George Ellis on top-down causation

In a recent OP at Uncommon Descent, Vincent Torley (vjtorley) defends a version of libertarian free will based on the notion of top-down causation. The dominant view among physicists (which I share) is that top-down causation does not exist, so Torley cites an essay by cosmologist George Ellis in defense of the concept.

Vincent is commenting here at TSZ, so I thought this would be a good opportunity to engage him in a discussion of top-down causation, with Ellis’s essay as a starting point. Here’s a key quote from Ellis’s essay to stimulate discussion:

However hardware is only causally effective because of the software which animates it: by itself hardware can do nothing. Both hardware and software are hierarchically structured, with the higher level logic driving the lower level events.

I think that’s wrong, but I’ll save my argument for the comment thread.

“Uncommon Descent” and “The Skeptical Zone” in 2015

(crossposted from here and here)

(Edited Feb 2, 2016 to add eight figures)

Since 2005, Uncommon Descent (UD) – founded by William Dembski – has been the place to discuss intelligent design. Unfortunately, the moderation policy has always been one-sided (and quite arbitrary at the same time!) Since 2011, the statement “You don’t have to participate in UD” is not longer answered with gritted teeth only, but with a real alternative: Elizabeth Liddle’s The Skeptical Zone (TSZ). So, how were these two sites doing in 2015?

Number of Comments 2005 – 2015

year 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015
UD  8,400 23,000 22,400 23,100 41,100 24,800 41,400 28,400 42,500 53,700 53,100
TSZ  2,200 15,100 16,900 20,400 45,200

In 2015, there were still 17% more comments at UD than at TSZ – 53,100 to 45,200.


Though UD is still going strong, there is a slight downwards trend (yellow line) in the daily number of comments.
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How and Why: questions for scientists and philosophers?

The late John Davison often remarked that science could only answer “how” questions, not “why”. It seems to me philosophers, perhaps I’m really thinking of philosophers of religion rather than in general, attempt to find answers to “why” questions without always having a firm grasp on how reality works. Perhaps this is why there is so much talking past each other when the explanatory power of science vs other ways of knowing enters a discussion. Continue reading

Conservation and function of long noncoding RNAs

How about some cool science as we head toward the weekend?

Let’s talk about long noncoding RNAs (lncRNA) – they are (somewhat arbitrarily) defined as stretches of DNA that are at least 200 base pairs in length that are transcribed into mRNA but have little potential to code for proteins. Determining the function (if one exists) of a particular lncRNA can often be difficult.  In part, this may be due to the fact that lncRNA evolve much more quickly than protein-coding genes do and therefore exhibit a much smaller degree of sequence conservation, which can make identifying orthologs in other related organisms more difficult.  Nevertheless, if a particular lncRNA is functionally important, we would usually expect to see copies of it in related organisms, so finding these homologs can be an important indicator of function.

A new paper in Genes and Development by Quinn et al. is a useful demonstration of this.  The authors find evidence of 47 homologs of roX, an lncRNA involved in X chromosome dosage compensation,  across 35 fruit fly species.  The researchers identity roX homologs based on a combination of short regions of sequence conservation (“microhomology”), RNA secondary structure and synteny (i.e., similarity in location along a chromosome)  Here is the abstract (I believe the paper itself is open access): Continue reading sides with UMC against the DI / ID.

Here’s the article in full:

Christian Today Article

The best bit?:

….However, the UMC has taken the view – expressed though it is in dusty legalese – that in allowing the promotion of intelligent design at its conference would to connive at something which is, not to put too fine a point upon it, not true.

In this respect, it is surely right. It’s always possible to find things about life and its development that evolutionary theory has not yet succeeded in explaining. To argue from this that the answer must be “God did it” is ultimately self-defeating. Science advances, the number of unknowns diminishes, and God is driven into a smaller and smaller space accordingly. This “God of the gaps” approach has long been discredited.

The UMC appears to have taken the view that giving a platform – no matter how small – to a view as mistaken as this undermines the credibility of the gospel because it encourages people to believe things that aren’t true. Building a faith around falsehood is putting people’s souls in peril. The Discovery Institute may not like it, but the UMC is surely right to stand its ground.

(format not the same as the original). Thoughts?

The Reasonableness of Atheism and Black Swans

As an ID proponent and creationist, the irony is that at the time in my life where I have the greatest level of faith in ID and creation, it is also the time in my life at some level I wish it were not true. I have concluded if the Christian God is the Intelligent Designer then he also makes the world a miserable place by design, that He has cursed this world because of Adam’s sin. See Malicious Intelligent Design.
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Excilience and Contextomy

consilience. : the linking together of principles from different disciplines especially when forming a comprehensive theory.

contextomy. : an informal fallacy and a type of false attribution in which a passage is removed from its surrounding matter in such a way as to distort its intended meaning. Quote mining.

excilience. : the linking together of Contextomies from different disciplines especially when forming a comprehensive theory. Thought mining.

The Quote Mine Project provides excellent examples of contextomy. Uncommondescent provides excellent examples of excilience.

The practices lend themselves to all kinds of humorous incongruities. Among them are:

1. free will vs predestination
2. deism vs interventionism (Michael Denton vs Michael Behe)
3. front loading vs twiddling (Mike Gene vs gpuccio, etc.)
4. ascentism vs degenerationism (Chardin vs Sanford)
5. old earth vs young earth
6. realism vs last thursdayism
7. biblical literalism vs inspirationism

There are probably a lot more, but these come up frequently. The humor comes from observing that the armies of ID clash by night, without ever mentioning or discussing their differences and their contradictory assumptions and conclusions.

Food for discussion.

Math Genome Fun 2, UPB and beyond?

This is a follow-on from the original “Math Genome Fun” thread here

I think it’s time to test out GAs on a bigger problem, the old one was at the boundary of home computation for an exhaustive search (OMD I said “search!” get on that Mung) – but I’m going to propose a *much* bigger search / smaller target.

Friends, you target is Pi

I’ve chosen Pi because of its qualities, being irrational and transcendental you cannot describe it in an equation, only approximate it.

Our target is the first 150 digits of Pi.

Our vocabulary is the same numbers and operators as before: [1,2,3,4,5,6,7,8,9,+,-,*,/], but this time they can all be used as often as required and the genome can be anywhere from 1 to 1000 characters in length.

The design approximation is now harder due to the decimal place and the absence of zeros in our vocabulary (but there’s quite a few in Pi).

I’ve done no computation on this myself, can a GA find that proverbial needle in a haystack?


Multicellularity? Not a problem.


“Our experiments show how biological complexity can evolve though simple, high-probability genetic paths,” said Thornton, who served as co-senior author. “Before the last common ancestor of all animals, when only single-celled organisms existed on Earth, just one tiny change in DNA sequence caused a protein to switch from its primordial role as an enzyme to a new function that became essential to organize multicellular structures.”

Let’s hope filling this gap creates two more, either side of it!