The 39th edition of Gene Genie has been posted at Genetics & Health [Gene Genie #39: Personal genomics, health and evolution]. Welcome to the 39th edition of Gene Genie, the carnival of clinical genetics and personalized medicine.The beautiful logo was created by Ricardo at My Biotech Life.
Personalized genomics are all over the news lately, so let’s jump right and see what’s going on.
Most of you should recognize this molecule. You must describe both parts of the molecule, making sure to state clearly what you are seeing. As an extra challenge, you have to specifically mention something that is not shown even though it might be normally considered part of the complex.
The Center for Inquiry, Toronto and The University of Toronto Secular Alliance are sponsoring a lecture by PZ Myers this Friday evening (Halloween). Contact me if you want to meet PZ.See the PZ Myers Visit website for more information, including how to get tickets and how to get to the MacLeod Auditorium.PZ Myers Presents: Science Education: caught in the middle of the war between science and religion
Friday, October 31, 7:30 pm - 9:30 pm
MacLeod Auditorium
2158-1 King's College Circle,
Room 2158, Toronto, ON, M5S1A8
The Spandrels of San Marco and the Panglossian Paradigm is one of my favourite science papers. As someone who accepts natural selection as a powerful evolutionary mechanism, but who considers that there are other, equally, or perhaps more, powerful mechanism out there, such as genetic drift, this paper resonated a lot with me. To summarise the paper (if you haven’t read it, please do), not everything that happens in evolution occurs because it was selected for. Like spandrels, things can happen as a consequence of other events. To summarise the summary, sh*t happens.Welcome to the blogosphere, Chris. With an opening like that, we expect big things in the future.
Here I’d like to develop that theme using Anomalocarus.
1. I still remember how excited he and Saint Andrew (Andrew MacRae) were when the curators at the Royal Ontario Museum pulled out their famous fossil of Anomalocarus to look at. Chris and Andrew, being paleontologists, were the only ones allowed to touch it. Chris was also thrilled to see the trilobites with bite marks. Read his posting to see why.
Meet my (probably mythical)1 ancestor, Marcus Antonius (83 BC - 30 BC), better known as Mark Antony. (Color photo not available.)
Claudius married Valeria Messalina (granddaughter of Octavia) and their daughter was Genvissa (Venus Julia). Claudius then married Julia Agripina and had more children, including Emperor Nero. We aren't interested in Julia Agripina except to note her scientific contribution to the understanding of eukarotic transcription [Mushrooms for Dinner].
This data represents only a small percentage of the genetic variation in Europeans. Much of the remaining variation does not show a geographic distribution like the one in the figure because the variants arose much earlier. They have had time to spread to all subpopulations, or perhaps they pre-date the founding of the European population.1. See comments. It looks like Genvissa, the presumed daughter of Claudius, is a mythical character made up many centuries after her presumed marriage to the King of the Siluria.
Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR, Stephens M, Bustamante CD (2008) Genes mirror geography within Europe. Nature, Published online 31 August 2008 [doi:10.1038/nature07331]
Niall Nóigiallach is a very famous man (Nóigiallach is Gaelic for "having Nine Hostages"). He was an Irish King who lived from about 350 to 405 AD. The "nine hostages" refers to hostages that he kept from each of the places that owed him allegiance. 
Niall is also famous for another reason. DNA studies indicate that one in twelve Irish men carry a Y chromosome haplotype that traces back to Niall. The haplotype is also common in Scotland and England, and on the continent. This makes Niall one of only a handful of men who have millions of direct male descendants. (Genghis Khan was another [Genghis Khan a Prolific Lover, DNA Data Implies].)
Today is "Mole Day," celebrated as part of National Chemistry Week. You can read all about it on Adventures in Ethics and Science [Happy Mole Day! (What's a mole?)].1. What would you call 6.02 × 1023 Cindy Crawford moles?
One of Ms. Sandwalk's ancestors is William Playfair (1789 - 1823). Her great grandfather—the great-great-grandfather of my children—was John Playfair Leslie. John's mother is a direct descendant of William Playfair. 
William Playfair was born in Scotland and lived with his older brother John Playfair in Edinburgh. John Playfair was a distinguished Professor of Mathematics at the University of Edinburgh. Their other brother was the architect James Playfair.
From Amazon.com.Before he began his recent travels, it seemed to Phil Zuckerman as if humans all over the globe were “getting religion” — praising deities, performing holy rites, and soberly defending the world from sin. But most residents of Denmark and Sweden, he found, don’t worship any god at all, don’t pray, and don’t give much credence to religious dogma of any kind. Instead of being bastions of sin and corruption, however, as the Christian Right has suggested a godless society would be, these countries are filled with residents who score at the very top of the “happiness index” and enjoy their healthy societies, which boast some of the lowest rates of violent crime in the world (along with some of the lowest levels of corruption), excellent educational systems, strong economies, well-supported arts, free health care, egalitarian social policies, outstanding bike paths, and great beer.
Zuckerman formally interviewed nearly 150 Danes and Swedes of all ages and educational backgrounds over the course of fourteen months, beginning in 2005. He was particularly interested in the worldviews of people who live their lives without religious orientation. How do they think about and cope with death? Are they worried about an afterlife? What he found is that nearly all of his interviewees live their lives without much fear of the Grim Reaper or worries about the hereafter. This led him to wonder how and why it is that certain societies are nonreligious in a world that seems to be marked by increasing religiosity. Drawing on prominent sociological theories and his own extensive research, Zuckerman ventures some interesting answers.
This fascinating approach directly counters the claims of outspoken, conservative American Christians who argue that a society without God would be hell on earth. It is crucial, Zuckerman believes, for Americans to know that “society without God is not only possible, but it can be quite civil and pleasant.”
”Most Americans are convinced that faith in God is the foundation of civil society. Society Without God reveals this to be nothing more than a well-subscribed, and strangely American, delusion. Even atheists living in the United States will be astonished to discover how unencumbered by religion most Danes and Swedes currently are. This glimpse of an alternate, secular reality is at once humbling and profoundly inspiring — and it comes not a moment too soon. Zuckerman’s research is truly indispensable.”It's not just Denmark and Sweden. Many European countries are essentially secular as are many parts of Australia, New Zealand and Canada. Even in the USA, there are pockets of the country where the influence of religion is minimal.
—Sam Harris
[Hat Tip: RichardDawkins.net]
Bishop James Ussher (1581 - 1656) was Archbishop of Armagh and Primate of All Ireland. He calculated that the universe was created on this day in 4004 BC, or more correctly the night before this day. 
"for the discovery of the production of mutations by means of X-ray irradiation"
Hermann Joseph Muller (1890 - 1967) won the Noble Prize for showing that X-rays could induce mutations in Drosophila melanogaster. He was able to isolate and map specific mutations caused by X-rays showing that these were stable genetic changes. It was known, already at the turn of the century, that apparently sudden changes may appear spontaneously in the hereditary mass, which result in changes in the characteristics of the organism. We now know that these changes may be of different types, and among them occur also disturbances in individual genes. These are very rare, however. Even in such a convenient experimental object as the banana fly, introduced by Morgan, where the generations succeed each other rapidly, and thousands of flies can be examined, it is only seldom that mutations are observed. Muller grappled with the task of trying to change the frequency of mutations. He first created procedures, technically extremely elegant, by which the mutation frequency could be measured exactly. When this task - which took several years - had been completed, the effect of different agents on the frequency of mutations was investigated, and the discovery for which the Nobel Prize is now awarded was made, viz. that irradiation with X-rays evokes large numbers of mutations. Experiments could be arranged, for instance, so that nearly 100 per cent of the offspring of irradiated flies showed mutations. Thus a possibility had been created for the first time of influencing the hereditary mass itself artificially.
This discovery aroused a great sensation already when it was first published in 1927 and rapidly led to a great deal of work of different kinds and in the most varied directions. The mechanism of the effect of rays was studied by many research workers, with Muller at their head. Greatly simplified X-ray irradiation, as also ionizing irradiation, could be likened in general to a shower of infinitely small (even compared with the individual cell) but highly explosive grenades, which explode at different spots within the irradiated organism. The explosion itself (or the fragments it throws up) tears the structure of the cell to pieces or disturbs its arrangement. If such an explosion happens to take place in or close to a gene, its structure, and therewith also its effect on the organism, may be changed.
Muller's discovery of the induction of mutations by means of rays has been of tremendous importance for genetics and biology in general.
A posting on the Scientific American website describes the view of Francisco J. Ayala, a man who was ordained as a Dominican priest who is also an excellent scientist [The Christian Man's Evolution: How Darwinism and Faith Can Coexist .Ayala graduated in physics at the University of Madrid, then worked in a geneticist’s lab while studying theology at the Pontifical Faculty of San Esteban in Salamanca, Spain. By his ordination in 1960 he had already decided to pursue science instead of a ministerial role. At the monastery Darwinism had never been perceived as an enemy of Christian faith. So a year later, when Ayala moved to New York City to pursue a doctorate in genetics, the prevailing U.S. view of a natural hostility between evolution and religion was a shock.I've already commented on the National Academys' sellout to political correctness and on the fact that Ayala was Chair of the committee [Richard Dawkins on the Michael Reiss Affair] [National Academies: Science, Evolution and Creationism]. The fallacy here is something called The Doctrine of Joint Belief.
Ever since, Ayala has attempted to address religious skepticism about Darwin’s theory. At first, he recalls, his scientific colleagues were wary and took the position that researchers should not engage in religious discussions. By 1981, when the Arkansas legislature voted to give creationism equal time in schools, the mood began to change. The National Academy of Sciences prepared an amicus curiae brief for a Supreme Court case on the Louisiana “Creation Act” and asked Ayala to lead the effort. The booklet became the 1984 Science and Creationism: A View from the National Academy of Sciences.
For the second edition in 1999 Ayala presented the idea of incorporating the words of some theologians but recalls, “I was almost eaten alive.” In the third edition, published this year, one section features statements by four religious denominations and three scientists on the compatibility of evolution with religious beliefs.
1. "Sally Lehrman teaches journalism in the public interest at Santa Clara University."
