Conventional Wisdom

I haven't written on here in a while, and it's really mostly a placeholder to prove that I came up with the idea first in case someone else tries to copy my idea.

However, I was reminded today of something from graduate school, and so I hearby invite you to join me as a member of the ASPCDSF: the American Society for Prevention of Cruelty to Dead Salad Fixings.

Across the street in graduate school was a small lawyers office. One of these lawyers had a bumper sticker on the back of his car that said, "Thou shalt not kill- go vegetarian."

If vegetables are not alive, then why are agriculture and plant physiology and similar majors considered part of Biology, the Life Science?

The lawyer probably saw himself as a crusader. I don't buy the premise. Lettuce is alive too, at least until I transfer it to the saline resistance chamber...

Marvel: Human Brains

This is an original article today from a colleague that I wish to repost here.

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It ain't much to look at.

Two, maybe three pounds of grayish-white goop. It's not even solid in a living person. More like Jello that floats around in it's vault.

But it's amazing. From that sloppy goop has come remarkable stuff. It's sent a robot to land on a moon of Saturn. It's explored the bottom of our deepest oceans. Built the Taj Mahal. The Great Wall of China. Painted the Mona Lisa.

Go listen to the remarkable Bach's "Toccata and Fugue in D minor". Not just the famous opening 30 seconds or so, but the whole 9-10 minute thing. That all came from the goop, long before it was heard or played on an instrument, it was just a series of electric signals jumping from nerve to nerve. The piece is over 300 years old. The mind that created it has been dead for over 250 years. And humans will likely be listening to it long after my great-great-great-grandchildren are dust.

The soul is there. The heart is amazing, but for all our romantic beliefs about it, who we really are is floating around in the goop. It's where hate, love, and everything in between comes from.

It's capable of terrible evil, such as the Holocaust, and remarkable good. Look at the outpouring of altruism that follows disasters. I love my dogs, but if something bad happens to a dog on the next street, they're not going to care. Yet the goop wants to help people who we've never met and have no direct impact on our own lives

My regular readers know I'm interested in maritime history. Why? I have no idea. It's just been a subject I've loved as long as I can remember. I've never been in the navy, or lived near the ocean. The family military history consists of grandparents who served in the army, but never were sent overseas. I can only assume there is some particular molecular structure in my goop that makes me interested in it. Or that made me want to treat other people's goop for a living.

Twin and biological studies have shown that most of who we are is how we came here. Yes, life experiences and background count for something, but the goop is most of it. People with conservative beliefs raise kids who turn out to be liberals, and vice versa, now matter how hard they may try to pass on their beliefs.

Coke vs. Pepsi. Dogs vs. Cats. Mac vs. Windows. I suspect whatever makes us fall on one side or the other of these great philosophical issues is 95% or more in the goop, and we just come that way.

Everything you are, have been, and will be. Have desired, dreamed of, and done. Have felt. It all comes from a few pounds of goop.

And this fascinates me. Because, let's face it, we're just another part of the planet. A collection of complex molecules, electrical impulses, and chemical reactions. That's all people. Anatomically, all humans are pretty much the same. And we're not that different from other mammals. The difference in our genetic sequence vs. that of a mouse ain't much.

And yet that small amount of difference has led to amazing results. The ability to think beyond our own biological needs and to see the world around us for the beauty it contains. To watch a sunset and be in awe, even though we understand the science behind it. And to look up at the night sky, and wonder.

And that never bores me.

Coincidence and Causality

In recent days, we've heard lots of editorials masquerading as news. They tell us that the economic rebound, the successful rescue of the captain of the Maersk Alabama, and housing starts are due to the president's economic plan, which hasn't even hit the ground yet. We hear from DHS that subversive militias are recruiting former members of the military in an attempt to overthrow the government. We hear that the world hates America because we are greedy.

What we don't hear should shock you. What we don't hear is that the pirates are attacking convoys of food and earning $150 million per year in ransom money. What we don't hear is that the Commander of the USS Bainbridge gave a split second decision command to fire that saved the captain of the Maersk Alabama. What we don't hear is that compared to last quarter, housing sales are actually down, but it seems up because fewer homes are going on the market so the percentage is down (my realtor gave me the stats herself on this).

Last night in class, we discussed one aspect of bad science- the ipso facto logical fallacy. They assume that because certain things are concurrent that one causes the other. You can't say that. At best, evidence suggests a link, but on further experimentation we can easily dispell this. One example in class deals with a woman whose flashlight doesn't work. She changes the batteries and it works. What if it hadn't? What other things could it be? We ignore so many things because we do not think of them. My students came up with some good ones: corroded connections, burnt out bulb, batteries inserted incorrectly, etc. Just because new batteries don't fix it doesn't mean they're bad either. Sometimes it's a matter of compounding variables.

Another powerful example, since I live in Nevada, is the roulette wheel. Many novice gamblers assume that because black has come up ten times in a row that it's red's "turn" to get a shot and they bet on red. Truth is that on the next spin, there are the exact same chances of black turning up again, and they don't have abetter chance of being right about red. Unless you remove a number when the ball falls on it, it doesn't change the chances of subsequent draws. It is mathematically possible on an unaltered roulette wheel for a ball to land on 17 black EVERY SINGLE TIME, however unlikely that might be.

See one other problem lies in differences between circumstances and operators. Every person performs experiments differently. A coworker called me yesterday to ask me how I innoculate a specific culture because it only works 50% of the time for her and it has so far always worked for me (most things don't work that frequently). Variations and variegations influence outcomes. We cannot predict the future because the circumstances are NEVER the same in subsequent trials. Things unseen and unknown change all the time, so no matter how well we try nothing is ever an exact replicate. Not even identical twins share everything.

I spent probably 75% of my time in laboratory troubleshooting to pin down unexpected outcomes and link them to unaccounted variables. About half of the rest of the time, I had to explain differences between trials to justify omission of results. Some scientists get excited apoplexy when they "discover" something new, when more often than not they are ghosts and not a result of our manipulations. Just because two things coincide does not mean they are linked. Just because they are linked doesn't mean one is causative. Sometimes things just happen and there is no real good reason.

Red Devil About Red Meat

Meat makes man mortal. Ok, that's not so bad if, like I do, you also hope one day to die. The bad news is the way in which your mortality becomes more apparent through eating red meat.

Red meat consumption is linked to higher heart disease and cancer. Ok, are they causative? Not necessarily, but this is a problem with all science, which creates knee-jerk reactions of all kinds leading the banning of DDT, CO2, and now 2,2,4-trimethyl pentane and beef (which is also threatened by the Flattulence Tax).

Here's the codicil:

The study relied on people's memory of what they ate, which can be faulty.
In the analysis, the researchers took into account other risk factors such as smoking, family history of cancer and high body mass index.

Ok, now, I support this. Why? Scientifically, meat is high in nitrogenous waste, which must be purged immediately to keep the blood from being toxic. Secondly, most amino acids cannot be directly incorporated into proteins, so they must either be modified or metabolized. Third, animals do not eat the best foods- mad cow disease by way of example comes from feeding cows the ground up meat from other cows, and if that includes brain matter of a diseased cow the consuming cow will catch it. Even in Austria, which is a green and organic country, guess how they fertilize the fields of grass? They spray liquid cow dung on it. Gross.

Finally, meat must be cooked to be edible. Even if only one bacillus survives, E. coli doubles fast enough that one survivor can pollute you with millions in rapid succession. During cooking, the chemical structure, and therefore the utility, of components falls apart, making most of it of little use except as glucose substitutes. Also, if you cook it poorly, via charring, an innocuous enzyme in the liver can turn that harmless byproduct into a carcinogen.

Some people claim that you can't bulk up without meat, but cows just eat grass, and they bulk up just fine. Do you need meat? No. I love fish, and a really, really, really good steak tastes good now and then.

Math Conundrums

If according to Dante 1+1=1 (one government plus one people to rule equals one society), then according to Tolkien, 3+7+9=1 (three rings for the elves, seven for the dwarves, and nin for men equal one master ring).

Also, 1 does not equal 1, else my one soldier could defeat your one army, or my one experiment should trump your one career.

Food for thought...

My Beef With Organics

This past week, I butted heads with a good friend over the issue of organic foods. As soon as I explained why, she understood where I came from and seemed less adverse to my reasoning for opposing organics as presently constituted.

As a graduate student, I studied secondary metabolism deposition in plant tissues. We measured volatiles and terpenoids primarily in root, shoot, and berry throughout the vegetative process through to post-veraison. Results for Vitis vinifera varietals demonstrated how secondary metabolites are processed.

My problem with organics is how they come to market. We could track based on chemical properties to the exact day when fruit was ripe and ready for picking. Many organics are, like the foods they replace, picked before they are ripe for transport. Our research demonstrated that most of the chemoprotectants for which we consume plants (like tocopherols, resveratrol, etc.) remain in tissues we don't consume until the plant is absolutely certain the fruit will be set. A day or two prior to ripening, the plant starts shuttling these metabolites from leaves and stem to the fruit, and not before.

For this major reason, organic foods come to market as bereft of the nutrients for which we eat them as their inorganic counterparts, offering no added nutritional benefit, often at much higher cost. If you eat them because they come without hormones or inorganic phosphate, fine, but if you think you're getting better nutrition, consider from whence they come.

The best way to get pure unadulterated foods is to grow as many of them yourself as possible. That way you control the food you eat from seed to salad. You raise it without exogenous chemicals. You pick it at the height of ripeness. You consume food that you know meets all of your criteria. If you buy it because it says organic assuming it's better for you, it might be, but chances are it's just a more expensive fecal precursor than that which your neighbors buy and offers no more chemoprotectants to countermand assaults on your health than inorganics. Caveate empor.

Conditionalities of the Unseen

I was just talking to a friend about how we're smack dab in the middle of cold and flu season. Some rather famous personages, including Rush Limbaugh, despite the medications and precautions they take, managed to catch flu, colds, or bronchitis so far this season. Not that I think colds are bad; by contrast, I think that periodic infections are good. Note that most of the major pandemics break out in civilized countries. Said virologist Gerald Lancz, we're scrubbing our kids down so much that we can't help but expect them to get sick.

By contrast, I cannot honestly remember the last time I "caught a cold". This might seem odd or perhaps by my own measurements alarming if you don't consider what I do for a living. As part of the microbiology lab in which I'm involved here, I obtain, maintain, and retain a series of strains of infectious microorganisms, including LVL2 Biohazard microbes (including E. coli, Diptheria, Cholera, and similar). The practical application of this I suppose is that periodic subclinical infections keep my immune system regularly challenged, such that it leaves little opportunity for opportunistic infections to take hold.

Without this information, it might seem that I'm more resilient against infection or that I'm "due" to catch something. Reality indicates however that I'm regularly and constantly under assault, but that my body is always ready to turn back the tide of invaders.

Some of the people I know who get flu shots complain that they don't work, and many people complain about responses of plants for which they care even after I dispense advice. What they do not realize is that that microbial world remains largely invisible to me. IN the first case, they probably catch the common cold, bronchitis, or even pneumonia after a flu shot and not the flu, such infections made possible by the fact that the body starts a primary response to influenza (which is a virus and MUST be fought by a secondary antibody-mediated immune response). In the second, they pretend that plants don't catch "colds" per se. Tobacco mosaic virus is basically akin to catching leprosy for a plant, but we don't pay it much mind.

Many things in science are not paid much mind. Touching plants induces genes. A failure in my building's climate control system shuts of laminar hood air flow (which was bad when I was mixing acetone and petroleum ether). However, I do not believe there are any coincidences. The problem for researchers is that when people discover unexpected things in science, they often don't provide public explanations if they come up with them at all. More often than not I observed scientists omit "anomalous" outliers in order to publish results when the outliers more accurately reflected the truth about that phenomenon.

When I studied diterpenes and volatiles in Vitis vinifera, we found, much to the chagrin of the funding agency that resveratrol increased only twofold in the berries but fiftyfold in the leaves under abiotic stress. That makes perfect sense biochemically now that I think about it, but if you're selling wine as an herbal supplement, that doesn't help your marketing. If you're making tea out of grape leaves, it's tantamount to a breakthrough. It wasn't what they wanted, but it was still useful.

One other thing that threw off our calculations was the alfalfa field adjacent to the vineyard. Overflow runoff from irrigation of that field influenced the grapes immediately antecedent, so once we were able to identify the source of the error, we omitted that one block out of the six total blocks of data available (a loss of 15 plants per subset out of 90 total biological replicates) until the situation rectified itself. Arbitrary omission or fanciful inclusion would have rendered our data irrelevant even if correct because it was founded on bad science.

Much goes on that we cannot see. The kind of scientific investigations in which I engaged as a graduate student involved ppb measurements, far below the detection levels of almost any human sense except taste/smell (which isn't quantitative). Just because we cannot see it doesn't mean it doesn't exist.

Yet my colleagues by and large also remain skeptics and atheists, except when they want me to buy their conclusions in peer review.