Gone fishin’

We have been gibbering for many, many pages, at least nominally on the topic ‘Common Design vs Common Descent’. I’d like here to discuss an interesting fact I discovered during the course of this. I mentioned it twice, but readers seemed underwhelmed by what, to me, looks like a genuine scientific discovery (I haven’t searched exhaustively for priority). More importantly for present purposes, it provides a useful test-bed for several concepts that regularly do the rounds.

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The Evolution of Sex

This has long been an interest of mine. It dates back to the old talk.origins days, prompted by a Creationist taunt with familiar tone – “I’d like to see someone explain the evolution of sex …” (with the implicit “hurr, hurr”). I articulated some thoughts, then was rounded on by the ‘mainstream’ community. I got a flavour of the world through Creationist eyes – an equally familiar tone: some very sharply expressed contempt and an invitation to f*** off back to high school and learn meiosis.

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WJM throws ID under the bus

I’m really not a fan of doing what I’m about to do.

But anyways, this is WJM @ UD

To be fair, when the proponent of a theory who claims that theory to be scientific fact provides little or nothing in the way of falsifiable predictions and offers largely only sweeping narratives and historical inferences based on ideological assumptions and/or an imagined infinite pool of unqualified possibility, it’s impossible for the opposition to offer specified rebuttals.

Until proponents offer specified, falsifiable predictions, the proper response to such a theory is to “lump everything into a single bucket and dismiss the entire topic.”

What’s the point?

We are all too familiar with the schtick of certain posters. I’d like to know what they hope to achieve by pounding their limited collection of nails year in year out.

One could summarise the entire output of some in a dozen or so sentences. They KNOW that no-one will answer their challenges to their satisfaction. They KNOW (rather, they think they know) that this is because their challenges cut right to the heart of the matter, and evolutionary theory (“which evolutionary theory?”, a poster mutters for the thousandth time) is not an arena of explanation that will satisfy them. So, once you have satisfied yourself that this is the case, why keep buzzing against that glass like a trapped house-fly?

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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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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Genetic load and junk.

Mung, to petrushka, elsewhere:

Everyone does not understand “genetic load” and those that do claim to understand are probably wrong. Why don’t you start an OP on genetic load and the genetic load argument? That would be interesting. Betting you won’t.

This is such an OP. I believe the genetic load argument*** was initially proposed by Susumu Ohno in 1972, whose paper also introduced the then-scare-quoted term “junk”. It’s brief, accessible, and worth a read for anyone who wishes to offer an opinion/understand (not necessarily in that order).

The short version: sequence-related function must be subject to deleterious mutations. Long genomes (such as those of most eukaryotes) contain too many bases for the entire genome to be considered functional in that way, given known mutation rates. The bulk of such genomes must either have functions that are not related to sequence, or no function at all.

Interestingly, the paper is hosted on the site of an anti-junk-er, Andras Pellionisz, a self-promoting double-PhD’d … er … maverick. Also of interest is that, contrary to some ID narratives, the idea was initially resisted by ‘Darwinists’, if that term is understood not as people who simply accept evolution, but as people who place most emphasis on Natural Selection. Perfectionism is not the sole preserve of Creationists.

More recent work has characterised the nonfunctional fraction, and this lends considerable empirical support to Ohno’s contentions.

[eta: link to comment]
***[eta: in relation to genome size, not the first time anyone, ever, discussed genetic load!]

Phylogeny – the Bigger Picture

During recent discussions on phylogeny, we saw a distinct failure to communicate, probably felt by both sides. The ‘evos’ attempted to consider the role of molecular data in determining relationship. Given that an obvious cause of common sequence is common descent, due to the significant but not perfect fidelity of the DNA replication process, the phylogenetic inference is that sequence similarity is indicative of common descent. This, critics feel, is a circular argument. Continue reading

Why I’m a Dinosaur

There has been much discussion, here and elsewhere, on ‘epigenetics’, broadly understood as the control of gene expression. People who cling to ‘classical’ models are portrayed, by revolutionaries and their cheerleaders, as dinosaurs standing in the way of progress.

I could perhaps explain, to any interested bystander, my own rationale for my position, since I’ve requested that of others. Continue reading

Chemtrails and other conspiracies

A Facebook friend of mine is a conspiracy nut. She was tagged in a post by a friend of hers, so up in my ‘news’ feed comes a post offering incontrovertible evidence that persistent contrails are in fact chemical spraying of the populace or the planet for nefarious purposes. I was dimly aware of this notion but was taken aback when encountering such people in the (virtual) flesh. Continue reading

Species

A perennial topic. The organisms we see cluster around specific, distinct types. We can identify an individual as belonging to that type because it has the distinctive characteristics of that type. We know what the characteristics are because we see a lot of such individuals.

To the some Creationists, those types represent essential, immutable forms, perhaps with some post-Ark latitude, and a bit of variation around the ‘norm’. It is as if those forms were cast from a mould, with small manufacturing defects. The mould is eternal, unchanging. Continue reading

Evolution Is A Force For Good

Not really, of course, that’s just click-bait – it is merely science. But at least one person has been turned from a dodgy path by, in part, considering the dissonance between his faith and scientific evidence. Non-UK residents won’t be able to hear this, but the essence is contained here.

It’s an issue that cross-references many familiar themes – religion, morality, homosexuality, science – so I thought I’d toss it into the arena.

Ashley Madison hack

Our default position towards infidelity is that it is Wrong. I’m not here to argue otherwise, but the moral dilemma thrown up by this case is that someone has made it their business to interfere in the lives of strangers in order to promote their own moral stance. This has led to two (unconfirmed) reports of suicide, and the potential damage caused by a discovered affair is enormous. Of course, one can say the cheats should have thought of that in the first place, but we are calculating creatures, and the genuine, if naive, belief is that if the other party does not find out, no harm is caused. If you choose to expose a cheat, you are directly crystallising the potential harm, with no knowledge of individual circumstances.

Real people have real circumstances, and real desires, wants and needs. It is not always a simple black-and-white matter of ‘leave first’. While I don’t condone the actions of marital cheats, I find myself more incensed by the interfering, scattergun actions of these busybodies.

On the Probability of Two Things Happening

On the ‘Evolving Complex Adaptations’ thread, a side-discussion arose with CharlieM over Behe’s ‘CCC’ argument. In summary, Behe places an event of probability {10^{-40} as the upper bound or ‘Edge of Evolution’. If a specific single mutation has a probability of {10^{-10} of arising in any one replication event, a specific double mutation has a probability of {10^{-20}, a triple {10^{-30}, and a quadruple {10^{-40} – that is, if four independent changes must happen simultaneously before a particular step is achievable, then that step cannot realistically have occurred in the history of life on earth. Behe thinks he has found a case with a {10^{-20} probability in the resistance to chloroquine in the malaria parasite Plasmodium falciparum.
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Equivocation

Just out of interest … this word gets bandied about a lot, mainly by evolution opponents hereabouts. They seem to use it when a word with multiple meanings is used. The accusation tends not to be withdrawn even when the intended meaning is unequivocally clarified – a bizarre situation where someone commits to a meaning and is still equivocating!

A typical definition is “The use of ambiguous language to conceal the truth or to avoid committing oneself”. There is a veiled hint of dishonesty – making an honest mistake with alternative definitions of a word is not strictly equivocation as defined there. That is, it is not merely ‘using ambiguous language’, still less ‘confusing two definitions of one word’, but purposefully being vague or misleading. But the use of the word rarely seems appropriate to me in the contexts in which it is used – generally, even the charge of ambiguity is unjustified, let alone nefarious motive. Numerous derails are provoked when one party says ‘you are equivocating’ and the other says ‘no I’m not’. I almost invariably find myself siding with (or being) the ‘no I’m not’ party (or, for self-referential funzies, “maybe I am, maybe I’m not”!).

Is this a quirk of American English (Americans forming the majority of opponents in these discussions)? Or is it a meme that has been unconsciously passed from one to another among the evolution-skeptical fraternity? Or something else?