We’re only 10% human. According to…who?

Reading an interesting post at Genomes Unzipped, “Human genetics is microbial genomics“, which states:

Only 10% of cells on your “human” body are human anyway, the rest are microbial.

Have you read a sentence like that before? So have I. So has a reader who left a comment:

I was wondering if you have a source for “Only 10% of cells on your “human” body are human anyway, the rest are microbial”

It’s a good question. Everyone quotes this figure, almost no-one provides a reference. Let’s go in search of one.
Read the rest…

Snippets: guts, cancers, statistics

File under “interesting articles that I don’t have time to write about at length.”

  • Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents
  • Long ago, before metagenomics and NGS, I did a little work on detection of Archaea in human microbiomes. There’s a blog post in the pipeline about that but until then, enjoy this article in PLoS ONE.

  • Mutational heterogeneity in cancer and the search for new cancer-associated genes
  • This article is getting a lot of attention on Twitter this week. Brief summary: cancer cells are really messed up in all sorts of ways, most of which are not causal with respect to the cancer. Anyone who has ever looked at microarray data knows that it’s not uncommon for 50% or more of genes to show differential expression in a cancer/normal comparison, so this is hardly a new concept. I think we need to move away from ever-more detailed characterizations of the ways in which cancer cells are “messed up.” We know that they are and that doesn’t provide much insight, in my opinion.

  • The vast majority of statistical analysis is not performed by statisticians
  • Interesting post by Jeff Leek, summarized very well by its title. It points out that many more people are now interested in data analysis, many of them are not trained professionally as statisticians (I’m in this category myself) and we need to recognize and plan for that.

Bonus post doing the rounds of social media: Using Metadata to Find Paul Revere. Social network analysis, 18th-century style. Amusing, informative and topical.

#arseniclife: the genome

It’s about one year since the science story dubbed #arseniclife hit the headlines. November 30th saw the release of a draft genome sequence for Halomonas sp. GFAJ-1, the bacterium behind the furore.

As Iddo pointed out on Twitter, sequencing the DNA from GFAJ-1 is itself strong evidence against arsenate in the DNA backbone, since the sequencing chemistry would be highly unlikely to work in that case. However, if like me you think that a new microbial genome provides the most fun to be had in bioinformatics [*], you’ll be excited by the availability of the data.

In this post then: where to get it, some very preliminary analysis and some things that you might like to to with it. Projects for your students, perhaps.

[*] note to self: why, then, am I working on colorectal cancer?
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.