Bacteria and Alzheimer’s disease: I just need to know if ten patients are enough

You can guarantee that when scientists publish a study titled:

Determining the Presence of Periodontopathic Virulence Factors in Short-Term Postmortem Alzheimer’s Disease Brain Tissue

a newspaper will publish a story titled:

Poor dental health and gum disease may cause Alzheimer’s

Without access to the paper, it’s difficult to assess the evidence. I suggest you read Jonathan Eisen’s analysis of the abstract. Essentially, it makes two claims:

  • that cultured astrocytes (a type of brain cell) can adsorb and internalize lipopolysaccharide (LPS) from Porphyromonas gingivalis, a bacterium found in the mouth
  • that LPS was also detected in brain tissue from 4/10 Alzheimer’s disease (AD) cases, but not in tissue from 10 matched normal brains

Regardless of the biochemistry – which does not sound especially convincing to me[1] – how about the statistics?
Read the rest…

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:

Read the rest…

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.

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.

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:

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:

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