Some of you aren't familiar with TED talks so the recent criticism doesn't make sense (e.g. The Trouble with TED). Here's an example of one of the problems with TED talks. This is a "gosh, gee whiz" kind of talk that's almost completely devoid of information.1
The talk has pretty pictures of the developing human embryo/fetus accompanied by the kind of music that evokes mystery and awe. The author of the video talks of the mystery and why it makes him think of divinity.
The first divinity-inspiring observation concerns collagen. Most collagen molecules form fibers (see Collagen) but those in the eye form sheets in the basal lamina. This is because the eye collagen is a different type of collagen. Here's what Wikipedia says [Collagen IV] ...
Type-IV collagen is a type of collagen found primarily in the basal lamina. The type IV collagen C4 domain at the C-terminus is not removed in post-translational processing, and the fibers link head-to-head, rather than in parallel. Also, type-IV lacks the regular glycine in every third residue necessary for the tight, collagen helix. This makes the overall arrangement more sloppy with kinks. These two features cause the collagen to form in a sheet, the form of the basal lamina.
Does that make you think of god(s)?
Would you pay several thousand dollars to hear this TED talk?
1. Recall that the theme of TED is "Ideas worth spreading." Which ideas in this talk are worth spreading?
I recommend this article by Enrico Uva: Changing Ideas About The Origin Of Life.
Here are the main points—but you should read the whole thing.
- Primordial catalysts were probably not proteins nor RNA
- First Energy Source Likely Involved Proton Gradients
- Knowledge of New Bacterial Kingdoms Downplays Role of Fermentation In First Cells
You should also read The beginnings of life: Chemistry’s grand question by Ashutosh Jogalekar. Here's an excerpt.
While Miller and his fellow “soupists” blazed the initial paths in origins of life research, a startling new era dawned in the 80s with the discovery of potential life-sustaining factories in the most unlikely environments. The finding that life thrives in deep hydrothermal vents opened a whole new chapter in the field, again avowedly chemical. Black smoker chimneys located miles beneath the ocean have for millions of years been orchestrating a tumultuous union of hot, metal-rich, acidic chemicals arising from volcanic vents with cool alkaline waters. The unholy meeting of these two chemical opposites leads to a violent precipitation of minerals including the silicate mineral olivine, one of the most ubiquitous components of our planet’s rocky landscape. The precipitation of these minerals results in chimney like structures that can be miles high. The convecting thermal currents in these chimneys provide an abundant source of life’s sine qua non – energy. The metals can act as catalysts for simple reactions which involve sulfur, carbon monoxide and water. In recent years, because of the sheer energy hidden inside them, their capacity to catalyze key reactions like the Krebs cycle and concentrate reactants and products in microscopic pores and the uncanny resemblance of some of the iron and sulfur compounds to crucial iron-sulfur cores found in proteins, these mighty smokers have been considered by many scientists to precede or at least accompany the origin of life on the surface. Prominent among the “smokers” are scientists like Nick Lane and the patent attorney Günter Wächterhäuser who moonlights in the field as a “hobby”. These theories provide the “metabolism first” counterpart to the “replication first” camp. Together they may account for both genetic inheritance and chemical metabolism.
It doesn't matter whether you're a soupist or a smoker but you'd better be aware of the controversy. Too many scientists think that the primordial soup is still the best, and only, game in town in spite of its severe problems.
Some of you might recall the recent Chromosome 2 kerfuffle. It started when Carl Zimmer asked David Klinghoffer a simple question. Zimmer asked him to describe the evidence to support his claim that the fusion site didn't look like it should if two primitive ape chromosomes had fused to produce human chromosome 2.
Rather than simply answer the question, the IDiots circled the wagons then went into attack mode. Eventually, after a lot of pressure, they got around to answering the question; apparently there is no evidence to support their claim [And Finally the Hounding Duck Can Rest].
Of course by then they were so deep in their hole that the sun don't shine.
It's Tuesday, so it must be time for Monday's Molecule.... Oops.1
Last week we looked at an important intermediate in the Calvin cycle—the main pathway for fixing carbon dioxide in many species [Monday's Molecule #179]. Today we're going to look at the intermediate in another pathway. Name the molecule, the common name will do.
Discovery of this molecule, and the pathway it's involved in, was an important contribution to understanding basic metabolism in most cells. The enzyme that makes it has been characterized. It's now one of the most widely studied enzymes in biochemistry. The pathway is essential for all species, with a few minor exceptions.
This knowledge has been exploited by technology to an extent never imagined only 50 years ago. Name the technology and how it makes use of what we know about the enzyme and the pathway. For extra bonus points, explain how the molecule got it's root Japanese name.
Post your answers 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 with a very famous person, or me.
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.)
Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)
In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.
Winners will have to contact me by email to arrange a lunch date. Please try and beat the regular winners. Most of them live far away and I'll never get to take them to lunch. This makes me sad.
Comments are invisible for 24 hours. Comments are now open.
UPDATE:The molecule is 5-enolpyruvylshikimate 3-phosphate an intermediate in the chorismate pathway and the synthesis of tryptophan, phenylalanine, and tyrosine. The enzyme that produces this product is EPSP synthase and some bacterial versionsof this enzyme are resistant to glyphosate, the active ingredient in the herbicide Roundup®.
The gene for the resistant enzyme can be inserted into crop plants making them resistant to Roundup®.
The winner would have been Ben but I can't identify that person. The winner is Raul A. Félix de Sousa.
Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa
June 25: Raul A. Félix de Sousa
July 2: Raul A. Félix de Sousa
July 16: Sean Ridout, William Grecia
July 23: Raul A. Félix de Sousa
July 30: Bill Chaney and Raul A. Félix de Sousa
Aug. 7: Raul A. Félix de Sousa
1. I got confused because yesterday was Simcoe Day.
Blogging is fun. I love it when a serious discussion breaks out in the comments. Sometimes I love it even when the discussion is not serious.
Back in the olden days I used to love the newsgroups, especially talk.origins but I don't read it much any more. (Don't worry, I won't shut off the talk.origins server.)
Lately I've been spending more time on Twitter, Facebook and Google+ to see if there's anything there worth reading. It seems to be a mixed bag. The ratio of interesting vs non-interesting stuff seems to be a problem.
Perhaps that's just because I'm not following the right people?
Let me know if you find something worthwhile. My Twitter account is @larryon sandwalk, you can reach me on Facebook at Laurence A. Moran, and on Google+ I'm Laurence A. "Larry" Moran.
An awful of of people seem to waking up to the idea that TED talks are not what they're supposed to be. They attract a lot of kooks who can speak well and exude enthusiasm. How many times have you listened to a TED talk in your area of expertise and wondered how the heck that person got on the stage?
TED talks are just big soundbites and soundbites are not good ways to explain complicated, and potentially revolutionary, ideas.
I just heard about the NAFTA Superhighway. It's going to be as wide as four football fields. Is that Canadian football fields, Mexican football fields, or American football fields?
I can't wait 'till it's finished.
The good news is that I should be able to drive from Toronto to Texas in less than 24 hours.
The bad news is that Texans will be able to drive to Toronto in less than 24 hours.
I hope they have Tim Hortons at the rest stops.
The term "pH" is used to measure acidity. Strong acids, like hydrochloric acid or sulfuric acid, have very a very low pH while weaker acids, like acetic acid (vinegar), have pH readings that are higher. A "neutral pH" is 7.0, this is close to the pH value of the cytoplasm in living cells.
Higher pH values are "alkaline" rather that acidic. The highest pH value is usually shown as 14 and the lowest pH value is shown as 0.
Acidity is a function of the concentration of hydrogen ions (H+), or protons. The strength of alkaline solutions is measured by the concentration of hydroxide ions (OH-).
There's a reciprocal relationship between the concentrations of these two ions because we're dealing with aqueous solutions (water). Water molecules dissociate into H+ and OH- ions so in pure water there will always be equal concentrations of both ions.
The extent of this dissociation determines the concentration of these ions in pure water. We express the extent of dissociation using a term called the equilibrium constant (Keq) that is defined as the concentration of the products of a reaction over the concentration of the reactant(s).
For the dissociation of water, the actual equation is ...
Paul McBride is causing quite a stir among the creationists. His review of Science & Human Origins was so devastating that they couldn't ignore it.
Jonathan McLatchie (Jonathan M) is the latest creationist to attempt a defense of the home team. He concentrates on defending the Intelligent Design Creationist position on junk DNA [A Response to Paul McBride on Junk DNA].
On this topic (junk DNA), the IDiots make a lot of errors. One of them is to deliberately conflate "junk DNA" and "noncoding DNA" so that when they come up with evidence for function in noncoding DNA they can tout this as evidence against junk DNA. This error is so pervasive in the IDiot literature that Paul McBride even predicted that Casey Luskin would make this mistake in the book.
Today is the day that the Mars rover Curiosity landed. A remarkable American technological achievement. There have been many other technological achievements in the past century and it's wise to remember them
[reposted from August 6, 2009 (slightly modified)]
At 8:15 AM on August 6, 1945 an atomic bomb was detonated over Hiroshima, Japan. Approximately 78,000 civilians were killed on that day. Six months later the death toll had risen to about 140,000 people.
There are many arguments in favor of dropping the bomb, just as there are many arguments against it. What's clear is that in the context of 2012 we are not in a good position to judge the actions of countries that had been at war for many years.
The most important lesson of Hiroshima is that war is hell and many innocent people die. It's all very well to enter into a war with the best of intentions—as the Japanese did on December 7, 1941—but it's foolish to pretend that when you start a war there won't be any suffering. When you do that, you can really say that the victims of Hiroshima will have died in vain.
The killing and maiming of civilians is an inevitable outcome of war, no matter how hard you might try to restrict your targets to military objectives. Before going to war you need to take the consequences into account and decide whether the cost is worth it.
One of the many mistakes in Iraq was the naive assumption that it would be a clean war with few casualties and no long-term consequences for the Iraqi people. Yet today, the numbers of innocent lives lost in Iraq is comparable to the numbers lost in Hiroshima and Nagasaki. And what is the benefit for Iraq that outweighs the cost in human lives? Is it "freedom" and "democracy"?
Hiroshima was not a glorious victory. It was ugly, heartbreaking, and avoidable. War is not an end in itself, it is the failure of peace. War is not an instrument of your foreign policy—it is an admission that you don't have a foreign policy.
[The top photograph shows the mushroom cloud over Hiroshima on the morning of August 6, 1945 (Photo from Encyclopedia Britanica: Hiroshima: mushroom cloud over Hiroshima, 1945. [Photograph]. Retrieved August 7, 2007, from Encyclopædia Britannica Online.
The bottom image is taken from a Japanese postcard (Horoshima and Nagassaki 1945). It shows victims of the attack on Hiroshima.]
Dr. Greg Wells is a professor in the Faculty of Kinesiology and Physical Education at the University of Toronto. He's the author of Superbodies and he's one of the people commenting on biochemistry on Olympic broadcasts in Canada (see Muscles and the Lactic Acid Myth). It's somewhat unusual to promote yourself as "Dr. Wells" with a Ph.D. in physiology but that's his right.
Here's what he says on his blog,
Greg Wells, Ph.D. is a scientist and physiologist who specializes in health and performance in extreme conditions. Most recently, Dr. Wells was the host of the Gemini-Award winning “Superbodies” segments for Canada’s national Olympic broadcast and the on-camera sport science and sport medicine analyst for the CTV Broadcast Consortium, ABC News and ABC’s 20/20 during the 2010 Vancouver Olympics. Dr. Wells’ on-camera analysis will be a part of CTV’s 2012 Olympic broadcast in London.
Here's one of the "Superbodies" clips that are being shown on Canadian television. Most of them are quite interesting and informative even if Greg Wells does talk about lactic acid from time to time.
I was checking out his blog and found this interesting article: Olympic Science Blog: The science of exercise and ageing.
It is well established that training helps to improve pretty much every organ system in the body including the muscles, blood, brain, nervous system, skin, heart among others. Check out the book "Spark" to read about how exercise can help the brain! But new research shows that exercise can protect our genes as well!
In a recent study, researchers examined the DNA of young and old athletes and healthy control non-smokers for a total of four study groups. As expected, the researchers were able to demonstrate that the athletes had a slower resting heart rate, lower blood pressure and body mass index, and a more favorable cholesterol profile. But the surprising finding was that the rate of accumulated damage to the DNA was much less in the older athletes (average age: 51) than the older healthy non-athletes. In fact, the DNA of the older athletes was “younger” than the younger non-athlete participants. Researchers measured the ends of the chromosomes that contain our DNA. The ends of the chromosomes are called telomeres, and can be thought of as being similar to the caps on the end of your shoelaces (they’re called aglets in case you’re wondering) that prevent the laces from fraying. The scientists who discovered telomeres and how they work won the Nobel Prize in Physiology and Medicine in 2009. Telomeres control the number of times that a chromosome can divide when replicating itself as happens through our lifetime. Cells naturally grow, divide to replicate themselves and then die off. Gradually through this replication process, telomeres shorten and when they become “critically short” the cell dies. On the whole body level this may lead to ageing and a shortened lifespan. Scientists have shown that exercise activates an enzyme called telomerase that protects telomeres and chromosomes and that this has an anti-ageing effect, especially on the cardiovascular system.
World class athletes are training smarter, eating better, and recovering more effectively than ever before. The combination of these factors is helping athletes to have longer and more successful careers. So while you're watching our athletes compete in London and marveling at their performances, think about getting out and doing some exercise yourself! You'll be helping your body - right down to your DNA!
There's a lot wrong with this claim. First, it's not clear that there's a cause-and-effect relationship between telomore length and aging in spite of what some people claim. In fact, the correlation between age and telomere length is barely significant in most studies.
Second, it seems very unlikely that Lamarck was correct and it seems very unlikely that exercise has an effect on expression of the gene for telomerase.
Third, do you suppose it could be possible that when you get older and your health deteriorates for various reasons (disease, aging, accident) you tend not to continue to be an athlete? Thus, the only old athletes you measure are those that are still in good health?
Fourth, what's the evidence that telomere length has more of an effect on the cardiovascular system than on other parts of your body?
Casey Luskin has posted an email message that he recently sent to someone who inquired about Intelligent Design Creationism. It describes his view of the debate between Intelligent Design Creationists and scientists [Personal Attacks Against ID Proponents Say More About the Attackers than the Abused].
With that, please let me give you a little introduction to how this debate works. Evolutionists regularly accuse their critics of being "dishonest" and "deceiving." It's a primary tactic they use to respond to criticism and intimidate critics into silence. You're not allowed to dissent from their view and be (a) informed, and (b) honest. Many of them can't fathom the possibility that a person on the other side of the debate could be both.
Here's a fact you might ponder: Virtually every single major person who has criticized the Darwinian viewpoint has faced personal attacks on his or her character. It happens to everyone, myself included. So one of two things are true: Either (1) virtually every single critic of Darwinism (of which there are many) is "dishonest" and "deceiving," or (2) evolutionists habitually respond to scientific challenges with personal attacks.
There's more than two choices here. Let's list the possibilities. Most creationist critics of evolution are ....
- Uninformed and honest
- Uniformed and dishonest
- Informed and honest
- Informed and dishonest
There are creationist critics of evolution who fit into all categories but category #3 is the least populated. I think Michael Denton and Michael Behe qualify. They seem to have a pretty good knowledge of evolutionary biology and they seem to be sincere in their criticism
Category #4 is tricky. There are some creationist critics of evolution who should be informed but they still say some very silly things. This leads me to suspect that they are being dishonest. Jonathan Wells is a good example.
Categories #1 and #2 contain the vast majority of creationist critics of evolution. They really don't know what they're talking about but it doesn't prevent them from talking. I think most of them are honest IDiots—Casey Luskin is an example and so is Phillip Johnson. Some of them are uniformed and dishonest, that's where I would place Bill Dembski and David Berlinski.
Casey Luskin is wrong when he claims that we accuse all creationist critics of evolution of being dishonest and deceitful. Mostly we just accuse them of being uninformed but acting as if they were.1 That's probably due to stupidity and not malevolence.
I've left out a huge number of creationists, including the theistic evolutionists who fall mostly into category #3: informed, honest, but wrong.
Where do the rest of them fit in?
1. Being uninformed is perfectly okay. Most of us are uniformed about a lot of things. You aren't stupid or an idiot just because you don't know something. You become an IDiot when you don't recognize how little you know about a subject but still feel qualified to tell the experts that they are wrong.
A few months ago I posted an exam question from my course on evolution [Exam Question #1]. It was designed to test student's understanding of phylogenetic trees—a serious problem in evolutionary biology. That post generated quite a few comments.
Take a look at this figure from a 2008 issue of Nature. Do you see the problems?
If not, read David Morrison's guest post on Scientipoia: Ambiguity on Phylogenies. He patiently explains all the common misconceptions about phylogenetic trees and references all the important articles in the scientific and pedagogical literature. Once you read his article you will never look at trees the same way again.
You will also be astonished at how bad the scientific literature has become when it comes to explaining phylogenies based on these trees. You would think that evolutionary biologists would have long ago stopped thinking about directions in evolution but it's surprising how often the great chain of being creeps into modern scientific papers.
[Hat Tip: Mike the Mad Biologist]
If you've been watching the Olympics, you've heard the story many times from coaches, athletes, and even team doctors. They all tell you that the performance of endurance athletes is limited by the buildup of lactic acid in their muscles and this is what causes the pain and limits their ability to win a gold medal.
It's the acid that does it and that acid is caused by synthesis of lactic acid taking place during anaerobic exercise, or so the story goes. That happens under extreme conditions when the energy needed by working muscles exceeds the ability to produce it by normal aerobic oxidation. It all sounds so logical ... and so biochemical.
It's all a myth. Lactic acid has nothing to do with acidosis (the buildup of acid in the muscles). In fact, it's not even clear that acidosis is the problem, but let's deal with that another time.
Assuming that acid buildup in muscles is what causes the pain of the long distance runner, where does that acid comes from? In order to answer that question we need a brief lesson on acids.
The word "stasis" entered our consciousness when Gould and Eldredge promoted the concept of punctuated equilibria (see Darwin on Gradualism ). Their observations of the fossil record showed that the morphology of many species remains unchanged for millions of years. Change occurs during speciation by cladogenesis when the new daughter species fixes morphological change, thereby allowing us to recognize it as a different species.
Stasis is an important observation. Here's how Gould describes it in The Structure of Evolutionary Theory (p. 759).
Abrupt appearance may record an absence of information but stasis is data. Eldredge and I became so frustrated by the failure of may colleagues to grasp this evident point—though a quarter century of subsequent debate has finally propelled our claim to general acceptance (while much about punctuated equilibrium remains controversial)—that we ureged the incorporation of this little phrase as a mantra or motto. Say it ten times before breakfast every day for a week, and the argument will surely seep in by osmosis: "stasis is data; stasis is data ..."
Okay, we get it.
What causes stasis? There are many possible explanations. One of the most common is stabilizing selection or the idea that a species is so well-adapted to its environment that any change will be detrimental. According to this view, evolution only occurs when the environment changes.
