Graduation and Utah

Yesterday, I graduated from Penn State.  Fortunately, I was spared the pomp and circumstance by being 3,455 kilometers to the west, in Cedar City, Utah.  Instead of the Bryce Jordan Center, today I spent the day exploring Bryce Canyon, a huge amphitheater filled with limestone towers called 'hoodoos' created by the erosive effects of rain and frost.  I definitely win.

Bryce Canyon is the fourth and final national park Bryan and I will be visiting in Utah.  By my estimation, four national parks in four days is a pretty solid indicator of a good trip.

Three days ago on Thursday the 11th, we arrived in Moab, Utah, coming from Rifle, Colorado.  The drive wasn't too long, so we had much of the afternoon to spend exploring Arches National Park.  It was my first encounter with the desert, and I absolutely loved it.  I stopped briefly to take a call from my future research adviser, seeking out cell service on the top of one of the huge limestone fins filling the park.  We started our hike in 'Devil's Garden', took a primitive trail loop, and found a deep hole bored into the limestone by rushing rainfall and filled with water (and life) and a huge arch tucked away among the limestone fins.  We didn't bring nearly enough water and were run pretty ragged by the end of it, but it was well worth it.  For dinner: delicious pasta dishes, jalapeno fries, and a pitcher of pale ale at the Moab Brewery.

On Friday the 12th, we spent the morning taking care of logistics online before heading out to Canyonlands National Park.  Also down the highway from Moab, Canyonlands borders Dead Horse Point State Park.  The landscape we encountered there was desolate and alien.  After staring out at the incomprehensibly massive objects comprising the view from 'The Neck', we headed out in the opposite direction down the sparsely-marked Neck Springs trail.  The first two of the six miles on this trail take place on one massive slab of slickrock; hikers are guided by rock cairns constructed every ten or so meters.  Through a desert prairie and up to the lip of the canyon, the trail then switchbacks its way past cacti and abandoned horse troughs to the canyon floor.  The environment there was surreal: the wash drew upon a wide enough area to support surprisingly verdant plant life, which brought with it all types of insects and small mammals.  As the sun set and the nearly full moon rose, a strong current of cold(!) air began rustling the leaves at the very bottom of the canyon wash.  Bats flitted in the twilight.  Before long we were relying on moonlight, and in the long shadows of the canyon walls, a single headlamp, to seek out the next cairn and keep moving.  Snakes and chipmunks made an appearance, and the bats increased in number.  We wound our way up and down through numerous tributary ravines before finally ascending out of the canyon and returning to the road.  While Bryan practiced some astrophotography, I laid down and took in the stars.  The Perseid meteor shower was mostly drowned out by the extremely bright moon, but a single fireball cut through and fell to the horizon.  On the drive back, we saw a mule deer grazing along the road and the flashing eyes of something vaguely canid (a coyote?) picking over some roadkill.  It was after 10:30 when we arrived again in Moab, but fortunately the Moab Brewery was still open.  Vegetable burritos, another plate of jalapeno fries, and a pitcher of stout finished off the day.

As we left Moab late the next morning, I made note of one more thing.  Right near the entrance to Arches National Park, we saw signs for the 'UMTRA Project'.  While the signage indicated that it was DOE-sponsored, it wasn't clear at all what was actually happening there.  Turns out: they're reclaiming the site of an old uranium processing plant, digging up 16 million tons of soil contaminated with uranium tailings (a waste product from processing) and burying it in a permanent containment site down the street at Crescent Junction.  The official DOE project page: http://www.gjem.energy.gov/moab

(To Be Continued: Zion Canyon, Bryce Canyon, and 'nitrogen-enriched' gasoline)

Chemical Engineering Education, Part Two

At a large public research institute such as Penn State, it is all-too-obvious that teaching comes a distant last on the list of priorities.  Which is a real shame... what happened to the original Land Grant rationale that founded the place?

In the course of advising friends-of-friends and just talking to people casually, I come across stories like this all the time:

http://loose-screws.tumblr.com/post/1461795697/honors-programs-cannot-survive-bad-professors?ref=nf

Amen.  The clear philosophy here is that anyone who can get a PhD is automatically competent enough to teach the material covered in an undergraduate course.  As someone who spent two years teaching privately and two more teaching for the University, I am reasonably qualified to attest that this is simply not true.  Just because someone can understand something complicated does NOT mean they have the skills to effectively communicate the ideas to someone else.  If the academic hiring process isn't carefully screening for communication skills (and it is definitely not - RESEARCH GRANTS bring money and prestige to a place like this, not teaching awards), then the damage to the quality of undergraduate education is immediate and obvious.


Fact is, the PhD process teaches you nothing relevant to actually being a professor.  Having completed virtually all of the requirements for an MS in ChemE, I can attest that success in the program has nothing to do with real talent and is really only a measure of resistance to abuse.  The material covered in the 'core courses' is arbitrary and irrelevant to an extent that is actually quite amazing.

The understanding is that if you can survive the academic hazing, you're in the system... and there is essentially zero oversight from there on out.  Student evaluations like the SRTEs?  They reward the panderers who give little and ask for little in return.  Faculty teaching evaluations?  I saw you having a beer together on Friday night and you babysit eachothers' kids, so give me a break: there is no way anyone can be professionally evaluated by their best faculty buddy down the hall.

The situation is (hopefully) better at places where the undergraduate student as seen as more than just a necessary inconvenience.

This Should Not Be Up For Debate, Part II

From an article in the Health Behavior section of MSNBC:

Researcher Nina Kraus said the data strongly suggested that the neural connections made during musical training also primed the brain for other aspects of human communication.

"The effect of music training suggests that, akin to physical exercise and its impact on body fitness, music is a resource that tones the brain for auditory fitness and thus requires society to re-examine the role of music in shaping individual development," the researchers said in their study.

This result is pretty intuitive.

The typical criticism leveled at this type of study is that it is very difficult to remove the confounding influence of social and economic wealth; studying music takes time and money, and those who have the resources for such a pursuit often come from favorable socioeconomic positions.

The researchers' take on this problem?  Make music available to more people!:

The researchers concluded that there needed to be a serious investment of resources into music training in schools accompanied with rigorous examinations of the effects of such instruction on listening, learning, memory, attention and literacy skills.

Full Article: http://www.msnbc.msn.com/id/38342541/ns/health-behavior/
And the technical version: http://www.sciencedaily.com/releases/2007/03/070312152003.htm

##Image from OpenClipArt.org

Wheels of Time

Plants, animals (including humans), and even many bacteria have internal clocks that give the organism some sense of what time of day it is.  Chronobiology is the branch of science that studies the regulation and biological significance of these cyclic phenomena.

Plants have photochemical clocks that utilize photoreactive pigments such as cryptochrome to detect the length of the nighttime, allowing them to determine what time of year it is.  They use this information to correctly time critical plant events like dormancy (summer for deserts, winter for temperate regions) and flowering.  There is no point in wasting energy on flowering if other flowers and the proper pollinators aren't available!

Human life is largely constructed around the Circadian rhythm, which matches the 24 hour cycle of day and night.  Light is the primary means by which the Circadian rhythm is kept in time with, or 'entrained', to the cycle of the Sun; other minor 'Zeitgebers' (from the German for 'time-givers') include temperature and patterns of eating and social interaction.  Artificial lighting disturbs this normal cycle, as can disorders such as Delayed Sleep Phase Syndrome and Non-24-Hour Sleep Wake Syndrome.

---

When left to my own devices, I regularly go to bed between 3 and 5am.  I often find myself wide awake long after everyone else is asleep.  My peak work productivity usually falls between 10pm-3am, and I am almost completely nonfunctional before 10am.  To force myself to be awake at the 'regular' times, I pull all-nighters at a frequency of about once per week so that I am awake in the morning, become exhausted, and can fall asleep at a 'normal' hour.

For these reasons, I've often wondered if I have either DSPS or Non-24.  Many sleep disorder practitioners recommend keeping a sleep journal, but a more practical way to analyze activity patterns is to make use of activity data that you already have on-hand.  For my analysis, I graphed several months of time-stamped text message and Google search records:

Though this is a graph of received text messages, texts are usually exchanged in volleys, so this should provide some quantitative sense of when I am awake.  The text message data will tend to underestimate my probability of consciousness during the hours when no one in their right mind is awake (3-8am).

This data is much more useful, because it includes a much larger sample size and is not reliant on the participation of others.

The International Classification of Sleep Disorders diagnostic criteria for DSPS include:

1.  ...a chronic or recurrent complaint of inability to fall asleep at a desired conventional clock time together with the inability to awaken at a desired and socially acceptable time.

5.  Sleep-wake logs and/or actigraphy monitoring for at least two weeks document a consistent habitual pattern of sleep onsets, usually later than 2 a.m.

6.  Occasional noncircadian days may occur (i.e., sleep is "skipped" for an entire day and night plus some portion of the following day)

7.  The symptoms do not meet the criteria for any other sleep disorder causing inability to initiate sleep or excessive sleepiness.

Bingo.

This Should Not Be Up For Debate, Part I

Music is something that almost anyone can do.

You don't need to be an aspiring music professional, or even particularly gifted in the musical arts, to appreciate music and benefit from a musical education.

Patience, persistence, and the art of practice - the music-making process emphasizes skills that are useful in all life paths.

Learning music isn't just akin to learning a language, art, skill, or culture: music education explicitly includes elements of all of these endeavors.

Making music is a perspective-expanding experience, and provides an introduction to new ways of thinking about, identifying connections within, and interacting with the world.

Music is capable of eliciting emotion in ways, and to extents, that are not achievable by other means.

"Why music?"

If you have to ask... you'll never know.


LINK: "...the cost of education is far less than the cost of ignorance."

Keyboard Layouts

This page has moved!  Access the updated post by clicking above.  In the interest in preserving the information integrity of the Internet (1), the original post is still available below.

(1) Tim Berners-Lee would be proud.

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QWERTY is not the final word on keyboard layouts!

The standard English QWERTY layout is very poorly designed.  When one looks at the letters in the 'Home Row' (A-S-D-F-J-K-L-;), it's probably not too hard to believe that less than one-third of your typing is going to take place on these keys.  This is significant, because these are the key that do not require you to move your fingers to strike them!  The result is that the English typing speed is significantly slower than it could be, if the keyboard had been organized to put the most-used keys on the Home Row.  This layout is purely an historical artifact, and was designed to conform to the needs of 1890's typewriter technology, which would often jam if two adjacent keys were struck rapidly in succession.

The best example of a keyboard that actually makes sense is probably the Turkish layout:

The language uses the Turkish Latin alphabet, and therefore requires its own dedicated keyboard.  The layout was developed in collaboration with the Turkish Language Institute with the goals of maximizing use of the Home Row, locating the other often-used keys in places that are anatomically easiest and fastest to strike, and evenly distributing the typing load between the left and right hands.  These design criteria have resulted in the most efficient keyboard layout to-date; the fastest Turkish typists regularly outpace the fastest typists in the rest of the world.

The English-language user has not been left out!  The Dvorak layout, named after inventor August Dvorak and commonly known as the American Simplified Layout (ASK), has sought to correct some of the issues with the standard English QWERTY layout.  The Home Row (A-O-E-U-H-T-N-S) actually makes sense, and maximum typing speed is increased.  The Dvorak layout is standard enough that it comes installed with most modern operating systems, so making the layout switch is fairly straightforward.  The downside?  You have to learn it, which takes time.  Websites like Dvorak Keyboard Training provide interactive practice to get you moving in the right direction.

What if you're learning another language?  You have several options: learning the obnoxious Unicode input codes, settling for 'ss' and 'ae' when you really mean ß and ä, or... changing your keyboard layout.  There are very many keyboard layouts currently available, so it's just a matter of figuring out exactly what you're looking for and changing some operating system settings (you do NOT need to buy a new keyboard!).

Take the standard German layout, for instance: it is based on the English QWERTY, but with Y and Z switched and quite a few changes to the locations of the symbols and other miscellaneous things.  It includes the German-specific characters (Ö-Ä-Ü-ß) and an increased number of dead keys (keys that change the function of the other keys, like SHIFT).  There are two dead keys for accented characters (á, ê, í); while these characters aren't actually used in Germany, a European German user is very likely to deal with Spanish, French, and other languages that do.  Not surprisingly, this layout comes standard with all operating systems, and making the layout switch to German is very straightforward.

...but I just said that QWERTY (or QWERTZ in this case) is slow!  Never fear; the Neo Users Group has created the German equivalent to the Dvorak layout.  This doesn't ship with most operating systems, but installation is pretty straightforward if you follow the directions on their website.  Can't read the website?  If you don't know German, why are you trying to install a modified German layout?!

Most modern operating systems allow for rapid switching between the different keyboard layouts that you have installed.  In Windows 7, for instance, you can rapidly switch between multiple input languages and keyboard layouts by clicking on the little icons that appear in the system taskbar:

Do you have any experience with alternative keyboard layouts?  Do you think keyboard layout makes a difference to typing speed?  Would you be willing to try a new layout?  Comment!

Laptop Overheating

My Dell Inspiron 6400 laptop has been getting slower and slower since I first purchased it new around three years ago.  I had assumed that this was due to the inevitable degradation of Windows Vista, but a fresh reinstall of Windows 7 didn't help.  When I burned myself on the bottom panel of the laptop, that was a pretty good indication that I should check for an overheating problem.

I installed I8kfanGUI, a handy little program for monitoring Dell Inspiron, Latitude, and Precision laptop temperatures, fan speeds, and CPU speeds and loads.  It allows you to manually control the speed of the laptop fan; I used this to max the fan speed, hoping to bring the processor core temperatures down to something reasonable.  Under high load, temperatures were still staying as high as 85C, and the laptop's performance was suffering as Windows automatically 'throttled' the processor speed to keep the temperatures from continuing to increase.

Time for more drastic measures.  Using this helpful guide to disassembling a Dell Inspiron laptop, I completely took the machine apart.  Inside: giant dust bunnies, completely clogging up the heatsinks at the end of the heatpipes that cool the CPU and GPU.  These could not have been removed simply by blowing some canned air through the external vents on the laptop; I had to use tweezers to dig out them out.  The fan was still spinning, but the air wasn't getting where it needed to go to keep things cool.

Success!  I reassembled everything, fired it up, and the load temperatures were down into the 60's.  Still pretty warm, but no CPU throttling and no performance loss.

Loss of computer performance over time is NOT normal.  If a fresh install of a stable operating system doesn't solve the problem, heat management may be the issue.  A computer is just like any other piece of machinery, and a little routine maintenance can make all the difference.  It can be a real pain to take a laptop apart and put it back together again, but an hour of effort can make it usable again.

Analyzing the global psyche with Google

{Query} [Google-Recommended Completion]

{How to}
tie a tie
kiss
lose weight fast
get pregnant
get a girl to like you
write a cover letter
write a resume
solve a rubix cube
make jello shots
make it in america

{How do I}
find my ip address
get a passport
know if im pregnant
get my work copyrighted
love thee
delete my facebook account
download youtube videos
look
delete my myspace
breathe lyrics

{What is}
my ip
my ip address
love
lady gaga's real name
a good credit score
chatroulette
the meaning of life
cinco de mayo
autism
twitter

{My girlfriend and I}
have nothing to talk about
fight all the time
are growing apart
are having communication problems
have nothing in common
are on a break
are bored
always fight
are going to different colleges
broke up

{My boyfriend and I}
fight all the time
have nothing to talk about
are growing apart
are on a break
can't communicate
are fighting
are bored
fight a lot
always fight

Summary:

The average internet user is most concerned about finding a mate, a complicated process which often involves ties, jello shots, and kissing.  To impress potential mates, the average internet user is: looking for a good job; traveling to other countries; losing weight; writing books; and solving Rubix cubes.  To avoid scaring off potential mates (and perhaps potential employers), the average internet user is considering closing their accounts on various social networking sites.  Perhaps the only thing the average internet user is as interested in finding as true love is their IP address.

Once they have found a mate, the average internet user is desperately unhappy.  Regardless, the average internet user proceeds to make babies (a poorly-understood process).

The Brewing Continues

Both fermenters are bubbling like crazy today; I don't have a rotameter hooked up, but I would guess that carbon dioxide production is peaking in excess of 100mL per minute.  Everything in the must is now suspended, buoyed by the bubbles rising from the yeast, which are now floating in a cloudy layer near the surface.

It's obvious enough that yeast produces a ton of carbon dioxide during anaerobic growth... but how?  Molecular oxygen is not present to act as the final electron acceptor in oxidative phosphorylation, so the TCA cycle (the source of the carbon dioxide produces by you right now) certainly isn't active.  For a closer look, we go to the basic (unbalanced) bioreaction stoichiometry:

C₆H₁₂O₆ (sugar) + CH_1.9O_0.51N_0.23 (protein) -> CH1_1.77O_0.49N_0.24 (biomass) + C₂H₆O (ethanol)

Most available protein is going to biomass (which has almost the exact same stoichiometric ratios as protein), along with some of the sugar.  Most of the sugar will go toward generating reducing equivalents (NADH) and energy carriers (ATP), in which it will be almost stoichiometrically converted to ethanol.  If you take a look at that stoichiometry:

C₆H₁₂O₆ (sugar) -> C₂H₆O (ethanol)

Glucose on the left has a 1:1 C:O ratio, whereas ethanol has a 2:1 C:O ratio.  Carbon dioxide has a 1:2 C:O ratio, so this is a likely solution for closing the mass balance!  Of course, this is all nasty global inference, which should be left to systems biology (fake science).

What really happens?  Pyruvate decarboxylase (using thiamine pyrophosphate [pictured] in an acid-catalyzed reaction) hacks pyruvate into acetaldehyde and carbon dioxide.  The acetaldehyde is converted into ethoxide by reaction with NADH, and is then protonated to yield ethanol.  This is 'Ethanolic Fermentation'.

(Isn't mechanistic biochemistry so much more satisfying?)

Let The Brewing Begin

Oh school - the more classes you've taken, the more doing well just comes down to going through the motions and taking the time.  Unfortunately, all of this fake learning has been keeping me from doing the stuff I really want to do.

I'm headed to Germany in two weeks, but I wanted to get one solid project going before I head out.  Fairly quick to set up with long wait times to product?  Brewing fits the bill perfectly.

I kind of feel like 'brewing' with store-bought malts is sort of a cop-out.  I'd rather go with something simple and straightforward, do it right (meaning without too much cheating), and expand upward as I get better at it.  There are many indications that mead was one of the first fermented beverages, even predating agriculture itself, so it seemed like the perfect place to start.

Setting everything up was very straightforward.
Follow this project's progress in my Brewing Notebook.

Environmentalism Extrema

I mentioned on Sunday that most environmentalists aren't calling for a reduction in the human population.  Some, however, are!  Others have messaged me saying they indirectly support human population reduction through better availability of contraceptive methods and education.  I've also heard the argument made that voluntary population control could help stabilize the economies of extremely depressed regions in Africa.  I guess it's worth keeping in mind that a reduction in per capita consumption only really has an effect if the population is fairly stable or declining.


The Voluntary Human Extinction Movement has a very interesting stance.  From their website:

"Phasing out the human race by voluntarily ceasing to breed will allow Earth’s biosphere to return to good health. Crowded conditions and resource shortages will improve as we become less dense."

Everyone likes to discuss 'carbon footprint', but perhaps 'carbon legacy' is just as important: if my six-person family severely limits its use of natural resources but still consumes more overall than a three-person family with a much higher per capita usage, who is 'more green'?

If I drive a Prius 30 miles to work every day and my coworker drives his old gas-guzzler but lives only 5 miles away, who is doing more to conserve?

Can you really claim to be an 'environmentalist' if you live in a climate where you need to heat your living space five months out of the year?

Should conservation be measured on a 'per-lighbulb' basis, or is it really only a relevant concept when it is considered in terms of all of the decisions an individual makes, including what they buy, what they eat, where they live and work... even how much they reproduce?

Discuss!

(thanks to Kyle for the link, Ben for the 'legacy' concept, and Mr. Somers for a really good point)

Environmentalist's Dilemma

The environmentalism movement has an image problem.

At first glance, it's difficult to see how this is possible.  Environmentalists, at the most basic level, are simply interested in finding and implementing steady-state solutions for humanity's mass and energy balances.  They want to protect the planet's natural biological diversity, and preserve natural environments and ecosystems for the enjoyment, use, and contemplation of future generations of our own species.

When many people think 'environmentalist', a number of images come to mind.  Let's take an analytical approach to analyze some of these images (so if you're not a Rational, stop reading here).

"Environmentalists think *insert endangered species* are more important than people"

Ecologically-speaking, humans are the top of the food chain, the highest of the high predators.  Granted, a lion could certainly do a number on you if you come across one, unarmed, in the savanna... but humans for the most part live in hives (cities, suburbs) where we kill and eat as we please.  Many high predators act as a check and balance on the population of the species they prey on (think foxes and rabbits); we have gone so far as to domesticate and raise our own prey, and when we do come in contact with wild populations that are tasty and easy to catch, we have a very long history of wiping them out completely.  We chop down forests and replace them with monocultured fields of turfgrass, corn and wheat; we destroy habitats that are overflowing with biological diversity, and only pidgins, rats, cockroaches, and housecats remain.  We have no stabilizing purpose in the biospheres we inhabit.

Take, for instance, the Pacific Yew (the original source of the anticancer agent Taxol), or pretty much any other native tree or plant: at the very bottom of the food chain, they provide food and shelter to countless other organisms.  From a biological perspective, plants are absolutely critical for regulating the global carbon redox balance (carbon dioxide vs. reduced carbon).  Humans, at the very top, serve no critical ecological functions.  If you were to wipe out a species of plant, or insect, or fungus, it would almost certainly cause major environmental destabilization; wipe out humans, and the result would be a net STABILIZING effect.

There are many, many humans - probably around seven billion at this point - and it would be next to impossible to wipe them all out.  Tigers, on the other hand?  ~2,000 in the wild.  (One tiger = 3.5 million humans?)

So, if you want to pick things apart rationally: humans ARE quite the invasive species, and global ecology would only really benefit from a reduction in their population.  This doesn't jive very well with the "god put us on this planet to kill, eat, and pillage whatever we want" mentality that the majority of Americans seem to embrace, so the source of anti-environmentalism animosity is not too hard to find.

The thing is, 99.99% of environmentalists are NOT advocating doing anything to reduce the human population (which would probably be the most straightforward, surefire solution...) - they're only saying that we need to reduce our per-capita rate of consumption of natural resources to limit the destabilizing effects that we have.

Disagree?  Open-fire below.

Tomorrow: "Environmentalists are against progress and technology"
This Week: "Environmentalists don't care about jobs or the economy"
Later: "Redox Balances, Global Warming, and The History of The World"
           "Environmentalism: what is it really protecting?"

Perfect Pasta

Getting pasta 'just right' takes patience and practice.

It helps to start with the best possible ingredients. White, tasteless, bleached-to-death pasta, a horrible holdover from the days of Wonder Bread and the 'faux-wood-and-gold' style, is no longer the only option: many companies are now offering whole-wheat and multigrain pastas that offer superior taste and nutrition.

White, Wheat, and 7-Grain pastas. Data from NutritionData.com and Ronzoni Healthy Harvest

While all products made from wheat flour will have the same glycemic index, whole grains include the bran component, which contains additional dietary fiber and B-vitamins.

Strangely, whole grain products tend to be more expensive than their bran-removed, bleached counterparts... I would think that whole grain products would involve fewer processing steps and therefore end up cheaper. It may be related to economies of scale - the typical American still prefers the bleached, tasteless stuff for a few cents cheaper per pound.

Unshod (Day Two)

Went for a jog in my new shoes again today to loosen up some stiff muscles.  The weather has been absolutely beautiful this week, which reminds me... "can I go back to California yet?"


Some sources suggest that unnatural form, and not solely heel-striking, is to blame for many running maladies.  This seems likely, though I would still argue that overzealous, running-shoe-enabled heel-striking is one of the most common sins.

The root of the problem seems to be 'unnatural running' and the modern equipment that enables it - the overpadded shoes, the asphalt and concrete, treadmills, perfectly flat and uniform tracks.

Asphalt and concrete have extraordinarily high elastic moduli, though it could be argued that we've been running on a variety of similarly-rigid surfaces for a very long time.

Treadmill junkies and track runners are blowing knees and ankles every quarter-mile on REAL surfaces, and how is it at all surprising?  All of that oversupported, flat, uniform, rigid, endless straight-line running does nothing to condition the stabilizing muscles that are absolutely necessary for robust real-world running.  Treadmill running makes you really good at treadmill running, and that's about it.

A good analogy would be the typical gym rat - comically oversized muscles, obscene single-rep maximum loads... but when placed in an environment with REAL resistance (jiu jitsu, for instance), they just don't measure up.  Time after time, I was surprised by how easy it was to overpower (not just outmaneuver) these types.  The reason is the same: picking up and setting down a heavy object, over and over again, makes you you really good at picking up and setting down that heavy object.  If that's your goal, that's fine, but useful power comes from realistic training.

Unshod (Day One)

"Heel-toe, heel-toe," like they say it in phys-ed, is fine for walking... but humans were never designed to run this way.  The unnatural heel-striking gait favored by many joggers and runners transfers far too much energy to the knee, resulting in a host of joint maladies.

To confirm this statement, try running "heel-toe" barefoot on a hard surface - the result is quite painful.  The only reason people tend to run this way is because it is encouraged by the running shoes that we wear, the vast majority of which feature extreme amounts of heel cushioning.

'Running shoes' were invented in the 1970's by corporations eager to cash in on the jogging craze.  Most are designed to protect the wearer from damage caused by bad running form, which in turn encourages bad form and leads to long-term injury.  Running shoes also restrict the natural movement of the ankle, foot, and toes.

Humans had been running a long time when the 70's came around.  Since the dawn of the species, we have been running barefoot or wearing moccasins or sandals which protect the feet from cuts and abrasions but do not offer any padding.  Running this way encourages proper form that reduces the impact of the motion, strengthening stabilizing muscles in the toes, foot, ankle, and calves, and lessening eccentric loading of the knee.

I've hated shoes, running shoes especially, since I first wore them for baseball, basketball, and soccer in elementary school.  Summers spent barefoot are a fond memory.  I regularly mountain bike in flip-flops or light sandals, but there is a price to be paid - rocks and branches can be very sharp and unforgiving.  

Enter a new type of shoe: Vibram FiveFingers

The best description would probably be 'foot glove'.  This shoe is little more than a sole coupled with a snug-fitting leather or synthetic foot covering.  The toes each have their own 'compartment', like with a toe-sock, and are free to move independently.  They are typically worn without socks.

Walking in them feels just like going barefoot, minus the hazards of sharp rocks and broken glass (and apparently bizarre parasites, if you live in the right places).  Biking in them is a similarly pleasant experience.

Now here's the real project:

I have never been much for running because of the stress it puts on the knee, which has given me problems since 6th grade.  I went on my first run in these shoes last night, covering about 3.5 miles of grass, dirt, gravel, and asphalt.  The sensation of running is fantastic - I can actually feel the surfaces underneath me as I traverse them.  While it's much too early to tell how I will fair in the long-term, the shoes are definitely doing their job: my toes, feet, ankles, and calves are quite sore in unexpected places.

I will keep track of my progress with the aim of giving a final recommendation in a few months.  Thanks to Kyle for telling me about these shoes back in August, and finally convincing me to try them out!

Smell That?

The return of the earthy scents is one of my favorite parts of the transition from winter back into spring.  Of all of the flavors, the scent of rain is the most unmistakable.

One of the primary contributors to this distincitive smell is the bicyclic organic compound shown here, geosmin.  According to Wikipedia, it is produced by a number of soil bacteria such as the Actinomycetes (which also have a variety of biotechnological uses), and is also responsible for the earthy taste of beets and bottom-dwelling freshwater fish.  The human nose can detect geosmin at vanishingly low parts-per-trillion concentrations.

Ahhh... the sweet smell of microbial metabolic biochemistry.

Chemical Engineering Education, Part One

It occurred to me yesterday that I have no idea what the top ten bulk chemical products in the world are.  I cannot connect the common names (limestone, potash) to the most basic of chemical reagents, and I have no idea where or how they are derived.  I just barely grasp the general processes that occur in an oil refinery, and I know next to nothing about any other industrially-relevant chemical transformations.

I can recite Avogadro's Number far beyond a reasonable number of decimals, but I have no idea how the number was discovered or derived and I can't explain its significance outside of its relationship to the seemingly arbitrary definition of the 'mole'.  The same goes for the Boltzmann constant, the Faraday constant, the ideal gas constant.  I have no idea who Avogadro, Boltzmann, and Faraday where.  I have only a hazy understanding of where chemical engineering came from - arisen somehow in the leap from alchemy to industrial chemistry, tied to the Industrial Revolution and the steam engine - and this is only due to a few minutes here and there of my own efforts.

For all of the Liberal Artists endlessly beating the drum of 'general education', higher education's efforts to instill something beyond the knowledge of a handful of mathematical relationships seem to have failed outright.  A third of my education in college, and a full four-fifths pre-college, has technically been in the 'liberal arts'.  The failure began in what was NOT emphasized: how my chosen discipline connects to the real world.  The lack of history and the absence of those people and the discoveries they made robs science of it humanity and strips it of the logical progression of our understanding that makes it all make sense.  Without history, there is no foundation upon which to consider the present.  The failure ends at the feet of the Ivory Tower Intellectual, who deems it all (reality) to be too complicated and too practical, and makes the decision to leave it all out entirely... in favor of a grand meaningless molecular understanding.

So we sit around and type away at our computers and derive silly things at the atomic level, all the while remaining ignorant of the REAL chemical engineering that goes on right in front of us!

Science is a story of the most improbable happenings and the people who made them happen, and it is a story that continues to the present.  To deny the connections science has with the real world is to turn away from practicality, applicability, usefulness.  The drive for academic prestige (a synonym for 'complete irrelevance') has enabled the Ivory Tower Intellectual to move in on the discipline - even at the good old Land Grant universities, which have pledged from the beginning to serve the people by ensuring that knowledge is applied.

If Chemical Engineering wishes to avoid becoming a wanna-be Chemistry, the philosophy with which it is taught must change.  Every course must be organized from general to specific, providing the real-world context to keep students' interest and attention.  Every course needs to start with the history: where did all of this come from?  How and why was it discovered?  Who discovered it?

Give Newton and Leibniz a rest - analytical mathematics is NOT the future of this discipline.  Invite Johannn Becher to pull up a chair instead, and perhaps we'll all learn a thing or two.

Router Configuration, Part One

If you are on the market for a router, the Linksys WRT54GL is an excellent choice.  The reason it has won 30+ consecutive 'Newegg Customer Choice' awards is simple - by upgrading the software that runs on the router hardware itself ('flashing the firmware'), this ~$50 router can be made to do advanced networking tasks that it would take a several-hundred-dollar router to do otherwise.

The upgrade process itself is fast and simple: download the appropriate Linux-based firmware from this site, then log onto the router itself and flash the new firmware using the 'Update' administration tab... but perhaps I should start at the beginning.

The Router
A router is a piece of networking hardware that allows computers on a network to communicate with eachother, and with outside networks, by routing packets of data within and between networks.  In the typical home use, the router serves as an interface between the Local Area Network (LAN; the computers in your house) and the Wide Area Network (WAN; your Internet Service Provider's hubs that connect to the Internet).  The router is the gatekeeper, directing requests and data between the LAN computers and the Internet.  A process called Network Address Translation (NAT) allows the router to 'hide' the LAN from the WAN ('IP masquerading'), and the router also acts as a hardware firewall to screen out unauthorized data traffic.

IP Addresses
Traffic is routed on networks by assigning an address to each node in the network.  Internet Protocol version 4 ('IPv4') addresses are formatted as follows: 192.168.1.1; this particular representation is known as 'quad-dotted decimal notation'.  To connect you to the internet, your ISP assigns you an IP address.  Your router then assigns private IP addresses to itself each of the computers on the LAN; the addresses assigned are in the 'private IP address space' (which has been defined by the Internet Engineering Task Force (IETF) ) and only apply internaly on the LAN.

The router therefore has two different addresses: the WAN address assigned by the ISP and applicable to the Internet, and the LAN address assigned by the router itself and applicable within the LAN.  Why doesn't the ISP just assign WAN addresses to every computer on your network?  There are a finite number of IPv4 addresses, and they are rapidly running out!  For the Internet to function, all LANs behind a router are free to use duplicate addresses, but WAN addresses must be unique; by only assigning one WAN address to the router, WAN IPv4 addresses are conserved.  This problem eventually must be overcome by changing to a new format that allows a much greater number of IP addresses (IPv6).

LAN, WAN, and MAC
To see information on your network connection on a Windows computer:

1. Hit 'Windows-R' to bring up the 'Run' dialog
2. Type 'cmd' and hit enter to bring up the command prompt interpreter
3. type 'ipconfig /all'

Dig through the resulting output to find the description of the network adapter that you use to connect to the internet (usually 'Wireless LAN adapter' or 'Ethernet LAN adapter'):

• 'Physical' or 'MAC Address' - unique ID assigned by the manufacturer; AA-BB-CC-DD-EE-FF
• 'IPv4 Address' - your computer's LAN IP address
• 'Default Gateway' - the LAN IP address of your Internet Gateway (your router)

To find the WAN address of your router, just head to http://whatismyip.com.

When you're surfing the internet, your computer is sending requests for Internet information to the LAN IP of your router; the router uses NAT to hide the LAN IP address of your computer, and sends the request off into the Internet superstructure (a future article!).  The Internet replies to the WAN IP of the router, which then forwards the reply to the LAN IP of the requesting computer.  Fortunately, not too complicated!

Now that you know a little about LAN, WAN, and MAC addresses, you're ready to access and configure your router!  Stay tuned for Part II.

Anatomy of an Exam

Yesterday, I took the least satisfying exam I have ever had the misfortune of encountering.  (Note that this isn't a case of sour grapes on my part; I scored fine, and my cumulative marks are safely in the 'good range'.)

The Content
Some of the questions on this 25-question, multiple-choice molecular genetics final included:

Q: "Which domain(s) recognize(s) methylated histone tails?"
a) Chromo domains    b) Bromo domains     c) Both Chromo and Bromo domains

Q: "Yeast Gal4 is one of the most well-characterized transcription factors in eukaryotes. What type of activating region does Gal4 have?"
a) Gln-rich region      b) Acidic region      c) Pro-rich

Q: "6S RNA in E. coli cells downregulates gene expression in the stationary phase.  What protein is the target for 6S RNA binding?"
a) Large ribosomal subunit    b) Sigma70 RNA polymerase holoenzyme    c) Aminoacyl-tRNA synthetase

The answers are a, a, and... it doesn't matter; the minutiae addressed in this exam are completely irrelevant to understanding the course topic, to the point of this being discernible to someone unaffiliated with the biological sciences.  The professor has wasted his one opportunity to determine whether students understood the important concepts covered in the course, in favor of testing for the ability to memorize thousands of unrelated facts.  Asking questions such as these in molecular biology is akin to testing a geography student on their ability to match countries with their capitol cities, instead of on their knowledge of, say, geography's effects on the development of civilization.  This only reinforces my suspicion that many professors do not know what the main concepts are in the courses that they are assigned to teach.  This is probably a side-effect of the extremely narrow focus of most professors' research.

The Format
Exam format is also at issue.  Four multiple choice, 25-question exams are the only method of evaluation in this 400-level junior/senior class.  While I understand that this is partially due to the course's size (120+ students), this limitation does not prevent the questions themselves from being much better than they are.  All 25 questions had only three possible answers, turning the whole affair into something of a stochastic crapshoot.  It's not like we pay a lot for this or anything.  I really hope this professor is a class-A researcher.

With such a simple format, proofreading also would have been fairly straightforward and much appreciated:
     "Answer which one determines the copy number of plasmid."
     a) an origin of replication      b) selection marker      c) multiple clorning site

It's Not That Hard
Writing decent exam questions that actually address concepts is not difficult; as an unpaid undergraduate TA last spring, I came up with:

"In the DNA, G can be converted to 8-oxo-G and 5-methyl-C to T by various biochemical mechanisms.  What is a 'failsafe glycosylase'?  How would you design a failsafe glycosylase to address the two base conversions described above?"

"Consider the structure of RNA versus that of DNA.  How do their structural differences reflect their different functions in the cell?"

"The Gibbs free energy is used to evaluate the thermodynamics of biochemical transformations in living organisms.  How is this thermodynamic potential an appropriate choice for this application?"

"The partial hydrolysis of a nucleotide triphosphate into a nucleotide monophosphate and a pyrophosphate is only moderately favorable (X kJ/mol), while the hydrolysis of pyrophosphate is more favorable (Y kJ/mol).  How does a difference of (Y-X) kJ/mol influence the equilibrium position of these reactions?  Why is this important in the process of DNA synthesis?"

The topics of these questions have a lot of overlap with the material covered in this molecular genetics course, and I think they're sufficient to illustrate the point.

-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

So what do you think: do I have a point here?
Why is it so hard to get your money's worth at a university these days?

How To Set Up A Website

Gone are the days when setting up your own website meant bribing the neighborhood genius to give you some space on the server farm in his parents' basement!  There are now a number of private companies that will sell you 'virtual personal server' space to store the files that make up your website.  This isn't 'Geocities' garbage either; you can have your own personal URL that points to your site (ala www.brandoncurtis.net) instead of a URL that just describes a subdomain of your hosting company (ala www.brandoncurtis.MyHostingCompany.net).

(A better title for this article might be: 'How To Get Hosted Webspace For A Website'.  Future articles will deal with website basics, including webpage design.  See 'How To Set Up A Wiki' and 'Content Management Systems for Web Design' for other modern options that you can install and host using your webspace)

Choosing A Web Host

There are dozens of such web hosting companies around.  I will use WebHostingPad as an example, because they offer a low-cost, full-feature web hosting plan that offers all of the features that MOST people are looking for in a hosting service, and I have had a good experience hosting my own stuff with them.  If you are a little more experienced or you know that you need SPECIFIC functionality to do the things you want to do, make sure to check out the feature list and to read some web hosting reviews before choosing a website host.

First, set up an account with your web host of choice.  This is often VERY inexpensive; WebHostingPad, at the time of this posting, is offering three years of hosting for only $2/month (less than 7 cents a day).  A quick search might net you a web hosting coupon; in my experience most coupon codes posted on the web do not work, but I was able to get 25% off of my hosting purchase with one of these.

Registering A Domain Name

Many hosts will provide you with a free domain name when you sign up.  You usually have the choice of '.com', '.net', '.org', and a few others; which one you choose will not change ANYTHING about your site, but you can read more about the generic top-level domains here.  If you are not offered a domain name, you must get one from a Domain Name Registrar.  You'll need to interact with this company to enter some configuration information (or at the very least to transfer management of your domain name to your chosen hosting company), so it's worthwhile to read up on them.  Fortunately, almost all modern hosting companies offer you a domain name when you sign up for hosting, so you don't have to worry about this.

If you have a website and you want to SWITCH hosts, you will need to transfer your domain name.  How this is done varies widely from company to company, but hosts have a vested interest in keeping this process simple and they usually document it well on their websites.

Choosing A Web Host
Now, you have a domain name that will refer visitors to the files on your personal server space!  If you point your browser to your new URL right away, you will get whatever default 'HTTP 404' error that your hosting company uses; it make take a few hours for your host to get everything set up, and you need to move your site's files to your server space before you can access them.

Many hosts, including WebHostingPad, enable simple access to your website's management and configuration tools through an online utility such as CPanel.  Simply point your browser to the CPanel login address specified by your host, and you can log in and access simple and advanced tools for uploading files, password-protecting directories, building databases, implementing subdomains, &etc.  If you're new to web design and you don't have any idea what half of these tools do, don't worry about it; you generally just learn them as you need them.

While web hosting control panels are great for many aspects of web administration, they are usually horrible for uploading and moving files around in your server space.  For this task, you will want a utility such as the free, open-source FileZilla, which makes use of FTP (File Transfer Protocol) to directly link up to and interact with your server.  File transfer and reorganization is as easy as drag-and-drop in modern FTP clients!  Use the FTP login information provided by your web host to access your server space; once you have everything set up, logging in is as easy as selecting your site from the 'Site Manager' button's dropdown menu on the upper-left corner of FileZilla.

Good modern web hosts will provide you with a directory labeled something like 'www'; only files in this folder are accessible from the internet.  Configuration information and other stuff is stored in the other directories, and you should feel free to make your own directories to store things that you don't want to be publicly-accessible.


Now What?
There are a million different directions you can take to build a functional site in your new space.  Some are simple: tools like Dreamweaver provide a simple interface for piecing together a website, and don't require any knowledge of the web languages (xhtml, css, php, etc) to use.

Some are even simpler: Drupal, Google Apps, Wikimedia, WordPress and many others can be installed in your serverspace to provide you with 'out-of-the-box' website functionality, with no page-by-page construction necessary.  See 'How To Set Up A Wiki' and 'Content Management Systems for Web Design' for more information.

Many blogging sites and other online content creation services give you the ability to 'reroute' your blog through your webspace.  You can have your Blogger site accessible, for instance, at www.MySite.com/blog.  Your blogging site's webpage will have more information if this is available.


Future articles: web design with WordPress and other platforms; web design with KompoZer and Dreamweaver; domain design and administration with Google Apps