Congratulations to our resident theoretical biologist of high renown, Joe Felsenstein, on his presentation, yesterday, of the 37th Fisher Memorial Lecture. [ETA: I’ll post a separate announcement of the video, when it is released.] Following are the details provided by the Fisher Memorial Trust (with a link added by me).
Title: Is there a more fundamental theorem of natural selection?
Abstract. R.A. Fisher’s Fundamental Theorem of Natural Selection has intrigued evolutionary biologists, who wondered whether it could be the basis of a general maximum principle for mean fitness of the population. Subsequent work by Warren Ewens, Anthony Edwards, and George Price showed that a reasonable version of the FTNS is true, but only if the quantity being increased by natural selection is not the mean fitness of the population but a more indirectly defined quantity. That leaves us in an unsatisfactory state. In spite of Fisher’s assertion that the theorem “hold[s] the supreme position among the biological sciences”, the Fundamental Theorem is, alas, not-so-fundamental. There is also the problem that the additive genetic variances involved do not change in an easily predictable way. Nevertheless, the FTNS is an early, and imaginative, attempt at formulating macro-scale laws from population-genetic principles. I will not attempt to revive the FTNS, but instead am trying to extend a 1978 model of mine, put forth in what may be my least-cited paper. This attempts to make a “toy” model of an evolving population in which we can bookkeep energy flows through an evolving population, and derive a long-term prediction for change of the energy content of the system. It may be possible to connect these predictions to the rate of increase of the adaptive information (the “specified information”) embodied in the genetic information in the organisms. The models are somewhat absurdly oversimple, but I argue that models like this at least can give us some results, which decades of more handwavy papers on the general connection between evolution, entropy, and information have not.
Welcome to TSZ, Dr. Ali.
There were some other continuity problems with the World Magazine story.
Alan Fox,
Thanks!
Alan Fox,
Hey, wait. How’d you know I’m a doctor?
Faizal Ali,
Apologies. I peeked at your registration when releasing your first comment from the moderation queue.
Alan Fox,
No problem. 🙂
I perused Joe Felsenstein’s 1978 paper through J-stor. As always, his math is beautiful to study.
Ironically, I’ve had sharp disagreements with the majority of the ID community in conflating Shannon Information Entropies with Thermodynamic Entropies.
Thermodynamic entropies are a SUBSET of all possible Shannon Entropies and in many cases the Shannon Entropies can be defined or erased based on purely conceptual constructs. This makes it difficult if not impossible to tie thermodynamic entropies with information entropies of the genetic code (or whatever hypothetical code is in the hypothetical population Joe describes).
There are two problems, one conceptual, and one numerical.
I illustrated one of the problems with estimating the Entropies of 500 copper coins.
Here are 3 acceptable answers:
A. 500 bits (heads tails entropy)
B. 4245 bits (orientation entropy )
C. 8.636 x 10^25 bits, etc. (standard molar thermodynamic entropy)
All these would be correct answers depending on how the observer chooses to recognize microstates and associated probability of each microstate!
The thermodynamic answer of 8.636 x 10^25 bits is a whoppingly large number. It totally dwarfs the 6.6 gigabits in the human genome for example — but this is comparing apples to oranges.
So let’s compare apples to apples.
The standard molar entropy in a human is greater than 116,677 J/K based on the water content alone. Using the conversion factor from J/K to shannon bits which both Gordon Davisson and I agreed on, this equates to
116,677 J/K / (1.381x 10^-23 J/K) / .693147 = 1.22 x 10^28 bits
This number dwarfs by 19 orders of magnitude the information bits in the human genetic code which is only 6.6 giga bits in the 3.3 giga bases of DNA.
So the problem is conceptual in as much as how one will count the microstates to compute entropy. If it is purely thermodynamic (according to standard engineering practice) entropy calculation is not so bad. Adding other layers of shannon information (as was done with the coins) adds a layer of complication that is not universally agreed upon how to connect to traditional thermodynamics.
The discussion centers around the Landauer principle, which is much easier to apply (relatively speaking) to the origin of life problem.
https://en.wikipedia.org/wiki/Landauer%27s_principle
Even supposing we used Landauer’s principle (whose validity is not without controversy) and could add the various layers of information entropy above into a thermodynamic calculation, the numerical problem kicks in. What do I mean?
Consider the copper coins entropy. Let’s hypothetically sum all the conceptual entropies:
500 bits (heads tails entropy) + 4245 (orientation angle entropy) +
8.636 x 10^25 bits (standard molar thermodynamic entropy) ~=
8.636 x 10^25 bits
Thus the quantity of interest, the proscriptive information entropy (the DNA type information entropy) of what we might consider as bits and bytes is swamped by the standard molar thermodynamic entropy. Thus calculations involving energy flow will result in making any theoretical calculations practically unmeasurable numerically with respect to the proscriptive (DNA-type) information.
Hence, ironically, I’ve told ID proponents to drop thermodynamics altogether from their information arguments. It’s fallen of deaf ears. The better information arguments are better formed with genetic analysis such as done by Basener and Sanford.
Personally, I’ve all but abandoned information oriented ID arguments have have gone back to the old Behe and Dean Kenyon biochemical arguments.
I use information concepts still, but minimize it’s use in evolutionary discussions. For example I calculated each human cell has about 80 megabytes of shannon information in the Chromatin Random Access Memory. I found out, recently that this number was independently arrived at in a paper in PLOS (3 years before I did the calculation, DARN!). But I sure as heck am not going to tie the possibility of evolution and thermodynamics to this number. That’s courting disaster, imho.
Here was my version of that calculation:
http://www.creationevolutionuniversity.org/public_blogs/skepticalzone/paper31.pdf
and
This equates to:
16,500,000 nucleosomes * 40 bits/nucleosome * 1 byte/8 bits * 1 megabyte/1024/1024 bytes = 78.67 megabytes per cell
That was my calculation in Spring 2015.
Contrast to PLOS 1 calculation 2012:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0035703
I don’t think the issue is a disregard of the effect of nearly neutral mutations. Rather, I suspect it has to do with the magnitude of the effect of beneficial mutations, combined with the ratio of beneficial-to-deleterious mutations.
I think Sandford has been on the record before saying something to the effect that he thinks beneficial mutations have very low beneficial effects. IIRC he considers it basically impossible that a mutation could double fitness. I remember reading something about that in this thread: in this thread. My guess is he’s poisoned his treatment of Fisher’s Theorem with the same assumptions he makes in his Mendel’s Accountant program.
It may be worth revisiting the meaning of fitness yet again. For example, how is Lenski’s bacteria are always increasing in fitness, yet when released in a normal environment, they die?
One can’t make much sense of the following experiment using population genetic definitions of fitness if the population is isolated. This applies also to Lenski’s isolated bacterial populations, whose evolving fitness I consider relatively meaningless:
http://genetics.org/content/148/4/166
The issue is that “fit” is defined relative to the present environment, not fit in the medical sense or in Darwin’s sense that fit is a design of some sort. This is like the blind cave fish issue where we measure fitness in terms of the degree of blindness, but what defines fitness for the fish is the reversed in an environment with light.
I find that context-dependence of the S-coefficient not very satisfying mathematically. Given Lenski’s bacterial populations are always growing in fitness in the lab but aren’t viable outside of that environment can be also interpreted that Lenski has made his creatures UN-fit. Claims of fitness increase are just mathematical whitewashing and equivocation of the fact the creatures are functionally unfit in more general (rather than specialized) environments. So which definition of fitness is right? Well, the fact there isn’t an answer is a bit of a problem, imho.
The problem with any fundamental theorem in population genetics as far as the evolution of coordinated functional systems like eyes is that fitness coefficients are a poor way of characterizing the system or its parts. Many parts in isolation from a working whole are neutral at best, unfit at worse.
Say a creature develops an insulin regulated metabolism. Without concurrent evolution of an insulin regulating mechanism, this newly evolved metabolism could be DOA (dead on arrival).
Sal:
Come on, Sal. Fitness is relative to the environment. Do you really think that if desert mice don’t thrive in the Amazon basin, that means they’re unfit — period?
How does Lenski measure increase in fitness exactly?
I don’t have specifics right now, but it would be worthwhile for everyone to work out an example of how to do it based on the equations in Joe Felsenstein’s book (freely available online): Theoretical Evolutionary Genetics.
I minimize my time with population genetics relative to studies in biochemistry — so that’s my excuse for not being able to answer your question! Sorry!
J-mac,
Here is the thread where Joe started walking me through the process of calculating fitness. I never got around to working out a specific example because shortly thereafter I started studying biochem at the NIH.
But anyway, here is what little discussion there is in calculating fitness. There was also a passing discussion of Fisher’s theorem there as well.
Thanks Sal. I was just curious….
I had a similar discussion with Joe on natural selection on the OP most of the mutations where we were discussing the strong element of randomness in natural selection…
I realize that fitness is often assumed based on survival. Out of 120.000 fertilized eggs of green frog only 2 survive. Based on what evidence does the population genetics assume that those 2 individuals were selected by nature? Because they were the fittest? Or because they survived? How do they know that those 2 didn’t have average fitness? Do you follow?
I have been very clear about that. In any case that other thread is where to discuss this (endless) objection. I have explained many times how population genetics models this. Go to the other thread if you want to go around on this again. Not here.
Fitness of extant strains is measured by competing them against the ancestral strain that has been kept in the freezer. Both strains are mixed in a liquid medium, incubated for a while, and then plated on petri dishes. The strain that has the greater number of colonies on plate, has the higher relative fitness. It is basically a test of growth rate in the presence of a competitor.
What is “average fitness”? Could you please bracket that?
Oh, and let’s take it to the appropriate thread if you feel like taking that subject up again.
You’ve managed to confuse yourself quite a lot here.
In Lenski’s experiment the fitness definition is actually extremely simple. It is defined as the average reproductive rate of the population, compared to the ancestral population, in direct competition in the same environment.
The ancestor with which the whole experiment was started had a particular reproductive rate (doubling time) in fresh media in the flasks. This reproductive rate was recorded, and in any case they have frozen samples of the ancestor than they can thaw and re-test for it’s reproductive rate in the flasks.
Later descendants of the ancestor also have a reproductive rate in the flask environment, but it is significantly higher. So fitness of the population has increased.
Fitness is of course always context dependent. In this case, fitness is defined in the context of the flask environment and is compared to the ancestor which is tested along with the descendant. The organisms in the experiment has continued to adapt to the flask environment, they have become more fit than their ancestors to that environment. Because they reproduce significantly faster, they outcompete their ancestor.
This is not unusual, the same is true of pretty much any species on Earth. When terrestrial organisms evolved, they became better adapted to life on land, but they lost fitness in aquatic environments. Evolution adapts populations of reproducing organisms to the environments in which they live.
It should not be a surprise that when the E coli strain that has evolved for over 20 years to the flask environment, is put back into their “natural” habitat from which they were originally first taken, they are no longer well adapted to that environment.
It would be like taking whales and expecting them to do well on land. Or throwing pigs and goats in the deep ocean.
It’s possible that Sanford made more than one error, though, isn’t it? I do see that he mentions neutral mutations in the theoretical discussion in the first part of the paper, but it is not clear to me that his calculations take them into account.
This highlights something that creationists have a hard time appreciating about the Lenski experiment: It provides clear cut empirical refutation of many of the key claims of ID. The ID creationists can try all they want to play with their pocket calculators and come up with big numbers that supposedly show that evolution is impossible. However, Lenski has shown that all you need to do is put a bunch of bacteria in a bottle and watch them. Evolution will then happen right before your eyes.
From one clonal population, 12 completely distinct populations have emerged. If speciation was impossible, we wouldn’t see that.
And the fact that every single one of those populations is better adapted to their environment shows that evolution can produce beneficial new genetic information. There just is no other explanation.
So when.e.g. Michael Behe decides to invent his own new category of “gain of function” mutations and argues that these did not occur in Lenski’s lab, it is irrelevant. All it shows, is that, even if Behe’s definition means anything, evolution does not require such “gain of function” mutations to proceed.
Joe’s 1978 paper has some beautiful math, even the basic stuff forced me to recall some forgotten principles.
The very first equation in the paper:
dA/dt = alpha – A lambda
is a variant of something that is highly foundational to Electrical Engineering.
I had to think about it for a couple minutes, and this is a first order ordinary differential equation whose solution is a decaying exponential. It’s just a tad more complex that a simpler form that looks like:
dx/dt = -X
which is recast as
-dx/X = dt
and integrating both sides
-lnX = t + C
and exponentiating both sides and making Exp(C) = A_initial
X = A_initial Exp (-alpha t )
But working with the more complex form in Joe’s paper:
dA/dt = alpha – A lambda
dA/(A-alpha) = dt
Ugh! I forgot how to integrate that! Ugh! That’s trivial stuff, back to the old math books. Told you my math is getting rusty.
Corneel and Rumraket,
Thanks for your comments. I learned something!
You’re saying that each petri dish contains two strains — right?
Joe,
Do you know when the video will be available?
Joe has told me that the organizers will be editing the video, and that he doesn’t know when they will release it. He’ll let me know when it’s available, and I’ll do another OP to announce it.
Thanks for the update.
Correct, one of the strains carries a genetic marker that allows researchers to distinguish the strains.
Makes it very easy to just count the number of colonies and compare them.
Relative Fitness Data Through Generation 10,000.
It really is quite remarkable how many common creationist canards are demonstrated false with that single experiment.
Corneel,
I’m for letting creationists off with a year of probation and 1000 hours of public service, provided that they have that image tattooed on their foreheads.
[latex exploded will try again shortly.]
Apologies to Joe Felsenstein as I believe I totally mangled the meaning of what he was trying to say.
With respect to
I believe when Joe said equilibrium is reached, that implies
which yields
adding to both sides
dividing both sides by yields
Which is the equilibrium point he mentioned. I sort of see the math, but I don’t yet see the formal reason will be true at some point except informally this must be some sort of decaying exponential.
I tried to find that decaying exponential by solving the differential equation implied by Joe’s formula.
So I started here:
multiplied both sides by and divided both sides by
Integrating both sides:
which implies
to solve this integral
let
and
then
so
which without loss of generality can be reframed as
exponentiating both side yields a bit of mess
which looks like a decaying exponential I guess, but I can’t see it as decaying with respect to T. I did something wrong.
There’s a really easy way to solve that. But instead of me explaining it, why don’t you ask the guy who wrote …
this
Congrats Sal!
That’s a really good article!
I haven’t laughed like that about evolutionary nonsense for a long time…
You have a very good sense of humor, Sal… 😉
If promoting YEC doesn’t fulfil your expectations, stand-up comedy could be your next choice… though,as you already know, I highly recommend quantum mechanics…
Remember, comedy, at the expense of others; in this case having a good laugh at the expense of Joe Felsenstein, is not as fulfilling as learning quantum mechanics…
” After you learn quantum mechanics, you are never really the same again.”
I tentatively decided to start an internet text and video series on quantum mechanics. Some of it will be insanely boring. I spent an hour last night reading through and re-learning Schrodinger’s equations and Hamilton’s equations and Dirac notation. But I found some gems for ID proponents and creationists in the process of reading which I didn’t catch the first time round.
Nothing personal intended against you, Joe. That was just business. Sorry you had to see what I say outside of TSZ.
“Salvador Cordova has appeared on National TV, radio shows, newspapers, books and magazines for his work in promoting Intelligent Design and Creation Science. He is a former scientist and engineer in the aerospace and defense industry and presently serves as a professor and researcher in the area of Christian apologetics at small Bible College through the generous support of a private foundation. He also manages a small privately held investment fund which he has run on the side since 1997. He has 4 science degrees including an MS in Applied Physics from Johns Hopkins University and is presently working on a PhD. On April 28, 2005, he became one of the few creationists to ever appear in a cover story of the prestigious scientific journal Nature which covered his work on behalf of intelligent design. The most famous member of the Intelligent Design club he organized at George Mason in 2005 is Biologist Caroline Crocker who was featured in the Ben Stein’s motion picture documentary Expelled.”
HAHAHAHA. You wrote that shit yourself didn’t you?
Sal:
I’m sure it will be as spectacularly successful as your Creation Evolution University was.
Bwahahaha.
Are you suggesting it isn’t true?
Or you just don’t know what to write, so you decided to mock?
I’m suggesting it’s supposed to look pretty, while having no actual value. Creationism is about appearance. It’s really just an attempt to look like you’re doing science. It’s an act. A performance.
It’s pretentious bullshit designed simply to impress gullible sychophants. Reminds me of “Dr” Kent Hovind. Who got his “doctorate” at Patriot Bible University. Which you can see here in all it’s glory:
Rumraket’s assessment of Sal deserves a repost:
I found some of the fundamental stuff of QM a bit boring… but I always look at it from the prospective of understanding it why QM works the way it does…
If the universe, life, as well as consciousness, on subatomic level, is built and operating by QM, it is the essence of everything, I would like to know as much as possible…
Or, is there a deeper level of complexity and everything that is based on dark energy and matter? This is harder to break down as no one knows what they are… we only know that they have to exist…
Keep me updated on your QM endeavours, if you can…
I always thought that the goal of scientific research is the pursuit of the truth and not to support preconceived ideas?
Do you disagree?
J-Mac,
What does that have to do with Sal’s pompous self-puffery?
Why should you be sorry?
Isn’t at least a part of your “calling” to expose false ideas?
If someone you like promotes false ideas, are going to let slide because it’s his birthday?
I may like Joe, but I don’t necessarily have to respect what he does and how he does it…
It must be a sad business one where you’re expected to make fun of people just because you’re too stupid to understand the points they make, and because you oppose the person’s scientific field.
Making fun of someone is always personal. When I make fun of you, at least I do it in your face. Not only that, I do it because you deserve it for being the illiterate fool who quotes from articles that show you wrong, imagining that they show you right. I make fun of you because you presume of a high intellect while showing astounding incompetence.
If you’re working on a PhD reading articles the way you read biology articles to quote in this forum, you must be doing quite an idiot out of yourself. If so, I hope they have the guts to fail you, even if that made you a martyr, in your own eyes, for the bullshit that you represent.
Never understood why doing something slimey for money or personal gain is somehow better than doing it because you honestly dislike someone. Seems more hypocritical.
Because I like Joe.
I only pointed out how funny it was to commemorate the deceased (RA Fisher) by pointing out one his great accomplishments in the name of Darwin wasn’t so fundamental. But if you’re going to trash someone at their funeral, do it the way the preacher did whom I quoted:
But business is business, and crev.info is in the entertainment business….
Personally, the best way to learn, imho, is to have a little entertainment mixed in. That Quantum Mechanics book by Griffiths which I’ll be basing my QM series on has subtle humor in every chapter.
See, this is one of the things that creationists do not understand about science. Taking a colleague’s work seriously enough to evaluate it thoroughly in attempt find its faults and weaknesses is a sign of respect, not disparagement.
Compare that to the mindless tribalism of creationism, where even a disagreement as fundamental as whether the universe is 14 billion years old or 6000 (LOL!) is just swept under the rug and not openly debated. It’s more important to present an appearance of unanimity because for creationists skeptical investigation, the heart of the scientific method, is considered a sign of weakness.
It would be good for its readers to know that the crap in there shouldn’t be taken seriously. It’s just entertainment passing for creationist bullshit. You’ve heard of Poe’s law, haven’t you? You better put your confession about the true business of that web site up front so people don’t get so exited by the bullshit that’s found in there.
stcordova,
What about you wrote something about your incompetent reading of biological articles in there? The title could be “Famous IDiot demonstrates astounding illiteracy,” or “Famous IDiot shots himself on the foot … repeatedly.”
That would be very funny, entertaining, and there would be something to learn about what it takes to be an IDiot like yourself.