I Found Theoretical Chemistry Blogs!!!

So I did find some theoretical chemistry blogs, and a good handful of them. Once the semester slows down some more, I will begin posting weekly links to interesting posts made by these blogs. Hopefully, it will expand the exposure of these blogs (and mine) and establish a community and network amongst us like-minded bloggers.

My New Blog

I will be in the process of moving over my material to my new blog. It is located here:

Chymico-Physico Elucidations

I'll steal from the first entry the intents and purposes of the blog:

I am a senior in chemistry and physics at Louisiana State University. I am interested in theoretical chemistry, particularly the interface of quantum physics and quantum field theory in chemical systems. I am simply trying to survive my senior year, from taking GREs to writing my senior thesis to fulfilling the last of my requirements to graduate in the spring.

I have owned many different types of blogs, ranging from horribly written poems and fan-fiction to deep philosophical musings on life, liberty, and science. The scope of this new, and henceforth permanent, blog is an outlet for me to discuss the science which truly encompasses and surrounds my interests. So, there will be a lot of discussion on quantum chemistry and other aspects of theoretical chemistry. Hopefully, this will be an exercise to fulfill two goals:

1. Increase my capability to convey science to a generally scientifically literate audience
2. Increase my understanding of the very field I am interested in making a career out of

I am inspired by the many different bloggers at ScienceBlogs. Personally, I know of no such blog concerning theoretical chemistry. However, please tell me if you know of any.

Louisiana and the Future of Science Education May Be At Risk

I am a strong proponent of proper science education. Science is an orchestrated methodological study of the occurences and phenomena experienced by both ourselves and our instruments. It rests in operational language based on empircal backings and theoretical frames with no invocation of a priori intuitions or expectancies.

This is the fabric of science. Yet, there will always exist people who desire, whether with ulterior motives or due to their lack of comprehension, to ruffle the very fabric of the scientific enterprise. Science is used to such ruffling, but sometimes the demagogues in control are too convincing for the ignorant and naive public. Thus, their pseudoscience becomes commonly accepted amongst the non-scientific minded, and accepted into the minds of the laymen as if the mechanics of the pseudoscience was how science operated and function.

Intelligent design creationism (IDC) is the major culprit of the modern era, moreso than persistent quantum physics and relativity deniers and people who still think the caloric is a measurable quantity. It plagues this nation like an annoying flea, hopping from location to location to test the waters of local, state, and federal governments.

Through the decades, creationism has tested itself in the higher courts and utterly failed to present itself as a valid source of instruction. Again and again, its blatant errors being pointed out by not only those who are at the top of their fields of speciality but also by their very students. Even I who have had very little formal training in biochemistry and evolutionary biology can see the errors in those respective fields.

IDC is a mockery not only of the sciences which they attempt to represent in their faux mannerisms, but IDC also makes a mockery of the scientific method in general. By attempting to circumvent the necessary requirement of determining the existence of a designer but instead concentrating on hypotheticals of "designed systems", they fail to meet the requirements of developing a proper operational definition backed with empirical as well as theoretical framework for support. IDC is all presentation with no calculation and no attempt to present itself honestly to an informed audience in the fields tangentially addrsssed by the proponents of IDC.

But why do I bring up IDC? Because the governor-elect of Louisiana, Bobby Jindal, has stated that intelligent design is on equal footing with the theory of evolution as a scientific topic to be taught in science class. I fear that the flea infestation is about to begin. Though I do plan on continueing addressing modern research concerning the interface of chemistry and physics, I have a deep commitment to proper science education and the future of my state. Expect more diverging topics in the future.

The Templeton Foundation: Purpose of Universe?

I guess I will have to wait twenty or more years before I could get on the list of "leading scientists and scholars" according to the Templeton Foundation, but I would like to chime in on the "Big Questions". This week's question is: "Does the universe have a purpose?"

The answer is simple, really. The universe does not have a purpose. The universe's only concern is to minimize the potential energy across the entire space time continuum. This is the only concern of the universe, and it is from the mechanics of this minimization which arises localized packets of "energy beings" or "energy peaks" such as ourselves. Our thoughts, feelings, friendships, and knowledge are all due to a localized peak in a vastly minimized energy spectrum.

So, there is no ultimate purpose. We could create a purpose for our packet of energy, but this purpose does not transcend ourselves beyond the scope of our humanity and level of sentient thought. We could create meanings from our biological consequences, but they are no more beyond us than our muscles or epidermis are beyond us. No need to invoke immaterial spirits or sprites and forces unable to be studied under scrutiny when the reality faces us squarely in the face.

The universe could obliterate us in a second without a care. The universe existed before we evolved from Cro-Magnon ancestors, and it will exist after we die, and it will continue to exist even if humanity becomes extinct. It seems rather chauvinistic to think the universe cares about us, and it is really disturbing to see people act like it does.

Just some personal reflections on the "big question". Go design your own purpose in life. It is just as correct as the next guy's purpose.

The Chicago Moron on Dawkins and Militant Atheism

I previously mentioned at the beginning of the semester a trend in student journalism toward folly and doltishness. Within a one-week period, Yale, Ohio, and my school managed to publish outlandish claims. I commented on the Yale article. Now, it is time to address an opinion editorial from the Chicago Maroon, the University of Chicago student newspaper. Just like before, I will address each claim developed in the editorial.

The tradition of atheism is certainly long-standing and stretches back at least as far as Western classical antiquity, but the modern trend of liberal, militantly atheist academics and of “scholars” who declare war on religion—or, more simply, a person’s belief in God—is vicious, disrespectful, and an abuse of the scholarly platform.

Somehow, as an academically inclined individual, I am supposed to believe that I am being viciously disrespectful anytime I remark about the inanity of belief in god? If I am, so be it. I would rather be disrespectful to entities and ideas which I see are socially and ethically unhealthy than become an appeaser to the evils wrought by chronic religiosity.

Dawkins insists that our beliefs should be based on evidence, specifically that which can be tested and definitively proven by the scientific method...What Dawkins fails to realize, though, is that no science, however advanced or “enlightened,” can ever prove the existence of God.

Here is a subtle admission made by Lee. To Lee, knowledge is determined by more than empirical methods. That is nice to know forthright. However, if he had realized he made this admission, he would then realize his entire grief with Dawkins is the discrepancy between their epistemologies. As a self-reported "analytic philosopher", I am a bit surprised he did not realize this.

Dawkins, like other like-minded individuals, demand a high level of empiricism in determining knowledge; that is, Dawkins desires a high-level of precise knowledge. I need to make a distinction between precise knowledge and imprecise knowledge. Imprecise knowledge can be considered any constituent which requires accepted definitions or beliefs as opposed to elements which stem from the scrutiny of empiricism. Language is an imprecise knowledge based on this definition. Words have meanings and associations that have been determined through the course of human history. Essentially, our ancestors bequeathed to us their vocabulary and grammar the same manner in which we will give our vocabulary and grammar to the next generation. These meanings are accepted universally. A cat is a cat because we say it fits our definition of being a cat. Thus, any sense of nomenclature is an imprecise knowledge, meaning we simply use such items as tools to communicate and connect patterns of thought together.

Science is a precise knowledge which, like logic, suffers from the aspect of being corroded by imprecise language. As much as we as scientists try and maintain a certain diction and jargon to separate the imprecision of colloquialisms from ruining our ability to communicate science, it is inevitable that imprecision prevails. hence, the existence of Creationism and the persistent mantra of evolution is just a theory.

But I digress some. It is true that Dawkins requires precise knowledge in making epistemological claims, such as knowing the existence of God. To Dawkins, it is better to know
whether something exists rather than simply believe it exists without any ability to determine whether it exists or not. This segues into Lee's next sentence:

Trying to use the limited perspective of humanity and the simple scientific methods we have at our disposal to prove beyond a shadow of a doubt that God exists is a waste of time. The nature of God is found far beyond the reach of even the most advanced scientific instrument.

There is one ultimate premise introduced by Lee here: humanity is limited (the claim concerning the scientific method is an easy corollary). Now, this instigates a question: Is humanity truly limited? Indeed, we are limited by our size and physical capacity; we can not do everything ourselves. However, we can develop tools and methods to achieve an expected end. That is the basic premise of engineering. So, as engineers, are we truly limited? I would argue no. Humanity is not ultimately limited. We are temporally limited, but being temporally limited does not easily translate to being completely or truly limited. Let us look at some case examples.

I am walking through the woods and happen to come upon a banana tree. I see a deliciously ripe banana at the top of the tree, but the tree is twenty feet tall while I am only six feet. What am I to do? I could obtain a ladder to help aide in my advent. Or, I could utilize a mechanical cherry picker to lift me to the top branches. In this example, ladders have been around in various shapes and constructs for centuries. The mechanical lift is relatively new in terms of the history of humanity. Where a ladder suffers from certain construction constraints (mainly stress as the ladder becomes "taller" and has more "lean" on a wall), a mechanical lift can be constructed overcome the shortcomings of the ladder. So where medieval man could only climb so high on a ladder (or build a certain level of stairs), modern man can construct a better mechanical lift. It follows that medieval man was temporally limited to the extent of technologies available to him versus modern man who has modern technologies. In the future, I could possess a fuel-efficient jet-pack to springboard myself to the top branches. Thus, my future self is temporally saturated versus the modern me who is, in comparison to the future me, temporally limited.

This occurs throughout the history of the sciences as well as other disciplines. The Native American civilizations knew nothing about the European civilizations until the Spanish conquistadors arrived. Thus, those Native American civilizations were temporally limited in their knowledge concerning Europe. It was not until the arrival of colonists and exhibitions did the Native Americans become aware of the existence of foreigners and distant lands.

So, where am I getting at with this digression? Simple. Were the Native Americans ultimately limited? No, they learned about the foreigners. Was I ultimately limited in those three different time periods to get the banana? No, I was only limited to the variety of technologies available. But overtime, these limitations decreased. Essentially, things expanded beyond the limits.

This is the pursuit of science: to go beyond the limits of human knowledge to forge new knowledge. And the major driving force of science to develop this new knowledge is, indeed, the scientific method. Empiricism is the copilot of science. To science, our only limitations are the available current knowledge and our ingenuity.

Thus, it amazes me for someone to say bluntly and factually that God is beyond human comprehension. Is it perhaps instead that God is simply currently unable to be comprehended due to a temporal limitation? Or, as Dawkins tends to assert which makes people unhappy, science has indeed breached this temporal limitation and have seen the lack of god everywhere?

Moreover, Dawkins incorrectly applies the sciences of biology, chemistry, and physics.

For instance, instead of using evolution and natural selection as examples of a harsh, Godless reality, he should realize that the complexity, intricacy, and beauty of a living organism further reinforce the reality of the supernatural. It also leads someone with an open heart and mind to the unmistakable conclusion that the cell or molecule under observation had to have been designed before it ever evolved to its current state.

We have three gauche concepts expressed by Lee above: complexity, intricacy, and beauty. How is a cell beautiful? How is a conjugated alkane chain complex? How is the Krebb's Cycle intricate? I would have to know the answers to these specific questions before fully analyzing his argument.

However, as a cursory observation, I would like to see what he means by being designed as opposed to having been evolved. Did God simply insert the Krebb's Cycle into a cell? Did God fashion the cell together mechanically, piece by piece, with his own (magical?) hands? Did humans simply appear out of the sky (or from the dirt, as Genesis implies) instantaneously? What is the mechanism by which God "designed" these things which people claim are "intelligently designed"? Those would be standard questions posed by one who demands empiricism to substantiate truth claims over those who desire other methods.

This is what Dawkins and other ID critics ask in their books and criticisms. If those who see design in nature do not desire to speak in terms of science but instead bury themselves in rhetorical devices and imprecise reflections, than so be it. There are people who demand strictness in knowledge and those who do not. One easily sees where the other lies upon the words they choose to answer the questions in the preceding paragraph.

If he wants some rational arguments for faith, I would encourage Dawkins to read some St. Thomas Aquinas before vomiting up his next accusation against religion.

Interesting. For someone who claimed to have read The God Delusion, Lee must have forgotten that Dawkins devoted an entire chapter to deflating the claims of Thomism.

To give an example of one of Dawkins’s logically flawed arguments, one need look no further than the fourth chapter of The God Delusion. One of his main claims is that because the universe is so enormous and contains so much information and substance, God must also be enormously complex. This complexity predisposes God to extreme improbability. I, along with a host of analytic philosophers, do not understand why this has to be so. Must God be infinitely complex to have designed something more complex than himself? Why does his simplicity prevent him from doing certain things? Michelangelo painted the Sistine Chapel, Handel composed the Messiah, and Gustave Eiffel designed and built the magnificent Eiffel Tower. In each of these cases—and there are countless more—one person produced something so much more intricate than himself that the world still marvels at his ability and vision.

No surprise really that I see a hint of Plantinga in Lee's rhetoric. However, Lee, like Plantinga, nearly straw man Dawkins' intent. Dawkins wrote in The God Delusion concerning the Ultimate Boeing 747 gambit:

1. One of the greatest challenges to the human intellect, over the centuries, has been to explain how the complex, improbable appearance of design in the universe arises.
   
   
2. The natural temptation is to attribute the appearance of design to actual design itself. In the case of a man-made artefact such as a watch, the designer really was an intelligent engineer. It is tempting to apply the same logic to an eye or a wing, a spider or a person.
   
   
3. The temptation is a false one, because the designer hypothesis immediately raises the larger problem of who designed the designer. The whole problem we started out with was the problem of explaining statistical improbability. It is obviously no solution to postulate something even more improbable. We need a "crane" not a "skyhook," for only a crane can do the business of working up gradually and plausibly from simplicity to otherwise improbable complexity.
   
   
4. The most ingenious and powerful crane so far discovered is Darwinian evolution by natural selection. Darwin and his successors have shown how living creatures, with their spectacular statistical improbability and appearance of design, have evolved by slow, gradual degrees from simple beginnings. We can now safely say that the illusion of design in living creatures is just that – an illusion.
   
   
5. We don't yet have an equivalent crane for physics. Some kind of multiverse theory could in principle do for physics the same explanatory work as Darwinism does for biology. This kind of explanation is superficially less satisfying than the biological version of Darwinism, because it makes heavier demands on luck. But the anthropic principle entitles us to postulate far more luck than our limited human intuition is comfortable with.
   
   
6. We should not give up hope of a better crane arising in physics, something as powerful as Darwinism is for biology. But even in the absence of a strongly satisfying crane to match the biological one, the relatively weak cranes we have at present are, when abetted by the anthropic principle, self-evidently better than the self-defeating skyhook hypothesis of an intelligent designer.

In short, Dawkins indicates that evolution via natural selection explains observable complexities in biology successfully compared to design theories. Then, Dawkins indicates the triviality of nearly improbable statistics for "finely tuned variable" due to the anthropic principle, thereby illuminating such confusions espoused by design proponents. It follows, then, that Dawkins' argument comprises of only the classic "Who designed the Designer" question. That is, Dawkins reduced the entire design argument into question begging: a designer designed the universe because the designer was un-designed. Or, in more succulent terms, Dawkins discredits the notion that the universe is designed as well as questions the aspect that a God is undesigned.

So, I fail to see where Lee gets his "infinitely complex" verbage from. Dawkins presented an argument questioning if God is necessarily uncaused. Though Lee would say yes, strict scrutiny yields otherwise.

I encourage the theists of this campus to stand up against this type of insidious “academic” persuasion and firmly assert the existence of God.

If I do indeed get accepted and attend University of Chicago for graduate studies, I will gladly be the nuisance of a student who will persistently call anyone out who asserts that the existence of God is true and not a mere opinion. As a "peer" in terms of age, it saddens me that Lee presents the foolish side of those who study science. He is no "peer" by my standards, though, because I have enough sense to back up my own words and not expect a student newspaper to publish my trash.

(Hat tip: Pharyngula)

Freshman Inanity at Yale

Note: This post is copied from my former blog The Natural Skeptic. I reposted it for future reference.

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This month seems to be the month for poorly written opinion pieces at college newspapers. My school had one concerning same-sex marriage, and Ohio University had blatant racism flash their student newspaper. Now, a freshman at Yale places a foot in his mouth concerning atheism and its "lack" of morality.

He writes:

Christians and other theists have raised the objection that naturalistic materialism — the notion that only the physical world exists — can provide no foundation for morality. That’s not to say that naturalists cannot behave morally, but merely that they can have no real and consistent reason for behaving morally. As this has been a long-standing and widespread objection to naturalism, it would seem only reasonable to expect atheists to devote careful attention to the question of morality.

Atheistic philosophers have, indeed, spent time describing a naturalistic morality. Where has this kid been? Our moral tendency develops as a result of our ability to possess empathy toward others. It is a natural human condition to project oneself into the situations experienced by others, because chances are we have experienced said situation. Our knowledge grew not from revelation or "magic" but by human experiences and human observation. We know stealing requires removing possession of property from one individual to another. We know rape involves sexual penetration and violence. We know the result of murder is the vanquishing of a life. We have experience and knowledge of the results and outcomes of given circumstances.

Morality is nothing more or a less than a reflection of knowledge. It is not a gene, and it is not a a deus ex machina. I find it a bit repugnant to declare that the sole reason beings are moral is due to posthumous judgment by a mythical being who supposedly walked the earth and floated into the sky or any other fancy mythology one can contrive. I act righteously because I have the ability to discern how the other individual desires to be treated. I act according to the law because that is what I accept as being a citizen of the nation. No need to call forth Jesus, Zeus, or any other deity of desire.

Concerning our ability to choose to act rightly or wrongly, the author writes:

C.S. Lewis puts the matter nicely: “If a man asks what is the point of behaving decently, it is no good replying, ‘in order to benefit society,’ for trying to benefit society, in other words being unselfish (for ‘society’ after all only means ‘other people’), is one of the things decent behaviour consists in; all you are really saying is that decent behaviour is decent behaviour.”

You are certainly free to disobey the moral tendency and do wrong and violence on to others. However, with every wrong committed a person exists who desires justice for the wrong. Hence, our morality stems from the social contract, an extension of our human empathy.

The freshmen enters into the famous is-ought paradigm: "naturalistic materialism gives no basis for this ought." Indeed, no such system has a true basis for an ought, and he is blinded to think religion does. The simple existence of a system or parameter does not necessitate the individual to follow said parameter. In the Christian tradition, no one is forced to act morally, that is there is no forced reason to commit oneself to ought statements. It is only inner volition which causes one to follow the oughts prescribed by Christianity, Judaism, or any other flavor of theism imaginable. Why limit the is-ought problem to only naturalism when it equally applies across the board? As stated previously, the individual can fall outside of the bell curve for following the natural moral tendency, but our social order determines the reaction to this individual's actions. Again, the social contract is held.

The author fails to convince the reader that morality is dependent upon God. The onus is on him to demonstrate how theism transverses the is-ought problem of philosophy. I am content with my naturalistic morality and its source, and I am content following the ought parameters established. I have no need to call forth supernatural entities to determine not to kill, to bathe every day, and to conserve energy and materials. Does the author only act morally because he is afraid of the lake of fire? What a prick to act out of fear of the unknowable and unseen and then condemn those who act due to their knowledge of the world and humanity.

The NWF in Greenland

During the summer, a few members of the National Wildlife Federation took a a trip to Greenland to observe firsthand the effects of Global Warming on the region. They have produced YouTube videos of their obersvations and time spent. I have included them below.

Studying for the GRE General Test

I am taking the GRE General Test tomorrow, and I wish I had prepared more for the verbal section. If I could redo everything all over again, these are the changes I would have done.

I would have started early on vocabulary. How early? I am thinking starting a vocabulary building excercise when I was in high school. yes, that would not only have helped me for the SAT, but also build my vocabulary for writing assignments and the GRE General. Now, I am reduced to recognizing key roots in words to guess a general meaning. Though not a bad technique, knowing the actual definition would make the analogies and antonym sections a little less difficult.

I would have started early on building my analytical writing skills. ETS gives out the entire pool of topics for both the issue and the argument sections of the analytical writing section. had I known this before a week ago, I would have started giving preliminary answers to each question to develop an idea of what I would address on test day. Also, this would keep building the necessary skillset to answering each anlytical writing section to satisfaction.

I let the GRE General slip by some. Though rumor has it that the GRE General is not as important as the subject tests are, I seriously doubt any school would admit a graduate student who scored below a 400 on the GRE verbal.

Wish me luck. After the GRE nonsense is all done, I'll post some chemistry topics of interest.

Hello World

I am a senior in chemistry and physics at Louisiana State University. I am interested in theoretical chemistry, particularly the interface of quantum physics and quantum field theory in chemical systems. I am simply trying to survive my senior year, from taking GREs to writing my senior thesis to fulfilling the last of my requirements to graduate in the spring.

I have owned many different types of blogs, ranging from horribly written poems and fan-fiction to deep philosophical musings on life, liberty, and science. The scope of this new, and henceforth permanent, blog is an outlet for me to discuss the science which truly encompasses and surrounds my interests. So, there will be a lot of discussion on quantum chemistry and other aspects of theoretical chemistry. Hopefully, this will be an exercise to fulfill two goals:

1. Increase my capability to convey science to a generally scientifically literate audience
2. Increase my understanding of the very field I am interested in making a career out of

I am inspired by the many different bloggers at ScienceBlogs. Personally, I know of no such blog concerning theoretical chemistry. However, please tell me if you know of any.

I have a Technorati Profile, and this link allows me claim it. So, disregard this.

Retiring This Web Log

I am in the process of retiring this web log. I'm changing my scope to reflect the science I am more passionate about (chemistry) than the science which is the primary target of idiocy (biology). So, I'm reviewing what I have written and the ones I like will be moved with me and the ones I do not will remain until I decide to delete everything.

I'll post the URL to my new blog when I come up with a title.