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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Journal club – Protein Space. Big, isn’t it?

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Simplistic combinatorial analyses are an honoured tradition in anti-evolutionary circles. Hoyle’s is the archetype of the combinatorial approach, and he gets a whole fallacy named after him for his trouble. The approach will be familiar – a string of length n composed of v different kinds of subunit is one point in a permutation space containing vn points in total. The chance of hitting any given sequence in one step, such as the one you have selected as ‘target’, is the reciprocal of that number. Exponentiation being the powerful tool it is, it takes only a little work with a calculator to assess the permutations available to the biological polymers DNA and protein and come up with some implausibly large numbers and conclude that Life – and, if you are feeling bold, evolution – is impossible.

Dryden, Thomson and White of Edinburgh University’s Chemistry department argue in this 2008 paper that not only is the combinatorial space of the canonical 20 L-acids much smaller than simplistically assumed, but more surprisingly, that it is sufficiently small to have been explored completely during the history of life on earth. Continue reading →

Response to Kairosfocus

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[23rd May, 2013 As Kairosfocus continues to reiterate his objections to the views I express in this post, I am taking the opportunity today to clarify my own position:

  1. I do not think that OM was calling KF a Nazi, merely drawing attention to commonality between KF’s apparent views on homosexuality as immoral and unnatural to those of Nazis who also regarded homosexuality as immoral and unnatural.  However, I accept that one huge difference is that KF appears to considers that homosexuality is non-genetic and can be cured; whereas Nazis considered that it was genetic and should be eradicated.
  2. I agree with KF that inflammatory comparisons with those one disagrees with to Nazis is unhelpful and divisive.  I will not censor such comparisons, but I will register my objections to them.  This includes OM’s comparison (although I find KF’s views on homosexuality morally abhorrent, and factually incorrect, his view is profoundly different to those of the Nazis), and it also includes KF’s frequent comparisons of those of us who hold that a Darwinist account of evolution is scientifically justified to those “good Germans” who turned a blind eye to Nazi-ism.
  3. When referring to CSI as “bogus” I mean it is fallacious and misleading.  I do not mean that those who think it is calculable and meaningful are being deliberately fraudulent.  I interpret AF to mean the same thing by the term.  However, even if he does not, I defend his right to say so on this blog, just as I will defend KF’s right to defend CSI (or even his views on homosexuality) on this blog.]

I will move this post to the sandbox shortly, but as I am banned from UD, and therefore cannot respond to this in the place where it was issued, I am doing so here.  Kairosfocus writes:

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Complex Specified Information: breaking the mould of Darwinistic evolution or bogus concept.

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Aplologies straight away for clogging up such an excellent site with this old chestnut but in the light of GEM (Kairosfocus) having apparently directing a long OP at me over some exchanges in an earlier thread, and as Kairosfocus has closed comments I feel I ought to take an opportunity to respond here. I’ll put everything else below the fold.

Click to continue at your peril!

The Dialectic of Darwinism and Anti-Darwinism

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I here present a number of theses, each of which deserves an independent argument in support of it, but which I think are both true and defensible:

(1) The resistance to Darwinism as expressed by creationism and by intelligent design largely arises from treating “Darwinism” as a scapegoat for the social ills produced by capitalism.  It has become commonplace among creationist and other anti-Darwinists to blame Darwinism for any and all of the following: eugenics, acceptance of homosexuality, sexual promiscuity, genocide, school shootings, abortion, and decline of ecclesiastical authority.

(2) Though the obsession with sexuality and anxiety about the ambiguity of embodiment are standard-fare among the religious far-right, my interest here lies in what it is about contemporary presentations of Darwinism that make it such a tempting target for these anxieties.

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Asymmetry

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When I started this site, I had been struck by the remarkable symmetry between the objections raised by ID proponents to evolution, and the objections raised by ID opponents to ID – both “sides” seemed to think that the other side was motivated by fear of breaking ranks; fear of institutional expulsion; fear of facing up to the consequences of finding themselves mistaken; not understanding the other’s position adequately; blinkered by what they want, ideologically, to be true, etc.  Insulting characterisations are hurled freely in both directions. Those symmetries remain, as does the purpose of this site, which is to try to drill past those symmetrical prejudices to reach the mother-lode of genuine difference.

But two asymmetries now stand out to me:

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What would Darwin do?

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At Evolution News and Views, David Klinghoffer presents a challenge:

Man needs meaning. We crave it, especially when faced with adversity. I challenge any Darwinist readers to write some comments down that would be suitable, not laughable, in the context of speaking to people who have lived through an event like Monday’s bombing. By all means, let me know what you come up with.

Leaving aside Klinghoffer’s conflation of “Darwinism” with atheism, and reading it as a challenge for those of us who do not believe in a supernatural deity or an afterlife (which would include me), and despite lacking the eloquence of the speakers Klinghoffer refers to, let me offer some thoughts, not on Monday’s bombing, specifically, but on violent death in general, which probably touches us all, at some time.  Too many lives end far too soon:

We have one life, and it is precious, and the lives of those we love are more precious to us than our own.  Even timely death leaves a void in the lives of those left, but the gap left by violent death is ragged, the raw end of hopes and plans and dreams and possibilities.  Death is the end of options, and violent death is the smashing of those options;  Death itself has no meaning. But our lives and actions have meaning.  We mean things, we do things, we act with intention, and our acts ripple onwards, changing the courses of other lives, as our lives are changed in return.  And more powerful than the ripples of evil acts are acts of love, kindness, generosity, and imagination. Like the butterfly in Peking that can cause a hurricane in New York, a child’s smile can outlive us all. Good acts are not undone by death, even violent death. We have one life, and it is precious, and no act of violence can destroy its worth.

Belling the Cat

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As Aesop didn’t actually say:

The Mice once called a meeting to decide on a plan to free themselves of their enemy, the Cat. At least they wished to find some way of knowing when she was coming, so they might have time to run away. Indeed, something had to be done, for they lived in such constant fear of her claws that they hardly dared stir from their dens by night or day. Many plans were discussed, but none of them was thought good enough. At last a very young Mouse got up and said: “I have a plan that seems very simple, but I know it will be successful. All we have to do is to hang a bell about the Cat’s neck. When we hear the bell ringing we will know immediately that our enemy is coming.” All the Mice were much surprised that they had not thought of such a plan before. But in the midst of the rejoicing over their good fortune, an old Mouse arose and said: “I will say that the plan of the young Mouse is very good. But let me ask one question: Who will bell the Cat?”

More heat than light seems to me to be generated by the demand for IDists to “define CSI” and the equations that are fired back in response. Nobody is disputing that we have plenty of equations.  Here is that bright young mouse, Dembski’s:

χ= –log2[10120 · φS(T)·P(T|H)]

The problem seems to me to lie in Belling the Cat.

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Andre’s questions

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Andre poses some interesting questions to Nick Matzke. I thought I’d start a thread that might help him find some answers.  I’ll have first go :

Hi Nick

Yes please can we get a textbook on Macro-evolution’s facts!

I’ll make it easy for you;

1.) I want to see a step by step process of the evolution of the lung system.

Google Scholar: evolution of the lung sarcopterygian

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