Quantum Gradnamics

Jorge Cham has a very good wit to him. I have enjoyed reading Piled Higher & Deeper comics since my freshmen year. His Quantum Gradnamics series is perhaps one of the funniest series he has yet, in my opinion.

Egg on Netflix's face?

The arXives blog has an interesting post. It seems a group of bored computer scientists have managed to de-anonymize the data set of Netflixes $1 million contest.

I wonder if those bored computer scientists will eventually win the prize. It does put a whole new meaning to the phrase trend setting.

Davies Writes Ridiculous NYT Op-Ed

Society seems to move faster than my ability to comprehend science. As I struggle to understand both the history behind and the solutions to the N-representability problem (eg. utilizing an electron pair representation of the electronic energies to solve many-electron problems) as coined by Professor John Coleman, society seems more than able to confound itself in basic principles. This is no different with Paul Davies, who as a notable popularizer of physics and a college professor, ought to know better than to cultivate confusion in the general populace over what physics says, physics implies, and what physics does not do for either at the moment.

All science proceeds on the assumption that nature is ordered in a rational and intelligible way. You couldn’t be a scientist if you thought the universe was a meaningless jumble of odds and ends haphazardly juxtaposed. When physicists probe to a deeper level of subatomic structure, or astronomers extend the reach of their instruments, they expect to encounter additional elegant mathematical order. And so far this faith has been justified.

Complete nonsense. When a physicist smacks a molecule with a femtosecond pulse, s/he certainly expects a certain result based on hypotheses rooted in conjecture formulated from prior observations. But our expectancies are not allows the result. Consider the Franck-Condon principle. The FCP is an elegant mathematical model of expected vibronic transitions, yet in photoinonic studies the FCP breaks down at energies in large excess of the energy of a chemical bond. This is due to the effects of Cooper minima on molecular vibrations (an effect of the change in sign of the dipole matrix element versus photon energy). The breakdown of FCP required experimental evidence to indicate the presence in photoionic spectroscopy, and the explanation later came from the mathematical model and how this model does not interfere with the previously established model.

Though physics is not a reduced form of phenomenology, it ultimately requires some phenomena to map mathematically. Certainly a desire of several mathematical physicists is to be able to start from various basic mathematical axioms and derive the entire universe. However, their derivations ignore the history of science which built such principles on established knowledge rather than prior dispositions.

A classic relic from the history of science is the birth of quantum physics during the late 19th and early 20th centuries. As physicists discovered the electronic freedoms of hydrogen and other gaseous elements, they found themselves in a quagmire. Classical physics simply failed to account for the electronic freedoms of atoms and molecules. However, classical physics gave a certain mathematical tool set that was able to be adapted and fitted into solving the problems faced by the turn-of-the-century physicists.

Planck utilized his knowledge of oscillators to give a mathematical derivation of the black body spectrum. Einstein used his knowledge of colliding particles to initially describe the photoelectric effect of metals. Bohr incorporated the discretized energies of gas spectrum and Rutherford's planetary model of electronic orbits and fashioned his quantized model that forced electrons into energy orbits and defied the Larmor formula which dictated that accelerating (and thus, orbiting) electrons emit E&M waves.

Sometimes...no, I would say all the time, science is dictated by what is observed and not by what is expected. Scientific knowledge is highly provisional, and we cannot create discrepancies with science due to this provisional limitation. But provisional knowledge is not what the general populace desires, and the acceptance of non-concrete answers to certain questions often invoke confusion and anti-science in audiences. So I can empathize with the scientific popularizer in the difficulties of addressing science to a general audience.

When I was a student, the laws of physics were regarded as completely off limits. The job of the scientist, we were told, is to discover the laws and apply them, not inquire into their provenance. The laws were treated as “given” — imprinted on the universe like a maker’s mark at the moment of cosmic birth — and fixed forevermore. Therefore, to be a scientist, you had to have faith that the universe is governed by dependable, immutable, absolute, universal, mathematical laws of an unspecified origin. You’ve got to believe that these laws won’t fail, that we won’t wake up tomorrow to find heat flowing from cold to hot, or the speed of light changing by the hour.

I have never been instructed as such. I have always been told that the laws and theories came from observational evidence. As a student I have even tested the various classical laws and theories that are simply time-tested (eg. electron diffraction indicating the wave-like nature of electrons and photoionization indicating the particle-like nature of electrons). I have always been told that these laws are provisional. They could potentially change tomorrow; however, the likelihood is slim. And if they do change, there is a discoverable mechanism that shows how it changed.

Note I did not say why. Personally, I think why questions are unnecessary in science and cannot be answered as precisely and accurately as how questions. Ultimately this leads into a rhetorical battle of words, but this essentially rooted in the previous provisional knowledge of science. Scientific knowledge is rooted in operational language. This is due to two reasons: (1) the heavy reliance of observational data and (2) the heavy reliance of concise definitions. More on this later.

If the laws of physics were just any old ragbag of rules, life would almost certainly not exist.

Poppycock. I doubt it has been determined that simply changing the permittivity of space would disallow the formation of molecules that look very much like the metabolic process we observe in organisms. Since that is the defining feature of life-- metabolism-- I think it is a bit rash to conclude that only this set of universal constants are necessary for the universe to produce through time intelligent observers.

This is why I like PZ Meyers' summary of the anthropic principle: "[a] tiresome exercise in metaphysical masturbation that always flounders somewhere in the repellent ditch between narcissism and solipsism." I wish I was a mastery of words like this biologist.

(Note: Peter Woit seems to blame Davies' hang-up on the anthropic principle and multiverses on string theory. I agree. String Theory gets too much hype from pop science authors where there is little experimental linking. But that's a digression.)

In other words, the laws should have an explanation from within the universe and not involve appealing to an external agency. The specifics of that explanation are a matter for future research. But until science comes up with a testable theory of the laws of the universe, its claim to be free of faith is manifestly bogus.

Now we come to the culminating end, and Davies' defeat at supporting his argument. As John Wilkins at Evolving Thoughts points out, Davies suffers from two gross fallacies: an enthymeme and a fallacy of reification. Davies takes the universe and assigns it as having the certain property of possessing laws.

I promised to return to the operational description of scientific knowledge and where it was going in this conversation. Wilkins has allowed me to springboard into this discussion. There is a difference between words and the world. As humans, we often believe our words are the world. But they are not. They are our attempts to describe the world through our words. Mathematics is elegant and much of our understanding of the world can be expressed in such elegant terms, but mathematics is not the world. Mathematics is the language, and physics is the study. The laws do not necessarily exist beyond our observations and use of them. The universe simply is, and though that is such profound statement to many, often inciting displeasure and discontent amongst the populace, it creates none where it is understood.

Note: The Edge seems to be gathering a list of responses.

Letters about NOVA:"Judgment Day"

NOVA (viz. PBS) recently aired a wonderful documentary on the Kitzmiller case. Being someone who has followed closely the entire intelligent design movement, the documentary did not really expand much of my knowledge. However, I found it to be a concise representation of the events surrounding the trial and the occurrences within the court room. I highly recommend it to anyone who desires to know more about the so-named Dover trial.

What I find more interesting, however, are the responses to the NOVA film. I figured that there would be both positive and negative feedback on the documentary, but the level of inanity expressed by the responders was unexpected. PBS Ombudsman has displayed several of the responses from viewers. I recommend reading all of them to create a clearer picture of the necessity of adequate science education in public schools. I have chosen a few that I find necessary to address.

Then, there's the immoral implication of evolution. "Survival of the fittest" follows from evolutionary theory. Evolutionists, to be logical and true to their faith (it takes faith to believe in it since there is no clear, unimpeachable physical evidence for macro-evolution) should see nothing wrong with what Hitler, Stalin, Pol Pot, etc., did in the genocides of millions of people. Since the exterminated ones were "weak," in terms of evolutionary faith, evolution proponents should all just shrug off these murders as being inconsequential (which is how the ones responsible for the murders saw them). But most don't, and the reason is we know those were atrocities. We know to murder another human being is wrong. And we know this because we have consciences given to us by our Creator.

I disagree. Why would "evolutionists" be forced to believe that those who lost their life to socially powerful dictators be considered "weak" and their death ultimately necessary or predictable? Also, I doubt the dictators considered the killings inconsequential considering each murder had a specific agenda or goal to acquire. Yes, oddly enough, though somewhat twisted in certain instances, the mass murders had a certain directive to achieve according to the ones who committed such atrocities.

My question to this viewer would be how does evolution require me to allow such actions to occur? I am not one who thinks dictators are deservedly powerful, and their means are often self-destructive to them as well as destructive to the society. Ultimately, why must I agree with the dictator due to me recognizing evolution as a reality?

And do I not murder because Providence forbids murder, or do I not murder because I recognize the humanity within other individuals? I choose the latter. One could argue that the Divine allowed me to recognize such humanity, but that is really on equal footing with my reasoning acquiring such a position independent of such divine revelation. That is, we simply do not know, and I have no reason to provisionally accept the position of divine revelation when other concepts derived from human reasoning cannot be explained by divine revelation.

The recent Nova special on Intelligent Design vs. Evolution was one of the most blatantly biased pieces of so-called "journalism" or scientific documentary. It was extremely insulting to the idea of Design. The whole tone of it was very sarcastic against Intelligent Design and completely victimized evolutionary thought by the evil villains of religious ignoramuses. It gave precious little air time to ID scientists who have plenty of legitimate research, but gave plenty of time towards evolutionary research. This was especially evident during the reenactment of the trial, when all evolutionary thought was propagated without rebuttal. However, the design theory was constantly interrupted with instances of anti-design narrative and arguments from outside the dramatization.

I invite this reader to read up on the details of the case. They will find (as the documentary does point out) that the prominent figureheads of the ID movement (1) had removed themselves off the defense witness list during the trial and (2) refused to hold an interview with NOVA unless unprecedented guidelines were imposed. Secondly, the evolution research discussed was that which appeared in the trial, or that which occurred during the trial (such as the fossil find Tiktaalik).

Intelligent Design is not religion. The end of the lesson does not offer any path to eternal salvation, claim that we are spiritual beings, or delve into supernatural phenomena; it merely states a theory of the origin of humankind that people in any arena should not be afraid to discuss. If public schools are assuming the responsibility of telling students to tolerate alternative lifestyles (which really has no place in the atmosphere of academia), then they should certainly open up the dialogue of alternative theories of evolution.

A religion does not need to address humanity as spiritual beings or address life after death. Though those are the qualities most modern religions have, a religion is simply anything which deals with non-natural phenomena. Despite your claim to the contrary, ID requires a discussion of non-natural entities, notions beyond the scope of testability and measurement themselves, or else such mechanisms are neither intelligent nor design based on the definitions provided by ID. Thus, if nothing else, ID is religion. And to state that ID is on even an equal plane concerning evidential claims is rather laughable.

As to the program's claims regarding Intelligent Design being taught in the public classroom as a violation against the First Amendment — it was completely out of line. The First Amendment says nothing of the "separation of Church and State." It says "Congress shall make no law respecting an establishment of religion or PROHIBIT the free exercise thereof." It protects religion from being persecuted by the State, not the other way around. If anything, the Constitutional First Amendment protects Intelligent Design being taught in school, and anything less is a violation of said Amendment.

The viewer missed the first clause, also called the Establishment clause, which prevents the government from mandating the instruction of religious thought. Ergo, a separation of church and state. And the second clause (the Free Exercise clause) does not extend into a public school setting. That is, it is true that the student can believe if humans emerged from a sea of Pepsi Cola and the student may not be jailed, fined, or censored for such thoughts. However, the clause does not protect the school's ability to teach the Pepsi Cola origins story since the school is effectively the government.

And the theory of evolution has been left wanting in lieu of proven concepts of science such as the Anthropic Principle (design and purpose in the universe), and the Second Law of Thermodynamics (everything unravels into chaos without an outside source of energy to bring order and purpose).

The anthropic principle only accounts for the existence of observers in a universe and our relation to making observations in such a universe. It is more of an application of science to philosophy of mind more so than an actual advent of scientific inquiry. This viewer's definition of the second law of thermodynamics is a bit off the beaten path. The second law is only concerned with the transfer of heat from one body to another. In an isolated system, heat transfers from the hotter body to the colder body. It requires work on the system to transfer heat from the colder body to the warmer body, and this application of work makes the system no longer an isolated system.

The Sun supplies energy and thus work onto the surface of the Earth. Thus, the Earth is not an isolated system (if we were, there would be no need of wind as temperature gradients would not exist across the surface). Also, concerning entropy and biochemical reactions, I think I recall a lecture on the mechanisms involved in DNA replication. Effectively, the reactions follow normal thermodynamic expectancies, and the side-reactions which give rise to genetic mutation also follow normal thermodynamic expectations. The unmutated DNA (aka "product") is more favorable; however, nature is quirky in that simply because one product is more favorable does not mean it is the only product produced. This is a consequence of the statistical nature of chemical reactions occurring at a given temperature. So, effectively, if I recall correctly from the lecture, the biochemical mechanism which gives rise to mutations in DNA replication is, ironically, thermodynamically sound (But, I will look into this further at a later date, and feel free to correct me in my comments).

Isn't it interesting, when evolutionists speak of ORIGINS they go into a long winded explanation of life on earth and how things operate and function, yet never tell you the source or offer a SCIENTIFIC EXPLANATION OF THEIR TRUE ORIGIN. And according to their own definition of the word science, it's only that which can be TESTED AND MEASURED THAT SHOULD BE ACCEPTED AS VALID. You may be able to test, examine and explain many things, yet if you cannot put the ORIGIN OF THE MATERIALS to the same LITMUS TEST OF EXAMINATION AND MEASUREMENT, then your position is just another theory or religion as well. THEREFORE, LOGICALLY, Biological Evolutionists are forced to do one of two things, they are forced to acknowledge and accept that their position ULTIMATELY cannot be tested according to their own DEFINITIONS AND CANNOT STRICTLY BE CLASSIFIED AS SCIENCE. Or, they are forced to accept as VALID, theories that use the same logical reasoning processes like that of Intelligent design TO OBSERVE WHAT IS OBVIOUSLY DESIGN IN NATURE.

The hypotheses concerning the origin of the starting organic materials necessary for organic life are, indeed, simply hypotheses. Most of these hypotheses are rooted in experimental studies, however. For example, it is not an absurd notion that inorganic materials, such as methane, carbon dioxide, water, and ammonia, can give rise to certain amino acids. Similar results have been shown with other simpler organic materials, and it has been shown that certain clays can catalyze various pertinent organic reactions to abiogenesis studies. But it is the humble scientist who recognizes that such searches would never lead to a definitive scenario concerning the source of beginning organic materials. No, but it gives a provisional concept rooted in experimental evidence, and it is this experimental evidence which makes such scenarios more scientific than creationism via the *poof* mechanism. Secondly, evolution in general applies only to populations that reproduce.

I will never understand an individual who believes that ID is an actual scientific avenue. Only time will tell if it falls by the wayside like other preposterous notions in history or it manages to manhandle itself into school curricula by political and legal persuasion.

What Once Was Few Now Is Many

This blog has cameos at -1:16 and -0:23.

(via Pharyngula)

Much Needed Update

I have been a bit overwhelmed with academics and nearly forgot that I had this blog. But, with the dust settling, I can focus more on my passions and less on my obligations.

I have been perusing the internet for decent tutorials on physical chemistry. I was hoping to find something short and concise and would stress the overall importance after the derivations. Yet, alas, I have not found any to my liking. I might be too picky, however.

I simply desire a good reference on the basics I can point newcomers to so any preliminary/elementary questions can be answered there. For instance, in my current line of work, it would bog me down every time to describe the sign problem with the fermion density matrix in the canonical partition function for the Feynman path integral expression.

However, I guess if one is not pleased with the current selection, one needs to fix the situation themselves. It will be odd sprinkling introductory quantum and the necessary mathematics while commenting on current research, but I guess a challenge is necessary for one to grow.

Chemistry GRE Reflection

I have to admit that the last organic class I had taken as an undergraduate was my freshmen year. Granted, that is still no excuse for not refreshing my memory on the reagents necessary to undergo various reactions (eg. anti hydroxylation of alkenes), but what is done is done.

However, was it me, or did there seem to be more protein chemistry than necessary?