The LCI and Bertrand’s Box

Tom English has recommended that we read Dembski and Marks’ paper on their Law of Conservation of Information (not to be confused with the Dembski’s previous LCI from his book No Free Lunch). Dembski also has touted the paper several times, and I too recommend it as a stark display of the the authors’ thinking.

Most people won’t take the time to carefully read a 34-page paper, but I submit that the authors’ core concept of “conservation of information” is very easily understood if we avoid equivocal and misleading terms such as information, search, and target. I’ll illustrate it with a setup borrowed from Joseph Bertrand.

The “Bertrand’s box” scenario is as follows: We’re presented with three small outwardly identical boxes, each containing two coins. One has a two silver coins, one has two gold coins, and one has a silver coin and a gold coin. We’ll call the boxes SS, GG, and SG. We are to randomly choose a box, and then randomly pull a coin from the chosen box.

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Natural Selection- What is it and what does it do?

Well let’s look at what natural selection is-

 “Natural selection is the result of differences in survival and reproduction among individuals of a population that vary in one or more heritable traits.” Page 11 “Biology: Concepts and Applications” Starr fifth edition

“Natural selection is the simple result of variation, differential reproduction, and heredity—it is mindless and mechanistic.” UBerkley

“Natural selection is the blind watchmaker, blind because it does not see ahead, does not plan consequences, has no purpose in view.” Dawkins in “The Blind Watchmaker”?

“Natural selection is therefore a result of three processes, as first described by Darwin:

Variation
Inheritance
Fecundity

which together result in non-random, unequal survival and reproduction of individuals, which results in changes in the phenotypes present in populations of organisms over time.”- Allen McNeill prof. introductory biology and evolution at Cornell University

OK so it is a result of three processes- ie an output. But is it really non-random as Allen said? Nope, whatever survives to reproduce survives to reproduce. And that can be any number of variations taht exist in a population.

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Reservations About ID, Rottenness in Creationism

As a card carrying creationist, I’ve sometimes wanted to post about my reservations regarding the search for evidence of Intelligent Design (ID) and some of the rottenness in the search for evidence in young earth creation. I’ve refrained from speaking my mind on these matters too frequently lest I ruffle the feathers of the few friends I have left in the world (the ID community and the creationist community). But I must speak out and express criticism of my own side of the aisle on occasion.

Before proceeding, I’d like to thank Elizabeth for her hospitality in letting me post here. She invited me to post some things regarding my views of Natural Selection and Genetic Algorithms, but in the spirit of skepticism I want to offer criticism of some of my own ideas.So this essay will sketch what I consider valid criticism of ID, creationism in general and Young Earth Creationism (YEC) in particular.

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No Free Lunch

My husband, mother, father, myself, and my four-year-old son were going out for a walk.  It was raining. My son refused (as usual) to wear his raincoat.  Instead, he carried a cup, which he held out in front of him.  He argued that he was going to catch the rain drops in the cup so that by the time he got to the place the raindrops had been, they’d be in the cup and he’d be dry. Half an hour later, four adults were still standing around, drawing diagrams on the backs of envelopes, arguing about Pythagoras and trigonometry, all to no avail.  We went out, with cup, sans rain coat.  My son got wet.  He insisted he remained dry.

Bryce Canyon, Utah.

I’ve got as far as Chapter 5 of Dembski’s book No Free Lunch, the chapter called Evolutionary Algorithms, and about which he says in his Preface: “This chapter is the climax of the book”.  He claims that in it he shows that “An elementary combinatorial analysis shows that evolutionary algorithms can no more generate specified complexity than can five letters fill ten mailboxes.”

I think he’s making the same kind of error as my son made.

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Why the NDE/ID Debate Is Really (For Most) A Proxy Fight

To define:

NDE (Neo-Darwinian Evolution) = OOL & evolution without prescriptive goals, both being nothing more in essence than functions of material forces & interactions.

ID (Intelligent Design) = Deliberate OOL & evolution with prescriptive goals

(I included OOL because if OOL contains purposefully written code that provides guidelines for evolutionary processes towards goals, then evolutionary processes are not neo-Darwinian as they utilize oracle information).

I’m not an evolutionary biologist, nor am I a mathematician. Therefore, when I argue about NDE and ID, the only cases I attempt to make are logical ones based on principles involved because – frankly – I lack the educational, application & research expertise to legitimately parse, understand and criticize most papers published in those fields. I suggest that most people who engage in NDE/ID arguments (on either side) similarly lack the necessary expertise to evaluate (or conduct) such research on their own.

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Natural selection can put Functional Information into the genome

It is quite common for ID commenters to argue that it is not possible for evolutionary forces such as natural selection to put Functional Information or Specified Information) into the genome. Whether they know it or not, these commenters are relying on William Dembski’s Law of Conservation of Complex Specified information. It is supposed to show that Complex Specified Information cannot be put into the genome. Many people have argued that this theorem is incorrect. In my 2007 article I summarized many of these objections and added some of my own.

One of the sections of that article gave a simple computational example of mine showing natural selection putting nearly 2 bits of specified information into the genome, by replacing an equal mixture of A, T, G, and C at one site with 99.9% C.

This post is intended to show a more dramatic example along the same lines.

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“Tiktaalik”, Why it is a failed Prediction

Tiktaalik is still being used as a successful prediction of something. I know it was supposed to be a successful prediction of universal common descent because it is A) Allegedly a transitional form between fish and tetrapods and B) It was found in the “correct” strata because allegedly no evidence of tetrapods before 385 million years ago- plenty of fish though and plenty of evidence for tetrapods around 365 million years ago- Tiktaalik was allegedly found in strata about 375 million years old- Shubin said that is the strata he looked in because of the 365-385 range already bracketed by existing data.

The thinking was tetrapods existed 365 mya and fish existed 385 mya, so the transition happened sometime in that 20 million years.

Sounds very reasonable. And when they looked they found Tiktaalik and all was good.

Then along comes another find that put the earliest tetrapods back to over 390 million years ago.

Now had this find preceded Tiktaalik then Shubin et al. would not have been looking for the transitional after the transition had occurred- that doesn’t make any sense. And that is why it is a failed prediction- the transition occurred some 25 million years before, Shubin et al., were looking in the wrong strata.

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Functional information and the emergence of biocomplexity

Journal club time again 🙂

I like this paper: Functional information and the emergence of biocomplexity by Hazen et al, 2007 in PNAS, and which I hadn’t been aware of.

I’ve only had time to skim it so far, but as it seems to be an interesting treatment of the concepts variously referred to by ID proponents as CSI, dFCSI, etc, I thought it might be useful.  It is also written with reference to AVIDA.  Here is the abstract:

Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define “functional information,” I(Ex ), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA–GTP binding energy), I(Ex ) = −log2[F(E x)], where F(Ex ) is the fraction of all possible configurations of the system that possess a degree of function ≥ Ex . Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of function.

I thought it would be interesting to look at following the thread on Abel’s paper.  I’d certainly be interested in hearing what our ID contributors make of it 🙂

 

Objective and subjective

This is a topic where we can discuss what we mean by “objective” and by “subjective”.  It is not tied to anything specific.  We don’t have to reach a consensus.

Here are a couple of examples to illustrate the issues:

  1. Is mathematics objective or subjective?  On the one hand, it is mostly a mental construct, so in some views that would make it subjective.  On the other hand, there is very strong agreement between mathematicians, and that seems to suggest that it is about as objective as anything could be.
  2. If we assume Berkeley’s idealism (the world is nothing more than a mental construct derived from our perceptions), would that imply that everything is subjective and nothing is objective?  Or, since we seem to all refer to the same things (cats, trees, etc) should we say that those are objective even if only mental constructs.

 

The Rules of Right Reason

Barry Arrington and StephenB at Uncommon Descent have frequently invoked “the rules of right reason” in their arguments.

Today, Barry posts them thus:

The Rules of Thought.

The rules of thought are the first principles of right reason. Those rules are:

  • The Law of Identity: An object is the same as itself.
  • The Law of Non-contradiction: Contradictory statements cannot both at the same time be true.
  • The Law of the Excluded Middle: For any proposition, either that proposition is true or its negation is true.

And claims:

Note that the three laws of thought cannot be proven. They are either accepted as self-evident axioms – or not. The fundamental principles of right reason must be accepted as axioms for the simple reason that they cannot be demonstrated. There is no way to “argue for argument” and it is foolish to try to do so. If one’s goal in arguing is to arrive at the truth of a matter, arguing with a person who rejects the law of idenity is counterproductive, because he has rejected the very concept of “truth” as a meaningful category.

 

This seems to me fallacious. (heh.)

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With much fear and trepidation, I enter the SZone

Here’s some personal correspondence between Liz and me. I presume that she checks posts before allowing publication, so if this is inappropriate I claim innocence.

Dear Liz,

As you know, I have great respect for you, even admiration, but I suggest the following.

You wrote:

The reason I get exercised about ID is that I do think, in simple scientific terms, that it is fallacious. Not because there couldn’t have been an ID, nor because science demonstrates that there wasn’t/isn’t one, but because the inference is, IMO, fallacious.

I respond:

The reason I get exercised about the proposed creative power of the Darwinian mechanism of random errors filtered by natural selection is that I do think, in simple scientific terms, that it is fallacious. Not because this mechanism couldn’t possibly have produced all that it is credited with, but because evidence, logic, and simple probability calculations demonstrate that this proposition is fallacious.

Thus, it seems to me, we are separated by an immense chasm over which there is no bridge.

Gil

Let’s face it, the ID versus materialism debate has profound scientific, philosophical, theological, and even ethical implications, which is why passions run so high.

Someone is wrong and someone is right. I just want to know the truth.

Anecdotal evidence

The ‘here’ in the first para refers to Secular Cafe, from which this is reposted.

In a number of threads, here and in other places, I’ve seen discussions – sometimes more than a little vituperative – concerning the value or otherwise of anecdotal evidence.

To start with my current position on it before commenting further.

I think that anecdotal evidence is evidence, but with three little caveats.

It is often, IMV, poor evidence, it is sometimes evidence of something other than what the anecdote purports to be evidence of, and it is rather infrequently later confirmed by later observations which have physical rather than anecdotal evidence behind them.

Having got that out of the way, an in-exhaustive list to identify the sort of alleged phenomena in which anecdotal evidence raises its head, in no particular order but as they spring to mind, with a few exceptions which I am anxious to include.

Ghosts, the effectiveness of clairvoyance, the effectiveness of astrology, the effect (or otherwise) of the full moon on madness,  hospital admissions et al, sightings of monsters on various lakes, UFO sightings, alien abductions, the power of prayer, what may broadly be called religious or spiritual experiences, unusual and hard or impossible to replicate physical phenomena.

For all of these, and others, I’d see it as important to keep a few things in mind.

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Methodological Naturalism

I’ve always understood Methodological Naturalism to mean the assumption we make in science that things are predictable, probabilistically at any rate.

It needn’t be true, and nor do we make any conclusion as to whether it is true or not, we merely proceed under that assumption, because it underlies the methodology that we call science.

But clearly some people, often citing Plantinga (here and here) regard it as some kind of error made by scientists that enables them to fallaciously reject religion, or at least compromise “religious neutrality”.
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Critical thinking means never having to say you’re certain.

This was originally intended as a brief reply to the comment by William J Murray but it sort of grew into something a little longer so I thought, since everyone else is doing it, I’d put it up here.

William J Murray:
I think that any fair reading of UD will show that the vast majority of pro-ID posters there, and certainly the moderators and subject contributors, are not “anti-science” at all, nor “sneer” at science; rather, they have what is IMO a legitimate concern over the anti-religious, anti-theist, pro-materialist agenda that many of those currently in positions of power in the institutions of science blatantly demonstrate.

I would agree that not all contributors to UD are anti-science but there is, nonetheless, a prominent strand of such thinking there. Many of the original posts mock the speculative excesses of evolutionary psyschology, for example, or seem to gloat over instances of where science has apparently got it wrong. Those occasions where the author of such comments has got it wrong themselves pass largely unremarked. The overall impression is of an anti-science advocacy site.

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Is materialism a form of dualism? I think maybe it is.

While I tend to see materialism, or any ism really, as misguided attempts to to translate the epic poem of reality into a language of limits, the universe to an Upanishad, the unknown and unexpected cuisine of eternity into bite sized morsels of processed food by-product. Ultimately, I think isms, including materialism narrow the minds of the porters stuck with the baggage. Like a person forced to wear a hat two sizes too small, like a fundamentalist’s child taught to feel shame at the first whiff of curiosity about something potentially interesting, isms discourage freestyle boogie on the cranial dance floor. They attempt to definitively answer the important question, “Why?”*. At least, that is my general attitude. I can and occasionally do trot out tome lubricant for my neurons in order to formulate a logical support for the idea, but I just ran across a printed copy of this paper in a file folder which accidentally traveled with me this week. Continue reading

Truth, free will, logic

Questions about truth, free will, logic have been raised in another thread.  To help clarify the discussion, let’s separate those from the “necessary premise” discussion.

Here’s an example of the argument being raised:

True statements can only be expected to exist, and we can only expect to be able to deliberately discern them, if we assume the universe is governed by logic (necssarily rationally ordered) and if we assume for ourselves the libertarian free will causative capacity to discern them.

This seems a rather strange claim, given then many people believe that our best and most reliable true statements are those coming from science, and based on describing our world in terms physical causation.  Moreover, science is often considered to provide our best examples rationality and logical reasoning.

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