Tuesday, August 29, 2006

tasting sour on your tongue and in your spine

Here's another intruiging science-of-food result, published in last week's Nature. (Link may require Nature subscription, sorry.) A team of scientists in San Diego wanted to figure out exactly how we taste sourness, such as the fantastic acidic taste of a white balsamic vinegar. People already knew how sweet, bitter, and umami tastes work, what chemical receptors are triggered when each of those flavors touch your tongue, but sour and salty receptors had yet to be identified. The scientists figured it out, and made a second discovery that it seems to me might suggest how the ability to taste sourness could have evolved. The same chemical receptor that detects acidity (sourness) on the tongue also detects acidity in the cerebrospinal fluid around the spine, and transmits that information to the brain.

The researchers proceeded by first using information about where different proteins are physically located in the body, then used genetically-modified mice to confirm their result. They initially found in a bioinformatics database about 30,000 proteins that are expressed on the outside of cells, and could thus interact with the chemical environment outside the cell.
They screened these by assuming that a taste receptor would only be found in a small number of tissue types (specifically tongue taste cells). That whittled the list down to 900. They then looked for gene patterns known to exist in other taste receptors, leaving a single protein called PKD2L1 as a prime candidate.

To check on the action of PKD2L1, the team created genetically engineered mice that produced a toxin in cells expressing PKD2L1, killing these cells. Probes placed inside the mouse brains then showed that no neural activity was prompted by sour-tasting foods in these mice... And their behaviour changed to match: they kept licking sour foods, whereas normal mice would run away from acidic snacks (only humans have a taste for sour foods; other animals avoid them).
That is, mice without this protein, the only protein that is expressed on the surface of a cell, that is present on the tongue, and that is not present in other taste buds, these mice acted exactly like you would expect from mice that could not taste sour things. They tasted everything else like normal mice, but without the cells with this one protein, they couldn't detect the acid levels in food.

They then wondered if that same protein was used anywhere else in the body. They used a staining technique to find out that the only other place where this acid-detecting protein was expressed was in neurons surrounding the spinal cord. This is interesting. It seems like that same protein may be used to detect deviations from the proper pH (acid/base levels) in the spinal fluid. Low-level parts of the brain stem control a large number of biological processes in the body, such as temperature regulation and the regulation of chemicals and hormones. If levels of chemicals go out of balance, you could get very sick or die, and in some cases imbalances are consciously perceived as feelings of malaise or internal pain. Some parts of the system that regulates pH in the blood and spinal fluid had previously been known, but not the precise receptor in the spinal column. Now, after this research on taste buds, it's known. (At least for mice.)

The researchers don't seem to explicitly mention it, but this result seems to hint at a mechanism for the evolution of the ability to taste sourness. The regulation of pH in the spinal column is doubtless a very old adaptation in vertabrates, and it would probably not be a surprise to find out that a very similar acid-detecting protein exists in a large number of animals with nervous systems. However, the taste of acidity might well be a much newer adaptation, perhaps due to some sort of poison or irritant in food. You can easily imagine a population of ancient animals that would suffer from eating acidic food, but have no ability to detect sourness. A mutation that caused the already-existing PKD2L1 protein to be expressed in some taste buds would cause an immediate selection advantage, and the mutation would quickly spread throughout the population, where it remains today, an exaptation that allows us to taste lemonade.


Wednesday, August 23, 2006

Guest Post: Uncle Ron on Heart Surgery

My Uncle Ron, an engineer living in Austin, TX, had heart surgery recently to replace an aging replacement valve that had been giving him trouble. He's recovering well, and wrote a great letter to his relatives about it. "I found the combination of low tech (sawing thru the bone, needle and thread) and hi-tech (carbon fiber valve and the computer with megabytes of mememory in my chest) very interesting," he said. He's given me permisison to post the letter here, and I hope you find both his description of the procedures and his personal reaction to them as compelling as I did...
Friends and family,
If you did not know, Wednesday I had heart surgery. I
am home and feeling great. I don't have a real blog,
so I'm sending this email about what happened.

The reason I had the surgery is that there were a
couple of indications that the aortic valve
replacement I had in 1988 was was getting worn and
caused my minor stroke in March. So we decided to
replace it with a new one of new design and new

When Dr. Oswalt opened things up on Wednesday morning
there was lots of scar tissue including some that had
grown over the artificial valve. So immediate proof
the the surgery was needed. Dr. Oswalt removed the old
valve and cut a nice opening to fit the new valve. He
stitched the new one in place making tiny stitches in
the muscle of the heart to hold the valve in place. In
a couple of places these stitches where in the scar
tissue, but all was fine until he was almost finished.
Then one of the stitches in the scar tissue tore
lose. Not good! So he took it lose and started over.
The only alternative was to make the stitches where
there was scar tissue a bit larger. Not a problem but
surgeons really take pride in their tiny stitches!

As it turns out the signal from the brain to cause
the heart to beat arrives at the upper chamber at a
transmission point and is sent to the muscle in the
upper chamber via some transmission cells. A nerve
runs from these cells to anther set of transmission
cells that delays about 1/5 of a second and sends the
beat signal to the lower chamber where the aortic
valve resides. In fact this second set of transmission
cell is right next to the aortic valve.

Dr. Oswalt had a quandary. If he made the stitches
larger he might injure this second set of
transmission cells. I did not want to live with a
leaky valve, so I voted we worry about that later and
get the valve sewed in. So he did, and the rest of the
surgery went well.

It is standard practice to attach a temporary
pacemaker during heart surgery just is case the
trauma of the surgery causes an irregular rhythm.
After surgery it showed that in fact the second set of
transmission cells in the lower chamber were not
functioning. The pacemaker compensated by sending a
beat signal of its own to the lower chamber.

There is a real possibility this condition is
temporary and the transmission cells are just stunned.
By Friday they had not improved. Huddle time. We
decided to put in a permanent pacemaker. This one is a
small computer only about the size of a silver dollar
and sits just under the skin next the collar bone.

Actually the device they put in is misnamed. It is
really not a pacemaker, it is a pacemaintainer. It
watches the transmission cells in the upper and and
lower chamber. If the upper transmitters fires and the
lower ones do not, it steps in and sends the signal to
the lower chamber for it (with the 1/5 second delay).
Pretty neat, huh?

Now here is the really cool part for a computer person
like me. As it watches the signals sent by the
transmitters in the upper and lower chamber, it
stores a record of it in the computer's memory. So it
maintains a history of every heart beat for the life
of the computer (it must be replaced every 2 years or
so). So if I go in to my doctor and say, last
Thursday afternoon I had this strange heart beat
sensation. They can just wrap a small wand around my
neck and plug it into a laptop and create reports and
graphs of just what was happening to to the heart last
Thursday afternoon. They can then search the
computer's memory for any other similar occurrences. I
can imagine a day when everyone has a similar device
connected to all your major organs.

Anyway, I am home now recovering not from the valve
replacement or the pacemaker install, but from the
injury they had to do to my lungs and chest to make it
happen. It is already starting to happen, but one
day soon this will all be done without they bone
breaking they do today. Bypass and valve replacements
will be done with only a few days recovery.

As a repeat customer, I can notice the improvements
they have made in the last 18 years. I don't remember
to many specifics, but I know I am feeling much better
than I did one week after my first surgery. I walked
three brisk miles in the hospital yesterday. I'll have
to have someone haul me to the mall to do my walking
today. 100+ degrees is too much for me.

I hope this finds you well. I am going to have plenty
of time to answer email, so don't hesitate to respond.

The really neat thing about this is, I am feeling
great but can't do any work, so I am just forced to
catch up on my reading. Darn!

Waiting to hear from you,

Cyborg Ron

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Monday, August 21, 2006

dark matter

In astrophysics and cosmology, dark matter is a postulated form of matter that acts like normal matter when it comes to gravity, but does not interact with normal matter in other ways (like collisions). Apparently, the amount of visible stuff in galaxies (stars, gas, black holes) isn't nearly enough to account for the ways galaxies behave gravatationally, so researchers basically made up this new sort of matter, that no one had ever seen, in an effort to make the numbers work.

And it looks like they were right. One of NASA's orbiting telescopes, the Chandra X-ray telescope, was used to measure the concentration of hot gas in a pair of nearby galaxies, while another optical technique was used to estimate the density of stars. The two galaxies had collided and passed through each other relatively recently. The really cool thing is that dense things, like stars, act like dark matter and don't lose velocity when galaxies collide, but non-dense things, like gas, do lose velocity in the collision. That means that if you can measure where this dense stuff is, and also where the non-dense stuff is, and they don't line up, and additionally if the dense stuff isn't nearly dense enough to account for visible gravitational effects, then you've basically proved that dark matter exists.

The blog Cosmic Variance has a really nice detailed explanation of this research, complete with pictures and a link to this video that shows a simulation of what the researchers think happened. Go read it. It's really easy to understand, and it's one of the more significant astrophysics results in recent years.


Thursday, August 17, 2006

carbon sequestration as agricultural fertilizer

The journal Nature has a couple of interesting essays in last week's issue about carbon sequestration as a solution to global warming. In general, I'm somewhat skeptical about carbon sequestration, where excess carbon dioxide is pumped underground or down to the sea floor or something like that. It's treating the symptom, not the problem, it doesn't deal with the problem of peak oil, it might not work very well, and some failure modes could result in huge amounts of carbon dioxide being released into the atmosphere all at once. Imagine 50 years of sub-ocean sequestered carbon dioxide bubbling to the surface all at once, and what a potential climate shock could result!

This article (Nature subscription required, so probably only readable from a University network) proposes a different solution. Instead of storing carbon dioxide as a gas, with the risk of an accidental release, take carbon out of the agricultural cycle by turning waste products (like corn stalks) into a charcoal-like product. The mostly-carbon char, made by smoldering it in an oxygen-poor environment can then be used as fertilizer for fields. This way, the carbon that would otherwise have been released when the corn stalks are burned (as ethanol, say) or decomposed (if tilled into the earth) stays in the ground.
The particles of char produced this way are somehow able to gather up nutrients and water that might otherwise be washed down below the reach of roots. They become homes for populations of microorganisms that turn the soil into that spongy, fragrant, dark material that gardeners everywhere love to plunge their hands into.
Even better, the fertilized soil with the additional structure from the char keeps the carbon rather than releasing it into the air. Studies show that perhaps 2 1/2 times as much carbon can be stored in a field fertilized with char than without.
...[T]urning unimproved soil into terra preta [soil enhanced with char] can store away more carbon than growing a tropical forest from scratch on the same piece of land, before you even start to make use of its enhanced fertility. Johannes Lehmann of Cornell University in Ithaca, New York... estimates that by the end of this century terra preta schemes, in combination with biofuel programmes, could store up to 9.5 billion tonnes of carbon a year — more than is emitted by all today's fossil-fuel use...
It's even possible to generate fuels from the gaseous products of making charcoal, fuels that are actually "carbon-negative" once the beneficial effects of the char fertilizer are taken into account. It's quite a remarkable process and I'm very much impressed with the research. Perhaps carbon sequestration has promise after all?

One issue pointed out in the article is worth a mention here. There's a conflict in agriculture between growing organic and growing sustainably that doesn't always get talked about. In recent years, growers have started to use "no-till" approaches to growing various crops. Instead of plowing the earth periodically to kill weeds and loosen the soil, herbicides (relatively benign ones like Roundup) are used to kill weeds and eliminate the need for plowing. Corn stalks and so forth are left in the fields to eventually decompose and aid soil development. A major benefit of no-till farming is that topsoil doesn't get lost in runoff, and in fact plowing causes a lot of the carbon stored in soil to be released or washed away. No-till farming generally can't be used with organic crops, since the weeds are too much of a problem if you can't spray and you can't till up the earth. Arguably, non-organic no-till farming is better for the soil (in some ways) than at least some approaches to organic farming with a plow. (Organic no-till would likely be best, but it seems to be very hard to make work, and I don't think it's really being used yet.) The issue with char fertilizer is that the powdered charcoal really needs to be mixed into the soil by tilling; it's not effective if it's just dumped on top where it can easily blow away. In order to get the benefits of char, adding carbon to the soil and sequestering it from the atmosphere, you actually have to stop using one of the more environmentally-friendly agricultural practices of recent years, a practice that by itself significantly helps retail carbon in the soil! Still, on balance it sounds very promising...


Sunday, August 13, 2006

New Mexican enchiladas

OK, I'm back from the trip and from some fairly stressful grant-writing at work... hopefully I'll be writing here a bit more again...

In my parents' home state of New Mexico, enchiladas are unique in a couple of ways. Instead of being a tortilla rolled around a filling and covered with sauce and cheese, the tortillas are flat, with the filling in between. The most traditional New Mexican enchiladas are layers of tortillas and cheese, with red chile sauce (made mostly from dried red New Mexican chiles, the mild but flavorful chiles you see in ristras), and with a fried egg on top. (This reminds me a little of the Korean dish bibimbap for some reason!) I wish I knew the origin of these somewhat unusual variations, but Google was, for a change, no help at all.

I have two interesting variations on the basic recipe (whose main appeal is that it can be scaled up, either by making a casserole, or by, well, just cooking it on a really huge griddle). One is my re-creation of a recipe I had at the Double Eagle restaurant in Old Mesilla, NW. It's a vegetarian enchilada, made with three layers of fillings, one black beans, one corn and tomato, and one garlic, squash, and lime. Of course it uses the traditional red chile sauce and has some cheese and a fried egg on top. Here's the recipe...

The other variation is one I created for a Mexican-themed dinner with my cooking club. I adapted bits of several other recipes to make appetizer-sized enchiladas with wild mushrooms, a green tomatillo-based sauce, a red chile sauce, and fried quail eggs for the top. Despite my using the wrong type of Mexican cheese and not making enough green sauce, they were very good (and pleasantly photogenic!). Along with the photo, here's that recipe...


Tuesday, August 01, 2006


Looks like three days of 100 degree humid weather here in New York. Hooray. On the way into work this morning, I snapped this cell photo of a road construction area near my apartment....

Doesn't it look happy, next to the 8 foot tall concrete thing that's been parked on the street for six months?

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