Tuesday, April 22, 2008

Year 3 Sem 2 modules

This Semester, I am taking 4 modules, excluding the UROPS module - LSM 4253 (Behavioural Biology), LSM 3251 (Ecology and Environmental Systems), LSM 3252 (Evolution and Comparative Genomics) and SSS 1207 (Natural Heritage of Singapore).

Doing UROPS, I learnt more about research and writing of paper and skills basically.

LSM 4253 also trained me in retrieving information from journal papers and writing papers as I attempted the term paper and wrote of carotenoid as an indicator of quality leading to subsequent dichromatism in Northern Cardinal. My biggest mistake is probably choosing my term paper topic, not based on what there is to find out, but based on the species Cardinal cardinalis which I adore. There was actually nothing significantly new about this topic or things I could expound on, but I search deep and hard to come up with a hypothesis, which does not hold water in the end. If I could redo this term paper, I would first do an extensive literature review on my areas of interest and what is lacking research/review papers in. My topic was very narrow as well, might not be the best choice to focus on that species alone... There was quite little papers, I realised, comparing to my friends who had 50 over. I only had perhaps not more than 20 references.

So did LSM 3251 trained me in writing papers and searching and skimming of journal papers. This it did so for the practical report on how the crustacean community structure changes with high and low tides.

I feel like I am undergoing training for Honours Year this Semester. It is something I am very grateful for. As I know how critical these skills are, struggling with them doing the papers and reports.

Very interestingly, I like the modules LSM 4253 and LSM 3252 more than LSM 3251 and SSS 1207. I find they stimulate my thinking more and require less intensive reading work than the other two. Maybe they're more interesting too?

It's very interesting how I prefer studying some things over others. But whatever it is, I will need to enjoy whatever I'm studying, in order to be a true biologist and to reap the true joy of learning. :)

Tuesday, April 15, 2008

Advice to a Young Scientist by P. B. Medawar

Once again, stumbled across a book in the Plant Systematics Lab library.

Once again, captivated by the preface. The reading of the preface is a relatively new habit, which I didn't use to do. I used to read mainly for the content and knowledge acquirement. Nowadays, I find myself reading, because I enjoy it. And the preface contains the heart of the writer. Why did he do it? What inspired him? Who helped him and made it possible?

"I use the word opinion to make it clear that my judgments are not validated by systematic sociological research and are not hypotheses that have already stood up to repeated critical assaults. They are merely personal judgments, though I hope som eof them will be picked up by sociologists of science for proper investigation."

"A good tutor taught the whole of his subject and not just that part of it in which he himself happened to be especially interested or proficient; to 'teach' did not, of course, mean to 'impart factual information,' a relatively unimportant consideration, but rather to guide thought and reading and encourage reflection."

How Can I Equip Myself to Be a Scientist or a Better One?

"The beginner must read, but intently and choosily and not too much."

The Scientific Process

"A young scientist has now a meter or so of bench space, let us say, a white coat, authority to use the library, and a problem that he has thought up himself of a senior has asked him to look into. To begin with, anyway, it is almost certain to be a small problem - one of which the solution will facilitate solution of something more important, and so on, until the long-term objective of the enterprise is in sight. Nonscientists cannot immediately see the connection between the lesser problem and the greater. It must often occur to a humanist as he reads the minutes of the board of the faculty of science that young scientists are engaged in comically specialized activities. A scientist might equally well wonder what there could be to engage a grown man in the study of the parochial affairs of Tudor Cornwall, because he does not realize that such an investigation is about the Reformation, a very great affair indeed."

hypothesis = imaginative preconception

"Thus the day-to-day business of science consists not in hunting for facts but in testing hypotheses - that is, ascertaining if they or their logical implications are statements about real life, if inventions, to see whether or not they work."

experiments = acts undertaken to test a hypothesis

"In the outcome, science is a logically connected network of theories that represents our current opinion about what the natural world is like."

"As a point of logic that has some bearing on the way he thinks he goes about his business, a young scientist must always avoid saying or thinking that he 'deduces' or 'infers' hypotheses. On the contrary, a hypothesis is that from which we deduce or infer statements about mattersof fact, so that, as the great American philosopher C. S. Peirce clearly recognized, the process by which we try to think up the hypotheses from which our obesrvations will follow is an inverse form of deduction - a process for which he coined the terms retroduction and abduction, neither of which has caught on."

"Before he sets out to convince others of his observations or opinions, a scientist must first convince himself. Let this not be too easily achieved; it is better by far to have the reputation for being querulous and unwilling to be convinced than to give reason to be thought gullible. If a scientist asks a colleague's candid criticism of his work, give him the credit for meaning what he says. It is no kindness to a colleague - indeed, it might be the act of an enemy - to assure a scientist that his work is clear and convincing and that his opinions are really coherent when the experiments that profess to uphold them are slovenly in design and not well done. More generally, criticism is the most powerful weapon in any methodology of science; it is the scientist's only assurance that he need not persist in error. All experimentation is criticism. If an experiment does not hold out the possibility of causing one to revise one's views, it is hard to see why it should be done at all."

By P. B. Medawar from Advice to a Young Scientist (1979). London: Pan Books (From this book! Not plagarism!)

Wednesday, April 9, 2008

How to Write a Review Paper by R. A. Day

Characteristics of a Review Paper
"The purpose of a review paper is to review previously published literature and to put it into some kind of perspective."

"However, the really good review papers are much more than annotated bibliographies. They offer critical evaluation of the published literature and often provide important conclusions based on that literature."

Preparing an Outline
"The cardinal rule for writing a review paper is to prepare an outline."

"aim, scope, and relevance of the topic to be reviewed"

Importance of Introductory Paragraphs
Of both the paper and of each major sections. Crucial as reader decides whether to read it or skim it or ignore it altogether based on their first impression.

Importance of Conclusions
Because the review paper covers a wide subject for a wide audience...

Wednesday, April 2, 2008

How does phylogenetic analysis enable evolutionary history to be traced?

Snippets from Phylogenetic Interpretations of Primate Socioecology: with special reference to social and ecological diversity in Macaca by Leslie K. W. Chan

"In recent years, however, there has been substantial development in the application of phylogenetic methods to the analysis of behavioural, ecological and social patterns in diverse groups of organisms. One common approach, referred to as character mapping or character optimization method, consists of establishing genealogical relationships of the species being compared first, and then asking whether similar traits observed among species arose in a common ancestor and have persisted, or whether they arose independently due to convergent adaptation to similar environments. This approach emphasizes the importance of a species' evolutionary history in constraining both the features it curently displays and the subsequent directions and rates of evolution open to it.

A key assumption of this approach is that just as the evolution of morphological and life-history traits, behavioural and social evolution take place in the context of phylogeny. It follows that mapping or superimposing these biological or behavioural features on a well-established phylogentic hypothesis, we may estimate when, and how many times, an observed characteristic arose in the group being studied. We can also gain insights as to which features are highly conservative, and which are most liable. In other words, this approach allows us to compare similar traits across species and to distinguish those similarities that are most likely due to descent from a common ancestor from those that evolve independently."