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Wednesday, January 23, 2013

Teaching Developmental Biology

PZ Myers posted some lecture notes from his developmental biology course [What I taught today: molecular genetics and basic concepts ]. Here's part of what he said ...
Think about that. In the early days of developmental biology, we didn’t even know whether there was differential gene activity or not; it was considered a reasonable possibility that all the genes were just doing their work, whatever it was, all the time in every cell, and that differences between cells emerged farther downstream, in biochemical interactions. But they knew this was an important question. They knew that we had to look at the activity of individual genes…they just didn’t have the tools yet. So it was back to hacking up embryos and trying to infer causes from aberrations.

The change emerged gradually, but there were a couple of watershed moments where everyone looked up and noticed that hey, we do have ways of looking at genes directly. One was the work of Ed Lewis, a most excellent geneticist who used the tools of genetics to look directly at mutations that caused changes in fly morphology, in the 1960s. This was amazing stuff — the papers he wrote were beautiful and complex and very, very genetical — but it was written in a language that most developmental biologists of the day were unprepared to read. They were genetics papers. But I think they laid a foundation: if you want to do development, you’d better learn about genetics.

The second big event was the saturation mutagenesis screen of Christiane Nusslein-Volhard and Eric Wieschaus, about 20 years later. This work was also built on an understanding of genetics, but also used the tools of molecular biology. It was another lesson: if you want to do development, you’d better learn about molecular biology.
I used to teach this stuff in the 1980s and I certainly agree with PZ that you need to understand molecular biology and gene expression.

When it came time to write my first textbook I incorporated the examples I had used in class. The first ones I described were: the early to late switch in gene expression in bacteriophage T4, sporulation in Bacillus subtilis, and the genetic switch in bacteriophage lambda. These were well-studied examples from experiments carried out in the 1970s. They teach fundamental concepts in developmental biology and they have an additional advantage; namely, they get students thinking about species that aren't animals.

These are still excellent examples that are well-understood at the molecular level. They are much easier to understand than Drosophila or plants. Unfortunately, we've educated an entire generation of developmental biologists who have never heard of these elegant examples.

Is this a good thing or a bad thing? Do students need to know the real history of developmental gene expression as worked out by scientists who studied phage and bacteria?


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