We got married forty-four years ago today.
Ms. Sandwalk hasn't changed a bit.
Thursday, August 09, 2012
"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?
Casey Luskin Wants Us to Categorize Evolution Critics
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.There's more than two choices here. Let's list the possibilities. Most creationist critics of evolution are ....
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.
- Uninformed and honest
- Uniformed and dishonest
- Informed and honest
- Informed and dishonest
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.
Understanding Phylogenetic Trees
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]
Saturday, August 04, 2012
Muscles and the Lactic Acid Myth
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.
Friday, August 03, 2012
The Paradox of Stasis?
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.
On the Evolution of New Enzymes: Completely Different Enzymes Can Catalyze Similar Reactions
In many cases, new enzymes evolve from primitive enzymes that catalyzed similar reactions [see The Evolution of Enzymes from Promiscuous Precursors]. It's quite easy to see how this could happen by gene duplication and there are tons of examples.
But what about the first primitive enzymes themselves? Presumably, they evolved all on their own. When scientists think of this problem, they usually think in terms of evolving a specific modern enzyme. This looks like a long shot, similar to the probability that a specific person will win the lottery tomorrow. What they don't realize is that this is an unnecessarily restrictive scenario.
Advice to New Creationist Students
In many cases, students will have graduated from high school with only a rudimentary knowledge of some important topics. This isn't necessarily a bad thing as long as they realize that they still have lots to learn. It becomes a bad thing when they think they know the subject but what they know is wrong.
Universities are places that challenge your beliefs and force you to think. New students should embrace this challenge and look forward to giving up misconceptions and ideas that can't stand up to critical analysis. The last thing you want to do as a new student is to begin university with the idea that your high school ideas are always right.
Which brings us to creationism. A large number of students enter university with little or no knowledge of evolution but they are convinced that it's wrong. They will soon encounter teachers who try to convince them that evolution is true. How should students react to this challenge?
David Klinghoffer1 proposes one solution on the Intelligent Design Creationist blog Evolution News & Views. Here's his advice [A Piece of Unsolicited Advice to Students].
The practical question is nearly self-answering. You should be very, very circumspect about even hinting at your views to people who will end up giving you grades. But beyond that fairly obvious and uninteresting advice, I wanted to add that you should, in your own mind, strive to give respect to your Darwinist teachers no matter how firmly convinced you are that they are wrong.In other words, hide your views because your professor might punish you. Recognize that your professor thinks he/she knows more than you do but be confident that they're wrong. Realize that when you encounter professors in class they probably don't understand their subject even though they've devoted their lives to studying it. They might be a bit angry if you exposed them so keep you mouth shut.
If I were a professor and had a student who walked into my class intending to inform me that my fundamental views on the subject of my professional training were in error, I can well imagine thinking the kid deserved a good smack. Unfair? Yes, but true. Overturning scientific theories is not the job of an undergraduate student. A student's job is to learn what his teacher has to teach him, so that perhaps later when the student is intellectually ripened, he can lead or participate in a revolution. It's not at all that you need a PhD to hold a dissenting view, but age, thought and experience count for a lot.
At an emotional and personal level, I can sympathize with the Darwinist prof who resents his openly Darwin-doubting student. What arrogance, it must seem, to imagine that what I spent decades mastering, you a little pipsqueak think you're ready to discard half-way into the semester. Imagine yourself in your teacher's place. To him, this is about you, in your ignorance and arrogance or at best innocence, sitting in judgment of the system to which he's devoted his professional life.
Above all, resist the temptation to learn and to question your beliefs. You already know the right answer. University is not the a place for learning.
Here's my advice. It you don't want to learn then don't go to university. If your belief in creationism is really strong then don't ever take a biology class—it might turn you into an atheist and your parents will be very upset. If you need the grade, then take the class, but be prepared to fail. It takes courage to openly stand up for what you believe, especially if there might be consequences. But it's the Christian thing to do.
Most professors love it when students challenge their ideas in class. We prefer those kind of students even if they are wrong. You will never fail a course because of your ideas and beliefs as long as they don't conflict directly with scientific facts. If you believe that the Earth is 6000 years old then you will not pass a geology course or a biology, unless you lie. If you dispute the existence of junk DNA then you could get an excellent grade as long as you get your facts correct.
1. I don't think Klinghoffer has ever been to university. None of the creationist websites mention any university degrees.
Wednesday, August 01, 2012
Our genome is degenerating, but wait, someone is coming to help us
According to plant geneticist, John Sanford, the human race is degenerating rapidly. It's one of the trade secrets of biology. Every population geneticists knows that it's true.
Sanford has even written a book about this trade secret: Genetic Entropy and the Mystery of the Genome
Now if humans are degenerating at the rate of 1% or so per year then this must mean that they were perfect only a short time ago—like maybe 6000 years?
Are humans doomed just as described in scripture? Yes. Is there any hope for us? Our only hope is Christ.
Interesting. Sanford doesn't exactly say exactly what Christ will do to fix all the mutations in our genome. Will He invert better DNA repair enzymes? What's taking Him so long? And why weren't we better designed to begin with?
Sanford has even written a book about this trade secret: Genetic Entropy and the Mystery of the Genome
Now if humans are degenerating at the rate of 1% or so per year then this must mean that they were perfect only a short time ago—like maybe 6000 years?
Are humans doomed just as described in scripture? Yes. Is there any hope for us? Our only hope is Christ.
Interesting. Sanford doesn't exactly say exactly what Christ will do to fix all the mutations in our genome. Will He invert better DNA repair enzymes? What's taking Him so long? And why weren't we better designed to begin with?
[Hat Tip: Uncommon Descent]
Carnival of Evolution #50
Welcome to the 50th edition of the Carnival of Evolution! In keeping with the name of the blog, this edition will have an educational theme to it. The posts are categorised into modules. Each module has an introduction by me about why it’s important to learn about it, and each post has a short blurb by me on the post’s content and, if appropriate, personal comments. I include a further reading list with links to relevant books and review papers for further discussion/background information. Most of these papers are behind draconian paywalls. If you don’t have institutional access, my e-mail can be found here. Just saying.I've got seven posts from Sandwalk on the list. That's a record for me and it means one of two things: (a) my posts are getting more interesting, or (b) they were hard up for posts this month.
The next Carnival of Evolution (August) will be hosted by The Stochastic Scientist. If you want to volunteer to host others, contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before. 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.
Why Should an Atheist Care About the Problem of Evil?
There are thousands of gods that I don't believe in. Some of them have imaginary reputations of cruelty, some of them are supposed to be kind, and some of them are indifferent. It doesn't matter to me because the one thing they all have in common is that they don't exist.
I'm told that some people believe in gods who are supposed to be kind. Those people have trouble understanding why the world is evil. It's a problem that has spawned an entire discipline called theodicy. Bully for them. It's their problem, not mine. I don't accept their premise.
For reasons that seem incomprehensible to me, there are some atheists who really like to talk about the problem of evil as though it were a real problem. Jason Rosenhouse is one of them. You can read his latest at: The Only Reasonable Reply to the Problem of Evil. Jerry Coyne is another. See his post from yesterday at: More Sophisticated Theology: The world’s worst theodicy.
They Like Me, They Really Like Me!
Just think. Imagine you're one of those undecided fence-sitters on the Darwin question that he thinks he's appealing to. Or say you're a journalist, reflexively pro-Darwin but one who's never had an occasion to follow the controversy in the past. Now something's come up in the news that touches on evolution and you figure you'll sample the arguments on both sides with a view to writing on it.Happy to oblige.
You stumble upon the blog, named in honor of Charles Darwin's famous "Sandwalk," of a University of Toronto biochemist and man of mature years who writes this way, over and over and over. He will, for example, reproduce a photo of an Internet Darwin critic with the words "I'm an IDiot" superimposed. This same biochemistry professor and Darwin advocate writes blog posts trying to defend and recommend this approach, including his favorite term "IDiot," to others. Are you impressed? That's a self-answering question.
Of course it would be different if Moran were not a guy who teaches in a relevant scientific field at a university you've heard of. If he were just another one of those pseudonyms that populate comment boxes around the Internet, and who dish out their own vicious/viscous stuff, no one would care. Much as it's distasteful to read Moran's blog (as I very rarely do), there's reason to be grateful for its existence.
Now watch, he's going to trawl the Internet for a picture of me and write "I'm an IDiot" on it and post that.
If I were purely strategic, I would say: Give us more, Larry Moran! Pour it on. Please!
Tuesday, July 31, 2012
Carbon Dioxide Fixation in the Dark Ocean
These species are called "autotrophs'" The most familiar are the plants. As most of you know, plants can grow quite successfully in a glass of water (with minerals). Animals are the most obvious example of "heterotrophs," species that need to be supplied with complex organic molecules in order to survive. We can't survive on water alone. We need to get sugars and a host of other compounds from eating other (mostly dead) species.
Oscar Miller (1925 - 2012)
Those of us so fortunate as to have worked under his guidance learned how to think freely, yet rigorously, and how to dream big and gamble on new adventures. We learned from Oscar how to free ourselves from convention, yet abide by the principles of science as crafted by its most honorable pillars. We remember two pieces of advice given by Oscar: “Don't believe everything you read in the scientific literature” and “There are a thousand Ph.D. thesis projects in a mound of dung.” The latter brings to mind the famous phrase of Vannevar Bush that science is an “endless frontier.” Oscar Miller was comfortable on the frontier of the unknown; he taught us that it is only on the frontier that discoveries of significance can be made. Our community of science will miss Oscar, as will all his dear friends and family. A good man has passed.Most of you have never heard of Oscar Miller but you've seen his work. He invented a technique for looking at genes in the electron microscope. The beauty of his technique, called "chromatin spreads" is that it shows genes in action. They are captured in the act of being transcribed and you can see the RNA being produced.
The initial transcripts are quite short but as the transcription complexes progress along the gene they get longer and longer giving rise to the Christmas tree structure. You can learn a lot from looking at these fantastic pictures. Notice that there are multiple ribosomal RNA genes arranged in tandom along the genome with relatively short spacers between them. These photos were taken before cloning and sequencing were invented so it was our among our first clues about gene organization in eukaryotes.
There's not much actual data from the 1960s that's still shown in modern textbooks. Remember Oscar Miller the next time you see his work.
McKnight, S., Beyer, A., and Gall, J. (2012) Retrospective. Oscar Miller (1925-2012). Science 335:1457. [DOI: 10.1126/science.1220681
Monday, July 30, 2012
Monday's Molecule #179
What is this molecule (IUBMB name) and why is it important?
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 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 2-carboxy-3-ketoarabinitol 1,5-bisphosphate, an intermediate in the reaction catalyzed by rubisco (ribulose 1,5-bisphosphate carbozylase-oxygenase). This is the main enzyme responsible for carbon dioxide fixation in plants and one of the most enzymes on the planet.
This week's winners are Bill Chaney and 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
Stephen Fry and the Two Cultures Problem (Brits vs Americans)
Here it is again because it's relevant to our discussion about IDiots. It's from: Getting Overheated (Nov. 19, 2007).
We must begin with a few round truths about myself: when I get into a debate I can get very, very hot under the collar, very impassioned, and I dare say, very maddening, for once the light of battle is in my eye I find it almost impossible to let go and calm down. I like to think I’m never vituperative or too ad hominem but I do know that I fall on ideas as hungry wolves fall on strayed lambs and the result isn’t always pretty. This is especially dangerous in America. I was warned many, many years ago by the great Jonathan Lynn, co-creator of Yes Minister and director of the comic masterpiece My Cousin Vinnie, that Americans are not raised in a tradition of debate and that the adversarial ferocity common around a dinner table in Britain is more or less unheard of in America. When Jonathan first went to live in LA he couldn’t understand the terrible silences that would fall when he trashed an statement he disagreed with and said something like “yes, but that’s just arrant nonsense, isn’t it? It doesn’t make sense. It’s self-contradictory.” To a Briton pointing out that something is nonsense, rubbish, tosh or logically impossible in its own terms is not an attack on the person saying it – it’s often no more than a salvo in what one hopes might become an enjoyable intellectual tussle. Jonathan soon found that most Americans responded with offence, hurt or anger to this order of cut and thrust. Yes, one hesitates ever to make generalizations, but let’s be honest the cultures are different, if they weren’t how much poorer the world would be and Americans really don’t seem to be very good at or very used to the idea of a good no-holds barred verbal scrap. I’m not talking about inter-family ‘discussions’ here, I don’t doubt that within American families and amongst close friends, all kinds of liveliness and hoo-hah is possible, I’m talking about what for good or ill one might as well call dinner-party conversation. Disagreement and energetic debate appears to leave a loud smell in the air.
There Are Many Ways to Improve High School Education: Dumbing It Down Is NOT One of Them
If Andrew Hacker has his way, people who can't pass a simple math course will never have to apologize again. He proposes, in the New York Times, no less, to eliminate algebra from high school [Is Algebra Necessary?]. (Andrew Hacker is a former professor of political science.)
Darwinists Don't Believe in Junk DNA
It caught my attention because my name was mentioned. Apparently some "ID opponent" read my take-down of Jonathan Wells' book The Myth of Junk DNA. This prompted the following response from "news" (lawyer, Barry Arrington).
"The Myth of Junk DNA" is actually quite easy to read. We’ve excerpted a number of passages here at UD. The interesting part is that Darwinists thought that the presence of huge amounts of junk DNA was evidence for their position.If Barry Arrington had bothered to read my review of Wells' book he would know that this is a lie. You can read the entire series of posts at: The Myth of Junk DNA by Jonathan Wells but I want to draw your attention specifically to my comments on the history of the controversy: Junk & Jonathan: Part 1—Getting the History Correct] [Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?].
Sunday, July 29, 2012
Ophelia, Daniel, I Respectfully Disagree
No insulting people. This means not calling them abusive names or making insulting insinuations about them which according to my judgment unnecessarily demean them as a person or which I take to be intended to demean them as a person. You may charge that people’s ideas are false, harmful, irrationally derived, etc. You may substantiate charges that someone’s personal behavior deserves moral disrepute where that’s relevant. You may critique an individual’s standards of evidence or question their commitment to reason over faith. But when you do things like this, stick to substantiatable charges. Use words which clearly specify what specific thing makes a person or institution’s ideas, beliefs, behaviors, attitudes, etc. worthy of criticism. Abusive names (like “stupid”, “moron”, “asshole”, “jerk”, “douchebag”, “idiot”, “motherfucker”, “dick”, “cunt”, “nigger”, “Feminazi”, “shitbag”, “mental midget”, “twat”, “fuckwad”, “retard”, “homo”, “fag”, “tranny”, “bitch”, “nutcase”, “crazy”, etc.) are emotional expressions meant solely to hurt other people. They are social equivalents of physical assaults.I know where they're coming from. They're talking mostly about racist and sexist comments since that's their main concern on Freethought Blogs, for now.
For the record, I do not condone those kind of insults. Nor do I condone accusing someone of racism or sexism without very good evidence.
On the other hand, I frequently use insulting words to describe stupid people. The most obvious example is my use of "IDiot" as a shorthand for Intelligent Design Creationist. A commenter on Daniel Fincke's blog suggested that words like "stupid" were okay since they aren't homophobic, sexist, or racist. Here's how Fincke responded ...
“Stupid” is just not a word that smart people have ruining their self-esteem from the time they’re little kids.When I use the word "IDiot" I fully intend to bash the IDiots for their stupid ideas. Why? Because their ideas are stupid and they really are idiots.
And even yet, it is a false and belittling word that is counterproductive to constructive discourse. Calling someone stupid tempts them to either slink away in shame or to fight back with equal emotional abuse.
There are perfectly good words for telling someone that a specific idea is no good. False, empirically refuted, fallacious, absurd, illogical, unsupported by evidence, irrational, rationally indefensible, superstitious, biased. All these might work and many more. There’s no need to then personalize it by calling the person stupid or the idea stupid, which has the implication of bashing the person for thinking it.
Here's where Daniel gets it wrong. I don't expect to convince the IDiots of the error of their ways any more than they intend to convince scientists by using insulting terms like "Darwinist," "materialist," and "stupid." There's no such thing as "constructive discourse" with creationists.
The general public needs to hear what passionate scientists really think of these IDiots. The best way to do that is to fight fire with fire. The idea is to plant in the public's mind the notion that these creationists are crazies and kooks, not respectable scientists with a different, but scientifically valid, opinion. We tried treating them politely for several decades and what did it get us? It got us leaders and politicians in many countries who think it's perfectly respectable to believe that evolution is false.
We were up against people like Jerry Falwell, Rush Limbaugh, and Michele Bauchmann but we were fighting with one hand tied behind our back. That's no way to win a fight like this.
The good news for the more polite proponents of rationalism, like Ophelia Benson and Daniel Fincke, is that they can be the "good cops."
What's Wrong with this List?
Those thoughts are short-lived. It never takes the IDiots more than a few hours to disabuse me of any such sympathies.
Yesterday, for example, Sal Cordova (scordova) posted one of the most stupid things I've seen in a long, long, time. He was bragging on Uncommom Descent about a paper by Todd Wood that
But he couldn't leave it at that. Look what he said next [Creationist Paper Published in Peer-Reviewed Biology Journal, UD Author Cited — Origins 2012 Conference] ...
Also congratulations to our very own Uncommon Descent author johnnyb (Jonathan Bartlett) for his work being mentioned in Wood’s paper. To my knowledge, the current tally of Uncommon Descent authors and commenters that have been published or mentioned in scientific journals: William Dembski, Michael Behe, Nick Matzke, Rob Sheldon, Caroline Crocker, Winston Ewert, Paul Nelson, Cornelius Hunter, Granville Sewell, John A. Davison, Allen MacNeill, Andrea Bottaro, Abbie Smith, Peter Olofsson, Albert Voie, Andras Pellionisz, Albert De Roos, Walter ReMine, Paul Giem, Jonathan Sarfati, Arthur Hunt, Steve Matheson, Larry Moran, johnnyb, Eric Anderson, Casey Luskin, and yours truly scordova. [If I missed anyone, please chime in.]IDiots! There's no other word to describe them.
Friday, July 27, 2012
What Do Scientists Know about Ethics?
As a first step, geneticists need to step back from the current curriculum and decide what 21st century students really need to know about genes and inheritance. These decisions should be based on how students will use what they learn, and not on what we as geneticists value.She proposes that modern genetics courses should concentrate on subjects that really interest students. Subjects like ...
Is genetic testing a wise thing to do? Is it a sound financial investment? Should I have full access to my genetic information? Should my insurer and my employer? Should athletes be tested for genetic modifications (“gene doping”)? Is it ethical to DNA-fingerprint all convicted criminals? All suspects? Did my genes make me gay? Are genetically modified foods safe? Are cloned animals ethical? How different are human races, and how different are we all from chimpanzees and gorillas?I explained in an earlier posting why I think this is wrong: Questions for Genetics Students. My main concern was that we might be sacrificing fundamental concepts and principles of genetics (i.e. science) in an attempt to appeal to students.
Rosie's goals sound like noble goals but is it even realistic to address these issues in a genetics course? That's the question that Heather Zeiger asks in her post on Genetics Class 2.0.
Many of these questions are ones bioethicists have been contending with for years. Bioethics is a multi-disciplinary field that is usually occupied by philosophers and healthcare professionals, but in the last twenty years it has seen an influx of lawyers, scientists, and people from many other disciplines.Now, I rarely agree with anything posted on The Best Schools but this is a legitimate concern.
Redfield suggests that it is the role of the scientist to address ethical questions. However, something that Redfield does not state in her paper, is that scientists are rarely trained in anything that would be helpful in assessing ethical issues, such as moral philosophy or rhetoric, and most programs do not include history and philosophy of science.
My position is that philosophers and healthcare professionals have been spectacularly unsuccessful at clarifying bioethical questions. I cringe just about every time I see a "professional" bioethicist on television. Most of them can't separate science from ethics and most of them are more concerned about appeasing religion than getting to the bottom of a difficult issue.
Scientists often make much more sense but that doesn't mean that all scientists are good at dealing with ethical issues. I teach a course that deals with ethical issues (cloning, reproductive technology, immunization) and I find that it's an excellent way to get students to think critically. However, I've learned a lot from my colleagues about ethics and philosophy over the years and I don't think I would be very effective without this background1.
I doubt very much that the average genetics teacher or TA can really be effective at handling ethical debates in their classrooms. I don't think you should build a course around such issues no matter how much the students want it.
My friend, Rob Allore, taught with me for several years. He's a scientist and a Jesuit priest. This year I'll be teaching with another friend, Chris DiCarlo, a philosopher and author of How to Become a Really Good Pain in the Ass: A Critical Thinker's Guide to Asking the Right Questions.
Redfield, R. (2012) "Why Do We Have to Learn This Stuff?"—A New Genetics for 21st Century Students. PLoS Biol 10(7): e1001356. [doi:10.1371/journal.pbio.1001356]
NASA Confusion About the Origin of Life: Part II
We don't know how life began but one of the more fanciful hypotheses is that it began in a primordial soup of organic molecules supplied by meteors, comets, and violent lightening storms. The idea is that the ocean was full of glucose, amino acids, and nucleotides. Glucose and similar carbohydrates supplied the energy for life. Amino acids spontaneously came together to form proteins. Nucleic acids arose by stringing together pre-existing nucleotides or nucleosides.
In the most extreme version, the ocean itself was the primordial soup and concentrations of organic molecules were sufficient to drive the formation of life. A simple back-of-the envelope calculation indicates that the concentration of typical amino acids would have been about 0.1 nM (10-10 M) [Can watery asteroids explain why life is 'left-handed'?]. This is an unlikely scenario [More Prebiotic Soup Nonsense]. You won't get spontaneous formation of polymers in water at that concentration.
High School Students Find LUCA!
Biology New Net posted a press release today from the American Institute of Physics: Researchers dig through the gene bank to uncover the roots of the evolutionary tree. It advertises the work of William Duax and his colleagues, including some high school students who work in his lab on Fridays.
Ever since Darwin first published The Origin of the Species, scientists have been striving to identify a last universal common ancestor of all living species. Paleontological, biochemical, and genomic studies have produced conflicting versions of the evolutionary tree. Now a team of researchers, led by a professor at the State University of New York at Buffalo and including area high school students, has developed a novel method to search the vast archives of known gene sequences to identify and compare similar proteins across the many kingdoms of life. Using the comparisons to quantify the evolutionary closeness of different species, the researchers have identified Actinobacteria, a group of single membrane bacteria that include common soil and water life forms, as the base of the evolutionary tree. They will present their findings at the annual meeting of the American Crystallographic Association (ACA), held July 28 – Aug. 1 in Boston, Mass.
Thursday, July 26, 2012
The Evolution of Enzymes from Promiscuous Precursors
There are two principle ways to evolve related modern enzymes with specific activities. The first way postulates an ancestral enzyme that catalyzes a specific reaction (e.g. A1 → B1). Following a gene duplication event, one of the copies evolves an enzyme that catalyzes a completely different (but chemically related) reaction: A2 → B2.
Most people think that this is by far the most common pathway. That's because they are used to thinking that enzymes are highly specific—that's what's emphasized in most biochemistry courses. They think that it should be possible to reverse engineer the evolutionary pathway on the right-hand branch and thus transform one enzyme to another.
Wednesday, July 25, 2012
Winners of the Google Science Technology Fair
An expectant crowd gathered last night inside an airplane hangar at a flight school in Palo Alto, California to hear the winners of the second annual Google Science Fair. The grand prize went to Brittany Wenger, 17, of Sarasota, Florida, who wrote a computer program to help doctors diagnose breast cancer less invasively. Jonah Kohn, 14, of San Diego, Calif. won his age category for creating a device that converts sound into tactile vibration to improve the music-listening experience for the hearing impaired; and a trio from Spain won the 15 to 16 age category for documenting the hazardous and non-hazardous organisms found in water from different parts of their country.Anna Kuchment works for Scientific American and posts on a blog called Budding Scientist: Everything you always wanted to know about raising science-literate kids.
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