There have been a number of interesting comments lately here at TSZ that referred to viruses.

Are viruses pre-biotic entities, and did they contribute to the origin of life?

Are viruses alive?

Do viruses evolve?

Are viruses an example of what evolution is capable of?

Did viruses contribute to the evolution of life?

Should be fodder for some discussion.

Hoist on its own petard: ENV’s two “fake science” stories turn out to be genuine

Two articles exposing “fake science” claims have recently been published over at Evolution News and Views. One article attacks the fossil evidence for whale evolution, while the other seeks to discredit the claim that human and chimp DNA are 99% identical. Both articles suffer from serious scientific flaws.

“Fake science” Story No. 1: Whale evolution – too little time for it to happen?

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Common Design

One of the densest Creationist tropes has to be ‘Common Design’. It is proposed as a direct competitor to Common Descent – template mediated copying of DNA – as an explanation for the high sequence similarity of two DNA segments. But what is actually held in common? If we look at a particular transposon sequence, and find it is in A and B but not C, and another that is in A but not B, etc, we can generally organise a set of such markers into a ‘tree’ structure, much as would be predicted by Common Descent. But no, we are assured that these apparent markers are in fact part of the ‘design’. If A is a whale, B a pig and C a deer, there is something that is vital for the function of both whale and pig but is definitely not required in deer. Instead, a sequence which, in whale and pig, sits either side of the insertion, runs uninterrupted in the deer. That, too, is functional, supposedly, even though the insert would give a product which was the A/B one with a gap and possibly a frameshift, if it were transcribed.

But this is held to be the case even if the sequence, with and without transposon, is never transcribed. A sequence that does nothing, and organises hierarchically exactly as would be expected of common descent, is nonetheless functional … because?

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Coyne’s latest defense of determinism: why it fails

Edge‘s big question for 2017 is: “What scientific term or concept should be more widely known?” The compilation of answers (205 in all) makes for fascinating reading. For his part, Professor Jerry Coyne has nominated physical determinism as “a concept that everyone should understand and appreciate.” Unfortunately, Coyne’s defense of this concept leaves a lot to be desired. As I’ll argue below, even if you reject interactionist dualism (as most scientists do), you can still believe in libertarian free will.

Professor Coyne begins by mis-defining determinism as the notion that “all matter and energy in the universe, including what’s in our brain, obey the laws of physics.” I know of no philosopher who defines determinism in this way. The Stanford Encyclopedia of Philosophy, for instance, roughly defines causal determinism as “the idea that every event is necessitated by antecedent events and conditions together with the laws of nature.” Coyne says nothing about antecedent conditions, and fails to even mention the notion of necessitation.

To illustrate what’s wrong with Coyne’s definition, I’ll use an analogy which is often cited by philosophers: the game of chess. All the pieces obey the rules (or laws) of the game, but those laws don’t tell the player where to move the pieces. Even if the pieces were capable of moving themselves without the help of an outside agent, nothing in the rules of the game would determine the moves that followed. That’s because the rules of chess merely constrain the set of moves which are allowed, without determining the movement of any of the pieces. What Coyne needs to show is that the laws of physics are more than mere constraints, and that for any given collection of molecules, they narrow down the set of possible outcomes to just one, and no more.

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The ‘How Many Theories Of Evolution Are There?’ Thread

Certain commentators seem surprisingly agitated about pursuing the idea that there is no ‘theory of evolution’. Some mean there is no single theory, although on examination the things they see as separate are frequently simply different components of the same broad process. Or, alternatively, they are referring to evolution in other senses, or in non-biological contexts. Others say there is no theory at all, as if that against which they argue does not even exist.

A theme has emerged that TSZ is somehow suppressing their concerns. So, in the spirit of suppressive dictatorships everywhere, here is a thread for people to say whatever they want about this vital topic. Hopefully without pasting in vast swathes of something already posted elsewhere – a link will suffice.

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Knowledge As Articulated Insight

The standard definition of knowledge, canonized in epistemology textbooks, is that knowledge is “justified true belief.”

I think that this is badly wrong, and to put it right, we should return to where this idea comes from: Plato’s argument (“argument”) in Meno. I suggest, based in part on Plato, that we should reject the JTB definition of knowledge in favor of knowledge as articulated insight.

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Who’s Skeptical of the Extended Evolutionary Synthesis?

Is anyone here skeptical of the Extended Evolutionary Synthesis (EES) in biology/biological sciences? If so, why? If not, why not?

Background: A couple of days ago I interviewed one of the participants in the Royal Society’s recent ‘New Trends’ meeting (audios now available), who is obviously pro-EES ,as part of a nearly completed research project from the past couple of years.

My interviewee gave the (ahem) ‘brilliant’ answer of a stone when asked to speak about ‘things that don’t evolve’ (one of those interviewer places where it’s really hard to mask a delighted smile with neutrality!) after claiming not to understand the question: “What are the limits of evolution as a scientific theory?” (we had already been discussing its ‘possibilities’ and I explained earlier that I would ask both about the possibilities and the limits of evolutionary theories). Undergrad students around the world chuckle when they hear the Rock answer (as if geological evolution doesn’t exist in the minds of biologists)!

It’s just a ‘play of scales,’ after all, that slips us into the ‘evolution of everything,’ don’t forget 😉

Objects fall off kitchen counters in haunted flat!

This video is doing the rounds:

To those that believe in such things as ghosts and poltergeists (Clive @ UD I’m looking at you), does this video demonstrate that the realm of ghosts is real? If not, why not?

To the believers, is it possibly a real video or must it have been faked?

To those that don’t believe in such things, has this video converted you? Why not?

Is it relevant that the video was sourced from the Daily Mail? Does the messenger matter?


The credibility of the Christmas story

As the Christmas season is drawing to a close, I thought I might put up a post with some useful links for people wishing to argue for and against the credibility of the Christmas narratives in the gospels of Matthew and Luke, and let readers draw their own conclusions.

On the skeptics’ side:

The Star of Bethlehem: A Skeptical View by Aaron Adair. Onus Books, 2013.

The Nativity: A Critical Examination by Jonathan M.S. Pearce. Onus Books, 2012.

For Jonathan M.S. Pearce’s recent posts on the Nativity, see here:

Debunking the Nativity: The Gospel Sources
Debunking the Nativity: The Virgin Birth
Debunking the Nativity: The Mistranslation of “Virgin”
Debunking the Nativity: The Male Genome
Debunking the Nativity: Contradictory Genealogies
Debunking the Nativity: To Bethlehem or Not to Bethlehem
Debunking the Nativity: Boney M
Debunking the Nativity – Quirinius vs Herod and the Ten Year Gap

On the believers’ side:

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