An open letter to Oprah Winfrey

 
Rebecca Watson of Skepchick publishes An open letter to Oprah Winfrey. Here's part of it ....

And then there’s Dean Radin and The Secret. Oprah, you promoted a “documentary” that claims to show proof that you can literally alter reality by wishing. We’re not talking about the power of positive thinking; we’re talking about the ability to create a pony that farts rainbows by merely thinking about it. Anything is possible, they say. They use a poor muddling of quantum physics to try to confuse people into believing their nonsense. That’s like me claiming that I have a scientific theory to back up my ability to read the future in caramel fudge sundaes: it’s called stratigraphic succession. This proven scientific theory, first developed in the early 19th century, deals with the careful study of layers, and how we can use layers to obtain a deeper understanding of time. Following in the footsteps of the revolutionary researchers who discovered this amazing theory, I simply take it to the next logical level and apply stratigraphic succession principles to the world around me, allowing me to “see” ahead into time.

Did you understand any of that? No? That’s okay, I’ll publish a whole book of that complete and utter nonsense and then come on your show and explain it to you and your audience of millions, going very slowly using the exact same words. Then you can cut me a big check and I’ll buy myself a god damned swimming pool full of caramel fudge sundae. Every year or so I’ll put out another book with the same words rearranged in a different order, and as the money rolls in I’ll laugh at all the suckers who keep me swimming in ice cream for the rest of my diabetes-ridden days.

Monday's Molecule #14

 
Name this molecule. You must be specific. We need the correct scientific name.

As usual, there's a connection between Monday's molecule and this Wednesday's Nobel Laureate. Bonus points for guessing Wednesday's Nobel Laureate(s).

Comments will be blocked for 24 hours. Comments are now open.

The Central Failure of Evolutionary Psychology

 
We wish to question a deeply engrained habit of thinking among students of evolution. We call it the adaptationist programme, or the Panglossian paradigm.
S.J. Gould & R.C. Lewontin (1979) p. 584There are lots of things wrong with evolutionary psychology. One of the most important is the tendency to construct just-so stories about the evolution of human behavior. Most of these stories don't make any sense to people who really understand evolutionary theory. A recent editorial in ScienceWeek makes this very point [History Denied: The Central Failure of Evolutionary Psychology].

On close examination, it becomes apparent that the central failure of evolutionary psychology as an effort to understand human behavior is that it essentially ignores two important corollaries of this major premise concerning universality of behavior across present-day cultures. The first corollary is that any behavior pattern that is NOT universal across cultures is NOT derived from Darwinian evolution, but probably derived from cultural evolution plus individual learned experience. The second and more important corollary is that any behavior pattern within a culture that is not universal across decades, or generations, or centuries, or even millennia is also NOT derived from Darwinian evolution, and more likely derived from cultural evolution plus individual learned experience. On these small time scales, Darwinian evolution just doesn't have enough time to work and cannot be responsible for any behavior changes within a culture.

Thus the central failure of evolutionary psychology is the failure to recognize that universality across both time AND geography are necessary to identify a behavior pattern derivable from Darwinian evolution.

Does Darwinism (sic) Predict Anything

 
The collection of IDiots at Cornell University have put together a webpage called The Design Paradigm. It consists mostly of the usual whining by commentators who are afraid to use their real names on a blog. (In fairness, I would also be embarrassed to use my real name on some of those postings.) One anonymous IDiot asks Does Darwinism predict anything?

We’ve heard over and over again from the Darwinist side of this debate that ID offers no novel predictions. Intelligent design actually offers many intriguing and novel predictions (you can head over to ResearchID.org to see some of them), but what about Darwinism?

I would love it if some of our commentators or readers would offer what they think are predictions of Darwinism. The definiton of Darwinism that we’ll use is the following proposition:

"The origin and diversity of life has occured solely by undirected processes such as natural selection."

For a prediction to count, of course it will have to be one that only Darwinism makes.

These are supposed to be university students. The fact that they can't tell the difference between evolutionary biology and "Darwinism" speaks volumes about their intelligence. It's not as though the difference hasn't been explained over and over and over and over ...

The "definition" they use is not a definition of evolution and it's not a description of evolutionary theory. However, it is a reasonable conclusion (or "prediction") based on everything we know about science. Purists will argue that ruling out God in evolution is philosophical naturalism and this goes beyond the methodological naturalism that's required in science.

Whether this is strictly true or not is debatable but that's not the point. The IDiot students have carefully phrased the question in a way that requires scientists to prove a negative. The kind of "predictions" they're looking for are those that "prove" unguided and undirected processes.

Don't believe me? Just watch how they respond to my evolutionary theory-based prediction that whenever we start using a new drug to treat bacterial infections we will soon discover bacteria that are resistant to the drug.

This is standard freshman biology stuff. Either the IDiot club at Cornell is full of people who don't understand first year biology or they intend to use rhetorical trickery to reject all predictions that they don't like.

Meanwhile, I'm going to hop on over to ResearchID.org to see what kind of predictions the IDiots have come up with.

IDiot Predictions

 
ResearchID is a Wiki devoted to Intelligent Design Creationism. One of the pages conatins Predictions of intelligent design. Let's see what kind of "predictions" you can generate by postulating a supernatural creator who's in charge of designing life.

It's really hard to sort though the gobbledygook to find solid predictions but I think I've found four that count as partially scientific. For each of them I'll quote the ReseardID.org prediction in yellow. My prediction follows.

Much so-called “junk DNA” will turn out to perform valuable functions.

The classic Darwinist prediction about junk DNA would be that none of it is really junk. That's because classic Darwinism attributes selectable function to almost everything and there's no place for things that have evolved by accident. My prediction is that most junk DNA will always be junk. That is, it has no function in the cell and is free to evolve randomly by accumulating mutations that become fixed by random genetic drift.

Natural structures will be found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information).

Based on my understanding of evolutionary biology I also predict that we will continue to discover natural structures that look like molecular machines. Such structures will be complex and they will catalyze highly specific reactions. This is exactly what we expect of an evolved structure.

In general, vestigial organs (sic) will yield some function for the organism.

Many vestigial structures such as rudimentary eyes in cave-dwelling fish, tiny wings on flightless beetles, small useless hind limbs within the body of whales, wisdom teeth that fail to erupt, and pseudogenes, will continue to provide evidence for evolution and evidence against an "intelligent" designer.

The correlation between habitability and discovery will strengthen.

IDiots will continue to say the stupidest things in an effort to sound scientific.

Oprah Has a Secret

 
UPDATE: Mike beat me to it. Read his posting [Here's The Secret: Blame the Victim]. He has videos!

Oprah Winfrey is a sucker for new-age psycho-babble. The latest people to dupe her are some kooks who've discovered "THE SECRET." The secret, as it turns out, is to think positively and radiate good thoughts. If you do that then good things will come back to you.

Apparently this latest version of self-help nonsense was triggered by a movie called The Secret produced by an Australian named Rhonda Byrne. (Why is it always Australians who cause trouble?) She discovered that the The Secret has been around since 3500 B.C., although it seems to have been forgotten from time to time. (Like you're going to forget the secret that makes your life wonderful?)

It wasn't long before others recognized a good thing. In this case people like Rev. Dr. Michael Beckwith and James Arthur Ray. These are two of the charlatans who conned Oprah into advertising their ignorance on national television.

If you want to profit from the secret it helps if you accept Jesus as your Saviour. (Apparently atheists aren't very good at radiating good thoughts. Who knew?)

Michael says The Secret involves the laws of the universe and they, in turn, describe the nature of how God works. "[Jesus] said, 'Pray believing that ye have that ye may receive.' That's The Secret in a nutshell," he says. "Pray believing and feeling and sensing that you already have it, and then you're available to receive it."

Millions of American and Canadian women (and a few hundred men) have been transformed by discovering The Secret. In less than a week their lives have changed dramatically. Oprah broadcast the first show about ten days ago and she had to follow up with a repeat performance yesterday. She was just as gullible the second time, and so was the audience.

Maureen Dowd watched the Oprah show and wrote a column aboout it in today's New York Times [A Giant Doom Magnet]. Here's part of what she says ..

So I was sitting around watching “Oprah” yesterday afternoon when I realized how I could stop W. and Crazy Dick from blowing up any more stuff.

All I needed to do was Unleash my Unfathomable Magnetic Power into the Universe!

Energy flows where intention goes. Or maybe it’s the other way around.

Anyhow, Oprah taught me how to stop abusing myself and learn The Secret. I finally get it: because the Law of Attraction dictates that like attracts like, my negativity toward the president and vice president is attracting their negativity and multiplying the negative vibrations in the cosmos, creating some sort of giant doom magnet.

In spite of Maureen's sarcasm, this is actually very serious. If people like Oprah Winfrey can't tell the difference between truth and nonsense then we're in big trouble. It's bad enough that she fell for John Edward. Now she falls for this?

People should speak out. We need to get out the message that this stuff is unacceptable in a rational society. It's weird. It's like believing in witchcraft.

Gene Genie: The First Issue

 
Gene Genie is a blog carnival that discuses human genes.The first installment of Gene Genie has been posted on ScienceRoll.

Gene Genie is a new carnival and judging by the first issue it's going to be a great one. You can learn about all kinds of things. Check it out.

Here are the human genes covered today: GDF5, DARPP-32, HSPA5, GAA (acid α-1,4-glucosidase, SHH (sonic hedgehog). Only 23,995 to go!

The coffee plant genes, SUS1 and SUS2. are also described.

Shermer v Dembski

 
Michael Shermer and Bill Dembski debated evolution and intelligent design last night. You can read two very different versions of the debate. Jason Rosenhouse posted a summary on The Panda's Thumb. He thought Shermer was good and Dembski wasn't. Salvador Cordova over at Uncommon Descent says Dembski won the debate.

Basing my conclusion entirely on the credibility of the two reporters, I'd say Shermer had a good night.

A Prelude to War

 

WASHINGTON (Reuters) - Stepping up the Bush administration's financial pressure on Iran over its nuclear program, the U.S. Treasury Department labeled three Iranian companies on Friday as proliferators of weapons of mass destruction, banning U.S. transactions with them.

The Treasury, invoking an executive order recently used against Iranian state-owned banks, said it would also seek to freeze any U.S. assets of Kalaye Electric Co., Kavoshyar Co. and Pioneer Energy Industries Co.

It said the companies are either owned by, controlled by or acting for the Atomic Energy Organization of Iran, the government agency that manages Iran's overall nuclear program.

"Treasury is taking this action to deny Iran access to the materials and services that support its nuclear ambitions," Stuart Levey, the Treasury's under secretary for terrorism and financial intelligence, said in a statement. He added that the action was consistent with the U.N. Security Council's recent resolution aimed curbing Iran's nuclear program.

Some People Defend Lying for Jesus

 
Judging by the number of different opinions on the Marcus Ross case, there appear to be a variety of standards for the Ph.D. degree at different universities. Several bloggers think that it's okay to lie in your thesis about which scientific facts you accept and which ones you reject.

The University of Toronto has a Code of Behaviour on Academic Matters that specifies how students and teachers are supposed to behave in an academic environment. Here's part of the preamble,

What distinguishes the University from other centres of research is the central place which the relationship between teaching and learning holds. It is by virtue of this relationship that the University fulfils an essential part of its traditional mandate from society, and, indeed, from history: to be an expression of, and by so doing to encourage, a habit of mind which is discriminating at the same time as it remains curious, which is at once equitable and audacious, valuing openness, honesty and courtesy before any private interest.

This mandate is more than a mere pious hope. It represents a condition necessary for free enquiry, which is the University's life blood. Its fulfilment depends upon the well being of that relationship whose parties define one another's roles as teacher and student, based upon differences in expertise, knowledge and experience, though bonded by respect, by a common passion for truth and by mutual responsibility to those principles and ideals that continue to characterize the University.

This Code is concerned, then, with the responsibilities of faculty members and students, not as they belong to administrative or professional or social groups, but as they cooperate in all phases of the teaching and learning relationship.

Such cooperation is threatened when teacher or student forsakes respect for the other—and for others involved in learning—in favour of self-interest, when truth becomes a hostage of expediency. On behalf of teacher and student and in fulfilment of its own principles and ideals, the University has a responsibility to ensure that academic achievement is not obscured or undermined by cheating or misrepresentation, that the evaluative process meets the highest standards of fairness and honesty, and that malevolent or even mischievous disruption is not allowed to threaten the educational process.

Call me old-fashioned, but I believe in those values. I believe that truth and honesty are essential requirements in a university environment. I believe that freedom of enquiry is threatened when a student misrepresents the truth and makes it hostage to expediency. I believe that students who violate the fundamentals of a university should not graduate, especially with the highest degree that the university can offer (Ph.D.).

Jason Rosenhouse put up a message on EVOLUION BLOG [Why is This in the New York Times?]. Jason says,

This is a complete non-story. By all accounts Ross produced competent scientific work. That he was effectively an actor playing a character reflects very badly on him, but does not reflect badly on URI. If he chooses to use his degree to lend credibility to asinine religious ideas that's his business. The rest of us will have to settle for bashing him for the things he now does. It's not the job of URI, or any other university, to pass judgment on the religious views of others.

It's not the job of a university to discriminate on the basis of religious beliefs. However, it is the job of a university to uphold minimal standards of honesty and accuracy. Ross misrepresents his position when he writes about 65 million year old fossils in his thesis. He doesn't believe that any of those fossils are more than a few thousand years old. He can't honestly discuss explanations for the extinction of marine reptiles at the end of the Cretaceous without revealing that he rejects any explanation that dates this event to the ancient past.

But apparently that's exactly what he didn't do. He misrepresented his true scientific opinion in his thesis. He did this deliberately because he knew that telling the truth in his thesis would probably mean it would be rejected.

John Pieret says,

Some people have questioned whether such a person is engaging either in a mammoth mental disconnect or deliberate deception and, in turn, whether he should be awarded the Ph.D. I think that that is a dangerously slippery slope to climb onto, given the relative risk posed.

The difference between "mammoth mental disconnect" and "deliberate deception" isn't as great as you might imagine. It only requires that before deceiving others you take the time to deceive yourself. In either case the candidate is guilty of stupidity for not accepting the scientific evidence and deception for hiding it. Universities should not award Ph.D.'s to students who are either stupid or intellectually dishonest; and they should definitely not award advanced degrees to students who are both.

This is a slippery slope. It's only asking for trouble when we excuse stupidity and dishonesty because it's part of a religious belief. You don't deserve a free pass through a university just because you get your ignorance from the Bible. Religious students should be subjected to the same rigorous standards as all other students.

No atheist student would get a Ph.D. in paleontology if he rejected all the evidence for an ancient Earth and claimed that our planet was built by aliens 10,000 years ago, and all species were created in just a few days. Such a student would be laughed out of the Ph.D. oral exam—if he ever got to it.

Another Boring Just-so Story

 
From ScientificAmercian.com.

Child molestation and rape top the social taboo list, according to a survey of 186 people between the ages of 18 and 47, and smoking marijuana ranks lowest among the 19 choices of forbidden behavior. In the middle—worse than robbing a bank but better than spousal murder—lies incest between brothers and sisters. Given the deleterious genetic impacts of offspring from such mating, some researchers have suggested that there may be an evolved mechanism designed to prevent that from occurring. And now evolutionary psychologist Debra Lieberman of the University of Hawaii–Honolulu believes she may have elicited some of its functions from this simple questionnaire....

The evolutionary psychologists hypothesize that some form of mental mechanism assesses various cues to come up with an estimate of how related two people are. "The real question is: What are these cues?" Lieberman says. "A potent cue is seeing your mom caring for a newborn. That would have served as a great cue that the infant is a sibling, at least a half sibling." But for younger siblings, who would have no opportunity to make this observation, another cue might be the amount of time spent living with another child/potential sibling. Dubbed the "Westermarck hypothesis"—after the Finnish sociologist who first noted it in a book published in 1889—it posits that children reared together do not often end up being sexually attracted to each other.

How to Save Yourself in a Falling Elevator

 
Friday's Urban Legend: FALSE

Imagine the cable on your elevator breaks and you're in free fall for ten stories. What do you do? Maybe you should wait until the elevator is just about to hit the ground then jump up as high as you can?

Bible Skeptics Conference

 
Come with us to the Bible Skeptics Conference in Whitby (East of Toronto) on Friday Feb. 23 and Saturday Feb. 24.

What the heck is a Bible Skeptics Conference? It's not what you think ...

At this conference named after you, the skeptic, we hope to challenge your views on evolution and ultimately the meaning of life. We promise no singing (not that there's anything wrong with that), no offering plate and no pressure to join a denomination or church - just reasonable arguments for the existence of a creator - and that His book is the Bible.

It should be a barrel of fun! (The Institute for Creation Research will supply the barrels and the fish.)

Another Canuck Atheist

 

I had lunch at the Faculty Club today with a fellow atheist who lives in the Toronto area. Mike McCarron and I have a lot of things in common so we'll undoubtedly be seeing more of each other in the future. Meanwhile, check out his blog Mike's Weekly Skeptic Rant.

Gene HSPA5 Encodes BiP-a Molecular Chaperone

 
Molecular chaperones are proteins that help other proteins to fold properly (see Heat Shock and Molecular Chaperones). The most important chaperones were indentified as heat shock proteins because they were produced following exposure of cells to excess heat. Their role in heat shock is to repair misfolded proteins and their role in normal cells is to assist in the proper folding of newly synthesized proteins.

The most important chaperone is HSP70 (Heat Shock Protein, M_r=70,000). It is present in all normal cells where it binds to polypeptide chains as they are being synthesized. Most cells contain multpile versions of HSP70. The different members of the gene family occupy different cell compartments. For example, there are distinct HSP70 chaperones in mitochondria, chloroplasts and cytoplasm.

The endoplasmic reticulum (ER) is a network of membranes within eukaryotic cells. Proteins that cross the ER membrane end up inside the ER in a special compartment that's isolated from the cytpolasm. Most of these proteins are destined to be exported from the cells in vesicles that bud off of the ER.

Proteins that need to be imported into the lumen of the ER are synthesized on the membrane surface. As they exit the ribosome tunnel they pass directly through a pore in the membane. When they reach the interior of the ER they are helped to fold by a member of the HSP70 gene family called BiP (Binding Protein) or GRP78 (Glucose Regulated Protein). BiP binds to the newly synthesized peptide while it is being made and while it is passing through the ER pore complex.

The HSP70 chaperones are interesting because of the role they play in protein synthesis but they are also interesting because they are the most highly conserved proteins in all of biology. This makes them ideal candidates for studies of molecular evolution. Several thousand sequences are available (HSP70 Sequence Database). The BiP gene in mammals is called HSPA5—a name choice made by the HUGO (Human Gene Organization) Naming Committee [HSPA5]. (HUGO tends to ignore names given to homologues in other species and choose human specific names. The gene is called BiP in most other species.)

HSPA5 is located near the end of the long arm of chromosome 9 at 9q33-q34.1 (chromosome map NCBI, chromosome map UCSC Genome Browser). The Entrez Gene Locus is GeneID=3309 and it lists 7 different independently-cloned genomic sequences and 8 full-length cDNAs. My favorite site is the SwissProt database (P11021) because it combines all the sequence information from each clone into one annotated sequence.

The HSPA5 gene has 8 exons in a relatively compact gene spread out over 6.5kb (6,500 bp). See the sequence [here]. There's nothing particularly unusial about this gene other than the fact that the introns are smaller than normal. All of the mamalian genes have the same intron/exon organization but other eukaryotic BiP genes may have fewer introns or none ar all.


The gene encodes a proein of 654 amino acid residues with a relative molecular mass of 72,300 (close to 70kDa, which is typical for HSP70's). The protein contains an N-terminal leader sequence that controls its import into the ER and a C-terminal ER retention signal that keeps it in the ER lumen. The rest of the sequence closely resemble all of the other members of the HSP70 gene family.