Anniversary day for Code for life

It’s year since my first article on this blog. Happy blogoversary to me!

Although I wrote a couple of guest posts at Alison’s bioBlog before starting Code for life, and recycled my ‘About’ page as an introductory post on September 24th, my first article, Scientists can’t write?, was written on September 30th, 2009. (I also published just two articles online in 2002 in an aborted bioinformatics/science column.)

I’ve posted 360 articles (excluding this one) and received 1790 comments. (Bear in mind I often use comments to add follow-up information.) I’ve received whole lot more spam – over 63,000 spam comments and counting…!

I’m allowed to indulge myself for one day, I think. Below are some I have gathered (far too many) picks from my first year of blogging. This list is really for my own use but you’re getting the benefit. Or misery depending on your point of view. Well, you don’t have to read them: you can ignore them…

These aren’t necessarily the ’best’ of what I’ve written, nor the articles that have attracted the most comments (which tend to be health-related issues that got over-taken by advocates). They’re just ones that appeal to me.

Science

• Monkey business, or is my uncle also my Dad? I’m still getting a couple of visits a day to this early post. For male pygmy marmosets, their genetic father could be their uncle. Confused? Check it out.
• Metagenomics-finding organisms from their genomes I’d write this differently now, but it’s an interesting topic.
• 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 both unnatural really.
• 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 are in some aspects of epigenetics: here I make a gentle prod at a journalists’ over-selling epigenetics’ claims.
• Aww, crap. Some pitcher plants have adapted to be tree-shrew toilets…
• Testing common ancestry to all modern-day life A gentle introduction to Theobald’s work providing quantitative evidence that life on earth has a single origin.
• 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 also tie knots, threading the chain through itself.
• Epigenetics and 3-D gene structure This article was probably a bit much for most readers, but it is an attempt to gently introduce one of the best-studied examples of epigenetics controlling the 3-D structure of a gene and hence how it functions.
• 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.
• Autism – looking for parent-of-origin effects The last few years have seen large-scale efforts to locate the genetic components of autism. One promising avenue is to look to epigenetic effects.

Science communication

• Scientists can’t write? Numero uno. My first article, quibbling at Allan citing Stead’s historic words of advice to editors.
• Science journalism–critical analysis, not debate A bit of a tricky subject, but one at the heart of much poor presentation in the media.
• Note to science communicators–alleles not ’disease genes’ Misuse of this term gets my goat sometimes.
• Media thought: Ask what is known, not the expert’s opinion It’s not opinion that matters, but what is known.
• Post-embargo publication delays: be gone Seeing articles about papers that are post-embargo but not yet available is just plain annoying and wrong.
• Molecular biology in museums This didn’t seem to appeal to readers, when I look at science communication in museums, I worry molecular biology is poorly represented.
• Writing a popular science book; links and writers’ warnings One day I might be foolish enough to try write my own…
• To link or not to link: is that the question? and To link or not to link: mainstream media and no links at all I joined in the endless effort of encouraging mainstream media to use links in their online stories.
• XMRV prompts media thought: ask for the ’state of play’ I decided to use the continuing saga of the ‘possible’ association of XMRV with chronic fatigue to illustrate a need for media to consider the ‘state of play’ of the science being reported. (The comments got taken over by those with particular positions on the science, not the media issues.)
• Vitamin C, swine flu, media, lawyers A local documentary with a very uneven presentation prompted some concern.

Health-related

I’ve written several posts head-butting various natural health lunacies over the year. I’ve opted to skip most of them here. They’d make this collection grumpy and beside they feel repetitive to me as the people promoting these ’cures’ make the same errors repeatedly…

• Autistic children and blood mercury levels Leaving aside autism, the study covered here reveals where we get mercury from.
• Book excerpt — Losing the faces of your wife and children A rather touching, and intriguing, excerpt from a book I was reading at the time.
• Genetic tests and personalised medicine
• Minorities, disabilities and scientists Even if this is too much to read, the silly pictures were fun. Hearing aids like you’ve never seen…
• Monday potpourri: maps, malaria in the USA, cholera in Dunedin and vaccines Three very short pieces chain together a line of thought.
• Popularity does not mean effectiveness or sensibility This short post is my attempt to show up a common fallacy in a fun way.
• 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.
• Homeopathy check-up: Not in the health system, disclaimers on labels Homeopathy is one of the silliest things around… (I’ve written a lot on homeopathy. It is admittedly a soft target: that it even exists ’in this day and age’ is bizarre.)

Bioinformatics and computational biology

• Computational biology: Natural history v. explanatory models ‘Stamp collecting’ or constructing models to hang data on?
• Bioinformatics — computing with biotechnology and molecular biology data Reviving a piece originally published in 2003 in a local scientific journal.
• Retrospective–The mythology of bioinformatics My most-visited article over the year was this retrospective (originally published in 2002) looking at the origins of bioinformatics.
• Developing bioinformatics methods: by who and how Best that the developer be someone with a genuine need for the algorithm themselves and actively use it.
• External (bioinformatics) specialists: best on the grant from the onset Talk to the specialists you are likely to need for your research before writing the grant application.
• Reproducible research and computational biology Academics’ main aim to create papers: is their work fully reproducible to others?
• The roots of bioinformatics Introducing a series of perspectives on the origins of bioinformatics, with some thoughts of my own.

Computing

• Windows 7 on Apple computers Virtualisation opens doors.
• Linking text and visual content Towards better interactive online documents and content.
• Bibliographies-why can’t research papers self-document what they are? I’d like to see documents have DOIs as meta-data (not in the text, in the encoding of the document).
• The iPad: a device to consume, not produce In which I think David Pogue has a good point about the early iPad reviews.
• The iPad: a cat toy? and iPads for the disabled both present video of usages exploiting the simple manual interface of the iPad, the first cute, the second serious.
• Consumer brain-computer interface A remarkable interface that ‘learns’ basic brain patterns to let users control their computer mentally.

Practicing science

• Buddies, annoyances and depression Although understandably not a popular topic, I think universities and research institutes could offer more pro-active support for their students and post-docs.
• Forgetting older science In which I worry that PubMed (and it’s ilk) are causing a (temporary) lost of older science.
• Advice for students heading to university Encouragement for suggestions, starting with a few of my own.
• A course for all degrees: PHIL 105, Critical Thinking I never had formal training in philosophy or logic, but this looks to be a course every student should take.
• You can change the ideas, but not the data I overhead Professor Lawrence saying this to religious students that crowded around him after his public lecture. It resonates with me and not just in science: advocates of pseudo-science (e.g. those pushing unsubstantiated ’remedies’) often try replace data with ideas of their own.
• Professors, lost souls with great oratory power? Leading from a charged passage in a novel I was reading, I asked if readers thought this a stereotype of professors. (Some didn’t.)
• What is your relationship with your research notebook? We all have notebooks of one kind or other, but relate to them differently.
• Describe your fantasy institute I picked up a meme travelling around the science blogs – invent your dream institute, offering a few of my wants.
• This discovery is mine (for a little while) That little passage of time that you know something no-one has is a motivating force for many scientists.
• Know the history of your field, be it science or pottery Knowing the history of your field clues you into why things are as they are, beyond pure logic taken at face value.
• Career paths, redux – the academic research career is the exception In this article, I gather the thoughts from several older articles that suggest Ph.D. graduates, and academia in general, need to look more widely at where post-graduate degrees are used.

Trivia and fun

I’ve presented a lot of these, but have left most aside as these most often highlight someone else’s content (esp. videos) rather me bringing much to them.

• Digital smiles I rather like this little piece, although as so few people read it I guess I am alone in thinking that!
• Fellatio by Fruit Bats Prolongs Copulation Time The post barely says anything, but who could pass up an opportunity to write a title like that?
• Visual illusions, change blindness and autism and Too much attentiveness leads to inattentiveness look at attentive blindness.
• Neti pots now validated as sound science? What a photo.
• Scientific baking. Great for those lab meetings or kids’ parties Science-themed cookies galore.
• All this talk about 3-D movies and TVs is depressing I can’t see in 3-D… here I also write about viewing 3-D graphics, which I do as part of molecular modelling.
• Map shows New Zealand with lowest death rate on earth in 1856, over 11 in 1000 dying Ian York is great at digging up historic maps related to medicine. While exploring one on his blog, I spotted a connection with early NZ medical history.
• Preconceptual science, the dismissal-ness of it all I put this up in part because of the pseudo-science of many natural health promoting take a similar approach.
• Rex and The Wrong Trousers – uncanny resemblance? Aardmann kindly allowed me to compare The Wrong Trousers with Rex.