Codes and DNA

I am still trying to assemble an explanation of the term “DNA code” and explain what it is and is not. Older posts on this can be found here and here.

“Code” may be defined as any of the following:

1) a set of rules for converting information into another form or representation (encoding) for later retrieval
2) a set of rules or principles or laws (not applicable in this case)
3) a system of transmitting messages for brevity and/or security (also not applicable)
4) the symbolic arrangement of data or instructions in a computer program or the set of such instructions

Is DNA a code?

A DNA molecule is, itself, neither a set of rules, nor is it symbolic of data or instructions. DNA molecules are sequences of nucleotides which can be broken down into reading frames, promoters, enhancers, structural and spacial segments, and so forth. Since the DNA molecule has such variability and physical functionality inherent within it, the metaphor of DNA being information or a “code” is both overly simplistic and inaccurate.

What about RNA?

Additionally, functional segments of the “code” exist without ever being “decoded.” Some segments of RNA, for example, spliceosomes, ribozymes, and ribozomes are in the same sequences as the DNA template.  Even ignoring the function inherent in many RNA transcripts (spliceosomes, ribozymes, ribozomes, etc.) which are still “the raw code,” we can continue on both ends. The DNA sequence itself, as well as the transcripts which are translated into proteins, are similarly not information. While codes rely upon symbolic arrangements to transmit data or instructions, the arrangement of DNA merely serves as a template by which RNA transcripts are made; this is more like a mold than a code as the resulting copy of a DNA template is the reverse and opposite of the template itself: the DNA sequence 5′AAGCTTGGCAT3′ is transcribed into the RNA sequence 5′AUGCCAAGCUU3′. What, also, is the magical “information” this DNA sequence is supposed to carry? Thus far, it appears the RNA is not information, nor is the DNA itself information.

Proteins?

Could it be the proteins which result from some RNA transcripts which are the “information” in DNA? No. Proteins also do not transmit information; while the protein is useful, it is as much “information” as a car is a manual to assemble a new one. Proteins were never “encoded” from protein to RNA to DNA in order to be properly “decoded,” the function of a protein is based upon its physical structure, as is the function of RNA and DNA.

Well, what is the “genetic code?”

We hear this phrase all the time, mostly by individuals who have no understandings of even the basics of genetics. The genetic code is the means by which we (humans) organize DNA into bits which we can understand. We remove the three-dimensional context and focus exclusively on the sequence. From this, the simplistic explanation (DNA->RNA->”magical protein”) that DNA is arranged in codons. These codons hold the “magical information” which becomes “magical protein,” which as we all know, is what DNA is all about. This is where the confusion lies. DNA does not just contain sequences for protein; functional units exist outside of any reading frames including promoters, enhancers, suppressors, etc. Other functional segments exist as well (centromeres, telomeres, and origins of replication) which contradicts the idea that DNA is like a software program. The genetic code is, in this respect, a human construct to understand specific regions of DNA which do contain sequences used for protein production. This is the only use this phrase has.

The biochemistry of ethanol consumption

Well, this is really about alcohol consumption in general, coupled with, I hope, a decent review of the underlying mechanisms of what happens psychologically and chemically.

I will be covering the biochemistry in several aspects. The metabolism of ethanol is central to this. Some ethanol is produced by bacteria in the gut, so everyone has, at the very least, a low level of ethanol metabolism. Once ethanol is consumed, it then begins being oxidized by an alcohol dehydrogenase. This enzyme converts ethanol into acetaldehyde. Acetaldehyde is a much more directly toxic substance. Acetaldehyde is then converted to acetic acid which is then converted to acetyl-CoA. At each step of this, the substances have physiological effects on the body which I shall briefly discuss.

Ethanol is an allosteric modulator of GABA_A. Since GABA_A is an inhibitory neurotransmitter receptor, which causes a decrease in neuron firing, GABA_A is essentially a depressant receptor. Continuous activation of GABA_A results in it being downregulated to allow for the nervous system to function properly. This is what partially causes alcohol tolerance and physical dependence. Complete withdrawal from alcohol after prolonged heavy use can result in uncontrolled synapse firing. (siezure, convulsion, etc.)Some medications can reduce this hypersensitivity of neurons. This is why severe alcoholics generally must undergo “detox” to treat these physiological effects of alcohol dependence prior to a therapy to prevent relapse.

Acetaldehyde is one compound which contributes to hangovers and is partially responsible for the damage associated with alcohol consumption. It has been hypothesized that cirrhosis may partially be due to acetaldehyde. Additionally, prolonged use of alcohol results in fatty deposits in the liver, although the exact mechanism of this is unknown. Acetaldehyde also is a potent carcinogen and mutagen which is partially responsible for many of the cancer and disease risks associated with smoking, car exhaust, and alcohol consumption.

As for the beneficial effects of ethanol consumption in low to moderate levels (less than two drinks per day), there is good evidence that this is the case. These include a decreased incidence of cardiovascular disease and some protection from some infectious diseases and diabetes. In higher levels, however, these benefits seem to be countered by greater than two drinks per day. The optimal point of mortality associated with alcohol is near the one drink per day mark.

As for the physiological effects of alcohol withdrawal, these are slightly more complex. The most severe of the symptoms are anorexia, delirium tremens, diarrhea, hyperthermia, nausea, seizures, sweating, and tachycardia. All of these are due to the overexcited state of neurons. Typically given to suppress these effects are a range of GABA modulators such as benzodiazepines, Carbamazepine, and Flumazenil. These medications are typically given due to the ease which these can be metered.

Superstimuli

What is a superstimulus? I hope that helped to clear it up.  Pascal Boyer is putting forth an argument that religion is, in fact, a superstimulus (pdf). This idea of “spandrels” arising from evolutionary characteristics is not unheard of. Since evolution acts upon the entire organism and not specific traits, what can arise as a result can be something which was never selected for in the first place.  It is not very long; only two pages. Read it. It’s good stuff. I am also posting a few videos below the fold.

The farce is strong with this one

I will first state that I am not trying to be condescending, it just comes out that way. I am not trying to ridicule, it’s just so difficult to not ridicule the ridiculous.

I want these!

Ok, New Scientist has found some awesome robotic ideas, might this mean fire ants could be used for walkway lamps and wild pigs for tractors?

Religion (or lack thereof)

While perusing the internet, I discovered a commenter on a blag who genuinely seems like a wonderful person. On this individual’s profile, however, was a statement which I feel necessary to explain:

Even if they’re one word platitudes now, hope, wonder, love, forgiveness and healing are the most beautiful ideas I’ve ever encountered.

Since nothing is not, how did this become the atheists’ primary cause?

While it may seem to the average theistic individual the causes of the atheistic are those of “nothing” or “lack of something,” this could not be farther from the truth. Many who are atheistic, myself included, simply wish to not be judged based upon their lack of belief. We do not want individuals automatically assuming we are amoral and cruel. Additionally, it would be quite nice to not be required (de facto) to worship (or pretend to worship) a deity in order to be elected to public office in our secular country. I, personally, am not seeking you to drop your belief in your superstition (although that would be wonderful). What is my mission with this blog? Why did I name it “Mors dei” and why do I constantly argue against the use of religion as a tool for censorship, violence, and imposing one’s view of morality? I can answer these in three very short (not including subordinate clauses, brackets, and parentheses) sentences:

1) I blog about nature, human life, politics, and so forth  [from the perspective of a young individual with a college education in the sciences who (having grown up in a semi-Catholic household and more familiarity with fundamentalists than I would care to discuss) feels evidence and understanding, not faith, should be the basis of moralities (yes, it is plural), governments, educations, and lives] when I find something interesting.

2) The answer to the name question can be found here; additionally, it’s a catchy Latin name.

3) Using religion for anything outside of personal use opens it up to scrutiny, [if you do not wish for your religion to be scrutinized, then don't put it out in daylight (read "keep it to yourself")--for this reason, using it as a vehicle to impose your beliefs upon others without presenting evidence (all evidence, not just cherry-picking) will result in their justifications to be ripped apart as the hot air (read "flatulance") which it is] which means when I sink my teeth into a juicy chunk of superstitious nonsense that you hold dear and use to justify your bigotry, I won’t let go just because you scream “I’m offended.”

I hope that clarifies why I blog about religion so much, I find it offensive to use theology to justify ANYTHING. There are more parsimonious explanations for anything than your preferred deity.

Cyborg Names

Since all the cool people are doing the cyborg name thing, why the hell not.

Get Your Cyborg Name

Repair brainwashed minds, destroy myths, infiltrate cults?

Natural “Remedies”; or Natural “Cures” for Proper Biological Function

Naturopaths love those few “remedies” they have that get some results; Zicam was one of them. It works by drying out the sinus mucosa which reduces congestion, coughing, etc. Unfortunately, it also has the potential to result in permanent loss of smell. This has also been KNOWN since 2003 and it is not the same as a “side effect” as one would commonly think of it. This is permanent nerve damage as a result of a “remedy” not having a proper regulation and reporting during a highly controlled prescription phase. The FDA finally did something 6 years later. Some presription medications are trials for broader release (Loratadine) which allows for a far better reporting of problems. “Natural” substances require no such regulatiory phase prior to being available over-the-counter.

Other “natural” remedies which are dangerous include:

1. Menopause “remedies” such as soy, ginseng, thyme, and liquorice can promote tumor proliferation
2. Tea tree oil (look at this list of supposed uses!) even though there is nearly no evidence to support the claims other than its usefulness as an antiseptic. “Boosting” the immune system is similarly something you never want to do. Either one’s immune system functions properly, or it does not. One does not want an overactive immune system.
3. Capsicum for hemeroids? I’m just a stupid Cajun, but I know what hemeroids are, and I know what capsicum does… This just doesn’t sound fun.

People, seriously, at least investigate the crap naturopaths and other quacks push. Read about the ingredients in medications you are considering. No matter how corrupt you might think the pharmaceutical industry actually is, it’s better than most of this shit.

Spontaneous generation

I was reading about spontaneous generation a short time ago when doing some research for my little book project and, of course, someone completely misunderstood the difference between spontaneous generation and modern abiogenesis. The first thing which I must address is that spontaneous generation relied upon matter to become complex organisms. The equivocation between the two ideas is similar to the equivocation between the geocentric model and the  heliocentric model. The main point about spontaneous generation is that complete organisms come from other substances.

1. And, by the way, some of the grey mullet species are not produced from copulation, but grow spontaneously from mud and sand.
2. Cockles and clams and razor-fishes and scallops row spontaneously in sandy places.
3. The hermit-crab grows spontaneously out of soil and slime, and finds its way into untenanted shells.
4. Sponges grow spontaneously either attached to a rock or on sea-beaches, and they get their nutriment in slime: a proof of this statement is the fact that when they are first secured they are found to be full of slime.
5. Other insects are not derived from living parentage, but are generated spontaneously: some out of dew falling on leaves, ordinarily in spring-time, but not seldom in winter when there has been a stretch of fair weather and southerly winds; others grow in decaying mud or dung; others in timber, green or dry; some in the hair of animals; some in the flesh of animals; some in excrements: and some from excrement after it has been voided, and some from excrement yet within the living animal, like the helminthes or intestinal worms.

Each and every one of these consists of the spontaneous generation of a multicellular organism in a nonhereditary fashion. Abiogenesis, on the other hand, follows all we know of modern heredity, seeking to extend it into self-replicating chemical structures of short nucleotide chains, chrystaline structures, or any of the other possible mechanisms. The key point which spontaneous generation lacks is that all orgnisms come from a similar parent. Virus offspring also come from other viruses. Extending the concept of heredity back to a point which something can be considered nonliving is abiogenesis. When creationists state that “abiogenesis was disproven by Pasteur,” you can firmly state that this was spontaneous generation, not modern abiogenesis. Some aspects of abiogenesis do have supporting evidence.

“Support the troops”

Have you ever wondered what that statement means and what it implies? While I members of the U.S. military elisted voluntarily, I cannot help but wonder what it means to “support” them.  The word “support” has many, many meaning:

1. give moral or psychological support, aid, or courage to
2. the activity of providing for or maintaining by supplying with money or necessities
3. support materially or financially
4. aiding the cause or policy or interests of
5. back: be behind; approve of
6. hold: be the physical support of; carry the weight of
7. a military operation (often involving new supplies of men and materiel) to strengthen a military force or aid in the performance of its mission
8. confirm: establish or strengthen as with new evidence or facts
9. documentation: documentary validation
10. subscribe: adopt as a belief
11. the financial means whereby one lives
12. corroborate: support with evidence or authority or make more certain or confirm
13. supporting structure that holds up or provides a foundation
14. defend: argue or speak in defense of
15. the act of bearing the weight of or strengthening

So let us first figure out what possible meanings to “support” in this sentence may be.

Removing all which do not apply to individuals (7, 8, 9, 10, 12, 15) I suppose one could argue rather effectively that we already (willingly or not) give support according to definitions 2, 3, and 11, so they shall be removed, leaving 1, 4, 5, 12, and 14.

Considering one does not have to necessarily approve of what the troops are doing to “support them” as stated by thousands of politicians, this removes definition 5 from the running.

Considering most military personnel have little or no say in cause or policy, and most citizens do not have access to information which would allow for a presentation of some kind of evidence to support them as per 12, it similarly cannot be definitions 4 or 12.

To claim to “speak in defense of” all military personnel is a bit of an over-generalization as a number of military personnel have done illegal activities. This leaves only definition 1 remaining.

1. give moral or psychological support, aid, or courage to

What would be the most psychologically beneficial activity one could do for the individuals still overseas? Support the troops; get them the psychiatric help many of them need. Support the troops; don’t send them on three tours in rapid succession. Support the troops; except the commanders using people as pawns in a very deadly game of chess.

Individuals using this phrase to mean “don’t say bad things about the war or the soldiers fighting for us,” while they imply it only means “comfort them.” Such phrases with hundreds of possible meanings are worse than useless. Do I agree with what they are doing? Yes and no; I appreciate them enlisting in the military, but I do not support the reason for our military being in Iraq (or still being in Afghanistan). Both of these military opperations were as organized as a herd of cats. How about we apologize to our military personnel for putting them in this situation?