Mendel's Garden #18

 

The 18th version of Mendel's Garden has just been posted on Balancing Life [Mendel’s Garden at Balancing Life]. Can you guess which one of my recent postings is included?

Monday's Molecule #42

 
Today's molecule is a very big molecule. You have to describe what you are seeing in the photograph and then relate it to this Wednesday's Nobel Laureate(s). Extra points if you can relate it to a recent posting. [Hint: The Nobel Prize is the most innovative, creative, and daring prize that the Nobel Committee has ever awarded.]

There will be no free lunch this week because the contest is too easy. You can win bragging rights by sending your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the photo and the Nobel Laureate(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. This way I may select multiple winners if several people get it right.

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

Parole Officer Can't Make You Attend Alcoholics Anonymous (because It's Religious)

 
A few months ago I posted a message about Alcoholics Anonymous. It was news to me that the program was very religious and required belief in God.

Friendly Atheist reports on a recent court decision in the United States [Forced Attendance at Alcoholics Anonymous is Unconstitutional, Says Court]. You should read the entire story as he reports it. A Buddhist was released on parole on condition that he attend a Salvation Army treatment program that included Narcotics Anonymous. The Buddhist went to some meetings but refused to participate and was sent back to jail.

The court ruled that,

… requiring a parolee to attend religion-based treatment programs violates the First Amendment… While we in no way denigrate the fine work of (Alcoholics Anonymous and Narcotics Anonymous), attendance in their programs may not be coerced by the state.

The Centre for Inquiry (Toronto) sponsors the Secular Organizations for Sobriety Group of Toronto (SOSGT), a non-religious organization for alcoholics [SOSGT].

SOSGT credits the individual for achieving and
maintaining his or her own sobriety and is ideal for those
uncomfortable with the spiritual content of 12-step programs.
The group is secular and religiously neutral.

Atheist Win Another One by Huge Majority

 
The results of a new Pew Research Center poll are just out. People were asked if they would be less likely to vote for someone with a variety of characteristics, including not believing in God. FriendlyAtheist has summarized the results as shown in the table on the left [I Would Be Less Likely to Vote for a(n) _____ as President].

Atheists win again! That makes it several hundred years in a row that Americans hate us more than anyone else—although those pesky Muslims are gaining.

You know, this is all because of Dawkins, Hitchens, and Harris. It's all their fault. Nisbet and Mooney warned us this would happen.

Neville Chamberlain Would Love this one!

 
Most of you probably don't realize that Richard Dawkins has a new book called The Fascism Delusion. Those people who criticized his earlier book (The God Delusion) have been quick to jump all over this one. Check out this devastating review at the Valve [More on Dawkins]

[Hat Tip: PZ Myers at Pharyngula (Dawkins demolished]

As It Turns Out, Not all Conservatives Are Smart ....

 
In an earlier posting I commented on how pleased I was that some of John Tory's supporters realized that teaching creationism is wrong [see John Tory Tries to Clarify]. I'm still pleased with the majority of conservative commentators but, naturally, there are some who still don't get it.

One of them is Matthew at ThePolitic.com, a widely read Canadian political blog. Mathew reveals that some Canadians are IDiots [Warren Kinsella’s Documentary Sequel]. Matthew really crams his foot in his mouth all the way up to his kneecap but I won't bore you with all the details. Instead, let me just mention one or two of the most obvious examples of stupidity.

5) Creation science is a real scientific theory — if you want to challenge it, please don’t insult us by just offering a fancy and long-winded “nuh-huh”. I find it funny that Wikipedia attempts this too, but I’ve seen this movie before; it’s called the Consensus on Climate Change (and we all know how that one will end!).

Where do these IDiots come up with stuff like this? Creation science is not a real scientific theory by any stretch of the imagination. If Matthew is talking about Biblical Creationism then that fairytale has been disproved by science. If he's talking about any other version of "Creation science" than it's either; (a) also disproved, or (b) vacuous.

The fact that Matthew is so confused about this means that it's extremely important that we teach evolution in school. It's pretty clear that Matthew skipped all the science classes when he was in school. Probably because they required more than 6th grade mathematics.

6) Someone still has to address for me how teaching an alternative view on the origin of species will forever ruin students’ lives and deny them jobs, houses and weekends up at the cottage. They’re not your kids so what do you care what they learn if it doesn’t affect you?

Look at it this way Matthew. We have basically two choices in the classroom. We can teach children things that are correct or we can teach them lies. Call me old-fashioned, but I think it's better to teach the truth. It makes for better citizens in the long run.

I actually think we should address Creationism in school. Traditionally we use astrology as the example of something that masquerades as science. It's a way of teaching what science really is and it provides a good lesson on how to think. Creationism would be another good example. We should make sure that all children learn why Creationism is not science.

9) Ala the Flintstones comment, blindly believing in evolution is like believing Star Trek is a documentary about the future. Reality is though that we’re not eliminating all wars, humanity isn’t evolving past its character flaws and evil tendencies and no matter how much some in our society might like it, we’re not going to grow beyond religious faith. Even the television series outlived this optimistic faith in the human will by DS9. Evolution might be wonderful science fiction with things spontaneously mutating everywhere, but we shouldn’t be confusing it with a scientific principle. Maybe we should also be keeping it in it’s proper place too — media class!

No comment, other than to point out there's a reason why we call them IDiots.

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[Photo Credit: The photograph shows a typical Boston Red Sox fan celebrating something that got them all excited (Red Sox Connection). (I think their team just lost another game against Toronto.)]

[Hat Tip: Canadian Cynic]

Gene Genie #15

 

The 15th edition of Gene Genie has just been published on Cancer Genetics [Gene Genie #15].

As you might expect, there's a lot of stuff about Craig Venter's genome. You won't read anything about it here so if you're really interested in Craig then your kicks from the carnival postings.

Play Creationist Bingo!

 
The rules are on Skeptico [ID Creationist Bingo].


[Hat Tip: FriendlyAtheist]

Theories Don't Become Laws

 
I'm pleased by the almost universal condemnation of John Tory's remarks about creationism in schools [John Tory Promotes Creationism]. Letters to the newspapers are running overwhelmingly against the leader of the Ontario Progressive Conservatives. However, there's still lots of misunderstanding out there even though their hearts are in the right place.

In today's Toronto Star there's a letter from a reader in Barrie, Ont. The title is Misunderstanding of the word `theory'. I'll quote most of the letter ...

John Tory's statement appearing to equate Darwin's theory of evolution with "other theories that people have out there" comes from a common misunderstanding the general public has about the scientific meaning of the word "theory."

When a scientist has an idea he or she wishes to test through observation or experimentation, this is termed a hypothesis.

Once a body of scientific data has been accumulated in support of the hypothesis, it is elevated to the status of theory.

After a time, certain theories receive considerable support from various scientists and no contradictory evidence turns up. Then, the theory may be elevated to the status of law.

There is now so much evidence from many branches of science supporting Darwin's theory of evolution by natural selection, that it may be time to give it the status of a law.

This is not right. Theories are explanations of natural phenomena and laws are simple descriptions of phenomena. Boyle's Law, for example, simply states that "For a fixed amount of gas kept at a fixed temperature, P and V are inversely proportional." It does not explain why this is so. That's what the theory of the behavior of gases would do.

Evolutionary Theory is a complex subject that attempts to explain how species evolved. It incorporates Darwin's Theory of Natural Selection and other things like random genetic drift and mechanisms of speciation. Evolutionary Theory will never become a law. Theory is as good as it gets in science.

Waiting for the Paradox

 
John Dennehy's citation classic for this week is Gunther Stent's Molecular Biology of Bacterial Viruses [This Week's Citation Classic]. This reminds me of the time when I was an undergraduate in 1966 and I first read about the Phage Group in Phage and the Origins of Molecular Biology (1966). The book was a collection of articles by workers who had been influenced by Max Delbrück, on the occasion of his 60th birthday.

A few years later I got to meet most of them at the annual phage meetings in Cold Spring Harbor. It was an exciting time. I remember Stent as one of those people who is so smart it's scary. Little did I know at the time that I was witnessing the end of an era.

Stent's contribution to Phage and the Origins of Molecular Biology was an essay with the cryptic title "Waiting for the Paradox." He describes some of the early history of the phage group and Delbrück's attempts to define the gene in 1940. This influenced the physicist Erwin Shrödinger who wrote a famous little book called What is Life?. It stimulated many physicists to enter biology—including Francis Crick.

The key passage from Shrödinger's book is described by Stent. Schrödinger defines an important credo (quoted by Stent) ...

In fact, this credo was probably the most important psychological incentive for physicists to turn to biology in the first place: "From Delbrück's general picture of the hereditary substance it emerges that living matter, while not eluding the 'laws of physics' as established up to date, is likely to involve 'other laws of physics' hitherto unknown which, however, once they have been revealed will form just as integral part of this science as the former." Thus it was the romantic idea that 'other laws of physics' might be discovered by studying the gene that really fascinated the physicists. This search for the physical paradox, this quixotic hope that genetics would prove incomprehensible within the framework of conventional physical knowledge, remained an important element of the psychological infrastructure of the creators of molecular biology. [my emphasis - LAM]

By 1966 it was clear that no new laws were going to be discovered although there was still the hope that something mysterious was going on inside the brain. Some people were still waiting for the paradox.

Today we teach our students that the most remarkable thing about biology is that life obeys the laws of physics and chemistry.

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[Photo Credit: The book cover shows the 1992 expanded edition of Phage and the Origins of Molecular Biology. A new Centennial Edition is due out next month.]

John Tory's Self-Immolation

 
This is from the National Post. They're supposed to be on the same side as the Progressive Conservatives. It's too cute to pass up [Colby Cosh: Tory's tumble].

EDMONTON -Where were you when John Tory lost the Ontario election? I was at my usual post in far-off Alberta, but even here Tory's Wednesday self-immolation cast a glow that you could almost warm your hands by.

As I hear it told, a radio reporter looking for a new angle asked the Conservative leader whether the fully funded religious schools he wants to pay for as premier would be permitted to teach creationism.

There's no word on whether Tory actually expressed gratitude for the layer of gasoline he had just been super-soaked with: he just went ahead and whipped out the Zippo. Creationism? Sounds great! Why, it's just one more of the menu items our $400-million will buy us! Say, why's my tie melting?

Genomics Is Dead! Long Live Systems Biology!

 
When you're an old fuddy-duddy like me you've lived through several revolutions in biology. I still remember when recombinant DNA technology was going to change the world. Then it was developmental biology and evo-devo. Along the way were told with a straight face that sequencing the human genome would cure cancer and everything else.

After a while it all got very boring. We put up with the hype on the grounds that it was good spin framing for the general public. If it brought in lots of money then what's the harm? Well it turns out there was some harm done. We scientists are losing our credibility.

I've gone way beyond being bored by this kind of nonsense. Now I'm angry—especially when it seems that those who are ignorant of history are doomed to misrepresent it. Here's the opening paragraph of a press release on Systems Biology [Systems Biology poised to revolutionize the understanding of cell function and disease]. It summarizes the contents of a report to the European Science Foundation.

Systems Biology is transforming the way scientists think about biology and disease. This novel approach to research could prompt a shake up in medical science and it might ultimately allow clinicians to predict and treat complex diseases such as diabetes, heart failure, cancer, and metabolic syndrome for which there are currently no cures.

I wonder if they just reuse the reports from years past substituting "systems biology" for "genomics," or whatever the last cure for cancer was supposed to be? This kind of stupid motherhood hyperbole would be laughable if it wasn't for the fact that these people are deadly serious. That makes it pathetic.

Look what one of authors of the report has to say ...

Until recently, researchers tended to focus on identifying individual genes and proteins and pinpointing their role in the cell or the human body. But molecules almost never act alone. According to Lilia Alberghina from the University of Milano-Bicocca, Italy: “There is a growing awareness in medical science that biological entities are ‘systems’ – collections of interacting parts."

I suppose this depends on what you mean by "recently." If it's 40 years then maybe the statement might make some sense but even then it's a gross misrepresentation of the truth. Of course we isolated genes and proteins one-at-a-time but the goal was always to put them back together to make molecular machines. Does Lilia Alberghina really think that older scientists were completely unaware of the fact that biological entities are "systems"? I wonder if Alberghina is aware of metabolic pathways that were worked out half a century ago, or ribosomes, or DNA replication complexes, or muscle, or the complement system, or Drosophila embryogenesis, or any number of other systems that haven't just sprung into existence in the last few years.

Most scientist are already tired of these fads masquerading as revolution. I wonder how long it will be before the public and the politicians catch on?

How Logical Are You?

 

You Are Incredibly Logical

Move over Spock - you're the new master of logic You think rationally, clearly, and quickly. A seasoned problem solver, your mind is like a computer!

How Logical Are You?

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[Hat Tip: GrrlScientist at Living the Scientific Life (How Logical Are You?]

Don't Trust All DNA Sequences

 
I've been interested in sequence errors and cloning artifacts for many years. I have a thick file of papers that have uncovered numerous examples of DNA sequences that are just plain wrong. It's one of the reasons for being at least a little bit skeptical of any unusual discoveries in DNA sequences.

Now, I'm not saying that you should take this skepticism to extremes; I'm saying that you should keep your mind open to the possibility that the data might not be real. Just because it's published in the peer-reviewed literature doesn't mean it's right.

Sandra Porter has an interesting example over on Discovering Biology in a Digital World [Digital Biology Friday: What sequences do you believe?]. She describes the process she went through when she first heard about the discovery of a β-lactamase gene [Penicillin Resistance] that was supposedly from Streptococcus pneumoniae. I'm not going to spoil the punchline by revealing it here. You'll have to read about it on Sandra's blog.

Keep this lesson in mind. It's what good science is all about.

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Figure Credit: The image of the common (but old) cloning vector pBr322 is from Horton et al. 4th ed. (2006). The amp^R gene encodes β-lactamase.]

Bloggers for Peer-Reviewed Research Reporting

 
Bloggers for Peer-Reviewed Research Reporting is a fledgling organization that's going to try and impose some standards on the reporting of peer-reviewed papers by bloggers. Here's their mission statement at [BPR3.org].

Bloggers for Peer-Reviewed Research Reporting strives to identify serious academic blog posts about peer-reviewed research by developing an icon and an aggregation site where others can look to find the best academic blogging on the Net.

The idea is to list all blog posts about peer-reviewed scientific literature on one site (with an RSS feed) and to identify all such blogs with a copyrighted icon.

What's the point of that, you might ask? Well, it's because BPR3 wants to impose some sort of standards on the blogging community. Here's how Dave Munger describes it on the BPR3.org website.

Here’s how I imagine we might handle this issue:

• Credentialling of blog authors is probably a bad idea — some expert bloggers have good reasons for being anonymous, and there are many blogs run by graduate students, journalists, and others without PhDs that offer thoughtful commentary on peer-reviewed literature


• Instead, we could have bloggers register their blogs here. Then we will (eventually) have an aggregation system which will allow links to those blogs’ posts about peer-reviewed research to appear on this site.


• If a blog appears to be abusing the system, either by not meeting our definition of peer review, or not commenting thoughtfully on the article, then readers could alert us and we could remove them from the list of registered blogs. How exactly would that process work? We’re open for suggestions.


• A secondary process could be used to combat abuse of the icon itself (whether or not the blog is actually aggregated here). This would require BPR3 to maintain copyright of the icon, so that we could deny permission to use the icon to those who abuse it. Again, we’d love to hear suggestions about how that might work.

Any other ideas/suggestions? Let us know in the comments.

I write a lot of articles about peer-reviewed research so this is right up my alley. I've got to say right up front that I'm not very enthusiastic about the proposal. Any attempt to impose order on the blogging community is doomed from the start, in my opinion. Furthermore, I don't see any advantage for most bloggers. What's in it for them?

We already have a sort of system that mimics this "peer review" of blog articles. It's the various carnivals that are published every week (see my list in the sidebar). The idea is that the carnival moderator will pick the best of the blog articles that have appeared recently and collect them on a single site. You can judge for yourself whether this has been a remarkable success over the years. From my perspective the quality of the articles in most carnivals varies enormously and I've no reason to suspect that the same won't happen on the BPR3 site.

What does everyone here think? Is this an idea that's going to work?