Cool Science

Jenn rightly teased me for rehashing my movie list post, but I just couldn't resist. Sorry.

I've thought about writing this up as a more formal essay at some point, but for now will use the blog to help figure out some of my thinking. The bottom line : I'm uncomfortable about the 'scientific method' as it is taught in middle and high schools, particularly with the way in which hypotheses are presented. It may or may not come as a shock that practicing scientists who are extremely successful at advancing the forefront of knowledge stray significantly from hypothesis-driven research as it is conventionally defined. And they need to.

Perhaps scarred just a bit from my own experience, but having seen the 'scientific method' regurgitated enough in print, I am worried about the appearance (and more importantly the consequences) of a too-rigid, rote view of how science is done. I can tell already I'm going to need a couple of posts to explain this right.

In my view the most wonderfully subversive thing about teaching students the hypothesis driven approach to science is that it is supposed to condition students to tackle a problem by asking well-phrased questions. In my view, a hypothesis is a very well phrased question that is asked in a way that can be interrogated by experiment. Is that controversial? Maybe it is.

To be clear, right now my feelings on this are anecdotal and I'm wondering if I have the time/inclination to research this right, but my sense is that there has been a distortion of what a hypothesis should be. My view that a hypothesis should be presented in question format seems to be a minority view. I will call this a question-based hypothesis. But the popular view is that a hypothesis is a guess about how the world works that can be tested by experiment. I will call this a law-based hypothesis, which is admirable on the surface, but quite dangerous.

I've invented a simple example, which is a bit flawed, but shows the point. Suppose your friend the hunter tells you he saw a purple deer once. A scientist who formulates a question-based hypothesis might say: "If I find out what colors of deer are observed in a large population and with what frequency I might spot a trend that will solve this mystery". A scientists who formulates a law-based hypothesis might say: "I assert purple deer are genetically prohibited, simply don't exist and expect that a field survey will show 0 instances of purple deer". After hiring tons of graduate students to perform field work, both scientists count 0 instances of purple deer. The latter scientist submits a manuscript to Nature entitled 'Purple deer do not exist in the wild type population' to state his new law. The former scientist submits a paper to Hunter's Quarterly reporting,'Advice to hunters: although there are no purple deer in the wild, many reddish shades are observed which, when considering the spectrum of light that shines through atmospheric pollution at dawn and dusk when hunting is popular may create an illusion of purple deer'.

A law-based hypothesis promotes the need for a boolean right or wrong answer and tempts one to overstate results (there is no such thing as purple deer). A question-based hypothesis should insist on advancing knowledge (cataloguing deer colors; finding that environmental conditions may trick an observer to perceiving a deer as purple), but does not need to state a law or solve a problem on the first go (since no reasonable experiment can measure the colors of all deer, living or deceased, it is not possible to prove there are no purple deer).

Posted by Dave at 11:49 PM | Permalink | Comments (0) | TrackBacks (0)

So I thought I would post a comment on the aforementioned blog entry on the CNN site. I commented "Does CNN think this is science?". Kept it simple, to the point. Naiively I thought it might provoke a response from the editor/author. It never made it through the moderator who I assume is the author. In the meantime at least one other post did. I am forced to conclude that I've been censored by CNN. I think I feel pretty good about that actually. Yes, it would seem that CNN has very complex emotions about science.

Today was a good day. Got recommended for tenure and promotion. Yeah! Thought I'd shout that out to cyberspace. Maybe I should go totally controversial and risque with this blog now - woo hoo!!! Yeah, right. Let's face it -I don't have the guts.

I'm really in the mood for some whacky, nerdy movie tonite for emotional catharsis for the last five and half years. In the spirit of CNN I propose a post that has nothing to do with science. Let's talk about the movies nerds like me love (in no particular order)

1. The Princess Bride - sure laugh, but it's the only chick flick that ever attracted a male audience

2. Ghostbusters - "back off man, I'm a scientist" ; should I say any more?

3. Akira - a disturbing hand-drawn masterpiece that makes you wonder 'how'd they do that?'

4. The Matrix - Neo was the everyman hero for the digital age

5. Star Wars (4-6) - Show them to Henry in a few years I will.

6. Buckaroo Bonzai - Bigboote! (if you don't get it, then you obviously have no appreciation for the fine arts); did I mention that Peter Weller references Mr. Wizard?

7. Big Trouble in Little China - "Jack Burton, Me!"

8. LOTR - extended editions of course

9. Jurassic Park - forget the CGI dinos, this is the movie that depicted a 3D computer GUI that drove all us computer types crazy and which Apple has a huge headstart on over Microsoft, according to patent drawings.

10. All Star Trek movies: Kahhhhhn! Am I the only one totally sick of the whale movie?

11. Jackie Chan - you must learn to say this like one word: Jackiechan! Then you will truly know the awesomeness of the drunken master.

12. Doom (the video game) - movie was a good try but didn't work (sorry - that's the way it is).

13. Civilization (the video game) - even science types like me were embarrassed to admit how addicted we were to this. But it didn't change the fact that we played it until carpal tunnel set in.

...back to movies...

14. Steel Dawn - the movie Patrick Swayze wishes he never made, but which got me through college.

15. Blade Runner - a gorgeous, musing film predicated on the famous 'Turing Test'

16. Fifth Element - supergreen

17. Predator - groundbreaking cinematography and sci-fi; true fans recognize how significant this flick is.

18. Tremors - a lesson on whose basement not to break in to. OK, a lesson on how low-budget sci-fi can be totally awesome. Think about it - this is the movie that made the Blair Witch possible.

19.The Keep - so overlooked it is not even on netflix; you are a true fan of the genre if you know this one, featuring Ian McKellan, Gabriel Byrne and Scott Glenn; eerie, wandering, frightening movie with some social commentary thrown in. You are a truer fan if you are drawn to this movie because of the superb score by Tangerine Dream.

20. Bill and Ted's Excellent Adventure - a most unprecedented movie; see the above comment about Tremors.

That should do for now.

Posted by Dave at 08:15 PM | Permalink | Comments (2) | TrackBacks (0)

I really do try not to let this get under my skin, but CNN just continues to sink deeper and deeper into abysmal science reporting. I just stumbled across this inane review of a WWE Smackdown videogame on their 'scitech' blog, which is supposedly a blog about "coming to terms with our relationship to our home planet". Is this some kind of a joke?

Posted by Dave at 09:49 PM | Permalink | Comments (0) | TrackBacks (0)

When penicillin was discovered by accident, could they at least have had the courtesy to also discover a miracle antiviral compound at the same time? On day 6 here of an extremely annoying cold and wondering why nobody has addressed this yet.

On the subject of a completely different virus, I heard a talk about corporate drug development to combat HIV and I had to share. In our own cells, our body goes to a lot of lengths to make accurate copies of our DNA for cell division. But in HIV it's a completely different story. HIV carries around its genetic information as a single stranded RNA molecule. When HIV attaches to and invades a CD4 cell (unfortunately CD4 cells are part of our immune system) the first order of business is to make a DNA copy of the HIV's RNA. This process is called reverse transcription. In HIV, this process is highly error prone. HIV intentionally makes a lousy DNA copy of its RNA. Why? It means that HIV mutates at an incredibly fast rate. In fact, so fast that it is morally unethical to treat a patient with any single drug since it is guaranteed that a mutant HIV strain will arise very quickly in the patient with resistance to this drug. To combat the high rate of mutations that HIV undergoes, modern treatments uses multiple drugs simultaneously, putting HIV in an evolutionary conundrum where it needs an exquisitely improbable set of simultaneous mutations to have any chance of adaptation. In quite a number of patients, this is extremely successful in suppressing the virus over long times.

Despite this, it does seem to still adapt, but much, much more slowly. So what do they do? I know drug companies take a tough rap sometimes, but I have to tell you this is amazing. They try to anticipate and profile the mutant HIV that successfully evade one cocktail of drugs and develop new drugs to attack that mutant and so on. Some hold out hope that a 'magic combination' of drugs can one day be developed to which there is no possible evolutionary trap door escape for HIV. As Jeff Goldblum's character cautioned in 'Jurassic Park', will we be humbled since "nature finds a way"? That the possibility of cornering HIV is even on table gives some hope I think, as it would have been unthinkable 10-15 years ago.

Posted by Dave at 08:55 AM | Permalink | Comments (0) | TrackBacks (0)

Henry counts to thirteen, which is awesome, not only because it's prime and a good place to take a breather before heading into those foreboding high teens, but because of all the numbers he invents after 13: eleventeen is my favorite. Can I claim that means he can count to 110? I'm ready to call mensa.

Speaking of which, a recent article I stumbled across asked where all the geniuses have gone. Could Einstein have been the last genius, it postulated. The article talked about the rise of collaborative science, and argued that individual contributions seemed to be on the decline.

But it's not bleak at all. A trend has emerged based on 'group leaders', professors or industry leaders who are quite bright who lead teams of scientists to make progress that no one person could on their own. Take for example the trend of awarding Nobel prizes to teams of scientists. On an everyday basis, everybody in science sees that this is true. My last lab where I postdoc'd had 20-25 postdocs. My Ph.D. lab was the same. Both of these were mini-corporations whose 'jobs' were to push the envelope of science. Both were led by brilliant scientists.

A nice example of an extremely talented team leader industry was Elmer K. Bolton, who led chemical research at DuPont in the first half of the 20'th century. Under his leadership, Du Pont produced nylon, neoprene and many modern wonders we take for granted. A mild-mannered Bucknell alum of 1908, Bolton would have to select which few of a myriad of projects his scientists brought to him every week would go forward, and had a knack for picking not just winners, but big winners. He is perhaps best recognized for deciding to find new and cheaper routes to nylon when others had given up on it. Bolton humbly never accepted scientific credit for the discoveries of others in his team, yet his mystique is that none of these things would have come to pass without his leadership and he was widely recognized for this.

Where are the geniuses? First of all, what is genius? In my book, it is the ability to recognize that something is true without necessarily knowing why. Was Bolton a genius? Hard to say - but nobody is that lucky so he was at least close. But the famed mathematician Ramanujan illustrates exactly this. He died far too young, but left behind a tremendous number of theorems, which mathematicians have steadily tackled and proven over the years. Richard Feynman, anybody? Love him or hate him, he was the real thing. He once tried to describe how things worked in his head. He wrote about how he would form abstract models in his mind and try to "fit" them together. With Feynman you have to ask if he was just saying this for fun or if he really meant it, but I'll go with the latter. English mathemetician Andrew Wiles proved Fermat's Last Theorem; to be fair, Wiles was standing on the shoulders of giants, but it was a one man show all the same.

Posted by Dave at 10:12 AM | Permalink | Comments (0) | TrackBacks (0)

I'm trying to decide if I feel like opining on this. But I'm caving in and doing it. I get these regular newsletters from a London university where I studied for a year. One of their professors has written a book wondering why it seems that the universe is so perfectly suited to us. This is the kind of tempting argumentative writing that attracts attention and is designed to sell books, but is completely flawed. And as I did throughout high school and college, I plan on analyzing the book without ever reading it.

First, it is we who are somewhat compatible with the universe. Natural selection has favored any mutation in a species that resulted in better adaption (chance for reproductive success) to the environment (a.k.a. the universe). An unimaginably large number of mutations together with billions of years of natural selection have resulted in species like humans that seem to be well adapted to their environment. Except that we need shelter, we also perish easily in extreme weather, we have dangerously long periods in which the young are helpless without parenting, etc. And no human or any other higher species on Earth has any chance of existing in the cold vacuum of space. That's right, we are not very well adapted to the universe at all.

When we drive around a fancy car, enjoy a nice filet mignon and then sleep for 12 hours between silk sheets, (FYI : I do none of these things) it may seem that we are masters of our universe, a perfect fit in every way. No, we're just spoiled and we shouldn't read anything more into it.

To make an example, nobody has (publicly) figured out a good solution to how humans are going to survive the lethal high energy background radiation of the universe (and solar flares) when we try to leave low Earth orbit and the protective cocoon afforded by Earth's magnetic field. Even the ISS is in low earth orbit so that it is protected from solar radiation. So in fact the universe is not well suited to us at all, and while we seem to do ok, natural selection has several billion years to go before we have any chance of being considered well suited to the universe.

Posted by Dave at 10:41 PM | Permalink | Comments (2) | TrackBacks (0)

...I've had that I'd like to share. First is that cable tv is awful. I spent two nights in a hotel and thought cable would be great to have again. No. It's flooded with commercials (how is it that you *pay* for cable and yet they subject you to an onslaught of ads?). The content is inane (thank you to the 'scientific' documentary that hyped up extrasensory perception - I was physically cringing when these guys tried to explain their theories- 'it's like the force in Star Wars' says one dude trying to sound really authoritative and sciency) Would the free HBO save me? No, they were harping on about some boxing match and showing '27 dresses' in between. So cable was really disappointing.

Second is that conferences are exhausting. When I was a student watching my bosses go off to fancy conferences I thought that must be really great. But while it's nice to put your work out there, the conference experience is always draining. Trying to focus on the umpteenth talk, visiting all the vendors, glancing at all the posters, and so on... Like broccoli and carrots and such, all of this is technically very good for you but that doesn't make it any easier. Every night, you just collapse on your bed and wish for it to be over. Back home now, throwing down fresh baked cookies and sipping wine after taking the dog out for a spin - couldn't be happier.

Some random science mixed in with anime: the other day I watched Patlabor WXIII. I'd give it a 3 out of 5. It had standard themes of anti-imperialism and cautionary warnings about technology that are staples of anime; but it didn't bring much new to the table or have the kind of character complexity that anime can achieve when it is at its best. But the best part was a surprisingly good exposition on telomeric DNA, apoptosis and on the enzyme telomerase, and the importance of this biochemistry to the plot. I kept waiting for them to get silly with the science, but with the exception of a gigantic mutant monster (don't worry, not a spoiler) they stuck to surprisingly conventional science and in fact got it right. It was refreshing.

Posted by Dave at 10:56 PM | Permalink | Comments (0) | TrackBacks (0)