About Code for Life

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

Welcome to Code for Life.

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 permanent. One day (…) I may replace with something reflecting the blog contents. The image shows 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 of my articles target a general audience. I’ll try let you know if I think an article is a bit geeky. (Once in a while I assume some basic background for those with deeper interests.)

Topic areas include:

• Genetics, epigenetics, genome editing and gene therapy, genomics, 3-D genome structure, evolution and so on. Science produces stunning and unexpected findings each week…
• Human biology, esp. cognitive neuroscience and rare diseases or disabilities.
• ’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 commentary.
• ‘Natural remedies’ vs. science-based medicine. The naïve presentation of some of the ‘woo’ can be appalling.
• Vaccination. (I now write on this less often: this is Helen’s specialist area and covered in her blog, Diplomatic Immunity.)
• Genetically modified-organisms (GMOs), genetic engineering (GE) and gene therapy.
• Issues within science, especially within New Zealand. Science is a great enterprise, but there’s always room for improvement.
• Developments in computational biology.
• 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. I’m frequently embarrassed by things I didn’t know… 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

For readers of the blog, my background covers molecular biology, (molecular) genetics, bioinformatics and some important related aspects like evolution. Molecular biology and molecular genetics underpin a great deal of modern biology—almost all of it—and apply to many seemingly different topics.

My formal training is in both biology and computer science. Readers might think a computational biologist mostly reads computer methods. I read these, but more often read biological research, the source of the data and questions I work with.

Original science writing involves a strong understanding of the concepts involved in biology. To make meaningful representations of biological systems, you need a sound understanding of the core biology. This working from core concepts underpins a lot of my writing. They’re a natural fit.

Work-wise 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’. 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 offer science writing, or other work related to science communication (e.g. editing). Currently (2019) I am focusing on writing projects.

Disclaimers and all that

Once in a while someone opposed to GMOs, glyphosate, vaccines, or similar accuses me of writing on behalf of companies, usually implying a multinational agricultural or pharmaceutical giant.

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, ‘chemical’ or pharmaceutical companies. My research work is not dependent on GMOs, vaccines, etc., either. (The work I do is computational analysis of genomes and other molecular biology data, or science writing – not experimental work.)

My writing here is my own. I’m an independent consultant. These leave 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, bring what is known or not to people, without potential biases from contributing to making these products, or by having financial benefits.

Contrary to what some think, I spend a great deal of time trying to understand people’s objections. It’s hard to do that. Many insist on being combative. Some block people with open views from their forums, disabling me from learning what troubles them. Despite this, I do what I can.

I have not been paid to write any of the articles I have written on Sciblogs. (I am open to contracts for science writing as an independent, freelance science writing or consulting work. For either, being allowed to write (or speak) independently and freely matters to me.)

On product names and (apparent) endorsements

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

Comments

(These suggestions reflect how I view comments. Sciblogs has a formal comment policy that runs over-and-above these.)

Friendly and open discussion is encouraged. Feel free to put forward your views or ask a question – don’t be shy, jump in! The main thing I ask is that people be respectful of others.

The first time you comment, it’ll be held up for approval. This is just a simple way of filtering out spam. Once your first comment is approved, your comments will post immediately.

More than two links included in a comment will cause it to be held up for moderation. (This is also related to filtering spam; comments with many links tend to be spam.)

I prefer people to use full real names as it encourages open discussion. While readers can use pseudonyms please don’t use companies’ or organisation names, or other people’s names. You’ll want to have a wee think and get your username right the first time, as changing them is discouraged (to avoid sock-puppets).

Comments should contribute to discussion of the topic introduced in the article. Natural digressions as discussions evolve are fine, but please don’t use comments to promote or introduce your own, unrelated interests.  Make your own blog for that!

If comments read as promoting a business they’ll likely be treated as spam and deleted, or edited. It’s a judgement call; please don’t get annoyed about it.

Comments cannot be used to attack people. I will call people out on this.

(Now mostly for historical interest: To help keep conversation open and friendly, if a commenter continues to be argumentative, slighting others, etc., after being asked not to I may suspend them from commenting for a few days. If a commenter tries to write to me or the blog while they are ‘on probation’ the suspension is extended, cumulatively. Best to sit it out. 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 or permanently block them.

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 with no commercial interest where the content might be useful to others. Commercial outlets should be aware that unlike most of those writing at Sciblogs I don’t do this writing on the back of a salary, and so tend to have similar views to freelance writers.

Writing samples

I’ll try update this… some time! In particular it mostly leaves out several large topical issues like genetic engineering, gene editing.

Below is a list of articles for general readers that give some feel for my short(er)-form writing interests. Generally older articles are nearer the top. I have, for the time being, left out most of my writing not related to 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 effort using narrative form to explore 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 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). Some time I should add newer examples, too! 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, epigenetics, the 3-D structure of genomes, gene therapy efforts and so on.

[Last updated 13-February-2019.]