Monday's Molecule #198

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

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

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

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

Vote for Your Favorite Theory of Evolution!

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

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

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

Nobody has voted for "Theistic Evolution."

VOTE NOW!

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WTF Is Science?

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

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

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

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

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

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

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Herd Immunity

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

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

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

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[Hat Tip: Mike's Weekly Skeptic Rant]

That's Extraordinary! Homeopathy

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

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The NRA Anti-Obama Ad

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

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


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

Here's another version of the ad.

NRA - Stand and Fight Parody - watch more funny videos

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[Hat Tip: Pharyngula]

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

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

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

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

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50th Anniversary of Ramachandran Plots

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

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



THEME:

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

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

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.

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[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

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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.

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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.

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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?

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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."

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