Ecology

Mike the Mad Biologist

Category archives for Ecology

A Handy Transformation for Microbiome Data

When worked on the human microbiome, I regularly confronted a problem with the data. Species frequencies are almost never normally distributed (‘the bell curve’), and if you want to use standard statistical techniques the data should be normally distributed. The second problem is that the data often have a lot of zero values. That is,…

Consider this a post wherein I engage in some speculation, and hope that I’m very, very wrong. You see, the ‘German’ E. coli O104:H4 outbreak (‘HUSEC041′) has taken a confusing turn: The strain of E. coli blamed for 46 deaths in Germany appears to have resurfaced in France, the French Ministry of Health said. The…

Or maybe wild-ass speculation. As the data continue to come in about the E. coli outbreak in Germany caused by E. coli O104:H4 HUSEC041 (well, everything but the public health and epidemiological data which are a contradictory, incoherent mess), it appears that one of the things that has made this strain so dangerous is its…

When Economists Misunderstand Biology

It really does matter: if economists are going to use biology as a model for their discipline, we need them to understand ours, to help improve theirs. But I’m getting ahead of myself. By way of Brad DeLong, we stumble across this Russ Roberts piece discussing the question of what kind of science (if any)…

I don’t see the need to redescribe the recent paper about the discovery of bacteria that can might replace, in extremis, phosphorus with arsenic, which was overhyped by NASA, was poorly covered by most journalists, and which has compromising methodological problems (for good coverage, read here, here, and here; and snark). But what the paper…

Reporting on the human microbiome–the microorganisms that live on and in us–is quite the rage these days. As someone who is involved in NIH’s Human Microbiome Project, it’s a pretty exciting time because the size and scale of the data we’re able to generate is unprecedented. This also means we have to figure out how…

Philip Mirowski has a must-read article in The Hedgehog Review about ‘The Great Mortification‘: the soul-searching (such as it is) that the economics profession has undergone since 2007. Two key points in Mirowski’s article are really important–and are relevant to most, if not all, intellectual disciplines. The first is “This Is What Happens When You…

While I’m away at ASM, here’s something from the archives for you When I read Olivia Judson’s post about hopeful monsters, I didn’t think she used the term correctly (here are some good explanations why), but I was surprised by Jerry Coyne’s response.

One of the key biological questions about antibiotic resistance is to what extent is the spread of resistance due to the evolution of new resistant strains versus the spread of existing resistant strains. With MRSA (methicillin resistant Staphylococcus aureus, it’s been thought that epidemic spread of a few resistant genotypes (strains) is responsible for much…

A recent paper examined if use of the antibiotic cotrimoxazole was correlated with resistance in three different bacterial pathogens, Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. To quickly summarize, in one species, S. pneumoniae, resistance was correlated with use, whereas it was not for the other two species. While the study is fine for what…