BMC Biology has a piece and video interview on John Mattick, entitled “The evolution of gene regulation, the RNA universe, and the vexed questions of artefact and noise“. Mattick is one of those fringe dwellers in science, a contrarian who likes things like lateral transfer as a contradiction to Darwinian tree thinking (it isn’t, IMO) and here, the utility of RNA derived from “junk DNA” as a regulatory mechanism. Some may be, but I suspect, as an amateur, that he oversells both claims.
Jim Griesemer, one of the most interesting philosophers of biology around at the moment, reviews another of the most interesting philosophers of biology, William Wimsatt, and his book Re-Engineering Philosophy for Limited Beings (my copy is signed by the author), but lacking access to journals at the moment (long story) I can’t comment on it. Thomas Pradeau reviews Alex Rosenberg’s and Dan McShea’s What Philosophy of Biology Should Be, also in Philosophy and Biology.
More philosophy: Julian Baggini explains why I won’t read your earthshattering manuscript. Tim Dean explains why moral variety is the spice of life (hint: it’s just like MHC molecules). Sebastian Lutz blows my mind about the Received View of theories. John D at Philosophical Disquisitions considers the morality of being surveilled by CCTV. There’s a debate at Leiter’s blog on whether Revise and Resubmit should be abandoned for journal reviews. Brandon at Siris takes PZ Myers to task for a bad post on Pascal’s Wager. I agree it’s a bad post, but I think that the Wager only works under artificial assumptions (such as, the choice is between the Catholic God and no god; if there are an infinite number of possible pantheons, which trivially there are, then the likelihood of any one choice being true reduces to nearly zero).
Some science: Remember when I bagged Andrew the Dolt about GMO species escaping in the wild and breeding with wild plants? It’s happened, and may have evolved a hardy weed species that will be a devil to control. Chris Nedin at Ediacaran shows pretty decisively why the recent “metazoans” at 2.1Gya are microbial mats.
Okay that’s seventeen links…
Regarding the Baber situation.
Just shows Philosophy shouldn’t be done in newspapers and blogs
I agree on Pascal’s Wager and disagree on Brandon’s insistence on larger complexity lost in short format newspaper opinion writing.
Actually I think Pascal’s wager is a better argument applied for atheism.
As you said only if you can prove the dichotomy, that at specific god exists does the wager acually apply else as you said an infinite number exist (we don’t even know mathematically the degree of infinity even) and the odds drops to near zero making a very bad wager to bet on god(s).
It’s a good day to be agnostic
At the very least it means that we can’t use simple likelihood arguments to make a choice of metaphysical commitment in that way. We need at least some Bayesian priors to restrict the set of alternatives, and since there are none that are rationally universal, the decision is not a rational one.
Brandon’s claim is that subtle arguments need subtle treatments is correct, and Paul’s discussion indeed has the attributes he ascribes, but the sting is reduced somewhat by the vacuity of the Wager itself.
“Some may be, but I suspect, as an amateur, that he oversells both claims.”
And I suspect, also as an amateur, that he is not overselling the claim WRT non-coding RNA at all. In fact, he may well be underestimating the actual influence.
It’s a matter of parsimony, especially its inappropriate application. In evolution, the fact that a particular mechanism is sufficient to explain an observed function never rules out the presence of another mechanism for the same function in another location. Any mechanism that’s possible is potential grist for the mutational mill, and any mutation that’s adaptive (or even isn’t non-adaptive) can become established and even widely expanded as a developmental mechanism.
Thus the fact (if true) that an expansion of regulatory DNA sequences and logic could explain all the increased complexity (which IMO it could many times over) doesn’t rule out the possibility that all this transcribed non-coding DNA plays a major, perhaps even dominant, role.
Consider that there’s no reason to assume that the complexity of the regulatory network will be at the minimum necessary to produce the observed morphological complexity. And the more redundant complexity is present in the network, the greater the potential for increased robustness, evolution of increased morphological complexity, or both. IMO it’s perfectly plausible that a random (mutational) 10-fold or so increase in network complexity (while supporting the same morphology) could contribute as much to setting the stage for a massive round of adaptive radiation as the adaptive superiority of the morphology itself.
A point I find particularly telling is the 30-fold expansion of RNA editing in the human brain relative to the mouse. Although I’m a little skeptical of his claim for environmental influences (pending my own examination of the research if any), even if all this editing is completely determined by the RNA sequence/structure it argues for a large and very critical role for ribozymes (one type of non-coding RNA) in controlling brain development and/or other activity.
OTOH, it seems likely to me that there are DNA-based mechanisms involved in the regulatory networks that haven’t been identified yet, because nobody has looked for them or noticed them when they showed up by accident in research results, again due to a mis-application of parsimony.
A point I find particularly telling is the 30-fold expansion of RNA editing in the human brain relative to the mouse.
I would find that telling too, except that the kind of RNA editing being discussed (A to I) strikes me as a fairly blunt instrument. And so many RNA microarray reports in the past have been debunked as artifacts and noise. Also, having watched too many horror flicks in my youth, I wonder where they got their human brains so as to make that measurement. I found this in one of the papers comparing mouse and human brains:
Adult rat whole-brain RNA (Sprague Dawley) was isolated as previously described (Burns et al., 1997), and human whole-brain RNA was purchased from BioChain Institute.
I’ll leave it to you to decide whether the BioChain institute might have some kind of conflict of interest in favor of hyping the kinds of discoveries that can be made using microarrays.
What annoys me most about folks like Mattick is their apparent core belief that humans are the pinnacle of evolution – far more complex than any other species – even though our genome size is the same as all other mammals and our proteome size is about the same as all other animals. He thinks that RNA regulation is something newly re-evolved for use in us complex beasts. Isn’t it more likely that it is universal in eukaryotes, has been around since the RNA World, and that its loss in prokaryotes is a derived trait?
Whoops, I failed to close the italics at “I’ll leave it to you”.
“[...] the kind of RNA editing being discussed (A to I) strikes me as a fairly blunt instrument.”
It’s not, really. Changing the side groups on a base changes the way that link in the RNA chain fits “around corners” in building up the 3-D form of the ribozyme. The key is not the change, but where it’s made in the molecule and how the selection of base(s) for editing is determined.
One of these days I’m going to have to pry loose the time to do a post on the subject, but hopefully the above is clear enough to communicate my point. Meantime, I’ll note the role of edited bases in the structure of tRNA, and interested readers can chase down more info from there. (My original source is a biochem textbook no longer available to me.)
Whatever the merits of the Wager, I agree PZ’s take on it was disapppointing. It looks uncomfortably close to the tactics and style of his intelligent design/creationist opponents: scoring points with his supporters by taking cheap shots at a strawman.
What is even less savory is the jeering and cat-calling that fill the comments. It reads like there are a lot of people there who take their lead from whatever Myers writes, rather than, say, reading Baber’s article and trying to think through her arguments themselves.
If Myers writing is being shaped by what he thinks his audience wants rather than needs to hear – and they want to be outraged by religious duplicity and philosophical sophistry – then that is just rabble-rousing and no whit better than the evangelical demagoguery he and many others, including me, despise.
This is saddening because he has a great talent for writing about science with a common touch which gives it vigor and clarity.
It reads like there are a lot of people there who take their lead from whatever Myers writes, rather than, say, reading Baber’s article and trying to think through her arguments themselves.
I think that’s probably spot on. I have to admit that I read PZ’s blog (and similarly this blog among others), but rarely read the articles he’s commenting on. Time is an issue, as is attention span. That said, I rarely comment on his blog because it’s a mosh-pit in there, too hard to keep up and not get squashed by the surge. I like PZ for his in your faceness.
I think that the Wager only works under artificial assumptions (such as, the choice is between the Catholic God and no god; if there are an infinite number of possible pantheons, which trivially there are, then the likelihood of any one choice being true reduces to nearly zero)
I think the artificial assumptions criticism is an interesting criticism, because in an important sense it’s true and in another it is trivial. It’s certainly true that the Wager presupposes certain fairly restricted assumptions. They are more or less explicitly made in Pascal himself (reasonably so, because he clearly has a very specific audience in mind) and the sort of casual disregard for those assumptions that’s common among, say, theistic apologists vitiates their versions entirely. But Wager arguments are arguments of practical reason, and all practical reasoning operates under fairly restricted assumptions; there are, logically speaking, infinitely many choices available to us at any given moment, but for practical purposes our decision matrices never have infinitely many cells, and the fact that they leave infinitely many logical possible alternatives out doesn’t automatically ruin them as arguments. That would depend chiefly, I think, on the immodesty of the conclusion demanded (and, as Baber suggests, on things like whether you take an optimizing strategy or some kind of satisficing strategy). In Pascal himself, for instance, the argument is not for the conclusion that everyone must judge that God exists but explicitly for the conclusion that, given the sort of inquiry involved, Christians have reasons not to suspend judgment, and also that the urbane Catholic-culture agnostics Pascal is specifically addressing have reasons not to suspend inquiry on the subject in the way they had been advocating. This is a modest conclusion that matches very well the restricted assumptions with which Pascal began. Wager arguments vary widely in how modest they are, and many of the modest ones may still be viable; at least, the only way the infinite possibilities objection could vitiate all forms of Wager argument is if it is taken to mean that formal decision theory is practically impossible. All decision-theoretical problems can be reformulated as wager arguments of one kind or another; so any problem for wager arguments generally is a problem for decision theory generally.
John, after reading Baggini’s article, am I to take it that you won’t read, then unreservedly endorse my Earth-shattering thesis that explains consciousness, Quantum Mechanics, Relativity and anything else that might be considered important? No?
Yours, maybe. But definitely not PZ’s.
But you’re still BFF with old Paul Zachary no?
By the way, my Earth-shattering, research stopping thesis can be summed up in this pithy phrase: ‘shit happens’. It’s all a brute fact, no big meaning, so get on with it. Do you think it’ll convince the masses?
He’s the evil twin and I’m the good twin in the attic. No, wait…
Anyway, I think everyone is convinced that shit happens. But they want it to smell better than it does.
But they want it to smell better than it does. You’ve refuted, or at least shown worthless, my thesis. Glad I didn’t type it up and format it before sending it to you then.
I’m admire your philosophical or adult ability to like PZ while finding his thinking shite. I do find it hard sometimes to separate how I feel about a persons ideas from the person.
Paul is a good man who makes the occasional false step. I hope to be as good as him that way myself. I also make the occasional false step, like spending thirty years doing philosophy instead of developmental biology.
To give a few examples, I can’t but help feel Steve Feilding is a moron, Andrew Bolt is a p***, and Darth Ratzinger a negligent b******. This is because of how their ideas, and the way they seem so smug about spreading what I see as ideas with really negative outcomes. Perhaps they’re all top blokes, who are worth knowing. But I don’t see it.
You do know PZ, and thus can see both sides. I reckon PZ is a good bloke, because he writes in a way I like and I roughly share his views. Probably an echo-chamber effect in my case, where I like (my idea of) a bloke who is apparently likable, but not because of what he’s like, but because I like what he says most of the time. Anyway, too much navel gazing.
When I came along there were 16 comments. Now there are 17.
Thx for the Lutz link. My own thinking on theories, modeling, and reductionism have been leaning toward an anti-realist position which I am now learning to name “positivism”. It is nice to learn that some people with better credentials are thinking in that direction too.
May I ask why you say that Lutz blows your mind? Because he seeks to resurrect such an unfashionable viewpoint? Because he claims that that viewpoint fell from fashion for such technical reasons? For such wrong reasons?