Monday, December 27, 2010

Updates in December.



Dear everyone How are you doing? I apologize for not writing as much as I should.Here it goes:


The Spring 2009 Issue of the has recently been published with my article on invasive species. At this time of writing, we are currently submitting our articles for the Fall 2009 to our faculty advisors (which are profs in NUS) We have already submitted our articles to the international liteary board. For checking For this issue I have already submitted my SUJA for this issue as I am short of time to write another essay. With some edits and rearrangments and updates , the article should be ready for publication after the profs have gone through it =)

This semester, besides my writing work, I have become involved in the admin stuff of TTH. I have been promoted to Managing Editor “unoffically”. From the compliation of articles for the Spring issue to the handling of recruitment matters. This was also my job for the Triple Helix. We have succcesfully recruited some new writers for ourselves. So I handle interviews with my colleagues and sometimes with my editor in chief. I must thank Mabel, my editor in chief, for patiently instructing me in my new duties and her trust in me =) and my various colleagues who I worked with this semester for a good working relationship. =)

On the 16th December, my auntie who is mum's younger sister came to Singapore with her family. She stayed in MBS with her family for one night. My mum and sis and I came to the hotel room and stayed the night there. We did ate a lot as they went out quite a lot to eat. We ate in the food court at MBS which recently opened in the afternoon and ate at Gluttons Bay at night. My cousin brought for me Wendy's for lunch when I came to the hotel. Yum.Besides, this we went swimming in the infinity pool. Sounds Cool?



Cheng Long rang me up on last Wed to inform me that one of our 4E1 friend's mom had just passed away and asked me whether i wanted to go to the wake. So for the next couple of days, I found myself at someone's else wake for the first time in my life. (Yes, I am such a greenhorn at life) On Thursday afternoon, I metup at Cheng Long's house and we went to the wake in Toa Payoh. I was told by Chenglong that the block of flats where the wake is being held used to be the residence for 2 of our 4E1 classmates. At least I learnt about something new that day.

We were not the only ones to take the time out for our friend in his time in need. We saw some of our 4E1 mates taking time out to attend the wake. We caught up with them over a very simple lunch of fried rice and other stuff like salted vegetable and over peanuts. We spent the the rest of the afternoon folding paper ingots. After a crash course in paper folding by Cheng Long and Kai Siang, I was managing passable efforts in making paper silver ingots that just manage to resemble like ingots and maintain their shape.

At night, only Cheng Long and Binzan and I stayed back for dinner. It was stuff like braised prok buns and curry. There was ceremonies throughout the night and Cheng Long did explain to me their significance as best as he could. We kept ourselves occupied by playing games with his iPad which he already showed me once after school on the bus back home. Nevertheless, it showed me how good were my game playing skills ---- which is simply awful. No matter what game they played, I found myself at the losing end.Nevertheless, it was a great way to keep us entertained.We got back home after witnessing the burning of the paper house ,servents and ingots. It was 11.30pm by the time we got back.

The next day, we were back at the wake in the morning. The rest of the guys were present as well. Kai Siang drove us to Mandai cermatorium. We witnessed the last rites and saw the coffin wheeled out to be cremated. It was a solemn time for the rest of us. After that , it was back at the wake for lunch before we went off.

We hung around together in Citysquare mall. (This was the first time I have been there with friends previusly I have been there with parents). We explored the mall and some of us took the chance to do last minute Christmas shopping for girlfriend visit/ gift exhange/ whatever. We browsed toy stalls, NTUC and Best Denki electronics stall etc (It was fun to peek at 3D TV at the latter.) After that, Kai Siang drove us all back home in his car. It was the end of an eventful 2 days for me.

At Christmas, my family went to Sakura at Shaw house for dinner. I received biscuits and choco pie for Christmas. We definitely ate a lot until I had a bloated tummy, which was easily resolved by chinese rubbing oil and powder for tummy troubles.

Merry Christmas and Happy New Year!!

Saturday, November 6, 2010

Updates

After a long semester, i have now come to the last week of this sem. Then it would be reading week then it would be exams with the LSM3212 exam starting at 20 Nov to the last exam LSM 3261 starting at 30 Nov. Some updates:

This semester, i have been more involved in the Triple Helix, besides writing articles for the triple helix, i have taken other functions such as helping out my editor in chief with production matters, interviewing prospective writers etc. I will be promoted to Managing editor soon. Also , we have just released our Spring 2010 issue (with my Invasive species article in it) and will be releasing a fall 2010 issue soon (I contributed my SUJA for that issue as there was no time to write a new article from stretch). However, our activities are taking a backseat now due to the coming exam and will be continue in this December.

Yesterday, I met up with Joyce and Jun Yun at City Hall yesterday. It was planned to be a class meeting but only me showed any interest in meeting them up. Joyce brought her CHC (incidentally, if you know my sister, you would know that my sis goes there as well) friend along. We had a last minute decision to head to CHIJMES and ate in a Spanish restaurant there. I had grilled chicken in honey mustard sauce with creme catalonia for dessert. The girls did had other appetizers and we chatted over dinner. Apparently, Joyce had decided to give in to the iPhone revolution and brought her own one. We chatted on investing ans stuff like that. By the time we finished, it was 10 pm at night. As we parted at the City Hall NRT station, we did mutally agree that a full class gathering was long overdue =)

Coming up after the exam: Invasive Biology for Dummies.

Tuesday, September 7, 2010

Holiday Update

OK...this may come quite late.... but more stuff on what I did for the holidays

On the 16th of July, I had the pleasure of attending a talk about Alfred Russel Wallace by the author Paul Spencer Sochaczewski. Wallace was a contemporary of Charles Darwin who travelled in the Amazon and South East Asia. He was quite productive for 8 years in which he collected 125660 specimens including 212 new bird species, 900 new beetle species and 200 new species of ants. Besides that, he was a codiscoverer of evolution by natural selection together with Charles Darwin. The talk examines his journeys through the Amazon and the South East Asia rainforests abd also examined the reasons why Wallace became obscure in the history of science and Darwin has been lionized as one of the greatest biologists in history.(Conspiracy? Later in life Darwin lobbied hard for a pension to be given to Wallace. Was Darwin doing this because he was feeling guilty of plagarizing or because he was just nice? You should make up your mind =))

On the 23rd of July, I went to JB with my sister and her boyfriend. It was my first overseas trip. We hung out at the shopping centre close to the immigration centre for lunch and we went shopping for cheaper goods. We ate at the HK cafe and I had pasta with bacon for lunch. I found it quite fun and would love to go there again soon.

Saturday, July 3, 2010

Holiday update Part 1

I haven't updated the blog for a very long time..yucks! Where should I start?

Exam results? BLAHHH!!!

SSS1207 A
LSM2201A B
LSM 2103 F
GE 2220 B-
CM1101 B+

Yupped, you saw it correctly..I did flunked my cell biology. Now it looks like i have to repeat my module next sem =(

Oh yeah The F means my CAP is still stuck at 2.92. No UROPS i guess =(

I asked for a review of my script, so I was going to school to meet Prof Yeung. She showed me my exam script and it was pretty obvious even with a passing grade of 30% for module, she was already quite generous with my marks. Well, she also gave me a lecture on how important grades are. LOL =)

Drats, still pretty gutted about it. It is like England did not qualify for Euro 2008 and thrashed 4-1 by Germany at the World Cup: simply crap results and underperforming
Must spend less time at the computer.

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Recently, (well in 22-23 may) , I spent 2 afternoons as a volunteer in the Operation No Release. Basically, volunteers were posted all over the central nature reserves, to educate and stop any people releasing any animals for Vesak Day for good karma. It turns out that is an appalling poor idea. The ecological balance to the nature reserves simply get screwed up( like competition with native species). Secondly, 80%- 90% of the animals simply do not survive the release, as most of the released animals are pets who do not know how to look after themselves. ( I guess if my Mom simply walked out of the house today , I will also get screwed as well. For a start, I don't know how to cook). On the 22 May I got posted to the Dairy Farm Nature Park and the day after that to Upper Selatar. On both days though we ( pairs of volunteers will get posted to variuos stations )did not see any animals releasers.However, we watched the NParks officals stop a running group that was intending to run in the forest in which entry was forbidden. We also saw a group of nature photographers in the where we were stationed. They were very happy to explain to us what are they doing and showed us an assassin bug on the tree trunk. Overall, it was a good experience for me and i saw a lot of animals like monitor lizards, long tailed macaques and a very big millipede.
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As for the Triple Helix article i was writing, the professor has now revised my article and I have submitted it for a yet final round of revision. Yes
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That is all for now =)
See you soon..

Wednesday, May 5, 2010

Hi guys?

How are you doing?

It is now May and my exams are effectively over.. Yahoo!!!

Yup yup.

Overall, I had a good semester the exams were a blast =)

LSM2103? Yucks!!!..I didn't managed to read finish Alberts et al.. I can't recall anything for the essays questions(per usual since O level Biology) and the MCQs were so confusing as everything looked quite plausible =( Just like the CAs. Let's hope that it does not pull down my CAP a lot...

CM1101? I had consultation with Dr. Tan the day before the exam on Molecular Orbital Theory. On the exam, i still didn't know how to do =( but the rest of the exam was OK =) I hope i can have an A grade for the module.=)

GE2220? It was quite all right as the essay section was 40% of the total marks and my MCQs and calculations was all right. So still can pass =). Prof Terry was a good lecturer and a friendly man =)I had quite a lot of consultations in the office and his advice helped me a lot =) For example, I told him about a paper I was reading for the module and he was interested enough to ask where did i got it from LOL. Too bad that i am not planning to read natural hazards ( which he is teaching)for next sem as I don't need it for Geosciences minor. Hmmmmm, maybe next time?

SSS1207? The exam was open book. It was quite easy but tedious to complete as i always felt I was in danger of not completing it. And i am a Life Sciences major, so woe to the other majors i guess. I brought my textbook and my singapore science centre guidebooks. I finished the exam 5 mins before time. Maybe an A?

It is the holidays now. Probably i will finish the last draft of the TTH article that I am writing after my article has be vetted by the profs=)After that, it will be published =)

I was on the train after my last exam when Cheng Long asked to the movie at 8.30pm...the problem was he called me at 8.20pm and there is no way that i am going go to the theatre on time as he thought that I was at home. Sigh...maybe another day?

Till next time,
Sin Wei

Wednesday, April 14, 2010

LSM 2201A : The End

I am sorry that I have not been blogging for quite some time. I was busy with quite CM1101 and LSM2201A Lab reports.

Today we had our second CA worth at least 50% of our final grade for LSM2201A. After failing the first CA with 40% and rushing through the lab report, the CA is a must win for me. And I am very glad to say that I have won. For the first time since i studied biology at O level., I actually knew enough to fill up the entire answer booklet. I pumped my fists in the air in happiness and in victory. Of course it helps that Prof Chung decided to give us a mock CA in preparation for today's CA as all of the concepts came out in the actual CA

After that, I asked Prof Chung how it is relevant to my concentration in Biology (Environmental). He replied that without a knowledge of proteins, i can only observe life and not to theorize how life works. He cited the example of plant stress proteins and genes which requires a knowledge of proteins and their purification. He also told me that even sometimes doctors do not know the importance of biochemistry in their career.In other words a knowledge of proteins is essential for any biologist. Gee maybe I should take LSM 3231 next semester. =)

Overall, I had a enjoyable time in the module . It is not a evil module as its reputation and student number might suggest (37 only) Working in the lab with my lab mates was fun and enjoyable. With a friendly and approachable professor and a helpful TA, i really felt that i have learned something from this module.

I think i should blog about the Life Sciences Society Field Trips to the Herbarium and Sungei Buloh the next time.

Monday, March 15, 2010

What i have been doing for LSM2201A: PAGE

Hi guys,

Today I will like to report on what I have done so far for our LSM2201A.

For our last 2 practicals, we have been doing polyacryamide gels electrophoresis(PAGE). What is that? Basically, PAGE is a common method of analysing proteins. There are 2 kinds of PAGE: native and SDS.
Firstly, we have to prepare the polyacylamide gels. Polyacylamide gel is the preferred choice for electrophoresis due to the following factors. It ,depending of how you might want to vary your recipe, can form in a wider range of pore sizes.( for reasons we might want to see later.) and compared to the other common gel medium, agrose, it is more durable and resilient. Usually, most of the time, the gel would be 2-layered discontinuous system: Resolving gel at the bottom and stacking gel at the top. The theory behind this set-up are out of scope for this post but this discontinuous set up promotes better separation of the proteins (resolution) Polyacryamide gels are composed of mainly acylamide monomers and N,N methylene bis acylamide monomers to cross link the chains formed. As a result, we can get a uniform mesh of pores through biomolecules can migrate. This reaction needs radicals to get going so to do just that, we can add ammonium persulphate with N,N,N,N tetramethylethylene diamine to generate free radicals. For those who have some chemistry background, you will be certain to understand this point more better. After we prepare the gel, we loaded our gel into the electrophoresis apparatus provided to us and loaded our protein samples (prepared from our previous experiments) into the wells in our gels using the micropipette. My TA made sure that everyone of us had a go at that as that is an a important skill in modern biology. Sounds difficult, but it becomes not as difficult as it seemed once I and my lab mates had a go at it. =). After we had loaded everything, we switched on the power supply. Once the electrophoresis started, usually It will take some time to perform the process. So we had 1 hour to go for lunch break and got to know my lab mates better =). When the protein reached the other end of the gel, we stopped the process and removed the gel. Very carefully indeed. Now we have a new problem: the protein bands are totally invisible...and how on earth are we going to see them? Usually, the gels undergo staining and de staining with the dye Coomassie Blue, which stains proteins and give blue bands we can see. Staining stains the whole gel blue and de staining removed any dye that have not bound itself to the protein, thus leaving the blue bands.

OK...so you may ask: what is the difference b/w the native and SDS PAGE?

For that the key concept is that electrophoresis is a good way to separate proteins as a result of an applied electrical field. Now this separation is determined by both size and net charge of the proteins. Let's us take two proteins with the same molecular mass and shape. The one with the greater net charge will go faster towards the other side of the gel. Native gel electrophoresis is usually carried out if we want the proteins to remain in their natural shape and conformation. Why would we want to do that? Well, one reason for that would be if we wanted to carry out activity staining. For our experiment, to test for the dehydrogenase activity we used tetrazolium salts which are lightly coloured when oxidised and coloured when reduced.. This stains the bands and allowed us to see in which band has the most enzyme content and activity.

DS stands for sodium dodecyl sulphate. SDS makes a good detergent which can create a good lather: in fact it is found in products like toothpastes, shampoos and other cleaning and hygiene products. Now, SDS binds to the hydrophobic areas of proteins causing them to unfold into polypeptide chains. Molecular mass is now the sole determining factor on the migration rate of the protein. Shape is no longer a factor due to the fact that the native structure are completely unfolded by the SDS so the shapes are the same. Proteins bind to the same number of SDS such that they have the same amount of negative charge. Larger proteins will have slow migration rates than smaller proteins due to the fact that they cannot pass through the pores of the gels as easily as their smaller counterparts. The end product is that on the gel, we can see a series of protein bands arranged in terms of molecular weight. By plotting the ratio of the distance moved by the protein band and the distance moved by the proteins (called the Rf value)against the log of molecular mass (Log transformation to give the straight line) of known proteins standards, we can figure out the mass of an unknown protein. Cool =) However, the method has certain setbacks. One possible one if the protein has post-translation modifications like glycoxylations made to it, it will move anomalously on the gel and give a misleading result.

Just realized the week I have 2 full labs: LSM2201A (the fith practical) and CM1101. Fun!!!

Till next time =)

Saturday, March 6, 2010

Chinese New Year

Chinese New Year was an eventful (and a very profitable one)one for me. Having fallen in the midst of recess week, there was plenty of time to celebrate. The pessimistic ppl would probably think that the recess week was desingned to allow the Chinese students to go back to China or something. On the eve on Chinese New Year, my extended family visited my house for reunion dinner. Then I went to River Hongbao with my sister and her boyfriend. It was a beautiful sight to see to all the decorations. The next day, we were off to our paternal grandmother's house in Toa Payoh. On both of these nights, after the visiting was over, we went over to Selagie Road for LAN gaming to play Left for Dead 2. It was my first time playing, and while i succesfully completed the frist campaoign with my sister without 'dying', I didn't quite make it for the rest of the rounds.=( Nethless we had an enjoyable time with her friends fromwork.
A couple of days later, I had my aunt from Australia visiting us. We headed towards Sentosa and ate in Resorts World. She gave me $100, A$100 and US$100 sealed in a big red packey =)=) We tried some of the food and we found the food deliclious. After that, while my aunt decided to gamble and win $500 at the casino, we went to visit Underwater World.

My Underwater World videoclip can be seen here:
http://www.youtube.com/watch?v=lMyHc-DF8gs

I brought the A Guide to Sponges of Singapore at the giftshop. After that we went walking in Vivocity. I brought a packet of assorted chocolates at the Candy Empire. Overall, it was a nice day out for us.Haha. The next day, I went with my nephew and his mum to his party at Hougang. He , before he went to RI, he went to St'Andrews Junior School and his CCA is rugby. That party was their Chinese New Year Reunion party and the party was held at one of theparents house. Netheless, me and my nephew played with the roulette wheel and the poker cards with his friends =)=) And eating all kinds of yummy food. Oh, before i went home, i watched Everton beating Man United 3-1 on cable TV..Drats.=(
The sum total of these outings? 18 red packets and $520 dollars. By my standards, it was a rich pickings this year. Usually, my extended family gives $120 in all.
How do you guys celebrate Chinese New Year?

Sunday, February 28, 2010

Blast from the Past Part 2

Please see below for the background.

Below is the SUJA, finally published after 1 year of dormancy =) Quite unfortunately, it wasn't really selected for publication on the Science Faculty website so I will be publishing it myself here on my blog. As noted on the last post, my topic was on the extinction of the dinosaurs and how fast it happened. In other words were the dinosaurs in decline millions of years before the end of the Cretaceous period or the meteorite put an end to the age of dinosaurs to a sudden stop? UPDATE:(An updated version of this will be published in the Fall 2009 issue of the Triple Helix NUS. There will be substantial differences, so do have a look at the issue when it comes out as well)

INTRODUCTION
Dinosaurs are the most famous prehistoric animals ever known. Many books have been written about them for the laymen. People continue to be fascinated by dinosaurs which first evolved about 225 million years ago (MYA) in the Late Triassic and went extinct 65 MYA in the Late Cretaceous Period. During their 160 million years reign on Earth, they evolved into all shapes and sizes. The vast majority of scientists agree that modern-day birds are actually direct descendants from the dinosaurs. In other words, evolutionarily speaking, birds are dinosaurs. However, in this essay the word “dinosaur” is used to mean “non-avian dinosaurs”.
Since the discovery of dinosaur fossils in 1819, scientists have wondered what had caused their demise and have suggested over 80 theories just to do that.[1]Some of the more sensible ones are extraterrestrial body impact, volcanism, sea level changes and climatic changes. However, there are also the less credible theories like a mass death by a virus and aliens taking the dinosaurs away.[1] This divergence of theories is because there are many lines of evidence, both geological and biological and they can be interpreted in many ways. However, there is reason to believe that the most likely cause of their extinction is a catastrophic end by an extraterrestrial body as it accounts for the vast majority of the evidence and observations. The understanding of the extinction of the dinosaurs may give us an insight on what will happen if, however small the likelihood might be, if an asteroid were to hit the Earth. The study of mass extinctions also gives us insight on how biological systems may recover from an ecological crisis.
In the light of the current human-caused ecological crises with a high rate of species going extinct, this knowledge is invaluable.[1] In this article, the Cretaceous-Tertiary extinction is abbreviated as the K-T extinction. “Cretaceous” is abbreviated as “K” to avoid confusion with the Carboniferous Period (300 MYA). So far, the most accurate dating of the K-T extinction event is that it took place 65.95 MYA give or take 40,000 years. [2] But before we go into specific details of this extinction, we need to consider the nature of extinction and the potential pitfalls in determining it from the fossil record.

THE NATURE OF MASS EXTINCTIONS
A species goes extinct only when its last living member dies out. There are two types of mass extinction. One way is through background extinction. By nature, extinction is a normal outcome of evolution and usually species dies out in a constant way. Well known dinosaurs like Allosaurus, Iguanodon, Brachiosaurus and Stegosaurus probably went extinct through this process which is known as background extinction. However, when a large number of species goes extinct within a short period of time, it is said that a mass extinction had occurred. Researchers postulate that there have been 5 mass extinctions though geological history. The first occurred in the Late Ordovician 438 MYA and the fifth and most recent K/T extinction at Late Cretaceous 65 MYA. [3]Figure 1 below shows mass extinction events through the last 500 million years. The x-axis represents the time in million of years ago. The y-axis represents the percentage of marine animal genera going extinct. In general, extinction events have been shown to occur at regular intervals. The bigger the extinction event, the more infrequent it is. There is no major difference between a background extinction event and a mass extinction event, other than a mass extinction event is greater in magnitude.[4]

FOSSILS AND INTERPRETING OF THE FOSSIL RECORD

Researchers into extinctions obtain the evidence and develop their theories by studying fossils, the subject of the next section. What is a fossil? Fossils are basically the preserved remains of organisms from the prehistoric era. In general, organisms preserved this way are only called “fossils” only if they are older than 10,000 years ago. There are two types of fossils: body and trace fossils. Body fossils are the remains of an animal's body while trace fossils preserve an organism's activities like eggs and track prints. Fossils are preserved in general by the following process. Firstly, after death, the soft tissues of a dead body of an animal must decompose. Then the hard parts like bones, teeth and shells must be transported to their final resting place. The hard parts are rapidly buried and mineralized into rock. Finally, erosion by the elements eventually brings the fossils to the surface where they can be found. However, not all organisms have an equal chance of being fossilized [5]. A body can decay and break down very quickly. For example, in the tropical forest, a gorilla body can become a skeleton in ten days and disappear within three weeks --- without taking into account scavengers like hyena, which can chew its bones. The environment affects the changes of fossilization. Mountains are poor habitats for fossilization as no burial takes place, only erosion occurs. Forests are also not good for preservation as any bones can dissolve in the more acidic soils. Aquatic animals fossilize more readily than land animals as rapid burial takes place more often than on land. The type of organism also affects the likelihood of preservation. Animals without any hard parts like jellyfish leave little, if any, evidence in the fossil record.[6]

How are fossils studied? Well, scientists basically go to the fossils, dig them up and go home. However, fossil-hunting requires a lot of luck, patience and a trained eye. Fossils are studied in scientific institutions equipped with high technology equipment like computers, scanning electron microscope, geological analytical equipment and a good library [5].

From the fossil record, we have learnt a lot about the history of life. For example, we have reconstructed the history of life on Earth. [1] Many evolution lineages have been reconstructed due to the fossil record, most notably that of horses, whales, humans and the horned dinosaurs.[1] We also use fossils to reconstruct phylogenies, which are studies to show how organisms are related to each other. And finally, fossils are used to deduce how extinct organisms might have lived and looked like. [5]

PITFALLS OF THE FOSSIL RECORD

Interpreting fossil record is an art and there are potential pitfalls in using the fossil record to interpret mass extinctions events. One issue is that rocks do not preserve all the time that has elapsed. The problem is that the time period is only preserved in the fossil during the deposition of sedimentary rocks. Without deposition, there can be no record. There are some times and some places that have no sedimentary deposition, so there will be no record preserved. In the case of the K-T extinction, the only good fossil sites that preserve the very latest part of the Late Cretaceous are in the Great Plains of North America[7]. It can be seen that trying to reach global conclusions with evidence largely coming from only North America is simply questionable.

Another important issue is that not all organisms that have been living are represented as a fossil. Only the occasional fossil site preserves almost all the original biodiversity, a conclusion that has been reached from the fact that their biodiversity is similar in extent and in number to modern ecosystems.[1] With both issues discussed above, we can conclude that it is not to easy to elucidate the events of a particular extinction. As a result, the less we can tell about the different events in an extinction, the more the apparent abruptness due to the lack of information.

The third important issue is what we call the Signor-Lipps effect. [8] The argument is that the fossils in question are distributed regularly in the fossil record. The dividing line separates the fossil-bearing rocks from the non- fossil bearing ones. After this line, the organism can been said to have gone extinct. Suppose that the dividing line is approached from the oldest rocks from the bottom, as it is approached closer, the likelihood of finding the fossil decreases as the amount of rock the fossil can possibly be found decreases. So instead of the fossils being found up to the dividing line, the last occurrence of the fossil will be found below the line. Even if the extinction event is abrupt in nature, to the uninitiated laymen, it will seem gradual. This can be seen from Figure 2 below. [1, 8]

How do researchers gauge the magnitude of an extinction? The intuitive way is to use taxa at species level to calculate the percentage of the biota that has gone extinct. However, the problem is that very often a bunch of old bones cannot be identified down to species level. For example, while a lion and tiger are different species, their skeletons shows a high degree of similarity. The usage of higher taxa is problematic as it is quite subjective due to the fact that there is no set definition on taxa like family and order etc. What can be one person's family can be another person's two families. [1]

IMPACT THEORY

The impact theory postulates that the cause of the K-T mass extinction is by an impact by a extraterrestrial body, hitting Earth in what is now the Yucatan peninsula in Mexico. Many short term and long term effects of the extraterrestrial body,most likely an asteroid ten kilometres wide or a comet,[9]have been suggested. For the dinosaurs, the impact and aftermath of the asteroid hitting the Earth would have made living conditions impossible, resulting in its extinction over a short period of time. Figure 3 illustrates what it may be like at the point of impact.

EVIDENCE OF THE IMPACT THEORY
With the above in consideration, the arguments in favour of the impact hypothesis can be presented. There is both geological and biological evidence to support this hypothesis.

Where K-T sediments are exposed, the following arrangement can be seen. Cretaceous sediments are at the bottom with Tertiary sediments at the very top. In between these two layers is a clay layer rich in iridium. Figure 4 shows the K-T boundary. This is unusual as iridium is one of the rarest elements on the surface of the Earth but is present in the Earth's interior and in extraterrestrial objects like meteorites and asteroids in great abundance [10]. It has been suggested that this is representative of an asteroid striking the earth and throwing up a dust cloud. This dust cloud is represented by the clay layer formed at impact [11].

Further geological evidence can been seen from the shocked quartz was found at the K-T boundary. This is a form of quartz, a type of mineral, that possess an altered structure due to the enormous pressure resulting from the impact[12] Microtektites, which are small, rounded and circular silicate glass particles, [13] were also found at the K-T boundary all over the world . They are believed to be material from the meteorite that had molten and solidified, being thrown up to the atmosphere during impact.

This leads us to the million dollar question: Where is the crater if there was an asteroid hit the Earth? A most likely candidate is the Chicxulub crater near the Yucatan peninsula. It has been dated at 65 MYA which correlates well with the K-T boundary. [1] Glass from Haiti had been proven to come from the crater and shocked quartz had also been found in the crater itself.[1] Evidence for a tsunami after the impact have been found in certain sites in North America. Also, the K-T boundary in the crater was thicker compared to the other parts of the world. This represents material that did not got thrown up into the atmosphere. [9] The crater was close enough to have caused all of the observations after the impact. The formation of the shocked quartz can be attributed to the asteroid impact. Large amounts of water could have been displaced during an impact at sea, causing tsunamis to form.[3] There are also several lines of biological evidence to prove catastrophism by a asteroid. There is some proof from the fossil record of marine micro-organisms called foraminferia. In today's ocean, they are a constituent of the plankton in the oceans. Since the 1970s, most scientists have agreed that according to the fossil record for marine micro-organisms,the extinctions at the K-T boundary was abrupt.[1]. This is supported by a study of calcareous nanofossils, another group of organisms that corroborates the case for an abrupt extinction. [14] Both groups of micro-organisms show an abrupt pattern of extinction. Another study, using foraminferia, observed a very serious decrease in the primary productivity i.e. a decrease of organic matter synthesized by organisms using inorganic chemicals and sunlight over 3 millions years at and after the K-T Boundary [15]. This may be caused by the blockage of sunlight by the dust clouds and atmospheric aerosols thrown up by the asteroid which deprived them of sunlight which is an essential ingredient for photosynthesis. In general, the consensus is that according to the evidence from the marine microbes, the extinction is abrupt. But how abrupt would the extinction appear to be with regards to other groups of organisms?

The plant record also supports a catastrophic impact event. Studies have shown an increase in the prevalence of fern spores in many parts of the world during the K-T boundary. This increase in the amount of fern spores is taken as an indicator of fern populations at the time. Therefore it can be deduced that there is an increase in the population of ferns post impact. The pattern of the changes seen in plant biota was very similar to what may be expected by conditions seen after an “impact winter” or global wildfire [16] possibly caused by the heat build up during impact. Similar patterns of succession with ferns as a pioneer species have also been seen after major disasters like volcanic eruptions [17]. Also the plant record in North America suggests there is a major, abrupt plant extinction at the K-T boundary [18] These results suggest the rise of ferns at the expense of flowering plants due to a global disaster like wildfires at the K-T boundary caused by the impact.

Does the vertebrate record support the impact theory? In general it has been shown that animals that depended on detritus i.e. dead organic matter like marine scavengers, small mammals, and river animals were better off. The presence of a dust cloud or perhaps atmospheric aerosol thrown up by the impact of an extraterrestrial body may cause photosynthesis to cease. As a result, animals that depended on plants died off whereas animals depending on detritus would still have a food source due to the large amounts of dead organisms[19] Also animals that are small in size or were living in aquatic conditions had a high rate of survivability due to the simple fact they can avoid the adverse conditions at the surface just by hiding in the soil or just staying deep underwater.[20,21] Taken together, the evidence suggests that life on earth pre impact was undergoing a “business as usual” condition and most taxa underwent a drastic decline in diversity after the impact.

Despite being the “stars” of the K-T extinction, dinosaurs have not been well studied. While initially, they seemed to show a gradual pattern of extinction [22], the current consensus is that dinosaurs did not show a gradual decline but it was “business per usual” up to the point of impact [1, 23]. This is shown through statistical analysis of dinosaur diversity at both genus and family level. The number of taxa did not change significantly during the last few million years of the Cretaceous. In fact they have seemed to have maintained high diversity during this period. [23,24] However , the main obstacle to unlock the true pattern of extinction is that the only good dinosaur fossils site dating from the latest Cretaceous are only restricted to North America. There is a general lack of material from the other parts of the world. More study on fossils from across the world will be needed for a more accurate determination of dinosaur diversity and the pattern of dinosaur extinction.

In summary, post-impact, Earth was shrouded by aerosols of dust. This blocked out the sunlight. In the ocean, the deprivation of sunlight caused a decrease in the biomass of phytoplankton of the ocean. The decline of these primary producers would have caused a collapse of marine food chains. [24] Only animals which are hardy generalists and could feed on dead organic matter which could have piled up in huge amounts could survive the extinction. On land, tsunamis could have killed any land organisms living on the coast that have survived the initial blast. Any organisms that survived all of that must contend with wildfires set off due to the great amounts of heat produced by the impact. Plant diversity suffered due to the lack of sunlight needed for photosynthesis and the wildfires. For the herbivorous dinosaurs, they would have died out due to the lack of food. When the last carcasses of dead prey ran out, the carnivorous dinosaurs also went extinct due to starvation. The animals which could survive the extinction were mainly small such that they did not need a large amount of food to survive or could burrow underground to escape the adverse conditions above. As the earth recovered, large amounts of land were vacant and the first plants to resettle on the land were hardy species like ferns. Flowering plants settled after the ferns. The main survivors of the extinction like the mammals quickly diversified to fill the ecological niches left vacant by the now extinct dinosaurs.[25]

COUNTER ARGUMENTS OF THE IMPACT THEORY

What are some arguments against the impact theory? There were some suggestions that the shocked quartz and microtektites can be attributed to tectonic activity. Indeed, the Late Cretaceous was marked by an increase in tectonic activity in general. In India there is a series of lava flows called the Deccan Traps formed during the period between 65-60 MYA . The plateau that makes up a major portion of Southern India was caused by the lava flowing out of holes in the Earth's crust. Any volatile gases produced could have affected temperature globally. However, there are two problems to this. The Deccan traps have been dated to be slightly younger than the K-T boundary. Secondly, the shock metamorphic features that volcanic activity produces were different from the ones at the K-T boundary. [1]

Another theory is that marine regression was responsible for the death of the dinosaurs. There is a general consensus that there was a drop and rise in sea levels at the K-T boundary. There are some scientists who believe that this caused changes in the distribution of the seas and continents. Seas shrank while new land was opened up for terrestrial organisms. These changes resulted in ecological havoc to weaken the dinosaurs and made them vulnerable to environmental changes [26]. However, there is no geological evidence in North America that supports their theory that the drop of sea levels caused the decline of the dinosaurs.

It has also been suggested that climatic change may have contributed to dinosaur extinction. A cooling trend at the end of the Cretaceous has been generally recognized. A low ratio of 18O/16O in the shells of molluscs and brachiopods suggests a decrease of temperature in the ocean. The plant record in North America confirms the same thing on land.[3] However, just as we noted already, the results were taken mainly from the North American fossil record and it is not wise to assume a global climate change based on such localized data.

It has also been alleged that the dinosaurs gradually declined due to the rise of the angiosperms (flowering plants). Dinosaurs were thought to be not used to feeding on angiosperms and were believed to have fed predominantly on gymnosperms (non flowering seed bearing plants) as shown by teeth design of plant-eating dinosaurs and the presence of gymnosperm remains in coprolites (fossil faeces) [27]. However angiosperms were very likely to have evolved about 40 million years earlier and dinosaurs should have time to adapt to the appearance of angiosperms . There was also an increase in dinosaur diversity during the late Cretaceous especially in the hadrosaur (duck-billed dinosaur) and ceratopsian (horned dinosaur)groups. This would debunk the theory the angiosperm diversification resulted in dinosaur decline.

CONCLUSION

In conclusion, the other theories offered for the extinction of the dinosaurs are difficult to substantiate in comparison to the impact theory of catastrophic impact by an asteroid 65 MYA. Whether the dinosaurs were already in decline before this or not, the impact ended the reign of dinosaurs and changed the course of the history of life forever. For without the impact, mammals would not have evolved to dominate the Earth and therefore humans would not have evolved to prove that a group of reptiles once ruled his planet. No matter how they died out, palaeontologists will be continuing to work to uncover the mystery of dinosaur extinction.
3,501 words
References:
[1] D. Fastovsky & D. Weishempel (2005) The Evolution and Extinction of Dinosaurs 2nd Edition
[2] http://www.sciencedaily.com/releases/2008/04/080424140400.htm “When Did Dinosaurs Go Extinct? Cretaceous-Tertiary Boundary Dating Refined” Accessed on 17 Feb 2009
[3] A.Hallam (1997) Mass Extinctions and their Aftermath
[4] D. Raup & J. Sepkoski (1984) “Periodicity of Extinctions in the Geological past” Proceedings of the National Academy of Sciences, USA 81,801-805
[5] M. Benton & D. Harper (1997) Basic Palaeontology
[6] O.Judson (2008) http://judson.blogs.nytimes.com/2008/12/30/reflections-on-an-oyster “Reflections on an Oyster” Accessed 21st Mar 2009
[7] D. Fastovsky & P. Sheehan (2005) “The extinction of the Dinosaurs in North America” GSA Today March 2005
[8] P. Siggs & J. Lipps (1982) “Sampling bias, Gradual Extinction Patterns and Catastrophes in the Fossil record” In L. Silver & P. Schaltz (eds) “Geological Implications of Impacts of Large Asteroids &Comets on the Earth” Geological Society of America Special Paper No.190 pgs 291-296
[9] D. Carlisle (1995) Dinosaurs, Diamonds and Things from Outer Space
[10] N. Greenwood & S. Earnshaw (1997) Chemistry of the Elements
[11] L. Alvarez (1983) “Experimental Evidence that an Asteroid Impact led to the Extinction of Many Species 65 million years ago” Proceedings of the National Academy of Sciences USA 627-642
[12] www.scn.org/~bh162/shocked_quartz.html “WHAT IS "SHOCKED QUARTZ"?” Accessed on 1st Mar 2009
[13] http://www.agu.org/revgeophys/claeys00/node4.html “Tektites, Microtektites and Impact Glasses” Accessed on 6 March 2009
[14] J. Pospichal “Calcenous Nanofossils and Clastic Sediments at K-T Boundary, NE Mexico” Geology Vol 24 no. 3 pg 235-258
[15] S. D'Hondt, P. Donaghay, J. Zachos, D. Luttenberg, & M. Lindinge (1998) “Organic Carbon Fluxes and Ecological Recovery from the Cretaceous-Tertiary Mass Extinction” Science Vol. 282. no. 5387, pp. 276 - 279
[16] V. Vajda, I. Raine, & C. Hollis (2001) “Indication of Global Deforestation at the Cretaceous-Tertiary Boundary by New Zealand Fern Spike” Vol. 294. no. 5547, pp. 1700 – 1702
[17] G. Smather , D. Mueller-Dombois(1974). Invasion and Recovery of Vegetation after a Volcanic Eruption in Hawaii, Scientific Monograph Number 5. United States National Park Service. Retrieved on 6 March 2009
[18] P. Wilf and K. Johnson (2004) “Land plant extinction at the end of the Cretaceous: a quantitative analysis of the North Dakota megafloral record” Paleobiology 30:347-368.
[19] P. Sheehan and T. Hansen (1986) “Detritus feeding as a buffer to extinction at the end of the Cretaceous” Vol. 14,No. 10, p. 868-870
[20] D. Robertson, M. McKenna,O. Toon,S. Hope and J. Lillegraven (2004) “Survival in the first hours of the Cenozoic” GSA Bulletin,Vol. 116, No. 5-6, p. 760-768
[21] P. Sheehan and D. Fastovsky (1992) “Major extinctions of land-dwelling vertebrates at the Cretaceous-Tertiary boundary, Eastern Montana” Geology,Vol. 20, No. 6, p. 556-560
[22] R. Sloan, J. Rigby Jr, L.Van Valen, and D. Gabriel “Gradual Dinosaur Extinction and Simultaneous Ungulate Radiation in the Hell Creek Formation” (1986) Science Vol. 232, no. 4750, pp. 629 – 633
[23] P. Sheehan, D. Fastovsky, R. Hoffmann, C. Berghaus, and D. Gabriel (1991) “Sudden extinction of the dinosaurs: latest Cretaceous, upper Great Plains, USA” Science Vol. 254. No. 5033, pp. 835 – 839
[24] K. Pope, S. Hundt and C. Marshall “Meteorite Impact & Mass Extinction of Species of The Creteceous-Tertiary Boundary” Proceedings of the National Academy of Sciences USA Vol 15 No.19
[25] M. Novacek (1999) “100 Million Years of Land Vertebrate Evolution: The Cretaceous-Early Tertiary Transition”Annals of the Missouri Botanical Garden, Vol. 86, No. 2 (Spring, 1999), pp. 230-258
[26] W. Clemens, J. Archibald and L. Hickey (1981) “Out with a Whimper not a Bang” Paleobiology, Vol. 7, No. 3 (Summer, 1981), pp. 293-298
[27] G. Lloyd, K. Davis, D. Pisani, J. Tarver, M.Ruta, M. Sakamoto, D. Hone, R. Jennings, M. Benton. (2008) ”Dinosaurs and the Cretaceous Terrestrial Revolution”. Proc R Soc B 275:2482 7

Edit(22-8-2010): By the time of writing, this topic was quite controversial. However in March this year, a team of 41 scientists has published in Science to reaffirm the single asteroid theory of dinosaur extinction. It is now clear to almost all scientists in this field that a single asteroid caused dinosaurs went extinct because of the overwhelming evidence. As such, the topic is no longer contentious as before

Blast from the Past Part 1

Just a short post here.

Quite some time ago in my 2nd semester, i took a course SP1202 Communicating with the Academy. Basically this is the course teaching you how to write and communicate in science like writing science papers and reports etc. As part of the course, we were required to do a 3000 word essay(SUJA) based on a topic of controversy. We were required to give a 10 minute oral presentation based on the SUJA.

My topic was on the extinction of the dinosaurs and whether their extinction was gradual or very sudden.

The links below shows the video of the OP posted on my youtube page:

Enjoy!!


Monday, February 8, 2010

Week 4 stuff

Dear everyone,

How is everybody?

This week was OK for me..

Had a packed Tuesday in which i had a CM1101 Lecture, CM1101 Tutorial , GE2220 lab and LSM2103 lecture in one day. For the GE lab we were required to work in pairs or 3s. Instead, i chosed Guo Zheng. He had been one of my groupmates during the practicals for GE2229 last semester. I have chosen to continue the working relationship in GE2220, which he is also taking. Besides GE2220, he is also taking CM1101 with me as well. Will be meeting up with him tomorrow to discuss this week practical after the GE2220 lecture 2morrow. We have a tighter deadline as we are supposed to hand in the assignment the week after the practs unlike GE2229 which is 2 weeks after the pract...=(

This Friday i skipped my LSM2103 lecture for CCA meeting. The Triple Helix held its first meeting. Basically, it gives us new members knowledge on how our new CCA functions. The Editor in Chief gave us members of the literacy board(I hold the post as writer) a idea of our work schedule. Apparently, our 1st draft is due on 24 Feb. After the meeting and updates, our assigned editor discussed our proposed topics. Nevertheless, it is apparent that to nail down my chosen topic, i need more research. =) I think that my topic wld be on the field of biodiversity and conservation. Outline due end of this week=)

Despite being a science blog, all i have been talking about is my school life. =( What I should be wiritng about in here???!!!


Monday, February 1, 2010

Week 3 events

Hi everyone!!!

I hope that you guys are doing OK. =)

This week i had a long Wednesday in the Lab... It is LSM2201A again.....My groupmates and I were having slow progress on our experiments that we finished at 7pm...Yikes... Our TA was quite nice to stay with us to supervise our experiment where he could have ate dinner at 5pm.=) But, generally it was quite enjoyable and fruitful day..I think i have gained more confidence in using the micro-pipette =)

Our experiment firstly were to isolate and purify lactate dehydrogenase from rat liver. In case that “lactate dehydrogenase” sounds like Greek to you, it is the enzyme that catalyzes the reaction from pyruvate to lactate in anaerobic respiration . Generally, the reason why you have sore muscles after running is due to the formation of lactate in your muscles. As you run, your muscles will utilize anaerobic respiration to fulfill their oxygen debt. Lactate is formed and as it decreases the pH inside the muscles, it becomes toxic, resulting in pain.

We got the buffers we prepared a fortnight ago from the freezer. What is a buffer? A buffer is basically a solution that has a weak acid/base with its conjugate base/acid. The pH will change very little when a small amt of strong acid or base is added to it. Buffers have a wide variety of applications. The chemistry of buffers can be summed up in the Henderson-Hasselbalch equation: ph = pKa + log [A/HA]

As most biochemical processes have low tolerance to extreme pH, buffers are common in living organisms. For example, the hydrogen carbonate and carbonic acid one in blood. In the biochemical lab, one common buffer is tris(hydroxymethyl)aminomethane, affectionally known as “tris”. This is a major component in the buffers we use.

We put the liver extract by affinity chromatography through a column. Affinity chromatography is a method of separating biological mixtures in a lab on the basis of a reversible interaction between a protein and a ligand (which has a similar structure to a substrate and a cofactor) in an immobile phase, which is usually a form of a gel.. This form of separation has several uses like the purification of an antibody in an blood serum. Whereas the protein we want is trapped to the gel, the other proteins will not be trapped. After we remove the other proteins, we can wash out our desired protein using another buffer. This process is usually termed elution. In our experiemnt, we use the blue gel called affi -gel blue. The dye has a similar structure to NADH and NAD, which allows the dye to bind to a wide variety of proteins. There was a problem with the rat liver extract we were originally given which were too lumpy which clogged up our column, as a result we couldn't get our fractions. We had our 12 fractions later when we were given more homogenized liver extract.

We set out to find how much enzyme activity and how much the protein we had in our fractions to figure out which fraction had the most enzyme. I worked on the enzyme activity assay while my lab mate worked on the Protein assay. I used a spectrophotometer which is an instrument that measures intensity as a function of light or color. Basically it measures the transmittance of light between a reference solution and a test solution. Light from the source lamp is diffracted to a series of individual wavelengths of light. Light of a single frequency is then passed through a sample. This intensity is measured with a light sensor and the transmittance is compared with the transmission through a reference sample. Before we start the machine, we have to zero the sample to set a baseline in which all other readings are compared relative to the zeroed sample. Usually the machine would give a reading of % absorbance. Spectrophotometers have a wide variety of uses, and in this case by monitoring the change in absorbacne over time, we can measure the activity of the enzyme..cool huh..

When we were finished with our experiments, we handed over the samples to our TA and went back finally to home. Whew!!! A long day for us and the TA too!!!=)


Monday, January 25, 2010

Week 2 Stuff


Hello how are you guys doing, There have been 2 major issues...

My application to Join the NUS chapter of the triple helix organisation has been successful...YES!!!! My job is to be a writer for the journal they will be publishing. My first task is to come up with a topic exploring the relationship between science and society and submit the abstract on 31 Jan 2009...Thought up a few possible leads....will decide about it soon =) So i have got a CCA already..haha =)
Just came back a few hours ago from my JC mini class gathering. Boon Yen is leaving Singapore soon for work at Down Under. So this called for a class gathering....(We had a precedent donkey years ago where we sent off Karen to NY). Only a third of them showed up
Boon Yen, Joyce, Joycelyn,Jun Yun, Andy , Zhi Wei and well yours truly. We ate at Marche@ 313 Somerset I ordered a rosti with smoked salmon, Oringina, and chocolate fudge cake and creme burlee ice cream....(Mom wasn't too pleased at the bill receipt though when i came back home).. I think Marche can be a bit expensive... We chatted about our lives and blah blah blah... After that, Andy and Zhiwei went back home first when I went with the girls to window shop and have a post-meal walk.Yup yup, They wanted to buy clothes for Chinese New Year....After that home sweet home..Nice meeting up with all of them again =).

See ya guys..Time for bed =)








Saturday, January 16, 2010

New Semester

Hihi how are you guys doing?

A new semester has arrived and I will be taking these modules for the new semester:

 CM1101 PRINCIPLES OF MODERN CHEMISTRY

 GE2220 TERRESTRIAL AND COASTAL ENVIRONMENTS

LSM2103 CELL BIOLOGY

LSM2201A EXPERIMENTAL BIOCHEMISTRY

 SSS1207 NATURAL HERITAGE OF SINGAPORE

Bidding went very well for me as planned except for the experimental module. I got outbidded for both the molecular biology and microbiology ones. Anyway, so does everyone else in the biochem module =) Our first practical was quite simple as we created buffer solutions. What the heck is that? More on that on a future post....

Have to wake up quite earlier in the morning to attend chemistry class at 8am. Our first lecture was on atomic quantization and quantum physics. Quite difficult, if i had not worked on my chemistry during the holidays, I don't think i would have understood anything.. Of all the 5 modules, I was quite apprehensive about taking this module at first as i can't S/U that module. But i decided to keep the door open in doing a chemistry minor anyway.. Looking forward to the lab =) This would be the first time i am studying chemistry in a year. haha =)

GE2220 would be the first lesson of my week. Our 1st lecture covered an introduction to geomorphology and weathering. Already i started to like Prof Terry as he is a friendly and jovial guy. Haha.. Looking forward to the lecture every week. And yes, maybe i will do a geosciences minor in the future..

SSS1207 is the module on the natural heritage in singapore. Prof Chou joked a lot during his introductory lecture. I got to meet Dr Ng (my lecturer for LSM1103) again during the lecture. Anyway, this will be an interesting module. I am currently looking for field trip kakis for this module..so if you are reading this, drop me an email soon...=)

On a lighter side, for this Tuesday i had a lots of free time like from 10am to 6pm. Don't ask why my timetable is weird, ask the scheduling guys. I studied at the table outside the science library, near the lifts when my JC friends said  hello. Charles and Rebecca said hello. Rebecca offered me her Natural heritage book when she learned that i am taking the module. Thanks for the kind gesture, Rebecca. =) but i need the latest edition with its updates...=)

I had lunch today with Guo Zheng. Guo zheng was one of my group mates during the GE2229 module and he is taking CM1101 and Ge2220 with me as well. So we will get to see each other again and hopefully will work with each other again ,especially for our new Geography module. Haha=)

On a lighter side, I will be meeting up with my JC friends next week. "For what?" you may ask. But it will have to stay hush hush for now. =)

That is what i have to got to say for today...

BYE BYE =)