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Evolution Friday : Jim Miller

A friend of my parents wrote an amusing entry about the Bible and evolution. It was originally available here, from the Rapid City Journal.

Noah and evolution
Does a biblical story support evolution? John Tomasin of New Jersey recently pointed out that the story of Noah and his boat may support the theory of evolution.
Accordingly, all human beings alive today are direct descendants of eight survivors of the great flood. These include Europeans, Africans, Asians, Native Americans, Norwegians, Eskimos, Hebrews, Muslims, Buddhists, Pygmies, and you and me. If we look at the diversity, the results seem to point to an evolutionary process at work.
Can we then conclude that to deny that this diversity is due to evolution is to deny the Holy Scriptures?
JIM MILLER
Rapid City

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Delta G

Faithful viewer, One Day at a Time, asked how I knew that the the combustion of wax resulted in carbon dioxide and water vapor. Well, there are two things to this problem: stoichiometry and thermodynamics. Let’s tackle the thermodynamics first.
Every molecule has a certain amount of energy that it took to make it from its atomic parts. This energy is called the “Gibbs Free Energy” or just G for short. There are published tables that show the Gibbs Free Energy (G) for different molecules. For example, here is a short list of G values for various molecules:

Molecule G (kJ/mole)
CH4 (methane) -50.8
O2 (oxygen) 0
CO2 (carbon dioxide) -394.4
H2O (water) -237.2

Delta G is the term used to describe how much energy is released durnig a chemical reaction. Delta G is calculated from the sum of G for the reactants minus the sum of G for products.
So for this reaction:

CH4 + 2 O2 –> CO2 + 2 H2O

We can look up the G values for all four molecules involved. The left hand side has G of -50.8 kJ/mole. The right hand side has G of -868.8 kJ/mole. The difference (delta G) is -818.0 kJ/mole. A negative number like that indicates that the reaction produces a lot of energy. If you were to try running the reaction backwards (ie. to make wax out of water vapor and carbon dioxide), you would find that you had very little success. This is because you would have to add 818 kJ of energy per mole of reactants. Never mind what a kJ is or what a mole is. Suffice to say that that requires a lot of energy for not much stuff.
So in summary, by using thermodynamics and Gibbs Free Energy, we were able to discover that the chemical reaction of turning wax plus oxygen into water and carbon dioxide produces a lot of energy. This is useful, because if it doesn’t produce energy (e.g. has a postive delta G) then the reaction won’t happen.
It’s also import to make sure we don’t create or destroy matter. In other words, there must be the same number and kind of atoms on both sides of a chemical reaction. That is what they mean by stoichiometry. Thus “methane plus oxygen makes water and carbon dioxide” must be balanced. You’ll notice that in the above equation, I added a “2” in front of the water molecule product. That’s because for every molecule of methane that burns, two molecules of water are produced. Also, you’ll notice that I had to put a 2 in front of the oxygen as well. In that form, every molecule is accounted for. Of course, many more molecules are involved when burning an actual candle (on the order of 602,300,000,000,000,000,000,000 molecules), but the ratio ( one methane : two oxygen : one carbon dioxide : two water ) is conserved.
Now quiz yourself. Here are some chemical reactions that aren’t stochiometrically balanced. Try to figure out what terms to add to make the reaction balanced. (click and drag to select and see the hidden answer.)
1. H2 + O2 –> H2O  clickndrag—> Answer: 2 H2 + O2 –> 2 H2O —>tohere
2. CH3CH3 + O2 –> CO2 + H2O  clickndrag—> Answer: 2 CH3CH3 + 7 O2 –> 4 CO2 + 6 H2O  —>tohere

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The old candle in the glass trick

So we were at a fancy dinner party the other night, and so naturally that was a perfect moment for kitchen chemistry. You may know the rule put down by my overbearing spouse — no chemistry in the kitchen. Which is what leaves me no other outlet but my friend’s kitchens or at fancy company dinner parties.
We took a burning candle and placed it on a saucer full of water. It was a mostly burnt out votive candle, so it floated nicely. I then put an inverted water glass over the candle. The flame went out, and water was drawn up into the glass.
This is a fun thing to do any time you are around candles and water glasses.
Here is what’s going on: Wax is a hydrocarbon — which means it is made of polymers composed of two hydrogen atoms and one carbon atom. Well, that isn’t entirely true — it is approximately true. For example, octane is a molecule that is a hydrocarbon with a formula C8H18. Dodecane has the formula C12H26. As the molecules get larger, they approach the 2:1 ratio. So to simplify our stoichiometry we’ll say that hydrocarbons are basically CH2. Molecular oxygen is O2. And this is how a hydrocarbon burns:

CH2 + 2 O2 –> CO2 + H2O

All off those molecules are gas (water is a gas at the temperature of combustion). So why does the water level go up? Two reasons: 1) The water vapor will condense and 2) The carbon dioxide may dissolve in the water. Thus the net reaction is consuming more gas than it produces, reducing the pressure inside the glass. Water is pulled up into the glass by the greater pressure exerted from the outside atmospheric pressure.

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Evolution Friday : Drug Resistant Pathogens

Today’s evolution piece is going to be short, due to the fact that I put it off until so late in the day. The topic is “drug resistance” — and it is a tragic and very real example of evolution in action. Through the course of a few years, or even less in laboratory conditions, strains of bacteria develop resistance to antibiotic drugs used to treat them. The process whereby fortuitous mutations confer special abilities which improve survival is called “natural selection”. Natural selection is a fundamental principle that explains how evolution occurs. This is a very real danger for modern medicine; one of my favorite celebs, Jim Henson, died from a drug resistant strain of streptococcus.
Drug resistance isn’t the only thing that pathogens evolve to cope with. Our immune system presents another sort of obstacle to their prosperity. Every year (in Asia it seems, for some reason) a new strain of the flu evolves. The new strain is sufficiently different than last year’s that the antibodies you’ve developed are no longer effective. (The flu is actually a virus, but it is able to evolve nonetheless since its genetic principles are the same as real living things.)
So there you have it. If evolution didn’t work, we wouldn’t all be coughing and sneezing (or worse) every January.

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9V battery

The other day I was thinking about 9V batteries. I was wondering about their shape, and why are they a different shape than other batteries such as a C or D cell. Then two things occurred to me: First, the shape of a nine volt is not square on the bottom — it is a rectangle with a ratio of about 2 across by 3 down. You could fit six cylinders inside it neatly. Also, 9 is 6 times 1.5, which is the voltage of an AAA, AA, C or D cell battery. So then I thought, you know what, I bet a nine volt is made of six small batteries wired up in series. Sure enough….
View image

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Evolution Friday

No, its not Illustration Friday — a website that encourages people to draw something once a week. In reaction to the unending, uneducated, and overly vocalized mantra of creationists heard in school board meetings across the country, I’m launching “Evolution Friday”. My intent is to combat the their “creation science” drivel. As a veteran scientist — hmm, can I call myself that? A war “veteran” is someone who served in a war — even if only for a short time. I have served in science for six years, so I think I ought to qualify. But still, it sounds far to pretention to call myself “veteran”. How about “former”?. As a former scientist, I’ve seen first hand a lot of things that confirm the theory of evolution. It seems the least I could do is share it with you.
Today’s Evolution Friday Topic : Convergent Evolution.
As a student of Ichthyology, I spent a fair amount of time in the lab classifying fish species. Fish inhabit a wide variety of environments: Open ocean, shorelines, estuaries, rivers, streams, lakes, caves and even some extreme environments like arctic waters where the temperature is below freezing. Carl Linneaus (he was working in plants at the time, but his work applies to all living things) noticed that some species were quite similar to one another (such as two species of Oak), but were different than other species. He created a system called Taxonomy, by which he organized species based on these similarities and differences.

0.jpg 1.jpg
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One interesting thing about Taxonomy is that something that seem quite similar are in fact quite different. For example, consider sharks, rays, walleye, and flounder. Superficially it seems that the shark and walleye are more similar based on their overall shape. Rays and flounder, on the other hand, while similar to each other, have a much different shape than the shark and walleye. So it would seem that the shark and the fish should be closer together taxonomically, as should the ray and flounder.
But upon closer investigation, it becomes clear that actually the shark and the ray are more similar to each other than either is to the walleye or flounder. And the walleye and flounder are quite similar as well. The shark and ray both have cartilagenous skeletons, whereas the walleye and flounder have bony skeletons. The shark and the ray both have seven gill slits, whereas the walleye and flounder have a single gill structure covered with a bony operculum. The walleye and flounder have different kinds of teeth than the shark and ray. Only the walleye has a swim bladder. Walleye and flounder have scales, the shark and ray have denticles. On a molecular level, the shark and ray share a greater percentage of their nucleic acid sequences than do the flounder and walleye.
This presents a riddle for Creationists. Why are similar functions “designed” in different ways. Both the ray and the flounder are bottom dwellers that move about using vertical oscillations of their limbs, but their structural make-up are radically different. Furthermore, why is the flounder built with a bizarre twisted face, so that one eyeball isn’t wasted staring at the mud? Wouldn’t it make more sense for a designer to build a flounder with its eyes evenly spaced on top? Why would a designer reinvent muscle fibers, skin coverings, neural circuitry, etc. to achieve the same purpose?
These strange observations are easily explained by the theory of evolution. The flounder and they walleye are descended from a common ancestor that looked much like the walleye does today. However, in one lineage, flounder’s ancestors found a good living was to be had by hiding on the sea floor. Eventually random changes accumulated that made flounder’s nearer ancestors more successful at that; it learned to swim on its side, its face started to twist, etc…. A similar process happened with the ray. An ancestral fish, probably lived in a way similar ot the dogfish (a kind of shark) does today — by skulking around on the bottom. Fins got longer and longer, as fish with bigger fins could skulk better. Eventually the fish looked and swam more and more like a ray.
This process by which two species acheive similar functionality via different processes is called convergent evolution. For the flounder and the ray, each acheive the abilities so hide on the bottom of the ocean and swim with vertical oscillations — but acheived them through separate processes. The natural world is filled with other examples of this process. Evolution explains it; creation science cannot.

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Intelligent Nutrients….(snicker)

A new restaurant opened near us recently called “Intelligent Nutrients”. We could see the sign for it from I-35W just after you got on going south. It had a curious purple, orange and green color scheme that made us think — hippie, new age, organic and maybe even vegetarian. Thus we had to give it a try.
We tried to find out what their business hours were on their website. Good luck! It has lots of glitz but not so much content. No business hours, no menu… what were getting ourselves into? In any case, we decided to risk it. So last night we drove over along with our trusty companions Tismo & One Day at a Time. Boy were we in for a surprise.
First of all, to get to the restaurant, you must pass through a gift shop of sorts. It is more like a shrine to the pure, lofty, and guady — all of which was empregnated with essential oils. Truffles for “Aphrodite” or “Motivation” — listing the essential oils which endowed those properties (ginger, lemon peel, etc…). We were right, everything was “organic”. But more than that — they actually touted that some of the foods were “harmonically grown”. Do they have a zen master do feng-shui on the crops?
The seemed to specialize in jewelry with audaciously large glass stones. Like the size of a 50 cent piece or bigger. I can’t imagine that looks good as a necklace.
I just couldn’t fathom the point of this establishment. Why do people believe that giant gems will make them healthy? Why are combinations of essential oils believed to enhance attribute X — and if they do, why is that any different than a drug that do so? Steroids are bad, but this essential oil of stamina is okay?
The restaurant, when we finally made it there, seemed pleasant. It had a giant projection TV displaying geometric shapes that danced with the new-age music the drifted through the air. The employees were smartly dressed in white chef’s outfits. However, the menu was just as weird as the gift store. I bet the food was interesting, but I got the feeling that it would be more of an “experience” than it would be “satisfying”, if you know what I mean. Lima beans are great and all, but now what I’d consider a suppertime main dish. We decided we’d try it some other day, when we weren’t so hungry.
On final reflection, even though we didn’t understand what this place was about we figured it boded well for us. Intelligent Nutrients seemed very Boulder-esque. New age, hippie, granola, tree-hugger, etc… Say what you will about Boulder, CO, you might love it or think it is hoaky. But real estate prices in Boulder are a Mile High, and I own a home from what appears to be the beginnings of the new Boulder in Minnesota. Moo ho ha ha haha!

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Calling all creative light blinkers

I’m runing out of time to complete the christmas present for my nephews. I’ve created a “build your own robot” kit. I have pretty much all the hardware assembled, but I have only a few days to write the software. That’s where you come in — I want suggestions for the most intersting ways to program my little beasts.
First, let me describe what they are: It is a small rectangular assembly of electronic parts and wires. It has one light sensor, two small switches (dip switches), a motor and lots of lights (I’m able to selectively turn on and off six different ones).
The kit will involve some amount of physical “put it together”. This includes attaching the wire legs, and clipping an off-center weight to the motor. The off center weight will make the robot appear to “walk” because it will vibrate the entire thing as it spins. You could also put a pinwheel or a spiral shape on the motor — which would look cool but wouldn’t make it move. You might even find a way to put a light spinning on the motor if you could find a way to make contact with a spining thing.
What kinds of behaviors should the robot have? With two dip switches, I have the ability to select up to four different behaviors. My current ideas are:

  • The robot starts to walk when it detects light. I’m including a small flashlight in the kit, so they can turn the robot on in the dark, and then illuminate it to start it going. What should the lights do during this time? Flash, pulsate, or be off, or on solid or dim?
  • The robot flashes its lights mimicing the pattern that it receives from the light sensor. So if you flash long, short short long, it would do that back.
  • The robot sits dark and quiet until the light level changes — then it goes bezerk. This is the ‘guardian’ mode and you could use it to guard your room.

Any other ideas of cool things the robot could do? What about cool ways that it could be accessorized, to make it more interesting to play with?
What are some nifty patterns of lights? With six lights available, I can do quite a few combinations of patterns…

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Comment SPAM

{sigh} Some moron named “TOM” keeps posting Spam comments on my blog. It is up to about four a day, and I delete them, and I block his IP address, but he keeps coming back.
So I’ve disable comments on all old posts — and moving forward I’ve change the id tags of the form data so that his script or whatever he is using won’t work anymore (I hope). In a way this is a challenge to see who is cleverer – me or Tom.
We will see. It is a toss up.

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USB PicKit tools for Mac OS X

A person named Orion created a nifty utility for programming PIC controllers. PICs, as you may recall are the brains of my robots. Specifically, this program controls the Microchip PicKitâ„¢ 1 Flash Starter Kit.
Orion called his software USB PICKIT.
Unfortunately, when Microchip, Inc. updated their software to version 2.0.2, Orion’s software stopped working on the Mac. This is because his comnputer got sent to Alaska. Go figure.
Fortunately, he posted his source code. So I took it and patched it up (which was not too hard, but did require making things more “Mac”centric, because the libusb support on Mac OS X isn’t the same as on Linux. Namely, interrupt mode didn’t seem to be supported.)
So, in order to be a good internet citizen, I’ll put up my Mac OS X version of usb_pickit for others to use.
Download file This is a Mac OS X 10.3 binary file in a zip archive.
For some reason I felt obligated to rename it Ezload. This wasn’t really intentional, oh well.
The way I did this was rather hacky… so I won’t post the source unless someone wants it.
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Update, I’ve cleaned the code a little bit and tried to integrate my changes in a way that won’t break the linux build either.
Download file
This version now has a UI, and as soon as you connect a device it either uploads or downloads. I’m also including all the source and the project file.
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Update, August 2011. The Download link above has been modified to reflect the new location on Google Code.