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.

Whodunnit? Finding the mystery 1080 testing lab - Code for life

Dec 01, 2019

1080 is used to control pests in NZ. Its use is contested by a noisy few. A new report claims high levels of 1080 in rats washed up on a beach. Flora and Fauna of Aotearoa (F&F) won’t name the laboratory that did their testing. It has sparked a hunt for the mystery 1080 testing lab. It’s just the sort of thing my readers might spend some idle time on Sunday searching for clues. Whodunnit? Readers can tackle Farah Hancock’s and Dave Hansford’s coverage (published in that order), and the Science Media Centre’s Expert Reaction report for background. You can also read the report itself (PDF file; obtained from a link in the SMC Expert Reaction report). Let us know what you think! F&F spokeswoman Di Maxwell claimed to Dave Hansford their tester previously … Read More

Measles vaccination a priority for travel to islands and Phillipines - Code for life

Nov 25, 2019

The Ministry of Health has announced that “people under the age of 50 travelling from New Zealand to Samoa, Tonga, Philippines and Fiji” are now on the list of national priorities for MMR vaccination. Given the outbreaks of measles in Samoa, Tonga, Philippines and Fiji, the Ministry of Health is asking primary care providers to ensure vaccinations are up-to-date for any individual (aged 50 and under) who indicates they will be travelling to one of these areas, or any country that has an active outbreak of measles. We also recommend infants aged six to 11 months travelling to an outbreak area have one dose of MMR. Please remember that any child vaccinated before 12 months of age will still need two further doses of MMR. All people need to be vaccinated at least two weeks before travel. More generally … Read More

Political parties and GMOs: we all need to move on - Code for life

Nov 14, 2019

Recently more than 150 post-graduate students and young scientists presented an open letter to the Green Party via The Spinoff, encouraging them to reconsider their position on genetic modification. Their target is tackling climate change issues.[1] Can any party continue to be dismissive about genetic modification (GM) contributing to better agriculture? We all want safe food, and the environment and climate change are important issues to tackle. New varieties can contribute, including those developed using GM. All political parties have quietly let the GM legislation slide, not just the Green Party. It is unimpressive no party has moved the temporary legislation on. (Such outstanding timidity! Such an excellence of hand-sitting![2]) It’s an issue politicians avoid, I believe, because the core of opposition to GMOs is about some people’s beliefs, not science, and politicians are reluctant to deal … Read More

1000 of these now - Code for life

Nov 09, 2019

Some days I sit and think, “what will I write…?” What do you say when you get to 1000 posts? Maybe you just start where you are, diverge to where this all began, then offer a collection of reader’s favourite posts, and a few of your own? (And throw in a few pictures.) Slow to fall This piece started a long time ago at a café table in Melaka, the laptop in front of me with a sweet kopi susu[1] carefully placed to one side. The book is, Biopunk dystopias: genetic engineering, society, and science fiction, by Lars Schmeink. Who can resist a title like that? This photo is from Kuching (not Melaka), taken from outside the cafe, looking out over the lake. It’s a favourite place for me in this town. ©Grant Jacobs, 2019-. I ponder my next … Read More

Film trailer towards gene editing in humans - Code for life

Mar 11, 2019

Here’s a film trailer of the documentary Human Nature that looks at a future of gene editing[1] – The film is to be released soon in Australia and elsewhere. Here’s their blurb, The biggest tech revolution of the 21st century isn’t digital, it’s biological. A breakthrough called CRISPR gives us unprecedented control over the basic building blocks of life. It opens the door to curing disease, reshaping the biosphere, and designing our own children. Human Nature is a provocative exploration of CRISPR’s far-reaching implications, through the eyes of the scientists who discovered it, the families it’s affecting, and the genetic engineers who are testing its limits. How will this new power change our relationship with nature? What will it mean for human evolution? To begin to answer these questions we must look back billions of years and peer … Read More

Published review of Wilyman’s anti-vaccine thesis says fail - Code for life

Mar 06, 2019

A few years ago several of us at Sciblogs took objection to one of the trashiest theses we’ve seen. (Which we, naturally enough, trashed.) Now there’s a review of the thesis published in the scientific journal, Vaccine. The review looks a thorough job… and the conclusions don’t look good. Essentially the author’s review of Wilyman’s anti-vaccine thesis review says “fail”. Politely. But definitely fail. It’s open-access: anyone can read it. A review of the review If I had a criticism of the review it would be it’s too kind. Scientific journals use very polite language, so a conclusion like, This thesis is notable for its lack of evidence of systematic liter- ature review. Despite its extensive claims, there is no primary research, but there is abundant evidence of strong bias in selecting the literature cited and sometimes outright … Read More

Autism revisited: genetics, environment, not vaccines - Code for life

Mar 05, 2019

Researchers are pounding the trail of the genetics of autism. There is also more evidence that vaccines don’t cause autism. More interesting is what does cause autism. (Those looking for the vaccine bit should track down to the section, Another nail on the coffin.) Not the Rain Man People with autism or autism spectrum disorder find social communication and interaction difficult. Austism can also show up in repetitive behaviour such as stacking the cans, ordering toys in rows, or strong interests on particular narrow topics. Autism occurs in around 1-2% of people and affects 4 to 5 more males than females. It has a broad definition and is often found with other neurological conditions. Hollywood movies like Rain Man and TV dramas popularised autism. These often idolise autistic savants, not ‘ordinary’ autistic people. Curiously Kim Peek, the real-life inspiration … Read More

A summary of the evidence for the main vaccine concerns - Code for life

Feb 19, 2019

Vaccine-preventable disease outbreaks are happening everywhere. Measles is on the rise worldwide, including in Europe and the USA. Over 900 have died in Madagascar alone since October 2018.[1] Most will be infants. Japan’s rubella epidemic has prompted traveller warnings. 367 cases have been reported this year. Venezuela has considerable problems, not helped by diphtheria coming back. The list just goes on. Many outbreaks feature those who’ve chosen not to vaccinate.[2] The WHO has called ‘vaccine hesitancy’ one of their top-ten global health threats. It’s appalling, really, that it’s come to this. I feel for parents and parents-to-be facing the claims made by the few who oppose vaccines. We all worry about kid’s safety. Recently I wrote a few suggestions for new parents or parents-to-be facing vaccine opinions. Just out is summary of the evidence for … Read More

Not cow farts - Code for life

Feb 09, 2019

You may have heard or read media outlets talking of cow farts.[1] This tweet from  University of California at Davis animal biotechnology/genomics scientist, Alison Van Eenennaam might help – I’m sure I’ve been guilty of lazily using it. Eructation is a very polite and fancy way of saying burp. As the dictionary puts it, “a belch”. (Yes, I check these things too!) It can also be called ructus or eruptus. I like eruptus. It resonates with the action so well. But back on track. Methane emissions from bovines. As Alison explains, bacteria in cattle break down cellulose in their rumens. Ruminants like cattle have four stomach compartments. A cow or cattle beast’s first stomach is called the rumen. The other parts are the reticulum, omasum and the abomasum. Plants have a lot of cellulose. Mammals have very limited ability … Read More

Taming inaccurate health and science news: could editors help? - Code for life

Feb 07, 2019

A recent study found most of the 10 most popular ‘health’ articles of 2018 were inaccurate. Similar but less skewed results were seen for the top 100 articles. I dislike pointing fingers. For these things, they tend to point at journalists and social media. Instead, I’d like to highlight something less talked about when discussing inaccurate health and science news: could editors help? Many newspapers position themselves as fighting fake news. That’s mostly for politics, but there’s a lot that news outlets might do for science and health news, too. Ideally these inaccurate stories would never published in the first place. Then we wouldn’t have to worry about what’s in social media! In reality there will always be some inaccurate stories in social media, but news outlets can play their part. It’d be great to see more editors offer strong … Read More