John Timmer explains some experiments in physics that have exposed some unexpected behavior by protons. Read that article to get the story, but this little bit jumped out at me as universally applicable to all science.

This may sound like a minor puzzle, but remember that the proton’s radius is tied into theories like the Standard Model, so the result suggested that there might be something wrong with our understanding of some basic physics. Theorists, naturally, responded with enthusiasm and developed some new models that added an additional fundamental force that influenced the muon’s interactions with the proton.

Show a scientist a problem, a real problem with data to back it up, and scientists naturally respond with enthusiasm. That’s the Standard Model of Scientific Behavior.

When scientists respond with a groan and a facepalm when you tell them your new theory for how humans evolved, or how chi flows through the body, or how to cure cancer with mango smoothies, or worse, announce that your scientific explanation is invalid because it doesn’t include the Bible or the Koran or the Bhagavad Gita, it’s because you don’t understand how science works. Real difficulties with an idea get us worked up and excited. Imaginary difficulties lacking in substantial evidence are uninteresting and mean we have to shoo away an annoying loon.

We’ve already confirmed that some people are irrational and ignorant. That observation has been replicated repeatedly and doesn’t enthuse anyone at all.

Related: here’s a professional physicist who consults with self-taught “theorists”.

The majority of my callers are the ones who seek advice for an idea they’ve tried to formalise, unsuccessfully, often for a long time. Many of them are retired or near retirement, typically with a background in engineering or a related industry. All of them are men. Many base their theories on images, downloaded or drawn by hand, embedded in long pamphlets. A few use basic equations. Some add videos or applets. Some work with 3D models of Styrofoam, cardboard or wires. The variety of their ideas is bewildering, but these callers have two things in common: they spend an extraordinary amount of time on their theories, and they are frustrated that nobody is interested.

She charges $50 for 20 minutes of consulting, in which she directs them towards current literature and advises them on the deficiencies in their background that they need to fill. I’ve had so many of these kinds of people harangue me with their ideas and objections to evolution, but I never realized I should be charging for the service.

Except, for $50 they’d probably expect me to be nice.

Sometimes, New Scientist puts a strange twist on their stories — like this one, Universal ancestor of all life on Earth was only half alive. I got stuck on just the title. “Half alive”? What does that mean? It’s describing a paper that did a comparative analysis of genes found in 1800 bacteria and 130 archaea to identify what was common between them, which would suggest what genes were present in the last universal common ancestor.

Now we have the best picture yet of what that ancestor was like and where it lived, thanks to a study that identified 355 genes that it probably possessed.

“It was flabbergasting to us that we found as many as we did,” says William Martin of the University of Dusseldorf in Germany, who led the study. The findings support the idea that the last universal common ancestor (LUCA) lurked in hydrothermal vents where hot water rich in hydrogen, carbon dioxide and minerals emerged from the sea floor.

“It’s spot on with regard to the hydrothermal vent theory,” Martin says. He describes LUCA as half-living, because it may have depended on abiotic reactions in the vents to produce many of the chemicals it needed.

That last bit is where they lost me. I’m about 0.4% salt, which is abiotically derived…does that mean I’m only 99.6% alive? And what about water? I’m 60% water, which means I’m now 39.6% alive, or mostly dead. If you’re just talking about chemical reactions, I don’t have an autonomous power source, but rely on daily input of organic material produced by other living creatures. So by that definition, I am a mostly dead, or undead, zombie PZ that lives by ghoulishly feasting upon the bodies of the living.

When I put it that way, it doesn’t sound so bad.

But I think what is messing us up here is a continuing bias towards vitalism — there is no distinction between “life” and “chemistry”. If you just accept that, we’ll all stop wasting our time trying to figure out what part of our biology is life vs. not-life. This video is a nice simplified approach to the problem of the origin of life, but it also seems hung up on a pointless distinction between “dead chemicals” and “living cells”.

At least the story does make the case for the increasingly dominant hypothesis for the origin of life on earth — that it came from reactions that exploited electron gradients found at deep-sea hydrothermal vents.

One characteristic of almost all living cells is that they pump ions across a membrane to generate an electrochemical gradient, then use that gradient to make the energy-rich molecule ATP. Martin’s results suggest LUCA could not generate such a gradient, but could harness an existing one to make ATP.

That fits in beautifully with the idea that the first life got its energy from the natural gradient between vent water and seawater, and so was bound to these vents. Only later did the ability to generate gradients evolve, allowing life to break away from the vents on at least two occasions – one giving rise to the first archaea, the other to bacteria.

It’s lunchtime!

Oh, hang on a sec, Jennifer Raff has a new post up. About…the history of human cannibalism?

Lunchtime is over!

By the way, Raff will be a speaker at Skepticon, giving you yet another reason to go.

Because if you are, you might not want to watch this video of Bryan Fry collecting sea snakes. There’s one scene where he’s got a fist full of multiple venomous snakes all writhing about that might give you the heebie-jeebies.

A True Scientist is supposed to be aloof, objective, dispassionate, and unemotional. This isn’t just a stereotype, it’s part of a set of social mores that are imposed on individuals who belong to this community of scientists.

And yet, at the same time, we’re part of a larger society that sometimes has serious problems that scientists are among the first to see. Should climate scientists be dispassionate about global climate change? Should medical doctors be unemotional about dishonest tobacco advertisements? The best scientists I’ve known have also had causes: for instance, George Streisinger, the fellow who started this whole business of zebrafish as a model system, was also a peace activist who was very concerned about nuclear war.

So when Shiv writes about the use of the word “activist” to demean scientists, I know exactly where that’s coming from. I’ve seen it way too many times.

Being an activist means you are aware and working to change the world. There’s nothing in that that implies you are cavalier with the evidence — often, it means you are acutely conscious of the facts, and passionate about the truth.

The fifth of August is the anniversary of the landing of the Curiosity Rover on Mars…and it’s programmed to sing a song to itself? That’s just saddest robot ever.

Maybe “One is the Loneliest Number” would have been more appropriate, but NASA probably didn’t want to deal with a robot breaking down in tears every year.

Our summer research program is winding down, and preparation for the fall semester teaching is winding up. My student, Katrine Sjovold, and I have been trying to figure out what early melanocytes are doing — it’s a very simple and accessible system to observe cell motility, because the cells label themselves with melanin and we don’t need to do any of that persnickety cell injection stuff, or buy expensive dyes, or buy expensive cameras capable of detecting fluorescence (although we’ve tried a little of that here at the end of the summer, and I’ve been appropriately impressed that my research camera actually can see DiI fluorescence, even if it’s not designed for it).

Anyway, one of the things we’ve been doing is making time-lapse videos of melanocytes after they start making pigment and as they’re linking up and consolidating to form stripes. Here’s one example, a time-lapse where we take one image every 3 minutes over a day and an evening of growth.

You can see that we’re looking down on the dorsal side of the animal, in the region of the hindbrain (see the fourth ventricle, and the ears, deep and out of focus?). You may also notice that one of the melanocytes spontaneously decides to die and quickly breaks down into a few darkly pigmented blobs.

I’ve also uploaded a few other videos, but keep in mind these aren’t polished, perfect videos — these are bits and piece of our working data collection.

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