How Linus Pauling Discovered the α-Helix

Biochemistry students have been learning this little bit of history for over fifty years. I discovered, quite by accident, that there's a video of Linus Pauling telling the story ...

---

[Hat Tip: The Biochemistry Questions Site]

Do You Want to Go to a Conference?

There's a conference in April called the Westminster Conference on Science and Faith. It takes place in a church in Philadelphia. Here's the trailer. How many of you just can't wait to register?

---

Annual Darwin Lecture at the University of Toronto

The Department of Ecology & Evolutionary Biology and the Royal Ontario Museum present the Annual Darwin Lecture: Darwin, Lizards, and Evolutionary Biology in the 21st Century. The speaker is Jonathan Losos and the lecture takes place tomorrow, Thursday, February 7, 2013 in the Earth Science Centre Auditorium, Room 1050, at 8pm.

Brief Description: Modern day evolutionary biologists combine DNA studies with field experiments that can detect Darwinian evolution in real time. Lizards are an ideal subject for such research.

---

Five Million Pageviews!!!

This is just a little blog. It's taken me more than six years to reach five million pageviews. The big guns get that many every month.

Nevertheless, it's a significant milestone. Please help me to celebrate by reading the top five Sandwalk posts since November, 2006. Four of them are science posts! Only the non-science post generated a significant number of comments and that's because so many people tried—and failed—to meet my challenge ....

I challenge all theists and all their accommodationist friends to post their very best 21st century, sophisticated (or not), arguments for the existence of God. They can put them in the comments section of this posting, or on any of the other atheist blogs, or on their own blogs and websites. Just send me the link.

February 26, 2007
The Genetics of Eye Color

May 11, 2007
Regulating Glycogen Metabolism

June 30, 2010
Smart Crocodile Eaters?

September 25, 2012
A Challenge to Theists and their Accommodationist Supporters

August 1, 2011
Carnival of Evolution #38

There are three other posts that are inching their way up toward the top five ...

December 15, 2012
Ann Gauger Describes the Intelligent Design Creationist Version of Population Genetics

May 22, 2011
Junk & Jonathan: Part 4—Chapter 1

February 23, 2007
Genetics of ABO Blood Types

---

Golden Palace Egg Rolls

I've been getting Chinese food (Canadian style) at the Golden Palace restaurant for over fifty years. The restaurant is on Carling Avenue in Ottawa (Ontario, Canada) in the neighborhood where I grew up.

I've taken many friends to the restaurant and recommended it to visitors. Recently the talk.origins moderator, Dave Greig, sampled the food and pronounced it tolerable. More recently, I brought lots of food to the hotel at Eschaton 2012 and treated PZ Myers, Veronica Abbas, Chris DiCarlo, and Ophelia Benson. They all liked the egg rolls. Everyone likes Golden Palace egg rolls.

The new, 3rd generation, owner, Bill Kwong is a friend of my cousin. Bill has kept all of the traditional servings at the restaurant (you don't mess with success). But he's done one thing that the previous owners never did—he's selling Golden Palace egg rolls at hockey games!

Check out the TV report to see how the egg rolls are made: Golden Palace egg rolls score big at Scotiabank Place.

UPDATE: Ms. Sandwalk recounts how we used to get our egg rolls 50 years ago [Golden Palace egg rolls].

---

Saint Andrew at Work

Andrew MacRae used to be very active on talk.origins. At the time he was studying Burgess Shale fossils and his expertise was much appreciated. He earned the nickname "Saint" Andrew because he was kind to, and patient with, most creationists. Many of us weren't.

Andrew was also interested in "Polystrate" Tree Fossils because creationists often used them as "proofs" that evolution is wrong.

Here's Andrew extracting a fossil tree from the Joggin Fossil Site in Nova Scotia (Canada). He looked a bit younger when I last saw him in Toronto in 1998.

---

God and the Problem of Pain

Jeffrey Shallit is making a heroic sacrifice. He's attending a series of lectures on God and Reason. This is a legitimate dichotomy, either you believe in God or you accept reason. You can't do both.

Unfortunately for Jeff, he is being subjected to a bunch of lectures from real Professors on how to rationalize belief in God with being reasonable. The latest was a lecture on God and Reason - Lecture 3 - John North - The Problem of Pain.

The argument goes like this ...

1. Assume (withou any evidence) that god(s) exist.
2. Assume (without evidence) that your favorite god is good and wouldn't allow pain.
3. Since pain exists then ...

• god is mysterious and we don't understand her motives OR
• god wants us to have free will and be capable of voluntarily choosing pain and suffering OR
• temporal pain is transitory, we will be free of pain once we reach heaven

This is an example of Christian reasoning? Jeff, you have my sympathies ... and thanks for reporting on the best that sophisticated theology has to offer.

---

Join Us on Friday to Discuss "Thoughts on Science: Evolution versus Intelligent Design (Part I of an indefinite number of parts)"

Rufina Kim has organized the second meeting of her group Thoughts on Science. We will meet on Friday, February 8, 2013 at 5 pm in room 5253 of the Medical Sciences Building on the University of Toronto St. George campus. The meeting is scheduled to end at 7:30 pm.

Here's the description form the Facebook page ...

Discussion of the controversies that lie within the question "How did organisms on earth come to be?"

Ideally, an equal number of evolutionary biologists and creationists will attend.

All are welcome, even spectators.

When I open a page of Darwin I immediately sense that I have been ushered into the presence of a great mind. ... When I read Phillip Johnson, I feel that I have been ushered into the presence of a lawyer.

Richard Dawkins (1996)Please join us. The last meeting [What Is Science? - Still No Answer!] was a lot of fun.

Here's a list of some topics we could discuss. If you can only read one then choose Creationism Continuum because it helps if you understand the meaning of "creationism."

The Discovery Institute Presents the Case for Magic
Five Myths (?) About Intelligent Design Creationism
How Do Intelligent Design Creationists Define "Creationism"?
The "Intelligent Design" Version of Creationism
Creationism Continuum
Casey Luskin "Explains" Intelligent Design Creationism
A Torley Defense of Irreducible Complexity
Blown Out of the Water
"Impossible" Molecular Machines
Will the Real IDiot Please Stand up?

And here, for no particular reason, is a quote from George Orwell.

The power of holding two contradictory beliefs in one's mind simultaneously, and accepting both of them... To tell deliberate lies while genuinely believing in them, to forget any fact that has become inconvenient, and then, when it becomes necessary again, to draw it back from oblivion for just as long as it is needed, to deny the existence of objective reality and all the while to take account of the reality which one denies – all this is indispensably necessary. Even in using the word doublethink it is necessary to exercise doublethink. For by using the word one admits that one is tampering with reality; by a fresh act of doublethink one erases this knowledge; and so on indefinitely, with the lie always one leap ahead of the truth.

George Orwell, Nineteen Eighty-Four

---

Goodby Penny!

Beginning yesterday the Canadian penny is being removed from circulation.

Everyone is supposed to round off to the nearest nickle. That's means that things that used to cost 16 or 17 cents will now cost 15 cents and things that used to cost 18 or 19 cents will now cost 20 cents.

---

Reviewing the "Arseniclife" Paper

Many of you will remember the "arsenic affair" from a couple of years ago. Here's what I wrote in February 2012 once we knew that the main result of the paper had been disproven by Rosie Redfield. We now know that there was no arsenic in the DNA (Erb et al. 2012, Reeves et al., 2012).

The "arsenic affair" began with a NASA press conference on Dec. 2, 2010 announcing that a new species of bacteria had been discovered. The species was named GFAJ-1 (Get Felisa a Job), by the lead author Felisa Wolfe-Simon. GFAJ-1 was grown in a medium that lacked phosphate and contained high concentrations of arsenic. The paper, published that day on the Science website, claimed that arsenic was replacing phosphorus in many of the cell's molecules, including nucleic acids.

Like many other scientists, I was very skeptical from day one. The results reported in the press conference just couldn't possibly be true unless everything we knew about chemistry and DNA was very wrong.

How did this paper ever get published in Science? I was suspicious that the normal peer review process had been skipped in order to get a major discovery into press as soon as possible.

Turns out that wasn't true. There were three reviews and they were all glowing. We know this because USA Today has obtained copies of the reviews through the Freedom of Information Act in the USA [Glowing reviews on 'arseniclife' spurred NASA's embrace] [Excerpts for the "asreniclife" investigation file]. Here are excerpts from the three reviews—I've never seen such glowing reviews.

Review 1

The manuscript Wolfe-Simon et al. demonstrates for the first time that a microorganism is able to use arsenic in place of phosphorus to sustain growth and life. This was done by using a rather simple initial selection on synthetic growth medium followed by a more in-depth analysis of the isolated organism with regard to the path of arsenic from uptake to incorporation into various cellular fractions using ICP-MS, 73As labeling and X-ray absorption near edge spectroscopy (XANES).

The results are exceptional as they show that arsenic, yet believed to be highly toxic for most organisms, in GFAJ-1, a member of the Halomouadaccae, can substitute for the lack of phosphate, a major building block for various macromolecules present in all cells, namely nucleic acids, lipids and proteins.

The methods applied are straightforward. The most surprising and acknowledgeable aspect of the work is its simple approach.

I have only a few minor points regarding the overall presentation.

Review 2

The manuscript by Wolfe-Simon et al. is well-written, concise, to the point and provides exciting novel results. The authors provide many lines of evidence to prove their point that the isolated novel bacterium (at least to some extent) can replace phosphate by arsenic in its biomolecules. It's a pleasure to get a well-conceived and carried-out study to review.

Review 3

Reviewing this paper was a rare pleasure. It is clearly-written and well-reasoned. The authors choose the right methods, designed the right experiments, obtain solid data supporting the conclusion that GSAJ-1 uses As in place of place of P. They use appropriate caution in interpreting results. I think the paper is just about publishable as is; my comments for revision are below. Great job! I look forward to seeing follow-up work in the future.

Looks like we can blame the reviewers, or perhaps the editor for choosing the wrong reviewers.

---

[Hat Tip: Michael Eisen (@mbeisen) (#arseniclife)]

Erb, T.J., Kiefer, P., Hattendorf, B., Günther, D., and Vorholt, J.A. (2012) GFAJ-1 is an arsenate-resistant, phosphate-dependent organism. Science, 337: 467-470. [doi: 10.1126/science.1218455 ]

Reaves, M.L., Sinha, S., Rabinowitz, J.D., Kruglyak, L., and Redfield, R.J. (2012) Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells. Science, 337: 470-473. [doi: 10.1126/science.1219861]

Wolfe-Simon, F., Switzer Blum, J., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D. and Oremland, R.S. (2011) A bacterium that can grow by using arsenic instead of phosphorus. Science. 332:1163-1166. Published online 2 December 2010; published in Science magazine Jun 3, 2011 [doi: 10.1126/science.1197258]

Become an Atheist

How can you resist this ad from Cult of Dusty?

---

[Hat Tip: Friendly Athiest: The Atheist Super Bowl Ad You Didn’t See]

Happy Groundhog Day!

Wiarton Willie says we're going to have an early Spring.

None of these groundhog festivals compare to the one in movie starring Bill Murray and Andie MacDowell. It's one of the best movies ever.

---

Jenny McCarthy Dumped

Wow! That was quick. I just wrote my letter a few hours ago and just posted to my blog at 11am [Why Is Jenny McCarthy Going to Ottawa?].

CTV News is now reporting that Jenny McCarthy Dumped from Bust A Move Ottawa event.

Actress Jenny McCarthy has been dumped again. McCarthy won't be in Ottawa for Bust A Move.

The Ottawa Regional Cancer Foundation reacted today to a public backlash in signing the anti-vaccine campaigner to the Ottawa breast health fundraiser.

McCarthy was to headline a fitness class for the March 2nd fundraiser at the Ottawa Athletic Club.

Social media websites exploded with negative reaction to McCarthy's choice for Ottawa's Bust A Move celebrity.

Twitter featured hashtag #DropJenny.

McCarthy has been replaced by fitness guru Tommy Europe.

Kudos to CFI Canada and Ottawa Skeptics. Well done!!!

---

What Is a Mutation?

I've said it before and I'll say it again, biology is messy. It's really hard to rigorously define simple terms because there are always exceptions. Just think of the problems we've had trying to define a gene [What Is a Gene?].

"Mutation"¹ is almost as difficult. First, we want to distinguish between a mutation and DNA damage. DNA damage occurs when various enzymes make a mistake and damage the nucleotides in a DNA molecule. Damage also occurs when outside forces such as X-rays or chemical mutagens attack DNA. Examples are thymidine dimers or cleavage of a base from a nucleotide. DNA can also be broken into two or more pieces.

This damage is never copied and passed on to the next generation. Either it is fixed in some way or it is lethal. When the damage is fixed it may end up being identical to the original DNA molecular or it may be altered in some way that is passed on. Thus, mutation is (semi-)permanent change that is heritable.

In the example shown here, the damage is deamination of cytosine, a very common spontaneous reaction. It is usually repaired fairly quickly but if the DNA is replicated before repair it will result in a switch from a G/C base pair to an A/T base pair at the same site. This change is inherited in all subsequent generations ... it is a mutation.

The genetic material is DNA in most cases but RNA genomes (viruses) can also be mutated. There are many different kinds of "genomes" that have to be covered in our definition. This include virus genomes, mitochondrial genomes, chloroplast genomes, plasmids, and mobile genetic elements (mostly transposons).

Any alteration in the sequence of a genome counts as a mutation, not just those that occur in a gene (whatever that is!). This is important because some of the traditional definitions of mutation are restricted to genes.

Here's a good definition from the Wikipedia site ...

In genetics, a mutation is a change of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element. Mutations result from unrepaired damage to DNA or to RNA genomes (typically caused by radiation or chemical mutagens), from errors in the process of replication, or from the insertion or deletion of segments of DNA by mobile genetic elements.[1][2][3] Mutations may or may not produce discernable changes in the observable characteristics (phenotype) of an organism.

The Understanding Evolution at UC Berkeley defines mutation as ...

A mutation is a change in DNA, the hereditary material of life. An organism's DNA affects how it looks, how it behaves, and its physiology. So a change in an organism's DNA can cause changes in all aspects of its life.

This isn't good because it doesn't cover RNA genomes and it doesn't distinguish between DNA damage and fixed, heritable, change.

Theme

Mutation

-definition
-mutation types
-mutation rates
-phylogeny
-controversies
The Genetic Science Learning Center at the University of Utah offer this definition.

A mutation is a permanent change in the DNA sequence of a gene. Mutations in a gene's DNA sequence can alter the amino acid sequence of the protein encoded by the gene.

That's no good because it restricts mutations to protein encoding genes.

A quick Google search will reveal many other definitions but none as as good as the Wikipedia entry.

As usual, the standard dictionary definitions are not helpful. They are usually quite poor at defining biological terms. Merriam-Webster defines mutation as ...

a relatively permanent change in hereditary material involving either a physical change in chromosome relations or a biochemical change in the codons that make up genes

This is actually better than some of the definitions from scientists. It's main deficiency is that it restricts mutations to genes.

---

1. The word comes from the Latin mutare, to change.

What About Grandfathers?

Judith Shulevitz is a journalist with no particular science background as far as I can tell. Her latest work is a piece published in The New Republic with a provocative title: Why Do Grandmothers Exist? Solving an evolutionary mystery. She writes ...

From these slim clues, Hawkes and her colleagues developed the "grandmother hypothesis," which holds that women past childbearing age helped not just their children, but their children's children, and lengthened the human lifespan in the process. Without babies of their own to lug around, grandmothers had both time and a very good reason to be useful. When they eked out food for their daughters' children, they reduced the chance that those children would die. That gave the grandmothers a better chance of passing on their own predisposition to longevity. (In general, grandmothers appear to have helped daughters' offspring more than sons'; evolutionary theorists explain this by pointing out that a daughter's maternity affords a surer genetic connection than a son's paternity, unless you all but imprison your daughter-in-law.2)

I've written about the Grandmother Hypothesis before [The Adaptive Value of Menopause] [How Women Got Their Menopause ]. It's an adaptationist just-so story that makes no sense whatsoever as soon as you start thinking critically.

But that's not what worries me today. What troubles me is that grandfathers don't seem to figure into these stories. Why is that? Are we completely irrelevant to our children and grandchildren?

---