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.

Making a list of books to share? Link to review or author sites, not that company - Code for life

Dec 08, 2018

It’s that time of year that people share lists of books that others might like to read. Often book lists offer a link to where a reader might get the book. Please don’t link to companies. Link to review or author sites. If you’re like me, you love to see new reading ideas. Even if they make your wallet wince… But it’s frustrating to see book list after book list promote a company. Book lists (and their makers) can be neutral just as easily by linking to review sites, or with a little more effort link to author sites. Review sites will, in turn, link to all of the main resellers and they offer immediate access to reviews. I typically use GoodReads, but there are alternatives. There’s no extra effort involved. You do the same search for the title … Read More

Neti pots to brain infections - Code for life

Dec 08, 2018

A few years ago I posted this startling picture. I’ll admit using neti pots looked pretty potty to me then. It still does. I thought it looked like the sort of thing someone would do for a party trick. Y’know: eww, look at the water come out my other nostril. A quick look around the internet revealed it has it’s practitioners. It looks innocent enough, but spare a thought for a Seattle woman who died of a fatal amoebic brain infection after using a neti pot. Hannah Rodriguez’s article is an excellent piece of medical science reporting and well worth reading. (Go the Seattle Times — it’s great to see an editor taking on this sort of material.) It might be OK for occasional use I noted in my earlier piece that, perhaps surprisingly, there is evidence that used … Read More

Genome-edited babies – what’s the worry? (#1) - Code for life

Dec 03, 2018

He Jiankui’s[1] experiment has brought the world’s first deliberately gene-edited babies into the world, twins nicknamed Nana and Lulu. He edited the DNA of their embryos, hoping to make them resistant to infection by HIV. I see a lot of people writing comments like, “Genome-edited babies – what’s the worry? We’re going to start it sometime. We can start here.” This misplaced enthusiasm thinks genome editing ‘just works’, but it’s not that simple. In the longer-term broad genome-edit embryos might be inevitable, but what was done in this case is not “OK”. Balancing this is misplaced worry, not helped by sensationalist headlines. The devil is in the detail, they say. Here I’ll give a ‘lite’ take on the biological issues. This one is for every reader. If there is interest I can give geekier a take later. I’ll leave ‘administrative’ concerns … Read More

Human gene-edited babies: hold the horses - Code for life

Nov 28, 2018

Time moves on; this story has too. Readers might like to try my more recent piece, Genome-edited babies – what’s the worry?, which covers the biological aspects of what was done. For those following the news that a Hong Kong-based researcher claims to have brought to term human gene-edited babies: hold the horses. I’ve been trying to put a story on this together. I see cracks in the story and now some extraordinary claims made online from sources that at least deserve consideration. Something doesn’t look right, likely a lot of things. A retrospective approval? Like a few others I noted that the English-language clinical trial approval is retrospective. That form is dated as being registered on 11-November-2018, and refreshed on the 26th November. The accompanying Chinese-language paper form (which I can’t read) is dated 7th March 2017 … Read More

Glyphosate and TIME magazine: writer employed by advocacy group a dubious choice - Code for life

Nov 24, 2018

TIME magazine has a story on DeWayne ‘Lee’ Johnston who took Monsanto to court claiming RoundUp caused his non-Hodgkin lymphoma.[1] The story has obvious appeal, but is crying out for balance and it’s provenance is, to be kind, awkward. I’d love to read his account of his experiences since the trial — but from a source I can trust. I’m dubious that a writer employed by an advocacy organisation can be sensibly used as a journalist. A reply I responded on TIME’s Facebook page, I’d encourage TIME to use independent science writers to cover contentious science-related stories. Your magazine has, or should have, a higher standard than drawing emotive pieces from advocacy groups unchallenged by balance. That Johnson’s version of his story has obvious human appeal ought to be … Read More

The origin of a false claim: projecting demons - Code for life

Oct 24, 2018

Seeing the origin of a false claim from its very beginning gives insight into where they come from. Contentious topics have many claims online, many completely untrue. Knowing how false claims arise might help us resolve them. It’s also a reminder if you see a claim, especially an emotive one, it pays to check first. Here’s one from people projecting something they oppose onto a straight-forward, accurate information source. They didn’t ‘misinterpret’ something complex, they put their projection on something that had emotional resonance. Let’s have a closer look. A deer covered in fibromas (benign growths) This photo has gotten about in some circles on the internet,[1] Some people say the deer developed these fibromas from eating plants sprayed with glyphosate. Not true, not at all; more on that later. How did this claim come about? When I … Read More

NZ EPA is to review 40 chemicals, not glyphosate - Code for life

Oct 18, 2018

The NZ EPA is to review 40 chemicals it has selected as of highest concern. This list doesn’t include glyphosate. We all like to know what we’re up against when using chemicals, so that we can avoid unnecessary risk. That’s one of the aims of the EPA:[1] to offer rulings and information to help us. I’m interested in genetically-modified organisms (GMOs) and other genetic techniques like gene editing. Knowing the history of a topic helps to see where things are coming from. Glyphosate (and RoundUp[2]) has been demonised by groups opposed to GMOs: attacking glyphosate is seen as a way to ‘get at’ one company that produces GMOs, Monsanto. It’s also leveraged by some pushing ‘organic’ farming. Where do things stand with glyphosate, and how does the EPA’s shortlist reflect Eugenie Sage’s statement that she was considering asking the EPA … Read More

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