Friday, October 5, 2012

I never chose to be this great. It was Natural Selection.


"The world becomes full of organisms that have what it takes to become ancestors. That, in a sentence, is Darwinism." - Richard Dawkins
Evolution is the concept which states that even with the huge range of diversity between organisms, we are all of the same ancestral background and that the diversity is the result of change over time. It occurs ever so slowly and subtly, it is difficult to identify evolution actually happening without a long-term study where enough data is collected for a comparison between the past and present. Some, even to this day, claim that evolution is a myth. Ironically enough, these people are also the ones who are least susceptible to accept change - whether it be their change of mind or the evolutionary changes going on around them. 

1. Explain the concept of natural selection using the snails as an example.
Charle's Darwin has brought forth natural selection as a theory and defined it as the process where organisms better suited to their environment out compete those who are less adapted. This causes the better suited organisms to reproduce more, resulting in an overproduction of the better suited organism as their advantageous characteristics are passed down to their offsprings. Natural selection identifies the variation between different organisms and within the same species, therefore natural selection can also be seen as one of the processes that lead to evolution.
Taking the Cepaea nemoralis, a species of land-snails, as an example, the process of natural selection can be clearly seen in their different characteristics within their population and their overall geological distribution. These land snails vary in their shell color and patterns, which plays an immense role in their chances of survival than just to look pretty under a magnifying glass. The color ranges from brown, pink and yellow where the brown and pink shelled snails are considered to be the darker snails. Their patterns are either branded or unbranded, branded meaning they've got several distinct lines going down their shells. What determines the color and pattern of the shells is genetics. The dominant genotype celebrates it's victory in showing up as the organism's phenotype for all to see. Like so, the dominant characteristics of a snail, that is the characteristics that are advantageous to the snail's survival, is what is past down. It must be kept in mind though, that the parents have no choice in choosing which gene goes to which offspring. I may have gotten lucky with my draw, but I never chose to be this great and neither did my parents. It was naturally selected. This concept is natural selection, the survival of the fittest. But what determines which characteristics to be advantageous or not? The ecology of the organism's location. Studies have shown that there are more darker shelled snails in Northern Europe where the temperature and climate are much cooler than Southern Europe. Further into the study, it was found this is because snail with darker shells are able to absorb solar radiation more effectively compared to snails with lighter colored shells. The better absorption of solar radiation allows the snails with brown/pink shells to thrive better in cooler temperatures where there is an adequate amount of heat. In contrast to that, snails with yellow shells thrive better in areas with higher temperatures, such as Southern Europe, because they can withstand the abundant solar radiation which would overheat and kill the brown/pink shelled snails. It is important to keep in mind that having a darker shell can be an advantage in cooler climates but a disadvantage in areas with hotter climates. The same feature can be a threat or a helping factor to an organism's chances of survival depending on their environment.
Along with the temperature and climate of the snail's environment, other organisms inhabiting the area also affect their survival rate. Yellow snails are more easily identified in woodlands compared to brown/pink snails causing their predators such as the song thrush to feed on them more often. On the other hand, this means that brown/pink snails stand out more in grasslands and therefore are more frequent fed upon than yellow snails. Again, depending on their environment, the same features can be seen as an advantage or a disadvantage. With abiotic factors like climate and temperature affecting the distribution of brown/pink snails and yellow snails, and biotic factors such as the snail's predators, it is evident that any organism's relationship to their ecological niche is crucial in determining their chances of survival. This is natural selection.

2. Research another case of natural selection in action.  Write a summary of this research (1-2 paragraphs).  Site your source(s) at the end of the summary.
The fact is, evolution and natural selection that will continue so long as there is life on this Earth. As we are all inhabitants of this biosphere, we somehow affect the evolutionary changes we each go through one way or another. Yes, "we" includes humans too. As much as we would like to see ourselves as completely different species, we are as much of an inhabitant of this Earth as the little cockroaches we all unanimously seem to hate. Now because we share Earth as our home, affecting the evolutionary changes some organisms go through is inevitable. On the other hand, there are cases where we greatly affect the evolution of some organisms which may, and most would argue, should be stopped. An immediate example of this would be African Elephants and human predators, hunting for their ivory tusks.
Studies have shown that in 1930, an approximation of 1% of all African elephants did not have tusks. From this percentage, it is clear that back the, having tusks was a rare feature. But it was soon found that ivory hunters of the area would often dismiss these elephants while those with ivory tusks were mercilessly hunted and killed. Even while some of the hunters ripped off the tusks without actually killing them, the elephants would eventually die out because the tusks were essential to daily performances; especially in river valleys where they are needed to dig mud and in savannas where trunks are used to break branches and pick food. As the elephants with ivory tusks were brutally murdered, the elephants without tusks became the dominant species. Being the dominant species, this means that these elephants outnumber and reproduce more than the other species of elephants.
It may questioned as to how the elephants without tusks were able to survive when most of the elephants who had their tusks ripped off would die out after a few days. The answer to this is most likely the fact that these elephants with such a rare trait are used to it and never had the choice to rely on tusks. Another answer can be the fact that for the elephants to have the genes determining their no-tusk trait, at least one of their parents must have had no tusks as well. Coaxed by their parent(s), it is most likely that they were brought up to cope with the rare trait. However, it has been proven that these rare traits are no longer 'rare' in our modern world today. The alleles making up the no-tusk genes have been passed down to the offsprings of the dominant elephant species that now, up to 38% of African elephants have no tusks. Natural selection has taken place where having no tusk proved to be a more advantageous trait than having tusks, therefore the elephants without tusks have increased greatly in population. Again, like the previous example of the land-snails, both the abiotic and biotic factors affected and continue to affect the elephants chances of survival.
Article on African Elephants: 
http://science.howstuffworks.com/environmental/life/evolution/natural-selection5.htm
Quick facts on African Elephants:
http://www.tenan.vuurwerk.nl/reports/eversdal/grade6.htm

3. Explain the relationship between evolution, ecology and genetics.

With the two examples shown above, it is evident and almost undeniable that evolution, ecology and genetics are all tied together. Ecology, defined as the study of an organisms' relations to one another and to their surroundings, clearly determines the changes the organism undergoes. Genetics comes in to determine which characteristics are an advantage or a disadvantage. This is stated by the idea of biological success. Biological success is the concept where an organism's offspring is able to reproduce. Relating it to evolution, this means that an organisms' trait can be seen as advantageous when it helps the chances of it surviving and reproducing offsprings with the same trait. As in genetics, how an organism evolves is not determined by the parents or by any form of authoritative figure. It is inherited at random, which is why the process of natural selection has been accurately titled. It is not always the case that the dominant gene brings forth the advantageous trait, like seen in the previous example of African Elephants. However, it is very likely that eventually through evolution, the advantageous trait will show more commonly in the organism's phenotype because the dominant species will reproduce more. Proven by the examples of land-snails and African Elephants, without a doubt, ecology and genetics influence the process of evolution greatly.

To end this post with a little humor, would it be going too far to see the world as "The Hunger Games"? The biosphere as the arena, our parents as our mentors and each living organism as a tribute taking part in the game of evolution. 
A rare and even dangerous combination, imagination and science, but nevertheless,
"May the odds be ever in your favor."


Sunday, April 29, 2012

lincRNA and Cancer? Beats me!

*Red Numbered footnotes (1) are links that will take you to the sites that were quoted/referred to. They are sited in MLA format below.

Open Itunes. Play your favorite song. Close your eyes and just listen. Soak up every single component the music offers to you. Are the lyrics what makes this song your favorite? The rhythm? The tune? Or is it the melody that sews these notes as a favorite? Without all that, what would be left?
The beats of any given song in music are very much like the long intergenic non-coding RNAs (lincRNAs) that have been pushed aside in the field genetics - necessary for the whole but rarely noticed. The term intergenic refers to a sequence of DNA that do not hold genes but are found between clusters of DNA that do. Non-coding RNA (ncRNA) is defined as a RNA molecule that is not translated to proteins. Because of this, until recent studies and researches, scientists have overseen the full potential, importance and function of these non-coding genes. One of these ncRNAs that scientists have classified as "junk" are the lincRNAs. Recent researches contradict this classification as lincRNA's have now been proven to carry out essential functions for organisms such as guiding proteins to their attachment sites on specific RNAs/DNAs , as well as organizing the pluripotency of embryonic stem cells.(1) But even with these functions necessary for life, primitive discoveries a relationship between this particular ncRNA and the causation of cancer due to another one of it's functions of regulating the process of rapid cell growth, or cell profileration.
 Why I refer to this discovery as primitive is because scientists have only recently decided that these lincRNA's are not worthless. Currently studying lincRNA, assistant professor of Stem Cell and Regerative Biology at Harvard University, John L. Rinn stated through his research, the Rinn Lab(2), that any misregulation of lincRNAs can result in tumor. This misregulation of lincRNAs can occur due to factors due to in malfunctions in the organism's status of epigenetics, cell division and cell cycle. How Rinn and his crew sought out to clarify between this fatal disease and this particular non-coding RNA by profiling lincRNAs to different types of cancer in order to specify which lincRNA plays a role in the actual formation and growth of cancer. Why this is such an extreme and crucial contribution to the field of genetics is because retracing cancer back to it's origin may lead to further discoveries of how to cure it and even further, how to prevent it.
Howard Hughes, from the Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, is also conducting researches/studies between lincRNA's and the progression of cancer. The first point he makes in his publication, Long Intergenic Noncoding RNAs: New Links in Cancer Progression (3), is that the lincRNA's ability to control transcriptional alteration leading to the differences between normal cells and cancerous cells indicate there is a direct link between lincRNAs and cancer progression. Another point Hughes discusses is the fact that several types of lincRNAs have the ability to control gene expressions. It does so with a process called chromatin modification where the lincRNA attaches specific histone-modifying enzymes to chromatin. Chromatin modification is an epigenitc process when disturbed, can lead to uncontrolled cell division that will result into a tumor. Traits of these epigentic changes such as it being long-lasting/stable and being heritable provide the same traits to cancer. For example, cancer is divided into stages that measure the degree of seriousness, the potential harm it can cause to the patient, how far it has spread/size of the cancerous tumor and whether it can be removed. (4) Because the epigentic changes that can lead to the formation of tumors are long-lasting and stable, once the cancer reaches a certain stage, it becomes too late for a cure or method to remove it. It is also a common practice for doctors to ask their patients whether there they have had relatives with cancer during their diagnosis. This is because of the heritable traits of epigentic alterations made during chromatin modification. The chances of these alterations being passed down are still unknown because only 1% of the 3,000+ lincRNA's identified (scientists say there are bound to be more) have been characterized. It is also uncertain which type of lincRNA's have the ability to control gene expression and chromatin modification. And even if scientists did eventually uncover every lincRNA there is to be uncovered, identify each one and come to a conclusion as to which type of lincRNA controls gene expression, the concept of randomness and mutation would still affect the probability of a person getting cancer instead of their two younger siblings because their grandmother had suffered from it. (5)
The new found information of lincRNAs and the relationship it has to cancers is extremely beneficial to not only understand our biological make up and functions, but also for a possible cure for cancer as well. For example, Stephen Baylin from Johns Hopkins University School of Medicine is trying to nurture the epigentic alterations begin tumors to form using drugs such as azacitidine and entinostat. (6) Baylin and his team combined the two drugs in order to prevent tumor growth on patients who have gone through treatments that showed no signs of success. As a result, 28 of the 62 patients were given the drug combination and other chemotherapies. 8 of those patients responded successfully to the treatment. His conclusion also claims that the epigenetic treatment also stimulated the patients' immune systems to attack tumors. As you can see, scientists are constantly finding new contributions, theories, and information through researches and experiments to uncover the potential change a mere noncodingRNA can bring to human life and the topic of genetics. So next time you tune out the world with your iPOD, make sure you're keeping up with the beat of the music - it could be in sync with the very heartbeat your DNA works for. 


MLA Citations:
1) Saey, Tina Hesman. "Missing Lincs - Science News." Science News. 11 Dec. 2011. Web. 1 Apr. 2012. <http://www.sciencenews.org/view/feature/id/336570/title/Missing_Lincs>.
2) Rinn Lab 2009. "Large Intergenic Non-Coding RNAs (lincRNAs)." Rinnlab.com. Broad Institute, 2009. Web. 11 Apr. 2012. <http://www.rinnlab.com/research.html>.
3) Hughes, Howard. "Long Intergenic Noncoding RNAs: New Links in Cancer Progression." Cancer Research. American Association for Cancer Research, 1 Jan. 2011. Web. 16 Apr. 2012. <http://cancerres.aacrjournals.org/content/71/1/3.full>.
4) "Staging." American Cancer Society. Cancer.org, 2010. Web. 29 Apr. 2012. <http://www.cancer.org/Treatment/UnderstandingYourDiagnosis/staging>.
5) Klitzman, Robert. "Am I My Genes?" Genetics as Rorschachs: Pondering Our Genes and Our Fate. Psychology Today, 29 Mar. 2012. Web. 1 Apr. 2012. <http://www.psychologytoday.com/blog/am-i-my-genes/201203/genetics-rorschachs-pondering-our-genes-and-our-fate>.
6) Saey, Tina Hesman. "Old Cancer Drugs Offer New Tricks." Science News. 2 Apr. 2012. Web. 17 Apr. 2012. <http://www.sciencenews.org/index/generic/activity/view/id/339613/title/Old_cancer_drugs_offer_new_tricks>.

Tuesday, April 17, 2012

How to Train A Dragon? No. How to Train Your DNA.

 "Tired of your look? Want to change your body? Get off your lazy butt and EXERCISE!" Everyone has been called lazy at least once in their lifetime and who can we blame? Life does get tiring sometimes, but for those athletes, fitness freaks and jocks, working out is an everyday goes-without-saying activity. They aspire to change their body for the better. Little do they know that as they work to change their body, they are actually changing their DNA methylation for the better as well.
DNA methylation is when certain expressions of the gene are turned 'on' or 'off' in accordance to improving the organisms bodily functions. It has bee hypothesized  that exercise changed your genetic code entirely, but this hypothesis was ruled out by scientists such as Professor Juleen Zierath. Zierath proved that the alteration in DNA methylation caused by exercise led to better protection of cells from oxidative damage along with improved transport of fats, sugars and other nutrients throughout the body. Her study involved observing the muscle tissues of a group of people that just carried out a 20 minute workout session and comparing their muscle tissues to a group of people who did not participate in the workout. She also compared the workout group's skeletal muscles 3hours before and after the workout to further identify the alterations. It became evident from this comparison that he alterations made in DNA methylation were to improve and make better the body's performance.
It was also stated by another researcher who contributed to Zierath's study, Dr. Donal O'Gorman, that regular exercise and workout activities were essential for metabolic health and prevention of diseases. Regular exercises are needed because the alterations in methylation are not permanent, they are, in simplest terms, our body's response to exercise. To get this response, we must workout regularly and even daily, as though to 'remind' our DNA to turn certain expressions 'off' while leaving others 'on'. By exercising, it is as though we teach our DNA to transport nutrients more efficiently, build muscle, and improve our bodily functions to be healthy.
Another article that supports the fact that exercise affects our DNA expression and how these affects can lead to prevention of diseases can be found through this link:
http://www.naturalnews.com/035259_daily_exercise_DNA_disease_prevention.html