On the Probability of Two Things Happening

On the ‘Evolving Complex Adaptations’ thread, a side-discussion arose with CharlieM over Behe’s ‘CCC’ argument. In summary, Behe places an event of probability {10^{-40} as the upper bound or ‘Edge of Evolution’. If a specific single mutation has a probability of {10^{-10} of arising in any one replication event, a specific double mutation has a probability of {10^{-20}, a triple {10^{-30}, and a quadruple {10^{-40} – that is, if four independent changes must happen simultaneously before a particular step is achievable, then that step cannot realistically have occurred in the history of life on earth. Behe thinks he has found a case with a {10^{-20} probability in the resistance to chloroquine in the malaria parasite Plasmodium falciparum.
Continue reading



A little bit of this and a little bit of that. A new and cheap way to implement genetic engineering, and a way to bypass the usual rules of population genetics.

The stakes, however, have changed. Everyone at the Napa meeting had access to a gene-editing technique called Crispr-Cas9. The first term is an acronym for “clustered regularly interspaced short palindromic repeats,” a description of the genetic basis of the method; Cas9 is the name of a protein that makes it work. Technical details aside, Crispr-Cas9 makes it easy, cheap, and fast to move genes around—any genes, in any living thing, from bacteria to people. “These are monumental moments in the history of biomedical research,” Baltimore says. “They don’t happen every day.”

ANY GENE TYPICALLY has just a 50–50 chance of getting passed on. Either the offspring gets a copy from Mom or a copy from Dad. But in 1957 biologists found exceptions to that rule, genes that literally manipulated cell division and forced themselves into a larger number of offspring than chance alone would have allowed.

A decade ago, an evolutionary geneticist named Austin Burt proposed a sneaky way to use these “selfish genes.” He suggested tethering one to a separate gene—one that you wanted to propagate through an entire population. If it worked, you’d be able to drive the gene into every individual in a given area. Your gene of interest graduates from public transit to a limousine in a motorcade, speeding through a population in flagrant disregard of heredity’s traffic laws. Burt suggested using this “gene drive” to alter mosquitoes that spread malaria, which kills around a million people every year. It’s a good idea. In fact, other researchers are already using other methods to modify mosquitoes to resist the Plasmodium parasite that causes malaria and to be less fertile, reducing their numbers in the wild. But engineered mosquitoes are expensive. If researchers don’t keep topping up the mutants, the normals soon recapture control of the ecosystem.

Push those modifications through with a gene drive and the normal mosquitoes wouldn’t stand a chance. The problem is, inserting the gene drive into the mosquitoes was impossible. Until Crispr-Cas9 came along.

Emmanuelle Charpentier did early work on Crispr.Today, behind a set of four locked and sealed doors in a lab at the Harvard School of Public Health, a special set of mosquito larvae of the African species Anopheles gambiae wriggle near the surface of shallow tubs of water. These aren’t normal Anopheles, though. The lab is working on using Crispr to insert malaria-resistant gene drives into their genomes. It hasn’t worked yet, but if it does … well, consider this from the mosquitoes’ point of view. This project isn’t about reengineering one of them. It’s about reengineering them all.

Principle of Sufficient Reason (PSR)

The Principle of Sufficient Reason is a powerful and controversial philosophical principle stipulating that everything must have a reason or cause. This simple demand for thoroughgoing intelligibility yields some of the boldest and most challenging theses in the history of metaphysics and epistemology. In this entry we begin with explaining the Principle, and then turn to the history of the debates around it.

Principle of Sufficient Reason

Continue reading

A Minimal Materialism

From Victor Reppert:

I am convinced that a broadly materialist view of the world must possess three essential features.

First, for a worldview to be materialistic, there must be a mechanistic base level.
Second, the level of basic physics must be causally closed.
Third, whatever is not physical, at least if it is in space and time, must supervene on the physical.

This understanding of a broadly materialistic worldview is not a tendentiously defined form of reductionism; it is what most people who would regard themselves as being in the broadly materialist camp would agree with, a sort of “minimal materialism.”

To the atheists:

Some of you know you’re materialists, some of you suspect it, others try to deny it or don’t like to be identified as such. But if you’re an atheist what else do you have?

Jonathan Bartlett’s “open-ended loop” argument

In the “Evolving complex features” thread, TristanM asks:

I’m curious what the group’s thoughts are on Jonathan Bartlett’s (AKA “JohnnyB”) argument about open-loops in the AVIDA program?

I haven’t studied Jon’s argument yet, but I think some of you have. What did you think?

Why I Love AVIDA – Detecting Design in Digital Organisms

Thoughts on Parameterized vs. Open-Ended Evolution and the Production of Variability

Irreducible Complexity and Relative Irreducible Complexity: Foundations and Applications


Just out of interest … this word gets bandied about a lot, mainly by evolution opponents hereabouts. They seem to use it when a word with multiple meanings is used. The accusation tends not to be withdrawn even when the intended meaning is unequivocally clarified – a bizarre situation where someone commits to a meaning and is still equivocating!

A typical definition is “The use of ambiguous language to conceal the truth or to avoid committing oneself”. There is a veiled hint of dishonesty – making an honest mistake with alternative definitions of a word is not strictly equivocation as defined there. That is, it is not merely ‘using ambiguous language’, still less ‘confusing two definitions of one word’, but purposefully being vague or misleading. But the use of the word rarely seems appropriate to me in the contexts in which it is used – generally, even the charge of ambiguity is unjustified, let alone nefarious motive. Numerous derails are provoked when one party says ‘you are equivocating’ and the other says ‘no I’m not’. I almost invariably find myself siding with (or being) the ‘no I’m not’ party (or, for self-referential funzies, “maybe I am, maybe I’m not”!).

Is this a quirk of American English (Americans forming the majority of opponents in these discussions)? Or is it a meme that has been unconsciously passed from one to another among the evolution-skeptical fraternity? Or something else?

Baby or Vat?

Zachriel asks, at UD:

Here’s a simple thought-experiment. There’s a fire at an fertility clinic, and there is precious little time before the entire building is engulfed in flames. Down one hallway, there’s the soft purring sound of an incubator with a thousand frozen embryos; down the other hallway, the cries of a newborn baby. Which do you choose to save?

Usually, people answer “the baby” and the interesting debate then concerns why.

Continue reading

Evolving complex features

The Lenski et al 2003 paper, The evolutionary origin of complex features, is really worth reading.  Here’s the abstract:

A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features. We examined this issue using digital organisms—computer programs that self-replicate, mutate, compete and evolve. Populations of digital organisms often evolved the ability to perform complex logic functions requiring the coordinated execution of many genomic instructions. Complex functions evolved by building on simpler functions that had evolved earlier, provided that these were also selectively favoured. However, no particular intermediate stage was essential for evolving complex functions. The first genotypes able to perform complex functions differed from their non-performing parents by only one or two mutations, but differed from the ancestor by many mutations that were also crucial to the new functions. In some cases, mutations that were deleterious when they appeared served as stepping-stones in the evolution of complex features. These findings show how complex functions can originate by random mutation and natural selection.

The thing about a computer instantiation of evolution like AVIDA is that you can check back every lineage and examine the fitness of all precursors.  Not only that, but you can choose your own environment, and how much selecting it does.  There are some really key findings:

Continue reading

The Cosmological Argument

I am currently working my way through the book A Natural History of Natural Theology: The Cognitive Science of Theology and Philosophy of Religion.

There is already a thread here dedicated to the book, but I decided to separate the thesis of the book from the actual natural theological arguments themselves. The evidence that the premises upon which these natural theological arguments rest are natural and intuitive are the subject of that thread.

In this thread I’d like to explore how the cosmological argument for the existence of God is presented in the book and provide a place where these cosmological arguments can be examined and criticized.

Continue reading