Darwin re-visited

[Pyrotex]

I'm amused by the various "headlines" quoted in the posts on this page. "Is Darwinism Past its Sell-By Date?" -- "Tree of Life Goes in the Recycling Bin"...

They all sound like one-liners on a Creationism website.

And typically, in the body of the article, one discovers that, No, Darwinism is not past its SBD, and the TOL is alive a kicking, except for that "10%" of all animals -- which turns out to be bacteria.

Yes, hybridization and DNA swapping and methylization and pseudo-lamarckian transwhateverism are ALL taking place -- or occassionally take place -- or have probably taken place at some time -- in some branches of the TOL -- during certain phases of the Moon -- and these things are all definately important and need to be studied. But none of them invalidates Darwin's original perception and insight.

The Tree of Life is still an important visual tool for understanding evolution. The Sell-By Date keeps getting annual extensions. Lamarck's central theory is still wrong, no matter how ingeniously we snip off little pieces of it and generously slather on 'spin' and 'recontextualization'. Darwin's mistakes, though numerous, were all tiny, inconsequential in the light of his main theory, and generally derive from his understandable ignorance of genetics, and the scarcity of geological and biological data that we take for granted today.

In this, the 200th Anniversary of Charles Darwin's birth, let us not forget that had any of us been in his shoes in the mid-nineteenth century, wandering the planet in search of adventure and a meaning for our lives, we, too, may have amassed an enviable collection of fossils and bugs, and may have written entertaining travelogs, and may even have earned an honored place in 'polite society'.

I seriously doubt that ANY of us could have put it all together and so logically and persuasively revealed to the world the core principle of biological evolution and its mechanisms of operation as he did.

[Biochemist]

Originally Posted by Pyrotex

I seriously doubt that ANY of us could have put it all together and so logically and persuasively revealed to the world the core principle of biological evolution and its mechanisms of operation as he did.

Nice post, and nice perspective, Pyro.

I think it is worthwhile to summarize the core issues that (one could argue) remain open, while, at the same time, noting those that are closed.

On the closed front:

1) The tree of life (for higher phyla) is incontrovertible. Those of us who still had questions in the '80s (mostly due to the incomplete nature of the fossil record) have had the TOL confirmed by the proliferation of genetic maps of species.

2) Relatedly, common descent (at least back to the early eukaryotes) is a given

Still open:

1) the primary mechanism for speciation (any perhaps more importantly, phylogenation) is open. The uneven arrival of phyla, and their "peak" at 70 phyla about 500 million years ago, is not cleanly supportive of any sort of gradualism. Gradualism may be a primary factor, but the lack of new body plans in the last 500 million years is indeed troublesome.

2) The degree of "front loading"- The surprising degree of biochemical complexity (completely unknown to Darwin) continues to rise. If you couple the massive chaotic complexity in later phyla with the advent of lysosomes in the first eukaryotes (thus essentially "locking in" the intracytoplasmic machinery at the first eukaryote), it suggests that the "end game" was somewhat decided, or at least limited at the first eukaryote. It remains surprising that the early biochemical cytoplasmic machinery could support such a broad array of body plans, and that such a broad array of body plans could arise without significant change in the cytoplasmic machinery.


Film at 11.

[Pyrotex]

Originally Posted by Biochemist

...
1) the primary mechanism for speciation (any perhaps more importantly, phylogenation) is open. The uneven arrival of phyla, and their "peak" at 70 phyla about 500 million years ago, is not cleanly supportive of any sort of gradualism. Gradualism may be a primary factor, but the lack of new body plans in the last 500 million years is indeed troublesome.

Gradualism means slowly, be small degrees, in an accumulated fashion. There are no tenets demanding that the change always be at the same rate, in the same direction, or accumulated in a certain way. Why "70 phyla"? Why not? It had to be some number! It turned out to be 70. That is NOT a problem. Had it been 40 or 140 or 1400 phyla, I suspect you would STILL be complaining that it, "is not cleanly supportive of any sort of gradualism".

The lack of new body plans in the last 0.5 Gyr is not troublesome at all. I wonder where you got that? A new body plan represents a major departure from predecessors. Would you not agree to that? To create a new body plan, one of two situations must occur:
1) the "mutation" can be relatively simple, but ONLY IF the animal itself is simple and generalized.
2) animal can be arbitrarily complicated and specialized, but THEN the mutation must be equally complicated in order to relocate organs, redefine skeleton, interface new organs/components in with existing specialized body systems -- and is therefore EXTREMELY UNLIKELY to succeed.

The more complex and specialized a lifeform is, the less any single mutation will affect its body plan. On the other hand, we know that among the simple segmented worms (very old critters), it only takes a single mutation to increase or decrease the number of segments, or to change a pair of legs into a pair of antennae.

2) The degree of "front loading"- ....

I got a meeting. Will tackle this point later.

[Biochemist]

Originally Posted by Pyrotex

Gradualism means slowly, be small degrees, in an accumulated fashion. There are no tenets demanding that the change always be at the same rate, in the same direction, or accumulated in a certain way. Why "70 phyla"? Why not? It had to be some number! It turned out to be 70. That is NOT a problem. Had it been 40 or 140 or 1400 phyla, I suspect you would STILL be complaining that it, "is not cleanly supportive of any sort of gradualism".

Hmmm. I didn't mean to be particularly contentious here. I was merely suggesting that if the number of phyla went form 3 to 70 to 30 in roughly equal LONG time periods (3 about a 750 million years ago, 70 about 500 million years ago and 30 now) this is not particularly consistent with gradualism.

Originally Posted by Pyro

The lack of new body plans in the last 0.5 Gyr is not troublesome at all. I wonder where you got that? A new body plan represents a major departure from predecessors. Would you not agree to that?

Yes.

Originally Posted by Pyro

To create a new body plan, one of two situations must occur:
1) the "mutation" can be relatively simple, but ONLY IF the animal itself is simple and generalized.
2) animal can be arbitrarily complicated and specialized, but THEN the mutation must be equally complicated in order to relocate organs, redefine skeleton, interface new organs/components in with existing specialized body systems -- and is therefore EXTREMELY UNLIKELY to succeed.

The more complex and specialized a life form is, the less any single mutation will affect its body plan.

All true, Pyro (thanks) but not really my point. No one was requiring that all new phyla only come from more complex species. There would be nothing stopping the existing lower forms (or, more succinctly, the lower forms 500 million years ago) from creating additional new primitive branches in the tree.

But they didn't. And I am just suggesting that this set of fact does not really support gradualism as a generalized mechanism for speciation. It certainly does not refute it, but it also certainly does not particularly support it.

[Pyrotex]

Originally Posted by Biochemist

Hmmm. I didn't mean to be particularly contentious here. I was merely suggesting that if the number of phyla went form 3 to 70 to 30 in roughly equal LONG time periods (3 about a 750 million years ago, 70 about 500 million years ago and 30 now) this is not particularly consistent with gradualism.

Hmmm...63 phyla per 250 MYr = approx 1 new phyla every 4 MYr. That sure seems "gradual" to me, BC. Then a loss of 40 phyla per 250 MYr = approx -1 phyla for every 6 MYr. That still looks "gradual". So, I guess you're gonna hafta explain to me what you mean by "gradualism" cause I just don't get it yet.

...No one was requiring that all new phyla only come from more complex species. There would be nothing stopping the existing lower forms (or, more succinctly, the lower forms 500 million years ago) from creating additional new primitive branches in the tree. But they didn't...

Well, maybe they did but you weren't looking!
Seriously, you make a good point. If any new phyla were going to appear over the last 250 MYr, the odds are, they're going to branches off the more primitive lifeforms, like worms and sponges and algae.

But consider this--when a new body plan spun off 500 MYr ago, what was its environment? Any sophisticated crabs, sea urchins, fish, snakes, sharks around to gobble them up? Not likely. Things were a lot easier for new body plans back then. An extra pair of legs or an extra pair of eyes might be just the ticket. For a while.

But today (meaning the last 100 MYr or so), the competition is a lot rougher. The sea is chock full of mean teeth, jaws, spikes, poisons, pincers and stabbie-thingies. The chemical nature of the oceans themselves are different. The ecosystems are all different. Everything is different.

So maybe worms and spongiglumphs are still creating new body plans, but they have no chance to thrive in today's environment. Some of those OLD body plans thrived for many 100s of MYrs, before they suddenly went bye-bye. What changed? Their environment and the sophistication of their predators and the availability of their prey. So, in hind sight, this all makes perfect sense.

And besides, just how many body plans do you think a planet can support? Doesn't it make sense that there would be a "ceiling" on the number of body plans, and that that ceiling just might drop slowly as the sophistication of ecosystems, plants and animals kept driving upward?

[Biochemist]

Originally Posted by Pyrotex

Hmmm...63 phyla per 250 MYr = approx 1 new phyla every 4 MYr. That sure seems "gradual" to me, BC. Then a loss of 40 phyla per 250 MYr = approx -1 phyla for every 6 MYr. That still looks "gradual". So, I guess you're gonna hafta explain to me what you mean by "gradualism" cause I just don't get it yet.

Gradualism does not require (or even imply) species or phyla need to go extinct slowy. Only that they accrue slowly. And the slow growth should be "reasonably" consistent (e.g., generally logarithmic) over long time horizons.

Originally Posted by Pyro

Well, maybe they did but you weren't looking!

I know you were joking on this, but it is true that new phyla actually may have shown up, and we missed them.

Originally Posted by Pyro

But today (meaning the last 100 MYr or so), the competition is a lot rougher. The sea is chock full of mean teeth, jaws, spikes, poisons, pincers and stabbie-thingies. The chemical nature of the oceans themselves are different. The ecosystems are all different. Everything is different.

This is a valid hypothesis, but it feels more like a postulate. It is a little tought to falsify. Further, we are accepting that speciation occured regularly over the last 500 million years, but no phylogenation. This alone seems to argue against the postulate that the "niches" were all "filled up". Besides, the niches that were vacated actually had "time" to be repopulated by similar phyla. We have had twice as much time since we lost them as it took to generate them.

Again, my only point is that this is not particularly consistent with gradualism.

Originally Posted by Pyro

And besides, just how many body plans do you think a planet can support? Doesn't it make sense that there would be a "ceiling" on the number of body plans, and that that ceiling just might drop slowly as the sophistication of ecosystems, plants and animals kept driving upward?

This seems completely at odds with the experimental data (such as we have it). There may well be a ceiling, but we would not expect the ceiling to fall. We might expect the phyla/species count to approach the ceiling asymptotically, but not to hit it and fall backwards.

Reiterating, I an not suggesting your suggestions are unreasonable. Just that they are not particularly consistent with gradualism.

[Pyrotex]

Okay, I'm cool.
Personally, I feel the problem is sufficiently complex, that we can't establish expectations of how phylogenation "should" or "should not" occur over 100s of MYrs. It's all one huge number of chaotic systems within chaotic systems within chaotic systems...

Or as the Buddha said, "it's turtles all the way down."

My feeling is that certain body plans are much more adaptable (that is, they wound up that way) than others, and better able to speciate in order to fill suddenly vacated niches. Over the long haul, then, we would expect the number of beetles to explode in a bewildering variety of forms, and the number of centipedes to peak out and slower decline. Beetles can evolve new forms and fill niches faster than the 'pedes. On another planet, it could just as easily turn out the other way, with their "beetles" slowly dwindling in number and variety as they are edged out by "speedi-pedes".

I am always cautious when the conversation turns to "how evolution is supposed to go" this way or that.

[Biochemist]

Originally Posted by Pyrotex

Okay, I'm cool.
Personally, I feel the problem is sufficiently complex, that we can't establish expectations of how phylogenation "should" or "should not" occur over 100s of MYrs. It's all one huge number of chaotic systems within chaotic systems within chaotic systems...

This is undeniably true.

Originally Posted by Pyro

My feeling is that certain body plans are much more adaptable (that is, they wound up that way) than others, and better able to speciate in order to fill suddenly vacated niches.

Very likely to be true. And your argument above that higher phyla are less likely to branch is a strong one as well.

Originally Posted by Pyro

I am always cautious when the conversation turns to "how evolution is supposed to go" this way or that.

Absolutely agree. But the core of the scientific method is prediction and falsifiability. If we posit gradualism based on serial incrementalism, we should either defend (or question) the predictions, modify the hypothesis, or throw it out.

I continue to think the argument for gradualism is weak. We have strong examples of genetic drift, but these seem to be cases of selection of recessive alleles. There is just so much assumption about how those recessive alleles got there.

[Michaelangelica]

More epigenetics, or something else going on?
This process must speed up genetic changes but should't there be more genetically damaged (or exceptional) people?

Jumping Genes Discovery Challenges Current Assumptions

ScienceDaily (June 13, 2009) — Jumping genes do most of their jumping, not during the development of sperm and egg cells, but during the development of the embryo itself.
The L1 family of retrotransposons comprises about 17 percent of the human genome. Eventually, continuous jumping by retrotransposons expands the size of the human genome and may cause shuffling of genome content.
For example, when retrotransposons jump, they may take portions of nearby gene sequences with them, inserting these where they land, and thereby allowing for the creation of new genes.
Even otherwise unremarkable insertions of L1 may cause significant effects on nearby genes, such as lowering their expression.
. . .

Jumping Genes Discovery Challenges Current Assumptions

[riper]

Originally Posted by Michaelangelica

NB
This is not a thread for Darwin Denialists but it is for those who would like to discuss, explore their understanding of, or disagree with, or even add to, or expand on Darwin's theories-- but not as Darwin's ideas conflict with the literal interpretation of the Bible.


It is interesting to note that the most vulnerable to the next Bird Flu are those with the best immune systems
Those between 15-20+ age group
How does this gel with Darwin's survival of the fittest (for the given environment)?

when we talk about survival of the fitest we do not mean the strongest. if the bird flu affects those with strong immune system mostly then those with weaker ones are meant to survive it.
imaging this. the people who live in areas with more cleaner air, air free of CO2, in villages, are said to be more healthier than those living in town, breathing polluted air. but in the period of global warming it is possible that the amount of CO2 will be so much that people will start dying from it. the ones who where living in a more polluted environment will survive better. because their lungs are more adapted to breath in the CO2. so in this case the weaker ones will survive. it all depends on the conditions we are talking about.