Extended essay.

The link at the end of the page leads to an online copy of one of my last drafts of my extended essay on Biology HL for the IB. The following paragraphs are the abstract of my EE in case someone wanted to read a brief summary of what it is about:

One of the main products of fermentation which has had an incredibly important role through human history is wine, and it has become a topic of my  own interest for different reasons I mentioned within the following extended essay. There is a surprisingly large number of varieties of wine, but the two most common are red wine and white wine. They both come from same genus of grape, vitis,  but they have different alcohol graduation, where red wines have an average percentage alcohol of 12º to 14º and white wines 10º to 12º. If the percentage alcohol in a fermented liquid depends on the microorganisms that have fermented it, this leads to the following question: To what extent does the type of grape, red or white, affect the growth rate and therefore the growth curve of leavening agents?

Colorimetry is commonly used in microbiology in order to determine the turbidity of a liquid. This allows quantification of the number of microorganisms in it. A colorimeter was used to measure the turbidity of grape juices inoculated with bakers yeast at specific time intervals over the course of a week. This was used to calculate the population growth curves of the microorganisms in the different samples. The population growth curves obtained of the red and white grape juice samples showed an statistically significant difference which was calculated through a paired T-Test.

A trend was present in all the populations of white grape juices. They started declining before the red grape juices populations, suggesting that there are less sugars in the white grapes than in the red grapes and therefore less alcohol can be formed by the yeast, leading to the conclusion that this may be one of the reasons why the alcohol graduation is lower for white than red wine.

Link to my Extended Essay:

https://www.scribd.com/document/325372393/Biology-Extended-Essay-Final-Draft

Working experience.

This last summer has been a busy summer. Apart from the September tests, extra reading, and summer work, I was able to do three weeks of working experience on a biochemistry laboratory, and I can’t be more happy about taking that decision.

In August, during three weeks, I worked in the biochemistry and hematology laboratories of Hospital La Beata Santa María, in Madrid. There I worked in a professional environment mainly in the blood analysis process and identification of pathogens in body fluids such as urine through different chemical tests. It really helped me to develop my lab skills, my efficiency and made me use to work in a lab environment and also to discuss topics related to it. The people I worked with were amazingly helpful, and I would like to give thanks again from here to Cata, Vio and Paz, cause they made the experience as amazingly productive and instructive as fun. 

I’m not going to post a lot of pictures in the blog due to the privacy of both patients and workers of the centre, but I would like to at least post this one picture that particularly attracted me, which is the coagulated blood from a patient “frotis” with high level of eosinophils. 

Again, thank you very much,Beata team, this experience couldn’t have been better.

Water transport in plants. Potometer!

Back to college! After loads of tests and deadlines, there’s some free time, so I can finally type some posts. This year in Biology HL we’re starting with plant biology. One of the experiments we did in order to show in real life what we’re learning from the book used a potometer. A potometer consist in a glass tube with several apertures and it's used to show water uptake from plants and how it is transported in the Xylem through pressure changes. A potometer is shown in the following picture. 

In order to show the water uptake from the plant, the tube was completely filled with water and the plant was introduced into a bung which then was used for sealing the potometer. After that, as the water was absorbed from the tube by the plant, some air would get into the tube on the opposite howl, so then a water cup had to be situated under the opposite hole in order to seal it. A small bubble of air should be then seen inside tube, and as the water is taken up on the right hand side of the potometer, pressure goes down so the bubble moves in that direction. The distance the bubble moves in a fixed amount of time can be used to calculate the rate at which water is absorbed by the plant.

Although a Potometer can be based on a really simple principle and it’s very useful to show water uptake by plants, it can be a bit tricky and tedious to set up. First of all, no air can be getting into the tube apart from the bubble, and in order to seal all holes a substance like vaseline has to be used to cover the space between the plant and the bung. also if there’s some air left in the tube it can separate the water from the roots of the plant, so no water uptake will take place.

Plant biology, although it can look a bit boring at the beginning, becomes really interesting in terms of transport of nutrients through the plants. The point that makes it more interesting for me is that no mechanical procedure can be used to do this and plants still find ways to achieve this without any problems, fact that I find particularly astonishing.

The Origin of Meiosis and How Sexual Reproduction Prevailed.

We’re studying now one of my favorite topics, evolution. The other day, we went after school to watch with our teacher the documentary film “Charles Darwin and the Tree of life”, presented by David Attenborough. I really enjoyed the documentary, but after watching it a question arose in my mind:

Supposedly, a characteristic doesn’t just appear. Is a step by step process, where each of these steps are a random mutation which presents an advantage for the individual which will increase the probability that the individual will survive and will pass it’s genes to it’s offspring. But what if this steps didn’t have any advantage to the individual at first and the process would not be beneficial until it was completed? 

The process I was thinking of was meiosis. If you think about it, what would be the advantage of an early meiosis without any outcome? It could not just appear like a complete process, and, In case it was an advantage on it’s first steps, why can we not find any organism which present this intermediate state of primal meiosis? 

For this reasons I decided to do some research on this topic.

The Origin of Meiosis

The Origin of Meiosis is still Unknown, but there are two main theories which try to explain where it evolved from:

—} Meiosis Evolved from Mitosis: 

In this theory, supposedly the first prokaryotic cells evolved Mitosis first. Then, when Mitosis was settled, Meiosis and sexual reproduction appeared.

The main support for this theory is that both Mitosis and Meiosis are very similar in terms of steps and they use almost the same molecular machinery (For example, The use of Spindle Fibers generated by the centrioles which separate the chromosomes during Anaphase). 

But this still doesn’t explain how variation processes appeared, like Chiasmata and crossing over.

—} Meiosis Evolved from prokaryotic sex:

Prokaryotic sex is a complex process which in simple terms consists in one bacteria releasing (Usually a plasmid of) DNA to the surroundings which is then taken up by another Bacteria and binds to it’s own DNA. This the simplest and most ancient way of achieving variation inside a single “specie”.

Support for this theory is that the earliest eukaryotic cells carry the genes for early meiosis, but are not expressed. This happens for example in Giardia Intestinalis.

However neither of this theories show in a clear way what was the origin of Meiosis.

How is Sexual reproduction an advantage? How did it prevailed?

An obvious advantage of sexual reproduction is that it leads to variation. However, this is a long term process, and Evolution doesn’t work like that. Evolution is based on short term advantages, advantages which increase the probability that the mutated individual would pass it’s genes to the offspring. Long term processes which don’t help the individual to survive in it’s first stages are much less likely to pass to the next generation, because they aren’t an advantage for the individual even though it takes energy for carrying it out.

This shows how improbable it was for Sexual reproduction to appear. The first Sexual reproductive individuals would be in competition with self replicating/cloning organisms and they would have to survive until sexual reproduction was actually an advantage.

With the next diagram I want to show how Sexual reproduction is a long term advantage over self replicating. 

During the second generation of sexual reproductive individuals, There would be both weak individuals and Strong individuals which reproduce this way, and they would have to compete against self replicating “normal” individuals. During this first competition, weak sexual reproductive individuals would die against normal self-replicating individuals, lowering drastically the amount of sexual reproductive organisms. However, Strong sexual reproductive individuals would survive, and normal self-replicating individuals would die against them. 

Therefore, over time, strong sexual reproductive individuals would be the only ones to prevail showing how variation is a long term advantage over cloning and self replicating. The survival of the fittest.

This is one of the blog posts that have taken me more time to do, but it can’t express how I feel about this topic and how amazingly interesting it can be. 

Our own GMO. Glowing E. Coli!

We just finished genetics a week ago in biology IB. We’re starting Taxonomy now, but before that, we finished one of my favorite topics with one of the experiments I’ve most enjoyed this year. 

The experiment consisted in, by genetic engineering, trying to insert a gene into E-coli bacteria in an LB agar sample which allowed it to glow under UV light.

For doing this, we prepared four plates of LB agar. The first one didn’t have anything in special apart from LB agar. The second and the third one one had ampicillin (A type of antibiotic) apart from LB agar. The fourth one, apart from this two, had Arabinose on it, which is a type of sugar.

In my group we did also plate 5 and 6 because we had extra LB agar. They were the same than plate 4.

Then we prepared four samples of E-coli for each of our plates. The first two didn’t have anything in special, but in the other two we inserted a vector named P-Glo, which can be seen in the diagram: 

(Diagram credit: http://microbesrule.blogspot.co.uk)

The vector presents 3 important parts. First of all, a promoter sequence of DNA based on the presence of arabinose sugar attached to the green fluorescent gene. This means that for the gene to be translated into a protein, there has to be arabinose sugar in the sample. The green fluorescent gene translates into a protein that allows the organism to glow under UV light. The other important section is the gene of ampicillin resistance, which will allow the bacteria to survive even if there’s ampicillin in the sample. 

For introducing the genes into the last two samples, we poured some vectors of the gene that was a previously copied by a PCR machine into the two last samples with E-coli. Then we putted both samples in a water bath at 42 degrees. This would make the bacterial membrane of the E-coli permeable for the Vector P-glo to pass through and being used by the bacteria.

Then we letted the bacteria to grow and multiply for two days and we got the following results:

-The first plate had a big group of E-coli visible on it, but these ones didn’t have anything in special because we didn’t inserted the vector on them. 

-On the second plate, all the E-coli had died. This is because the Agar had ampicillin on it and the antibiotic killed the bacteria.

-The third plate had E-coli on it but they weren't able to glow. The reasons for this is that even if they had the P-glo vector inside of them (Which gave them the resistance to the ampicillin, the reason why they survived), there wasn’t any arabinose sugar on the sample. Because of this, the promoter didn’t activate, and the glowing gene wasn’t translated into the protein.

-Finally, on the fourth plate we had glowing bacteria! In this case there was arabinose on the sample, so the glowing gene was translated into a protein that gave the E-coli the ability to glow under UV light.

I’ve really enjoyed this experiment and shows me that biology is even more fun than what I expected. We’re starting Evolution now with our other teacher, let’s see how it goes!

Creating our own little "Earth".

As I said in my previous blog posts, we’re studying ecology at the moment in Bio HL IB. The other day, having a lesson about the same topic than in my last blog post (The correlation between CO2 levels and global temperature), we carried out a really simple experiment with the aim of showing us that this correlation can actually exist in a much smaller level if he have three things: Carbon dioxide, a sealed mini-atmosphere and a source of light.

The experiment consisted in the following steps:

-You take two flasks.

-Cover the base with a thing layer of water.

-Put a thermometer in each flask.

-in a side of one of the flasks, we fill a conic flask with Calcium Carbonate (CaCO3) and we seal the top of the conic flask connecting a tube from it to the nearest flask.

-We cover both Flasks with a plastic layer, leaving a space for the thermometers and the tube in one of the flask that is connected to the conic flask. 

-We uncover the conic flask and we pour hydrochloric acid. Immediately after that, we seal the conic flask again, which is connected to the other flask.

-We put both flasks under a source of light like a lamp, arranging them in a way that both get the same amount of light.

So what do we expect to happen?

Both flasks should have the same initial temperature, 21ºC in my case, but when they are heated by the light, the one that is connected to the conic flask should become hotter, because CaCO3 reacts with Hydrochloric acid forming CO2 (Which will pass through the tube), CaCl2 and H2O (Which will remain in the conic flask). As we end up having more CO2 in one flask than in the other one, we should end up with more temperature in the flask with extra CO2.

And this actually was what happened, after 30 minutes, the normal flask ended up having 30ºC and the one with extra CO2 ended up having 32ºC. It may not look as a big difference, but we have to take in count a lot of factors. Although the Extra-CO2 flask should had a bigger temperature because the CO2 traps heat and doesn’t let it get out of the flask, there wasn’t a lot of time for this to happen. Also, it will loose a bit of heat because the room was at a much lower temperature. The water would also have an effect, as it has a high specific heat (Amount of energy needed to heat or cool down an object), but it is needed because it makes much easier to measure the temperature with the thermometers… And even with all this factors, the CO2 was able to rise the temperature 2 centigrades! This shows us how CO2 levels have and incredible effect in global temperature and how they are absolutely linked together.

How a little fern called Azolla drastically cooled down the earth 50 million years ago.

As I said a couples of posts ago, we have started Ecology in Biology IB. Today in our lesson, we talked about climate change. more particularly, about how the CO2 levels affect to the global temperature and they both increase and decrease together at the same rate.  

(Photo credit: Bioknlowledgy)

This afternoon I was watching a couple of videos from SciShow (https://www.youtube.com/channel/UCZYTClx2T1of7BRZ86-8fow) and I was really surprised when I realized that yesterday they posted a video about this exact same thing!

Link to the video:

https://www.youtube.com/watch?v=LUnpHax9EwA

What the video is talking about is one of the main hypothesis about how the earth’s temperature drastically decreased 50 million years ago. And this reason is a Fern called Azolla, a small fern that lives over fresh water which flourished around 50 million years ago in the northern arctic sea, covering millions of square kilometers and almost lowering the CO2 levels in the atmosphere by half. By doing this, as CO2 is a gas which contributes to the greenhouse effect, the temperature was reduced drastically, leading to a new glacial period.

A lot of research is being done at the moment about Azolla, and one of the main questions that the researchers want to solve is… Would Azolla be able to cool down the earth AGAIN under the right conditions?

But this is just a little summary, in the video they explain it much deeply and better, so, go check it out!