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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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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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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Why David Madison’s Slam Dunk Isn’t One

David Madison is a minister-turned-atheist, who has a PhD in Biblical Studies from Boston University. Madison was raised a liberal Protestant, but he gradually lost his faith while serving as the pastor of two Methodist parishes in Massachusetts. He went on to pursue a business career, but he’s recently written a book titled, Ten Tough Problems in Christian Thought and Belief: A Minister-Turned-Atheist Shows Why You Should Ditch the Faith (see here for one critic’s review and here for a more favorable review).

However, what put me off Madison’s book is what he’s written on his own Web page. His recommended reading list of 200 books, put together for people who want to “find out how Jesus, Christianity and theism have all been so convincingly slam dunked,” includes dozens of books by authors defending the kooky view that Jesus never even existed (a view not shared by any reputable historian – and no, Dr. Richard Carrier doesn’t count as one; nor does Dr. Robert Price, who got trounced when he debated Dr. Bart Ehrman last year on the historicity of Jesus, as Carrier himself admits), and only a handful of books addressing the traditional philosophical arguments for the existence of God, of which Raymond Bradley’s God’s Gravediggers: Why No Deity Exists (Ockham Publishing, 2016) and Michael Martin’s The Cambridge Companion to Atheism appear to be the most substantive. (There are other books attacking Intelligent Design on Madison’s list, but these are beside the point, as ID proponents don’t maintain that their arguments, taken by themselves, prove the existence of any Deity.) And believe it or not, H. L. Mencken, whose credibility on religious and moral issues I have demolished here, here, here and here, makes the list, too. Richard Dawkins’ The God Delusion is on the list (has Madison ever read John Lennox’s response, I wonder?), as well as Bertrand Russell’s Why I Am Not a Christian, which has been refuted ably by David Snoke.

For the benefit of his readers, Madison has also kindly provided chapter summaries for his book, which (I am sorry to say) do not inspire confidence. A few excerpts:

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Worse than Watergate? Bias in the mainstream media

With the mainstream media mocking what they describe as President Trump’s delusional claim that former President Obama ordered Trump Tower’s phones to be tapped, I thought it would only be fair to invite readers to look at the other side. In a 12-minute video, Mark Levin, a lawyer who was a chief of staff for Attorney General Edwin Meese during the Reagan administration, has laid out what appears to be overwhelming evidence that backs up Trump’s wiretapping claims. Newt Gingrich offers his take here. Matthew Vadum’s article, Obama’s Wiretaps?, in FrontPage magazine, makes for very disturbing reading. Vadum doesn’t pull any punches:

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The Christian God and the Problem of Evil

Both Mung and KeithS have asked me to weigh in on the question of whether the existence of evil counts as a good argument against Christianity, as KeithS has maintained in a recent post, so I shall oblige.

It is important to understand that the problem of evil is not an argument against the existence of God or gods, but against what KeithS calls the Christian God (actually, the God of classical theism), Who is supposed to be omniscient, omnipotent and omnibenevolent. KeithS succinctly formulates the problem as follows:

Let’s say I claim that an omniGod named Frank exists — omniscient, omnipotent, and omnibenevolent. Suppose I also claim that Frank regards seahorses as the absolute height of evil. The world contains a lot of seahorses, and Frank, being omnipotent, has the power to wipe them off the face of the earth. Why doesn’t he? Why does he countenance a world full of seahorses?

KeithS emphasizes that it is not enough for the Christian to show that God is on balance benevolent. Rather, the Christian needs to defend the claim that God is omnibenevolent:

The Christian claim is that God is omnibenevolent — as benevolent as it is logically possible to be. Finding that the items on the “good” side of the ledger outweigh those on the “bad” side — if that were the case — would not establish God’s omnibenevolence at all.

Finally, KeithS provides his own take on the problem of evil:

The problem of evil remains as much of a problem as ever for Christians. Yet there are obvious solutions to the problem that fit the evidence and are perfectly reasonable: a) accept that God doesn’t exist, or b) accept that God isn’t omnipotent, or c) accept that God isn’t perfectly benevolent. Despite the availability of these obvious solutions, most Christians will choose to cling to a view of God that has long since been falsified.

He even suggests how he would resolve the problem if he were a theist (emphasis mine – VJT):

Suppose God hates evil and suffering but is too weak to defeat them, at least at the moment. Then any such instances can be explained by God’s weakness.

It addresses the problem of evil without sacrificing theism. I’m amazed that more theists don’t seize on this sort of resolution. They’re too greedy in their theology, too reluctant to give up the omnis.

I think KeithS is onto something here. In fact, I’d like to ditch the conventional Christian views of God’s omniscience, omnipotence and omnibenevolence. It’s time for an overhaul.

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Gay atheist media star interviews bishop: what do you think?

I found this interview on the Website of Brandon Vogt, a Catholic blogger and speaker who’s the Content Director for Bishop Robert Barron’s Word on Fire Catholic Ministries. Allow me to quote from Vogt’s introduction:

A few months ago, a man named Dave Rubin reached out to us at Word on Fire to ask if Bishop Barron would be open to an interview. (Apparently lots of Dave’s Twitter followers suggested the idea.)

To be honest, we didn’t know much about Dave at the time. But after some Googling, we discovered he’s a well-known comedian and host of the super popular “Rubin Report”, a show that airs directly through YouTube. “The Rubin Report” has over 350,000 subscribers and 100 million views. It’s one of the most popular YouTube channels in the world…
Dave is an interesting guy. One website describes him as a “rising media star” and “the voice of liberals who were mugged by progressives.” It says he’s “a 39-year-old pro-choice, pro-pot, recently gay-married atheist with a strong allergy to organized religion.”
In other words, the anti-Bishop Barron…

I encourage you to watch both parts of the interview. Bishop Barron did such a marvelous job. He was smart and eloquent, even when Dave pushed the discussion toward hot-button issues…


So, what do viewers think of this interview? Does anyone feel that the bishop made an interesting case for belief in God?

Two kinds of complexity: why a sea anemone is not a Precambrian fossil rabbit

The British biologist J.B.S. Haldane is said to have remarked that the discovery of fossil rabbits in the Precambrian would falsify the theory of evolution. Over at Evolution News and Views, Dr. Cornelius Hunter has argued in a recent post that the sea anemone (whose genome turns out to be surprisingly similar to that of vertebrates) is “the genomic equivalent of Haldane’s Precambrian rabbit – a Precambrian genome had, err, all the complexity of species to come hundreds of millions of years later.” Apparently Dr. Hunter is under the impression that many of these ancestral genes would have been lying around unused for much of that time, for he goes on to triumphantly point out that “the idea of foresight is contradictory to evolutionary theory.” RIP, evolution? Not by a long shot.

An unfortunate misunderstanding

Dr. Hunter seems to have missed the whole point of the report that he linked to. A sentence toward the end of the report would have set him right, had he read it more carefully (emphases and square brackets are mine – VJT):

It’s surprising to find such a “high level of genomic complexity in a supposedly primitive animal such as the sea anemone,” [Dr. Eugene V.] Koonin [of the National Center for Biotechnology Information (NCBI) in Bethesda, Md.] told The Scientist. It implies that the ancestral animal “was already extremely highly complex, at least in terms of its genomic organization and regulatory and signal transduction circuits, if not necessarily morphologically.

That’s right. Genomic complexity and morphological complexity are two completely different things. That was the take-home message of the report. It was also the message of the other report cited by Dr. Hunter:

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