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.

Newspaper warns of human-induced climate change in 1912 - Code for life

Aug 17, 2018

We’ve had more than 100 years of warnings of human-induced climate change now. It’s nearer 200 years, really. Before records were taken they would be extrapolations rather than observations. Extrapolations are harder for those outside of science to trust, but extrapolations are part of what science does. Looking to where things might go is useful. This pithy, insightful newspaper article is doing the rounds of social media again: The basic idea was in fact well established by then. Alexander von Humboldt is a legendary figure.* In his day he was the equal of Darwin or Goethe. He theorised about human-induced climate change from 1799 onwards. He was one of the first, if not the first, to raise it. His ideas came from observing the effects of deforestation, from seeing changes in flora at different altitudes, and later from … Read More

USA Court ruling on glyphosate— the role of IARC and Eugenie Sage’s call - Code for life

Aug 13, 2018

A lot has been said about a recent court case ruling about Monsanto’s Roundup. Let’s look just at the role of IARC and Eugenie Sage’s call for the New Zealand Environment Protection Agency (NZ EPA) review their stance on Roundup. The role IARC seems to be very little understood. Many media reports (worldwide) on this court case offer a throw-away statement that the IARC report and regulatory rulings conflict. They are not in competition. The regulatory bodies have not “set aside” or “overlooked” the IARC findings. (That’s a lobby-group line.) In practice, regulatory bodies are using the IARC reports as they are meant to. This seems to have confused by objections to IARC’s findings, a parallel issue. Adding to the mix, in New Zealand the Associate Environment Minister, Eugenie Sage, has said she will ask the NZ EPA to … Read More

The ‘Impossible Burger’ is not genetically modified - Code for life

Jul 06, 2018

In the New Zealand media and social media people are talking about this genetically modified ‘Impossible Burger’. Except it’s not. Sorry everyone, but it really isn’t genetically modified. What was genetic engineered is a yeast that makes one of the ingredients used in the ‘Impossible Burger’. It’s just a different way of making that ingredient. The ingredient is the same as in soy plants. All the ingredients in the burgers are the same as in ‘natural’ plants.* A noisy few rush to declaim loudly everytime someone mentions genetic engineering or GMOs, calling to banish the use of a technique, rather than look at each application. Let’s look at this one. A key part of what gives the burger it’s ‘meaty’ taste is a “blood” protein, leghaemoglobin. The one used is actually from soy plants, not animals. Like the similarly-named haemoglobin … Read More

‘Fake author’ papers opposing HPV vaccine retracted, editor’s defence - Code for life

May 28, 2018

‘Fake author’ papers opposing HPV vaccine by ‘Lars Andersson’ are being retracted. The editor of one of the papers has offered an extraordinary defence, railing at the Karolinska Institute. Earlier this month I wrote about a research opinion piece claiming that the HPV vaccine increases cervical cancer in some patients. Among the faults of the comment article were that the sole author faked their name and institution, and that the people it pointed to were almost entirely not vaccinated. I’ve just been alerted that the publisher of this paper, the Indian Journal of Medical Ethics (IJME), has retracted the paper.* According to Retraction Watch three more ‘Lars Andersson’ papers in the Journal of Internal Medicine are also to be retracted. (In a twist of fate perhaps, the editor of this journal is a professor at the Karolinska Institute that … Read More

Apple boards bendy once again - Code for life

May 26, 2018

As you age history repeats itself. Anyone over about 30 will know what I mean. Today I was reading over at ArsTechnica how some of the Apple 6 phones were bendier than earlier models, and Apple knew it. The writer reports, These touchscreen-controlling chips became unseated from the logic board due to bending and flexing with normal use. Back in the day—you knew this would start this way—Apple’s boards flexed all by themselves. Or at least the clones did. As an undergraduate student I spent a vast sum of money on a Sundox, a Taiwanese clone of Apple’s vaunted ][e computer. The ‘e’ stood for enhanced. This model came with 64 kilobytes of RAM, rather than 48. And we could program it using a high-level language that the university taught us called Pascal, named after the famous mathematician … Read More

HIV infection animated - Code for life

May 13, 2018

Here’s a great video of HIV infection animated, showing molecular life at play – Molecular life is fascinating stuff. Complex molecules getting around making life happen. I’ve been following it for 30+ years and it continues to amaze me. It’s a realm where chemistry and physics merge to become life. In this case, an HIV infection taking place. There’s a narrated version on the Science of HIV animations page. I’ve told my version* of the story at the end of this post; see the section What’s happening in the video? below. All that science! The video gives an idea of the rich collection of details scientists use to draw a (mental) picture how life works. Here we’re seeing it visualised. One thing that might not be obvious is just how much work is. Each of the molecular structures and what … Read More

Faking HPV vaccine claims, in more ways than one - Code for life

May 11, 2018

When the author and the core claims of the paper aren’t real, you’re faking HPV vaccine claims in more ways than one. A new paper in the Indian Journal of Medical Ethics (IJME) claims that the HPV vaccine causes an increase in cancers in some patients. It’s first problem is that the author is fake. A fake author Yes, you read right. (There’s irony, too, seeing this in a journal about ethics.) Several sources—including the Skeptical Raptor and Retraction Watch—highlight that the author faked their name. The author claimed to be a Lars Andersson hailing from the Department of Physiology and Pharmacology of the distinguished Karolina Institute in Sweden. The department says that they have no Lars Andersson.[3] Amazingly, the journal acknowledges the author faked his name, but has decided it is OK for him to continue with … Read More

New code for controlling new food varieties (FASNZ; GMO, or not) - Code for life

Apr 09, 2018

New Zealanders and Australians might like to contribute (last-minute!*) submissions to revise Food Standards Australia and New Zealand’s code for controlling new food varieties, FSANZ is seeking input from the community on whether food derived using new breeding techniques (NBTs) should be captured for pre-market approval under the Code, and whether the definitions for ‘food produced using gene technology’ and ‘gene technology’ should be changed to improve clarity. You’ll want to read the consulting paper that comes with this call for submissions. Comments and suggestions welcome I’ll add my thoughts on the need to revise the code tonight, and perhaps an outline of what I might submit. In the meantime I can at least let readers know of the call for submissions.** Late last year I offered an outline of things to consider with current ‘GMOs’. My … Read More

A new organ? - Code for life

Mar 30, 2018

Media outlets the world over are touting the “discovery” of a new organ in humans. I’m not alone in protesting, I agree.[1] The new organ claim is not made in the research paper Importantly, the research paper doesn’t claim a new organ — that’s a claim made outside of the research paper, made by one of the authors. The uncritical repeating of this claim is disappointing, if sadly typical of a social media-driven fuss. That’s click-bait, right? The research shows the presence of collagen-bundle structures in the interstitial space. The paper speculates these might have a “shock-absorbing” role.[2] How the research was assessed matters The author says the research paper was rejected from 8 other journals before getting it out in SciReports, a journal whose peer-reviewers are advised that, Manuscripts are not assessed based on their perceived importance, … Read More

More Wellcome reading - Code for life

Feb 09, 2018

I know many of my readers are, well, readers. (Ha!) I like book prize longlists, as they give you a selection to browse, all of which will be great efforts. (I’d also encourage browsing around the booksellers’ and publishers’ websites, and bookstores: there are excellent books not on any prize shortlist.*) The Wellcome Trust, one of largest medical research charities in the world,** funds an annual award for books, fiction or non-fiction, that “have a central theme that engages with some aspect of medicine, health or illness.” The books “can cover many genres of writing – including crime, romance, popular science, sci fi and history.” To find the blurb for each book on the longlist on their website, you have to visit each page in turn. To help my readers a little, I’ve listed the books with the short topic and … Read More