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.

COVID-19: sequence the viral genomes of all border cases - Code for life

Aug 17, 2020

New Zealand has an advantage in managing COVID-19: all our cases come from the border, one way or other.[1] We can exploit this in how we shut down outbreaks. One way is to have at the ready the viral genomes of all border cases. With this we can quickly find the starting point of any outbreaks inside the country. If the genome sequence of a case within the country very closely matches a case at the border, that’s likely where it started. Because our cases come from the border, viral genome sequences can be a shortcut to find the index case, a key to finding all people in an outbreak. To be in with a chance of finding a match this way, we need to collect all the viral genomes from positive cases at our borders we can. Joep de … Read More

Lifting our game against COVID-19 - Code for life

Mar 23, 2020

We need to be lifting our game against COVID-19. [Edit: this was written before to the announcement of the Level 4 lockdown, and the National State of Emergency. The explanation of why we’re doing this, and general points should still be useful.] You and I need to help those working to prevent the spread of COVID-19 while they’re trying to lift the testing and treatment efforts. We don’t want to be playing this game running backwards. Best to play it solidly forward, from the start. So, what you and I need to do, and why?[1] Don’t overwhelm critical care We do not want the health system overwhelmed. It all comes back to this. Forget that detailed stuff about case fatality rates, R0s, whatever. If the health system is overwhelmed everyone who needs that care is affected – not just people with COVID-19. And … Read More

Is 2019-nCov a pangolin coronavirus? - Code for life

Feb 08, 2020

Tonight’s news suggests the coronavirus outbreak may have originated from pangolins. Details are very sketchy, almost nothing at all beyond a claim of high similarity. My impression is this claim comes from a press release by South China Agricultural University. Initial discussion online suggests this is a more likely candidate for an intermediate host than previous speculations. It is also ‘science by press release’, where claims are made in advance of publication of preprints, research papers or data. Spiny anteaters Pangolins are also known as ‘spiny anteaters’, small mammals covered in scales that feed on ants and termites. They’re nocturnal, and roll themselves into defensive balls when provoked.[1] Are you in there, Mum? Pangolins are known to curl up into a ball in defence. I’m no pangolin biologist. Perhaps tired Mums also roll up when they want a … Read More

The 2019-nCov coronavirus outbreak: all together now - Code for life

Feb 01, 2020

There’s so much being reported about the ‘Wuhan’ 2019-nCov coronavirus outbreak it’s confusing. Here’s an outline of some aspects of what scientists are looking at, some places to follow the story, and a few tips for reading the science. Yesterday Tedros Ghebreyesus, the Director General of the World Health Organisation (WHO) wrote, calling for a public health emergency – I am declaring a public health emergency of international concern over the global outbreak of #2019nCoV, not because of what is happening in #China, but because of what is happening in other countries. Not (yet) a pandemic call The WHO International Health Regulations Emergency Committee is not calling 2019-nCov a pandemic.[1] Formally it is a ‘public health emergency of international concern’ (PHEIC). The aim is to assist countries that are less able to prevent entry and spread of the illness. For example, … Read More

The coronavirus outbreak: what is R0? - Code for life

Jan 29, 2020

There are a few misunderstandings about the coronavirus outbreak from Wuhan getting around. Below is a short explanation of one of them: what is R0, and what does it mean. Current estimates for R0 centre around the mid 2s—call it 2.5 or thereabouts—not the higher values some are scare-mongering online. In following posts I may explain other things—if there’s something you’d like covered, let me know. What is R0? R0 (R-naught) is the basic reproduction rate, how many other people one infected person typically infects. I’ve emphasised typically as it is an average of many different scenarios. R0 estimates also assume everyone is susceptible to the disease. You’ll often see these quoted as a single number. In practice a range of scenarios are played out in modelling, with a range of values for R0 estimated. The single figure … Read More

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