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Sunday, December 01, 2013

Elizabeth Pennisi writes about Richard Lenski's long-term evolution experiment

Elizabeth Pennisi has written about the long-term evolution experiment of Richard Lenski [The Man Who Bottled Evolution]. The experiment is in it's 25th year and it is entirely appropriate that Science magazine devotes several pages to describing the results. There have been some remarkable discoveries.

But I want to focus on a couple of things that Pennisi says in her article. There has also been a discussion on Panda's Thunb: Lenski’s experiment: 25 years and 58,000 generations. Pennisi writes ...
Lenski's humble E. coli have shown, among other things, how multiple small mutations can prepare the ground for a major change; how new species can arise and diverge; and that Gould was mistaken when he claimed that, given a second chance, evolution would likely take a completely different course. Most recently, the colonies have demonstrated that, contrary to what many biologists thought, evolution never comes to a stop, even in an unchanging environment.
Let's talk about two issues in that paragraph.

Gould was mistaken

Stephen Jay Gould wrote an excellent book on the Burgess shale back in 1989 (Wonderful Life).1 The title refers to a movie with a similar name (It's a Wonderful Life). In the movie, George Bailey, played by James Stewart, is taken back in time and shown how his life has changed so many other lives for the better.

In his book on the Burgess shale, Gould introduces the "tape of life" and defends the position that if we rewind the tape of life and replay it, the results will be entirely different. Gould is referring to evolution over the long term (macroevolution is his schtick) and he specifically mentions things like random extinctions, chance, and asteroid impacts. The history of life, like the history of George Bailey's life, is contingent on everything that went before and small changes can have huge impacts. (Think of the Back to the Future movies.)

Gould was not referring to stepping back just a few generation and seeing if the same one or two mutations could happen again. That's not at all what he meant.

So, Elizabeth Pennisi is not being fair when she says, "Gould was mistaken when he claimed that, given a second chance, evolution would likely take a completely different course." She probably never read Wonderful Life so she doesn't understand what Gould actually said. Evolution seems to be some sort of mysterious dark matter to Elizabeth Pennisi.

In Lenski's long-term experiment, one (and only one) of the cultures evolved the ability to utilize the small amount of citrate in the medium. This gave that culture an enormous advantage. The other eleven cultures failed to evolve in this direction. I'll post a description of what happened but the evidence is clear. In order to evolve the ability to utilize citrate a number of improbable mutations had to arise in the correct order. The end result was contingent on chance events. It's pretty good confirmation of Gould's point about the tape of life [see Lenski's long-term evolution experiment: the evolution of bacteria that can use citrate as a carbon source].

And that conclusion is the exact opposite of what Pennisi says. Isn't that strange?

Biologists thought that evolution could stop

Elizabeth Pennisi says that, "contrary to what many biologists thought, evolution never comes to a stop, even in an unchanging environment." She claims that biologists (some? many?) thought that evolution would come to a stop in an unchanging environment. If they thought that, then they would have to believe two things.
  1. There's no such thing as random genetic drift or that fixation of deleterious alleles or nearly neutral alleles by random genetic drift doesn't count as evolution.
  2. Most species are perfectly adapted to their present environment so that further adaptation is no longer possible. You have to believe this because new mutations are happening all the time and if evolution by natural selection has stopped then none of these new mutations can be beneficial.
I suspect that Pennisi is right and some biologists really are ignorant of random genetic drift and really do think that natural selection is so powerful that every species is at the top of an adaptive peak.

However, what she says is unfair because that's not what evolutionary biologists think. Surely there aren't many evolutionary biologists who just learned about random genetic drift from reading Lenski's papers? Surely there aren't many evolutionary biologists who thought that E. coli was perfectly adapted to growth in minimal medium?

Once again, Pennisi is conveying false and misleading information to her readers. Lenski is not stupid. When he started his experiment 25 years ago he fully expected to see evolution and when the first papers were published they did not come as a great shock to evolutionary biologists in spite of what Elizabeth Pennisi would have you believe.

Is it true that many biologists don't know enough about evolution to realize that it occurs in an unchanging environment?2 I suspect it might be true. I also suspect it's a common belief among members of the general public because that's the way evolution is usually taught. I suspect it's what Elizabeth Pennisi believed.

What does the future hold?

Richard ("Rich") Lenski has a blog. Here's what he recently wrote [Fifty-Thousand Squared],
Both of these have got me thinking about the long-term fate of this long-term experiment. Should the experiment continue? For how long should it continue? Who will take it over when (or before) I retire? And after that person retires, then what? How will they sustain it? Will they rely on the usual competitive grants? Would an endowment be more suitable? How does one raise an endowment
If the USA can afford to spend enormous amounts of money on physics experiments and huge sums on NASA, then why not spend a few million on an endowment to make sure Lenski's long-term evolution experiment continues far into the future?

1. I'm not interested in quibbling about things that Gould got wrong in his book or about Conway Morris and his silly ideas about convergence. Save that for another day. The point here is whether Pennisi was fair.

2. Please, let's not get dragged into a lengthy discussion about stasis and punctuated equilibria. What Eldredge and Gould showed was that morphological change could be locked in by speciation (cladogenesis). In most cases, the speciation event occurred in the same environment and both species continued to exist side-by-side for millions of yeas. Neither Eldredge nor Gould ever believed that no evolution was occurring during periods of stasis.


Marcoli said...

Thank you especially for bringing up the clarification of what Gould actually said on whether evolution would follow the same course if history could be re-wound to a start again. On more than one occasion I had seen people declare Gould was wrong on this (with too much glee, IMO) while they were referring to microevolution, when actually Gould was writing about very long term macroevolution.

Anonymous said...


I know I have been a pest, (it's my nature; I'm asperger's if you can appreciate that) but this post made my day.

Larry, that is why I start my day by drinking coffee while reading your blog. Well that is not entirely true but your blog is up there.

BTW: Didn't I make it clear in the past??? I'm not a creationist....I CAN'T BE. WHO IN THE WORLD WOULD THINK THAT? NEG-ENTHROK? COME ON!!! GET A LIFE!!

Newbie said...
This comment has been removed by the author.
judmarc said...

Thanks for this - Wonderful Life is probably my favorite Gould book (as a layperson I've not yet decided whether to tackle the big evolutionary theory book), and Lenski's experiment is something I've admired tremendously for its elegance of design and care of execution. If he gets together an endowment fund (government funding for such a long term experiment seems way too politically contingent to me, unfortunately), I'd love to know where to sign up.

Regarding your two points:

- How can anyone do sufficient research to write about Lenski's experiment for Science and so misunderstand what it says about contingency? (The experiment sheds light on many other things besides the role of contingency, of course.)

- As a layperson, the concept that evolution would stop in stable environments is nonsensical to me. First, where exactly is the environment stable for lengths of time relevant to speciation for every form of life in a particular location? Second, how many forms of life are incapable of spreading into new environments, microscopic or macroscopic? Certainly e. coli have spread through many different locations and environments. (Highly recommend Carl Zimmer's Microcosm.) As you say, there are always new mutations, and if they are not seriously deleterious in the varied and changing environments in which they find themselves, there's a chance they'll catch on.

W. Benson said...

Neutral evolution by drift is verified mathematics. A biological science reporter not knowing that neutral evolution is unstoppable approaches incompetence. Natural selection may also proceed despite a constant environment, but I have not heard an airtight argument that it is inevitable. When you get lots of species together, even in an unchanging physical environment, coevolution seems to promote increasingly complex contrivances, with lags and unexpected disequilibria, like when a disease pops up, challenging all at irregular intervals. In principle, there should be [IMHO] a threshold when evolution, like fire, is self feeding. Pennisi should go back and meditate on her metaphysics.
Two asides: 1) although some of the pronouncements of Steven J. Gould can be questioned, his view that evolution is not determinant is unquestionable. Twin worlds will not be evolutionary photocopies. 2) I think Darwin pretty much accepted by 1859 that evolution was self-generating without needing outside environmental challenges.
Although Lenski’s bacteria continue to increase in fitness, and are not projected (do I remember rightly?) to reach a fitness plateau, only time will tell if the adaptive evolution of Lenski’s bacteria finally stalls. I bet they will stop evolving, even if a few adaptive mutations still arise along the way. If his bacteria were inserted into a more or less complex ecological microcosm (a few protozoans, some nematodes, a few additional bacteria), I would bet not only that adaptive evolution would be more brisk, but that replicates would differentiate more markedly. Now that tried and true protocols exist, someone might run an experiment to see how and if ecological complexity affects the tempo of adaptive evolution.

chemicalscum said...

Gould's assertion " that if we rewind the tape of life and replay it, the results will be entirely different." is not only true for macroevoution but but for genetic drift as well. It is a direct consequence of quantum mechanics. Which mutation appears where and when is totally stochastic as the genetic material is molecular, Schrödinger was able to predict this in the 1940's purely on the basis of quantum mechanics from the fact that X-rays generate mutations.

Though a whether a specific mutation in a specific genome is fixed in a specific population size is effectively deterministic. The change in a specific genome over time is not deterministic. There is a vast number of branching paths for the neutral evolution of this genome to take. If we accept Everett's position that the wavefunction does not collapse then this evolution takes place in Hilbert space. The neutral evolution of a molecule of genomic DNA in an organism matches the evolution of its wavefunction and all the resulting "worlds" are equally real.

This presents a large number of possible genomes for for natural selection to operate on in parallel. Consequently at the level of macroevolution "if we rewind the tape of life and replay it, the results will be entirely different." This is in part due to the quantum stochastic processes underlying neutral (and nearly neutral) genetic drift.

Robert Byers said...

What they call "living fossils" is a hit against Evolution going constantly on in unchanging niches.
Did this experiment create new species with new names in the lists??
Was it anything other then ordinary attrition in nature even with a new mutation helping out?
If it doesn't leave its kind its not important as a evidence for evolution. Evolution means crossing thresholds of biology to advance complexity and diversity of note.

anthrosciguy said...

It might be worth noting that an unchanging environment is impossible. All climatic variation, all other species, including microorganisms, everything must stop for there to be an unchanging environment. How is that even remotely possible.

judmarc said...

What they call "living fossils" is a hit against Evolution going constantly on in unchanging niches.

Hi, Robert. What I see from laypersons in my particular area of expertise (law) is that they take one little bit of knowledge and incorrectly apply it to the entire field - i.e., they over-generalize. And that's what you just did in the statement above. All that has to happen for so-called "living fossils" to exist is that some species relatively closely resemble their ancestors over extremely long periods of time. For animals and plants large enough to make fossils, that does happen, though my impression is that it is relatively rare. Nothing very surprising about that, and certainly no challenge to evolutionary theory.

judmarc said...

Yes, quantum mechanics is involved, since quantum mechanics is a fundamental feature of the universe, so it's involved in pretty literally everything everywhere. But you don't really need quantum mechanics concepts (e.g., the uncertainty principle) to capture the concept of contingency in evolution. After all, asteroids are massive enough that quantum effects are quite small, and DNA copying errors would still exist in the absence of mutations caused by radiation.

Larry Moran said...

There are no known example of species that haven't evolved at a relatively constant rate over milllions oy years. The are a few examlpes of species where that evolution didn't result in big changes in gross morphology but even there you can measure changes if you look closely enough. The idea of "living fossils" is a myth.

Robert, your other questions are irrelevant. Nobody ever claimed that this experiment would produce new species. Your attempt to redefine evolution is pathetic.

Pedro A B Pereira said...

Personaly I don't have much of a problem with the concept of "living fossils". I like Dan Graur's view on the issue:

"""The following paragraphs are taken from a draft of a new book on molecular evolution. I use “living fossils” to illustrate the disconnect between molecular and morphological evolution.

I would greatly appreciate all those objecting to the term “living fossil” to let me know (dgraur at uh dot edu) what’s wrong with my text, and how should it be changed (in addition to updating my references to include the new reports on the Latimeria genome).

“Living fossils are defined as taxa that have not changed morphologically for long periods of time (say, 100 million years). As far as living fossils are are concerned, it is of interest to find out whether the morphological stasis is also accompanied by molecular stasis.

Quite early in the history of molecular evolution, it was noted that sharks, which have not changed to any conspicuous degree since the Devonian, evolved at about the same rate as other “nonfossil” organisms (Fisher and Thompson 1979; Kimura 1989). Furthermore, the mitochondrial DNA of the alligator (Alligator mississippiensis), which is also considered to be a living fossil, evolves much faster than that of birds, which presumably appeared on the evolutionary stage much more recently (Janke and Árnason 1997). Turtles, on the other hand, which have remained morphologically unchanged since Triassic times, seem to evolve at the molecular equivalent of a “turtle’s pace” (Avise et al. 1992). A similar case is observed with the coelacanth species belonging to Latimeria, which before their discovery in 1938 were believed to have been extinct since the end of the Cretaceous, about 65 million years ago (Inoue et al. 2005).

The most spectacular example of a lack of relationship between morphology and molecular evolution is most probably that of the horseshoe crab (class Merostomata), which despite their name are more closely related to scorpions, spiders, and mites than to the crustaceans. While the morphology of horseshoe crabs has changed little in the last 500 million years—indeed, one extant horseshoe crab, Limulus polyphemus is almost indistinguishable in its morphology from its extinct Jurassic relatives—their rates of molecular evolution are unexceptional (e.g., Nguyen et al. 1986; Tokugana et al. 1993). Thus, there seems to be no obvious relationship between morphological and molecular change.”""

Pedro A B Pereira said...

""" How is that even remotely possible."""

You should tell that to the hyppies and some people at Greenpeace.

chemicalscum said...

Copying errors occur at the molecular level and are quantum stochastic processes. Andy Albrecht argues that all probabilistic processes are fundamentally quantum mechanical, On this basis one needs to understand the implications of this for all stochastic processes in understanding evolution both at the molecular level and for macroevolution. The quasi-classical world is fundamentaly quantum mechanical and this has ontological implications.

John Harshman said...

I would point out that all of Graur's "living fossils" (except the horseshoe crabs) are diverse clades within which there is considerable extant morphological disparity. To claim that they haven't changed in two or three hundred million years is to ignore both extant and fossil disparity. It's like saying that mammals are living fossils because Morganucodon has all the features of extant mammals.

So yes, I do have an objection.

Horseshoe crabs are a bit different. There are only a few species, and to my eye they do all look quite similar to each other and their fossil relatives. The differences are there, but they're subtle. Not so for the others.

Pedro A B Pereira said...

""""So yes, I do have an objection.""""

Fine by me, I'm a microbial ecologist, so I don't care about those pesky anatomical details anyway ;p Your should email Graur, then. He's honestly interested in other's opinions on the subject for his book. And I will buy the book, so the more discussion of opinions the better.

""""Horseshoe crabs are a bit different. There are only a few species, and to my eye they do all look quite similar to each other and their fossil relatives. The differences are there, but they're subtle. Not so for the others.""""

So there's "living fossils" after all? ;)

Kidding asside, Graur does say in another post that:

"""On the other hand, living fossils do exist. For a species to be considered a living fossil, it must possess a great number of plesiomorphies (i.e., ancestral traits), and these ancestral traits must be shown to be of great antiquity. How many plesiomorphies and what constitutes “great antiquity” should be specified in each case under study. Opinions may vary on these two issues, and some researchers, like Mark Robinson-Rechavi, may find the term objectionable a priori as it tends to color subsequent inferences. Nonetheless, it is possible to define objectively a taxon as a living fossil."""

So it seems that there is some significant arbitraritry to what should constitute enough differences for something to be called a living fossil or not.

Anyway, keep the discussion going, I'm interested.

Arlin said...

No, no, this is not correct. It's easy to be misled because quite a lot of nonsense has been written on this topic by biologists and philosophers who apparently have not discussed the issue with their local quantum chemist. Just because something happens at the molecular level does not mean it is "microscopic" in terms of quantum indeterminacy. This is a common misconception, e.g., it's in Monod's _Chance and Necessity_. Most of biochemistry is "macroscopic" relative to quantum effects.

For instance, when computational chemists model the folding of a protein they use classical dynamics with force-fields-- think of taking a physical model of a molecule made out of springs and magnets and so on, and throwing this physical model in a clothes dryer for a few hours to see how it folds. That is the kind of process that they are modeling, which includes no quantum magic.

*Some* things that happen at the molecular level are subject to quantum indeterminacy. For instance, some enzymes appear to make use of quantum tunneling in their active sites. Anything involving electromagnetic radiation of course is subject to indeterminacy. But not all mutations involve radiation, and even the ones that involve radiation only involve it in an early step, i.e., a UVB or X-ray photon causes (indeterministically) the formation of a reactive species such as peroxide, which then diffuses (quasi-deterministically) and causes damage, which is repaired (quasi-deterministically) by enzymes, which is where the mutation comes in. Of course the causal chain leading to the mutation is indeterminate if any event in the chain is indeterminate.

chemicalscum, I think you left out "not" in the sentence "whether a specific mutation in a specific genome is fixed in a specific population size is effectively deterministic." The chance of fixation for a new mutation is 1/N for a neutral mutation (haploid case) and ~2s for a beneficial mutation.

Arlin said...

Creating a "living fossil" category isn't the issue. The classical neo-Darwinian view of the Modern Synthesis is that species generally are close to an adaptive optimum. If the environment shifts, they quickly adapt via available variation. If a species is not exhibiting changes, this would mean that the environment is not changing.

There has long been another line of argument that species may become burdened with a tangle of "constraints" that prevents effective change.

I think it is fair to say that there has been a widespread belief in stasis as an evolutionary pattern (I'm not sure if this is what Pennisi is saying). It hardly matters to the paleontological pattern of stasis that some molecules are changing invisibly! One still has to explain the pattern of stasis in those features for which there is stasis! In a nutshell, the neo-Darwinian view is that everything varies, and selection is powerful. The only way these 2 things can be true in the case of stasis is if the species is at an optimum.

judmarc said...

There are a few examlpes of species where that evolution didn't result in big changes in gross morphology

That is what I meant by "some species relatively closely resemble their ancestors."

judmarc said...

In a nutshell, the neo-Darwinian view is that everything varies, and selection is powerful. The only way these 2 things can be true in the case of stasis is if the species is at an optimum.

As a layperson I'm probably missing something relatively elementary here, but what if the vast majority or even all of the variation is with respect to alleles that are neutral wrt selection? (Say for example that any variation of non-neutral alleles is very tightly constrained.)

The whole truth said...

The idea of an unchanging environment (in the wild) seems counter-reality to me. Something that should be considered when talking about unchanging environments or stoppage of evolution is scale or degree. On what time scale (or other scale) is an environment unchanging and on what time scale can or does evolution stop?

As anthrosciguy said:

"All climatic variation, all other species, including microorganisms, everything must stop for there to be an unchanging environment."

Even if that could happen, for how long could it last? A nanosecond, a minute, an hour?

The whole truth said...

Larry said something that I think relates to what I said about scale/degree:

"The are a few examlpes of species where that evolution didn't result in big changes in gross morphology but even there you can measure changes if you look closely enough."

Yes, even in cases where changes aren't easily noticeable, if a close enough look is taken and enough time is allowed, changes will be apparent and measurable, and I would think that this applies to life forms and everything else in the universe.

Robert Byers said...

It is a creationist point about how some creatures have not changed in looks for claimed ages in millions. Quite a lot of millions of years.
I have heard the present denial there are "living fossils" a word coined be evolutionists previously.
Yet if morphology is so similar , after so long, then it suggests that constantly evolving is practically, i say practically, non existent. Looking for differences is looking too hard. People have more differences then many creatures noted by posters here and many more mere millions of years old. Horses for example are said to look exactly, almost, like they did 20 million years ago in the miocene. etc.
in fact our own body parts could be said to be living fossils. Our eyes, hearing, immune system , liver, etc are identical to claimed relatives which must mean from that common descent there has been LITTLE or no evolution in great time periods.
I think evolution should cling to PE and not constantly evolving concepts. Just leaps and great stasis.

Konrad said...

Ludicrous that Lenski still has to compete in the regular NSF pool to keep this going. Perhaps the most remarkable aspect of the experiment is that it didn't get randomly defunded by a grant panel somewhere along the way.

Konrad said...

Actually, the beat poet seems to have stumbled on something useful upthread. I think I'm going to adopt "ordinary attrition in nature with new mutations helping out" as my new favorite definition of evolution.

Q: How are new species created?
A: Ordinary attrition in nature with new mutations helping out.

What could be more apt than that?

Konrad said...

Aaargh, I left the "u" out of "favourite"! Living in the USA is really screwing up my English :-(

The whole truth said...

Byers said:

"Yet if morphology is so similar , after so long, then it suggests that constantly evolving is practically, i say practically, non existent."

What difference does it make whether evolution occurs "constantly" or not when it comes to supporting your religious fairy tales? Even if ALL evolution were to take a million year break now and then that wouldn't add one bit of evidence to support your ridiculous YEC beliefs.

Whether evolution occurs "constantly" or in spurts or a mixture of the two, there's NO way, other than by deluding yourself, that the evidence of the multi-billion year history of the Earth and the evolution of its life forms can be crammed into a 6,000 year time span.

un said...

I found this quote from a paper by Lenski et al. in a presentation that Graur put up a couple of days ago, and it might be relevant to the first point you raised, Larry:

"The evolution of a phenotype is contingent on the particular history of a population. Historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection."

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

Arlin said...

I don't think you are missing anything. It's just that your scenario conflicts implicitly with the premise that selection is powerful. If selection is ultra-powerful, then there can't be any neutral variation.

The way that neo-Darwinians have negotiated this implicit conflict is to suppose that there are important features directly impacted by selection, and non-important ones that are hidden. The old neo-Darwinian rules still apply to everything important, but they don't apply at the "molecular level".

This resolves the seeming conflict in which "living fossils" (horseshoe crab, coelocanth, platypus, snapping turtle, crocodile, chambered nautilus, etc) are morphologically stable for 10s or 100s of MY, yet still change at the molecular level.

However, we still have to explain stasis in the "important" morphological features of all those "living fossils", and the neo-Darwinian explanation is, as always, selection. If important things change, it's selection. If they don't change, that's due to selection as well.

judmarc said...

Thanks Arlin, got it. Just for clarity, would you care to provide a summary of a non-ultra-adaptationist alternative?

Arlin said...

There are many alternatives to the Darwin-Fisher extreme view in which everything varies and selection keeps the population close to the current optimum.

Wright's alternative doesn't really challenge this presumption, but emphasizes the importance of interactions, such that there are better optima that are not locally accessible via continuous upward (in terms of fitness) shifts. An interconnected set of demes that are individually subject to drift can overcome this challenge via the shifting balance mechanism (in theory). This is sort of like turning up the heat in simulated annealing.

There is a structuralist alternative (invoked for over a century) that focuses on the idea that the organism is not infinitely malleable. Only certain types of changes are genetically-developmentally possible. When these "constraints" are limits on the variation that the system is capable of generating (i.e., system A can't generate a variant B), then it is clearly an alternative to the standard view. When "constraints" are understood as effects of selection (we can't get from A to B to C because B has a lower fitness), then this is less of a departure. Often it's hard to tell. But the structuralist would argue that stasis is often due to "constraints". When constraints are due to selection this is only slightly different from the Darwin-Fisher view, except that structuralists tend to rejection the assumption of natura non facit saltum.

IMHO, this ambiguity is a reason that "constraints" has faded away as an alternative paradigm. If the currently accepted paradigm is P, then it's pretty hard to sell I-just-can't-decide-between-P-or-Q as a revolutionary alternative.

There may be other views of stasis but nothing occurs to me at the moment.

chemicalscum said...

The copy of GAMESS (General Atomic and Molecular Structure System) that I have on the hard drive of this computer has routines for doing QM/MM calculations and using FMO (Fragment Molecular Orbital Theory) that enables calculations on very large systems. These routines can be used as part of protein folding studies.

However this is not important. Like the ab initio, semi-empirical and DFT QM calculations I perform as a pharmaceutical chemist on much smaller systems, the calculations use the time independent form of the Schrödinger equation and treat the wavefunction of the molecule as a standing wave. In determining a molecular structure the QM programs seek out thermodynamic minima just the same a molecular mechanics (MM) ones do. This is static not dynamic and therefore is not relevant to evolutionary processes as here the wavefunction does not evolve.

What is interesting are quantum processes where forking into different states is possible, such as the Schrödinger cat thought experiment. Here we have the (sorry about the bad spacing) density matrix in Dirac notation:

|cat alive> |cat alive + cat dead>
|cat alive - cat dead> |cat dead>

Decoherence (interaction with the environment) destroys the off-diagonal elements of the matrix) leaving behind the trace, here two vectors in Hilbert space: |cat alive> and |cat dead> which continue to evolve independently and in parallel.

This can simply be changed for a specific mutation in DNA that is caused by a QM event to this density matrix:

|no mutation> |no mutation + mutation>
|no mutation - mutation> |mutation>

Again were are left with two vectors which continue to evolve independently and in parallel in Hilbert space. That is there are two different genomes evolving independently and in parallel in Hilbert space.

The Löwdin mechanism proposed for some DNA mutations uses quantum tunnelling and thus is definitely a quantum stochastic process.

I would draw attention to Andy Albrecht's arXiv paper I reference above where he argues "using simple models that all successful practical uses of probabilities originate in quantum fluctuations in the microscopic physical world around us, often propagated to macroscopic scales". In the above analyses the quantum event is clearly propagated to the macroscopic scale.

Arlis you are right about the not. I didn't really think about the not vaguely remembering lots of deterministic looking equations when I tried to do a bit of self study of population genetics. Then it is dealing with probabilities and as argued above all probabilities ultimately derive from the quantum level. Dealing with populations is a bit like statistical thermodynamics, at root there is quantum indeterminacy at the atomic and molecular level which even Boltzmann didn't know about but for large ensembles there is FAPP determinism. Its when you deal with interesting complex individual things like cats and an individual DNA molecules that "worlds" or "histories" (use your favourite terminology here) split and evolve on separate parallel pathways.

There is no classical world as quantum indeterminacy is continually welling up to the macroscopic level. This is why we live in a stochastic quasi-classical world.

Robert Byers said...

The difference was important relative to the discussion. Your changing the thread here.
Its a good point for creationism about claims that creatures lived soooo long but look so alike to modern relatives YET are said to have been evolving ever since the old fossil was found.
Very unlikely for a system saying evolution is constantly going on in all creatures.
The living fossil thing says otherwise at the least.
In fact there is no evidence any evolution going on. Just evidence for diversity within types. Anyways only the geology is "evidence" for evolutionary change. The biology of data points is silent.

Arlin said...

chemicalscum, thanks for writing this. You seem to know more about this issue than I do, though I'm quite skeptical of the claim in the arXiv paper that you cite. My experience is that I have seen many naive claims from biologists who don't know about physical biochemistry, physicists who don't know about the biology of mutation, and philosophers who don't know about either one, and I've discussed some of the issues with a colleague who is a quantum chemist (first author of, now retired). I'm currently writing a paper on mutation and randomness and I want to be sure to get this part right. Can you contact me to discuss this offline? I'm easy to find.

Arlin said...

Oh, and by the way, I stand corrected-- I mis-spoke when I said "classical dynamics". This is the point in chemicalscum's first paragraph-- the calculations in GAMESS are based on molecular orbital theory, which is based on quantum mechanics. So, this is not "classical dynamics", although in practice this kind of calculation does not allow quantum uncertainty to percolate up and result in indeterminate folding outcomes (if I understand correctly, this is the point in chemicalscum's second paragraph).

Arlin said...

And if anyone wants to read an article that (judging from the abstract) is going to present what I would call the conventional view linking stasis to stabilizing selection, see:

Estes, S. and S.J. Arnold, Resolving the paradox of stasis: models with stabilizing selection explain evolutionary divergence on all timescales. The American Naturalist, 2007. 169(2): p. 227-44.

The whole truth said...

Robert, you're the one who tries to change a thread every time you post a comment in one. All you do is deny anything that pertains to actual science and you push your YEC religious beliefs. You obviously think that your assertions and questions are legitimate and sciency but it's abundantly clear that you just won't accept anything that challenges or refutes christian YEC fairy tales.

One of the points of mine that you are ignorantly dismissing is that no matter how much you try to to assert that evolution is "Just leaps and great stasis" or that "there is no evidence any evolution is going on" or that "constantly evolving is practically, i say practically, non existent" or that "there has been LITTLE or no evolution in great time periods" (make up your mind), the universe, the Earth, and life on Earth are OLD. Very, very OLD. Billions of years OLD.

The other point is that none of your inconsistent or erroneous assertions about evolution and science provide any supportive, scientific evidence for your religious beliefs.

By the way, how can there be "great time periods" if the whole universe is only 6,000 years old?