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

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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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Review: Climbing the Steiner Tree

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Overview

Winston Ewert, William Dembski, and Robert J. Marks II have made available a paper titled Climbing the Steiner Tree — Sources of Active Information in a Genetic Algorithm for Solving the Euclidean Steiner Tree Problem wherein they claim to have identified sources of “active information” in a genetic algorithm used to find solutions to a Steiner problem. The problem referenced in this paper was originally described by Dave Thomas on the Panda’s Thumb almost six years ago. I developed a GA to solve the problem that Dave posed as a challenge a few weeks later, as did a number of other people.

This paper suffers from numerous flaws, starting with a fundamental mischaracterization of the purpose of Thomas’s solution and including general misunderstanding of genetic algorithms, misapplication of the No Free Lunch theorems, spurious claims about “active information”, and incorrect and unsupported assertions regarding the impact of certain GA implementation details.
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Evidence

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A question has come up in another thread about the term “evidence”, and what qualifies (and does not qualify) as evidence.  This particular debate has come about when Elizabeth said, in relation to an ongoing description of my model of “how things work” (free will/psychoplasm), said:

The problem it seems to me, with your model is that a) there is no evidence to support it whatsoever and b) we have a supported model that works pretty well.

I then challenged that assertion about the state of evidence with:

Can you support your assertion that “there is no evidence to support it whatsoever”?

She responded:

No, and I will qualify: I am aware of no evidence to support it, and I speak as one fairly well acquainted with the empirical literature.

Which I found odd, since I had given testimony (or, as Robin later said, “claimed”) that this model apparently worked well for me, others I know, and had in this thread and the Free Will thread pointed ouit various other similar doctrines that are chock full of such testimony (or “claims”). So, I asked:

So, my testimony, and that of others through various media, is not evidence?

Unfortunately, Elizabeth has yet to respond to that question. However, Robin contributed his/her answer:

No. Claims are never evidence of what is being claimed; they are solely evidence that someone made a claim. Why? Because anyone can make a mistake or even lie.

I think this deserves its own thread, for reasons I think will become clear. Before responding to Robin, though, I’d like for others to weigh in on the question of if testimony (not in the court sense, but in they typical “claim” sense), through various forms of media, is evidence.

Reservations About ID, Rottenness in Creationism

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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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Todd Wood on the Tennessee bill (and falsification)

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He makes some very interesting comments, and also this point, which I think is worth making:

I know for a fact that evolution cannot be falsified; it can only be replaced.

“Falsification” has become kind of shibboleth that in my view has outlived its usefulness as a criterioin for what is, or is not, science.  We don’t actually proceed by what people usually mean by “falsification” in science, IMO, we proceed by replacing existing models with better ones (in that sense, of course, all models with a better fit to data than a previous model “falsify” the previous model – but that’s not what people usually mean).  So I think Todd, as so often, is right here.  Of course I think he is radically wrong about the age of the earth, but that’s another story!

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Privileged Planet

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Toronto posted this comment on another thread:

A privileged planet, ( for observation of the universe ), would be one that could see “most” of the universe, i.e. not part of it.

We would sit on “top” of the universe so we could see more star systems than having to look “through” a mass of stars.

This position would also cut down on the effects of gravitational lensing.

We would also have a unique orbit both within our solar system, and as part of it.

Our solar system’s orbit would take us close to other star systems so we could investigate them without having to build spaceships that take more than a scientist’s lifetime to get anywhere.

Our atmosphere would shield us from almost any deadly radiation but not impede any signal we require for observing the universe.

Sadly , none of these things are true.

In reality, like any other planet, our positions are relatively fixed for much longer than our lifetime and radiation from the stars would kill us if we got close enough to observe them, provided the gravitational forces or asteroid impacts don’t kill us first.

which sparked a lengthy discussion, which at first I moved to Sandbox, but will now move here.

Enjoy 🙂

Libertarian Free Will

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The concept of Libertarian Free Will (and the contextualizations that must accompany it) is really just too big to tackle all at once, so I’m going to begin with a thread to serve as a basic primer about my view of Libertarian Free Will (LFW) – what I posit it to be, ontologically speaking, and how I describe it.

The basic difference between compatibilist free will and libertarian free will is that compatibilist intents are ultimately manufactured effects of unintentional brute processes. No matter how many layers of “pondering” “meta-pondering” one adds, or how many “modules” or “partitions” are added to the mix, it all still ultimately boils down to intentions being sufficiently explained as effects of brute (unintentional) forces. That is the root of all will in the compatibilist view; ultimately, humans do as they will, but do not will as they will, regardless of how many pre-action “intentions” they put in the chain.

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Intention and action

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The subject of intention and action has come up few times, so I thought I’d start a thread.

From my point of view as a cognitive neuroscientist,  decision-making (which action to take) is best conceived of as a kind of winner-take-all arm-wrestling competition, in which competing programs (represented as networks of active neurons) of action exert a mutually inhibitory effect on on the other, while each receives excitatory input from various other other networks, each of which in turn are engaged in a kind of subsidiary arm-wrestling match with some networks and a mutually cheer-leading match with others.

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Semiotic theory of ID

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Upright BiPed has been proposing what he has called a “semiotic” theory of Intelligent Design, for a while, which I have found confusing, to say the least.  However, he is honing his case, and asks Nick Matzke…

…these three pertinent questions regarding the existence of information within a material universe:

  1. In this material universe, is it even conceivably possible to record transferable information without utilizing an arrangement of matter in order to represent that information? (by what other means could it be done?)
  2. If 1 is true, then is it even conceivably possible to transfer that information without a second arrangement of matter (a protocol) to establish the relationship between representation and what it represents? (how could such a relationship be established in any other way?)
  3. If 1 and 2 are true, then is it even conceivably possible to functionally transfer information without the irreducibly complex system of these two arrangements of matter (representations and protocols) in operation?

… which I think clarify things a little.

I think I can answer them, but would anyone else like to have a go? (I’m out all day today).

A Second Look at the Second Law…

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…is the title of Granville Sewell’s manuscript that almost got published in Applied Mathematics Letters last year. It was withdrawn at the last minute by the editor, but you can still download the manuscript from Sewell’s web page. The purpose of this thread is to discuss the technical merits of Sewell’s arguments.

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No Free Lunch

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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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Intelligence and Design.

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My copy of No Free Lunch arrived a few days ago, and there are a couple of posts I want to make about it, but the first thing that struck me, reading the preface, and not for the first time, is how little Dembski (and other Intelligent Design proponents) seem to know about either Intelligence or Design.

As it happens, I have a relevant background in both.  I’m a cognitive scientist, and I came into cognitive science from a background in educational psychology, so I’ve always been interested in intelligence – how it works, how it is measured, what factors affect it, etc.  And, somewhat unusually for a cognitive scientist, I also have a training in design – I trained as an architect, a design training that is specifically focussed on “problem solving”, but I also applied that training to other “design” modalities, including composing music, and writing children’s books that attempted to explain something, both to commission, and therefore with a “design brief”.

And in both areas, what is abundantly clear, is that learning is critical.

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Does intelligence violate the 2LoT?

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Granville Sewell’s argument that evolution does so, therefore evolution must be caused by intelligence, rests on the odd assertion that intelligence (our own, for instance) does violate the 2LoT.

Bruce David, a UD poster I have a lot of respect for, writes:

I realize that to say that something, anything, violates the Second Law is an anathema to most people who have had a normal scientific education. And I have had the experience on these threads of explaining Dr. Sewell’s point in what I thought was very clearly reasoned prose to people like Elizabeth Liddle, who is intelligent, a scientist, and generally does give her fellow commenters a respectful hearing, only to get the terse response, “Nothing violates the Second Law.”

However, Dr. Sewell’s point, as I understand it, is that both life and human activity in fact do violate the Second Law, and in the case of humans it is clearly our creative intelligence that does this. And if ID is correct, then it is only intelligence that does this. Personally, I think it is a point worth making, even if it falls on deaf ears most of the time. And also, I think that precisely because it contradicts one of the most respected principles of science, and because of the implications for the nature of intelligence and thus the nature of human beings, that it has massive implications for science, philosophy, spirituality, and religion, and therefore, again, needs to be brought to light.

Yes indeed.  If ordinary human intelligence regularly violates the Second Law of Thermodynamics, that would indeed have massive implications, for all kinds of things, not least our energy requirements.

hmmm.

Creating CSI with NS

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Imagine a coin-tossing game.  On each turn, players toss a fair coin 500 times.  As they do so, they record all runs of heads, so that if they toss H T T H H H T H T T H H H H T T T, they will record: 1, 3, 1, 4, representing the number of heads in each run.

At the end of each round, each player computes the product of their runs-of-heads.  The person with the highest product wins.

In addition, there is a House jackpot.  Any person whose product exceeds 1060 wins the House jackpot.

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Dembski’s CSI

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(5th April, 2013: stickying this, for a bit, as it has come up.  Mung might like to comment).

Time to look at this in detail, I think 🙂

His definitive paper to date on CSI, is Specification: The Pattern That
Signifies Intelligence. It is very clearly written, not very mathy, but, by the same token, a paper in which it is easy (IMO) to see where he goes wrong.

Here is the abstract:

ABSTRACT: Specification denotes the type of pattern that highly improbable events must exhibit before one is entitled to attribute them to intelligence. This paper analyzes the concept of specification and shows how it applies to design detection (i.e., the detection of intelligence on the basis of circumstantial evidence). Always in the background throughout this discussion is the fundamental question of Intelligent Design (ID): Can objects, even if nothing is known about how they arose, exhibit features that reliably signal the action of an intelligent cause? This paper reviews, clarifies, and extends previous work on specification in my books The Design Inference and No Free Lunch.

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

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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

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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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