IB Biology Ecology Fieldtrip

The Biology fieldtrip was an amazing and extremely fun experience which was organized at Pranburi, Thailand and allowed us to investigate different factors in the ecosystems: Mangrove forest and the man-made Rocky shore. The factors that were being observed included biotic such as amount of individuals of each species, competition within the ecosystem and water supply, and the abiotic factors included temperature, pH level, turbidity, other nutrients in the water (ammnia, phosphate, nitrate, oxygen) and etc. 

Mangrove

In the Mangrove forest, we were divided into two groups to go to two different sites (Site A and Site B).  Site A was located further away from the river where there were more mostly Red Mangroves which grow in soft mud in that area.  Red Mangroves are characterized by their prop roots which supply air to the underlying roots and provide support and stability to the red mangrove. In site A, we observed the light intensity of the water was quite low compared to the light intensity of water in site B since the water was cloudy and the sunlight was blocked by the leaves of the Mangrove trees.  Site B is located next to the river and further into the forest. Slightly different methods were use in the two sites to obtain the measurements since site A has water on its site, therefore, we can directly take the sample from the site and use different probes to measure the different factors. However, Site B consists of solid soil where we have to take sample of the soil and dissolve it in distilled water to gain most of the measurements except for water temperature and turbidity where we can measure it from the river next to the site using a thermometer and turbidity kit. The technique that was used in Site A was placing a quadrat by random sampling and the technique that was used in Site A was a transect line.

Figure 1: Comparing eight different abiotic factors in Site A and Site B of the Mangrove Forest

According to figure 1, it can be see that some of the other abiotic factors that were observed were air temperature, water temperature, dissolved oxygen in water, pH level of the water, turbidity and other nutrient concentrations in the water. We can see that there are no significant differences in the measurements of each abiotic factor for the two areas. The only two measurements that are different are air temperature and water temperature. The lower air temperature in Site A may result from the observation that was made earlier about the branches and leaves of the Mangrove trees that cover the place. This high density of mangrove population may block the amount of sun and wind penetrating through the forest, thus lowering the air temperature.  Since this reason cannot account for the higher water temperature in site A than in site B, other factors such as time of the day may have affected this. All these factors will affect the distribution of different species in the area which will be discussed further on the biotic factors.

The biotic factor that was investigated was the distribution of species in the two areas which can be seen in Figure 2.

Figure 2: Comparing the amount of individuals in each species in Site A to Site B 

We can see that there are not much significant differences in the amount of individuals of each species in the two sites except for the Red Mangrove and seeds where we can see slight differences. We can also observe that the Lichen green and Lichen yellow are very numerous compared to other species. The seeds are more commonly found in Site B which may be explained by the fact that these seeds need a more solid area to grow since unlike mangroves, they do not have air roots to allow them to live in the water. The Red Mangrove is more commonly found in Site A since they are more adapted to living in the damp area as opposed to the solid soil in site B. From this graph, we can estimate and conclude that the diversity in the two areas are relatively very close. This may be because even though they are located in different areas, they are still in the same ecosystem with very similar abiotic components. The water of the damp soil in Site A probably originates from the river next to Site B.

Rocky Shore

The Rocky shore we investigated was man-made where rock piles extend approximately 40 meters into the ocean. The method that was used in the rocky shore area was different from what we did in the Mangrove Site A since instead of using random sampling of quadrats, we used a transect line (As shown in the picture below). By using a transect line, we can observe the changes in the distribution of living organisms of different species from the rocks into higher depth of water. 

The abiotic factors that were being measured included temperature of water, wave frequency, wind direction, aspect and light intensity. Temperature of the water can be easily measure using a thermomter while the wave frequency can be obtained by the counting the number of waves that crashes into the shoreline per minute. The wind direction and light intensity are just direct observations. The aspect was obtained by calculating the slope of the angle of the rocky shoreline where we had to use a protactor to see that the line between two poles is around 90 degrees. The values of these measurements are shown in Figure 3.  

Figure 3: The measurement values for different abiotic factors on the rocky shore

Abiotic Factors	Measurement Values
Temperature of water	31.5 ºC
Wave Frequency	48 tides per minute
Wind direction	Northeast
Aspect	70ºNW
Light Intensity	Partially clouded

Acorn Barnacles

Other than these abiotic factors, we also investigated the biotic factors which are the different amount of species that live on the rocky shore. We had to count the amount of different species per quadrat along the transect line. The species that was the most abundant was the barnacles. Barnacles (right) are crustaceans that are recognized by their jointed legs and shells of connected overlapping plates. Unlike other organisms, instead of crawling after food, they attach themselves to rocks, ships or even whales and wait for food to wash by with the waves. When the waves wash over them or when the barnacles are submerged under water, they reach out their legs to filter out plankton and absorb oxygen. This is the reason why barnacles are the most abundant species on the Rocky shore.  This also explains the correlation between the amount of barnacles and depth of water (distribution of barnacles). More barnacles were counted in the quadrat where the barnacles are slightly submerged under water.

Knobbly Periwinkle Snails

This is because they will have constant food supply in the water and obtain oxygen at the same time. Another organism that was also abundant was the knobbly periwinkle snails(left).  It is believed that the shells of these snails help them withstand the high temperature. The other two organisms that were observed were rocky periwinkle snails and limpets. The distribution of some of these organisms is shown in Figure 4 which is a kite diagram of the abundance of species along the Rocky shoreline. We can see that the abundance of species changes as the depth of water is higher (Quadrat 1 low depth to Quadrat 9 high dept). For example the Acorn Barnacles with the most abundance in quadrat 7 where it is almost fully submerged and the abundace is rare for quadrats below quadrat 4 since these areas are the areas where the waves do not crash into as much. We can also observe that the amounts of rocky periwinkles is almost stable throughout the quadrats while the limpets are considered to be rare. 

Figure 4: The Abundance of Four different Organisms Along the Rocky Shoreline

There were several learning outcomes of going to this trip. Firstly was to learn how to do measurements of different factors that are essential in an ecosystem. Secondly, I believe this is a more direct way of learning how the distribution of certain organisms change according to competition with other organisms or the other abiotic factors. By 'direct' I mean we get to actually carry out experiments using quadrats and transect lines instead of just studying from the textbook and trying to grasp on the ideas. For example the barnacles that prefer to live nearer to the water or the Red Mangroves which would be abundant in damp areas. I also learned that there are many abiotic factors which can contribute to determining the characteristics of an ecosystem even though we had investigated only a few. The slightest changes in these factors may affect the organisms in that ecosystem. Lastly, another valuable thing that I learned was that biology trip is the one of the most awesome trip ever and starfish is the best team ! :) 

Starfish FTW :D

Natural Selection

Natural selection is a process that demonstrates that evolution is not just based on chance but other factors and that not all individuals will survive. The survival of individuals is determined by their surroundings and the compatibility of their characteristics with those surroundings. In a population, there will be overproduction of offspring and in those offspring, there will be variations from one individual to another due to genetic differences.  Using the snails as an example, each individual has shell that varies in color (pink, brown, yellow) and number of bands.  These variations may be useful if they allow an individual to have a better chance of survival or may be harmful if they make it difficult to survive. The different colored shells have different thermal properties. Darker shells (brown and pink) are more efficient in absorbing solar radiation than do the yellow shells. As a result, darker snails are better suited to cooler climate as they use the heat to keep themselves warm, while snails with yellow shells are better suited to warmer climates because they can tolerate the heat. Snails with yellow shell also tend to live in open grassland and pink and brown unbanded shells in woodland. This is because yellow snails are more heavily predated in woodland due to their bright colors against the dark background of the woodland floor. As opposed to brown and pink snails that are better camouflaged and able to avoid predation. Since their genetic characteristics are poorly adapted for their environment, there will be a decrease in snails with yellow shells in woodlands and decrease in snails with brown/pink shells in grassland because they will have less of a chance of surviving to maturity. The better-adapted individuals (yellow shell snails in grasslands and brown/pink shell snails in woodlands) will survive to adulthood since they have a better chance to reproduce and to pass on their successful genetic characteristics to the next generation.

Another case of natural selection is the deer mouse in the Sand Hills of Nebraska and is one of the quickest-evolving examples of natural selection in animals. Their adaptation in variations of fur color is similar to the variations in the shell color of the snails in avoiding predation in their habitat. The deer mouse is normally dark-brown which is suitable for mice living in the woods where it is dark and they can blend in with the surroundings thus hiding from predators. However, when these dark-colored mice are in the Sand Hills, it would be easily spotted by the predators against the area’s light terrain. As a result, over time the deer mouse with the darker colors will die and the deer mouse with the lighter colors will survive and pass on these preferable characteristics to its offspring. Over many generations, the accumulation of changes in the heritable characteristics of a population results in evolution and the gene pool has changed. The mice living in Sand Hills quickly evolved lighter coloration. Light coloration arises from increased activity in a single gene which is called Agouti and is being inherited through several generations. This increased expression is associated with the deletion of a single amino acid, a process that appears to be under natural selection. This Agouti mutation generates wider pale bands on dorsal hairs, making the entire animal appears golden rather than brown.  Scientists predicted that predation would drive virtually all individuals in the area toward pale coloration within 8,000 years.

Ecology is the study of the relationships that organisms have with other organisms and their environment. As we can see from the examples of the snails and mouse, organisms interact with other organisms and the environment in ways that will alter the characteristics of their variations. Some characteristics will be preferable over the other to maintain the survival of the organism. As a result, over a period of time and generations, the characteristics that were influenced will be altered which results in evolution. Evolution is defined as the process of cumulative change in the heritable characteristics of a population. Evolution is possible since these preferable characteristics are passed on to successive generations through genetics thus impose changes in the gene pool of the population.

http://news.harvard.edu/gazette/story/2009/08/mice-living-in-sand-hills-quickly-evolved-lighter-coloration/

Expanding the Genetic Alphabet

The Scripps Research Institute has conducted a study on the DNA replication and found that the genetic instructions in living things is wider and varies more than just the four natural bases that are currently known- adenine, thymine, cytosine, and guanine. This expanded DNA alphabet that was discovered can carry more genetic information than the natural bases and thus, code for more molecules. This study which was in the issue of Nature Chemical Biology has show how these bases can go through the replication process as normally as the four bases. Floyd E. Romesberg, associate professor at Scripps Research, principal developer of the new DNA bases, and a senior author of the new study states that "We now know that the efficient replication of our unnatural base pair isn't a fluke, and also that replication is more flexible than had been assumed."  In the year 2008, Romesberg discovered the two efficiently replicating bases, NaM and 5SICS. They pair up together as a double helix just as normally as guanine pairs with cyotosine and guanine pairs with adenine. Then, Romesberg demonstrates in his lab that these two bases can be transcribed into RNA in the lab dish. However, their base pairing success still remains a mystery since it is clear that their chemical structures lack the ability to form hydrogen bonds like those that join the natural base pairs. In addition, the two pairs does not adhere to the Watson-Crick geometry of base pairing because they do not bond but rather join in a loose, “intercalated” fashion. First it was thought that this ‘mispair’ bases will not be recognized by the DNA polymerase during replication, but it was false since after several tests, the NaM-5SICS pair was replicated efficiently. Further support shows that even though the base pairs did not maintain the Watson-Crick geometry, but they do adopt the structure when gripped by the DNA polymerase during replication. Maylshev says that, “The DNA polymerase apparently induces this unnatural base pair to form a structure that’s virtually indistinguishable from that of a natural base pair.” The two bases which are not held by hydrogen bonds are instead held together in the double helix structure by “hydrophobic” forces. This causes the bases to repel water molecules and thus cling together in a watery medium. "It's very possible that these hydrophobic forces have characteristics that enable the flexibility and thus the replicability of the NaM-5SICS base pair," said Romesberg. 


http://www.sciencedaily.com/releases/2012/06/120603191722.htm

Stem Cell Treatment and Cartilage Growth

            (The research project is below, on Epigenetics, not this one)  In the article from ScienceNews magazine, scientists have found in their study, a new molecule called "kartogenin" that encourages stem cells to take on the characteristics of cells that make cartilage--a strong flexible, substance in your body, especially around your joints. This treatment using kartogenin allowed many mice with arthritis-like cartilage damage in the knee to regain their ability to use their joints without pain. This study has shown light on a potential treatment for patients with osteoarthritis(the most common joint disorder, which is due to aging and wear and tear on a joint) by finding a way to regenerate cartilage.  The way kartogenin works is that, it touches on the mesenchymal stem cells, which are in cartilage plus giving rise to cells that make connective tissue. This also includes chondrocytes which are the only cells in your body that manufacture cartilage. Kartogenin allows these stem cell to differentiate into cells that take on the role of making cartilages or in specific, to take on the role of chondrocytes. Results from lab work shows that kartogenin inhibits a protein called filamin A in the mesenchymal stem cells. This releases other compounds that can the regulate the activity of genes essential in transforming the stem cells into functional chondrocytes.This helps protect and repair cartilages. I believe that this potential technique gives hope to millions of people that are likely to become victims of osteoarthritis since cartilages wear off as everyone ages. It is an unevitable process that everyone has to go through. 

"Our cartilages wasn't meant to live this long," says molecular biologist Mary Goldring of Weill Cornell Medical College in New York.


http://www.sciencenews.org/view/generic/id/339669/title/Stem_cell_treatment_spurs_cartilage_growth

Epigenetics and Disease Susceptibility

                  Randy Jirtle (right), a professor of radiation oncology at Duke university, has worked with Michael K.Skinner, a geneticist at Washington State University, on the study of epigenetics’ influence on disease susceptibility. Epigenetics, or literally translated as “on”genes, refers to the modifications, mitotically or meiotically, in the gene expression which are heritable, but do not involve a change in DNA sequence. This is not similar to genetic mutation because epigenetic changes are likely to be reversible. Since genes carry ‘blueprints’ to the production of proteins in cells, DNA sequence can be further transcribed into RNA, which is then translated into proteins. Epigenetic modification works by turning “on” or “off” the genes, which allows or prevents the genes from being available to make certain proteins. Some common forms of epigenetic changes are through DNA methylation and histone modifications. During DNA methylation, an additional methyl group (a carbon atom plus three hydrogen atoms) is being added to specific bases on the DNA sequence. This intervenes with the chemical signals that would order the gene into action and therefore silences the genes. However, in histone modification, it involves the fact that DNA is wound around proteins known as histones and is unwounded to be transcribed, therefore, alterations to the histone orientation (DNA packaging) causes some genes to be more or less active to the cell’s chemical process and thus effects the gene expression in a similar fashion as in DNA methylation


In the study of epigenetics by Jirtle and Skinner, it is suggested that environmental exposure early in development have a role in susceptibility to disease later in life which seem to be passed on through successive generations. The study is supported by using the evidence from animal studies which indicates that prenatal and early postnatal environmental factors—including nutritional additions, xenobiotic chemicals, behvaiourial cues, reproductive factors, and low-dose radiation—can result in altered epigenetic programming and the risk of developing disease. Agouti mice, which are characterized as fat and yellow, were used in the experiment since they carried the agouti gene which makes them prone to cancer and diabetes. When agouti mice breed, a typical result is that they are identical to their parents (yellow, fat, and susceptible to life-shortening disease.) However, in this experiment, an offspring with alternated looks were produced (brown, slender, and lived till old age). In addition, the parents’ susceptibility to cancer and diabetes were eliminated.

The mother agoutic mouse (right)  has given birth to the young mouse that has completely different appearance and  disease susceptibility

The approach that the researches had taken did not involve any alternation of a single letter of the agouti mice’s DNA but rather, they changed the maternal dietary. The coat color is primarily yellow in the offspring that are born to unsupplemented mothers, whereas it is mainly brown in offspring from mothers that were supplemented with methyl-donating compounds (picture below). Before conception, the mother mice were fed with a diet rich in methy donors that is, folic acid, choline, vitamin B12, and betaine (common in onions, garlic, beets, and in the food supplements often given to pregnant women), which are small chemical clusters with the ability to attach to a gene and turn it off. The way this chemical works after being consumed by the mother is that, it attaches onto the developing embryos’ chromosomes and the critical agouti gene. As a result, the agouti gene is still passed on to the offsprings, but due to the methy-rich pregnancy diet, the gene acts as a chemical switch that diminishes or inhibits the gene’s deadly effects. Methylation-sensitive restriction-enzyme analysis followed by PCR amplication have been used to identify the set of genes and other DNA sequences with altered DNA methylation that is epigenetically reprogrammed.

a. Group of mice with dietary supplementation of methyl donating substances to female mice during pregnancy vs. the group without dietary supplementation./ b. The effects of maternal dietary supplementation on coat colour distribution. The coat colour is primarily yellow in the offspring that are born to unsupplemented mothers, whereas it is mainly brown in the offspring from mothers that were supplemented with methyl donating substances.

Furthermore, epigenetics involves transgenerational inheritance in which is the transmission of a biological trait to successive generations through the germ line and in this case, without changing a single gene sequence. Michael skinner proved this to be true in 2004 after he discovered an epigenetic modification in rats that lasts for at least four generations. Another study done by biologist Emma Whitelaw in 1999 (using mammals) also supports that epigenetic marks could be passed through to subsequent generations. Another research conducted by the research team in Linköping University in Sweden also reaches an analogous conclusion by using chickens (shows eight generations of epigenetic marks). At the moment, evidence is only enough to be done with animals, but there are still gradual evidence that epigenetic modifications might work in humans as well. 


 In conclusion, the study done by Jirtle and Skinner has highlighted the indication that environmental factors are able to alter gene expression and change phenotype by modifying the epigenome. Moreover, if these environmentally induced epigenetic adaptations occur at crucial stage of life, they can potentially change behavior, disease susceptibility and increase possible chances of survival. They can be used as therapeutic approach for early diagnosis of individuals with a tendency for adult-onset disease. 


 "Epigenetics is proving we have some responsibility for the integrity of our genome," Jirtle says. "Before, genes predetermined outcomes. Now everything we do—everything we eat or smoke—can affect our gene expression and that of future generations. Epigenetics introduces the concept of free will into our idea of genetics."


MLA:
 1. Downer, Joanna. "Backgrounder: Epigenetics and Imprinted Genes." Johns Hopkins Medicine, Based in Baltimore, Maryland. Web. 29 Apr. 2012. . 
 2. Watters, Ethan. "Living World / Genetics." DNA Is Not Destiny. Nov. 2006. Web. 29 Apr. 2012. 
 3. "Inherited Epigenetics Produced Record Fast Evolution." ScienceDaily. ScienceDaily, 29 Feb. 2012. Web. 29 Apr. 2012. . 
 4. PDF file: http://www.geneimprint.com/media/pdfs/17363974_fulltext.pdf

Flood week

This picture is the picture of my house during the flood. As you can see, my house is guarded with the sandbags while the water is trying to push into the house. The water level is quite high to the point that normal level automobiles could not go through without dying in the middle of the water. I chose this picture because firstly, it is how I personally relate to the flood and secondly, it has created some troubles for me and my family. However, I believe that it is also a result of the poor government we have, that is inadequate of telling us exactly what actions we have to take. My parents had to spend thousands baht to protect the house with the thought that it would've created more damage if the water was really going into the house and swollen up our newly placed wooden floor.
It is pretty heartbreaking to see that my house is a mess with all the furniture carried up to the second floor, the refrigerator on 3 levels of bricks, and our family evacuating from the house. At first my parents didn't want to move out since we could still walk out of the house (wearing boots), but we finally decided to move out because it of the tension of worring about the situation all the time. One of the reasons why I hate the flood is that my dogs have to move to another place since my family and I are currently staying at our condo in Ekamai, but they do not allow dogs to enter. It's been about a week since we moved out the house and from here we saw that the water isn't rising any further and we've realized that we've spent all those money for nothing. As I have said, if the government could tell us which areas will be flooded, then we wouldn't have to worry and panic about the situation around our neighborhood.
I think Thailand has learned its lesson that results from the flawed system of our water management. However, it is impressive on what the flood can do. We can see through the news about people helping each other by bringing in food, supplies, and needs for those who are in trouble. The flood brings the people together because we all have to help out in order to pass one of the major crises in the history of our natural disaster. There is also one quote that I think is remarkably true which says “คนไทยไม่ทิ้งกัน” which means that Thai people will never give up on one another. I think if we remain like this, helping each other out, then there wouldn’t be any red shirts, yellow shirts, pink shirts, and one day Thailand might reunite as one again.

Homeopathy

Homeopathy is a system based on the principle that a much diluted preparation of a substance that causes symptoms in healthy individuals can cure disease that causes the same symptoms in a sick person. Homeopathy is different from other treatments for allergy in that it creates a remedy which caused the same symptoms in a healthy person and use it in homeopathic dilution to treat that patient. However, in my opinion, I do not think it works, firstly because it contradicts the current laws of physics, chemistry, and pharmacology. Therefore, in order for it to be true, scientists would've had to rewrite the whole textbook. Also, it relies on anecdotes rather than empirical evidences because it requires its consumers to believe in a certain level of 'magic.' The technique of homeopathy simply cannot work according to modern science.Homeopathy has been tested in several, reliable trials and the results show that it works at the same level as the placebo control, meaning that it has no therapeutic effect. It does not have enough support to claim that homeopathy truly works. If a doctor were to prescribed me with homeopathy, I could only hope that it would work which would probably be if I were to believe in miracles.