Wednesday, November 30, 2011

Joseph Hoffmann Responds

 
Joseph Hoffmann thinks he knows a lot about modern atheism so he wrote an insulting and rather stupid attack: Atheism’s Little Idea. A lot of atheists were offended and took the time to try and educate Hoffmann. My own contribution was: On Being a Sophisticated Atheist.

Hoffmann noticed that there was less than unanimous agreement with his position so he replied on his blog The New Oxonian: The Sure-Fire Atheist Rapid Response Manual.

You really have to read it to see just what a sophisticated response from a Harvard/Oxford intellectual looks like. I think he's a bit annoyed at all the attention he's getting.


How to Fix CFI Canada

 
In my opinion, there are two immediate things we need to do to fix CFI.

The first is more openness. To that end I think the December 11th meeting in Toronto should be open to any member of the Centre for Inquiry. The meeting is at 10 am (Sunday). I assume it's at the CFI offices in Toronto.

I expect that several people, including Justin Trottier and the Directors, will want to speak at that meeting. The objective is to explain exactly what's going on and how we got into this mess.

The second thing we need to do is add more Associate Members. Candidates for Associate Membership can send an application to the Board of Directors.1 The Board must approve these applications. Associate Members elect the Directors. There are only a dozen or so Associate Members and it's not clear how many of them are active in the Centre.

If you have any ideas about what should, or should not, happen next, please bring them up in the comments below.

Check out ...
Ian Bushfield (Vancouver): Beyond CFI Canada–Reasons for optimism


1. You can contact me for the application form.

Tuesday, November 29, 2011

IDiots and Incivility

 
This is just a heads-up to let you know that Casey Luskin is about to post a series of examples of bad behavior by ID critics [The Uncivil Style of Intelligent Design Critics]. Apparently it's going to be a long series ....
I'm going to let ENV readers in on a little secret: When many of us in the intelligent design (ID) movement read the arguments coming from our critics, we're surprised at their low quality and style. We don't rejoice at this -- we'd much rather see a robust, civil, and fruitful scientific debate over the relevant questions. But the incivility, basic inaccuracy, and unserious tone characteristic of so many criticisms of ID all make you wonder: If the critics had stronger rebuttals to offer, wouldn't we be hearing them?

...

There are so many examples of incivility among ID-critics that it's hard to know where to start. And I'm not just talking about the usual Internet suspects, like PZ Myers, Jerry Coyne, or Larry Moran.
On a completely unrelated topic that has nothing to do with Darwinist incivility ...

While you're checking out Evolution News & Views you might want to read a fascinating article by Richard Weikart defending his books From Darwin to Hitler: Evolutionary Ethics, Eugenics, and Racism in Germany and Hitler's Ethic: The Nazi Pursuit of Evolutionary Progress [Robert J. Richards and the Historical Record]. It even has a photo to illustrate the point about Darwin (see below).


This is a follow-up to a very civil article posted last month: Can Darwinists Condemn Hitler and Remain Consistent with Their Darwinism?.
I threw down the gauntlet to many of my Darwinian opponents by telling her that if Darwinism is indeed a purposeless, non-teleological process, as many evolutionists and biology textbooks proclaim, and if morality is the product of these mindless evolutionary processes, as Darwin and many other prominent Darwinists maintain, then "I don't think [they] have any grounds to criticize Hitler."

According to Flam, these are "fighting words." However, I have spoken with intelligent Darwinists who admit point-blank that they do not have any grounds to condemn Hitler, so I am not just making this up. Many evolutionists believe that since evolution explains the origin of morality -- as Darwin himself argued -- then there is no objective morality. The famous evolutionary biologist and founder of sociobiology, E. O. Wilson, and the prominent philosopher of science Michael Ruse co-authored an article on evolutionary ethics in which they asserted, "Ethics as we understand it is an illusion fobbed off on us by our genes to get us to co-operate."
Anyway, let's not forget the important point and that's Casey Luskin's upcoming series on the incivility of ID critics.


David Berlinksi Prays for Me!!!!

 
Over at Evolution News & Views, Casey Luskin is ranting again about not getting no respect [The Uncivil Style of Intelligent Design Critics]. While checking out recent postings on that site to see whether the evil Darwinists were being treated respectfully, I came across a post by David Berlinski on Phillip Johnson. Imagine my surprise when I read this ....
At the Discovery Institute we often offer an inter-faith Prayer of Thanksgiving to the Almighty for the likes of P.Z. Myers, Larry Moran, Barbara Forrest, Rob Pennock and Jeffrey Shallit.
Thank-you to all the inmates at the institute. I really appreciate your thoughts and prayers.

Next time, could you ask him to send money?


Monday, November 28, 2011

On Being a Sophisticated Atheist

We atheists really have a hard time pleasing theists and philosophers who insist that we immerse ourselves in the study of gods before declining to believe in any of them. Apparently it's not sufficient to simply reject as unconvincing all of the arguments for the existence of god. We also have to study apologetics, which takes the existence of god as a premise!

As if that weren't bad enough, we now have a group of philosopher types who insist that we study every atheist who ever lived. One of those philosopher types is R. Joseph Hoffman, a graduate from Harvard Divinity School and the University of Oxford. He is mainly interested in early Christianity. Hoffman is a nonbeleiver who posts at The New Oxonian. His latest post is: Atheism’s Little Idea.

Is the Burzynski Clinic Full of Quacks?

The Burzynski Clinic is located in Houston, Texas, United States. It charges a lot of money to treat cancer patients and the treatment is probably not effective according to Andy Lewis at The Quackometer: The False Hope of the Burzynski Clinic.

Andy Lewis received a letter from someone named Marc Stephens who claims to represent the Burzynski Clinic. You have to read this letter to understand what's going on [The Burzynski Clinic Threatens My Family].
Le Canard Noir / Andy Lewis,

I represent the Burzynski Clinic, Burzynski Research Institute, and Dr. Stanislaw Burzynski. It has been brought to our attention that you have content on your websites http://www.quackometer.net/blog/2011/11/the-false-hope-of-the-burzynski-clinic.html that is in violation of multiple laws.

Please allow this correspondence to serve as notice to you that you published libelous and defamatory information. This correspondence constitutes a demand that you immediately cease and desist in your actions defaming and libeling my clients.

Please be advised that my clients consider the content of your posting to be legally actionable under numerous legal causes of action, including but not limited to: defamation Libel, defamation per se, and tortious interference with business contracts and business relationships. The information you assert in your article is factually incorrect, and posted with either actual knowledge, or reckless disregard for its falsity.

The various terms you use in your article connote dishonesty, untrustworthiness, illegality, and fraud. You, maliciously with the intent to harm my clients and to destroy his business, state information which is wholly without support, and which damages my clients’ reputations in the community. The purpose of your posting is to create in the public the belief that my clients are disreputable, are engaged in on-going criminal activity, and must be avoided by the public.

You have a right to freedom of speech, and you have a right to voice your opinion, but you do not have the right to post libelous statements regardless if you think its your opinion or not. You are highly aware of defamation laws. You actually wrote an article about defamation on your site. In addition, I have information linking you to a network of individuals that disseminate false information. So the courts will apparently see the context of your article, and your act as Malicious. You have multiple third parties that viewed and commented on your article, which clearly makes this matter defamation libel. Once I obtain a subpoena for your personal information, I will not settle this case with you. Shut the article down IMMEDIATELY.

GOVERN YOURSELF ACCORDINGLY.

Regards,

Marc Stephens
Burzynski Clinic
9432 Katy Freeway
Houston, Texas 77055
What would a normal person do after receiving such a letter? Ask for more information about the "defamatory" content. That's what Andy Lewis did and here's part of the response.
If you had no history of lying, and if you were not apart of a fraud network I would take the time to explain your article word for word, but you already know what defamation is. I’ve already recorded all of your articles from previous years as well as legal notice sent by other attorneys for different matters. As I mentioned, I am not playing games with you. You have a history of being stubborn which will play right into my hands. Be smart and considerate for your family and new child, and shut the article down..Immediately. FINAL WARNING.

Regards,

Marc Stephens
Yep, that's a threat you see in that paragraph.

Here's a few people who think that the Burzynski Clinic deserves more publicity.


"Yes," "No," and "I Don't Know"

John Wilkins has continued the discussion about agnosticism, atheism, and the meaning of debate [Once more into the fray, dear agnostics]. I'll try and respond to the specific points he makes in a minute or two, but first I need to make my own position (more) clear.

I teach a course on critical thinking about scientific issues such as evolution/creationism. Most (all?) of the "scientific" debates that enter the public realm can be divided into two groups: those where one side is right and the other side is wrong, and those where the issue is controversial. From a personal perspective, that means you can have three responses when asked if you agree with a scientific argument: "yes," "no," and "I don't know."

Monday's Molecule #151

 
This is a very complicated molecule so I'm not going to ask for the IUPAC name. You can win with the common name but be sure to get it right!

This molecule has played a very important role in elucidating some basic concepts in molecular biology but its structure is rarely shown in 21st century biochemistry textbooks.

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: The molecule is rifampicin, an inhibitor of bacterial RNA polymerase. The winner is Philip Rodger. Congratulations Philip, please send me an email message so we can arrange lunch.

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)


Sunday, November 27, 2011

NASA Confusion About the Origin of Life

NASA-funded researchers have evidence that some building blocks of DNA, the molecule that carries the genetic instructions for life, found in meteorites were likely created in space. The research gives support to the theory that a "kit" of ready-made parts created in space and delivered to Earth by meteorite and comet impacts assisted the origin of life. [NASA Researchers: DNA Building Blocks Can Be Made in Space]

Most scientists are not thinking critically about the origin of life. It is extremely improbable that asteroids could have delivered enough amino acids or purines to make a difference. Given the known stability of these molecules in the ocean, you would have to achieve an enormous delivery rate to make a concentration sufficient to drive polymerization. It's much more likely that the first complex amino acids, and the first purines and pyrimidines, were synthesized in special environments on Earth using simple inorganic precursors. This is the origin of life scenario promoted as "Metabolism First" [More Prebiotic Soup Nonsense].

I wish NASA astrobiologists would stop making the assumption that all they have to do is discover complex organic molecules in asteroids in order to solve the origin of life. There are a lot of steps between finding purines in asteroids and making a prebiotic soup that could contribute to the origin of life. Those steps need to be spelled out in their press releases so the public can evaluate the discovery.

Here's what I wrote a few years ago .... [Can watery asteroids explain why life is 'left-handed'?]
In order for extraterrestrial organic matter to have fueled the origin of life, a lot of meteorites carrying organic matter had to arrive on the primitive Earth. The problem of amino acid concentrations and stabiltity were discussed in a classic paper by Jeffrey Bada published in 1991.

Some of his calculations are worth remembering.

The current flux of extraterrestrial organic material is about 3 × 108 grams per year from cosmic dust and micrometeorites. About 1% of this is amino acids and most of them are not the ones found in living organisms. This should give rise over time to a concentration in the oceans of about 0.1 nM (10-10 M). That's not sufficient for life to have originated.

The flux in the past was almost certainly much greater and lots of organic material might have been delivered by large meteorites; however, it's unlikely that amino concentrations in the oceans could ever have been more than 10-100 pM for all amino acids combined.

Most amino acids will spontaneously degrade over time. There's a window of opportunity that only lasts about 10 million years because in that time all the water in the oceans will pass through hydrothermal vents and the high temperature will destroy most chemicals—including amino acids.
I don't know whether the NASA astronomers are aware of this problem but have developed a scenario to overcome it, or whether they just haven't thought about the problem.


Bada, J. (1991) Amino acid cosmogeochemistry. Phil trans. R. Soc. Lond. 333:349-358.

Saturday, November 26, 2011

The Implosion of CFI Canada

The Centre for Inquiry - Canada "... promotes and advances reason, science, secularism and freedom of inquiry in all areas of human endeavour." It is affiliated with the Center for Inquiry in the United States, headquartered in Amherst, New York (near Buffalo).

The Canadian Centre for Inquiry was founded in 2007 and the inaugural meeting was held in their rented facilities just south of the University of Toronto and a short walk from my office [Centre for Inquiry: March 10, 2007]. Justin Trottier was the new director.

CFI - Canada has now grown from the original Toronto (Ontario) branch to include branches in Vancouver, Okanagan, Calgary, Saskatchewan, Ottawa, Montreal, and Nova Scotia. There's paid staff in Toronto and there are now paid employees (usually part time) in several other centres.

Friday, November 25, 2011

Zoë Is Coming for Christmas

 
My granddaughter Zoë is coming for Christmas, from Los Angeles. She's bringing her parents. That means two of my little girls (mother and daughter) are coming home for Christmas.

Here's an atheist video from Australia. It's about Christmas, family, love, and a little baby girl who grows up. Can you get through it without shedding a tear? I couldn't.

TimMinchin the songwriter and singer in this video, grew up in Perth, Australia. He lives with his wife, daughter, and son in London, England. The song, White Wine in the Sun was first released in December, 2009.




[Hat Tip: Pharyngula]

De mortuis nil nisi bonum

De mortuis nil nisi bonum is a Latin phrase which indicates that it is socially inappropriate to say anything negative about a (recently) deceased person. Sometimes shortened to nil nisi bonum, the phrase derives from the sentence "de mortuis nil nisi bonum dicendum est" and is variously translated as "Speak no ill of the dead", "Of the dead, speak no evil", "Do not/ Don't speak ill of the dead" or, strictly literally, "Of the dead, nothing unless good".
There are times when social conventions need to be violated. This is one of those times.

Lynn Margulis died last Tuesday (November 22, 2011) at the age of only 73. Margulis is rightly famous for her endosymbiotic theory of the origins of mitochondria and chloroplasts. We known that she was right and she deserves credit for that part of her theory.

However, since then (about 1970) her record has not been stellar and it's only appropriate that we keep this in mind as we reflect on her contribution to science. Here's a video of Lynn Margulis "defending" science by promoting the idea that one of the buildings of the World Trade Center in New York was brought down on Sept. 11, 2001 by explosives that had been planted in the building months before.




[Hat Tip: Why Evolution Is True]

John Wilkins on Sandwalk

 
I like John Wilkins. If he lived in Toronto I would want to talk to him several times a week and I'd even pay for the the coffee and lunches. It's embarrassingly easy to teach me things I don't know, or correct my errors, but John has done way more than his fair share over the past twenty years.

I think he's mad at me [Prescriptions for atheists].
First, Larry points out that arguments about the existence of God require one to take a position on fairies. One can only be agnostic about gods to the extent one is agnostic about fairies. My previous argument that this is comparing unlikes has, in one fell swoop, been demolished! Of course, there must be other reasons for thinking that we can rule fairies out of contention (let us call them faeries to avoid confusion) which do exist but are undetectable. It cannot be the principle that “if it is unscientific it is irrational” for that would be the positivist presumption and that would be unscientific. I know I am wrong about positivism here, because Dan Hicks pointed out that some positivists weren’t positivists about everything. So positivism is never self-defeating, even when the positivist presumption is applied by some to everything.

Larry must have other reasons for showing that faeries do not exist – other than being uninterested in what some people claim; this, as Larry must appreciate, is not about what I the reasoner think is true, but about what others who make these claims must be called. I look forward to him enlightening me on this.

Friendly Atheists and the Other Kind of Atheist


We've been discussing the perceived conflict between agnosticism and atheism. I believe they are compatible. Most prominent atheists are also agnostic about the existence of supernatural beings.

Part of the discussion has to do with how you define atheism. Many philosophers (professional and amateur) maintain that atheism is defined as "the view that there is no God." This is the definition taken from The Internet Encyclopedia of Philosophy, which claims to be a "peer-reviewed academic resource" [Atheism]. It seems to me that this view of atheism is widespread among philosophers, lending support to those who use it to justify rejecting atheism.

Thursday, November 24, 2011

Defining Atheism

 
Most people know that there are two common definitions of atheism/atheist. Here's an excellent example from two different dictionaries.

atheist: a person who denies or disbelieves the existence of a supreme being or beings [dictionary.com]

atheist: a person who does not believe in the existence of God or gods [Oxford Dictionaries]
The first definition defines an atheist as someone who maintains that gods do not exist. The second defines an atheist as someone who is not a theist.

The distinction is relatively unimportant in everyday usage since most of us who are nontheists will argue that gods do not exist. But when you're arguing with a philosopher you need to pick nits since philosophical arguments often turn on definitions. No intelligent atheist wants to be trapped into arguing that gods do not exist since that's like trying to "prove the negative" and we all know that it is impossible to prove the nonexistence of something.

What William the Conqueror's Companions Teach Us about Effective Population Size

 
My mother has been working on genealogy for several decades. She recently gave me a little book called My Ancestors Came with the Conqueror by Anthony J. Camp, first published in 1988. Camp is a professional genealogist. Before discussing this book, I should let you know that the relationship between professional genealogists and the amateur genealogy found on ancestry.com is similar to the relationship between scientists and Intelligent Design Creationism.

It's estimated that half the population of Great Britain claims to have descended from William the Conqueror who defeated King Harold at the Battle of Hastings in 1066. Not all claims meet the rigorous standards of professional genealogists but it's quite reasonable that there are millions of direct descendants of William.

Back in 1400 it was less likely that you were a descendant of William because there were fewer generations and fewer descendants. This was a problem for aspiring nobility and minor landholders so they tended to settle for the next best thing—they claimed descent from one of the companions of William who accompanied him from Normandy and fought at the Battle of Hastings. Gradually the list of companions grew and grew because if you couldn't prove you were related to an existing companion, you just made one up.

Many genealogists and historians have analyzed the various lists of companions. Some lists have over three hundred names but there are only about 20 companions who are definitely known to have been present at the Battle of Hastings in 1066 [William the Conqueror's Companions, The Companions of the Conqueror]. The Order of the Conqueror’s Companions is part of a genealogical society that traces descendants of the companions of William the Conqueror. They list 39 known companions.

Let's assume that there are 20 well-documented companions. Only one of these (William Mallet) has possibly passed on his Y chromosome to the present time and even that male line of descent is disputed. This is fully consistent with our understanding of genetics when you consider that most male lines are likely to die out in a few generations. Those that survive ten generations or so are unlikely to become extinct since there will likely be several male lines at that time.

Only 10 of the companions have descendants who are alive today. This could be due to the fact that genealogists don't have perfect records for all the companions and their families but it's also quite in line with expectations.1 You don't expect that all 20 families will avoid extinction. What this means is that for a random "population" of 40 individuals (20 companions plus their wives), only 20 of them contributed alleles to the present population after 50 generations.2

The take-home lesson from these genealogical studies is that the actual population size at a given point in time is not the same as the actual number of individuals who contribute to the gene pool over the long term.

This has long been known to population geneticists. They define a new term, Ne, called the "effective population size." In order to understand the definition of effective population size, you have to keep in mind that most of the variation in a given population is due to the presence of nearly neutral alleles whose frequency is fluctuating under the influence of random genetic drift. The parameter of interest, Ne, represents the theoretical number of individual in a population of size N who actually contribute to the variation in a population.

The definition is from Sewell Wright [Effective Population Size] ...
Effective population size is "the number of breeding individuals in an idealized population that would show the same amount of dispersion of allele frequencies under random genetic drift or the same amount of inbreeding as the population under consideration."
The effective population size is always less than the actual population (Ne < N). Sometimes it's a lot less. In most vertebrates, for example, the long-term effective population size is calculated to be about 10,000.

Why is this important? It's important because evolution is important for understanding biology and in order to understand evolution you need to understand population genetics. One of the important lessons from population genetics is that the relative important importance of natural selection and random genetic drift is dependent on effective population size. This is a major theme in Michael Lynch's book The Origins of Genome Architecture.

He argues that the effective population size of most large multicellular animals (e.g. Homo sapiens) was small enough to render natural selection impotent for most alleles that might have been somewhat beneficial in larger populations. This led to loss of such beneficial alleles by random genetic drift and to frequent fixation of mildly deleterious alleles by drift. Thus, even if the accumulation of large amounts of junk DNA, for example, was slightly deleterious, it cannot be eliminated by natural selection when the effective population size is small.

Furthermore, many alleles with small beneficial effects cannot possibly become fixed in such a population so it's silly to construct a model that relies on fixation of alleles with a small advantage. This leads to his theory of the evolution of genome complexity by nonadaptive processes. According to Lynch, the default explanation is random genetic drift and because this accounts for much of genome architecture, there's no reason to invoke natural selection to explain what we observe.

Lynch devotes an entire chapter (Chapter 4) to Why Population Size matters. I'm hoping to get more people interested in this subject by giving them a simple example of the difference between actual population size (N) effective population size (Ne).

This isn't only important in genome evolution. As most of you know, the effective population size is an important consideration in recent human evolution [From genes to numbers: effective population sizes in human evolution] and many other disciplines.


1. The reason we focus on nobility isn't because they are more important, genealogically, than the 8,000 other soldiers at the battle. It's because we don't have any records of those other potential ancestors.

2. This doesn't mean that all of the alleles in the other 20 individuals were lost because many of them could have been passed down from siblings, aunts, uncles etc.

Tuesday, November 22, 2011

Trying to Understand Agnostics

 
John Wilkins has tried, again, to explain the difference between an atheist and an agnostic [Positivism about agnosticism].

My position is similar to that of Richard Dawkins, and many others. I am an atheist (i.e. not a theist) because there is no convincing evidence for gods, in my opinion. Thus, I do not believe in them (not-a-theist).

There is always a possibility that gods actually exist even though I see no evidence for them. I cannot prove that they are all non-existent. Thus, I am, in a sense agnostic on the possibility of gods existing, although I think the odds are incredibly small.

Like Dawkins, "I am agnostic only to the extent that I am agnostic about fairies at the bottom of the garden." I am a practicing atheist because I do not believe in gods but I am philosophically agnostic as well. I have theist friends who believe in God but are also agnostic.

John says,
Let me be quite clear on this: I do not think there is evidence for a God, as an agnostic. And I certainly think there is evidence against many stories and characterisations of gods. But, and this seems to be the point that strong “skeptics” like Hecht cannot get into their heads, not all. So long as there is a formal possibility that some gods might exist, and no general evidence against it, the rational thing to do is hold off judgement on the (empirically permissible) claims. So Thor doesn’t exist, but Leibniz’s deity might.
Like me, John, doesn't believe in gods—he is not a theist. But he is not an a-theist in spite of the fact that if you followed him around for several days you could not distinguish his bevavior from that of any other non-believer.

We agree that there's a possibility that some sort of gods exist but we both have declined to become believers (theists). Yet, I am a strong atheist/agnostic while John is a nonbeliever but only an agnostic.

Have I got that right, John?

As an amateur philosopher, it seems to me that you could apply the same logic to the existence of fairies or UFO astronauts with a fixation on body openings. There's no evidence that they exist so we don't believe in them. But as long as there's a formal possibility that they exist—and there is—we have to be agnostic about their existence.

For some reason we don't go around announcing to the world that we are agnostic about the existence of fairies, UFOs, and Santa Claus. Why? Doesn't the formal possibility of their existence merit consideration? Don't we recognize that we could never PROVE that fairies don't exist?

The word "agnostic" only ever applies to the belief in gods and never—in common speech—to fairies. We all know the reason for this. It's accommodationism. It's a way to avoid insulting our religious friends by proclaiming you don't believe in their gods. Too bad it's almost always atheists who are so sensitive. You don't see many theists avoiding the word "theist" in favor of "agnostic."

Part of the problem is that agnostics like John tend to use a different definition of "atheist" than we do. He seems to think that it means we deny the possibility that gods exist. I think that's why he considers "atheist" and "agnostic" to be non-overlapping sets.


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.

Monday, November 21, 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.


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?


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


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?


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

Thursday, November 17, 2011

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.)



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.


Wednesday, November 16, 2011

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?


Tuesday, November 15, 2011

Monday, November 14, 2011

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


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.

Sunday, November 13, 2011

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.

Jonathan Wells Sends His Regrets

Paulmc visited Uncommon Descent in order to defend junk DNA [Here’s Jonathan Wells on destroying Darwinism – and responding to attacks on his character and motives]. Now Wells has responded to several of paulmc's points [Jonathan Wells on Darwinism, Science, and Junk DNA].

We'll get to those issues in another post but right now I want to take note of something Wells said at the end of his article.
Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.
I can understand why Wells might decline to post a comment on Sandwalk. Many of us know what it's like to try and argue with the readers of the intelligent design blogs. Wells would meet the same reception here that we get over there.

But that doesn't preclude Wells from posting on Uncommon Descent or Evolution News & Views. If he really believes that my review of his book is an example of "confused thinking and malicious misrepresentations of my work"1 then why not back up such a statement with a thoughtful response on a friendly blog? Evolution News & Views would be ideal since comments are banned.


1. Wells has accused other scientists of misrepresentation. It's a common theme in The Myth of Junk DNA and in Icons of Evolution. I quoted this passage in Junk & Jonathan: Part 13—Chapter 10.
Coyne and Avise are professors of genetics at major universities, so they cannot claim ignorance of the genomic evidence without thereby admitting negligence or incompetence. In fact, one of Coyne's colleagues at the University of Chicago is James Shapiro, co-author of the 2005 article cited in Chapter 6 that listed over 80 known functions for non-protein-coding repetitive DNA. [The other author is Richard (von) Sternberg ... LAM] But if Coyne and Avise were not ignorant of the evidence, then they misrepresented it—and they continue to do so. Like Dawkins, Shermer and Kitcher they have forfeited any claim they might have to be speaking for science.
I can understand why Wells is reluctant to defend such statements. It's because they are indefensible.

Saturday, November 12, 2011

A New View of Evolution

There have been lots of new books about evolution in the past decade or so. I tend to divide them into three categories:
  1. The Standard View: These are books that basically support the Modern Synthesis with some small tweaks here and there. They do not advocate major shifts in the way we look at evolution. Books by Richard Dawkins (The Greatest Show on Earth: The Evidence for Evolution), Jerry Coyne (Why Evolution Is True), Sean B. Carroll (Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom, The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution), and Ken Miller (Only a Theory) fall into this category.
  2. The New View: Some books make the case for a new way of looking at evolution. I'll call it the "New View." Many of Stephen Jay Gould's books fall into this category (The Structure of Evolutionary Theory). He refers to it as extending the modern synthesis. Most of the "extension" is based on a pluralist, rather than an adaptationist approach but other modifications are important. Two recent books by Michael Lynch (Origins of Genome Architecture) and Eugene Koonin (The Logic of Chance: The Nature and Origin of Biological Evolution) fall into this category. It's a view that I share.
  3. The Radical View: Some books advocate a more-or-less complete overthrow of the Modern Synthesis, replacing it with the author's pet theory. Examples are: Marc Kirschner, and John Gerhart (The Plausibility of Life: Resolving Darwin's Dilemma), James Shapiro (Evolution: A View from the 21st Century), Lynn Margulis and Dorion Sagan (Acquiring Genomes: A Theory Of the Origin Of Species), Massimo Pigliucci and Gerd B. Müllerand (editors) (Evolution - the Extended Synthesis), many others.

Friday, November 11, 2011

The Problem with STEM


The new buzzword in science education is STEM: science, technology, engineering, and math. In America, there are dozens of studies on how to improve STEM education at all levels—including universities. Leading scientists have signed on.

Here's the problem. "Science" is NOT the same as "technology" and not the same as "engineering." There's a big difference between learning science and learning how to build things. The purpose of a degree in technology and engineering is obvious—it's job training. The purpose of a science education is quite different—it's supposed to teach you how to think critically.

But that distinction seems to have been lost on politicians, the general public, the media, and—most disappointingly—my fellow scientists. A recent article in The New York Times illustrates the extent of the problem [Why Science Majors Change Their Minds].

Thursday, November 10, 2011

The New Scientific Version of Intelligent Design Is Compatible with Junk DNA

 
Over on Uncommon Descent we've been discussing junk DNA [Here’s Jonathan Wells on destroying Darwinism – and responding to attacks on his character and motives]. One of the IDiots (Joseph) has proposed a modification of the existing scientific theory of intelligent design. The new version now accounts for junk DNA.

You might think this is just his personal take on intelligent design but I asked everyone else to comment if they objected to his ideas. After more than 24 hours, nobody raised any objection so I assume Joseph's ideas are acceptable to the other IDiots.

The new version goes like this .....
  1. You can have junk DNA because physical constraints and design compromises prevented a perfect design.
  2. Due to genetic entropy the originally designed genomes might have degenerated.
  3. Junk DNA could have been put in the genome by the intelligent designer as preparation for future creations.
  4. Some of the junk DNA is redundant functional DNA that's present in case a gene breaks down.
This new version of intelligent design is not in conflict with the presence of large amounts of junk in our genome.

The evolution side should know about this new development just in case we're ever accused of not keeping up with the latest advances in Intelligent Design Creationism.

UPDATE: Some readers are a little confused by this article. Of course there's no "new" version of Intelligent Design Creationism. Joseph's speculations are completely at odds with the views of the leading IDiots like Dembski, Myers, Wells, Behe etc. Most of the "leading lights" think there's a serious problem with junk DNA. According to them, ID predicts that most of our genome will be functional.

The point of my article is that the IDiots never criticize or correct their friends no matter how stupid they get. That's why you won't see any proponents of intelligent design posting comments below that question Joseph's statements.

BTW, Joseph, or Joe G, is a field service engineer. Please refrain from making unflattering comments about The Salem Conjecture. (That's my job.)


The Wreck of the Edmund Fitgerald

 
Twenty-nine men died on November 10, 1975 when the S.S. Edmund Fitgerald sank in a storm on Lake Superior.




Wednesday, November 09, 2011

Ahem!

 
David Klinghoffer is at it again: How Ignorance Insulates the New Atheists
First, that's because the key argument against belief in God lies, as it always did, in the attempted critique of the design argument. New Atheists like Richard Dawkins recognize this, and so does Coyne. Otherwise why would he name his blog, a venue overwhelmingly devoted to religion bashing, "Why Evolution Is True"? Yet the New Atheists have uniformly kept themselves just as ignorant of modern expressions of the design argument as they have of adult religious beliefs. When Dawkins goes after Darwin-doubters, he ignores -- will not debate, will not grapple with in print, probably doesn't even read -- proponents of intelligent design, a credible scientific alternative to and critique of Darwinian evolution. So too with Coyne. When Dawkins or PZ Myers or the rest does critique a Darwin doubter, it's always some hapless creationist, apprehended unarmed in the Internet wasteland and presenting a nice easy target. Like a schoolyard bully, they will pick on the little kids, but never on an opponent their own size.
Aside from David Kinghoffer, I don't usually pick on hapless creationists. I'm more than happy to pick on the very best that Intelligent Design Creationism has to offer. Problem is, they don't listen to me.

Is that because the IDiots prefer to attack the small fry rather than stand up to someone their own size (or larger)?


Carl Sagan Day

 
Happy Carl Sagan Day.
In every such society there is a cherished world of myth and metaphor which co-exists with the workaday world. Efforts to reconcile the two are made, and any rough edges at the joints are tend to be off-limits and ignored. We compartmentalize. Some scientists do this too, effortlessly stepping between the skeptical world of science and the credulous world of belief without skipping a beat. Of course, the greater the mismatch between these two worlds, the more difficult it is to be comfortable, with untroubled conscience, with both.

In a life short and uncertain, it seems heartless to do anything that might deprive people of the consolation of faith when science cannot remedy their anguish. Those who cannot bear the burden of science are free to ignore its precepts. But we cannot have science in bits and pieces, applying it where we feel safe and ignoring it where we feel threatened—again, because we are not wise enough to do so. Except by sealing the brain off into separate compartments, how is it possible to fly in airplanes, listen to the radio or take antibiotics while holding that the Earth is around 10,000 years old or that all Sagittarians are gregarious and affable?

Carl Sagan, The Demon-Haunted World (1995) P. 297.

Visit Bad Astronomy: On the birthday of Carl Sagan to hear Carl Sagan read his famous essay "The Pale Blue Dot."




Tuesday, November 08, 2011

I would so go to this if I were in Madison

 
Upcoming lecture in Madison1



1. Coincidentally, Ms Sandwalk and I were just talking—less than 15 minutes ago— about how long it would take to drive to Madison from Toronto. I think we could do it in 12 hours.

Monday, November 07, 2011

Haught vs Coyne: The Q&A

Here's an excellent summary of the Q&A from the debate. It's from Eric MacDonald at Choice in Dying: Q&A: Haught on God: Bitter, Impolite and Wrong.

He has a blow-by-blow account of the questions and answers following the debate but I especially like this ....
The assumption that science decided to leave out questions of god, meaning, purpose and value is a caricature of the history of science, and Haught, who claims to be making a serious attempt to show the compatibility of science and religion, must know this. If he doesn’t, and he really thinks that science made such a decision — how does “science” do this, by the way? — then his misunderstanding of the relation of science and religion is total.

When Haught turns around, then, and castigates Jerry by saying that everything that he said was a caricature, that every quotation that Jerry took from Haught’s work was taken out of context, and that instead of reading carefully and thoughtfully Jerry got his idea of god and theology from creationist websites, this was undoubtedly the most aggressive and impolite move of the whole debate. Listen to what he says:

Remember that John Haught is a Roman Catholic theologian. As far as I know he has never dissociated himself from the main teachings of the Roman Catholic Church. If he doesn't believe in any of the stuff that Jerry mentioned then isn't it up to him (Haught) to clarify what he does believe in?

Does he believe in the resurrection? Does he believe that humans have souls? Does he believe in miracles? Does he believe that God answers prayers? Does he believe the Nicene Creed? Are all these things compatible with science?