Darwin re-visited

[Biochemist]

Originally Posted by 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?

This is a really interesting development, MA. Your point is valid, but since the retrotransposon activity is embryonic, it also suggests that genetic changes that would result in death of a fertilized ovum now will only result in death of an early embryo cell. Essentially, it raises the probability of embryonic survival, and increases the probability off a functional cell mosaic (whether good or bad).

Really interesting. Also, I never saw the numbers (noted in the summary) that L1 retrotransposons are 17% of the human genome. This is roughly six times the portion that transcribes proteins.

Bio

[Biochemist]

Originally Posted by riper

when we talk about survival of the fittest we do not mean the strongest.

Nice point, Riper. Darwin should probably have said something like "survival of the most opportune variant in the niche", but it doesn't quite roll off of the tongue as well.

[Pyrotex]

Originally Posted by Biochemist

Nice post, and nice perspective, Pyro....
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...

Hi Bioch,
and thanks.

Again, I am not surprised at the "front loading". Remember, it took from 3 BYrA to .6 BYrA to achieve eukaryotic complexity, with all the cellular machinery that multi-celled plants and animals required BEFORE they could start evolving.

Call it 2.5+ BYr to evolve *just* the basic floor plan of the single cell, with its mitochondrial energy-plant, the lysosomes, the cytoplasm, the DNA, the messenger RNA, the standardized use of 4 amino acids to construct all proteins/enzymes which become the "tools", "agents", "end effectors", "sensors", "gateways", "garbage collectors" and "structural elements" of the fantastically complex cell machinery.

Yes, there was a LOT of front loading going on. But that front loading took 4 or 5 times longer (~2.5+ BYr versus ~.6 BYr) then the development of ALL the body plans that ALL plants and animals have developed since.

Sounds about right to me. More later.

[Biochemist]

Originally Posted by Pyrotex

Again, I am not surprised at the "front loading". Remember, it took from 3 BYrA to .6 BYrA to achieve eukaryotic complexity, with all the cellular machinery that multi-celled plants and animals required BEFORE they could start evolving.

Call it 2.5+ BYr to evolve *just* the basic floor plan of the single cell.....[the] "structural elements" of the fantastically complex cell machinery.

Yes, there was a LOT of front loading going on. But that front loading took 4 or 5 times longer (~2.5+ BYr versus ~.6 BYr) then the development of ALL the body plans that ALL plants and animals have developed since.

All true, and a good point. I still am surprised (and it seems somewhat counterintuitive) that after "carving into stone" so much of the standardized cell infrastructure, that we could generate such a remarkable diversity in body plans without significant alteration to the standardized machinery.

My opinion on this (completely unsubstantiated, of course) is that the tendency toward life (in fact toward the tree of life that we see) is intrinsic in the fundamental molecular structure of the basic molecules. That is, development of life is similar to the order created when solids crystallize. The difference is (of course) that crystallization happens rapidly, so we can test reproducibility.

I would hypothesize that if similar conditions arose again, we would get a very similar tree of life again, and arrive at a very similar "end point" again.

Bio

[Pyrotex]

Originally Posted by Biochemist

All true, and a good point. I still am surprised (and it seems somewhat counterintuitive) that after "carving into stone" so much of the standardized cell infrastructure, that we could generate such a remarkable diversity in body plans without significant alteration to the standardized machinery...

Hmmm, he said while scratching his chin

But why would a different body plan (3 body segments vs. 2; 8 legs vs. 6; etc.) need different machinery at the cellular level? The cellular machinery (CM) exists only for the benefit, survival and reproduction of the cell. Well, 99%, anyway. Nothing in the CM "knows" about the "body plan", whether there are 2 heads or 1, or any at all, 2 eyes or 3, antenna or none, etc. The only "external" factors the CM knows about are a select few chemical reactions. Excess potassium or sodium outside the cell will trigger protein gates buried in the cell walls. There exist a few "communication" processes whereby one cell can initiate a process in another. Apoptosis comes to mind. Among some bacteria, if their "wastes" become concentrated enough, all the cells imbedded in that waste change mode or form. Like, growing spores, shutting down metabolism, extruding a protective glue, growing structural fibers between cells, etc.

On the other hand, I could argue that multicelled organisms, like duckweed and giraffes, DO have macro large scale functions that demand a "different" kind of cell. Well duh!!!
They evolved a host of NEW CELL TYPES to support those new functions. The nerve cell has a significantly different CM than a blood cell, or a muscle cell or a bone-growing cell.

So, you were onto something, but just not what you anticipated.
CM did not have to change to support new body plans.
NEW types of cells with a modified CM evolved to support new body structures.

Now, given that any animal needs a nervous system and a digestive system, which are infinitely flexible in terms of size and configuration, animals can evolve an arbitrary number of body plans without any further changes to CM. Kind of a "one size fits all" solution.

The paucity of body plans, IMO, is due strictly to the non-viability of most body plans under evolutionary stresses. Eight-legged gazzelles never evolved because eight-legged lizards never evolved because eight-leg-segmented vermicular pseudopedes never evolved because their immediate predecessors took the path of developing a "spine" and becoming chordates at the point where their body plan was 4-symmetric, and mutations toward 8 legs after that point really fucked up the embryonic nervous system, and left the progeny too clumsy to fend off fangy predators.

Once the complexity of the body plan increased past a certain point, older elemental parameters of the body plan (like, number of legs) get frozen in. More recent "emergent" parameters of the body plan (like, scales vs. hair) can still mutate for a few score MYrs, until those too are frozen in.

[Symbology]

It's just amazing what a difference a few courses in zoology, biology, and/or genetics do to the vocabulary, sentence structure, and viewpoints of the posts around here.

I wonder if we could make that a prerequisite for some threads around here?

Or even better the reverse! I mean just think of how much more fun some of the threads could be if we could exclude all the people who actually know something about the subject that is being talked about!

[Michaelangelica]

Originally Posted by 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..

yes i know, isn't that fun?
The reason we get visits from so many 'nice', Yank fundamentalists.
and
the reason I put the new rider in post # one of the thread recently
see riper's post above.

Despite all this, I still can't nail the basket, Darwin

[Michaelangelica]

Very interesting conversation Pyrotex and biochemist. Could you break it down a bit for "bears of little brain"
Otherwise I will have to resort to being silly, silly like:-

[Pyrotex]

Originally Posted by Michaelangelica

Very interesting conversation Pyrotex and biochemist. Could you break it down a bit for "bears of little brain"...

[This post has been edited to correct a stupid mistake]

Mangel,
I would never in 984,625 years ever think of you as a bear of little brain. Poo!

But, assuming that there might be a few lurking around, I will give it my best shot.

Evolution: Body Plans and DNA

DNA does not code for body parts. There are no genes for a trunk. You cannot, even in principal, splice some genes from an elephant into a giraffe, and get a giraffe with a trunk. What DNA does is code for chemistry -- and 99% of that is code for producing proteins. Proteins have no relation to body parts or body plans. Proteins encode for something else that we might call "Effect" -- this includes the shape of the protein, its ability (if any) to fold or shift into an alternate shape, the charge-density map of its shape, its sensitivity to external electric fields, and its electro-mechanical behavior in the presence of certain "trigger" molecules or levels of acidity (pH).

Proteins (by and large) are the Universe's smallest machines. [hypothetical scenario] Along comes an amino acid a nucleotide and a specific protein will respond to its (and only its) electric field and will change shape and "grab" the amino acid nucleotide. This alters the protein's charge-density, which is detected by another protein which attractes protein #1 over to a nest of tightly coordinated proteins that are building a segment of RNA. Protein #1 is leveraged into position by electric fields. A free electron is pumped into Protein #1 and it releases its amino acid nucleotide and reverts to its default shape. Protein #1 drifts away to start the process over again, and the amino acid nucleotide is strung onto the end of the RNA strand.

So, at a higher level of abstraction, we can say that proteins have functionality. They "do" things; they make things happen.

Now look at a primitive strand of DNA in an organism from the Cambrian Era. The DNA creates proteins in a certain sequence. The proteins take on certain shapes and do certain functions. One patch of DNA generates the shape of a body segment. Another patch of DNA generate a string of proteins that triggers the first patch at a certain "time" in the sequence. Patch #2 typically generates a string of 4 trigger proteins; they trigger the creation of 4 body segments: head, thorax1, thorax2, tail.

Thorax1 and thorax2 are nearly identical, containing buds for a pair of legs.

Head is quite similar; it also contains buds, but they will develop into antenna/eye complexes. Tail also contains buds, but they develop into orifices.

You have the standard 4-leg body plan: lizards and mammals.

A mutation occurs, and patch #2 now generates a string of 5 trigger proteins. Bingo, you now have the 6-leg body plan, containing thorax1, thorax2 and thorax3. Thorax2 is the "new" segment, and is identical to thorax 1.

Later on, other mutations occur in DNA patch #2, yielding the 8-leg, 10-leg, 24-leg, and 96-leg body plans: spiders, squids, worms, centipedes.

Now slip ahead a few tens of Millions of years. The DNA of each body plan has evolved tremendously. The individual "body segments" have to some extent merged, and to some extent, each gone their own way, developing their own refined attributes. Thorax1 and thorax2, among the lizards, have specialized, with thorax1 focused on heart and lung development. Thorax2 focused on digestion and reproduction. The division between these two segments has blurred and disappeared, unless you notice the diaphragm inside.

NOW--consider what would happen if we had another mutation in DNA patch #2 at THIS point of evolution. When it happened in the Cambrian Explosion, it resulted in primitive critters with 6, 8, 10, or more legs. Which survived, and each evolved in their own independent direction.

NOW--it produces a lizard with six legs, two hearts, two pair of lungs, two diaphragms, a really screwed up spine and nervous system and the agility of a mushroom. It's dead, Jim!

Why? Several reasons. The lizard is now 1,000 times larger than its Cambrian ancestor. Mechanical repetition of body segments doesn't scale up. Each segment has evolved its own functions which cannot be improved with mere organ duplication. Each segment has evolved its own internal mechanical, nervous and fluidic structures which can only be botched if you throw in extra components.

And so, whereas the proto-critter back in the Cambrian could alter its basic body plan with a single mutation, its descendents tens of MYrs later CANNOT execute the same kind of change and survive. Too much DNA superstructure and organ evolution, and specialization has taken place, and you collapse that "house of genetic cards" if you start slipping in a new pair of arms at the "bottom of the house".

A body plan can therefore be "frozen in" by all the changes that take place afterwards. At one time, our arms could have had as many joints as you can imagine. Look at the joints in antennae which are modified limbs. But once 3 joints (shoulder, elbow and wrist) had been around for a while, evolution of muscles, nerves, tendons, veins took place on top of that, to take whatever mechanical and fluidic advantages there were in each arm segment. Each joint evolved to take advantage of its special place and function in the arm. So now, 3 joints is also "frozen in".

Given that there are people with 6 fingers and cats with 7 toes, I conclude that the "body plan" of the hand (or paw) is not yet "frozen in". But if specialization and functional extention of the the fingers/toes takes place over a long enough time, then that too will become "frozen in" and a mutant with 6 fingers may not even be able to survive!

That, in a nutshell, is how and why body plans can only be created at very early stages in the evolution of any creature. At a stage when no superstructure has been built upon, and is tightly dependent upon, a certain number of: legs, segments, vertabrae, eyes, whatever. But after that superstructure has evolved, the body plan underneath is "frozen in" and cannot change.

Metaphor: think of an evolving organism as a personal computer. When it was simple (back in the 80's) you could slap in a new, faster CPU and take off. By the late 90's, peripheral extensions, such as video boards, sound boards, array processors, external drives, etc., had progressed so far that making a new, faster CPU chip that was universally backward compatible was nearly impossible.

Thanks for the question!!!

[modest]

Originally Posted by Pyrotex

That, in a nutshell, is how and why body plans can only be created at very early stages in the evolution of any creature. At a stage when no superstructure has been built upon, and is tightly dependent upon, a certain number of: legs, segments, vertabrae, eyes, whatever. But after that superstructure has evolved, the body plan underneath is "frozen in" and cannot change.

Thank you, Pyrotex. Your post makes brilliant sense and it's really well explained

I'm wondering if it is possible in your estimation for another body plan explosion to happen today. Of course, it wouldn't happen as you say with one of the more complex phyla. But, with one of the early branches of the animal tree like a sponges or flatworms—sponges don't have nervous, digestive or circulatory systems and their cells are very unspecialized—might they find themselves in a position one day to branch out into a new assortment of body plans?

My first thought is that this is more unlikely today than it was in the pre-Cambrian because competition is greater now. There aren't as many vacant niches in the ecosystem which would drive such a change. Why, for example, would a sponge develop legs to scurry around the ocean floor if crabs and lobsters are already expertly filling that niche?

But, it might be just as likely (and I frankly am not informed enough to know) that sponges and other simple animal phyla are not genetically in a position right now for a body plan explosion. Perhaps one day a species will come to a point where evolving new body plans is easy and favorable.

I'm curious what you think.

~modest