Still a Theory in Crisis

Posted on February 1, 2016 by Mung

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Michael Denton’s new book is out, Evolution: Still A Theory In Crisis.

Denton’s stance is for structuralism and against functionalism, especially as functionalism appears in it’s current form as the modern synthesis or neo-Darwinism (the cumulative selection of small adaptive changes).

Denton argues for the reality of the types, that “there are unique taxon-defining novelties not led up to gradually from some antecedent form” and that the lack of intermediates undermines the Darwinian account of evolution. He also argues that a great deal of organic order appears to be non-adaptive, including “a great number of the taxa-defining Bauplans,” and that this also undermines the Darwinian account of evolution. Evo-devo is also showing us that “Darwinian selection is not the only or even the main factor that determined the shape and main branches of the great tree of life.”

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George Ellis on top-down causation

Posted on January 30, 2016 by keiths

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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

Posted on January 27, 2016 by DiEb

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(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?

Posted on January 24, 2016 by Alan Fox

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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

Posted on January 21, 2016 by Dave Carlson

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 →

Christiantoday.com sides with UMC against the DI / ID.

Posted on January 21, 2016 by Richardthughes

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?

Alternatives to Methodological Naturalism Conference

Posted on January 17, 2016 by johnnyb

I thought some of you might be interested in an online conference April 16, Alternatives to Methodological Naturalism. The goal of the conference is to have a discussion among interested researchers about what other modes of investigation one might employ that were counter to methodological naturalism.
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The Reasonableness of Atheism and Black Swans

Posted on January 16, 2016 by stcordova

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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

Posted on January 13, 2016 by petrushka

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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?

Posted on January 10, 2016 by Richardthughes

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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.

Posted on January 8, 2016 by Richardthughes

Re http://sciencelife.uchospitals.edu/2016/01/07/a-single-billion-year-old-mutation-helped-multicellular-animals-evolve/

“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!

ID falsifiable, not science, not positive, not directly testable

Posted on January 7, 2016 by stcordova

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There was a time when people believed the moon craters were the product of intelligent design because they were so perfectly round “they must have been made by intelligent creatures living on the moon”. That idea was falsified. If hypothetically someone had said back then, “The Flying Spaghetti Monster (FSM) made the moon craters”, the claim would have been falsifiable, but it really doesn’t make a positive case for the FSM, doesn’t make the FSM directly testable, doesn’t make the FSM science. Substitute the word “ID” instead for “FSM”, and one will see why I think even though ID is falsifiable, I don’t think ID has a positive case, and I don’t think ID is directly testable, and I don’t think ID is science at least for things like biology.

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Featured Thread

Posted on January 7, 2016 by Mung

Featured threads ought to be featured because of their content, not because their content suppresses dissent.

The amazing sudden disappearance of the Feature posts here at TSZ is puzzling.

Math Genome Fun

Posted on January 6, 2016 by Richardthughes

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You have thirteen characters: the numbers 1-9 and the operators for Plus, Minus, Divide and Multiply. Arrange them in a string so they have the highest possible value, or write a program to do this for you. If a string cannot execute as a mathematical function, it scores zero.

Full list [1,2,3,4,5,6,7,8,9,+,-,*,/]

There are 13! possibilities. How many score more than 0 (are mathematically viable)? How many steps did you program take / candidates did it evaluate. How did you know when to stop?

It is a sampling error to use marine mammal vestigial parts as evidence for evolution.

Posted on January 6, 2016 by Robert Byers

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I note many public evolutionists, Prothero and Shermer and many others always stress the cases of vestigial parts in marine mammals as evidence for evolutionary biology.

Yet in reality this is a sampling error that in fact makes the opposite case against evolution.

I agree marine mamnmals once were land lovers and only later gained features to surbvve in the water. Not the impossible steps said by evolutionists, as Berlinski demonstrates, but some other mechanism.

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