Here's the problem. Jonathan Wells wrote an entire book on The Myth of Junk DNA. Wells says that back in the early 1970s a substantial number of scientists—he calls them Darwinists—said that all noncoding DNA was junk.
Thursday, August 09, 2012
Still Digging: Part I
Here's the problem. Jonathan Wells wrote an entire book on The Myth of Junk DNA. Wells says that back in the early 1970s a substantial number of scientists—he calls them Darwinists—said that all noncoding DNA was junk.
"Curiosity" Driven Science
Have you been wondering about the scientific mission? The search for life is getting all the publicity but, let's face it, the chances of success are slim.
What about the other missions? Rebecca Ghent of the Dept. of Earth Sciences at the University of Toronto explains why she's interested in the data that "Curiosity" will collect [Curiosity: planetary science and the latest Mars mission].
One of the things I'm interested in is the physical characteristics of planetary regoliths - the surface layer of broken rock, dust, etc., that covers planetary surfaces. It's important to understand how this layer formed and has evolved, because it holds a record of the geological processes that have occurred on each planet. Mars has a very complex surface geological record involving the actions of wind, volcanism, impact cratering, and possibly, water; so this new information about the composition and physical characteristics of the rocks at the Curiosity landing site will provide valuable new insights into the roles of these various processes in forming Mars' surface rocks.For scientists, the best is yet to come. I hope the science journalists can keep the public focused on the real mission and the importance of the data.
Wednesday, August 08, 2012
Charles Darwin at the London 2012 Olympics
Those Brits know what's important! (They also had a picture of some other scientist, I think his name was Isaac.)
[Hat Tip: Ms. Sandwalk]
TED: Alexander Tsiaras, "It was hard not to attribute divinity to it"
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] ...
Would you pay several thousand dollars to hear this TED talk?
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?
Tuesday, August 07, 2012
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
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.
Note to David Klinghoffer, When You find Yourself in a Hole, Stop Digging
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.
Monday's Molecule #180
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.
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.
Newsgroups, Blogs, Twitter, Facebook, and Google+
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.
Monday, August 06, 2012
The Trouble with TED
TED talks are just big soundbites and soundbites are not good ways to explain complicated, and potentially revolutionary, ideas.
The NAFTA Superhighway
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.
What Does "pH" Mean?
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 ...
Intelligent Design Creationists Attempt to (re)Define Junk DNA
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.
On this Day in 1945
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.]
Sunday, August 05, 2012
Dr. Greg Wells Writes about Athletes and Telomeres
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!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.
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!
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?
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