My thoughts on JohnnyB’s new view of Irreducible Complexity

Jonathan Bartlett, known here as JohnnyB, has written a very thought-provoking post titled, A New View of Irreducible Complexity. I was going to respond in a comment on his post, but I soon realized that I would be able to express my thoughts much more clearly if I composed a post of my own, discussing the points which he raises.

Before I continue, I would like to say that while I find JohnnyB’s argument problematic on several counts, I greatly appreciate the intellectual effort that went into the making of his slide presentation. I would also like to commend JohnnyB on his mathematical rigor, which has helped illuminate the key issues.

Without further ado, I’d like to focus on some of the key slides in JohnnyB’s talk (shown in blue), and offer my comments on each of them. By the time I’m done, readers will be able to form their own assessment of the merits of JohnnyB’s argument.

Continue reading

Confabulation

An interesting essay in Aeon by neurologist Jules Montague:

Why is the brain prone to florid forms of confabulation?

She had visited Madonna’s mansion the week before, Maggie told me during my ward round. Helped her choose outfits for the tour. The only problem was that Maggie was a seamstress in Dublin. She had never met Madonna; she had never provided her with sartorial advice on cone brassieres. Instead, an MRI scan conducted a few days earlier – when Maggie arrived at the ER febrile and agitated – revealed encephalitis, a swelling of the brain.

Now she was confabulating, conveying false memories induced by injury to her brain. Not once did Maggie doubt that she was a seamstress to the stars, no matter how incongruous those stories seemed. And that’s the essence of confabulation: the critical faculty of doubt is compromised. These honest lies were Maggie’s truth…

‘Memetics is a Dumb Explanation’ says Dennettian ‘naturalist’

The resident professional ‘philosopher’ of TSZ recently wrote this:

“’memes!’ is a dumb explanation.”

Yes, I agree! (Although that person doesn’t seem to know the difference between ‘memes’ and ‘memetics.’ – e.g. I don’t mind ‘memes’ used for popular shared internet links, but that’s not ‘memetics.’)

Well, given the weekend’s significance for a billion+, let’s ‘crucify’ memetics then. Why is ‘memetics’ a dumb explanation? And there’s no need to hold back with merely ‘dumb’. If one is an ideological ‘naturalist’, isn’t one forced into something like ‘memetics’ because they share the same materialist, naturalist, agnostic/atheist worldview as (chuckling at his own supposed lack of self-identity!) Daniel Dennett? Isn’t the built-in materialism of ‘memetics’ what made it so attractive to certain people and for the same reason obviously not attractive or believable to most others?

Continue reading

RNA editing in cephalopods

From Wired:

But when Stanford University geneticist Jin Billy Li heard about Joshua Rosenthal’s work on RNA editing in squid, his jaw dropped. That’s because the work, published today in the journal Cell, revealed that many cephalopods present a monumental exception to how living things use the information in DNA to make proteins. In nearly every other animal, RNA—the middleman in that process—faithfully transmits the message in the genes. But octopuses, squid, and cuttlefish (but not their dumber relatives, the nautiluses) edit their RNA, changing the message that gets read out to make proteins.

In exchange for this remarkable adaptation, it appears these squishy, mysterious, and possibly conscious creatures might have given up the ability to evolve relatively quickly. Or, as the researchers put it, “positive selection of editing events slows down genome evolution.” More simply, these cephalopods don’t evolve quite like other animals. And that could one day lead to useful tools for humans.

From the paper itself:

Continue reading

Evidence for the Resurrection: Why reasonable people might differ, and why believers aren’t crazy

Easter is approaching, but skeptic John Loftus doesn’t believe in the Resurrection of Jesus. What’s more, he thinks you’re delusional if you do. I happen to believe in the Resurrection, but I freely admit that I might be mistaken. I think Loftus is wrong, and his case against the Resurrection is statistically flawed; however, I don’t think he’s delusional. In today’s post, I’d like to summarize the key issues at stake here, before going on to explain why I think reasonable people might disagree on the weight of the evidence for the Resurrection.

The following quotes convey the tenor of Loftus’ views on the evidence for the Resurrection:

Continue reading

Dennett in The New Yorker

I wanted to bring to your attention a lovely profile piece on Dan Dennett, “Daniel Dennett’s Science of the Soul“.  It’s nice to see a philosopher as respected and well-known as Dennett come alive as a human being.

I’d also like to remind those of you interested in this sort of thing that Dennett has a new book out, From Bacteria to Bach And Back: The Evolution of Minds. The central project is to do what creationists are always saying can’t be done: use the explanatory resources of evolutionary theory to understand why we have the kinds of minds that we do. There are decent reviews here and here, as well as one by Thomas Nagel in New York Review of Books that I regard as deliberately misleading (“Is Consciousness an Illusion?“).

[Note: The profile and/or the Nagel review may be behind paywalls.]

 

Is it easy to get a new protein? A reply to Ann Gauger

In a podcast on the show, ID the Future (March 14, 2017), Dr. Ann Gauger criticized a popular argument that purports to show how easy it is to get new proteins: namely, the evolution, over a relatively short 40-year period, of nylonase. (Nylonase is an enzyme that utilizes waste chemicals derived from the manufacture of nylon, a man-made substance that was not invented until 1935.) While Dr. Gauger made some factual observations that were mostly correct, her interpretation of these observations fails to support the claim made by Intelligent Design proponents, that the odds of getting a new functional protein fold are astronomically low, and that it’s actually very, very hard for new proteins to evolve. Let’s call this claim the “Hard-to-Get-a-Protein” hypothesis (HGP for short).

To help readers see what’s wrong with Dr. Gauger’s argument, I would like to begin by pointing out that for HGP to be true, two underlying claims also need to be correct:

1. Functional sequences are RARE.
2. New functions are ISOLATED in sequence space.

In her podcast, Dr. Gauger cites the work of Dr. Douglas Axe to support claim #1, when she declares that the odds of getting a new functional protein fold are on the order of 1 in 10^77 (an assertion debunked here). Dr. Gauger says little about claim #2; nevertheless, it is vital to her argument. For even if functional sequences are rare, they may be clustered together – in which case, getting from one functional protein to the next won’t be so hard, after all.

If claims #1 and #2 are both correct, then getting new functions should not be possible by step-wise changes. Remarkably, however, this is precisely what Dr. Gauger concedes, in her podcast, as we’ll see below.

Continue reading

Contradictions in the Christian Bible

Contradictions are rife in the Christian bible. Here at The Skeptical Zone we have recently discussed those surrounding how Saul died. We’ve also noted the two conflicting accounts of Judas’ death and what he did with the thirty pieces of silver. There are dozens more.

The Skeptics’ Annotated Bible and The Thinking Atheist are two of several excellent resources on biblical contradictions and absurdities. The sheer volume of contradictions, though, is best demonstrated visually as is done at BibViz:

The creators of this site started with a cross-index of topics in the bible and pulled out those that contradict each other. You can click on the links to get more detail. As a bonus, the site includes references to the sections in the bible that contain Scientific Absurdities & Historical Inaccuracies, Cruelty & Violence, Misogyny, Violence & Discrimination Against Women, and Discrimination Against Homosexuals.

Obviously most Christians aren’t foolish enough to claim their bible is inerrant. Those that do, in the words of Desi Arnaz, have “got some ‘splainin’ to do.”