Newly Discovered Functions of “Pseudogenes”

Abstract

Researchers have noted that there are portions of the DNA that look similar to functional genes, but contain lesions or premature stop codons. These genes have been assumed to be largely non-functional, but recent research suggests that many of these ‘pseudogenes’ are actually functional.  This paper is an overview of some of the research done in the area of  pseudogene functionality. I address several recent advances in the  area of genetic research regarding pseudogene functionality  chronologically, starting from one of the first discoveries of a  functional pseudogene and ending with a paper from this year (2013). Broadly speaking, it would seem that the assumption of non-functionality has been overturned regarding many pseudogenes, and the evidence suggests that many more pseudogenes may have a function that has yet to be discovered.

Introduction
pseudogene_important_role_wide Pseudogenes have been typically understood as portions of DNA  that have lost their function and remain in the DNA as a relic that  signifies past functionality. The prefix ‘pseudo-‘ indicates that  something is fake or false, and a pseudogene is a portion of DNA  that looks like a functioning gene, but is not actually functional. Pseudogenes have been placed in the ‘junk DNA’ category, ‘dead’, non-functional by-products of evolution. If a pseudogene is transcribed at all, it is often considered to be largely a neutral process that hasn’t been weeded out by selection. However, recent evidence has shown that many pseudogenes have very important functions in the genome of nearly every organism, humans included. There are very good reasons to revise the definition of ‘pseudogene’ to include a wide variety of biological functions, from gene expression and cellular function to gene regulation and tumor suppression. The newly discovered functions are making the term ‘pseudogene’ notoriously ambiguous. This review will analyze a small handful of functions discovered for pseudogenes that were previously assumed to be non-functional byproducts of genome evolution. It is not intended to be an exhaustive treatment of newly discovered pseudogene functionality. Functions are being ascribed to pseudogenes on a fairly regular basis in contemporary genetics literature, and some of the literature is reviewed in chronological order.
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The Responses of Anuran Species to Varying Levels of Ultra Violet (UV-B) Radiation


Ultra Violet Radiation and Its Role in Frog Ecology and Evolution
Ultra violet radiation, especially UV-B radiation (280 – 320 nm), has been hypothesized to be one of the major contributing factors to the decline of amphibian populations worldwide (Gardner 2001, Houlahan et al. 2000, Keisecker et al. 2001). UV-B radiation has been known to cause an increase in the likelihood of premature death, as well as malformations and deformations in a large number of frog (order Anura) populations (Han et al. 2007, frog_farm Keisecker et al. 2001, Blaustein et al 2003). While the exact effects UV-B  radiation has on frog development is currently being investigated and  debated,  many conclusions can be drawn from past and current  research. UV-B radiation  by itself is a known problem, but when  combined with other factors (pH,  temperature, water depth, mold) it can  cause a synergistic and additive effect  (Bancroft et al. 2008, 2nd  reference, Gardner 2001).

There has also been a variety of research investigating the role of physiological, molecular and behavioral (Han et al. 2007, Blaustein et al. 2003) adaptations in frog populations. These adaptations are in response to the recent increase in UV-B radiation on the surface of the planet, which has been caused by the recent decrease in stratospheric ozone (Bancroft et al. 2008, Diamond et al. 2002). In some cases, the size of the population may also have an influence the effects of UV-B radiation (Houlahan et al. 2000).

Effects of UV-B Radiation on Anuran species
Exposure to UV-B radiation can cause various types of lethal or sublethal effects on amphibians (Han et al. 2007). These effects include genetic deformations, improper development, various forms of skin malformations, and premature death (Diamond et al. 2002). Due to the recent decrease in stratospheric ozone and the decrease in surface water level in frog habitats, there has been a significant increase in the amount of exposure to UV-B radiation in frog populations (Bancroft et al. 2008).

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You Can’t Bring Them with You – Virtue Ethics & Organ Donation

           Biomedical technology is one of the fastest growing areas of research in modern society. Whether it is reproductive technologies, cloning, genetic engineering or any other topic, people generally approach these with an attitude of both awe and hesitation. Most of us recognize the seemingly limitless potential of new technologies when it comes to curing diseases, elongating lifespans or increasing quality of life. At the same time, we also recognize that these new technologies bring difficult (and seemingly unanswerable) ethical questions. It seems that the reason many people find these questions so hard to answer is that they don’t have a well-established ethical framework from which to answer them. Once we establish an ethical framework, we can explore the answers to the difficult questions. In this paper, I am going to take a virtue ethics perspective on the topic of post-mortem organ donation. I don’t plan on defending virtue ethics as a theory, but I will clarify some of the important issues as they relate to the donation of organs after death.

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A brief look at the medical statistics reveals a significant problem; there is ahuge disparity between those who are waiting for organs and the number of organs available. “According to the United Network for Organ Sharing (UNOS) 83,472 people were waiting for an organ transplant in the United States as of January 2004. From January to October of 2003, 19,101 transplants were performed” (Glannon, 2005). As of today (December 3, 2013), there are 120,845 people waiting for organs in the United States (www.unos.org). The number has increased by approximately 37,000 people in only 9 years, and doesn’t show any signs of decreasing. It is obvious that the human body is a valuable resource, and until medical technology researchers develop fully functional artificial organs, the human body is the primary source for the ‘spare parts’ used in organ transplants. It is also clear that “… we are being prodigally wasteful in our funerary practices and stupidly selfish in our use of vital organs while we live and even more so when we die”. (Fletcher, 1979) So what should we do? Should we donate our organs after we die? When approached from a virtue ethics perspective, we may have a moral obligation to donate our organs after our death. Donating our organs may be how we could continue behaving virtuously even after our life is over.
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Homo sapiens, Neanderthals and Denisovans… did they interbreed?

Recent discoveries in DNA have shed light on the relationship of Homo sapiens and extinct hominids, Homo neanderthalensis and Denisova hominins. There is evidence to suggest that all three lived around the same time, and possibly in the same area (Krause et al., 2010)(Meyer et al., 2012). If these three groups lived close together, it should be possible to detect whether or not theyinterbred. If H. sapiens interbred with H. neanderthalensis and D. hominins, we should be able to find genetic evidence of this interbreeding in modern H. sapiens genomes. Using modern genetic examination (Gibbons, 2010), scientists have determined that H. sapiens did interbreed with both H. neanderthalensis (Green et al, 2010)(Hawks, 2013)(Meyer et al, 2012) and with D. hominins (Hawks, 2013)(Meyer et al, 2012).

article-1058538-02B984B100000578-348_468x342Homo neanderthalensis fossils were first discovered in 1856 in Germany, and ever since, scientists have been exploring the relationship of Neanderthals to modern humans. (Gibbons, 2012) The first “draft sequence of the Neanderthal genome” was published in 2010 (Green, et al), and that has given us insight into the relationship of Neanderthal DNA to the DNA of modern humans. Using data obtained by the Human Genome Project (Intl Human Genome Sequencing Consortium, 2001), scientists can compare human and Neanderthal DNA in order to discover the genetic relationship between the two.  The evidence suggests that Neanderthals lived in both Europe and Asia before going extinct around 30,000 years ago (Green et al, 2010). However, many of the Neanderthals interbred with H. sapiens before going extinct. According to Green and colleagues (2010) andHawks (2013), modern humans living outside of Africa represent between 1% and 4% of ancestry from Neanderthal populations. It is possible, with modern genomic technology, for the average person to send a sample of her own DNA to a lab (ex: ‘23andMe’) and get results showing her ancestry. If she has European ancestry, it is possible that she will also have some small percentage of Neanderthal ancestry (Gibbons, 2012). These sorts of results would only be possible had the Neanderthals interbred with direct ancestors of modern humans. Not all of the evidence suggests that Neanderthals interbred with the ancestors of modern humans, however. A study showed that there were no contributions from Neanderthal mtDNA to modern human mtDNA from a specimen recovered from Mezmaiskaya Cave in the northern Caucasus. (Ovchinnikov, 2000) This is not necessarily contradictory data from the other studies; it shows that not all Neanderthal populations interbred with modern human populations.
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Rethinking Aristotle: The Unwarranted Rejection of ‘Final Causation’ in Modern Evolutionary Biology

Why is the polar bear’s fur white? Why does the snake have the ability to unhinge its jaw? At first consideration, the answers to these questions are fairly straightforward. A polar bear has white fur for camouflage and the snake can unhinge its jaws to eat large prey. However, behind these questions lies a larger question, a question that is not directly answerable by describing the function of a certain feature. This question is of final causation, purpose or teleology. Does the polar bear have white fur because camouflage was the purpose of white fur? Is the snake’s unique unhinging jaw a result of a purposed process, with eating as a goal? Or are these features just the accidental by-products of the purposeless mechanism of evolution? Aristotle was under the impression that you do not fully understand an object unless you understand all of its explanations, including teleology, which Aristotle referred to as ‘the final cause’. Is that standard of explanation accepted today? And if we don’t embrace a teleological explanation today, is that rejection justified?

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“Aristotle was one of the greatest philosophers and scientists the world has ever seen”. (Dunn, 2005) He was one of the first people to propose a formal logical system, a functioning ethical system, a methodology concerning causality and a systematic way of studying the natural world. During his study of the natural world, he spent a large portion of his time studying life; a field that we now know of as biology. “Aristotle’s studies encompassed the entire world of living things. Many of his descriptions and classifications remain sound today” (Dunn, 2005)

In addition to his study and classification of organisms in the natural world, Aristotle had a very specific way of looking at natural and man-made objects. In Metaphysics, Aristotle explains the 4 different types of aition, often translated as ‘explanations’ or causes’. He believed that in order to fully understand something, you have to understand it in light of the four causes. If you didn’t understand all four of the causes, you didn’t actually understand the object in question.
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