The scientific method applied to the theory of Evolution

[otseng]

The theory of evolution is the dominant theory to explain life that we see on Earth. This theory is the gold standard in which to compare all other theories of life since it is by far the most widely accepted theory in society in regards to life.

What I would like for us to explore is to apply the scientific method to the theory of evolution.

So, for discussion:
What are the relevant terms that must be defined in discussing biological evolution?
What is the hypothesis?
What are the predictions?
What are the evidences that correlate (or does not correlate) with the predictions?

If there are any other things you feel should be added to the list of questions, feel free to bring them up.

I anticipate this will become a lengthy thread. So, I would like to encourage people to spawn off new threads if an area is brought up that requires deeper discussion.

[juliod]

I don't want to spend much time quibbling over semantics, but again, a major concept to me would involve a high level concept that is an essential element for understanding the theory. Major concepts would be more what would be taught in Evolution 101.

Again, you won't find the scientific method in an intro-level textbook. Textbooks only have a shallow treatment of the "major concepts" that are the conclusions of a million observations.

Jose, bless his little heart, thinks that by giving examples of the SM, and presenting more evidence, that students can be brought to more fully accept/understand evolution. I don't share that point of view, but since he is a perfesser, I will defer to him.

It's always possible for laypersons (including creationists) to bring up an infinity of unreasonable objections to any scientific work. You can spend your whole life trying to answer them.

The SM, as I have said, takes place at the extreme details of current scientific research. Down there we form a hypothesis (usually implicit rather than explicit) and test it. To succeed you have to get enough data to accept or reject the hypothesis. That's the point: via the SM we rule out all other explanations based on the available evidence. Good science forms firm conclusions.

And to criticize another scientists work, it is not enough to cast doubt on it. You must formulate a hypothesis of your own and test it. If you produce no evidence of your own then you fail automatically because you don't provide an alternative.

Science proceeds by the hypothesis, evidence, conclusion scheme. You simply can't use this scheme to examine evolution from a textbook.

(And at the detailed level, 100% of biological research supports evolution, of course...)

DanZ

[Jose]

Bless his little heart, Jose also had the curious circumstance of being his department's Associate Chair for a decade or so, in charge of assigning everyone else what courses to teach, and also being the lucky guy to whom students complained about everyone's teaching.

My first task, it turned out, was to meet with the honors ecology class after the grades had been turned in (the students feared retribution). All of 'em were being given D's and F's, but all of them also had GPA's of 3.8 or higher. They were all very annoyed.

The insight came when one of them, whom I knew because her lab and mine were having joint group meetings, complained about the paper they'd been assigned. It was supposed to deal with some question or other. She'd asked her research advisor to read it, and see if it was OK. Her advisor said, "it's great!" So, she turned it in... and got a D because it didn't address the question. So, here we have the situation: two perfessers read the same assignment, read the student's paper, and one of 'em says the paper is great, while the other says it doesn't even address the question that was assigned. No wonder the student is confused.

It boiled down to this: in the ecology course, it was assumed that everyone would follow The Scientific Method for everything they ever did. The students' prior courses had all been in "the molecular tradition," which doesn't use the "scientific method." Therefore, in the words of the perfesser, "they didn't know how to do science."

Now, in the journals we publish in, Dan, we present an experiment, then consider alternative explanations, then present an experiment or two that can distinguish among them. We go on like this until we've made our case.

In many of the organismal biology courses, it's not like that. The hypothesis must be stated in the introduction. The experimental procedures, logic, everything must be in the Methods section. The Results section cannot say anything about experimental logic, ever. I quote the entire Results section from a paper provided to me by a friend, as an example: "The results of experiment 1 are shown in figure 1. The results of experiment 2 are shown in figure 2." The Discussion section must then compare the observed results to the predicted results, and may state its conclusion as "the null hypothesis is supported."

In these fields, it is forbidden to write about two experiments that follow one after the other, because you can't put the hypothesis for the second experiment into the Introduction.

In these fields, this is the only way to do science. Anything else isn't science. Unless you state your hypothesis first, it's not an experiment, because you've done it wrong.

So, it actually is valid to apply "The Scientific Method" to evolution, even starting at the beginning. I wouldn't a thunk it some years ago, but now I recognize that in some fields, it makes sense.

I might also note, just for laughs, that the SM follows a tradition of organismal and field biologists over many, many decades, and is probably the version of scientific investigation that is closest to that of Darwin himself. Those of us who use the "biochemical tradition" are the new ones.

*see the May issue of The American Biology Teacher, page 262 for a more extensive discussion. It's not in digital form on the web yet, but I may edit this to include the URL when it finally shows up.

[otseng]

Sorry, I tend to use the actual scientific terminology. I feel that most other terms are in some form misrepresentations, often devised for the purpose of misrepresentation to then attacks and then say "see, evolution is wrong." And then we go on for 50-100 posts with the "is/aint" stuff. Trust me, I have seen that many times.

I can believe you because I as well have seen this too many times. That is why I'd like for us on the onset to be clear on the terminology.

You keep on qualifying the ToE with the "Scientific" ToE. I am not familiar with this terminology. What is the difference between the "Scientific Theory of Evolution" and the "Theory of Evolution"? How would you define each?

creation, intelligent design, and common features due to a common designer The question is "what is the evidence for evolution," not "what is the evidence for ruling out a god that can create everything just as it is, and may have done so yesterday, giving us memories of things that never happened." We must look at the evidence that exists, and see where it leads us.

I don't want to spend too much time in this thread on creationism/ID. There are already plenty of threads covering those. I would agree that the purpose of this thread is to present the evidence for the ToE. However, I would add something that you had mentioned before:

It is insufficient merely to show that there is evidence for something. It is also necessary to show that said evidence cannot be explained by alternative models.

So, that is why I made the comment about using Linnaeus' taxonomy. Offering it as evidence of common descent doesn't really apply since he believed in creationism, not common descent, when he classified organisms.

What would help in explaining homologous features is connecting the dots between microevolution and homology. That would be better evidence of using homology to support the ToE.

microevolution and macroevolution
We know a lot about mutations that alter these genes, or the patterns of expression of these genes. We can, therefore, account for macroevolution--as initially defined--by the exact same process as microevolution. The only difference is which genes are involved.

From my current understanding of macroevolution, the only difference between microevolution and macroevolution is the time span involved. I am of the impression that macroevolution is a bunch of microevolutions added up over several population generations. Whereas, a macromutation is a "large" change from one generation to the next (like the Antennapedia mutation).

Do we buy this mechanism? Are we agreed that we can rule out the mythic "changing individual" as a component of evolution?

We can safely rule out Lamarkianism. Organisms do not pass on traits that have been acquired during their parents' lifetime. My future kids will not have big muscles if I work out every single day (though wouldn't it be easier if it did work out that way).

[Jose]

creation, intelligent design, and common features due to a common designer The question is "what is the evidence for evolution," not "what is the evidence for ruling out a god that can create everything just as it is, and may have done so yesterday, giving us memories of things that never happened." We must look at the evidence that exists, and see where it leads us.

I don't want to spend too much time in this thread on creationism/ID. There are already plenty of threads covering those. I would agree that the purpose of this thread is to present the evidence for the ToE. However, I would add something that you had mentioned before:

It is insufficient merely to show that there is evidence for something. It is also necessary to show that said evidence cannot be explained by alternative models.

I think we are saying the same thing. There are plenty of other threads for exploring creation/ID. Here, we're dealing with ToE. We agree we should deal with the evidence.

So, that is why I made the comment about using Linnaeus' taxonomy. Offering it as evidence of common descent doesn't really apply since he believed in creationism, not common descent, when he classified organisms.

I agree. It is not "evidence" per se, but it is a part of the dataset that led people to propose the theory in the first place. [Earlier, we had thought it would be useful to identify some of those initial observations, which include the hierarchical relationships.]

Clearly, hierarchical relationships alone would not convince anyone of anything much. But, let's think of it this way: What are all of the possible models we can imagine for how the existing hierarchical relationships came to be?

• god created everything that way (can't be tested; we'd have to ask god)
• there's some kind of family relationship (ie common descent)(testable, makes predictions)
• space aliens put everything here (silly, but potentially testable; if we ever encounter them again, perhaps we could ask them)
• it's always been like this; we don't know why, but that's just how it is (also testable; predicts that changes don't happen)

There may be other explanations that we could think up.

The next step is to evaluate the alternatives. For models that make predictions, we should be able to test the predictions.

So, you're right. Bringing in Linnaeus isn't evidence in itself. It merely highlights the fact that the physical relationships of living things have long been known. But, once we observe these physical relationships, it becomes interesting to ask whether they reflect genetic relationships. That is, if these relationships result from common descent, then there must be a genetic mechanism that we can uncover, that is in operation today, and that we can observe directly (albeit for a very tiny slice of geological time).

From my current understanding of macroevolution, the only difference between microevolution and macroevolution is the time span involved. I am of the impression that macroevolution is a bunch of microevolutions added up over several population generations. Whereas, a macromutation is a "large" change from one generation to the next (like the Antennapedia mutation).

You are essentially correct. We get macroevolution if microevolution occurs for a very long time. Probably, millions of generations is what we need to have it become evident.

As for Antennapedia (Antp), it and similar mutations (such as bithorax, postbithorax, Ultrabithorax, proboscipedia, nasobemia, and all of those that distinguish different varieties of Brassica napus (broccoli, cauliflower, brussels sprouts, cabbage, kohlrabi, etc) are just mutations. They are mutations in genes that control the expression of other genes, and therefore alter the pattern of development. But, they are not "large" mutations, even though early evolutionary biologists imagined that some kind of "large" mutation ("macro" mutation) would be necessary to do that. Now that we know how it works, we know that these are just ordinary genes that mutate just like any others. They are subject to microevolution, just like any others. The only thing that could be considered "special" about them is that they control the expression of other genes, and thus "call up the subroutines" that create particular structures.

Knowing about these developmental-control genes makes it much, much easier to understand evolution. We can see how lobe-finned fish could give rise to tetrapods because we know most of the genes involved in limb development, so we have a sense of how minor changes in these genes (or their expression) can lead to seemingly-large changes in limb morphology. This, in turn, makes it much, much easier to understand "homology," in the sense that all of the tetrapod limbs share common developmental features determined by common genes.

But this gets a bit ahead of ourselves. I think it might be profitable to explore the predictions that are made by the various models we can envision to explain the hierarchical relationships of living things. Homology and all this other fun stuff will eventually fall out of that exploration. So: If common descent were the actual explanation of the relationships among living things, what must be true? What predictions does this model make?

[steen]

Sorry, I tend to use the actual scientific terminology. I feel that most other terms are in some form misrepresentations, often devised for the purpose of misrepresentation to then attacks and then say "see, evolution is wrong." And then we go on for 50-100 posts with the "is/aint" stuff. Trust me, I have seen that many times.

I can believe you because I as well have seen this too many times. That is why I'd like for us on the onset to be clear on the terminology.

You keep on qualifying the ToE with the "Scientific" ToE. I am not familiar with this terminology. What is the difference between the "Scientific Theory of Evolution" and the "Theory of Evolution"? How would you define each?

When I see "ToE," it frequently is coupled with "only a theory" claims. The correct description is the SToE, just as is the case with all other Scientific Theories of.... (More of a stickler point, but in some discussions it does matter. "theory" in general language is very different than the meaning of "Scientific Theory" in science. What is generally understood as "theory" in general terms is at best the equivalent of a Scientific Hypothesis, the 1st step of the Scientific Method, not the last)
.....

microevolution and macroevolution
We know a lot about mutations that alter these genes, or the patterns of expression of these genes. We can, therefore, account for macroevolution--as initially defined--by the exact same process as microevolution. The only difference is which genes are involved.

From my current understanding of macroevolution, the only difference between microevolution and macroevolution is the time span involved.

Well, you can have microevolution go on forever, and you can have macroevolution over just a few generations. It is a matter of whether the changes occur on one population or whether the population somehow gets split up.

But then, the classical example is that of ring species, where a population as it migrates around a mountain, the globe or something like that eventually meets up with its originator but is a different species at the interface.

I am of the impression that macroevolution is a bunch of microevolutions added up over several population generations. Whereas, a macromutation is a "large" change from one generation to the next (like the Antennapedia mutation).

It can also result from a single mutation, though. The nylon bacteria is a classic example Nylon bug

[otseng]

So: If common descent were the actual explanation of the relationships among living things, what must be true? What predictions does this model make?

This seems to be a premature approach at this point in time. Rather, shouldn't we first seek to find what evidence would lead to the formation of the hypothesis of the ToE? But, if this is the approach you would like to present first, I don't mind. But, I'd like to eventually see what I suggest at some point in this thread.

You keep on qualifying the ToE with the "Scientific" ToE. I am not familiar with this terminology. What is the difference between the "Scientific Theory of Evolution" and the "Theory of Evolution"? How would you define each?

When I see "ToE," it frequently is coupled with "only a theory" claims. The correct description is the SToE, just as is the case with all other Scientific Theories of.... (More of a stickler point, but in some discussions it does matter. "theory" in general language is very different than the meaning of "Scientific Theory" in science. What is generally understood as "theory" in general terms is at best the equivalent of a Scientific Hypothesis, the 1st step of the Scientific Method, not the last)

You still have not provided a definition of the SToE and the ToE. I would suggest for the purposes of the discussion here that they are the same thing. Until definitions can be provided that shows that these two terms are different, I will continue to refer to it as the "Theory of Evolution".

From my current understanding of macroevolution, the only difference between microevolution and macroevolution is the time span involved.

Well, you can have microevolution go on forever, and you can have macroevolution over just a few generations. It is a matter of whether the changes occur on one population or whether the population somehow gets split up.

Could you elaborate on macroevolution occurring over a few generations? This is something that I also have not heard about. How would you classify something as having macroevolved?

[Jose]

So: If common descent were the actual explanation of the relationships among living things, what must be true? What predictions does this model make?

This seems to be a premature approach at this point in time. Rather, shouldn't we first seek to find what evidence would lead to the formation of the hypothesis of the ToE? But, if this is the approach you would like to present first, I don't mind. But, I'd like to eventually see what I suggest at some point in this thread.

I think that this is part of what you're after. It's just that my brain works in weird ways, from what I hear, so it seems like we're off on a tangent. In an earlier post, I'd suggested that the hierarchical relationships among living things represent one of those bits of evidence that led to the formation of the ToE. I'm following that up.

For the sake of our current discussion, in which we're trying to distinguish between creation and evolution, the hierarchical relationships require very different types of explanations. The creation model requires that we imbue god with a certain whimsy, or at least some odd sort of notion that life should be related-looking in this particular way. Now, if I were creating life, I'd make all kinds of different things, without restricting myself the way life on earth is restricted. But, that's just me. Maybe god had some sort of restrictions placed upon him somehow.

By contrast, ToE pretty much requires hierarchical relationships--which is why I asked the question quoted above. Evolution cannot produce anything but hierarchical relationships. That is, evolution (common descent) provides a very simple explanation for this observation.

So, there's step one. Hierarchical relationships are exactly what we'd get through evolution. Therefore, such relationships provide the first bit of evidence upon which ToE was founded.

If this is acceptable logic, I'll go on.

I'll go on anyway. Let's consider dog breeding, or any other breeding program (horses, corn, rice, chickens, etc). Humans have demonstrated many, many times (enough so that we can call it fact) that it is possible to change the character of a lineage just by choosing which individuals will be the parents of the next generation. In our small population of dogs, there are some whose characters we like, so we use them as parents. The others had very similar characteristics, but in the overall diversity of our population, there are a few that we like best. We do this generation after generation after generation.

After a while (usually, a very long time, like 5000 years), the dogs we have are unlike the dogs we started with, in a great many ways. More interestingly, different groups of dogs are different from each other. They were bred by different groups of people for different characteristics. This includes not only morphology (whippets vs chihuahuas vs retrievers vs border collies), but also behavior (herding instinct, retrieving instinct, digging instinct, pulling instinct).

In any one generation, however, we can't tell that anything is happening. Our dogs are born, live their lives, and die. Some have puppies, some don't. All we see is the diversity among our dogs, and we think that some are "really good dogs" compared to the average.

OK. That's the next observation. Selective breeding changes the character of populations over time. Along with hierarchical relationships, the ability of living things to change over time (not individually, but as the array of characteristics in the population), provide information that led to the formulation of ToE.

(to steen) You still have not provided a definition of the SToE and the ToE.... I will continue to refer to it as the "Theory of Evolution".

ToE is fine. Steen's point (pardon me, steen, if I mis-speak) is to distinguish the scientific definition of "theory" from the colloquial definition of "just a guess." It is also to distinguish the actual mechanism from the misconceptions that many people have (such as "evolving in order to survive, or individuals changing, rather than populations showing different frequencies of various traits). Because these are such common misconceptions, and because our teaching does not dispel them (but sometimes establishes them), I hope that any of our readers will ask what the heck we're talking about, if it sounds like we're not describing evolution as they unbderstand it.

Could you elaborate on macroevolution occurring over a few generations? This is something that I also have not heard about. How would you classify something as having macroevolved?

This is a simple result of creationists having re-defined "macroevolution." All of the evolutionary biologists I know use "macroevolution" to refer to a "change in morphology." This used to be equated with formation of species, because we didn't know the mechanism. Now that we do know the mechanism, it's no longer considered to be part of speciation.

By this definition, all of those different breeds of dogs, that look so different from each other, differ by macroevolution events. These macroevolution events occurred by the mechanism of microevolution; the genes that were involved were those that control various aspects of embryonic development. There weren't significant changes in genes that control egg/sperm fusion, or other critical aspects of reproduction, so the different breeds remain a single species. So, here we have macroevolution without speciation.

Mutations in developmental-control genes can give morphological change in a single generation. The infamous 4-winged fly illustrates this, although creationists like to say that this is irrelevant and not evolution. Despite what they say, this is morphological change in a few generations, and therefore macroevolution (without speciation).

On the other hand, it is also possible to have speciation without macroevolution. Sunflowers that become tetraploid are no longer cross-fertile with their diploid progenitors, and represent a new species. But, this species looks like the original, so there's no macroevolution. Drosophial melanogaster and D. simulans look so similar that I can't tell them apart. Yet, they produce sterile hybrids, and are thus different species. Again, here is speciation without macroevolution.

In the Grand Scheme of Things, most different species show morphological differences. Certainly, different genera show morphological differences. So, in a vague, general sense, we see the results of macroevolution when we look at the overall diversity of life.

[steen]

Rather, shouldn't we first seek to find what evidence would lead to the formation of the hypothesis of the ToE?

That has been done the last 150 years. (Well, actually, the expansion of this intital hypothesis. The original hypothesis was mainly formulated on the Data Darwin collected on his trip on H.M.S. Beagle.

You keep on qualifying the ToE with the "Scientific" ToE. I am not familiar with this terminology. What is the difference between the "Scientific Theory of Evolution" and the "Theory of Evolution"? How would you define each?

When I see "ToE," it frequently is coupled with "only a theory" claims. The correct description is the SToE, just as is the case with all other Scientific Theories of.... (More of a stickler point, but in some discussions it does matter. "theory" in general language is very different than the meaning of "Scientific Theory" in science. What is generally understood as "theory" in general terms is at best the equivalent of a Scientific Hypothesis, the 1st step of the Scientific Method, not the last)

You still have not provided a definition of the SToE and the ToE. I would suggest for the purposes of the discussion here that they are the same thing. Until definitions can be provided that shows that these two terms are different, I will continue to refer to it as the "Theory of Evolution".

Well, from a scientists's perspective, they are the same. From a creationist view, ToE is "only a theory," which is why I don't like the over-simplification. Yes, I know I am a stickler here, but I have been in enough arguments in creationists to insist on that one to avoid misrepresentations/deceptions down the line when other posters butt in.
But what IS the SToE? The most basic one can be exprerssed rather simply (with a few important elaborations in parenthesis) as: The allele expression in a population changes over (generational) time (in response to environmental changes).

From my current understanding of macroevolution, the only difference between microevolution and macroevolution is the time span involved.

Well, you can have microevolution go on forever, and you can have macroevolution over just a few generations. It is a matter of whether the changes occur on one population or whether the population somehow gets split up.

Could you elaborate on macroevolution occurring over a few generations? This is something that I also have not heard about. How would you classify something as having macroevolved?

Well, first of all, "macro-evolution" used to mean the evolvement of new species. But when creationists started using it and found out that new species had indeed been directly observed to have evolved, they rapidly started shifting the goal post (Another reason why we so often find creationists to be dishonest). So now it has to be "different" species, like "but they are all finches and not ostriches, so no macro-evolution occured," or "But they are still fish." So what the creationists see as the boundary is rather fluid, vague and undefined. It can be anythign from a new species to an entirely new class. The original meaning though, was to distinguish between species, which is how I use it when I use it at all. To me, the point is meaningless because it is all "Evolution." There is no change in mechanisms, process, or potential changes that makes some into "micro" and other changes into "macro"

But given that this meaningless claim is butted around, yes there are examples of even single mutations leading to new, novel species with completely different function, food sources etc.

An easy one is the mutation into a nylon-digestive bacteria. Fascinating reading:
http://www.nmsr.org/nylon.htm
One single mutation caused an entirely new bacteria, digesting nylon which had never existed before in the world's history. It is a novel and unique change that led to the use of a new and abundant resource with no competition.

And, of course, talk.origin has several links to the observed emergence of new species. Finally, the nylon bug site has a link to other new mutations with significant changes in populations:
http://www.gate.net/~rwms/EvoMutations.html

[otseng]

For the sake of our current discussion, in which we're trying to distinguish between creation and evolution, the hierarchical relationships require very different types of explanations.

Some more comments about hierarchical relationships. I think hierarchical relationships is more of a result of how the human mind likes to organize things, than necessarily indicating any particular lineage between things. This is demonstrated by the fact that practically anything can be organized into hierarchical relationships. As stated here, "Almost anything, animate objects, inanimate objects, places, and events, may be classified according to some taxonomic scheme." Even when I program in Java (and this goes the same for any Object Oriented Programming Language), one of the first things I do is organize classes into a hierarchical pattern. This does not mean that one class has descended from any other, but simply that they share properties that allow creation of a hierarchical diagram.

However, I will agree that hierarchical relationships is a necessary element for the ToE. Though I think we both agree that it is insufficient to lead to the hypothesis.

Now, if I were creating life, I'd make all kinds of different things, without restricting myself the way life on earth is restricted. But, that's just me. Maybe god had some sort of restrictions placed upon him somehow.

There certainly are restrictions on how life can come out. Biochemical and physical constraints impose a restriction on what life can be like. Some of the restrictions I've mentioned here (water based, carbon based, light based).

Hierarchical relationships are exactly what we'd get through evolution.

Let me quibble a little bit over this. Hierarchical relationships would be what we should see if the ToE is true. However, the hierarchical relationships that we do see would still need to be explained. To put it another way, we'll need to be careful about using circular logic by saying hierarchical relationships leads to the ToE. And the ToE leads to hierarchical relationships. So, a bit more evidence will need to be introduced to break the circular argument.

Let's consider dog breeding, or any other breeding program (horses, corn, rice, chickens, etc).

How would this be different from Mendelian genetics? In your example, a dog is still a dog, even though they would have morphological differences.

ToE is fine. Steen's point (pardon me, steen, if I mis-speak) is to distinguish the scientific definition of "theory" from the colloquial definition of "just a guess."

Good. I'll continue to use ToE. Also, to clarify my position, when I use the word "theory" in the "theory of evolution", I use the term in the scientific sense, rather than "just a guess".

Mutations in developmental-control genes can give morphological change in a single generation.

For further terminology clarification, could you comment on single generation mutations versus saltationism?

[Jose]

As always, otseng, you raise valid and interesting points.

You are right that one can devise a dichotomous key for most things, and according to this key, the things show a hierarchical relationship. This would be something like alive vs not-alive, plant vs animal, etc. I've done the same thing with furniture to illustrate the basic principle of "phylogentic trees." The question then becomes: what is the history that led to this particular relationship?

Here's where the scientific methodology comes in. We suggest possible explanations, then go to the next step: test those explanations. The best way to test them seems to be to determine whether they make predictions that are borne out.

One explanation is that our hierarchical tree is an artifact of our classification-happy minds. This explanation predicts that other features that we did not use in the classification process will be scattered randomly among the different organisms. The strongest test would be to look at characteristics that weren't known when the tree was first built--perhaps biochemical aspects.

An alternate explanation is common descent. Now, if the relationships result from common descent, then the various biochemical aspects should also show the same hierarchical relationships. That is, different kinds of characters should be congruent with the same tree, even if those charactes were previously unknown.

There's always wiggle-room, though, which is where things get complicated. We should predict also that we are imperfect, and that we will find some examples of characteristics that seem to contradict the general pattern. Do these examples disprove common descent, or do they prove that we were naive in our earlier understanding and predictions?

In such a case, we need to examine the examples more carefully, examine our previous assumptions about relationships more carefully, and ask what's wrong. It could be that the common descent idea is wrong, or that the biochemical characteristics are actually very different, but we don't realize it, or that we used inappropriate characters to make our tree initially (like color, or like wings vs no wings.)

We'd predict that, if we understand the different characteristics well, then we should find that many of them follow the same hierarchical pattern. This gets us to the definition of "homology," which the ID folks explain as circular reasoning and therefore hogwash. The point, really, is to compare apples with apples and oranges with oranges, rather than apples with duodenums.

If, on the other hand, everything was created by an all-powerful god who therefore had no constraints, then we predict none of these things. We predict that no two organisms have any reason to be similar in any particular way. We have no reason to imagine the same chemistry, the same basic rules of metabolism, or anything. Of course, we also predict that no matter what we actually find, we will always be able to say "that's how god made it." However, we might begin to wonder why an all-powerful god would constrain himself to a very narrow window of all possible chemistries, if we find that life is so constrained.

(re: dog breeding) How would this be different from Mendelian genetics? In your example, a dog is still a dog, even though they would have morphological differences.

There are two flavors of answers to this question. One is historical: Darwin didn't know about Mendel when he used selective breeding as an example of morphological change over time. He simply said "gosh, look at that. If individuals with certain traits are selected as the parents for the next generation, then those traits tend to become common among the offspring. Over several generations, they become common in the breed of dogs. Maybe the same kind of thing happens in the wild, but with environmental conditions determining which individuals have more or fewer offspring."

The other flavor of answer is that it is exactly Mendelian genetics. Now that we know what Darwin didn't, we can say that's how evolution works. We can also say that it should have been obvious to us that there's no way evolution could work except by normal everyday mechanisms, of which genetic inheritance is one.

Dogs are still dogs? The only bearing that this has on the issue is in terms of giving us a time frame. It looks like wolves were domesticated (ie became "dogs") 60,000 years ago (or maybe 100,000). The molecular evidence indicates that there has been a fair amount of cross-breeding, and occasional back-breeding with wolves. This might actually be a kind of selection against mutations that would affect sperm/egg recognition, or chromosome segregation at meiosis, and would tend to maintain this diverse group as a single species.

Otherwise, the fact that dogs are still dogs tells us that there's no reason to imagine that evolution has to occur really fast, or in any magical way, or in sudden leaps in which creatures become wildly different all at once. The idea that there should be some kind of sudden appearance of new traits, and that this is what causes speciation, is a misconception. By normal Mendelian mechanisms, what happens depends on which genes are involved, but it's always the same methods. It's just plain genetics.

Mutations in developmental-control genes can give morphological change in a single generation.

For further terminology clarification, could you comment on single generation mutations versus saltationism?

In biology, saltation (from Latin, saltus, "leap") is a sudden change from one generation to the next, that is large, or very large, in comparison with the usual variation of an organism. The term is used for occasionally hypothesized, nongradual changes—especially single-step speciation—that are atypical of, or violate, standard Darwinian evolution. The unorthodox emphasis on saltation as a means of evolutionary change is called saltationism.

I'd never heard of saltationism before, so what I will say is based on Wiki's definition. I think one could imagine that when a plant becomes tetraploid through an error of cell division in early embryogenesis, and thus becomes a new species in a single generation, then this is a saltation event. It's single-step speciation using a non-Mendelian mechanism of altering genetics. It lacks any "large" changes, however, and thus doesn't fit the "occasionally hypothesized" notion of sudden morphological change.

By contrast, a homeotic mutation such as that which turns cabbage into cauliflower, or that turns a wild rose with 5 petals and a hundred stamens into a 'double' rose with 55 petals and 50 stamens, is a single-gene mutation that alters morphology. These are normal Mendelian genetics, simply resulting from mutations in genes that determine which "developmental pathway" (or developmental subroutine) the cells follow. In cauliflower, the flower-initiation pathway is turned on reiteratively. In double flowers, the cells that would normally form stamens turn on the petal-development pathway. I wouldn't call this "saltation," but merely "mutations in developmental control genes."

Saltation may be what creationists imagine when they think of punctuated equilibrium. The (incorrect) notion would be that things go along with no evolution happening, then all of a sudden there's a saltation event, which punctuates the equilibrium, and causes massive macroevolution really quickly. It's instructive to look at some of the punctuations, and think about this. After some (most? all? I'm not sure) of the mass extinctions, new life forms arose in a roughly similar time frame. There was a sort of an equilibrium when the dinosaurs were alive, in which evolutionary change was moderately slow. The dinosaurs lasted a couple of hundred million years. There were changes, but they were moderately gradual.

During this time, mammals arose, but spent a hundred million years not going anywhere. Their environment was pretty stable--full of carnivores, full of effective herbivores with whom they couldn't easily compete.

Then, wham-o! The dinos are gone. The equilibrium is broken. Mammals are able to enter new habitats that were off-limits to them before. Occasional mutations that would have been selected against before are now sometimes kinda useful, and are selected for. Pretty soon, we have a new equilibrium with a new environment, with mammals in the roles of herbivores and carnivores, and with flowering plants as the ecological producers. The rate of change slows down.

How fast was this rapid diversification of mammals? The geological data tell us that the dinosaurs bit the dust (iridium dust, probably) at 65MYA. The adaptive radiation of the mammals was mostly over by 55MYA. That "saltation" of "sudden appearance" of lots of mammals, that rapid change between equilibrium states, took 10 million years. So, rapid evolution seems to occur on a time-scale of millions of years, or even tens of millions.

This is plenty of time for normal, garden-variety Mendelian genetics to work. Morphological change, which seems so hard to imagine between species, and which is so obviously just diversity within species, results simply from the diversity within species being amplified over time. Population A diversifies in one direction, and population B diversifies in another direction. In time, we've got two species that look kinda different. It's Mendelian genetics and it's every species reproducing according to its kind. It's just that "kind" includes genetic diversity, and diversity allows the "kind" to change over time.