Archive
How to be a good graduate student
Rather then trying to reinvent the wheel, let’s have a look at what is out there on the web. Are there good assays about graduate school and graduate students?
Well, this appears to be the case. So, there is no need to reinvent the wheel. Here are 7 assays of how to be a good graduate student:
How to be a good graduate student – Marie desJardins – [PDF version]
How to be a good graduate student (PDF) – Deirdre N. McCloskey
How to do research at the MIT AI lab – Davis Chapman
Advise for graduate students (synopsis) – Frank Vahid – [book]
Unsolicited advice IV: How to be a good graduate student – Sean Caroll
Hitchhikers guide to surviving graduate school (computer science) – Ron Azuma
How to be a good graduate student (PDF of PPT with presentation below) – Biswanath Mukherjee
Evolution in Pictures
Darryl Cunningham is an artist who explains science through comics. His most recent works is on evolution and is a great throwback to the intro to evolution class we took as undergrads. Here’s the first panel:
Check out the entire comic in the works here. Thanks Katarzyna Koscielska for the find!
“GFP” for electron microscopy
Author Summary
Electron microscopy (EM) once revolutionized cell biology by revealing subcellular anatomy at resolutions of tens of nanometers, well below the diffraction limit of light microscopy. Over the past two decades, light microscopy has been revitalized by the development of spontaneously fluorescent proteins, which allow nearly any protein of interest to be specifically tagged by genetic fusion. EM has lacked comparable genetic tags that are generally applicable. Here, we introduce “miniSOG”, a small (106-residue) fluorescent flavoprotein that efficiently generates singlet oxygen when illuminated by blue light. In fixed tissue, photogenerated singlet oxygen locally polymerizes diaminobenzidine into a precipitate that is stainable with osmium and therefore can be readily imaged at high resolution by EM. Thus miniSOG is a versatile label for correlated light and electron microscopy of genetically tagged proteins in cells, tissues, and organisms including intact nematodes and mice. As a demonstration of miniSOG’s capabilities, controversies about the localization of synaptic cell adhesion molecules are resolved by EM of miniSOG fusions in neuronal culture and intact mouse brain.
Link to original article in PLoS Biology
Discussion of this article in BioTechniques
Great interview with Richard Lewontin
Richard Lewontin is a well known evolutionary biologist. A while ago he was interviewed for the Conversation with History series at UC Berkeley on Nov. 20th, 2003. Especially the first 10 minutes of this hour long interview, Lewontin touches upon the importance of talking to your peers in science.
Note: not just the first 10 minute are great to watch, the entire interview is more then worth watching. Grab a glass of your favorite drink and enjoy!
“I am right!” – about the origin of human reasoning
A translation by Daniël Melters of an article from a Dutch popular science website, called Noorderlicht.
by Bouwe van Straten
Why are people sometimes excellent in reasoning, but at other time they are horrible at it? Because you are searching for confirmation of your point-of-view, your conviction. Reasoning is not a method to find the truth; it evolved to convince others, according to a new theory.
The philanthropist George Soros became of the most successful investors of all times in the 70s and 80s. What was his secret? He assumed that his ideas about reality – and thus about the financial markets – were probably wrong. This didn’t discourage him. On the contrary, he kept on searching for indications, arguments and reasonings that could disproof his theories, and improve them where needed.
Whether Soros’ financial success was because of his use of the ‘radical fallibility‘ principle remains speculative (just like the rest of the stock market, ed.). But his approach does show what you can achieve with reasoning: it can lead to new and better knowledge to facilitate the decision making process.
Rather obvious, maybe. Maybe a little too obvious. So obvious that most scientist assume it is a fact and they do not bother themselves with checking if it is true. Especially, because there are reasons to doubt this assumption. Because if reasoning was truly evolved as a means to gather knowledge to make better decisions, why don’t more people take the route Soros took? That most people didn’t take his route, has become apparent in many studies. Most people suffer from what is known as confirmation bias: they seek for facts and reasons that fit their ideas and thoughts.
For argument’s sake
Not that useful, you would think. Before you know it, you have wrong and outdated thoughts and ideas. But this confirmation bias isn’t so bad, show the cognition scientists Dan Sperber and Hugo Mercier in Behavioral and Brain Sciences. According to them, reasoning wasn’t invented to find the truth. From a evolutionary point of view, the primary reason reasoning evolved was to convince someone else that you are right. You don’t want to find the truth, you want to win an argument in your favor. And it is rather useful to confirm your point-of-view with cherry-picking of facts.
With the Argumentative Theory of Reasoning – as Sperber and Mercier named this new theory – the two scientist try to explain how the human capacity to reason arose They do this with a cognitive experiment. Imagine that two of our great great grandparents try to work together, before they could reason. Once they would start disagreeing, a deadlock would arise, because they couldn’t reason with each other and thus convince one another that they are right because of a, b, and c.
Reasoning is critical in collaborations. And it is known that people collaborated millennia ago. Not only for gather food and hunting, but also to raise children. But an inevitable side-effect of communication is: how do you know that your partner doesn’t try to fool you? If you would believe anything that is said to you, you could be easily manipulated.
An easy response would be to not believe what is being told to you. Otherwise you would be vulnerable. But it is not smart to be extremely suspicious of other, because there is a possibility the other is right. And here comes the capacity to reason into play. On the one hand, you could convince other by reasoning and using argument. On the other hand, you can also check or evaluate the other who tries to convince you.
Using reasoning for arguing, not for gather knowledge. A nice theory, but does it hold up? With many theories about the origin of human (psychological, ed.) characteristics this is hard to verify; you can think of an evolutionary origin for just about anything. Such theories are hard to test, because we do not know how things were in the past.Just-so stories, as they are called.
Not just-so
But this theory does make some predictions, and these are testable. If reasoning is arguing, then you would predict that people who are alone would reason poorly. And this is precisely what is observed. Various studies, which Mercier and Sperber evaluated, show that people who are alone are highly susceptible to confirmation bias. Put them in a possition where they can exchange ideas with others, and their views change accordingly. Despite that everyone initially kept to their ideas, they became unsustainable when they have to be defended in a group. After a while the group reaches the right conclusion that they were initially set out to find.
The theory also explains the existence of the confirmation bias. So there is empirical evidence in favor of the Argumentative Theory of Reasoning. This is probably also the reason why this paper has been well-received by fellow scientist. ‘Original and provocative‘ (Steven Pinker), ‘the solution to one of the most important questions in psychology’ (Jonathan Haidt), are just a few of the many positive reviews.
The researchers are already seeing various ways to apply their new theory, for instance in education – now you can teach kids better in groups about difficult and abstract problems – and in politics – people should share their ideas about society to come to new insight.
But what happens when you apply the Argumentative Theory of Reasoning to science itself? Scientists are ultimately searching for the truth. Or are they only working on confirming their own ideas and perceptions? If they would be working alone, would that be jeopardizing the enterprise of science? Not all scientists have the same approach as George Soros, but it is a good thing that science is a team sport. This way scientists can filter out each others confirmation bias to reach a solution for the questions they trying to answer.
Hugo Mercier en Dan Sperber, ‘Why do humans reason? Arguments for an argumentative theory’, in Behavioral and Brain Sciences, april 2011.
Special Guest Seminar by Dr. Richard Kuhn
Special Guest Seminar
“Replication and Assembly of Dengue Virus”
Dr. Richard J. Kuhn
Director, Bindley Biosciences Center
Purdue University
Tuesday June 28, 2011
12:10 – 1:00 PM
CNPRC Seminar Hall
bmcdb
