Collecting Data like Ecologists, Chasing Each Other like Seniors

One would assume that a group of students going on an Ecology field trip would find many different types of organisms in the Mangrove forests and along the Rocky shores. However, though there were indeed a lot more organisms outdoors, the ironic truth is, there was more life indoors along the hotel corridors and auditorium than anywhere else during the entire four-day weekend.

Mangrove forests

Heading to the Mangrove forests, my Green Turtles observed the Avicennia marinas, also known as the grey mangroves and the Rhizophora mangles, also known as the red mangroves. There were distinct abiotic differences between the two areas with different dominant mangrove species. We found that the grey mangrove area had higher air and water temperatures than the red mangrove area. It can be inferred that this is so because of the physical differences between the two mangrove species. Red mangroves are much taller than grey mangroves and have large, extensive roots and branches which often overlap and tangle with other red mangrove trees. As the structures of the red mangroves cover the sunlight and offer more shade, the light intensity decreases and cools the air temperature below. On the other hand, the grey mangroves grow upright, are much less extensive and cover very little space compared to the red mangroves. This allows for sunlight to pass through, causing the grey mangrove area to have a higher light intensity; which as a result leads to higher air temperatures.The same goes for the water temperature. The more the water is hit by light, the warmer it will become. It is also important to keep in mind that the grey mangroves were in immediately next to a river. This river had no extensive branches or large leaves offering shade and had direct sunlight hitting its surface. Meanwhile in the red mangrove area, water temperature was measured when the tides began to enter. Since the water is moving from one location into another, the water is exposed less to direct sunlight and are much cooler. From the differences between the light intensities as well as the temperatures of air and water between the two areas, it can be said that even whilst both species are seen as mangrove types, each mangrove type has its own distinguishable relationship to its environment.

The variations between the abiotic factors also show a potential possibility for the biotic factors to be just as variant. This was definitely the case since as I mentioned before, the grey mangroves were closer to the river. By being so close, the grey mangrove area had a chance of having marine organisms whilst the red mangrove area did not. The difference between the river and water flowing into the red mangrove area is that the river is always there regardless of the time of date whereas the tides come in usually during noon or even after. So predominantly in the red mangrove area, the soil is very damp due to the tides but stable and dry enough walked on. With having the river nearby, there were organisms such as guppies, periwinkles and waterstriders which were all present in the grey mangrove area but unidentified in the red. But organisms such as flies, mosquitoes and snails all known to be flexible and tolerant to harsh conditions and extreme conditions, were spotted in both mangrove communities. Lichens, fungi and algae were all seen growing among the soils, roots, barks and even branches within the two mangrove types. Another organism seen in both communities was the mud crab. Unfortunately, my group didn't see any of them in the grey mangrove area but saw plenty in the red. The only reason we knew there were mud crabs in the grey mangrove community was due to the other groups sharing what they had seen. We feel that the reason our group did not see these crabs was because the soil in the grey mangrove area was equally damp but sandier compared to the soil of the red mangrove area. From their names, it can be assumed that these mud crabs would most likely prefer damper soil, which is more similar to mud than to sand. Therefore, it could be hypothesized that perhaps the soil for the other groups in their line transect may have been damper than the soil in our line.
Clearly, the organisms inhabiting each of the mangrove communities are similar. However, the richness or abundance of each organism also need to be evaluated. To quantify the abundance within the two areas, we found the total number of organisms we spotted as a group. There was a total of 48 organisms counted in the red mangrove community and 77 in the grey mangrove community. These numbers are a result of using the transect line method in both of the communities. Clearly from our data, the grey mangroves are inhabited by a large population than the red mangroves. To be fair though, in my own personal experiment I found that the red mangroves had a higher biodiversity than the grey mangroves. But this was found through quadrat sampling. So in order for the data to be fully justified for a reliable and valid conclusion, it is essential to replicate the use of both methods to measure the richness and evenness of the organisms present in the ecological area.

Rocky shores
After a few hours of in the mangrove forests, we headed down to the Rocky shores to do a similar form of data collection. Here, we used quadrat sampling on a line transect, where 6 quadrats adjacent to each other along the line were used. The length of the line was 4.1 meters, tied to one pole in the water and one up on the rocks. The line was not horizontal since the rocks were at a higher elevation compared to the water, meaning that the line had an angle of elevation. Within the two poles were the 6 quadrats used for data collection. The first three quadrats were in the water entirely, while the fourth included water and surfaces of a rocks while the last two quadrats were entirely with casual tides flowing in. As our data was collected, we found that the water temperature was 27°C with a partially cloudy scenery. The wind was blowing in a northeastern direction and there were 27 tides which hit the rocks in one minute. Same as the mangrove forests, there are clear reasons to the distribution of organisms along the line transect depending on these specific abiotic factors.

First, we were able to identify two species of periwinkles along our line transect, the knobbly periwinkle and the rock periwinkle. We found that the knobbly periwinkle were more evenly distributed along our line than the rock periwinkles which were only found in quadrats 3, 4 and 5. After some external research, it was understood that the rock periwinkles usually wedge into crevices of rocks and are naturally known to be clumped together in one location. This explains why the knobbly periwinkles were more spread out. Rock periwinkles are most active at night or in cool/rainy days, which is a possible reason as to why they were found in the middle quadrats between the rocks and the tides. The tides are able to cool off the rocks, especially when it is 27°C. On the other hand, knobbly periwinkles are also usually found in the cracks between rocks. They have a rougher shell than the smooth shells of the rock periwinkles, thus enabling them to withstand higher temperatures and rougher tides. When they are up high on the rocks, their shells keep them cool. When they are in the lower areas, the shells protect them from the tides. They are usually dry throughout the day, so the medium light intensity as mentioned previously allows them to attach to the rocks without getting burnt. These characteristics are possible reasons as to why the knobbly periwinkles were found in all but the first quadrat. The first quadrat had no rock surfaces above the water which is a very likely reason as to why none of the two types of periwinkles were identified there.

While there is a difference in the distribution of the two periwinkles, there is a similarity between the distribution of the acorn barnacles and the knobbly periwinkles. Both of these organisms were identified in all but one quadrat. The acorn barnacles were not identified in the 6th quadrat, one which consisted only of rocks with little to no tide. This difference was caused most likely due to the fact that acorn barnacles are able to successfully attach to hard surfaces by excreting 'glue' through their cement glands - which the periwinkles do not have. The 'glue' is so strong it is common for the barnacle's shell to stay in place even after it is dead. Therefore, even with the tides or wind direction, the barnacles are able to hold their position without being dragged off. This explains why all of the acorn barnacles identified were all seen in the first 5 quadrats where the waves were clearly hitting on the rocks. Also, we found that these barnacles were clumped together just as the rock periwinkles. The reason for this is because barnacles have reproductive organs of both genders and having a community is an advantage for cross-fertilization, especially when fastened in one position. 

After a day of back straining work climbing through mangroves and bending over in the rock y shores to collect data like ecologists do, we headed back to the hotel. Physically, our bodies had faced a challenge but mentally, we were provided with a lot of new information. The variety of abiotic and biotic factors identified in the mangrove forests and the rocky shores demonstrate how each organism reacts according to the biotic factors present in their environment. This is ecology. And although it may have taken a huge amount of time to collect all of this data, as my Green Turtles group would say, slow and steady wins the race. With biology and fun so closely tied together by this one trip, we found that even after a long day of chasing mud crabs for a quick photo, we still had enough energy to keep our vigour as high as the red mangroves and chase after each other. So, if we were to sum up the fun and academic side of this trip, it could probably be done by the phrase:

Slow and steady wins the race, but wild and cheery starts the chase.

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."

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>.

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.

A link to this article:
http://www.naturalnews.com/035327_exercise_DNA_expression_health.html

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

Brain: Playground Swing or Rocking Chair?

Being young at heart can be a little problem for those who've lived more years than they'd like to admit. And of course, solutions involve people dying a few strands, having a lift here and there or shaving off a few years to seem, look and appear young. But is appearing young the real issue? What if your brain aged faster than other people's? What if you're young at heart, high on the swing when your brain is already resting on a rocking chair?

Reported by Tina Hesman Saey in ScienceNews, Ahmad Salehi's study with pilots show that a specific version of a gene may impact the aging of a person's brain. The specific version of a gene is called BDNF. Specifically, Salehi's research involved the performances of pilot's distinguished into two groups - one group made up of pilots with the BDNF gene and the other group with those who don't -  on a flight simulator test. The study carried out for over two years and the results proved that pilots who had the BDNF gene showed a drop about three times more in their flight stimulator test compared to the pilots who didn't. Differences in scores were seen in areas such as reaction time, navigational skills, positioning of planes and performance/decision making in emergency situations.
There was also an obvious decrease in areas associated to learning and memory in the brain for those who had the BDNF gene. For example, those who had this particular gene had lost more volume of their hippocampus (part of the brain used for navigation and spatial memory) in comparison to those who have the normal version of the gene. This contributes to the possibility that the BDNF gene impacts the brain to age faster as all of the pilots that had the volume of their hippocampus measured were 65. Although they were all the same age, their hippocampus volume differed due to the presence of this gene.
But having this gene does not cause a person to be at a disadvantage at all. "The drop in scores was not so dramatic that pilots should be removed from the cockpit", as Tina Hesman Saey quotes Salehi. None of the pilots were more or less capable than the others at a drastic measure. It is also important to keep in mind that the degree of impact this BDNF gene has on the brain aging is not clear entirely as it is still an ongoing research topic and is fairly recent. A neurologist and neuroscientist from University of California, William Mobley, states that "It could be one of a thousand factors that play a role (in the brain aging)". With this statement, other scientists are trying to figure out how to counteract this gene and possibly slow the brain aging. But until further research is done, for now, whether you have this brain aging gene or not, it seems as though being young at heart is the best young you can be.