I know I said the next post would be more on epistemology, but in the meantime we've had a whole bunch of visitors who have made my life unnecessarily difficult. So, a quick primer on farm life.
We live in an antique farmhouse on 2 acres. A good portion of that 2 acres has been made into a vegetable garden and orchard. We also keep poultry, unfriendly cats and two giant livestock guardian dogs. We heat the house by means of a wood stove. Lots of people think it would be lovely to visit a real antique New England farmhouse, complete with ghosts, from leaf peeper season right through the holidays.
1. The combination of "antique," "fireplaces" and "giant dogs" means the house is not child-friendly. We have uneven floors, creative wiring, weird handmade door latches, an extremely hot wood stove and an open fireplace large enough to walk into. The dogs perceive children as a kind of sheep to be herded. We have a barn full of sharp yet rusty hay-making and gardening equipment. The chickens will peck, hard, at things they don't understand, such as inquisitive five-year-old fingers. The swimming pool is not typically supervised, is eight feet deep, and no, there is no magic chemical that makes pee disappear or that successfully kills ALL diarrheal bacteria. Those pretty plants in the garden that your child is so joyfully wrecking? Those are my groceries for the next three months, thanks. Replacing them at the Stop & Shop will run to about $900. If you bring a young child to this house, be prepared for a lot of crying, a lot of scraped knees and boo-boos while Junior learns that the whole world is a dangerous place. Better yet, leave Junior at home with a sitter.
2. About Chores:
2a. The chores do not stop because you're visiting. The chickens and weeds do not bow to your presence. For that matter, neither do my experiments. If early morning noise bothers you, bring earplugs. Bring a book to read or make your own entertainment plans. Be aware that chores last from early in the morning to late at night. Depending on what needs to be done that day, I may not get any time off to relax between 5am and 9pm. And no, I can't just do it some other day--an animal or a food-producing plant can die in 24 hours of neglect, depending on the time of year. If I don't run the wood stove for a few days, I rack up one hell of a fuel oil bill. Chores are part of farm life. "Real" farmers don't get days off or sick days either.
2b. The most helpful thing you can do is make a second pot of coffee when you roll out of bed. Most farms have their own set-up, and unless someone specifically shows you how you can help, generally assume that you cannot do anything without making more work. The second most aggravating thing is when people say, "Oh, let me help you!" and proceed to tear out perfectly good garden veggies ("I thought they were weeds! I've never seen ones like that at the supermarket!"), attempt to maintain the wood stove ("What do you mean, the wood has to cure? Wood is wood!"), or attempt to clean something inappropriately ("I bleached the perches in the chicken coop, they were all dirty!"). Either wait to be shown what to do, or stay out of the way.
3. You'd think this would be elementary, but apparently it isn't: Eat the food that is put in front of you. If it bothers you that the food on your plate was recently growing in a garden, or that the napkin you're given was dried by means of sunlight, or that the meat was recently munching hay, don't ask too many questions about it. Or announce before dinner time that you will be eating at a restaurant. You don't need to say why. But for the record, the air in your electric/gas dryer is in fact dirtier than the sunlight (the UV in sunlight kills germs), and the food at the grocery store is many weeks old by the time it hits the shelves, in addition to having been picked and processed by someone who for sure did not have sufficient sick days and probably did not wash their hands. Most agribusiness-type farms don't even have port-a-potties in the fields for their workers, so guess where the farmhands at the mega-corporations go to the toilet? Now wouldn't you rather have veggies picked by someone who you personally KNOW washes their hands, whose septic system is always in good working order and who prepared the food in a clean kitchen right in front of you?
4. The house is antique. A-N-T-I-Q-U-E. That means that it will be drafty and there's no cable TV. Why are you visiting me if all you want to do is watch TV? I thought you wanted to hang out with us, talk, do things you can only do here. You can watch TV at home. Put a sweater on and quit complaining or go home to your nice overheated hermetically sealed McMansion and watch TV. No, I'm not cold, probably because I just did 12 hours of heavy labor. Yes, I did eat a lot at dinner, and no, I don't think I'll get fat. That 12 hours of heavy-duty farm work probably has something to do with it...
5. Farms have poop. We've got kitchen waste, chicken poop, leaf mold, dog poop and compostable cat litter. Generally, it stays contained in two mega compost heaps by the outhouse and a manure barn, but the chickens have been known to drop crap-bombs directly on people. The dogs are reasonably well trained, but they are first and foremost guard dogs--they jump on people. Garden clogs, Wellingtons, sneakers, hiking boots and paddock shoes are good footwear choices. Metallic strappy Manolo heels, not so much. Dress in layers to accommodate the weather and the relative dirt: It's really easy to throw a cheap windbreaker in the wash if it gets dirty, especially if you have a sweater and long sleeved t-shirt on underneath. More difficult to clean a satin halter top with matching see-through shrug if that's all you're wearing when the dogs decide that you'd look great with a big muddy paw-print on your boob.
Saturday, January 3, 2009
Monday, December 22, 2008
Been busy.
Been busy with various things the past 10 weeks. PSA: Never never never buy a real antique house. Buy a reproduction. I fell in love with my house because it smelled like my uncle's old farmhouse: wood smoke, lemon-scented cleaner, a hint of cattle/horse manure, and this dusty old musky floral smell that old houses seem to acquire over centuries. I am a moron and a sucker and I bought the thing, despite the inspector's warning that it needed a LOT of work. No less than 12 contractors later, I am back to Contractor #7, whose timescale is clearly different from the rest of humanity's, but was the only one who listened to a word coming out of my mouth and had a reasonable estimate. It's not just the work that needs done, it's that contractors are demons from the nether regions of heck.
Anyway. The subject of today's post shall be Epistemology: The Theory of Knowledge.
The reason this comes up is that in the daily course of events, I run into people who do or say something clearly hazardous, stupid, that puts their own lives and the lives of people around them in jeopardy. When it is pointed out (gently, politely) that what they just said or did is perhaps unwise, the response is, "oh yeah? well all them experts don't know nuthin'."
Experts? You need an expert to tell you that the sky is blue?
Relying on expert opinion is a shortcut in thinking. There's no inherent value judgment to shortcuts, as long as you realize their limitations. It's quicker and easier to use a computer program to solve a math problem than to do it yourself with paper and pencil, as long as you realize that the computer is going to use an algorithm that might add a certain measure of error to the result. The problem with relying on expert opinion is that you're adding their potential errors in thinking to your own--and for someone who isn't an expert in the field themselves, knowing which experts to heed and which ones are blowhards, isn't obvious.
The "ask an expert" algorithm is one we're all raised with, though. When you're a small child, teachers and religious leaders and parents are all experts who guide you through worldly perils. Many churches continue to exploit this algorithm, interpreting holy texts and dispensing wisdom through "expert" designees. Our society is not designed to give people a lot of opportunities to discover things on their own--we are structured and have grown around the concept of specialization and expertise, rather than generalization and discovery. Partly, that's because it's much faster to memorize knowledge on a particular subject from an expert than it is to re-create it for yourself. However, it seems we've gotten to the point that now the process of creating new knowledge is, in itself, a specialty task few can undertake.
I think that for the good of society and education in general, this is wrong. People should be able to gather and analyze data on their own. But our popular media is such that it's difficult for many people to tell the difference between a fact and an opinion. Opinions and controversy and debate sell more papers and get more viewers than simple data sets, unfortunately. Worse, our educational system has collapsed to the point that even when simple data sets are published, most folks don't know what to do with them. The thinking processes that are used to design a question to be answered, the mathematics used to separate the questioner's bias from the data set, are not commonly taught outside of a few post-secondary-school disciplines.
So, let's start with what data is and how to recognize it:
The word data is from the Latin datum (datus, data, datum, 2nd declension neuter), a derivative of the verb dare, do "to give." Data are "givens," i.e. things that exist on their own independent of opinions on them.
Examine these statements:
"The average global temperature is rising at a rate of 1.3 degrees per 100 years; when examined over the past 50 years, the average global temperature increased at a rate closer to 2 degrees per 100 years."
"Global warming will be the next major crisis of humanity"
"Global warming is not caused by human activity."
The first one is data--pure information, no interpretation involved. The latter two are interpretations, although they are presented as facts. The problem with the interpretations is, whose might be more accurate? Most folks, including many scientists, use number of credentials and prestige as a shortcut to decide whose interpretation is best, but unless there is a pressing time constraint (decisions and actions required in a matter of days, rather than months or years) there's no reason to use that mental shortcut. You can collect your own data and decide whether or not your data set matches the data set of any individual "expert," all on your own.
In the global warming example, the National Oceanic and Atmospheric Administration collects temperature data from their weather satellites, and stores it in a database that is freely open to the public. You could select random longitude and latitude locations around the globe, evenly distributed over the planet, and look up the historical temperature readings in the database over several decades. Then you could graph the results over time, and see if your result matches that of any particular expert. All you need to do this exercise is high school algebra, a pencil, and some graph paper.
Another question about data and how to interpret it is, how do we know that any one particular method of collecting data is correct? How do we know that the satellites that measure the earth's surface temperature are measuring correctly--hell, they could be running on Windows or something. To be sure that our data is true, and not an artifact of the data collection method, we validate the data against some other method that collects similar information.
For example, we know that warmer temperatures will melt ice. We should see more polar ice melting overall, and sea levels rising as a result, if indeed the earth's temperature is rising. And indeed, polar ice is melting quickly.
But I don't have a satellite, and probably neither do you. How could we validate the warming curve in our own backyards? After all, I've got 2 1/2 feet of snow in my back yard, and the polar bears are welcome to borrow some, right?
1. Investigate historical information, and keep diaries of dates for the first snowfall of winter, the first real frost of autumn, the last frost of spring, and the first appearance of spring flowers in your backyard. In my little corner of New England, we normally have the first snow with accumulation (as opposed to flurries) by Thanksgiving, but recently it's not shown up until closer to Christmas. I've been able to keep my swimming pool open till October, rather than September, as frosts come later and later. The last frost date for my area is 1 May, but we haven't had a late April / early May frost in at least five years. Track daily temperature highs, lows, and averages.
2. Make notes of the arrivals and migrations of seasonal birds and insects in your area. When does the first hummingbird show up at the feeder, and when do they leave? When did you see the first robin, the first swallow or flycatcher? I'm looking at my bird feeder and there's a red-bellied woodpecker eating the suet--a bird that rarely overwinters this far north.
3. You can also track reports of insect-borne diseases online, such as EEE and West Nile Virus. In temperate or cold climates, warmth-loving insects like mosquitos can't survive, so northern areas generally have fewer problems with these diseases than warmer areas. If the world wasn't warming up, we would expect that these diseases would stay mostly within their geographic confines.
4. Count the number of annual heat-related deaths vs. the annual number of cold-related deaths. Elderly people and small children typically die of heatstroke or dehydration, although outdoor workers and athletes can also succumb. We would expect the ratio of heat related deaths : cold related deaths to increase over time as the temperature increases.
Which do you think is a better method to determine facts from interpretations? Asking an expert, or independent validation by another means of measuring the same parameter? We can test data by means of validation, or we can trust someone because they've got a bunch of letters after their name.
Next post: Assertions, questions, and logic.
Anyway. The subject of today's post shall be Epistemology: The Theory of Knowledge.
The reason this comes up is that in the daily course of events, I run into people who do or say something clearly hazardous, stupid, that puts their own lives and the lives of people around them in jeopardy. When it is pointed out (gently, politely) that what they just said or did is perhaps unwise, the response is, "oh yeah? well all them experts don't know nuthin'."
Experts? You need an expert to tell you that the sky is blue?
Relying on expert opinion is a shortcut in thinking. There's no inherent value judgment to shortcuts, as long as you realize their limitations. It's quicker and easier to use a computer program to solve a math problem than to do it yourself with paper and pencil, as long as you realize that the computer is going to use an algorithm that might add a certain measure of error to the result. The problem with relying on expert opinion is that you're adding their potential errors in thinking to your own--and for someone who isn't an expert in the field themselves, knowing which experts to heed and which ones are blowhards, isn't obvious.
The "ask an expert" algorithm is one we're all raised with, though. When you're a small child, teachers and religious leaders and parents are all experts who guide you through worldly perils. Many churches continue to exploit this algorithm, interpreting holy texts and dispensing wisdom through "expert" designees. Our society is not designed to give people a lot of opportunities to discover things on their own--we are structured and have grown around the concept of specialization and expertise, rather than generalization and discovery. Partly, that's because it's much faster to memorize knowledge on a particular subject from an expert than it is to re-create it for yourself. However, it seems we've gotten to the point that now the process of creating new knowledge is, in itself, a specialty task few can undertake.
I think that for the good of society and education in general, this is wrong. People should be able to gather and analyze data on their own. But our popular media is such that it's difficult for many people to tell the difference between a fact and an opinion. Opinions and controversy and debate sell more papers and get more viewers than simple data sets, unfortunately. Worse, our educational system has collapsed to the point that even when simple data sets are published, most folks don't know what to do with them. The thinking processes that are used to design a question to be answered, the mathematics used to separate the questioner's bias from the data set, are not commonly taught outside of a few post-secondary-school disciplines.
So, let's start with what data is and how to recognize it:
The word data is from the Latin datum (datus, data, datum, 2nd declension neuter), a derivative of the verb dare, do "to give." Data are "givens," i.e. things that exist on their own independent of opinions on them.
Examine these statements:
"The average global temperature is rising at a rate of 1.3 degrees per 100 years; when examined over the past 50 years, the average global temperature increased at a rate closer to 2 degrees per 100 years."
"Global warming will be the next major crisis of humanity"
"Global warming is not caused by human activity."
The first one is data--pure information, no interpretation involved. The latter two are interpretations, although they are presented as facts. The problem with the interpretations is, whose might be more accurate? Most folks, including many scientists, use number of credentials and prestige as a shortcut to decide whose interpretation is best, but unless there is a pressing time constraint (decisions and actions required in a matter of days, rather than months or years) there's no reason to use that mental shortcut. You can collect your own data and decide whether or not your data set matches the data set of any individual "expert," all on your own.
In the global warming example, the National Oceanic and Atmospheric Administration collects temperature data from their weather satellites, and stores it in a database that is freely open to the public. You could select random longitude and latitude locations around the globe, evenly distributed over the planet, and look up the historical temperature readings in the database over several decades. Then you could graph the results over time, and see if your result matches that of any particular expert. All you need to do this exercise is high school algebra, a pencil, and some graph paper.
Another question about data and how to interpret it is, how do we know that any one particular method of collecting data is correct? How do we know that the satellites that measure the earth's surface temperature are measuring correctly--hell, they could be running on Windows or something. To be sure that our data is true, and not an artifact of the data collection method, we validate the data against some other method that collects similar information.
For example, we know that warmer temperatures will melt ice. We should see more polar ice melting overall, and sea levels rising as a result, if indeed the earth's temperature is rising. And indeed, polar ice is melting quickly.
But I don't have a satellite, and probably neither do you. How could we validate the warming curve in our own backyards? After all, I've got 2 1/2 feet of snow in my back yard, and the polar bears are welcome to borrow some, right?
1. Investigate historical information, and keep diaries of dates for the first snowfall of winter, the first real frost of autumn, the last frost of spring, and the first appearance of spring flowers in your backyard. In my little corner of New England, we normally have the first snow with accumulation (as opposed to flurries) by Thanksgiving, but recently it's not shown up until closer to Christmas. I've been able to keep my swimming pool open till October, rather than September, as frosts come later and later. The last frost date for my area is 1 May, but we haven't had a late April / early May frost in at least five years. Track daily temperature highs, lows, and averages.
2. Make notes of the arrivals and migrations of seasonal birds and insects in your area. When does the first hummingbird show up at the feeder, and when do they leave? When did you see the first robin, the first swallow or flycatcher? I'm looking at my bird feeder and there's a red-bellied woodpecker eating the suet--a bird that rarely overwinters this far north.
3. You can also track reports of insect-borne diseases online, such as EEE and West Nile Virus. In temperate or cold climates, warmth-loving insects like mosquitos can't survive, so northern areas generally have fewer problems with these diseases than warmer areas. If the world wasn't warming up, we would expect that these diseases would stay mostly within their geographic confines.
4. Count the number of annual heat-related deaths vs. the annual number of cold-related deaths. Elderly people and small children typically die of heatstroke or dehydration, although outdoor workers and athletes can also succumb. We would expect the ratio of heat related deaths : cold related deaths to increase over time as the temperature increases.
Which do you think is a better method to determine facts from interpretations? Asking an expert, or independent validation by another means of measuring the same parameter? We can test data by means of validation, or we can trust someone because they've got a bunch of letters after their name.
Next post: Assertions, questions, and logic.
Monday, September 15, 2008
Cultural differences
So in discussing the Boobywars on ScienceBlogs, one commenter made a point of telling other ladies to show off their feminine attributes without fear, because we could not live our lives in fear and must, at some point, square our shoulders and work to change our culture. However, she also mentioned that she was surprised that junior scientists and students in her lab had intimated that they had used their feminine wiles to get grades, assistance, etc. and then went on to joke a bit about the importance of putting various unguents on one's breasts to make them more lustrous. I joked back, well, a better option might be glue, all things considered--I don't want to put on a peepshow by mere accidental stumble. She was not amused by my joke and seemed a bit horrified, as if the joke had been pushed too far for her liking. Maybe it was.
But the more I thought about it, the more it struck me that she must come from an extremely different world than me, money-wise. I went to school in economically depressed areas of the US, where double-digit unemployment was the rule rather than the exception. Women students at my alma mater frequently did put themselves through school by gluing things to their breasts and then jiggling the results at paying men. That was not unusual in the least; it was seen as just another option for a part-time job in college, like bartending. It paid rather better than most other part-time jobs, but this was looked on as hazard pay, similar to any other dangerous job that is done by part-time contractors (crab fishing, lumberjacks, etc.) and can only be done by the relatively young and healthy. Nor was it unheard-of for undergrad women to collect their tips from their own university department heads. The women themselves saw their own bodies as a straightforward economic resource, not a game. They wouldn't have found the commenter's joke funny, merely puzzling. Why would you put Vaseline on your breasts for any reason? Didn't she know it would make your skin break out? Then they'd expound on the many types of body make-up, relative pricing, ease of use, and so on. Some worked as prostitutes, also.
I cannot emphasize enough how normal and regular this was, especially for working class students. Lower-middle class students, whose parents were just barely able to send their daughters to school, but not able to afford them the tutoring and private schools that would have given them enough academic skills to compete, were more apt to trade their bodies for grades and favors. They didn't have any other means of getting grades enough to meet their aspirations, although those aspirations were not usually any different from those of wealthy students whose parents expected them to become doctors, lawyers and chief executives.
{Male students who needed to raise money in a hurry usually used their organic chemistry skills to manufacture LSD. You could correlate the student drug busts exactly with the announcement of tuition increases and the bursar's billing schedule. Students who only occasionally deal drugs aren't good at avoiding police detection. Basically, there's just not enough financial aid for students who need it, there aren't enough jobs for students who need them, and the jobs that exist don't pay enough. A temporarily crummy or black market job to get a leg up in the class wars is worth it to some people. They've seen how their parents live and don't want to die like that. But I digress.}
For decades, my alma mater's chemistry department was run by a man who did trade grades for boobage. All the chemistry teachers were known for grading their large lecture sections hard, and women especially. Some of my friends would experiment on their professors by coordinating their answers with the male students, then comparing grades. Male students got A-s and B+s for the same exam answers that merited a C- from female students. When this was brought to the attention of the department head, they were given the option of trading oral sex or stripteases for a revised grade. This scam went on for many years before the department head in question tried it on the wrong student, who promptly sued. One of my undergrad advisors argued on his behalf in court that it was grossly unfair of the school to fire him, since he had tenure.
When I went to grad school in an area that was far from economically depressed, in an area that was in the midst of a small boom, there were no strip clubs, no bad part of town where hookers cruised, no known whorehouses, and a few college bars which any respectable person could be publicly observed. Only a few students ever complained to me that they needed financial aid, and for the most part they managed to get scholarships or additional loans. The lower-middle class kids did offer to trade sex for grades, but this was fairly infrequent and many professors were horrified by the propositions they received.
It struck me that the commenter and I are coming from such different experiences. I don't think to show off any of my feminine attributes, well fit as they are, because when I was a lass showing off your figure was something women might do for money, certainly not for free, and it was a job I didn't want. There were professional jobs that I wanted to have, grubby jobs I didn't want to have, and showing off your feminine wiles was grouped along with "scrubbing toilets" and "car salesman" under the Jobs I Don't Want heading. Things I might have to do out of economic necessity, but would prefer not to do if at all possible. Yet to the commenter, her breasts and sexuality are toys, a joke, a fun part of her appearance and something she can afford to lecture other ladies about. If she ever struggled with a difficult class, no doubt her first tactic was to study harder, get tutored, attend extra study sessions. She didn't have to do the calculus of X hours in class + Y hours at work = no additional time for studying, and wonder how to pass a needed course at her wits' end. She cannot see how her economic advantage shaped her thinking on the matter, or how she can afford to be brave in the confidence that she has many other options for battle or for escape if she encounters a sexist situation.
But the more I thought about it, the more it struck me that she must come from an extremely different world than me, money-wise. I went to school in economically depressed areas of the US, where double-digit unemployment was the rule rather than the exception. Women students at my alma mater frequently did put themselves through school by gluing things to their breasts and then jiggling the results at paying men. That was not unusual in the least; it was seen as just another option for a part-time job in college, like bartending. It paid rather better than most other part-time jobs, but this was looked on as hazard pay, similar to any other dangerous job that is done by part-time contractors (crab fishing, lumberjacks, etc.) and can only be done by the relatively young and healthy. Nor was it unheard-of for undergrad women to collect their tips from their own university department heads. The women themselves saw their own bodies as a straightforward economic resource, not a game. They wouldn't have found the commenter's joke funny, merely puzzling. Why would you put Vaseline on your breasts for any reason? Didn't she know it would make your skin break out? Then they'd expound on the many types of body make-up, relative pricing, ease of use, and so on. Some worked as prostitutes, also.
I cannot emphasize enough how normal and regular this was, especially for working class students. Lower-middle class students, whose parents were just barely able to send their daughters to school, but not able to afford them the tutoring and private schools that would have given them enough academic skills to compete, were more apt to trade their bodies for grades and favors. They didn't have any other means of getting grades enough to meet their aspirations, although those aspirations were not usually any different from those of wealthy students whose parents expected them to become doctors, lawyers and chief executives.
{Male students who needed to raise money in a hurry usually used their organic chemistry skills to manufacture LSD. You could correlate the student drug busts exactly with the announcement of tuition increases and the bursar's billing schedule. Students who only occasionally deal drugs aren't good at avoiding police detection. Basically, there's just not enough financial aid for students who need it, there aren't enough jobs for students who need them, and the jobs that exist don't pay enough. A temporarily crummy or black market job to get a leg up in the class wars is worth it to some people. They've seen how their parents live and don't want to die like that. But I digress.}
For decades, my alma mater's chemistry department was run by a man who did trade grades for boobage. All the chemistry teachers were known for grading their large lecture sections hard, and women especially. Some of my friends would experiment on their professors by coordinating their answers with the male students, then comparing grades. Male students got A-s and B+s for the same exam answers that merited a C- from female students. When this was brought to the attention of the department head, they were given the option of trading oral sex or stripteases for a revised grade. This scam went on for many years before the department head in question tried it on the wrong student, who promptly sued. One of my undergrad advisors argued on his behalf in court that it was grossly unfair of the school to fire him, since he had tenure.
When I went to grad school in an area that was far from economically depressed, in an area that was in the midst of a small boom, there were no strip clubs, no bad part of town where hookers cruised, no known whorehouses, and a few college bars which any respectable person could be publicly observed. Only a few students ever complained to me that they needed financial aid, and for the most part they managed to get scholarships or additional loans. The lower-middle class kids did offer to trade sex for grades, but this was fairly infrequent and many professors were horrified by the propositions they received.
It struck me that the commenter and I are coming from such different experiences. I don't think to show off any of my feminine attributes, well fit as they are, because when I was a lass showing off your figure was something women might do for money, certainly not for free, and it was a job I didn't want. There were professional jobs that I wanted to have, grubby jobs I didn't want to have, and showing off your feminine wiles was grouped along with "scrubbing toilets" and "car salesman" under the Jobs I Don't Want heading. Things I might have to do out of economic necessity, but would prefer not to do if at all possible. Yet to the commenter, her breasts and sexuality are toys, a joke, a fun part of her appearance and something she can afford to lecture other ladies about. If she ever struggled with a difficult class, no doubt her first tactic was to study harder, get tutored, attend extra study sessions. She didn't have to do the calculus of X hours in class + Y hours at work = no additional time for studying, and wonder how to pass a needed course at her wits' end. She cannot see how her economic advantage shaped her thinking on the matter, or how she can afford to be brave in the confidence that she has many other options for battle or for escape if she encounters a sexist situation.
Saturday, September 6, 2008
Mad busy!
Things have gotten insanely busy at work AND at home.
Home first: It's harvest time in the Reasonable household, which means that every single weekend I have to can or freeze something, mulch something else, weedwack another thing. Plus, I am writing this in the few minutes I have before I have to clean out my car to get a new puppy. Then I have to train said puppy. Also, we are collecting quotes for structural work on our house. I hate contractors. Hate 'em. They're all evil. And I'm acclimating my chickens to their new coop, which is a bit of a Process. They've been in there a week, and I still haven't scrubbed out their old coop. And Mr. Reasonable tells me that his high school buddy will be visiting in a couple of weeks, so I need to prep my office for a guest room, which involves shampooing the cats' favorite couch, moving litterboxes, and cleaning off my desk.
Work: I am informed that if I don't get the effing manuscript for one of my projects into the Legal department's hands by the end of the month, I will not be allowed to go to the really good conference I want to attend. Manuscript is, like, 1/3 written, although all the data has been collected. I am sort of stupid on how I should do the figures, despite the Author Instructions on various journal websites. There are multiple ways of presenting the same data, and I'm messing around with which one looks the coolest, and also procrastinating a lot. I'm going to end up refuting one of the field bigwigs, and that makes me a wee bit nervous because I'm still more of less nobody (my brain is exceptionally wide, but not deep on any particular subject). Plus I have all my regular projects to puzzle over, and new equipment arriving next week. On top of that, I am covering for my co-worker who is off doing something, I forget what, with her kids. Also, we are losing executive staff left and right, but they all assure us that it's not because the new president of research is evil or anything. Yeah, right.
Must go clean out the car and line it with puppy pads. And probably fill up the carpet shampooer.
Home first: It's harvest time in the Reasonable household, which means that every single weekend I have to can or freeze something, mulch something else, weedwack another thing. Plus, I am writing this in the few minutes I have before I have to clean out my car to get a new puppy. Then I have to train said puppy. Also, we are collecting quotes for structural work on our house. I hate contractors. Hate 'em. They're all evil. And I'm acclimating my chickens to their new coop, which is a bit of a Process. They've been in there a week, and I still haven't scrubbed out their old coop. And Mr. Reasonable tells me that his high school buddy will be visiting in a couple of weeks, so I need to prep my office for a guest room, which involves shampooing the cats' favorite couch, moving litterboxes, and cleaning off my desk.
Work: I am informed that if I don't get the effing manuscript for one of my projects into the Legal department's hands by the end of the month, I will not be allowed to go to the really good conference I want to attend. Manuscript is, like, 1/3 written, although all the data has been collected. I am sort of stupid on how I should do the figures, despite the Author Instructions on various journal websites. There are multiple ways of presenting the same data, and I'm messing around with which one looks the coolest, and also procrastinating a lot. I'm going to end up refuting one of the field bigwigs, and that makes me a wee bit nervous because I'm still more of less nobody (my brain is exceptionally wide, but not deep on any particular subject). Plus I have all my regular projects to puzzle over, and new equipment arriving next week. On top of that, I am covering for my co-worker who is off doing something, I forget what, with her kids. Also, we are losing executive staff left and right, but they all assure us that it's not because the new president of research is evil or anything. Yeah, right.
Must go clean out the car and line it with puppy pads. And probably fill up the carpet shampooer.
Saturday, August 23, 2008
Keep your eyes in your head
There's currently a debate over at Thus Spake Zuska about the mysterious grey area where a glance at a breast becomes an unwelcome stare. So far the main talking points seem to be:
-It's biological, people can't help looking at an attractive person
-Humans are sexual creatures and it's unreasonable of society or anyone to expect people to leave their personal foibles and bad habits at home
-People shouldn't be so easily offended, AKA Some women like it
-People should cover up in burkas if they are so incredibly gorgeous
Zuska has done a wonderful job of dispelling the last of these: In countries where women do wear burkas, they get much more harassment than they do in countries with more liberal clothing policies. As to the other three...
It's biological, people can't help looking at an attractive person
Lots of things are biological, and yet we train ourselves out of them in polite company. Adults are potty-trained, eat food with silverware, wear clothing outdoors and in mixed company, and bathe themselves, all means of overcoming natural biological things that are offensive to polite society. You don't get a pass on those, so why should I give you a pass on where you rest your eyes? Practice the good habit of looking someone in the face, always, until you get it right. If prolonged eye contact feels uncomfortable, look at a spot beside their ear, gaze into a notebook or coffee cup, or look to one side while you talk. You can help it. If you can master the art of not picking a wedgie in public, then you can learn to look at someone politely. The added bonus of this good habit is that people truly feel like you are listening intently to them, even if you're only contemplating the pimple on their nose. Male or female, when someone feels like they are being listened to intently, they usually feel a lot better about your conversation even if they did all the talking.
Humans are sexual creatures and it's unreasonable of society or anyone to expect people to leave their personal foibles and bad habits at home
It's not unreasonable. It's just not, and there's an end of it. You don't pick your nose, pick your butt, squeeze pimples or masturbate in public, and those are perfectly reasonable expectations. If you want to know someone better, ask them out for coffee or beer. If you absolutely must know if they are generally attractive on the outside, use the miracle of peripheral vision or look from a respectable distance such that no one could tell if you were checking out boobs or merely trying to recognize the person. It's just not that hard. It's bad for your career to flirt at work anyway.
People shouldn't be so easily offended,
Some people are offended. If you offend people, it's very easy for you to be labeled That Guy in your social circle, in which case you will have to make some friends outside your circle because no one wants to hang out with That Guy, and it's so much easier to cut That Guy out of activities than it is to deal with angry, offended people making the occasion uncomfortable for everyone. Arguing that they should not be offended is missing the point entirely: They are offended no matter what you intended. Your choices consist of finding a new workplace, finding new friends, or apologizing for the offense and making a concerted effort not to do it again. "No one should mind my disgusting lack of socialization" is not a viable option here.
AKA Some women like it
And some don't. Yes, there are people out there who have a higher bullshit tolerance than others, bless their hearts. I'm sure not one of them, and I'm not alone. Some people are into all sorts of fetishes and bad habits that others find perfectly repulsive. The difference is, they know that their bad habit/fetish is not everyone's cup of tea, and keep that to themselves in mixed company. This is why the good Lord created the VCR, the DVD player and the internet, so you can keep your voyeurism in the privacy of your own home.
-It's biological, people can't help looking at an attractive person
-Humans are sexual creatures and it's unreasonable of society or anyone to expect people to leave their personal foibles and bad habits at home
-People shouldn't be so easily offended, AKA Some women like it
-People should cover up in burkas if they are so incredibly gorgeous
Zuska has done a wonderful job of dispelling the last of these: In countries where women do wear burkas, they get much more harassment than they do in countries with more liberal clothing policies. As to the other three...
It's biological, people can't help looking at an attractive person
Lots of things are biological, and yet we train ourselves out of them in polite company. Adults are potty-trained, eat food with silverware, wear clothing outdoors and in mixed company, and bathe themselves, all means of overcoming natural biological things that are offensive to polite society. You don't get a pass on those, so why should I give you a pass on where you rest your eyes? Practice the good habit of looking someone in the face, always, until you get it right. If prolonged eye contact feels uncomfortable, look at a spot beside their ear, gaze into a notebook or coffee cup, or look to one side while you talk. You can help it. If you can master the art of not picking a wedgie in public, then you can learn to look at someone politely. The added bonus of this good habit is that people truly feel like you are listening intently to them, even if you're only contemplating the pimple on their nose. Male or female, when someone feels like they are being listened to intently, they usually feel a lot better about your conversation even if they did all the talking.
Humans are sexual creatures and it's unreasonable of society or anyone to expect people to leave their personal foibles and bad habits at home
It's not unreasonable. It's just not, and there's an end of it. You don't pick your nose, pick your butt, squeeze pimples or masturbate in public, and those are perfectly reasonable expectations. If you want to know someone better, ask them out for coffee or beer. If you absolutely must know if they are generally attractive on the outside, use the miracle of peripheral vision or look from a respectable distance such that no one could tell if you were checking out boobs or merely trying to recognize the person. It's just not that hard. It's bad for your career to flirt at work anyway.
People shouldn't be so easily offended,
Some people are offended. If you offend people, it's very easy for you to be labeled That Guy in your social circle, in which case you will have to make some friends outside your circle because no one wants to hang out with That Guy, and it's so much easier to cut That Guy out of activities than it is to deal with angry, offended people making the occasion uncomfortable for everyone. Arguing that they should not be offended is missing the point entirely: They are offended no matter what you intended. Your choices consist of finding a new workplace, finding new friends, or apologizing for the offense and making a concerted effort not to do it again. "No one should mind my disgusting lack of socialization" is not a viable option here.
AKA Some women like it
And some don't. Yes, there are people out there who have a higher bullshit tolerance than others, bless their hearts. I'm sure not one of them, and I'm not alone. Some people are into all sorts of fetishes and bad habits that others find perfectly repulsive. The difference is, they know that their bad habit/fetish is not everyone's cup of tea, and keep that to themselves in mixed company. This is why the good Lord created the VCR, the DVD player and the internet, so you can keep your voyeurism in the privacy of your own home.
Saturday, August 9, 2008
Animal rights activists firebomb university scientists
Winning hearts and minds.
Disclaimer: I have done animal research in the past on rats, mice and squirrels, although I don't do that currently. I raise cage-free, extremely spoiled chickens in my barn, and occasionally have to cull them if they are injured or ill beyond recovery. I fish regularly, and eat local venison when they feast on my garden. I have no compunctions about killing wasps, mosquitoes, aphids, slugs, wireworms, or any other garden pests. I keep an extremely spoiled dog and several cats. So I probably qualify as Evil as far as animal rights go.
In my experience, the animal rights folks--and I know many, my mother included--don't have an awful lot of experience working with actual animals. They specifically don't want any, either, which seems odd to me, since a horrible lot of animals end up in rescue situations where they could use some love and support from a hairless monkey with compassion and time to spare. In a sort of circular logic, I can see this, if you're starting from the point that it's wrong to domesticate animals at all for any reason. That this first point is obviously wrong doesn't seem to matter to them--is it also wrong to wear clothing, cook food with fire, eat with silverware or take birth control? We've domesticated ourselves to a large extent, too. I guess it's OK to domesticate yourself because you're doing it to yourself, but that argument also applies to human babies and plants--is it wrong to eat any kind of tomato that isn't a landrace, or eat maize in any form, or consume the many Rosaceae derivatives that have been domesticated these past few millennia? Or is that OK because plants aren't sentient? How do you know for sure they aren't sentient, though? Lots of things don't look like animals but really are, and other things that look sentient really aren't at all. You end up with the whole epistemology question again.
True story: I had a philosophy professor once, a seriously involved animal rights activist, who said that we should all use traditional Chinese medicine because it's so much kinder to animals. Yeah, she really said that. And many of the animal rights people I know feel that we should use something other than animals because there are all these alternative ways of doing things out there. Only, in actual point of fact, when you ask them what specifically these ways are and how they've been validated, because our animal rooms are damn costly and a real pain in the arse to staff, they haven't got any answers.
Quite frankly, I don't think many scientists really enjoy doing the animal work. I don't know any who wouldn't rather use something else if they possibly can. Petri dishes don't need fed on weekends, they don't bite, they cost about a buck, one tech can manage about a thousand of them, and you get results in a couple of days rather than a couple of months or a couple of years. Here's the alternatives we've got and their relative drawbacks:
Genomics: There are several techniques in genomic analysis and transcriptome analysis. The most developed one is probably the AffyChip system. Error rates for the Affy system are about 10%; that is, 10% of the hits you get as "gene expressed/present in this sample" are wrong. To some extent you can correct by using longer oligos, better computer algorithms, but really you do have to run RT-PCRs to confirm hits. The initial capital equipment investment is not small either. And the fundamental problem is, this only tells you about genes, and genes aren't everything. There are several other levels of molecular control, which an Affy system will tell you nothing about.
Proteomics: There are several proteomics workbenches on the market. They also have some nasty error rates. The proteomics problem is, there are a couple million proteins in any human and they can all have their own subtle differences even with the same transcript. So most people focus on a single tissue. However, this often produces as much gobbledegook as actual data, as proteins tend to be very subtle things rather than the simpler on/off mechanisms that genes have.
Metabolomics: We don't have any good models yet. We just don't. Although folks have been trying for many years to cobble together models of the pathways, they are still not good predictors and at best can only work with extremely simple control loops. Whole people aren't simple.
Tissue culture: OK, so let's say I add Drug X to my dish of human liver tissue to see how it behaves. My liver tissue is immortalized through various means; how do I know that the immortalization process (whether through viral transfection or creating lesions in the DNA or by creating hybridomas) didn't screw up the metabolic processes? Because it usually does, to some extent. But let's take it for granted that this liver culture is pretty good, and also that the lack of an epithelium to affect uptake and diffusion isn't a problem. Even assuming that my liver tissue culture will do a decent approximation of first pass kinetics, how do I know that other tissues won't be affected by the metabolites? Do I test all the thousands of tissues in a human? We don't have cultures for all of them, but we do have cultures for many of them. We do, in fact, have high throughput systems and liquid handling mechanisms that we could probably test a couple thousand tissues in triplicate on a gradient. That still doesn't tell me whether or not all the tissues working together will behave the same way.
And the error rate due to the immortalization process is cumulative. Cell cultures drift over time, in many cases over a fairly short time--say, three months. It's the nature of immortalized tissue to drift genetically, because it hasn't got the control mechanisms to correct its own genes. Worse that that, tissue cultures can be very delicate things. You've seen news stories about Compound X that "kills cancer in tissue cultures"? Everything, except possibly sterile heat-treated fetal calf serum, will kill a cancer cell in a tissue culture! Other cancer cells in the same bloody dish will kill their neighbors in tissue culture! The mere shear stress of pipetting the cells up and down too often kills cancer cells in tissue culture, but that doesn't mean that if you ride enough roller coasters you won't get cancer. Tissue cultures are not stable critters.
Co-culture in a reactor to produce complex systems: Sometimes these are advertised as "growing organs," but they're more like growing a piece of an organ rather than the whole thing. Again, you've got a piece of a cancerous growth in a highly-oxygenated, extremely artificial condition. It may share a proteome with a human tissue, but it sure doesn't quantitate expression the same way.
So, we could use some other tools. Hey, animal rights folks say we should develop them, and I agree. I don't like having to wait two months for Drug X results, either. It seems to me that since animal rights groups have many dedicated people and get plenty of donations, that they should establish some cell & molecular biology scholarships and fellowships, fund a grant or ten, and develop us some better tools. I would love, LOVE to have a metabolomics in silico model of a human, to start with, and that only requires a bunch of textbooks, a UV-Vis spectrometer, some Sigma-Aldrich reagents and a couple of good computer programmers. If I had a couple of good engineers and didn't have to work full-time, I'd do it myself. Most of my colleagues have been begging our bosses to let us do it, but they are fussy about having us focus on curing cancer and stuff, they don't want us to spend a lot of time developing tools as we are not a tool-making company. You could sell such a model for a small fortune to various drug companies, thereby eliminating much animal suffering and experimentation, as well as earning a living and being able to quit your day job. The cost of the grant to fund it would be, oh, let's put it at $125,000/year for three years, meh, round it up to $500,000. Surely some animal rights group has $500,000 to spare? Isn't that, like, a fraction of their advertising budget?
Disclaimer: I have done animal research in the past on rats, mice and squirrels, although I don't do that currently. I raise cage-free, extremely spoiled chickens in my barn, and occasionally have to cull them if they are injured or ill beyond recovery. I fish regularly, and eat local venison when they feast on my garden. I have no compunctions about killing wasps, mosquitoes, aphids, slugs, wireworms, or any other garden pests. I keep an extremely spoiled dog and several cats. So I probably qualify as Evil as far as animal rights go.
In my experience, the animal rights folks--and I know many, my mother included--don't have an awful lot of experience working with actual animals. They specifically don't want any, either, which seems odd to me, since a horrible lot of animals end up in rescue situations where they could use some love and support from a hairless monkey with compassion and time to spare. In a sort of circular logic, I can see this, if you're starting from the point that it's wrong to domesticate animals at all for any reason. That this first point is obviously wrong doesn't seem to matter to them--is it also wrong to wear clothing, cook food with fire, eat with silverware or take birth control? We've domesticated ourselves to a large extent, too. I guess it's OK to domesticate yourself because you're doing it to yourself, but that argument also applies to human babies and plants--is it wrong to eat any kind of tomato that isn't a landrace, or eat maize in any form, or consume the many Rosaceae derivatives that have been domesticated these past few millennia? Or is that OK because plants aren't sentient? How do you know for sure they aren't sentient, though? Lots of things don't look like animals but really are, and other things that look sentient really aren't at all. You end up with the whole epistemology question again.
True story: I had a philosophy professor once, a seriously involved animal rights activist, who said that we should all use traditional Chinese medicine because it's so much kinder to animals. Yeah, she really said that. And many of the animal rights people I know feel that we should use something other than animals because there are all these alternative ways of doing things out there. Only, in actual point of fact, when you ask them what specifically these ways are and how they've been validated, because our animal rooms are damn costly and a real pain in the arse to staff, they haven't got any answers.
Quite frankly, I don't think many scientists really enjoy doing the animal work. I don't know any who wouldn't rather use something else if they possibly can. Petri dishes don't need fed on weekends, they don't bite, they cost about a buck, one tech can manage about a thousand of them, and you get results in a couple of days rather than a couple of months or a couple of years. Here's the alternatives we've got and their relative drawbacks:
Genomics: There are several techniques in genomic analysis and transcriptome analysis. The most developed one is probably the AffyChip system. Error rates for the Affy system are about 10%; that is, 10% of the hits you get as "gene expressed/present in this sample" are wrong. To some extent you can correct by using longer oligos, better computer algorithms, but really you do have to run RT-PCRs to confirm hits. The initial capital equipment investment is not small either. And the fundamental problem is, this only tells you about genes, and genes aren't everything. There are several other levels of molecular control, which an Affy system will tell you nothing about.
Proteomics: There are several proteomics workbenches on the market. They also have some nasty error rates. The proteomics problem is, there are a couple million proteins in any human and they can all have their own subtle differences even with the same transcript. So most people focus on a single tissue. However, this often produces as much gobbledegook as actual data, as proteins tend to be very subtle things rather than the simpler on/off mechanisms that genes have.
Metabolomics: We don't have any good models yet. We just don't. Although folks have been trying for many years to cobble together models of the pathways, they are still not good predictors and at best can only work with extremely simple control loops. Whole people aren't simple.
Tissue culture: OK, so let's say I add Drug X to my dish of human liver tissue to see how it behaves. My liver tissue is immortalized through various means; how do I know that the immortalization process (whether through viral transfection or creating lesions in the DNA or by creating hybridomas) didn't screw up the metabolic processes? Because it usually does, to some extent. But let's take it for granted that this liver culture is pretty good, and also that the lack of an epithelium to affect uptake and diffusion isn't a problem. Even assuming that my liver tissue culture will do a decent approximation of first pass kinetics, how do I know that other tissues won't be affected by the metabolites? Do I test all the thousands of tissues in a human? We don't have cultures for all of them, but we do have cultures for many of them. We do, in fact, have high throughput systems and liquid handling mechanisms that we could probably test a couple thousand tissues in triplicate on a gradient. That still doesn't tell me whether or not all the tissues working together will behave the same way.
And the error rate due to the immortalization process is cumulative. Cell cultures drift over time, in many cases over a fairly short time--say, three months. It's the nature of immortalized tissue to drift genetically, because it hasn't got the control mechanisms to correct its own genes. Worse that that, tissue cultures can be very delicate things. You've seen news stories about Compound X that "kills cancer in tissue cultures"? Everything, except possibly sterile heat-treated fetal calf serum, will kill a cancer cell in a tissue culture! Other cancer cells in the same bloody dish will kill their neighbors in tissue culture! The mere shear stress of pipetting the cells up and down too often kills cancer cells in tissue culture, but that doesn't mean that if you ride enough roller coasters you won't get cancer. Tissue cultures are not stable critters.
Co-culture in a reactor to produce complex systems: Sometimes these are advertised as "growing organs," but they're more like growing a piece of an organ rather than the whole thing. Again, you've got a piece of a cancerous growth in a highly-oxygenated, extremely artificial condition. It may share a proteome with a human tissue, but it sure doesn't quantitate expression the same way.
So, we could use some other tools. Hey, animal rights folks say we should develop them, and I agree. I don't like having to wait two months for Drug X results, either. It seems to me that since animal rights groups have many dedicated people and get plenty of donations, that they should establish some cell & molecular biology scholarships and fellowships, fund a grant or ten, and develop us some better tools. I would love, LOVE to have a metabolomics in silico model of a human, to start with, and that only requires a bunch of textbooks, a UV-Vis spectrometer, some Sigma-Aldrich reagents and a couple of good computer programmers. If I had a couple of good engineers and didn't have to work full-time, I'd do it myself. Most of my colleagues have been begging our bosses to let us do it, but they are fussy about having us focus on curing cancer and stuff, they don't want us to spend a lot of time developing tools as we are not a tool-making company. You could sell such a model for a small fortune to various drug companies, thereby eliminating much animal suffering and experimentation, as well as earning a living and being able to quit your day job. The cost of the grant to fund it would be, oh, let's put it at $125,000/year for three years, meh, round it up to $500,000. Surely some animal rights group has $500,000 to spare? Isn't that, like, a fraction of their advertising budget?
Friday, August 1, 2008
Anthrax researcher dies
I'm actually quite interested to see how this case turns out. So far every article posted on CNN, BBC, etc. have been very lite on facts. Although I did some work for ECBC (the Fort Detrick bioweapons center) myself as a contractor, I didn't know Dr. Ivins.
From what the half-arsed articles say, the FBI's case is basically, "he swabbed some areas without getting official approval first, and it turned out the swabs did find anthrax in those areas, where it wasn't supposed to be." They declare this highly suspicious on the grounds that he should have gotten approval first.
O RLY? What if, say, his results demonstrated that the Fort Detrick containment system was a joke, and that there was no place safe in the whole building from the bugs they had stored there, and that the senior management knew this and put all the workers and contractors in danger on a daily basis because it would be Too Expensive to pack up the hazards, ship 'em to CDC, and re-engineer the whole entire lab complex from the ground up? What if his results would have caused a major scandal for the organization and about a zillion lawsuits? What if his boss, upon receiving Dr. Ivins' request for permission to swab those areas, realized what havoc a positive result would wreak, and therefore said Absolutely Not?
Anyone who thinks that senior managers don't knowingly pull shenanigans with highly dangerous stuff hasn't been out in the working world long enough. Talk to an environmental engineer who does fieldwork and Due Diligence for chemical company acquisitions. Talk to the industrial hygienists who clean up after regular everyday hazards in coal mines, chemical plants and steel mills on a daily basis. Just two years ago, about an hour up I-95 from me, a big paint manufacturer went kaboom, leaving naught but a giant crater where the building used to be. Turned out that management and their process engineers had knowingly created a faulty flammable liquid handling manufacturing method that resulted in the explosion. Miraculously, no one was killed, only injured. It would not surprise me one bit to find out that USAMRIID managers calculated the risk of what could happen if it turned out the cooties had indeed escaped the lab, and turned Dr. Ivins reasonable and concerned request down. And then decided to throw him under the bus. Unfortunately, government officials and senior managers with a lot of money and their own personal careers at stake, really don't have a great track record on accountability and integrity. They've got a great track record for scapegoating though. That's just the working world for you.
And sadly, I don't know that Agent Scully, with all her science, actually works at the FBI. You have to be a bit of a specialist even as a scientist to understand why a microbiologist might go around swabbing stuff after their boss told them it was a bad idea, and then understand what the molecular diagnostics mean and how to interpret them. Did the FBI have such a specialist review the sequencing results thoroughly, including the bioinformatic logarithms of the computer program used to analyze them, and troubleshoot accordingly? Were the sequences double-checked by some other method? What level of identity was considered a reasonable match, and how was that acceptable mismatch level calculated? Were they working from theory or from a library or what? Did the FBI know to ask this stuff? Or did they just take Dr. Ivins' boss' word for it that everything was done properly? Did they seize the notebooks and samples and try to re-create the results? If not, why not? I would think that the very first step in such an investigation would be to figure out who might be telling a tall tale, especially who might have a vested interest in blaming someone whose career is conveniently over, but then again I am not a criminal investigator. I don't even play one on TV.
From what the half-arsed articles say, the FBI's case is basically, "he swabbed some areas without getting official approval first, and it turned out the swabs did find anthrax in those areas, where it wasn't supposed to be." They declare this highly suspicious on the grounds that he should have gotten approval first.
O RLY? What if, say, his results demonstrated that the Fort Detrick containment system was a joke, and that there was no place safe in the whole building from the bugs they had stored there, and that the senior management knew this and put all the workers and contractors in danger on a daily basis because it would be Too Expensive to pack up the hazards, ship 'em to CDC, and re-engineer the whole entire lab complex from the ground up? What if his results would have caused a major scandal for the organization and about a zillion lawsuits? What if his boss, upon receiving Dr. Ivins' request for permission to swab those areas, realized what havoc a positive result would wreak, and therefore said Absolutely Not?
Anyone who thinks that senior managers don't knowingly pull shenanigans with highly dangerous stuff hasn't been out in the working world long enough. Talk to an environmental engineer who does fieldwork and Due Diligence for chemical company acquisitions. Talk to the industrial hygienists who clean up after regular everyday hazards in coal mines, chemical plants and steel mills on a daily basis. Just two years ago, about an hour up I-95 from me, a big paint manufacturer went kaboom, leaving naught but a giant crater where the building used to be. Turned out that management and their process engineers had knowingly created a faulty flammable liquid handling manufacturing method that resulted in the explosion. Miraculously, no one was killed, only injured. It would not surprise me one bit to find out that USAMRIID managers calculated the risk of what could happen if it turned out the cooties had indeed escaped the lab, and turned Dr. Ivins reasonable and concerned request down. And then decided to throw him under the bus. Unfortunately, government officials and senior managers with a lot of money and their own personal careers at stake, really don't have a great track record on accountability and integrity. They've got a great track record for scapegoating though. That's just the working world for you.
And sadly, I don't know that Agent Scully, with all her science, actually works at the FBI. You have to be a bit of a specialist even as a scientist to understand why a microbiologist might go around swabbing stuff after their boss told them it was a bad idea, and then understand what the molecular diagnostics mean and how to interpret them. Did the FBI have such a specialist review the sequencing results thoroughly, including the bioinformatic logarithms of the computer program used to analyze them, and troubleshoot accordingly? Were the sequences double-checked by some other method? What level of identity was considered a reasonable match, and how was that acceptable mismatch level calculated? Were they working from theory or from a library or what? Did the FBI know to ask this stuff? Or did they just take Dr. Ivins' boss' word for it that everything was done properly? Did they seize the notebooks and samples and try to re-create the results? If not, why not? I would think that the very first step in such an investigation would be to figure out who might be telling a tall tale, especially who might have a vested interest in blaming someone whose career is conveniently over, but then again I am not a criminal investigator. I don't even play one on TV.
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