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.

A gene drive in mice – but only for females - Code for life

Jan 24, 2019

What if you could change a gene in a population by introducing laboratory-prepared animals then just letting nature take it’s course? A gene drive is the informal name given to a process where a genetic variation is set up so that it will be inherited more often in the offspring than it would by chance.[1] In a gene drive each generation has a better than 50% chance of inheriting the new variant, so over time the chosen variant becomes the dominant variant of that gene in the population. Not a new idea and common in nature It’s not a new idea. It’s also something that is actually common in nature. The idea has been around since at least the 1960s, and that ‘selfish’ genetic elements can spread through populations has been known for over a hundred years. What is … Read More

Strongest opponents of GM think they know best but actually know the least - Code for life

Jan 17, 2019

A study just out shows that the strongest opponents of GM (genetic modification) think they know the subject well, but in fact know the least. What does this means for science communication? Especially contentious topics. Doubly so where deliberate misinformation is being offered. Similarly are their lessons for politicians? In New Zealand politicians seem too timid to try correct the legislation and resolve the issue. Invisible faces The paper in question isn’t looking at the Dunning-Kruger effect but it helps to know what this is first. You have to laugh at the example that prompted what has become known as the Dunning-Kruger effect, a bank robber who was baffled to be caught after rubbing lemon juice into his face in the belief it would make him invisible to security cameras At first this seems to just be an example … Read More

Tired of flipping USB plugs over? - Code for life

Jan 10, 2019

If you’re anything like me, flipping USB plugs over is irritating. It’s not as if it takes much time, just that you have to do it at all. Here’s a tip I stumbled onto a few years ago: (advertising) logos face up. When you put the cable or device in, keep the advertising logo face up. I can’t guarantee that will always work—there’s bound to be a few companies that are just ‘different’—but try it with the cables and devices you’ve got, it might be all you need. It may also be one of those cases with crass marketing concerns are actually useful. USB cables are meant to be labelled with an embossed forked-wire icon on the ‘up’ side, like the cable shown on the right. The connecting pins are exposed on the side with the USB logo. This … Read More

Blogimmuniqué 31 December 2018 - Code for life

Dec 31, 2018

Blogimmuniqué – one of my irregular communiqués about the Code for life blog. The end of the year is a time for gathering up stuff, and a time for reflecting. In my case I’d like to let readers have a chance share their thoughts about what directions I could take this blog. (If you haven’t time for reading this, feel free to skip to the sections that interest you, even straight to the comments!) I’d also like to give a bit of an idea of what I’ve been up to over the last few years. Those old drafts If you’re familiar with writing, you’ll know many drafts don’t get published. They pile up over the years! Over the last few days I’ve gone through my drafts and ideas for Code for life. I have 17 pages of drafts for this … Read More

Scientific paper has a face in a turd. Who could it be? - Code for life

Dec 15, 2018

Today I read that a scientific paper has hidden a face in a turd. Who could it be? The paper is research in faecal genomics, sequencing DNA in turds.     It’s aims are fair enough. It’s easier to collect DNA from faeces than from wild animals. A catch is that faeces tend to have DNA from a lot other things in their guts, like gut bacteria. If you’re wanting to DNA sequence the animals that pooped, that’s a hassle. It there a way to do better?     On the third page in the top-left of Figure 1 there is a baboon.     The baboon looks as if it’s just pooped. (And is looking at its turd?)     Looking closer, that turd might have a face in it.   … Read More

Go voyage the great beyond - Code for life

Dec 13, 2018

They charted our lives. As children we read of their plans and their laboured construction. We watched them delivered, blasted into the heavens by the Titans. From time to time we heard of their long journey. They sent us photographs as they passed the outer planets. This week the last left flew past the light of the sun to voyage the great beyond. We grew up in the era of exploring the outer planets. The arc of the lives of those adventurous probes mirror our own. They were the travellers of the Planetary Grand Tour. Not a day seized, but a rare, years-long alignment of the planets. Some of us share their wanderlust to stray far to find the company of unfamiliar things. To visit those places and write to … Read More

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