Thursday, 6 September 2012

08:52 – For about 20 years, I’ve been ordering bulk pipe tobacco from Craig Tarler at Cornell & Diehl. I order five pounds at a time, which lasts me a few months. I store the gallon ziplock bags in the freezer. So, the other day I finished off a bag and pulled a new bag out of the freezer. It felt light, so I tossed it on the shipping balance, which indicated only 14.4 ounces. The empty bag with label weighed 0.5 ounces, so that meant there was only 13.9 ounces of tobacco in the bag, more than 2 ounces short. The remaining bags weighed 15.1, 14.8, and 15.3 ounces.

I’ve been dealing with Craig for 20 years, since soon after he opened his business in 1990, so it never even crossed my mind that the shortage was intentional. I figured his balance must be miscalibrated, so I called yesterday and asked to speak with Craig. He wasn’t available, so I told the guy who’d answered the phone about the problem. He apologized profusely and said they’d ship replacement tobacco. I thought no more about it.

Then, this morning, I fished an email out of my trash folder. It was a forwarded message saying that Craig had died recently. Wow. I’d never met Craig, and spoke to him on the phone only every few months, but it still feels like I’ve lost a friend. Craig was never in a hurry when I spoke to him. We’d finish our business in the first couple minutes, and then talk for 10 or 15 minutes more about stuff in general. Craig was the last blending tobacconist left in the United States. He had thousands of individual customers like me, who ordered their pipe tobacco directly from C&D. He also supplied most of the independent tobacconists in the US, both with his standard blends and with custom blends made only for them. He produced many fine tobaccos, and was a wonderful person. He’ll be missed.

16:31 – Like many scientists, I’ve tried to take some time today to look over the results released yesterday by the ENCODE group. I’m seldom overwhelmed and intimidated by a new science paper, but this group of 30 related papers is difficult to take in, to say the least. Someone said this was the greatest breakthrough in genomics in 20 years, which I don’t think exaggerates the importance of this work.

Briefly, this massive project relates to so-called “junk DNA”, which I’ve always preferred to think of as “dark DNA”. It always seemed presumptuous to me to assume that because we don’t know what some parts of the genome do they must do nothing at all. Some evidence that that is not the case has been around for 20 years, and every year there’s more added. Until now, things related to dark DNA were murky, to say the least. This consortium of scientists has at least opened the door to starting to understand what dark DNA does. Until now, we’ve known that small parts of dark DNA–it was never really very clear which small parts–had a bearing on many things that are not well understood. Still, the assumption remained that the vast majority of dark DNA was just flotsam in the genome. As of now, we have strong evidence that the majority of “junk DNA” is anything but. It appears that at least 80% of what most people formerly called junk DNA is in fact biologically functional and important. Which begs the question, if 80% is important, why not assume that all or nearly all is equally important.

This really is a breakthrough, with potential implications for everything from cancer to Alzheimers to many other diseases that have genetic components. The work hasn’t really yet begun, but at least these scientists have shown us good places to start looking. Now, if we only had enough scientists working on all of the potential paths.

22 thoughts on “Thursday, 6 September 2012”

  1. While I object very strongly to cigarette smoke and smokers I’m not bothered by pipe smoke. My father had a pipe but I don’t remember seeing him use it. He smoked cigarettes, – started during WWII and gave up in the mid Sixties. Within months he couldn’t stand being near smokers. The older brother of one of my pals when I was about 10 smoked a pipe, he used a brand called “Blend 11”, which I thought smelt wonderful.

    I did a year of ancient Greek with an elderly pipe smoker. I was his only student that year and we sat at his dinner table while I was trying to pick up Greek. He smoked a pipe, but unlike cigarette smoke it didn’t annoy me in the least. He died in November of that year of esophageal cancer, aged about 73.

  2. That’s pretty common. Barbara can’t tolerate cigarette or cigar smoke, but she actually likes pipe smoke as long as it’s not too heavy.

  3. I was a heavy cigarette smoker (2-3 packs per day) for several years, but I quit cold turkey almost 3 years ago. Cigarette smoke bothers me because it’s unpleasant smelling and because everytime I smell it I realize I’m also inhaling it. As someone who went through the process of quitting it bugs me that I still get stuck inhaling other peoples smoke.

    However, my father smoked pipes and cigars and I love the smell of that smoke. It triggers a lot of pleasant nostalgia. So, the local bar I frequent most when I want a drink is actually a cigar bar. I go sit in the corner, order my double whiskey, neat, and enjoy the arome. I realize that secondhand pipe and cigar smoke is just as bad as secondhand cigarette smoke, but the pleasant aroma that reminds me of my father is more than enough to get me to ignore the health risk.

    When I see a cigarette smoker I think, “They’re feeding their addiction.” When I see a pipe or cigar smoker I think, “They’re enjoying some tobacco.”

  4. Actually, I’ve seen no convincing evidence that casual second-hand smoke is harmful to non-smokers, other than those who are allergic or otherwise extraordinarily sensitive. In terms of lasting effects on health from casual exposure, there’s no evidence to support it.

  5. What makes me laugh is the people who make the claim that second hand smoke is more dangerous than smoking directly!

    I quit cold turkey in 1998 and had my first cigarette in 1965 at the tender year of six. I am like most other people who have quit in that I don’t mind being around other smokers, but I have never liked the smell it leaves on clothes. Pipe tobacco is much more fragrant, but the best smell for me is unburnt pipe tobacco.

  6. I had my first and last ciggie when I was 12. I about coughed up a lung and never smoked again. My entire family smoked, but quit or died (other causes than smoking). I, like the others here, am annoyed by ciggie smoke, but have no problem with pipe smoke.

    My worst experience was as a young 2d Louie flying on a C-141 to Germany for REFORGER. That was back when smoking was allowed on military aircraft. The air was “blue” for the whole trip. I probably got cancer just sitting there. lol Even when I started flying Blackhawks there were still ash trays in the doors.

  7. Even when I started flying Blackhawks there were still ash trays in the doors.

    You should have done like they do in TN. At the first intersection they stop at they roll down the window and toss out their butts. Most intersections in town are littered with the remnants of inconsiderate smokers.

  8. My worst experience was as a young 2d Louie flying on a C-141 to Germany for REFORGER. That was back when smoking was allowed on military aircraft. The air was “blue” for the whole trip. I probably got cancer just sitting there. lol Even when I started flying Blackhawks there were still ash trays in the doors.

    I was in the USAF from 1995 – 1999. Aircraft were all non-smoking, but we used to do it anyway. I was enlisted aircrew on C-5’s and I used to just go down to the cargo compartment, go stand near a door, and smoke. Cargo planes tend to leak like a sieve, so all of the smoke was blown through the leaky seal around the door and out the side of the plane. You couldn’t always do it. Sometimes there’d be some asshole on your crew that got off on bustng airmen for stupid shit. Sometimes you were carrying explosives and couldn’t smoke. However, on long flights I was usally able to sneak one cigarette and on the rare occassion when a non-smoking crew member came down to the cargo compartment at the same time and saw me, they usually just waved and went about their business.

    There were a couple of grisled old colonels and generals (probably the very last of the active duty Vietnam Vets) who would smoke while the plane taxied and when they got to the active runway would then flick their cigarette out of the cockpit window, latch the window, and then advance throttles and take off. They had to fly a sortie every 60 days to maintain their flying status and no one would dare point out that they were violating regs. Definitely difference between the old officers and the new. These days a USAF officer wouldn’t dare smoke. It’s very taboo for them. Sort of those unwritten rules of getting promoted as an “O”: Non-smoker, be married, wife should be active in Officer’s Wives Club, get your graduate degree before you’re up for Major, etc.

  9. Actually, I’ve seen no convincing evidence that casual second-hand smoke is harmful to non-smokers, other than those who are allergic or otherwise extraordinarily sensitive. In terms of lasting effects on health from casual exposure, there’s no evidence to support it.

    I would agree. For me it is more of a perception thing. Like when I smell automobile exhaust. I realize that catching a nose full of someone’s clunker car isn’t going to create any health problems, but I still can’t shake the feeling that I just inhaled something my body was never intended to inhale and something that in higher concentration for longer periods of time would be deadly. So, it triggers that “Poison!” alarm in my brain despite any actualy danger.

  10. Yes, well a favorite maxim among toxicologists is that the dose makes the poison. Some compounds have no discernible effect on health, good or bad, even at pretty high levels. Others, such as vitamin C, are essential for health at moderate levels, and not harmful even at relatively high levels. Still others are either essential or harmless at some level, but toxic beyond a threshold level. And then there are those that are lethal even at extremely low levels, things like dimethyl mercury and many alkaloids.

    And, as any chemist can tell you, just because something smells very good doesn’t mean it’s harmless, and just because something smells very bad doesn’t mean it’s harmful.

    And, as I’ve said more than once, the last time anyone tried doing scientifically controlled experiments on humans, they hanged the experimenters. Of course, they still use the data, tainted as they are. The fact that Nazi physicians who experimented on people were vicious, evil human beings doesn’t change the fact that at least some of them were good scientists. We’re never going to get scientifically valid data on humans simply because it’s unethical and rightly illegal to experiment on them. We just have to do the best we can using animals and large-scale population studies of humans. But that lets an awful lot slip through the cracks.

  11. We’re never going to get scientifically valid data on humans simply because it’s unethical and rightly illegal to experiment on them.

    You ever been to Walmart at 2:00AM? Some of those people look like the end result of some very dangerous experiments.

  12. Well, frankly, I think it should be legal to experiment on humans if you have their permission to do so. I’m thinking about situations like someone who will die imminently, has exhausted all approved treatment alternatives, and wants to do a Hail Mary by undergoing treatment with new drugs whose safety has not yet been tested. If someone knows that there’s a 0.9999 probability that he will die soon and a new drug has only a 0.9998 probability of doing nothing or killing him, that’s still a 0.0001 probability in his favor. But as things stand, he won’t get the treatment even if he begs for it.

    A big part of the problem is liability and lawsuits. I still maintain that a competent adult should be allowed to disclaim all liability and save someone harmless for actions taken with that person’s consent. Of course, the lawyer lobby will never allow that to happen, as reasonable as it is.

  13. The trick to conducting ethical human studies is to find subjects who
    look human and respond as humans would to drugs or whatever, but which
    aren’t human. Lawyers or politicians (some category overlap may be
    noticed) would be reasonable test subjects. (Though I’ll concede that in
    the case of career politicians, the “look human” test may fail.)

  14. I know that you will disagree, but I believe the human body to be a marvelously designed piece of engineering work. There are chemical factories in the human body that cannot be duplicated much less run by us in any efficient manner. The human stomach is an EPA superfund site with a pH of less than 2.0. The materials used in the human body are just amazing and usually do work well for a number of years. Show me another single pump system that has the capability of lasting over 100 years without serious maintenance. Of course, I am an engineer and do think of most things in engineering terms.

    When my Dad had heart valve replacement surgery in 1999, I was surprised to find out that the heart lung machine has to process three times as much blood in order to approximate a human set of lungs. So, the docs crank the velocity of the blood 3X and feed it to your brain first to get the most oxygen enrichment. Of course, this causes lesions in your brain due to the high speed blood going through it for 4 to 6 hours but it is better than being a veg.

    I just wish that we had a readily available spare parts bin and a complete set of user manuals. The Bible is a great introductory user manual but very incomplete on the human body details.

    I keep on arguing with myself on the design life of the human body. I first thought 30 years, then 35 years and now 45 years. Why 45 years? Because that is when presbyopia starts up and is the first clear sign of aging. The other signs are tooth loss and hair greying. BTW, I get really odd looks from members of my church when I talk about the design life of the human body. People tend not to like thinking about God as an engineer.

  15. I am not sure what convincing evidence would be, and if all the known studies aren’t it. However, I can toss this in: When the first two Swiss Canyons prohibited smoking in restaurants, bars, and workplaces, and they saw an almost immediate drop in heart attacks. 20%. This wasn’t expected, and is clearly documented in hospital admissions.

    What I don’t have is a breakdown of the 20% into smokers and nonsmokers. I It also isn’t really important. What seems clear is that spending hours in smoked-filled rooms was causing heart attacks.

  16. This in the morning paper: The FDA has started anti-terrorism inspections of Swiss food manufacturers who export to the US. You know, terrorists might poison a piece of cheese. Assuming this is a world-wide program, the sheer size of it must be astounding.

    Of course, like TSA, there is no legal requirement to put up with the searches. Just the question: “Do you want to export today?”

  17. You have to be careful about cause and effect. The example I use frequently is the strong correlation between marriages and housing starts. That makes sense superficially, until you consider that very few newly-married young couples are in a financial position to build a new house. Certainly, one can argue displacement, with newlyweds starting a household and the people they buy or rent from moving up, but the correlation becomes much weaker the further you delve into it.

    Similarly, I was just reading an article the other day that correlated serum concentrations of some environmental chemical or other with strokes or some other serious health issue. The non-scientist thinks, “Aha. High levels of this chemical cause strokes.” The scientist counters, “Or perhaps people who are more likely to have strokes are also more likely to bioaccumulate this particular chemical.” Those are two very different things, and determining which, if either, is true is often difficult or impossible.

    As to autocorrect, I remember the time I was writing an RFP for a new mainframe. The current mainframe was a Unisys, so the RFP was full of references to Unisys. WordPerfect’s spell checker corrected all instances of “Unisys” to “anuses”, which I thought was oddly appropriate because most of the Unisys reps I dealt with were assholes.

  18. Oh, yes, I remember Unisys all too well…

    Regarding causation vs. correlation: I understand the point, but I am at a loss to see how else to interpret this data. A 20 decrease in heart attack rates is pretty dramatic. For this to happen in the weeks following an indoor smoking ban – it could be coincidence, though any other explanation fails me. However, if it is correlated, it seems to me that the causation can only flow in one direction.

  19. I’m not a doctor, but I would suspect something other than smoking cessation alone to have such a dramatic effect. Perhaps very elderly smokers or the environment itself they smoked in. Maybe they weren’t drinking as much or their stress levels changed because they couldn’t go to their typical smoking place to bitch about life.

  20. That’s not a bad theory. It is certain that bars had less traffic, so there was likely also a drop in alcohol consumption.

  21. I am not a doctor either, but there are 4 in the close family. All of them agree that smoking degrades life—especially for the end. The one most recently out of medical school has indicated to me that smoking (including second-hand), coats the arteries and veins with stuff that isn’t good for you, impedes functioning of the lungs leading to emphysema in many people, and causes wrinkles and premature aging of the skin and other body parts. Even people who live into their 80’s or so, would have lived longer if they did not smoke, so she claims. I have no idea what studies are involved, but I do note one big difference between the US and Germany. US doctors would not touch a smoke if their life depended on it, whereas in Germany you see doctors regularly coming out of the hospitals to stand outside for their smoke break. The German doctor who attended to me when I fell off the skateboard, was nearly a chain smoker. He did his residency in NYC, but apparently never picked up the American doctor’s abhorrence for smoking.

    But I am glad to have left the US 1950’s in terms of smoking—which is what Germany today is—and returned to the land of the smoke-free. Even smokers here cower and go far away when you look at them with the proper expression. And cigarette butts are almost non-existent on the ground in the US. They were everywhere in Berlin—especially after they fired the guys in orange with the brooms and trash cans on wheels.

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