Common Descent!

[Furrowed Brow]

This is probably reheating an old theme.

In the God Delusion - Ch 4 Here

Further, creationists do not totally reject evolution. Rather the main issue is the inadequate support for common descent.

I have been thinking about this same point recently as I have been debating the issue on a completely different forum. It is an area I still need to get my head around.

Why do some find common ancestry so unreasonable?
What would count as reasonable support for common ancestry?
What argument/evidence do creationists require?

[otseng]

I was aiming at the point that the factors are unknown, so any odds must be arbitrary.

Even Furrowed Brow quotes: "The odds against the formation of RNA are akin to a ball finding its way around all 18 holes of a golf course dues to natural causes."

[otseng]

So you present two picture of evolution that appear incongruent. A telling point for you. Jose points out that there is no real incongruence going on here because the view the pictures offer is out of shape. A telling point for Jose.

We'll find out. I've asked Jose for all the phyla that first appear in the Precambrian. Aftwards, I'll demonstrate all the ones that first appear in the Cambrian. We'll then compare notes.

The answer is an earlier, softer kind of egg.

A softer kind of egg? That would be the explanation between live-birth and egg-laying? If it is hundreds/thousands of generations of microevolved animals, it would be much more complex than this.

[Furrowed Brow]

I was aiming at the point that the factors are unknown, so any odds must be arbitrary.

Even Furrowed Brow quotes: "The odds against the formation of RNA are akin to a ball finding its way around all 18 holes of a golf course dues to natural causes."

I'd add one needs to be careful how one interprets this. Yes the odds of RNA spontaneously generating do appear vanishingly small (at present). I think if you had asked someone fifty years before the Wright brothers what were the chances of manned flight and you would have got fantastic odds.

However as I pointed out guys like Benner are trying to bring those odds down to something more realistic. I'd also say that arguments from probability in no way imply God or design, but we have been over that ground in the debate for Nature's Destiny.

[Goat]

You know, a religious web site is not the place I would go for informaiton about science.

There is nothing inherently wrong with using a "religious" web site. If the evidence is incorrect, then you are free to point out the errors.

But, with that said, I do prefer to use secular sources. However, if it is erroneous, I avoid using them.

For example, here is one chart that shows the first appearance of Metazoans.


http://www.ucmp.berkeley.edu/phyla/metazoafr.html

It gives the impression that the fossils of the differing phyla are spread out among various time periods, with concentrations at the Cambrian and the Cenozoic.

But, after some research, I've determined that the graph is unusable. And as I concluded in that post "there is no reason to doubt what the vast majority of biologists claim in that all the phyla appear during the Cambrian Explosion."

And there is no difference between 'micro-evolution' and 'macro-evolution' except that micro is within a few generations, and 'macro' is over hundreds of generations.

Looking at the Cambrian fossils, we do see examples of microevolution among the trilobites. There is a great diversity among the types of trilobites. However, we see no evidence of trilobites evolving into something else. Or any other animal evolving into something else. If microevolution spans hundreds or even thousands of generations, we should see evidence of a smooth and gradual evolution between various animals. However, fossils that we see are distinct and quite different from the others. I give some of the fossils found in the Cambrian here.

The statement 'if micro-evolution spans hundreds or even thousands of generations' is making an assumption that in and of istslef is false.

"micro-evolution' can span just a few dozen generations.. or it coudl take several thousand. The key in the equiation, aside from some random variation, is changes to the environment. The cambian had a lot of change in the environment, due ot hte influx of free oxygen, caused when the iron in the water finally rusted out.

So, the whole basis for their conclusions is based on false assumptions.

[Fisherking]

Many of you may have allready read the Theobald/Ashby debate but if you haven't, it's a very informative debate regardless of which side you stand on issues of common descent and macro-evolution.

Theobald:
29+ Evidences for Macroevolution

Ashby:
Exposing the Myth of Evolution

Theobald:
29+ Evidences for Macroevolution
A Response to Ashby Camp's "Critique"

Ashby:
Camp Answers Theobald
Reply to Theobald’s Response to Part 1 of Critique

[honegod]

one needs to be careful how one interprets this. Yes the odds of RNA spontaneously generating do appear vanishingly small (at present). I think if you had asked someone fifty years before the Wright brothers what were the chances of manned flight and you would have got fantastic odds.

I think part of the problem is trying to assign a probability for the production of a SPECIFIED molecular configuration out of all the possible configurations that the atoms commonly found on earth will naturally fall into.

this applies to common descent when 'natural selection' is added to the mix.

when life first 'started' there is no reason to believe it was a sharp event comprising a single molecule that took off and populated the world all by it's lonesome, with all the stuff of life floating around not being used by life the generation of all possible molecules could proceed freely so there could be a near infinite range of carbon based molecules all interacting randomly with each other.

so instead of an hourglass shape, a wide selection of chemical processes coming together to form a single molecule which then splits up into all the myriad forms of life, I am seeing more like a rope with lots of individual strands that weave together and apart again until strands with complementry curves come together and are 'selected' into an offshoot which flops around until it collides with another offshoot and forms a better rope, or DNA double helix.

sort of thing.

[Jose]

I can understand how naturalists can arrive at this. But as I've mentioned, it's primarily a result that there are no other natural explanations. Since it is the only natural explanation, it would be the only step. So it would not matter if it was a small step, a big step, or a massive step.

The tricky bit here is deciding which supernatural explanations to include. Do we allow that of Wen The Eternally Surprised, and posit that god destroys and re-creates the universe every instant? Sure. Why not? There's no evidence against it. Our memories don't count, if god can create us with them already in place. Or, do we use the supernatural explanations of fundamentalist Hindus? Or do we posit a great metaphorical turtle?

It's not that naturalists don't allow supernatural explanations, though this is typically what is taught. It is that science starts with data, and infers explanations therefrom. If the gods would show their hand, and present data of their existence or their action, then they would figure into the explanations. Alas, they've played their cards very close to their chests.

The challenge for creationists is to step back, and look at the entire suite of data, and set aside their belief. Without the clues provided by one religion out of many, how do you interpret the data? People don't like to do this, because they fear that they'll conclude that the scientific explanation is more likely. Of course, scientists don't like to do this either--set aside their favorite explanation and look at the data from the viewpoint of one of their competitors--but that's the nature of the world we live in, so we gotta do it. There's no penalty for changing your mind, except knowing that you didn't get there first. That's a big contrast from the possibility of losing Eternal Salvation if you look at the data with a blank slate.

I'll bring up one case. The route from egg-laying to live-birth and vice versa. Each one requires a complex set of requirements. How can animals microevolve from one to the other?

It's actually pretty straightforward. Animals have eggs. Initially, they were all squirted out into water. Then, for protection, they developed some kind of coating--think of a frog egg with a Jelly Coat. The jelly coat is analogous to the white of a chicken egg. (The yellow part is the egg itself.) Once you start using internal fertilization, then there are all sorts of options. You can plop the fertilized egg into water. Or, you can secrete a shell around it, and bury it in the sand. Or, you can secrete a shell around it and plop it anywhere. Or, you can skip the shell, and let the fertilized egg develop inside you. If it does this, you can let the little critter out when it's tiny, or you can let it develop a bit longer and then crawl into your pouch and lick milk from your fur. Or, you can let it invade you and build a placenta, so you can feed it until it's much older. If you take the latter route, you can ditch the jelly coat altogether, because there's nothing to protect the egg from. You can even ditch the idea of producing yolk proteins (in your liver, as it turns out), secreting them into your bloodstream, and having the egg take up the yolk proteins and store them in little droplets inside the egg. If your egg is going to have to develop on its own, you need to give it food. If you're going to feed the embryo, why bother with the yolk?

Of course, animals don't evolve from one to the other and back again. Egg-laying came first. Some species have developed strategies of not laying the eggs--and there are many different strategies among different kinds of animals.

Now “soft bodies first” does not seem to me to be evolutionary theory bending over backwards to explain away data, quite the reverse, I would be unhappy with an evolutionary picture that did not posit soft bodies first, and as a consequence a lack of fossil evidence for the soft bodied era.

For a long time, it was a matter of positing soft bodies first. But, that was before the discovery of the Edicaran fossils. Now we know. There were soft bodies before the Cambrian.

Now, some creationists discredit these fossils by (a) not accepting geological dating, and (b) saying that the fossils don't look like anything we recognize, so they can't be ancestors of the current phyla. I won't comment on argument (a). For argument (b), we have to ask whether there's any reason to expect to recognize as "familiar" a critter that's a common ancestor of dogs and shrimp. If you tried to predict what such a critter might be like, you'd need to focus on just the feature that dogs and shrimp have in common. You'd get something unfamiliar.

[otseng]

Of course, animals don't evolve from one to the other and back again. Egg-laying came first.

Not sure what you mean. There are several examples of going back and forth.

One example is the monotremes.


http://www.usatoday.com/tech/columnist/ ... uest_x.htm

According to the chart above, mammals came about 200 mya. Monotremes came about 110 mya. Except for the monotremes, all other mammals are live-bearers. So here is one example of going from live-birth to egg-laying to live-birth.

[McCulloch]

Of course, animals don't evolve from one to the other and back again. Egg-laying came first.

Not sure what you mean. There are several examples of going back and forth.

One example is the monotremes.


http://www.usatoday.com/tech/columnist/ ... uest_x.htm

According to the chart above, mammals came about 200 mya. Monotremes came about 110 mya. Except for the monotremes, all other mammals are live-bearers. So here is one example of going from live-birth to egg-laying to live-birth.

I think that current evolutionary thought is that the early mammals were not live-birth but monotremes or monotreme-like. The marsupials and placentals evolved from that more primitive common ancestor.

[Jose]

Greetings Jose, it's been awhile since we've been head-to-head. Smile

Actually, I'm already stretched a bit too thin now....

And greetings to you, my friend. It has, indeed, been awhile. Actually, I'm already stretched a bit too thin now... but that's all just part of life's rich pageant, you know.

Let's start off with this because it relates to how we're defining common descent. I provided a definition earlier: "all living organisms on Earth are descended from a single organism." For the purposes of this thread, this is how I'm referring to common descent.

but, the genetics and population biology for the common descent of all organisms from a common ancestor follow the same rules as the common descent of all duck-like birds from a common ancestor of duck-like birds. There are, therefore, several issues here:

• do you accept that some species can have a common ancestor?
• do you accept the genetic mechanisms of inheritance of DNA from the parents, mutation of DNA, the dependence of phenotype on genotype, and the dependence of reproductive success on phenotype?
• what observations make common descent within certain animal groups acceptable, while the same mechanisms for "deeper" common descent between groups is unacceptable?

You see, genetically, it is impossible to separate deep-level common descent from recent, within-kind common descent. The data point to both levels being equally plausible, and identical in mechanism. I suspect that, like the Big Bang, the diversification of the first multicellular, soft-bodied animals is a target simply because there are fewer data. The precise route that evolution followed is not well known, so it's easy to say "okay, show me." But, it's impossible to escape once one looks at biochemical, DNA-level relationships--the only other way to produce the data is to say "apparently god wanted to make everything look evolved."

I'm not stating that there are no fossils prior to the Cambrian. Even in the chart above shows phyla prior to the Cambrian. ... Could you give references to exactly all the differing phyla that are found in the Precambrian?

That's a little like asking for the "current-animal name" of the common ancestor of cats and dogs. Since it was neither cat nor dog, it would not have a name as "cat" or "dog." Similarly, the precursor of two phyla would not fit into either, and would be called neither. Now, perhaps this reasoning indicates that the creationist argument that many phyla first appeared in the Cambrian represents nothing more than semantics. We couldn't call them by extant phylum names until they kinda looked like 'em. There was lots of evolution before that, but the names were different.

In noodling about the literature, I've also learned that early paleontologists tried very hard to shoehorn Cambrian fossils into phyla that were known. Again, this is a matter of semantics. Does fossil XXX really belong to phylum chordata, or was it something else? What the hey--let's call it chordata anyway.

The phylum is the highest division except for kingdom, and these metazoans certainly belong in the animal kingdom. Since every living organism fits neatly into an extant phylum, there is a tendency to think that every extinct organism should fit neatly as well. --http://www.darwincentral.org/blog/2006/ ... evolution/

One further aspect about these now extinct basal taxa is that they would have accumulated their own autapomorphies not possessed by the extant taxa. As a result, these basal fossil taxa are bound to differ from the extant clades: they will not be diagnosable as members of those clades; and they will show a confusing mixture of some but not all features of those clades, together with a set of features absent from them. It should be noted that this characteristic mix has been repeatedly noted in Cambrian fossils.
--The Cambrian fossil record and the origin of the phyla. Budd, G. Integrated Comprehensive Biology. 2003, 43, 157-165.

Because the fossils of soft-bodied things are rare and hard to find, and because the morphology of the earliest members of a phylum may be unrecognizably weird, many researchers have turned to DNA phylogeny to sort this out. This requires calibrating the molecular clock using branchpoints that are known from fossils of Cambrian age or younger, so there's a bit of extrapolation into the Precambrian. There are results such as this:

In the past, molecular clocks have been used to estimate divergence times among animal phyla, but those time estimates have varied widely (1200-670 million years ago, Ma). In order to obtain time estimates that are more robust, we have analysed a larger number of genes for divergences among three well-represented animal phyla, and among plants, animals and fungi. The time estimate for the chordate-arthropod divergence, using 50 genes, is 993 +/- 46 Ma. Nematodes were found to have diverged from the lineage leading to arthropods and chordates at 1177 +/- 79 Ma. Phylogenetic analyses also show that a basal position of nematodes has strong support (p > 99%) and is not the result of rate biases. The three-way split (relationships unresolved) of plants, animals and fungi was estimated at 1576 +/- 88 Ma. By inference, the basal animal phyla (Porifera, Cnidaria, Ctenophora) diverged between about 1200-1500 Ma. This suggests that at least six animal phyla originated deep in the Precambrian, more than 400 million years earlier than their first appearance in the fossil record.
--http://www.pubmedcentral.nih.gov/articl ... id=1689654

Proc Biol Sci. 1999 January 22; 266(1415): 163–171. Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi. D Y Wang, S Kumar, and S B Hedges

It's unrealistic to expect (and biologically impossible anyway) that a new morphological feature will suddenly pop into existence in a single mutation. It will take multiple mutations over multiple generations to change a characteristic enough that we'd call it "new."

I think there are those who would disagree with this, but let's go with this. How can it empirically demonstrated that multiple mutations over multiple generations can generate something new?

Which part would they disagree with? Do they argue that there is hard data that show that new features really do pop into existence with a single mutation? I bet not. Rather, I bet that they claim that evolutionary theory posits this, and then wax poetic about what a dumb idea it is.

If a single mutation just can't do it, then it must require multiple mutations. Since we know that a single new mutation cannot become fixed in a population without the passage of several generations, I think we're safe in saying that multiple mutations must require even more generations to become fixed. Since each mutation can do no more than change some existing trait, it must obviously require multiple changes before a trait can become different enough to call it "new."

Now, if people argue that there aren't enough mutations to have them accumulate over time, all they have to do is look at the DNA sequences of recently-diverged species. Take, for example, Drosophila melanogaster and Drosophila simulans. Look at the DNA sequences between genes. There are lots of differences. That's lots and lots of mutations.

I'd even question whether we should call things "new features" sometimes. Bird wings, bat wings, seal flippers, primate hands, and horse feet are all variations of the same thing: vertebrate limbs. And those are just variations of coelacanth fins, another variation of which is "ordinary" fish fins.

From my definition of common descent above, it is a requirement that new features be introduced in the evolutionary tree. If we go from a single cell organism to the variety of plants and animals on Earth, new features must have been introduced.

Indeed. But not in a single, magical leap in a single mutation in a single generation. The progenitor vertebrate limb had proximal bones and distal rays. In the lineage that became the ray-finned fish, the proximal bones were lost, and the rays expanded. In the lineage that became land animals, the rays were lost, and the bones expanded. This gives us fish fins and animal feet, one of which probably fits your definition of being "new." None of the individual changes were big enough to say "aha! from the last generation to this one, we've had the creation of a new feature." But after enough changes, we can look at the two lineages and say "gosh; these are different."

It's the same thing with "becoming multicellular." You start with cells being able to recognize each other and have what passes for sex (as in yeast). You move from there to cells being able to recognize each other and assemble into larger groups, as in stromatolites. From there you go to being able to adopt different "cell types" and play different roles in the loose assemblage of cells, as in sponges. From there, you go to more cell types and more complex roles...and here we are. No single change was very dramatic, but if we look at what we have now, compared to what we started with, whooooeee, lookit that!

But, after some research, I've determined that the graph is unusable. And as I concluded in that post "there is no reason to doubt what the vast majority of biologists claim in that all the phyla appear during the Cambrian Explosion."

This is not a valid conclusion. The vast majority of biologists--at least, the vast majority of those I know--would go to UCMP to find out what the current thinking is. It doesn't matter what people used to think, except as an interesting study in how our understanding changes as more data are discovered.

And there is no difference between 'micro-evolution' and 'macro-evolution' except that micro is within a few generations, and 'macro' is over hundreds of generations.

Looking at the Cambrian fossils, we do see examples of microevolution among the trilobites. There is a great diversity among the types of trilobites. However, we see no evidence of trilobites evolving into something else. Or any other animal evolving into something else. If microevolution spans hundreds or even thousands of generations, we should see evidence of a smooth and gradual evolution between various animals. However, fossils that we see are distinct and quite different from the others. I give some of the fossils found in the Cambrian here.

"Microevolution" is the change in allele frequencies; "macroevolution" is a longer-term change in morphology, including speciation and higher-level diversification. The trilobites certainly diversified into multiple genera and even families before they succumbed to the Permian extinction. They might well have given rise to other types of things had they not become extinct.

Again, it's no more compelling to say "Cambrian fossils are all distinct types" than to say "today's animals are all distinct," or to say "Ediacaran fossils are all distinct." The only way to justify claiming that organisms appeared suddenly with no prior evolution is if there are no prior fossils. That's what created the myth of the Cambrian Explosion--the fact that it took a long time to find Precambrian fossils, so it kinda looked like, maybe, there were no prior animals that could have been ancestors. Once we know there are fossils, and know there were prior life forms, we can no longer argue with any shred of validity that the Cambrian critters had no ancestors. Rather, the question becomes, "which of the fossils could possibly represent the ancestors of the Cambrian critters? Or, which could be relatives of the direct ancestors?" The puzzle now is to figure out what an animal might be like that had only one or two (ancestral) Hox genes, rather than multiple clusters of Hox genes in a large gene family.