Finding the truth is a waste of time, scientists say

Before bioinformatics, I worked in both biochemistry and microbiology labs, including a stint in the field of extremophile biology. So like many other people, I’ve been following the “arsenic life” story with great interest.
It seems that far more has been written about the publication, the manner of its announcement, the ensuing online debate and the personalities involved than about the principal scientific question: can arsenate substitute for phosphate in biological molecules? My opinion, for what it’s worth, is that the Science paper presented no compelling evidence for covalently-bound As in DNA and that the editors should have asked the authors either to do better experiments or tone it down.

Now, Nature News reports that the criticisms are in, the authors have responded and as part of their response, they are willing to share samples of the bacterium with other researchers for further analysis. Good on them – that’s the right thing to do. What’s bewildering and saddening are some of the responses to the offer. They include (paraphrased): “I wouldn’t waste my time because I don’t believe it”, “if there is no arsenate in the DNA, how could I publish in a high-impact journal and get a job?” and “I have the technology to do it but I have better things to do.”

Is this what biological science has become? The single-minded, career-oriented selfish pursuit of the high-impact publication to the exclusion of everything else – including the truth? I’m afraid that the answer is “yes” and I suspect this attitude is what got the authors of this Science paper into trouble in the first place.

This is what those who imagine some glorious future open-science utopia are up against. All I can say is: be thankful for Rosie Redfield and her lab.

Poor reporting: the anti-freeze that wasn’t

Generally, I don’t cover “mainstream” science reporting, but this is too poor to let it pass.

Nature Genetics features a fascinating article about the properties of haemoglobin from the extinct woolly mammoth. Briefly, the researchers sequenced DNA encoding haemoglobin subunits from a sample of mammoth bone and compared it with that of modern elephants. They then altered the modern elephant DNA sequence to match that of the mammoth, expressed mammoth and elephant protein in E. coli and compared the oxygen affinity of each protein. Their conclusion: the amino acid substitutions in mammoth haemoglobin result in an enhanced ability to release oxygen to tissues at low temperature.

You will not find the words “anti-freeze” anywhere in the article. Bear that in mind, as we survey the reporting of this story by various news outlets:

Darwin 2009: multimedia and more

Good to see that the BBC are getting into the Darwin anniversary celebrations. Here’s their informative website with TV/radio shows and special features.

BBC Radio 4 also have a Darwin website. You could do a lot worse than start by listening to Melvyn Bragg’s 4-part Darwin series from the show “In Our Time”. It’s available via the iplayer or as a podcast.

Elsewhere in the UK there are Darwin 200 events organised by the Natural History Museum and the Wellcome Trust.

When information retrieval goes…weird

Bar-tailed godwit

This is a little odd – the tale of the publication that isn’t.

Update: the “missing article” surfaced in my RSS reader on Nov 1; here’s the link

Giant panda genome: mapped or sequenced?

I’m with Ogden Nash who said:

I love the baby giant panda,
I’d welcome one to my veranda

This week, I learned via Keith that Chinese scientists announced the completion of the giant panda genome. An impressive achievement, given that the project was announced in March this year, but what exactly has been completed? Has the genome been sequenced – that is, there are strings of A, C, G and T covering most chromosomes, or mapped – that is, the approximate chromosomal location of most genes determined? The media seem unsure.

• The Australian: Scientists in China have mapped the genome of the giant panda…
• Window of China (the official source, it seems): Chinese scientists have completed sequencing the genome of giant pandas…
• The China Post: The Chinese-led genome-mapping effort…
• Melbourne Herald Sun: Genome sequencing confirms pandas are bears…but then “endangered giant pandas have had their genomes mapped…”
• Indian Express: Genome mapping to find out why Pandas are sex-shy…
• Discovery Channel: Scientists Map Giant Panda Genome…but then later on “by sequencing the genome, we have laid the genetic and biological foundation to gain a deeper understanding of this peculiar species”

And so on. Here’s a Google News search with more hits.

So what has been achieved – sequencing or mapping? If the former, is it really complete (I doubt this) or draft – and if draft, what kind of quality? And where are the data? Nothing in the genome project section of NCBI as yet.

IgNobels 2008

I mark the passing of the years in a couple of ways. One is natural events: the coral tree flowers in mid-winter, the jacaranda flowers in spring, the comings and goings of Queensland’s bird species.

The other is the annual IgNobel award ceremony. 2008 is a vintage year:

• List of winners
• BBC News story
• The Guardian story

It’s hard to choose a favourite this year. Armadillos and archaeology would have to be up there, but based on the idea that how much you laugh correlates with how much you relate, I’m going with: “You Bastard: A Narrative Exploration of the Experience of Indignation within Organizations”, from the journal Organization Studies.

Automatic content for the people

Anyone who has ever built a website knows that maintaining it is a lot of work. There’s just making sure it hasn’t gone offline because the httpd daemon died. Constant monitoring for script kiddies and their SQL injections. Not to mention continually feeding it with fresh content, lest your audience become bored and desert.

I’ve always thought it would be cool to build a site that could more or less look after itself. There’s a myriad of content management systems to choose from, most of which are somewhat hackable in whatever language they happen to be coded in. One of the more mature in this respect is Drupal – which is the engine behind Eureka! Science News. It’s a fully-automated science news portal, using a bunch of customised Drupal modules to aggregate, cluster, categorise and rank articles.

First impressions are excellent. Coders will enjoy this post at Drupal explaining how it all works.

Life on Mars

Late one evening back in July 1997, I was alone in the lab writing my Ph.D. thesis, several months behind schedule. I fired up the web browser (probably Mosaic in those days) on our single computer and discovered that a tiny rover was about to land on Mars. Live, on the web!

When people use the phrase “web design circa 1996″, this is what they mean. It was all very exciting back then. Up came the first image, in near-real-time. Wow!

I’ve been a Mars geek ever since. Yesterday morning there I was again, except this time I was watching live streaming video of the Phoenix lander. After a near-perfect landing, the science is set to begin and it could be pretty exciting. Phoenix is the first lander since the Viking program to dig into and analyse the Martian surface. If there ever was (or is?) microbial life there, Phoenix has a pretty good shot at finding the signs.

Get the news as it happens from:

• Phoenix Mars Mission website
• Spaceflight Now mission status centre
• And even – the MarsPhoenix Twitter channel

Science publication and assessment: our national debate

The Australian, our national newspaper, is usually not my preferred read but does have a good higher education section. Our new government has just thrown out an assessment exercise named the Research Quality Framework (RQF) – it will be replaced with something very similar, no doubt. Disturbingly, Thomson Scientific were given a licensing agreement by the previous government to supply the data for the RQF.

Imagine my delight to find newspaper articles discussing the shortcomings of impact factors, the rise of Google Scholar and the open-source software of Anne-Wil Harzing:

• Research Review Heats Up

“…commercial rivals such as Elsevier’s Scopus database and software built on Google Scholar have entered the market while the rise of research assessment linked to promotion and funding has made academics ask searching questions about the integrity of Thomson ISI as the key player.”

• Metrics debate is the rule

“Australia’s closer embrace of metrics comes at a time of fierce international debate about research assessment.”

Not entirely unrelated:

• Scientists ‘obliged’ to share wisdom – so says the science minister
• Science left to rue a roo genome – on the sorry state of genomics in Australia

Two more signs

1. The blogosphere is alight with the announcement from Science Commons of a protocol for implementing open access data. This Technorati search with keywords “science commons open data” throws up 528 posts, many of which are relevant. I suggest that you also follow developments via Deepak’s blog and links therein.

   Now, this is great news for those of us who care about all things open – open access, “open science”, open data; and people who follow developments in web technology. However, we need to make it relevant and accessible to the people who matter: interested research scientists with the question “how can I make my data more accessible”. Those people are unlikely to subscribe to the W3C mailing list. So rise up blogging community – start writing short, clear informative posts in non-specialist language, aimed at explaining to a bench scientist why they should care and what they should know concerning this protocol.

2. John Hawks has had a busy week following his major publication on accelerated evolution. He writes:

What I most want to point out is that the discussion on blogs is at a very high level — people are reading the paper with much more precision than I have ever experienced in the peer review process

If I could have one wish come true in 2008, it would be for more scientists in academia to realise that so-called “non-traditional” modes of publishing, debate and communication are of equal value (for me personally, higher value) to the old ways that they insist on defending, regardless of the evident flaws in those ways.