Acid Test

Acid Test

I’m sorry. I just can’t take it any more. I’m going to stop the world and get off. Yes, that’ll make the oceans slosh and drown everyone else. You should have thought of that before you bored me.

Okay, you ask. What is it now?

Drivel framed in drivel. (No, I don’t have a link to the original. I can’t be arsed. It’s in the Proceedings of the National Academy of Science.) Study: men with genetic variant struggle with commitment Or this one from the New Scientist: Monogamy gene found in people

What if you could tell whether a man is husband material just by peering at his genes?

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Your Blogscientist has been falling down on the job. A few days ago I saw plenty of headlines about new nanoscale batteries. Everything’s nano-whatnot these days. I figured I’d read about it later. No doubt somebody had an extra 5% improved energy yield or something.

Turns out, no, this is really new. A team at MIT has genetically engineered bacteriophages — a kind of virus that normally attacks bacteria — to assemble batteries. Put them in a soup with the right ingredients and they pull out what they need to assemble anodes, cathodes, and, in short, batteries. (Abstract of Proceedings of National Academy of Sciences article.)

It’s lab bench work at this point, but as Belcher says,

“[R]ight now the thing is trying to make the best material possible, and if we get a really great material, then we have to think about how do you scale it.”

Scaling up means laptop batteries, car batteries, and — shoot for the stars, any damn fool can hit the ground — electromagnetic rail gun spaceship launching batteries.

Technorati Tags: batteries, nanoscale, virus, Belcher, Hammond, Chiang, MIT

Via Slashdot I found this Science News article which links to a mathematics site that’ll blow your mind up like bubble gum. It’s visualizations by mathematicians and graphic artists of four- and more-dimensional shapes. Plus, if you have any mathematical ability, in other words if you’re not like me, you may even understand what they’re talking about. But understanding isn’t needed to feel your mind expand.
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Interesting times. From universetoday.com (via Slashdot):

The White House is Briefed: Phoenix About to Announce “Potential For Life” on Mars
It would appear that the US President has been briefed by Phoenix scientists about the discovery of something more “provocative” than the discovery of water existing on the Martian surface. … Whilst NASA scientists are not claiming that life once existed on the Red Planet’s surface, new data appears to indicate the “potential for life” more conclusively than the TEGA water results. Apparently these new results are being kept under wraps until further, more detailed analysis can be carried out….

These new MECA results are, according to the Phoenix team, a little more complex than the water “discovery.” Scientists are keen to point out however, that this secretive news will in no way indicate the existence of life (past or present) on Mars; Phoenix simply is not equipped make this discovery. What it can do is test the Mars soil for compounds suitable to support life. The MECA instrument does have microscopes capable of resolving bacterial-scale life forms however, but this is not the focus of the forthcoming announcement, sources say.

They seem a bit desperate not to find evidence of life. Mustn’t upset anyone entitled to their own facts, I guess.

The likeliest scenario is that this will turn out to be evidence of some carbon-based compounds. That, together with the earlier evidence that the Martian soil at the Phoenix site has water and Earth-like pH all points toward increased probability that there was or is life on Mars.

It’s bacterial life, at most, but that would be huge. Vast. Impossible to overstate. Because it means one of two things: either that life generally appears when there is carbon-based chemistry in the presence of water, or that some bacteria can make it through space often enough to seed life wherever conditions support it. Or both.

Either way, it would mean that life is common in the universe, not rare.

Technorati Tags: Mars, Phoenix, water, life

This is one of those feel-good stories that just lights up my day. (It’s night here, but you know what I mean.)

NZ dolphin rescues beached whales.

… The pygmy sperm whales had repeatedly beached, and both they and the humans were tired and set to give up, he said.

But then the dolphin appeared, communicated with the whales, and led them to safety.

The bottlenose dolphin, called Moko by local residents, is well known for playing with swimmers off Mahia beach on the east coast of the North Island. …

Technorati Tags: dolphins, whales, interspecies, communication

The Second Law, that is. This should not be possible unless you add energy to the system. For instance, if there were a giant fan in Los Angeles, blowing their so-called air out to sea.

But there is no giant fan.

I saw this while hiking northwest of LA, and it’s not the first time I’ve seen it. This is what the plume of LA pollution normally does. It’s not a matter of ground and upper level winds either. The pollution is near ground level and so was I, going from sea level to about a thousand feet up a coastal mountain.

How does dirty air move out into the ocean against the wind? How? This is really bothering me. If anyone knows how this happens, tell me!

Update: a commenter on this post at Shakesville suggests what I think may be the answer:

OK, maybe…
The polluted air is denser and lies along the ground. Ground drag doesn’t allow it to move as readily as the cleaner, eastbound air above, which thus moves across the top of the smog bank and, being cooler, sinks, displacing the polluted air, which moves west because it is blocked by the coastal mountain range to the east.
cory | 03.11.08

Technorati Tags: pollution, inversion, convection, Los Angeles

What’s not to love?

(Via Wired.com)

(Well, to be absolutely honest, I’d still rather have an Aptera….

)

The planet’s big problems relate to energy. Using it is warming the planet. Getting it is causing wars. Running out of it will end in poverty and famine. Now that we’re getting closer to the apocalypse, it looks like the four horsemen are all riding one cloned horse.

The first task is to figure out the scope of the problem. How much energy do we use? How much will we need in, say, 2050? (That’s a favorite year for projections: it’s nice and round, and within many current lifetimes, but not so close that there’s no hope.) The next task is to consider which types of energy could supply the needs. And the final task would be to go out and do it. The system breaks down at that crucial point. There are solutions to the energy crisis. We’ll soon find out if there’s a solution to the “people’s heads in a place where the sun don’t shine” crisis.

(Fair warning: this is another one of my interminable posts…) Read more »

What can I say?   I love these things.

These are some new friends I recently met at Point Dume near Malibu.  During very low tides, such as we had at the end of December, you can just wander around among the tide pools and find things that you’d normally only see snorkeling.

Crossposted to Shakesville.

Technorati tags: sea squirts, tunicates, Malibu, Pyura haustor

You know, so long as you avoid politics and stick to science, the world is full of wonderful stories.

Via Wired Blog:

A young professor has used her favorite childhood toy, a laser printer, and a toaster oven to make microfluidic devices - tiny computer chips with plumbing that are usually fabricated in multimillion dollar labs.

Microfluidics are essential to the whole new field of genomics and proteomics, which are at the center of the new advances we hear about in curing things like multiple sclerosis, diabetes, cancers, alzheimers, etc., etc. Her method makes the guts of the microfluidics chip in a few hours for a few dollars without a clean room. The others take a few months, cost thousands, and can’t survive without the aforementioned multimillion dollar lab.

Michelle Khine, as a new faculty member without a lab, figured out how to make a “lab on a chip” in her kitchen using Shrinky Dinks. It’s like something straight out of Heinlein.

The actual article is here. I may be wrong, but I’d be willing to bet that the way her name appears last in the list of authors is one of the clearer symptoms of typical academic politics at work that you’ll see.

Crossposted to Shakesville

Although, really, I guess that would depend on how you define their work. Let me put it this way: the government is continuing not to protect and help the citizens who pay the government to help and protect them.

Via Shaker Nik E. Poo, another depressing bit of news.

Despite the protests of more than 50 scientists, including five Nobel laureates in chemistry, the U.S. Environmental Protection Agency on Friday approved use of a new, highly toxic fumigant, mainly for strawberry fields.

The new pesticide, methyl iodide, is designed for growers, mainly in California and Florida, who need to replace methyl bromide, which has been banned under an international treaty because it damages the Earth’s ozone layer.

I happen to live a few miles away from some of the strawberry fields in question. (Upwind, luckily.) The procedure when they’re fumigating the fields is to cover them in acres of plastic. Great rolls of white stuff, about six feet wide, are rolled out and taped at the seams. Then a couple of guys dressed in white moon suits show up. These are the full biohazard overalls, with their heads completely enclosed in a gas mask sort of thing. They pace around, doing something obscure with hoses and stuff. They have a pickup-sized truck with a metal tank. Once they start pumping the gas under the plastic it billows in a dreamy way. It continues billowing for a few days. Anything alive under there is killed. I drive by with my windows rolled up, wondering how well those seams are holding up.

Meanwhile, a couple fields away, dozens of farmworkers are bent over, picking celery, or cabbages, or carefully hand-weeding a sod farm. When they’ve finished picking a box load, they run to the collecting truck. Then they run back. It’s not easy work, they do it for at least eight hours, and there’s probably scarcely a minute when they’re not breathing hard.

I can hear people sputtering, “Why the HELL don’t the farms just go organic!”

They can’t. If they tried to, it would take about three years before the soil microbiology and organisms built up to the point where something besides pests could live in those fields. Three years of paying taxes on the land and no income to show the shareholders is not something any agribusiness wants any part of. It’s not that they’re against organic farming as such. (Really. Organic farms are often more profitable after the transition period.) It’s that they can’t stand not making money all the time.

So they have to keep killing everything that moves. But life is very adaptable, especially pestiferous life, and there aren’t many poisons that will do that. Methyl bromide was a fumigant that did. It’s a very light molecule that went floating straight up into the stratosphere where it destroyed ozone. Bad for the planet.

But the farms that need a fumigant couldn’t function without it, so even though the stuff was outlawed years ago, it continues to be used with “exemptions” in quantities of thousands of pounds. (When an exemption is a continual thing, is it still an exemption?)

Now, I guess, the EPA has decided it has to get serious about stopping the use of methyl bromide. If you look at that column of elements in the periodic table, you see fluorine, chlorine, bromine, and iodine. All truly vicious toxins, which is why they work as disinfectants. Iodine is a bigger atom than bromine, so when it’s attached to a methyl group, you have a heavier compound. Methyl iodide does not go straight to the stratosphere. It hangs around where we are and gets into the groundwater. Bad for people.

So that’s the choice the “hydroponic” model of agriculture has given us. Kill the planet (and us, eventually), or kill (some of) us now.

There’s an interesting twist at the end of the LATimes article:

The manufacturer [of methyl iodide fumigant], Arysta, has spent eight years and more than $11 million collecting toxicological and environmental data to persuade the EPA to register methyl iodide as a pesticide.

Arysta’s former chief executive, Elin Miller, is now a top official at the EPA and was appointed administrator of its northwest region last year.

Evidence from a sudden climate warming 55 million years ago suggests that increased production of methane by warming bogs accelerated the warming. Feedback loops are something scientists have been worrying about for years. They could speed up warming beyond any hope of controlling it. One of the scary loops is coral reef dieback, and the millions of tons of carbon locked up there dissolving into the ocean. The other real biggie is what happens when all the carbon locked up in frozen northern bogs starts unfreezing. Well, roads in Alaska are buckling as the permafrost melts. The Northwest Passage is opening up. So far, scientists have just been predicting what it all means. Now there’s geological evidence that they’re perfectly right. (Speaking as a scientist: DUH!)

Chronic fatigue syndrome may be due to an intestinal virus. “Eighty-two percent of stomach biopsy samples from 165 chronic fatigue syndrome (CFS) patients tested positive for enterovirus infection versus 7% of samples from controls (P<0.001), John K.S. Chia, M.D., and Andrew Chia, of EV Med Research, reported in the Journal of Clinical Pathology." (The p<0.001 means there's less than one in a thousand chance that the results are meaningless.) Another "it's all in your head" explanation falling by the wayside?

White blood cell transplant may help fight cancer. From the BBC. These are not the usual T-cells and B-cells that stem cell and monoclonal antibody research has worked with. These cells are granulocytes, which people had thought acted only against bacteria. Turns out, some people have cancer-killing granulocytes that keep working even in a petri dish. Transplanted to patients, maybe they could do the same thing. The bad news (there’s always bad news) is that foreign cells lead to rejection, which can be so severe it kills the patient. Another therapy where embryonic stem cells (which don’t have the same rejection issues) might be the answer?

[First posted at Shakesville]

Amoeba zombies, that is. As a headline in thedailygreen.com put it, “Brain-eating Amoeba Deaths Spike in Warmer U. S. Climate.” [link not working, deleted, 2007-10-22]

These brain-eaters are for real. They’re amoeba that like warm water, live in lakes, infect swimmers via the nose, migrate to the brain, and start living it up. Naegleria fowleri is said to be very rare. But as lakes warm up, it’s getting less rare.

From the LATimes report:

“This is definitely something we need to track,” said Michael Beach, a specialist in recreational waterborne illnesses with the Centers for Disease Control and Prevention. “This is a heat-loving amoeba. As water temperatures go up, it does better. In future decades, as temperatures rise, we’d expect to see more cases.”

To be less tabloid about it, it’s not that many cases. The national yearly average has gone from about 2.3 deaths to 6 this year. But though the absolute numbers are small, that’s more than a doubling. If it does that every ten years, in fifty years we’d be up to some 200 cases. Compare that to a total of 27 SARS cases in the US at the height of that scare in 2003. The country was ready to shut down over that.

Also compare the approximately 10% mortality rate in SARS with the near-100% rate from the zombie amoeba. That’s what it is at this point. Amoebic diseases are notoriously difficult to cure. I could see people start to avoid every fresh body of water, including swimming pools (it turns up in less-than-pristine pools), and having to do that right when it’s 110F outside.

But global warming is nothing to worry about. It’ll be nice to spend less on heating, and to have a Northwest Passage, and to grow corn in Canada. No problem. Nothing to see here.

First posted at Shakesville

One bizarre effect of global warming is how it’s become a reason to make the problems worse.

Global warming is so bad, that we have to pull out all the stops. That’s true. So far, so good.

But then people go on to lobby for fuel that doesn’t reduce greenhouse gases, that takes land away from food production, and that’s already causing food crises and environmental destruction. They lobby for hydrogen made from coal, because hydrogen is so clean-burning. (No, no, don’t look at the coal plant. Look over here at the hydrogen car.) And they lobby for nuclear power. The first application in over twenty years to build a new nuclear reactor was recently submitted to the Nuclear Regulatory Commission.

The nuke stuff just blows me away. At least the other technologies haven’t been tried on a national scale in the US. If you’re stupid, you could pretend you can’t figure out what the problems are. But nukes have been tried. They did not work. They do not work. They will never work, because they can’t work.

Let me go over exactly why that’s true.
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We’ve heard it all by now. “Stem cells will cure everything.” “Stem cells kill embryos.” “Stem cells are overrated.” We hear much less about the science of it all. (Oh, no! Not science!) And that’s too bad, because it can tell us a lot about the rest of what we hear. Let’s get to it.

Think of stem cells like tiny organ transplants, and you’ll be pretty close to grasping the essentials. If you could grow a new heart from your own tissues, there wouldn’t be any need to worry about transplant rejection. That’s how adult stem cells work when used in the adult they came from. Used in another person, they’re like a transplant. Anti-rejection drugs need to be taken for the duration.

So, conceptually, stem cells are simple. Politically, it’s another matter. I’m going to try to give the Cliff Notes version of both the science and my take on the ethics, as well as what we can realistically expect in the way of cures in the near term.

Intro … at warp speed

Adult stem cells are a very rare cell type, are hard to grow, and are hard to turn into useful tissues. Embryonic stem cells are easier to find because they’re present in much higher proportions relative to the total number of cells in the embryo. The earlier the embryonic stage, the more stem cells, until at the very earliest stages (zygote, blastula) it’s pretty much all stem cells. Embryonic stem cells are easier to grow and mature. They can generally be coaxed to mature into a wider variety of tissues.

Also, the earlier the stage, the less developed the immune system is, so the less chance there is of rejection even when the tiny cell transplant is given to an unrelated person. However, due to research restrictions in the US, there hasn’t been enough work done here to know whether rejection will be an issue or not. Research is being carried forward elsewhere (Britain, South Korea, Australia, Singapore, China, Brazil, and other countries), but I haven’t heard about definitive results on this question yet.

The downside of stem cells is that they can have a nasty tendency to turn cancerous. There’s some evidence (eg here, and here) that at least some cancers get their start as stem cells that lose the fine-grained regulation necessary to grow and differentiate into something useful. Instead, they just grow. However, it’s still not clear whether so-called cancer stem cells start as normal stem cells or just look like them in some ways.

There are also other down sides. One is that more research really does need to be done. We’re just taking the first baby steps in this field.

Some results are being obtained now, and those are therapies for conditions due to malfunction of a single cell type. Things like macular degeneration blindness (retinal cells), replacing insulin-producing cells, and regrowing damaged nerve cells, such as in Parkinson’s (simpler, here), and brain or spine damage. But we’re years away from growing new organs.

[update, Sept. 4. The hardest thing about writing this post is that the field overtakes me before I have the paragraphs finished. The scuttlebutt is that Israeli researchers have grown a whole heart from embryonic stem cells. So we're obviously not years away from growing new organs. We're not even days away, if that report is right.]

Getting a stem cell to mature into one cell type is just a matter of figuring out how to trigger it and then keep the cells alive while they grow. An organ is dozens (hundreds?) of cell types, all of which have to be perfectly placed together in order to function. At this point, we’re miles (but not light years) away from understanding cell growth regulation well enough to know how to do that. Figuring out how far away we are from growing new hearts or limbs is an unknown itself. It’s like trying to figure out how far away a mountain peak is when you’re hiking. If you’re seeing the whole mountain, it’s on the horizon and maybe fifty miles away. If you’re only seeing the tip, then the base is around the curve of the Earth somewhere and it could be 500 miles away. We don’t know enough about growth regulation to know how far we have to go, but we can see the peaks in the distance.

And then there’s the huge downside that people get hung up on stem cells, especially when they’re from an embryo. So let’s just dive right into that issue, since it has to be addressed before anything else can be done.

[Fair warning: this is a long post...] Read more »

You know those “How to tell if you’re a redneck” lists? This morning it occurred to me that there’s a foolproof way to tell if you’re a geek: getting up at three a.m. to stare at the moon for a couple of hours because it’s a funny color.

Better than television, as far as I’m concerned. Way better. Pictures below the fold.
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