On The Origin of Species, read by Richard Dawkins (2007)

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There is grandeur in this view of life, with its several powers having been originally breathed into a few forms or into one, and that while this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning, endless forms most beautiful and most wonderful have been, and are being, evolved.

These are the closing words of Darwin’s On the Origin of Species, read abridged in an audio recording by Richard Dawkins from 2007.

How should we read Darwin’s book today?

Should we read it as history? Is On The Origin of Species a Hopeful Monster of a theory lacking a mechanism and made irrelevant by more recent discoveries?

As politics? Is the book no more than a privileged English gentleman naturalist explaining interesting but unsupportable things to his own social class?

As science? Is it no more than a naturalist’s attempt to synthesise what was known or speculated from biology, geology and paleontology, physics and chemistry as it was known at the time?

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Final word to KF

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In response to KF here: In my view it is no more, or less, slanderous imply a relationship between “Darwinism” and Nazi-ism than it is to imply a relationship between “anti-homosexualism” and Nazi-ism.  To point out that the Nazis conviction that the “unfit” should be “culled” may have owed something to their reading of Darwin, is at least equivalent, I would say, to pointing out that the Nazi’s conviction that homosexuals should be “culled” may have owed something to the view that homosexuality is deviant, immoral and dangerous.  To say the first is not to say that Darwinists are Nazis; to say the second is not to say that anti-homosexualists are Nazi.  To insist that the first is justifiable but the second slander, is, I suggest, to impose a double standard.  Moreover, to suggest, as KF does, that by “enabling” posters here to suggest a comparison between the anti-homosexualism of some religious views and the anti-homosexuality of the Nazis I am somehow comparable to the “good” Germans who “enabled of Nazi-ism is at least as “slanderous” as the comparison he objects to.  However, I can live with that.  The best response, in my view, to slander, is effective rebuttal, not censorship.

I agree with KF that comparisons to Nazis is inflammatory.  That is as far as I will go.

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FOR RECORD: An explanatory note to KF of UD

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Re this:

The principles on which this site is run are summarised here and here.  The key rule is: “assume other posters are posting in good faith”.

That does not mean that you have to believe that they are posting in good faith, simply that you should make that assumption for the purposes of discussion.

I will not “correct” posts – people are responsible for their own posts, and for any errors they contain.  I will not delete posts, although I may move posts to a different thread, or to the Sandbox or to Guano.  They remain publicly viewable. I will however, delete links to porn or malware, and posting such links or material are the only grounds on which I will ban anyone.  Posters are complete free to disagree with me, with each other, and to be mistaken.

UD is run on different lines.  Fine.  I prefer mine.

Denis Noble again….

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Denis Noble has a new review out, in Experimental Physiology called Physiology is rocking the foundations of evolutionary biology.  Unfortunately the article itself is behind a paywall, but here is the abstract:

The ‘Modern Synthesis’ (Neo-Darwinism) is a mid-20th century gene-centric view of evolution, based on random mutations accumulating to produce gradual change through natural selection. Any role of physiological function in influencing genetic inheritance was excluded. The organism became a mere carrier of the real objects of selection, its genes. We now know that genetic change is far from random and often not gradual. Molecular genetics and genome sequencing have deconstructed this unnecessarily restrictive view of evolution in a way that reintroduces physiological function and interactions with the environment as factors influencing the speed and nature of inherited change. Acquired characteristics can be inherited, and in a few but growing number of cases that inheritance has now been shown to be robust for many generations. The 21st century can look forward to a new synthesis that will reintegrate physiology with evolutionary biology.

It’s a nice synthesis of the views he expresses in his book, The Music of Life, which I mentioned a previous post, Reductionism Redux , but he also lays out very clearly the ways in which four assumptions that have underlain much thinking in evolutionary biology since the “modern synthesis” (not so modern now), need to be revisited.

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Specification for Dummies

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I’m lookin’ at you, IDers 😉

Dembski’s paper: Specification: The Pattern That Specifies Complexity gives a clear definition of CSI.

The complexity of pattern (any pattern) is defined in terms of Shannon Complexity.  This is pretty easy to calculate, as it is merely the probability of getting this particular pattern if you were to randomly draw each piece of the pattern from a jumbled bag of pieces, where the bag contains pieces in the same proportion as your pattern, and stick them together any old where.  Let’s say all our patterns are 2×2 arrangements of black or white pixels. Clearly if the pattern consists of just four black or white pixels, two black and two white* , there are only 16 patterns we can make:

Patterns1And we can calculate this by saying: for each pixel we have 2 choices, black or white, so the total number of possible patterns is 2*2*2*2, i.e 24  i.e. 16. That means that if we just made patterns at random we’d have a 1/16 chance of getting any one particular pattern, which in decimals is .0625, or 6.25%.  We could also be fancy and express that as the negative log 2 of .625, which would be 4 bits.  But it all means the same thing.  The neat thing about logs is that you can add them, and get the answer you would have got if you’d multipled the unlogged numbers.  And as the negative log of .5 is 1, each pixel, for which we have a 50% chance of being black or white, is worth “1 bit”, and four pixels will be worth 4 bits.

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Protein Space and Hoyle’s Fallacy – a response to vjtorley

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‘vjtorley’ has honoured me with my very own OP at Uncommon Descent in response to my piece on Protein Space. I cannot, of course, respond over there (being so darned uncivil and all!), so I will put my response in this here bottle and hope that a favourable wind will drive it to vjt’s shores. It’s a bit long (and I’m sure not any the better for it…but I’m responding to vjt and his several sources … ! ;)).

“Build me a protein – no guidance allowed!”

The title is an apparent demand for a ‘proof of concept’, but it is beyond intelligence too at the moment, despite a working system we can reverse engineer (a luxury not available to Ye Olde Designer). Of course I haven’t solved the problem, which is why I haven’t dusted off a space on my piano for that Nobel Prize. But endless repetition of Hoyle’s Fallacy from multiple sources does not stop it being a fallacious argument.

Dr Torley bookends his post with a bit of misdirection. We get pictures of, respectively, a modern protein and a modern ribozyme. It has never been disputed that modern proteins and ribozymes are complex, and almost certainly not achievable in a single step. But

1) Is modern complexity relevant to abiogenesis?

2) Is modern complexity relevant to evolution?

Here are three more complex objects:

DESCRIPTION HERE

Circuit Board

DESCRIPTION HERE

Panda playing the flute

DESCRIPTION HERE

er … not yet in service!

 

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Prizegiving!

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Phinehas and Kairosfocus share second prize for my CSI challenge: yes, it is indeed “Ash on Ice” – it’s a Google Earth image of Skeiðarárjökull Glacier.

But of course the challenge was not to identify the picture, but to calculate its CSI. Vjtorley deserves, I think, first prize, not for calculating it, but for making so clear why we cannot calculate CSI for a pattern unless we can calculate “p(T|H)” for all possible “chance” (where “chance” means “non-design”) hypotheses.

In other words, unless we know, in advance, how likely we are to observe the candidate pattern, given non-chance, we cannot infer Design using CSI. Which is, by the Rules of Right Reason, the same as saying that in order to infer Design using CSI, we must first  calculate how likely our candidate pattern is under all possible non-Design hypotheses.

As Dr Torley rightly says:

Professor Felsenstein is quite correct in claiming that “CSI is not … something you could assess independently of knowing the processes that produced the pattern.”

And also, of course, in observing that Dembski acknowledges this in his paper, , Specification: The Pattern That Signifies Intelligence, as many of us have pointed out.  Which is why we keep saying that it can’t be calculated – you have to be able to quantify p(T|H), where H is the actual non-design hypothesis, not some random-independent-draw hypothesis.

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DonaldM, at UD, asks…

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…an odd, but revelatory, set of questions:

1. How do you know scientifically (and I emphasize “scientifically” here because I want to make it clear that theological, metaphysical or philosophical opinions – while important for other reasons – have no bearing on the question at hand) that the properties of the Cosmos are such that any apparent design we observe in natural systems can not be actual design, even in principle?

I don’t.

2. How do you know scientifically that Nature (or the Cosmos) is a completely closed system of natural cause and effect? (Recall Dawkins claim that a universe superintended by a Deity would look much different than ours as he says in The God Delusion several times)

I don’t.

3. How do you know scientifically that the properties of biological systems are such that any apparent design we observe in them can not be actual design, even in principle? (The Blind Watchmaker and Dawkins’s claim that “Biology is the study of complicated things that give the appearance [emphasis mine] of having been designed for a purpose.”)

I don’t.

4. How do you know scientifically that no supernatural being, if such actually existed, could ever take any action within nature itself that would produce observable phenomenon or effect any change in the arrangement of matter or energy anywhere in the Cosmos?

I don’t.

Does anyone here?  And does any one make any such claims?  I don’t.

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Is Darwinism a better explanation of life than Intelligent Design?

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I recently bumped a post by keiths: Things That IDers Don’t Understand, Part 1 — Intelligent Design is not compatible with the evidence for common descent as it had come up in a recent discussion.  Vjtorley has responded on UD with a post called Is Darwinism a better explanation of life than Intelligent Design?

I’ve unbumped keiths’ post, as the thread was getting rather long, and in any case, it would be good to respond to vjtorley, who is, of course, very welcome to come over here in purpose.  I like Dr Torley, and do hope he will drop by, but in any case, the loudhailer seems to work reasonably well!

Feel free to continue the discussion that had been renewed on keiths’ post in this one (or on the old one if you like, using the link).

Dr Nim

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It has struck me more than once that a lot of the confusion that accompanies discussions about stuff like consciousness and free will, and intelligent design, and teleology, even the explanatory filter, and the words “chance” and “random” arises from lack of clarity over the difference between decision-making and intention.  I think it’s useful to separate them, especially given the tendency for people, especially those making pro-ID arguments, but also those making ghost-in-the-machine consciousness or free will arguments, to regard “random” as meaning “unintentional”.  Informed decisions are not random.  Not all informed decisions involve intention.

This was my first computer:

It was called Dr Nim.  It was a computer game, but completely mechanical – no batteries required.  You had to beat Dr Nim, by not being the one left with the last marble, and you took turns with Dr Nim (the plastic board).  It was possible to beat Dr Nim, but usually Dr Nim won.

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Things That IDers Don’t Understand, part 3 — We still make choices, even if free will is illusory

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Over at UD, Salvador Cordova criticizes a statement by Jerry Coyne that appeared in a USA Today column:

So if we don’t have free will, what can we do? One possibility is to give in to a despairing nihilism and just stop doing anything. But that’s impossible, for our feeling of personal agency is so overwhelming that we have no choice but to pretend that we do choose, and get on with our lives.

There are a lot of problems with Cordova’s post (which we can address in the comments), but I do agree that Coyne’s statement is problematic and warrants criticism. Ironically, Coyne’s misunderstanding is shared by many ID proponents — hence the title of this post.

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Englishman in Istanbul proposes a thought experiment

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at UD:

… I wonder if I could interest you in a little thought experiment, in the form of four simple questions:

1. Is it possible that we could discover an artifact on Mars that would prove the existence of extraterrestrials, without the presence or remains of the extraterrestrials themselves?

2. If yes, exactly what kind of artifact would suffice? Car? House? Writing? Complex device? Take your pick.

3. Explain rationally why the existence of this artifact would convince you of the existence of extraterrestrials.

4. Would that explanation be scientifically sound?

I would assert the following:

a. If you answer “Yes” to Question 4, then to deny ID is valid scientific methodology is nothing short of doublethink. You are saying that a rule that holds on Mars does not hold on Earth. How can that be right?

b. If you can answer Question 3 while answering “No” to Question 4, then you are admitting that methodological naturalism/materialism is not always a reliable source of truth.

c. If you support the idea that methodological naturalism/materialism is equivalent to rational thought, then you are obligated to answer “No” to Question 1.

 

Well, I can never resist a thought experiment, and this one seems quite enlightening….

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Eppur si muove

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Cornelius Hunter has a particularly odd post up, called: More Warfare Thesis Lies, This Time From CNN.  He takes issue with a report by Florence Davey-Attlee, on Vatican seeks to rebrand its relationship with science.  His complaint is that it promotes what he calls “the false Warfare Thesis, which pits religion against science” and “is too powerful and alluring to allow the truth to get in the way”.  He writes:

The key to a good lie is to leverage the truth as much as possible. In this instance, we have two truths juxtaposed to make a lie. You see Bruno did argue for an infinite universe, and he was burned at the stake. But those are two distinct and separate facts. The implication is that the Church burned Bruno at the stake because of his scientific investigations about the universe—a perfect example of the Warfare Thesis.

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Philosophy of Mind: A Taxonomy

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I consider the following to be a “work in progress,” and will make changes as others here contribute corrections and suggestions.

The so-called “mind-body problem”, as bequeathed to us by Descartes, has invited various solutions over the centuries.  In the classical version, the basic positions were dualism, materialism, and idealism — each of which has its sub-varieties.

What is meant by “mind”?  Well, there are characteristically mental phenomena have been presented as candidates for what is essential to mindedness: rationality, intentionality, subjectivity, volition, or consciousness.  (That these don’t all overlap can be seen by asking, “are there unconscious mental states or processes?”, “what sorts of minds do non-rational animals have?” “are there purely qualitative, non-intentional mental states, e.g. pains?” and so on.)

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A materialist defends substance dualism

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At UD, Vincent Torley links to an odd little paper by William Lycan, a philosopher at the University of North Carolina, entitled Giving Dualism Its Due.

The abstract reads:

Despite the current resurgence of modest forms of mind-body dualism, traditional Cartesian immaterial-substance dualism has few if any defenders. This paper argues that no convincing case has been against substance dualism, and that standard objections to it can be credibly answered.

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