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A Reflection on Biological and Chemical Networks

The history of science can be viewed as a large, ever-changing network, with increasing knowledge of seemingly unrelated fields shaping the direction of scientific research in the modern day. We often hear of the “Hierarchy of Science,”  made humorous by the popular xkcd comic, of how biology is applied chemistry, which is simply applied physics, which in turn is just applied math.

However, these connections aren’t simple directed edges – they go both ways (as much as the physicists and mathematicians would say otherwise). As a senior double majoring in Biology and Chemistry, I am forced to see connections between these two fields on a daily basis. This is true especially now as I consider the current state of the life and physical sciences, most especially now as I am going to enter either the job market or research, jumping to the node that will hopefully connect in the future to the most pressing and relevant scientific work.

So where do my peers and I go from the Ivy Tower on the Hill? In heading towards the future, we first turn to the past. We now speak of biology and chemistry in coexistence, in networks, but this certainly wasn’t the case 50 years ago. Let’s look at synthetic organic chemistry, a field I considered entering, as an illustrative example. The origins of that field, and indeed chemistry in general, lie in the concept of the atom, of a fundamental particle with certain physical properties. Motivated by physics, scientists largely focused on analyzing and understanding individual, pre-existing molecules. We discovered the concept of chemical structure, especially that of carbon lattice structures, the breakthrough that ignited the field of organic chemistry. Synthetic organic chemistry followed soon after, with an explosion of research in the mid-nineteenth century on the creation, optimization, and isolation of single chemical species in a series of defined chemical reactions.

But today I am told (albeit very informally and off-the-record), that pure, traditional synthetic organic chemistry is now a dying field. Why? Because chemistry is now moving towards the field of biology (incidentally, where all the money is now) – towards the study of systems. New chemistry is emerging out of biology and vice versa, new fields like synthetic biology or systems chemistry, in which complex dynamic phenomena are expressed by a group of reactions. The goal now is to create a whole system of chemical systems with emergent properties from the interactions of different chemical networks. Instead of bemoaning chemical mixtures (the old chemist’s mantra: purity, purity, purity), we now desire engineered chemical networks.

Thus, the study of networks is becoming ever more relevant, especially as academic fields coalesce and influence one another. We see the same models that apply on the macroscale, in economics and social networks, on the microscale, in biology and chemistry. For instance, we see Braess’ Paradox at work in systems chemistry. After correcting for reversible pathways (i.e. chemical equilibria), researchers have used computational methods and discovered the same counter-intuitive result: enhanced product formation when a chemical pathway was removed, and decreased product formation when a pathway was introduced. The paradox is also encountered in nanostructures, in semiconductor mesoscopic networks. Just as car drivers seek to minimize time spent on the busy road, molecules seek to minimize their free energy, and both “individual” actions may be influenced by interactions with others.  These results have a profound impact on drug discovery and design, the field that I want to enter one day. Drugs are often designed to interrupt a reaction pathway by inhibiting an intermediate; however, by the Braess’ Paradox, there may be circumstances in which the synthesis of the final, deadly product is made more efficient. In some cases, we may literally be engineering our own deaths, or at least hastening the process. 

We do have to keep in mind though, that the examples we have discussed in class are linear, and we look at behavior in the steady-state. However, we should still keep networks in mind, especially when thinking about our future careers. Looking at the research questions within drug discovery in journals, though I’m no certified expert, I see a real push towards using computational methods to understand physiology and disease from the level of molecular pathways and regulatory networks in cells, tissues, organs, up to the entire organism. Especially after the sequencing of the human genome, there has been a tremendous investment in genomics and screening technologies to develop large databases of protein interactions and differential gene expression in cells. The fields range from the more popular topics of metabolic networks to the more esoteric ones, like evolutionary game theory. We speak of humans maximizing utility or happiness, and we investigate now too if cells maximize their own version of “utility,” or molar yield of pathway products (seems like they don’t). We no longer speak of science in isolation anymore – it’s all about the networks.

I like to think of the different sciences as clusters of interconnected nodes once held together by weak bridges, the occasional collaboration, the awkward biophysicist (although these nodes definitely still exist). However, the connections between fields are clearly no longer weak (for that, God forbid, would violate the principles of strong triadic closure). It’s time to reshape our old Hierarchy into a new paradigm, a Network of Science, one we should take care to observe as we leave Cornell and enter the real world.    

 

 

http://chemistry.st-and.ac.uk/staff/dp/group/page1/page1.html

http://www.nature.com.proxy.library.cornell.edu/nchembio/journal/v3/n9/full/nchembio0907-521.html

http://link.springer.com/article/10.1007%2Fs10910-010-9746-7#page-2

http://www.pubfacts.com/detail/22913510/A-new-transport-phenomenon-in-nanostructures:-a-mesoscopic-analog-of-the-Braess-paradox-encountered-

http://www.nature.com/nbt/journal/v22/n10/full/nbt1017.html

http://www.nature.com.proxy.library.cornell.edu/nature/journal/v462/n7274/full/462736a.html

http://vcp.med.harvard.edu/braess-paradox.html

http://www.sciencedirect.com/science/article/pii/S0022519307006340

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