The ID Report

by Denyse O'Leary
ARN correspondent

Here's my Mercator.Net story on Francis Collins as new NIH head:

President Obama has chosen an evangelical Christian as the new head of the National Institutes of Health. He is coming under fire from both sides of the culture wars.

[ ... ]

Of course, his advocacy of faith as a public scientist has received mixed reviews, to the point of attracting histrionics about looming "theocracy."

But now that Collins faces confirmation hearings before the Senate, the focus will shift from his persona to his view on issues relevant to his new job. He seems much more relaxed about abortion and human embryonic stem cell research than the average evangelical leader, so it will be interesting to see if he attracts any flak on that account.

Go here for more.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

This was the question:

Here's On the Epistemological Crisis in Genomics by Edward R Dougherty, which moved in Current Genomics, April 2008.

Abstract

There is an epistemological crisis in genomics. At issue is what constitutes scientific knowledge in genomic science, or systems biology in general. Does this crisis require a new perspective on knowledge heretofore absent from science or is it merely a matter of interpreting new scientific developments in an existing epistemological framework? This paper discusses the manner in which the experimental method, as developed and understood over recent centuries, leads naturally to a scientific epistemology grounded in an experimental-mathematical duality. It places genomics into this epistemological framework and examines the current situation in genomics. Meaning and the constitution of scientific knowledge are key concerns for genomics, and the nature of the epistemological crisis in genomics depends on how these are understood.

He kvetched,

The rules of the scientific game are not being followed. Given the historical empirical emphasis of biology and the large number of ingenious experiments that have moved the field, one might suspect that the major epistemological problems would lie with mathematics, but this is not the case. While there certainly needs to be more care paid to mathematical modeling, the major problem lies on the experimental side of the mathematical-experimental scientific duality. High-throughput technologies such as gene-expression microarrays have lead to the accumulation of massive amounts of data, orders of magnitude in excess to what has heretofore been conceivable. But the accumulation of data does not constitute science, nor does the a postiori rational analysis of data.

What's happened since? Another black hole?

Contest question, for a free copy of Expelled?: What rules of science are relevant for genomics. Are they being followed?

This one didn't attract a lot of entries and they were all from the same person. Principally, I suppose, that is because many people interested in genomics react to the "crisis" the way I reacted to a recent claim about a "crisis" in cosmology around gravity. To most of us, a crisis is when you lock yourself out of the house and see through the window that the dog has tipped the candlabra and set fire to the carpet. If you don't do something useful right this minute, you soon won't have a house or a dog.

Okay, and the winner is, by acclamation, Lock, for 2:

From Edward R Dougherty: "But the accumulation of data does not constitute science, nor does the a postiori rational analysis of data."

I assume he uses an a priori framework with which to make that judgement?

Of course he does. And rightly so. And that lens is the one science should be using (and does ... but not consistently).

Here is the insanity ... science uses this lens religiously, except that when doing so the evidence points to religious conclusions.

Denyse, you asked: "What rules of science are relevant for genomics?"

Available empirical data examined consistently through the lens of the 'law of non-contradiction'.

"Are they being followed?"

Really now ... is that question necessary?

While Lock says he already owns Expelled, it may make a handy gift item, so he needs to be in touch with me at oleary@sympatico.ca, to arrange shipment of his prize.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

In "Why microbes are smarter than you thought," Michael Marshall at New Scientist (June 30, 2009) intros and links many stories of the amazing ways microbes manage without brains and can even appear to think ( well, not really, but ... ). Here's my favourite, but go here for more:

Many single-celled organisms can work out how many other bacteria of their own species, are in their vicinity - an ability known as "quorum sensing".

Each individual bacterium releases a small amount of a chemical into the surrounding area - a chemical that it can detect through receptors on its outer wall. If there are lots of other bacteria around, all releasing the same chemical, levels can reach a critical point and trigger a change in behaviour.

Pathogenic (disease-causing) bacteria often use quorum sensing to decide when to launch an attack on their host. Once they have amassed in sufficient numbers to overwhelm the immune system, they collectively launch an assault on the body. Jamming their signals might provide us with a way to fight back.

How about a culturally (so to speak) adapted version of "Suicide is Painless"?

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

In "The Quantum Life" (Physcisworld.com, July 1, 2009), Paul Davies, astrobiologist and director of BEYOND: Center for Fundamental Concepts in Science at Arizona State University, examines the case for quantum mechanics kickstarting the origin of life (Q-life):

But why should quantum mechanics be relevant to life, beyond explaining the basic structure and interaction of molecules? One general argument is that quantum effects can serve to facilitate processes that are either slow or impossible according to classical physics. Physicists are familiar with the fact that discreteness, quantum tunnelling, superposition and entanglement produce novel and unexpected phenomena. Life has had three and a half billion years to solve problems and optimize efficiency. If quantum mechanics can enhance its performance, or open up new possibilities, it is likely that life will have discovered the fact and exploited the opportunities. Given that the basic processes of biology take place at a molecular level, harnessing quantum effects does not seem a priori implausible.

It's intriguing, the way he attributes to "life" and, elsewhere, "evolution" the attributes of a planning and thinking intelligent agent.

He almost persuades himself but

Although at least some of these examples add up to a prima facie case for quantum mechanics playing a role in biology, they all confront a serious and fundamental problem. Effects like coherence, entanglement and superposition can be maintained only if the quantum system avoids decoherence caused by interactions with its environment. In the presence of environmental noise, the delicate phase relationships that characterize quantum effects get scrambled, turning pure quantum states into mixtures and in effect marking a transition from quantum to classical behaviour. Only so long as decoherence can be kept at bay will explicitly quantum effects persist. The claims of quantum biology therefore stand or fall on the precise decoherence timescale. If a system decoheres too fast, then it will classicalize before anything of biochemical or biological interest happens.

. So we are now into the business of persuading ourselves that, based on a few studies, that would not be the normal fate of Q-life. And in the end,

How would Q-life evolve into familiar chemical life? A possible scenario is that organic molecules were commandeered by Q-life as more robust back-up information storage. A good analogy is a computer. The processor is incredibly small and fast, but delicate: switch off the computer and the data are lost. Hence computers use hard disks to back up and store the digital information. Hard disks are relatively enormous and extremely slow, but they are robust and reliable, and they retain their information under a wide range of environmental insults. Organic life could have started as the slow-but-reliable "hard-disk" of Q-life. Because of its greater versatility and toughness, it was eventually able to literally "take on a life of its own", disconnect from its Q-life progenitor and spread to less-specialized and restrictive environments - such as Earth. Our planet accretes a continual rain of interstellar grains and cometary dust, so delivery is no problem. As to the fate of Q-life, it would unfortunately be completely destroyed by entry into the Earth's atmosphere.

All this reminds me of a beautiful Edith Wharton short story, "Pomegranate Seed", on line here, and not wrecked by some clueless ethnicity/class/gender-driven analysis. The point of the story is that it looks as though a ghost drove a story character to suicide - but there is no actual evidence. (If you ever think of writing a ghost story, take Wharton as your guide. What make her stories work is: No one can prove anything happened, apart from catastrophic emotional impacts, and yet everyone is sure that something happened.)

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).