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


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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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?

Clinical ethics and materialism

In a variant of the hoary old ‘ungrounded morality’ question, Barry Arrington has a post up at Uncommon Descent which ponders how a ‘materialist’ could in all conscience take a position as clinical ethicist, if he does not believe that there is an ultimate ‘right’ or ‘wrong’ answer. I think this betrays a fundamental misunderstanding of clinical ethics. In contrast to daily usage, ethics here is not a synonym for morality.

I can understand how a theist who believes in the objective reality of ethical norms could apply for such a position in good faith. By definition he believes certain actions are really wrong and other actions are really right, and therefore he often has something meaningful to say.

My question is how could a materialist apply for such a position in good faith? After all, for the materialist there is really no satisfactory answer to Arthur Leff’s “grand sez who” question that we have discussed on these pages before. See here for Philip Johnson’s informative take on the issue.

After all, when pushed to the wall to ground his ethical opinions in anything other than his personal opinion, the materialist ethicist has nothing to say. Why should I pay someone $68,584 to say there is no real ultimate ethical difference between one moral response and another because they must both lead ultimately to the same place – nothingness.

I am not being facetious here. I really do want to know why someone would pay someone to give them the “right answer” when that person asserts that the word “right” is ultimately meaningless.

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Atheists are bad people – discuss

This comes up from time to time, so I felt it merited its own thread. Here in the UK, atheism is typically a mark of nothing more than disbelief in gods. I have few friends who attend church, which is less a reflection of my choice of friends than the demographic of the country I live in. I tend not be exposed to bigotry as a result of denoting myself as such. I go online for that!

I don’t wear a badge or steer the conversation towards the subject, but it’s no secret either. No-one cares. If I wanted to run for public office it would be no barrier; people don’t appear to trust me any less, or assume amorality or a lack of goodwill on my part.

But other countries are different. Atheism is the ‘state religion’ in some, in others it can still be a reason to put you to death (surely one of the densest ideas ever dreamed up). I am interested in experiences, and in how you view ‘the other side’. Over to you.

Randomness and evolution

Here’s a simple experiment one can actually try. Take a bag of M&M’s, and without peeking reach in and grab one. Eat it. Then grab another and return it to the bag with another one, from a separate bag, of the same colour. Give it a shake. I guarantee (and if you tell me how big your bag is I’ll have a bet on how long it’ll take) that your bag will end up containing only one colour. Every time. I can’t tell you which colour it will be, but fixation will happen.
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The stolen “Stolen Concept Fallacy” fallacy.

The Fallacy of the Stolen Concept was coined by Ayn Rand, to point out the absurdity of arguing against a position when the argument depends upon that position – setting up a kind of indirect (and hence not so obviously paradoxical) version of Epiminedes-style “this sentence is false”. For example, to argue that all consciousness is really dreaming requires that there be some state one could recognise as ‘waking’, in order that dreaming could be distinct from it. One steals the concept of ‘waking’ (on whose existence ‘dreaming’ depends) in an attempt to argue there is no such thing.
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Protein Space and Hoyle’s Fallacy – a response to vjtorley

‘vjtorley’ has honoured me with my very own OP at Uncommon Descent in response to my piece on Protein Space. I cannot, of course, respond over there (being so darned uncivil and all!), so I will put my response in this here bottle and hope that a favourable wind will drive it to vjt’s shores. It’s a bit long (and I’m sure not any the better for it…but I’m responding to vjt and his several sources … ! ;)).

“Build me a protein – no guidance allowed!”

The title is an apparent demand for a ‘proof of concept’, but it is beyond intelligence too at the moment, despite a working system we can reverse engineer (a luxury not available to Ye Olde Designer). Of course I haven’t solved the problem, which is why I haven’t dusted off a space on my piano for that Nobel Prize. But endless repetition of Hoyle’s Fallacy from multiple sources does not stop it being a fallacious argument.

Dr Torley bookends his post with a bit of misdirection. We get pictures of, respectively, a modern protein and a modern ribozyme. It has never been disputed that modern proteins and ribozymes are complex, and almost certainly not achievable in a single step. But

1) Is modern complexity relevant to abiogenesis?

2) Is modern complexity relevant to evolution?

Here are three more complex objects:


Circuit Board


Panda playing the flute


er … not yet in service!


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Journal club – Protein Space. Big, isn’t it?

Simplistic combinatorial analyses are an honoured tradition in anti-evolutionary circles. Hoyle’s is the archetype of the combinatorial approach, and he gets a whole fallacy named after him for his trouble. The approach will be familiar – a string of length n composed of v different kinds of subunit is one point in a permutation space containing vn points in total. The chance of hitting any given sequence in one step, such as the one you have selected as ‘target’, is the reciprocal of that number. Exponentiation being the powerful tool it is, it takes only a little work with a calculator to assess the permutations available to the biological polymers DNA and protein and come up with some implausibly large numbers and conclude that Life – and, if you are feeling bold, evolution – is impossible.

Dryden, Thomson and White of Edinburgh University’s Chemistry department argue in this 2008 paper that not only is the combinatorial space of the canonical 20 L-acids much smaller than simplistically assumed, but more surprisingly, that it is sufficiently small to have been explored completely during the history of life on earth. Continue reading