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Tuesday, January 15, 2008

Best Canadian Sci/Tech Blog 2007

 
Nominations have closed and the voting has begun for the best Sci/Tech blog in Canada. Here's the ballot.

The nominees are ....
The only blogs that I've read before today are Eastern Blot and The World's Fair. Should I be reading the others? Please let me know if you think any of these are science blogs worth reading. Several of the Canadian science blogs that I read every day are not on the list.

Is there an easy way of finding out how popular those blogs are? There must be some tool out there that will tell me the average number of visits per day/week/month for each of the nominees.


Monday, January 14, 2008

What Is this Dog Thinking?

 
If you think you know what's going on in the mind of this dog, get over to Friendly Atheist and enter the contest [Friendly Atheist Contest #14: Dog Prays to God].

Remember the rules. According to Hemant Mehta, "Funny and creative answers will have a shot at winning."

You can enter as often as you like.

Here's what the boy is thinking, "This is so embarrassing. I'm soon gonna have to break it to him that I'm an atheist."


Insurance Against Alien Abductions

 
According to some studies, up to four million Americans may have been abducted by aliens [Abduction by Aliens or Sleep Paralysis?]. I often use this information when questioning religious people about the rationality of their inner convictions. As it turns out, most theists reject the silly beliefs of alien abductees without seeing any connection between this and their own proof of God by religious experience.

A group of people have banded together to exploit help those who fear being abducted by aliens. They have prepared special dog tags [www.earthbounddog.com].
Picture yourself lost in the galaxy...UFO sightings and Alien Abductions are on the rise...Will you return to tell the story?

In case of alien abduction these dog tags may save your life. The crucial data an alien will need to get you back to Earth is die stamped into these dog tags.

The design is based on NASA research for the Pioneer 10 Space Mission that used a gold plaque attached to the craft to inform any Extraterrestrials of it's Earthly origin.
You can buy them for only $12.99 (US). I suggest you buy several sets of dog tags for all your close friends. Do not buy them for other people.


[Hat Tip: Bad Astronomy]

Convocation 2007

 
A few months ago I told you about my first convocation as a Professor [Bruce Alberts in Toronto]. Here's the formal photograph of the main participants. Don't we look pretty?




Monday's Molecule #58

 
This is one example of a very common molecule found in every cell. You have to give us the common name of this molecule and identify the species. You'll be pleased to know that I don't need the systematic IUPAC name for this one.

There's a direct connection between this molecule and Wednesday's Nobel Laureate. Your task is to figure out the significance of today's molecule and identify the Nobel Laureate who studied its function. (Hint: The Nobel Laureate is a Canadian—there aren't very many Canadian Nobel Laureates so this is a very big hint.)

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate. Previous winners are ineligible for one month from the time they first collected the prize. There is one ineligible candidates for this week's reward because Sandwalk readers were not very successful in December. The prize is a free lunch at the Faculty Club.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk(at)bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and the Nobel Laureate. Note that I'm not going to repeat Nobel Laureates so you might want to check the list of previous Sandwalk postings.

Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: We have a winner! This one proved to be far more difficult than I imagined. Everyone got the Nobel Laureate (Sidney Altman) but very few people got the molecule correct. Some people failed to identify the species correctly even though I specifically asked for the species. Most people said that the molecule is RNase P but that isn't quite correct.

The molecule is the M1 RNA subunit of RNase P from E. coli. The other subunit is a small protein called the C5 protein cofactor. This RNA is sometimes called RNA P and that would have been an acceptable answer.

Only one person got everything right and that response just arrived a few minutes ago. Congratulations to PonderingFool for knowing that the molecule was the M1 RNA component of E, coli RNase P and the Nobel Laureate is Sidney Altman.



Creation Science Papers

 
Phil Plait of Bad Astronomy must have had a great deal of free time on his hands now that the asteroids have missed us and the galaxy isn't going to be consumed by a hydrogen cloud for at least 40 million years. He was thinking of writing a paper for a new journal sponsored by Answers in Genesis [Creationists: publish and perish].

Phil was interested in the first two papers that were published in the Answers Research Journal. One was a geology paper and one was about microbiology. Phil wanted to know how good they were.

Being as relieved as him about the fact that the Earth survived the near miss, I decided I could spare a few minutes to read the microbiology article. It's by Alan L. Gillen from that famous center of research called Liberty University. Here's the abstract.
The world of germs and microbes has received much attention in recent years. But where do microbes fit into the creation account? Were they created along with the rest of the plants and animals in the first week of creation, or were they created later, after the Fall. These are some questions that creation microbiologists have been asking in recent years. Ongoing research, based on the creation paradigm, appears to provide some answers to these puzzling questions. The answers to these questions are not explicit in Scripture, so the answers cannot be dogmatic. However, a reasonable extrapolation from biological data and Scripture can be made about the nature of microbes in a fully mature creation. This article attempts to provide reasonable answers to when microbes were created and is meant to stimulate discussion and further research in this area.

Very little has been written in Bible commentaries or in creation literature on the subject of when microbes were created. Some have postulated that microbes were created on a single day of Creation, such as Day Three—when the plants were made. This is partially due to the “seed-like” characteristics that bacteria and fungi have—therefore classifying microbes as plants. In addition, we observe microbes (such as Escherichia coli) isolated in the lab and we tend to think of microbes as individual entities much like birds or fish or animals and, therefore, created on a single day. However, in nature, the vast majority of microbes live in biological partnerships, not in total isolation. The natural symbiosis of microbes with other creatures is the norm. Therefore, we postulate that microbes were created as “biological systems” with plants, animals, and humans on multiple days, as supporting systems in mature plants, animals, and humans. This idea is further supported by the work of Francis (2003). Francis calls microbial symbiotic systems a biomatrix, or organosubstrate. He proposes that microbes were created as a link between macroorganisms and a chemically rich but inert physical environment, providing a surface (i.e., substrate) upon which multicellular creatures can thrive and persist in intricately designed ecosystems. From the beginning, God made His creation fully mature, and complex forms fully formed. This would insure continuity and stability for the times to come. Although we cannot be certain as to specifically when the Creator made microbes, it is within His character to make entire interwoven, “packaged” systems to sustain and maintain life.
I didn't read any further.

Phil, the bad news is that this is a pile of crap. The good news is that you won't have to waste very much time writing a paper for this journal. You can probably knock it off in an afternoon.


[Image Credit: The Complete Idiot’s Guide to Just Doing It]

Scientific Illiteracy About Death Rates

 
Here's part of an article on ScienceDaily about death rates in New York City [New York City Death Rate Reaches Historic Low].
The death rate in New York City reached an all-time low in 2006, the Health Department reported today, as the number of deaths fell to 55,391 -- down from 57,068 in 2005 and 60,218 in 2001. Mortality declined in eight leading categories, including diabetes, HIV, chronic lung disease and kidney failure. The only leading killer that increased significantly was substance use (up 8%). Heart disease and cancer remained the city's biggest killers, claiming 21,844 lives and 13,116 lives, respectively. The figures come from the latest Annual Summary of Vital Statistics, the definitive registry of births and deaths in New York City.
The numbers of deaths are not death rates. This is one of my pet peeves. I get angry when newspaper reporters screw it up but this is much worse. It's from a website that's supposed to specialize in science ("Your Source for the Latest Research News").

The raw numbers are available at Summary of Vital Statistics 2006: The City of New York. They show that the death rate did, indeed, fall from 7.0 per 1000 citizens in 2004 to 6.7 per 1000 citizens in 2006. In 1916 it was 14.0 while in 1980, 1990, and 2000 it was 10.0, 10.1, and 7.6 respectively.

The absolute numbers of deaths tells you nothing about death rates. For all we know, the population of New York City could have fallen from 2004 to 2006 and the death rate could have gone up. (Incidentally, if you look at the raw data you'll see an interesting footnote. The rates in 2004-2006 were revised downwards when the 2007 census data for population was used. Previous estimates were based on the population according to the 2000 census.)


[Image Credit: New York City in 1916 from The University of Texas at Austin]

Sunday, January 13, 2008

Scientific Mistakes

 
During a recent discussion with undergraduates, they mentioned that it would be a good idea to discuss the more recent scientific papers in class. They seemed to be very impressed with a course that presented papers published within the past few months.

I pointed out that there's a problem with that kind of course. If the goal of a course is to teach fundamental principles and concepts then it's very unlikely that recent papers are going to advance that goal. Why is that? Because much of the scientific literature is either trivial or incorrect. You don't know that it's trivial or incorrect until some time has passed and other scientists react.1

If the goal of a course is to teach how science is done on a day-to-day basis, then a key part of that course should be to drive home the concept of skepticism. Don't believe everything you read in the latest journals. An important part of that teaching goal is to pick examples of important mistakes in older literature.

John Dennehy has helped us out this week by posting a "citation classic" that turned out to be wrong [This Week's Citation Classic: Being Wrong]. In my opinion, it's far more important to look at examples like this than to expose undergraduates to several dozen hot new papers that are supposedly at the cutting edge.

The paper that John choose is by Paul Boyer who subsequently won the Nobel Prize in Chemistry [Nobel Laureates: Paul Boyer and John Walker] for his work on the mechanism of ATP synthase [How Cells Make ATP: ATP Synthase].


1. Sometimes it takes a long time for scientists to react to mistakes in the literature. Wrong ideas can be perpetuated for decades after they've been refuted, especially if the original papers were widely referenced. I was reminded of this the other day when listening to a graduate student seminar—coincidently, on the structure of ATP synthase. The student posted an old-fashioned, out-of-date view of the citric acid cycle as an introduction to the function of ATP synthase. I have challenged my undergraduate biochemistry class to find a single example of a web site that gets the entire citric acid cycle correct. There's a prize. They can't use the IUBMB site, they can't use my sites, and they can't make one of their own. So far nobody has collected the prize.

How Much Junk in the Human Genome?

Ryan Gregory has another contribution to this question that's well worth a read [Is most of the human genome functional?].

Among other things, Ryan picks on the views of John Mattick who has got to be one of the worst scientists in the field. Whenever I read a paper by Mattick I revise my opinion of the value of peer-reviewed literature. It's bad enough that Mattick has silly ideas but it's even sadder that his "peer" reviewers don't recognize it.

Here's a quote from Mattick that I discussed in my article on the The Central Dogma of Molecular Biology. It's obvious that he doesn't understand the real meaning of the central dogma. Can you pick out the other conceptual flaws in this paragraph? [Hints: Worst Figure Ever and Dog Ass Plots.]
The central dogma of biology holds that genetic information normally flows from DNA to RNA to protein. As a consequence it has been generally assumed that genes generally code for proteins, and that proteins fulfil not only most structural and catalytic but also most regulatory functions, in all cells, from microbes to mammals. However, the latter may not be the case in complex organisms. A number of startling observations about the extent of non-protein coding RNA (ncRNA) transcription in the higher eukaryotes and the range of genetic and epigenetic phenomena that are RNA-directed suggests that the traditional view of genetic regulatory systems in animals and plants may be incorrect.

Mattick, J.S. (2003) Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. BioEssays 25:930-939.


Graduate Students Need to Publish Papers

 
In my field it takes five, or even six, years to complete a Ph.D. program. This time could be significantly reduced if there wasn't pressure on students to produce publishable work. The reduction in time is even more obvious at the M.Sc. level where it often take far more than two years to get a degree.

One could make a case for an M.Sc. degree that was not a "research" oriented degree. These programs would be useful for high school teachers, for example, or patent attorneys, or even physicians.

But those are exceptions. In most research departments the thesis is based on scientific research. Does that research have to produce results that can be published in the scientific literature? Yes it does.

T. Ryan Gregory explains why [Why would advisors encourage students to publish?]. (This is a repost of an article that he published earlier on Genomicron but it's still relevant and topical, especially in our department where we are grappling with the issue of long times to completion.)


[Photo Credit: Graduate students in the Department of Biochemistry 2007-2008.]

Friday, January 11, 2008

Test Your God Logic

 
Here's a quiz you can try to see if your positions on atheism and religion are consistent [Battleground God]. Be careful, this quiz has many pitfalls. I took three hits and a bullet but it's not because I'm illogical, in my opinion. It's because questions can be interpreted in several different ways.

Here's one of the questions that caused me trouble.
It is foolish to believe in God without certain, irrevocable proof that she exists.
I answered "true." What I mean by that is that you require evidence to believe in something. What the authors of the study mean is that "certain, irrevocable proof" is inconsistent with my answer about evolution! They say,
You stated earlier that evolutionary theory is essentially true. However, you have now claimed that it is foolish to believe in God without certain, irrevocable proof that she exists. The problem is that there is no certain proof that evolutionary theory is true - even though there is overwhelming evidence that it is true. So it seems that you require certain, irrevocable proof for God's existence, but accept evolutionary theory without certain proof. So you've got a choice:

Bite a bullet and claim that a higher standard of proof is required for belief in God than for belief in evolution.

Take a hit, conceding that there is a contradiction in your responses.
I did, indeed, reply "true" to the statement that evolutionary theory is essentially true. But that's only because I wasn't given the option of replying to the statement that evolution is a fact. I accept evolution because there is certain proof that it exists. I assumed, incorrectly as it turns out, that they were using "evolutionary theory" as a synonym for "evolution."

In order to be consistent I guess I should have replied that "evolutionary theory" is not essentially true.

Watch out for Question 15. It's also a trap.

Read the comments on FriendlyAtheist. Quite a few people got through the test with no hits. I wonder how they answered the question about evolution.


Vegetarian Humor

 
Today after class we were having a wide-ranging discussion about all kinds of issues when one of my students announced that she was a vegan. She claimed that all us meat-eaters were ignoring the slaughter of animals required to justify our habit.

I retorted with the standard reply that she was conveniently ignoring all the plants that had to die for her. Her response caught me off-guard—it was new to me but may be old hat to you. Anyway, she said, "I'm not vegan because I love animals, I'm a vegan because I hate plants!"

The original quote is ...
I am not a vegetarian because I love animals; I am a vegetarian because I hate plants.

                                             A. Whitney Brown
I like it. From now on I'll say that I'm an omnivore because I hate all living things!






The photo honors National Meatloaf Appreciation Day. At least one animal, and several plants, were seriously injured during the making of this photo.

Electoral Compass

 
I'm a sucker for these things but take them with a huge grain of salt because I'm not an American. Some of the questions were very difficult to answer and I ended up having to guess what they wanted a socialist like me to say.

Why isn't Kucinich on the chart? How accurate are the positions of the candidates?



Stop the Presses! Denyse O'Leary Says Something Thruthful!

 
You'd better sit down before I tell you this. Over on Uncommon Descent Denyse O'Leary has just posted an article complaining about evolution, as Intelligent Design Creationists tend to do1 [Today at Design of Life: The Avalon explosion: Another intricate, Darwin-busting puzzle].

But she really blows it in the first sentence when she accidentally gets something right, suggesting that she is finally beginning to understand what we've been telling her for years.
Contrary to popular misconceptions, the history of life shows no steady Darwinian march of progress ...
Congratulations, Denyse. You finally understand that there's no progress in evolution. There's no purpose either.


1. They think that criticism of evolution is the same as promoting Intelligent Design Creationism—but then, that's why we call them IDiots.

What's Going On Here ?

 


Go to easternblot to find out. The photos were taken in the 2nd year introductory Cell and Molecular Biology course at the University of Toronto.