Life in the Context of Thermodynamics

I remember now that I made a wordpress account for voicing out my philosophical inquiries regarding the nature of God. It was an emotionally stressful night that finally led me to write a blog entry. However, I let this account gather dust because I was afraid that the people who raised me as a conservative Catholic would happen upon this page and be extremely disappointed. Perhaps my high school self would be disappointed as well. But in time, I have learned to accept that I am an agnostic. I’ve heard most of the arguments for the existence of a God and I’ve pondered on them (mostly before exams because my brain loves to distract itself with philosophical musings when it’s working on full blast).

One of the arguments I used to hear often was that life is too complex to have arisen on its own. There must be an intelligent designer that engineered the mechanisms of life processes. I found this reasoning disconcerting because it assumes a being that we can neither prove or disprove to exist. We just need to accept the limitations of Science in answering this fundamental question regarding life.Even if I try forgetting this question, it always comes back to haunt me.

How do you reconcile the complexity of life with the Physical laws that govern the universe?

I recall even asking this question when I had the dengue fever. In Chem 16, we were taught the basics of thermochemistry and it was then that I wondered how the 2nd law of thermodynamics seem to contradict life itself. The entropy of the universe is always increasing but why is life incredibly complex? In retrospect, I think this question stems from my failure to completely understand the second law. Organisms are open systems where energy and matter can flow freely; the net entropy of the universe still increases despite a local decrease in entropy.

This is where non-equilibrium thermodynamics come into play. I was introduced partly to this concept while reading Biochemistry by Mary Campbell and was completely enamored by it when I read quanta magazine’s article about Jeremy England’s take on this issue (https://www.quantamagazine.org/20140122-a-new-physics-theory-of-life/). According to him, life is not just consistent with the laws of thermodynamics; they DEMAND life to exist.

In my capacity as a biology student to understand what was going on, I think that when a system is pushed very far away from equilibrium through an input of energy, it can organize itself into something more complex so as to dissipate excess energy more efficiently. To illustrate, think of a mixture of biooligomers in solution. The number of favorable reactions in that system is dwarfed by millions of reactions that happen within a bacteria of comparable mass. Hence, the net entropy in living organisms is far greater than that of biooligomers in solution.

I think it’s humbling to think of life simply as efficient machines to increase the entropy of the universe. A lot of people would not probably agree with me when I say I find this extremely satisfying to think about. Here is a set of fundamental laws that can explain the dynamic complexity of life in a few set of equations. While it doesn’t answer the very important question of why the universe had such low entropy during its inception (was it because of God? :O), it does put life in a different context–an important framework that facilitates scientific inquiry.

Refolding of Proteins to their Native State

So I spent a solid two hours just trying to get reliable sources on this article I saw on the internet where researchers supposedly “unboiled” an egg (http://www.cnbc.com/id/102364302). I happened upon that article a few days ago when my Orgo chem classmate shared it on Facebook. My initial reaction was that of amazement. One of the first things you learn in basic biochemistry is that it’s extremely difficult to renature a protein once it has denatured. The free energy landscape consists of numerous energy minimas where a protein can get trapped in when it attempts to refold properly. Armed with this knowledge, my excitement slowly died down to skepticism. CNBC is a reliable news network but it often happens that journalists misrepresent recent discoveries in Science. I had to understand what was going on.

This article gnawed at me ever since I read it because the headline sounds too good to be true. So I tried reading on the vortex fluidic device (VFD), the machine that was used in the experiment. However, it’s an extremely difficult read unless you’re a Chemist or an Engineer. One of my frustrations as a biology major is that I’m not equipped with the technical knowledge to understand complex machines. I supposedly have “biotechnology” in my degree as well but I think I only have superficial knowledge to actually merit that title in my diploma when I graduate. I once attempted to read a paper on a continuous process for producing biofuels from algae a few years ago and I can’t even say I understood 25% of what the authors wrote. There was simply too many references to unit operations and chromatography techniques that I have no prior knowledge on. I downloaded that paper and hoped that someday I will be able to understand what the researchers did.

Going back to the article I read, the VFD is essentially a machine that spins liquid into a very thin film in order to speed up a chemical reaction. You get a similar vortex when you mix powdered drinks like Tang in a glass of water. It’s just that this process is more controlled. I eventually found a freely available preview page from the original paper published. It included Weiss, who co-authored the first Chemical Biology textbook as my batchmate, Mao, pointed out (I won’t digress again from the discussion. I’ll probably just make another entry about my fascination with Chemical Biology in the future)  Being a preview page I only got a glimpse of the paper but I think this summarizes what they did:

“We imagined applying the VFD with a similar range of input energies to the refolding of proteins…”

Since the folding of a protein to its native state is just a thermodynamic process, I think they just made the the folding more favorable. However, I’m really disappointed because I can’t get into the details because the paper is behind a paywall. While I understand that publishers need to get money from papers, I hope that my university can provide us with subscriptions to these publications. We are a state university after all