The Biochemical Essence of Life: Carbon

June 6, 2010

I recently had a discussion with some friends of mine about life on other planets, a field called Astrobiology (or Exobiology) that was partly started by a hero of mine, Carl Sagan. The discussion unfolded into pondering what other forms of life could exist, and what it takes to make life. Two theories became apparent:

1) Extremes in the environment of other planets could allow for life to be based on different elements and processes that we don’t know about.

2) On the other hand, it seems like the elements and processes that exist here on Earth are so much more likely to be the gestalt of life that theorizing about other ways that life could arise is pointless.

Here’s why i think the second explanations is the correct one:



The basic building block of life on the planet is carbon. Carbon is a divine element. What makes carbon so special is that it has the ability to make four bonds to surrounding atoms. Even more importantly, it can bind to other carbon atoms very easily, making it essentially a 4 sided building block for the creation of multi-atomed molecules. Ever see a picture like the one on the right? Every kink in the chain is a carbon molecule.

Other molecules more rapidly crystallize into uniform structures, like this depiction of a salt crystal.

This is vital for the creation of life. The components of life are all created with carbon: carbohydrates, lipids, proteins, and nucleic acids (DNA & RNA). No other elements have properties to create such diverse, large and structurally unique molecules. Heavier elements are too large to create thin chains, and usually form uniform crystal lattices instead of unique structural combinations. In fact, the only other element that has properties like carbon and could be considered suitable for creating life is silica and it also tends to crystalize, rather than allow for complex structures to be created.

In contrast, look at the incredible properties of carbon-based molecules: Diamonds are pure carbon and are the hardest substance known to man. No other material can cut them. Carbon nanotubes can self assemble and provide not only incredible strength, but also electrical, optical, thermal and kinetic properties like no other materials. Graphite, also a pure carbon-based molecule is the lead in your pencil. Oil in your car is made of carbon, and the plastic of your keypad is carbon-based.

Try making such a diverse array of properties out of any other element! Metals will give you alloys, but will pretty much still be a metal. Gasses can be liquified but, once they are made solid, require some seriously extreme environments that would in-of-themselves cause a lot of complications for life to be sustained. Any expert chemist will quickly tell you that carbon is the only element that can be the backbone of so many different types of molecules with the properties required for organisms.


Another key feature of carbon is that its bonds are strong enough to resist environmental stresses, but weak enough to be manipulated by our bodies with enzymes. This is a requirement of any organism’s metabolism.

A basic depiction of how we take our carbon-based molecules and interchange them freely into the rest.

When we eat a piece of pork knuckle, the cooked muscle of another animal is chopped up into tiny pieces inside our guts, absorbed, and then reassembled into either our own muscle (if we are weight lifters), immediate fuel (in the form of sugars), or into fatty tissue (if you are like me) that deposits around your thighs (women) or bellies (men) and sits there until you are starving and require it, which in the Western world pretty much never happens.

Throughout these processes, we are either breaking bonds between atoms, or forming bonds between atoms. What this all leads to, is a net gain of energy into our bodies. We are taking this animal muscle, which has a higher state of energy, and we are ultimately excreting a much lower energy byproduct. The excess energy we gain from all of this is stored within the carbon-based molecules inside our bodies.

The ability of carbon-based molecules to so easily store and release energy is a necessary requirement for life. Other elements simply can not be manipulated like this to utilize, store, and relocate energy.

Compartmentalization and Water

Life would also require some sort of compartmentalization to exist. This is an assumption that I think can be assumed to be true. You can not have a uniform hunk of metal or cloud of gas be alive. You need to separate things from each other. There are always detriments inside life forms that need to be stored away safely (usually the left over waste from energy stores), and there are molecules that need to function in a specific environment. Furthermore, the life form itself can’t be exposed to the environment because that would be too risky. It would need something covering it to keep its insides safe, like skin on us or exoskeletons on arthropods (insects, crabs, etc.).

When we compartmentalize molecular substances, we need to have some sort of matrix to sustain everything in. Here on earth that matrix is water. If there is any element that I give most praise to, it’s carbon, but if there’s any molecule I give most praise to, it’s water. A simple bonding of two hydrogen atoms on either side of a much larger oxygen atom creates a unique molecule that should be a gas, but whose properties allow it to remain a liquid at a much higher temperature than expected of such a small molecule.

One of the greatest properties of water is that it has a very strong polarity. Essentially, there are polar molecules (hydrophilic), like water, and there are non-polar molecules (hydrophobic) like oil. These opposite polarities prevent them from mixing, like two ‘poles’ on the opposite side of a magnet. So one easy way to keep things separated from each other within a life form is by using either polar or non-polar liquids as a matrix for the rest of the working molecules, and using another substance of opposite polarity to compartmentalize things from each other.

To imagine this, think of dropping a dye into a glass of water, and then imagine dropping a dye into a glass of water with some olive oil poured on top. The dye would have a difficult time working its way down through the oil into the water below because it is water based and is repelled by the oil!

To bring this back to the original point: Carbon can be used to create oily substances that then allow us to compartmentalize cellular components from each other within a water matrix. So for life to be created from another element would require that element to be able to create both polar and non-polar forms of molecules.


In the earliest origins of life, there must have existed a single molecule that could duplicate itself. Hot streams with glaring sunlight, volcanic heat, acidic environments, and a multitude of other environmental factors allowed for the existence of one molecule to replicate. Even if only to act as a template for other atoms to gather on top of it and form another type of molecule, this new cast could have allowed for corresponding atoms to rebind and form another form of the original molecule. This is the most basic way life formed and going into it any further would require a lot more words than it’s worth mentioning at the moment.

So what types of molecules could recreate themselves? As was mentioned before, these molecules would need to be based on an element that can form bonds capable of being strong enough to last for some time, but weak enough to be broken. It would be chain-like so as not to miss any hidden areas inside of it when replicated.

Today we know that this original molecule was probably a nucleic acid sequence that was similar to our DNA and RNA, our blueprints. Once again, the energy needed to create strands of a self-replicating molecule from elements more rare or non-existent in our life today would be tremendous. For life to form in such a manner, only the elements that we are made of would be able to be accomplish this.


Finally, it should be noted how long it took life to form on our planet in this more simple and obvious way than many theorize. The earth is about four and a half billion years old. It took a billion years for life to occur on the planet. How much longer would it take for life to form in a more complex manner or with elements that are statistically less likely to develop into life? Twice as long? Ten times as long? The Universe itself is only 14 billion years old. The formation of life is not something that has infinite time to develop. There really is a time-limit involved, and for life to evolve using element other than carbon would certainly take a much higher amount of time to occur.

“Silicon-Based Life”

Finally, with all of this talk explaining how life can only form from carbon, I would like to mention that carbon-based life is not the only life that could exist. We can not forget robots. Life can exist “in-silico” once we create it. In this sense, life will definitely be different from how we know it. Robots with artificial intelligence are very likely to be invented sometime and this is the main life-form that I think could exist outside of a carbon-based design.

Already we are living in a time where people have microchips implanted into their brains, pacemakers into their hearts, and bionic limbs into their nervous systems. It would be interesting to see if life on earth continues to be biological, or strays into an in-silico form (or perhaps a combination).


Coolest Bird Ever? Terror Birds

April 4, 2010

When birds evolved from dinosaurs in the Jurassic period (about 150 million years ago), they were tiny creatures like the ones we see on a regular basis. Many of these smaller birds evolved into beautiful parrots, others into waterbirds, and some would become aggressive predators. In every ecosystem there are always apex predators that find a niche at the top of the food chain. Behold Phorusrhacidae, commonly known as the Terror Birds.

These monstrosities were up to 3 meters high and could swallow a dog in a gulp. Their heads were the size of a horses. One of the largest, Phorusrhacidae titanis, was the only one to travel into North America when the bridge between South and North America had formed. This migration and intermixing of species was called the Great American Interchange and P. titanis’ habitat reached form Texas to Florida according to fossil specimens.

Some terror birds, specifically Mesembriornis, could run at over 60 miles per hour, comparable to that of a cheetah. And since they were flightless, their bones were found to be dense enough to be used to shatter the bones of their prey to reach the delicious marrow inside. Yummy!

It fascinates me how dinosaur-like these birds had become. Even though they existed only 2 million years ago, they demonstrate similar characteristics to theropod dinosaurs that went extinct around 65 million years ago. This sort of convergent evolution occurs if animals are put under similar stressors from their environment. In this case, a predatory lifestyle selected characteristics very similar to those of theropod dinosaurs, which held a similar position at the top of the food chain.

Take for example the “ostrich dinosaurs”, Ornithomimosauria. These dinosaurs had similar body shapes and even evolved beaks.  Of course, their arms had not passed through an evolutionary flying adaptation, so they were more handy at grasping.

But what the Terror Birds’ upper limbs lacked in weaponry, their beaks made up for. I know myself the strength of a beak. I once owned an African Grey parrot (named Albert) whose beak had evolved to crush nuts. That thing could bite through my finger if it wanted to. Now imagine a bird towering over you whose beak hadn’t evolved to crush nuts, but rather evolved to crush your skull. Researcher working for the Discovery Channel reconstructed the neck muscles and skull of a Terror Bird and found that it was easily capable of driving its beak into a skull like a sledge hammer. Especially while running as fast as a car….

So if you’re ever asked what your favorite bird is, answer whatever you please but remember that there were birds on this planet a hell of a lot cooler than a bald eagle.

CAM in the Health Care Reform Bill

March 27, 2010

This week President Obama will sign the final piece of health reform legislation, concluding an epic battle that ultimately lead to the passage of the Patient Protection and Affordable Care Act (PPACA). The bill enforces the largest change to US healthcare for decades and has provided an opportunity for Complementary and Alternative Medicine (CAM) advocates to be federally endorsed in our future healthcare system.

CAM proponents tout a few sections in the PPACA as a victory for their cause. One of these sections is 3502, entitled Establishing Community Health Teams To Support The Patient-Centered Medical Home, which endorses government grantsto establish community health teams,” which are defined as “community-based interdisciplinary, interprofessional teams.” It goes on to say that such a ‘team’ may include, “doctors of chiropractic, [and] licensed complementary and alternative medicine practitioners[1].

The requirements of such a health team are listed and one of them ultimately reads, “to provide support necessary for local primary care providers… to provide coordination of the appropriate use of complementary and alternative (CAM) services to those who request such services.” What this entails, is that there will be an influx of federal spending into CAM services with the enactment of the new bill.

Fortunately, the section provides other requirements for ‘health teams’ such as,

to support patient-centered medical homes, defined as a mode of care that includes… safe and high-quality care through evidence-informed medicine, appropriate use of health information technology, and continuous quality improvements.

Health teams will also be required to (bare with me here),

“provide support necessary for local primary care providers to… provide quality-driven, cost-effective, culturally appropriate and patient- and family-oriented healthcare… [and]collect and report data that permits evaluation of the success of the collaborative effort on patient outcomes, including collection of data of patient experience of care and identification of areas for improvement.”

This could mean that even though CAM will be supported by our government plan there will be some restrictions in place requiring CAM therapy to adhere more to an ‘evidence-informed’, ‘quality-driven’ and ‘cost-effective’ form of medicine. Guidelines may be implemented to track the progress and efficacy of health teams using CAM therapies. If this was true, I would suspect an initial rise in CAM from the increase in government funding but an ultimate demise in the long-term as an enormous surge of government-sponsored data separates cost-effective treatments from sham.

Unfortunately, this hasn’t been shown to be true in relation to The National Center for Complementary and Alternative Medicine (NCCAM), which has been criticized for spending hundreds of millions of tax dollars on studies of CAM and never confirming the efficacy of a single therapy nor declaring any as ineffective. This shows that data gathered from CAM due to the healthcare reform bill might never actually lead to any meaningful conclusions or changes in healthcare.

Another section of the PPACA, supported by herbalists, is number 4206: Demonstration Project Concerning Individualized Wellness Plan[2]. The section describes the establishment of “a pilot program to test the impact of providing at risk populations… an individualized wellness plan that is designed to reduce risk factors for preventable conditions.” The program will include nutritional counseling and will provide dietary supplements that have health claims approved by the FDA. Examples include calcium supplementation for those at risk of osteoporosis and prenatal folic acid to decrease the incidence of neural tube defects. Seeing as this is guided by the FDA’s recommendations I can only join in the approval of such a “wellness plan”, and expect it to be a big hit in the new healthcare system.

Chiropractic has found a niche in the soon-to-be National Healthcare Workforce Commission as described in section 5101[3] of the PPACA. “The Commission,” as it is referred to, will be responsible for analyzing and disseminating information to the government, state and local agencies, Congress, healthcare organizations, and professional societies about the US healthcare workforce. It will be responsible for developing and commissioning “evaluations of education and training activities to determine whether the demand for healthcare workers is being met.”

In so doing, it will recommend to the government which institutions deserve grants for the government in order to “develop a fiscally sustainable integrative workforce that supports a high-quality, readily accessible healthcare delivery system that meets the needs of patients and populations.” It will also “study effective mechanisms for financing education and training for careers in healthcare.” Basically, the Commission will be channeling tax dollars to different healthcare institutions based on their analysis of demand in our healthcare system.

The Comptroller General, Gene L. Dodaro, will appoint the members of the Commission no later than September 30th of this year. It will consist of 15 members representative of the healthcare workforce, employers, third-party payers, representatives of consumers, State or local workforce investment boards, and educational institutions. It seems like there will be a host of different viewpoints and interests influencing the recommendations that this commission will be making.

Therein lies the problem. The section about the Commission specifically defines the ‘healthcare workforce’ as, “all healthcare providers with direct patient and support responsibilities,” and specifically includes licensed CAM practitioners and chiropractors in the definition. If proponents of such CAM therapies infiltrate the Commission, taxpayers could end up funding disproportionate amounts of money to medical therapies unsupported by science.

Another section of the PPACA that has been hailed as a victory by CAM proponents, especially chiropractors, is section 2706 in the Senate-approved H.R. 3590 bill, which prohibits “discrimination” against any health care provider. Chiropractors who feel they are being ‘discriminated’ against in the medical community see this as an end to their problems. Interestingly, this section is colloquially dubbed the “Harkin amendment”, after the Iowa Senator’s introduction of the section into the new healthcare reform bill. David Gorski has written about him on a number of occasions. Tom Harkin is the man most responsible for the creation of the aforementioned NCCAM and also the Dietary Supplement Health and Education Act (DSHEA) of 1994, which allows “herbal supplement” manufacturers to make dubious health claims with little or no regulation.

Fortunately, I couldn’t find any sign of section 2706 in my ‘quick’ look-through of the 2,407 page PPACA (my web browser crashed every time I tried searching the document) but it may crop up somewhere in the overwhelmingly lengthy and technical health reform bills so let’s keep a look out for it. The American Chiropractic Association (ACA) is saying, however, that the amendment did pass and will become law once Obama signs the bill this week.

On a positive note, the PPACA bill has in it a section on immunization[4] and describes a new program that will come into effect to maximize vaccinations throughout the country. This is a huge blow to the anti-vaccine movement, which has been surprisingly quiet about this.

In summary, we should be prepared for an infiltration of CAM therapies into the new healthcare system that will come into effect starting this year. The PPACA healthcare bill is not a disaster for science-based medicine by any means, but it is not bullet proof. The bill specifically mentions it’s endorsement of CAM and the more it acts on this, the more difficult it will be to eradicate passionately advocated therapies with no evidence supporting them in the years to come. Now is the time, more than ever, to ensure that the US health care system does not begin to excessively promote sham therapies. Otherwise, we will risk developing a foundation to the new healthcare system that incorporates scientifically unsound medicine.

[1] Page 1049 of the PPACA

[2] p1215 of the PPACA

[3] p1255 of the PPACA

[4] p1199 of the PPACA

Why I’m Blogging

March 8, 2010


Hello World!!!! Welcome to my blog!

I hold the belief that my first blog should be something special. This is probably a false concept and I will no doubt cringe at the site of this many years from now, as I do with everything that I have written in the past.

Thankfully, the reason for this is because I have slowly improved my writing quality over time and I can’t stand reading my own work prior to the improvements. With all the rote memorization in medical school, I’ve almost forgotten what it’s like to write. This blog will provide me with the medium for my thoughts, beliefs and understandings that I have so desperately been needing.

I don’t have many people with whom I can discuss deeper ideas. Even my fiance gets sick of my science-based rants and intolerance of ignorance. She does her best to act interested, but I can see it in her eyes that she would prefer a less serious form of discussion. Yet she is one of the very few who I actually attempt to engage in such conversations because others don’t even try to pretend they are interested.

There is a famous quote by Eleanor Roosevelt; one that has been a favorite of mine for many years. It goes like this,

“Great minds discuss ideas. Average minds discuss events. Small minds discuss people.”

Let me reassure you, I will certainly be discussing all three things in my subsequent blog posts. However, ideas will be the foundation of this blog. These ideas will be discussed from many viewpoints, and I hope to demonstrate that the best viewpoints are those of an unbiased, evidence-based, scientific and impartial nature.

In this way I hope to educate my readers not necessarily on topics but rather on how to think. I also hope to educate myself through the research that I do and by consciously improving my mistakes and shedding my own dispositions, as hard as it may be for me to do so.

Finally, I am using this blog as a springboard for future blogs that I may contribute to or start myself. I hope that I can attract interest from others and prove a devotion to educated writing.

I hope you enjoy what’s yet to come and learn a thing or two in the meantime.

Signing off!