Hot Paperback

The Hot Zone


by Richard Preston

Boy, if you aren't squeamish or hypochondriacal and you haven't read it yet, this is must read material. I'm only about half-way through and there are some unsolved mysteries just unfolding now, but it is, as the cover says, a terrifying true story of the world's most fearsome (in terms of kill rate and the violent deaths they produce) pathogens - the filoviruses (named for their thread-like structure as seen left), which include Ebola (90% fatality rate within a couple of weeks after exposure) and Marburg ("only" about a 25% rate - quite lethal already compared with other pathogens).

I'll spare you the gruesome details of how these viruses kill. It is so disturbing that I don't plan to recommend it to my students without some parental notification in the future - I could easily see kids having nightmares or turning into total germophobes. Of course I read the thing sitting on a NY City subway car surrounded by the hacking, wheezing and sneezing masses. It's an interesting context in which to read a book that could easily induce acute anxiety attacks in more than a few people that I know.

It's not all about blood and guts. Preston is a great story teller with a gift for getting inside people's heads. The parallel stories that go from African or Asian rainforests to suburban DC and back again give you a real sense of how small the world has become - and how dangerous that smallness may prove to be. Did I mention that this is a true story?

Image Source

Recipe for "success"

At least some level of success, as in a passing grade for the marking period at the very least.

I always assumed there was a correlation between completed work and grades but now I have a little data to back it up, thanks to the magic of electronic gradebooks and excel. I noticed it almost by accident as I was sorting grades the other day. Let's get the graphic out of the way:

Sorry it's a bit fuzzy, I'm not sure what is the best method for converting an excel chart into a jpeg for posting on the internet - if I figure it out I'll come back & fix it.(See Update)

Missing assignments are on the X axis, grades on the Y. The general trend is pretty obvious and allows me to make a few generalizations. Trendline shows a clear negative correlation between missing work and grades - As missing assignments increase, grades decrease.*

1. Although it is not an official policy of mine, it seems virtually, mathematically impossible to fail my class if you do all the work. Based on this observation, I'm now willing to make it official policy - I guarantee you will receive a passing grade if you DO all your work. Of course this does not include work copied from a friend just to hand something in or habitually late work (as in a week after the marking period ends!).

2. More work = higher grades. Of the relatively small number of students who have zero missing work, the grades range from 84-101 (I give extra credit occasionally). One missing assignment and the range goes to 72-98. And so on. It's not a perfectly smooth trend, as some assignments carry more weight than others. Some reasonably diligent students still get low test scores and some less-than-diligent students do really well on tests and quizzes. Still the trend is clear.

3. Finally, it's never been my policy to fail a student just because X number of assignments is missing. But as I think more and more about what success means in the real world (It's not what you know but what you do), I'm planning on revising that policy. I don't know exactly what X will be, yet, but I will impose a minimum amount of work requirement from now. Failure to complete that minimum will result in a failing grade regardless of how the numbers compute.

*Yes, I'm aware that there's a certain "duh" factor here. Every assignment not turned in counts against your grade so of course there would be a correlation. But as obvious as it is, I can only conclude that this realization simply hasn't dawned on many of the students who turn in no work and then come to me full of desperate hope that they will somehow still receive a passing grade. So I'm actually using this data in class to have students look at, think about, and discuss what it takes to succeed.

UPDATE

It looks like GIF is the way to go with charts. Click on the small picture above to see larger (clearer) version. I copied the chart from excel and pasted into photoshop (elements), saved as GIF.

How to pass the regents exam

As we pass the mid-point of the year and start thinking more seriously about passing the regents exam in June, a few thoughts on what it takes to do well in biology. I always get a flurry of hits on the blog around regents time, and I suspect they are from desperate students looking for some magical solution to their last minute concern with passing the exam. Alas, I have no such elixir. Hopefully a few will read this well enough in advance and take it to heart.

These suggestions assume that you are an average student or better who can read at, near, or above grade level.

1. Pay attention in class. This is the number one most important thing you can do. If you can't do anything else, like homework, or projects, or studying, then do this. Listen to the class discussions & the lectures. Watch the demonstrations, animations, slide shows. Ask questions. Take notes. Add your own insights or comments to the teacher's notes.
   
   
   Why? Biology is a huge subject. Your textbook gives far more detail than you can possibly take in. Class lectures and discussions serve to narrow down the content to the most important concepts and terms. Your teacher will also try to clarify concepts that are usually confusing and put things into a context that the book doesn't always do well. I also try to personalize the content so students will develop an understanding of how the biology relates to them. You will only get this kind of guidance in class, and without it you are likely to be overwhelmed and confused.
   
   
2. Labs. We do labs for a variety of reasons, but the most important is probably the understanding of the scientific process itself. This is a fairly substantial part of the regents exam, and few people can grasp the scientific method by simply reading about it - it is a skill that must be practiced and that's what labs are really about. Yes, some of them also teach you important content -related understandings, but that is usually secondary and not terribly efficient. You can spend a lot of time in lab and only learn a very limited amount of "content." Labs are really a subcategory of "paying attention in class." If you go through the motions of filling out the lab report without actually focusing on it, you're wasting your time.
   
   
3. Textbook Homeworks. Homework can make class discussion more meaningful and class discussions can make homework more meaningful. Either way, doing your homework will help you get the most out of the course. Or homework can just be a laborious waste of time. It all depends on HOW you do it. Do you skim the chapter looking for the shortest answer to the questions so you can hand something in and pretend you "did your work?" Or do you read the chapter, study the diagrams, and answer the questions in your own words?
   
   
4. Projects. The textbook usually does a good job of teaching very narrowly focused content objectives. The regents course emphasizes big ideas and major understandings. The purpose of projects is usually to bridge the gap and bring together the disparate ideas presented in the textbook. Your teacher probably does this in class, at least I do. I always try to make connections between what we learned last month and what we are learning now. But at some point you the student must jump in and piece that puzzle together for yourself. I try to design projects that require you to make those connections.
   
   
5. Regents Review. If you've done everything else, then this part will actually be a little fun. You will see that many regents exam questions are like riddles, and solving them will make you feel good about yourself. You will take delight in realizing how ridiculous some of the multiple choice answers are and how easy it is to rule out 2 or 3 of them with little effort. It's like watching Jeopardy and realizing that the questions often contain dead give-away clues for anyone who has a little knowledge of the subject.

Well, I hope that helps. This is just my personal take on things, your teacher's list might be different.

Addendum

I just realized I didn't mention the word "study." When I think of studying I think of "cramming" for the exam. It's not very effective and not usually necessary if you've done everything else. There are some things you should know, and if that means "studying" then you will have to include that. I prefer the term "review." Examples of things you should review are the formulas for photosynthesis & respirations, the cell organelles and their functions, the human body systems and how they function, DNA structure/replication/protein synthesis, etc. I still think that the amount of studying or review necessary will be minimal if you do the right thing throughout the year. And your regents review will give you plenty of opportunity to do most of this, well, "review."

Here We Go Again

This is my last post on this issue, it's clearly not going away.

From Today's New York Times article on magical thinking:

If the tendency to think magically were no more than self-defeating superstition, then over the pitiless history of human evolution it should have all but disappeared in intellectually mature adults.

How exactly does magical thinking lead to disadvantages in terms of survival or reporductive success? Evolution doesn't lead to a loss of habits just because they are silly or irrational.

The article does go on to describe how magical thinking can actually be an advantage in certain situations (it reduces stress and gives some poeple the motivation or confidence to do things that they might otherwise not do - but that can cut both ways when it leads to risky or foolish behavior), but it still leaves the impression that if something is not necessary it should disappear from a population.

Update

OK, I just realized the writer provided some wiggle room with the phrase "self-defeating," which I overlooked, since there's zero explanation of how wishful thinking might be self-defeating. Not one example. I can think of a few, but these excesses would in fact likely be weeded out by natural selection, assuming that magical thinking is not an either/or trait but exists along a continuum. On the most obvious level, magical thinking that leads to totally ridiculous acts of "bravery" or daredevil stunts would likely lead more often to death or injury.

Phineas Gage

I'm almost finished with this short (86 pages) book about the life of a man who had a 3 foot iron tamping rod rammed through his skull in a freak accident that changed his life and taught us some things about how the brain works.

If I were to pick a single book to have everyone in my science classes read, it would be this one. Short enough to get through in a brief amount of time, interesting, engaging, detailed information presented in small chunks, and the main story, which is quite compelling, can be followed even if some of the details are a little too advanced for most students. A great accompaniment to a nervous system unit.

Phineas's accident left him "physically" unharmed - he could still function physically as well as he did before the accident. He remained strong, fit, lost no coordination or physical abilities that could be detected. His memory was intact, as well as his mathematical reasoning ability and attention span. However, Phineas was no longer his old self. The iron rod tore through his frontal lobe destroying an area of the brain that is today associated with "sociability" - the capacity to interact with others by reading and responding appropriately to their verbal and nonverbal cues as well as the overall social context in which these interactions take place. Here's a quote:

Humans have always argued about what makes us human. Is it our ability to walk on two feet? To hold tools in our hands? To speak and hear language? To worship a supreme being? The case of Phineas Gage suggests that we are human because our frontal lobes are set up so that we can get along with other humans. we are "hard-wired" to be sociable. When we lose that ability, we end up like Phineas.

I'm not sure the answer actually follows - there are plenty of social animals who are "hard-wired" to get along with other members of their own species. The question itself is probably moot. There is no single quality we possess that other animals do not. It becomes a matter of degree and the unique combination of characteristics we exhibit. The book raises a number of interesting questions that bridge science, philosophy, and psychology. Just the kind of ideas I like to discuss with my students.

Image Source (Wikipedia)

Book Recommendations

I took the advice of the english teacher in my school and made up a list of 6 books that students could purchase at a discount from Barnes & Noble. I ordered extra copies that students could borrow. Here's the list:

The Case of the Monkeys That Fell from the Trees: And Other Mysteries in Tropical Nature

172 pages, a collection of mysteries in Nature. Young adult audience.

Susan E. Quinlan, Susan E. Quinlan (Illustrator)

Format: Hardcover

ISBN: 1563979020

An American Plague: The True and Terrifying Story of the Yellow Fever Epidemic of 1793

192 pages, written for young adult readers.

Jim Murphy

Format: Hardcover

ISBN: 0395776082

Phineas Gage: A Gruesome but True Story about Brain Science

86 pages, young adult audience.

John Fleischman

Format: Paperback

ISBN: 0618494782

Great Mythconceptions: The Science Behind the Myths

224 pages, large type and illustrations. Young adult audience.

Karl Kruszelnicki, Adam Yazxhi (Illustrator)

Format: Paperback

ISBN: 0740753649

Stiff: The Curious Lives of Human Cadavers

304 pages, adult themes – not for the faint of heart.

Mary Roach

Format: Paperback

ISBN: 0393324826

Hot Zone: A Terrifying True Story

418 pages, a real suspense-filled true story of a nearly disastrous biological accident at a government laboratory.

Richard Preston

Format: Mass Market Paperback

ISBN: 0385479565

And here's the
Order Form that I used.

An occasional quote

As I'm reading I keep coming across interesting passages that I would like to share. Here's the first.

In the future, humans may well be able to engineer themselves, be it by better drugs or better genes, to live as long as they please, but the cost may be twenty year olds with all the vigour, appetites and charm of the middle aged.

Armand Marie Leroi, Mutants

This is based on the idea that there is in inseparable linkage between the vim & vigour of youth and life span. As life span increases, youthful vitality will be diminished. This hypothesis is born out by experiments with fruit flies that have been bred for longer life. They produced fewer offspring, and lived a much slower, almost sloth-like existence.

Nature abounds with other examples of a connection. In a species of marsupial mice in Australia, the life of an adult male is a playboy's fantasy, or so it might appear, culminating in a 2 week period of repeated 12 hour frenzies of copulation. But then the mouse dies at the end of that single breeding season, "spent" in every sense of the word.

Conversely, the British Royal family's geneological history (with meticulous records dating over many centuries) shows a correlation between the lifespan of its members and their fecundity - Those who died shortly after menopause had on average 2.4 children. Those who lived a substantially longer life (past 90) averaged 1.8 but nearly half of the nonagenarians had no children at all.

Not exactly a slam dunk case, but interesting to think about as I approach middle age territory and watch the wrinkles grow.

Well I thought it would be fun...

...to have the kids personalize the digestive system a little by photoshopping their own faces onto a diagram of the digestive system.

So I lined up the assignment and told everyone to get their head shots ready and brought in the laptops to the classroom...

...only to find the laptops don't have photoshop loaded. So much for planning ahead and checking the software availability FIRST!

Anyway, a couple of students also expressed some reservations about putting their pictures on a body like this, so I gave them the option of picking a celeb to attach...*

Who knew bush was in such good physical condition (or Mr. Gatton for that matter!).

*I also thought better of it and found a different diagram of the digestive system and manipulated it a little to make the "private parts" a little more private.

Image Source

Lamarckianism

I like to use the example of the blind cave fish to test whether my students still harbor Lamarckian notions about evolution or if they have really caught on to the idea of natural selection. It's a good example because the Lamarckian explanation is so tempting. It just seems so logical that the cave fish lost their eyes because in total darkness they just don't need them anymore.

I bring this topic up again after mentioning it last week regarding wisdom teeth. Then yesterday reading an excellent book called simply Mutants, about all the things that can go wrong in a developing human embryo, I stumbled across this line (italics mine):

...But delightful as it may be to look at, red hair is not good for anything at all (i.e., has no adaptive survival value in any environment in which humans live ). MC1R (for simplicity's sake, the gene that causes dark hair when it functions "properly," red hair when it doesn't) may simply be a gene that is decaying because it is no longer needed, rather as eyes decay in blind cave-fish.

Now, I'm reasonably certain that the author is a hundred times more knowledgeable about biology, genetics and evolution, than I am, and yet either through carelessness or brutal editing, has issued a Lamarckian explanation for an evolutionary phenomenon. It's an otherwise fabulous book.

I started doubting myself, maybe I don't know as much as I thought I did. Maybe decay is the answer and I just haven't thought it through thoroughly enough to see how it works. But alas, serendipitously, I found PZ Myers' article in Seed Magazine on the very topic of HOW THE CAVEFISH LOST ITS EYES.

The Mexican blind cavefish raises the challenging evolutionary question: Does disuse lead to degeneration or disappearance of a feature? Here, an answer Darwin would have loved.

I certainly can't do the article justice by summarizing, so I'll leave you to go and read it for yourself. It's relatively short and sweet. I'll give you a hint about the ending - it's not Lamarck.

That Wasn't So Bad

I really expected to be in the oral surgeon's office for a couple of hours of excruciating discomfort. All those horror stories about wisdom tooth extraction. Turned out that it was over in a matter of minutes.

The worst pain is of course the injections of Novocaine, 4 to be exact. The doctor said I seemed to handle the harder ones better than the easy ones. Maybe I just got used to it. Anyway, I sat there a few minutes expecting the whole side of my face to go numb like the last time I had tooth work done, but he explained that upper teeth are easier to numb and wouldn't be so bad. The most noticeable effect was a loss of feeling in the roof of the mouth - otherwise the cheek, eye, ear, lips, felt pretty normal (ALL those areas were numb when I had lower tooth work done). All-in-all a much more pleasant experience than having a crown which required two separate numbing experiences!

What was a little freaky was the sound of the cracking tooth being extracted. Even with the heads-up that I would hear it and not to worry about it, it's a little disconcerting.

I also have learned that I do not savour the taste of blood. That oddly salty, almost sweet, raw steak quality is decidedly unpleasant. I would not make a good vampire. And a gaping hole in your mouth tends to take a while to stop bleeding, so every 30 minutes or so I change the gauze that I' m supposed to bite down on to apply pressure. SO I'm off now to change the dressing and get ready for bed. SO far not too much pain or discomfort. But I am taking pain killers prophylactically as advised.

Wisdom Teeth

I have a long history of tooth problems, dating back to early childhood. I grew up in the rural south with unfluorinated water and super sweet iced tea and soda and candy and a general lack of awareness concerning good oral hygiene. And I didn't inherit the best genes either - my father had a complete set of false teeth in his 30s and mom has had her share of tooth problems over the years. Needless to say, all my experiences with dentists have been of the painful variety, which in turn led me to avoid the dentists as much as possible which in turn again ensured that when I did visit it would be an unpleasant experience.

So about a year & a half ago I was compelled to visit the dentist to get a crown. He informed me at the time that I had a wisdom tooth that would need to come out soon. He expressed surprise that it had not already caused me trouble or pain, and said he would leave it for the time being - the tooth would let me know when it was time to go. This week the tooth started talking to me. It's scheduled to come out on the 8th. Meantime I have to take antibiotics and I have a prescription for pain killers to get me through. I am trying to avoid the pain killers as much as possible - it's just barely tolerable on ibuprofen, we'll see if it gets worse.

Of course this got me thinking about the whole concept of wisdom teeth and why we have them when they cause so much trouble - a rather "unintelligent" design flaw to say the least - and the irony of then calling them "wisdom" teeth is inescapable. Nothing wise about a set of teeth that your mouth doesn't have room for.

The obvious (not necessarily correct, just intuitively obvious) explanation is that in our evolutionary history the modern human mouth (the jaw, really) decreased in size but the number of teeth remained the same as our larger-jowled ancestors. Scientists debate why this event occured: Was it a change in diet and eating habits or the necessary by-product of an increase in brain size? In other words, did the change in diet and subsequent decrease in jaw size allow the development of a larger brain or did the development of the larger brain drive the decrease in size of the jaw? I don't see why these two alternatives are mutually exclusive and I can see how both forces could have been at work simultaneously. Although it's not obvious why a larger jaw for a third set of molars would in itself be disadvantageous for eating softer or cooked foods.

Whatever the ultimate driving force, it seems the wisdom tooth problem is a pretty nice argument for evolution and illustrates the way evolution works- and perhaps more importantly how it DOESN'T work. It produces characteristics that are not perfect, just "good enough" to allow for survival. Who knows, perhaps given more time and a more primitive technological world, the wisdom tooth would not be such a problem - either we would have settled for a larger jaw or the wisdom-toothless trait would have become the norm. As it is, the wisdom tooth is not a fatal (normally) condition and even then it usually causes trouble relatively late in life - thus there's really no evolutionary mechanism for eliminating it.

In cursory research of this topic, I stumbled across this article from the Columbia News Service. Columbia as in Columbia University. It's an article by a journalism student, so I'm more than willing to cut a little slack here, but I still expected to find a pretty accurate and intelligent story. Unfortunately the author completely botched the concept of evolution generally & natural selection in particular. Here's a quote:

Scientists agree the human race is advancing -- if very, very slowly -- along the evolutionary track by shedding unnecessary parts like the wisdom tooth, though there's debate about what is causing it to disappear.

I'll just mention without going into the details that the whole concept of evolution representing some sort of "advance" in any metaphysical or cosmic sense is pretty much a dead topic and a little jarring to see people still discussing it in those terms.

What strikes me more is the Lamarckian explanation for the way in which the wisdom tooth is supposedly disappearing, the idea that we are shedding wisdom teeth simply because we don't need them. I read the whole article looking for a clarification of this simplistic explanation, but there is none. It reminds me of those stories I heard when I was younger about how we are losing our little toes because we don't use them any more. I also looked elsewhere for data that support the idea that we, as a species or even a population in the US, are losing the wisdom teeth at all. I browsed a couple of studies from PubMed that looked at wisdom teeth in a sampling of students. Both put the number at around 10% showing no wisdom teeth (congenitally missing) but neither refer to any change in this percentage over time. So I'm not even sure the general statement is supported by the evidence and I can't think of any plausible explanation for how it would occur. In general, here's what would have to happen.

Assumption: Congenitally missing wisdom teeth is an inherited condition - it is not a result of pre-natal or post-natal nutrition or the texture of the food eaten in early childhood or adolescence. If this trait is becoming more prevalent, then one of the following conditions would have to be met (there may be others, but these are the obvious possibilities.)

1. People who inherit congenitally missing wisdom teeth have an advantage over people who are born with wisdom teeth. By advantage, I mean ONLY that they are able to survive longer and produce more offspring. In the modern world this seems a rather unlikely scenario. I could be wrong, but an article that asserts an increase in the number of people who do not have wisdom teeth (as a result of evolution) needs to address this issue - do a significant number of people die as a result of having wisdom teeth compared with those who do not? Do the wisdom-toothless live longer and thereby produce more offspring? Are they more attractive and therefore find mates more successfully? Again, none of these possible explanations seem plausible.

2. The second possibility is that congenitally missing wisdom teeth is bundled with some other trait that is advantageous - a stronger jaw line, which seems to be a particularly attractive male feature (if less so for females), for example. Again this seems rather implausible, and in fact the opposite would seem more intuitively correct - a stronger jaw line would be more likely to have room for the extra set of molars.

3. Genetic drift - by pure chance a slightly larger number of offspring are produced with the missing wisdom teeth, and over time we have drifted toward a decrease in the incidence of wisdom teeth in our population. Like tossing a coin and getting 7 heads and 3 tails out of ten, this possibility is more likely in small isolated populations (If a subset of a population is getting 7/10 heads, by chance, another subset is just as likely to get 7/10 tails - when they commingle the outcome is back to the expected 5/10 each). I'm not sure this is a plausible answer given the large population size we are dealing with and the constant influx of immigrants from around the world into the gene pool.

I have absolutely no data to support or refute any of these possibilities. I also realize there may be more complicated factors at work. I'm just wondering where the author got her data and arrived at her conclusions. I'm always interested in how people imagine evolution occurs, and Lamarckian "disuse" seems to be a particularly common conception.

PS- Alexbarnett gets the award for most catchy title relating to this topic: An Inconvenient Tooth