Why You Should Become a Postdoc Instead of Taking a Job in the Private Sector

Eric Lewellyn is an enthusiastic postdoc in the Drubin/Barnes Lab at US Berkeley. (They work on membrane trafficking.)

Eric tries to convince you to stay in university using song and dance. He describes all the good things about slaving away enjoying science in a research lab. I don't know Eric but I have met his mother—she's the cousin of one of our best friends.

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What Does the Liberal Party of Canada Stand For?

I've long been a supporter of the Federal Liberal Party of Canada. It's the party of Mike Pearson and Pierre Elliot Trudeau—two Prime Ministers that I greatly admire. I even like Jean Chrétien!

Lately I'm having trouble understanding what the Liberal Party stands for. They've just had two leaders (Michael Ignatieff, and Bob Rae) who are complete mysteries to me. I really don't know what they stand for, or what they're passionate about.

Apparently I'm not alone. Here's the view of Thomas Walkom from a column in the Toronto Star a few days ago [Do Canada’s, or Ontario’s, Liberals matter any more?].

On the other hand, it’s not clear what the Liberals represent any more. They would like voters to think of them as the non-Conservatives — the alternative to Stephen Harper federally or to Tim Hudak in Ontario.

But are they?

Paul Adams, an astute political observer writing in iPolitics, argues that the federal Liberals have transformed themselves into the old Progressive Conservatives, socially progressive but fiscally to the right.

I’d go further. I reckon the old PCs of Joe Clark would find federal Liberal leadership candidate Martha Hall Findlay’s talk of dismantling farm marketing boards a bit too right-wing for their tastes

Similarly, Liberal front-runner Justin Trudeau’s enthusiastic embrace of the Alberta oilsands would probably be seen as a tad naive by the Red Tories of former Ontario premier Bill Davis, most of whom believed that strong business required equally strong regulation.

As a party, the Liberals haven’t had a new idea since the 1980s. Individual party members have (Stéphane Dion’s green shift comes to mind).

But the party, as a whole never signed onto Dion’s environmental agenda. Nor has it signed onto anything else.

The Liberals talk of holding policy conventions that would replicate that golden period of the 1960s, when the party embraced medicare, public pensions and welfare reform.

But they never do. Former federal leader Michael Ignatieff hosted a thinkers’ conference that headlined prominent conservatives. Nothing came of it.

The conventional wisdom among Liberals is that strong policy positions should be avoided at all costs in order to avoid alienating voters. Instead, Liberals prefer to talk about what they call values.

We've been discussing this issue with our former Liberal MP, Omar Alghabra, who happens to be a member of Justin Trudeau's team. Justin, for those of you who don't follow Canadian politics, it the son of Pierre Elliot Trudeau and he's running for the leadership of the Federal Liberal Party. We want Justin, and all the other candidates, to speak out on what the Liberal Party stands for.

Omar sent us a link to this video. It's obvious that Justin is avoiding the question. He stands for some trivial issues like legalizing marijuana but what about the bigger issues? How do I tell the difference between the Liberal Party and Conservative Party or the New Democratic Party? I don't think I can vote for Justin Trudeau or for any of the other leadership candidates. In fact, I'm not sure I can vote for the Liberal in the next election. The NDP is looking very attractive.

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What Is Science? - Still No Answer!

We had a fun meeting last night thanks to Rufina Kim [WTF Is Science?]. A bunch of students showed up along with Steve Livingston, the new co-Chair of CASS (Committee for the Advancement of Scientific Skepticism), and David Bailly, Chair of The Association for Science and Reason (Skeptics Canada).

Unfortunately we were not able to come to an agreement on "What Is Science."

Now we have to meet again in a couple of weeks!

We talked about whether there was a scientific method and whether falsifiability is part of the definition of science. The Wikipedia article on falsifiability is a good place to look for background information. Here are two sections from that article to get you started.

Paul Feyerabend examined the history of science with a more critical eye, and ultimately rejected any prescriptive methodology at all. He rejected Lakatos' argument for ad hoc hypothesis, arguing that science would not have progressed without making use of any and all available methods to support new theories. He rejected any reliance on a scientific method, along with any special authority for science that might derive from such a method. Rather, he claimed that if one is keen to have a universally valid methodological rule, epistemological anarchism or anything goes would be the only candidate. For Feyerabend, any special status that science might have derives from the social and physical value of the results of science rather than its method.

...

In their book Fashionable Nonsense (published in the UK as Intellectual Impostures) the physicists Alan Sokal and Jean Bricmont criticized falsifiability on the grounds that it does not accurately describe the way science really works. They argue that theories are used because of their successes, not because of the failures of other theories. Their discussion of Popper, falsifiability and the philosophy of science comes in a chapter entitled "Intermezzo," which contains an attempt to make clear their own views of what constitutes truth, in contrast with the extreme epistemological relativism of postmodernism.

Sokal and Bricmont write, "When a theory successfully withstands an attempt at falsification, a scientist will, quite naturally, consider the theory to be partially confirmed and will accord it a greater likelihood or a higher subjective probability. ... But Popper will have none of this: throughout his life he was a stubborn opponent of any idea of 'confirmation' of a theory, or even of its 'probability'. ... [but] the history of science teaches us that scientific theories come to be accepted above all because of their successes." (Sokal and Bricmont 1997, 62f)

They further argue that falsifiability cannot distinguish between astrology and astronomy, as both make technical predictions that are sometimes incorrect.

There's no such thing as a universal scientific method and falsifiability doesn't describe how the scientific way of knowing actually works.

I made up an example of a Professor of English whose research focuses on how the English language actually sounded in the time of Geoffrey Chaucer (about 1370)¹. Is she doing science? If not, what kind of way of knowing is she using?

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1. This is roughly the time of World Without End. If the characters actually spoke in 14th century dialect we probably wouldn't have understood a word.

Teaching Developmental Biology

PZ Myers posted some lecture notes from his developmental biology course [What I taught today: molecular genetics and basic concepts ]. Here's part of what he said ...

Think about that. In the early days of developmental biology, we didn’t even know whether there was differential gene activity or not; it was considered a reasonable possibility that all the genes were just doing their work, whatever it was, all the time in every cell, and that differences between cells emerged farther downstream, in biochemical interactions. But they knew this was an important question. They knew that we had to look at the activity of individual genes…they just didn’t have the tools yet. So it was back to hacking up embryos and trying to infer causes from aberrations.

The change emerged gradually, but there were a couple of watershed moments where everyone looked up and noticed that hey, we do have ways of looking at genes directly. One was the work of Ed Lewis, a most excellent geneticist who used the tools of genetics to look directly at mutations that caused changes in fly morphology, in the 1960s. This was amazing stuff — the papers he wrote were beautiful and complex and very, very genetical — but it was written in a language that most developmental biologists of the day were unprepared to read. They were genetics papers. But I think they laid a foundation: if you want to do development, you’d better learn about genetics.

The second big event was the saturation mutagenesis screen of Christiane Nusslein-Volhard and Eric Wieschaus, about 20 years later. This work was also built on an understanding of genetics, but also used the tools of molecular biology. It was another lesson: if you want to do development, you’d better learn about molecular biology.

I used to teach this stuff in the 1980s and I certainly agree with PZ that you need to understand molecular biology and gene expression.

When it came time to write my first textbook I incorporated the examples I had used in class. The first ones I described were: the early to late switch in gene expression in bacteriophage T4, sporulation in Bacillus subtilis, and the genetic switch in bacteriophage lambda. These were well-studied examples from experiments carried out in the 1970s. They teach fundamental concepts in developmental biology and they have an additional advantage; namely, they get students thinking about species that aren't animals.

These are still excellent examples that are well-understood at the molecular level. They are much easier to understand than Drosophila or plants. Unfortunately, we've educated an entire generation of developmental biologists who have never heard of these elegant examples.

Is this a good thing or a bad thing? Do students need to know the real history of developmental gene expression as worked out by scientists who studied phage and bacteria?

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What's Wrong with These Sentences?

Here's a short paragraph containing three sentences from my textbook (page 584). Is there anything wrong with any of these sentences?

Under physiological conditions, double-stranded DNA is thermodynamically much more stable than the separated strands and that explains why the double-stranded form predominates in vivo. However, the structure of localized regions of the double helix can sometimes be disrupted by unwinding. Such disruption occurs during DNA replication, repair, recombination, and transcription.

Having trouble seeing where I went wrong, according to some people? Check out this and this.

Oh, and don't forget this.

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Onion Talks: Social Media

Everyone knows about TED talks (Ideas Worth Spreading). They know that TED talks are "riveting talks by remarkable people." Or at least that's what they would like to believe [TED Tries to Clean Up Its Act].

Here's some worthy competition to TED talks from The Onion. It's title is Using Social Media To Cover For Lack Of Original Thought.

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[Hat Tip: Mike the Mad Biologist]

The Revisionaries Is Coming to Television

The Revisionaries is a documentary about the Texas state board of education and their attempt to suppress science in Texas public schools.

It will be aired on PBS starting January 28th. It's due to be broadcast in my area (WNED) on Feb. 3, 2013 at 11pm and on Feb. 8, 2013 at 4am.

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[Hat Tip: Mike the Mad Biologist]

Monday's Molecule #198

The last "Monday's Molecule" was 2R,3S-isocitre [Monday's Molecule #197]. The winner was Evey Salara. She's probably too far away to come for lunch.

This week's molecule is very strange looking but it serves a very important role in some species. What is the molecule, what species have it, and what does it do?

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Vote for Your Favorite Theory of Evolution!

I'm conducting a poll on topics that some people would like to add to modern evolutionary theory in order to create an "extended" modern synthesis [Which subjects need to be added to current evolutionary theory to create a new extended synthesis?].

So far there are almost 200 votes and "EvoDevo" is leading the pack (Boo!). I'm delighted to see that "Nonadaptive Evolution of Complexity" is getting a substantial number of votes. It suggests that there are people who really do understand Michael Lynch and Eugene Koonin (among others).

"Epigenetics" is way too popular. It is NOT an addition to evolutionary theory, in my humble opinion.

Nobody has voted for "Theistic Evolution."

VOTE NOW!

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WTF Is Science?

Join us for a discussion about science and its relevance in the real world. This group will meet regularly every few weeks and it's open to everyone.

The topic for the first meeting is "What Is Science?" Check out the facebook page at: WTF Is Science?.

Wednesday, January 23, 2013 at 6pm.
Room 5243, Medical Sciences Building (5th floor)

You are welcome to bring food and (non-alcoholic) drinks.

Here are some definitions of science from the Oxford English dictionary.

1. The state or fact of knowing; knowledge or cognizance of something specified or implied; also, with wider reference, knowledge (more or less extensive) as a personal attribute.
2. Knowledge acquired by study; acquaintance with or mastery of any department of learning. Also +pl. (a person's) various kinds of knowledge.
3. A particular branch of knowledge or study; a recognized department of learning.
4. In a more restricted sense: A branch of study which is concerned either with a connected body of demonstrated truths or with observed facts systematically classified and more or less colligated by being brought under general laws, and which includes trustworthy methods for the discovery of new truth within its own domain.
5. The kind of knowledge or of intellectual activity of which the various `sciences' are examples. In early use, with reference to sense 3: What is taught in the schools or may be learned by study. In mod. use chiefly: The sciences (in sense 4) as distinguished from other departments of learning; scientific doctrine or investigation. Often with defining adj. as in 4 b.

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Herd Immunity

Have you ever heard anyone say that they don't need to get a vaccination because they never get the disease and, even if they do, it's never very serious?

That's fine if the only person you care about is you. Maybe you live in a cave. Maybe you never visit old people in a retirement home. Maybe you are never near babies. Maybe you don't have a spouse or a partner. (I can't imagine why such a self-centered person would not have a partner.)

Or maybe you just don't understand the concept of herd immunity. Ignorance can be cured ....

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[Hat Tip: Mike's Weekly Skeptic Rant]

That's Extraordinary! Homeopathy

Here's a new video from Centre for Inquiry, Canada. Homeopathy is ridiculous, pseudoscientific, nonsense. It's about time that all intelligent people recognized this fact. Tell your friends.

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The NRA Anti-Obama Ad

If you live outside of the USA you may not have seen this television ad paid for by the National Rifle Association.

It's tantamount to a declaration of war on the issue of gun control. What this means is that there is no compromise or middle ground with these people. I hope Obama accepts the challenge and takes on the gun lobby. Last I heard, they were not a democratically elected part of the legislature.


BTW, if members of the NRA are really interested in protecting their children from the risk of being killed by guns then they should send them to school in the UK. Even Canada would be better.

Here's another version of the ad.

NRA - Stand and Fight Parody - watch more funny videos

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[Hat Tip: Pharyngula]

Which subjects need to be added to current evolutionary theory to create a new extended synthesis?

Here's a list of subjects that have been proposed as extensions to the so-called "Modern Synthesis" of evolution. Some of them are radical changes and others are more subtle.

I'm not going to explain all of them because that would take many posts and a lot of time. Besides, most of them have been openly debated on numerous blogs over the past decade or so.

Choose the one(s) that you think are the most important.

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50th Anniversary of Ramachandran Plots

This year marks the 50th anniversary of the publication of Ramachandran plots (Ramachandran 1963).

Don't know what I'm talking about? Read Ramachandran Plots.



THEME:

More posts on
Protein StructureChirag Vora was kind enough to alert me to this anniversary. Check out his blog at: Golden Jubilee of Ramachandran Plot.

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Ramachandran, G. N., Ramakrishnan, C. T., and Sasisekharan, V. (1963) Stereochemistry of polypeptide chain configurations. Journal of molecular biology, 7:95-99.