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.

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