Not the best microbiology reporting: New Scientist on Lonely Bacterium

Too traumatized by the events in Connecticut to write much here but trying to focus on work for but so here goes.

Uggh. This article does not sit well with me: World's loneliest bug turns up in Death Valley - life - 13 December 2012 - New Scientist

The parts of the article I don't like?

• "Uniquely, the bacterium has evolved to do without the sun's energy, relying only on hydrogen and sulphate, which can form naturally in its subterranean home." Umm ... how is this unique? What about all the other chemoautotrophic microbes known? What about deep sea vent communities? WTF this claim is so completely wrong I don't know what to say.
• The article implies that one can use percent identity of the DNA of microbes to tell us how recently they shared a common ancestor. Hmm ... Is that under the model of "all organisms evolve in exactly the same way"? 
• "Until recently, biologists thought that the species was confined to South Africa's depths". Really? So - the organism was discovered in one place and therefore we the biologists thought that it was confined there? 
• Title: "World's loneliest bug turns up in Death Valley".  Sure - in the one system in South Africa this did seem to be a relatively lonely organism.  But to presume that this was the only place the organism was found was just silly. 

There.  Alas, writing this did not make me feel any better.  But it did distract me for a bit

Appendix story in need of an asterix and appendix and a retraction

The appendix. What is it good for?

That was the topic of a series of news stories and a press release last week that somehow I did not blog on even though Thomas Goetz sent me the story. I was busy at a conference mind you but this is such easy pickings. This has got to be one of the poorer science reporting jobs done in a while and also one of the most misleading press releases I have seen. In the press release there are a series of phrases that make it seem like the scientists have discovered a major function for the appendix:

Appendix Isn't Useless At All: It's A Safe House For Good Bacteri

AND

William Parker, Ph.D. is one of a team of scientists to discover that the appendix has a function -- protecting beneficial bacteria.

And the reporting seems to have bought this hook line and sinker. See

• The appendix does have a use – re-booting the gut
• Appendix: It’s not useless after all
• Scientists discover true function of appendix organ
• Purpose of Appendix Believed Found
• Study: Yes...your appendix has a purpose

The problem? Wanna know what they actually did in their paper? Well if you have a subscription to the Elsevier published Journal of Theoretical Biology you can go read the paper here. If you do not have a subscription I quote some of the abstract for you

We propose that the human appendix is well suited as a “safe house” for commensal bacteria, providing support for bacterial growth and potentially facilitating re-inoculation of the colon in the event that the contents of the intestinal tract are purged following exposure to a pathogen

The key word here is "propose." In the paper, they do not actually really show direct evidence for any function. And the title of the journal should hint at this - the Journal of Theoretical Biology. It is a place for scientists to put out new hypotheses, including those that have little evidence behind them. Nothing is wrong with such a journal. Hypotheses are a good thing.

Sometimes things in this journal have lots of evidence and in other cases they do not. In this case I do not think they present any direct evidence and the evidence they present is at best circumstantial and unconvincing. Basically, they lay out a hypothesis that the appendix may have some role in the immune system. Then they highlight a further series of circumstantial connections and inferences to come to the idea that the appendix may have some role in harboring "beneficial" microbes in the gut.

It is an interesting theory. It could be true. But the evidence they present is very very circumstantial and weak at best. They seem to claim that stronger evidence would be impossible to obtain since doing experiments on humans is not easy. But given the large number of people who have had their appendices removed, one could actually do a retrospective study of how well such people recover from pathogen attacks or the use of antibiotics. Until such a study is done, it would be wrong to say these authors discovered anything. What they did is propose a hypothesis for a function of the appendix. The hypothesis might stimulate discussions and some research but lets not oversell it.

In many ways you could consider their hypothesis much like the hypothesis that microbial life existed on Mars. This Mars idea is plausible. But there is currently no evidence for it. Imagine if the reporters said "Life found on Mars" in relation to a paper proposing that life might have existed on Mars. The reporting here is no different - though the stories got it wrong. In part this is because the press release is so misleading. But reporters have got to go beyond the press release or the initial story. Just see Carl Zimmer's blog for a great example of bad reporting.