Category Archives: Evolution

Macro/microevolution

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A number of posts have appeared at Uncommon Descent on the topic of macroevolution. Comments here have been appended to other threads, but I thought it an appropriate subject for its own thread.

The posts start here with a link to chemist James M Tour’s blog, on which he posted some personal musings on the creation-evolution debate. Numerous follow-on posts have appeared on UD subsequently, in a rather recursive comments-becoming-posts-spawning-more-comments-that-become-posts manner. I won’t detail them all, but they comprise the bulk of UD threads between 18th and 22nd February.

Tour admits his lack of credentials in the subject, but fundamentally expresses doubts that microevolution (which he accepts) leads to macroevolution. The issue has taken a bizarre turn since, apparently, a couple of UD regulars have offered to stump up costs for Nick Matzke to have lunch with Tour in a meeting that will be witnessed by one of them (it’s his dollar!) but, at Tour’s request, will not be recorded or discussed externally. A personal tutorial. Matzke’s mission, should he choose to accept it, is to prove to Tour’s satisfaction that the extrapolation is justified – that macroevolution is sufficiently explained by iterating the small degrees of microevolution.

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Is evolution of proteins impossible?

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At Uncommon Descent, “niwrad” has posted a link to a Sequences Probability Calculator. This webserver allows you to set a number of trials (“chemical reactions”) per second, the number of letters per position (20 for amino acids) and a sequence length, and then it calculates how long it will take for you to get exactly that sequence. Each trial assumes that you draw a sequence at random, and success is only when you exactly match the target sequence. This of course takes nearly forever.

So in effect the process is one of random mutation without natural selection present, or random mutation with natural selection that shows no increase in fitness when a sequence partially matches the target. This leads to many thoughts about evolution, such as:

  • Do different species show different sequences for a given protein? Typically they do, so the above scheme implies that they can’t have evolved from common ancestors that had a different protein sequence. They each must have been the result of a separate special creation event.
  • If an experimenter takes a gene from one species and puts it into another, so that the protein sequence is now that of the source species, does it still function? If not, why are people so concerned about making transgenic organisms (they’d all be dead anyway)?
  • If we make a protein sequence by combining part of a sequence from one species and the rest of that protein sequence from another, will that show function in either of the parent species? (Typically yes, it will).

Does a consideration of the experimental evidence show that the SPC fails to take account of the function of nearby sequences?

The author of the Sequences Probability Calculator views evolution as basically impossible. The SPC assumes that any change in a protein makes it unable to function. Each species sits on a high fitness peak with no shoulders. In fact, experimental studies of protein function are usually frustrating, because it is hard to find noticeable difference of function, at least ones big enough to measure in the laboratory.

ID, ENCODE and the Happy Isles of Fitness

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As Neil Rickert was foolish enough to grant me posting rights, I had better take advantage of the offer before the sysops sensibly change their minds.

Consider an argument used consistently by the ID community: that the natural processes of genetic mutation and environmental selection acting upon the resultant variation are incapable of generating speciation.

Their recurring metaphor is of improbable islands of fitness separated by unbridgeable seas of non-functionality. Even if the hill-climbing capability of “random mutation plus natural selection” is real (and even incorporating unselected allele frequency changes), evolution can’t work because “you can’t get there from here”. For brevity, let me acronymise this argument as CANTSWIM.

CANTSWIM has a great many shortcomings as a metaphor for how evolutionary processes actually work, and you don’t need me to enumerate them. But let me hand over the title deeds to the evolutionary farm, and assume that CANTSWIM is factual.

At the same time, the ID community has adopted the claim made by the leadership of the ENCODE program that >80 per cent of the human genome is functional. The devil, of course, is in the detail of how “functional” is defined.

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On Paul Nelson on macro-evolution

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Paul Nelson has argued against macro-evolution, and I sense that some folk here want to discuss it.  So here’s a thread where we can do that without taking other threads off-topic.

First, some references.  There are three UD threads on this:

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An Invitation to G Puccio

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gpuccio addressed a comment to me at Uncommon Descent. Onlooker, a commenter now unable to post there,

(Added in edit 27/09/2012 – just to clarify, onlooker was banned from threads hosted by “kairosfocus” and can still post at Uncommon Descent in threads not authored by “kairosfocus”)

has expressed an interest in continuing a dialogue with gpuccio and petrushka comments:

By all means let’s have a gpuccio thread.

There are things I’d like to know about his position.

He claims that a non-material designer could insert changes into coding sequences. I’d like to know how that works. How does an entity having no matter or energy interact with matter and energy? Sounds to me like he is saying that A can sometimes equal not A.

He claims that variation is non stochastic and that adaptive adaptations are the result of algorithmic directed mutations. Is that in addition to intervention by non-material designers? How does that work?

What is the evidence that non-stochastic variation exists or that it is even necessary, given the Lenski experiment? Could he cite some evidence from the Lenski experiment that suggests directed mutations? Could he explain why gpuccio sees this and Lenski doesn’t?

It’s been a long time since gpuccio abandoned the discussion at the Mark Frank blog. I’d like to see that continued.

So I copy gpuccio’s comment here and add a few remarks hoping it may stimulate some interesting dialogue. Continue reading →

Is ‘Design in Nature’ a Non-Starter?

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A row is ready to erupt over two competing notions of ‘design in nature.’ One has been proposed under the auspices of being a natural-physical law. The other continues to clamour for public attention and respectability among natural-physical scientists, engineers and educators, but carries with it obvious religious overtones (Foundation for Thought and Ethics, Wedge Document and Dover trial 2005) and still has not achieved widespread scholarly support after almost 20 years of trying.

One the one hand is the Discovery Institute’s notion of ‘design in nature,’ which is repeated in various forms in the Intelligent Design movement. Here at TSZ many (the majority of?) people are against ID and ID proponents’ views of ‘design in nature.’ The author of this thread is likewise not an ID proponent, not an IDer. On the other hand is Duke University engineering and thermodynamics professor Adrian Bejan’s notion of ‘design in nature’ (Doubleday 2012, co-authored with journalism professor J. Peder Zane), which rejects Intelligent Design theory, but contends that ‘design’ is nevertheless a legitimate natural scientific concept. Apropos another recent thread here at TSZ, Bejan declares that his approach “solves one of the great riddles of science – design without a designer.”

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James Barham on Mary Jane West-Eberhard and teleology

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UD has featured a post by James Barham on the work of Mary Jane  West-Eberhard.  I shall be questioning Barham’s conclusions.

Unlike the subject of my previous column in this series, James A. Shapiro, she does not present her ideas as revolutionary or as a mortal threat to the Darwinian worldview.

In my opinion (as a non-biologist), she is entirely correct about that.

And yet, I shall argue that West-Eberhard—who is a researcher at the Smithsonian Tropical Research Institute in Panama, as well as a professor of biology at the University of Costa Rica—has made a foudational contribution to a new and revolutionary approach to evolutionary theorizing that bids fair (whatever her expressed intentions) to turn mainstream Darwinism on its head.

Perhaps it challenges the strawman version of Darwinism that creationists and ID proponents love to criticize.  But I don’t see it as any challenge at all to Darwinism. Continue reading →

Gil Dodgen on “Transparent Lunacy”

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In a recent UD post, Gil has been more specific than he often is, so I thought I would respond here:

The resolution of the debate about the creative powers of natural selection is dead simple and utterly trivial to figure out.

  1. Natural selection throws stuff out. Throwing stuff out has no creative power.
  2. Existing biological information, mixed and matched, can be filtered by natural selection, as in sexual reproduction, but nothing inherently new is created.
  3. Random errors can produce survivability quotients, but only in circumstances in which overall functional degradation supports survival in a pathological environment (e.g., bacterial antibiotic resistance), and only given massive probabilistic resources and a few trivial mutational events capable of producing the survival advantage.
  4. Random errors are inherently entropic, and the more complex a functionally-integrated system becomes, the more destructive random errors become. Anyone with any experience in even the most elementary engineering enterprise knows this.

To his first, I cite this:

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Cornelius Hunter vs William Dembski?

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Cornelius Hunter has posted an odd argument:

Is there evidence for evolution? Sure, there is plenty of evidence for evolution. But there are significant problems with evolution. There is plenty of evidence for evolution just as there is plenty of evidence for geocentrism. But the science does not bode well for either theory.

So the evidence for evolution follows this general pattern: Even at its best, it does not prove evolution to be a fact. And furthermore, the evidence reveals substantial problems with evolution.

So how can evolutionists proclaim evolution to be a fact with such fervor? There seems to be a glaring mismatch between the evidence and the truth claims of evolutionists. The answer is that evolutionists use contrastive reasoning. Evolution is not claimed to be a fact based on how well it fits the evidence, but rather on how poorly the alternative fits the evidence. Evolution is proved by the process of elimination.

In other words, Hunter is arguing directly against Dembski:.

In eliminating chance and inferring design, specified complexity is not party to an argument from ignorance. Rather, it is underwriting an eliminative induction. Eliminative inductions argue for the truth of a proposition by actively refuting its competitors (and not, as in arguments from ignorance, by noting that the proposition has yet to be refuted)

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Granville Sewell vs Bob Lloyd

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Bob Lloyd, professor emeritus of chemistry at Trinity College Dublin, wrote an opinion article in Mathematical Intelligencer (MI) commenting on Sewell’s not-quite-published AML article. This was mentioned in a previous thread, where Bob briefly commented. Granville was invited to participate but never showed up.

In response to Lloyd, Sewell submitted a letter to the editor. On advice of a referee, his letter was rejected. (Rightly so, in my view. More on that later.) Sewell has now written a post on Discovery Institute’s blog describing his latest misfortune. The post contains Sewell’s unpublished letter and some of the referee’s comments. I invite you to continue the technical discussion of Sewell’s points started earlier.

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More on Marks, Dembski, and No Free Lunch, by Tom English

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Tom English has a great post at his blog, Bounded Science, which I have his permission to cross post here:

Bob Marks grossly misunderstands “no free lunch”

And so does Bill Dembski. But it is Marks who, in a “Darwin or Design?” interview, reveals plainly the fallacy at the core of his and Dembski’s notion of “active information.” (He gets going at 7:50. To select a time, it’s best to put the player in full-screen mode. I’ve corrected slips of the tongue in my transcript.)

[The “no free lunch” theorem of Wolpert and Macready] said that with a lack of any knowledge about anything, that one search was as good as any other search. [14:15]And what Wolpert and Macready said was, my goodness, none of these [“search”] algorithms work as well as [better than] any other one, on the average, if you have no idea what you’re doing. And so the question is… and what we’ve done here is, if indeed that is true, and an algorithm works, then that means information has been added to the search. And what we’ve been able to do is take this baseline, that all searches are the same, and we’ve been able to, in cases where searches work, measure the information that is placed into the algorithm in bits. And we have looked at some of the evolutionary algorithms, and we found out that, strikingly, they are not responsible for any creation of information. [14:40]

And according to “no free lunch” theorems, astonishingly, any search, without information about the problem that you’re looking for, will operate at the same level as blind search.” And that’s… It’s a mind-boggling result. [28:10]

Bob has read into the “no free lunch” (NFL) theorem what he believed in the first place, namely that if something works, it must have been designed to do so. Although he gets off to a good start by referring to the subjective state of the practitioner (“with a lack of knowledge,” “if you have no idea what you’re doing”), he errs catastrophically by making a claim about the objective state of affairs (“one search is as good as any other search,” “all searches are the same”).

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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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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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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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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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“Tiktaalik”, Why it is a failed Prediction

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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

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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 🙂

 

Intelligent Design is NOT Anti-Evolution

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Thank you Elizabeth for this opportunity-

Good day- Over the past many, many years, IDists have been telling people that intelligent design is not anti-evolution. Most people understand and accept that, while others just refuse to, no matter what.

With that said, in this post I will provide the evidence (again) that firmly demonstrates that ID is not anti-evolution. I will be presenting several authoritative definitions of “evolution” followed by what the ID leadership has to say about evolution. So without any further adieu, I give you-

Intelligent Design is NOT Anti-Evolution

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