Most useful paper I’ve read this week

I’m teaching our science writing course in the Fall, and I’m also one of the instructors in our teachers’ workshop next month (we still have room for more participants!). And now I’ve found a useful, general, basic paper that I have to hand out.

Motulsky, HJ (2014) Common Misconceptions about Data Analysis and Statistics. JPET 351(1):200-205.

What it’s got is clear, plain English; brevity; covers some ubiquitous errors; will be incredibly useful for our introductory biology students. You should read it, too, for background in basic statistical literacy. Here’s the abstract.

Ideally, any experienced investigator with the right tools should be able to reproduce a finding published in a peer-reviewed biomedical science journal. In fact, however, the reproducibility of a large percentage of published findings has been questioned. Undoubtedly, there are many reasons for this, but one reason may be that investigators fool themselves due to a poor understanding of statistical concepts. In particular, investigators often make these mistakes: 1) P-hacking, which is when you reanalyze a data set in many different ways, or perhaps reanalyze with additional replicates, until you get the result you want; 2) overemphasis on P values rather than on the actual size of the observed effect; 3) overuse of statistical hypothesis testing, and being seduced by the word “significant”; and 4) over-reliance on standard errors, which are often misunderstood.

I can probably open any biomedical journal and find papers that commit all four of those errors.

We’re all gonna die of cancer

Not this again. CNN is running another article about “X causes cancer!”, where in this case X is coffee. Not regular coffee, just very hot coffee. That is, coffee served at a temperature high enough to cause painful burns might also increase the incidence of esophageal cancer.

Huh. OK. You know, living causes cancer. Epidemiological studies like the one cited are important for identifying possible problems, but your whole life is a great long exercise in risk management where you balance doing things against cowering in terror. We have to consider realistic assessment of risk. So I was going to actually read the study (the short summary given is that an analysis of a thousand studies found that “drinks consumed at very hot temperatures were linked to cancer of the esophagus in humans”, but no numbers were given), but CNN screwed up: their link to the study goes to a paper on the carcinogenicity of pesticides in the Lancet instead. I thought I’d rummage around and try to find it myself, but instead I found this editorial in the latest issue which was pretty good, much better than yet another study that finds a superficial cancer link. So I’m including the whole thing right here.

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Slithering cells

I’m working with a student this summer on a project to measure the dynamics of a migrating cell population, and in addition to making pretty pictures and collecting data, we’re going over papers in the scientific literature. One of those papers is about filopodia as sensors.

For those of you who don’t know your cellular anatomy, migrating cells have this kind amoeboid movement in which their cytoplasm oozes in a kind of bulk flow into expanding volumes of membrane, but they also may make long, spindly, delicate ‘antennae’ that reach out in multiple directions. These filamentous processes are called filopodia. Moving cells probe their environment by sending out these little scouts that can sense signals, either repulsive signals that tell the cell to not go that way, or attractive signals that can trigger the cell to flow in a particular direction.

The illustrations in this paper are kind of quirky, but nice. To show how cells respond to signals in the environment, they use an octopus as a stand-in for the cell, with its arms representing filopodia.

Repulsive and attractive interactions in axon pathfinding. A) Repulsive interaction. When the cell contacts the target, the forward momentum of the growth cone is halted. The movement of the veil/lamellipodium resumes at the right or left of the contact site. As a result, the growth cone turns aside. The formation and turnover of FCs within the filopodium are correlated with its behavior during this interaction. B) Attractive interaction. The cell contacts a stationary target and binds tightly to it.

Repulsive and attractive interactions in axon pathfinding. A) Repulsive interaction. When the cell contacts the target, the forward momentum of the growth cone is halted. The movement of the veil/lamellipodium resumes at the right or left of the contact site. As a result, the growth cone turns aside. The formation and turnover of FCs within the filopodium are correlated with its behavior during this interaction. B) Attractive interaction. The cell contacts a stationary target and binds tightly to it.

Despite the blatant octopomorphization, something about this appeals to me. I’ve been describing these cells we’re watching as spidery, but clearly I’ve been using the wrong phylum as a metaphor.

I like the bandaged arm image. One of the things we’re sometimes seeing is that cells don’t just retract and limp away, sometimes they literally die and explode into little fragments. This needs an octopoid illustration.

Really…not alien, not alien at all

alienocto

Almost a year ago, I briefly wrote up the results of the cephalopod genome sequence— a sequence, which thanks to a few off-the-cuff, silly remarks by one of the authors, had turned into an assertion by irresponsible journalists that science had proven that octopuses were aliens. They haven’t. Researchers actually found many commonalities — cephalopods are a branch of the animal family tree, and share genes with all other organisms on the planet.

But hey, what do you know, deja vu all over again. Inanity re-emerges, with a recent article titled SCIENTISTS CONCLUDE OCTUPUS DNA IS NOT FROM THIS WORLD.

Thanks to the first-ever full genome sequence, researchers have found that octopuses (NOT Octopi) are in fact entirely different from any other animals on our planet. Their genome shows a never-before-seen level of complexity with a staggering 33,000 protein-coding genes identified, more than in a human being.

US researcher Dr. Clifton Ragsdale, from the University of Chicago, said: The octopus appears to be utterly different from all other animals, even other molluscs, with its eight prehensile arms, its large brain, and its clever problem-solving abilities.

“The late British zoologist Martin Wells said the octopus is an alien. In this sense, then, our paper describes the first sequenced genome from an alien.”

What Wells said is what is known on planet Earth as a “joke”. An exaggeration for humorous effect.

Apparently, scientists have just proven that journalists are aliens, lacking normal human feeling and appearing incapable of comprehending the behavior of bipedal mammals.

They are also prone to lying.

Octopuses have an alien genetic baggage. The scientific report mainly concluded that Octopuses share ‘Alien’ genes.This has been a ground shaking claim in the scientific community which caused an upheaval among marine biologists who seemed to be shocked and intrigued at the same time.

None of this is true at all.

Casey Coates Danson, you are an incompetent, dishonest hack. Resign from your job. Never ever even attempt any science reporting ever again.

The Science Press Release Hype Machine claims a “second layer of information in DNA”

dnasecondlayer

I hate it. Mainly because I get swamped with people asking me to explain crap, and even more, because there’s a whole lot of people who enthusiastically embrace the crap. The crap in question is this press release from the University of Leiden, Second layer of information in DNA confirmed.

The press release is bullshit, OK? But for some reason, people really want to hear that there is some other magical kind of external information that, I don’t know, frees them from the tyranny of genetics, or something. See also epigenetics, which also appeals to the lay public for all the wrong reasons. The paper isn’t talking about a “second layer of information” — it’s talking about mechanical effects of the nucleotide sequence. That’s it. Everyone can calm down now.

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Friday Cephalopod: Force of arms

octopusarmimage

Who among you has taught or studied vertebrate anatomy? I have. It’s cool. Skeletal and muscular anatomy are weird, though, because we so take the principles for granted that we’re often not aware of it. We can move because we have a jointed framework, a collection of levers that are moved by the contractions of muscle fibers, which have distinctive attachments and insertions via tendons on those bones (or, in some cases, the muscles attach to sheets of connective tissue called fascia). The musculoskeletal part of anatomy classes consists of a lot of memorization of muscles, their origins and insertions, and the effect of the action of contracting the muscle. In some ways, vertebrate limbs are actually rather crude, made up of bony rods with joints that are prone to failure (I am very aware of that as I get older), with a collection of long muscles cobbled together to carry out specific movements.

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Parks have rules for a reason

Jebus, people. Lately it’s nothing but bad news about people doing stupid things in our national parks: ignoring signs and strolling out to fragile ponds, picking up abandoned bison calves, getting up close to adult bison and getting trampled for their trouble, and now the most horrible story of them all: a young man left the boardwalk and fell into a boiling hot spring.

The grisly death of a tourist who left a boardwalk and fell into a high-temperature, acidic spring in Yellowstone National Park offers a sobering reminder that visitors need to follow park rules, park officials and observers said.

Efforts to recover the body of Colin Nathaniel Scott, 23, of Portland, Oregon, were suspended on Wednesday after rangers determined there were no remains left in the hot spring.

There’s just a thin mineral crust over the seething water, which is highly acidic, so boiling a body in that for a day leaves nothing. Stay on the designated trails. Wild animals are wild and active volcanic springs are deadly dangerous.

Also to keep in mind, besides personal danger: it’s a good thing the body dissolved, because park rangers were risking their lives trying to recover the remains, until it became pointless.