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 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

The loose boobies of deathly cold, humour, entertainment, and science communication - Code for life

Feb 02, 2019

Last night a clever tweet written by art+science fan ‘girlyratfish’ (@girlyratfish) amused me: – Her riff of the TV news image uses a clever analogy to explain why climate change has affected the polar vortex. It reminded me of an issue in science communication: how do you reach those who never watch or read science news? There‘s a suggestion in the science communication literature that most adults get their science information from entertainment. The thing there is that they’re not looking for science, they’re looking for entertainment and whatever science they get is on the by-and-by. In the salon Forgive me for the stereotypical setting ladies, but imagine our not-seeking-science gal is setting in the salon looking in the magazine pile for something to read while her turn comes up. Is she more likely to … Read More

For new parents or parents-to-be facing vaccine opinions - Code for life

Jan 29, 2019

For new parents or parents-to-be the wildly different opinions about vaccines must be very confusing. This one’s for you. It’s also for people who pass on vaccine messages to their parent or parent-to-be friends. (If you’re concerned about the apparent length of this article, the main body of the article is short.) Half of all parents with small children are shown what people or groups opposed to vaccines say. That finding is from a report by Royal Society for Public Health in the UK. I imagine it’ll be same here. There’s a lot of misinformation out there; they miss the real comparison. The real comparison The two options are, vaccine or no vaccine. So the real comparison is: are you better off with the vaccine than without it? What we all want is the safest of the two options. Read More

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 Dunner-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 Dunner-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