing at the Karolinska Institute. Earlier this month I wrote about a research opinion piece claiming that the HPV vaccine increases cervical cancer in some patients. Among the faults of the comment article were that the sole author faked their name and institution, and that the people it pointed to were almost entirely not vaccinated. I’ve just been alerted that the publisher of this paper, the Indian Journal of Medical Ethics (IJME), has retracted the paper.* According to Retraction Watch three more ‘Lars Andersson’ papers in the Journal of Internal Medicine are also to be retracted. (In a twist of fate perhaps, the editor of this journal is a professor at the Karolinska Institute that … Read More

Apple boards bendy once again - Code for life

May 26, 2018

As you age history repeats itself. Anyone over about 30 will know what I mean. Today I was reading over at ArsTechnica how some of the Apple 6 phones were bendier than earlier models, and Apple knew it. The writer reports, These touchscreen-controlling chips became unseated from the logic board due to bending and flexing with normal use. Back in the day—you knew this would start this way—Apple’s boards flexed all by themselves. Or at least the clones did. As an undergraduate student I spent a vast sum of money on a Sundox, a Taiwanese clone of Apple’s vaunted ][e computer. The ‘e’ stood for enhanced. This model came with 64 kilobytes of RAM, rather than 48. And we could program it using a high-level language that the university taught us called Pascal, named after the famous mathematician … Read More