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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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.”

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?

 

Is the scientific revolution the result of Christianity’s influence in Europe? No/Yes!!

the issue/question of why europe became the origin for the scientific revolution has been said by many, now and in the past, to be the unique result of christian thought and could not of happened elsewhere in the world and thats why it didn’t.

I see many Christians, of all types, who care about science and who want to resist attacks about Christian beliefs being opposed to science MAKING these claims.

They say conclusions about God and order and laws is from Christian faith and led to seeing this in nature etc etc.

I say this is not true. Christian thought/beliefs had nothing to do with the science revolution and Europe’s superiority.

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You and your future self

In my final months at work, I had many conversations about retirement with friends and colleagues who asked about my plans and preparations and shared their own. I was struck by the wide range of attitudes they expressed. For some, retirement was a concrete reality, something they had visualized and thought about in detail. For others it was more abstract, as if it were going to happen to someone else entirely. You might expect this to correlate straightforwardly with age: the closer to retirement, the more concrete the thinking about it. That didn’t seem to be the case for many people.

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On the reception and detection of pseudo-profound bullshit

This 2015 paper ought to provoke provoke an interesting discussion:

On the reception and detection of pseudo-profound bullshit

Abstract

Although bullshit is common in everyday life and has attracted attention from philosophers, its reception (critical or ingenuous) has not, to our knowledge, been subject to empirical investigation. Here we focus on pseudo-profound bullshit, which consists of seemingly impressive assertions that are presented as true and meaningful but are actually vacuous. We presented participants with bullshit statements consisting of buzzwords randomly organized into statements with syntactic structure but no discernible meaning (e.g., “Wholeness quiets infinite phenomena”). Across multiple studies, the propensity to judge bullshit statements as profound was associated with a variety of conceptually relevant variables (e.g., intuitive cognitive style, supernatural belief). Parallel associations were less evident among profundity judgments for more conventionally profound (e.g., “A wet person does not fear the rain”) or mundane (e.g., “Newborn babies require constant attention”) statements. These results support the idea that some people are more receptive to this type of bullshit and that detecting it is not merely a matter of indiscriminate skepticism but rather a discernment of deceptive vagueness in otherwise impressive sounding claims. Our results also suggest that a bias toward accepting statements as true may be an important component of pseudo-profound bullshit receptivity.