50% bananas


Today in “blog posts that have spent two years in the draft folder” – “Humans are 50% banana.”

“Humans are 50% banana.”

Perhaps you have heard this statement, or one like it. It seems to be widely-quoted. As an example it’s hard to go past this article from UK tabloid The Mirror which, in addition to the banana, also informs us that “the entire internet weighs about the same as one large strawberry”. I don’t even know where to begin with that one.

A couple of years ago, between jobs and with time on my hands, I thought I’d go in search of the source for this factoid.

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Venn figures go wrong

6-way Venn banana

6-way Venn banana

I thought nothing could top the classic “6-way Venn banana“, featured in The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.

That is until I saw Figure 3 from Compact genome of the Antarctic midge is likely an adaptation to an extreme environment.

5-way Venn roadkill

5-way Venn roadkill

What’s odd is that Figure 2 in the latter paper is a nice, clear R/ggplot2 creation, using facet_grid(), so someone knew what they were doing.

That aside, the Antarctic midge paper is an interesting read; go check it out.

This led to some amusing Twitter discussion which pointed me to *A New Rose : The First Simple Symmetric 11-Venn Diagram.

[*] +1 for referencing The Damned, if indeed that was the intention.

A new low in “databases”: the PDF

I’ve had a half-formed, but not very interesting blog post in my head for some months now. It’s about a conversation I had with a PhD student, around 10 years ago, after she went to a bioinformatics talk titled “Excel is not a database” and how she laughed as I’d been telling her that “for years already”. That’s basically the post so as I say, not that interesting, except as an illustration that we’ve been talking about this stuff for a long time (and little has changed).

HEp-2 or not HEp2?

HEp-2 or not HEp2?

Anyway, we have something better. I was exploring PubMed Commons, which is becoming a very good resource. The top-featured comment looks very interesting (see image, right).

Intrigued, I went to investigate the Database of Cross-contaminated or Misidentified Cell Lines, hovered over the download link and saw that it’s – wait for it – a PDF. I’ll say that again. The “database” is a PDF.

The sad thing is that this looks like very useful, interesting information which I’m sure would be used widely if presented in an appropriate (open) format and better-publicised. Please, biological science, stop embarrassing yourself. If you don’t know how to do data properly, talk to someone who does.

I give up

It’s what – 10 years or more? – since we began to wonder when web technologies such as RSS, wikis and social bookmarking sites would be widely adopted by most working scientists, to further their productivity.

The email that I received today which began “I’ve read 3 interesting papers” and included 1 .doc, 3 .docx and 4 .pdf files as attachments is indicative of the answer to this question, which is “not any time soon.”

I’ve given up trying to educate colleagues in best practices. Clearly, I’m the one with the problem, since this is completely normal, acceptable behaviour for practically everyone that I’ve ever worked with. Instead, I’m just waiting for them to retire (or die). I reckon most senior scientists (and they’re the ones running the show) are currently aged 45-55. So it’s going to be 10-20 years before things improve.

Until then, I’ll just have to keep deleting your emails. Sorry.

Factoids (and using R as a simple calculator)

Wikipedia defines factoid as “a questionable or spurious—unverified, incorrect, or fabricated—statement presented as a fact, but with no veracity.”

Last night I was enjoying a TV documentary series, The Story of Science, when I heard a startling factoid, namely:

If the “empty space” inside the atoms that make up people were removed, the entire human population would fit inside a sugar cube.

What the? Can we improve the veracity of this factoid?
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