Note: This is a theory I've been working on for a while, but lack the access to a lab to put it to the test. I think that mapping the genome of various species and a better understanding of epigenetics can shed a greater light on this. Is this concept really scientific? If not, what can be improved?

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It is currently scientific fact that natural selection is a key mechanism in biological (or Darwinian) evolution. Natural selection is, of course, the process by which heritable traits that make it more likely for an organism to survive and successfully reproduce become more common in a population over successive generations. Is our current scientific data relating to the process of natural selection actually evidence of biological evidence, as is currently assumed? The answer is surprisingly not as definite as you would believe.

Natural selection works on the physical traits of an organism, or the phenotypes. These phenotypes are controlled by genotypes (or alleles), which give a reproductive advantage that will increase in frequency over following generations. What you see in an animal, though coded for and expressed at the genetic level, is not always exclusively what is in a species' genotype. What this meas is that an animal can carry the genetic information for a different color of fur that is not expressed physically due a more dominant color gene being expressing physically instead. When/If this animal produces offspring it's offspring could express the recessive gene, if the right conditions were met genetically. As you can probably guess this kind of genetic variation can result in adaptations that specialize organisms for particular ecological niches and may eventually result in the emergence of what we currently refer to as a new species. Is this biological evolution? Yes and no. Why is it not so clear?

To understand this better you must understand what speciation is. Speciation is the process by which a group of animals can no longer mate with what was formerly it's original group (Notice that my definition varies greatly from the official definition). To comprehend this let me give you an example of what I'm taking about. Let's use an example of Allopatric speciation, by which a population splits into two separate geographical locations (perhaps an earth quake caused a huge rift down the center of their natural habitat, thereby stranding half of the population separate from the other half). The isolated population can then be subject to genotypic and/or phenotypic divergence because they could be faced with dissimilar selective pressures. They could also undergo simple genetic drift. What is really happening here? Is a new organism being created, as suggested by the official definition of speciation? No.

[edit on 22-7-2009 by one_enlightened_mind]

Originally posted by scraze
You're stating that the seemingly different species are still the same; they share the exact same gene pool. Differences in phenotypes simply reflect differences in expression, not differences in DNA.

It is unclear to me whether you feel that all organisms of one species share the exact same DNA, or whether there are small differences possible.

Oh dear. I haven't made myself as clear as I had hoped... a troubling realization indeed.

You are correct in thinking that I see seemingly different species as all sharing the same gene pool, and the observable differences are differences in expression and not DNA.

Do they all share the same DNA? This is where it all comes down theoretical thinking on my part. I think it is possible that two seemingly different species can share the very same DNA and still have vast variation in observable traits. I understand this concept is... not exactly a kosher scientific concept. So in order to explain why I believe this to be the case I mentioned Epigenetics.

Imagine two identical twins, both have the same DNA, but one twin expresses a physical trait ever so slightly different than the other. How so? Epigenetics has been observed by the scientific community as the answer. The problem is that it's not 100% understood. There are questions as to how it all works.

So... yes... I understand the problem, and perhaps I'm on the wrong track... I am willing to admit that. But from what I understand currently it just seems like the most plausible answer.

Should I clarify further?

Addition:
I do acknowledge differences, of course. I suppose the difficulty in other people understanding is that the concept needs to be refined. While I do acknowledge differences I question our full understanding of them. Why is a trait seemingly lost in several generations, only to suddenly appear again in later ones? If the generations leading up to that re-ermerging trait lacked it... where was it hiding? Perhaps deeper research is in order... maybe the answer is in a book I've not yet read.

[edit on 22-7-2009 by one_enlightened_mind]

Thanks for the explanation; I might have failed to read careful enough in the first place. It occurred to me that I replied solely to content, less to the scientific validity or format; sorry for that. But I trust that discussing the content leads to a clear view of the scientific validity anyway hope you agree.

Although it's a bit clearer to me now, in a way the question whether your hypothesis assumes that organisms of one single species share the exact same DNA remains. The part of the hypothesis stating that two phenotypical different isolated populations may share the exact same gene pool is clear to me; however, the following is what confuses me.
When the gene pools of two isolated populations contain the same information, there are still two possibilities regarding the DNA between all of the organisms; 1) either they all have the exact same DNA 2) or they differ (whether slightly or significantly is less relevant in this differentiation). When the DNA between organisms of one species differs, the gene pool is the sum of 'reproducable' genes; as the DNA is not the same among all organisms, some genetic information may not be present in all organisms of that species. However, they are still present in the total gene pool.

Forgive me if I missed it; so far it seems like your hypothesis requires all the organisms to share the exact same DNA - but as I stated earlier, I assume you acknowledge differences in DNA between organisms of one species, as made evident by the success of DNA technology (which isn't too valid an argument - I'll get back on that if my assumption turns out to be wrong).

So please forgive me for asking the same thing again; is your hypothesis based on the assumption that organisms of one species share the exact same DNA, or are small differences possible?

I guess it should have been clear to me already, but at any rate - now I can be very certain

The hypothesis states that new species are never created. This is equivalent to saying that a species' gene pool never changes. If you don't mind me being hyper-interactive; is that correct?

If the hypothesis indeed states that a species' gene pool never changes, it poses a slight problem for the assumption that DNA may differ between organisms. If some genetic information is not present on all organisms, it is entirely possible that the organisms without the genetic information are the only ones to survive (given a specific situation in the environment); in that case, has the gene pool not changed?

This thread is so awesome! Flag.

I never like to think a new species is ever created. Well, I mean, obviously we say so and we categorize into species based on common traits to a certain degree and to make our cetegorization easier... and to groups together common organisms which can reproduce.

But really everything is just a different mutation, or set of mutations, from an original.

Speciation is weird. Because humans are the same species as other humans, but not all humans are able to reproduce with each other because of some sex chromosomal abnormalities which can leave humans with an extra x or y chromosome or a few.

But they're still the same species.

And some completely different organisms, like types of canines, have very different traits and histories but are able to reproduce young which can then reproduce.


I had a huge debate with my zoology teacher awhile ago about tarsiers and aye ayes. They are very similar, but grouped differently primarily because of location. I don't think that's right, especially not today. I think genetic drift is common enough now that you can't find a python in London and call it one thing, and find a slightly different one ten years later in Mexico and call it something else, if you know what I mean.

I think DNA is a good enough indicator at this point that a species should be defined by a certain area of similarity in the DNA code.

BUT. Some species differ primarily because of location. I don't think they should differ much, but since taxonomy is weird and typically a species name can even be "extra," adding "Floridensis" to a common type of fern that has specific differences in Florida can be useful to scientists. And some species in some areas just develop differently, and one may evolve past another to a point where it becomes too different to group with the organism that is most like the original.

Originally posted by scraze
The hypothesis states that new species are never created. This is equivalent to saying that a species' gene pool never changes. If you don't mind me being hyper-interactive; is that correct?

Ah. Here is the difficult thing to explain. Let's say we have a population of lizards who are sexually compatible with each other (or a supposed species). Now should genetic drift occur then part of the population's gene pool, while wholly the same, would contain changes in the expressions (or observable traits) Nothing is wholly gained or lost.

What I mean is that the gene pool will remain stagnant (or possibly altered... but through gene frequencies...) but the genes have multiple possibilities stored within it. The various possibilities are selected for and expressed based on environmental pressure. So what we are interpreting as the gene pool changing is actually something else.

I never denied that there is genetic variation within the gene pool. It exists and is required for a species to adapt to a new environment. I think where my theory needs refinement is genetic mutation resulting in the loss, or addition, of genetic information. Should a small population lose a gene for a certain color... or... lose some defense mechanism... then the gene pool may or may not be altered. If it is... maybe it can be restored... depending on whether or not that population is still able to reproduce with it's former population. Same principle with a population picking up genotypes from another. This is the area I need to really concentrate on and do further research.

If the hypothesis indeed states that a species' gene pool never changes, it poses a slight problem for the assumption that DNA may differ between organisms. If some genetic information is not present on all organisms, it is entirely possible that the organisms without the genetic information are the only ones to survive (given a specific situation in the environment); in that case, has the gene pool not changed?

Since the gene pool remains the same there are options for adaptation. The options are stored in the overall genepool, but expressed differently.... certain genotypes are active while others remain dormant. Overall the entire species (or multiple versions of it) the genepool is the same.

Addition:
The gene frequencies are changed... the genes are not.

[edit on 22-7-2009 by one_enlightened_mind]

[edit on 22-7-2009 by one_enlightened_mind]

I feel like I may have offended you; in that case, my sincere apologies. It seems the way I write appears harsh to others.. I mean nothing of the kind!

I think I finally understand your vision on the matter; genetic variations between organisms may exist, but they do not disturb the 'core' DNA of the species. Thus, even if all but two organisms die, the gene pool remains stagnant; the whole species will be able to reproduce with the same exact traits as the previous population.


Once more, is this correct? (hope you don't mind!)

As happens every now and then, I wrote a huge post only to have lost it. If this one seems a bit brief, you know why!

Back to the point of scientific validity; as you know a good hypothesis needs to be falsifiable. For this hypothesis to be falsifiable, there should be a bit more information on what kind of variations a species might express simply by phenotype, and what kind of genetic variations are possible in the DNA among with an explanation of how different genotypes are preserved in the DNA of each single organism of the species.
Formulated without the above, the hypothesis merely states that the variations of phenotypes are either caused by irrelevant genetic differences (not variations in the species' DNA) or features of the core DNA. While it's quite a complete statement, as an hypothesis it lacks a way to be tested. how exactly is the 'core DNA' defined? Is it a certain group of alleles? Is it a specific portion of the DNA strains? If I could show an example in which that portion of the DNA did mutate, would you consider that as proof that there is no such thing as an undisturbed portion of DNA, or would you redefine your concept of the core? These gray lines make the hypothesis relatively untestable at the moment.
However, on a greater scale, your hypothesis can be tested more easily. Since it states a species' gene pool is stagnant, it would be impossible for one species to diverge into different species over the course of millions of years. This means that the hypothesis is falsifiable by demonstrating that one species became more than one species.
Yet again, there is a problem of criteria; when do two species differ? Take our own species; I could show you how our skull has expanded over the course of tens of thousands of years. I could argue that our gene pool is now different than the gene pool of that time; in this gene pool, the skull size is different. Most probably, we would still be able to reproduce, and hence are labeled as the same species. When we go further back in time, we will notice bigger differences. The problem is this; I can argue those differences are differences in core DNA / gene pool, while you might say it's outside of the core. The older the specimen, the greater the differences; so a criteria for this aspect would be the amount and/or type of differences between two populations (in time, or place). For example, if I could show you a branch of a species that developed wings - would that be adequate as proof that a new species can evolve?

Rephrased to one question - in regard of this hypothesis, how can we test whether a gene pool has changed or not?

Then there are some details of the hypothesis that can be tested; if I understand correctly, the genetic frequencies you are talking of are coded in the DNA. This differs from the original definition in which the genetic frequencies refer to the observed frequencies of genotypes. If it is possible to show that genotypes are not shared with all organisms of one species but only present in some, and that the DNA does not store genotypes it does not use, would that suffice as evidence that a species' gene pool is not stagnant?
A different matter I worded a lot better in the lost post, is how the hypothesis implicates that all species be present on earth from the first point in time, or requires periodical addition of species from a different plane of existence. As the second possibility cannot be tested, only the first can be studied with a scientific eye.


I hope this makes sense - it's a bit shaken up, I feel. Am curious to hear your thoughts about it!

You are right that testing this is difficult. I think I can solve that problem.

There exists experiments already that claim to prove evolution, but they are quite flawed. I'm sure you've heard of the experiments with E. coli, and how over many generations it "evolved" the ability to consume a new kinds of food. As amazing as this report seemed to be on the surface, upon further research I discovered that E. coli was already capbable of consuming the food that was claimed to be previously inconsumable by it. I will grant the scientists performing the experiment the fact that E. coli did not metabolize it well in the original generations. The fact still remains that it was possible to metabolize it. This does not demonstrate evolution, but instead shows that an organism can adapt to a hostile environment. This is key for any organism's survival.

I propose that if you really are going to test evolution you must perform a similar E. coli test, but instead of using a food it can metabolize, you must only use foods it is incapable of metabolizing. Should the virus suddenly gain a tolerance for it then there is something to this evolutionary theory. It does not prove it completely, but now you have a starting point! Now something has happened to E. coli that has never happened before. Ever.

As far as your mentioning the fossil record as proof I'm afraid that is also flawed. We have no undeniable DNA evidence that hominids are our ancestors, as opposed to non-human primates. Yes, Chimps share from 96-98% of our DNA, but what does that mean? Is it proof of evolution? No. the genes are presumed to be the same gene, merely mutated in different directions over millions of years of supposed evolutionary history. Well, if you examine them more closely you see that the 2–4% difference in the genomes is actually millions and millions of bases (individual components of DNA). Besides those enormous numbers of difference, is it possible that the genes for an organism to have two arms and two legs can be universal to all organisms that have such features? This would not imply they are from a common ancestor, but only that they have two arms and two legs. The genes for the nervous system of sponges are similar to the genes for our own human nervous system... and that could simply mean the genes for such a system are universal to the organisms that have said feature. It does not, in any way, imply a common ancestor.

Until you can show an organism, giving birth a brand new and entirely different organism (over millions of generations), and, that new organism has about 90-99% similar DNA, then you cannot say beyond any doubt that evolutionary proof is in our similar genes. You must prove it before you can state it as fact.

What would provide that proof of evolution? The problem with that question is that I don't know if science is ready to come up with an answer. Similarity is not going to prove it because the similarity we see does not mean modern humans split off from a common ancestor. It has not been proven.

Addition:
The experiment I propose can have a predictable outcome. Because E. coli does not have the genes that code for it to metabolize anything that is not what it considers to be food, it will be unable to adapt because it has no genes to select in order to metabolize the entirely foreign (possibly poisonous) substance. I predict evolution never occur.

[edit on 24-7-2009 by one_enlightened_mind]

[edit on 24-7-2009 by one_enlightened_mind]

[edit on 24-7-2009 by one_enlightened_mind]

Originally posted by scraze
By the way, I looked over this:

I'd say there are two possibilities; one in which the trait hid on recessive genes, temporarily overruled genotypes or circumstantial phenotypes; the other in which the trait really disappeared, but was recreated in the same way as the first time. The latter is what I think to be the case with bacteria getting immune for antibiotics; this seems to happen when you use antibiotics on too many patients in the stage of onset. In this case, most of the bacteria die in the first instance, but the one that survives is the immune one that reproduces. The fact that all the other bacteria die shows me that the trait wasn't hidden on the DNA; it really wasn't there. The only bacteria to survive is the one that has the correct genetic information.

On the surface I would agree that perhaps the trait simply wasn't there, but when I think back to E. coli experiment I can't help but remember how generations just failed to adapt entirely because they simply had so much trouble metabolizing the supposed inconsumable food. This would indicate to me that the genetic information wasn't there to efficiently metabolize it. Fortunately, for the scientists performing the experiment, one generation finally adapted as if something was suddenly switched on.

I guess both possibilities offer an explanation. It still remains to be evident to me that the genes of an organism have the ability to adapt to an extent. Should the organism enter into an environment for which it has no genetic variation to select for, in order to deal with environmental pressure, it will die off. Evolution would not be able to save it because DNA does not function in a way for genetic code to randomly appear. Mutations can only take you so far.

For example, if global warming were true, then penguins could go extinct due to increasing heat, and I seriously doubt an evolutionary replacement would arise. That species would cease to exist because their DNA says they require a colder climate. If that climate vanishes their genetic code will allow them to adapt only so far. When the environment crosses their allowed threshold it's game over. Their DNA is stagnant as penguin DNA.

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