Monday's Molecule #128

 
Name this molecule. Include the IUPAC name and a brief description of its function.

One Nobel Laureate got the prize for contributions to organic chemistry, including working out the structure of this molecule.

The first person to identify the molecule and the Nobel Laureate, wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Òscar Reig of Barcelona, Maria Altshuler of the University of Toronto, Mike Fraser of the University of Toronto, Jaseon Oakley of the University of Toronto, Bill Chaney of the University of Nebraska, Ian Clarke of New England Biolabs Canada in Pickering ON, Canada and Dima Klenchin of the University of Wisconsin at Madison.

Dima has donated his free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours.

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Are Creationists Rational?

 
I don't think that creationism is a rational choice, especially Young Earth Creationism. John Wilkins isn't so sure [Are Creationists Rational?].

I highly recommend his article. It addresses the reasons why creationists think the way they do. I disagree with John's conclusion that you can't change the minds of most committed creationists and I disagree somewhat with John's definition of science. John seems to imply that science is what scientists do whereas I see science as a way of knowing that permeates all aspects of knowledge discovery. I would even argue that John is using the scientific way of knowing in his philosophy papers.

If you disagree, John, can you identify the other way of knowing that you are using?

I think that science as a way of knowing&mdashbased on evidence and rationality—should not only be taught in science classes. It should also be part of the core concepts in history, geography, English, civics, and social studies.

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IDiot Contest Question

 
Denyse O'Leary continues to look for ways to give away a few copies of the Expelled DVD. In order to win you have to write a 400 word essay on a particular topic and Denyse will pick the one that best conforms to her personal criteria.

This time Denyse is worried about Rob Day (aka Canadian Cynic) so she asks ... [Uncommon Descent: Contest Question 7: Foul anonymous Darwinist blogger exposed. Why so foul?]

Why do so many of Darwinists spout so much filth, hostility, and aimless detraction?

Realizing that she might get the wrong answers she adds another rule to the contest.

Note: Entries that merely claim it isn’t happening will not be judged. Too many people here know otherwise.

On a completely urelated topic, here are some interesting quotations from Conservapedia ...

Dr. Josef Mengele's evolutionary thinking was in accordance with social Darwinist theories that Adolph Hitler and a number of German academics found appealing.[15] Dr. Joseph Mengele studied under the leading proponents the "unworthy life" branch of evolutionary thought.[16] Dr. Mengele was one of the most notorious individuals associated with Nazi death camps and the Holocaust.[17] Mengele obtained a infamous reputation due to his experiments on twins while at Auschwitz-Birkenau.[18]

Prominent evolutionist and atheist Richard Dawkins stated the following regarding Adolf Hitler in an interview: “What’s to prevent us from saying Hitler wasn’t right? I mean, that is a genuinely difficult question."[19] The interviewer of Richard Dawkins wrote the following regarding the Richard Dawkins comment about Hitler: "I was stupefied. He had readily conceded that his own philosophical position did not offer a rational basis for moral judgments. His intellectual honesty was refreshing, if somewhat disturbing on this point."[20]

In addition to greatly influencing Hitler's Nazism, evolutionary ideas influenced the thinking of the Communists, including Marx, Engels, Vladimir Lenin, and Joseph Stalin.[21] Marx wrote, "Darwin's book is very important and serves me as a basis in natural science for the class struggle in history."

...

As noted earlier, evolutionary ideas contributed to the scourge of racism. [25][26] Charles Darwin and Thomas Huxley contributed greatly to the theory of evolution broadly being accepted in the 1900s. [27] Darwin, Huxley, and the 19th century evolutionists were racist in sentiment and believed the white race was superior.

And here's an interesting posting from Denyse O'Leary herself: If you accept the argument in Descent of Man, you accept a racist argument . Now don't get me wrong, I'm not saying that the creationists are being mean and hostile by accusing evolutionists of racism and genocide. No siree, not me. I'm sure they wouldn't do that.

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Quacks in the ER

 
Here's what the emergency room would look like if homeopathy and naturopathy became real medicine instead of alternative medicine.

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[Hat Tip: Pharyngula]

Nobel Laureate: Leopold Ruzicka

 

The Nobel Prize in Chemistry 1939.

"for his work on polymethylenes and higher terpenes"




Leopold Ruzicka (1887 - 1976) won the Nobel Prize in Chemistry for his contributions to organic chemistry—especially the structures of polymethylenes and higher terpenes.

One of the structures that Ruzicka solved was that of muscone, the molecule responsible for the smell of musk. The perfume industry required large supplies of this molecule which could only be prepared from the musk gland of musk deer. The preparation of synthetic muscone probably saved the musk deer from extinction.

Ruzika was born in Austria-Hungary but he spent most of his career in Switzerland. Do to political circumstances in 1939, the prize was awarded at a special ceremony in Switzerland in January 1940. Ruzika attended another ceremony in Sweden at the end of the war. He shared the 1939 Nobel Prize with Adolf Friedrich Johann Butenandt.


The special award presentation describes the work on sex hormones.
THEME:
Nobel Laureates

When studying the natural odorants occurring in musk and civet, muscone and civetone, little known until then, Ruzicka obtained fundamentally new and surprising results during the years 1924-1926. He discovered that the molecule of muscone as well as that of civetone contains one single ring of carbon atoms, the number of which was considerably larger than that in all hitherto known cyclic molecules, larger even than had been considered possible. During his investigations of these odora he synthesized many kindred macrocyclic compounds, and drew attention to the plant-physiologically remarkable fact that these could be prepared from natural fatty acids.

Many interesting relationships exist between the polyterpenes studied by Ruzicka and a series of physiologically and medicinally important groups of compounds, viz. the bile acids, the sterols and the sex hormones. Among the many interesting results obtained by Ruzicka and his collaborators with sex hormones, the preparation of compounds with the same action as male sex hormones is of signal importance. It is his merit that by establishing preparative methods for androsterone and testosterone the technical synthesis of these two hormones has been made possible.

Moreover, the numerous new related compounds prepared by Ruzicka have contributed fundamentally to our knowledge of the physiologically so very important sex hormones, thus creating a sound basis for future investigations.

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[Photo Credit (bottom): ETH-Bibliothek Zürich, Bildarchiv: Creative Commons License]

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Nobel Laureate: Hans Spemann

 

The Nobel Prize in Physiology or Medicine 1935

"for his discovery of the organizer effect in embryonic development"

Hans Spemann (1869 - 1941) won the Noble Prize in 1935 for his contributions to developmental biology. He worked mostly with the eggs of newts and frogs and through careful observation of the developing embryo he was able to work out the fate of many cells in the early embryo.

Spemann reasoned that some cells in the early embryo were able to direct the fate of other cells. By transplanting parts of one embryo to specific locations in another embryo he determined which cells acted as organizing centers, presumably by secreting regulatory molecules [see Monday's Molecule #126 and The Spemann–Mangold organizer experiment in 1924].

Here's an excerpt from the Presentation Speech.
THEME:
Nobel Laureates

Much thought has been given to the nature of the forces and causality regulating this development. It is at this point that Spemann's researches begin. He used eggs of various animal species which differ in colour, and with his simple instruments transplanted small pieces of tissue in different stages of development. By this means he was able to establish that, for example, a cell mass normally destined to become ventral epidermis - Spemann calls it presumptive ventral epidermis -could develop into nerve tissue if it were put in the place where the spinal cord was to develop. Hence, the course of development of these cells was not laid down in advance or it could - if such was the case - be altered by transplantation; so that the transplanted portion adjusted itself to its new environment. When Spemann then transplanted the anterior lip of the blastopore of an embryo into the ventral side of another embryo it grew a new brain and spinal cord. This brain and spinal cord did not arise from the transplanted cell material, but from the presumptive ventral epidermis whose course of development was thus altered by the presence of the blastopore. From this Spemann could ascertain that the blastopore had an organizing influence on its environment. The cell material which was grafted into the ventral epidermis and caused the development of the new spinal cord was actually of the kind that, developing normally, would have given rise to the notochord. Further experiments showed that it is the notochord primordia which organize the development of the primordial spinal cord, while, on the other hand, the mesoderm in the head causes the development of a primordial brain. Near this arise the so-called optic vesicles which are the origin of the retina of the eye. Where these approach the ectoderm of the head they organize the development of the lens of the eye. Or, to take another example: the anterior end of the primordial gut (the oesophagus) organizes the development of a primordial mouth and primordial teeth inside it. Thus, we now see how cell masses originally undifferentiated have the course of their development laid down by the influence of rudiments of organs formed earlier. Thereafter, a cell mass such as this can assume the role of organizer in relation to its environment.

In this way we begin to understand how the laws of development work. We begin to perceive why a primordial head arises at the anterior end of the embryo, why a brain always arises in the head and never anywhere else, or why the mouth always has its place below the primordial brain and never elsewhere.

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[Image Credit: E. M. De Robertis and Hiroki Kuroda (2004)]

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Canadian Cynic Is Coming to Town

 
Don't forget that Canadian Cynic is giving a talk tomorrow night at CFI Toronto [Creationism, ID and the Douchebaggery of Really Bad Arguments: An Evening with the Canadian Cynic].

This is your big chance to meet the man behind the blog.

We'll be getting together for food and beverages before his talk. Email me if you'd like to join us.

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Monday's Molecule #127: Winner

 
The molecule is muscone or [R]-3-methyl-cyclopenta-decanone. This is one of the main ingredients in the musk odor used in perfumes. The original chemical is the R-enantiomer shown below. It was extracted from the musk glands of musk deer (right). Modern perfumes are made from synthetic muscone, which is a mixture of the R- and S-enantionmers.

The Nobel Laureate is Leopold Ruzicka, who worked out the structure of muscone.

This week's winner is Dima Klenchin of the University of Wisconsin.

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Today's molecule stinks.¹ You have to identify it by giving me the common name and the IUPAC name.

There's only one Nobel Laureate whose name is linked to this molecule. The Laureate was responsible for determining its structure.

The first person to identify the molecule and the Nobel Laureate, wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Michael Clarkson of Waltham MA (USA), Òscar Reig of Barcelona, Maria Altshuler of the University of Toronto, Mike Fraser of the University of Toronto, Jaseon Oakley of the University of Toronto, Bill Chaney of the University of Nebraska and Ian Clarke of New England Biolabs Canada in Pickering ON, Canada.

Bill Chaney has donated his free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

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

---

1. Opinions may vary.

Genes, Phylogeny, and Orangutans: A Correction

 
In a recent posting I described how New Scientist devoted several pages to the idea that orangutans could be our closest relatives [Genes, Phylogeny, and Orangutans. Here are my exact words,

It's a lesson that New Scientist should have learned. They devote several pages to the Grahan and Schwartz paper thereby giving it much more publicity than it deserves [Could the orang-utan be our closest relative?]. The article is written by Graham Lawton who you might remember from the "Tree of Life" episode [see: Explaining the New Scientist Cover]. The editors of New Scientist knew full well that their decision would be controversial so they took a proactive position by writing a short editorial [In praise of scientific heresy ]. [my emphasis - LAM]

I've received an email message from Graham Lawton, Deputy editor of New Scientist and the author of the article. He points out correctly that the article was exactly two pages long and the editorial was 400 words. He thinks that this is significantly less than "several pages" and asks me to correct my "mistake."

So, for those who think that two pages and a short editorial don't qualify as "several pages," I apologize for my "mistake." I only wanted to make it clear that the coverage was not just a few lines in their weekly survey of press releases.

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Does Teaching Science Lead to Atheism?

 
Does science lead to atheism? My short answer is "no" just like the answer given by John Wilkins and Matt Young. Their emphasis is on whether scientists are always atheists and whether those who are atheists became atheists because of science or whether they picked science as a profession because they were nonbelievers. Not all scientists are atheists, therefore science doesn't inevitably lead to atheism. That's their position.

Let's ask a different question. Would good science education in the public schools convert religious students to atheism? No, it is not true that exposing students to good science teaching will inevitably make them abandon their religion.

Is that all there is? No, the question can't be answered in such a simple manner. I think that a good science education will threaten most religious beliefs and in some cases will cause students to abandon those beliefs.

Let's imagine what a good science education would look like. The teachers would explain how science works. They would teach that scientific explanations require evidence and logic and that everyone should learn to be skeptical of all claims. Teachers would use examples like evolution, plate tectonics and cosmology to describe good science and how new ideas are incorporated into our understanding of the way things work. They would use astrology, homeopathy, and the deluge as examples of how some explanations do not conform to the expectations of science. The goal is to stimulate students to think and teach them how to do it in a scientific manner.

Imagine that there are religious students in the class. There seem to be three possible ways they could incorporate their knowledge about science into their religious worldview.

1. It will have no effect on their beliefs.
2. It will cause them to question and possibly abandon some of their beliefs.
3. It will reinforce and strengthen their beliefs.

I strongly suspect that more students will start questioning their beliefs when they are exposed to good science education but I admit I have no data to support that suspicion. Does anyone think that the net effect would be to strengthen beliefs or leave them unaffected?

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Genes, Phylogeny, and Orangutans

Jeffrey H. Schwartz is well known to talk.origins veterans because we discussed his book (Sudden Origins: Fossils, Genes, and the Emergence of Species) back in 1999. Schwartz tried to make the case for a "groundbreaking and radical new theory of evolution." This "theory" was based on the idea that new species spring into existence very quickly when a mutation in a homeobox (HOZ) gene arises in a population. It's a "theory" of saltation but it's based on such a flawed understanding of genetics that you really have to read to book to see just how bad it is. Sudden Origins is a leading candidate for the worst science book ever published.

In case you want to see a shorter version, the basic idea is explained in Schwartz (1999).

Over the years, Schwartz has published many other ideas that are controversial. Lately he has been pushing the concept that molecular phylogenies are unreliable. In part this is because he is opposed to gradual change as documented in the record of the genes. He thinks that real evolution takes place when alterations of regulatory genes result in major new phenotypes. Thus, the best way to discover the history of life is to examine anatomical homologies and differences.

But part of the problem lies in Jeffrey Schwartz's idiosyncratic understanding of genetics and molecular biology. When you put these together, this is what you get in Schwartz (2009).

This having been said, systematics and evolutionary biology need not remain estranged. Developmental biology increasingly makes clear that organismal change (and by extension, evolution), is not how it was imagined when the synthesis emerged (see reviews in Schwartz 1999, 2009b; Maresca and Schwartz 2006). Further, because of the interrelation between, e.g., the physical properties of cells, signaling pathways, epigenetic effects and development and consequently the origination of form, the false dichotomy of ‘‘molecules versus morphology’’ that resulted in the 1980s from the dethroning of morphology by the hegemony of molecular analyses is no longer tenable (Schwartz 2009a). Indeed, the undeniable hierarchical continuum from the molecular through the morphological, firmly centralizes morphology (as understood via development) in systematic endeavors (Schwartz 2009a).

Grahan and Schwartz (2009) have just published a paper in which they claim that orangutans are more closely related to humans that are chimpanzees. According to them, the molecular data is not reliable. They claim that detailed morphological comparisons show that orangutans are our closest ancestor.

John Hawks asks the question "Are orangutans our closest living relatives?" and he comes up with the best possible answer to scientists with a well-known history of promoting "unusual" positions on evolution.

It's a lesson that New Scientist should have learned. They devote several pages to the Grahan and Schwartz paper thereby giving it much more publicity than it deserves [Could the orang-utan be our closest relative?].¹ The article is written by Graham Lawton who you might remember from the "Tree of Life" episode [see: Explaining the New Scientist Cover]. The editors of New Scientist knew full well that their decision would be controversial so they took a proactive position by writing a short editorial [In praise of scientific heresy ].

If its claims are so outlandish, should the research even have been published? Some scientists would clearly have preferred it if the paper had never seen the light of day, and question the judgement of the journal.

That is territory we should tread with care. Ideas that mainstream opinion "knows" to be wrong occasionally turn out to be right. The insights of Galileo, Stan Prusiner - who discovered prions - and many others were once denounced as heresy. And even those that are wrong can be valuable.

Science proceeds by questioning its own assumptions and regarding every "fact" as provisional, so alternative hypotheses should be given an airing, if only to reaffirm the strength of the orthodoxy. Science that pulls up the drawbridge on new ideas risks becoming sterile. The journal recognised that and should be applauded for its decision to disseminate this challenging paper.

There's some truth here, but only some. You can't use Stanley Prusiner as an excuse to publish every crazy idea that comes along. Some ideas really are crazy—they are not revolutions in disguise. The plain fact is that Jeffrey H. Schwartz has already had his chance to make his case and he has not been successful. How many chances does he get before we draw the obvious conclusion?

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1. The article was two pages long and the editorial was much less than one page. This may not qualify as "several" pages by some definitions.

[Photo Credit: Daily Mail]

Grehan, J.R. and Schwartz, J.H. (2009) Evolution of the second orangutan: phylogeny and biogeography of hominid origins. Journal of Biogeography, published online June 22. 2009. [doi:10.1111/j.1365-2699.2009.02141.x]

Schwartz, J.H. (1999) Homeobox genes, fossils, and the origin of species. Anat Rec. 15:15-31. [PubMed]

Schwartz, J.H. (2009) Reflections on Systematics and Phylogenetic
Reconstruction. Acta Biotheor 57:295–305 [doi: 10.1007/s10441-009-9078-9]

What Can Scientists Do to Help Science Journalism?

 
This week's issue of Nature has a number of articles devoted to science journalism. Their publication coincides with the 6th World Conference of Science Journalists in London, UK.

One of the articles is an editorial, Cheerleader or watchdog?, about what scientists can do to help science journalism.

Scientists can do little to stem this bloodletting. But whatever they can do to engage with those caught up in it, and ensure that questioning and informed science journalism persists, will be worthwhile. If there is to be a transition to new — perhaps philanthropic — business models for in-depth reporting or new types of analytical media, science journalism will integrate into them all the better if scientists are taking an active interest in its health. And if the future of the media truly is a dire landscape of top-100 lists, shouting heads and minimal attention span, then such efforts might at least defer the grim end.

Even amid the turmoil, however, scientists can help ensure that reporting about science continues to be both informed and accurate.

I agree that scientists should work on trying to make science reporting more accurate. So far, we haven't been too successful.

But there's another important contribution we can make. We can help clean up our own act so that less bad science is published. This will not only make science better, it will have the spin-off effect of making life easier for science journalists. At the very least, we should make sure that press releases coming from our institutions are accurate. Every scientists should have to stand behind and endorse the press releases from their supporting institution. Let's take responsibility.

Also, wouldn't it be nice if most of the papers published in the scientific literature were careful to put their work in the proper perspective? Wouldn't it be nice if scientists themselves stopped exaggerating their contributions and stopped making outrageous claims? Science journalists have not done a good job of sifting the wheat from the chaff, in spite of what they think. They are far from blameless but scientists carry a bigger share of the blame for the sorry state of science literacy.

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Campus Excitement

 
There's usually something exciting happening on the University of Toronto campus during the summer.

It's a popular location for shooting movies and TV shows and you never know what you'll find on any given day. This is the scene that greeted me today when I emerged from the subway station. It took a few seconds to realize that I wasn't in the middle of a real emergency.

Last week the front campus was the scene of a bank truck robbery in Germany, just in front of a sidewalk café. I wish they'd left the outdoor tables and umbrellas and kept serving the wine and food.

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Monday's Molecule #127

 

Today's molecule stinks.¹ You have to identify it by giving me the common name and the IUPAC name.

There's only one Nobel Laureate whose name is linked to this molecule. The Laureate was responsible for determining its structure.

The first person to identify the molecule and the Nobel Laureate, wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Michael Clarkson of Waltham MA (USA), Òscar Reig of Barcelona, Maria Altshuler of the University of Toronto, Mike Fraser of the University of Toronto, Jaseon Oakley of the University of Toronto, Bill Chaney of the University of Nebraska and Ian Clarke of New England Biolabs Canada in Pickering ON, Canada.

Bill Chaney has donated his free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours.

---

1. Opinions may vary.

Grandpa Burger

 
When I was (much) younger I used to order the Teen Burger when we went to the A&W. Even after I stopped being a teenager I still got the Teen Burger 'cause I wasn't really eligible for any of the others.

While we were living in Europe there were no A&W's in our part of the world so I didn't have a problem choosing what to order. By the time we returned to Canada, Jane had been born and I could order the Papa Burger without feeling guilty.¹

Here I am at the the A&W yesterday, trying out the Grandpa Burger. Technically, I won't be officially eligible for the Grandpa Burger until next January. Coincidentally, that's when my daughter Jane and her husband Michael will be able to buy the Mama and Papa Burgers.

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1. I sometimes cheated and ordered the teenburger anyway.

[Hat Tip: A&W Grandpa Burger commercial.]