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Real Time Evolution “Happening Under Our Nose”

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A couple of weeks ago a friend forwarded me a link to this recent article about “ongoing research to record the interaction of environment and evolution” by University of California, Riverside biologist David Reznick. Reznick’s team has been studying adaptive changes in guppies. Reznick’s work focuses on tracking what happens in real-world situations in the wild, rather than the somewhat artificial environments in the lab. As a result, Reznick has gathered some of the more trustworthy and definitive data about changes over time in a real-world environment, largely free from the intervention and interference of the coated lab worker.

The article states:

The new work is part of research that Reznick has been doing since 1978. It involved transplanting guppies from a river with a diverse community of predators into a river with no predators – except for one other fish species, an occasional predator – to record how the guppies would evolve and how they might impact their environment.

In the recent follow-up research, Reznick’s team studied “how male color pattern affected” their differential survival in the environment. Significantly, the team even gathered DNA from the guppies over time to track who their parents were and reconstruct a guppie pedigree to help determine the reproductive success. Without going into all the details, which are interesting in their own right, the key point for my purposes today is that this adaptive change occurred extremely quickly.

Graduate student, Swanne Gordon, noted,

Our research shows that these fish adapted to their new habitats in less than one year, or three to four generations, which is even faster than we previously thought.

Reznick adds,

People think of evolution as historical. They don’t think of it as something that’s happening under our nose. It is a contemporary process. People are skeptical; they don’t believe in evolution because they can’t see it. Here, we see it. We can see if something makes you better able to make babies and live longer.

What Really Happened?

Now normally when my friend forwards a link, I will just review the article, realize it is making claims beyond the data, and move on. But coincidentally, just days earlier I had been reading Chapter 7 of Lee Spetner’s 1998 book, Not by Chance!

Part of Spetner’s argument is that many adaptive changes we see in nature are in fact not examples of a Darwinian process of chance changes + natural selection, but instead the result of specific programming capabilities in the organism to allow it to respond to changes in the environment. Indeed, what caught my eye about the article my friend forwarded is that Spetner had discussed Reznick’s earlier experiments in that very context.

After describing two different predators of the guppies: (i) the cichlid, which prey on large mature guppies; and (ii) the killfish, which prey on small immature guppies, Spetner continues:

Reznick and his team took 200 guppies from the Aripo [river in Trinidad] and put them in a tributary of the river that is home to the killfish but has no cichlids and had no guppies. Changes soon appeared in the newly introduced guppies. The fish population soon changed to what would normally be found in the presence of the killfish, and Reznick found the changes to be heritable.

The full change in the guppy population was observed as soon as the first samples were drawn, which was after only two years. One trait studied, the age of males at maturity, achieved its terminal value in only four years. The evolutionary rate calculated from this observation is some ten million times the rate of evolution induced from observations of the fossil record [Reznick et al. 1997].

Reznick interpreted these changes as the result of natural selection acting on variation already in the population. Could natural selection have acted so fast as to change the entire population in only two years?

Spetner goes on to argue that the adaptive change observed in the guppies is more likely the result of a programmed response to environmental change, and provides several examples of such changes in other species.

Where is the Darwinian Evolution?

Darwinian evolution, as we know, is supposed to work by natural selection weeding out random variation. The Neo-Darwinian model has traditionally gone a step further, suggesting that those random variations are genetic in nature — taking place in the DNA as a copying error here, a misplaced sequence there, an accidental cut-and-paste elsewhere . . .

So the question arises: do the kinds of rapid, adaptive, reversible changes Reznick observed owe their existence to this kind of Darwinian process, or are they the result of a pre-programmed genetic response to environmental changes?

Spetner makes a good argument that we are observing the latter. He goes on to show that even many of the classical examples of Darwinian evolution — you know, the examples of random mutation + natural selection that even most evolutionary skeptics have tended to accept: convergent “evolution” of plants in similar environments, the “evolution” of bacteria to live on lactose or salicin — are not good examples of Darwinian evolution at all. Even that icon of icons, finch beaks in the Galapagos, is likely not a good example of the alleged Neo-Darwinian mechanism of random mutation + natural selection.

All of this prompts me to ask a simple, but pointed, question:

How many good examples are there of Darwinian evolution?

The more research I do the more I come to the same conclusion Spetner did, namely that most adaptive changes are not the result of the random, purposeless changes Darwinian evolution posits as the engine of biological novelty.

Even skeptics of the grand evolutionary claims tend to accept, either specifically or implicitly, that Darwinian evolution can produce all kinds of minor adaptive changes, the so-called microevolutionary changes: variations in finch beaks, insect resistance to insecticides, coloration of peppered moths, and so on. And indeed, the “selection” side of the formula seems to work well, which is simply the somewhat pedestrian observation that if an organism is poorly adapted to its environment it has a poor chance of surviving.

Yet the engine of the novelty, the alleged random variation that is supposed to provide all this adaptive variability on which selection can work its magic, seems stubbornly absent. Even these most common of examples, on closer inspection, do not support the Darwinian claim. Thus the doubts multiply. If Darwinian evolution cannot even claim explanatory credit for things like bacteria being able to metabolize lactose, what can it explain? The more closely we look, the more anemic the Darwinian claim becomes.

Now we could be intellectually lazy and call every adaptive change we observe an example of “evolution.” But the problem with observing a change and claiming that we have observed “evolution” is that (i) we rob the word of explanatory value if it is applied indiscriminately, and (ii) we trick ourselves into thinking we have an explanation for what occurred, when in fact we have have no idea what is happening at the molecular level or the organismal level to produce the change. Claiming that we are witnessing “evolution” in such circumstances becomes then not so much an explanation as a confession of ignorance.

Real Darwinian Evolution

There are no doubt quite a number of legitimate, confirmed examples of random mutation + natural selection producing an important biological effect. For example, I think Behe’s review of malaria/sickle cell trait is a legitimate example of Darwinian evolution in action. And the circumstances of that example are rather telling: (a) large population size, (b) meaningful amount of time, (c) very strong selection pressure, (d) and change that can be caused by one or two single-point mutations.

If we see adaptive change outside of these parameters — small population, short timeframe, an adaptation that requires significant genetic change — we might be better served to suspect that we are witnessing a programmed adaptive response, rather than Darwinian evolution. And rather than being naively impressed with the great power of Darwinian evolution to act more rapidly than anticipated, we should be prompted to look deeper to find what is actually taking place.

Your Turn

In addition to the malaria/sickle cell example, what other examples of legitimate, confirmed Darwinian evolution can you think of?

Comments
Eric Anderson: So are you arguing that the landscape is the result of deterministic forces? Certainly many aspects of the environment are the result of deterministic forces, such as sunshine. Eric Anderson: Regardless, it certainly isn’t the Neo-Darwinian mechanism of DNA mutations that is driving the situation in this case. Ghalambor links plasticity with adaptive evolution. Eric Anderson: No subsequent details about evolution, common descent or otherwise need be provided. We can limit the guest post to the question of abiogenesis. They can't be unlinked. If someone denies evolutionary adaptation, for instance, then talk about early replicators wouldn't have a connection to extant life.Zachriel
October 20, 2015
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What makes you think I am confused about mutations?
You say things like
The question is whether there are other genetic changes besides mutations
What is a non-mutational genetic change?wd400
October 19, 2015
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Zachriel @306: That specific offer related to your claim about abiogenesis. No subsequent details about evolution, common descent or otherwise need be provided. We can limit the guest post to the question of abiogenesis.Eric Anderson
October 19, 2015
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Zachriel @278:
At least part of that landscape is due to basic physics; fusion on the Sun, rotation and revolution of the Earth, the collection of water in basins, rain, snow, ice, the formation of land, etc. Other aspects of the environment are biological organisms themselves, including competitors.
Of course. So are you arguing that the landscape is the result of deterministic forces? Or the result of chance?
See Ghalambor et al., Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature, Nature 2015.
Phenotypic plasticity is indeed an interesting phenomenon. And what do you suppose drives that plasticity? Epigenetic activity in most cases. Regardless, it certainly isn't the Neo-Darwinian mechanism of DNA mutations that is driving the situation in this case. Which is precisely the point.Eric Anderson
October 19, 2015
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What makes you think I am confused about mutations? I have already agreed with your statement that mutations appear to be essentially random with respect to fitness. That is not the question. The question is whether there are other genetic changes besides mutations. There is growing evidence that such changes can and do exist. As I said earlier, I'll hopefully get to that in another post. Briefly, however, Spetner describes a couple of examples in his book, including experiments with Salmonella bacteria and E. coli. Regardless, independent of the above, the real issue of the OP is how some people seem to jump from meager observational evidence to larger unwarranted conclusions about the power of the evolutionary mechanism.Eric Anderson
October 19, 2015
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The evidence for divergence from common ancestors is an important clue as to the origin of life.
There isn't any such evidence so that would be a problem.Virgil Cain
October 19, 2015
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Zachriel:
The offer is appreciated. However, such a discussion presupposes the validity of evidence for evolution, and the history of common descent. Not sure how to engage such a discussion without those already being established.
Translation: Zachriel is too chicken to make a claim it has to actually support.Virgil Cain
October 19, 2015
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Again, the question at stake is not whether organisms poorly adapted to their environment are less likely to survive than those that are better adapted. That is obvious and we don’t need evolutionary theory to tell us that. Nor do we need a convenience label.
You keep saying stuff like this as if it's related anything I've said. Which leads me to a question: what do you think happens to a population where the degree to which individuals are adapted to their environment is not heritable?wd400
October 19, 2015
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EugeneS: This is complexity in principle. Z: Of course there is complexity involved. EugeneS: Heterogeneous systems to replicate require the existence of: 1. memory; 2. a symbolic representation of the system being able to be stored and retrieved from memory; 3. a reader/writer of these symbolic representations to/from memory; 4. a processor which actually executes instructions in order to rebuild the system using the representation. What Crick conjectured, based on evolutionary principles half a century ago, is now known to be possible, a molecule which can act as 1. memory; 2. a symbolic representation of the system being able to be stored and retrieved from memory; 3. a reader/writer of these symbolic representations to/from memory; 4. a processor which actually executes instructions in order to rebuild the system using the representation.Zachriel
October 19, 2015
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Zachriel, How complex a constituent sub-problem is does not matter. The point is the resultant structure must cater for replication and autonomy. This is complexity in principle. Heterogeneous systems to replicate require the existence of: 1. memory; 2. a symbolic representation of the system being able to be stored and retrieved from memory; 3. a reader/writer of these symbolic representations to/from memory; 4. a processor which actually executes instructions in order to rebuild the system using the representation.EugeneS
October 19, 2015
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EugeneS: Zachriel seem to have recognized the problem of initial complexity as they stated that for evolution to even start, one needs membranes and replication. Some sort of segregation may be required. A lipid membrane is a reasonable and available mechanism. EugeneS: I read this ‘and‘ as a tacit recognition of initial complexity necessary in order for life to even start. Of course there is complexity involved. EugeneS: The next step they need to take is recognize the huge difference between replicating homogeneous structures and replicating heterogeneous structures. A dividing membrane is among the simplest of problems. A molecular replicator is the hard problem.Zachriel
October 19, 2015
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Eric Anderson: What evolutionary theory has to bring to the table — in the context of the present discussion, what the Neo-Darwinian random-mutations-in-DNA mechanism has to bring to the table is an explanation of how the organisms in all of their varieties came on the scene in the first place. We can’t just assume it happened by mutation. Case in point. The evidence for divergence from common ancestors is an important clue as to the origin of life. But if you reject this billions year history of divergence, then you will find assertions concerning the trunk of that tree to be unfounded.Zachriel
October 19, 2015
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Eric Anderson: I hereby offer you a guest post opportunity to support the following claim you made with respect to the origin of life: “the evidence indicates a natural cause” The offer is appreciated. However, such a discussion presupposes the validity of evidence for evolution, and the history of common descent. Not sure how to engage such a discussion without those already being established.Zachriel
October 19, 2015
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Virgil Cain, I mostly agree with you. However, I have problems with 'directed evolution'. I think that this is an oxymoron. I believe there is hardly any evolution at all, where by evolution I mean undirected oscillations around attractors in the parameter space. Darwinian evolution is dwarfish and cannot account for novelty. Perhaps all behavioural intelligence of an organism is built-in as a template. It manifests itself as meaningful genetic responses to external stimuli.EugeneS
October 19, 2015
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Hi Eric Anderson:
By the term “random with respect to fitness” wd400 uses, it is meant that the mutation is indeed “happenstance,” as you suggest.
And yet directed mutations can be random wrt the current fitness.
For clarity of discussion, we should distinguish these from “mutations.” They are not random, they are not errors, they are purposeful and controlled. “Genetic changes” yes, but not “mutations.”
Yes, "mutation" seems to imply "accident, error and mistake".Virgil Cain
October 19, 2015
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You appear to be confused about what mutations are - do you want to describe one of these non-mutational genetic changes?wd400
October 19, 2015
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Popperian, This is how I see this whole business. Zachriel seem to have recognized the problem of initial complexity as they stated that for evolution to even start, one needs membranes and replication. I read this 'and' as a tacit recognition of initial complexity necessary in order for life to even start. The next step they need to take is recognize the huge difference between replicating homogeneous structures and replicating heterogeneous structures. This difference is not a difference of degree but a difference of kind. There is absolutely no way out of the reductionist conundrum. Either reductionists honestly accept the need for starting complexity or they will never get the correct picture. The start of life could not be simple in principle. The start of life is absolutely dependent on there being a starting irreducibly complex structure including data, a program to read this data in and do something meaningful about it, and the processor which will translate the program and execute it.EugeneS
October 19, 2015
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Virgil Cain @276: Thanks for your comments. Just one clarification on terminology: By the term "random with respect to fitness" wd400 uses, it is meant that the mutation is indeed "happenstance," as you suggest. As far as we know, most mutations appear to be random, without regard to whether they will help the organism survive or not. And the overwhelming majority do not help the organism survive or are outright harmful -- which is precisely the problem for Neo-Darwinian theory. In contrast to these "mutations," there are examples of controlled genetic changes that some organisms initiate, among other things, in response to environmental cues. For clarity of discussion, we should distinguish these from "mutations." They are not random, they are not errors, they are purposeful and controlled. "Genetic changes" yes, but not "mutations."Eric Anderson
October 19, 2015
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wd400 @286: Well, we've finally pinned down the source of your misunderstanding.
If you accept mutation is random then if follows the standin[g] variation is the result of a random process.
No, it does not follow at all. It only follows if we assume that mutation is the source of the variation. If something else is the source of the variation, something other than mutation, then it doesn't follow at all. Again, the question at stake is not whether organisms poorly adapted to their environment are less likely to survive than those that are better adapted. That is obvious and we don't need evolutionary theory to tell us that. Nor do we need a convenience label. What evolutionary theory has to bring to the table -- in the context of the present discussion, what the Neo-Darwinian random-mutations-in-DNA mechanism has to bring to the table is an explanation of how the organisms in all of their varieties came on the scene in the first place. We can't just assume it happened by mutation. It has never been demonstrated that mutations have that creative ability; indeed the evidence points strongly to the contrary.Eric Anderson
October 19, 2015
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Zachriel @245: I hereby offer you a guest post opportunity to support the following claim you made with respect to the origin of life: "the evidence indicates a natural cause" Let me know if you want to take up the opportunity and we'll get your guest post up for discussion.Eric Anderson
October 19, 2015
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Biological Darwinism is real if and only if living organisms arose from non-living matter and energy via stochastic processes.Virgil Cain
October 17, 2015
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The whole argument is whether or not all mutations/ genetic change are accidents, errors and mistakes. That is why the OoL is KEY. If the OoL = Intelligent Design it would be a given that the genetic changes are NOT accidents, errors and mistakes.
I'm suggesting the fundamental issue is between the idea that designers create the knowledge they use to solve problems and the idea that knowledge doesn't genuinely grow at all. It just gets moved from one place to another or is mechanically extrapolated though observations. But the latter does not withstand rational criticism. The contents of theories do not come from observations. They start out as conjectures (guess) that we then criticize and discard error we discover. There is no guarantee that our conjectured theories about how the world works will solve the problems we want to solve. Nor is it guaranteed that it will not solve some other problem we didn't intend to solve, either. If the contents of theories did come from observations then we should be much father along because all you'd have to do is observe something and you would be guaranteed to get the right theory from those observations every time. Nor should there be significant gaps in how we make progress. Rather it should be very linear and continuous. Yet, this doesn't describe progress in science. IOW, human intelligent designers create knowledge though a process of trial and error, which is darwinian in nature. It's part of a universal explanation of the growth of knowledge. In the case of biological Darwinism, the process isn't just random, but random to any particular problem to solve. Unlike people, bacteria or individual cells do not conceive of problems like we do. But that isn't a insurmountable problem because we start out with variation on existing knowledge that we do not know will solve the problem we want to solve, either. In both cases, variation is not guarantee to solve problems. Both represent variation controlled by criticism. Human knowledge is explanatory in nature, while biological knowledge is non-explanatory. It reprints useful rules of thumb. While people can create both explanatory and non-explanotry knowledge, only people can create explanatory knowledge because only people are universal explainers. People can conjecture explanations about how the world works to solve problems. However, bacteria are not universal explainers because they cannot conceive of problems, let alone conceive of theories of how to solve them. So, what's key is that there are diffident kinds of knowledge. Explanatory and non-explanatory. For example, imagine I’ve been shipwrecked on a deserted island and I have partial amnesia due to the wreck. I remember that coconuts are edible so climb a tree to pick them. While attempting to pick a coconut, one falls, lands of a rock and splits open. Note that I did not intend for the coconut to fall, let alone plan for it to fall because I guessed coconuts that fall on rocks might crack open. The coconut falling was random in respect to the problem I hadn’t yet even tried to solve. Furthermore, due to my amnesia, I’ve hypothetically forgotten what I know about physics, including mass, inertia, etc. Specifically, I lack an explanation as to why the coconut landing on the rock causes it to open. As such, my knowledge of how to open coconuts is merely a useful rule of thumb, which is limited in reach. For example, in the absence of an explanation, I might collect coconuts picked from other trees, carry them to this same tree, climb it, then drop them on the rocks to open them. However, explanatory knowledge has significant reach. Specifically, if my explanatory knowledge of physics, including inertia, mass, etc. returned, I could use that explanation to strike coconut with any similar sized rock, rather than vice versa. Furthermore, I could exchange the rock with another object with Significant mass, such as an anchor and open objects other than coconuts, such as shells, use this knowledge to protect myself from attacking wildlife, etc. So, explanatory knowledge comes from intentional conjectures made by people and have significant reach. Non-explanatory knowledge (useful rules of thumb) represent unintentional conjectures and have limited reach. Knowledge can be created without intent in the form of useful rules of thumb. The knowledge of how to build biological adaptations isn’t explanatory in nature but non-explanatory and occasionally results in useful rule of thumb that improves biological adaptions.Popperian
October 17, 2015
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@box#292
Materialist simply assume the continued existence of replicators in all sizes and shapes — although that doesn’t make sense from the perspective of physics.
Can you kindly point out what part of the quote or the paper "doesn't make sense from the perspective of physics"? Thanks.Popperian
October 17, 2015
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Physicists meet to discuss the discovery of "highly organized information systems in nature". The conference "intends to address the "in vivo" (role of information in nature)", http://www.informationuniverse.rug.nl Physics joining ID in taking the lead in Evo Bio. Good on them.ppolish
October 17, 2015
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The whole argument is whether or not all mutations/ genetic change are accidents, errors and mistakes. That is why the OoL is KEY. If the OoL = Intelligent Design it would be a given that the genetic changes are NOT accidents, errors and mistakes. And Intelligent Design OoL means that evolution is directed, for the most part. Directed evolution is exemplified by evolutionary and genetic algorithms. The point of DNA repair is it is obvious it is a directed process. Transposition is also a directed process with the transposon containing the coding for two of the enzymes it requires to move around.Virgil Cain
October 17, 2015
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WD400 Please do tell hoe did a random process create a non random process to prevent random processes from happening?Andre
October 17, 2015
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Popperian #287, Your non-response illustrates clearly the point I was making: the blindness of materialists for the unlikelihood that bags of chemicals (or any dynamic conglomeration of chemicals) are dynamically stable. The writers of the paper you cite obviously suffer from the same blind spot. Materialist simply assume the continued existence of replicators in all sizes and shapes — although that doesn't make sense from the perspective of physics. I understand that this baseless assumption is foundational to your absurd belief. Probably foundational to the extend that reflecting on it is no longer possible. In the imagination of Darwinians, life-forms are easy to find and come in extreme abundance and variety. In that context, there is constructive "natural selection" for the pruning of all that excessive stuff.Box
October 17, 2015
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What's with all these spammy posts Mung? DNA repair doesn't lead to a change in genetics from one generation to the next, which is the relevant point for evolution. It's also random with respect to fitness -- if it wasn't then mutations would not be either. But surely you know this? So why all these silly comments?wd400
October 17, 2015
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wd400:
You seem to be confused about what mutations are in the other comment — instead of playing games do you want to say what non-random genetic changes (that aren’t mutations?) do you have in mind?
Let's start with DNA repair. DNA repair isn't mutations. It is non-random. And it affects the genome. Why in your mind does DNA repair not meet the definition?Mung
October 17, 2015
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For one because all the extra stuff actually clouds the point. For instance, there are almost certainly combinations of alleles ("genetics") that did not exist in "at least one organism in the original pool" that are present in the evolved population. That's one result of selection on heritable variants over generations that isn't included in your infantile "translations" of natural selection.wd400
October 17, 2015
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