Saturday, March 31, 2007

The need for Vigilance in Science

In science, contrary to popular thinking, many hypotheses are incorrect. In fact, considering all the published papers, most of the ideas presented will eventually turn out to be substantially false. The importance of these ideas, even those that will become false, comes from the rigorous testing methods that can prove the veracity or errors present in the initial hypothesis. As a tool, the scientific method can become useful in assessing the likelihood that a given theory can be upheld with incoming data. Science therefore, must be supported through experimental means, beyond theoretical assumptions. The tools at our disposal, are far numerous to count. As an example, computer simulation can be a powerful determinant when it comes to proving certain hypothetical claims. Further, numerous analytical techniques can correlate data into a comprehensive understanding. When considering evolutionary theory, Natural Selection remains supported through hundreds of different methods present at a scientist's disposal. Through molecular genetics, radio-isotopic analysis, taxonomy, paleontology, comparative anatomy, and numerous other converging fields, the Theory of Evolution through Natural Selection is not only supported, but strengthened and refined. With the development of newer tools and even more specialized techniques, specific details can emerge and add to the mountain of data already present.

Having been exposed to the thrills and rigor of evolutionary theory, it's striking that as comfortable as one becomes with a given subject, the likelihood for a breach in upholding the standards practiced at first, increase rather substantially. Since the field of evolution is so vast, theories abound in a seemingly chaotic fashion. Some remain conserved from the moment of inception, and others are as likely to change as autumn leaves in temperate locales. It seems as though some theories are presented just to strengthen the opposing argument while others are just like small stepping stones, aiding to an all encompassing bigger picture. With so much mercurial transition, the danger of complacency increases in a staggering manner. Certain theories seem logical, and therefore, so intuitive that they are grasped as though they were proven with little doubt. These are "fashionable" ideas that can vary from replicable and probable, to absolutely impossible. An example is the radiation of mammals during the Cretatious/Tertiary era (approximately 80 million years to about 40 million years ago). It was long assumed that before the extinction of dinosaurs as well as 75% of other organisms on Earth, mammals were simple, shrew sized animals living nocturnally and barely scraping through an existence. Further, it was only after the K/T (65 Million years ago, otherwise known as the end of the Dinosaur Age) extinction event that mammals had the freedom to radiate and fill various ecological niches. As intuitive as this theory may seem, it has recently been proven largely false. As it turns out, through molecular analysis (of various mammalian DNA), it turns out that most modern mammals had 2 major radiation events where they evolved into numerous species. The first was well within the Dinosaur age, at about 80 million years ago, while the second event was well after the extinction event, dating to approximately 55 million years ago. Those mammals that did radiate directly after the K/T extinction were eventual evolutionary dead ends. They have left no known modern ancestors. The Mammals that exist on Earth today are a result of the aforementioned radiation events, and not the latter that lead to the post-extinction radiation. With the molecular data pointing to these two dates, the challenge now falls upon the paleontologists to match the fossil record with that of the molecular evidence. What this new finding means is that although early mammals were indeed the size of shrews, they were genetically very diverse. They went through two periods of explosive diversity, followed by slower evolutionary changes. Although this new data increases our understanding as per the dates of the events, theories as to why these occurred when they did are now being published. What lead to these two periods of radiation? Was it subtle changes in the Earth's climate? The configuration of the continents? The diversity of flowering plants, or insects, or items that were consumed by mammals?

Having spoken of the dinosaur age, certain assumptions of fossilizations must also be disassembled. It was long thought that fossils could not preserve any genetic material for tracing. Until recently, most paleontologists expected fossils older then 50,000 years to have very little chance of preserving any observable material. They assumed that mineralization of the tissues would be complete, and no actual tissue could be left preserved. Even insects fossilized in amber were thought to mineralize from the chemicals present, and have no usable tissue remaining. The assumption was proven wrong when a paleontologist by the name of Mary Higby Schweitzer of North Carolina State University and colleagues, recovered what seemed to be actual tissue from a Tyrannosaurus Rex sample. As it turned out, this fossil was preserved in sandstone, and even delicate details were present. With further processing and new molecular imagine techniques, some actual collagen (connective tissue) was recovered for DNA analysis. As it now turns out (with further independent verification required), T-rex was closely related to modern day Chickens. Birds therefore, are a direct descendent of a meat eating, bipedal, therapod dinosaur.

Having earlier delved through the confusion that abounds in mammalian diversity, other aspects of evolutionary theory are just as difficult to understand. The former example (of mammalian radiation) provided the fallacy of "compound intuition". The next example will shed light on the fallacy of "convergent observation". Certain parallel behaviors that we observe in nature can seem to have a common root. A common fallacy is to assume that perhaps those behaviors share a genetic basis. In fact, what we observe can in fact be due to convergent evolution that uses an optimal survival strategy. It will become apparent that an organism doesn't necessarily need a specific "gene" for useful strategies to perpetuate its survival. For example, just as a tropical fish will flee into a small crevasse in coral to escape a predator, an arctic lemming will dive into a small hole to do the same. Although these two strategies seem similar superficially, the organisms do not share a "flee into a small hole" gene. Their strategies are the optimal best to ensure survival therefore they remain within those organisms. The genetic tools they use to escape are completely different, even though the end result ensures survival. Similarly, genes that control social organization among species can vary greatly. The same optimal survival strategy that dogs use in pack situations, ants use in colonies, and naked mole rats use within their own hierarchy is similar to those of our own species. Organizing into cohesive social units furthers our chances of survival, although the genes that govern this behavior are completely different. Moreover, similar convergence in evolution can be found in the development of the eye. As it turns out, the ancestors of various modern species evolved eyes completely independent of each other. The eyes of the box jelly fish, or the mantis shrimp, are completely different then that of human eyes. Yet, in an organism's development, some genetic sequences that govern the placement of the eyes are very similar (hox genes for example). This similarly however, does not mean that there is a genetic link between the development of the eye in these organisms. What actually happens is that the environment dictates the advantage of a sensory organ for sight, and as certain evolutionary trends evolve, gene sequences are used that are similar between these organisms for the same function. To simplify, if jelly fish and humans both use the "Z" gene for eyesight, it doesn't necessarily mean that they both had a common ancestor that used the "Z" gene for sight. At some early phase of development, the ancestors of jelly fish and humans acquired a certain gene sequence ("Z") that independently resulted in governing the development of the eye in these two organisms. If looked at superficially, it would seem to some that this ancestral organism (Concestor, using a word invented by Richard Dawkins-- one of the most well known evolutionary biologists) had used the "Z" gene for eyesight and then the branch the lead to the jelly fish/human split acquired this characteristic. In reality, the Concestor passed on the gene first, and then some time later, the progenitors that resulted in jelly fish acquired the usage of the gene for eyesight, just as those early organisms that resulted in humans did independently as well. Naturally, this is an oversimplification, because the common ancestor between what later became humans and jelly fish existed over 500 million years ago.

Finally, after Gregor Mendel's legendary experiments with peas and genetics, followed by the discovery of the actual carrier molecule for those genes (DNA), many geneticists felt that soon, genetic inheritance would be completely uncovered. It was assumed that within a few decades after the initial discovery of DNA, all would be known about genetic inheritance. As it turns out, those assumptions could not have been more wrong. As we've come to realize, genetic inheritance isn't as simple as once was thought. The simple assumptions that the interplay between dominant and recessive genes, along with the sexually selected genes determined inheritance. It was also thought that each gene coded for a single protein, but as our understanding of molecular biology and chemistry improves, we now know that things are far more complex than assumed. The same genes can code for various different proteins if they are placed different locations with different activator sequences. Other genes code for nothing but unused DNA. Furthermore, the concept of imprinting greatly compounds our understanding of Mendelian Inheritance. With mammalian imprinting, the male or female parental genes can disable the other partner's and as a result, the offspring will only retain one copy of that gene. In other words, the gene becomes useless because it's function is blocked by one of the parents. Although some traits can easily be explained through Dominant and Recessive genes, other traits are a result of the complex interplay between numerous genes and imprinted genes within an individual. In fact, even environmental changes can determine the expression of certain genes. Not only genes in an existing individual, but the changes in certain sequences can effect individuals many generations down the line. For example, under the newfound field of epigenetics, scientists are realizing that obesity can alter genes in such a way that many generations of descendents can be effected by Diabetes, among other medical ailments. In essence, the processes are so complex, that it could take hundreds of years to decode the workings well.

In essence then, science will always shift in new directions, with additional information arriving. Observation is thus, the most important trait in science, and as we invent new tools to further our observation, and then theorize and explain those observations, our understanding of the universe will continue to grow. As certain theories are invalidated, our understanding strengthens because now we can rule them out. Further, even more questions will arise, as some of those are answered and others discarded. This is ultimately the beauty of science. Errors will always be useful because they help focus our understanding and strengthen or weaken existing theories. Science is therefore alive and will evolve with our progress. As an example, before the car existed, the wheel must have been invented, followed by the cart, carriage, etc. Similarly, incremental steps are so important, that we cannot take them for granted. After all, a ladder can't be climbed by great leaps, but step-by-step (of course, occasionally, you can take two or three steps up the rungs, but you also risk falling, just as is done in science). Thus, most apparent breakthroughs are not enormous leaps but lead to rapid descent followed by yet another surge towards the top. Therefore, with vigilance comes momentum and progress.

Thursday, March 15, 2007

The Rifle Shot that Blew my Mind

Having just seen the Oscar winning movie Babel, a few realizations of human nature, and our consequences on the fabric of the world come to mind. Without spoiling too much of the movie, the whole movie can be summarized as consequences from actions that seem trivial and insignificant at first which can subsequently snowball into complex and intertwined larger problems. A "causality cascade" as I will call these types of events can occur without anyone's knowledge, and with no determined directionality. In the movie, an avid hunter from Japan leaves behind a rifle in gratification for the good job his Moroccan guide did providing him with optimal hunting locations. This rifle, eventually getting in the hands of mischievous children, leads to a shot on a tour bus, that snowballs into a causality cascade, eventually resulting in a complex interwoven story of how separate lives can combine through a rather insignificant event. Had the hunter never made it to Morocco, or had the rifle never exchanged hands, or any number of other scenarios, the actions that resulted in tragedy and loss would never have occurred. All of these events, therefore, transpired without any predetermination in the part of the people involved at the fate of their lives. Events such as these are nothing new to philosophers and even scientists have mathematical equations describing these cascade events known as Chaos Theory.

A causality cascade could be anything that snowballs into something larger. In effect, it's like an uncontrolled chain reaction with no predetermined intention. When an atomic bomb undergoes fission, the neutrons in the atoms start a cascade chain reaction effecting others exponentially until the immense powers of those nuclear reactions are released. In this instance, there is a clear predetermination as to what the subsequent result will be. The neutrons do not undergo uncontrolled chain reactions like the causality cascades, because the end result is a mushroom cloud, and everything must result in precise timing. Causality cascades on the other hand, as already mentioned are not predetermined, and are extremely uncontrollable. Events can effect other events in such ways that could never be imagined, because there are an infinite amount of possible outcomes from each event. Chaos theory attempts to describe these events, whether they involve atoms, computer generated fractals, or even human actions, into a mathematical model that attempts to predict various probabilities on possible outcomes. At the point of infinite variation, it's impossible to predict exactly how an event that is so complex will turn out, yet there are events that can be more likely to occur then others. It's similar to quantum effects* on atoms. It's impossible to predict the exact location of an electron orbiting an atom because measuring and observing the location of the electron forces it to change, and alter its initial state. Therefore, the best one can hope for is to determine a probability of where the electron may be. There is a chance that the electron itself can be found at the other end of the universe, and with trillions of electrons, it's very likely that one may end up there through some complex quantum effects. Yet, through probabilities, the electrons are more likely to be found in certain regional distributions, and the greatest amount will be found in certain areas orbiting atoms. Taking this in mind, it's possible through causality cascades to have a butterfly flapping its wing in Mexico, effecting the weather to the point of a hurricane developing in the Indian Ocean. The displaced air molecules from the butterflies wings can convert into a type of chain reaction and eventually lead to enough "momentum" building in the changes of air flow to feed a system over the Indian Ocean, resulting in a Hurricane. The probability of this specific event may be extremely low, but with all the air molecules, and all the small effects of butterflies, birds, dragonflies, and other such causational events, the probability that these can cascade into a large scale atmospheric event is almost certain. There is no way to predict which specific butterfly can cause it, but it's possible to predict the probability that these small scale events have in effecting larger ones (100% since all larger events start with smaller ones that cascade).

Our actions on a daily basis will therefore, inevitably lead to an infinite number of causality cascades, some which we consider good, and others which we consider bad. For example, perhaps giving the right of way to a driver waiting on a busy free-way onramp, will result in that driver's awareness of others, and through due course and time, this will cascade into good will spread upon numerous individuals, perhaps cascading into someone's life being saved. In the same token, it's also possible that cutting somebody off, will result in the driver's behavior to become erratic, and through numerous other chain reactions, one of the angry drivers along the way will do something rash enough to cause an accident and involuntarily take a life. Finally, a third possibility is that what one perceives as a positive event can become negative to others. For example, taking the same driving scenario mentioned, perhaps suddenly breaking to avoid large debris on the freeway may be beneficial to the individual driver, and the avoidance a positive event, yet, the reaction may cause more disastrous results to drivers following behind. It may be a positive event to one life, but its negative impact may be felt by dozens of others following behind. In another example, if a small child was choking on food particles, and one were to assist in saving the child's life, it would definitely seem like a positive event. However, what if this child in turn became a Tyrannical leader who's path of destruction lead to the death of millions, wars of aggression and perpetual hostility? Then what seemed like a good deed, could in fact have been a great disservice. If one knew ahead to time, that said child would turn out to be Hitler, the morality of the situation would definitely be difficult to assess. These scenarios show the complexity of causality cascades, and how their effects cannot be trivialized or minimized. There is no way to avoid effecting events along the chain when one has no predetermined notion as to what will follow. Yet, there are scenarios high in probability that are more likely to occur when one analyzes the events thoroughly and attempts to discern some form of causality.

Having defined and explained causality cascades, one need look no further then those individuals in prominent positions of government to realize just how much power they have over events that effect every individual's life. The causality cascades that you or I are able to initiate in our lives are infinitesimally small, compared to those that Bush, as well as other "leaders" are capable of. Bush's decision to launch an aggressive war on Iraq leads to the destruction of an infinite amount of lives, over such flimsy reasons as weapons of mass destructions. When the excuse for invasion failed to materialize, other excuses such as freeing the Iraqi people, or spreading democracy in the region were provided. Ultimately however, countless lives have been directly changed on account of specific actions taken without much consideration to possible outcomes of events. The civilian lives that have been taken in Iraq as a direct result of these actions, along with the billions of lives in the world that have changed, are the result of one man's determined and faulty mind. When we elect those who are supposed to represent the people, we rarely consider just how much power we are providing them. These people shape the future of the world. Going back to Bush's example, not only did his invasion cost over 3200 American soldier's lives, it also cost over 100,000 Iraqi civilian lives, and indirectly, the infinite lives of those who would have been born had their predecessors not have been killed. Perhaps one of those soldiers would have fathered (or mothered) a child who would have discovered the cure for AIDS. All of these potential human beings will never exist because their parents were killed as a result of a few poor decisions. What would the world have been like if Gandhi's father was killed by the British? Or how different would civil rights in the United States have been had Martin Luther King's mother been lynched? What if Philip of Macedon, Alexander the Great's Father, been killed in an intradynastic feud? All of these questions become obvious when we realize that each person has the potential to influence countless other lives, either positively or negatively. Most of us influence lives completely oblivious to the chain of events that unfold, but other's have so much power, that their decisions determine the course of human history a thousand fold as compared to ours. Although we are all able to determine the course of history because just being alive and interacting with the world changes the causality of the situation, the scale at which we do it can differ. Those who hold the reigns of authority have the power at larger scales then others. We are enabling them to determine the fate of the world, and are oblivious to the nature of their capabilities.

Ultimately, causality cascades can be found in the same uncertain philosophical grounds as notions of morality such as good and bad. Attempting to define causality cascades as good, and other's as bad can seem like a moot point, considering our ignorance at the ultimate effects our actions may take. However, just being aware of the profound multilayered interactions of our lives can be illuminating in itself. Knowing that defining such events as good and bad can become a lesson in futility, the act of defining cannot be completely dismissed when taken in an attempt at furthering our thinking. The traits that have allowed human beings to transcend simple instinctual urges, and have allowed us to pause and reflect, are thus furthered with the knowledge and questions that we ask about our nature. Causality cascades are an important aspect of self definition and growth because we have the heightened senses to be capable of the awareness of our actions and the possible consequences they may entail. Yet, just because the potential exists for such deep introspection, the application of it is based on an individual basis. Most of us have the tools to further our understanding of the universe and ourselves, but because of various barriers and filters (Such as certain religious beliefs, cultural nuances, social standing, and serendipity of living comfortable enough lives to be so introspective), many are not able to exercise such potential. The most unfortunate side effect of this wealth of potential, is that those who should be required to tap these tools within us live their lives thirsting for material gains, power control and petty squabbles that don't matter much to the greater world. By this, I mean the elected "representatives" of the world. How long will we allow these bickering, selfish, self absorbed, narcisstic, and ineffective individuals ruin our futures before we stand up and fight? We are lead to believe that the most important things in life are acquisition of wealth, and superficial trappings of civilization, when in fact, we're ignorant of the greater good that society can offer. We are so entrenched in our immediate lives, that we're ignorant of the greater potential for humanity. We watch news to uncover updates on Anna Nicole Smith and Paris Hilton, when in fact, we should be concerned about the advancement of our species and the survival of our planet. In the end, the future of the world will rest with how we define ourselves, and come to understand the consequences of our actions upon the planet. Just like a butterflies wings, small effects can have enormous unintended consequences. We are all small effects, but we're not inconsequential. After all, causality cascades cannot rule out the potential for even one human being (further reducing that idea, such cascades cannot even rule out the behavior of an atom, but with human beings, our actions can be consciously analyzed, and reflected upon).

*Quantum Theory in Physics describes the interaction and effects among subatomic particles.

Saturday, March 10, 2007

Charles Darwin: Myth from Reality

Through countless conversations with most intelligent people who are not well versed in topics of Evolutionary Biology, I have come across a thread of resistance because of who they think Charles Darwin Represents.

To many, Charles Darwin is an antagonistic entity, bent on destroying faith, and relegating mankind to nothing but oblivion. Some philosophers, having absorbed evolution and natural selection have become Nihilists, envisioning no purpose in life, and exhibiting the lack of hope associated with their lack of faith in anything. It's easy to fall prey to hopelessness when one's faith and beliefs are shattered, but as I have attempted to explain in my previous essay, just because we find ourselves insignificant to the universal order of things, it does not mean we are insignificant to each other. What matters is our relationship to those around us and our world. The Earth is our only home, and every human being who has ever existed was born here (paraphrasing Carl Sagan). Perhaps one day, there will be other worlds to inhabit and other places humans will be born, but until that day is here, our planet is the most significant thing in the universe because it is tied to our existence.

What Charles Darwin uncovered, was the process through which we came to exist on this planet that has and will, for the foreseeable future, be our home. The process of Evolution through Natural Selection has existed on Earth for Billions of years. In fact, it's possible that life on Earth in its infancy was seeded from perhaps rudimentary amino acids, or even something as complex as bacteria, from outside our planet. Yet, this does not change the fact that for at least the last 3.5 billion years, organisms have evolved to inhabit every corner of our planet. Darwin is vilified for any number of reasons, but all he did was uncover a process that had existed with or without his scientific contribution. Darwin did not invent Evolution because it had existed before him. Many religious extremists will deny these facts, but that is in large part to their ignorance as it pertains to science, and biology. We don't celebrate Charles Darwin's discovery because it destroys the faith in some people, but we celebrate it for helping us better understand the world that we live in. When Newton and subsequently Einstein described the laws and function of gravity, they only helped uncover forces that had existed since the dawn of the universe. Scientists are ultimately detectives who after coming across clues and evidence, eventually build a better picture of the world to help solve certain mysteries. We should appreciate the fact that those very same evolutionary processes that help a dolphin or bat to echo-locate, or a snake to swallow pray larger then their heads, also helped shape and force our minds to communicate through language. We can't fall into the trap of expecting a miraculous or divine process to suddenly develop language in an upright largely hairless ape. We were lucky enough to be shaped by our environment to communicate effectively and intelligently with each other. We can convey such complexities through words alone, that in of itself, is an amazing development. Just because it's amazing however, does not make it miraculous. It's true that some aspects of this development are still uncertain, but through rigorous testing, simulating and understanding, we will get that much closer to perceiving these natural processes.