Merry Christmas!

I wish you all a very Merry Christmas!

I realize that I've kind of drifted from the original tack of this blog, so the New Year will bring some changes in the type of stuff that gets put up here. And hopefully, I'll be able to update more regularly.

Our tree is a real tree, about 3 feet tall, blinged out in red and gold. Those are the colors we use as our main decor, too.

Real Greenies Don't Recycle

We recycle only about half the glass that comes into our apartment--mostly the wine bottles, and then only if I can't use them for a vase (some of them are really fugly).

The other half does not get thrown out. It gets put to good use--holding screws, blackberry jelly, acting as pseudo-tupperware, holding things like corks and pencils and beads, as containers for stock, etc. I sometimes wonder how I ever got along with virtually no glass jars.

Why do we recycle at all? There are only two good reasons to recycle:

1) Essentially nonrenewable resources: paper, for instance. Yes, I know, trees are grown in specially manicured forests etc etc, but the fact is they grow at a much slower rate than our current need for paper. Hence the "essentially".

2) To decrease the amount of crap going to the landfills. Especially the nonbiodegradeable crap. Like glass. And styrofoam, too--but that one might actually degrade, given enough gasoline.

From some points of view, recycling is a terrible waste of resources. You have to drive a special truck to pick it up. The crap gets sent down lots of conveyor belts--using tons of electricity from what is most likely going to be a fossil-fuel burning plant. People get paid to sift through it. More resources are used to reconstitute the crap into its original form.

Is it worth it? When you consider how much crap we throw away on a daily basis--coffee filters, coffee grounds, small paper scraps, food scraps, broken things, food containers--one must wonder exactly how much of a difference a single can of Coke is going to make to the net amount of crud going to the landfill.

But then consider how many resources are devoted to, say, quarrying aluminum, hauling the raw ore to a refinery/smelting plant, smelting out the metal from the slag, shipping it to companies who bang on it and make nuts and bolts and cans, etc.

Recycling is worthwhile. But it should not be considered Green, but rather as the lesser of two evils.

Why conserve?

Water is too cheap, which is why people don't care about wasting it.

There is also the fact that if you don't use it, it just evaporates, floats around as a cloud for a while, and then drops back to earth again, as rain. The water cycle, believe it or not, still works in the same way it did when you were a kid in elementary school. So really, there's no real shortage of water.

Except when there is:

It is impossible to predict which year will be a drought year. In the 1990s, when I lived in/around Philadelphia, there were at least two summers where you could be forgiven for wondering what happened to summer, because everything was brown. It didn't rain for three weeks straight, once--and given the average temperature of a Philadelphian summer, that's a big strain on plant life.

It is becoming even more difficult thanks to the weird climate changes we are all experiencing. Drought and famine in Africa. Drought and famine in India. Glaciers melting, Venice under water. Northern Europe caught in a web of freezing cold. More powerful hurricanes.

The problem is not that water actually runs out. It is that it runs out where people live. But it's not like you can keep it, either--evaporation occurs, no matter what.

So why "save" water?

1) Why not? If you're not using it, why run it? It's a profligate waste of money and resources.

2) Those "just a few bucks" you save--any little bit helps if you're struggling. Turn off the faucet, fix those leaks, and you'll breathe just that much easier.

3) Peace, quiet, and no green streaks. When I was in college I lived in an apartment where the bathtub's faucet leaked all the f*cking time. Eventually we were able to summon a groundskeeper to fix it, but by that time there was an irremovable scum of green stuff staining the white tub, marking where algae had grown along the trace of the water. Dripping faucets drive me nuts in general.

4) Water damages. See #3 about green scum. But a drippy pipe can cause floorboards and cupboards to rot, and those cost a helluva lot more to replace than calling the plumber to fix the leaks.

5) Save your skin. Washing too often dries out your skin, and washing your hair too often sucks the natural oils that give it shine right out. I wash my (long) hair every other day--it's oily--which is just about right.

Bailing out!

The latest talk around the economic round table is on bailing out the auto industry. Don't worry, this won't turn into a long rant about the auto industry and how unions screw things up. The human cost if the Big Three went under would be tremendous--not necessarily catastrophic, but definitely painful--but at the same time, one must wonder whether the environment would see it that way.

If we go by the standard 10,000 miles driven per year, 15 mpg (we're talking SUVs, not Priuses), and 23 pounds of CO2 gas emitted per gallon, that adds up to almost 8 tons of carbon dioxide in the air per SUV, per year. Multiply that by however many millions of SUVs are idling in parking lots (er, I mean freeways) not just in the US, which is by far the biggest consumer but by no means the only one, China, and Europe, and it's a wonder that the oceans are still able to keep up.

This doesn't even take into consideration the acts of finding oil, drilling for it, shipping, and refining it, all of which produce their own small environmental catastrophes (and larger social ones, but I'm not up to dealing with things this complicated this late at night). Or the effects that roads have on the landscape--and how they shape the movements of animals, and the effects that has on conservation efforts. It's enough to give even an environmentally-inclined blogger a headache.

The point is that driving with reckless abandon will wreck the world--if you happen to live in Nigeria, then you know firsthand that it does, in fact, wreck your world. I'm not one to put much faith in doomsday prognostications of a world without oil, but let's realize: 1) oil renews itself at a much slower rate than we use it up (think millions of years--unless you're Sarah Palin and your brain can't physically cope with the idea that the world might be older than Genesis), and 2) there are much, much more urgent uses for oil than merely making things go zoom or zap.

It is actually the second that worries me more. It is possible to live without cars (we do). It is possible to deal without central heating, to scrape by on candlelight, and make do with microwaves.

But imagine a life without plastic, or try to--I can't. Most of the the world we live in is plastic. The couch I'm sitting on is plastic. My laptop--encased in plastic. Even the most plastics-averse person (my boyfriend) thinks nothing of buying chicken encased in a plastic box--and doubt anybody would even think of buying meat any other way. Consider how they keep things sterile in hospitals. Consider what rubber gloves are made of. Consider a life without polyester.

At some point in the (hopefully) far future, we're going to have to make decisions about what we can do without. Delaying this particular inevitable is one I think we can all agree on.

Does not compute

My lab works on proteins. A few of the people run "dry" experiments, meaning they enter equations and run simulations of molecules and how they interact with proteins. Needless to say, being as inept with computers as I am, I normally don't deal with that.

But recently I was giving a box of 32 compounds that I had to test for allosteric activity. According to the computers, they were all allosteric enhancers.

According to my experiments, they're not.

Admittedly, a hit rate of 3-4 out of 32 isn't half-bad. Random screening without using computers to narrow down the list of criteria for our allosteric compounds would have me pulling my hair out of pure stress--when you're testing that many compounds, you have to make sure that the labels on one tube matches the label on the other, or else...

The point of all this is that life doesn't compute well. We can plug data into our computers until we're blue in the face, and get all types of random, seemingly meaningless correlations (rainy weather, autism), or important, seemingly significant ones (cholesterol, heart attacks). But it takes getting your hands dirty--designing the surveys, running the statistics, cracking the math--before you might turn up something useful.

And all too often, you don't.

I've still got a few more tests to run, but at this point they're more for verification of what I already know (most of the compounds are not allosteric modulators) than to get new data.

Bitten by the Bug

Politics and science are usually separate fields. Certainly, politicians control the money that scientists get, and within the scientific communities you get political squabbles. But mostly, science is a meritocracy and politics is a popularity contest. In politics it doesn't matter if you're as dumb as a rock as long as people like you. You don't have to know what you're talking about as long as you can "connect; as long as people like the way you say it, you could suggest eating babies. After all, if Hitler could get elected...

But every now and then they come together, namely in the election years, when we decide who gets to make the policies for the next two, four, or six years (depending on who's running). Most of the time science gets pushed aside as people discuss the issues more relevant, so they think, to the most people: taxes, health care, and that mythical thing called Reform, during which they swear to end corruption and limit the influence of the very cronies who are paying them to say that.

But I, and most scientists, probably, would argue that the state of scientific research in the United States is critical to the welfare of the country. Not just because Big Pharma makes all manners of lifesaving drugs (well...okay, maybe not), but because supporting the infrastructures that do the scientific research, be it particle physics or grizzly bear DNA, generate their own economies. To say nothing of the knowledge that gets put out there--knowledge that transforms industrial practices, knowledge that increases our understanding of the world we live in. Sarah Palin may mock the grizzly bear study, but won't she be sorry if hunters shoot the last bear?

Several factors contribute to the robust health of the intellectual sphere: The budget of the NIH to fund studies is still, despite cuts, larger than the GNP of many countries. The flexibility of the English language ensures that ideas can be communicated. The diversity of those involved in research guarantees that many ideas will be generated, and the system of peer review helps ensure that only the best succeed.

The problem is that politicans often have no idea what constitutes science. Scientists are already prone to interpreting data along the lines of their own personal beliefs, but politicians will flat-out deny the existence of data.

Basing public policies on what you want to think is the truth is very different from basing public policies on what is actually the truth. The truth is: evolution happens, stem cell research is no more or less evil than abortion, mercury in our water systems is bad, and climate change is a fact. Simply because these are inconvenient to us does not change that tey are, and we need politicians with the balls to acknowledge that we do not dictate how the world runs, the world runs and we deal with it.

Whenever and wehere ideology takes the place of knowledge--be it in tribal Pakistan or the halls of the Senate, in the Supreme Court or sub-Saharan Africa, in money or in medicine--shit happens. Ideology has its place; it gives us a platform from which we can jump off as we learn new things, but it should never replace knowledge. Let's pick a prez who knows the difference.

Feeling Good

Ups and downs are a normal part of life. In my day job, I'm a scientist/lab tech, and I'd recently mastered the art of a cAMP assay. This is a long, complicated assay involving live cells, lots of clear liquids in lots of clear plates, and calculations and back-calculations. It is, in many ways, the worst kind of assay one can run: expensive, easy to screw up, and completely dependent on how you grow your cells.

Recently my cells have been giving me a lot of flak, and after two weeks of piddling about and hoping that they'd come around, we've finally decided to just use new cells. What a bummer--I've lost two weeks' worth of work.

But oddly, despite the troubles these past two weeks, and the shortening days (anybody who says seasonal depression isn't real has never met me), I'm actually feeling quite good. Probably from a combination of chocolate, love, biking to and from the train stations, and the giddiness from not having eaten enough all week.

Feeling good, according to neuroscientists, is about brain biochemistry: having the right amounts of all the neurotransmitters in all their correct balances. Some people have a harder time of attaining this balance, others are magically "normal".

How do we go about assigning hedonistic values to the aspects of our lives that warrant it?

Science is not scientific: how to tell cells from cells

I go birdwatching on a regular basis--my favorite birds are waterfowl, and at this time of year there are a lot of migratory species coming through Holland (it's a very good time to have a pair of 8 x 56's). As with any region, you have your native common fauna, which consists of the same old 15-20 species you see EVERY time you go out, your native less-common fauna (the 10-15 species you don't see every time and are excited when you do), the non-native fauna (10-15 species that are SOO COOL! when you see them), and the rare birds.

When you pick up a birdwatching guide, it will contain a long list of field markers, habitats, songs, behaviors, notes about plumage changes, differences between age groups--there is no way to memorize all of the information. Yet I can tell you, sitting in a train whizzing by at 60 mph, that that white-ish goose is a domestic goose and that other white-ish goose is a dark variation of the snow goose.

OK, so compulsively reading my bird guide probably has something to do with this. But more than that is practice. It's how you learn to tell black-headed gulls apart from common gulls (red feet, red bill) during the winter, when they don't have their black heads. I don't check plumage points, behaviors, habitats, unless I'm really uncertain about a new strange bird--and the only reason it's new and strange is because I haven't seen it in the wild before, as most of the time I know where it is in my book and I can turn right to it.

But if you were to ask me how I go about quickly spotting birds and making my identificataions--what thoughts go through my head--I couldn't tell you. Just as I couldn't tell you exactly what makes my cells healthy and what makes them not--why I say they're "not behaving" even though they look plump and otherwise healthy. I don't think anybody who does cell culture can accurately describe what "healthy" cells look like, but they know "unhealthy" cells when they see them.

You might wonder why there's any fuss over the health of cells at all. Turns out that many of the assays run depend on the cells being "healthy"--i.e., not contaminated, in the log phase of their growth, not newly-split, not "hungry" (believe it or not, you can tell when they are), with a slightly-acidic-but-not-too-much media, evenly dispersed--the criteria go on and on, but the gestalt picture is that the cells just look "healthy".

When you work in science, you eventually acquire a feeling as to what should work and what doesn't. The minutiae of your system become intuitive--you know that's not a pigeon, even if all you can see is a black blob against a blue sky. You know your cat isn't feeling well, even if it's not doing anything other than what it normally does. You know that even if the protocol says nothing about gently stirring your reaction mixture, you'd better do it gently if you want results. You know that some equations are better than others.

This is the daily in-and-out of experimental science, ladies and gentlemen. It is predicated on a long list of assumptions, some of which only may be true. It is not very scientific at all.

Weight loss secrets, revealed!

One of the "hot research" areas I've been following for the past few months concerns the melanocortin receptor (I'm a pharmacology geek, what can I say?) and the regulation of appetite, the cooperation with dopamine receptors for pleasure, and the nebulous (so far) link with the hormones that are thought to regulate appetite: ghrelin, leptin, CCK (cholecystekinin), NPY (neuropeptide Y), and so on. Briefly, researchers are finding that melanocortin receptors cooperate with dopamine receptors to produce the hedonistic pleasure brought on by food. Exactly how the cooperation occurs and the effects of it are more technical matter that I will not get into here.

The article in question is, unfortunately, a closed one, meaning that you either have to be at a university library or pony up $32 to view it, unless Google has archived it somewhere.

But the main point is that this essentially debunks the "genetic set point" that irritates the hell out of me. The set point refers to a range of weights in which your body will fall, given an endless amount of food and constant metabolism. For most people, alas, this set point is not at the waif-like weight of what is being sold as beauty, but substantially above it.

There is no question that one's weight is naturally predisposed to falling at/around a certain point, and that for everybody, this point is different. For a society trained to find pixie sticks beautiful, this point is much heavier than what they would like it to be.

Allow me to digress a moment to point out that the pervasiveness of the diet industry is unique to the United States, and I would venture to guess that its success is largely unique to the US. Undoubtedly there are diet companies in Europe, but aside from an occasional flyer advertising a gym, there are few ads for apple cider vinegar pills, dietic green tea drinks, or body wraps. There is no media pressure to conform to a slender physique, though there is plenty of social pressure--for starters, cars are expensive, fuel even more so, and the stores catering to expansive waistlines are few and far between.

Anyway: it should come as no surprise, then, that one's weight tends to be a function of one's daily habits. Eating, drinking, sleeping, and all that good stuff. The operative words are "daily habits"--patterns of learned behaviors and thought that circumscribe everyday operation.

Behavioral experts say that it takes 2-3 weeks of sustained effort to create a new habit, and if my nail-biting is an accurate indicator, and old habits can never be fully destroyed--they can be overridden, but never vanquished.

What does this have to do with the set point?

My problem with the idea of a genetic set point is that it assumes that your body is entirely independent of your brain. If you've got a lifetime of, say, comfort eating (guilty) behind you, it is going to take much more than six weeks of bikini-body-dieting to break you of the habit of responding to emotional triggers with food. And, most likely, you'll find that no matter how long it's been, you'll probably relapse occasionally (guilty, too). When you go about "remaking yourself", not only do you have to learn a new habit to override the old one, you have to learn a new way to activate the pleasure centers to get that sense of achievement. This is hard. Very hard.

That young children have remarkably plastic brains is no surprise. Kids can learn to speak perfect French or Chinese if they start early enough, while adults might be able to if they persist at it for a decade or two. But what we have yet to appreciate is the full spectrum of plasticity of the adult brain. We, too, can train ourselves to like broccoli and delight in string beans. We, too, can teach ourselves new habits. It is hard. It takes a damn long time, and not only does it take a long time, it often involves pushing ourselves out of our comfort limits.

But it's not like we don't have that choice.

Science is not scientific

My background is scientific: I've got a BS in biology and biochemistry, and I've worked in pharmacology and/or molecular biology ever since I started working. Even my hobbies outside of work are more or less scientific; readers of my personal blog will probably wince in recollection of my birdwatching lists, and I prefer reading nonfiction (Brian Greene's The Fabric of the Cosmos is one of my favorites, while The Elegant Universe is on my reading list) to fiction.

So it always astounds me when people believe that science is scientific--that is, precise, exact, where the proof is irrefutable and the data conform to nice and pretty graphs. It's not. Science does allow you to answer the most mundane questions ("How do we taste?") in the most amazing ways, and if it's done properly you'll even be correct. But it's not math--that is, there is always uncertainty, there is always room for error, and different interpretations, and you may find that a solid, well-thought-through hypothesis is shot to hell when you do one more test as an afterthought.

Good science is not about doing good experiments as it is about asking the right questions. That is, the clinical trials that the people at Science-Based Medicine love to espouse are really just demonstrations of safety and/or efficacy, rather than actually uncovering anything new. One could argue that the science that led up to the development of drugs ready for clinical trials is good science, and I would have to concede that point--but few studies actually purport to change the way we think about the human body, or anything else, for that matter; the studies that actually add to our body of knowledge are usually not of social interest. I.e., you don't see membrane-protein crystal structures making the front page of anything except Science (which is a very remarkable feat and one that rightfully deserves all of the attention and praise that it gets, but I don't think mobs of girls are going to be swarming over to the Scripps Institute begging for autographs). If you don't know why crystal structures of membrane proteins are so important, that sort of proves the point--that the good science simply doesn't engender social interest.

Allow me a moment to rant about the science that does interest people: dieting and weight loss, drugs against obesity, and drugs against drug addictions (funny how the phrasing works out). For the most part, these studies are flawed, some more than others--the ones that are less-flawed tend to be the basic-science ones, where they find that Molecule Zed makes a mouse skinny or fat and then elucidate the pathway by which Molecule Zed works. They tend to rely on statistics and epidemiology, which in turn make the assumption that the people answering the questions are honest, or that there's no other compounding factor. I always read these studies with a skeptic's eye (though I don't always disagree with the findings), but it's ironic, in my book, that the studies that interest people are the ones that are the most lax in how they are controlled.

What I call "good science" is less a question of method and more a question of...well, questions. Methods can be improved--someone who wants to study the effects of acupuncture could do worse than stick random needles into random people--but you can't get more basic than asking whether acupuncture works, and how (answer is probably not, in case you're wondering). Asking the right questions makes good science far more than running the most rigorously-controlled experiments; asking the right questions usually requires a divergence from the state of reality as we know it today.

Aside: I am afraid my posts will continue to be sporadic. Suffice it to say that life is crazy.