Why Physics is Awesome

One common application of the atomic force microscopes that we make is to measure properties of bio-molecules. AFM’s have long been used to image DNA strands, but the more interesting work is when you functionalize the probe, and then try to “pick up” a bio-molecule (like a protein).

I am working on definition of improvements to our analysis software, and since I know squat about biology, I found a series of lecture notes from UIUC’s Bio Physics course. I am flying through the early lectures, getting the correct mindset, and it dawns on me. Physics is everywhere, and it is always useful.

In the second lecture, the discussion goes to molecular reactions, and to define the probability of a reaction happening you need to measure the probability of finding a set of constituent molecules in the right state.

How do you do that? Oh yeah, the Partition Function from statistical mechanics. Bang, suddenly I “get it”.  Of course I took Stat Mech close to 20 years ago, so it is a bit rusty, but the application of the formula is simple enough.

One more comment. I do not know the lecturer, but from his lecture presentations/notes, I am sure I would like him.

I don’t know enough to understand the WLC model of protein unfolding, but I will soon.

@$$hole driving

I often flow with traffic keeping a low key, and cluck-cluck people who do dumb a-hole driving stunts around me. Phoenix (and SE Phoenix) drivers rarely fail to amuse me.

But once in a while, I get an itch, and to scratch it, I need to drive like an a-hole. Honestly, it can be fun, as long as you do it in limited doses, and take care to not be near Johnny Law when you break free. Last night was one of those occasions.  I noticed that my usual path out of work was jammed, so I flipped a bitch, and hightailed it to back streets. Nothing like revving Stewie up, and rowing the gear box. The hard compound street tires (Yokohama S-Drives) have a little give, yet they break free fairly predictably. Make fun for aggressive cornering.

I got my start in aggressive driving tactics a long time ago. After the CX500 got wrecked, my next street bike was a 1979 XL500S. I lost the Titanic-sinking stock muffler, put on a SuperTrapp, and went about terrorizing neighborhoods. That was a fun hooligan bike, and it taught me how to be an a-hole, yet not get caught.

My first 4 wheeled A-hole-ness was in an old RX-7.  I think it was an ’83, or maybe older. It was quick, light, handled well, and had OK brakes. It was a lot of fun to cut in and out of traffic in.

My '05 Honda S-2000. The best car I have ever owned
My ’05 Honda S-2000. The best car I have ever owned

Fast forward to now, and I drive probably the most balanced, reasonably prices sports cars around, a 2005 Honda S-2000. Affectionately known as “Stewies”, it is a blast to drive. Now most of the time, I do my sedate 15 mile round trip to the office at the speed limit. But once in a while, I feel the need to air it out. And the car has the pedigree to do it. Redline at 8K RPM, 6 speed transmission (4th gear at redline is just 100 mph), and the vtec hit at 6K RPM when the valve timing changes is fun.

Of course, I am cautious to never cut loose in front of the po-po. And the great thing about the Stewie is that you don;t have to get to supra legal speed to have fun driving it. Taking a 90 degree corner at 45mph, kissing the apex, and drifting back into the lane is just fun, (but a little reckless)

Growing up “Gifted”

In a prior post, I discussed how a pretty big familial change greatly affected me during a critical period of development. Now I would like to discuss another, somewhat related, topic.

Bart backs into the gifted program, where he doesn't fit in
Bart backs into the gifted program, where he doesn’t fit in

In the third grade, I was identified as “gifted”. This means that I scored high on the standardized tests, and consequently, I was “invited” into the advanced learning program. This was 2-3 hours 3 days a week in a special program. Like the episode from the first season of The Simpsons, where Bart “steals” the test of the smart kid, and gets pulled into a special school where he really didn’t belong, I was pulled into this group where I “did” belong. It wasn’t structured learning, but it allowed us in the program to explore whatever interested us. There was a complete set of SRA materials, at the time pretty leading edge, self paced curricula, with a lot of science and mathematics focus (hey, I did grow up in Silicon Valley after all). I did enjoy having the freedom to branch out and learn at my own pace, and that opportunity trained me well. Today, I still go off on intellectual whims for as long as I am interested (History of Mathematics, US History, European history, and others recently).

But it wasn’t all grins and giggles. The problems manifested themselves early. First was the fact that being plucked from your class, your “peers” singles you out. I was never one to have many close friends, but those that I had established pretty much avoided me (much in the same way Bart’s friends did in the Simpsons episode above.) This would have been fine, had I made many friends in this new peer group, but I didn’t form any close bonds. The program mixed students from 3rd through 6th grade, and since I was at the lower end of the age spectrum, I was odd man out.

Second, the home situation wasn’t great at this time. The alcoholic, abusive stepfather that I mentioned in my prior post was against me being part of this group from the beginning. He had an irrational distrust of authority, and felt that such a program was “indoctrination”. There were many fights at home over this, and I remember this troubling me greatly.

Lastly, also due to the situation at home, there were some activities that were part of the program that cost money. Since money was very tight, I wasn’t able to participate in these programs. The one that I recall clearly was model rocketry. For a nominal fee (certainly less than $10) we would be able to build an Estes model rocket, and launch it. Then we would calculate trajectories and other cool things that tied to our advanced math work. But I just got to watch.

It wasn’t all bad. I did gain a healthy habit of learning (not studying), and realized that I could do more on my own that in the tutelage of the teachers. But due to lack of support at home for the program, and being left out of some of the more interesting activities, I believe it could have been a huge boon to my confidence. But alas, it fell short of such lofty deliverables.

Today, I wonder what would have happened had I been in one of the nurturing families, who encouraged their children to grab at these handholds to success. Would I have become less cynical, and more accepting? Would I have tried harder in high school? Would I have applied to MIT, CalTech or Stanford? Who knows, but at one time, I was really smart.

Weight Loss Update

Two weeks ago, I lamented the need to get back on the horse and lose some weight. Of course, I know the formula, and I have tools to help me with my endeavor. But it is difficult to train the body to accept the new status quo.

For the stats:

Starting Weight: 232#

Today’s weigh in: 225#

Total lost – 7#

Not a bad first two weeks, but a lot more to go (my goal is 190#). In the last two weeks, I haven’t cooked anything extraordinary. We had visitors, so I made Pizza (by request) and had only one piece. I have been quite good about not snacking between meals, and not eating dessert. Lots of Lean Cuisine (good for portion control and balance, but big bad on the Sodium content. A willing trade).

By my tracking tool, the “Perfect Diet Tracker”, I am allocated about 2100 calories a day, and I consistently am eating about 1400 – 1500 a day. I am hungry, but not starving.

Exercise is the tough one. I can’t run anymore (last time I lost weight, and for years after, I did about 5m of running at lunch every day. Now the Plantar Fasciitis prevents that), so I walk when I can at work. Good for about 3.3 miles, it does burn some calories, and it gets me off my butt. This last weekend I brushed the dust off my bicycle, and put on about 36 miles.  Felt good (legs are a little stiff today, but I am seriously saddle sore), but need to keep the habit up.

There was a facebook status a week or so ago, one of those funny e-cards that said: “I know the feeling of skinny.  It feels hungry”. That sums it up exactly.

Where have all the UFO pictures gone?

Lately I have been grooving to the X-Files episodes over on Netflix streaming. I remember waiting with baited breath each week for the next episode, and cursing the creators when they used a cliffhanger at the end of the season.

I want to believeIf you haven’t watched the show, it has a fairly large portion of its episodes based on the idea that extra terrestrials (aliens, little green men what have you) are visiting the earth, and the government is covering it up. Of course, from the 1940’s on, there have been an endless stream of stories about UFO sightings, abductions, encounters with ET’s, and all that rigmarole. Often, with photographic evidence. Fuzzy pictures of lights in the night sky, to fantastic views of saucer like ships in the day time.

With all this photographic evidence captured over the decades, I would expect (if there were real events) that with the digital camera revolution that if there really were events and activities, it would be captured by multiple people, and shared endlessly on social media. Or that there would be a never ending stream of “very high quality” fakes created in photoshop.

But curiously, I don’t see that. Yes, the usual conspiracy nut groups still exist, and live in their bubble chamber devising conspiracy theories. But it appears that the general population has moved on to the Angry Cat and other memes for entertainment, and that the whole belief in ET visitations are nonsense.

For the record, I believe that there are likely other intelligences in the universe, but I also know that interstellar “warp” drive is a figment of science fiction authors, and that the time of travel between star systems, even at relativistic speeds, is far too long to allow “visitation”. In that vein, the correct way to search is via programs like SETI.