Devolution (genetically speaking) - Tree of Life loops

[OrdinaryClay]

For this discussion I would like to define devolution as the lose of genetic material.

The notion of Devolution came up in another thread. I understand that we do not see this in modern biology, at least to any significant degree. My question is why. There is nothing inherent in evolutionary processes that prevent a species from losing genetic material as an adaptation. The fact that we have a plethora of niches filled with genetically simpler organisms clearly shows that these organisms can compete. So why is it that the tree of life does not have loops?

There clearly seems to be a direction?

 

[Chesterton]

Are you talking about say, a population of bacteria evolving into mere self-replicating molecules, or a population of humans evolving into chimps? I've wondered about that.

 

[Mallon]

For this discussion I would like to define devolution as the lose of genetic material.

The notion of Devolution came up in another thread. I understand that we do not see this in modern biology, at least to any significant degree. My question is why. There is nothing inherent in evolutionary processes that prevent a species from losing genetic material as an adaptation. The fact that we have a plethora of niches filled with genetically simpler organisms clearly shows that these organisms can compete. So why is it that the tree of life does not have loops?

There clearly seems to be a direction?

I'm really not clear on what you're saying, here. Could you please rephrase your question? It would help if you could define what you mean by "information" and "loops".

 

[OrdinaryClay]

I'm really not clear on what you're saying, here. Could you please rephrase your question? It would help if you could define what you mean by "information" and "loops".

Sure. I did not use the term information, but what I mean by the "loss of genetic material" is that the total number of base pairs in a genome would significantly decrease. The clear direction is for an increase or an approximate maintenance of existing levels. Note this is different from the simple loss of a trait. The genetic evidence is that traits are frequently lost while still maintaining the genetic markers for them in the genome. I don't mean for example why doesn't a bird evolve into a "lizard". Vertebrates all have about the same order of magnitude number of base pairs - about 10**9. Free living bacteria have about 10**6 or so. Why don't metazoans devolve into protists, for example? It sounds like a silly question, but based on the raw mechanism of evolution there is no reason why this could not happen - that I can see.

What I mean by loops are strictly not loops, but rather a case where the tree would kind of turn back on itself with regard to species complexity, as reflected by genetic complexity.

 

[OrdinaryClay]

Are you talking about say, a population of bacteria evolving into mere self-replicating molecules, ...

Interesting question. I am even more curious why we see no proto-life "ecosystems" on earth today. At least bacteria and archaeans exist within our current ecosystems. Conveniently the most important question about life has a mysteriously missing piece.

I'm pretty sure the least complex free living prokaryote living today still has about 10**6 base pairs.

 

[Assyrian]

Aren't tasmanian devils threatened by a cancer that can actually spread from animal to animal, in other words the cancer cells are acting like bacteria? At the same time any analysis of the cells would show them distinctly eukaryote, the same dolphins while they have returned to the sea and taken on the streamlining of sharks, are still distinctly mammal. With the devolution idea, it is worth remembering that while speciation and adaptation involves selecting certain parts of the genome, at the same time, new genetic material is constantly being added every generation, each of us was born with about 120 new nuceotides our parents never had. Your loss of genetic material through adaptation can be seen in the divergence between human and chimps over, what is it, 7 million years, but that matches quite nicely the rate at which we see new genetic material being added.

 

[OrdinaryClay]

Aren't tasmanian devils threatened by a cancer that can actually spread from animal to animal, in other words the cancer cells are acting like bacteria? At the same time any analysis of the cells would show them distinctly eukaryote, the same dolphins while they have returned to the sea and taken on the streamlining of sharks, are still distinctly mammal. With the devolution idea, it is worth remembering that while speciation and adaptation involves selecting certain parts of the genome, at the same time, new genetic material is constantly being added every generation, each of us was born with about 120 new nuceotides our parents never had. Your loss of genetic material through adaptation can be seen in the divergence between human and chimps over, what is it, 7 million years, but that matches quite nicely the rate at which we see new genetic material being added.

Contagious cancer is an interesting idea. Are you sure the carcinogenic agent is not the contagion as opposed to the cancer itself? There are several issues with cancer becoming contagious: transmission and immunological rejection. I have not heard of this; though, it is not implausible. Technically this is not a loss of genetic material.

Where did you read about the addition of 120 nucleotides(60 base pairs?) per generation? I suppose you mean the growth of "junk" DNA. Do you have a source for your claim?

Speciation is not strictly a loss of genetic material - it may be, but usually it is not. Speciation is as much a matter of gene expression/suppression as it is the loss or gain of genetic material. Note: I'm not interested in "noise" in base pair numbers. I'm talking about long term genetic trends. The trend is very clear. Losses are minor over all. The direction is to larger numbers and increasing complexity.

 

[Mallon]

I think I have a better understanding of where you're coming from now, OC. I can think of three topics that pertain to your question:
1) resource competition
2) developmental canalization
3) concepts concerning the "left wall of minimal complexity" and the "drunkard's walk"

Have you heard of the last concepts? Gould wrote a lot about them. You might try checking out his work.

 

[Mallon]

Oh yeah. And:
4) adaptive landscapes

 

[OrdinaryClay]

Oh yeah. And:
4) adaptive landscapes

I assume you are suggesting possible explanations for why devolution (as I described it) does not occur, but I fail to see the explanatory power in these subjects with regard to my question. The fact that simpler systems can compete is clearly evident by the success of simpler systems. A complex system, while certainly effective at competing, still has the higher cost of complexity. It is not apparent to me why complexity is maintained.

 

[Mallon]

A complex system, while certainly effective at competing, still has the higher cost of complexity. It is not apparent to me why complexity is maintained.

It is maintained because those costs can be met.

 

[OrdinaryClay]

It is maintained because those costs can be met.

This explains why some complexity still exists. Not why complexity does not evolve into simple forms. Why no "cycles" in the graph of life. Why don't we see any lineage that flows from low genetic complexity to higher back to lower.

 

[Mallon]

This explains why some complexity still exists. Not why complexity does not evolve into simple forms. Why no "cycles" in the graph of life. Why don't we see any lineage that flows from low genetic complexity to higher back to lower.

Define "complexity". Many istances of character reversal and vestigiality have been noted in evolution. Is this what you are referring to?

 

[OrdinaryClay]

Define "complexity". Many istances of character reversal and vestigiality have been noted in evolution. Is this what you are referring to?

I did define it for goodness sake. I defined devolution as a "large" loss of genetic material.

 

[gluadys]

I assume you are suggesting possible explanations for why devolution (as I described it) does not occur, but I fail to see the explanatory power in these subjects with regard to my question. The fact that simpler systems can compete is clearly evident by the success of simpler systems. A complex system, while certainly effective at competing, still has the higher cost of complexity. It is not apparent to me why complexity is maintained.

I don't know if this question fits or not in this topic, but I wonder if part of the answer lies in how much of the genome effectively impacts the organism. We have a much larger genome than bacteria, but bacteria have much less non-coding DNA. Perhaps if we looked only at the part of the mammalian genome that is expressed, it wouldn't be that much more than what you find in prokaryotes.

Dawkins suggests in The Selfish Gene that surplus DNA may be a sort of genetic parasite--"a harmless, but useless passenger, hitching a ride."

 

[OrdinaryClay]

I don't know if this question fits or not in this topic, but I wonder if part of the answer lies in how much of the genome effectively impacts the organism. We have a much larger genome than bacteria, but bacteria have much less non-coding DNA. Perhaps if we looked only at the part of the mammalian genome that is expressed, it wouldn't be that much more than what you find in prokaryotes.

Dawkins suggests in The Selfish Gene that surplus DNA may be a sort of genetic parasite--"a harmless, but useless passenger, hitching a ride."

There are real gene number differences, also the whole idea of "junk DNA" is being seriously questioned right now. The current thinking is that while there is undoubtedly DNA sequences that do nothing but take up space the percentage that falls in to this category is far smaller then once thought.

This does not address the core issue of why there is no large reduction in base pair values in any species over great periods of time.

 

[metherion]

Is there a reason for it to be? Remember, there must be selective pressure on something for changes in it to be passed along.

For argument's sake, let's say 15% of our example animal is actual, honest to goodness, not coding, can be lost with no harm, truly junk DNA. The ones that do take up space. Currently noncoding is a lot more, but 15% is actually junk. What pressure would make this animal get rid of 15% of its DNA? Where would the mutation to stop coding DNA come from? How would it get only that 15% or so gone but keep the rest that is necessary? Etcetera etcetera etcetera. Remember, changes don't just randomly happen, they happen IN the DNA, as mutations or other methods. So there would have to be a change IN the DNA to make some of the DNA stop being coded, but only parts that are ACTUALLY junk, and it would have to confer enough of an advantage in the environment to be worth keeping. Since such a change hasn't arisen, we wouldn't see what you wonder about.

Metherion

 

[OrdinaryClay]

Is there a reason for it to be? Remember, there must be selective pressure on something for changes in it to be passed along.

For argument's sake, let's say 15% of our example animal is actual, honest to goodness, not coding, can be lost with no harm, truly junk DNA. The ones that do take up space. Currently noncoding is a lot more, but 15% is actually junk. What pressure would make this animal get rid of 15% of its DNA? Where would the mutation to stop coding DNA come from? How would it get only that 15% or so gone but keep the rest that is necessary? Etcetera etcetera etcetera. Remember, changes don't just randomly happen, they happen IN the DNA, as mutations or other methods. So there would have to be a change IN the DNA to make some of the DNA stop being coded, but only parts that are ACTUALLY junk, and it would have to confer enough of an advantage in the environment to be worth keeping. Since such a change hasn't arisen, we wouldn't see what you wonder about.

Good point, but you almost seem to be proposing a law that there will never be selective pressure to reduce "junk" DNA. This does not seem plausible to me. The advantage of not having junk DNA would be an energy advantage at the very least. The energy used in mitosis and transcripting useless DNA could be significant. Even if we are in an energy rich environment it still means more energy could be used in valuable biomass as opposed to useless biomass.

 

[metherion]

Good point, but you almost seem to be proposing a law that there will never be selective pressure to reduce "junk" DNA. This does not seem plausible to me. The advantage of not having junk DNA would be an energy advantage at the very least. The energy used in mitosis and transcripting useless DNA could be significant. Even if we are in an energy rich environment it still means more energy could be used in valuable biomass as opposed to useless biomass.

I'm not trying to formulate a law saying that it can't happen. Yes, it could very well be an advantage, a huge advantage! But it would need a huge complicated system that would need to do many things:
1. Determine some way to sort useful and useless dna.
2. Copy only the useful stuff.
3. Discard the useless stuff.
4. Oh wait. All the useless stuff is gone. This system has no more use.

It would be pretty much a one shot thing. After it gets used once, there is no more need for it for... well, long enough for more true junk to get built up. And in the meantime this system would basically BECOME junk in and of itself, right?

The thing is... generation to generation change is the name of the game. We don't tend to see a lot (if any, I know of exactly zero) big one-shot changes that occurred in one organism and spread to the rest to be used once and then kind of 'fall off'. Evolution doesn't really work that way as far as I know.

So yes. Cutting out a bit less than 15% of the mass and energy species X would need to survive would be very useful. But a system like that wouldn't really arise via any known means to be used for one shot. It would be formed most likely in successive steps, since it would be quite complicated, have to have some way of determining useful and useless remnants, which would as far as we know require intelligence and a catalog/map of the entire species X genome, as well as a way to discard the stuff, and have each of these steps either do something useful to the organism (which they really wouldn't as described) or be part of a totally different system that changed function later. And since they would ALL have to be in and/or around the DNA reproduction genes it would seem really unlikely they would all arise.

Yes, the end result would be beneficial. But evolution is blind, it doesn't seem the end result, but each step. And since the steps would involve a lot of useless stuff being set up till near the end... it wouldn't happen. As far as I know. But a cellular evolutionary biologist would know more >.<

Metherion