On Corn & Carbon

In the fascinating, free 1st chapter of Michael Pollan’s new book The Omnivore’s Dilemma, he makes the point that American industrial agriculture is largely based on corn. Most of our livestock species are fed on corn, and a laundry list of comestibles contain additives derived from it. He goes on to explain that it is possible to quantify how much corn one consumes directly or indirectly due to the type of photosynthesis that corn engages in.

All forms of photosynthesis involve the fixation (harvesting) of carbon which is made into simple sugars subsequently consumed for energy. Photosynthetic types can be categorized, according to the specifics of the carbon fixation process, as C3, C4, or CAM. Corn is a C4 grass. This means that it has developed an adaptation to deal with dry, arrid climes. Specifically, the fixation of carbon is achieved first by PEP carboxylase, which basically buffers it. Plants absorb carbon in the form of CO2 through holes on their leaves called stomata. However, water can also be lost through these pores, so they must be closed to prevent dehyrdation. During these periods, the lack of available CO2 can become a problem because the costly reverse reaction of photosynthesis: photorespiration, occurs. Not so for corn and it’s C4 cronies; their buffer of carbon prevents wasteful photorespiring. In addition to this benefit, it turns out that there is another significant consequence of such a strategy: indiscriminate absoprtion of carbon isotopes.

Most (98.9%)of carbon is C-12, it has 6 protons and 6 neutrons. Almost the entirety of the remaining 1.1% is C-13, 6 protons and 7 neutrons, a mass difference of 1.6749 × 10^−27 kg. Most plants preferentially absorb C-12, but not C4 plants. Given such a minute difference between these atoms, it is quite amazing that plants have any ability to discriminate between them. It turns out that differences in the rate of (1) diffusion into the stomata, (2) absorption of C02 by water in the plant, and (3) diffusion of carbon out of the plant is what makes the difference1. Beyond these passive properties, PEP carboxylase has somehow managed to develop a bias in which type of CO2 (preferring C-13) it fixes. It is damned astounding that an enzyme can have such specificity, discriminating such a small mass difference (there is no charge & so probably not much of an electron-shell-structure difference). The end result of all this is that the ratio between the two isotopes in, for example, your flesh is informative about what type of plant supplies most of your carbon.

It is unclear if monitoring this value will ever be relevant to the individual. The potentially deleterious effects of eating large amounts of corn on health and well being are up for debate. It is immediately interesting, however, from a socio-cultural standpoint. Mr. Pollan makes this point quite well in an article he wrote for The New York Times2. He points out that the consequences of industrial monoculture farming are probably not sustainable in the long term. I firmly believe that questioning the long term feasibility of our life styles is important for continued human survival and happiness. The ability to measure corn consumption on a large scale will allow us to monitor and understand this potential problem in a very direct way.


1. Farquhar, G.D., Ehleringer, J.R., & Hubick, K.T. (1989) Carbon Isotope Discrimination and Photosynthesis, Annual Revews of Plant Physiology and Plant Molecular Biology, Vol. 40 pp. 503-537
2. Pollan, M. (2007) Unhappy Meals, The New York Times (http://www.nytimes.com/2007/01/28/magazine/28nutritionism.t.html)

On the Difficulty of Understanding Evolved Objects, Namely Biology

(a map of yeast protein interactions1

Imagine a machine designed to slice bread which, through some pathological design concept, posessed the trait that its blade was also somehow its power source. Removing the blade/power supply would clearly render the device inoperable, but understanding how this action had achieved its effect would be quite difficult. This is the essence one of the main problems which confronts anyone interested in teasing apart the complex web of interactions that is molecular biology.

For whatever reason, whether it be a basic feature of human intelligence or simply a sort of paradigmatic immaturity as a species, we tend not to design things in the same way the evolution does. By that I mean employing multi-purpose parts in the way the fictional device mentioned above does. One human-designed object posessing that property is the bicycle. There, it so happens, that the rotation of the wheels actually tends to keep the bike up-right. The wheels are like gyroscopes: their rotational intertia tends to keep them in their plane of rotation in the same way that the linear inertia of an object moving in a straight line tends to keep it on that trajectory. In the sense that the idea of the bicycle has retained this accidental advantage, it resembles an evolution-designed object. However, examples of human engineering that fit this category are few.

In biology, it appears, this type of overlapping, redundant functionality is the norm. For example, insulin is a molecule which is well known to many layman as being involved in the metabolism of glucose: the regulation of blood sugar. However, if one simply consults the wikipedia article on insulin, it immediately becomes clear that this is far to simple a tale. The functions of insulin listed there are:

1. Increased glycogen synthesis – insulin forces storage of glucose in liver (and muscle) cells in the form of glycogen; lowered levels of insulin cause liver cells to convert glycogen to glucose and excrete it into the blood. This is the clinical action of insulin which is directly useful in reducing high blood glucose levels as in diabetes.
2. Increased fatty acid synthesis – insulin forces fat cells to take in blood lipids which are converted to triglycerides; lack of insulin causes the reverse.
3. Increased esterification of fatty acids – forces adipose tissue to make fats (i.e., triglycerides) from fatty acid esters; lack of insulin causes the reverse.
4. Decreased proteinolysis – forces reduction of protein degradation; lack of insulin increases protein degradation.
5. Decreased lipolysis – forces reduction in conversion of fat cell lipid stores into blood fatty acids; lack of insulin causes the reverse.
6. Decreased gluconeogenesis – decreases production of glucose from non-sugar substrates, primarily in the liver (remember, the vast majority of endogenous insulin arriving at the liver never leaves the liver) ; lack of insulin causes glucose production from assorted substrates in the liver and elsewhere.
7. Increased amino acid uptake – forces cells to absorb circulating amino acids; lack of insulin inhibits absorption.
8. Increased potassium uptake – forces cells to absorb serum potassium; lack of insulin inhibits absorption.
9. Arterial muscle tone – forces arterial wall muscle to relax, increasing blood flow, especially in micro arteries; lack of insulin reduces flow by allowing these muscles to contract.

Even as I’m writing this, I have come across an article in Nature about a previously unknown action of insulin in a biochemical pathway involving a protein called TORC22.

Some would say that I am pointing to an inherent flaw in reductionist thinking. That our tendency to search for the smallest parts in order to build up a description of everything from the universe itself to the many varied forms of matter we find within it, cannot hope to penetrate these massively interconnected systems. It seems true that our current notions of what the smallest parts are will lead us to descriptions which are simply too large scale to be intuitively understood. However, this doesn’t necessarily point to a flaw in reductionism, especially since the alternative approach of holism doesn’t seem to offer any ways forward which circumnavigate such a problem. Rather, I would suggest that we need to fundamentally shift the way we think about evolved things in order to make significant progress towards understanding that which falls under the blanket term of “complex systems.”

Early in the last century, physics was spurred on by a shift in thinking: quantum theory, often thought of as one of the canonical scientific revolutions. I am hopeful that this century, or some time in mankind’s future, will do the same for biology, and complexity in general.


1. Durrett, Rick. Random Graph Dynamics New York: Cambridge University Press, 2006.
2. Dentin, R. Liu, Y., Koo, S.H., Hendrick, S., Vargas, T., Heredia, J., Yates, J. III, Montiminy, M. (2007) Insulin Modulated gluconeogenesis by inhibition of the coactivator TORC2 Nature 449: 366-369

Trees Can Talk to Each Other

How do plants converse with each other? As human beings, we posses probably the most sophisticated communication abilities of any species on the planet. This makes it very easy for us to forget that every form of life has some ability to transmit information between individuals. This is true even at a microscopic level where bacterial cell-to-cell signaling is a popular research topic (ref 1).

Having been around for a very long time and being unable to move much, it is no surprise that plants have developed many sophisticated adaptations for the purpose of communication. Plants can communcate in a host of ways, see (ref. 2) for a brief overview. One of the most fascinating of these is the use of “smoke signals.”

Ten years ago, researchers interested in plant biology and forest fires discovered that exposing seeds to smoke or certain nitrogenous compounds in smoke will induce germination (ref. 3). The evolutionary advantage of this behavior is presumed to be that forest fires leave an area rife for new growth.

The greater significance of this ability is our ongoing opportunity to learn from biological organisms. Although we use our intelligence to guide us in solving problems, we still use trial and error extensively. The greatest expert on trial and error is evolution. The process of evolving progressively more sophisticated life forms has relied on the use of trial and error for the last 3.7 billion years, and we would do well to realize that when it comes to the challenges of existing on earth, we’ve got a teacher who’s got a valuable store of experience.


1. Melissa B. Miller & ­ Bonnie L. Bassler Quorum Sensing in Bacteria Annual Review of Microbiology 55: 165-199 [doi:10.1146/annurev.micro.55.1.165]

2. Ragan M. Callaway & Bruce E. Mahall Plant ecology: Family roots Nature 448, 145-147 [DOI: 10.1038/448145a]

3. Jon E. Keeley & C. J. Fotheringham Trace Gas Emissions and Smoke-Induced Seed Germination Science 276: 1248-1250 [DOI: 10.1126/science.276.5316.1248]