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.

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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…

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:

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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:

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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.

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Why we probably don’t live in a computer simulation

Over at her blog, BackReAction, physicist Sabine Hossenfelder has written a cogently argued article titled, No, we probably don’t live in a computer simulation (March 15, 2017). I’ll quote the most relevant excerpts:

According to Nick Bostrom of the Future of Humanity Institute, it is likely that we live in a computer simulation

Among physicists, the simulation hypothesis is not popular and that’s for a good reason – we know that it is difficult to find consistent explanations for our observations…

If you try to build the universe from classical bits, you won’t get quantum effects, so forget about this – it doesn’t work. This might be somebody’s universe, maybe, but not ours. You either have to overthrow quantum mechanics (good luck), or you have to use qubits. [Note added for clarity: You might be able to get quantum mechanics from a classical, nonlocal approach, but nobody knows how to get quantum field theory from that.]

Even from qubits, however, nobody’s been able to recover the presently accepted fundamental theories – general relativity and the standard model of particle physics…

Indeed, there are good reasons to believe it’s not possible. The idea that our universe is discretized clashes with observations because it runs into conflict with special relativity. The effects of violating the symmetries of special relativity aren’t necessarily small and have been looked for – and nothing’s been found.

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Are atheists really atheists as they claim?

I’m pretty sure that most knowledgeable people know that someone who claims to be an atheist is just making an overstatement about his/her own beliefs. As most knowledgeable people who claim to be atheist probably know that even the most recognizable  faces  of atheistic propaganda, such as Richard Dawkins, admitted publicly that they are less than 100% certain that God/gods don’t exist.

My question is: Why would anyone who calls himself an atheist make a statement like that?

Do we have a duty not to procreate?

Writing in the Sydney Morning Herald recently, Australian journalist Ruby Hamad explained her decision not to have any children. Ecological considerations proved to be a “very compelling factor” influencing her decision, leading her to conclude that for her and her partner, having a child would be “the more selfish decision.” Ms. Hamad details her reasons in a passage that makes for disturbing reading:

Our planet is in trouble. We all know this. The Amazon is depleting so rapidly, we have already lost 20 per cent of it and will lose another 20 in the next two decades – just as children born today are coming of age. Lucky them!

The Great Barrier Reef is as good as dead, as everyone who is not Pauline Hanson will admit, but deforestation is also happening in the oceans, thanks to the rise in global temperatures. Meanwhile, the oceans will be commercially extinct by the middle of the century, and the entire Arctic is living on borrowed time…

For lay people, the knowledge that one child born today will add 9,441 metric tons of carbon to the atmosphere is enough to turn them off procreation. “You can never take it back,” said one American woman. “That stopped me in my tracks.”

So, is Ruby Hamad right? In today’s post, I’d like to explain why I believe her logic is profoundly mistaken.

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How Did The Designer/God do it?

I’m pretty sure that many creationists/ID proponents and skeptics about materialism have heard that question many times often when materialists get  cornered about their beliefs about the origins of life…The usual question posed by materialists is: How Did The Designer/God do it? We can’t recreate life, so tell us how was it created!

Does anyone have a theory about how ID/God/ET did it?

I have my own,  but I’m just curious how much smarter people than me would answer  the skeptics who often add to their skepticism: Did ID/God/ET just “poofed”  life magically into existence?