Question 1: The Fossil Record

[Simon]

According to Darwin, the absence of intermediate fossil forms "is the most obvious and gravest objection which can be urged against my theory." What new fossil finds, if any, have occurred since Darwin wrote these words nearly 150 years ago? Do they overturn Darwin's bleak assessment of evolutionary theory? If the absence of intermediate fossil forms holds as much today as it did back then, why should anyone accept evolution?

[Tortle]

My question is how does macro-evolution, as a theory, benefit science today? Does it matter that all the commonality in genetics between species can be traced back to common precursors, or is it more of the intellectual challenge to try to prove it? It seems like more of a geneological exercise to chart the family tree.

I think macro-evolutionary theory is very important to understand the intricacies of evolution so that we can accurately map phylogenies and predict relationships between species. Assuming micro-evolution in all cases might produce conflicting and confusing theories if macro-evolutionary forces are at work in a significant number of species.

[Jose]

Well, richic, let's see here....

As I see it, microevolution becomes what you call macroevolution if you just wait long enough. I think it's impossible to accept one but not the other. (Tortle, you may dispute this since you refer to macro-evolutionary forces, but I'm a reductionist, so I see it from the viewpoint of the molecules that make it work.)

You'll see discussions of micro vs macro in the evolution journals because scientists use the term "macroevolution" to refer to changes in morphology, rather than changes in allele frequencies. Creationists have picked up the term to refer to "common descent as illustrated in phylogenetic trees." So, when evolutionists are debating macroevolution, they are not debating common evolutionary descent. That issue was settled decades ago, and they've moved on to details of mechanism.

You are right that microevolution is critical for everyone to understand. From it come new strains of viruses and bacteria that can infect us in serious ways. From it come new strains of insects that can withstand our pesticides. We need to understand how it works in order to understand what's going on in our food supply and our medicine. We also need to know how it works so that we don't get tricked by charlatans who tell us wacky stories about what genetic modification will do. If we know what's going on, we're way better off.

What about macroevolution (common descent)? Well, it's the number one tool being used right now to develop new strategies for fighting diseases, both infectious and genetic. If we know that organism X is just like us in some critical respect, then we can use it as a "model system" to work out the specifics of the disease. In most cases, we use mice as a model, but there are plenty of instances where soil nematodes, fruit flies, or yeast are a good model. We have used these models enough to know they work. We also know the limitations, because of the evolutionary trees that tell us how similar or how different we are from other species.

Certainly, there's some of the general intellectual curiosity that any scientist brings to her work, which leads us to probe things we don't know. It does involve a bit of "let's see what we learn if we probe this a bit more deeply!" But from this kind of curiosity that probes in many different directions, we get the discoveries that turn out to be really important.

Initially, the question was "what are all the things that God created?" As we (meaning Darwin and his predecessors) found out what these things were (though by no means all of them, which we still don't know), the pattern of relationships became apparent. I should probably say, became even more apparent than it had been before. What fell out of the science of natural theology was the theory of evolution--based on the patterns of relationships that are the result of common descent. In other words, even if there were no "practical value" to it, it is something that resulted from the early studies that were designed to prove something else.

[richic]

What about macroevolution (common descent)? Well, it's the number one tool being used right now to develop new strategies for fighting diseases, both infectious and genetic. If we know that organism X is just like us in some critical respect, then we can use it as a "model system" to work out the specifics of the disease. In most cases, we use mice as a model, but there are plenty of instances where soil nematodes, fruit flies, or yeast are a good model. We have used these models enough to know they work. We also know the limitations, because of the evolutionary trees that tell us how similar or how different we are from other species.

When you say tool, how exactly do we use it? So what is it about the phylogeny tree that says this or that branch significant for use as a model system?

In other words, even if there were no "practical value" to it, it is something that resulted from the early studies that were designed to prove something else.

I know the debate between E's and C's isn't over, but if Creationsists had been successful in repudiating the theory of common descent, would that have really made any difference in our work with "like" species. I would guess we'd be in a paradigm where we view species as having common building blocks and still used rats and monkeys for experiments.

Practically speaking, the best model system for our experiments is really a human being, isn't it? If we didn't have a moral issue to deal with, I'm sure we'd use the sick, and the aged in our lab tests.

[Jose]

When you say tool, how exactly do we use it? So what is it about the phylogeny tree that says this or that branch significant for use as a model system?

One way that we use it is by comparison of DNA or protein sequences. If a particular part of the sequence is evolutionarily conserved, we know it is functionally important. Natural selection has maintained it; mutations that change it are deleterious. Another way is simply knowing what the relationships are. We know that yeast is pretty far diverged from humans, so we expect some significant differences in mechanisms, while mice are less diverged so we expect more similarities. The pattern of relationships is simply part of our basic understanding of life, and underlies all of biology. This seems vague, but it is essential. More recently, as we've determined the DNA sequences of more and more genomes, we do whole-genome comparisons. Looking at mouse DNA and human DNA, we find that there are lots of DNA sequences that are conserved, but are not protein-coding genes. Why are they conserved? Because mutations in them make the animals sick, so mutations are selected against. This comparison, and this discovery of these conserved sequences, led to the discovery of a major mechanism of gene regulation.

I've been involved in a museum exhibit on "genes and your health," in which alcoholism is discussed. Over years of selective breeding, researchers have produced a strain of rats that is alcoholic, and prefer alcohol over water. Careful genetics, and comparison of rat DNA to human DNA has identified at least two genes in rats that are involved in their alcoholism--which led to checking the involvement of the same genes in humans. Lo and behold, they are involved here, too. The rat was a model system that made it easier (maybe possible) to figure this out.

Practically speaking, the best model system for our experiments is really a human being, isn\'t it? If we didn\'t have a moral issue to deal with, I\'m sure we\'d use the sick, and the aged in our lab tests.

Think of the rats. Imagine 50 generations of arranged marriages, forcing the alcoholics to marry alcoholic brothers and sisters, regardless of any other aspects of their health or interests. We won't do it. Nor would we have time. One of the characteristics of model systems is that they have a short generation time, so that we can do multi-generational genetic studies. There are lots of these kinds of models being developed--for things like alzheimers and…uhh…I forget what others. The reason we know this will work is that our genes and their genes are evolutionarily conserved, and do the same things. Without common evolutionary descent, there would be no reason to expect this to be true.

[richic]

We know that yeast is pretty far diverged from humans, so we expect some significant differences in mechanisms, while mice are less diverged so we expect more similarities. The pattern of relationships is simply part of our basic understanding of life, and underlies all of biology. This seems vague, but it is essential.

But isn't that kind of intuitive? I would think after the discovery of DNA the next thought was 'Let's catalogue all species DNA and look for relationships'. Monkeys first.

The reason we know this will work is that our genes and their genes are evolutionarily conserved, and do the same things. Without common evolutionary descent, there would be no reason to expect this to be true.

But it seems like whether its common evolutionary descent or not, we would have the same expectation for like genes. If our theory was that all life is built using common building blocks we would think that like building block patterns would act the same.

[Jose]

We know that yeast is pretty far diverged from humans, so we expect some significant differences in mechanisms, while mice are less diverged so we expect more similarities. The pattern of relationships is simply part of our basic understanding of life, and underlies all of biology. This seems vague, but it is essential.

But isn't that kind of intuitive? I would think after the discovery of DNA the next thought was 'Let's catalogue all species DNA and look for relationships'. Monkeys first.

Yes, it's very intuitive. So much so that it seems obvious, just as you say. It turns out that we couldn't do the cataloguing right after we learned the structure of DNA, because we had to wait several decades to develop methods for sequencing it, but now that we can do so, we're making the comparisons. While it may be obvious in some sense, it is striking that the DNA sequence similarities pretty much follow the morphological similarities. Sure, this might be what you'd expect--but I think you'd expect it only if you had some reason to believe that creatures that are morphologically similar are genetically related. There are many ways to build similar structures; genetic similarity is by no means required. The fact that we find genetic similarity simply lets us go one step beyond the obvious, intuitive conclusion, and add to it: "gosh, it looks like all of this similarity, both morphological and genetic, results from genetic continuity--evolutionary descent."

The reason we know this will work is that our genes and their genes are evolutionarily conserved, and do the same things. Without common evolutionary descent, there would be no reason to expect this to be true.

But it seems like whether its common evolutionary descent or not, we would have the same expectation for like genes. If our theory was that all life is built using common building blocks we would think that like building block patterns would act the same.

Indeed, we would. But we wouldn't have any reason to think that there would be similarities in building block patterns if we thought that each species was created independently. We wouldn't even expect them to use the same chemistry. With creation, anything is possible--so why limit it to the same chemistry for everything? To turn this thought around, we knew about common evolutionary descent before we could sequence DNA. We started with our model systems before we really understood what genes are or how they work. It was through the model systems that we figured this out--and it applied 100% to humans. This was done with no knowledge whatsoever about sequence relationships, because no technology existed to figure out the sequences.

We can, if we like, think of the sequencing in much the same way as it was thought of initially. Here we have our theory of evolution, built from morphological comparisons, the fossil record, and knowledge of genetic mechanisms and geological mechanisms. Let's check whether this theory makes sense. We'll make a set of formal predictions based on this model, and then do the work to see if these predictions are met. We predicted that DNA sequence similarities and differences would exist, and that species we think are more closely related would have DNA sequences that are more similar. We predicted this without any knowledge of the DNA sequences. When we got the sequences, it turned out that our predictions were right. Well, not quite all of them…there are a few interesting exceptions, that tell us of "horizontal gene transfer" between unrelated organisms. The best example is the evolution of influenza virus, which causes pandemics when one of these kinds of horizontal gene transfer events occurs.

So, you could present the information as you suggest, as if we got all of this sequence data and found that there are some real similarities among similar-looking organisms. We could say, "now that we know this, we can explain why the things we've been doing for decades work." But, doing so would violate the Standards for science teaching, which include discussion of science as a human endeavor, with historical aspects as well as the current understanding. This is important, because it shows how science works, and shows that it is accessible to everyone, regardless of gender, race, nationality, or any other of the dividing lines we like to draw to separate people. If we are to teach it this way, then we have to bring in the thinking of several decades ago, in which we were using the model systems without the sequence information. Why did we think it was a reasonable thing to do?

We also have to answer the question, which is always raised by students, of why this pattern exists. Why are there DNA sequence similarities? Why do they happen to match the morphological similarities that Linnaeus used when he first set up the system of nomenclature for living things? The simplest answer is "common descent." We share sequences because we are genetically related.

[anchorman]

Lotan wrote:

Yes, a tiny minority of paleontologists are also creationists (although the term 'creationist' negates any sense of scientific objectivity). I managed to find 5 of them. In an attempt to alleviate my ignorance and bigotry I have researched their claims:

Lotan...you say that the term creationist negates any sense of scientific objectivity. This is the most hypocrytical statement I have ever heard from a person of science. Scientists have openly admitted that the idea of a creator can not be considered because it cant be tested. From square one science is not objective in the creation/evolution debate.

[Jose]

Lotan...you say that the term creationist negates any sense of scientific objectivity. This is the most hypocrytical statement I have ever heard from a person of science. Scientists have openly admitted that the idea of a creator can not be considered because it cant be tested. From square one science is not objective in the creation/evolution debate.

It is not hypocritical at all (and, of course, we shouldn't be casting aspersions at one another this way!). The fact, as evidenced by the Creation Science movement, is that these folks begin with the answer (Creation), and then look about for data that they can interpret to fit the answer. They either ignore contradictory data, or they invent odd scenarios to explain it away. The lack of objectivity is exemplified in the initial approach: Creation is the answer; the answer is defined before the experiment begins.

Scientists have, as you say, openly admitted that the idea of a creator cannot be tested, because the creator can create things to be exactly as they are now, and then hide from any investigative techniques. This does not make science non-objective. It simply makes it honest in stating that the supernatural is beyond the methods of what is usually called "natural science." Scientists generally say this to indicate that nothing they can do, or have done, can disprove the existence of God. But neither can it prove the existence of God, or prove Creation (at least, it has not yet been able to, despite a great deal of effort). All science can do is gather data from the world, look at those data carefully, and develop explanations that fit the data. It is neither the fault of science, nor bias on the part of scientists, that God has chosen to provide us with data that are best interpreted by purely natural mechanisms.

[Nyril]

It is not hypocritical at all (and, of course, we shouldn't be casting aspersions at one another this way!). The fact, as evidenced by the Creation Science movement, is that these folks begin with the answer (Creation), and then look about for data that they can interpret to fit the answer. They either ignore contradictory data, or they invent odd scenarios to explain it away. The lack of objectivity is exemplified in the initial approach: Creation is the answer; the answer is defined before the experiment begins.

Although this is not actively contributing, I saw a comic along those lines.

[YEC]

Nyrils comic above missed the point.

I've seen traffic accidents investigated. Using the comic as a guide one might say...look at the skidmarks on the highway (facts). What conclusion can we draw from it? The answer might be a car at the end of the skidmarks.

OR

We have a car that was involved in an accident (the conclusion). What facts can we find to support it? The answer might be skidmarks leading towards the car.

Both methods are scientifically acceptable Nyril.

Now on the other hand we have the evo community doing just what Nyril mocked the Creationist for doing.
An example of that is.....Here we have an animal (conclusion) lets look and see if we can find some transitional fossils (facts)

Science can be used to approach something from both directions