It’s more than genes, it’s networks and systems

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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.

bithorax.jpeg
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.

106 Comments

Good stuff.

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.

Okay, this has totally thrown me off guard here…

Not only is that formulation the easiest way to explain the whole process to a layman, but it will be even harder to explain how the populations and networks of different genes factor in. And by this I mean being more than just epiphenomenal things that take affect as a result of mutation and selection.

Thanks for clarifying it, I’ll be sure to send my partially retarded Xians here the next time I have to deal with someone who doesn’t understand evolution. I know they won’t actually read it, but they also won’t listen to me, so why bother wasting my time trying to explain it?

GuessWho said:

Not only is that formulation the easiest way to explain the whole process to a layman, but it will be even harder to explain how the populations and networks of different genes factor in.

Yeah, but that formulation is also simplistic verging on dodgy. Try “genetic variation and selection effects” … that sounds broad enough. After all, processes like sex, horizontal gene transfer, and the whole “tangled bank” of symbiotic coevolution can factor in, too.

This is exactly why the argument from ignorance and incredulity fails so miserably. An uninformed person can easily dismiss a simplified and fundamentally flawed notion. It takes an expert to understand all of the subtleties that go into modern evolutionary theory. FIrst, you must understand basic genetics. Then you must understand mutations. Then you must understand population genetics. Then you must understand developmental genetics. And when you have mastered all of that you can finally begin to grasp some of the complexities involved. That’s why uninformed people and people who are not equipped to look at evidence, or who simply refuse to look at evidence, are not entitled to an opinion. That is why we have experts in all of these fields. That is why we should listen to the experts. Blindly dismissing the experts, because you in your own ignorance cannot imagine how something could work, is simply arrogance.

I really like PZ’s explanations. The more we see the underlying details, the more they tie the processes of evolution to the physics and chemistry.

In the physics of complex systems subjected to their surrounding environments, it is often the emergent properties that guide subsequent stages of development within those environments.

Those emergent properties are usually unpredictable (before the fact) characteristics that are manifestations of myriads of underlying physical and chemical processes.

A nice example of selection of emergent features would be the stockiness of the limbs of ambulatory creatures in a gravitational field. As structures get bigger, weight becomes important and gravity becomes an environmental “pressure.” The strength of the emergent limb is proportional to the square of its dimension, i.e., its cross-sectional area. But weight is proportional to the cube of the dimensions of the creature, i.e., its volume.

Those morphological features are both emergent properties that are the result of many underlying processes, no particular one of which is the sole determiner of those gross features. But once those gross features become significant in a gravitational field, they become features which can be modified by selection in subsequent populations.

I like to think of a chain of populations as analogous to a single system that makes its adjustments to surrounding “pressures” by using time-sequenced surrogates of itself. In other words, if one were to take snapshots of successive adult representatives of a species throughout its evolutionary history and play them back in succession, it would look like a single individual changing through time.

A single system “relaxes into” its current potential wells by minimizing its potential energy in the most general sense. Reproducing systems do this through slightly morphed surrogates in successive generations.

DS said:

This is exactly why the argument from ignorance and incredulity fails so miserably. An uninformed person can easily dismiss a simplified and fundamentally flawed notion. It takes an expert to understand all of the subtleties that go into modern evolutionary theory. FIrst, you must understand basic genetics. Then you must understand mutations. Then you must understand population genetics. Then you must understand developmental genetics. And when you have mastered all of that you can finally begin to grasp some of the complexities involved. That’s why uninformed people and people who are not equipped to look at evidence, or who simply refuse to look at evidence, are not entitled to an opinion. That is why we have experts in all of these fields. That is why we should listen to the experts. Blindly dismissing the experts, because you in your own ignorance cannot imagine how something could work, is simply arrogance.

I think that argument applies to other scientific issues, like Global Warming.

For example, look at this comment made by a denialist on my blog:

http://circleh.wordpress.com/2009/0[…]#comment-646

Well as one of those filthy denier types,…

I go along with the basic outline.

But CO2 is 0.0383 per cent by weight or 0.06 per cent by mole for dry air. Air has on average 1 per cent water vapor.

So we have as a ratio 6 molecules of CO2 for every 10,000 other molecules. Now for those radiant absorption curves that indicate that CO2 has 32 per cent of the absorption spectrum, can you qualify what are the parameters of these measurements. I suspect that if air was used there would be no CO2 reading due to the 6/10000 washout.

Even this, what portion of CO2 is human compared to the carbon cycle?

I see a fraud here along the same lines as the homeopathy fraud, an exaggeration to extreme of the influence of a molecule.

There cannot be any feedback (+ or -) of a entity that is vastly overwhelmed by similarly acting molecules.

CO2 is a scarce resource that the planet has been sequendering for 3 billion years. CO2 is not a pollutant. As good citizens of the planet we need to be at peace with the workings of our blessing and not be distracted from the ever real problems we have to deal with. Fancy suggesting (others not here) a fix in the form of what we knew to be nasty and have seen the results from its reduction … sulphur dioxide.

That comment had “moron” written all over it. So I said:

Dale Husband: CO2 is indeed a trace gas, but it can still have a profound effect. Are you aware that there is even less ozone in our atmosphere than CO2, yet it is classed as both essential to life (since it forms a layer to shield us from ultraviolet radiation) and as a pollutant at ground level? Clearly, you haven’t read my other blog entry on the matter of CO2′s role as a greenhouse gas, have you? When you have, you will be much less ignorant, I hope. http://circleh.wordpress.com/2009/0[…]ouse-effect/

It’s doesn’t matter how small the amount of a gas appears to be. What matters is what empirical data shows regarding its effects.

Dale Husband said:

I think that argument applies to other scientific issues, like Global Warming.

For example, look at this comment made by a denialist on my blog:

http://circleh.wordpress.com/2009/0[…]#comment-646

Well as one of those filthy denier types,…

I go along with the basic outline.

But CO2 is 0.0383 per cent by weight or 0.06 per cent by mole for dry air. Air has on average 1 per cent water vapor.

So we have as a ratio 6 molecules of CO2 for every 10,000 other molecules. Now for those radiant absorption curves that indicate that CO2 has 32 per cent of the absorption spectrum, can you qualify what are the parameters of these measurements. I suspect that if air was used there would be no CO2 reading due to the 6/10000 washout.

Blah, blah, blah,

This is a perfect example of someone slinging numbers around in order to bamboozle, but who has absolutely no contact with the real world of science.

When I was doing work on infrared detecting CCD imagers, I had a blackbody source set up about 2 meters from my infrared spectrometer; in other words, the path through the atmosphere, through the spectrometer and to a liquid nitrogen cooled CCD imager being characterized was about 2 meters.

In just that short distance, the absorption lines for CO2 in the near to mid infrared were easily detectable and served as calibration lines for the spectrometer.

Just think what a hundred miles of atmosphere can do.

Actually, this PZ blog was oddly reassuring to me. I always knew that RM-NS worked, and I always knew it worked while I was asleep, awake, or not paying attention. This is not ‘rocket science’, it is infinately more intricate, and strangely, comprehensible.

Changes occur in populations, advantageous changes could lead to new phenotypes, this COULD give reproductive advantage, the environment could alter, the new advantage could become a disadvantage, the environment could change, new mutations (occuring as I sleep) COULD.… anyway you and I, and nature get the idea.

Mike Elzinga wrote

I like to think of a chain of populations as analogous to a single system that makes its adjustments to surrounding “pressures” by using time-sequenced surrogates of itself. In other words, if one were to take snapshots of successive adult representatives of a species throughout its evolutionary history and play them back in succession, it would look like a single individual changing through time.

And it would be profoundly misleading. One of the toughest notions to get across to lay people is that evolution is a population phenomenon and that diversity within a population is a critical variable. Evolution is not an individual morphing through time/generations, but rather a distribution shifting through time/generations. I know you know that, of course, but there really is difficulty in getting it across to lay audiences and that illustration makes it tough.

Oops. Read the OP before commenting, RBH.

So, looking at all these neutral mutations of cistrons,the ones that only change the nucletide but not the amino acid, and the further ones that make conservative amino acid changes, we can summarise that many improved mutations are just waiting for the correct complements to come along.

Point mutations of introns and intercistronic sequences have more immediate effects. If we propose that these regulate cistronic activity by their binding of proteins *like* transcription factors and cis/trans factors, *and* their binding of RNA sequences (let us regard these too as transcription factors) potentially with their own point mutations.

.….then there is considerable scope to modulate the expression of the cistronic genome without any significant alteration of coding sequences.

Yet I think it is not fair to disparage the simplistic model. It is fine for single-gene traits, particularly in bacterial genetics.

Rusty

Dale Husband said:

It’s doesn’t matter how small the amount of a gas appears to be. What matters is what empirical data shows regarding its effects.

Sigh, CO2 is indeed a trace gas. Which means that if it has an appreciable effect, it doesn’t take much in the way of an increment to have an appreciable effect.

I am willing to cut AGW skeptics a bit of slack – climate is a very difficult subject, and even the pros admit that sometimes the skeptics make good points. But they keep using up the slack. They have an unfortunate tendency to sound like creationists. Which is because a lot of them ARE creationists.

“You’ve got to include network theory and gene and environmental interactions to really understand the phenomena.”

You can include whatever you want - it will still remain the old darwinism in new clothes. The only difference is that this “network” enable darwinists to explain what is really observed in nature - sudden changes in morphology or saltationism. It was Richard Goldschmidt who observed and studied phenocopies on butterflies wings btw. As you may know this prominent geneticist dismissed darwinian model and coined the term “systemic mutation” to explain sudden changes observed in nature.

PZ Myers’”network” is now a new helper in this pseudo-scientifical narrative called neodarwinism. “Network” can somehow mysteriously accumulate enough “silent changes” only to expose them at the right moment as phenocopies or phenotypes - and doctor Myers obviously confound these two terms to support his “network” version of darwinism. Actually such “network” approach can inhibit evolution and not to promote it. See “Frozen evolution” or “Elastic not plastic evolution” by professor Flegr here:

http://www.ncbi.nlm.nih.gov/pmc/art[…]/PMC2823622/

Professor Flegr has mentioned also pleiotropy and epistatic interactions mentioned in PZMyers article using layman words. And so we can see - for one neodarwinist “network” can promote evolution and for another neodarwinist the same network inhibits evolution.

“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.”

Maybe better solution would be to issue a decree for “system biologists” how to interpret this mysterious “networks” in order to save neodarwinian narrative in the coming years.

PZ Myers Wrote:

Most of you don’t understand evolution.

Of course not, only Tony Pagano does. ;-)

Seriously, unfortunately I’ll be out of town for the next few days, and not be able to contribute much to this thread. Nothing much you said is new to me, but I often find it difficult to convey to others. Your explanation will make it a bit easier. Even when they have it explained to them at the “101” level most people have a habit of retreating to the media (& creationist) caricature. And that sadly includes many scientists who ought to know better. If anything I think fellow chemists have less of an excuse to allow media and creationist misrepresentation than biologists, because they are very aware that cells are not just a collection of molecules, but more importantly of reactions.

“You’ve got to include network theory and gene and environmental interactions to really understand the phenomena.”

You can include whatever you want - it will still remain the old darwinism in new clothes. The only difference is that this “network” enable darwinists to explain what is really observed in nature - sudden changes in morphology or saltationism. It was Richard Goldschmidt who observed and studied phenocopies on butterflies wings btw. As you may know this prominent geneticist dismissed darwinian model and coined the term “systemic mutation” to explain sudden changes observed in nature.

PZ Myers’”network” is now a new helper in this pseudo-scientifical narrative called neodarwinism. “Network” can somehow mysteriously accumulate enough “silent changes” only to expose them at the right moment as phenocopies or phenotypes - and doctor Myers obviously confound these two terms to support his “network” version of darwinism. Actually such “network” approach can inhibit evolution and not to promote it. See “Frozen evolution” or “Elastic not plastic evolution” by professor Flegr here:

http://www.ncbi.nlm.nih.gov/pmc/art[…]/PMC2823622/

Professor Flegr has mentioned also pleiotropy and epistatic interactions mentioned in PZMyers article using layman words. And so we can see - for one neodarwinist “network” can promote evolution and for another neodarwinist the same network inhibits evolution.

“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.”

Maybe better solution would be to issue a decree for “system biologists” how to interpret this mysterious “networks” in order to save neodarwinian narrative in the coming decades.

Mr G: Try “genetic variation and selection effects” … that sounds broad enough.

That leaves out a major process: genetic drift.

MartinC said:

You can include whatever you want - it will still remain the old darwinism in new clothes.

I tell you guys this OVER AND OVER! The term is “EVIL-utionism”! Can’t you get the least thing straight?

MartinC wrote:

“You can include whatever you want - it will still remain the old darwinism in new clothes. The only difference is that this “network” enable darwinists to explain what is really observed in nature - sudden changes in morphology or saltationism. It was Richard Goldschmidt who observed and studied phenocopies on butterflies wings btw. As you may know this prominent geneticist dismissed darwinian model and coined the term “systemic mutation” to explain sudden changes observed in nature.:

So evolution can sometimes proceed quickly and can sometimes proceed slowly. What exactly is your point? How is this a problem for evolutionary theory? Do you think that no real scientist has ever considered the effects of pleiotropy and epistasis? Do you honestly believe that these concepts are somehow a problem for modern evolutionary theory?

Here is a news flash for you, no one cares about “neodarwinism”. Darwin was right about many things. Darwin was wrong about many things. So what? All that we have learned about modern genetics shows that evolution is a complicated process that must be examined on many different levels. Or do you think that “poof” is a better explanation?

DS asks:

Or do you think that “poof” is a better explanation?

I suspect Martin Cadra thinks PEH is a better explanation!

Alan Fox said:

I suspect Martin Cadra thinks PEH is a better explanation!

Ah! An associate of the articulate and highly influential John A. Davidson, well known for his groundbreaking work on the leading fringes … er, edges of science.

Well, Martin still has not informed us of exactly what point he was trying to make. However, I did find this quote from the Flegr paper:

“It was argued above that adaptive evolution by means of Darwinian selection of individuals in a population, as well as by means of Dawkinsian competition between alleles in individual loci, is very difficult, if not impossible, in populations of sexual organisms. It is evident, however, that adaptive evolution operates on Earth and that this evolution is especially and extremely efficient in sexual organisms. It follows that a situation must occur, in which all three barriers to adaptive evolution are lifted, or at least temporarily operate with decreased efficiency.”

So you can quibble about “neodarwinism” or “Dawkinsian competition” all you want, but evolution is still real and still works in all organisms, whether sexual or asexual.

MrG said:

Alan Fox said:

I suspect Martin Cadra thinks PEH is a better explanation!

Ah! An associate of the articulate and highly influential John A. Davidson, well known for his groundbreaking work on the leading fringes … er, edges of science.

More proof that Creationists are pathological liars.

RBH said:

Mike Elzinga wrote

I like to think of a chain of populations as analogous to a single system that makes its adjustments to surrounding “pressures” by using time-sequenced surrogates of itself. In other words, if one were to take snapshots of successive adult representatives of a species throughout its evolutionary history and play them back in succession, it would look like a single individual changing through time.

And it would be profoundly misleading. One of the toughest notions to get across to lay people is that evolution is a population phenomenon and that diversity within a population is a critical variable. Evolution is not an individual morphing through time/generations, but rather a distribution shifting through time/generations. I know you know that, of course, but there really is difficulty in getting it across to lay audiences and that illustration makes it tough.

Indeed; I understand the notion of population. It has many of the same characteristics as the notion of ensemble in statistical mechanics.

And, in the case of ensembles, if it were not for the spread of energies, and if matter did not interact with matter, there would be no tendency for a thermodynamic system to come to equilibrium with anything.

Ensembles have statistical averages and distribution widths that are representations of the instantaneous state of the system to which they refer.

In the case of populations, any phenotypic feature would have a mean and a standard deviation. A representative member of that population would be one that has that mean phenotypic feature; and it is this representative that I was picturing as morphing through time.

So, as compared with a single system that adjusts to changes in its surroundings by spontaneously adjusting and morphing its current constituents or energy, I was suggesting that reproducing living systems adjust by making surrogates of themselves that contain the variations on which selection takes place. Those surrogates are the populations (ensembles) that respond to environmental changes by adjusting the mean and spread of any relevant phenotypic characteristics.

Obviously a single individual lives or dies, just as a particular state in an ensemble becomes available or unavailable.

The single system to which I was referring was the “ensemble average” of the population; it isn’t a real creature. The difference is the replication of surrogate ensembles through time.

But I think I see your point if you are suggesting that this would cause confusion for the layman. The notion of ensembles in statistical mechanics is important but perhaps a bit subtle for the layman also. Just as is the notion of entropy which refers to the number of ways one can spread a given amount of energy among the microscopic constituents of a system.

On the other hand, as I have frequently suggested, the fundamental misconceptions of the ID/creationists start with the notions of thermodynamics. They pushed these misconceptions hard in the beginning back in the 1970s and 80s. The conceptual confusions they reveal here are the same conceptual confusions that permeate everything else.

Dale Husband Wrote:

More proof that Creationists are pathological liars.

Some are. Some are liars but not the pathological “kind.” Some are just “possessed” by Morton’s Demon (including it’s OEC variants). Some honestly believe that they must tell fairy tales to save the world. Some (IDers) know better than to tell mutually contradictory fairy tales that don’t fit the evidence so they just promote unreasonable doubt of evolution and let the audience infer what makes them feel good.

And some, though now I’m referring to the rank and file, not the activists, have just been misled. Some irreversible, some reversibly.

That’s the “X-axis.” On the “Y-axis” we have everyone from the Flat, Geocentric Young Earthers to the common-descent-accepting Old Earthers, non-Biblicals, etc.

Any wonder why I rarely use the word “creationist?”

Two comments:

1)I think the knowlege we have gained in the past 10 years about what actually happens inside cells with regard to gene expression (Immediate Early Genes, etc) have made the fact of evolution even clearer. The Biology 101 “explanation” is an example of an overgeneralization that leaves out important details. When dealing with enthusiastic beginning students, I always thought it important to bring in Hardy-Weinberg even at the beginning levels because it is so powerful to develop population genetics generalizations earl–even if the students are not ready for all the genetics details. In the ‘90’s we waited until genetics (usually an upper 200 level course) to teach it. I have seen demo lessons to teach Hardy-Weinberg at the high school level conceptually, adding a short calculation for students who have the math skills.

2) I was a geologist before becoming a biologist, and I have some real problems with the current “climate science” that does not seen to take earth history into account. That global climate change has occurred in earth history is beyond dispute, but to claim that the earth is on a linear global warming trend caused primarily by human activity has many problems, not the least of which is that there has been an increase in global temperatures at the end of every interglacial period that had led (sometimes very quickly in a geological time frame) to new glacial advances and global cooling.

The science is not all in on this, and the science in no way dictates that the particular policies being bandied about by political bodies will have the desired effect. I am uncomfortable with the dogma that climate change must be linear and must be global warming, and that it must be stopped. And I worry that tying it to evolution–which is a demonstrated fact–is a mistake for the reasons I cite above. In fact, I often wonder if the political global warming hysteria tends to demonstrate that most people do not in fact understand evolution, since adaptation to changes in environment is part of that process.

Uh-oh. I’m sure glad I’m not standing close to the fan…

Elisheva Levin said:

I was a geologist before becoming a biologist, and I have some real problems with the current “climate science” that does not seen to take earth history into account. That global climate change has occurred in earth history is beyond dispute, but to claim that the earth is on a linear global warming trend caused primarily by human activity has many problems, not the least of which is that there has been an increase in global temperatures at the end of every interglacial period that had led (sometimes very quickly in a geological time frame) to new glacial advances and global cooling.

The science is not all in on this, and the science in no way dictates that the particular policies being bandied about by political bodies will have the desired effect. I am uncomfortable with the dogma that climate change must be linear and must be global warming, and that it must be stopped. And I worry that tying it to evolution–which is a demonstrated fact–is a mistake for the reasons I cite above. In fact, I often wonder if the political global warming hysteria tends to demonstrate that most people do not in fact understand evolution, since adaptation to changes in environment is part of that process.

Ironically, global warming can indeed cause a thermal backlash due to the Gulf Stream being pushed southward by melting ice water flowing into the north Atlantic from Greenland and Canada. Al Gore even mentioned this danger in his book An Inconvienent Truth. He noted that an inrush of water many thousands of years ago as glacial ice was melting at the end of the last ice age caused Europe to enter another cold spell.

So the issue is very complicated, but it’s all been dealt with by the experts and explained well enough for educated laymen like myself to follow.

Elisheva Levin said:

Two comments:

1)I think the knowlege we have gained in the past 10 years about what actually happens inside cells with regard to gene expression (Immediate Early Genes, etc) have made the fact of evolution even clearer. The Biology 101 “explanation” is an example of an overgeneralization that leaves out important details. When dealing with enthusiastic beginning students, I always thought it important to bring in Hardy-Weinberg even at the beginning levels because it is so powerful to develop population genetics generalizations earl–even if the students are not ready for all the genetics details.

I absolutely agree. It is necessary to state that evolution is a genetic phenomena and a population phenomena and to demonstrate why that is true. Hardy Weinberg is really rather easy, both conceptually and mathematically. Why not use it even in the most basic courses? Of course, it doesn’t lose any relevance in the more advanced courses where it can be even more fully developed in order to account for many genetic complexities. In the more advances courses, I think it is also important to emphasize molecular phylogenetics and developmental genetics as well. This can help to show how far our understanding has advanced since the time of Darwin.

Clearly, MartinC, you have discovered a fatal flaw in this theory. Perhaps you’d like to tell us what alternate theory you have that explains the same phenomena?

And since your complaint seems to be that PZ’s model allows for too wide a variety of different results, can we assume that your alternate theory has more stringent limitations on what things it predicts? After all, you would look pretty stupid if you first complained that the ToE is illegitimate because it allows for both fast and slow change, but then proposed an alternative that allows any change at any speed at all…right?

Ray Martinez said:

All Myers said is that “evolution-did-it.”

Creationism-ID says “Creator-did-it.”

If you’re an Atheist you have no choice but to accept evolution.

Bullpuckey. Meyer went into detail about mutation, selection, populations, gene networks and flexible genes. There is a vast scientific literature which contain evidence for everything that was discussed. But you did get one thing right, creationism and ID are rightly lumped together and neither one makes anything more than the vague unsubstantiated claim that somebody, somewhere did something, sometime for some reason.

As for atheists having to accept evolution, why would the most skeptical people in the world accept anything based on anything other than the evidence? Maybe they are just more able to accept evolution because they are not encumbered with so many preconceptions and blind spots. The fact is that everyone who is not convinced by the evidence is perfectly free to reject evolution. They won’t even be threatened by hellfire! Those who are unfamiliar with the evidence, or simply refuse to look at the evidence, are not entitled to an opinion on the matter. They can still have one, but no one will care.

Oclarki said:

I suppose that it is just that I cannot resist the…um…temptation…to challenge the assertations of apparent evolution deniers.

The issue is that you challenged THAT particular evolution-denier. That one gets banned from ANTI-EVOLUTION forums.

Sorry, I’m a bit late to the party here, but have a question for any experts still reading the thread. Would this indicate that if Dr. Lenski were to blend 4 or 5 of his different lines of non-Citrate-metabolizing bacteria, thus creating a population with a greatly increased allelic variety, then he would expect the ability to metabolize citrate to evolve faster than it was able to otherwise? Or does the asexual reproductive nature of e. coli preclude the effect?

Oclarki said:

Ray Martinez said:

If you’re an Atheist you have no choice but to accept evolution.

Sorry, but that claim is not accurate. An atheist could most certainly believe that the observed spatial and temporal distribution of life on Earth was directly cause by Martians…or Romulans.…or even little white mice. Or that atheist could simly claim that we do not yet have an explanation for that observed distribution.

There is no requirement that atheists must accept the theories of evolution in order to rationalize their opposition to the existence of deities. Indeed, there is no requirement that anyone must accept those theories. At least, the principles and methodologies of science include no such requirement.

Despite the long-winded evasion seen above, since no God exists Atheists have no choice but to believe that species generate species (= evolution).

DS said:

Ray Martinez said:

All Myers said is that “evolution-did-it.”

Creationism-ID says “Creator-did-it.”

If you’re an Atheist you have no choice but to accept evolution.

Bullpuckey. Meyer went into detail about mutation, selection, populations, gene networks and flexible genes. There is a vast scientific literature which contain evidence for everything that was discussed.

I never denied that Myer presented a long and complicated elucidation. My point was that these elucidations give birth and health to the over-simplifications that Myer complained about.

But you did get one thing right, creationism and ID are rightly lumped together and neither one makes anything more than the vague unsubstantiated claim that somebody, somewhere did something, sometime for some reason.

As for atheists having to accept evolution, why would the most skeptical people in the world accept anything based on anything other than the evidence? Maybe they are just more able to accept evolution because they are not encumbered with so many preconceptions and blind spots. The fact is that everyone who is not convinced by the evidence is perfectly free to reject evolution. They won’t even be threatened by hellfire! Those who are unfamiliar with the evidence, or simply refuse to look at the evidence, are not entitled to an opinion on the matter. They can still have one, but no one will care.

Again, since no God exists Atheists have no choice but to accept evolution.

Oh gosh, it’s evening, feeding time for the troll.

Ray Martinez said:

Despite the long-winded evasion seen above, since no God exists Atheists have no choice but to believe that species generate species (= evolution).

Since reading comprehension seems to be an issue here, I will be short. Your claim lacks logical support.

Oclarki said:

Your claim lacks logical support.

Well DUH. This is Ray Martinez. RAY! MARTINEZ! Google him, he’s very well known. Conversations with him are similar to working with a PC that has a system error suggesting it is going to crash at any moment.

Oclarki said:

Ray Martinez said:

Despite the long-winded evasion seen above, since no God exists Atheists have no choice but to believe that species generate species (= evolution).

Since reading comprehension seems to be an issue here, I will be short. Your claim lacks logical support.

It is perfectly logical.

Since no God exists, what other choice does the Atheist have but to believe that nature “created” itself?

You don’t like the fact because it makes “Christian” evolutionists look like buffoons.

On googling the name, add “creationist” to the search term – it’s a common name.

Ray Martinez said:

It is perfectly logical.

Since no God exists, what other choice does the Atheist have but to believe that nature “created” itself?

You don’t like the fact because it makes “Christian” evolutionists look like buffoons.

Christians who accept the theories of evolution as the best, most robust explanation for the temporal and spatial distribution of life on earth look pretty reasonable to me. Far, far more reasonable that those who reject those theories, ridicule those that accept them, and yet have a very, very difficult time coming up with anything even remotely as compelling.

Oops…I guess I am being long-winded again. Oh, well. Deal with it.

As for those athiests of yours, they could also believe that aliens created life on earth.

MrG said:

On googling the name, add “creationist” to the search term – it’s a common name.

No need…I see what you mean. Oh, well. I do apologize for the feeding.

Oclarki said:

Oh, well. Deal with it.

If you really think you have good reason to try to hold a conversation with a rambling paranoid schizophrenic, have at it.

Kevin said:

Sorry, I’m a bit late to the party here, but have a question for any experts still reading the thread. Would this indicate that if Dr. Lenski were to blend 4 or 5 of his different lines of non-Citrate-metabolizing bacteria, thus creating a population with a greatly increased allelic variety, then he would expect the ability to metabolize citrate to evolve faster than it was able to otherwise? Or does the asexual reproductive nature of e. coli preclude the effect?

Actually prokaryotes do exchange genetic material. My hunch is that this would result in citrate metabolism evolving faster in a more diverse starting population.

MrG said:

If you really think you have good reason to try to hold a conversation with a rambling paranoid schizophrenic, have at it.

I am not sure that this is actually a good reason, but I am all for giving creationists every opportunity to provide a substantive, credible alternative explanation to the theories of evolution.

Heck..I would settle for a substantive, testable alternative explanation for the temporal and spatial distribution of life as expressed in the fossil record. But then again, I am a geologist and so am perhaps a bit too narrow in my demands for most creationists.

The trouble is, in 30+ years of being open-minded, I have yet to encounter a convincing alternative explanation. I am about ready to give up, but in a way I cannot help but maintain a certain amount of openness to credible alternative explanations.

But the key word is credible.

Ray Martinez said:

Oclarki said:

Ray Martinez said:

Despite the long-winded evasion seen above, since no God exists Atheists have no choice but to believe that species generate species (= evolution).

Since reading comprehension seems to be an issue here, I will be short. Your claim lacks logical support.

It is perfectly logical.

Since no God exists, what other choice does the Atheist have but to believe that nature “created” itself?

You don’t like the fact because it makes “Christian” evolutionists look like buffoons.

The idea that nature “created” itself has nothing to do with evolution. You are thinking of the Big Bang.

Humans and other species on Earth could have been planted by some alien intelligence, not evolved.

Evolution does not prove atheism, not does atheism require evolution. There are plenty of reasons to deny God that have nothing to do with evolution.

About this Entry

This page contains a single entry by PZ Myers published on July 24, 2010 6:46 PM.

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