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.

[otseng]

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

Thank you. I take your comment with great weight coming from someone of your standing.

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.

I would agree. Please present the evidence of how the data correlates with each other.

The other flavor of answer is that it is exactly Mendelian genetics.

Are you saying that the ToE includes Mendelian genetics? If so, I would argue that the mechanisms for the two are completely different. Each has its own hypothesis which is completely different than the other. If not, how then can Mendelian genetics be used as evidence for the ToE since they are unrelated?

Saltation may be what creationists imagine when they think of punctuated equilibrium.

Even more new terminology in this thread. I have my own view of punctuated equilibrium, which is different from saltationism. But before completely leaving saltationism, would it be safe to say that saltationism is ruled out as part of the ToE?

As for punc-eq, I view that as more of an explanation of the "abrupt" changes in the fossil record, rather than directly related to the ToE. That is, does the ToE predict punc-eq? If so, how?

[juliod]

If not, how then can Mendelian genetics be used as evidence for the ToE since they are unrelated?

It's because of the simple and elagant interdigitation of the main unifying biological principles. In biology (via evolution) these really are unifying concepts.

What you and Jose have been talking about brings together three major fields. One is Mendelian genetics, which applies strictly to sexually-reproducing organisms. Another is population biology, or the study of properties of groups "in the wild". Another is evolution, or the principle of change in populations over time. And then there is molecular genetics. Oops, that's four major areas.

Oh, how the physicists are jealous!

Yeah, sure they can unify atomic physics with astrophysics, but it requires so much math that no one understand it. In biology each major area can explain and expand each other major area. Very neat.

DanZ

[steen]

But before completely leaving saltationism, would it be safe to say that saltationism is ruled out as part of the ToE?

I don't see why it would be. A significant mutation cna spread fast in a population, causing a significant cange over relatively few generations.

As for punc-eq, I view that as more of an explanation of the "abrupt" changes in the fossil record, rather than directly related to the ToE. That is, does the ToE predict punc-eq? If so, how?

The SToE doesn't really predict one vs the other. Rather, the data shows that P.E. is the actual occurence. SToE doesn't predict one over the other, though.

[QED]

Even more new terminology in this thread. I have my own view of punctuated equilibrium, which is different from saltationism. But before completely leaving saltationism, would it be safe to say that saltationism is ruled out as part of the ToE?

As I understand it, a genetic micro-mutation could be responsible for a macro-mutation in the appearance of an organism. Thinking of a computer program that prints out a row of three O's:

for i=1 to 3
print('O')
next i
run

OOO

If there was a power glitch that corrupted the memory storing the program, it might produce this when it was run again:

OOOOO

We certainly wouldn't expect to find the program in our corrupted memory looking like this:

for i=1 to 3
print('O')
next i
for i=1 to 2
print('O')
next i

But instead we would most probably find this:

for i=1 to 5
print('O')
next i

The point I'm making is that the mutation of a small genetic instruction could add a whole extra body-segment to an invertebrate.

[Jose]

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.

I would agree. Please present the evidence of how the data correlates with each other.

Here's a phylogenetic tree based on DNA sequence data:

Molecular tree DNA evidence, phylogeny reconstruction methods and models deliver a topology, or branching pattern of mammalian phylogeny. The dotted lines indicate aspects for which further corroboration is needed, and there is some debate about the molecular dating of the various branching events. The orders Afrosoricida, Eulipotyphla and Cetartiodactyla are recent orders developed due to genomic evidence. (Source: Adapted from Murphy et al. 2001, courtesy of Ole Madsen and Wilfried W. de Jong)

As we see from the caption associated with the tree, there are some dotted lines. These are not fully resolved by the current data, apparently. The caption also notes that the dating of the branches--as we'd imagine, since we're looking at existing DNA molecules, and the historical mutation rate is not recorded anywhere. We need fossil data to determine the time scale, and that's not included in this figure.

The little drawings on the right are of different groups of animals. We might, if we wanted, call them "kinds" of animals. In general, the ones that are most similar are linked by the shortest lines. For example, rodents and rabbits are side-by-side, just as the morphological relationships suggest. Monotremes and marsupials are separated from the placental mammals by the longest lines. This is a pretty low-resolution tree, however, so we're looking at the Big Picture among land animals. Still, the two datasets pretty much give the same picture.

There are controversies, or discussions, about the details when we get down to finer detail. Is the branching order ABCDE or ACBDE? When we hear of trees that don't match, it's not the big picture that's at issue--the macroevolution--but the more recent divergences--the microevolution. It's the specifics of the aspect of ToE that creationists accept.

In the even bigger picture, when we use DNA sequences to look at All of Life, we get this image:

This particular image doesn't have names on the bacteria, but it should do the job. Maybe I can replace it with a better one when I get a chance. Here, we can see some other things that aren't obvious otherwise. All of the bacteria are separated significantly from all of the eukaryotes (fungi, protozoa, plants, animals), just as cellular morphology would suggest. The bacteria are divided into two main groups, eucarya and archaea, which differ in significant biochemical ways (like the chemistry of the lipids in the cell membrane). Chemically, plants and animals are pretty similar, and on this tree, they are nearby twigs on the end of a branch.

The other flavor of answer is that it is exactly Mendelian genetics.

Are you saying that the ToE includes Mendelian genetics? If so, I would argue that the mechanisms for the two are completely different. Each has its own hypothesis which is completely different than the other. If not, how then can Mendelian genetics be used as evidence for the ToE since they are unrelated?

Indeed, ToE includes Mendelian genetics--as well as non-Mendelian genetics. ToE posits that heritable variation is the raw material for natural selection and genetic drift, which requires that there is some way of generating heritable variation. The "heritable" part comes from the DNA that codes for the proteins that build the organism. The "variation" part comes from the fact that DNA mutates, creating new "versions" of genes. Meiotic recombination can shuffle these mutations to increase the diversity by mixing and matching different versions of different genes.

It would probably be "allowed" to say that Darwin's original theory predicted that mechanisms should exist for producing heritable variation. He didn't know what kind of mechanism there might be, because he was unaware of Mendel's work. He favored Lamarck's notion that animals could change during their lifetime, then pass on the changes to their offspring. This turned out not to be true. Lamarck had a good idea, but life doesn't work that way.

Having to work with Mendel and random mutation makes the process harder to follow, because it introduces that confusing randomness. However, that's how genetics works, so we're stuck with having to understand it.

In any event, ToE and genetics are not unrelated, but deeply intertwined. Basically, Mendelian genetics says that organisms reproduce according to their kind, passing on their genes from parent to offspring. What Mendel showed is that genes come in different versions, and that sometimes, one version is "dominant" over another. It turns out, of course, that there are hundreds or thousands of different versions of most genes (1388 different ones for the cystic fibrosis gene). Very few genes show strict dominance, so I generally don't make a big deal of it when I teach about it (heretical notion, coming from a geneticist!). Rather, I say that different versions of genes are likely to influence the characteristics of organisms sooner or later, one way or another. When they do, then they can affect the reproductive success of the individuals that carry them.

And that causes evolutionary change.

Saltation may be what creationists imagine when they think of punctuated equilibrium.

Even more new terminology in this thread. I have my own view of punctuated equilibrium, which is different from saltationism. But before completely leaving saltationism, would it be safe to say that saltationism is ruled out as part of the ToE?

As for punc-eq, I view that as more of an explanation of the "abrupt" changes in the fossil record, rather than directly related to the ToE. That is, does the ToE predict punc-eq? If so, how?

Ah, yes...terminology. Hateful, isn't it? But, to talk about things, we have to call 'em something, so here we are. Well, ToE states that there is change over time. It does not state that individual animals change, even though Lamarck and Darwin thought it likely. Mendelian genetics explains that the mechanism is by the generation of diversity, from which selection determines which individuals, if any, have more offspring.

ToE does not address the rate of change, either. However, the rate is part of it, so we talk about it within the discussion of ToE. There are two issues. One is that we don't think we see lots of rapid evolution when we look around. Why not? First, we don't recognize extinction or the death of "mutants" as part of natural selection; we think "evolution" has to be "things getting better." Second, the environments we look in are relatively stable, so selection acts to keep things pretty much as they are. You know--mutants are "weird" so they are selected against.

It's typically during times of environmental change that evolutionary change occurs most rapidly. The rate of mutation doesn't change, but the selection conditions do. Therefore, mutations that might have been advantageous before may be less so now, and vice versa. That is, "weird" mutations might turn out to be helpful, and be selected for instead of against.

So, the sort of image we have of the rate of evolutionary change is that it's fairly slow in stable environments (equilbrium), but fairly rapid during times of environmental change (times that "punctuate" the equilibria before and after).

But, these are not abrupt changes. They are simply faster than during times of stability. We can get a measure of how long it takes for an "abrupt" change to occur by looking at the length of time it has taken to develop new species diversity after a major extinction. For the extinctions I've read about, it's been around 10 million years. This is an eyeblink in geological time, but it's still one heckuvalot of generations.

What it does not include is great morphological changes, complete with speciation, in a single jump between generations--you know, sort of like a small velociraptor suddenly laying eggs that hatch as chickens. I think that's the kind of scenario that is meant by "saltation." It made sense as a hypothesis when we didn't know the mechanism of morphological change. But now that we know it's just a matter of microevolution applied to genes that control embryological development, we can discard the idea.