About Code for Life

Re-introducing Code for Life: notes about what this blog is, disclaimers, comment policy, copywrite, and writing examples.

Welcome to Code for Life. I hope you get something out of my modest efforts to explore science.

What’s with the name of the blog?

Code4Life was a name I considered for my consultancy, BioinfoTools. It plays on a number of things related to my work and what I write about:

• My work involves programming (coding) for life sciences (molecular biology and genetics).
• The data I examine and write algorithms for are the sequences of bases in DNA (genes, genomes), the amino acid sequences of proteins (enzymes, hormone receptors, etc.) and the three-dimensional atomic structures of proteins. These are the codes in life, the ‘information base’ of biology and life. (If readers are interested in an introduction to this, let me know.)
• It can mean moral codes and other ‘rules’ people guide their lives with. I won’t be writing about this much about this in the sense of rules for life, but I may look at role of honest skepticism, logic and testing in science.
• You can stretch it to be about writing about life sciences, writing being a code of sorts.
• It has nothing to do with The Code for Life, an album of the heavy metal band Warrior. I am not a fan of heavy metal. (Sorry, heavy metal fans.)

The banner photograph

My current banner image is temporary (but seems to permanent); I hope to later replace with something reflecting the title of the blog. The image shows where the village I was based in on the Otago peninsula. (The image is open source, obtained from wikimedia and edited using GraphicConverter v6.5.1.)

Topics

Most articles target a general audience. I’ll try remember to let you know if I think an article is a bit geeky; once in a while I write assuming some basic background for those with deeper interests.

Topic areas include:

• Genetics, epigenetics, genome editing and gene therapy, genomics and evolution. Science is an endless outpouring of stunning or unexpected findings each week… (Readers might think a computational biologist mostly reads computer methods; I mostly read biological research, the source of the data I work with.)
• Human biology, esp. cognitive neuroscience and rare diseases or disabilities. The workings of our minds is fascinating stuff and it’s intriguing to explore others’ lives.
• ’What science is’, what the basic terms mean, how to read a scientific report, sorting out the good stuff from the bad.
• Science communication, including the media.
• ‘Natural remedies’ vs. science-based medicine. The naïve presentation of some of the ‘woo’ can be appalling.
• Vaccination. (I now rarely write on this: this is Helen’s specialist area, and covered in her blog, Diplomatic Immunity.)
• Genetically modified-organisms (GMOs) and genetic engineering (GE).
• Issues within science, especially within New Zealand. Science is a great enterprise, but there’s always room for improvement.
• Developments in computational biology (my research/consulting area – I also offer a sideline in science communication and editing).
• Computing & computers (the tools of my trade; geeky stuff can be fun!)
• Plain old ruminations. We all have our navel-gazing days…

Readers are encouraged to ask questions and suggest topics they’d like covered.

I don’t claim to be a gifted philosopher or an expert on matters far and wide, in fact I’m frequently embarrassed by my sheer stupidity… Aren’t we all? Readers are welcome to correct any errors but please substantiate your claims. You’ll help yourself if you are polite about corrections.

My scientific background

By training I’m a computational biologist, a biologist who applies computational methods (algorithms, statistics, etc.) to biological problems, and who develops computer tools for biologists to explore data from genes, genomes and proteins. I work as an independent scientist through my consultancy, BioinfoTools, contracting to research groups and biotech companies. More about my research interests can be found on the consultancy website.

A more commonly-known name for the field is ‘bioinformatics’ but strictly speaking that term originally applied to a subset of the field. Some of us who started before the genome era prefer the computational biology label, for a variety of reasons.

I also take writing contracts, or other work related to science communication (e.g. editing).

Disclaimers and all that

Once in a while someone accuses me of writing on behalf of companies, usually a large multinational agricultural or pharmaceutical giant. Those asking are typically opposed to, say, GMOs, glyphosate, vaccines or similar.

So here goes.

If you think I’m a ‘shill’, I’m still waiting for that large check you’re imagining. Or even a very small payment.

I have no ties with agricultural or ‘chemical’ companies. I’m not tied to making GMOs, vaccines, etc., in an academic setting either. My work is in computational analysis of genomes and other molecular biology data, or science writing.

My writing here is my own. I’m an independent consultant. It leaves me in a good position to speak on contentious topics. I can use my training as a biologist to get to the bottom of the issues, and bring them to people without having potential biases from contributing to making these products, or by having indirect benefits such as a research grant (i.e. income) that aims to work on, say, GMOs, etc.

Also: contrary to what some think, I spend a great deal of time trying to understand what people’s objections are. It’s hard to do that. Many insist on being combative. Some block people with open views from their forums, disabling me from accessing their views. And so on. Despite this, I do what I can.

On product names and (apparent) endorsements

Unless I explicitly endorse something, I’m not: mere mention of a product is not an endorsement.

Comment policy

More than two links included in a comment will cause it to be held up for moderation.

I would like to encourage friendly and open discussion. People are encouraged to put forward alternative views – don’t be shy, jump in! The main thing I ask is that people be respectful of others.

To help keep conversation open and friendly, if a commenter is too disruptive, continuing to be argumentative, slighting others, etc., after being asked not to I may choose to suspend them from commenting for a few days or a week. If a commenter tries to write to me or the blog while they are ‘on probation’ the suspension gets extended, cumulatively – best to just sit it out. I only set the initial week – extensions are in the hands of commenter. For a little ‘geek flavour’, the cumulative increase follows a Fibonacci series. Finally: I would like to never have to exercise this, but if someone persistently disrupts what I would like to achieve with this blog, I reserve the right to ban them.

Comments that I consider are aimed at promoting a business rather than contributing to a discussion will likely be treated as spam and deleted. (It’s a judgement call; please don’t get annoyed about it.)

Readers are welcome to use pseudonyms, but please avoid using commercial companies’ names.

Copyright

Journalists, editors & publishers, a gentle reminder: the material on my blog is copyright. You are welcome to contact me if you wish to use this material. Generally I’m happy to help those where the content might be useful. Commercial outlets should be aware that as a consultant I don’t do this writing on the back of a set salary, and so tend to have similar views to freelance writers.

Writing

Below is a list of articles for general readers that I consider are better efforts. Generally older articles are nearer the top. As this is intended to list those for general readers I have, for the time being, left out science-related trivia, book reviews and material aimed more technical audiences such as articles on computing technologies or computational biology.

• Monkey business, or is my uncle also my Dad? For male pygmy marmosets, their genetic father could be their uncle. Confused? I still get regular visits to this early effort.
• GMOs and the plants we eat: neither are ‘natural’ An attempt to point out that, among other things, both our ’natural’ foods and GMOs are not really ‘natural’.
• Deleting a gene can turn an ovary into a testis in adult mammals I was startled to learn that ovaries may not be permanently defined to be ovaries in some adult mammals.
• The inheritance of face recognition (should you blame your parents if you can’t recognise faces?) Prosopagnosia is surprisingly common and has fascinated me for years.
• Epigenetics, a confused muddle in the media My biological research interests involve some aspects of epigenetics: here I make a gentle prod at epigenetics being oversold in media.
• Aww, crap. Some pitcher plants have adapted to be tree-shrew toilets…
• Book sales, frumpy readers, and mental rotation of book titles While at the famous-in-Dunedin 24-hour book sale I wondered if there was a ‘right’ orientation to scan rows of books. (Nominated by a reader for OpenLaboratory 2010.)
• I remember because my DNA was methylated Epigenetics meets neural systems, meets memories. I get a little lyrical in the beginning, which I confess I enjoyed.
• Boney lumps, linkage analysis and whole genome sequencing Looking for the basis of inherited bone spurs.
• Temperature-induced hearing loss This was a surprise to learn: a few rare individuals have temperature-sensitive hearing, losing it when they have a high body temperature.
• Loops to tie a knot in proteins? How proteins fold is an interest from my Ph.D. student days. A few proteins do more than just collapse on themselves in folding: they tie knots, threading the chain through itself.
• Preserving endangered species — of gut microbes A interesting idea – new to me – that we should not only conserve rare species of animals but also microbes in our gut that reflect now-rare diets.
• Coiling bacterial DNA DNA in cells is rarely ‘naked’, it is packaged with proteins. This article presents a new model for bacterial DNA packaging.
• Finding platypus venom Researchers cleverly did not extract the venom, but created possible venoms by comparing the platypus genome with known venomous proteins and expressing the genes that matched. (One of my favourites, platypuses are extraordinary creatures.)
• Autistic children and blood mercury levels Where we get mercury from.
• Genetic tests and personalised medicine
• Monday potpourri: maps, malaria in the USA, cholera in Dunedin and vaccines Three very short pieces chained in a line of thought.
• Honey’s antibiotic properties found? One group played off different compounds found in honey to determine the contributions of each to antibiotic effect and the strength of combinations.
• Rubella, not a benign disease if experienced during early pregnancy As a ‘rubella kid’ this topic is close to my heart in it’s own way.
• Autism – looking for parent-of-origin effects Some genes are expressed in a way that depends on what parent the gene was from. I report on a study looking at autism this way.
• Doggie ERVs We have in our genomes endogenous retroviruses, ERVs. Turns out that man shares ERVs with his (her) best friend.
• Haemophilia – towards a cure using genetic engineering Using ‘designer’ zinc finger proteins to insert a working copy of a missing gene.
• Carrots for my neighbour A longer-form effort exploring growing veges, genetic modification and supplementing plants with additional minerals in this case, calcium.
• C’s founder is no more Explaining to non-geeks why Kernigan’s passing means much to those in the computer science and computing industries.

Footnotes

I hope to revise the list of articles above to strict reverse order of publication (i.e. most recent article first), and add newer examples. An older list of articles can be found on the anniversary of my first year of blogging.

I have countered various health claims and pseudo-science over the years through a perhaps misplaced sense of moral obligation. I suspect these articles stick in mind for some readers. For those readers, lest you come away with the wrong idea, I’ll tell you that prefer to write articles about science itself, particularly genetics and epigenetics.

[Last updated 26-August-2018.]