…and this is a 
Most of you don't understand evolution. I mean this in the most charitable way; there's a common conceptual model of how evolution occurs that I find everywhere, and that I particularly find common among bright young students who are just getting enthusiastic about biology. Let me give you the Standard Story, the one that I get all the time from supporters of biology.
Evolution proceeds by mutation and selection. A novel mutation occurs in a gene that gives the individual inheriting it an advantage, and that person passes it on to their children who also gets the advantage and do better than their peers, and leave more offspring. Given time, the advantageous mutation spreads through the population so the entire species has it.
One example is the human brain. An ape man millions of years ago acquired a mutation that made his or her brain slightly larger, and since those individuals were slightly smarter than other ape men, it spread through the population. Then later, other mutations occured and were selected for and so human brains gradually got larger and larger.
You either know what's wrong here or you're feeling a little uneasy—I gave you enough hints that you know I'm going to complain about that story, but if your knowledge is at the Evolutionary Biology 101 level, you may not be sure what it is.
Just to make you even more queasy, the misunderstanding here is one that creationists have, too. If you've ever encountered the cryptic phrase "RM+NS" ("random mutation + natural selection") used as a pejorative on a creationist site, you've found someone with this affliction. They've got it completely wrong.
Here's the problem, and also a brief introduction to Evolutionary Biology 201.
First, it's not exactly wrong — it's more like taking one good explanation of certain kinds of evolution and making it a sweeping claim that that is how all evolution works. By reducing it to this one scheme, though, it makes evolution far too plodding and linear, and reduces it all to a sort of personal narrative. It isn't any of those things. What's left out in the 101 story, and in creationist tales, is that: evolution is about populations, so many changes go on in parallel; selectable traits are usually the product of networks of genes, so there are rarely single alleles that can be categorized as the effector of change; and genes and gene networks are plastic or responsive to the environment. All of these complications make the actual story more complicated and interesting, and also, perhaps to your surprise, make evolutionary change faster and more powerful.
Think populations
Mutations are the root of biological variation, of course, but we often have a naive view of their consequences. Most mutations are neutral. Even advantageous mutations are subject to laws of chance in their propagation, and a positive selection coefficient does not mean there will be an inexorable march to fixation, where every individual has the allele. This is also true of deleterious mutations: chance often dominates, and unless it is a strongly negative allele, like an embryonic lethal mutation, there's also a chance it can spread through the population.
Stop thinking of mutations as unitary events that either get swiftly culled, because they're deleterious, or get swiftly hauled into prominence by the uplifting crane of natural selection. Mutations are usually negligible changes that get tossed into the stewpot of the gene pool, where they simmer mostly unnoticed and invisible to selection. Look at human faces, for instance: they're all different, and unless you're looking at the extremes of beauty or ugliness, the variations simply don't make much difference. Yet all those different faces really are the result of subtly different combinations of mutant forms of genes.
"Combinations" is the magic word. A single mutation rarely has a significant effect on a feature, but the combination of multiple mutations may have a detectable or even novel effect that can be seen by natural selection. And that's what's going on all the time: the population is a huge reservoir of genetic variation, and what we do when we reproduce is sort and mix and generate new combinations that are then tested in the environment.
Compare it to a game of poker. A two of hearts in itself seems to be a pathetic little card, but if it's part of a flush or a straight or three of a kind, it can produce a winning hand. In the game, it's not the card itself that has power, it's its utility in a pattern or combination of other cards. A large population like ours is a great shuffler that is producing millions of new hands every day.
We know that this recombination is essential to the rapid acquisition of new phenotypes. Here are some results from a classic experiment by Waddington. Waddington noted that fruit flies expressed the odd trait of developing four wings (the bithorax phenotype) instead of two if they were exposed to ether early in development. This is not a mutation! This is called a phenocopy, where an environmental factor induces an effect similar to a genetic mutation.
What Waddington did next was to select for individuals that expressed the bithorax phenotype most robustly, or that were better at resisting the ether, and found that he could get a progressive strengthening of the response.
The progress of selection for or against a bithorax-like response to ether treatment in two wild-type populations. Experiments 1 and 2 initially showed about 25 and 48% of the bithorax (He) phenotype.
This occurred over 10s of generations — far, far too fast for this to be a consequence of the generation of new mutations. What Waddington was doing was selecting for more potent combinations of alleles already extant in the gene pool.
This was confirmed in a cool way with a simple experiment: the results in the graph above were obtained from wild-caught populations. Using highly inbred laboratory strains that have greatly reduced genetic variation abolishes the outcome.
Jonathan Bard sees this as a powerful potential factor in evolution.
Waddington's results have excited considerable controversy over the years, for example as to whether they reflect threshold effects or hidden variation. In my view, these arguments are irrelevant to the key point: within a population of organisms, there is enough intrinsic variability that, given strong selection pressures, minor but existing variants in a trait that are not normally noticeable can rapidly become the majority phenotype without new mutations. The implications for evolution are obvious: normally silent mutations in a population can lead to adaptation if selection pressures are high enough. This view provides a sensible explanation of the relatively rapid origins of the different beak morphologies of Darwin's various finches and of species flocks.
Think networks
One question you might have at this point is that the model above suggests that mutations are constantly being thrown into the population's gene pool and are steadily accumulating — it means that there must be a remarkable amount of genetic variation between individuals (and there is! It's been measured), yet we generally don't see most people as weird and obvious mutants. That variation is largely invisible, or represents mere minor variations that we don't regard as at all remarkable. How can that be?
One important reason is that most traits are not the product of single genes, but of combinations of genes working together in complex ways. The unit producing the phenotype is most often a network of genes and gene products, such at this lovely example of the network supporting expression and regulation of the epidermal growth factor (EGF) pathway.
That is awesomely complex, and yes, if you're a creationist you're probably wrongly thinking there is no way that can evolve. The curious thing is, though, that the more elaborate the network, the more pieces tangled into the pathway, the smaller the effect of any individual component (in general, of course). What we find over and over again is that many mutations to any one component may have a completely indetectable effect on the output. The system is buffered to produce a reliable yield.
This is the way networks often work. Consider the internet, for example: a complex network with many components and many different routes to get a single from Point A to Point B. What happens if you take out a single node, or even a set of nodes? The system routes automatically around any damage, without any intelligent agency required to consciously reroute messages.
But further, consider the nature of most mutations in a biological network. Simple knockouts of a whole component are possible, but often what will happen are smaller effects. These gene products are typically enzymes; what happens is a shift in kinetics that will more subtly modify expression. The challenge is to measure and compute these effects.
Graph analysis is showing how networks can be partitioned and analysed, while work on the kinetics of networks has shown first that it is possible to simplify the mathematics of the differential equation models and, second, that the detailed output of a network is relatively insensitive to changes in most of the reaction parameters. What this latter work means is that most gene mutations will have relatively minor effects on the networks in which their proteins are involved, and some will have none, perhaps because they are part of secondary pathways and so redundant under normal circumstances. Indirect evidence for this comes from the surprising observation that many gene knockouts in mice result in an apparently normal phenotype. Within an evolutionary context, it would thus be expected that, across a population of organisms, most mutations in a network would effectively be silent, in that they would give no selective advantage under normal conditions. It is one of the tasks of systems biologists to understand how and where mutations can lead to sufficient variation in networks properties for selection to have something on which to act.
Combine this with population effects. The population can accumulate many of these sneaky variants that have no significant effect on most individuals, but under conditions of strong selection, combinations of these variants, that together can have detectable effects, can be exposed to selection.
Think flexible genes
Another factor in this process (one that Bard does not touch on) is that the individual genes themselves are not invariant units. Mutations can affect how genes contribute to the network, but in addition, the same allele can have different consequences in different genetic backgrounds — it is affected by the other genes in the network — and also has different consquences in different external environments.
Everything is fluid. Biology isn't about fixed and rigidly invariant processes — it's about squishy, dynamic, and interactive stuff making do.
Now do you see what's wrong with the simplistic caricature of evolution at the top of this article? It's superficial; it ignores the richness of real biology; it limits and constrains the potential of evolution unrealistically. The concept of evolution as a change in allele frequencies over time is one small part of the whole of evolutionary processes. You've got to include network theory and gene and environmental interactions to really understand the phenomena. And the cool thing is that all of these perspectives make evolution an even more powerful force.
Bard J (2010) A systems biology view of evolutionary genetics. Bioessays 32: 559-563.
Life Science
Comments
Posted by: Peter H
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July 24, 2010 7:57 PM
Another simplistic trap that creationists readily fall into is the conviction, born perhaps of a need to clutch straws, that any mutation must of necessity be degenerative and thereby not contribute to the possibility of the organism's enhanced viability but, rather, to increase the likelihood of its demise.
They often present this argument, but always fail to produce data or logical reasoning to support it. But you knew that.
Posted by: Kel, The Privileged View From Nowhere
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July 24, 2010 8:07 PM
Is this reason why in small populations that genetic drift can play a role in particular alleles being in 100% of a population?
Posted by: Brownian, Most Vicious & Petty of Pharyngulites
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July 24, 2010 8:08 PM
Excellent. Consider this one bookmarked for recurrent reading and rumination.
Posted by: Nerd of Redhead, OM
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July 24, 2010 8:12 PM
Dang, hard science late on Saturday (hic). But, the article expresses the way I have been thinking. Take Lenski's work with E. coli and citrate. It took two mutations to prime the pump for the third mutation that gave the germs the ability to metabolize citrate. All due to the fluidity of genes, with some mutations being neutral (the first two), but with one final mutation, giving a real effect. Now to be soundly refuted by those better versed in biology.
*assumes fetal position*
Posted by: morriganscrow
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July 24, 2010 8:15 PM
Fascinating stuff! Thanks PZ, for an article I'll be thinking about for some time.
Posted by: 'Tis Himself, Quel Dommage
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July 24, 2010 8:17 PM
Somehow I doubt PZ wrote this post on an iPod.
Posted by: Sven DiMilo
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July 24, 2010 8:18 PM
Of course, it is possible in many cases for a single point mutation to be strongly positively selected, and examples are known.
Posted by: Brownian, Most Vicious & Petty of Pharyngulites
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July 24, 2010 8:24 PM
Well, clearly he turned off 'shuffle'.
Posted by: Cuttlefish, OM, CR
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July 24, 2010 8:25 PM
The misunderstanding of this concept is the one thing that I dislike about Tim Minchin's "Tony the Fish": http://www.youtube.com/watch?v=4DXl68NF_uI
Otherwise, love it!
Posted by: Kel, The Privileged View From Nowhere
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July 24, 2010 8:29 PM
Yeah, that makes me cringe every time I hear it... until it gets to the punch-line which makes the misunderstanding worth it.Posted by: flawedprefect
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July 24, 2010 8:40 PM
Awesome! I learned something today!
Posted by: Peter H
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July 24, 2010 8:42 PM
Keep in mind that Tim Minchin's general audience is ordinary folk, not Philosophers, Sages, Luminaries & Other Professional Thinking Persons.
Posted by: Frank Lovell
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July 24, 2010 8:44 PM
Superbly articulated, PZ -- THANK YOU for taking the time to compose that essay, may the FSM bless you and the horse you rode in on!
Posted by: lumbercartel
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July 24, 2010 8:44 PM
And then there's the fact that the processes you describe are themselves only a lower level of the complexity -- because those traits interact with others in the environment, both intra- and inter-species.
As with the ether, and going back to the original example: that bigger brain might not be of much use unless the population with the somewhat-bigger brains also have the nutrition to support them, which depends on whether they have started cooking food, which is much easier when some of them have more dexterity, not to mention living in an area with ready fuel suitable to relatively crude firestarting methods ....
Drop one factor and the odds all shift. Chaos, in the mathematical sense arising from a complex network of nonlinear processes.
Posted by: llewelly
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July 24, 2010 8:46 PM
Why are we getting all this science on this blog? I thought this place was about calling creationists demented fucktards.
Posted by: Kel, The Privileged View From Nowhere
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July 24, 2010 8:46 PM
When I saw him last December, he went on about 5 minutes about post hoc ergo propter hoc.Posted by: Shplane, some shit in french
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July 24, 2010 8:47 PM
I would agree with you that it's absolutely shameful that evolution isn't being taught to our children properly, but then I remember that most people are far, far too stupid to understand the real thing.
Yes, the Standard Story is dumbed down, but it kind of needs to be. People would just stare at you and go "hnurrrrr" otherwise.
Posted by: Silič O'Nopolitanopoulos, Färschdbischuf Beesknees aus Ulm und Klein Elguth, Elector Pharynguline.
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July 24, 2010 8:47 PM
You're such a dick.
This makes it even harder to sum up Evolution in an elevator pitch.
Posted by: Thalamus
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July 24, 2010 8:48 PM
Recombination in meiosis, and sexual reproduction are the biggest source of variation within populations, but I think people tend to ignore them because the impression is that they aren't as dramatic (or as buzz-worthy) as mutation.
@Kel
One of the reasons is that small populations usually have a gene pool that is not representative of the larger population they have broken off of. If a small colony is founded by just a few individuals, those individuals will not encompass the full genetic variation of the species, and as such some alleles that are rare in the larger population may suddenly be instantly present in 100 percent of the individuals in the new population. In addition, some alleles present in the larger population will be missing in the smaller population. This is called the founder effect.
The reason mutations (or recessive or deleterious alleles) can move via drift easily in small populations is precisely because they are small. In sexual reproduction, there is a 50% probability that a chromosome (and the genes on it) will be passed to the offspring. However, this is not determinate, it is probabilistic. When you flip a coin, there is a 50% chance of getting heads, but sometimes you will get 10 heads in a row. Sometimes one allele will get passed on at a higher percentage than other alleles in it's series, simply because of stochastic processes. In a small population, because there are less individuals that make up the population, it is much easier for an allele to move to fixation via drift than it is in a larger population, where the probabilistic trend would have to go on much longer.
Posted by: DeusExNihilum
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July 24, 2010 8:50 PM
Thank you PZ for this article! My high school Biology teachers failed miserably at instilling much knowledge or understanding of Evolution (it was barely covered, and boringly so). To the point where, embarrassingly, I don't have the required knowledge to even understand this article fully :C
But it being put in fairly straight forward terms, presented in an enthusiastic way, really helps me (and no doubt others) understand an unmistakably inspiring, complex and important subject. Write more! Or let me steal you for private tutoring =D
Posted by: johnlil#0a224
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July 24, 2010 8:51 PM
Yeah, I admit that that was probably the general view I held of evolution.
It was probably a by-product of the gene that makes me able to spell "occurred" correctly.
Posted by: Pen
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July 24, 2010 8:56 PM
Well, the thing about the Standard Story is that it's a meme, if you like, that has itself evolved in the culture over time, and I'm afraid the more "complicated and interesting" version still has some work to do if it's to compete in that environment.
It's not even that people don't know any better (some of them anyway), it's just that the Standard Story has repeatability power. It's short, it's sweet. Kids can get it. Hell, even creationists can remember it. That's what you're up against.
Posted by: Cuttlefish, OM, CR
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July 24, 2010 8:58 PM
The emergence of some feature
Through selection of mutations
Doesn’t happen in one creature,
But across the populations!
Permutations, combinations,
Both additions and omissions,
Lead to phenotype creations
And their rapid acquisitions
Sometimes networks are redundant
And the extras act to buffer—
When mutations are abundant
We don’t always have to suffer!
And environmental factors
May give rise to phenocopy
Where the genes are not the actors
(Yes, it’s all a little sloppy).
So it seems that the initial
View of evolution’s liable
To be somewhat superficial
(Not as much, though, as the bible)
When the pressures of selection
Shape the feature’s distribution,
This determines the direction
Of the change called “evolution”.
(a bit more, at
http://digitalcuttlefish.blogspot.com/2010/07/evolution.html )
Posted by: https://www.google.com/accounts/o8/id?id=AItOawm4CYGXi1n4Armyc3H5WH0I3OSlKZ1Zvc4
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July 24, 2010 9:12 PM
Good explanation. However [as an evolutionary biology graduate student] I kind of thought it would be unnecessary; i.e. we all know that the 'simple explanation' is, well, simplified. From the many positive comments I see I was incorrect. Happily corrected. Out of touch, I guess, but then are not all graduate students 'out of touch'?. Keep up the good work PeeZed (that's Canadian for 'PeeZee')!
And get your book finished already! Jeez! And I thought I was a procrastinator... Oh shit! My dissertation is due within the week. What am I doing spending my time commenting?!? Arrghhhh!
Posted by: phylogenous
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July 24, 2010 9:12 PM
This post is a great example of my feelings that biologists are better off educating those that already accept evolution than trying to convince creationists of anything. I think the rewards will be greater if scientists focused on the former.
Funny that I was just thinking about networks while pondering how to write my blog post about how recombination has affected sex chromosome evolution. It's a complex topic but as you say, to ignore it renders evolution "superficial; it ignores the richness of real biology; it limits and constrains the potential of evolution unrealistically."
Great post.
-Kele
Posted by: Mattir-ritated
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July 24, 2010 9:14 PM
Yep, this is going into the homeschool biology curriculum. More like it would be great.
Posted by: cameron
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July 24, 2010 9:21 PM
Great post. Thanks for continuing to feed my layman's understanding of, and interest in, real science.
I will agree that the Standard Story you present is wrong, but I think it's wrong in the same way that Newton's understanding of how the universe works physically is wrong: it gets almost all of the story, but lacks the deeper layers of subtlety that have the most explanatory power. 99% of the arguments people have with creationists don't even require the more refined understanding of evolution, they can be dismantled just fine with the grade-school Standard Story.
Again, thanks for the write-up, I feel like my brain is larger than it was an hour ago!
Posted by: John Morales
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July 24, 2010 9:28 PM
Thanks, PZ. Informative.
(Thank you too, Cuttlefish).
Posted by: James F
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July 24, 2010 9:33 PM
Systems biology makes creationism look more mind-numbingly stupid than ever. Bravo, PZ, I hope that your book will include an "Evolution 201" section for the masses!
Posted by: RamblinDude
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July 24, 2010 9:42 PM
Man, I am gonna be so smart the next time I casually correct someone's mistaken notions about evolution.
Posted by: rturpin
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July 24, 2010 9:47 PM
Great explanation, but you left out the key thing: this all depends on sex. I think I'll link to your post under the title, "Why sex is important."
Posted by: jradxit
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July 24, 2010 10:04 PM
I just saw an x-ray in which the patient has small fifth and sixth ribs which decrease the diameter of his chest at these levels. This is almost certainly the result of a combination of gene alleles which, in isolation, result in little change but together have resulted in this particular deformity. Just happened upon this example after reading your post and thought I would share.
Posted by: cyan
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July 24, 2010 10:12 PM
rturpin,
No, its about mixin' genes together in novel combinations, then a change in the environment. Yeah, sex is one way to do do the mixing.
But a non-sexual way to do it has resulted in whole groups of organisms that are the most abundant on earth in terms of sheer numbers to be so very different that they've been classified into not just two different kingdoms but into two different domains.
We have more in common with eubacteria than eubacteria have in common with archaebacteria, where it counts, on the cellular level.
But sex is durned important to us, of course, so its phyllomorphic and metazoamorphic to say evolution all depends on sex.
...alright, fungimorphic, too.
Posted by: Lynn Wilhelm
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July 24, 2010 10:17 PM
Thank you for more education, PZ. Since I've been following you, Jerry and PT, I've learned so much (not to mention how much I don't know :-)) that informs my standard story.
One little thing I've trained myself to do is to say, "That's how it evolved", when my daughter (or anyone) asks why something is the way it is. I follow up with what I can, but I always recall that answers I heard to that question invoked a creator. You know, the typical, "It was made that way", or "That's how god made it". It's such a simple thing to do. My daughter will never hear such things from me.
Thanks to you for the verse Cuttlefish. Very good and educational in its own right. I'd comment on your blog, but it's a real pain. Won't you please get off Blogger?!!
Posted by: fernaldo
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July 24, 2010 10:21 PM
My kind of post, thank you PZ. I'd much rather read about this kind of thing than...
Posted by: Betelgeuse
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July 24, 2010 10:22 PM
Great post PZ!
I'm keeping that one on an easy reach shelf too, to use when its explanation time.
I can only hope that I'll be a tenth as clear.
Posted by: FossilFishy
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July 24, 2010 10:23 PM
Fuck yes! There's nothing better than to learn something demonstrably true on a Sunday afternoon. Thank you, thank you, thank you, PZ.
And a big thank you to Cuttlefish too. Once again you've proved that science can beget art.
Posted by: humanizzm
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July 24, 2010 10:28 PM
This is the kind of post I come here for. I love it when i leave this site not with a mere "yeah, he's right" in mind, but a "wow, I learned something" instead.
When I thought about what the mistake could be in the first paragraph, "well, it's dumbed down" was the thing that came to mind. But still reading the rest of the post shifted my perception of the scope of things quite remarkably. I had no idea that serious changes in drosophilia can be brought about in as little as 20 generations, and the complexety and variability of networks was something that I never gave a lot of thought.
Thanks alot! Consider this bookmarked for re-reading, spreading and referral.
Posted by: John Morales
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July 24, 2010 10:33 PM
[OT]
Lynn @34,
Kudos.
--
Similarly, I dislike 'creatures' (and typically use 'organisms' or 'animals' instead).
Not 'creation', but 'the universe'.
Not 'blessed', but 'fortunate'.
Etc, etc.
(Yeah, I buy into a weak form of Sapir-Whorf)
Posted by: Dave A
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July 24, 2010 10:36 PM
Thank you so very much for your work and your time. Thank you for the support that you give us all.
Posted by: chemicalscum
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July 24, 2010 10:47 PM
Funny, just before opening Pharyngula I was reading a paper by Pete Saunders where he discusses this very point and Waddington's work together with the phenocopy phenomenon:
"Darwinism and Economic Theory"
In Sociobiology and Bioeconomics (ed P. Koslowski). Springer, Berlin, 1999, pp. 259-278.
He emphasises that the genetic networks form non-linear systems but then he is a mathematician.
I found the paper on his KCL website:
http://www.mth.kcl.ac.uk/staff/pt_saunders/HANNOVER1.pdf,
Posted by: Sal Bro
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July 24, 2010 10:47 PM
THANK YOU for this, PZ. Even those of us who've had Evolution 201 need reminders, like this one, to drown out the overly simplistic noise.
Posted by: firebird
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July 24, 2010 10:51 PM
While I enjoy the takedowns of idiots, not least because sometimes I might not understand what they are doing wrong till it is pointed out, and then when I see it it can be very funny (and obvious), this post is very helpful and partly why I added this blog to my RSS feed.
I was raised in a fanatically, obsessively, psychotically Christian home, homeschooled in a religious curriculum. I may still own a couple AIG published books (I'll have to check) and I've been to one of their weekend "education" conferences as a teenager. All of that is to say that I am so ignorant I'm not sure I grasp the simple version, although I was happy to try wrapping my head around the broader version. Having heard the simple version only as a straw man argument from creationists, I appreciate learning about how evolution really works.
Posted by: McCthulhu is taking ∞ to eat all the pi
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July 24, 2010 10:54 PM
The EGF Pathway diagram is proof of the existence of the FSM. His noodly appendages are everywhere!
Posted by: rturpin
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July 24, 2010 11:05 PM
Well, you're right, Cyan. And the fascinating question is how that transition was made.
That said, I'm a metazoaphile.
Posted by: Glen Davidson
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July 24, 2010 11:08 PM
Depends on whether it's considered a summary explanation, or if it's presented as a fairly adequate explanation.
Takes a long time to cover it adequately, as this post shows.
Glen Davidson
Posted by: Sven DiMilo
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July 24, 2010 11:15 PM
Biology is always more complex than you think.
Posted by: John Morales
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July 24, 2010 11:16 PM
[meta]
firebird, you hearten me.
I suggest you might consider following the category tags at the top of the post, there're many many good posts like this in the archives.
Posted by: Nerd of Redhead, OM
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July 24, 2010 11:18 PM
That is why when folks ask about evolutionary pathways and describe several, and then ask which really works, I just say yes to all.Posted by: pjzen
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July 24, 2010 11:35 PM
Thank you PZ. I learn more about about biology reading your blog than I ever did in school. Of course I went to mostly private religious schools, and then their were the dark ages spent in the Utah public school system. I don't remember them teaching biology. They did have an animal husbandry class. I skipped that one.
Posted by: Bueller_007
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July 24, 2010 11:40 PM
tl;dr
Suffice it to say that genes interact and when you consider the 'environment' or 'ecology' in which genes are selected for/against you have to take into account the relative frequencies of other genes in the gene pool, their linkage to the gene of interest, the nature of the interaction, etc. Effects like pleiotropy mean that the interactions are rarely simple, and of course a change in environment can change the way in which genes interact.
This much was obvious, I thought. You'd even get a very basic grasp of that from Dawkins's rowboat analogy in The Selfish Gene, which is probably the progenitor of the "standard view" among laypeople.
Posted by: Kel, The Privileged View From Nowhere
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July 24, 2010 11:52 PM
So you're saying that Biology doesn't pass Occam's Razor? ;)Posted by: frustum.myopenid.com
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July 24, 2010 11:54 PM
On the section describing Waddington's experiment, while it is new to me, I'm not at all surprised. Years ago it was explained to me that when doing selective breeding, the trait being emphasized will quickly reach a plateau, and new stock has to be brought in to allow eventually reaching higher peaks. That is, the new stock isn't just to avoid the problems of inbreeding, but it is a necessary part of being able to breed for a trait.
This was all known for centuries by farmers, so I'm not sure why Waddington's result is controversial.
Posted by: octopod
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July 25, 2010 12:52 AM
Sometimes I worry whether even most paleontologists really understand this kind of stuff.
Posted by: John Morales
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July 25, 2010 12:53 AM
Bueller_007,
You thought wrong, and this was precisely PZ's point in the post — that many of those who don't dispute evolutionary theory are nonetheless unaware of its minutiae.
Posted by: Brainy Jello
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July 25, 2010 12:58 AM
A summary, by its nature, isn't complete. Even PZ's improved description isn't "complete," as no such work could really exist.
The Biology 101 example is less accurate than the 201, and it's also much shorter. PZ - what's the simplest conceptual model of evolution that you'd be content with the public having?
Posted by: hyoid
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July 25, 2010 1:02 AM
Thanks PZ! That was very helpful! I'm sure you just added, at least, 48 hours to my life span! My brain is all tickle-ly inside from the sudden rush of newly motivated synapses!
Posted by: Phro
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July 25, 2010 1:04 AM
Thanks so much for this post! I feel like I learned more in his one post than I did from my high school biology teacher. (I suspect he was a creationist, but fortunately he never mentioned it in class...)
More please!!!
Posted by: John Morales
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July 25, 2010 1:14 AM
Phro, cf. #48.
Goes for you, too.
Posted by: DLC
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July 25, 2010 1:14 AM
Why evolution can't be true
it can't account for me and you
for being different yet the same
as those apes with hairy manes.
descendant of primates just doesn't please us
therefore we ascribe it all to Jesus!
(with all due apologies to real poets like cuttlefish -- I'm much more Poe than Poet )
Posted by: natural cynic
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July 25, 2010 1:29 AM
Kel @52
So you're saying that Biology doesn't pass Occam's Razor? ;)
Occam's razor us qualitative, not quantitative. It says that the correct answer is most likely no more complex than it need be. All that is needed is the simplest explanation that takes into account all of the contributing factors. Contributing factors can be any number.
Great post, PZ.
Posted by: Roger F
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July 25, 2010 1:40 AM
.. and the one thing you didn't talk about was the fact that this is one way to look at the differences beteen sexual and asexual reprodution. It is often not understood why sexual reproduction is so much more powerful than asexual reproduction. The concept of variation with in a population gene pool and the shuffle of combinations only really applies if individuals sexually reproduce (or exchange genes in other ways).
I'll stop short there, but this would be a good blog top. Many books / biologists fail to capture the benefits of sexual reproduction (apart from the obvious joy of ..x)
oh and when you've done that how about symbiotic "borrowing" of genes. My fav is Elysia chlorotica.
Posted by: the__eye
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July 25, 2010 3:01 AM
*applauds*
Excellent post! Over the past three years as a zoology undergrad, I have been rapidly realising that evolution is so much bigger and more complex than I ever imagined, and more beautiful as well! It makes me wish the whole world could understand evolution in all its depth and beauty, and it really makes me pity creationists who, by choice, won't even begin to comprehend the simplest version of evolution.
Reading this post made me all fuzzy and happy inside. =)
Posted by: Glenn G
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July 25, 2010 3:24 AM
The funny thing is that I'm actually about to start my second year of evolutionary biology
and that simplistic "evolution 101" understanding at the beginning of the article applied to me :P
Posted by: dvizard
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July 25, 2010 3:39 AM
Uh, oh. You are gonna bring out that creationist who was trolling here, I think, maybe a year ago, who argued that pre-adapted genes were a result of design and the traits actually showed up before they were used, thus, of course, disproving evolution... (or did I read him on some other blog?)
Posted by: FrankO
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July 25, 2010 4:12 AM
This is a great post, PZ. Readers of Dawkins's early books should already appreciate clearly that evolution depends on population biology and gene networks: he really sets out this stuff with enormous clarity.
Two comments. The first is that this post should be mandatory reading for science journalists. They rush to repeat PR hype from universities that a scientist has found/will find the gene for a disease, and that will give us new drugs. Since the genetic role in disease is most often a consequence of the kind of subtle and complex events your post describes, having genomic information will not lead to anything of the sort in most cases. Genomics is just a tool, as PZ pointed out a couple of months back.
The second comment concerns mutation. We still think of mutation as a point phenomenon, affecting single bases. But — particularly in the microbial worlds, which PZ recently said he's learning to love — gene changes can often involve reassortments and rearrangements of whole chunks of genes. Many asexual fungi seem to cut and paste bits of genome as a means of keeping busy. We need to move away from regarding point mutations as the sole source of biological change.
Posted by: pallabbasu
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July 25, 2010 4:45 AM
Hummm...
learned something new !
Posted by: Stephen Wells
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July 25, 2010 5:13 AM
Simplest model the public should have:
"It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the external conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved."
Darwin, 1859 :)
He was a bit wrong about "use and disuse" but hey, cut a guy some slack.
Posted by: Donald Oats
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July 25, 2010 5:29 AM
And then there are copy number effects, where multiple copies of a particular gene occur along the DNA of a chromosome. A classic example is with the metabolism of codeine into morphine, which involves several steps and several different enzymes. There is one step in particular which has only one path, only one enzyme can do the job; without that step, a person's liver cannot produce the morphine from codeine at all. Extensive metabolizers are people who have a single copy (per strand) of the gene, and a good allele at that locus - typically. Poor metabolizers have one of the many dud alleles at the locus of the gene; about 7% to 10% of Caucasian people are in this category. Now to the crux of the copy number effect. Ultra-extensive metabolizers typically have multiple copies of the gene along the DNA strand, and typically have the efficient alleles at each of those gene loci. These people can be killed, or at least given a nasty trip, with a single panadeine pill (acetaminophen 500mg + codeine 8mg). The higher the copy number, the higher the production rate of the essential enzyme from the genes, so these ultra-extensive metabolizers get all of the morphine from the codeine extremely rapidly, compared to Joe and Jane Average. Since codeine is rarely consumed in the natural environment, such copy number variants of the gene would have been benign in the past. But not now.
Ain't evolution and natural selection grand?
Posted by: KingUber
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July 25, 2010 5:46 AM
Thanks for explaining that fruit fly experiment, a creationist once told me about it a while ago and said it disproved evolution.
Posted by: jasonandrewdasilva
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July 25, 2010 5:47 AM
Wonderful post, PZ. I thoroughly enjoyed it.
Posted by: jack.rawlinson
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July 25, 2010 6:37 AM
Love the poker analogy. I'm nicking that. :-)
Posted by: Maarten
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July 25, 2010 6:59 AM
Two comments. First comment: good contribution for those who like to know more about the subject; it's truly a good 'biology 201' introduction.
Now for the second comment: I'm not really sure about holding against the original simplification that it is just that: too simplified. If I draw an analogy to a subject which I hold dear (chemistry), then the simplified story would be about there being several kinds of bonds between atoms: ionic, covalent, perhaps atom too. Every chemist knows that this is a gross oversimplification: there's metallic bonds, and hydrogen bonds, and pi-bonds, and all that funny lanthanide business, and ... hell, the entire concept of a 'predetermined type of bond' is flaky to begin with as it all comes down to the various subtleties of orbital electrons of different atoms combining into newer structures. That this yields a more powerful view of what exactly goes on between atoms is clear as day; the question is then whether or not it is suitable for general consumption. (That would make for an interesting experiment in teaching, by the way.) I'm under the impression that something quite similar is present in this case, too.
Posted by: David N
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July 25, 2010 7:03 AM
OK, PZ, I'll bite (not having read the rest of your post), and by your standards I'm probably on Evolutionary Biology 101 (UK not US but I'm pretty sure I know what you mean).
Looks OK so far Not so good; mutations can be disadvantageous as well, surelyOr not, as the case may be (vide supra)
Presupposing that a larger brain is an advantage - needs to be demonstrated? [spelling police]Yes, very queasy[/spelling police]
OK, now I'll go back and read the rest of your post. Any corrections welcome
Posted by: John Morales
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July 25, 2010 7:09 AM
David N:
Do you include self-corrections in that invitation?
If so, I urge you to take advantage of it.
Posted by: MrJonno
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July 25, 2010 7:09 AM
Think PZ Myers is being a bit harsh. If you teach a complex subject that is absolutely nothing wrong in simplify it and possibly mention that it is not the whole story.
You don't teach the basic structure of the solar system and then suddenly jump in Einsteins theory of relativity or start going into gravitons or the fact that the sun is also moving.
For anyone who isnt a biologist by career but wishes to come across as a well rounded educated person then random mutation under natural selection quite sufficient. If you want to study it more then great.
Its a bit like someone bring up in a random conversation that the Earth isnt a sphere its an oblate spheroid. It doesnt make you a better physicist or geologist it makes you a bit of a twat given the context
Posted by: maureen.brian#b5c92
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July 25, 2010 7:15 AM
Just one correction. Read the post, then comment!
See especially the bit with the sub-head Think populations
Posted by: John Morales
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July 25, 2010 7:16 AM
PZ: Most of you don't understand evolution. I mean this in the most charitable way
MrJonno: [I] Think PZ Myers is being a bit harsh.
Perhaps, MrJonno.
Harsh but fair, or harsh and unfair?
That is the question.
(i.e. is PZ wrong?)
Posted by: KG
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July 25, 2010 7:19 AM
MrJonno,
I disagree. PZ is pointing out a fundamental misconception - that evolution is about individuals, when it's about populations - akin to thinking that substance have the colours they do because each individual molecule is that colour.
Posted by: maureen.brian#b5c92
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July 25, 2010 7:31 AM
Mr Jonno @ 76,
It is not Evolutionary Biology 101 you want but Literacy 101.
When PZ posts on something those of us last formally taught science in 1956 are going to find a bit challenging he carefully flags it up - see above. We then have the choice of reading or not reading. Or, sometimes, reading it,almost understanding it and being completely unable to explain it to anyone else. A common occurrence in these parts.
If PZ were to reduce this particular post to the level of simplicity which required no effort at all from you then
* there would have been no point in writing it at all (it i about one of the levels of complexity beyond the simple formula Mr Darwin came up with)
* those of us who do not subscribe to the theory the human brain will wear out if you use it would be deprived of an opportunity to learn.
And, no! I do not completely understand it and I am wonderfully untroubled by that.
Posted by: David N
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July 25, 2010 7:42 AM
@JM #75
Yes, working on it. To clarify, I have no doubts re evolution as the reason for why we have what we have. However, I don't see any specific problems with what I said in #74 (although I should have referred to neutral muatations explicitly, perhaps; I think it was implicit). I may be about to get a lot of crap about being accommodationist or whatever the current buzz-word is, but bottom line is that if you can get most people up to Evolution 101 that, surely, is progress. (Is everyone up to special relativity 101 or Green's functions 101? No chance.) Yes, I know (believe?!) that it's not as simple as 1 gene different = 2 cm height difference but I'm not sure that the emphasis is entirely appropriate; with PZ talking about populations, is he in danger of misleading re how selection works?
Anyway, I'm working tonight so need to get some sleep; will check in later.
@MB #77
More fun to comment and to try to work it out first without being much beyond 101?
Posted by: David N
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July 25, 2010 7:48 AM
Oops!
[spelling police re #81] mutations, not muatations[/spelling police]
Posted by: Kel, The Privileged View From Nowhere
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July 25, 2010 7:55 AM
If those same oversimplifications are at the heart of the arguments of so many who reject it, then I don't think so. It's important to properly understand the process because there are those who prey on the misunderstanding to promote a different agenda. Yet if there was a concentrated number of people who made issue around a geocentric earth and shunned relativity because of popular yet incomplete to the point of misleading understanding, then surely we could see the value in promoting a proper understanding. Think of the thought experiment involving the man in a moving train, have you heard the "what about a 3rd observer?" objection? If this objection were the focus for a widespread rejection of relativity, then surely it would be good to correct that naive understanding which leads to problems. But it isn't an oblate spheroid... don't you know there are mountains and valleys? ;)Posted by: Michelangelo
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July 25, 2010 7:57 AM
Well done!
Posted by: Kel, The Privileged View From Nowhere
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July 25, 2010 8:02 AM
And because it needs to be done: XKCD!
Posted by: stasiu88
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July 25, 2010 8:05 AM
The other common misconception about evolution is thinking, that "survival of the fittest" means "survival of the fittest organisms". No, it doesn't, all organisms eventually die. It really means "survival of the fittest genes" – the organisms are just by-product of the most evolved DNA.
Posted by: Dave_SE20
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July 25, 2010 8:47 AM
Many thanks for this clear explanation, PZ. I've just realised I've been misunderstanding genes, mutations and evolution.
Posted by: jcbmack
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July 25, 2010 9:14 AM
Sensible professors teach this in freshman Biology. Mine did. With introns discussed in a 1985 textbook the Microbial World as more than "junk DNA" and alternative splicing already hinted at back then in the same textbook it amazes me that more biology professors do not teach these basics in first year biology. The school I went to back a few years a minus a degree or two was Nassau Community College. I do enjoy your work PZ, however, this kind of stuff needs to be taught early as it is very fundamental early undergraduate material meant to form the foundation for future learning.I am glad that this blog shares such basic and vital information. Basic research and data that comes out of it needs to be disseminated freely and openly to educate the masses even if many will not listen at least they cannot accuse biologists and scientists in general of being elitists.
Posted by: DN King
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July 25, 2010 9:14 AM
Thank you for that nice breakdown. It also makes me happy in an ego-stroking way. Since reading your blog, Dawkins's blog and books, Dennet's books, and more, I have begun defining evolution as:
"An accumulation of mostly ambivalent genes that spread through a population creating genetic diversity that then enables a population to adapt through natural selection when conditions change. No genetic diversity, no evolution. No living thing can adapt by mutation after the environmental change, if that change is significantly crippling to the existing genotype/phenotype, which causes extinction events."
I'm still lacking much of the story, as you pointed out, but it is comforting to read that I have been learning from you and some Horsemen, and I am training my biology student mind in the right direction. Especially since I just had a minor argument with my entomology professor about specialization using this model to back my argument.
Posted by: jdifeo
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July 25, 2010 9:42 AM
Reminds me of synergy, the whole is greater than the sum of the parts...
Posted by: https://me.yahoo.com/a/3z7tDlkFvJnlvQqMIixgnfyQOWkH3QNjWw--#ffe82
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July 25, 2010 9:53 AM
This. It's at this very first hurdle- what Ernst Mayr called "population thinking"- that most people, eve most biology students, already stumble. Without a firm grasp on that there's no hope of understanding the significance of the other things PZ discusses above. The "man in the street" picture of evolution is NOT just a simplification, it's a profound misunderstanding.
Steve LaBonne
Posted by: Pen
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July 25, 2010 10:20 AM
Perhaps you're all too young to remember the 'adaptive at the population level' debacle, in which individual organisms cheerfully strove and sacrificed themselves for the greater good? I'm old enough to be cautious when I hear the word 'population'. OK, so evolution (the result) happens at the level of populations, no argument about that, but how easy is that to confuse with selection happening at the level of populations? Especially for the untutored.
Posted by: evogene
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July 25, 2010 11:12 AM
I really liked this article. It reminds me of some of the opposition that gene-based evolution gets, not only by Prof. Myers, but by Prof. Massimo Pigliucci as well. I wonder what Prof. Dawkins thinks of this point of view - if you want to call it that -. I have a question about speciation in this context, if in the case of sympatric speciation a particular adaptive mutation occurs in a population, how does natural selection ensure that this allele, that could give rise to a new adaptive trait, is expressed? It could well be that its interaction with other alleles makes it incapable of expressing a phenotypic difference that increases its Darwinian Fitness.
I am sorry if this question sounds like a silly question, but I am starting to do evolution 201 and I could use a clarification.
Posted by: Rik G
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July 25, 2010 11:20 AM
Thanks for the interesting post. I was already familiar with the concepts, but appreciate the clarification. Now how about a post on horizontal gene transfer? That's another concept I'm familiar with, but would like to understand better. You're on a roll, Professor; keep up the good work!
Posted by: MultiTool
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July 25, 2010 11:27 AM
By sheer coincidence, I've been writing a genetic algorithm where each creature's genome is a network (matrix) and each 'gene' is a node of that network (row of the matrix). When creatures have sex they exchange matrix rows.
Their genes are turned on only by other genes (the matrix feeds back on itself), and only ONE gene out of the whole bunch gets to express itself phenotypically. So all the genes of a creature live or die together depending upon how they express themselves through that one output gene.
For now, creatures are scored on how well that one gene turns on and off in imitation of a simple rhythm I made up.
What's interesting is that I set the mutation rate really high - HALF of all children are mutants, but once the population 'gets it' and individuals produce the exact desired rhythm, nearly all of the creatures score 100% correct even though half of them are freshly mutated.
What this implies is that the network-creatures have also evolved a robustness against mutation - most likely by accumulating many redundant node-genes.
My master plan was to make a game sort of like space invaders, except that all the aliens you don't kill get to have children who attack you more effectively than the previous generation...
Posted by: Tulse
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July 25, 2010 12:10 PM
Gould also emphasized the centrality of variance across a species, rather than looking at the species as a mean represented by some idealized individual. Species aren't one "thing", they are a collection of individuals, and such individuals vary.
Posted by: Sven DiMilo
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July 25, 2010 12:13 PM
Oh, this is only slightly less simplistic than your original formulation.
No gene is an island. The "fitness" of a particular allele is vetted only in the context of its phenotypic expression as part of an integrated organism (including all of the other alleles that contribute to the integrated phenotype) living in a particular environment (which includes both biotic and abiotic components).
Organisms matter. Adaptive evolution--i.e. the part that involves selection--is about organisms and gene combinations interacting within populations. Individual genes, not nearly so much.
Posted by: Citizen of the Cosmos
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July 25, 2010 12:30 PM
Awesome post. But I'm not going to lie - I will have to read this one again. :)
Posted by: Sven DiMilo
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July 25, 2010 12:35 PM
It's complexity all the way down, I'm afraid.
actually, no, I'm delighted
Posted by: P_Smith
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July 25, 2010 12:58 PM
One of the best descriptions of natural selection I ever heard of came from the cheesy 1980s TV series, "Night Heat". The newspaper reporter / narrator of the show said, "It's not about survival of the fittest. It's about who can survive on the least."
It's not always the biggest, fastest or strongest, but those that can find enough to stay alive, and that's probably true in evolution.
Posted by: Moveable Type
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July 25, 2010 1:22 PM
Thanks PZ, I haven't been called a bright young student for over 45 years. And, if I being honest I wasn't called a bright young student then either.
Well, thanks anyway!
Posted by: Sven DiMilo
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July 25, 2010 1:32 PM
Except when it's not. Or when it is. Different organisms, different environments, different pressures.
Another thing worth keeping in mind: selection is measured in units of reproduction, never survival per se.
Posted by: Sven DiMilo
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July 25, 2010 1:34 PM
Posted by: Aratina Cage
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July 25, 2010 1:44 PM
KG #79,
At first that seemed opposite to what Jerry Coyne wrote in "For the good of the species":
But now I am thinking that the difference is that PZ is talking about evolution in total while Jerry Coyne was talking about selection, an integral part of the process of evolution rather than the entire process itself, or did I just fail Evolutionary Biology level 201?
Posted by: Sven DiMilo
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July 25, 2010 1:54 PM
Selection "acts on" individuals: some leave more offspring than others in their population, sometimes/often/always (in part) for cause.
Evolution by selection happens to populations, as allele frequencies in the gene pool shift over generations because of the differential reproduction for cause.
Basically, Coyne is separating the causal mechanism (individual [reproductive] success) and the caused effect (evolution, i.e. "the spread of the genes [in the population's gene pool]".
Posted by: Kagehi
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July 25, 2010 2:16 PM
Unfortunately, this is in some respects a bad example. Unfortunately, the internet "was" intelligently designed, by a bunch of people, most of them having never bothered to follow the specifications, with the bizarre result that a connection can go down in LA, and, if you are in Arizona, you can't get to a server in Central Valley from there, but you can get to some place in Europe, since *both* go through LA, but someone severed the connection between northern and southern California, but only for people *outside* California, and south of Wyoming...
Sadly, what should have automatically "fixed" problems has turned into a damn mess that takes hours to work out something is wrong, and depending on how and *who* optimized it, can simply give up, having no bloody clue, and getting no help from the rest of the network, to re-route some connections.
Posted by: https://me.yahoo.com/a/tL1MkU0ghY0gNMrxrvSjJFsEYJYQ0ZIPjQ--#5f870
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July 25, 2010 3:00 PM
A new baseline for understanding? Bring it on!
Admonitions are beside the point. If a better base level of understanding is required, what gets incorporated into pedagogy? What do you tell your beginning wannabe biologists? I assume that what you've written here is a first draft at providing it.
Without good models, explanation stagnates. Experience — and that includes the highly refined experience produced by experimentation — must be ordered and logically related according to schemas.
Will network theory adapted to biological explanation provide a simpler and more inclusive way of organizing known interactions than its legitimate competitors? What unexpected testable predictions do its models make?
At the same time, it would be interesting to know how sophisticated network theory had to become to be a mathematical tool of sufficient power to be "thinkable" as source for a metaphorical transfer to biological explanation.
However, no model is true -- a fixation on “truth” is an almost unquestioned perversion of western thought by platonizing xians. What matters is increased informativeness which would include "predictions" (logical inferences made from the model) which can be tested.
the anti_supernaturalist
Posted by: entropia
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July 25, 2010 3:54 PM
Selection and recombination of variants after selection make use of pre-existing variation, which comes from mutations that, without the selecting environment, would pass unnoticed. This is fine. Introducing networks later is useless to make this point. Sure, networks change the shape and the extent of expression of variants (buffer both, up and down, depending on circumstances), but there is no need to introduce networks for understanding these experiments, nor for explaining the need to think about pre-existing variation, and of how effective can recombination be to potentiate new phenotypes (by combining different selected variants) when thinking evolution.
Networks are interesting, important, and have their effect on the shape of evolutionary histories. But are to be introduced at the proper stage.
If we wanted to introduce the concept of variation/selection/recombination to a creationist, introducing networks too is useless and noisy. It complicates the story beyond necessary.
Of course, my comment is nothing but an opinionated opinion coming from the trenches of teaching undergrads, and also from explaining the concept to creationists. Keep it simple enough. Introduce complexities only when ready and necessary.
Posted by: lautrec85
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July 25, 2010 5:42 PM
This very post could be used as a critique of Dawkins' main ideas about evolution:
- Selfish genes: Actually, genes have to collaborate in order to make copies of themselves in the host's offspring. A selfish gene which spoils the network he works in won't make it, so natural selection can't tell this gene apart from this gene and select it individually. Natural selection has to take or leave the whole thing, ie the individual.
- Extended phenotype: Individuals are not passive actors being pushed around by the environment; they modify and create their own environments. ALso, there's no gene "for" one particular behaviour. Thus, complex behavioural traits are the result of complex genetic networks being expressed in a phenotype that interacts actively with the environment. So we have a phenotype expressed by complex genetic networks working together and a bunch of interactions between the genes and between the expressed phenotype and its environment. Do you know how we use to call that? Individuals.
I think Dawkins famous persona has a lot to do with this simplistic version of evolution that a lot of for-science people hold.
Posted by: Aratina Cage
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July 25, 2010 6:10 PM
Thank you Sven DiMilo for the response (#105) about individuals being selected versus populations evolving, one being the causal mechanism the other being the effect. My own understanding of the word "evolution" is probably way too loose and may be what is causing me to be confused.
Posted by: entropia
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July 25, 2010 11:05 PM
Hey lautrec85,
I think you might have gotten it wrong. I have not read the extended phenotype, but I read the selfish gene (30th anniversary edition), where Dawkins also talks a bit about the extended phenotype.
For your complain about the selfish gene. Do these genes cooperate in networks and such and get no benefit themselves? In other words, they might have to collaborate, but they would not if they did not survive, right? Thus, that would not be altruistic behaviour. There are also many examples where the best explanation is "selfishness." Not a conscious selfishness, of course, but that the best explanation for some gene function is the benefit for the gene itself, rather than for the organism. So, selfish genes might not be the best explanation for everything evolution, and genes might not be the main beneficiary for natural selection, but there seems to be room for selfish-gene explanations.
For your complains about the extended phenotype. Well, Dawkins, in the selfish gene, goes long explaining that "genes for xxx" is an oversimplification. You seem to have it wrong about its meaning, because extended phenotypes are about effects of a gene in one organism affecting the environment, and affecting other organisms. Thus the qualifier "extended." So, I don't understand your complain. It does not seem to contradict what the extended phenotype is about.
Of course, Dawkins explanations go into so many complications, that it is easy to be mislead. I had to read the selfish gene twice in order to get it. (I might also be a bit slow).
Posted by: CherryBombSim
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July 26, 2010 12:02 AM
This was a good post. It might clarify for some people what the difference is between sorting and mutation, and how both are operating. Every once in a while, I come across some piece that claims to have discovered "rapid evolution" in a species subjected to some environmental change, and they never clearly explain that what is happening is that genes that already exist are being sorted; many readers are left with the impression that genes must be mutating at a furious rate to optimize adaptation.
Posted by: bcdurden
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July 26, 2010 8:30 AM
Wow, I'm blown away. Has anyone here dabbled in AI neural networks before? This is strikingly similar; in fact, I'm having trouble finding differences!
I should have figured it out a long time ago when I discovered for myself what genetic algorithms were.
Posted by: lautrec85
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July 26, 2010 9:00 AM
entropia,
"they might have to collaborate, but they would not if they did not survive, right? Thus, that would not be altruistic behaviour."
I didn't say altruistic, I said collaborative. I'm sorry, I think that "they collaborate, therefore they are selfish" is word twisting. If you want to say it, ok fine, but the point is that organisms do what is best for themselves, not for their genes. Genes aren't the unit for selection. Dawkins says "We are survival machines-—robot vehicles blindly programmed to preserve the selfish molecules known as genes." Well, no. Every organism is a lot more than that.
"extended phenotypes are about effects of a gene in one organism affecting the environment"
Yeah. And the vast majority of genes work in collaboration with , so you almost never can state the effects of "a gene". The expression of a gene is always affected by its genetic context, that is, the rest genes it works with, and the interaction of the phenotype with its environment. As PZ said, "the same allele can have different consequences in different genetic backgrounds". Think networks.
Posted by: https://www.google.com/accounts/o8/id?id=AItOawnG39uMFt69kwCKZ8DoxtmMCvmzr5chx94
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July 26, 2010 9:23 AM
OK. I think I see the point.
Next! How many here believe that Big Bang was an explosion? How many believe that it started at a point and expanded outwards in some sense? That is totally wrong. Really totally wrong, from a cosmologists point of view...
Anyway, thanks for these explanations! Expected more like that from Dawkin's "greatest show.." and must say I am a little disappointed, but I think there is more about it in some of his other books. Would actually like to see more about the math and theory e.g. on that "fixation".
Posted by: eyespy
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July 26, 2010 1:45 PM
"That is awesomely complex, and yes, if you're a creationist you're probably wrongly thinking there is no way that can evolve."
The only way something gets that pointlessly, ridiculously complex is if it evolved.
If you're god or jeebus and you're sitting around looking for a way to get EGF into the body, I would think creating something as tangled and illogical as the EGF pathway would be impossible to conceive for a perfect, omniscient being.
I would think they would just have the brain say "MAKE EGF GO NOW" and poof! there'd be EGF.
In fact, the need for EGF itself is needlessly complex. Why doesn't the brain just say "MAKE SKIN GO NOW" and poof! there's skin?
Finding proof of creation in complexity is such a fundamental denial of basic facts and logic I cannot get my head around the cognitive dissonance.
Posted by: hkdharmon
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July 26, 2010 2:02 PM
Thank you PZ. You have just greatly increased my previous understanding of evolution. I am going to have to think about this a lot to get the concept down.
I previously thought I had a fair handle on it for a non-scientist. But NOW I will have a fair handle on it for a non-scientist.
Posted by: entropia
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July 26, 2010 10:17 PM
Hey lautrec85,
But the opposite of selfishness is not cooperation, but altruism. This is the point. The point is not they collaborate thus they are selfish, but that collaborate does not preclude selfishness. No twisting, rather trying to untwist that confusion.
Then you add that other part which is not what you said initially. Of course organisms might do what is good for themselves, but it does not always look that way. If you moved the target to "what is good for its genes," you would include most of what is good for themselves (because the genes are part of the "themselves" bit), and other things that don't seem quite right with "what is good for themselves." But fine, I said that selfishness might not explain everything, but that there is room for selfish-gene explanations.
Then, of course you can talk about effects of "a gene." After all, it does not matter if we see the effects within/thanks-to a network. We might as well bother to talk about the effect of "a gene" given the network, or else in the organism and/or beyond it, thus obviating the network. The idea is about a gene or a set of genes affecting stuff beyond the organism where they reside (not directly necessarily). The interdependencies of such genes for having their way does not make the idea of effects beyond the organism where they reside wrong. Note too that for Dawkins "a gene" is not "one-gene-one-protein," but a DNA/chromosome/hereditary material segment that survives long enough to recombination to be an object of selection (might need a bit rethinking though).
Thus, I don't see cooperations and networks being precluded from selfish explanations. I don't see them contradicting extended phenotypes either.
Again, not that they explain everything, but there is room. A lot of room. Again, I said it is not easy to grasp, and taking a few bits/summaries here and there does not do justice to the explanatory power of the selfish-gene idea. Dawkins style does not help a lot either. I will check if the extended phenotype is in the library.
Posted by: entropia
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July 26, 2010 10:22 PM
A book that started me re-evaluating the selfish gene theory, and better understanding it, was "genomes: the autobiography of a species in 23 chapters" by Matt Ridley. After that I read the selfish gene for a second time. It made better sense.
Posted by: jaybgee
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July 27, 2010 8:31 PM
Great blog post. Sounds like a lot of positive feedback in the comments. I think most lay people are interested because they get so little of it. Hope you'll post more on basic biology. (I'm a bio major, but my job isn't really related to my study, so it's always nice to brush up on the basics.)
Posted by: dorght
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July 28, 2010 4:26 PM
Years ago as I read "Climbing Mount Improbable" I kept thinking this is too simplistic, genes aren't lone agents. PZ eloquently put a rational basis to my sketchy objections.
Posted by: azumahazuki
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July 29, 2010 10:04 PM
PZ, you ROCK. This is why I platonically-only-since-I'm-a-dyke love you.
Hard science. HardCORE science. Cutting-edge science. Explanatory science. Cutting through the soundbites that even the best and most well-intentioned people have internalized. I'm a geologist, not a biologist, so I had only a suspicion of the concepts you've enumerated here. You've explained like a zillion hours' worth of cognitive stalemating and introduced things, fundamental things, that I plain old DID NOT KNOW.
It's too bad you can't bronze a web forum post :)
Posted by: Julian Hart
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August 4, 2010 6:10 PM
PZ
You might find this new thinking of particular interest. It represents the generalisation of Darwin's thinking to include cooperation as well. It is presented through the lense of human society, but can quite obviously be generalised to natural systems. Indeed, evolution is very definitely much more than genetics.
http://www.scribd.com/doc/32856404/The-Origin-of-Man
http://www.scribd.com/doc/32852505/Theory-of-Social-Interaction
Posted by: Ezequiel
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August 9, 2010 6:51 AM
This is one step more to understand the biology complexity, but you do not have problems with creationist people,your dificulties deal with to understanding God´s nature. By the while you are only a drop in the vast ocean, one net increases the strenght, but the evolution theory o maybe the evolution only, does not have any force as the same way, no direction neither .
Posted by: htomfields
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August 23, 2010 5:05 PM
Researchers at INL are defining natural adhesive systems at the molecular scale and are exploring ways to recombine proteins to improve adhesives. Such new adhesives may more strongly bond to a wide range of materials and do so in an environmentally friendly and safe manner.
http://www.inl.gov/research/natural-adhesive-systems/
Posted by: Malachi Constant
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August 31, 2010 2:08 AM
I'm so late to this party, I imagine you, PZ, won't see this comment.
I'd just like to say that this post has given me a wonderful perspective on evolution just as I recently started reading Dawkins' "The Greatest Show On Earth".
It allowed me to see and understand some shortcuts he took while explaining the evidence for evolution and also to understand some of the subtler conclusions he was drawing, while he was still speaking to a lay audience.
I always appreciate being enlightened about what I don't know (though it can be embarrassing). It gives me a framework to understand what I'm being taught that I otherwise wouldn't have understood.
Thanks, and I think I understand evolution better now, though I thought I already understood it (almost) completely.
I'm a chemistry major, and learning what I don't know in fields outside my specialty is invaluable to me.
I'd urge you to write more posts like this whenever you see skeptics, atheists, scientists, etc., repeating irritating and uninformed stances that you feel qualified to correct.
This kind of detailed and rational explanation of a subject is very persuasive to me and enlightens my continuing education.
Posted by: sleeprunning
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January 7, 2011 4:24 PM
Our understanding is that the term "evolution" is misleading. What's more accurate? Descent?