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?

[richic]

Jose,

I just read through this thread from the beginning. Obviously my Darwin quote is incomplete. Please ignore. I would still be interested in your feedback on the other questions, though.

I also have another question. I've seen "intermediate" species mentioned. Are there actual species classified as intermediate, or do they belong to one class but have enough characteristics of the other to class them that way? Is there any minimum threshold of commonality to cause them to reach intermediate status?

[bernee51]

Are the paleo-anthropoligists still searching for the "missing link" or have they abandoned that quest based on new scientific theories?

Ah the 'missing link' - like Jose )or is it Obi Wan) - that is a name I have not heard in a long long time. I think Jose has covered the bases on this one.

[richic]

Ah the 'missing link' - like Jose )or is it Obi Wan) - that is a name I have not heard in a long long time. I think Jose has covered the bases on this one.

Yes he did. That's straight out of my Anthro 101 class 20 years ago with Tim White. I think the lecture was entitled. 'Lucy as the Link'. It seemed like a very promising theory at the time.

[Jose]

Thanks for all the answers. Here is darwin's quote:
Charles Darwin: ."(Since) innumerable transitional forms must have existed, why do we not find them imbedded in countless numbers in the crust of the earth? "Origin of Species", p. 162. "Why is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely graduated organic chain: and this perhaps is the most obvious and gravest objection which can be urged against my theory." "Origin of Species," p. 293.

Indeed, Darwin said that transitional forms should exist. But, he didn't describe what they should look like. I don't think we know what he imagined they should be.

He seems to believe that the record should show proof of gradual change.

Yes, that is what he believed. That is why the creationists jump on the concept of "gradualism" to say that "evolutionists don't believe in evolution," because we know it's not gradual. There are long periods when the environment is reasonably stable, so selection works to keep species more or less the same. Some species in some environments can remain fairly similar for very long times--look at coelocanths, for example. Some still exist, and look pretty darned similar to the originals. They must be in a pretty stable environment.

But, why would we expect gradual change? Why not expect change to be fairly rapid when a new environmental opportunity presents itself? Why not expect change to be slow when conditions stay the same?

Does this mean DNA can be re-programmed to produce something else? Is this something we can do in a lab, say take the DNA of 'x' species and modify it to produce 'y' species? Have we done any computer modeling of this?

At the simple level, yes, DNA can be re-programmed--all you have to do is change the sequence. In principle, we could change X into Y, if we knew what the changes were between X and Y, and if we did it properly. This wouldn't help us understand evolution, though, because we already know that different species have differences in DNA sequence, and all we'd be doing is changing the DNA of one species to match the DNA of a different species. We wouldn't be doing it the way evolution did.

Is homology the branch of science that covers this study?

No, unlike many of the other "ologies," homology isn't a science. The term means "derived from a common precursor." Structures are homologous if they share a common ancestral precursor in a common ancestor. Vertebrate limbs are homologous. Creationists get upset about this, because they claim that evolutionists say things are homologous because they look the same, and because they look the same, they must be homologous. In the early days, deciding what structures really are homologous was a bit tricky. Now we have more information, and can make the judgement more soundly.

In contrast to homology, there is analogy--things that have similar functions, but are not homologous (ie, of common evolutionary ancestry). The classic example is the wings of insects and the wings of birds.

I'm trying to get my arms around where we are then.
It sounds like we have agreement between creationsists and evolutionists that species mutate and evolve. We also have agreement that species share characteristics.

Today we don't have conclusive evidence of the mechanism for how one species evolves into another(a transitional form). I assume we also don't have evidence that they were all created and remain inside their respective species box.

Am I missing something?

Well, we do seem to have agreement that mutations happen, and that there can be changes in allele frequency in populations (ie. microevolution). Creationists usually insist that this is not "true" evolution, because no new species arise from it; it's just variation in kind. I also imagine that creationists accept the fact that species share characteristics, because we can look at them and see that this is so. Where creationists draw the line is at the prinicple of common evolutionary descent, which they refer to as macroevolution (using the term differently than in evolutionary biology).

Actually, we do have conclusive evidence of how a species evolves into another. Stated simply, it's mutations, which produce genetic variation, and changes in allele frequency in populations (due to selection). If the genes that happen to undergo mutation are genes that are important in courtship and mating, or egg/sperm recognition, then it's pretty easy to see how two populations of a species might become different enough from each other that they cannot interbreed. Then, we have two species, where before we had one. They may look pretty similar at first, but given time, as additional mutations and selection occur, they will become different.

Yet, at the same time that we got two species where before we had one, neither population actually "changed to a new species" in any sort of sudden change. Each population did what they always do: reproduce according to their kind. In a funny sort of way, each species is still the same species as it started out being, since it is the same population of organisms--even though the two species end up being different.

If you were to take random individuals from one of these populations at various times, and fossilize them, you'd have all of the transitional forms that you need. But, for each one, you'd have only representatives of the diversity that existed in the population at that time. You'd recognize each as a fossilized individual, but you'd have a hard time pointing to any one of them and saying, "this is THE transitional fossil" or "this is THE missing link." In this sense, all fossils are transitional forms.

[richic]

At the simple level, yes, DNA can be re-programmed--all you have to do is change the sequence. In principle, we could change X into Y, if we knew what the changes were between X and Y, and if we did it properly. This wouldn't help us understand evolution, though, because we already know that different species have differences in DNA sequence, and all we'd be doing is changing the DNA of one species to match the DNA of a different species. We wouldn't be doing it the way evolution did.

Could you build a computer model to evidence the mutation mechanism of macro-evolution? Let the computer run through all the potential mutations and see what you get. Or you could plug in x and y DNA and use the computer to fill in the blanks with a plausible mutation sequence.

Are there any rules on mutation that you could use to restrain your model?

This would seem to be quite conclusive proof that a creationsist would have to deal with.

[perfessor]

Could you build a computer model to evidence the mutation mechanism of macro-evolution? Let the computer run through all the potential mutations and see what you get. Or you could plug in x and y DNA and use the computer to fill in the blanks with a plausible mutation sequence.

Are there any rules on mutation that you could use to restrain your model?

This would seem to be quite conclusive proof that a creationsist would have to deal with.

Hmmm - I'm not sure how much you know about computers or programs - but computers are not some giant, all-knowing magic answer box. A computer will do exactly what the programmer tells it to do - nothing more, nothing less. Yes, you can do computer simulations of natural processes - weather systems, for example, like we see every evening on the news. There are also simulations, or "illustrations", of how evolution works. But as I said, they behave the way they were programmed to behave, so I doubt they would "prove" anything to a creationist. A good simulation would perhaps make the concepts easier to understand. For example, it could demonstrate how an ordered result can come from a random process, as described in the thread "Mutation is a random directed process" in this forum.

[richic]

Hmmm - I'm not sure how much you know about computers or programs - but computers are not some giant, all-knowing magic answer box. A computer will do exactly what the programmer tells it to do - nothing more, nothing less. Yes, you can do computer simulations of natural processes - weather systems, for example, like we see every evening on the news. There are also simulations, or "illustrations", of how evolution works. But as I said, they behave the way they were programmed to behave, so I doubt they would "prove" anything to a creationist. A good simulation would perhaps make the concepts easier to understand. For example, it could demonstrate how an ordered result can come from a random process, as described in the thread "Mutation is a random directed process" in this forum

Gosh I didn't realize about computers. I thought they were a lot smarter.

I'll read that thread. Can you point me to a website or research paper describing the most advanced simulation we have of the macro evolutionary process?

I had another question there regarding restraints we could put on the computer model. Do we see any patterns or constants in the micro-evolution mutation process that can be extrapolated to macro evolution?

[rjw]

Hello richic,

I cannot answer your question to Jose directly. However I can provide some input of relevance. Certainly experiments can be done in the lab to demonstrate what Jose was talking about and what your question was aiming at. (So why bother with computer simulations when a possible version of the real thing can be simulated in the lab.)

If you can get hold of it, have a read of the following:-

<i>Nature</i> <b>415</b> 21 Feb 2002, pp915

Insects are believed to have evolved from a crustacean like creature. The fossil record and molecular data tells us that this happened some 400 million years ago. The possible nature of this transition is a question which researchers put to a partial test some 2 years ago. They tested an idea concerning the evolution of the insect limb pattern, demonstrating that a simple change in expression of a certain inhibitor protein plus minor changes in the expression of a Hox gene of the purported ancestor, was all it took. The authors conclude:-

“Previous studies led us to propose that gain and loss of transcriptional activation and repression functions in Hox proteins was a plausible mechanism to diversify morphology during animal evolution. Here we show that naturally selected alteration of the Ubx protein is linked to the evolutionary transition to hexapod limb pattern.”

I guess my point is this – it would be beaut to be able to build the appropriate computer simulations. However, advances in genetics and laboratory techniques are beginning to allow us to explore these questions in the lab.


Regards, Roland

[Jose]

Are there any rules on mutation that you could use to restrain your model?
......

I had another question there regarding restraints we could put on the computer model. Do we see any patterns or constants in the micro-evolution mutation process that can be extrapolated to macro evolution?

Rules on mutation...I don't think so. Consider that for the DNA sequence AGCT, you can have an infinite number of mutations. You aren't constrained to changing A to G, C, or T, for example, but you can delete bases (e.g. AGCT-->ACT), or you can add bases (e.g. AGCT-->AGGGCT). You can add as many bases as you want, of any sequence--hence the conclusion that the possible mutations are infinite in number. There are also lots of ways of producing mutations, from simple errors of DNA replication or repair, to breakage and rejoining, to the duplication of large or small portions of chromosomes. Breakage and rejoining enables the creation of gene fusions, that produce proteins that fuse different portions of other, previously-existing proteins together.

In terms of the kinds of DNA changes, there are constraints only due to the chemistry of DNA. In terms of the information content--what genes there are, and how the gene products interact--the possibilities are constrained by what is already present. Mutations can "edit" pre-existing information easily, but it's hard to invent entirely new information that is functional. The increase in information that we see when we compare "complex" things to "simple" things comes from gene rearrangements, duplications, and occasional input from viruses which can act like mobile DNA-carriers.

There are constraints on what happens to mutations. If a plant or animal is born with a mutation that makes it "sick," then it dies or fails to produce offspring. The bad mutations are weeded out. If a plant or animal is born with a mutation that makes it a little more successful, then it may have more offspring, which will have offspring, and which may eventually out-compete the others in the population. This is, of course, "natural selection," which is what "directs" the process of evolutionary change.

The notion of editing pre-existing information, rather than inventing wholly new information has a significant influence on what you call macroevolution. Lobe-finned fish can give rise to tetrapods pretty easily, but not to trees or squids (at least, not without a huge amount of mutation and selection). This is why we have "lineages," and why the diagram of relationships looks like "branches on a tree."

I'll read that thread. Can you point me to a website or research paper describing the most advanced simulation we have of the macro evolutionary process?

I just did a quick search of PubMed , and found a couple of things that might be useful, if you can find the journals. There's a paper called Hetero: a program to simulate the evolution of DNA on a four-taxon tree and another called Tracking the trajectories of evolution. Both are pretty new (but I haven't read them myself, so I can't tell you whether they really answer your question). But, remember what perfessor said: computers do exactly what you tell them to, including the mistakes and preconceptions that you use in building the model.

[richic]

I was hoping to get some feedback on this question within this thread instead of starting a new thread.

It seems clear to me the importance of evolutionary theory to other scientific disciplines like genetics. The scientists posting on this site are quite detailed in their rationale. The benefits to mankind through this understanding have been well stated, I believe. I view this as the micro-evolution part of the story.

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.