This Year's Highlight (and I'm not even exaggerating or being a brownnoser either)

One the most awesome highlight of this year is the IB Biology Year Two HL field trip. I recalled us packing and loading up to two buses and heading off to Pranburi on the September 20, 2012. In addition to having memorable times there, we also conducted two experiments on the ecology of the rocky shore area of the beach and the ecology of the mangrove forests. We visited the mangrove forest near the Pranburi river and the man made rocky shore of the sandy shore beach next to the ocean. Thus, these two investigations will be explored in the following blogs.

Mangrove Investigation

During our time at the mangrove forest, our group was divided into two in order to investigate two areas. The first area, which is away from the river, will be referred as mangrove A and the second area, which is situated next to the Pranburi river, will be referred as mangrove B.  While mangrove A was surrounded by mostly grey and red mangroves, mangrove B was surrounded mainly by yellow mangroves. We investigated both the abiotic, including temperature, pH levels, water quality, turbidity, dissolved oxygen, water dept, salinity, light intensity, and substrate, and biotic factors, pertaining to the biodiversity, for each site. The results were then recorded and compared for further processing. To determine the biodiversity of each area, we used the Simpson’s Diversity Index and the observed number of organisms present per species. Although the data in mangrove A was collected via a restricted single 1 meter by 1 meter quadrat, the data in mangrove B was collected using a perpendicular transect that ran perpendicular to the river and is about one meter of width and 10 meters of length.

Even though this is not the first time I visited a mangrove forest, I am nevertheless amazed by it. The scenery of a beautiful mangrove forest filled with astonishing biodiversity stunned me. From what Sea, our expertise tour guide said, I learnt some of the mangrove fun facts including its salty texture, different species and its quality as valuable nursery areas for juvenile fish and crustaceans.  Our “Red Crabs” groups, led by our Ultimate Red Crab Queen Mendy, was divided into two groups, the R-1 and R-2 groups. Each group of 6 members collect their own data and thus two sets of data per site are represented and conclusions are drawn as shown below.

Table 1: The shows the abiotic factors of mangrove A and mangrove B. These factors include air and water temperature, dissolved oxygen levels, pH levels, salinity, substrate observed, water quality, turbidity, dept of water and light intensity.

Table 2: Shows the biotic factors in mangrove A and B, in which represent the species presented and the abundance of each species in two sites.

Figure 1: comparing species of abundance in areas mangrove A and mangrove B using graphical displays of the numbers of each species present at each site.

With this data and using the Simpson’s Diversity index formula where diversity (D) = [N(N-1)/∑ [ n(n-1)] with N as the total number of organisms and n as the number of organisms of a particular species, the biodiversity of each site is calculated. The larger the diversity or the D value, the more diverse. Using the data from our data collection for the abundance of species, the diversity for site A is 3.88 while the diversity for site B is 1.56. Therefore, it can be concluded that there is more biodiversity in site A, or areas away from the river, than site B, or the areas next to the river. However, it should be noted that the yellow mangroves are smaller species that live next to each other while the red mangroves live further away due to its sport stilt roots. This could contribute to the less amount of mangroves per quadrat in mangrove site A.

Comparing the abiotic factors, it is shown that mangrove A had higher air temperature and turbidity when compared to mangrove B. The soil is also muddier in mangrove A while mangrove B is sandier. Nevertheless, mangrove B had higher water temperature, dissolved oxygen, pH, salinity, and substrates observed. Both mangrove sites had low light intensity, mostly due to the tall mangroves blocking the sunlight. Although mangrove B has more dissolved oxygen and thus more nutrients than mangrove A, site B attract lesser organisms than site A. This may be a result of the sandy, dry texture of the soil in mangrove B. More over, mangrove A contained organisms, including crabs, fish and tapeworms that are adapted to saline and submerged surroundings.  From these information’s, I therefore learnt that even though the mangrove areas seemed harsh due to the inconstant tides, there are huge biodiversities due to its abilities to provide shelters.

Rocky Shore Investigation:

The rocky shore we investigated is actually man made structures that protrude into the ocean. Using a perpendicular transect, we observed the abundance of organisms as we went deeper into the ocean. We calculated the slope of the rocky shoreline. The quadrats that are 0.5 meter by 0.5 meter were placed contiguous to each other from the lowest pole to the highest one. The number of organisms was recorded per each quadrat. A tape measure was used to find out the total distance between poles and the distance perpendicular to the poles. In addition, we also measure the abiotic factors, including air and water temperature, wave frequency, aspect, light intensity, and wind direction.

Table 3: shows the abiotic factors of the rocky shore, indicating the air and water temperature, wave frequency, aspect, light intensity, and wind direction.

Table 4: shows biotic factors at rocky shore, indicating the abundance of each species per quadrat

Species

Figure 2: shows a kite diagram of species abundance, indicating the abundance of each species in the investigated rocky shoreline, having the first quadrat most far away into the ocean and the sixth quadrate out of water.

According to the kite diagram pertaining to the data collected, the abundance of acorn barnacles, limpets, knobbed periwinkles and the abundance of rock periwinkles increased as the area invested is closer into the ocean. There are nevertless optimal locations. For example, the optimal location for acorn barnacles is in the 5^th quadrat while the optimal location for rock periwinkles are in the third quadrat. There are no optimal location according to the observed data for limpets and knobbed periwinkles. However, if more observations were made in different areas, we might be able to find the optimal location for these organisms since our transect area does not cover all the rocky shore.

Here, other than learning that rocky shores (even though it’s man made) is beautiful and awesome, I learned that organisms are adapted in various places! Okay.. maybe this knowledge isn’t that NEW, but it’s still a cool fact worth mentioning. I just want to conclude that this biology trip is a highlight of this entire year. I don’t think any supposedly education fieldtrip can top this one. 

There’s Nothing Random About Natural Selection

"In the struggle for survival, the fittest win out at the expense of their rivals because they succeed in adapting themselves best to their environment." - Charles Darwin

1        1. Explain the concept of natural selection using the snails as an example.

Individuals in a population differ from each other. Some individuals will have characteristics that make them well adapted to their environment whereas others will have characteristics that make them less adapted to their environment. The better adapted individuals are the ones that are more likely to survive and produce offspring while the less adapted ones are more likely to die. This is called natural selection. Natural selection results in the better adapted individuals to pass on their characteristics to more offspring as the lesser adapted ones are more likely to die before they reproduce. Over time, this result accumulates and a new generation is created with the favourable characteristics that make this species better adapted to its environment. Natural selection has lead to the species evolving. The one of land-snails species, Cepaea nemoralis, for instance shows a clear example of a process of natural selection as seen in the casual relationship between their different characteristics within their own population and their overall geological distribution. These land snails vary in shell color and patterns, ranging from brown, pink and yellow where the brown and pink shelled snails are the darker snails and also ranging from unbranded to unbranded patter with the branded pattern with several distinct lines. These different colored and pattern shells may seem trivial but they play a significant role in the chances of survival. Genetics are what determine the color and the patterns of the shells, where the dominant genotype, like its name, is the dominant one and thus represents the organism’s phenotype. Like wise, the dominant characteristics of a snail are supportive of the snail’s survival and thus they were past down. Although some may claim that the causes of evolution may be arbitrary, there is actually nothing random about natural selection. It’s just simple algorithm: the more likely you are to survive, the more likely your genes are advantageous and the more likely your genes will be passed own. In the case of the snails, both the abiotic factors like the environment, climate and temperature affecting the distribution of brown/pink snails and yellow snails and biotic factors such as the snails’ predators are what determined its survival. There are evidence that pointed out that the darker shelled (brown and pink) snails are, the more likely they will survive in Northern Europe rather than in Southern Europe, where climate and temperature are much warmer due to its ability to absorb solar radiation more effectively in comparison to that of the lighter shelled snails. The less absorption of solar radiation propels the snails with yellow shells to thrive better in environments with higher temperature in places such as the Southern Europe because unlike the brown/pink shelled snails, the yellow snails are less likely to be overheated and died off. In colder areas, the brown and pink-shelled snails thrive because of their ability to trap scarce heat to warm them up. In addition, the environment and the other organisms living within the environment in which the snails live also affect the chance of survival. Yellow snails are noticeable in woodlands when compared to brown and pink snails. Thus, they are often fed in this area. However, the brown/pink snails are easily distinguished in grasslands and therefore are frequently predated in those areas. The same characteristic, in this case the shell color, can be a double-edged sword: it can either benefit you or harm you. This is simply 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 cases of natural selection in action are right in front of us. In reality, these cases are actually us, human beings. Are humans still evolving? The simple answer is yes, even if the changes are not obvious. Experts believe that about 9 percent of our genes are undergoing rapid evolution as we speak. The genes most affected by natural selection are those involving the immune system, sexual reproduction and sensory perception. Lactose intolerance is one example of natural selection. We are the only species that doesn't become lactose intolerant as we grow up. This case of natural selection in action can be supported by a case study by Sabeti in 2006.

The domestication of plants and animals roughly 10,000 years ago profoundly changed human diets, and it gave those individuals who could best digest the new foods a selective advantage. The best understood of these adaptations is lactose tolerance. The ability to digest lactose, a sugar found in milk, usually disappears before adulthood in mammals, and the same is true in most human populations. However, for some people, including a large fraction of individuals of European descent, the ability to break down lactose persists because of a mutation in the lactase gene (LCT). This suggests that the allele became common in Europe because of increased nutrition from cow's milk, which became available after the domestication of cattle. This hypothesis by Sabeti and colleagues was later eventually confirmed by Todd Bersaglieri and his colleagues, who demonstrated that the lactase persistence allele is common in Europeans (nearly 80% of people of European descent carry this allele), and it has evidence of a selective sweep spanning roughly 1 million base pairs (1 megabase). Indeed, lactose tolerance is one of the strongest signals of selection seen anywhere in the genome. Sarah Tishkoff and colleagues subsequently found a distinct LCT mutation also conferring lactose tolerance, in this case in African pastoralist populations, suggesting the action of convergent evolution.

Let me ask you one last question. Are you lactose intolerant? Well, many people are. In fact, the ability to digest lactose may be an example of adaptive evolution in the human lineage.

http://sysbio.harvard.edu/csb/research/sabeti.html

http://discovermagazine.com/topics/human-origins/human-evolution

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

Ecology is the study of the distribution of living organisms and their relationships to each other. Evolution involves the changes that take place as new species come about.  The ecology of an ecosystem changes as the biological diversity changes. For example, during the Jurassic period, the ecosystem involved large reptiles as the dominant animals. However, as the ecology changes overtime, the mammals evolve and the dinosaur eggs are destroyed, altering the population dynamics.  

In order for evolution to work, a mechanism that keeps trait discrete must exist. Genetics describes the pattern of inheritance. In order for evolution to work, a mechanism that keeps trait discrete must exist. Genetics describes the pattern of inheritance. A mutation is a change in DNA, the hereditary material of life. An organism’s DNA affects how it looks, how it behaves, and its physiology. So a change in an organism’s DNA can cause changes in all aspects of its life. Mutations are truly essential to evolution as they are the raw material of genetic variation. If the mutation made is beneficial to the organisms, the mutated genes will be passed on to the next generation. Without mutation, evolution could not occur.

Research Blog on “Genome-wide scan for loci of Asperger syndrome”

 

Asperger’s syndrome is a type of pervasive development disorder. Although Asperger’s syndrome is similar to autism, there are some major differences. Children with Asperger’s syndrome typically function better than those with autism. Furthermore, children with Asperger’s syndrome generally have normal intelligence and near normal language development. Since the first observations, problems with social interaction have been frequently observed in the family members of patients with Asperger’s syndrome and thus suggest familial and perhaps genetic aggregation of the syndrome. Several reports, including the original description by Hans Asperger (1944), have suggested that AS has a strong gnenetic component. In this research, the experimenters have performed a genome-wide scan on Finnish families specifically for Asperger Syndrome with a strictly defined phenotype, an observable characteristics of an individual resulting from the interaction of its genotype with the environment.

The aim of the current study, “Genome-wide scan for loci of Asperger syndrome,” is to identify genetic loci, a position of a gene, for Asperger Syndrome by analyzing Finnish families in which both the Asperger syndrome’s patient and one of their parents was affected.This analysis is done through a method called genome-wide scan. During a genome wide scan, the DNA, which has been extracted from the blood sample, has markers placed along the chromosomes, each of which are different sizes. This method of observation allows researchers to see whether a gene for the disorder lies near one of the markers to determine where the loci of Asperger Syndrome are. By identifying the loci of Asperger Syndrome, in the future, doctors can identify the loci that cause AS and perhaps fix or prevent the symptoms from happening even before the baby is born.

The method to analyze the Finnish families includes dividing these families into four groups: Asperger syndrome (narrow classification), Asperger syndrome (broad classification), unaffected, and other disorder. They are divided depending on health background and the results of their diagnostic interviews, which includes questions about behaviors that are frequently presented in individuals with AS. Individuals who fulfilled all criteria for AS during the diagnostic interviews will be labeled as “affected individuals, narrow classification” while individuals who had Asperger-like features but did not fulfil all the diagnostic criteria will be labeled as “affected individuals, broad classification.” By analyzing individuals with Asperger syndrome (whether they are narrow classification or broad classification), the unaffected, and the ones presented with other disorders, researchers can compare loci, identify the loci overlaps between people with AS, find the connection between the loci and the origin of the disorder, and deduce its connection with other genetic disorder.

After dividing the participants into different groups, genome wide scan is performed. This is done by extracting DNA through blood from the participants, placing markers in the DNA, performing polymerase chain reaction, and conducting gel electrophoresis. The tools for PCR and gel electrophoresis are stated in the videos

                                                Polymerase Chain Reaction

                                                       Gel Electrophoresis

After gel electrophoresis, data were extracted from the gels and the genotypes were assigned and verified.

The results of the genome wide scans are as followed: In the initial scan to find the overlapping of loci, Z_max>1.5 was observed on nine chromosomal regions, 1q21–22, 3p14–24, 3q25–27, 4p14, 4q32, 6p25, 6q16, 13q31–33 and 18p11. In the fine mapping stage, the highest two-point LOD scores were observed on chromosomes 1q21–22 (D1S484, Z_{max dom}=3.58), 3p14–24 (D3S2432, _{Zmax dom}=2.50) and 13q31–33 (D13S793, _{Zmax dom}=1.59). The loci on 1q21–22 and 3p14–24 overlap with previously published autism susceptibility loci, and the loci on 1q21–22 and 13q31–33 overlap with the reported schizophrenia susceptibility loci. This process is called linkage analysis. 

                                                                  Gene Linkage Study 

 

            In conclusion, the evidence for linkage was observed in the Asperger material throughout the 3q25-27 regions. To our knowledge, this study is the first genome wide screen in Asperger syndrome. Interestingly, the identified AS loci are overlapping some susceptibility loci reported earlier for autism and schizophrenia. The overlapping linkage regions between AS and other neuropsychiatric disorders do not necessarily mean shared genes, but rather implies that these genomic regions deserve additional analyses in the clinical study samples to find the relationship between these overlap linkage regions.

Other causes of Asperger Syndrome

In this article, it is implied that there is a linkage between Asperger syndrome and genes. Thus, the researchers are stating that Asperger Syndrome is a genetic disorder that is caused by AS susceptibility loci. However, other research studies show that Asperger syndrome is not caused only caused by genetic factor but is also caused by other factors.

mirror neuron theory

The mirror neuron system (MNS) theory hypothesizes that alterations to the development of the MNS interfere with imitation and lead to Asperger's core feature of social impairment. For example, one study found that activation is delayed in the core circuit for imitation in individuals with Aspergers syndrome. This theory maps well to social cognition theories like the theory of mind, which hypothesizes that autistic behavior arises from impairments in ascribing mental states to oneself and others, or hyper-systemizing, which hypothesizes that autistic individuals can systematize internal operation to handle internal events but are less effective at empathizing by handling events generated by other agents. Other possible mechanisms include serotonin dysfunction and cerebellar dysfunction.

Possible environmental causes of Asperger's
• Infectious disease
• Heavy metal toxicity
• Certain vaccinations

• Perinatal factors
• Stress.

Resources:

"New Genetic Study Of Asperger Syndrome, Autistic Traits And Empathy." Medical News Today. MediLexicon International, 17 July 2009. Web. 30 Apr. 2012. <http://www.medicalnewstoday.com/releases/157802.php>.

"TO WHAT EXTENT DO GENES CAUSE AUTISM?" Autism, PDD-NOS & Asperger's Fact Sheets. Web. 30 Apr. 2012. <http://www.autism-help.org/autism-heritability-parents.htm>.

Perry, Mark. "Asperger Syndrome Cause." Health Guidance. Web. 30 Apr. 2012. <http://www.healthguidance.org/entry/11545/1/Asperger-Syndrome-Cause.html>.

Stöppler, Melissa Conrad. "MedicineNet.com." MedicineNet. David Perlstein. Web. 30 Apr. 2012. <http://www.medicinenet.com/asperger_syndrome/page3.htm>.

Leite, Embrapa De. "BMC Genomics | Full Text | Genome Wide Scan for Quantitative Trait Loci Affecting Tick Resistance in Cattle (Bos Taurus X Bos Indicus)." BioMed Central. BMC Genomics, 30 Apr. 2010. Web. 30 Apr. 2012. <http://www.biomedcentral.com/1471-2164/11/280>.

Position Paper: con

            Golden Rice was meant to be launch on the market after over 10 years of research and development. Advocates maintain that there is no alternative to this genetically engineered rice variety in the fight against vitamin A deficiency and accuse government agencies and critics of endangering the lives of millions of children. Some even go as far as to charge government agencies and critics of being complicit in bringing about a “Holocaust.” To speed up market approval and limit expenses, they demand a general loosening of standards for the risk assessment of genetically engineered plants.

            However, this report shows that the managers of the Golden Rice project have demonstrated a disregard for necessary scientific accuracy and precision and thus I am against Golden Rice project. They have employed propagandistic methods to push the project beyond the issue of vitamin A deficiency, setting a precedent to increase the pressure on regulatory authorities and accelerate the introduction of agricultural biotechnology.

            It is still not possible to judge whether or not Golden Rice is even technically able to combat vitamin A deficiency. No data has been made available on the degradation rate of its B carotenoid content in our stomach during storage nor on its bioavailability. Any risks posed by the cultivation or consumption of Golden Rice has been largely ignored. Very little data is available on new active ingredients and changes in the metabolism of the plants, and on the reaction of the plants to changing environmental conditions. So far not a single feeding study on the rice has been published. In spite of all this, a trial has already been conducted on Chinese school children. This “experiment” on human alone is inhumane since golden rice can cause allergies from transferring genes from other species. A study has shown that putting a protein that kills pests into pea DNA and feeding that pea to mice have done this. It was found that the altered chemical structure of protein caused allergies in mice.

            It is highly likely that the commercial cultivation of Golden Rice will lead to the irreversible entry of this genetically engineered organism into the environment and to its crossbreeding with local rice varieties. It is not scientifically possible to predict the long term ecological consequences. Other than this, poor people have harder time to pay for the Golden Rice product. Therefore, I do not support the Golden Rice project.

           

In sickness and in health

This article stresses the importance of genetics in many diseases. For example, in cystic fibrosis, a single mutation in a single is enough to cause the disease. Other examples derive from a subtler cause, such as diabetes and asthma, which are caused by our slight and subtle genetic influence. Our class just took a test on DNA transcription, translation, and an introduction to genetics. In the latter, we explore the basis of genetic mutation, particularly base substitution mutation. This topic ties back to the article when it mentions a disorder that affects the blood’s oxygen carrying protein hemoglobin. According to the topic we’re learning, the disorder that derives from the base substitution mutation that affects the hemoglobin’s shape is known as sickle cell anemia since its shape looks like a sickle cell and thus has a harder time carrying oxygen throughout the entire body.