New Theory of Evolution

[Alighieri]

Spidergoat,

The article you posted a link to shows a transformation miniscule in comparison to the structures I described above. Also, the process outlined in the article allows for several transient generation, in the case of a proton motor also seen in E.coli, this is not possible.

I am not implying that Darwinian evolution does not occur, but I am saying that it is not the only force behind speciation; in fact I beleive it to be comparitively minor.

 

[Alighieri]

Vkotii,

Well said.

 

[spidergoat]

Spidergoat,

The article you posted a link to shows a transformation miniscule in comparison to the structures I described above. Also, the process outlined in the article allows for several transient generation, in the case of a proton motor also seen in E.coli, this is not possible.

I am not implying that Darwinian evolution does not occur, but I am saying that it is not the only force behind speciation; in fact I beleive it to be comparitively minor.

One so called "force" is the fractal nature of some natural structures, the result of a process following some simple rules.

I hope you aren't suggesting that there are biological structures that are irreducible, since that creationist argument has yet to be proven. Complex structures are the result of cumulative improvements.

Sometimes there is a mutation in the instructions on how to build a "modular" creature, the so-called Hox genes. This can cause a sudden change in basic structures.

 

[Alighieri]

I am not implying that these structures are irreducible, rather I propose that different genes encoding for different parts of a given structure combined into one another by means of colonization, differentiation and finally integration to produce a sequence of series of sequnces encoding for the overall structure. This new sequence for the resulting structure could also be integrated into an even larger genome to yield an array of new structures based on what ever other elemnts were present. This cycle of combining different sequences through an act of integration is what I refer to in the posted theory of 'integral forces'.

I do not dispute that evolution is a cumultive process, if fact it is the basis to a lot of what I am saying. Rather I do not agree with current beliefs on the major mechanisms by which this proccess progresses; namely, random mutation.

 

[iceaura]

As for your evidense that random mutation results in complex molecular machinery, it is not there.

It is all over the place - Darwin even, without the modern understanding of genetics or specified mechanism, was able to document extensive evidence of quite complex structures evolving by cumulative modifications of much simpler structures, in his studies of orchids and barnacles and other organisms.

It is very unlikely that a series of random mismatches could result in the staggering complexity and efficiency seen in 'simple' structures such as ATPase enzymes our prokaryotic flagellum motors. The intermediates mandated by Darwinian evolution would not function correctly and the organism would die, leading away from the structure.

This fallacy is the common creationist one, brought about by an initial bias toward purpose in the human mind, and an inadequate comprehension of Darwinian mechanism.

The "intermediates" would function (did function, and often do function still) in whatever their role - which need have no relation to whatever they do now. The "random mismatches" are not drawn from a pool of simple parts scattered around, but from a large pool of existing complex structures subject to continual minor variations and incorporated into multiple functions and interactions (even entirely separate organisms, as in symbiosis) already.

 

[Alighieri]

Ice Aura,

I think perhaps my writing has been vague and prone to misinterpretation.

I whole heartedly believe that evolution is a cumulative process and that Darwin's observations were accurate and brilliant. What I disagree with is the principle mechanism which he uses to describe the synthesis of complex structures.

Take the example of ATPase, which I mentioned before. I agree with your statement that the parts to construct such a biomolecule most likely came about independantly through random modification. So suppose two simple organisms each independantly developed subunites of the enzyme. One organism, has developed a catalytic domain enzyme which can efficiently phosphorylate ADP when coupled with an existing reaction such as glycolysis, this would be a precursor to parts of the F1 domain seen today. The other organism may have devloped an ATP dependant proton pump which creates a gradient which drives a proton motor flaggellum, resulting an increased motility, but still relies on primitive means to synthesize ATP. This is similar to what you outlined above. Now suppose, as you mentioned, that they become symbiotic, one organism donating ATP from efficient enzymes to drive the proton flaggelum of the other. Eventually the two organisms differentiate to the point where they are completely dependant on each other; they now act as a colony rather then a simple symbiotic pair. Eventually, the biological barriers between the two may breakdown, and geomes may integrate. Now a single genome exists which encodes for parts to a complex proton-driven, ATP catalyzing enzyme. Later genomes may have been integrated via tranformation, conjugation, etc to incorporate respiration to complete the mechanism.

The point here is that although Darwinian evolution may have resulted in the subunits by chance variation, the mechanism which brought them together was the integration of separate genomes. Random mutation may have preceded and proceeded the integration, but it was not the determining factor for the construction of the enzyme. So I beleive Darwinian evolution exists, but that it is a less profound mechanism that runs parallel to what I call 'integrative forces'.

 

[Fraggle Rocker]

You should all read Code of the Lifemaker by James P. Hogan. Humans discover a civilization populated by incredibly advanced machines who have a clever quasi-sexual way of reproducing. The machines have cracked the mystery of abiogenesis and manufacture primitive organic tissue as the basis for their technology.

When we show up they assume that we are the descendants of some other civilization's abandoned organic technology.

 

[iceaura]

The point here is that although Darwinian evolution may have resulted in the subunits by chance variation, the mechanism which brought them together was the integration of separate genomes. Random mutation may have preceded and proceeded the integration, but it was not the determining factor for the construction of the enzyme.

In the first place, you have no evidence for "integration of genomes" in the evolution of, say, flagella. That is not the currently most plausible and evidence-backed history for them- they seem to have evolved step by step, and only their incorporation into multicellular organisms even hints at such "integration" - or for many other complex structures such as eyes.

In the second place, aside from ordinary Darwinian mechanism there appears to be no obvious way to "integrate" the genomes of symbiotic organisms. What did you have in mind ?

 

[Alighieri]

iceaura,

Although I understand your argument, flagella are a poor example do the vagueness. There exists three completely separate structural designs for this complex in archaebacterial, bacterial, and eukaryotic cells. Eukaryotic flagella appear to be nothing more than a complex system of microtubules extending through the membrane and most likely have evolved through Darwinian measures. Archael and Bacterial flagella are far more complex rotation systems driven by chemical gradients and supplemented by a type III transport system. The latter systems require the interaction of complex subsystems which may have been derived in separate organisms. Your example of eyes, however, is an excellent example of pure Darwinian evolution. Due to homology amongst kingdoms and common genes, it is of little doubt that the eye evolved through natural selection.

The evolution of the eye is a perfect example of Darwinian evolution that preceded and followed an act of integrative evolution. The biggest example of integrative evolution is that which you cited above, the development of multicellular organisms. The eye no doubt began its evolution as a collection of light sensitive molecules within unicellular organisms, like those we see in protists such as euglena today. These organisms then symbiotically paired with a multitude of others to form a symbiotic colony. Eventually the colony would reach a state where its constituents are highly differentiated and completely dependant on each other, but still each maintain separate genomes. This is seen in complex colonial organisms such as Portuguese Men of War today. The next step would be the integration. Each single genome would integrate into a marcogenome. Now each differentiated component of the colony could develop from and carry the same genome. From here, even more specialized differentiation could occur as the cells work together in unison, taking the final steps to act as a single organism. Also, complex developmental plans could be embedded within the genomes of every cell, eventually leading to the evolution of a variety complex eyes seen today by the Darwinian evolution proceeding the integration.

As for your question on the integration of genomes, it happens constantly in all forms of life with the help of a variety of enzymes such as hydrolyses, proteases, and integrases. Viruses integrate and excise their genetic material into and from ours daily, sometimes remaining there for years as an endogenous form. Bacteria donate and receive genetic material via conjugation and can pick up and integrate environmental DNA via transformation; in fact this is the primary mechanism by which bacteria evolve antibiotic resistance. It is not difficult to imagine how one symbiotic organism could hydrolyze, import, and then integrate the material of another.

Integration is also seen in our own genomes. Aside from the viral factors, large sequences of genetic material in the form of transposons proliferate themselves throughout our code in a manner excision and integration by a variety of mechanisms. The fact is that they are all moving in a quest for increased genetic expression and is a microcosm to how organisms compete to proliferate their genes in an ecosystem. This is one reason why post-transcriptional editing is necessary; to prevent expression of certain sequences which were integrated into our genomes long ago and no longer serve any purpose.

Also, integrative evolution was an essential innovation for the development of our adaptive immune systems. The genomes of stem cells for T and B cells as well as the genes encoding for antibodies are all initially the same as the result of the integration of thousands of different types. However, in order to be functional, only one type of B-cell, T-cell, or antibody can exist for a specific antigen. And so, stem cells precursors 'de-integrate' themselves by removing vast amounts of DNA, resulting in a different genome then other cells in the body. For antibodies, mRNA is heavily spliced to ensure that only one type is made. This phenomenon of alternative splicing can be applied to a wide variety of eukaryotic proteins.

Also not that eukaryotic cells themselves are in a stasis of midintegration where not all components of the colony were integrated. Notably the genetic material of chloroplasts and mitochondria.

going back to your example of the eye, it is clear that eyes of all forms of life come from a common ancestor and developed by means of Darwinian evolution. However, without the integration of separate genomes into multicellular organisms, the complex eye could have never developed. This phenomenon of integration is extremely profound and I believe has occurred in many stages of evolution including the jump from RNA based organisms to DNA based organisms and prokaryotes to eukaryotes. As I outlined above, it also occurs constantly on a smaller level.