Is the party over?

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I’ve spent most of this year doing an honours degree studying genetic algorithms. As such, I’ve found reading the best and brightest ID proponent’s attempts to understand the genetic algorithm equivalent of a “Hello World” program – a simple string evolver, with no crossover and only one parent per generation – to be hillarious.

Anyway, it seems that they’ve finally managed to come up with a version of the program that doesn’t consist of a partitioned search. It mutates a single character per offspring, rather than giving each locus an independent probability of being mutated, but that’s a somewhat smaller flaw than most cdesign proponentist attempts to implement the Weasel program.

And then, GilDodgen came out with this:

No search is required, because the solution has been provided in advance. These programs are just hideously inefficient means of printing out what could have been printed out when the program launched. The information for the solution was explicitly supplied by the programmer.

Well, duh. That’s because it was a toy program, purely written to illustrate the difference between pure random chance and the accumulation of small changes. You may as well say that the entire software development industry is a waste of time and money because it would be easier to just create a file containing the string “Hello world” and print it to the terminal with cat.

The Weasel program does not attempt to show that evolution can produce novel information. It merely demonstrates that difference between selection and no-selection. If you want a computer simulation to demonstrate the power of evolution to produce novel structures, you could read one of any number of papers in which genetic algorithms or genetic programming have been used to find novel solutions to real-world problems. Or, heck, even read the rest of chapter three in TBW (the one which mentions the Weasel program), which is mostly about the far more interesting Biomorphs program.

Or, if you prefer, Gil’s conclusion:

The Darwinian mechanism as an explanation for all of life is simply not credible. Most people have enough sense to recognize this, which is why the consensus “scientists” — with all their prestige, academic credentials, and incestuous self-congratulation — are having such a hard time convincing people that they have it all figured out, when they obviously don’t.

If you like, you can download my version of Weasel. It’s written in C# and you’ll need at least .NET 2.0 to run it. Source and binaries are included in that download. It uses a population size of 200 and a mutation rate of 0.05.

Throwing modus tollens around like it was confetti

Cornelius Hunter, is, as usual, ridiculous, most recently in his commentary on a review of TGSOE.

After all, there are no fossil rabbits in the ancient strata. That’s right, no rabbits before the Cambrian era. Astonishing, evolution must be true.

For a start, the Precambrian rabbits are an example: anything so out of place would falsify evolution. The fact that nothing is out of place is not a “proof” of evolution, but it is a sign that this particular falsification test has been passed. With flying colours.

This was criticised in the comments (on UD), and Cornelius replied:

The very title of this blog post [No Precambrian Rabbits: Evolution Must Be True] is a complete and utter non sequitur, which no evolutionary biologist (least of all Richard Dawkins) has ever espoused.

I know it sounds absurd, but the Precambrian rabbit, and others like it, are precisely what evolutionists have seriously set for as falsification criteria / creation refuter.

Apparently, giving any falsification criteria is a modus tollens. Karl Popper must be rolling in his grave.

Testimony to our shared origins? Grand family tree? Evolutionists in the know are abandoning the venerable evolutionary tree, but don’t tell the people.

This section, specifically, was referring to “bats, monkeys, horses and humans”. These are all not only multi-cellular, but all mammals! Yes, the tree of life is tangled amongst single-celled organisms where lateral gene transfer is common, but unless he is seriously claiming that lateral gene transfer is common amongst mammals, or heck, even vertebrates, this is just a sign that he’s either blatantly misunderstood whatever magazine article he got his information about the tree of life from, or is deliberately being disingenuous.

There are multitudes of examples of similarities amongst the species that do not fit the evolutionary pattern. It is a glaring example of selecting the evidences that fit the theory, and ignoring the plethora of contradictions.

This was attacked in the comments, and his response was to post links to sections 4.2 and 4.3 here. These argue that new alleles can be created quickly and that there are ultra-conserved regions – true, but irrelevant, but it doesn’t come even close to addressing the point he was responding to – or even the claim he was attempting to make. The speed of genetic change can vary wildly – heck, that’s exactly what natural selection (for example) does – but it doesn’t change the simple fact that the similarities between genes conforms to the evolutionary predictions.

But it just wouldn’t be Cornelius Hunter without insisting that evolution was primarily religious. He picks out the following examples:

Glitches, like the laryngeal nerves that are so neatly laid out in fish but that must detour in animals with necks—by a crazy 15 feet (4.6m) in the case of giraffes—demonstrate the incremental, undirected business of evolution in touching detail.

Recurrent laryngeal nerveIn a shark, for example, branches from the vagus nerve are connected to the last three gills, passing behind the arteries as they do so. This is the simplest arrangement. However, if, for example, a giraffe had evolved from an organism with this arrangement, well, the gills would probably have been modified into things like thyroid or parathyroid glands, or the larynx, sharing the same nerve connections.

Although the larynx is now high in the neck, the recurrent laryngeal nerve still passes behind an artery in the torso! This goes well beyond mere theodicy. The picture on the right shows the path of the recurrent laryngeal nerve in a human neck – this is taken to extreme proportions in a giraffe, as the loop is repeated for the entire length of the neck. And why? Because, of course, humans and giraffes share a common ancestor with an organism in which putting the nerve behind the artery was the simplest way of doing it.

… among the many puzzles that evolution explains so well are the futility and suffering that are ubiquitous in the natural world. All trees would benefit from sticking to a pact to stay small, but natural selection drives them ever upward in search of the light that their competitors also seek. Surely an intelligent designer would have put the rainforest canopy somewhat lower, and saved on tree trunks? The cheetah is perfectly honed to hunt gazelles—but the gazelle is equally well equipped to escape cheetahs. So whose side is the designer on?

Cornelius Hunter comments:

With religious arguments like these who needs scientific evidence?

Apparently, now evolution isn’t allowed to answer questions about the natural world. But again, this is part of the nature of evolutionary arms races – a mutant cheetah which can run faster will catch more gazelles than non-mutants, and so be more likely to reproduce. As the population of cheetahs becomes faster, there is now a selective pressure on gazelles to become faster.

Theological attacks on evolution are common nowadays, and given this, it is hardly surprising that a defense of evolution would respond to these attacks. But the case for evolution can be made without this, obviously: Chris Colby’s article Introduction to Evolutionary Biology article on is an excellent example of this.

Review: The Greatest Show on Earth

[cross-posted onto Young Australian Skeptics]

In previous books, Richard Dawkins has looked to promote new perspectives on natural selection, and at barriers to the understanding of evolution. In The Greatest Show on Earth, however, he looks at the evidence for evolution. You can read extracts from chapter one and chapter two online.

One of the book’s major strengths is the level of detail that Dawkins goes to in explaining difficult concepts and interesting experiments. For example, in the chapter on embryonic development, we learn how (well, one of the ways) in which mutations in the genome actually affect what a cell can do. This level of detail is a recurring feature. For example, we are treated 14 pages of glorious detail on Richard Lenski’s E. coli experiments, much of which I personally hadn’t picked up on when the story broke.

Dawkins considers molecular evidence to be the strongest line of evidence for evolution, and so the fossil record is just a bonus. He clearly outlines the problems with claiming that “gaps” in the fossil record make an argument against evolution. As far as fossils are concerned, the focus is on some of the more recent finds – and what a selection he has to choose from! He discusses tetrapods, whales, manatees, pinipeds (seals, sea lions & walruses) and turtles. It’s certainly a daunting prospect, to be claiming gaps in the fossil record, in the face of just these recent fossils. The discussion of homology was strong, not least for explicitly reverting to a pre-evolution definition of homology.

I particularly enjoyed the sections on development and molecular evidence – not least because of my unfamiliarity with these areas, and thus there was plenty for me to learn. I’m somewhat hopeful I’ll manage to work some self-organising systems into my doctorate somewhere.

Maybe I’m just a fan of cladograms, but I feel a couple of high-level cladograms – one of vertebrates (with a particular focus on the varieties of fish) and another of sauropsids – would have been worth a thousand words or so each. Another sour note was the mention of Andrew Schlafly in the discussion of the Lenski experiments, which mostly reeked of schadenfreude. I would have also avoided including any Haeckel drawings to illustrate any points – you just know that Haeckel’s crustaceans are going to give the history-deniers an irrelevant point to scream about whilst avoiding substantive discussion.

The depth of description – of the experiments, the discussion of human ancestry, and of the details of molecular & developmental biology is magnificent. As we’ve come to expect from Dawkins’ books, the writing is flowing and understandable, even on technical topics. And, as someone who had constantly had to maintain both my place in the main text and in the footnotes whilst reading The Selfish Gene, I was glad to see that the footnotes are at the bottom of each page, as opposed to at the back of the book.

Of course, Jerry Coyne published Why Evolution is True earlier this year. Is it worth reading both? The answer: yes, emphatically yes! Both books have very different lines of evidence on which they focus – Dawkins, for example, is highly focused on experiments, whereas Coyne focused more on observation in nature and the fossil record. Many lines of evidence, or topics for discussion, are only in one or other, or emphasised differently. There’s also a distinct difference in how they discuss creationism – Dawkins only mentions it occasionally and tends to give the evidence for evolution on its own merit (except in the chapter on biogeography, really).

So, yes, go and buy it. More importantly, go and read it!