I’m still waiting for the PZome

“-ome” and “-omic” are overused, as Jonathan Eisen has been saying for years, and now the Wall Street Journal has taken notice. There are 404 “-omics” disciplines? It’s so silly that there is now a Badomics generator to invent new terms.

It’s still missing PZomics. I’m serious, it could be a real science, you know…I don’t know why researchers aren’t lining up to get cell samples from me. (There’s probably more money in Venteromics—I say “psshhht!” to their dedication to the principles of true knowledge over mere pecuniary gain.)

Live by statistics, die by statistics

There is a magic and arbitrary line in ordinary statistical testing: the p level of 0.05. What that basically means is that if the p level of a comparison between two distributions is less than 0.05, there is a less than 5% chance that your results can be accounted for by accident. We’ll often say that having p<0.05 means your result is statistically significant. Note that there’s nothing really special about 0.05; it’s just a commonly chosen dividing line.

Now a paper has come out that ought to make some psychologists, who use that p value criterion a lot in their work, feel a little concerned. The researchers analyzed the distribution of reported p values in 3 well-regarded journals in experimental psychology, and described the pattern.

Here’s one figure from the paper.

The solid line represents the expected distribution of p values. This was calculated from some theoretical statistical work.

…some theoretical papers offer insight into a likely distribution. Sellke, Bayarri, and Berger (2001) simulated p value distributions for various hypothetical effects and found that smaller p values were more likely than larger ones. Cumming (2008) likewise simulated large numbers of experiments so as to observe the various expected distributions of p.

The circles represent the actual distribution of p values in the published papers. Remember, 0.05 is the arbitrarily determined standard for significance; you don’t get accepted for publication if your observations don’t rise to that level.

Notice that unusual and gigantic hump in the distribution just below 0.05? Uh-oh.

I repeat, uh-oh. That looks like about half the papers that report p values just under 0.05 may have benefited from a little ‘adjustment’.

What that implies is that investigators whose work reaches only marginal statistical significance are scrambling to nudge their numbers below the 0.05 level. It’s not necessarily likely that they’re actually making up data, but there could be a sneakier bias: oh, we almost meet the criterion, let’s add a few more subjects and see if we can get it there. Oh, those data points are weird outliers, let’s throw them out. Oh, our initial parameter of interest didn’t meet the criterion, but this other incidental observation did, so let’s report one and not bother with the other.

But what it really means is that you should not trust published studies that only have marginal statistical significance. They may have been tweaked just a little bit to make them publishable. And that means that publication standards may be biasing the data.

Masicampo EJ, and Lalande DR (2012). A peculiar prevalence of p values just below .05. Quarterly journal of experimental psychology PMID: 22853650

I’VE BEEN WARNING YOU ALL

They’re evil…EEEEEEEVVVIIIIILLL.

In a horrifying study, ordinary housecats were fitted with little cameras to monitor their activities throughout the day and night. It turns out that cats are carnivores, real predators, that scurried about murdering little creatures. Are you surprised?

About 30 percent of the sampled cats were successful hunters and killed, on average, two animals a week. Almost half of their spoils were abandoned at the scene of the crime. Extrapolating from the data to include the millions of feral cats brutalizing native wildlife across the country, the American Bird Conservancy estimates that kitties are killing more than 4 billion animals annually. And that number’s based on a conservative weekly kill rate, said Robert Johns, a spokesman for the conservancy.

"We could be looking at 10, 15, 20 billion wildlife killed (per year)," Johns said.

When we had cats, they were confined to the house, and only allowed outside under close supervision, because we understood their savage, beastly natures.

I’m ready for my close-up

I’m getting a bit peeved at all this new technology. Why, back in the day when I was doing electron microscopy work, I’d spend days slicing up tiny fragments of zebrafish embedded in epon-araldite with an ultramicrotome, and I’d end up with hundreds of itty-bitty copper grids that I’d put in the EM one by one, pumping the chamber down to a good vacuum and scanning and focusing and taking pictures. On a film cartridge! That I had to take into a darkroom and process myself! Both ways, uphill, in the snow!

And now look at this. These guys can make a single thin section slice of the whole larva, throw it in a machine, and step back while it automatically scans everything, and then throws it all onto a digital image. Of course, in this case it took their machine 4½ days to shoot over 26,000 images and then stitch them all together, but that’s still far faster than I ever was. I’d slave away to get just one good picture of a chunk of synaptic neuropil maybe 20 micrometers on a side.

Damn. Now I know how John Henry felt.

So here’s a transmission electron micrograph of a zebrafish at low resolution, just to help orient yourself. Ah, this is all familiar stuff; I spent most of my time hanging out in the nervous system, but those blocks of muscle (pink) on the left are always beautiful to look at. That big hole in the middle is the swim bladder, and the guts are slung underneath that. This is a parasaggital section — just off the midline — so it slices nicely through the eye (the big dark circle on the right) and also catches one nostril, above (that’s right, not where you might expect it*) and to the right of the eye. The scattered fragmentary stuff at the bottom, in front of the swim bladder, are sections through the pharyngeal arches. Take a look at the pretty cartilaginous rods sliced through in there.


The virtual slide was recorded at 120 kV with a magnification at the detector plane of 9460. A set of points was manually selected to outline the zebrafish and the convex hull of these points was used to define the data collection area. A total of 26,434 unbinned 4k × 4k images was collected with a FEI Eagle CCD camera (>8 s readout time full frame) in 4.5 d. The sample was maintained at −1 µm defocus throughout the whole data collection. The resulting slide of 1,461 × 604 µm2 consists of 921,600 × 380,928 pixels of 1.6 nm square each. The net data content of this slide is 281 Gpixel.

This is at high enough resolution that you can browse around the brain and find synapses and vesicles. Oh, you can’t see that? Go to the visual browser, and you’ll be able to zoom in and in and in. Easily. With no effort. Just glide on in there and find what you want.

Unlike my old experience with EM. Hey, if any of you have a time machine handy, could you grab one of these gadgets and drop it off for me in Eugene, Oregon, about 1982? Thanks.

*In case you’re wondering how nostrils can be above the eye, visualize a bulldog. Now grab it by the snout, and lift upward, stretching the face up so that a forward view is just a shot of the jaws with eyes on either side. Or, better than a bulldog, start with Admiral Ackbar.

Frank G.A. Faas, M. Cristina Avramut, Bernard M. van den Berg, A. Mieke Mommaas, Abraham J. Koster, Raimond B.G. Ravelli (2012) Virtual nanoscopy: Generation of ultra-large high resolution electron microscopy maps. Journal of Cell Biology 198:457-469 DOI: 10.1083/jcb.201201140.

Botanical Wednesday: Baseball!

See? It’s a plant that looks like a baseball! And on Friday, the Minnesota Atheists Regional Conference will be sponsoring a baseball game in St Paul, the Mr Paul Aints vs. the Amarillo Sox. You should come. Here’s the schedule for the meeting: Dave Silverman, Hector Avalos, Ayanna Watson, Robert Price, Teresa McBain, J. Anderson Thompson, and me. Probably no baseball plants, though. They’ve been wiped out in the wild.

(via WebEcoist)