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Sunday, January 04, 2015

A physiologist thinks about evolution

Denis Noble is a physiologist at Oxford University (now Professor Emeritus). He is famous for his work on the physiology of the heartbeat and he is touted as one of the founders of systems biology.

Denis Noble wrote a book on evolutionary theory called The Music of Life. It's featured on The Third Way, a website created by James Shapiro to promote his version of a paradigm shift in thinking about evolution. All the usual suspects are represented on that site.1

Here's how the book is described on that website ....
What is Life? Decades of research have resulted in the full mapping of the human genome - three billion pairs of code whose functions are only now being understood. The gene’s eye view of life, advocated by evolutionary biology, sees living bodies as mere vehicles for the replication of the genetic codes.

But for a physiologist, working with the living organism, the view is a very different one. Denis Noble is a world renowned physiologist, and sets out an alternative view to the question - one that becomes deeply significant in terms of the living, breathing organism. The genome is not life itself. Noble argues that far from genes building organisms, they should be seen as prisoners of the organism.

The view of life presented in this little, modern, post-genome project reflection on the nature of life, is that of the systems biologist: to understand what life is, we must view it at a variety of different levels, all interacting with each other in a complex web. It is that emergent web, full of feedback between levels, from the gene to the wider environment, that is life. It is a kind of music.

Including stories from Noble’s own research experience, his work on the heartbeat, musical metaphors, and elements of linguistics and Chinese culture, this very personal and at times deeply lyrical book sets out the systems biology view of life.
I haven't read this book and I don't intend to read it. Having listened to a lecture by Denis Noble (below) I don't think I'm going to learn anything more by buying the book.

I urge you to watch the lecture. It's the plenary lecture at the International Conference of Physiological Sciences in November, 2012. Denis Noble is the President of the International Union of Physiological Sciences. The lecture is only 30 minutes long but it gives you a good introduction to the way many scientists from outside the field of evolutionary biology are thinking about evolution (and the Central Dogma of Molecular Biology). It's not a very pretty picture.

If you want a brief summary of what's wrong with this lecture see Jerry Coyne's blog website post: Famous physiologist embarrasses himself by claiming that the modern theory of evolution is in tatters.

1. For more on James Shapiro see: The Third Fourth? Way
Evolution: a View from the 21st century
Reply to Laurence A Moran’s review of Evolution: A View from the 21st Century
James Shapiro Responds to My Review of His Book
James Shapiro Never Learns
James Shapiro Claims Credit for Predicting That Junk DNA Is Actually Part of a "highly sophisticated information storage organelle"
Revisiting the Central Dogma in the 21st Century.


Geoff said...

You or Jerry need to put together a response to another popular challenger to modern evolution: Jeremy England's thermodynamic ideas from MIT. See for a talk; there's also a paper on ArXiv. While England's ideas may be a reasonable approach to abiogenesis, he seems to get carried away with the possible implications for biological systems in ways that are reminiscent of "quantum woo". And of course the popular press has seized on this in a series of very bad articles - the worst is in Salon, but don't waste your time.

Athel Cornish-Bowden said...

Denis Noble's book isn't as bad as you imply, and you might enjoy it more than you think, especially his rewriting of Richard Dawkins's famous description, "Now they [genes] swarm ... safe inside gigantic lumbering robots ... they created us, body and mind; and their preservation is the ultimate rationale for our existence". Also, his description of what happens during sexual intercourse is a tour de force.

Your "touted as one of the founders of systems biology" is a bit unfair. I don't think he touts himself that way, but maybe others do. It's a journalistic version of what he said to an interviewer once, after the interviewer explained to him what systems biology was and he said something along the lines of "Is that what it is? If so, I find I've been doing systems biology for 40 years without knowing it", like Monsieur Jourdain discovering that he had been speaking prose all his life. I'm pretty sure he doesn't see himself as a "founder" of systems biology.

"Systems biology" of course, is just a portmanteau term to describe anything that will extract money from grant givers. Most of the people who claim to be doing systems biology are just doing what they always did before the term was invented, but are doing it on a vast scale. The term was invented a surprisingly long time ago, by Mihajlo Mesarovic in 1968, but it didn't become fashionable until very much later.

Robert Byers said...

Interesting the author of the thread here segregates scientists from inside evolutionary biology and outside. AMEN. Evolutiondom however takes the whole tribe to back up evoplution as a settled scientific fact. They don't speciate when dealing with authority.
in reality very few scientists, whatever that is, get paid/or did to study/investigate evolutionary biology.

I only know this prof from another forums attention to him.
Yet he makes a historic creationist point.
Living life is not a sum of the parts of the material and/or its not just the parts.
life is from God's breath or rather immaterial and/or the life is joined at levels of information interactions. a common iD claim.
Not just molecules joinrf but they are a conduit for information.
in other words life is more complicated in its anatomy then the parts observed.

Athel Cornish-Bowden said...

When I wrote my comment above I hadn’t listened to his lecture in Suzhou, though I have heard him on three other occasions, in Grenoble, Bordeaux and Exeter, talking mainly about other things (his heart model), and I’ve read his book.

However, I’ve listened to his lecture now, and read Jerry Coyne’s criticisms of it. Some of them I agree with, but some are, I think, exaggerated. I’ll use Coyne’s sub-headings:

1. Mutations are not random. I agree with Coyne, and I was surprised that Noble made an issue of this.

2. Acquired characteristics can be inherited. “In support of this neo-Lamarckian view, Noble trots out the tired old horse of epigenetics, ...”. I don’t know a great deal about this, but I think Coyne is probably right.

3. The gene-centered view of evolution is wrong.  “Noble clearly has a beef about his colleague Richard Dawkins, and spends a lot of time in his talk arguing against both the notion of ‘selfish genes’ and the idea that the gene is the true unit of selection rather than, say, the cell.” OK, probably he does have a beef about this, but I’d love to hear the two of them arguing about it. Not all of Noble’s objections are invalid.

4.  Evolution is not a gradual gene-by-gene process but is macromutational. “Here Noble cites examples of entire blocks of genes being moved around, or acquired from other species, in a leap. This, he says, invalidates the neo-Darwinian view of gradual evolutionary changes in genes.” Again, I’m a bit surprised that Noble talks about this as if it’s a novel idea, but I think he’s right to emphasize that point mutations are not the whole story.

5. Scientists have not been able to create new species in the lab or greenhouse, and we haven’t seen speciation occurring in nature.  “This is what really burns my onions, because Noble is flat wrong here, and the study of speciation is my specialty.” That is very strange, and perhaps burns my onions as well (though I’m guessing what that expressions means).

At the end, Coyne says “However famous Noble may be in physiology, he’s a blundering tyro when it comes to evolutionary biology. He might try discussing his ideas with other evolutionists and listening to their responses. He obviously hasn’t done that, and yet travels the world trading on his expertise in physiology to show that the edifice of modern evolutionary biology is rotten.” I think he almost certainly has discussed his ideas with other evolutionists, and that’s why I’d like to see them argued about in a public session. He refers several times to Richard Dawkins as “Richard” (a familiarity he probably wouldn't use if they didn't know each other) and as they work in the same university I think it’s virtually certain that they do know one another and have argued about these things, though possibly talking past one another.

Re-reading what I’ve written, I see that I end up much closer to Coyne than to Noble, but I don’t think I’d call Noble a blundering tyro, and some of his points do require analysis.

AllanMiller said...

Noble was Dawkins's PhD examiner. They know each other.

Athel Cornish-Bowden said...

Ha. That is interesting. I didn't know that. How does one find out who was whose DPhil examiner? Is it recorded somewhere, or is it something you just happen to know?

Petrushka said...

“When I left you, I was but the learner, now I am the master.”
“Only a master of evil, Darth.”

Now back to your regularly scheduled program.

AllanMiller said...

It seems to be mentioned (online) in every third article containing the 2 names. I don't strictly 'know' it! Perhaps Noble himself simply mentioned it - or perhaps it is an untrue meme I am propagating! ;)

Diogenes said...

Reading Coyne's rebuttal of Noble, I am struck by how, though JAC is an @$$π0!£, he sure can land a punch.

Athel Cornish-Bowden said...

Is Jerry Coyne an @$$π0!£? I haven't found him to be so, and, rather to my surprise, I liked his book Why Evolution Is True better than Richard Dawkins's The Greatest Show on Earth: the Evidence for Evolution written at about the same time.

Larry Moran said...

I don't think Jerry Coyne is an @$$π0!£ but I strongly disagree with his view on academic freedom, his criticisms of religions, his reliance on American law to protect him from creationism, cats, cowboy boots, and his adaptationist leanings. Other than that, he a pretty nice guy who likes food.

John Harshman said...

I can see the rest, but cats? Criticisms of religion?

Rkt said...

From what I've observed, it would seem that Coyne and Shapiro consider one another to be @$$π0!£$. This is a mutual error from where I'm sitting as I think they both talk a lot of sense. Even about cats. Not sure what JS thinks about cats but JAC sees it about right (they beat canines by a mile). Anyway, Diogenes' remark also makes me wonder: if Jerry Coyne is an @$$π0!£ then for what reason, exactly? And what descriptor is then applicable to, say, PZ? Shudder to think.

John Harshman said...

What sense do you find in Shapiro?

Joe Felsenstein said...

Aside from all the cats and the issue of whether his website is a blog, Jerry is a great expert on speciation and an important researcher on it. His stout defenses of existing evolutionary biology against highly-publicized dismissals are excellent (for example, his recent articles defending of kin selection).

Shapiro imagines that living organisms have systems of genetic engineering built in that will somehow tend to do adaptive things. He has never explained how such a system could know what will be adaptive, or how any such capability could be maintained through long evolutionary times in the presence of mutation degrading it. Jerry's criticisms of Shapiro are spot on.

Joe Felsenstein said...

Typo: "defending kin selection"

Diogenes said...

Athel: "Is Jerry Coyne an @$$π0!£? I haven't found him to be so, and, rather to my surprise, I liked his book Why Evolution Is True better than Richard Dawkins's The Greatest Show on Earth"

I did too. I liked his book and it's better than Dawkins', though that's not saying much. On science issues, he's a wonderful writer. On philosophy issues/metaphysical arguments for God's existence, he writes very well.

But he's still an @$$π0!£. Yes, he banned me from his blog because I disagreed *with another commenter there* without insulting said commenter and without involving the fragile, precious Coyne. Then Coyne himself announced I had insulted my host! and must apologize or I will be banned forever. Coyne thinks disagreeing with him is insulting him, and he can't even distinguish between disagreeing with *another commenter* and *insulting him personally.* How insecure is that?

And what's intolerable is demanding that I apologize. If you can't debate and lose any debate based on the facts, and that makes you insecure, then just ban me and delete my comments like most of the creationist sites have done. Just ban me. Don't ask me to apologize when you can't even accurately describe what I wrote.

Coyne leads no third option of the form "Use evidence to persuade me that I have mischaracterized your point." No, that's not allowed-- he misrepresents what you wrote, then you get one chance to apologize for a thing you didn't do, and you better hop to it, or you're banned.

But he justifies it on the grounds that his bl*g is his "living room" and therefore he gets to lie about and misrepresent what you said, and then demand you apologize. I wouldn't visit anybody's living room if they announced ahead of time that was Da Roolz, as he says. He should simply be honest and write right in Da Roolz that he will lie about what you said and wrote, and then he will demand you apologize for a thing you didn't say or do.

Wonderful writer on science issues, I agree. But when I want a moralistic prick to lie about what I wrote and then ban me anyway, I go to creationist blogs.

Diogenes said...

Rkt: "And what descriptor is then applicable to, say, PZ? Shudder to think."

Oh, you wanna go there. PZ is a wonderful writer when he sticks to science. Smart about science, and his writing is spot on sometimes.

Where politics are concerned, he's a moralistic prig and sometimes insufferable. His crumbling a communion wafer stunt was quite childish and made atheists look immature. His dismissal of Robin Williams' suicide on the grounds that the media should *only* cover stories of black people getting shot by cops was insensitive, politically tone deaf, and morally disproportionate.

Rkt said...

@John Harshman: here is not, I realise, the ideal place to defend James Shapiro. A few brief points though. First, where bacteria are concerned, I'm persuaded that dying cells (or cells under great stress) may mutate parts of their own DNA, in an automatic manner (not ruling out that a range of different responses are built-in, even, so the process is subtly modified because of the effects of the stress the cell is experiencing). Second, in general terms, regarding multicellular organisms (with generation times far, far longer) got to where they are today at a cracking pace, and no-one has so far set down what, to me, suffices as an adequate picture of how. What do I mean by an adequate picture? That we are not yet seeing the totality, which has to include chaotic (perhaps explosive) change along the way. All the common-ground between biologists, visualising a daisy-chain of tiny alterations in respect to a gradual, polishing, meandering of the genome for generation after generation is beyond dispute of course. As I type this our cat is stretched out on the sofa near me. I can well accept that his ancestry (and mine) has had spells - spells of thousands upon thousands of generations - where this was the only change happening. Plenty of evidence of this type of evolution has been accumulated. What is beyond us is how to untangle the major episodes; the evolution events bizarre-and-strange. We simply are not there yet. That kind of abrupt change that is massively rare. You're question to me, inevitably, will be whether I think this change is 'directed' or 'guided' in any way. For myself, I would say _not_ (puts me in a clearly different place from Shapiro, I won't go along with his ideas about the DNA undergoing manipulation in some fashion. He hasn't shown evidence to back up those claims, and I think it unlikely he ever will). As a minor addition, let me say that Shapiro has got the wrong idea on 'junk-DNA' so I prefer Larry's view to a degree (but he seems rather hawkish, too theoretical for my taste). Lots to be unearthed in the non-coding parts of the genome (don't see the need to be quite so mega-skeptical unless this is being employed as a tactic).
@Diogenes: understood.

John Harshman said...

Rkt: We can agree that Shapiro has on occasion said some true things. Increased mutation rate as a response to stress in bacteria is one of those things. But what lesson does Shapiro draw from that? It's hardly a case of anything weird.

Your second point appears to be that we don't know everything. I agree, but as you admit that tells us nothing about Shapiro.

I don't know what you mean by "hawkish, too theoretical for my taste"; Larry has simply listed at various times the many reasons why we think most of the genome is junk. Certainly there are functional bits of DNA we don't currently notice, but the evidence tells us that all the functional bits put together can't amount to much more than 10% of the human genome. That isn't "mega-skeptical"; that's drawing conclusions from the evidence. It may be that you aren't acquainted with that evidence. In summary, it's the non-conservation of most of the genome over evolutionary time, the extreme variation in genome size among closely related taxa, the fact that much of the genome consists of broken transposable elements, and computations of genetic load. Only the last might be considered theoretical. (I may have forgotten a couple, but that's enough.)

J Wapatoo said...

> That is true, but says nothing about the randomness of mutations. What we mean by “random” is that mutations occur regardless of whether they would be good for the organism.

And regardless how good or bad that environement is to the organizm?
Has nobody noticed a cracked logic in this «excellent rebuttal»?