Random Genetic Drift: a controversy?

Over my time as a dilettante observer of the science blogging community, I have noticed a certain frisson of controversy over the idea of random genetic drift. Sewall Wright, who with Ronald Fisher and J. B. S. Haldane (Bill Bryson’s observations on Haldane’s research into diving and decompression are entertaining) established the science of population genetics, is credited with coining the phrase in 1929. Thanks to Professor Joe Felsenstein for pointing out his seminal paper. Continue reading

McKinnon’s Paper on Miracles

In the Alastair McKinnon paper (“Miracle” and “Paradox”) I cited in a recent comment, it is argued that miracles of a certain kind are impossible.  The impossible ones are the ones that would provide any evidence of supernatural objects or occurrences.

We can call any of those most wondrous miracles a “miracle1.”  Any other miracle, which would be more in the nature of an amazing coincidence, we can designate as a “miracle2.”  Note that there’s nothing about a coincidence that provides evidence of the supernatural (something beyond nature).  And what does it mean to be “supernatural”?  It means to violate a natural or physical law. Continue reading

Reliance on Testimony to Miracles

  • Humans acquire a vast amount of factual information through testimony, arguably more than they learn through experience.
  • The extensive reliance on testimony is remarkable given that one often cannot verify testimonial information.
  • What makes testimony distinct from storytelling is that it has an implicit or explicit assertion that the telling is true. The literary format and style of the Gospels is that of the ancient biography, a historiographic genre that was widely practiced in the ancient word. Thus, one can regard these accounts as a form of testimony.

A Natural History of Natural Philosophy (pp. 165-172)

Continue reading

What Are You (or Have You) Been Reading This Summer?

A couple of comments on another thread got me wondering about this.  In my own case, I’m re-reading Middlemarch (for a discussion at the Boston Athenaeum in September) and continuing my reading on the Russian Revolution. I’ve finished the The Great Russian Revolution, by V. Chernov, and am now into Agrarian Foes of Bolshevism, by O. Radkey.  Also finishing up D. Hausman’s Rationality, Self-Interest, and Welfare.

How about you?

Faith vs Fact (Coyne’s book reviewed by Steven Pinker)

http://www.cell.com/current-biology/pdf/S0960-9822(15)00743-5.pdf

Seems to fit in with recent threads.

His latest book, Faith Versus Fact, is
intended not to pile on the arguments
for atheism but to advance the debate
into its next round. It is a brief against the
faitheists — scientists and religionists
alike — who advocate a make-nice
accommodation between science and
religion. As with Michael Corleone’s offer
to Nevada Senator Pat Geary in The
Godfather Part II, Coyne’s offer to religion
on the part of science is this: Nothing.
This sounds more imperialistic and
scientistic than it really is, because Coyne
defi nes ‘science’ broadly, to encompass
any system of belief grounded by reason
and evidence, rather than faith. On
this defi nition, many of the humanities,
such as history and philosophy, count
as ‘science’, not just the traditional
physical and social sciences.

Coyne quotes several historical and
recent writers, particularly Carl Sagan
and the philosophers Yonatan Fishman
and Maarten Boudry, while adding some
examples of his own, to show how the
existence of the God of scripture is a
testable empirical hypothesis. The Bible’s
historical accounts could have been
corroborated by archaeology, genetics
and philology. It could have contained
uncannily prescient truths such as “thou
shalt not travel faster than light” or “two
strands entwined is the secret of life.” A
bright light might appear in the heavens
one day and a man clad in white robe and
sandals, supported by winged angels,
could descend from the sky, give sight
to the blind, and resurrect the dead. We
might discover that intercessory prayer
can restore hearing or re-grow amputated
limbs, or that anyone who speaks the
Prophet Mohammed’s name in vain is
immediately struck down by lightning,
while those who pray to Allah five times a
day are free from disease and misfortune.

Innate dualism and intimations of eternal life

Excerpts from a new article at Aeon by Natalie Emmons:

We see faces in the clouds and we might just see Jesus in our toast: the fact that we see anyone at all tells us that the human mind is actively searching for agents, even in the most ambiguous of situations.

…Bering and his colleagues set their sights on what psychologists call ‘intuitive mind-body dualism’ as an alternative…The study deliberately included a cluster of children too young to have been exposed to much religious testimony at all, to see whether even they had an inkling that a part of an individual survives death.

Continue reading

On the Probability of Two Things Happening

On the ‘Evolving Complex Adaptations’ thread, a side-discussion arose with CharlieM over Behe’s ‘CCC’ argument. In summary, Behe places an event of probability {10^{-40} as the upper bound or ‘Edge of Evolution’. If a specific single mutation has a probability of {10^{-10} of arising in any one replication event, a specific double mutation has a probability of {10^{-20}, a triple {10^{-30}, and a quadruple {10^{-40} – that is, if four independent changes must happen simultaneously before a particular step is achievable, then that step cannot realistically have occurred in the history of life on earth. Behe thinks he has found a case with a {10^{-20} probability in the resistance to chloroquine in the malaria parasite Plasmodium falciparum.
Continue reading

Crispr-Cas9

http://www.wired.com/2015/07/crispr-dna-editing-2/

A little bit of this and a little bit of that. A new and cheap way to implement genetic engineering, and a way to bypass the usual rules of population genetics.

The stakes, however, have changed. Everyone at the Napa meeting had access to a gene-editing technique called Crispr-Cas9. The first term is an acronym for “clustered regularly interspaced short palindromic repeats,” a description of the genetic basis of the method; Cas9 is the name of a protein that makes it work. Technical details aside, Crispr-Cas9 makes it easy, cheap, and fast to move genes around—any genes, in any living thing, from bacteria to people. “These are monumental moments in the history of biomedical research,” Baltimore says. “They don’t happen every day.”

ANY GENE TYPICALLY has just a 50–50 chance of getting passed on. Either the offspring gets a copy from Mom or a copy from Dad. But in 1957 biologists found exceptions to that rule, genes that literally manipulated cell division and forced themselves into a larger number of offspring than chance alone would have allowed.

A decade ago, an evolutionary geneticist named Austin Burt proposed a sneaky way to use these “selfish genes.” He suggested tethering one to a separate gene—one that you wanted to propagate through an entire population. If it worked, you’d be able to drive the gene into every individual in a given area. Your gene of interest graduates from public transit to a limousine in a motorcade, speeding through a population in flagrant disregard of heredity’s traffic laws. Burt suggested using this “gene drive” to alter mosquitoes that spread malaria, which kills around a million people every year. It’s a good idea. In fact, other researchers are already using other methods to modify mosquitoes to resist the Plasmodium parasite that causes malaria and to be less fertile, reducing their numbers in the wild. But engineered mosquitoes are expensive. If researchers don’t keep topping up the mutants, the normals soon recapture control of the ecosystem.

Push those modifications through with a gene drive and the normal mosquitoes wouldn’t stand a chance. The problem is, inserting the gene drive into the mosquitoes was impossible. Until Crispr-Cas9 came along.

Emmanuelle Charpentier did early work on Crispr.Today, behind a set of four locked and sealed doors in a lab at the Harvard School of Public Health, a special set of mosquito larvae of the African species Anopheles gambiae wriggle near the surface of shallow tubs of water. These aren’t normal Anopheles, though. The lab is working on using Crispr to insert malaria-resistant gene drives into their genomes. It hasn’t worked yet, but if it does … well, consider this from the mosquitoes’ point of view. This project isn’t about reengineering one of them. It’s about reengineering them all.

Principle of Sufficient Reason (PSR)

The Principle of Sufficient Reason is a powerful and controversial philosophical principle stipulating that everything must have a reason or cause. This simple demand for thoroughgoing intelligibility yields some of the boldest and most challenging theses in the history of metaphysics and epistemology. In this entry we begin with explaining the Principle, and then turn to the history of the debates around it.

Principle of Sufficient Reason

Continue reading