Wednesday, October 31, 2007

Legitimacy of the Founder Effect

One very pertinent question that always comes to mind when looking at the Founder Effect is the viability of the extant founder population and the subsequent deleterious effects from the lack of genetic diversity in their offspring. How is it possible for the offspring to continue to be viable when their genetic diversity is so severely reduced? We often hear about the likelihood that a population of less then 500 founding individuals is doomed to fail because they lack genetic diversity causing lethal alleles to accumulate through inbreeding. For example, the state of the Cheetah is in peril because their species went through a recent genetic bottleneck which lead to only a few individuals surviving and passing on their limited genetic diversity to future generations. In fact, cheetah's are so similar to each other that one can swap organs between two regionally distant animals and due to their histocompatability, their bodies will not reject the donor organ. This means that the organs of one cheetah are recognized by another cheetah's immune system as though they came from the same body. In essence, the variation between proteins on the surface of the cells (major histocompatability complexes) are small enough that there's a lack of an antibody mediated immune response, minimizing cross-donor rejection. This reduced genetic diversity limits the adaptability of the cheetah and major stressors can severely crash the population. Thus, the question once again can be restated by asking why are certain species able to cope with such limited founding diversity and suddenly flourish, while others are prone to extinction?

To further investigate this question, one must delve deeper into understanding not only the Founder Effect, but the interplay between Genetic Drift and Natural Selection as well. All of these factors occur to help perpetuate speciation. Speciation can occur when one or more daughter groups are isolated from the founding group, or the founding group itself branches into two or more extant populations that are isolated enough from each other to speciate. There are four main methods of speciation, ranging from complete geographic isolation, to mostly geographic, somewhat geographic, and finally no geographic barriers at all. Island populations that suddenly get cut off from the mainland when sea levels rise speciate due to complete isolation. Some species evolve to occupy certain ecological niches within the same geographic area. For example, perhaps a mutation for a slightly thicker bill in an outlying area within the same geographic boundaries results in a finch that has a thicker bill and perhaps the ability to extract insects from dead bark. This group then eventually exploits the rotten wood insect niche throughout the initial geographic range.

Genetic drift then is the random rate of variation that occurs within a given population and depending on the initial numbers and environmental conditions can be either kept in check by Natural Selection or allowed to proceed. Smaller populations are more likely to undergo genetic drift because of the limited genetic diversity, while larger populations intermix well and barring environmental changes that open new ecological niches for certain groups within the population to occupy leave little room for major drift. Natural Selection functions by allowing only those alleles that are biologically or reproductively adaptive to perpetuate, while genetic drift is just the random shuffling of alleles mostly irrespective of the adaptive pressure. Examples of Genetic Drift in Humans can include epicanthic folds in the eyes of Asians, increased hairiness in the bodies of Mediterraneans or Okinawans, Blond Hair and Blue Eyes in Scandinavians, wavy hair in Polynesians, and etc. Examples of Natural Selection in Humans on the other hand include darker or lighter skin, thicker, stockier builds in colder regions, barrel flared chests in Andean and Himalayan people, reduction of perspiration in Australian Aborigines, etc. It must further be noted that not all of these human characteristics are strictly a result of natural selection or genetic drift, some are a product of the interplay between the two forces.

Coming back to the Founder Effect then, we can look at a hypothesis as to how New World Monkeys came to Occupy the Americas when in fact, there was already a large gap between the continents when their ancestors branched from their African counterparts. It has been established, through the fossil record, and mitochondrial analysis that New World Monkeys emerged approximately 35 million years ago (link), during the early oligocene. At the time, the geographic distance between Africa and South America was at least 1300 miles (link) and therefore, quite a barrier for a founding population of pioneering monkeys. Vegetative Rafting has been proposed as a solution to the large oceanic gap that was bridged by these accidental voyagers. Due to the large volume of water discharged in the rainy season within Tropical locales, occasionally large swaths of vegetation get swept out to sea by huge rivers like the Amazon or the Congo. These vegetative rafts then float hundreds of miles out to sea, usually drying up. However, with prevailing winds and currents, some of these rafts can travel quite far, and this is the possible scenario that lead to the ocean voyage of some African Monkeys. This initial founder population then must have been very limited, perhaps a half dozen individuals. The genetic analysis has shown that they all originated from a small group of founders (just like a population bottleneck) but because of the rich geographic and environmental diversity, their populations exploded and speciated. In particular, population drift probably had a very large role to play in the diversity of current New World Monkeys and the ecological niches they occupy. The Question again is how this small founding population, with limited genetic diversity, blossomed into numerous species, irrespective of the initial inbreeding that could have resulted in numerous lethal alleles and population crashes. Several possible theories are likely, but none definitively stand out. Perhaps some animals are better able to cope with limited genetic diversity. Or, perhaps the new ecological niches helped increase the rate of speciation and variation within the population. Given that Genetic Drift had a large part to play with the small founding population, how did that effect the likelihood that lethal alleles were mitigated.

Such questions are the reason why Evolutionary Biology is such a fascinating field of study, and rarely are answers as complete as one would like. However, should anybody reading this have better knowledge on any of these topics or answers to my questions, please e-mail me or let me know in the responses what possible theories or holes in my reasoning can help to further illuminate this subject.

**02/17/2009 Update
The possible role of r/K selection in the founder effect.

The concept of r/K selection describes the selection of certain traits which promote success in particular environments. It comes about from an algebraic equation related to population dynamics. In general, species that are K strategists have increased investment in fewer offspring, while r strategists maximize the amount of offspring with as little investment as possible. Competition is the major key differentiating these two strategies. Since r strategists have little competition, they can focus on increasing their numbers as quickly as possible. Yet, once competition pressures increase as new species come about, other strategies, such as more investment in less offspring, evolve to cope. Ultimately, an ecological balance is reached between r and K strategists. From this, the relevance to the founder effect seems intuitive. Founder species, especially those like the ancestors of New World monkeys must have been r strategists. Finding themselves in an environment with countless niches, they must have reproduced quickly and evolved to fill them. Once enough speciation occurred to sufficiently increase competition, some monkey species may have adapted towards K selection.

Still, even though we can identify the ecological process that r/K selection plays within the founder effect, we must still explain the eventual success after the initial lack of genetic variability. Perhaps r strategists, with their hi fecundity, mutate rapidly enough that their genetic diversity is readily expanded within a few hundred generations, reaching a critical threshold when lethal alleles are balanced with genetic variability. The critical number of founders certainly differs among species, with those that are K-strategists probably requiring a larger gene initial gene pool. It's also possible that some species, regardless of their ecological strategies, are naturally prone to greater mutations; perhaps a less accurate DNA repair machinery, or environmental constraints that increase the adaptive advantage of survival through increased offspring variability.

Saturday, October 20, 2007

The Embrace of Atheism

Reading through some of my early blogs, even up to February of 2007, I realize how non-dramatic my acceptance of atheism has become. Initially, I viewed myself as an agnostic because I thought that there is no way to be conclusively sure that the physical universe is all that we have. Since we cannot rule out the existence of the supernatural, then agnosticism seemed the best view. The simple change that occurred was the inclusion of probability. The probability that something supernatural exists is infinitesimally small. We can't use the tools of science to prove the supernatural. We can attempt to explain the processes of the universe without invoking the supernatural, and through various fields of science, we have been able to probe and investigate our environment. We have developed tools that have shown the reason for the variability of species, why large bodies stay together, why subatomic particles don't float apart, etc. Just as the probability is infinitesimally small for the existence of gnomes that invisibly live in the attic of houses older then 100 years, yet, their existence cannot be proven because as soon as they are attempted to be found and sense this by magically disappearing, the probability of an invisible being occupying some unexplainable space controlling our every thought and answering prayers as sees fit is also just as unlikely. The difference being is that more people have faith in the omnipotent being then the attic gnomes. There may even come a time, after thousands of years that a large group of people come to believe in attic gnomes because nothing else, including their idea of ghosts can explain the noises. Yet, this doesn't change the fact that believe, either widespread, or limited, does not prove the existence of anything. With this in mind, I eventually realized that I cannot continue to remain "on the fence" just because some things cannot be disproved. Therefore, yes, however unlikely it is, there is a small chance, an infinitesimally small probability of the truth behind a religion or another but knowing how well science can explain and predict the universe (even with so many unknowns, the fact that we have grown so much in our knowledge within just the last 400 years), I can happily shed any remaining doubt and exist for this life that we have. Considering even one atom of change within any ancestors we may have had could nullify our existence, we should be happy to have the life that we have. We get one chance to live a life and use our potential as best we can. Sure, we can pursue a life of destruction, and neglect, but knowing that we only have one chance, and exercising the chance for the best possible outcomes is a venture that cannot easily be explained. Our destiny as a species is within our hands, not in the hands of some invisible beings, or whatever, but in our common goals for preserving this one world that every single creature we know of has called home. If we rely on some existential, outside force to govern our behavior, we are doomed to repeat the ineptitudes of the past, and never learn from our mistakes. To grow and prosper is to understand and love the world which we are a part of; to understand the creatures and use our knowledge for good. The topic of morality, and where it comes from in our evolutionary past, though still debatable is a part of our society. Although what we know as good and beneficial changes, the progress that we see can allow us to use our potential for good. We're still agnostic in understanding our evolution of morality and ethics, but with our skills as investigators, time is but a testing field for discovery.

Friday, October 19, 2007

Comfort in a warm religious blanket

Considering the extensive role that religion and spirituality have played in the lives of many, synthesizing a single explanation for those trends in the human species is a difficult, if not futile, prospect at best. However, keeping in mind that no single explanation can be effective in illuminating our understanding of why humans evolved, whether culturally or biologically, with some sense of the supernatural, we must nevertheless attempt to find a few basic root principles. Many of these principles have been expanded upon in great detail from authors such as Richard Dawkins, Daniel Dennett, and Jarod Diamond. The works of an evolutionary biologist, an evolutionary philosopher and a geographer with a linguistic background have greatly aided in our understanding of the biological, psychological, and environmental factors at play in allowing human beings to dominate most ecological niches and progress to our present form today. The concepts they discuss are just the beginning of a paradigm shift towards evolutionary explanations for physical, behavioral, and psychological traits. The belief in the supernatural therefore, has to take into account our evolutionary past. It should be understood that natural selection is not a wasteful process, and anything that is counter towards a species survival is culled before it can become well established. The belief in the supernatural can be a proximal product of some other evolutionary process, or a discrete product that aided our survival. At the moment, the range of opinion varies greatly, but each view is proposed in an attempt to explain the reasons for the expansive existence of religion and spirituality. Some behavioral and psychological traits among human beings are cultural in origin, while others are biological. Generally, the traits that the majority of human beings across different cultures share must have some basis in our evolutionary past. Laughter for example is a cross-cultural trait, and has been shown to have an evolutionary basis. Since spirituality and religion regardless of actual beliefs is a shared trait across the globe, an evolutionary biologist will look with interest into what processes evolved to help perpetuate it.

Of the various evolutionary traits that may provide the proximal outcome for religious belief, comfort and authority may be the most salient. As Richard Dawkins discusses in the God Delusion, authority is ingrained in us since childhood because it aids in our survival. Human children are born so helpless, that only through direct exposure in a culture, will they develop to their evolutionary potential. The initial learning required to effectively navigate through life, and therefore propagate to the optimal potential, requires at least two decades in human beings. We are social creatures, and with so much danger in the world, we're born with built in authority seekers. We need to learn from the experience of those older then us, especially parents, during our formative years. Perhaps this receptive ability towards authority when we're young blinds us to continue following authority when we're older. Certain traits don't necessarily shut off just because of an age difference. Although important for survival in our youth, this trait has lead us astray when we seek to follow those with authority who may actually not have our best interest in mind. For example, a parent might tell a child not to poke a sleeping bear with a stick, and if the child does not listen, then natural selection will effectively cull this trait from the gene pool. As the same child becomes an adult, perhaps the village chief will tell this individual that the only way the rains will return is if he pokes a bear with a stick. Now, this act is not in the best interest of the individual, but because of the authority seeking ability ingrained in us, most will do as told.

Another evolutionary trait that must be discussed is our need for comfort. This may not seem as discrete a trait as that of authority seeking, but it has a very large part to play with our persistent religious beliefs in the face of so much contrary evidence. As a species, feeling security is tantamount to survival. If there are large land predators around, then the security of a tree will aid in the survival of the individual. Similarly, as humans evolved from an arboreal species to a terrestrial species, we relied more and more on creative solutions to seek comfort. Various examples include enclosed dwellings, such as caves, or ones that we create ourselves, such as houses. Since we're able to control fire, this gives us an added feeling of comfort and security. As most mammals, it is ingrained in us to seek the shelter and comfort of our parents. Just as one cannot turn off the need for authority as an adult, one cannot just turn off the need for comfort either. Religion to some extent provides this safe cozy blanket that shields us from the harsh world around. It gives authority to the supernatural, and we justifiably feel safe from the cold reality of the world. Whether believers feel obliged to seek comfort in a singular authority like God (as in monotheists like Christians, Muslims, Jews, Sikhs, etc), or a varied scope like the Hindus (among other polytheists), they share the need for some comforting authority. Even among animists (non organized religion, or folk religion), like the folk religion of most early hunter-gatherers, they often sought comfort with the belief that their dead ancestors had control over their lives.

With comfort and authority in mind, it becomes partly obvious why people across different cultures reach to the supernatural when faced with so much contrary logic. Science cannot provide the same warm comforts, at least psychologically, that religion can. When one bases their belief in the physical world that we live in, it's somewhat disconcerting to realize that there isn't an omniscient and omnipotent authority figure looking after one's best interest. Conversely, without such an authority figure, it frees us to seek guidance in the realm of science and the laws of the universe. The meaning of life can change from "God wanted me on Earth" to "How do I understand the physical processes of this amazing and vast universe that I live in?" When one is freed from the bonds of religion and authority, the freedom that's available is refreshing. There may be a part that misses that warm comforting blanket, the reassuring being(s) looking out for one's best interest, but even then, it doesn't make the existence of a higher power more likely. Just because there is a need in people to feel comfort and security even in their adult years, it still doesn't necessitate the supernatural. For example, if a billion people on the planet think and need to believe that God created the Earth as the center of the universe for it's sheer importance, it doesn't change the fact that this belief is wrong. We know that the Earth is just the third planet, from a negligible star, in an ordinary corner of an ordinary galaxy and no matter how much one would like to believe otherwise, science through its empirical methods and scientific reasoning has shown us the truth.

One must therefore strive to seek comfort and security in the physical world as we know it. Some may argue that it's arrogant to think we evolved through natural selection and random chance mutations. Instead, these people think that we must submit ourselves to the will of some entity that is largely a creation of our amazing imaginations and our need for comfort and authority. Others will have spent years of their life in a religious institution that has never been able to properly investigate the universe around us. Without a deep understanding of the physical, biological, and chemical processes that makes our existence possible, how can one understand life? This is the ultimate reason why those of us who have embraced science to the fullest have no regrets or empty voids that must be filled through some supernatural means. Comfort is nice, blankets are warm, but without shedding the blanket and investigating our environment, we are no different than creatures which we consider inferior to our intellect.

Wednesday, October 17, 2007

Progress from Genocide Denial??!!?!!

Along the long global march towards technological progress and the expansion of our scope as individuals, our sense of morality and ethics has concurrently evolved. The progression of morality does not occur at the same rate throughout the world, but in most modern nations, what was once considered common behavior is now becoming obsolete. For example, slavery, which was once acceptable in various societies, is now obsolete as a social institution. Other examples of archaic beliefs include cannibalism, human sacrifice, medical procedures like trepanation, etc. Various other beliefs have been completely overturned, largely based on the scientific method, and technological advances. The reasons for these trends are debatable, but once comes away realizing that our sense of morality, ethics, justice, and equality have all progressed consistently. There will always be pockets of resistance, but eventually, even the most conservative positions will seem archaic. For example, if we take Western Europe in the late 19th century, many progressives (for their time) recognized that those of African extraction were born free and should never be thought of as slaves. Yet, even the most progressive and liberal individuals felt that they were superior in race to these very same Africans. Although such belief can still be encountered, many of the progressives today, recognize that race is largely a construct of our need to categorize, and that ultimately, there is not such thing as a superior race. Most of this modern progress was brought forth from the fallout of the Eugenics movement, and the Nazi regime's infatuation with superiority.

Having largely described the progressive trends that has been described as a Zeitgest (German for current at some point in time), it becomes clear why the thought of another event with mass casualties and large scale warfare like that from WWII is harder and harder to imagine. Hopefully, diplomacy is starting to win out over the need to launch such global scale wars. In fact, the unfavorable opinion of many from the current Iraq war makes us realize the loss of life to such ill conceived wars is become more and more unbearable to people. Thought the loss of life from Iraq from a military standpoint is less that that from the Vietnam war, people are less tolerant of such casualties. Furthermore, the loss of civilian life cannot be underestimated. We now have a deeper understanding of just how many lives these wars cost, thanks to a larger net of global information.

With social progress in mind, we must never forget how far we've come ethically and morally. In order to continue to move forward, we must accept our previous moral indiscretions and move on accordingly. This is why the Armenian Genocide Resolution in Congress is such an important event in the minds of many Armenians. The Turkish Government fears that recognition of the Genocide will result in restitutions to the families of the survivors. The truth is, restitution aside, it's our moral duty and obligation as human beings to begin to accept such acts and bear personal responsibility for such events. Another issue in Turkish denial is that the Modern Turkish people cannot fathom how their ancestors were able to accomplish such an act when they themselves have progressed. Yes, there are extremist elements in Turkey, and the Kurds are to some extent suffering similar fates, but even so, most enlightened Turks can't imagine massacring a people and culture. Yet, the overwhelming evidence, and the total destruction of the Armenian presence in Eastern Turkey is pretty damning and conclusive evidence as to which culture was on the wrong side of the Genocide. If Turkey was truly objective, why go to all the trouble erasing the past as it pertains to Armenians?

Worse then the Turkish denial, was what seemed to be the silent approval by certain allies of Turkey (Such as the United States and Israel, oh the Irony) because ultimately, Turkey provided friendlier to the interests of those states then other nations in the area. During the Cold War, Turkey was critical in Containing the Soviet Union, and helping support Israel. Since the collapse of the Soviet Union, Turkey has allowed itself to be further exploited by the West for profit. Our ethics and morality,especially in the sphere of government, obviously haven't evolved to where the majority think that profit is less important then the well being of others.

Granted, some may argue that due to current circumstances of the volatile Middle East region, acceptance of the Armenian Genocide measure by Congress will endanger the American Troops, and give free reign for Turkey to behave according to national interests. Well, if that's how an American ally will behave, "threatening to endanger our troops", then they aren't really allies in the first place (brings to mind that quote, "with friends like these, who needs enemies"). Besides, waiting for a perfect moment of acceptance of the measure will never occur, because the world is always in a state of flux, and there never is a perfect moment. As sure as the Germans recognized the Holocaust then, the Turks must recognize the Armenian Genocide. Some Cynics will argue that should the Armenian Genocide be accepted, then why not the Hawaiian Genocide, the Native American Genocide, the current Darfur Genocide, among many others. Well, why not accept all these events as genocide and move on. Throughout history, it has been shown again and again that there will always be powerful states, or societies trying to destroy weaker ones. Some are done in the name of god or gods, others in the name of the holy land (nationalism), still others in the name of xenophobia, internal strife, etc. Yet, all these events have a common link and that is that we must recognize so that we can move forward.

Should the Armenian Genocide Resolution not pass the House, or be blocked as it has been in the past, then whatever values those in Congress who didn't support the measure purport to have are completely groundless. The level of hypocrisy among these supposed progressive individuals is staggering. Ultimately, this isn't just a resolution for Armenians, it allows others who have been effected by such measures, such as the Japanese who were interred in US concentration camps during WWII, or Native Americans, Native Hawaiians, African Americans, to come together and build a coalition to prevent such tragedies from every happening again and stop those that are currently in progress (Palestine, Sudan, Zimbabwe, Iraq.....)

It is my hope that humanity will view the early 21st century as the critical moment in time when people stopped living for materialism or hatred of others, but progressed to accept all of humanity as a singular race. We as a species are obligated to help not only each other, but the world that we live in. We must accept and in due course, progress further from these shackles which restrain us to our past. Will civilized discourse and diplomacy win over war and genocide? Will we remain ignorant of other's inalienable right to freedom? Well progress lead us to view our current times as we now view the Middle Ages? Will we stop viewing the world in Black and White, and start reasonably assessing the gray areas in between? These, and many other similar questions should be on the forefront of everyones mind.