More Recent Comments

Friday, December 14, 2007

Biology Envy and Quantum Magic

In this week's issue of New Scientist there's a report of a recurring phenomenon—the desire of physicists to become biologists [Was life forged in a quantum crucible?].
AS if they don't have enough on their hands tackling some of the biggest questions about our universe, some physicists are muscling in on biology's greatest endeavour. Life, say the physicists, began with a quantum flutter.

The idea that quantum mechanics is key to explaining the origin of life was first raised as far back as 1944 in Erwin Schrödinger's influential book What is life?.
Seventy years ago, physicists took up biology for two important reasons: (1) they were expecting to find new fundamental laws in biology, (2) they wanted to show biologists how smart they were.

They partially succeeded in the second goal since some of the most important work in molecular biology was done by physicists who started to work on biological problems. However, the biggest lesson from this experience was that you need to learn how to think like a biologist—and not like a physicist—in order to make progress in the messy field of living organisms.

This is a lesson that physicists need to relearn frequently. The latest attempt to understand biology, while thinking like a physicist, comes from Johnjoe McFadden. In this case, McFadden is not a physicist but a genuine molecular bioogist. He thinks that primitive self-replicating RNAs have to spring up out of the primordial ooze in one fell swoop.
Yet even a primitive ribozyme is a complicated structure, McFadden explains, requiring 165 base-pair molecules to be strung together in the right order. In fact, 4165 possible structures - most of which are not self-replicators - could be made with the same starting ingredients. "That's more than the number of electrons in the universe," he says. What's more, life came about relatively soon after the planet formed, he says. "The puzzle is not only how life emerged, but how it emerged so fast."
The creationists are going to love hearing about those kinds of improbable events.

Most biologists don't think that life began with the sudden formation of a 165 bp ribozyme. Instead, they would postulate much more probable scenarios, including scenarios that precede the RNA world.

But such thinking doesn't concern a physicist because physicists are used to dealing with five or six improbable things before having breakfast. McFadden believes that an extremely improbable ribozyme can form spontaneously by invoking a short-cut in the search algorithm.
McFadden believes that nature employed a quantum trick to speed up the process of sorting through and discarding unwanted structures - the same trick quantum computers employ.

Quantum bits, or qubits, can take on many different values simultaneously, since the properties of particles are not set until they are observed. This means that quantum computers can, in theory at least, exploit this ability to whip through their calculations much faster than their classical counterparts.

McFadden thinks a similar process could have occurred in the chemical soup that spawned life. If many different chemical structures could exist simultaneously in multiple, slightly mutated configurations, they could essentially "test" a range of possibilities at once until they hit a self-replicating molecule. This could trigger the act of replication, he says, which could be violent enough to collapse the delicate quantum states, fixing that structure as a self-replicator.
Thanks for your input, Dr. McFadden, but those kinds of hand-waving explanations don't cut the mustard in biology. They may be acceptable in physics but most biologists have higher standards these days.

However, in fairness, there are a few biologists who find the idea of quantum magic quite attractive. Ken Miller writes in Finding Darwin's God (p. 241).
Even the most devout believer would have to say that when God does act in the world, He does so with care and subtlety. At a minimum, the continuing existence of the universe itself can be attributed to God. The existence of the universe is not self-explanatory, and to a believer the existence of every particle, wave, and field is a product of the continuing will of God. That's a start which would keep most of us busy, but the Western understanding of God requires more than universal maintenance. Fortunately, in scientific terms, if there is a God, He has left himself plenty of material to work with. To pick just one example, the indeterminate nature of quantum events would allow a clever and subtle God to influence events in ways that are profound, but scientifically undetectable to us. Those events could include the appearance of mutations, the activation of individual neurons on the brain, and even the survival of individual cells and organisms affected by the chance processes of radioactive decay.
Now you can add the formation of life itself to the list of subtle, scientifically undetectable, processes that can be used by God.

Johnjoe McFadden is the author of Quantum Evolution. As far as I can tell, McFadden is not promoting belief in the supernatural. Nevertheless, some of his writings appear to almost as mystical as those of Ken Miller. Here's a quotation from his website [Quantum Evolution].
We have all been brought up on the neodarwinian synthesis of Darwinian natural selection with Mendelian genetics that states that the only significant lifestyle change to befall any microbe – mutations – are entirely random. The dogma states that mutations provide the raw material for evolution but natural selection provides the direction of evolutionary change. This dogma has been the central plank of evolutionary theory for nearly a century. But is it always true?

The proposal that the genetic code may inhabit the quantum multiverse suggests that in some circumstances, it doesn’t hold. Mutations are the driving force of evolution; it is they that provide the variation that is honed by natural selection into evolutionary paths. Mutations have always been assumed to be random. But mutations are caused by the motion of fundamental particles, electrons and protons – particles that can enter the quantum multiverse – within the double helix.

When Watson and Crick unveiled their double helix more than half a century ago they pointed out that mutations may be caused by a phenomenon known as DNA base tautomerisation.

Tautomerisation is essentially a chemist’s way of describing a quantum mechanical property of fundamental particles: that they can be in two or more places at one. Quantum mechanics tells us that the protons in DNA that form the basis of DNA coding are not specifically localised to certain positions but must be smeared out along the double helix. But these different positions for the coding protons correspond to different DNA codes. At the quantum mechanical level, DNA must exist in a superposition of mutational states.

If these particles can enter quantum states then DNA may be able to slip into the quantum multiverse and sample multiple mutations simultaneously. But what makes it drop out of the quantum world? Most physicists agree that systems enter quantum states when they become isolated from their environment and pop out of the multiverse when they exchange significant amounts of energy with their environment, an interaction that is termed ‘quantum measurement’. Cells may enter quantum states when they are unable to divide and replicate – perhaps they can’t utilise a particular substrate in their environment. They may collapse out of those quantum states when their DNA superposition includes a mutation that allows them to grow and replicate once more. In this way the environment interacts with, and performs a quantum measurement on the cell, to precipitate advantageous mutations. From our viewpoint, inhabiting only one universe, the cell appears to ‘choose’ certain mutations.
Is this one of those times when a little knowledge of physics (and biology) proves to be a really dangerous thing?
"A little learning is a dangerous thing; drink deep, or taste not the Pierian spring: there shallow draughts intoxicate the brain, and drinking largely sobers us again."

Alexander Pope (1688 - 1744) in An Essay on Criticism, 1709


10 comments :

Acleron said...

"Tautomerisation is essentially a chemist’s way of describing a quantum mechanical property of fundamental particles"

A long time since I did any chemistry but I thought tautomerisation was a chemist's way of describing the change by moving a proton.

And if this theory is correct, shouldn't we have higher mutational rates of DNA irrespective of mutagen concentrations?

Timothy V Reeves said...

I am all for these kinds of risk taking, exotic, blue skies, weirdo, brainstorming ideas myself: Haven’t you heard Larry? Imaginative thinking is fun. It’s a bit like backing horses – it wouldn’t be half as much fun if you won every time. Besides the critical faculties can’t work unless something has been first created to criticize. Get enough creative monkeys on to a problem and one of them might just come up with something. Creativity and criticism must work together. I personally think that McFadden (and Miller) may have some ‘fun’ ideas worth looking into!

And don’t forget the role that multiverse ontology plays in some people’s thinking as they attempt to apply evolutionary-like notions to the very existence of the universe itself. There’s definitely some irony here!

Bet you’re the sort of guy who would write a book called “Elementary Biology for Physicists”

Torbjörn Larsson said...

Oy! There is so many confusions here, from Mcfadden, in New Scientist, and in the post, that it will exceed my detailed knowledge and nowadays more limited time. But I will try, because I'm fairly certain it will be a learning experience for me.

I better start with what the post gets right:

Is this one of those times when a little knowledge of physics (and biology) proves to be a really dangerous thing?

An insightful question, and I believe the answer is yes.

And it is, as also noted, not a good idea to believe that one scientific area works like another. I'm in complete agreement with the post here.

Biology Envy

I'm not exactly sure what "physics envy" entails, but if it is the wish to use physical methods and more extensive math, I'm sure the posts jests here - it is McFadden who seems to have physics envy.

As theoretical physicist Joe Polchinski has noted, as opposed to a mathematical theory which is as strong as its weakest link a physical theory is as strong as its strongest link, due to the interconnections between theories and facts. But I believe it is a mistake to assume that a more complicated area such as biology works in the same manner.

physicists are used to dealing with five or six improbable things before having breakfast

As physics is verifiable by solid observations, I suspect that the intention here is to imply "inconceivable things". Generally physicists have the comfort of being able to use observations or tests with low and well understood uncertainties, while biology and medicine may have distributions that overlap.

This is why physicists may engage in speculation at times. The observations will often sort it out later.

But I have also observed that biologists such as Koonin misunderstands physicists likelihood arguments. When he, in essentially the same quest as McFadden (to explain fast abiogenesis), in his papers on "Biological Big Bang" believes that anthropic principles are used to explain low probability phenomena instead of searching out high likelihood alternatives (weak AP).

Larry Moran said...

Torbjörn Larsson says,

But I have also observed that biologists such as Koonin misunderstands physicists likelihood arguments. When he, in essentially the same quest as McFadden (to explain fast abiogenesis), in his papers on "Biological Big Bang" believes that anthropic principles are used to explain low probability phenomena instead of searching out high likelihood alternatives (weak AP).

That's excellent! I didn't think of comparing McFadden and Eugene Koonin [Eugene Koonin and the Biological Big Bang Model of Major Transitions in Evolution.

There are a lot of similarities, aren't there? Should we add Stuart Kauffman?

Torbjörn Larsson said...

I would like to add Kauffman, as I don't find his ideas likable either. But it is harder for me to judge on them, as the biology is further removed from what I'm trying to grasp.

Perhaps we should discuss explicit examples of his?

Torbjörn Larsson said...

[Cont:]

McFadden believes that nature employed a quantum trick to speed up the process of sorting through and discarding unwanted structures - the same trick quantum computers employ.

I think New Scientist over-interpret McFadden here. While I haven't read the book or his original paper, nor the details of the exchange between the criticism of physicist Matthew Donald and McFadden et al, I understand McFadden's description as a selection when quantum systems comes out of isolation.

While this is akin to proposals of operation of quantum computers, it is well known that they will only give quadratic speed up in the general case. Computer scientist Scott Aaronson even subtitles his blog Quantum computers are not known to be able
to solve NP-complete problems in polynomial time
, because he is so tired of the usual unsupported claims and the confusion of quantum mechanics it is based on. Admittedly, a confusion many physicists helps spread, for much the same reason they should generally refrain to dabble too much in biology.

but those kinds of hand-waving explanations don't cut the mustard in biology. They may be acceptable in physics but most biologists have higher standards these days.

I noted in my previous comment why what looks like handwaving speculation may have fairly good support, or else why they often are acceptable as they will be tested sooner or later.

But I must also note that it is a physicist, Donald, who has extensively reviewed McFadden's book and criticized McFadden's and Al-Khalili's paper. I don't fancy Donald's "many-mind" interpretation much, but a quick glimpse of his criticism looks solid: no experiments on coherence or selection when the systems (DNA or cell) leaves the assumed coherence, and simple calculations on decoherence times such as physicist Max Tegmark's shows that a cell or its constituents decoheres much too fast to not be considered as well described by classical physics.

So I can ask, where there any biologists criticism at the time (2000-2001)?

Torbjörn Larsson said...

[Cont.:]

the idea of quantum magic

Again, I'm not entirely sure what this entails. I usually describe what Miller discuss as "quantum woo", as it doesn't follows from or is actually against what quantum theory proposes. Miller sees a guiding hand behind physical laws, while Bell tests experiments shows that there are no local hidden variables to a fantastically high certainty. (15 sigma, give or take.) The difference can be split by what empirically is as dubious as solipsism - last thursday scenarios explaining the actions of Millers supernatural phenomena.

DNA may be able to slip into the quantum multiverse and sample multiple mutations simultaneously

Finally, this I believe is another confusion of McFadden, albeit more on the semantical level.

The many-worlds interpretation of QM that he seems to lean against is neither proven nor a variant of multiverse ideas. As I understand it "the many worlds" are simply coexisting states in our universe, but inaccessible to each other after decoherence.

Hmm. I have to rest my case at this point.

If I'm not hammered on any of my own mistakes or misunderstandings on biology or physics as this at the moment is all hasty handwaving, it would indeed be interesting to review Kauffman's ideas to see where they fit among Koonin (supports anthropic reasoning) and McFadden (against anthropic reasoning, as I understand Donald).

A. Vargas said...

How about writing these books "the selfish quantum" or "big bang warming" (xxx flick?) Instant hits of daring modern science!!!

Are you guys telling me that Kaufman has been caught into the cheap quantum talking?

I don't trust Kaufman too much but I wasn't quite expecting that

A. Vargas said...

I honestly don't think that Kauffman has flopped as badly as the level of those other guys...
About Kauffman's thinking about the place of mankind in nature...I really have not read his stuff, but I don't think it's necessarily anthropic or wack...in fat, this is an unavoidable topic for any thinking person.

I will say though that structuralist thinking does not blend into a paradigm centered on natural selection as nicely as Kauffman seems to think. By trying, like everyone, to marry his ideas to natural selection, he has conditioned his entire contribution to possible irrelevance. Funny, huh?

Next to quantum mechanics, natural selection must be almost as badly abused. It's wanted to be connected to everything and, of course, explaining everything, with MANY eye-rolling "modern" quack hypothesis; for instance, "universe selection" cosmology in physics. Or take Dawkin's memetic explanation of cultural evolution, for instance. How daring! integrative! and...a total steaming piece of scientifically useless crap!!

Actually, it would be nice to see more red flags about "natural selection abuse" in modern pseudocience

A. Vargas said...
This comment has been removed by the author.