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.

[Jose]

Thank you, nikolayevich, for summarizing what we've said. It's quite helpful. Let me answer one of your direct questions first:

2. Another result is the hierarchical relationships that are seen in comparison of different life forms. It is the pattern of the hierarchical relationships that have led to the theory of common descent from a single common ancestor; evolution per se doesn't require a single common ancestor. There could have been many, but the relationships suggest otherwise.

I think that I gather what you are saying, but would rather not assume. If you could clarify what you mean by "...could have been many, but the relationships suggest otherwise"...

I was thinking that we could have had life originate several times, and create several distinct lineages. For example, maybe plants would be one lineage, animals another, and bacteria another. All could evolve from the ancestor that started each lineage. The relationship data that we have, however, indicate that there was only one ancestor, from which plants, animals, and bacteria all descended.

Perhaps we can look at Mendel's work on heredity and assess the limitations and loopholes, if you will, in genetic diversity and adaptation. How has our understanding been enhanced since his time (by Morgan et al) and what does it all mean for ToE?

Excellent idea. Much has been learned since Mendel--and Darwin formulated his original description of evolutionary mechanisms without even any knowledge of Mendel! As it turns out, when I teach genetics, I tend to down-play some of the Official Rules that Mendel described, because there is so much that doesn't work that way. A bit of genetics wouldn't hurt us when we discuss what I put as point 2 of Mechanisms.

You have helped us a lot by digging up the various definitions of "species." As I understand it, the "biological" concept (ability to interbreed) is generally the definition used for animals, while the "phenetic" concept is more often used for plants. That is, some sub-types of plants are grouped as separate species, rather than sub-species, based on visible characteristics rather than the "interbreeding test." Certainly, those that cannot interbreed are accepted as species by everyone. I think that we'll find it easier to discuss this rather large topic if we stick with the more stringent criterion of interbreeding.

Bacteria are a bit tricky, since they don't mate in the way that plants and animals do. I think, though, we can deal with them as a "special case" when they come up.

I believe between the various aspects of ToE mentioned so far, we can go quite far. Perhaps we could limit this list to 2 through 9 at the moment or simply for our discussion of common descent, since Abiogenesis rightly deserves its own thread, though I would accept as Otseng has done that this can be included in our discussion of ToE overall.

I agree with you that we might want to exclude Abiogenesis, for the simple reason that the mechanisms are quite different. With "straightforward" evolution, we can talk about known molecules doing the things they are known to do. When we venture back in time, before these known molecules were "up and running" so to speak, we have to think in terms of specific types of chemical reactions that would be possible in particular microenvironments. The kind of thinking is so different from that we will do in discussing evolution itself that I fear we'd be overwhelmed. A separate thread would be preferable, but perhaps after we've worked our way through this one somewhat.

[otseng]

I would like to nudge this thread and hopefully bring it back to life. In all of our debates on CvsE so far, we have not really spent a lot of time supporting the theory of evolution. I have mentioned that the ToE is the gold standard in which to compare all other models with in regards to life. Yet, surprisingly little has been discussed about it on this forum to support it.

So, here again are the questions for debate:

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?

As for the first question, rjw has offered this definition of the theory of evolution:

ToE is the theory that all extant life forms are related through a lineage of common descent, that began with a replicating molecule some billions of years ago and through a series of changes (mutations?), life adapted in various ways (was selected) to a multitude of environments. In the process a series of related genetic systems (and hence morphologies) developed, leading to the patterns we see in life today.

I can accept this definition. If there are any more input on this definition, or any other terms that needs to be defined, feel free to add it.

Next question, what is the hypothesis of the theory?

[Jose]

Good idea, otseng. Thanks for waking this thread up again.

I will quibble with the definition you cited, as well as with "the hypothesis." I can't help it, since my field of biology doesn't use "hypothesis" and "The Scientific Method" in the way that it has been caricatured in high school biology texts. Most fields don't, in fact. So, I'll probably end up saying this in an odd way...

I think the "theory" must be the mechanistic explanation of how we think things work. I also think the "hypothesis" must be a statement of our understanding, based upon this theory. The "predictions" are, then, things that should be true, based upon the hypothesis and upon the mechanism.

The mechanism is tremendously important, because if we imagine the wrong mechanism, we can develop goofy ideas that just don't make sense--ideas that are currently quite common as "misconceptions" about evolution.

The Theory of Evolution: The Mechanism

• Organisms inherit their genetic information from their parents.
• Genetic information is subject to mutation.
• Traits that are genetically controlled exhibit diversity in populations (because of mutation).
• Environmental conditions cause some genetic variants to be relatively unsuccessful, while others are more successful.
• The more-successful genetic variants have more offspring than the less-successful genetic variants, so their genes become more common in the population as one generation gives way to the next, and the next, and the next.
• Populations that are separated into sub-populations may have the same genetic diversity initially, but as time passes, their genetic diversity becomes different, because the mutations that occur in one population are unlikely to occur in another population (because there is no mechanism to "target" mutations to any particular gene, and thus they occur at random).
• Due to mutation and selection, separated populations become different; given sufficient time, they may become different enough that they can no longer interbreed--and they become different species.

The Hypothesis, Based Upon This Mechanism
Here, I would put rjw's statement:

ToE is the theory that all extant life forms are related through a lineage of common descent, that began with a replicating molecule some billions of years ago and through a series of changes (mutations?), life adapted in various ways (was selected) to a multitude of environments. In the process a series of related genetic systems (and hence morphologies) developed, leading to the patterns we see in life today.

This states our understanding of the relationships among different living things, and is therefore an official Hypothesis.

Now, I see as I write this, that Darwin started with this hypothesis, without knowing the mechanism. Therefore, what I have written above will be seen by some as wacky. I can imagine, however, that we have of necessity rephrased the theory and the hypothesis as we have learned more in the last 150 years. From Darwin's original hypothesis, we predicted that there must be a mechanism for genetic inheritance that enables the creation and inheritance of variation. Darwin did not know what such a mechanism could be. Now that we understand genetics, we do know. That is, Darwin's hypothesis predicted that genetics would be as it is: imperfect transmission of traits from generation to generation. Now that we know this, I think we need to include it in the official Theory. Indeed, the "Modern Synthesis" was a revision of Darwinian theory to include genetics, once it was known. Even then, there were mechanistic details we didn't know, so people imagined "micromutations" and "macromutations," terms which no longer have much meaning.

The Predictions
These must be mechanistically possible, given our understanding of the theory. Therefore, we cannot predict that there must be "intermediate forms" that are "caught in the act of changing from one species to another" because genetics doesn't work like that. The "intermediate forms" must conform to genetic mechanisms that are possible.

• All life forms should have DNA sequences that are related.
• Life forms that are most similar to each other should have DNA sequences that are most similar, as well as having morphological characteristics that are most similar.
• Life forms should be related in a hierarchical way. That is, there should be broad divisions of life that result from early speciation events. These broad divisions should each be subdivided into smaller divisions that result from later speciation events. These smaller divisions should be subdivided into yet smaller divisions resulting from later speciation events. This hierarchical set of relationships should extend to existing life forms, for which there should be "incipient" species in the form of varieties/ecotypes/races/subspecies/variants or whatever we like to call them.
• There should be fossils of earlier life forms.
• Fossils of a single age should represent that age's position in this hierarchical division of life forms.
• There should never be fossils that are "out of position," in which the genetic relationships contradict the fossilized history of the way life forms have changed over time.
• Morphological traits that change with evolutionary time should be controlled by genes that are subject to mutation (i.e. there should be a discoverable mechanism for the developmental production of morphological characteristics).
• Biochemical properties of living things should reflect their evolutionary history: there should be many biochemical characteristics that are shared among species, with the most similar biochemical details in the most similar species (e.g. different mammals), and the least similar biochemical details in the least similar species (e.g. mammals vs plants or mammals vs archaebacteria).

I suppose we could go on, but I'm running out of steam here.

Maybe it would also be useful to make a list of things we should not see, but that are commonly thought to exist, because this may be important.

Things we should not see--i.e. misconceptions

• There should never be "animals caught in the act of mutating."
• "Intermediate forms" should never be "intermediate" in all of their traits at once, nor should they be half-and-half (front-to-back, or top-to-bottom) chimeras.
• There should not be any kind of "plan" or "progress" to evolution. The "ladder of evolution" from simple to complex should be an artifact of the fact that life started at zero, and could only become more complex. If we could start evolution in the middle (i.e. introduce a species to a small island), sometimes it should result in life forms becoming less complex.
• Evolution should not always make species "better." Many species actually should not "evolve" into "better" forms, and should become extinct because of it.
• Species should not "evolve in order to survive." How could they, if they can't plan their mutations?
• New characteristics or new traits should not appear suddenly. Rather, new characteristics should only be modifications of prior characteristics.

There are probably more.

Please feel free to argue with any of the above!

[juliod]

I think it's time to know on the door and ask for Rodney Real.

This is way too big a topic to cover in a thread. Or even 100 threads.

If you want to analyse the modern ToE, then you are talking about thousands of major concepts, and millions of particular observations.

If you are talking about the original formulation of the theory by Darwin, then you need to read his books. But that's not very fruitful because his work is so badly out of date.

The Scientific Method is a means to do science, not a means to analyze existing theory. This is because it depends principally on the utility of prediction. In science you predict about things no one knows. You can't make predictions about experiments or observations that have already been made and published.

So in order to do science you must be working just beyond the limits of human knowledge.

Here's a hypothetical example. Let's say I discover a new species of bacteria. I show through typical microbiology experiements that it is not a known species. Under the microscope I see that it looks alot like Bacillus cereus (BC). So my hypothesis, guided by the ToE, is that this species is closely related to BC. In other words that they descended from a common ancestor comparatively recently. My prediction is that if I sequence the 16S rRNA genes of this new bacteria I will find that it matches BC closer than other common species in the genus, such as B. subtilis, B. anthracis, or[/i] B. thuringiensis[/i]. I then sequence the gene, and find out if I was right or not. If so, then it supports common descent of these two species, and through that the ToE.

DanZ

[Jose]

Agreed: it's one dang big topic. And yet...

There are a great many parts of it for which many of us don't know the supporting data. We've covered some of them in some of the more-specific threads. Perhaps, this thread can serve as a "parent" that we can use to identify the fundamental issues that people would like to discuss in more depth, and then turn to specific threads for each of them.

[juliod]

There are a great many parts of it for which many of us don't know the supporting data.

Yes, but that's not something we can use the SM for. Presenting supporting data is not actually part of the SM. The SM is all about hypothesis, prediction, observation.

Since supporting data is all about things already known, it is impossible to make predictions about it. We can only pretend we don't know the result already. That's fine for teaching the SM, but a bogus way to impliment it.

DanZ

[otseng]

Good idea, otseng. Thanks for waking this thread up again.

Thanks for responding.

I will accept the predictions and misconceptions that you listed. I'm sure there are more, and if others would like to add to them, please do so.

This is way too big a topic to cover in a thread. Or even 100 threads.

Of course. I fully expect this thread to spawn more threads.

If you want to analyse the modern ToE, then you are talking about thousands of major concepts, and millions of particular observations.

Thousands of major concepts? No wonder people don't really have a good grasp of ToE. What are some of the "thousands of major concepts" that you are referring to?

If you are talking about the original formulation of the theory by Darwin, then you need to read his books.

For discussions here, let's focus the ToE to the neo-Darwinian point of view, not from "The Origin of Species" point of view.

OK, to get to the meat of this topic. What are the supporting evidence for the ToE?

[Jose]

Thousands of major concepts? No wonder people don't really have a good grasp of ToE. What are some of the "thousands of major concepts" that you are referring to?

Yep, that's one of the reasons, all right. Another is that when we teach it as "facts" to memorize, it comes across as Received Wisdom--which puts in on a par with Creation. I'm becoming more convinced that it is essential to teach it by presenting the data, and asking students to figure out what the interpretations are. [I'll let juliod answer the last bit... He's the one who brought it up.]

OK, to get to the meat of this topic. What are the supporting evidence for the ToE?

Allow me to procrastinate. When you ask for supporting evidence, do you ask about the evidence that led to formulating the theory, or do you ask about testing the theory by seeking evidence for/against the predictions? Both are valid, but will take us in different directions.

Allow me also to play a game. I think I've done this somewhere else in these forums, but I'll do it again here. Take a DNA sequence, or any sequence of letters. Let it represent the genetic information of an animal. Imagine a whole bunch of 'em, and split 'em into two groups, A and B. Now follow A and B for a bunch of generations, with occasional random mutations happening. Write these down...maybe just one sequence from each population, to keep it manageable. What happens?

Now, let's continue by splitting A and B into two groups. Follow all 4 groups for a bunch of generations, again with random mutations happening.

Basically, this process models genetic inheritance. The splitting of populations models the real world, in which populations do become separated into sub-populations. If you want to make it more realistic, you can select against many of the possible mutations, and even tweak the "environments" so that A and B have different mutations that survive. This makes it more complicated, but it's possible to do (especially if you write up a little subroutine so the computer can do it for you). If you do this, you will get an evolutionary tree.

Now, we know how DNA is inherited, and we know that mutations happen, and we know they happen at random, and we know that populations get split up quite often, and we know that most mutations are selected against, but some are not, and we know that there have been lots of generations before now. Therefore, it seems to me, it is impossible to avoid the conclusion that evolution must occur. The above process models it.

The question, really, is what path has it taken?

I have a sense that a couple of the big issues revolve around how mutations can change traits (and thus be selected for or against), and the general problem of geological strata, fossils, and the ages thereof. I also have a sense that another issue is "certainty" vs "inference," and the validity of using one, or a few, examples to prove a principle, and then extrapolating that principle to situations in which we have not tested it.

But I don't want to pre-judge your questions. Can you give us some guidance by suggesting a couple of particularly troubling issues?

[juliod]

Thousands of major concepts? No wonder people don't really have a good grasp of ToE. What are some of the "thousands of major concepts" that you are referring to?

What I am saying is that if you want to apply the SM to evolution, you will need to be working (or at least talking) at the level of detail of research biologists, not at the level of an intro-level textbook. What I think you really want is evidence that shows evolution is true. I am saying that these are incompatible objectives.

Let me give just one example of a major concept in biology that might shed light in the extreme number of major concepts that support evolution.

The example is the relationship of members of the GAR protein family in species as distinct as mammals and yeasts. The concept is that the GAR domain is involved in modulating the protein- or RNA-binding properties of the proteins that contain it. A GAR domain is a (usually short) region of protein composed of repititions of the sequence glycine-arginine-arginine. It is typically present in proteins with other discrete RNA and/or protein binding domains. It is also not primarily responsible for binding functions, and at least several examples are known where the GAR domain can be deleted without destroying the function of the protein. GAR domains are present in the proteins of very different species, often highly conserved when there is not an otherwise high degree of identity. For example, the yeast gene NSR1 as compared to mammalian nucleolin. It remains, I believe, undecided whether NSR1 and nucleolin are homologs (i.e. descended from the same precursor) or whether they independantly evolved.

Now, in biological journals there is a fairly large collection of publications on these GAR proteins. Why has no one here other than I ever heard of them? Because the GAR paradigm is one of thousands and thousands of major concepts that are of too little public interest to gain the attention of the laity.

The GAR field is a subfield of (among other things) the assembly of ribosomal subunits with rRNA. That is a subfield of the assembly of ribosomal proteins into subunits. That is a subfield of the biogenesis of ribosomes. That is a subfield of protein synthesis. That is a subfield of cellular metabolism. That is a subfield of cell biology. And cell biology is a subfield of biology.

You could go back down the sub-sub-sub-fields to arrive at another one of the thousands of individual concepts that make up biology. And for 99.9% of them you won't find them in college-level textbooks.

That's where you will find the SM, and of course all those sub-sub-sub-fields support evolution in their own infinite variety....

DanZ

[otseng]

When you ask for supporting evidence, do you ask about the evidence that led to formulating the theory, or do you ask about testing the theory by seeking evidence for/against the predictions? Both are valid, but will take us in different directions.

You're right. I intentionally left it open-ended to allow freedom on how evolutionists would like to proceed. I would suggest first providing evidence that leads to the formulation. Then we can proceed to evidence in supporting the predictions. (This would be similar to how we approached the Global Flood model first and then the Flood as science next.)

Can you give us some guidance by suggesting a couple of particularly troubling issues?

Let me not taint the presentation yet with my critiques. Of course I have in mind troubling issues about evolution, and I think you are familiar with them. But, I'd like for us to lay the fundamental groundwork first before jumping into debate.

Also, let me add for all the readers that I am not entirely opposed to the ToE. There are many things about it that I consider to be true. But, I also believe that there are things about the ToE that are left wanting. I'm sure in time we'll get to those areas to debate on. But, in the meantime, I'd like for the foundational material to be laid out first.

Thousands of major concepts? No wonder people don't really have a good grasp of ToE. What are some of the "thousands of major concepts" that you are referring to?

The example is the relationship of members of the GAR protein family in species as distinct as mammals and yeasts.

I think we differ on what we view as a "major concept". A major concept of the theory of evolution to me would mean something along the lines of the mechanism of evolution that Jose brought up earlier. It would be a fundamental point of evolution that is required to be presented in order to understand what is the theory of evolution. I would not regard understanding GAR protein relationships as fundamental to understanding the theory.