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Wednesday, January 23, 2013

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.


Tuesday, January 22, 2013

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.



[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.



[Hat Tip: Mike the Mad Biologist]

Monday, January 21, 2013

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!


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.


Saturday, January 19, 2013

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 ....



[Hat Tip: Mike's Weekly Skeptic Rant]

Friday, January 18, 2013

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.





Thursday, January 17, 2013

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.



[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.



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 Structure
Chirag Vora was kind enough to alert me to this anniversary. Check out his blog at: Golden Jubilee of Ramachandran Plot.


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

Wednesday, January 16, 2013

Drive-Thru at Timmy's

It's been ages since I've posted anything about the Canadian institution known as Tim Hortons. Here's a photo from cheezeburger.



[Hat Tip: David Schuller.]

Why Do the IDiots Have So Much Trouble Understanding Introns?

Most eukaryotic genes have introns. Introns make up about 18% of the DNA sequences in our genome. Most of these sequences are junk but introns are functional and up to 80bp of each intron is required for proper splicing. The essential sequences contain the 5′ splice site (~10 bp); the 3′ splice site (~30 bp): the branch site (~10 bp); and enough additional RNA to form a loop (~30 bp). The branch site and the splice sites are where specific proteins bind to the mRNA precursor [Junk in Your Genome: Protein-Encoding Genes]. It turns out that within introns about 0.37% of the genome is essential and about 17% is junk.


What? Me Worry?

Alfred E. Neuman may not have had a care in the world but most of us worry about something. John Brockman of The Edge asks his bevy of followers this question for 2013: 2013: WHAT *SHOULD* WE BE WORRIED ABOUT?.

You'd think that most of the responses would be along the lines of global climate change, poverty, disease, crime, war, or the possibility that Earth might be destroyed by an asteroid impact. You'd think that the treatment of women in third (and second) world countries and the fanaticism of religious extremists might generate more than a few responses.

You would be wrong.

Here's what the best minds in the Western world came up with. I read most of them and I don't think I'll lose any sleep over any of these worries. I will, however, continue to lose sleep over women being raped in India and young children being shot to death in Connecticut.

Chinese Eugenics
What We Learn From Firefighters
That We Won't Make Use Of The Error Catastrophe Threshold
A Fearful Asymmetry: The Worrying World Of A Would-Be 'Science'
Misplaced Worries
We Are In Denial About Catastrophic Risks
The Disconnect
Unfriendly Physics, Monsters From The Id, And Self-Organizing Collective Delusions
Worry About Internet Drivel
We Don't Do Politics
The Black Hole Of Finance
The Opinions Of Search Engines
The Mating Wars
Computer-Generated Fascism
Who's Afraid Of The Big Bad Words?
Data Disenfranchisement
The Patience Deficit
The Underpopulation Bomb
Big Experiments Won't Happen
"Smart"
What—Me Worry?
by Craig Venter (one of the few decent responses)
The Promise Of Catharsis
I've Given Up Asking Questions
The Anthropocebo Effect
The Relative Obscurity Of The Writings Of Édouard Glissant
The Danger Of Inadvertently Praising Zygomatic Arches
The Loss Of Death
One Universe
The Rise Of Anti-Intellectualism And The End Of Progress
Applying Classic Science To Understand "Modern States" Shaped By Crime
Lamplight Probabilities
What Is Conscious?
Men
Science By (Social) Media
Unmitigated Arrogance
Technology May Endanger Democracy
"The Singularity": There's No There There
MADness
Blown Opportunities
The Power Of Bad Incentives
Quantum Mechanics
Are We Homogenizing The Global View Of A Normal Mind?
Science Publishing
Is The New Public Sphere... Public?
World As We Know It

Stress
by Arianna Huffington, who is one of the important causes of stress
Science Has Not Brought Us Closer To Understanding Cancer
Losing Touch
The Human-Nature Divide
Are We Becoming Too Connected?
Putting Our Anxieties To Work
Incompetent Systems
Too Much Coupling
Power And The Internet
Close To The Edge
The End Of Fundamental Science?
The Paradox Of Material Progress
The Fragility Of Complex Systems
by Randolph Nesse, worth a read
Rats In A Spherical Trap
Close Observation And Description
Global Greying
The Fourth Culture
The Coming Fight Between Engineers And Druids
Impact
The Complex, Consequential, Not-So-Easy Decisions About Our Water Resources
Children Of Newton And Modernity
The Teenage Brain
Augmented Reality
Where Did You Get That Fact?
Social Media: The More Together, The More Alone
Is Idiocracy Looming?
The Disconnect Between News And Understanding
Objects Of Desire
Say It Ain't So
Being Told That Our Destiny Is Among The Stars
Global Cooperation Is Failing And We Don't Know Why
Morbid Anxiety
Worrying About Children
A Synthetic World
The Death Of Mathematics
Losing Our Hands
Internet Silos
The New Age Of Anxiety
Does The Human Species Have The Will To Survive?
All The T In China
Neural Data Privacy Rights
Armageddon
No Surprises From The LHC: No Worries For Theoretical Physics
Losing Completeness
Worries On The Mystery Of Worry
The Growing Gap Between The Scientific Elite And The Vast "Scientifically
       Challenged" Majority
Presentism
Metaworry
Do We Understand The Dynamics Of Our Emerging Global Culture?
The Loss Of Lust
We Worry Too Much About Fictional Violence
The Consequences Of Our Increasing Knowledge Of What Causes Disease,
       And Its Consequences For Human Freedom
Natural Death
C.P. Snow's 'Two Cultures': The Nature-Nurture Debate
The Demise Of The Scholar
The Unavoidable Intrusion Of Sociopolitical Forces Into Science
Who Gets to Play in the Science Ballpark
Communities Of Fate
Working with Others?
Working with Others?
Super-A.I.s Won't Rule The World (Unless They Get Culture First)
Posthuman Geography
The Danger From Aliens
by Seth Shostak, way, way down on my list
The Role Of Microorganisms In Cancer Is Being Ignored By The Current Sequencing
       Strategies
Human Intuitions Will Stifle Technological Progress
Illusions Of Understanding And The Loss Of Intellectual Humility
The End Of Hardship Inoculation
An Exploding Number Of New Illegal Drugs
Superstition
by Matt Ridley, important but not in the top ten
History And Contingency
The Triumph Of The Virtual, And Its Consequences
There Is Nothing To Worry About, And There Never Was
The Cultural And Cognitive Consequences Of Electronics
Failure Of Genomics For Mental Disorders
Crisis At The Foundations Of Physics
The Behavior Of Normal People
Democracy
Human Population, Prosperity Growth: One I Fear, One I Don't
Magic
The Rise In Genomic Instability by Eric J. Topol, gimme a break
Can They Read My Brain?
by Stanislas Dehaene, who would want to?
A World Without Growth?
The Dangerous Fascination Of Imagination
Worrying
The Gift Of Worry
Not Enough Robots
Safe Mode For The Internet?
Life As We Know I
Unknown Unknowns
Our Blindspots
The Is-Ought Fallacy Of Science And Morality
The Loss Of Our Collective Cognition And Awareness
The Decline Of The Scientific Hero
by Roger Highfield, what's a
       "scientific hero"?
What Is A Good Life?
Digital Tat ...
Capture
Society's Parlous Inability To Reason About Uncertainty
Fast Knowledge
The "Nightmare Scenario" For Fundamental Physics
Homogenization Of The Human Experience
We Won't Be Able To Understand Everything
by Clifford Pickover,
       really? that worries you?
Systematic Thinking About How We *Package* Our Worries
The Real Risk Factors For War
by Steven Pinker, yes, we should be
       worried about war
Worrying About Stupid
The Belief Or Lack Of Belief In Free Will Is Not A Scientific Matter
Science Is In Danger Of Becoming The Enemy Of Humankind
Living Without The Internet For A Couple Of Weeks
by Daniel Dennett,
       not in my top ten


How Atheists Cope with Death

There are millions and millions of atheists around the world. Whether it's in Brussels or Beijing these atheists cope with deaths in the family in a variety of ways. None of them require the false comfort of god(s) or heaven.

I live in a (relatively) secular society. Most of my friends are nonbelievers. We are at the age where the deaths of friends and family members are not uncommon. In many cases, the memorial services are completely non-religious but even in those cases where the service takes place in a church my friends are not troubled by their lack of belief in god(s).

However, problems arise in societies where the vast majority of people are religious and where the believers have no concept of what it might be like to be an atheist. The problems aren't caused by the inability to cope with death in the absence of god, they are caused by intolerant and insensitive believers who can't, or won't, recognize that their false beliefs provide no comfort to an atheist. That's why there's so much talk these days about how atheists cope with death in the USA [After Tragedy, Nonbelievers Find Other Ways To Cope].

If you read the examples in that article, you will realize that the problems they face would not exist in non-religious societies. Their "problems" all stem from feelings of guilt about not believing or from interfering Christians. You won't see articles like this published in Brussels or Beijing.


What Exactly Is Evolution? Stated Clearly Gets It Mostly Right

Stated Clearly posts videos on YouTube. It is dedicated to "spreading the love of science to the world" [Stated Clearly, YouTube] [Stated Clearly, Website].

The video below, narrated by Jon Perry, answers the question, What Exactly Is Evolution. It starts with an excellent definition of evolution that closely resembles my own preferred, minimal, defintion of evolution at What Is Evolution?. Here's the definition in the video ...
(Evolution is defined as) any change in the heritable traits within a population across generations.
The first example involves a new mutation that arises in an amoeba-like organism. Because this new mutation in inherited by a daughter cell, the video declares that "evolution has officially occurred."

What this means is that mutation becomes a mechanism of evolution. I prefer to think of evolution as "heritable changes in a population spread over many generations" in order to make it clear that change in a single generation doesn't qualify. I also prefer to think of mutation as a mechanism for generating variation and not a mechanism for causing evolution but this can be legitimately debated.

The second example is two badgers mating to produce an offspring that has a different combination of characteristics than either parent. According to the video "evolution ... has officially occurred." This is incorrect. Populations evolve, not individuals. It's quite possible for the individuals in a given generation to have different combinations of traits than either of their parents while the frequency of alleles in the population remains unchanged. Thus, evolution has NOT occurred.

The idea that it's populations that evolve and not individuals is crucial to a correct understanding of evolution and it's a shame that the video promotes a common misconception.

Bug_girl at Skepchick liked this video and so did PZ Myers at Pharyngula.



Tuesday, January 15, 2013

WTF Is Science?

Rufina is a student at the University of Toronto and she's interested in setting up a group/club to discuss science. Here's what she has in mind.
The goal of this group is to meet regularly (~biweekly) to discuss/debate the hot topics in scientific controversy and their implications in the sociopolitical world. My personal aim in founding this group is to refine the art of delivering articulate and diplomatic scientific explanations to those who don't "believe" in science. In addition, I would like to expand our efforts to somehow elucidating to the general public/non-science students the importance of science in the progress of society.
I'm in.

The first meeting will be Wednesday, January 1623, 2013 at 6pm at a location to be decided. (Probably in my building.) The topic of the first meeting is "What Is Science."

Anyone else want to join us?


Monday, January 14, 2013

Is It Time for All Religions to Accept Evolution?

This is a BBC One program posted to YouTube on Jan. 13, 2013. The question is whether it's time for all regions to accept evolution. The answer is "yes" of course, but some religions are going to resist for a bit longer. Because this is Britain, it's not so much the Christians that are the problem but Muslims.

You will recognize some of the people on this program. Matt Ridley, for example, gives a pretty good answer to the question about whether there's a scientific debate about the fact of evolution. It's amusing to read the response of Cornelius Hunter who claims that everything Ridley says is a lie [Here is How Evolutionists Lie to the Public].

Hunter says,
That was such a dizzying flurry of big lies we, frankly, lost count. Those lies are so absurd, so unequivocally false, and spoken with such conviction, that the average person is sure to believe them.

Unfortunately such lies are the rule rather than the exception. This evolution propaganda segment was no mistake—it is unfortunately typical.

Of course one can make truthful arguments for evolution. And one can try to find scientific evidence to support it. It is not easy, but it can be done. But that is not what evolutionists do. They mandate evolution. They insist evolution is a fact in spite of the evidence. And that is a big lie.
I don't think we're ever going to succeed in teaching the Cornelius Hunter's of this world the difference between truth and lies but TV shows like this one are having an impact and I'm glad to see that some Muslims are willing to speak out.

Shows like this one were very rare in the 20th century. It's now become much more acceptable to challenge religious beliefs that conflict with science and I think that's because of outspoken atheists like Richard Dawkins, Daniel Dennett, Christopher Hitchens, and Sam Harris, along with many other so-called "New Atheists."



Monday's Molecule #197

The last "Monday's Molecule" was β-D-mannopyranose, shown in boat and chair configurations [Monday's Molecule #196]. The winners were Bill Chaney, Dima Klenchin, and Bill Gunn. Bill Gunn should contact me if he is within range of Toronto.

Students often find it very difficult to distinguish between various stereoisomers. For example, many of you thought that the last molecule was glucose. This week's molecule should present a real challenge for most of you. It's a common molecule, present in all cells and it has a common name by which it is identified in most textbooks. However, the common name isn't good enough because there are several different conformations. The conformation shown in the figure is the only one that's synthesized in the normal reaction. Name this molecule using whatever conventions you have to employ to identify it correctly. [Hydrogen atoms are omitted for clarity. You should be able to infer their positions.]

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.)

A New Year

Here's a photo of my granddaughter, Zoë, flying her kite on Santa Monica beach on New Year's Eve. The kite was a present from Santa Claus.

Zoë turned three years old on January 5th.


Friday, January 11, 2013

The Great Wrinkled Finger Debate

The students in my Molecular Evolution class have to read the Spandrels paper by next Tuesday.

Ryan Gregory explains why this 35-year-old paper is just as relevant and important today as it was when it was first presented in 1978 (published in 1979). Read aall about it at: The great wrinkled finger debate.

Please leave comments on Genomicron and not here.


The Problem with Selling the Homeopathic Product Oscillococcinum

A group of skeptics have banded together to sue Shoppers Drug Mart for selling the homeopathic product Oscillococcinum. Watch the video on Think Again! TV produced by Centre for Inquiry, Canada. This is a class action lawsuit and anyone who has purchased Oscillococcinum from Shoppers Drug Mart may join the plaintiffs.

CFI is not a plaintiff but it has agreed to provide the court with "accurate scientific data on the efficacy and substance of the product."



Thursday, January 10, 2013

Jim Yeager Shows Americans Why Banning Assault Guns Is Necessary

My American friends need to watch this video. Be afraid, be very afraid.

I don't know how many people think like this but if it's more than a few thousand there's going to be trouble.

Isn't threatening to kill somebody a crime? Isn't he advocating the overthrow of the democratically elected American government by force? I don't think that's in the Constitution.




Goodbye, Anonymous, It's Been Nice Knowing You

There are very few anonymous comments these days and those few that persist will not be missed. I've stopped accepting comments from people who won't identify themselves in some way.

I'd prefer if your identifier leads me to an actual name but for now I'll tolerate posting under a pseudonym as long as it's unique.


I Have the Least Stressful Job!!!

According to Careercast.com, I have the least stressful job of all jobs.1 Here's how it's reported in Forbes magazine by web staff writer Susan Adams: The Least Stressful Jobs Of 2013.
University professors have a lot less stress than most of us. Unless they teach summer school, they are off between May and September and they enjoy long breaks during the school year, including a month over Christmas and New Year’s and another chunk of time in the spring. Even when school is in session they don’t spend too many hours in the classroom. For tenure-track professors, there is some pressure to publish books and articles, but deadlines are few. Working conditions tend to be cozy and civilized and there are minimal travel demands, except perhaps a non-mandatory conference or two. As for compensation, according to the Bureau of Labor Statistics, the median salary for professors is $62,000, not a huge amount of money but enough to live on, especially in a university town.

Another boon for professors: Universities are expected to add 305,700 adjunct and tenure-track professors by 2020, according to the BLS. All of those attributes land university professor in the number one slot on Careercast.com’s list of the least stressful jobs of 2013. The ranking comes from an annual best and worst jobs list that began in 1995 under the auspices of the Wall Street Journal.
Ironically, this article comes out just as some of my colleagues are getting the bad news about their grant applications. Those who weren't funded face the end of their research career while they are still in their 40s. It also comes out at a time when two of my colleagues are starting to think about their applications for tenure. If they are unsuccessful, they will be out of a job in their late 30s with a family to support.

None of my colleagues took a month off at Christmas and I can assure you that all of my colleagues are here for almost the entire summer running a lab full of graduate students, post-docs, technicians, and summer students. The stress of running what amounts to a small business and getting papers published on things that nobody else has ever discovered is a lot more than most people could stand.

Read to the end of the Forbes article to see how the author responds to the many comments she received. The real problem here is that a prominent journalist could actually believe what she wrote in the first place!

I love the comment from Thomas Epps ...
Given your comment above indicating that you realize the source of your article was poor at best. I think you should consider retracting this article. I know that I would be severely sanctioned for writing this type of article with such questionable sourcing in my academic job. If the same is not the case in your job, then clearly your career is not a terribly stressful one. Maybe, "web staff writer" should be on the top of the "least-stressful jobs" list?

See ...
Do College Professors Have Less Stress?
Top 10 Reasons Being a University Professor is a Stressful Job
Before Professor comes Postdoc: Lower career rung, just as much job stress


1. I have no intention of supplying specific information about MY job but I'm happy to explain why every one of my younger colleagues is under a tremendous amount of stress every single day.

Proof of God #42: Laminin

No comment is necessary except to say that this man, Louie Giglio, was all set to deliver the benediction at Obama's upcoming inauguration until it was discovered that he hates homosexuals. For me, this video would have been enough to disqualify him.



[Hat Tip: Hermant Mehta at Friendly Atheist: Louie Giglio, Who Thinks Laminin Molecules Prove Christianity is True, Will Deliver Obama’s Inauguration Benediction]

Wednesday, January 09, 2013

A New Era at Centre for Inquiry Canada

The Board of Directors of the Centre for Inquiry, Canada has mailed out the following press release. Unfortunately, nothing has been posted on the website [The Centre for Inquiry].
The Board of Directors would like to thank Justin for launching CFI Canada, growing it from one location in Toronto to across the country in short order. There are few individuals who possess the dedication, passion and tenacity to accomplish this. Justin was instrumental in making CFI the premier voice for reason, secularism and skepticism in Canada. We were fortunate to have him. Justin leaves CFI in good hands with our National Director, Michael Payton, and our incredible branch leaders and volunteers who are committed to continuing our growth and influence.

Justin, we look forward to watching you make further positive and lasting contributions to society, as no doubt you will.

Board of Directors, Centre for Inquiry Canada
I'm delighted that The Board and Justin were able to reach agreement on a new direction for CFI and usher in a new era under new leadership. I agree with the Board that Justin did an excellent job of creating CFI Canada and leading it through its formative years. I was happy to work with Justin and support him during those early years of building an organization (see photo).

In the past year I've been very critical of the CFI Board of Directors because I think they mishandled the firings and re-hirings that took place in 2011 and 2012. This time I think they've done the right thing during recent negotiations. Congratulations to Kevin Smith (President) and all the Board members for working hard to ensure the future success of CFI.

The email announcement also contained a letter from Justin Trottier to the Freehthinker members of CRI. It begins ....
Special Note from Justin Trottier, Founding National Executive Director, Centre for Inquiry Canada

To My Fellow Freethinkers,

It is with mixed emotions that I take this opportunity to announce the upcoming end of my leadership role with CFI Canada. March 15, 2013 will mark the end of my full-time position as National Communications Director; however, I will consider, if I am asked, continuing in part time or other status until no later than July 31. I am immensely proud of the contributions I've made to the organization over the last six years and plan to continue as a volunteer and active participant in CFI events and initiatives, but now it is time to start making the transition from CFI and pursue other interests and employment.

It has been a pleasure working with so many amazing people to form a unique Canadian educational charity and expand it into a national voice for atheists, humanists and skeptics from coast to coast. Leading CFI as it came to establish itself as the most visible, active and professional freethought organization in Canada, with employees, infrastructure and a growing budget will stand as one of the most important and certainly, matchless accomplishments of my life.

...
I'm looking forward to rejoining CFI Canada in just a few months.


Friday, January 04, 2013

Jumping for Joy

Jerry Coyne has posted a video of a happy young antelope jumping up and down in a style called "pronking" or "stotting" [Antelope pronking].

If you're a certain type of evolutionary biologist you will immediately ask yourself what kind of selective advantage could have led to the fixation of stotting alleles in antelopes? Here's a list of possibilities that Jerry offers ...
  • It allows an animal to jump out of high grass to look for predators
  • The behavior startles the predator, giving the gazelle more time to escape
  • It’s an alarm signal (like bird alarm calls), alerting herd members that a predator is nearby. This would probably evolve only if herd members were closely related, so the behavior could evolve via kin selection (assuming it’s individually maldaptive, which isn’t proven).
  • It’s simply play behavior. But not only the young do it: adults pronk too when they’re chased by predators.
  • It’s a way, in young gazelles, of letting the mother know the baby has been disturbed. This may be one function, but doesn’t explain stotting in adults.
  • It confuses the predator. Presumably a herd of gazelle, all pronking, would puzzle a pursuing cheetah or wild dog, making it hard to pick out a given individual to chase. I don’t believe this for a second; predators aren’t that dumb, and in fact a predator would probably either learn to or evolve to concentrate on the stotting individuals because they might be easier to catch. (This “confusion” explanation was once used to explain zebra stripes: it might be hard to single out one zebra in a mass of fleeing stripey equids. But see my earlier post on another explanation for stripes.)
  • It’s a way to attract mates, possibly by showing how fit you are. Sage grouse in the western U.S. form “leks” in which males group together and jump up and down for hours (making loud noises at the same time) while the females watch from nearby. Invariably it is the males who jump the longest that are chosen as mates. Females want a fit father for several reasons. This doesn’t wash for gazelles since both sexes do it, and not in a sexual context.
  • This is a favored hypothesis: the “honest signal” theory. This posits that the behavior is saying to potential predators, “Don’t bother trying to catch me as I can bounce really high, so imagine how fast I could run if I wanted to!” In other words, the behavior deters the predator from attacking that individual.
  • This is the hypothesis I find most credible: stotting warns the predator that it has been seen, thus discouraging it from pursuing the stotting animal. (Predators like to sneak up on a prey, getting as close as possible before they’re detected.) That is, stotting evolved via individual selection. Remember that predators often don’t go after a whole pack of quadrupeds at once, but single out certain individuals—often young or weak ones—to pursue.
Here's another example of animals jumping up and down in a stylized manner. Surely there are specific alleles that make them behave this way? And the alleles must have become fixed in the Maasi population by natural selection. In other words, it has to be an adaptation, right?

How many just-so stories can you think of?



Beat Australia!

The Atheist Census is a project of Atheist Alliance International. You have to answer a few questions but it won't take more than a minute or two.

Please fill out the form if you are Canadian because the reputation of our country is at stake. So far the top ten countries are ...

1. United States of America: 51,541
2. Brazil: 10,971
3. United Kingdom: 10,683
4 Turkey: 9,795
5. Australia: 7,593
6. Canada: 6,852
7. India: 3,100
8. Italy: 2,948
9. Iran: 2,797
10 Poland: 2,679

Do you see what's happening? Some upstart British colony from the bottom half of the world is beating Canada! We can't let that happen. If you are Canadian get yourself over to Atheist Census right away. If you're from Australia you can get your vote counted at Atheist Census for Australians. (Agnostics need not apply.)



[Hat Tip: Veronica at Canadian Atheist: Canada Versus Australia.]

Scientific American Chooses ENCODE Project as One of the Top Ten Science Stories in 2012

It's pretty hard to ignore the ENCODE papers if you're selecting the top ten science stories of 2012. This doesn't mean it's a "breakthrough" as Science magazine claims [Science Magazine Chooses ENCODE Results as One of the Top Ten Breakthroughs in 2012]. And it doesn't mean that the results overthrow Darwinian evolutionary theory as implied by the Intelligent Design Creationists [Intelligent Design Creationists Choose ENCODE Results as the #1 Evolution Story of 2013].

The Scientific American article was written by Bora Zivkovic, a long-time blogger who knows the difference between hype and reality. He apparently knows which scientists to believe and which ones to ignore [The Top 10 Science Stories of 2012: Publication of the ENCODE Encyclopedia: A Milestone in Genome Research].
Unfortunately, much of the discussion surrounding the publication of ENCODE failed to focus on the usefulness of the catalogue and the techniques that built it. Instead, much of the debate centered on the failure to understand that transcription does not necessarily imply meaningful biological function. Cells are messy biological entities, with lots of gunk and goo floating around, so mistakes happen all the time. Many DNA sequences get translated into RNA, only to have the cell degrade that RNA. Much, perhaps most, of the DNA in our genomes—despite being occasionally transcribed, and thus recorded in ENCODE—is still functionless “junk DNA.” That is actually not surprising; it is in fact expected from evolutionary theory. Thanks to ENCODE, though, we should eventually learn which sequences are the junk and which are the gems of cell activity.
This is a very different take on the subject than that published by the editors of Science and the Intelligent Design Creationists.

I wonder why?


Intelligent Design Creationists Choose ENCODE Results as the #1 Evolution Story of 2012

The folks over at Evolution News & Views (sic) have selected the ENCODE papers as the Number 1 evolution-related story of 2012. Naturally, they fell for the hype of the ENCODE/Nature publicity campaign as you can see from the blog title: Our Top 10 Evolution-Related Stories: #1, ENCODE Project Buries "Junk DNA".

Most of the article is just the reposting of an article by Casey Luskin but some anonymous editor has added ...
Editor's note: For the No. 1 slot among evolution-related news stories of 2012, this one was an easy pick. The publication of the ENCODE project results detonated what had been considered among the sturdiest defenses that Darwinian evolutionary theory could still fall back upon: "Junk DNA." Casey Luskin's initial reporting is featured below. See also our response to the ensuing controversy over ENCODE ("Why the Case for Junk DNA 2.0 Still Fails").
Normally I would make fun of the creationists for misunderstanding the real scientific results in the papers that were published last September but, in this case, there are lots of real scientists who fell into the same trap.

Even Science magazine selected the ENCODE results as a top-ten breakthrough and noted that 80% of the human genome now has a function [Science Magazine Chooses ENCODE Results as One of the Top Ten Breakthroughs in 2012]. Oh well, I guess I'll just have to be content to point out that many scientists are as stupid as many Intelligent Design Creationists!

I can still mock the creationists for claiming that "Darwinian evolutionary theory" supports junk DNA.


Science Magazine Chooses ENCODE Results as One of the Top Ten Breakthroughs in 2012

Science magazine (published by AAAS) was one of the major news sources that fell hook, line and sinker for the ENCODE/Nature publicity campaign last September [Science Writes Eulogy for Junk DNA]. It even published a laudatory three page profile of Ewan Birney, the man responsible for misrepresenting the ENCODE results as evidence that most of our genome is functional [Ewan Birney: Genomics' Big Talker].

I was somewhat apprehensive when I saw that the editors of Science had picked the ENCODE results as one of the top ten breakthroughs [Genomics Beyond Genes]. Would the editors continue to promote the idea that most of the human genome is functional?

Carnival of Evolution #55

This month's Carnival of Evolution is hosted by Suzanne Elvidge at Genome Engineering. Read it at: Carnival of Evolution #55: New Year’s resolutions 2013 – evolution, evolution, evolution
Welcome to 2013 and to Carnival of Evolution #55, and Happy New Year to everyone from Genome Engineering. Have you made any New Year’s resolutions this year? Apart from the oft repeated ‘This year I will write my novel’, here are some of my New Year’s resolutions for 2013.

New Year’s Resolution number one: Deliver Carnival of Evolution on time

Okay – broken that one already – sorry. Hope it was worth waiting for. Now onto the rest.
There's no host yet for the next Carnival of Evolution (February, 2013). If you want to volunteer to next month or for March, April, or May, contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission.

Wednesday, January 02, 2013

This Is Why Christians Want Guns

I'm sure you've heard that Americans need guns so they can overthrow the government whenever it infringes on their personal beliefs. Many Americans believe they have a "right" to commit treason whenever they feel like it and, furthermore, that "right" must be protected by allowing them to bear arms, including assault weapons.

Here's what could happen. This is an interview by Janet Parshall of Mathew Staver. Believe it or not, Mathew Staver is Dean of the School of Law at Liberty University. He is also the Chair and Founder of a right-wing extremest group called Liberty Counsel. Mat is worried that the Supreme Court of the United States—the ultimate source of what's legal and what's not—could actually allow same-sex couples to get married!!!!

The consequences would be devastating, according to the Dean of Law. He says,
This is the thing that revolutions literally are made of. This would be more devastating to our freedom, to our religious freedom, to the rights of pastors and their duty to be able to speak and to Christians around the country, then anything that the revolutionaries during the American Revolution even dreamed of facing. This would be the thing that revolutions are made of. This could split the country right in two. This could cause another civil war. I’m not talking about just people protesting in the streets, this could be that level because what would ultimately happen is a direct collision would immediately happen with pastors, with churches, with Christians, with Christian ministries, with other businesses, it would be an avalanche that would go across the country.
I'm sure it's a great comfort to most Americans that these people have the weapons they need to start another civil war over legalizing gay marriage.




[Hat Tip: Hermant Mehta: Christian Right Leader: Legalizing Gay Marriage Will Result in Another Civil War.]