Alternative Mechanisms For Evolution?

[Agent Intellect]

There is a glaring misconception that Charles Darwin came up with the theory of evolution. It was actually concieved earlier, under the title Transmutation of species. What Charles Darwin proposed was a mechanism for this supposed transmutation of species, namely Natural Selection.

I generally find that a large portion of the population either has a woeful lack of understanding about the history, the mechanisms, and even the theory itself, of evolution (I'm sure I'm one of them) so the goal of this thread is for further understanding about the theory itself (whether one believes it to be true or not) and not to refute its existence nor to question it's merit as a scientific theory.

I don't mean for this to be a religious debate (hence why I put it in the "Pure Science" forum) but more of a discussion about other possible mechanisms for evolution. Intelligent design is one of the most popular alternatives, but ID has the problem of being untestable. What I'm interested in is evidence (or very solid reasoning) of other mechanisms for evolution.

Things like parasitism/symbiosis and horizontal gene transfer are possible ways for mutations to happen in our genes, but these seemingly random changes wouldn't have the benefit of natural selections explanation for which mutations would survive and which ones wouldn't.

A few other ways in which evolution can propagate is through Evolutionary Opportunism - but once again, it leaves out a mechanism for which genes survive.

What I'm wondering is, while most biologists (and scientists of many other fields) have a consensus that natural selection is the mechanism by which evolution propagates, I'm wondering what other theories are out there. Natural selection has been tested, and there is much supporting evidence, but is natural selection really enough to explain all of biological evolution? Is it the only possible mechanism, or could other mechanisms be at work, as well? What are some of the biggest 'gaps' or unexplained phenomena with the theory of Natural Selection (and what would have to be done to explore these areas)? What about the differing theories of punctuated equilibrium and phyletic gradualism, is there any mechanism that could explain either of those more accurately (particularly punctuated equilibrium)? Has Darwinian natural selection become too much of a scientific 'gospel' to allow dissenting scientific hypotheses to be tested?

Other resources (must read for anyone interested in evolution)

 

[Invoke Ninja's True Power]

supposedly light and radiation(specific types and frequencies) can have a profound effect on DNA

 

[nickgray]

supposedly light and radiation(specific types and frequencies) can have a profound effect on DNA

Yeah, an energetic photon can kick off some of the electrons from a part of the dna, either killing it or, by rare chance, introduce a mutation or destroy the part that prevents the cell from (sorta) reproducing itself infinitely. It's kinda fascinating how you can get cancer from smoking cigarettes - pure physics

 

[Yellow]

I dunno, while I know that natural selection is a good general outline, I'm more of a genetic drift* girl myself. I mean the idea of natural selection sounds almost just a more sciency form of creation. Things naturally drift towards a perfection or its weeded out.. meh. Genetic drift accounts for more randomness. Parasitism/symbiosis and horizontal gene transfer has been widely accepted as the reason for the emergence of Eukaryotes (cells with nuclei). In addition, there are theories that a virus caused uteruses to emerge though I'm very foggy on the details and the validity of the claim. Punctuated Equilibrium and Phyletic Gradualism are both accepted in regards to the timeline of emergence, and they have camps similar to that of natural selection and genetic drift. Some people are all for one or the other, but most fall somewhere in the spectrum (think I'm slightly on the PE side of neutral).


*

Spoiler

Genetic drift is what happens through the random reshuffling of a limited number of genes. If you were to flip a coin 100 times and come up with 800 heads and 200 tails, you'd distrust the coin. If you flipped it 10 times and got 8 heads and 2 tails, you'd probably chalk it up to change. Now imagine a small group isolated permanently from its original population. Throw this relatively small number of collective genes together and the next generation may well be skewed from the original, and likely to become increasingly skewed as time goes by. Perhaps someday, the differences would be so great that the two groups could be classified as different subspecies and eventually different species. The emergence of this new species would not have been in response to selective pressures, but a result of the random reshuffling of genes.

 

[Agent Intellect]

Genetic drift has seemingly too much attributed to chance. I'm sure it's a true phenomena, but could it really account for all of biodiversity? It seems like, even with genetic drift, there would still be some aspect of natural selection, as traits that are less suitable for survival would be killed off quicker. On the other hand, genetic drift would certainly account for the 'speed' of evolution that many people seem to point out as a flaw in the theory, but also in the same way that could be a bad thing if the change diverts too far from the edge of chaos.

I disagree with the the notion that natural selection is just a form of creation with a lab coat on. Natural selection is very much reactionary (much like a free market economy) while a creator is much more pro-active. Natural selection doesn't have any goal except to survive and pass on genes. Many people seem to think about it like some sort of 'force' or 'intent' but really all that's happening is that different traits are selected depending on the changing environment merely by having the less suitable ones die out.

The problem I have with punctuated equilibrium is that it seems like the emergence of new species would be much more sporadic (and, as a result, easily observable). That sort of speciation has really only been observed in the fossil record - and even there, transitional species have been found. I'm sure rapid evolution can happen (and in the event of catastrophic climate change or large disruptions in the local habitat, necessarily happens) but punctuated equilibrium doesn't appear, to me, a suitable theory to explain the evolution of species under normal circumstances.

 

[Yellow]

Genetic drift has seemingly too much attributed to chance. I'm sure it's a true phenomena, but could it really account for all of biodiversity? It seems like, even with genetic drift, there would still be some aspect of natural selection, as traits that are less suitable for survival would be killed off quicker. On the other hand, genetic drift would certainly account for the 'speed' of evolution that many people seem to point out as a flaw in the theory, but also in the same way that could be a bad thing if the change diverts too far from the edge of chaos.

I disagree with the the notion that natural selection is just a form of creation with a lab coat on. Natural selection is very much reactionary (much like a free market economy) while a creator is much more pro-active. Natural selection doesn't have any goal except to survive and pass on genes. Many people seem to think about it like some sort of 'force' or 'intent' but really all that's happening is that different traits are selected depending on the changing environment merely by having the less suitable ones die out.

The problem I have with punctuated equilibrium is that it seems like the emergence of new species would be much more sporadic (and, as a result, easily observable). That sort of speciation has really only been observed in the fossil record - and even there, transitional species have been found. I'm sure rapid evolution can happen (and in the event of catastrophic climate change or large disruptions in the local habitat, necessarily happens) but punctuated equilibrium doesn't appear, to me, a suitable theory to explain the evolution of species under normal circumstances.

I just don't like the "we are the apex of evolution/creation" spin pure natural selection has. Now I don't think its all genetic drift, just more so than natural selection. But genetic drift is very much observable. A group of salamanders down and up the length of a mountain range, and the ones at the end of the route are technically a different species from those in the beginning because of the random changes on the gene pool from point A to point B, yet we can see everything in between.

You do have a good point about punctuated equilibrium. But, it shouldn't be interpreted as some kind of over-night change. More of a over-thousands-rather-than-millions-of-years change. We may not have noticed it, because we haven't even finished cataloging all the different species yet, let alone able to observe them over that kind of time span. I feel that without a fair bit of punctuated equilibrium, we cannot account for all of the diversity that has developed in the last half a billion years since the cambrian explosion.... though perhaps there were a lot of different softer animals before then that have failed to produce fossils, and the "explosion" could have just been an instantaineous emergence of 'harder' creatures all over the world... I guess that would still be an explosion, hm?

I guess my rambing point is, I don't think any one mechanism is the driving force of evolution.. I think that all of them together and possibly in combination with something yet undiscovered allows the whole system to work.

 

[eudemonia]

I am not a scientist and do not understand all of this. So I wondered if someone could explain where the extra genetic material comes from? If we descended from a single cell amoeba I don't understand where the additional DNA comes from in order to create far more complex organisms. (I said I was dumb!)

I also don't understand the evidence of speciation. I mean I know that new species of fish can emerge from lakes originally inhabited by only one species but I don't know of any evidence of speciation that has generated new animal types altogether ie a fish morphing into a bird. And I don't understand how DNA appears to create a wing from no preceding genetic information regarding wings or eyes for that matter? And why does life get more and more complex - I can see why a more complex organism would have a survival advantage but I just don't understand why life should necessarily and ineluctably become more and more complex. Its almost as if there is an underlying drive to create complexity in the universe - why should this be the case? I mean its not inevitable that the amoeba should evolve at all. I'm sure all the answers are out there somewhere its just that I don't seem to be able to find them.

Sorry if these questions are a bit basic.

 

[Yellow]

I am not a scientist and do not understand all of this. So I wondered if someone could explain where the extra genetic material comes from? If we descended from a single cell amoeba I don't understand where the additional DNA comes from in order to create far more complex organisms. (I said I was dumb!).

Thats not dumb at all. DNA, as a whole, changes very slowly over time. When speciation occurs, it means the DNA has also changed (been added to, subtracted from, or just altered..but usually added to). We have, stored within us all kinds of "junk DNA". We call it junk because we do not know what it does and we are too conceited to admit it may have a purpose we do not understand. A lot of this junk DNA is stuff from our "evolutionary past" along with virus DNA that has integrated and other random, yet to be understood bits. The part that makes us, us is the part that is read and interpreted. DNA and RNA are amazing little chemicals which self-replicate. Well, while they can self-replicate with amazing precision, mistakes are occasionally made either by sheer chance or by eternal influence. This is called a mutation. Mutations can be good, bad or (usually) neutral. However, unless the mutation is bad enough to make it's organism in some way unable to survive/pass on genes, it will remain and perhaps be passed to the offspring ad infinitum.

I also don't understand the evidence of speciation. I mean I know that new species of fish can emerge from lakes originally inhabited by only one species but I don't know of any evidence of speciation that has generated new animal types altogether ie a fish morphing into a bird. And I don't understand how DNA appears to create a wing from no preceding genetic information regarding wings or eyes for that matter? And why does life get more and more complex - I can see why a more complex organism would have a survival advantage but I just don't understand why life should necessarily and ineluctably become more and more complex. Its almost as if there is an underlying drive to create complexity in the universe - why should this be the case? I mean its not inevitable that the amoeba should evolve at all. I'm sure all the answers are out there somewhere its just that I don't seem to be able to find them.

Sorry if these questions are a bit basic.

The reason there is no evidence of such drastic changes is that it doesn't exist. Changes don't happen so quickly. I mean there is evidence of a slow process leading to the emergence of say a new class of animals like birds, but nothing as drastic as the sudden emergence of wings. If you look at the bone structure of say a human hand, a cats paw, a whale's side-flipper-thingy (sorry, I can't think of the name of the stupid thing), and a bird's wing you can see they are the same structure that has been altered (a multi-step process to be sure). While every individual genetic alterations along the way may not be available, there is enough information available to safely draw these conclusions. As far as eyes, it was similar. There are some simple organisms with 'eye spots', some of which are more sophisticated than others. And it's not inevitable that anything should evolve (in my opinion). Some things do, most things don't.. we just don't hear about them so often.

 

[Latro]

Yeah, an energetic photon can kick off some of the electrons from a part of the dna, either killing it or, by rare chance, introduce a mutation or destroy the part that prevents the cell from (sorta) reproducing itself infinitely. It's kinda fascinating how you can get cancer from smoking cigarettes - pure physics

Cigarette cancer is related to substances, in particular certain aromatic molecules, getting entwined in the DNA strand and causing it to break down. There isn't really any involvement with high-energy photons there, as far as I know. High energy photons can do that, though.

On-topic:
Natural selection is almost certainly a major factor. Whether it's the only one is questionable. Note, though, that natural selection is compatible with any number of theories which explain how mutations occur, such as horizontal gene transfer. Natural selection only dictates which mutations survive to propagate themselves.

Thats not dumb at all. DNA, as a whole, changes very slowly over time. When speciation occurs, it means the DNA has also changed (been added to, subtracted from, or just altered..but usually added to). We have, stored within us all kinds of "junk DNA". We call it junk because we do not know what it does and we are too conceited to admit it may have a purpose we do not understand. A lot of this junk DNA is stuff from our "evolutionary past" along with virus DNA that has integrated and other random, yet to be understood bits.

There is a theory that junk DNA is present to soak up the brunt of the blow of, e.g. ultraviolet radiation, thereby protecting the small amount of truly important DNA in the nucleus. Whether or not this is really how things worked out (or if that answer is really even determinate) is questionable.

 

[Agent Intellect]

I just don't like the "we are the apex of evolution/creation" spin pure natural selection has.

I don't think natural selection asserts that. Evolution is an ongoing process - humankind is undergoing changes as we speak, but like the development of a child, one can't see it right before their eyes. The problem with humans is that there is nothing 'selecting' us from our perch at the top of the food web.

Now I don't think its all genetic drift, just more so than natural selection. But genetic drift is very much observable. A group of salamanders down and up the length of a mountain range, and the ones at the end of the route are technically a different species from those in the beginning because of the random changes on the gene pool from point A to point B, yet we can see everything in between.

Natural selection causes changes to organisms in different locations. Point A could have predators that select their prey based on trait Y that the organisms at point B have, or the organisms at point B might have a more abundant food source that requires trait X to eat. Animals are not confined to one area - new predators could be moving in from the direction of point A, or moving away from point B, or any number of things. Long story short, I still don't see how this diversity can't be explained through the theory of natural selection.

You do have a good point about punctuated equilibrium. But, it shouldn't be interpreted as some kind of over-night change. More of a over-thousands-rather-than-millions-of-years change. We may not have noticed it, because we haven't even finished cataloging all the different species yet, let alone able to observe them over that kind of time span. I feel that without a fair bit of punctuated equilibrium, we cannot account for all of the diversity that has developed in the last half a billion years since the cambrian explosion.... though perhaps there were a lot of different softer animals before then that have failed to produce fossils, and the "explosion" could have just been an instantaineous emergence of 'harder' creatures all over the world... I guess that would still be an explosion, hm?

Very true, but as I said, I do think PE necessarily happens, I just don't see it as the main method under normal circumstances. The cambrian explosion was a rare circumstance when the emergence of complex life came about - things either had to evolve or die. Once the complexity of multicellular organisms emerged, it was a race for the top. Competition spurs rapid change. It's slowed down now because anything that has to evolve now has a lot of tough competition - any slip in the gene pool can spell disaster.

One could almost look at it as if the cambrian explosion was evolution at it's terrible two's, like a child; it was running off in every direction and getting into everything, trying out anything that could work. This, I would contend, is why mass extinctions are probably actually quite necessary for the balance of nature, so that it can get a fresh start before it goes old - a mass extinction is analogous to the fountain of youth for our planets ecosystem.

I guess my rambing point is, I don't think any one mechanism is the driving force of evolution.. I think that all of them together and possibly in combination with something yet undiscovered allows the whole system to work.

No argument here.

I am not a scientist and do not understand all of this. So I wondered if someone could explain where the extra genetic material comes from? If we descended from a single cell amoeba I don't understand where the additional DNA comes from in order to create far more complex organisms. (I said I was dumb!)

Some of this could probably be answered in the links of my original post, but to sum it up: symbiosis and horizontal gene transfer. A lot of genetic material is shared through parasitism - our mitochondria are actually parasites that have become necessary in our own cells (not to mention the bacteria inside of our gastralintestinal tract).

Virus's and other phages attack cells by inserting their own DNA into the cell nucleus and causing it to create copies of the virus instead of protein strands - this is the method in which horizontal gene transfer works, when this process doesn't kill the cell, it retains some of the phages genetic material. Horizontal gene transfer has even been seen inside of multicellular organisms (also check this out from the bottom link of the same site).

Epigenetics, or adaptations in our genetic code due to external pressures, also cause our genome to undergo mutations.

I also don't understand the evidence of speciation. I mean I know that new species of fish can emerge from lakes originally inhabited by only one species but I don't know of any evidence of speciation that has generated new animal types altogether ie a fish morphing into a bird.

http://talkorigins.org/faqs/comdesc/section1.html#morphological_intermediates

And I don't understand how DNA appears to create a wing from no preceding genetic information regarding wings or eyes for that matter?

http://talkorigins.org/faqs/comdesc/section3.html#morphological_parahomology

And why does life get more and more complex - I can see why a more complex organism would have a survival advantage but I just don't understand why life should necessarily and ineluctably become more and more complex. Its almost as if there is an underlying drive to create complexity in the universe - why should this be the case? I mean its not inevitable that the amoeba should evolve at all. I'm sure all the answers are out there somewhere its just that I don't seem to be able to find them.

It's not inevitable for anything to evolve in any particular direction, and things don't necessarily move towards higher complexity. Competition is main driving force (in natural selection, anyway). Something would become more complex simply because it needs to 'one up' the next guy, or it won't survive.

An oversimplified, arbitray example: An animal might eat a plant for it's food, and maybe 1 out of every 50 plants of that type contain a poison that makes the animal sick. So, this animal will continue to eat the other 49 out of 50 plants, leaving only the ones that cary the mutation for being poisonous to survive, thereby allowing them to reproduce at a much faster rate then it's non-poisonous siblings. After several generations, 49 out of 50 of this type of plant will have the gene to produce poison. So now what does the animal that needs to eat this plant do? Well, 1 out of 20 of this particular animal has a resistance built up to the poison (perhaps it even built up this resistance epigenetically by eating the plant little by little and allowing it's body to become immune to it). Now, only these animals that have built up a resistance will survive to pass on their genes, and several generations later, all of this species will be resistant to the poison, and the cycle continues. A million years later, both the animal and the plant, going through this evolutionary dance, have become 'more complex' through a process of one upping each other, and are almost indistinguishable from their older ancestors.

 

[Invoke Ninja's True Power]

sometimes I wonder if we evolved from viruses

 

[Da Blob]

There is a glaring misconception that Charles Darwin came up with the theory of evolution. It was actually concieved earlier, under the title Transmutation of species. What Charles Darwin proposed was a mechanism for this supposed transmutation of species, namely Natural Selection.

I generally find that a large portion of the population either has a woeful lack of understanding about the history, the mechanisms, and even the theory itself, of evolution (I'm sure I'm one of them) so the goal of this thread is for further understanding about the theory itself (whether one believes it to be true or not) and not to refute its existence nor to question it's merit as a scientific theory.

I don't mean for this to be a religious debate (hence why I put it in the "Pure Science" forum) but more of a discussion about other possible mechanisms for evolution. Intelligent design is one of the most popular alternatives, but ID has the problem of being untestable. What I'm interested in is evidence (or very solid reasoning) of other mechanisms for evolution.

Things like parasitism/symbiosis and horizontal gene transfer are possible ways for mutations to happen in our genes, but these seemingly random changes wouldn't have the benefit of natural selections explanation for which mutations would survive and which ones wouldn't.

A few other ways in which evolution can propagate is through Evolutionary Opportunism - but once again, it leaves out a mechanism for which genes survive.

What I'm wondering is, while most biologists (and scientists of many other fields) have a consensus that natural selection is the mechanism by which evolution propagates, I'm wondering what other theories are out there. Natural selection has been tested, and there is much supporting evidence, but is natural selection really enough to explain all of biological evolution? Is it the only possible mechanism, or could other mechanisms be at work, as well? What are some of the biggest 'gaps' or unexplained phenomena with the theory of Natural Selection (and what would have to be done to explore these areas)? What about the differing theories of punctuated equilibrium and phyletic gradualism, is there any mechanism that could explain either of those more accurately (particularly punctuated equilibrium)? Has Darwinian natural selection become too much of a scientific 'gospel' to allow dissenting scientific hypotheses to be tested?

Other resources (must read for anyone interested in evolution)

In keeping with the original tone, I would like to make an observation. The science of genetics is an aspect of truth. It is a real and manipulated variable. I think the problem between religious seekers of truth and scientific seekers of truth occurs when the concept of genetic adaptation is extrapolated into the far distant past, a realm which simply is not accessible to true scientific investigations. Speculation is speculation, and adding the adjective 'scientific' does not change the guesswork into something valid.

At the basic level, discussion of possible alternatives to evolution via genetic responses to changes in the environment has to be conducted on the level of scientific variables. A variable, an agent of change, is seemingly the enemy of the status quo and the equilibrium provided in that status quo. Even at high levels of cognition a variable, a change, is considered a threat. There are programmed responses to threats, even at the level of the reptilian mind. It would not be unreasonable to assume that there is a similar program at a genetic level.

This would mean that variations in the gene pool are not totally random. In a stable environment, a species might have uniform and similar genotypes. It would only be after a change in the environment introduces a new variable into the equation that the species responds with its next generation itself being quite varied genetically. These offspring could adapt better to a hostile environment compared to their parents/ progenitors, who were the beneficiaries of a stable status quo.

I think that the gap that should be investigated, is - considering all of the man-made changes in the environment, if natural selection is valid, there should be millions of new species being observed. To date there have been few or none...

 

[Invoke Ninja's True Power]

Could it be possible that man-made changes actually cause de-evolution?

 

[Latro]

sometimes I wonder if we evolved from viruses

Current science would say "that is absurd" since current science deems viruses to not be organisms. The converse, however, is an interesting thought that has some merit. That is, that viruses originally were essentially "rogue nuclei" of their host species which then became parasitic. A big support for this involves the specificity of viruses. Unlike pathogenic bacteria, that can hurt a wide variety of different organisms, viruses are usually very specialized. This is why a lot of pet illnesses can't be transferred to people, and also why the occasions when they DO (e.g. avian flu) is catastrophic (no immunity and antivirals suck compared to antibiotics).

 

[Agent Intellect]

In keeping with the original tone, I would like to make an observation. The science of genetics is an aspect of truth. It is a real and manipulated variable. I think the problem between religious seekers of truth and scientific seekers of truth occurs when the concept of genetic adaptation is extrapolated into the far distant past, a realm which simply is not accessible to true scientific investigations. Speculation is speculation, and adding the adjective 'scientific' does not change the guesswork into something valid.

I kind of saw this coming, but I'll bite:

This is where the fossil record comes in. We've observed evolution happening in our time (contrary to what opponents of evolution want people to believe) and we can create a fairly comprehensive mapping of phylogenetic trees. One can easily deduce that the same changes that have been tested and experimentally verified were also happening in the past.

Of course this is guess work, but there is still constantly accumulating material evidence to back it up. It's like a detective on a crime scene that has evidence continually piling up that points to the suspect that he is witnessing doing the very crime that the evidence points to.

At the basic level, discussion of possible alternatives to evolution via genetic responses to changes in the environment has to be conducted on the level of scientific variables. A variable, an agent of change, is seemingly the enemy of the status quo and the equilibrium provided in that status quo. Even at high levels of cognition a variable, a change, is considered a threat. There are programmed responses to threats, even at the level of the reptilian mind. It would not be unreasonable to assume that there is a similar program at a genetic level.

Are you suggesting that genes would wipe out genetic mutations before they were able to propagate into the rest of the gene pool?

This would mean that variations in the gene pool are not totally random. In a stable environment, a species might have uniform and similar genotypes. It would only be after a change in the environment introduces a new variable into the equation that the species responds with its next generation itself being quite varied genetically. These offspring could adapt better to a hostile environment compared to their parents/ progenitors, who were the beneficiaries of a stable status quo.

Correct me if I'm wrong, but you basically just described natural selection.

I think that the gap that should be investigated, is - considering all of the man-made changes in the environment, if natural selection is valid, there should be millions of new species being observed. To date there have been few or none...

http://talkorigins.org/indexcc/CB/CB901.html
http://talkorigins.org/indexcc/CB/CB910.html
http://talkorigins.org/indexcc/CB/CB901_2.html
http://talkorigins.org/indexcc/CB/CB902.html


Once again, I urge anyone interested in evolution to check this sight out.



Edit: final note; I'm not going to respond to any more 'refutations' of evolution. There is mountains of websites with tons of literature on the subject, and 90% of all the arguments against it come from nothing more then ignorance about even some of the most fundamental aspects of evolution and are almost all addressed on Talkorigins.com

Questions about evolution are fine, but I'd rather leave the religious debating to the countless religious threads in the philosophy forum.

I'll be happy to debate the topic in another thread if someone finds any holes or misunderstandings in that site.

 

[walfin]

Punctuated equilibrium/phyletic gradualism both seem to still be based on natural selection.

I don't see why it can't be a mix of both (which would be the likely case if things were truly random).

The idea that an organism's DNA can be modified while it's still alive is an interesting thought, though. Seems like a modern day version of Lamarck's theory. If the cigarette had never come to being, would human evolution have taken a different course, and would humans be more intelligent today? After all it's conceivable that smoking might affect sperm/egg quality.

Current science would say "that is absurd" since current science deems viruses to not be organisms.

But what about abiogenesis?

 

[Latro]

But what about abiogenesis?

Viruses also lack a number of fundamental building blocks that are needed to create "organisms." Inorganic material has them, theoretically.

The other issue here is how viruses work. Viruses are highly specific about hosts, and die rapidly without a host. I suppose you could've had bacteria and then bacteriophages and then the bacteriophages somehow became the nucleus of some primitive eukaryotic cell through some kind of bizarre fusion...but that doesn't seem too likely to me. But then I'm no biologist so I'm not altogether qualified here anyway.

 

[Invoke Ninja's True Power]

I've read that bacteria and viruses can actually inject their DNA strand into an already existing DNA strand effectively altering it when they replicate.

 

[Latro]

I've read that bacteria and viruses can actually inject their DNA strand into an already existing DNA strand effectively altering it when they replicate.

That's how viruses work every time, though they kill the cell when they let their copies out. Bacteria don't do that normally though I dunno if they ever do it abnormally.

 

[Invoke Ninja's True Power]

That's how viruses work every time, though they kill the cell when they let their copies out. Bacteria don't do that normally though I dunno if they ever do it abnormally.

suppose the cell didn't die but emerged as a living synthesis of the 2?

 

[Latro]

suppose the cell didn't die but emerged as a living synthesis of the 2?

I suppose a complete failure of a virus might do that...

 

[Agent Intellect]

I don't think the emergence of biological material is the main gap with Abiogenesis, but goal seeking behavior is. Every living organism must have the will to survive and replicate - natural selection itself would fail without it. We already know that complex proteins can form even in the hostile environment of outer space (in nebulae). But how does this protein go from being molecules to being something that wants to survive? RNA could have evolved from something simpler, peptide nucleic acids - a deoxyribozyme can both catalyze its own replication and function to cleave RNA, all without any protein enzymes. But, I still have to wonder where the goal seeking behavior - replicating itself to stay 'alive' - came from anyway.

I would speculate that goal seeking behavior was an emergent property that starte off very simply. The 'goal seeking' that these primordeal organic chemicals performed wouldn't have looked like anything we recognize as goal seeking behavior. A goal for something as simple as the first RNA or deoxyribozymes would simply be that they 'navigate' towards larger sources of naturally accuring amino acids as they transcribe them into proteins to make themselves larger. There wouldn't be any real intent behind this 'navigating' towards amino acid sources, it would merely be a chemical thing - creating bonds with the amino acids would propel the incredibly simple organism along, so that it would always be moving in the direction of higher food sources.

This is where parasitism and symbiosis would come into play. With natural selection, two RNA's working together symbiotically (creating DNA) might have had a better chance of survival. The RNA's that formed into DNA (once again, no real intent behind it, simply just the RNA that had the right sequences for forming together) survived longer, were able to transcribe more complex proteins, and eventually were able to create a protein membrane of some sort around themselves, which had the ability to gather even more amino acids. More DNA strands would form symbiotic relationships, making themselves more and more complex, able to transcribe more and more protein strands.

And then something new happened: predation. Virus's found that it was easier to have other organisms transcribe proteins for them, and began preying on other microorganisms. Because it now became a game of survival, the need for more symbiotic relationships became very important, and this would eventually lead to multicellular and complex organisms - always playing this delicate game of one upping each other.

At least that's my hypothesis, anyway.

 

[merzbau]

Current science would say "that is absurd" since current science deems viruses to not be organisms. The converse, however, is an interesting thought that has some merit. That is, that viruses originally were essentially "rogue nuclei" of their host species which then became parasitic. A big support for this involves the specificity of viruses. Unlike pathogenic bacteria, that can hurt a wide variety of different organisms, viruses are usually very specialized. This is why a lot of pet illnesses can't be transferred to people, and also why the occasions when they DO (e.g. avian flu) is catastrophic (no immunity and antivirals suck compared to antibiotics).

this is interesting. it has always puzzled me why things like harmful viruses exist. as their purpose is self-defeating - to replicate and consume the host, until the host cannot sustain it anymore and it dies, making the virus' essential function suicide.

perhaps some ancient opportunistic organisms were able to develop "warrior" cells manufactured to take over other hosts, these eventually separated as independent agents, divorced from their original purpose they carry out a suicidal function? though the cross-species barrier would tend to work against this..

it would be far more advantageous for a virus to live in symbiosis with a host, consuming and replicating only enough to propagate itself in balance with the amount of material available to consume - much like the natural ecosystem.
i have read a theory that DNA was once a parasitic virus, and has evolved to live in symbiosis.

 

[Invoke Ninja's True Power]

I often speculate that there were civilizations before us that messed with genetic manipulation and disease manufacture. Perhaps melting of places with permafrost is a bad idea......

 

[Yellow]

this is interesting. it has always puzzled me why things like harmful viruses exist. as their purpose is self-defeating - to replicate and consume the host, until the host cannot sustain it anymore and it dies, making the virus' essential function suicide.

perhaps some ancient opportunistic organisms were able to develop "warrior" cells manufactured to take over other hosts, these eventually separated as independent agents, divorced from their original purpose they carry out a suicidal function? though the cross-species barrier would tend to work against this..

it would be far more advantageous for a virus to live in symbiosis with a host, consuming and replicating only enough to propagate itself in balance with the amount of material available to consume - much like the natural ecosystem.
i have read a theory that DNA was once a parasitic virus, and has evolved to live in symbiosis.

Viruses, the most successful viruses do take a long time ot kill the host, if at all. For a virus, killing a host isn't necessarily self-defeating. Killing it very quickly before it can spread, is. Often, when we notice new viruses emerge, quite a few people die right away. Then, people live with it a little longer and/or it becomes milder. When Syphilis came to Eurasia, it killed people very quickly at first. Then, it adapted to new hosts and became a more drawn out disease. If one little cluster of viruses can find a host, multiply, spread to several new hosts, it is very successful.

 

[Latro]

this is interesting. it has always puzzled me why things like harmful viruses exist. as their purpose is self-defeating - to replicate and consume the host, until the host cannot sustain it anymore and it dies, making the virus' essential function suicide.

perhaps some ancient opportunistic organisms were able to develop "warrior" cells manufactured to take over other hosts, these eventually separated as independent agents, divorced from their original purpose they carry out a suicidal function? though the cross-species barrier would tend to work against this..

it would be far more advantageous for a virus to live in symbiosis with a host, consuming and replicating only enough to propagate itself in balance with the amount of material available to consume - much like the natural ecosystem.
i have read a theory that DNA was once a parasitic virus, and has evolved to live in symbiosis.

My idea is more along the lines of nuclei with only partial DNA strands (sometimes even just RNA strands) that have broken off from their original cells and that now only "know" how to inject themselves into their host's DNA strands to replicate themselves. I dunno, though; I'd be somewhat interested to read what biologists think of the origins of viruses right now.

Viruses, the most successful viruses do take a long time ot kill the host, if at all. For a virus, killing a host isn't necessarily self-defeating. Killing it very quickly before it can spread, is. Often, when we notice new viruses emerge, quite a few people die right away. Then, people live with it a little longer and/or it becomes milder. When Syphilis came to Eurasia, it killed people very quickly at first. Then, it adapted to new hosts and became a more drawn out disease. If one little cluster of viruses can find a host, multiply, spread to several new hosts, it is very successful.

Definitely this, though. Viruses' goal is to replicate, not to kill the host (minus bacteriophages, which MUST kill the host to replicate since the host is unicellular). If they can kill some cells in the host, replicate many times, and then move to another host and continue to do this, they are "successful."

 

[Agent Intellect]

A virus killing it's host could possibly have the advantage of making sure that the host doesn't gain resistance to the virus and pass on those genes.

I found an interesting experiment, using a genetic algorithm with robots, that shows the novel adaptations that can arise from Darwinian evolution. The robots learned to actually break their programming and lie to each other.

One of the biggest differences between biological evolution and evolution with a computer model is that biological evolution is sort of a patchwork approach. Evolution is not a consciousness or a living being and cannot foresee problems in the future (the reason humans get lower back pain is because evolution didn't predict us evolving to walk upright, so there is a time lag involved), so adaptations can only be made within the scope of the current alleles.

While biological evolution can have novel solutions emerge to problems, they'll never be something as drastic as, say, a dog being born with wheels instead of legs. Most changes in the genome have to come from patches - a possible explanation for 'junk' DNA - in that the next generation won't simply be minus a gene, but a different gene will develop a pleiotropic expression, in which it will hinder or enhance the expression of another gene. Many of our genes have only the function of affecting the expression of another gene, and some of them will do this only for a short time during our development.

So, I have to wonder, if our genome is merely a series of patching itself over, where does an increase in genome complexity arise? Why do some organisms have more genes then others? Genetic drift doesn't seem to be a sufficient explanation for this, although I'm sure it has some affect - I would hypothesize that the reason humans have two connected chromosomes (chromosome 2), giving us two less then chimpanzees, is probably due to genetic drift.

Horizontal gene transfer is probably a more likely candidate, and it's also a good way to think about how an organism can become so dependent on it's environment. For example, those bugs that look like leafs may have actually acquired it's leaf-like attributes from a microorganism that transfers genetic code between the bug and the plants that it lives on (possibly through ingestion). This could almost be like reverse Darwinism - the insect preys on the plant, and as it does so, it's genes continue to acquire plant genetic code and makes the insect look more plant like. It didn't evolve to look plant like because it was a survival mechanism, but simply acquired the survival mechanism because of the change in it's phenotype - the change happened first, and then became necessary.

 

[Yellow]

Horizontal gene transfer has proven to cause some of the more complicated changes within a species. The shrinking and deformation of the Y chromosome is due to the elimination of some genes by accident, and by gene transfer to the X chromosome. Transfer of mitochondrial DNA has provided some complexities as well. Biologists routinely use gene transfer for all kinds of genetic research. Maybe it plays a bigger role in evolution than it is given credit for. I hadn't read before that gene transfer was responsible for that planty-bug type of camoflauge, but I suppose it makes sense.

 

[Agent Intellect]

Horizontal gene transfer has proven to cause some of the more complicated changes within a species. The shrinking and deformation of the Y chromosome is due to the elimination of some genes by accident, and by gene transfer to the X chromosome. Transfer of mitochondrial DNA has provided some complexities as well. Biologists routinely use gene transfer for all kinds of genetic research. Maybe it plays a bigger role in evolution than it is given credit for.

That's essentially the case I'm making. It would certainly be a reasonable explanation for how a genome can expand, and a mechanism for positive mutations (as most of them seem negative - ie cancer and down syndrome etc).

There isn't usually much mention of HGT and symbiosis in evolutionary literature, but I'd posit that it plays a very substantial role (I should apply for a patent).

I hadn't read before that gene transfer was responsible for that planty-bug type of camoflauge, but I suppose it makes sense.

It's never actually been written anywhere, I was merely musing on a hypothetical situation where HGT may have played a big role - there's a chance that I'm way off base, I just enjoy coming up with hypotheses.

 

[Yellow]

I hadn't read before that gene transfer was responsible for that planty-bug type of camoflauge, but I suppose it makes sense.

It's never actually been written anywhere, I was merely musing on a hypothetical situation where HGT may have played a big role - there's a chance that I'm way off base, I just enjoy coming up with hypotheses.

Well, maybe it is something that can be researched. With various genome projects going on, and the materials for testing it accessible... You would just need to isolate the genes that code for the camoflauge, and the genes that code for the texture and concentration of the chromoplasts within the plant. It is possible that the color similarities may even be the result of similar chemicals (though I will admit that I don't know much about the biochemistry of bugs).

 

[Latro]

That's essentially the case I'm making. It would certainly be a reasonable explanation for how a genome can expand, and a mechanism for positive mutations (as most of them seem negative - ie cancer and down syndrome etc).

Cancer is not a genetic mutation per se; while your genes mutate, that happens after you're alive and independent, and doesn't generally spread to your gametes. Down syndrome is a meiotic problem, where the male's sperm contains 2 copies of chromosome 21. It is thus also not technically a mutation. The positive individual mutations are most likely hard to see because they are small, but pretty much everyone has some of them; no meiotic process perfectly preserves the DNA of both parents.

 

[Agent Intellect]

Cancer is not a genetic mutation per se; while your genes mutate, that happens after you're alive and independent, and doesn't generally spread to your gametes. Down syndrome is a meiotic problem, where the male's sperm contains 2 copies of chromosome 21. It is thus also not technically a mutation. The positive individual mutations are most likely hard to see because they are small, but pretty much everyone has some of them; no meiotic process perfectly preserves the DNA of both parents.

Yes, but cancer is a mutation on the scale of microorganisms - we are essentially a collection of microorganisms. Transcription errors in the DNA during mitosis is essentially the same idea as genetic mutations of an organisms offspring. Not to mention that there is a genetic correlation with cancer cases.

But, on that note, point taken. The vast majority of genetic mutations are neutral, but the most noticeable ones are usually negative (genetic diseases and deformities).

I've just always wondered where some of the very specialized mutations come from, like the insects that look like plants, or angler fish, or flounders with both eyes on one side of their heads, or even an elephants trunk. Being able to gain genetic material from their surroundings seems like a fairly reasonable assertion, since something like genetic drift doesn't seems sufficient to explain such specializations - they almost seem like they require direct input from the environment.

 

[Yellow]

Yes, but cancer is a mutation on the scale of microorganisms - we are essentially a collection of microorganisms. Transcription errors in the DNA during mitosis is essentially the same idea as genetic mutations of an organisms offspring. Not to mention that there is a genetic correlation with cancer cases.

But, on that note, point taken. The vast majority of genetic mutations are neutral, but the most noticeable ones are usually negative (genetic diseases and deformities).

I've just always wondered where some of the very specialized mutations come from, like the insects that look like plants, or angler fish, or flounders with both eyes on one side of their heads, or even an elephants trunk. Being able to gain genetic material from their surroundings seems like a fairly reasonable assertion, since something like genetic drift doesn't seems sufficient to explain such specializations - they almost seem like they require direct input from the environment.

I see where you're going with this horizontal gene transfer now.. yes, I think it might play a bigger role than it is given credit for. However, I think mutation and selection may have accounted for some the features you've named. Now HGT may well be responsible for more random changes (one in a million of which may produce a viable organism), in the light of an angler fish, I can maybe see it. Some bugs as well. The flounder seems to dwell pretty solidly in the realm of more classic explanations. Mammals are often too complex to survive drastic genetic alterations, and a huge adapted nose and upper lip seen in elephants may look really weird, but isn't that big of a change. (And Downs Syndrome, remember, is a very very rare exception to the complex animal-lower survival of genetic mistakes-rule, and most younger, healthy women's bodies abort fetuses with this genetic alteration.. birth of these babies is usually only seen in women over 35.)
I think HGT is a very viable subject for research, and investigating it in otherwise unexplained cases may produce some interesting results. However, in large, complex animals, and more superficial alterations, normal mutation, natural selection and genetic drift are most likely the causes.

 

[Invoke Ninja's True Power]

sometimes I wonder if the organisms are just attracted to certain plants or if the plants created the organisms through some process unknown. I heard there is some species of tree that will only germinate if it is passed through the digestive system of a specific animal. There are some very strange symbiosis out there

 

[Agent Intellect]

I see where you're going with this horizontal gene transfer now.. yes, I think it might play a bigger role than it is given credit for.

It seems to have to make us rethink the idea of a selfish gene. I still wonder, though, whether HGT would fit in with Darwinian theory - is there any survival advantage on the genetic level for HGT, is it something that genes are supposed to do, or is it merely an accidental thing, or even a 'problem' that sometimes has positive effects?

HGT seems counter intuitive to the idea of germ-line replicators or alleles that 'want' to continue their lineages, as it necessarily changes the alleles if they are receiving new genetic material. This goes against the Darwinian idea of lineages struggling against everything else for survival - they're actually cooperative.

I suppose, though, that one could argue that genes have evolved in a way that allows this transfer of genetic material because its both self evident, in that they do undergo HGT (although that always feels like circular logic to me) and also that HGT seems like a major way in which genetic mutations could happen on quicker time scales - recombination (both in mitosis and meiosis) and genetic drift seem too random, and that most mutations would be negative, where with HGT the genetic mutations would be coming directly from the environment to which the organism is trying to adapt (perhaps HGT is why colds are so difficult to fight off, the virus being able to become resistant by gaining some of our own genetic code).

However, I think mutation and selection may have accounted for some the features you've named. Now HGT may well be responsible for more random changes (one in a million of which may produce a viable organism), in the light of an angler fish, I can maybe see it. Some bugs as well. The flounder seems to dwell pretty solidly in the realm of more classic explanations. Mammals are often too complex to survive drastic genetic alterations, and a huge adapted nose and upper lip seen in elephants may look really weird, but isn't that big of a change.

Understood, I was simply just throwing out some animals that seemed to have very specialized adaptations. Something like an animals skin color, or the size of their mouths or limbs are very easily explainable, but I do find things like angler fish and flounders to be wonders of evolution - and it often makes me curious as to why there aren't more such finely tuned adaptations, and the fact that if, for example, the prey stopped going after the angler fish bait, that they would die out very easily (they're incredibly dependent on this specialized adaptation).

There are theories to that (try reading "The Extended Phenotype" by Richard Dawkins) but it would take more typing then I care to do for the one or two people that actually read this thread.

(And Downs Syndrome, remember, is a very very rare exception to the complex animal-lower survival of genetic mistakes-rule, and most younger, healthy women's bodies abort fetuses with this genetic alteration.. birth of these babies is usually only seen in women over 35.)

Interesting. I knew a lot of pregnancies miscarried very early on, but I was under the impression that this was more of just a random thing. Has there ever been any studies as to what other sorts of mutations that get aborted, or as to how the female body knows when to do it?

I think HGT is a very viable subject for research, and investigating it in otherwise unexplained cases may produce some interesting results. However, in large, complex animals, and more superficial alterations, normal mutation, natural selection and genetic drift are most likely the causes.

HGT would probably still happen on a cellular level with macro organisms - the idea of irreversible complexity comes to mind, where the body produces an adaptation and then makes it necessary (sort of my example with the bugs). But I agree, I'm not trying to lord HGT as the only game in town as far as mutations, I'm sure, besides genetic drift, recombination, natural selection etc, there are probably even things we have yet to discover, and even unforseen ways in which the ones we do know can affect a species.

sometimes I wonder if the organisms are just attracted to certain plants or if the plants created the organisms through some process unknown. I heard there is some species of tree that will only germinate if it is passed through the digestive system of a specific animal. There are some very strange symbiosis out there

Interesting, do you have an example? I know that some pine trees require forest fires for the heat to open up the cones and let the seeds out. And, obviously, many flowers require insects to pollinate them. We even depend on bacteria in our gastrointestinal tract to assist in digesting our food for us.




Just as a lark, here's some cool pictures of strange animals (one must wonder what sorts of selection pressures and mutations allowed this to come about):

 

[NoID10ts]

Maybe this is the wrong place to post this, but in terms of evolution, what the hell is going on here ................

?

This lady in China killed this snake with a foot. My first reaction is that this is a fake, but I don't see any articles that indicate that it isn't real and it looks like some fairly reputable sources are reporting it.

Evolutionarily speaking, what, if any, significance does something like this have?

 

[Yellow]

Maybe this is the wrong place to post this, but in terms of evolution, what the hell is going on here ................

?

This lady in China killed this snake with a foot. My first reaction is that this is a fake, but I don't see any articles that indicate that it isn't real and it looks like some fairly reputable sources are reporting it.

Evolutionarily speaking, what, if any, significance does something like this have?

Wow. Well, photoshop could have easily produced this. If it is real though, I would venture to say that exposure to radiation could have caused this.. though it is more typical of amphibians and fish... I'm not sure if that readily happens in reptiles. A far-fetched idea would be that something mutanigenic, or some huge mistake happened and some old DNA was activated? I dunno, its just looks so disturbing I feel I have to have a reason for it.

 

[Agent Intellect]

What do people make of epigenetics? The basic idea behind it is that external effects can change the expression of genes (although not the actual genes themselves) which can alter a phenotype.

The current theory of epigenetics is that it's not hereditary - the epigenetic changes doesn't pass on to offspring.

DNA methylation is reprogrammed during gametogenesis based on the sex of the parent - a process thats controlled by genes. If a genes expression has been changed through epigenetics - the gamete basically being the phenotype of this expression - would that not necessarily cause genetic mutations in the gamete, which would lead to mutations (at least as far as differentiation from a Mendellian point of view) during meiosis?

Heterochromatin regulates genes by silencing them (one of the main tenets of epigenetics). Paramutation is basically HGT between two alleles on a pair of chromasomes (an allele that isn't transmitted can affect one that is), which also cause the genes to express differently.

I guess, to me, it seems like epigenetic changes would be inheritable, but I admit I haven't read much on it. Does anyone have any better expertise on the subject? Could this essentially be another method of genetic morphology (possibly even a sort of genetic drift)?

To me, it's interesting, because it's sort of backward sounding compared to natural selection. Genes aren't being naturally selected, but instead are changing according to selection pressures.

 

[Cogwulf]

Snakes are a very interesting subject in terms of evolution due to their being the only group of organisms (that I can think of anyway) to be epitomised by losing a feature so completely, and the only major differences between species are size and habitat.
Recent evidence from molecular biology suggests that snakes evolved from other reptiles very quickly, and the different types of snakes differentiated from each other just as quickly.

A very good explanation of the evolution of snakes is that the first members of the snake family were born with missing limbs due to DNA mutations, the missing limbs would have allowed the creatures to thrive as the absence of limbs allowed the creatures to find new niches in the environment that no species had been able to exploit previously, the creatures which started living in each niche differentiated into the different types of snakes we see today, and the parent species either became extinct or the mutation causing gene(s) died out in that species.

Genetic mutations causing extra or missing body parts are actually fairly common in most species, but 99.99999999999999% of the time these mutations either cause premature death or serious impediment to the mutated organism or are of no consequence at all, think of humans being born with webbed toes. The other minuscule percentage of mutations may provide some sort of advantage to the creature.

 

[Agent Intellect]

Genetic mutations causing extra or missing body parts are actually fairly common in most species, but 99.99999999999999% of the time these mutations either cause premature death or serious impediment to the mutated organism or are of no consequence at all, think of humans being born with webbed toes. The other minuscule percentage of mutations may provide some sort of advantage to the creature.

This is often something I've mused about. What if some disease or predator came about that only preyed on humans that are over 4 feet tall? After a few thousand years, all of humanity would be under 4 feet tall (with probably a large majority of them with dwarfism). I wonder what those people would think of their ancestors?

 

[Yellow]

What do people make of epigenetics? The basic idea behind it is that external effects can change the expression of genes (although not the actual genes themselves) which can alter a phenotype.

Well, epigenetics is responsible for things like cellular differentiation. While nearly every cell in our bodies have the same DNA, each type expresses and utilizes different pieces. Same with the whole extra 'x' crumpling in certain cells in women. If I remember correctly, a certian group of prions also utilize epigenetic change, because they stop certian bits of messages from being translated.

As far as evolution, it is an interesting idea. Each new organism within a species kind of starts with a 'blank slate' or tabula rasa (if you'll forgive the reference) as far as cell differentiation. They begin as stem cells and specialize from there. Therefore, most changes are not heritable. However, there are many, many cases where epigenetic changes have spanned generations. I was reading about rabbits a couple of years ago. See, rabbits can be scared to death. These researchers were conditioning these rabbits to not be so skittish. What they discovered, was that their offspring were born less easily frightened suggesting a heritable, genetic change within the original rabbits in response to environmental stimuli. As far as I know, there are dozens and dozens of similar examples throughout all living species. I see no reason why epigentic changes would not be a factor in evolution.

 

[Agent Intellect]

However, there are many, many cases where epigenetic changes have spanned generations. I was reading about rabbits a couple of years ago. See, rabbits can be scared to death. These researchers were conditioning these rabbits to not be so skittish. What they discovered, was that their offspring were born less easily frightened suggesting a heritable, genetic change within the original rabbits in response to environmental stimuli. As far as I know, there are dozens and dozens of similar examples throughout all living species. I see no reason why epigentic changes would not be a factor in evolution.

I think the main argument for this (and I admittedly haven't read up on epigenetics much, much less any studies done on it (which is why I'm asking and speculating so much on it )) is that epigenetic changes aren't actually genetic changes, but only changes in the expression of a gene. Therefore, even if there would be noticable changes in the phenotype, any genes passed on to offspring would retain the same original genetic code that they had before the epigenetic alterations.

It seems that, even if epigenetics itself isn't heritable, that some of the changes it causes would create different selection pressures. Many of our alleles are what's called 'coadapted genomes' in that, because of the alleles of other loci, a certain allele will be more likely.

This happens in two ways, one obvious and one slightly less obvious. The obvious one is, of course, that for the most part, we'll only acquire alleles for things we have - a human being will not inherit the genes for having black wings. The other way is that, for example, a frogs environment goes from very wet to considerably dryer, any epigenetic affects that happen will affect the alleles that display better fitness further down in the lineage - the epigenetic effects on certain alleles will coadapt with alleles that are not altered epigenetically (epigenetic changes could also alter paramutation affects on the chromosomes).

I think one of the biggest problems is trying to define what exactly a gene is, though. As far as I know, there isn't really a well agree'd upon concept of what a single gene is - some genes overlap on the DNA strand with other genes, some genes take up much more genetic code then others, and some genes only serve as expressers, activating another gene (could both be said to be 'genes' when they have such different jobs?). Epigenetics affects, mainly, the chromatin and methylation of DNA strands, so wouldn't it be possible that by affecting the expression of one 'gene' that it would also inadvertantly affect an overlappting gene, or a gene that the affected one works in conjunction with (either as an expresser or during paramutation)?

 

[Yellow]

...some genes overlap on the DNA strand with other genes, some genes take up much more genetic code then others, and some genes only serve as expressers, activating another gene (could both be said to be 'genes' when they have such different jobs?). Epigenetics affects, mainly, the chromatin and methylation of DNA strands, so wouldn't it be possible that by affecting the expression of one 'gene' that it would also inadvertantly affect an overlappting gene, or a gene that the affected one works in conjunction with (either as an expresser or during paramutation)?

Totally. In epigentics, the actual gene that is or is not being expressed hasn't been altered, its expression is. So, the genes controlling the expression of other genes can be altered while still calling it epigentics.

I think one of the biggest problems is trying to define what exactly a gene is, though. As far as I know, there isn't really a well agree'd upon concept of what a single gene is...

Oh, and tell me about it. A few years ago, it was one-gene-one-polypeptide (they even made us recite it). Now its one-gene-one-polypeptide-unless-its-one-enzyme-or-one-protien.

 

[Madoness]

sometimes I wonder if the organisms are just attracted to certain plants or if the plants created the organisms through some process unknown. I heard there is some species of tree that will only germinate if it is passed through the digestive system of a specific animal. There are some very strange symbiosis out there

Is it in any way an alternative for evolution? As far as I can understand if a species has evolved over the time with having one plant that may or may not be hard to digest, a major source of food, a species can have its digestion system only fit for it over the time. Is it not possible that this certain plant has evolved with symbiosis with a certain animal or a bird? It seems to be more of a proof of this theory not beginning of something alternative.

 

[Yellow]

Is it in any way an alternative for evolution? As far as I can understand if a species has evolved over the time with having one plant that may or may not be hard to digest, a major source of food, a species can have its digestion system only fit for it over the time. Is it not possible that this certain plant has evolved with symbiosis with a certain animal or a bird? It seems to be more of a proof of this theory not beginning of something alternative.

You're right. But I think, in general, this thread is not so much discussing alternatives to evolution, but additional mechanisms of evolution beyond what is classically taught.

 

[Madoness]

You're right. But I think, in general, this thread is not so much discussing alternatives to evolution, but additional mechanisms of evolution beyond what is classically taught.

Well, I understand what you're saying, but if we are talking about different mechanisms, then using aspects that fit in already existing ones are pointless.

 

[Agent Intellect]

Well, I understand what you're saying, but if we are talking about different mechanisms, then using aspects that fit in already existing ones are pointless.

Natural selection certainly has (in my and many other peoples opinion) the final say on which genes survive, but things like epigenetics and HGT have an almost Larmarckian way of catalyzing change, in that it seems a more top down approach.

The one weakness I see with Darwinian natural selection is that, over time, a lot of the alleles would become so homozygous that a species would become stagnant, unable to adapt and evolve fast enough to changes in the environment. This, of course, does happen a lot (higher than 99% of all species that have ever lived are extinct) but evolution is very flexible, and many of the things that we have been discussing here are mechanisms for the mutations that allow natural selection to even occur (as oppose to just saying "random mutations" that so many people ignorant of evolution seem to favor).

Evolution is the process of organisms essentially 'spreading out' genetically, like the branches of a tree, and then having the weakest branches sheared off - what's been discussed here is the mechanism by which new branches can continue forming even once the fittest ones have been solidified.

Now, I'd still be very interested in hearing any theories about the actual selection of the varying alleles that isn't the theory of natural selection - and perhaps it's only my lack of imagination that I can't really think of a superior explanation. Intelligent design is the only other hypothesis that's really been proposed (besides the ridiculous Larmarckian theory of evolution) but that's essentially a non-explanation, or "God of the gaps", and until there have been thoroughly researched and reproduced tests of it the way there has been for natural selection, I'll continue favoring natural selection is the best possible theory proposed so far.

 

[Madoness]

Natural selection certainly has (in my and many other peoples opinion) the final say on which genes survive, but things like epigenetics and HGT have an almost Larmarckian way of catalyzing change, in that it seems a more top down approach.

The one weakness I see with Darwinian natural selection is that, over time, a lot of the alleles would become so homozygous that a species would become stagnant, unable to adapt and evolve fast enough to changes in the environment. This, of course, does happen a lot (higher than 99% of all species that have ever lived are extinct) but evolution is very flexible, and many of the things that we have been discussing here are mechanisms for the mutations that allow natural selection to even occur (as oppose to just saying "random mutations" that so many people ignorant of evolution seem to favor).

Evolution is the process of organisms essentially 'spreading out' genetically, like the branches of a tree, and then having the weakest branches sheared off - what's been discussed here is the mechanism by which new branches can continue forming even once the fittest ones have been solidified.

Now, I'd still be very interested in hearing any theories about the actual selection of the varying alleles that isn't the theory of natural selection - and perhaps it's only my lack of imagination that I can't really think of a superior explanation. Intelligent design is the only other hypothesis that's really been proposed (besides the ridiculous Larmarckian theory of evolution) but that's essentially a non-explanation, or "God of the gaps", and until there have been thoroughly researched and reproduced tests of it the way there has been for natural selection, I'll continue favoring natural selection is the best possible theory proposed so far.

As far as I know of, cheetahs have the the problem of being too homozygous, being nearly identical with each other. The theory of evolution does not give any solution to avoid extinction, but how and why it happens sometimes.

I am too interested in hearing people giving different ideas that do not involve mechanics of evolution, that was why I had a say in here in a first place. I agree with you all the way, I myself cannot however come to solution that does not involve mechanics of evolution as the topic is is search for, but I can only give an idea when one has reached the topic, that is, a mechanic that is possible without us having include it into already known facts.

 

[Agent Intellect]

Interesting audio discussion about HGT and the 'unit' of selection.

 

[Agent Intellect]

Hmm, this thread might just turn into another one of my personal musing threads, but oh well.

I've recently been wondering about the "junk" DNA, or noncoding DNA, that comprises a large majority of every organisms genome. The size of the genome of an organism doesn't reflect what we would consider to be its complexity - there are very simple animals that have a genome much larger than ours.

This tends to raise the question, to me, about where the seeming complexity of our phenotype arises. Putting aside that some simple animals have larger genomes than more complex ones, just the fact that most of our genome does nothing means that we are an expression of only a small number of genes. Even if we figured that each of our coding genes had multiple pleiotropic affects, it still seems counter intuitive to think that such a small amount of information can give rise to such complexity.

Or course, it could possibly be explained by thinking of an "assembly line" type metaphor. The DNA really only has to code for a single cell, doing just a small job - then the cells themselves give rise to the more complex organism. The same idea as an assembly line - each person does a small job so as to simplify it - the DNA only has to do a small job of coding for a single cells job.

There have been several hypotheses about what the actual noncoding DNA really is. The most compelling one is that it's an artifact of our prior evolution. This could mean that every expansion to our genome up until now remains within our chromosomes. What this means is that any animal could be reverse evolved manually.

Another hypothesis is that the junk DNA is like parasitic or 'selfish' DNA. From a 'genes eye view' the only thing that matters is the propagation of the the gene into the next generation. Genes generally survive by coding for a phenotype that increases the fitness of the vehicle, or organism, that it resides within. But having a phenotype is not theoretically necessary for the survival of a gene if all it has to do is 'piggyback' on the success of other genes - they do nothing but continue to propogate by being attached to other successful genes that do code for proteins.

Another hypothesis is that the junk DNA has other regulatory affects that may have yet to be discovered, or may not be fully understood. Genetics and the study of DNA is actually a very young science, especially compared to something like physics which has been around for hundreds of years, and it makes sense that there would still be much that is still unexplained or misunderstood.

Edit:

Thinking about this, I've come up with some of my own hypotheses.

It's possible that, having evolved in a universe rife with wayward particles and radiation from the sun, this extra DNA is sort of a 'cushioning' against these threats. The more DNA there is for these threats to interact with, the less of a chance it has of hurting the DNA that is actually being transcribed.

It could also be a function, or result, or HGT. Perhaps organisms bodies create this excess DNA so that it can be transferred about to other organisms by means of virus (or other microorganisms), so that the other organisms can benefit from DNA an organism has that may be beneficial (ie resistance to some illness) - this noncoding DNA is rather like a quantized pool of genetic information that can pass between vehicles. Imagine, we may be more social with one another then we expect.

Epigenetics could have the purpose of switching different parts of this DNA on and off at different times. Possibly even expressing genes depending on the extremes of our environment?

Just some thoughts.