Science for the Future

Radical Incentives

2012-02-04T17:17:00.000-08:00

Like many people I have spent a lot of time in the last couple of years thinking about the nature of our economy. As I delved deeper and deeper, my interest peaked on the role of government and the possibilities of creative monetary policy. I should say that I am not an economist by training. I choose instead to study math and physics because I believe these fields subsume most others by teaching the language of numbers and measurement. Economics though is a particularly interesting amalgam of math and physics, because it involves human decisions that effect our physical experience. Despite the continued poor state of the economy, there is still hope because in the end, collectively, we have the power to change it.

There is a big difference between math and physics that most people don't often think about. Physics describes a language to use to think about and compute ontological facts, whereas mathematics presents the symbology of calculation and logic. In physics the axioms are built from observations, but in mathematics a collective of experts, have over time, decided on the rules that define its logic.

When we step back and look at human endeavor from a scientific perspective, we can measure its features in many ways, but the system as a whole looks more like Mathematics in that it's axioms have been decided by the collection of all human transaction though history. The economy can be described as the net effect of collective human reasoning on the physical reality of our environment. To put it clearly, the economy as a whole, is a human derived system that creates vast observable physical effects. We collectively have the power to decide what activities and products are valuable. The process of valuing some activities more then others creates incentives for people and businesses to act in a certain way. The theory of incentives is at the heart of my interest in monetary policy.

If I could create a theorem of economics it would go something like this: Given that incentives drive economic behavior, there exist some set of incentives that when combined unilaterally in one economic system, can create anything that is physically produceable. Our current economic system, where we exchange special kinds of value labeled paper for goods and services, is a small subset of the possible incentive systems we could create. The set of all possible incentive systems actually approaches infinity. The set is indeed best define by it's limits which are physical impossibilities and collective human imagination.

There are many features of our current value exchanging system and many are good, but there are definitely some bad features as well. On the good side, people pay for things that they want and thus democratically decide what is made. The other side of this though is that people must pay for the things they need to survive and can in effect become a slave to the system or end up with no way to earn a living. Another good aspect of our current system is that hard work has great potential to be rewarded. Again though the downside is that some people are also sometimes rewarded for doing effectively nothing or even for doing things that harm the value of our collective possessions.

A more perfect system would preserve the good aspects of our economy while reducing the negatives. And good economic policies could indeed help greatly to align incentives with the general public good. Unfortunately though, our current means of determining value is poorly defined. Under the current system, where we 'let the market decide' the valuable of things, the things local communities value are increasingly diminished in comparison to the things valued by the market. In fact as wealth accumulates in the bank account of the richest one percent these people gain increasing control over what things are valued over others.

The process of wealth inequality inevitably leads to the general alignment of economic incentives with the interests of the very wealthy. This is how civilizations have risen and fallen for all of human history. A small group of people eventually become too wealthy and make increasingly selfish decisions that completely undermine the pubic interest to the point of total collapse for everyone. What was the value of Nero's fiddle during the collapse of Rome? Rather then continue explaining why this is bad, I would share a somewhat radical idea that could salvage the good things in our current market system while better reflecting the value of close knit communities and collectively caring for each other.

This idea involves creating a new currency to be traded and exchanged along with the standard old currencies, but this new currency would have some special rules. The first and biggest would be that this money would only be exchanged for good deeds or necessities. For example if you saw a person on the street who needed help and you helped them you could submit a description of the good deed to the community bank and they would give you an appropriate amount of this special money based on some standardized and public algorithm. You could then take this money to purchase needed items such as food, housing, utilities and healthcare, but you could also exchange it for money at an exchange rate determined by some set of specially tailored economic algorithms.

I know that this idea sounds impractical and would certainly have many inadvertent effects that could not easily be predicted (Most of them would probably be positive though). The point, however, is to find ways to provide a general incentive for people and business to better value the welfare of their local community. In effect the system I propose would simply put a tangible monetary value on how well individuals followed the golden rule and treated each other as they would wish to be treated. I challenge anyone to come up with something better.

Occupy Knowledge

2011-10-17T23:23:00.000-07:00

As you may have gathered from my previous posts I really love science and technology. Having grown up with the digital age, computers seem more like a helpful sibling, than a scary alien technology bent on irrevocably changing the human experience. I am excited to see what the future brings, and dream of helping to usher in great new things myself. So it should not be too much of a leap to understand why I tend to worry more then most about the future of civilization. Civilization, more specifically the building of civilization, is the foundation for the vast majority of our scientific and technical advances.

Without civilization we are individuals living in a mad max style DIY driven existence. Some more ignorant folks might consider this an improvement to the status quo, but I would recommend that they take a trip to the third world where gangs and ruthless criminals run the show and then tell me which system they prefer. Even so, I feel like the social contract that has benefited those of us lucky enough to have one is increasingly under attack. Do billionaires truly believe that they will be better off if laws are only written for their benefit and taxes are something that only poor people pay?

I am truly amazed that there are actually billionaires out there who hold this concept of the world. I guess nobody ever told them that money is only a figment of our collective imagination. Were the proliferators of corporate greed to follow their own logic to its conclusion, they should not be surprised to wake up one day to find that a loaf of bread, a handful of beans or a clean drink of water will cost them much more than a measly billion dollars. It is nothing less than the potential of human endeavor that hangs in the balance.

Of course the alternative world view of empathy and cooperation is where brightest future of humanity lies. We can never hope to master the truly great feats that stand at the edge of our combined potential without being willing to freely invest in each other without the necessity of monetary return. The continued advance of science and technology is only one of the many benefits we could expect from such an investment. The internet is a perfect example of this. Without many voices and the many more millions of eyes the web would be completely pointless.

In this case we are compelled to invest in each other, but the internet is only the first manifestation of the potential of our possible joint ventures. There is no technical or scientific reason that all people can't live in prosperity together; free from need and with the continued opportunity for self betterment. In fact I find the very concept of poverty to be nothing less then the institutionalization of cruelty. Given that money is the abstraction of value, we must make rules to define the abstraction. Since these rules dictate how we trade with one another for goods and services, there is nothing to stop us from making rules that dictate everyone starts out with enough money to pay for a minimum of basic needs.

For the mega rich to deny the ensured stability of this economic safety net is the clearest breach of our social contract. Everyone should be given the opportunity to fail at some endeavor without the risk being forced to live on the streets, losing access to healthcare and healthy food. More over it is proof that they see themselves as kings and everyone else not as peasants, but as slaves. And that is what we will become if we don't stand up and reacquaint the most prosperous members of our community with empathy for the other 99% of us who haven't had the opportunity yet to be as fortunate.

Self Constructing Materials

2011-10-10T21:09:00.000-07:00

Imagine many small blocks that efficiently move by themselves could tightly lock together. You could design any 3D structure on a computer and wirelessly signal them to form that structure and lock into place.

In addition each individual piece would have sensors that could read its environment as well as its own functions, signaling to be replaced on detecting a structural failure. I'm not going to bother listing all of the things that could be made with this, because the metric of success is the range of different items or shapes that could be made in this way.

I'd write more, but to get into the details both gives too much away and would be a large amount of work. In addition, I have my own ideas as to how one could construct such a machine-material hybrid, but there are many possible solutions. I say let the best engineer win!

Biological Simulation Software

2011-09-28T13:57:00.000-07:00

If we can simulate the environment within and around our cells accurately enough, we could extrapolate to organs, regions and hopefully whole bodies. This in turn would allow us to simulate the molecular interactions of various diseases in our body. By recreating them in a simulator we could potentially reverse engineer the pathways of disease. We could test the effects of new medicines in an environment that more closely resembles our own then any lab animal ever could and thus remove the need to subject other creatures to an often cure and short life. As the simulations improve it will become easier and easier to root out side effects until our medicines cured diseases thoroughly without also causing others.

Medicine would become another programming language as we begin to truly understand DNA and our genome. Eventually, we could have a digital copy of our own unique physiology that doctors would then be able to analysis to prevent diseases long before they could even be diagnosed at present. And then there is a singularity, where this computer aided medicine not only makes us healthier for longer, but can also make us stronger, more durable, and especially smarter. Once we begin using computers to augment our biology, we will be able to accelerate the advance of our scientific and technological capability to levels are not merely currently impossible, but as unimaginable as the content of an actual singularity.

Consider the first gauntlet laid...

The Gauntlets

2011-09-28T13:54:00.000-07:00

Those of you who know me are probably curious as to why this blog seems so muted in comparison to the kind of ideas that I like to talk about in person. I often wonder this myself, and I think that the reason is that it has been very difficult to for me to find a tone to express my ideas that I feel comfortable putting into the public record. I have been rereading my previous posts with some dismay and among other things, found my most recent post to be uncomfortably cynical.

I wish that my post had been more akin to this, but there seem to be a lot of problems weighing on my outlook recently. If I wanted to blame something I would choose the recent news cycle. In one day to hear about the continued dismal economic news, coupled with this story of Bush era government incompetence and the continued wasteful release of greenhouse gas was a little disheartening. Additionally, seeing the news media get very excited about the potential of overturning important tenants of modern physics while failing to explain in a coherent way what was actually at question only added to my general consternation.

I am actually a hugh proponent of large scientific group effort, because it has the potential to produce such amazing results. The fact that the LHC has been focused on the edge of physical knowledge is still exciting, even though I personally feel that there are too many serious but mundane problems facing humanity that should really be attended to first. Imagine if the same amount of effort was put into developing a new sustainable super high-tech energy source. Given the vested interests holding firm to the status quo, this kind of project is currently impossible. The LHC, regardless of my feelings about it mission, is at least a forum where scientists can work together to create potentially big things, least we forget how to do this all together.

Anyway, I am going to attempt to take a new tact. On rereading some of my previous articles, I have realized that I am holding back too much to have any hope of accomplishing my goal of presenting ideas that genuinely express the true potential of the future of science. To mark this departure, in my next several posts I plan to lay down a series scientific gauntlets. I will attempt to present these ideas as concisely as possible, and I will not discuss all of the potential ramifications of each technology. I will leave that to later consideration and debate.

Most importantly though, the ideas I have in mind are big potentially game changing technology that could be achieved in a decade or so. Ideas like the moon launch and indeed the LHC, that with enough public interest and concerted group effort, are imminently possible. I feel like the general public discourse has been pretty pessimistic recently, and I would like to be more optimistic about the possibilities for the future. The gauntlets that I have in mind are my own answer to this.

I refuse to refight the battles of a reactionary past, posed by those who continue to be afraid of the future. Instead I'd like to offer a path to blase through into the future, by remembering the amazing things of which we are collectively capable. So without further ado, I will get started on writing up the first of my technological gauntlets.

Change

2011-09-27T00:45:00.000-07:00

I was very happy to hear about the recent findings from CERN last week that the muon neutrino was possibly able to defy the speed limit of light. I am happy mainly because nothing was shoved under the rug. Of course there are not many vested or extreme moneyed interests out there banking off the continued general acceptance of Einstein's relativity theory. Luckily relativity does not need well heeled proponents to make is case. It manages that by simply being congruent with 99.9% of all experiments conducted to test it over the last century, including the recent results of the gravity probe b experiment sent into orbit to measure frame dragging.

Given the unsurprising failure of the LHC to find the Higgs boson though perhaps it is not so surprising that they would release somewhat sketchy, but shocking headline worthy results at a time when Europe and the U.S. are tightening fiscal policy. This seems like a good way to stay relevant and I fully support it even if it does eventually turn out to be some kind of glitch.

A Futurist Manifesto (sort of?)

2011-06-13T22:54:00.000-07:00

I have been doing a lot of introspective reasoning of late and although I already knew it, I hadn't ever thought to declare the fact that I am a futurist. I believe in technology's ability to change our world entirely. For either good or bad and until it is almost entirely different from our current experience. The fact, that what we conceive has the possibility of becoming real, especially if we do the math beforehand, is a wondrous thing. I would go as far as to say that innovation is the only real form of magic.

In my teens I remember thinking about how much I loved imagining possibilities; events as perhaps they played out in a parallel universe. I started with art because it seemed the easiest way to bring imagination to life. It turns out that this is actually the hardest way, but I'll save that for some other time. I turned my pursuits away from art to learn what science had to offer. I did this for many reasons, but mainly because I had come to the conclusion at the end of high school that science was where the truth was. I have always loved good science fiction as well and though as I said, truth was the ideal, the futuristic technology I imagined late at night was the hook.

It's so easy to forget the imagination we have as children. I have a theory that as our brains get filled with more data our imagination has less active memory to simulate reality. I don't think that our imagination becomes worse, it just becomes more bounded. I can remember vividly imagining a world of advanced technologies, with things like interstellar space travel, artificial intelligence, a verity of human augmentations, and most of all a means to a peaceful and prosperous coexistence of humanity. I like to believe that I have simply become replaced with a more practical version of myself, but I was much more idealistic back then. I think that the biggest catalyst for this change has been the general reaction of people over the years to the climate change problem.

I've already written about climate change enough, so suffice it to say the list of amazing things that I longed to see science accomplish, has dwindled down to: "find a way to make current civilization sustainable." In my early twenties, the slow realization of the lack of imagination of others was a rather large comedown. Since then though, I have spent a lot of time thinking about the possible solutions for our many problems. To me, the only other choice is to give up on civilization and so far I still refuse to do that. Sometimes when I am worried about the fate of the world it helps to imagine solutions to the biggest problems. Problems so big and challenging, that if solved, would in turn provide an immediate solution to many other smaller problems. What is the best and most sustainable way to provide continuos power to civilization?

Realizing the scope of the amount of power we need, it was and is still, hard to believe that anything other then direct nuclear fusion would be sufficient. It would of course be best if we could limit ourselves to second hand sun power, but we can't seem to produce enough renewable energy to cover what we currently need and unless civilization collapses our power needs are only going to increase. Fusion could also provide the power source necessary for large advanced space travel. So this was my first real intellectual leap into the world of futurism. The decision that the future of technology is riding on our ability to generate electricity from fusion reactions. There are other ways to conceive of the future, but to me the grandest visions always involves fusion as the power source.

Over the years I thought up a dozen different ideas as to how this problem could be solved. I have no idea if any would actually work, but it seems clear even the scientists working on fusion currently have no idea whether their designs will work either. Of course, my favorite idea involves nanotech...

An Argument for Materials Science

2011-04-04T12:33:00.000-07:00

I want to make an argument for this period being the dawn of the condensed matter revolution. A big statement I know, but there are two specific and compelling reasons why I believe this to be the case. The first relates to the advanced materials currently in use in modern technology, specifically those used in computers. The second focuses on nanotechnology and includes a broader statement about the progress of technology and how condensed matter physics and materials science is on the cusp of breaking open a new frontier of possible applications.

The advance of computer technology has been following Moores' law very reliably for more then half a century. It has in effect become a self-fulfilling prophecy, as the industry that makes computer chips now uses this law as a strategic planning metric. The invention and continuing development of the transistor was arguably the first game changing material based technology. Game changing because the entire purpose of the computer is to augment human intelligence and productivity. I don't want to push this obvious point too hard, but when you ask the question of what can be done with intelligence augmenting technology, the power of the computer becomes apparent.

The question is not what can we do, but what will we do with computer technology, and that gets me to my second point. The better engineering becomes at simulating and controlling events, the more flexibility there is to manipulate substances into useful shapes and configurations. The art of developing new technology is compressible into a single concept: find the optimum geometry of a given substance or set of substances to achieve a desired result. Again a simple question: what happens when we can chose and manipulate substances in increasingly fine detail?

Effective nano-manipulation techniques will be the only way to solve what have so far been intractable problems. Real solutions for cancer, energy production/climate instability and perhaps even aging will be made accessible by the ultimate technological scalpel of nanoscale manipulation. I personally have some ideas about what can be done with current technology (which I will discuss in a future post) but, the landscape of possibilities for nanoscale fabrication technology is vast and anything I can think of is only an imperceptible scratch on the surface. The punch line though, is that while nano-manipulation and computers augment our technical abilities, neither compel us to use these tools creatively.

An NPR Connection

2010-04-17T14:57:00.000-07:00

I was listening to this science friday show today about earth day and among other things they mentioned this puzzle concerning the total energy being absorbed by the climate. Satellite data shows a certain amount of energy coming into the earth/climate system, but ocean temperatures and other readings don't correlate to account for all the energy being absorbed. After hearing this, an interesting thing occurred to me.

Last month I was listening to another interesting report about an increase in the level of seismic activity in the last decade. Is it possible that this missing energy could actually be found in the increased seismic activity? I think it might be and propose this hypothesis: The missing energy is being absorbed by the earth's crust, resulting in the thermal expansion of rock, especially metallic ore, and thus leading to greater amounts of seismic activity.

This hypothesis is in no way a slam dunk because the overall climate system is so complex, but the general calculation is straight forward. First find the area of the earths crust. Divide this area by percent composition of each material and use this to calculate the total thermal expansion of the system. This will then make it possible to calculate the total thermal expansion of the earth's crust as temperature increases.

Now, because the earth's crust is not uniform, some parts are going to expand more then others leading to pressure gradients. According to plate tectonics these gradients will eventually accumulate along known fault lines. Thus the increase in crust temperature could lead directly to an increase in seismic activity, with the energy dissipated in these events accounting for the missing energy being added to the global climate system.

In the NPR article I cited from last march, the geologist concluded that, though more study was needed, earthquakes are generally understood to be random events. Still though, there is a compelling case to be made for a link between earthquakes and global warming. Iron (II) and (III) oxide accounts for approximately 8.5% of the oceanic crust. A back of the napkin calculation tells me that a 1 degree celsius increase in ocean temperature will result in an expansion in the oceanic crust of about 1-3%. Given the total volume of the oceanic crust this quickly becomes a large number, adding pressure to the overall system.

So increased seismic activity could just be a coincidence, but then where does all of that extra volume go? It seems quite possible that the ocean floor is acting like a heat sink, expanding and producing more earthquakes, volcanos and other less predictable events. Regardless, adding energy to any closed system will ultimately increase its entropy. So it seems like a bad idea to do that to the climate we have no choice but to live in.

A Top-Down Theory on Colony Collapse Syndrome in Bees

2010-04-06T13:39:00.001-07:00

I want to put down a quick hypothesis on the commercial honey bee affliction know as Colony Collapse Syndrome (CCS from now on). Honeybees from my understanding do not have an internal immune system as humans do, but instead rely on the hive wall and behavior to protect them.

In the wild the hive wall would be constructed of wax and propolis (a tar-like antimicrobial secretion). This barrier actively protects bees from most environmental dangers, however there are still some diseases and parasite problems that can quickly damage or destroy an infected hive, especially if the hive is already weak.

Again from my understanding, the growing consensus among apiarist is that CCS is the caused by more then one vector of disease. So a hive killed by a case of CCS is often infected with at least one known parasite, microbe or virus. My hypothesis is that the final collapse of a hive with CCS is indicative of a virus, but that virus is not the lone cause of collapse.

The fact that the death of many beehives was so wide-spread, especially among commercial hives, is actually more interesting then the specific cause of the disease. Wide-spread death of such large numbers of bees suggest that the commercial bee gene-pool has become too shallow.

From the symptoms of CCS this would be the case for both individual commercial operations as well as the US industry at large. I don't know if commercial beekeepers take any measure to expand the gene pool of their hives, but I feel confident that if such measures were enacted, CCS and any future bee disease would generally be limited to isolated outbreaks.

So the short form solution for a shallow gene pool in hives would be to release more diverse drones in the vicinity of isolated commercial hives. This would be a relatively easy solution since drones travel between many different hives and and are responsible for half of the overall gene pool. It may even be that if the drone gene pool specifically becomes to shallow, CCS will become more prevalent over time. I therefore present this as a hypothesis for a future study.

On a personal note I am working on building remote sensors to easily track the internal hive environment. I would like to aggregate data in this way and use it to help conduct this research.

A History of Modern Theoretical Physic: Part One

2009-08-10T19:09:00.000-07:00

Don’t be fooled by the title, I am not going to describe all of the developments in theoretical physics from the last 110 years. It is important however that my story begins in 1899. This was the year that Max Planck discovered the quantum and began a great new movement in the search for ultimate knowledge of the universe.

It is probably not surprising to anyone that, though Planck began it, Albert Einstein was the driver of this movement. Planck was an example of a physicist who found something unexpected, and failed to believe it. Like a gardener who one day looked up and saw a sasquatch eating his tomatoes. Challenging long held beliefs when comfortably employed by an elite University is not as easy in some academic fields as others. Physics paradoxically can often be one of the most reactionary, because it is perceived as the guardian of empirical facts. Physicists, like most people are naturally skeptical of any large change and are usually not incentivized to challenge conventional wisdom.

To a large extent the natural human aversion to change was the reason the unique personality of Einstein was such a dynamo of scientific advance. Einstein saw Planck’s quantum dilemma and immediately recognized it’s significance, beginning the avalanche of what would become Quantum Mechanics. In the first twenty years of the 20^th century Einstein also revised classical mechanics, created a more accurate theory of gravity, invented a new field of statistics and brought about the invention of the atomic bomb. That’s a pretty hefty list for one person, but that is why Einstein has been synonymous with the word genius for the past 90 years. Unfortunately, Einstein also eventually succumbed to stagnant thinking, when he refused to accept the philosophical implications of quantum theory. Personally, I think that he realized that Quantum Mechanics and General Relativity were fundamentally incompatible. Thus when he was forced to decide which theory was right and which was not, he choose to believe that General Relativity was correct. Who could blame him?

The World: Part 1

2009-08-06T14:53:00.000-07:00

In addition to physics I also spend a lot of my time thinking about other large things. Getting to it from a navel-gazing perspective there are two incredible puzzles in the universe that deserve great attention. The first is of the physical world, which can be imagined as a near infinite list of 'How' questions. How is it put together? How does it work? How can we simulate it and reproduce it? How does it know to jump right instead of left, and so on. The second is the world of humanity and after spending too much time thinking about the first subject I realized that I have to live in a world with many other people.

Science and especially technology are dependent on the edifice of human progress that we call civilization. Civilization is however not a given. It is only a structure for the promotion of peaceful cohabitation. Peace is a fragile thing though because it is based on there being enough for everyone to the extent that we don't have to resort to physical violence to see who gets what they need. So in the long run it seems that if science wishes to continue enlightening the mysteries of the universe, it's going to have to figure out a way to provide the technology to make sure humanity continues to have enough for everyone to live.

LHC Update

2009-08-04T11:19:00.000-07:00

So it turns out that my skepticism towards the the Large Hadron Colliders' official time table was justified. Today's Science Times article confirms what I said in the last paragraphs of this post. My thinking on the LHC project has changed in the past few months. The reality of the current recession makes it clear that our priorities at the cutting edge of physics are unfortunately skewed. The main reason for building the LHC was to attempt to flush out a log jam in theoretical physics. The money and time would have been better spent researching and developing advanced energy technology.

Theoretical physics has a long way to go before it can really begin to understand processes that occur at the energy target set by the LHC. It is quite probable that the Higgs particle is just a fictional keystone created by the arch of the standard model to hold itself together. Even with the Higgs particle in place, the standard model still does not give an explanation for gravity, and thus it must be an incomplete theory. So the LHC's stated mission to search for the Higgs' particle was from the beginning a wild goose chase.

The reason I think the LHC was built, was to search for new information that might lead to a better theory. If you ask me groping in the dark is not a good reason to build a multibillion dollar project. This is especially true if it has only a limited chance for success. In a way it reflects the bull market mentality the globalized world has had for the last several decades. Our planetary civilization has spent such a great deal of time doing the things we wanted to do, instead of what needed to be done. Let's focus on the problem of keeping our civilization in tack for a while, and let the theorist come up with an experiment truly worthy of the time and energy that has gone into developing the LHC.

MRI and the microbleed phenomenon

2008-09-12T23:58:00.000-07:00

I have been thinking a lot about Medical imaging recently. My experience working at the hospital has given me some valuable first hand info on the general state of healthcare technology. Part of me is dismayed that we still have so far to go, but another is deeply interested in the abundance of improvements that can be made. From the diagnostic standpoint doctors and technicians use invasive procedures from simple blood draws to brain biopsies. Imaging technology however seems to have the potential to not be invasive. Unfortunately, much of the advanced imaging technology uses high energy radiation to produce its pictures and thus exposes delicate genetic structures in our bodies to potential damage.

Of course medical imaging is to powerful a diagnostic tool to abandon, and thus imaging procedures are undergone after an assessment of risk/benefit ratio. At least that's how it's supposed to work. In practice doctors and very poorly incentivized to limit imaging procedures. To them the potential risk of radiation exposure is weighed only against the potentially infinite danger of not knowing. Perhaps there is a technological solution to this problem, like advancing the resolution of ultrasound imaging or the gold standard: MRI. It turns out though that there is a distinct possibility that even the MRI process possess the potential for serious damage.

I like to state the basic problem with medical imaging in the following way. In order to see inside the body, something must go in and come back out. Before our understanding of physics became more sophisticated, the only way to do this was to cut someone open. Now that we have a better grasp of things like radiation and wave mechanics, it is possible to get a picture of someone's insides without cutting them open. Yet all forms of energy we use to get medical images still have to send in some amount of energy to get out any results. The real problem lies in the fact that the amount of energy used in any form, is correlated to the potential for possible harm.

For a long time MRI technology has been touted as being basically noninvasive. At the very least it is surely less invasive then nuclear medicine, but the micro-bleed phenomenon found in stroke patients given an MRI makes me wonder whether this is actually true. In a perfect world when using a high tech instrument on the body, there would be a way to measure the total damage done afterwards so that it might be mitigated. It would also be nice to know where the damage had been done if you had to do any invasive procedure regardless. The perfect situation would be to have a way to produce a damage map and from that, calculate the total potential damage for any procedure as a function of where or if damage tends to occur and how severe it is compared to the alternative.

Running a few searches brought up a two interesting points. The best number scale I found for injury damage, oddly enough, was the AA. Second, there has been research done on determining and tracking medical injuries, but not much visible discussion happening right now. So it would seem that there is no scale for procedural damage. Is it because of the potential medical liability related to keeping truly accurate records, or is the culture of hospitals is generally simply unscientific? My experience leads me to believe that both are true to some degree. I would love to see an general damage scale created to keep track of the true risk of invasive procedures in aggregate and also ways to use lower energy methods to get even better results.

While I'm dreaming I'd also like for all hospital employees to be competent, well payed and extremely detail oriented, but I'll probably have to wait until the robots take over for any of that to happen...

2008-09-11T14:56:00.000-07:00

There has been some discussion in the media lately about the slow progress of clinical advances in cancer therapy. Though a great deal of knowledge on the pathogenesis of many different cancers now exist, the efforts of medical research continue to take a long time to benefit patients and thus far have produced limited results. There have been plenty of possible explanations for this but, given the complexity and variety of the disease it is no mystery that researchers have not found a reliable cure. While there are many possible smoking guns to be analyzed it seems unlikely that a single silver bullet exists.
This realization has led scientist to pursue the prospect of personalized medicine which offers the possibility of treatment specifically targeted to individual cancer profiles. The effectiveness of targeted therapy, however is directly tied to the accuracy of the existing pathological models for the disease. One thing that has become increasingly clear from this move to monoclonal antibody therapy and the use of a gambit of small molecules that interfere with specific cancer pathology, is that we are dealing with a disease of extensive and diverse etiology. Unfortunately the realization that cancer pathology may not only be very specific to humans but that they could also vary significantly from one individual to the next. This means essentially that the models used to develop targeted therapies, such as transgenic mice, are most likely too general and thus will present a predetermined limitation to the eventual effectiveness of these treatments over a given population.
In my opinion most promising advance in the development of future therapies will be the advent of powerful computer technology capable of accurately simulating complete biological processes of individual patients. If cancer is indeed as complicated and diverse as researchers are beginning to believe, it seems that this is the most thorough way to achieve the full potential of individualized medicine. I have been following the work of the Folding@home project at Stanford and IBM's BlueGENE group. Both of these programs are working to accurately simulate the folding of specific proteins. While this is a far cry from what I am proposing that we eventually achieve it is indeed a step in the right direction.

The main problem that Stanford and IBM are currently facing is that in order to achieve the level of accuracy required the computing power needed for the advanced simulation I propose could be astronomical. There are however several possible end runs that could be made around the problem. One interesting attempt has come from a group of researchers at the University of Washington. Fold it has turned the problem of finding the correct shape of proteins into a game that people can play on their computers. I have been playing fold it for a few weeks with average results. Some people apparently are quite good a figuring out the correct processes to produce efficiently compacted proteins, but I personally have found the interface a little too clunky. The idea though is top notch. Computers are great at calculating but not yet very good at extrapolating. Having a large base of players intuitively tweaking proteins solves the problems of computing resources I mentioned earlier, but there are still ways it could be made more efficient. As far as fold it goes, I would be intrigued to see a virtual reality version of the game where I could use my hands to play rather then a mouse. Being able to manually manipulate a 3D object in VR could bring the efficiency of the game to a new level.

The other change that could be beneficial would be to introduce RNA and the ribosome into the game. These proteins don't come fully formed out of the quantum background (although they could with significant improbability). They come one amino acid group at a time as the ribosome unzips data from the RNA. This fact has got to effect the final shape of the protein because bonds are forming for each new amino acid as it is connected, which I imagine would cause it to curl up as it is being unzipped. I, however, am not a biochemist and it is possible that this is not actually the case. Regardless, I applaud the effort and with enjoy watching it develop.

The most fundamental problem with finding a cure for cancer is that all it takes is a single cell with faulty gene. The only way to cure cancer is to kill every single cell that has the dangerous mutation, but because that mutation wants to rapidly reproduce itself, this quickly becomes a problem of exponential mass. The bodies natural defense against the cancer process diminishes with age, and thus in a sense the problem becomes one of geriatrics. It seems to me that the way cure cancer is to augment our ability to defend against it. This will require more powerful simulation technology and possibly, in the distant future, gene repairing technology. Until that time cancer will most certainly be a limiting factor to human longevity, but as research continues we get a little bit closer to finding a solution each day, and that is always a cause for optimism.

Accelerators and Other Things

2008-02-27T17:59:00.000-08:00

As I mentioned previously, my last two years have been spent wandering the abstract and often bizarre halls of theoretical physics. Although I don't plan to devote all my writing to this topic, it will be the general theme of this blog. There are also a number of physics related topics currently on my mind. It seems fitting though that I should begin with the great multi-billion dollar search for the elusive Higgs particle.

There is a great deal of excitement being generated in the physics world by the anticipated activation of the Large Hadron Collider, which is supposed to come online sometime later this year. Most of that excitement revolves around the idea of finding the Higgs particle, which, along with its field, supposedly explains the origin of particle mass. The hype for this possible achievement has leaked into the mainstream in increasingly grandiose terms. Just to highlight this, there was a book written about the Higgs particle for popular consumption entitled "The God Particle."

Now say what you will about the possible importance of the Higgs particle, but I've noticed that a lot of physicists like to use religious terminology when talking about the frontiers of their field. I have to admit that the religious allegories that have been attached to some scientific pursuits has made me a bit uneasy. The popular nomenclature of the Higgs particle isn't even the worst of it. The goal sought by theoretical physicists and embodied most popularly by string theory is to create a consistent theory that takes into account all the major forces. The search for a Unified Field Theory has been called has been described as the "holy grail" of physics by prominent researchers in the field. The mystification of the development of a unified field theory seems contrary to the ideals of rigorous science, which after all is meant to explain rather then obfuscate the workings of nature.

In any event, the construction of the LHC on the boarder of France and Switzerland represents the next major leg of the journey to an eventual unifying theory. I think that some physicists realize that despite its hype, the Higgs particle is actually just a placeholder for physics at the edge of the standard model and beyond. Personally, the Higgs particle seems to be the keystone that prevents the standard model from collapsing in on itself. However, since it is generally agreed that the standard model is not the last word in theoretical physics it seems likely that if something were going to be wrong with it, Higgs theory is the most likely culprit. Regardless, it seems unlikely that a theory can explain a key concept like mass without also providing some insight into the nature gravitation. But then again, what do I know?

The 14 TeV energy will hopefully be enough to flush out a quanta of the Higgs field if it exists and even possibly a low energy supersymetric particle (although I find this extremely unlikely). What seems most probable to me is that new and as so far unpredicted physics govern this level of energy and will delay the project, as the limits of modern engineering are tested. I expect that the difficulty of the technical challenges involved, as engineers attempt to focus and optimise the proton beams, will increase dramatically.

It's hard to believe that the LHC will actually be running experiments by this summer. I am curious as to how operational the accelerator will be by the ceremonial opening event scheduled for October and am glad that I am not in charge of designating those dates. Anyway I will try to keep up to date on its progress in further posts and perhaps make some inroad with the people working on the project. For now I wish them well and hope that I am wrong about the probability of delays.

Ending a Long Hiatus

2008-02-05T14:10:00.000-08:00

I started this blog back in 2005 as a heated reaction to the hurricane Katrina disaster in New Orleans. I posted a few other things since then, most of which I took down thinking that I would eventually rewrite them. I didn't. Coming back to it now I find myself slightly amazed at what I left up: the original 'alarmist' essay, a paper I wrote as a freshman in college and a laughably pretentious piece on scientific reductionism.

A lot has happened since then. Politically things have gotten worse even as the entire scientific community and most reasonably well informed people, have recognized global warming as a problem, although I suspect most people haven't yet realize its actual scope. The climate scientists have been required to be cautious or risk loosing the clout they've so painfully built over the past few years. Even so, I've been hearing some pretty alarmist things coming from that sector, like the statement that without some drastic change in the next 4 years we risk global disaster. It is looking more and more likely that the major problems associated with global warming will accelerate at a frighteningly unexpected rate. I may have been wrong about the inevitable increase in hurricane activity, but that's only cause for more worry as hurricane strength storms remove a great deal of heat energy from the oceans. O discordia...

In any event I stopped actively working on the problems of sustainability (if what I was doing could truly be called such) to return to my original pursuits in theoretical physics. I have decided to resurrect this blog as a place to talk about what I've learned and in general, comment on the progress and possibilities of contemporary science and technology. Of course, in paying homage to the law of cause and effect, I have to concede that this decision was in part motivated by the spiritual awakening of two close friends. The first, in reaction to a perceived slowing of life has embarked on a vision quest that has taken him from coast to coast and finally all the way to Africa. The second upon a confrontation with some personal adversity has unleashed his immense talent and in doing so has discovered a new Joie de vivre which thrust him into a personal renaissance taking form in something he's dubbed 'hyperliving'.

Their condition has infected me with a new will to take a shovel back to the mountain that divides what is from what could be, and once again begin to dig. I pray what lies ahead will bare that out.

Philosophical Reductionism in Science

2006-02-28T14:19:00.000-08:00

Long ago I discovered reductionism in the way theorists talk about the progress of contemporary physical theory. I’m not a devote reductionist because my experience has shown that often complexity can render reductionism useless, but from an aesthetic perspective this philosophy has great merit. Suppose that a given problem in any scientific field can be reduced to and solved through knowledge of the most basic interactions present in a specific system. Riding the reductionist train of logic each scientific field can be thought of as knowledge pertaining to a specific scale of inquiry. As scale decreases so do the applicable disciplines where physics is typically the last stop, but let me begin here with an example.

The common cold is a typical annoyance this time of year. Those who get one display a variety of uncomfortable symptoms that are often readily observable. Medical Science has observed that the symptoms of a cold remain somewhat consistent from person to person, often involving an inflammation and congestion of the sinuses, headaches, dizziness, fever, and red irritated eyes and nose. Microbiology and virology tell us that these symptoms are caused by a virus (Rhinovirus to be precise). When this virus is placed in contact with the cells that form the lining of our nostrils, it attaches itself, enters the host cell and reproduces little copies of itself at the expense of the infected cell. Chemistry identifies a virus as a composition of proteins, lipids, carbohydrates, and nucleic acids that naturally form a specific chemical structure. To reduce this once more, we break these organic compounds down into atoms of specific elements, and again into subatomic particles which lands us firmly in the territory of Physics. The biological description of the process by which a virus gains entry and hijacks a host cell fall mainly into the realm of chemical reactions that are in turn dictated by specific physical forces.

This particular reductionist view so far though, lacks one important factor: utility. How is reductionism useful to science? From a big picture perspective, this philosophy is simply a byproduct of the way we’ve organized scientific inquiry. A complete understanding of the events we observe in the universe requires specific knowledge of the interactions that occur between the largest and smallest possible scales we can observe. The benefit of a reductionist perspective is that each different field of scientific study provides details about a specific scale. Of course, generally, physics describes interactions that span the scale of all of other fields, which incidentally, is the reason there exists specific branches of physics prefixed by each of the other major scientific fields (i.e. geo-physics, biophysics etc.).

The contention that I have with reductionism though, is that people assume that it attempts to simplify the questions in other branches of science to a matter of physical interactions. If anything, including physical observations in studies that are not necessarily physics related will generally complicate rather then simplify the problems of the specific study in question. However, if the physical observations pertaining to such a study are provided, more details about the specific object/objects under investigation are available, and can provide an added level of sophistication to the eventual scientific explanation. This does not mean that physics usurps or trumps other branches of science; it simply provides a means by which further detail can be considered in the scientific explanation of a specific experimental observation.

The form of reductionism I personally like most, and attempt to espouse to, is that there is a valid explanation for every scientific observation. In essence I believe that a consistent reductionist theory should be able to answer all of the specific “whys” that logically follow from the initial explanation of a given observation. To remain consistent with my examples lets say a small child observes someone with a cold and asks why people get sick. The conversation proceeds as follows.

A: People get sick because our bodies are vulnerable to diseases.

Q: Why are our bodies vulnerable to diseases?

A: Because our health requires the biological processes of our bodies to work in a specific way, and diseases can change the way our bodies work.

Q: How do diseases change the way our bodies work?

A: Our bodies are composed of different structures, each of these structures are composed of cells, and each cell contains a specific chemical structure that controls the chemical reactions in our cells, between our cells and between the different cells that compose the different structures of our bodies. Diseases interfere with these interactions.

Q: Why?

A: (Now adding physical detail) because the chemicals that control the way the cells in our bodies work are composed of different atoms of varying sizes that are held together in a very specific way by physical forces. These forces allow the specific structure of these chemicals to produce other chemicals that are used to build and send information to other parts of our bodies. The forces that dictate what forms these structures can take allow for a great deal of variation and when these chemicals are not exactly right or are interfered with, the processes of our bodies can change. Disease can be caused either by defects in the underlying chemical structures or by the introduction of some outside chemical structure or organism that interfere with the way our internal biological machinery is supposed to interact.

Continuing this line of reasoning and following all possible tangential questions could eventually cover all current medical knowledge. Understanding the physics of genes could give us the ability to control processes that occur on this scale and could potentially provide a way for medical technology to monitor and protect our health from all forms of disease (I’ll follow up on this next time). This doesn’t mean that medical science can be replaced by physics, it’s just a reminder that all areas of science are interconnect. From major benefit of this reductionist perspective is to provide a means of finding the holes in a specific explanation. By identifying the ideas or concepts that have no adequate explanation we can discover where further studies and experiments are needed which makes the philosophy of reductionism a vital part of the theoretic process in science.

Chemistry of the Virus

2005-11-04T12:22:00.000-08:00

Chemistry of the Virus

Towards the end of the 19th century a strange new pathogen was discovered. Dimitri Ivanovski, a young Russian botanist, found that the agent responsible for tobacco mosaic disease differed from most known bacterial pathogens. He found that the agent was both several orders of magnitude smaller then most bacteria, and that for some reason this pathogen could not be artificially cultivated.(Scott 12)
By the time Ivanovski was doing his work the germ theory of disease was well excepted thanks mainly to the work of Louis Pasteur and Robert Koch. However, Ivanovski was not prepared to go the extra step and declare the existence of a new pathogen. It wasn’t until a Dutch botanist by the name of Martinus Beijerinck repeated Ivanovski’s experiments and came to the conclusion that the new agent must be a unexpected form of chemicals able to reproduce but only by proxy inside a host organism. (Radetski 43) Since then the debate between whether the virus should be considered a living or nonliving entity has raged. Viruses have specific attributes which correspond to both living organisms and inanimate chemicals. Because of this it is fair to think of viruses as falling into both categories. However in essence the view I propose with be that viruses are simply replicating chemical structures.
Nucleic acids are quite possibly the most remarkable and dynamic of chemical compounds. They make life as we know it possible. However the same chemical process that allows all life to pass specific information from one generation to the next also makes the existence of viruses possible. Therefore the first step towards understanding viruses is to understand the chemistry of genes.
Without first understanding how normal cells work it is impossible to really understand what a virus does so this section is going to be devoted to the chemistry of nucleic acids, proteins, lipids, and carbohydrates.

Nucleic Acids

DNA is an acronym which almost everyone has heard of before, but DNA is actually only one particular compound in a larger group of chemicals known as nucleic acids. DNA stands for Deoxyribonucleic acid and it, along with Ribonucleic acid or RNA, make up the genetic material upon which life is based. Nucleic acids are of central importance to all life processes however they can not construct a living organism all by themselves. Nucleic acid’s main function is to encode information on how to produce specific subsidiary chemicals known as proteins. (Scott 21)
DNA stores this information by organizing several specific compounds known as nucleotides into specific sequences. These nucleotides are composed of three parts (see figure 3). A phosphate group and a nitrogenous base are connected by a special sugar ring know as deoxyribose. From this formulation four nucleotides (deoxyadenosine phosphate (A), deoxycytidine phosphate (C), thymidine phosphate (T), and deoxyguanosine phosphate (G)) are created (see figure 4). These compounds are the main constituents of the DNA molecule. In each of the different nucleotides both the phosphate group and sugar ring remain unchanged leaving the nitrogenous base group to display the dynamic qualities. The equally important RNA (ribonucleic acid) is almost exactly the same except in place of the base thymine it uses uracile (U), and a slightly different sugar ring is employed. (Scott 22)
So now that we have been acquainted the each of the pieces of the DNA molecule it’s time to talk about the famous Double Helix. DNA is actually two connected nucleotide strands. The nucleotide strand is connected by the deoxyribose sugar which bonds to two different phosphate groups. The phosphate group of one nucleotide forms a chemical bond with the oxygen of the lower outside carbon of another sugar ring forming the continuously repeating backbone of the molecule (see figure 5). (Scott 22)
separate DNA segments. This turns out to be the The nitrogenous base associated with each sugar group forms the connection between two specific nitrogenous bases which makes DNA coding possible. The actual double helix comes about when weak bonds form along the major grove between bases to form what are know as base pairs. Base pairs form between adenosine and thymine as either AT or TA and between cytosine and guanine as either CG or GC Therefore if we know the sequence of adenine and nucleotides for one stain then we can easily work out its complimentary nucleotide. This symmetry within the DNA molecule allows the replication of genes to occur. (Harper 43) Because the bonds holding the separate strains of the DNA together are weak the DNA can dividing along the center of the base pairs to produce two identical copies of the original molecule or reciprocal strains of RNA (see figure 7).

Proteins

This ability to produce basic RNA copies of genes is of central importance to the life of an individual cell and the organism as a whole. The process in which an RNA strain is produced from the original DNA marks the first step towards protein fabrication. This particular RNA is called a messenger RNA or mRNA. The mRNA is a replication or transcription of one strand of the original DNA know as the plus strand. mRNA acts as the middleman between all genes and protein production regardless of the type of organism. Protein manufacture occurs when mRNA comes into contact with a collection of RNA and amino acids called a ribosome. The ribosome moves along the mRNA strand and assembles a group of twenty amino acids into the specific order encoded on the mRNA. By this process all the proteins used for life functions are created. (Scott 23) This process if very important because as mentioned before all organisms use this process to create the essential proteins needed for life. In the case of viruses this preexisting machinery is exploited to produce the proteins required by the virus.

Lipids

Lipids are a large group of substances used in life processes. The one feature they all have in common is simply that none of them are soluble in water. Thus lipids are very important for creating the barriers between the watery environments of cellular life. The most interesting use of lipids as far as the subject of virology is concerned is their role as cellular membranes called the lipid bilayer. The bilayer organizes itself though the use of polar molecules. One end of the molecule is attracted to water and the other end is repelled by it organizing an effective barrier. Cellular membranes use this to regulate the content of the cell. The only way any given substance can gain entry to the cell is by passing through the lipids of the cellular membrane. (Harper 34)

Carbohydrates

Carbohydrates are a diverse group of chemicals used by most organisms as an energy source. Some common carbohydrates are the simple sugars (see figure 9). Carbohydrates represent only a very small part of the structure of viruses. However, they play a vital role in the form of glycoprotein which is a hybrid of protein and carbohydrate used by the virus to gain entry into the host cell. (Harper 36)

Virus Structure

Viruses come in many different varieties. One of the first viruses studied, the tobacco mosaic virus, also happens to be one of the simplest structurally, consisting of a single strand of RNA and one protein subunit (see figure 10). However some viruses that infect animals can be many times more complex. In general the virus is composed of a nucleic acid core which carries the genetic information for the virus and a protein coating called a capsid which serves as protection for the viral genome from damage outside the host cell (see figure 11).
The viral genome and the protein coat is together is often called a nucleocapsid. In some of the more complex viruses the nucleocapsid is further enveloped within a lipid bilayer. This structure is usually derived from the membrane of the host cell. The outer layer of the virus also has structures known as effectors. These structures are usually composed of glycoprotein and as mentioned previously make possible the entry of a virus into the host cell. (Strauss 14)
Keeping these basic structures in mind, viruses can come in a variety of shapes and sizes. The largest known viruses belong to the Poxviridae family and can be up to 2000 nanometers in length. Correspondingly, viruses in the Parvoviridae family can be as small as 24 nanometers in diameter (see figure 12). Shapes can vary from objects as simple as a protein coated helix (tobacco mosaic virus) to icosahedra to the complex insect-like shape of the bacteriophages. (Strauss 15)

Viral Life Cycles
This is a particularly dubious topic which brings us straight back to whether or not the virus is alive or inanimate. The main prerogative of all viruses is to preserve their genetic code. In essence though this is exactly the same for all other forms of life including humans. Of course humanity has many additional activities beyond replication, but the virus serves to put this into perspective. The virus represents the simplest form which genetic chemicals can assume naturally, and its basic function is to preserve itself. From this logic it is possible to assume that the inborn desire of living organisms for self preservation is in fact a function of the properties of a chemical. Of course this brings us full circle to the original question: what is it that defines a life form? Obviously this question is beyond the scope of deductive reasoning and thus let us proceed to the discussion of the viral “life” cycle.
Although diverse, the life cycle of viruses can be generalized to four different stages. These stages consist of the virion binding to the host cell, the introduction of the virus into the host cell, the replication of the virus, and finally the release of new virions from the cell. Each of these steps involve complex chemical processes and deserve a closer look.

Binding
The process that viruses use to bind to prospective host cells involves complex chemicals on the surface of the viral envelope. These structures are usually made out of glycoprotein. As previously mentioned these binding agents are a hybrid of protein and carbohydrate. The protein end of the compound binds to either the capsid protein or the lipid envelope of the virus while the carbohydrate end is attracted to the receptors of the host cell. These glycoprotein binding agents mimic the structure of specific compounds needed by the cell. This adaptation allows the virion to enter the cell by exploiting the receptors which are used to import needed compounds and nutrients. For example the Human Immunodeficiency Virus binds only to very specific receptors called CD4 receptors (see figure 13). These receptors are only located on the immune response T-cells found in the human bloodstream. This is why HIV causes the disease AIDS. The specific receptor the virus binds to creates a very localized infection killing the immune cells which protect against diseases and impurities in the body. (Radetski 123)

Virus Entry
Once a virus is bound to a cell the next obvious step is getting inside. This is achieved by the virus in three different ways depending on the structure of the virus. The first method of entry is called translocation. This occurs when the virus passes directly through the cell membrane into the cytoplasm. This method of entry is often employed by the smaller non-enveloped viruses such as the Picorna and Reoviruses, because it involves the virus passing though the small protein channel associated with the membrane receptors. Even small viruses can have difficulty entering though this pathway, so often the virus will simply inject their genome into the host cell. A good example of this is the bacteriophage. (Harper 32)
The second method a virus uses to enter the host cell is called endocytosis. This process is used by the cell to imbibe nutrients that require further digestion before the cell can use it. The virus exploits this by binding to the host cell and then being enveloped into a vacual which is internalized by the cell.
This process is used by the cell to absorb nutrients which for one reason or another are unusable in their current form. Therefore endocytosis in a mechanism for cellular digestion. Once taken in, the ph level inside the vacual is decreased in order to assist digestion of what is usually a complex carbohydrate. The virus takes advantage of this by utilizing the drop in ph level as a chemical trigger. Once triggered the virions capsid binds to the internal vacual walls and basically fools the cell into thinking that the contents of the vacual have been digested, releasing the virus genome into the cytoplasm of the cell. (Harper 32)
The third process the virus uses to enter the cell is called membrane fusion. This method is employed only by viruses which have a lipid membrane. After the viruses binding sites have latched onto the cells receptors the lipid coating the virus attaches and fusses to the cell membrane. This is possible because the virus has derived the lipid membrane encasing it from the cell membrane of its previous host cell. Due to the nature of the virus binding sites, which will only attach to specific receptors, the cell previously infected is of the same type as the cell currently being infected. (Scott 43) This is perhaps best shown by the HIV retrovirus. The reason HIV will eventually cause AIDS in the victims it infects is because the virus only attaches to the specific CD4 receptors. CD4 receptors are only expressed on the surface of specific cells called lympocytes which include T-cells and natural killers cells which are primarily responsible for initiating the bodies immune response. (Radetski 125)
Although these three processes embody all the conduits utilized by the virus to gain entry to the cell, many viruses use more than one of these methods. The most typical combination (and the one used by the Influenza virus (seen in figure 1.) employs both endocytosis and membrane fusion.

Viral Replication
Once inside the host cell the virus must do two things. The first is to make working replicas of their DNA or RNA sequences. The second is to create messenger RNA strains to produce the proteins needed for the viral capsid. Because the virus cannot do things on its own, in order for these two processes to occur the host cell must be redirected from its normal metabolic processes. How a virus goes about this varies from virus to virus and is not completely understood due to the complexity of chemical processes. Some viruses react quickly producing many new copies and killing the host cell immediately afterward, some (like the HIV virus) react much more slowly. In some situations the virus infects but does not kill the cell, and in still other cases the virus can actually change the genetic sequence of its hosts DNA. (Harper 50)
However, all a virus must do in order to reproduce itself is to hijack the host cells organelles. The virus seems to accomplish this by simply inserting its genetic material into the cells cytoplasm. In fact the main functions of a virus once inside the host cell are carried out by the viral DNA or RNA molecule. Thus the basic process a viral genome undergoes can be described by four steps mentioned earlier. The first is to make copies of its genetic material which is accomplished by the same method the cell uses when dividing. The second is the production of mRNA. The third is the production of the viral protein accomplished by the ribosome moving along the viral mRNA. The last process occurs when the new viral genome and the viral proteins are put together by cellular and viral enzymes to create a new virus within the host cell (see figure 14). (Harper 56)
This greatly simplified version of viral reproduction in essence encapsulates the power of the viral genetic material. It may seem amazing but the mere presence of DNA or RNA where it is not supposed to be can cause great difficulties for a host organism. It is, in fact, exactly this power of the nucleic acids that the premise of viral “life” is based upon.

The Bodies Defenses
The reaction the body undergoes after it is infected by a virus is called an immune response. The reaction of the bodies immune system to infection is, along with many other processes associated with the virus, an extremely complex one.
There are two basis steps of an immune response. The first is called the non-specific response and is the bodies first line of defense against infection. There are two different cells which responsible for this reaction, the first of which is called a phagocyte. This cell is found in the bloodstream or the lymphatic system, but can travel anywhere in the body. It is mainly responsible for attacking and destroying impurities in the body. Many potentially infectious viruses are found and destroyed by phagocytes long before they can cause illness. This process is called phagocytosis.
The second type of cell involved in the non-specific immune response is called a natural killer cell. This is a cell similar to the phagocyte, but attacks and destroys cells which are already infected. When a cell is infected by a virus it produces one or more of a number of chemicals called interferons. These chemicals do two things: 1st they warn other cells about the presence of a virus and 2nd, they attract natural killer cells which eventually destroy the infected cell along with the virus. (Scott 72)
After a virus has been in the system for a while the body can initiate a specific immune response. This process is extremely complicated and could easily take up many pages for a real description. Due to the scope of this paper I will limit the following explanation to a brief summery of the general process.
The specific immune response is mitigated by white blood cells called T cells and B cells. These two cells are responsible for the immune memory the body displays after having been infected by a specific pathogen. First a phagocyte carries a virus to a specific receptor on the T cell (or T lymphocyte). This specifically created receptor bind to the virus receptor site called the viral antigen. The millions of T cells in the body are capable of recognizing a huge number of antigens because each T cell can store several different receptors. Once a T cell recognizes a specific viral antigen presented to it by the phagocyte, the T cell then divides many times producing enough T cells with the specific antigen receptor to bind and destroy the offending virus and infected host cells. These cells also give off specific chemical messengers which can activate other defenses and convey specific information about the infecting virus. (Scott 73)
B cells are very similar to T cells. They can bind to viral antigens which cause them to multiply and can destroy antigen as well. However, instead of directly killing viruses and infected cells, B cells give off proteins known as antibodies. Antibodies are proteins that can bind with great specification to the antigen which provoked their creation. The antibodies work in two ways. The first is to render binding sites on the virus impotent making it impossible for the virus to attach to a host cell. The second is to bind to the chemical receptors of the host cell which has been infected by a virus. On the side of the antibody not responsible for binding to the antigen is another binding site to which a phagocyte can easily attach. Once the phagocyte attaches to the free end of the antibody it can proceed to destroy the entire virus or infected host cell (see figure 15). (Scott 75)
Presented are the two main processes by which the body defends itself from infection. Although greatly simplified this is the crux of the immune system.

Intervention
Although the body possesses powerful defensive tools viruses have found ways to subvert them. The battle that ensues between multicellular organisms and viral pathogens has seen many casualties on both sides. However through the means of science and further understanding of the nature of the pathogens which plague humanity it has become possible to fight viral infection though biotechnology.
In the late 1700’s a British physician named Edward Jenner made a startling discovery. He found that if a person were to become infected by a disease called “cow pox” the individual would then become immune to the similar, yet much deadlier disease know as small pox. This discovery marked the beginning of a process called vaccination. (Radetski 64)
Today vaccination is used to prevent a plethora of disease. How it works is by infecting an individual with a weakened or less dangerous form of a virus and the immune response and memory described earlier will immunize the individual against later infections by the full form of the virus. This basically simple idea discovered (if not understood) by Edward Jenner two centuries ago is still the best means available for preventing viral infection. (Strauss 132)
The frightening truth about viruses is that despite great leaps in medical technology in the last century, there is still no cure for any virus once a person has been infected. Once infection occurs we must rely completely on the strength of our immune system.
For many years scientists have been trying in vain to find the “magic bullet” which would prove effective against viral infection. Currently our understanding of certain processes within the realm of molecular biology and bio-chemistry is still incomplete. However the power of the virus is just beginning to be understood, and it is possible that in the not too distant future the virus could be made to work to our benefit. Processes that use viruses to make changes in our DNA could prove to be the most effective weapon against all variety of disease. Regardless of what the future holds, it is more then likely that the virus is here to say as our fellow traveler though time and life on this planet.

Global warming and Hurricanes

2005-09-19T23:40:00.000-07:00

The destruction and human suffering in the wake of Hurricane Katrina has many Americans (especially those on in the southeast) asking what, if anything can be done to prevent similar disasters in the future.
In the past thirty-five years the prevalence of powerful (category 4 and 5) hurricanes has almost doubled. NASA has recorded a new record for storm activity during the month of July and so far this trend has continued through August and September.
So what can be done about this very real problem? First we must admit to the underlying cause. Despite the general reluctance in the scientific community to acknowledge it, global warming is creating a very real impact on our climate. The recent increase in storm activity is just one effect we are going to have to face. Even though it is true that each storm is by itself is a random weather event, the overall trend is not.
Consider this, Hurricane Katrina hit the Louisiana and the gulf cost with the equivalent energy of a ten-megaton nuclear weapon ever twenty minutes. Of course the destruction of New Orleans was not quite as complete as it would have been had an actual atom bomb been dropped there, but that’s only because the atmosphere can’t release energy quite as fast as our weapons technology.
So where does all this energy come from? That’s right, the same place that 90% of the energy on this planet comes from. The Sun. And introducing greenhouse gases into the upper atmosphere traps more heat energy that otherwise would reflect back into space just. This energy is trapped in the oceans and in the air. But this energy can’t just build up forever; our atmosphere is a chaotic system and when extra energy is introduced the system naturally becomes more chaotic.
Of course without hurricanes and other storms dissipating some of this excess, the planet would be heating up much faster then it is currently. However I imagine that this is of little consolation to those people in the southeast who will be facing the wrath of progressively larger and more destructive storms in the near future. Not only will these storms be more intense, but contrary to the opinions of some scientists and the media the number of storms per season will also increase.
It is logically impossible for the intensity of storms to increase while their prevalence either stays the same or decreases. If a storm that would have been a category 3 without warmer oceans feeding it, becomes a category four hurricane doesn’t it seem reasonable that a storm that would have only been a tropical depression will now become a full hurricane. Even little storms that might never even have gotten out of the gate fifty years ago will now have the energy available to become another storm.
So now that we’ve admitted to ourselves that there’s a problem again I’ll ask the question: what can we do about it? I want to stress that this is not yet in a helpless situation. There are several things that we can do, the first of which is to build stronger better cities. Houses built on sand dunes or cities below sea level are not responsible uses of our resources. Secondly we can decrease the amount of carbon dioxide in the atmosphere, both by reducing emissions and by building chemical collectors, basically artificial trees, to filter out greenhouse gasses already present. If you would like to learn more check out this article from Discover magazine.
There is no doubt that working towards a solution for the problem of global warming will be difficult, but the potential cost of not doing anything now, while we still can, will be thousands of times worse. The current increase in Hurricane activity will be nothing compared to the devastation caused by rising sea levels and other effect of global climate change.
There is no way any one person can do this alone but if we join together anything is possible. The time to act is now. If we don’t work to preserve the delicate balance of our climate, the future will most certainly bring about disasters many times worse then what we have so far experienced. Please, help me to create a more responsible attitude in our government. We’re all in this together.

To get involved please send a short email to responsiblefuture@gmail.com