Friday, May 31, 2013

From Darwin's Dangerous Idea: why we can believe scientific theories

The following quotation is from Darwin's Dangerous Idea, by Daniel C Dennett.  This quote applies to all strongly-confirmed scientific theories, including global warming.

"The fundamental core of contemporary Darwinism, the theory of DNA-based reproduction and evolution, is now beyond dispute among scientists. It demonstrates its power every day, contributing crucially to the explanation of planet-sized facts of geology and meteorology, through middle-sized facts of ecology and agronomy, down to the latest microscopic facts of genetic engineering.  It unifies all of biology and the history of our planet into a single grand story.  Like Gulliver tied down in Lilliput, it is unbudgeable, not because of some one or two huge chains of argument that might–hope against hope–have weak links in them, but because it is securely tied by hundreds of thousands of threads of evidence anchoring it to virtually every other field of knowledge. New discoveries may conceivably lead to dramatic, even 'revolutionary' shifts in the Darwinian theory, but the hope that it will be 'refuted' by some shattering breakthrough is about as reasonable as the hope that we will return to a geocentric vision and discard Copernicus." [Emphasis in the original]."

Denialist "arguments" are rubbish because they don't unravel any strands, let alone enough to let Gulliver get up.

Everything you need to know to refute climate denial trolls

 ClimateProgress contains a superb reference for rebutting 99 climate-denial trolls.

Each troll (skeptic argument) is followed by a one-line rebuttal, a paragraph rebuttal, and links to multi-page references containing nothing established science.

Read this page, keep calm, and you *will* win any argument with the trolls.

Saturday, May 25, 2013

Proceedings of the National Academy of Sciences: P. furiosus turns CO2 directly into industrial chemical

UGA discovery may allow scientists to make fuel from CO2 in the atmosphere: http://news.uga.edu/releases/article/uga-discovery-may-allow-scientists-to-make-fuel-from-co2-in-the-atmosp/

Here is the abstract of the referenced article PNAS. I don't have a subscription:

Exploiting microbial hyperthermophilicity to produce an industrial chemical, using hydrogen and carbon dioxide:
http://www.pnas.org/content/110/15/5840.abstract?sid=7125bcb6-b8cb-41da-96f8-322cb6b641cc
Here is an earlier article from PNAS, in full:


Mechanism of oxygen detoxification by the surprisingly oxygen-tolerant hyperthermophilic archaeon, Pyrococcus furiosus: http://www.pnas.org/content/109/45/18547.full.pdf+html?sid=7125bcb6-b8cb-41da-96f8-322cb6b641cc

Tuesday, December 4, 2012

Deep learning: a sensational theorem and its evolutionary implications

 I recently stumbled upon this article in the New York Times: Scientists See Promise in Deep-Learning Programs These sentences initially caught my eye:

"But what is new in recent months is the growing speed and accuracy of deep-learning programs, often called artificial neural networks or just “neural nets” for their resemblance to the neural connections in the brain

'There has been a number of stunning new results with deep-learning methods,” said Yann LeCun, a computer scientist at New York University who did pioneering research in handwriting recognition at Bell Laboratories. “The kind of jump we are seeing in the accuracy of these systems is very rare indeed.' "

Intrigued, I followed the link to Geoffry Hinton's home page. There are links to many papers there, including: A Fast Learning Algorithm for Deep Belief Nets From the summary:

"...we derive a fast, greedy algorithm that can learn deep, directed belief networks one layer at a time..."

Folks, this is an astounding result!  One would imagine that training a neural net with N layers would require adjusting weights of all N layers simultaneously.  If instead, training can be done one layer at a time the computational complexity is reduced by a factor of N.

Furthermore, it is natural to conjecture that all, or almost all, evolutionary processes are in essence greedy algorithms.  Something like this algorithm likely explains how evolution has any chance of creating brains!

Wednesday, November 7, 2012

The diseases of the Republican Party

I rejoice that Barack Obama has won re-election.  It is terrifying that the Republican Party, as presently constituted, should control the White House.

I have stated many times that I believe that the United States needs two healthy political parties.  There is plenty of room for disagreement about a host of important topics.  This will always be so.

However, the Republican Party is in deep trouble.  It would be better for America, and better for the Republican Party itself, to rid itself of the following diseases:

1.  The Republican Party tolerates denialism.  It somehow feels free to deny scientific fact whenever those facts conflict with the financial interests of its wealthiest members.

2. The Republican Party is based on religious conservatism.  As a militant atheist, I regard any religious basis for political power as revolting opportunism, but basing a political agenda on the religious doctrines of a small minority of Americans is a recipe for permanent minority status.

3. The Republican Party is a party of fiscal and monetary chicken hawks.  Its leaders talk about reducing the deficit, but are, in fact, in favor of budget-busting programs such as the prescriptions drug benefit and the F-35 fighter.  John Mauldin, a prominent financial analyst, eloquently writes about the dangers of large deficits on the one hand, while on the other hand he counsels his rich clients about how to avoid taxes.  How can he not see the contradiction?

4. The Republican Party somehow believes that the wealthiest people in the United States should be exempt from shared sacrifice, and that the rich should be specifically exempted from higher taxes.  This is an absolute failure of political, economic and moral leadership.

5. The Republican Party embraces, rather than repudiates, the contemptible practices of Fox News.  It has become a party of 24/7 propaganda and self deception.  A healthy party would welcome real debate; the present diseased party tolerates the shouting down of all who would dare disagree with it.

To summarize, the Republican Party asks, "What can government do for me?" (less taxes, more contracts, more religious conformity), rather than, "What can government do for all its citizens?".  The Republican Party seems unable to confront the world as it is: a world that is mostly poor, mostly non-white, and deeply in danger of ecological calamity.  It is a party of the insulated and isolated privileged and of the religious fringes.  It can, and must, do better.

Why I am a miltant atheist

The short answer is, because all the facts and evidence demand that conclusion.  We can break down the argument into several parts:

1.  The theory of evolution disproves all super-natural theories of creation.

2.  The is absolutely no evidence for any of the world's religions.

Here are the major influences on my thinking:

1.  Stephen J. Gould. His wonderful popular books about paleontology, evolutionary theory and the history of science showed me how revolutionary evolutionary theory is.  They also showed me how beautiful and powerful science is.

2. Sam Harris, and especially his book, The End of Faith.  This book exposes the absolute lack of evidence upon which all religions are based, and confronts the real danger that religious ideas pose to the world.

3. The scientific journals, Nature and Science. These are the most exciting, the most informative, and the most important journals in the world today.

Once I saw the true beauty and power of scientific thought, it became impossible to believe the drivel that we know as religion and most (not all) forms of spirituality.  It became clear that religion is a crude form of political manipulation, with fear of eternal damnation as its only real weapon. There is no evidence whatsoever for such fear.  To give up religion is to give up the fear of death.

Seen in this light, the new atheists could be said to be stating the obvious.  However, there is a lot more that can be said on the topic of replacing religion with science.  I recommend the following YouTube videos as a starting point.

Richard Dawkins: Militant Atheism

Sam Harris vs an evangelical (The full debate is here.)

Sam Harris: Death and the present moment

Sam Harris: Science can answer moral questions

Harris and Dawkins are both respected scientists.  I recommend all of Dawkins's books.