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Contents 1 MathBio 1.1 Final and Submitted 1.2 Application 1.3 Structure 1.4 New Structure 1.5 Possible Things to Include 1.6 MSc Mathematical Biology Statement 1.7 MSc Mathematical Biology Statement, Version 2

[edit] MathBio

[edit] Final and Submitted

My first eye-opener to this area of Mathematical Biology was from a conversation with a neighbour who is CEO of a company called Ovasort. Ovasort is a biosciences company with an aim to develop molecules that can bind to novel surface proteins in X-chromosome sperm in order to separate them, meaning that semen used for artificial insemination can be gender-specific. This process has now found a possible new use in drug treatment of cancer. By detecting surface proteins on cancer cells, the drug can be targeted directed, which means that it would incur minimal side effects if any in comparison to radiotherapy. This project is still in progress, however what it has highlighted to me is how developments in genomics and proteomics have been a crucial aid to the company. These developments could not have been made without mathematics and computing inputs, for instance in scanning an entire genome looking for patterns to find genes and also detecting possible evolutionary changes. Ovasort has also benefited from the ability to predict locations of common genes in different species, for instance in cows and pigs. These areas of bioinformatics are current areas of research with a huge amount of scope that I would be very interested in learning more about.

Another project that has interested me recently is the "Blue Brain" project whose aim was to construct computationally an entire neural network of a human neocortex using an IBM supercomputer. Now that this is completed, the project will simulate parts of neocortex in order to try to understand the effects of altering certain genes, and how this can affect the higher functions of the brain. These higher functions are interesting in themselves, for instance, why can humans remember faces very well, yet find it very hard remembering words. Projects like Blue Brain attempt to find specific current genetic reasons for this. There are also sensible evolutionary reasons for these sorts of higher function phenomena.

On the topic of evolution, there are also many active areas of research, one such is how different units of selection are subject to evolution, for example, at the level of the gene where humans are vehicles and large protein coats for the genes to replicate. Also, entire organisms can be considered as units of selection, the original Darwinism, where survival of the fittest is the key concept. Group level selection or "Super-organisms" have also been hypothesised, even in groups containing different species where the entire group has common biological goals that aid the survival of the group, for example E.O. Wilson's work on ants. This concept of units of selection leads still further into philosophical ideas such as the Gaia Hypothesis in which the whole planet’s life can be considered as an evolving organism with an aim to survive. None of these ideas are firmly agreed upon within the scientific community therefore they still require significant research in order to test the theories, which is where mathematics and statistics come in, including on the "Evolution of Genetic Systems" module in the first semester of this MSc.

These units of selection also create other questions such as the famous nature/nurture debate. This can relate directly to the area of genomics, e.g. to find heritable genes that link with things like intelligence, and as mentioned earlier, problems involving genomics like this require mathematics. Extending this over time periods can create questions like: how has our biological evolution affected our cultural evolution and vice-versa, and at what rate do these interactions take place?

I will soon graduate with a maths degree from Bath. During my time here I have gained good knowledge of different areas of applied mathematics, statistics and probability alongside gaining knowledge of programs like Matlab and R which will also be needed during the MSc programme. I hope from the above I have outlined some of my interests in this field in which I will finally get to apply mathematics directly. I am very keen to start my research career in an empirical field which has a huge amount of opportunities for the future.

[edit] Application

If you are applying to do RESEARCH, please use this space to tell us about your research interests in as much detail as possible. If you have a full research proposal, you should write it here, or attach another sheet. (A research proposal is not applicable for the Department of Biology & Biochemistry. Please contact the Department directly for further advice). Please list your publications/reports, if any, and tell us if you wish to work with a particular member of staff at the University.

If you are applying for a TAUGHT COURSE, please tell us about any relevant professional experience you have, and about your reasons for wishing to study on this course. Attach another sheet/CV if necessary.

[edit] Structure

1. Reason for Applying
   1. Interest in evolution, using current mathematical knowledge to learn about a new field: Biology
   2. Interest in a research career and gaining a grounding in an empirical field
2. Current Interests
   1. Nature vs Nuture in neuroscience, Twin studies, Biological and Cultural Evolution
   2. Intraspecies vs interspecies selection (debate between dawkins and other dude)
   3. Game theory (tit for tat, prisoners dilemma, computer models for predicting social interaction between organisms)
   4. Evolution based on superorganism level instead of looking at it on the gene level (E.O. Wilson, might revolutionise biology)
3. Current Knowledge and Skills
   1. Matlab, R
   2. Already will have maths degree from bath

[edit] New Structure

1. Ovasort
2. Genomics/Proteomics
3. Uses
4. Blue Brain
   1. Cognition
5. Selection
   1. Unit of selection
      1. LUCA,panspermia, Gaia
   2. Bio/Cult Nature/Nuture
   3. ESS
6. Current State?
7. Future State?
8. Rate?
9. Current knowledge and what I can offer

[edit] Possible Things to Include

• population genetics

• structure of genetic systems

• genetic and molecular evolution

• methods for testing evolutionary hypotheses.

• always been intrigued by timescales of evolution

• nature vs nurture

• biological evolution vs cultural evolution

• neuroscience

[edit] MSc Mathematical Biology Statement

currently rubbish:

I am applying for the MSc in Mathematical Biology because I would like to gain a first grounding for a career in research. This course will provide me with the relavant mathematical and biological techniques in order for me to persue a career in the wide range of current areas of research.

More specifically, one of the things I am interested in is evolutionary psychology. Ever since understanding evolution at school, I have always been intrigued that we are using a brain that is built for the hunter/gatherer human, and we are actually using it to research the beginnings of the universe, to trade on the stock market, to try to cure cancer, to build computers that can attempt to model our brain, etc. From directly looking at ourselves and nature, there seems to be many unknowns still, for instance, why do we have an extraordinary ability of remembering faces, but then a limited ability in remembering words. There are so many questions, and now with today's computing power and such advances as the sequencing of the human genome, it seems that the answers to these large amount of questions may be closer.

I am also interested in how our current period of time may affect the evolution of ourselves and the environment in many years to come. These are very general problems but when thinking about them, they create many hypotheses in which to drive research in more specific areas such as protein structure prediction, comparitive genome analysis, computationally modelling the brain etc.

I also think that a thorough understanding of areas of statistics and probability is crucial in this area due to the huge amount of data we have of the past, and the even larger amount of possible outcomes for the future when considering any system.

I very much enjoyed my first year project on cellular automata and I would be very interested in extending this sort of analysis to epidemiology. I also feel confident in the use of Matlab, R and am interested in learning new skills in things like Maple

[edit] MSc Mathematical Biology Statement, Version 2

I am very interested in evolution and how it can display such a powerful explaination for the huge living diversity on this planet. I would like to use and develop my mathematical knowledge to learn about a new field, namely biology.

I am interested in a research career and gaining a grounding in an broad empirical field that has many future opportunities

My current interests surrounding this field are summarised in the following: For instance, there are many questions still to be asked about "nature versus nurture" in areas such as neuroscience, questions surrounding diverse behavioral traits. It seems so easy to accept a predominantly nurture basis as determining factors in ones knowledge of oneself, however, as in anything, a self observation is impossible to justify. Whether these questions can be answered any time soon yet another question, and whether that one can be answered is yet another question. And when we consider something as nuture, what does that consist of, this can also raise very interesting philosophical questions as well including the concept of free will. Reseach consisting of mainly twin studies have shown that "nature" influence is substantial in developmental psychology. Then there are the even wider questions that span multiple generations, for instance, how does our biological evolution affect our cultural evolution and vice-versa. Current analyses for these questions

Another area that is interesting is the huge amount of cognitive biases that we are subject to every single day, and how some people can notice them, yet others seem to not know, or choose not to know.

I have recently been reading about the "Last universal common ancestor" and the related question of "Panspemia", the seeds of life around the universe carried by metoerites

I have also recently been reading about EO Wilson's work with ants and the concept of a Superorganism, which then also extends to the Gaia hypothesis

Another unrelated area of interest has actually followed from myself reading about the prisoner's dillemma. I have now realised that this simple game can be extended in a huge number of ways in order to predict things like social interaction with different species, e.g. going back to the example of ants, the species called Myrmecia tend to be very aggressive and have powerful stings which is quite in constrast to the Polyergus who can't actually feed itself, but must rely on slaves of another species Formica to care for them that they stole from a Formica nest.

I am also interested in how our current period of time may affect the evolution of ourselves and the environment in many years to come. These are very general problems but when thinking about them, they create many hypotheses in which to drive research in more specific areas such as protein structure prediction, comparitive genome analysis, computationally modelling the brain etc.

Obviously I do not hope to address all these questions within a one year masters, even one question answered would be surprising, however I know that my interest will drive me to work with the rest of the research community to come ever closer to the answers of these questions.

I currently have basic knowledge of Matlab and R from my degree here at Bath and am very interested in expanding my knowledge in these areas.