Gobind Khorana (1922 - 2011)

 

Har Gobind (Hargobind) Khorana was a biochemist specializing in polynucleotide synthesis. He was awarded the Nobel Prize in Physiology or Medicine in 1968 along with Robert Holley and Marshall Nirenberg "for their interpretation of the genetic code and its function in protein synthesis."

Khorana was born in Raipur, Pujab, British India (now Pakistan) in 1922. After graduating from Punjab University in Lahore (British India) he went to the University of Liverpool (United Kingdom) to complete a Ph.D. Following several post-docs in Zurich (Switzerland) and Cambridge (UK) he accepted a job at the British Columbia Research Council, in Vancouver, Canada in 1952.

According to his colleague, Uttam Rajbhandary,

Gobind was so excited that he was going to start a lab of his own. He looked at the map of Canada, saw where Vancouver was for the first time, and off he went ...

In 1960 he moved to the University of Wisconsin, Madison (United States) and in 1970 he moved again, this time to the Massachusetts Institute of Technology in Boston (United States). Gobind Khorana died in Concord, Massachusetts on Wednesday, November 9, 2011.

Religion in Canada

There's news of an Ipsos Reid poll from September 2011 [Canadians Split On Whether Religion Does More Harm in the World than Good]. It surveyed Canadians about religion. Only 16% of Canadians attend church every week and about 30% of Canadian say they don't believe in God. Only 53% of Canadians say they believe in God. This is good news for those of us who think the trend is in the right direction. It's bad news for those who think that the religious views of society can't be changed.

Here's a news story from Global news on September 12, 2011 [Canadians divided on whether religion does more harm than good: poll]. Thanks to Canadian Atheist for bringing this to my attention.

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Whole Life Expo 2011

 

The 25th Whole Life Expo takes place next weekend in Toronto (Ontario, Canada) at the Metro Toronto Convention Centre [Whole Life Expo 2011].

Skeptics are definitely not welcome as some of them found out last year [Whole Life Expo 2010: A Personal Account]. This year will be different. A small army of skeptics is set to infiltrate the show [Getting Ready for the Whole Life Expo – Toronto, November 25-27].

They're in for a treat. Here are some of the talks you can attend if you have the stomach for it.

Charlotte Szivak, Animal Communicator (Hamilton, Ont.)

Be amazed by some of the hilarious adventures Charlotte has had while talking with animals. Explore through meditation techniques how the language of light will infuse a deeper connection and understanding with your companions. Together, elevate your healing abilities, overcome communication breakdown, and open your heart to infinite possibilities. Charlotte is the producer/host of the radio show “Goddess Alchemy: Divine Magic,” and a spokesperson for the HBSPCA. [I once tried talking to a cat. -LAM]

Dr. Cass Ingram, D.O (Chicago, Ill.)

In the northern forests of Canada are found powerful medicines of nature which everyone can use for better health. Research shows that wild chaga mushroom helps reverse arthritis, diabetes, heart disease, cancer, prostate disorders, and more. Wild green extracts are ideal for cleansing the liver, gallbladder and skin. Birch bark reduces obesity and high cholesterol. Wild berries help reverse circulatory disorders, eye diseases, varicose veins, and cancer. Find out how to use wild forest cures to stay healthy forever. [Eat a canoe and live forever. -LAM]

Liala Epstein

Explore the functioning of the human body as a transmitter and receiver of electromagnetic frequencies. Hear why EMF protection and structured water, free of negative energy patterns (from toxins), are vital. Learn about health benefits of water purification and EMF protection that functions using only natural laws. Sample structured water that is rich in bio-photonic energy, endorsed by scientists Dr. Fritz Albert Popp and Dr. Konstantin Korotkov. Sample an Earthcalm Nova Scalar Resonator and feel the difference as you ground to frequencies of the planet’s Schumman Resonance and your body dissipates out stress-inducing electrical currents. [So this is what they mean when they say you're "in tune" with the Earth? -LAM]

Lilly Rahmann (Deux-Montagnes, Quebec)

In this lecture you will learn how to reduce stress using crystals. How to increase your energy flow. How balancing your chakras and aura with crystals can help you keep healthy and happy. Lilly Rahmann is author of “Crystals Healing” and has been teaching and lecturing on crystal healing for many years. She is very passionate about her work on self healing. [Putting salt on my poutine does wonders for my aura. -LAM]

Eminé Piyalé-Sheard (Montreal, Quebec)

Water ionizers have been used in Asia for over 30 years and are certified in Japan and South Korea as an approved medical device. Ionizers produce both alkaline and acidic water that provide numerous health benefits. Drinking alkaline ionized water daily improves hydration, restores pH balance and slows down the aging of our cells. Find out how the quality and quantity of water we drink can have an impact on our overall health and wellness. [This could put homeopathy out of business. -LAM]

Janet Matthews and Alana Hewitt

This talk addresses an awareness of health and healing that is of utmost importance if you are seeking a vibrant and meaningful life. The speakers will discuss healing in its most subtle dimension, as it applies to all levels of your being: physical, emotional, mental, and spiritual. They will show you how to have unique and profoundly personal experiences of divine presence and guidance through the practice of simple visualization exercises. These techniques are for people of all faiths, and can be used by anyone seeking a more conscious awareness of the healing potential that comes from recognizing the role of divine spirit in their lives.[I guess you're screwed if you're an atheist. -LAM]

Michael Stern, B.A.Biology

Since 1998, when the Nobel Prize for Medicine was awarded for Redox Signalling, it has become a hot research topic worldwide, second only to stem cell research. With it is realized a new category of cellular communications that promises to make major improvements in health and wellness. A patented product, ASEA, has succeeded in stablizing the body’s native produced Redox Signalling molecules, which are able to replenish those criticial molecules in your cells to restore youthful healing. [Nobel Prize in Medicine 1998 -LAM]

Dr. Andrew Michrowski, PhD (Ottawa, Ont)

How do you cope with the invasion of wireless technologies when dealing with officials, suppliers, school boards, and even your neighbours when confronted with trespasses against you, and the lack of choice. New international government and judiciary interventionss are now on your side, and you can use their support to improve your health. [Do they know that there's WiFi at the Convention Centre? -LAM]

Valery Uvarov (St. Petersburg, Russia)

WHY RUSSIANS ARE BUILDING A PYRAMIDAL COMPLEX IN SIBERIA: In the last 15 years there has been an organized effort in Russia to study ancient technologies from around the globe, especially in Egypt. Studies conducted by top scientists from Russian academia, headed by Mr. Uvarov have made amazing findings. Come and find out why pyramids are being built, how the energy of pyramids and Wands of Horus influence the immune system; how pyramids are antennas and amplifiers of “life force” – energy bands that are beneficial for humans; how the pyramid’s energy field corrects/purifies all materials nearby, especially water; and what will happen in 2012. Mr. Uvarov has published two books about pyramids and the Wands of Horus. [I remember the Wands of Horus ... it's from Zork, right? -LAM]

Paul MacDonald

Would you like to be in perfect balance, physically, mentally, and spiritually? Join Paul MacDonald, preeminent Biontologist in North America, and learn how that balance can be achieved. Every living cell in the body emits biophotonic light. Paul will describe how chaotic light impulses indicate disturbance in the body, and how that light can be neutralized to successfully treat depression, heart disease, migraines, and other symptoms that incoherent light presents. You will also learn how to become a biontologist and set up your own practice. [Does your biophotonic light keep your partner awake at night? -LAM]

I'm tempted to say that you "just can't make this stuff up" but then I realized that's exactly what these quacks are doing! I can see why they they're afraid of skeptics. I wonder if any genuine newspaper reporters will cover this?

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Monday's Molecule #150

 

Today's molecule has a common name but this time I'll need the complete IUPAC name. There is considerable controversy over whether this molecule actually exists in most cells.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

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.) Every undergraduate who posts a correct answer will have their names entered in a Christmas draw. The winner gets a free autographed copy of my book! (One entry per week. If you post a correct answer every week you will have ten chances to win.)

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.

UPDATE: This one was more difficult than I expected. The molecule is oxalosuccinate or 1-oxopropane-1,2,3-tricarboxylate. I posted all the answers that used this IUPAC name or 1-oxopropane-1,2,3-tricarboxylic acid. This is clearly not the acid form of the molecule but that didn't make you ineligible to win the prize.

Oxalosuccinate is thought to be a transient intermediate in the reaction catalyzed by isocitrate dehydrogenase (citric acid cycle) but this is only a hypothesis—the intermediate has never been detected.

The molecule contains a chiral carbon atom (C3 of oxalosuccinate and C2 of oxopropane). I was expecting all answers to specifically identify the [2S] or [3S] stereoisomer, especially since we had recently discussed stereoisomers on this blog. "Cyau" was the only one to get this correct (on her second try) but she is not eligible because she didn't identify herself.

RaulFelix was the first person to name the molecule as 1-oxopropane-1,2,3-tricarboxylate and she would be the winner if I knew her real name. That means Vipulan Vigneswaran is this week's winner, beating out Joseph Somody by less that one minute.

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

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Don't Muzzle Our Doctrors

 
Last summer, the Ontario College of Physicians and Surgeons published a draft proposal on Non-Allopathic (Non-Conventional) Therapies in Medical Practice. It was horrible. As I noted at the time, "The document is flawed from the beginning because it gives credence and respectability to "alternative medicine," otherwise known as non-evidence based medicine or quackery" [Non-Allopathic (Non-Conventional) Therapies in Medical Practice].

Many groups took notice of the draft policy and criticized the Ontario College of Physicians Surgeons for their gutless response to a serious crisis in health. One of those groups was the Committee for the Advancement of Scientific Skepticism, a committee of Canada's Centre for Inquiry [Media Advisory: Ontario Doctors Given the Green Light to Promote Quackery]. The members of CASS worked hard to lobby for changes and they co-ordinated their activities with several other groups that are opposed to the weak-kneed position of the College.¹ The College conducted a survey of its members and discovered that 78% of them opposed the draft policy. About one third of the people who filled out the survey were directed to the site by CASS or its allies [Skeptical Activism Sends a Message to CPSO. Very impressive.

Those behind-the-scenes activities had an impact as more and more people voiced their criticism on the FeedBack Site.

All this lobbying convinced the Toronto Star newspaper that something serious was afoot and yesterday, Sunday Nov. 20, 2011, the newspaper published an editorial that sides with science [Don’t muzzle our doctors]. The paper deserves praise for getting it right and giving us hope that science will win in the end..

Patients walk into allergist Dr. David Fischer’s office almost every day expressing interest in trying “natural” therapies. These range from harmless diet changes to the truly bizarre, like applied kinesiology, says the Barrie physician. It’s an experience shared by other doctors. “We’re on the front line of dealing with ideas for which there is often a dearth of scientific evidence.”

Alternative medicine is booming even without much proof it works. A record 20,000 people are expected at Toronto’s Whole Life Expo at the downtown convention centre next weekend. Three-quarters of Canadians regularly use some form of natural health product, opening their wallets to spend at least $4.3 billion yearly. And the herbs and homeopathic tinctures they buy are just one facet of unconventional medicine — a thriving sector encompassing everything from acupuncture to zone therapy (supposedly stimulating the body’s organs through hand or foot massage).

Ontario’s College of Physicians and Surgeons is bending to the trend with a new policy inhibiting doctors’ criticism of unconventional therapies. In doing so it risks encouraging even broader use of dubious and potentially harmful treatments.

Make no mistake — blind trust in alternative cures can be dangerous. An unknown number of Canadians are opting out of science-based medicine to treat even deadly conditions, like cancer, with unproven “natural” approaches.

....

The field of allergy medicine, Fischer’s specialty, is especially prone to alternative approaches. Natural practitioners using applied kinesiology, for example, check for allergy by placing a food item in a patient’s mouth or in their hand. Then they pull down on the person’s free arm to assess its strength. If this “muscle testing” shows notable weakness, the patient is deemed to be allergic.

There is no good evidence that this method works, and no sound scientific reason why it should. Yet patients come in with an interest in that, says Fischer. “I’d like to be able to tell them it’s quackery.”

He may not be in a position to say so much longer under a new policy proposed by the college of physicians and surgeons. It states that doctors are obliged to give a patient their best professional opinion on an alternative treatment goal or decision, but physicians “must refrain from expressing personal, non-clinical judgments.”

....

There’s no denying alternative medicine is immensely popular. Patients are more independent than ever before, often researching their illness and trusting their own solutions. And a host of unconventional “natural” healers has risen capitalizing on that trust — offering unproven therapies with little validity and which, in some cases, are a menace.

The college shouldn’t seek to accommodate that trend or retreat to a neutral corner. Rather it should leave doctors free to punch hard against those peddling dubious cures and to challenge people’s comforting, but irrational, beliefs. Science-based medicine serves patients best. If doctors can’t vigorously defend it, who will?

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1. I'm a member of CASS but I had nothing to do with this campaign.

Blogiversary

 
I completely forgot about Sandwalk's blogiversary. It's a biggie!

My first post was on Nov. 4, 2006 [Welcome to my Sandwalk] so this makes Sandwalk five years old!

It was PZ Myers who got me started.¹ We were in England visiting Down House when he convinced me that starting a blog was better than posting messages on talk.origins. He took the picture of me on the upper-left-hand corner of this page Can you guess where we were? He also took the one in this post.

3811 posts later I'm still not sure whether to thank PZ or curse him.

On last year's blogiversary, none of the top five postings on Sandwalk were about science. This has now changed. As of today, four of the top five all-time postings are science postings.

The Genetics of Eye Color
Smart Crocodile Eaters?
Regulating Glycogen Metabolism
A Challenge to Theists and their Accommodationist Supporters
Carnival of Evolution #38

Sandwalk currently averages around 180,000 page views per month. This puts it at the low end of the middle group of science blogs. (Ranked number 36 this month.)

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1. He has a blog as well.

Medieval Teaching Methods

 
John Hawks posts a reference to an article in MacLeans magazine about undergraduate teaching. John supports a style of teaching that emphasizes "hands-on" experience over learning about theory [The Problem with Stem, A reason for practical genomic education].

Like many critics of education, John thinks that traditional lectures are old-fashioned and inefficient. I tend to agree with him on this point—we can do a much better job of education in a classroom setting. However, I part company with many critics who go overboard in rejecting traditional lecture formats as a way of communicating information. For example, I note that this style is readily accepted in many other contexts. John Hawks gave a talk last week n Madison that I would love to have attended [I would so go to this if I were in Madison]. There are all kinds of other public lectures that people pay good money to attend—we filled an auditorium when PZ Myers acme to town. Traditional lectures are very common at scientific meetings because nobody has figured out a better way to hear what an expert has to say.

The death of lectures has been greatly exaggerated.

Better Biochemistry: The Problem with Glycerol Phosphate and Citrate and What This Has to Do with Archaebacterial Membranes

Now that you've learned about Fischer Projections [Better Biochemistry: Fischer Projections] you're deady to tackle a more challenging problem. But first some background.

Glycerol phosphate is a major precursor in the synthesis of triacylglycerides and related compounds. These are the major lipid components of membranes. Here's a simplified pathway to show the importance of the glycerol backbone. ("R" stands for long-chain fatty acids.) I've deliberately avoided naming the glycerol-phosphate precursor because it requires a bit of thought.

Thinking Like a Theist

 

This figure is making the rounds with the title "When a theist starts a debate with an atheist." It's funny because it mocks the average theist who thinks that they have an overwhelming case for the existence of God. For some strange reason, theists don't think it's funny.

Brandon appears to be one of those theists. He's a Roman Catholic philosopher with a blog called Siris and he recently posted a rejoinder called When Atheists Try to Be Clever... .

Brandon noticed that the board has no kings. (Aren't those philosophers clever?) It also doesn't have any bishops but he doesn't mention that. In spite of the fact that the board is missing a few pieces, Brandon thinks that the standard rules of chess should apply ...

... it nonetheless ends up backfiring because ... it is logically and mathematically impossible, given any standard rules of chess, for either side to win this game. The rules of chess require an automatic draw if there is an impossibility of checkmate -- once it is established that no legal series of moves can reach checkmate, the game is over and both sides tie. A game with no kings has no possible checkmate, and so is an immediate draw. In trying to depict with a chessboard how much better their arguments are, a task in which they had perfect freedom to choose any possible chess set-up, they still managed to give themselves an unwinnable board. In other words, the atheist player doesn't know what he's getting into: the board is rigged so that the theist, with nothing but pawns, can guarantee a draw no matter how many queens the atheist has. Diabolically clever theist, getting atheist hopes up while making it impossible for them to win! That's on standard rules. And, of course, if the rules are supposed to be nonstandard, it is impossible to know what this board even means.

Looking at the board, you can can imagine that the contest will end when all the pawns have been wiped out and there are 15 queens left. At this point the theists will declare a draw because an imaginary, nonexistent, king has not been captured. Yep, that certainly sounds like an argument from a theist.

It also—for some strange reason— reminds me of The Black Knight. ("Right, we'll call it a draw.")

John Wilkins, who is also a philosopher, thought Brandon's "rejoinder" was clever enough to deserve a mention on his own blog [Agnostic versus atheist chess]. I guess you don't have to be a theist to believe in imaginary, nonexistent, chess pieces.

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Redundancy Explains Junk DNA, Redundancy Explains Junk DNA

 
From GilDogen, in a comment on: Jonathan Wells on Darwinism, Science, and Junk DNA.

Moran is particularly vicious concerning challenges presented by ID proponents. He’s a disturbed individual. (That’s not a personal attack, just an empirical observation, and I hope he gets over it somehow.)

Another factor in biology that should be considered is redundancy and backup systems, which are standard fare in human engineering. Redundant/backup systems ensure survival if one or more of the primary systems is disabled or compromised. In aviation, fly-by-wire systems (in which the pilot does not directly influence the aircraft’s control surfaces, but provides input to computer systems that execute the pilot’s commands) provide three or more redundant computers that process the pilot’s commands and vote about the outcome. If one computer disagrees, the majority wins.

I'll try really, really, hard not to be vicious or mocking in response to the redundancy argument. Instead, I'll just pose a few questions that occur to me.

1. Almost all IDiots intelligent design proponents accept microevolution. Why don't the unused redundant systems accumulate mutations and become junk?
2. Why would a truly intelligent, omnipotent, designer need to create redundant back-up systems?
3. When we look at genome sequences we don't see any evidence of redundant back-up systems for DNA replication, the citric acid cycle, or lipid metabolism (or anything else). Why?
4. Why are there so many genetic diseases if everything is backed-up?
5. I can see why I need two kidneys, but how come I've only got one heart?
6. Why didn't Wells mention redundancy in his book?
7. Where is the theory of redundancy published?

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When a theist starts a debate with an atheist ...

 
Also applies when a creationist starts a debate with a scientist ....

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[Photo Credit: imgur]
[Hat Tip: Friendly Atheist]

Jonathan Wells Talks About Sequence Conservation

Paul McBride (paulmc) tried to convince the readers on Uncommon Descent that there was evidence for junk DNA. One of the lines of evidence has to do with sequence conservation. If most of the genome sequences are not conserved between species this strongly suggests that they have no function, although it doesn't rule out a function that is independent of sequence.

Wells addresses this argument in: Jonathan Wells on Darwinism, Science, and Junk DNA. Before analyzing his response, it's worth reviewing what he wrote in The Myth of Junk DNA.

In chapter 5, Wells talks about sequence conservation as evidence of function—specifically the fact that the sequences of some potential pseudogenes are more conserved that would be expected if they were really pseudogenes [Junk & Jonathan: Part 8—Chapter 5]. That's an important argument and, if true, it would point to a function. The irony is that Wells doesn't believe in common descent so, from his perspective, these are not conserved sequences due to negative natural selection. Nevertheless, he is happy to use evolutionary arguments whenever it suits him.

Monday's Molecule #149

 

Today's molecule is one member of a large class. Give me the complete, unambiguous, name of this molecule to win a free lunch. Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

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.) Every undergraduate who posts a correct answer will have their names entered in a Christmas draw. The winner gets a free autographed copy of my book! (One entry per week. If you post a correct answer every week you will have ten chances to win.)

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!)

Name the molecule shown in the figure. Remember that your name has to be unambiguous. The best way to do this is to use the full IUPAC name but usually there are traditional names that will do. In this case there's a trivial name and that will suffice.

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

UPDATE: Several people got this one right. The molecule is prostaglandin H2. The winner is Thomas Ferraro. The undergraduate winner is "Vip" = Vipulan Vigneswaran.

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

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Better Biochemistry: Fischer Projections

Biochemistry is a three-dimensional subject but most of us aren't comfortable thinking in three dimensions. For example, we often have difficulty envisaging how a three-dimensional substrate binds to a three-dimensional enzyme.

The problem is exacerbated because we usually teach in two dimensions for simplicity—especially in textbooks.¹ There are certain rules that have to be followed when displaying a three-dimensional object on a two-dimensional page. This is especially true for metabolites where the stereochemistry is crucial. One of these rules is called the Fischer projection.²

Most students (and faculty) don't understand the relationship between a two-dimensional Fischer projection and the three-dimensional molecule it's supposed to represent. This is unfortunate because it means they don't really understand the three-dimensional conformation of metabolites.

Let's look at a simple three-carbon compound—glyceraldehyde. There are two different versions of glyceraldehyde: D-glyceraldehyde and L-glyceraldehyde. The two different molecules cannot be superimposed, that's why you know that they are different molecules. Enzymes can tell the difference; that's why D-glyceraldehyde is a common metabolite and L-glyceraldehyde is rarely found in cells.

Jonathan Wells Talks About Genetic Load

Most people don't understand the positive evidence for junk DNA—this includes most scientists. Paulmc tried to convince the readers on Uncommon Descent that they had been misinformed about junk DNA. The fact that our genome has huge amounts of junk DNA is not just an argument from ignorance—an argument that most IDiots are familiar with—because there are several good reasons for concluding that most DNA has to be junk.

Wells addressed those arguments in: Jonathan Wells on Darwinism, Science, and Junk DNA.