Monday, September 15, 2014

Looking for Frankenfood

The students in my third year lab course are about to test various food products to see if they contain any DNA from genetically modified organisms. They'll be using a variety of PCR primers to detect the Cauliflower mosaic virus 35S promoter and the nopaline synthase terminator sequence from the Ti plasmid of Agrobacterium tumefaciens [see Roundup Ready® Transgenic Plants ].

Every student has to bring in their own food sample to test but I'll be providing a number of "controls" that I picked up in the cafeteria and at the grocery store. Which ones are Frankenfood?


We're using some additional sets of primers as controls. One set detects a chloroplast gene (rbcL). We have two sets of primers for corn-specific genes (invertase and zein) and one set for a soybean specific gene (lectin). An important part of the exercise is figuring out what controls to use and what DNA samples to analyze. Each group of two students can do 24 PCR reactions. It's going to be a challenge for them to figure out which reactions are the most important.

(They were told that corn and soy products are most likely to test positive in the GMO assay.)


Friday, September 12, 2014

The logic of lawyers

Barry Arrington is a lawyer from Colorado [Encyclopedia of American Loons]. Here's an example of the logic of lawyers posted on Uncommon Descent [Not Merely False].
The following statements are so obvious as to be considered truisms.

1. The primordial datum: I am subjectively self-aware.

2. It is not possible even in principle to account for mental facts, such as the primordial datum, on the basis of physical facts. They are different sorts of things; therefore one cannot account for the other. Trying to account for subjective self-awareness by suggesting it is an epiphenomenon of the electro-chemical process of the brain is like saying the color blue can be reduced to its constituent banana peels.

3. It follows that a reductionist materialism is not merely false but obviously false.

4. Just as obviously, it does not follow that committed materialists will admit that reductionist materialism is false, for they have reasons to put their faith in their metaphysical commitments that have nothing to do with the evidence and logic of the matter.
I would not want him to defend me if I were innocent. On the other hand, he might be a good choice if I were guilty because I could easily fool him into thinking that I was innocent.


Thursday, September 11, 2014

The mystery of Maud Menten

Maud Menten is best known for the Michaelis-Menten equation and her work on enzyme kinetics. She was born in Port Lambton, Ontario and she is a graduate of the University of Toronto.

The "mystery" concerns her degrees and the year she graduated. The video below was prepared when she was inducted into the Canadian Medical Hall of Fame in 1998 [Maud Menten]. If you watch the first few minutes you'll hear that in 1911 Maud Menten was one of the first Canadian women to receive a medical degree. You find similar statements all over the web, although sometimes it says she graduated in 1913—as in the text on the Canadian Hall of Fame website.

Wednesday, September 10, 2014

The perils of genetic testing

Most people don't understand the consequences of genetic testing. You may think that you can handle all of the data and information but think again.

This is the story of someone who got their DNA tested by a commercial company and he persuaded his parents to participate as well. What could possibly go wrong? The title of the article tells the story: With genetic testing, I gave my parents the gift of divorce.

Turns out he has a half-brother! His father never mentioned that he had a son with another woman.
At first, I was thinking this is the coolest genetics story, my own personal genetics story. I wasn't particularly upset about it initially, until the rest of the family found out. Their reaction was different. Years of repressed memories and emotions uncorked and resulted in tumultuous times that have torn my nuclear family apart. My parents divorced. No one is talking to my dad. We're not anywhere close to being healed yet and I don't know how long it will take to put the pieces back together.
It's not always true that having information is better than not having information. If you beleive that then you are very naive.


The Non-Conference Is Coming


Website Countdown Clock


Do IDiots understand evolutionary theory?

Do Intelligent Design Creationists (IDiots) understand evolution? ... of course not.

It's been really frustrating over the past 25 years trying to explain modern evolutionary theory to IDiots. They continue to refer to "Darwinism" and "neo-Darwinism" but it's obvious that they don't have a clue what they mean by those terms. This become especially obvious when they discover, once again, that real evolutionary biologists don't accept the IDiots' version of evolutionary theory.

Check out the latest post by Casey Luskin on Evolution News & Views. It would be so easy for him to explain to his readers what the textbooks say on evolutionary theory and how it differs from what the IDiots are promoting in their own books and on their websites [Are Biologists Rejecting Neo-Darwinian Evolution?]. He doesn't do this, of course, and that's only partly because it suits his purpose to be dissembling. It's mostly because he really doesn't understand what he's talking about. We know this because dozens of people have tried to explain it to him over the years and he still doesn't get it.

In fairness, Casey Luskin is responding to an article on The BioLogos Forum by philosopher Robert C. Bishop [Two Rhetorical Strategies (Reviewing “Darwin’s Doubt”: Robert Bishop, Part 2)]. It's pretty clear that Bishop doesn't understand modern evolutionary theory either. Unfortunately, there are many scientists who share these misconceptions but that's not an excuse for Luskin and his fellow travelers since they are supposed to understand what they spend so much time attacking.


The atheist barmaid's error

I'm usually a big fan of Jesus and Mo but today's cartoon is a bit disappointing. It is "resurrected" from 2009 [nerve2] and it is prompted by an excellent article on militant atheists written by Nick Cohen [The phantom menace of militant atheism]. Even Jerry Coyne likes it [A wonderful attack on the "militant fundamentalist atheism" trope].


The issue here is whether an atheist needs to study all religions in order to be an atheist. The barmaid seems to concede that point since she advances arguments that require knowledge of specific religions. Both of her examples require the provisional acceptance of gods because they refer to particular properties of those gods (i.e. whether they can have sons and prophets).

A Christian, for example, would happily engage the barmaid in a debate about the the divinity of Jesus as long as they begin with the assumption that gods exist. In order to engage seriously in that debate, the barmaid would have to read a ton of Christian apologetic literature. In other words, she would have to understand "sophisticated" religion. She would not be defending atheism even if she won the debate since there are billions of religious people who don't believe in the divinity of Jesus.

But atheists, by definition, don't believe in gods. The only arguments that are relevant are whether gods exist. Those arguments are not specific to any particular religion and they certainly aren't going to be found in the Bible or the Qur'an. I do not accept the premise that gods exist so I'm not the least bit interested in studying the religious beliefs of anyone who begins with the "fact" that gods exist. I'm about as interested in debating whether any of the gods had children as I am in debating how many angels can dance on the head of a pin.1

The atheist barmaid made a mistake. She should have said "Let's see - I understand that all religions begin with the idea that gods exist. What evidence do you have that this is true?"


Or, for that matter, the problem of evil. If there are no gods then there's no problem. Debating the "problem" of evil or whether Jesus is the son of gods is just like debating the cut of the Emperor's new clothes [On the Existence of God and the Courtier's Reply].

Wednesday, September 03, 2014

Club Day at the University of Toronto

Today's the day that clubs strut their stuff and try to get new students to sign up. It's an important part of campus life and an important part of a university education even though the majority of students don't participate.

There's a club for just about everyone, even biochemists!

All of that will disappear when universities shut down and undergraduate education is confined to MOOCs and glorified Skype conferences. You can't join a rowing club if you're a thousand kilometers from the clubhouse.

I suppose there are lot of business types out there who don't care about this sort of thing as long as you pay your money, get a degree, and go on to a decent job where you can pay back your student loan.



Harrison Ford vs Ian McKellen

It's hilarious even when you know it's photoshopped.


Are universities doomed?

This month's issue of The Atlantic has another one of those boring articles on the imminent death of universities (colleges) [The Future of College?].

This time it's a new "university" called MINERVA that's going to kill off all the old-school schools. Minerva is a for-profit university where all the learning takes place in electronic seminars of up to 19 students. Sort of like a Skype conference call only it uses copyrighted software. Students will pay only $28,000 (US) per year for this experience.

There have been articles about the death of universities published every year for as long as I can remember. Almost all of them think that a "university" is just a place where you go to get an undergraduate education. That's because almost all of the potential murderers only experienced university as an undergraduate.

Tuesday, September 02, 2014

What are they playing?

Apparently the Queen's Guards surprised everyone by playing a new song during the changing of the guard at Buckingham Palace on July 15, 2014.

Name that song!



Do you know it?

Here's a hint ... the actual theme is better but it's the thought that counts.




The top ten cities in the world

The Economist has surveyed cities from all over the world to find the ones that are the most livable (i.e. best places to live). Here's a summary of the criteria described in the report [A Summary of the Liveability Ranking and Overview]
The concept of liveability is simple: it assesses which locations around the world provide the best or the worst living conditions. Assessing liveability has a broad range of uses, from benchmarking perceptions of development levels to assigning hardship allowance as part of expatriate relocation packages. The Economist Intelligence Unit’s liveability rating quantifies the challenges that might be presented to an individual’s lifestyle in any given location, and allows for direct comparison between locations.
Bjørn Østman alerted me to the list by posting a link to this article: The World's Most Livable Cities All Have One Big Thing in Common. What do the top ten cities all have in common?—none of them are in the USA.

Here's the list ....

1. Melbourne, Australia
2. Vienna, Austria
3. Vancouver, Canada
4. Toronto, Canada
5 (tie). Adelaide, Australia
5 (tie). Calgary, Canada
7. Sydney, Australia
8. Helsinki, Finland
9. Perth, Australia
10. Auckland, New Zealand

There's obviously more to "livability" than meets the eye. Some of these places are a lot less interesting than Paris, London, or New York.

I think the ranking also depends very much on how much money you have. I'd need to be offered a hell of a lot more money if I were to consider a move to Calgary, Helsinki, or Perth.1


1. I've never been to Perth but it doesn't seem like a place I'd like to live.

IDiots exploring evolution

Modern evolutionary theory is far more advanced than the simple version that's attacked by Intelligent Design Creationists. Neutral Theory, population genetics, and the importance of random genetic drift are just a few of the additions that were incorporated in the 1960s. (That's almost 50 years ago.)

Most IDiots are half-a-century behind in their knowledge of science. They think that random mutations and natural selection are the only way that evolution can occur.1 That's why they refer to evolution as "Darwinism."

Many of them have heard vague rumors of change, proving that from time to time they do, indeed, take their fingers out of their ears. They've discovered that modern scientists have moved well beyond natural selection as an explanation for every bit of evolution. This makes the IDiots very happy since, to them, it means that evolution is wrong. And if evolution is wrong then gods must exist.

They've even developed a course to explain why Neutral Theory and random genetic drift support the idea that gods must be making bacterial flagella and protein-protein contacts. It looks like a very interesting course ...




1. A few of them might know differently but they will never admit it in public.

Friday, August 29, 2014

What are students interested in and does it matter?

PZ Myers [Oh, dear] picked up on a tweet from Jeffrey Ros-Ibarra [Tell me botany doesn’t have a recruitment problem]. He posted the result of a survey of 800 first year students.


This shouldn't come as a big surprise to any Sandwalk readers. The question is, what should we do about it?

Most university professors share this bias so they are very comfortable with teaching biochemistry from a strictly animal (mostly human) perspective. When challenged, they point out that students are mostly interested in animals and themselves. They think we should design our courses to accommodate these interests because that's what students want to hear. I call these professors the "caterers."

A minority (that includes me) look upon this data as a challenge. Our goal is to convince students that they should broaden their interests and learn about other species. People like me will emphasize broad principles and concepts that apply to ALL living organisms. We teach comparative biochemistry and talk a lot about evolution. These guys are the "challengers." (They're also the ones with the low student evaluations.)

The easiest way to tell the difference between the two types of professor in introductory biochemistry courses is to see whether they teach photosynthesis or the glyoxylate shunt, and whether they spend as much time on gluconeogenesis (the most ancient pathway) as they do on glycolysis (the derived pathway). It's also informative to observe whether they cover the biosynthesis of amino acids or whether they treat amino acids as food.

It's a really bad sign if they spend any time at all on the difference between "essential" and "nonessential" amino acids.


Thursday, August 28, 2014

The function of IDiots

There aren't very many big questions left to answer. Most ot the great debates have been settled and we're now in a mopping up situation.

One of the few remaining questions concerns the function of IDiots. The Intelligent Design Creationist Movement has been a spectacular failure. The Wedge Document is a joke. They've failed to get creationism into American schools. People are abandoning Christianity. Their books have all been trashed by critics.

One wonders why they're still around. They must be thinking the same thing because David Klinghoffer has put up a recent post on this very issue [You're Welcome: Darwinists Should Thank Us for Quality Control, Fact-Checking]. It turns out that the function of IDiots is to keep real scientists honest by finding flaws in their reasoning and errors of fact.
Casey [Luskin] points out that in any marketplace—whether vendors are promoting consumer products or ideas about evolution—competition improves the products and the service. The absence of competition almost always results in shoddy products and poor consumer service, as anyone who has visited a socialist country can tell you. Darwin advocates should be thanking us.

Of course the flipside to all this is that for every orthodox evolutionist who is made more judicious and truthful in what he argues, there's probably another who prevaricates about the meaning of scientific data, because "What will the creationists say?"

Still, on the whole, they and everyone else who cares about getting at the truth in science ought to be glad we're here.
Who knew?