Darwin re-visited

[HydrogenBond]

One way to explain how genes, as a whole, can form the bulk characteristics of an animal, without there being distinct body part genes, is connected to potential gradients. In single cells, gradients are created between the inside and outside of the cell membrane. There is also a gradient between the inside of the cell membrane and the outside of the nuclear membrane and between the inside of the nuclear membrane and the DNA. The DNA also has a gradient between unpacked and packed DNA.

With multicellular critters, a different set of gradients are used, based on the surface of the cells. The neurons have the highest membrane potential of all cells and are therefore at the upper limit; exterior positive pole. The blood supply is slightly alkaline and defines the negative pole. The rest of the cell surfaces are in the middle.

If we go back to embryology, two basic body features that begin to differentiate, very early, is what will become the circulation and the nervous system. This is the primary gradient. These are specified by the DNA, with both poles having to contain enough final capacity to feed all the future cells and run all the systems connected to nervous tissue. That means the entire critter. This primary gradient then will subdivide into intermediate states (systems) which set their own gradients for other intermediate systems, etc..

If we take an elephant, the preliminary gradient of circulation to nervous has to contain both a future circulatory system and a future nervous system that can support all the tasks required to have an elephant. Within this gradient, the cells, via differentiation in the DNA, will try to connect the gradient with systems like muscles as a step down from the nervous system, while organs like kidneys is a step up the gradient from the circulation.

If we go back to single cells, the place of a cell within the external gradients of the overall form, will impact that cell's membrane potential, which through gradients, works it way back to the DNA. The DNA has its own gradient between packed, unpacked and active. This will define differentiation for that place in the external gradient.

Plants all begin with a primary gradient associated with a simple root and leaf. Based on the DNA, this primary pole contains the potential to subdivide further from both ends based on the DNA. This simplifies the tasks of the DNA, since the gradient offer a checks and balance for the parallel chemical feedforward.

These gradients may be hard to see with just the bio-chemicals. One needs to look deeper into hydrogen bonding, especially within the mediator of all the gradients, which is water. Water can transmit information through its hydrogen bonding from surfaces and solutes, using solutes and surfaces to help coordinate the genetic and gradient match.

If we look at genetic changes within conservative gradients, altering genes can alter the placement of systems within conservative gradients. One may not need an entire group of genes to change to define a new possible system, just a critical gene or two that can alter placement in the old gradient location. This makes space in the gradient for another system to appear to connected the gradient.

There is not a gene for an elephant trunk. It is due to a step down within a conservative gradient. Because the trunk is like an arm, it may have stepped down from the nervous pole, because the brain stepped up, making a new gradient location.

[Pyrotex]

Originally Posted by Michaelangelica

...Now lets try to see what the mangle-brain is about. The proteins that 'do things" or make things that make things happen must talk to each other right?
Otherwise how do you get chickens with teeth when you put the wrong activated / 'turned on' DNA next to an other. (The research is somewhere here??)
Now the proteins have to know where they are right? Otherwise we would have feet were the head it?...s.

Mangel,

another good question. I am pushing my meager knowledge of genetics and cell machinery to the limit here, so be aware I may make a mistake or two.

Proteins do not know "where they are". They simply be. What it is EXACTLY that the proteins DO is a function of where they are. A protein (let's call it George) in the mitochondrial complex may perform an entirely different function than the same protein (George) in the outer cell wall. Mechanically, they may be doing the same 'action' -- for example, if the local phosphorus ion concentration goes above some limit, George twists into a different shape -- no matter where George is. And when the phosphorus ion concentration falls back below the limit, George returns to its default shape.

But in the mitochondrial complex, a single George twisting into a different shape may cause an influx of ATP pre-cursor molecules, or cause a free electron charge to transfer from one molecule to another -- but in the outer cell wall, a cluster of 4 Georges twisting into a different shape may open up a tunnel to allow a string of RNA to leave the cell.

So, wherever George is located, it is sensitive to only 1 command: phosphorus ion level. And George has only 1 reaction: twist. But what that accomplishes may be a function of the specific local environment that George is embedded in.

{Add} All proteins are proteins (with certain exceptions). They are all made of amino acids. But each one is a unique machine. They may fold in just one way, or in two or more ways. They may be "triggered" by a variety of chemical or electrical stimuli, or they may have no trigger at all. They may serve as passive structural members or as active cogs in some larger machinery. Some "proteins" that behave like catalysts are called enzymes. Each and every protein has (typically) one "action" or "role" -- but that action or role may serve a different high-level function, depending on where the protein is located in the cell.

[Pyrotex]

Earlier, this thread had a misunderstanding (caused by me) as to how molecules were "transported" from one site to another in the cell. The article link for enzymes in the previous post speaks of coenzymes.

Coenzymes are small organic molecules that transport chemical groups from one enzyme to another. Some of these chemicals such as riboflavin, thiamine and folic acid are vitamins (compounds which cannot be synthesized by the body and must be acquired from the diet). The chemical groups carried include the hydride ion (H-) carried by NAD or NADP+, the acetyl group carried by coenzyme A, and formyl, methenyl or methyl groups carried by folic acid. ... about 700 enzymes are known to use the coenzyme NADH.

The purpose of enzymes (which are proteins) appears to be to speed up certain chemical reactions that would otherwise be too slow or too inefficient to support the life of the cell. For example, there are several enzymes that will add a methyl group (CH3+) to a specific substrate biomolecule. Each enzyme will add the methyl group to a different substrate peculiar to that enzyme. But for most or all of these enzymes, they obtain that methyl group from the coenzyme Formic Acid. (actually, Methyl Formic Acid) The enzyme grabs both molecules in its "active site", pops the methyl off the coenzyme, adds the methyl to the substrate molecule, then releases the products, ready for the next methylation.

The speed with which an enzyme can do this may be millions of times faster than would happen by "ordinary chemistry".

I think this is all just fr***in fascinating. I also am of the opinion that abiogenesis (the origin of "living", self-reproducing bio-molecular systems out of non-living molecules) may have been made possible by the origin of the process necessary to create proteins. That would include RNA. And it would include the first primitive RNA "reader" that read the nucleotides and converted them into a sequence of amino acids: the protein.

With a vast (and initially random) variety of proteins and enzymes whizzing around, the variety and speed of chemical reactions that COULD occur would have multiplied astronomically. Chemical reactions that occurred rarely, if at all, now could occur in microseconds. It was kind of like an "Inflationary Era" for biochemistry. Evolution of bio-molecular chemistry sped up by factors of millions or billions.

Leading to the very first prototype Model-T cell.

[Larv]

Originally Posted by Pyrotex

I also am of the opinion that biogenesis (the origin of "living", self-reproducing bio-molecular systems out of non-living molecules) may have been made possible by the origin of the process necessary to create proteins. That would include RNA. And it would include the first primitive RNA "reader" that read the nucleotides and converted them into a sequence of amino acids: the protein.

Pyrotex, I think the correct term is “abiogenesis.” And I also think that "reader" chemicals need a language—a digital language–in order to read the writing on those nucleic acids.

With a vast (and initially random) variety of proteins and enzymes whizzing around, the variety and speed of chemical reactions that COULD occur would have multiplied astronomically. Chemical reactions that occurred rarely, if at all, now could occur in microseconds. It was kind of like an "Inflationary Era" for biochemistry. Evolution of bio-molecular chemistry sped up by factors of millions or billions.

Leading to the very first prototype Model-T cell.

Please consider also that more than just chemistry is involved in abiogenesis. There needs to be an emergence of a digital genetic code, which allows structural information to be propagated from one generation to the next. Some scientists believe that “life”—more like "pre-life"—can form without such a code, but we know of no biological life forms, present or past, that ever existed without one. To me, at least, this is the most important aspect of abiogenesis, and I think Richard Dawkins would agree.

Question: How do you differentiate a “self-reproducing bio-molecular system” from a living organism?

[Pyrotex]

You're right. "Abiogenesis". Thanks.

How do I differentiate a "self-reproducing bio-molecular system" from a living organism?

Well, first, I start talking about protein structures and bipolar lipids, then I raise my arms to show that there is nothing up my sleeves, while at the same time tipping over my glass of iced tea, pointing at the window and screaming "LOOK! IT'S THE WINGED VICTORY OF SAMOTHRACE!!!" ...

I dunno. How do YOU differentiate a "self-reproducing bio-molecular system" from a living organism?

[Larv]

Originally Posted by Pyrotex

You're right. "Abiogenesis". Thanks.

How do I differentiate a "self-reproducing bio-molecular system" from a living organism?

I dunno. How do YOU differentiate a "self-reproducing bio-molecular system" from a living organism?

I differentiate the two on the basis of how structural information is propagated. Biological organisms store and propagate it using a digital language, while lesser self-reproducing bio-molecular systems do not.

[Ben]

Originally Posted by Pyrotex

How do I differentiate a "self-reproducing bio-molecular system" from a living organism?

You don't - although the "bio-" prefix is tautological. A life-form is classically defined just as you have described, mod the bio bit.

[Pyrotex]

So! The question: How do we distinguish a "self-reproducing molecular system" from a "living organism"? may (considering only extreme cases) be answered by determining whether "information" is stored in the form of a digital language (RNA/DNA, for example).

Now, there still remains a question, and that is what about the transition forms that are of neither extreme (not obviously molecular, not obviously living)? I like Ben's answer. You don't have to distinguish. The goal of the game is not distinguishing between molecular and living; the goal is to discover (hopefully) the (plausible) path of that transition.

I am of the opinion that the self-reproducing molecular systems (SRMS) began incorporating nucleotides and amino acids rather early in their evolution, long before DNA was used to "store" a list of proteins that the SRMS would need in order to reproduce itself.

[HydrogenBond]

Using a computer analogy, the modern genetic material is analogous to the hard drive of the cell. It contains the operating system and all the programs for the cell. Before computers had the large modern hard drives, programs ran directly off disks. if you needed to run a program, a disk was inserted. The disk had to remain inserted, for the program to be used, since it was sort of an external hard drive.

What that analogy suggests are smaller pieces of DNA/RNA, inserted, like disks, to run programs. For example, a cell might be generating extra mRNA, with these being exported like boot leg programs, simply due to inefficiency in usage and recycle. These little disk programs will work in other cells, but because they are mRNA, they will only work when inserted. Virus may have been the next step, adding the ability to insert the disk and copy the contents directly to the hard drive.

[Larv]

Originally Posted by HydrogenBond

Using a computer analogy, the modern genetic material is analogous to the hard drive of the cell. It contains the operating system and all the programs for the cell. Before computers had the large modern hard drives, programs ran directly off disks. if you needed to run a program, a disk was inserted. The disk had to remain inserted, for the program to be used, since it was sort of an external hard drive.

What that analogy suggests are smaller pieces of DNA/RNA, inserted, like disks, to run programs. For example, a cell might be generating extra mRNA, with these being exported like boot leg programs, simply due to inefficiency in usage and recycle. These little disk programs will work in other cells, but because they are mRNA, they will only work when inserted. Virus may have been the next step, adding the ability to insert the disk and copy the contents directly to the hard drive.

When biologists, especially molecular biologists and evolutionary biologists, get a full purchase on this concept, HydrogenBond, I think we can make progress by explaining life dimensionally, as I am becoming more and more suspicious that life is a dimensional thing. Viruses in computers, as you have explained, and not merely metaphors of the viruses that attack living organism. Dimesnioally that are the same thing; indeed they are both coded digitally.

There is no chemistry in the universe that subordinates itself to digital code, except for the chemistry of life. Therefore, it is more than chemistry and physics. Life is an orchestration of digital genes, exactly as Richard Dawkins explains (River Out of Eden, 1995, p. 19):

Genes are pure information—information that can be encoded, recoded and decoded, without any degradation or change of meaning. Pure information can be copied and, since it is digital information, the fidelity of the copying can be immense. DNA characters are copied with an accuracy that rivals anything modern engineers can do. They are copied down the generations, with just enough occasional errors to introduce variety. Among this variety, those coded combinations that become more numerous in the world will obviously and automatically be the ones that, when decoded and obeyed inside bodies, make those bodies take active steps to preserve and propagate those same DNA messages. We—and that means all living things—are survival machines programmed to propagate the digital database that did the programming. Darwinism is now seen to be the survival of the survivors at the level of pure, digital code.

Dawkins therefore identifies a new dimension—a digitally coded dimension—in which, or upon which, life is allowed to exist and evolve.

I’d appreciate any intelligent feedback on this. It seems to me that for us to move forward in understanding the relevant principles of life and its origin we must now stand on Dawkins’ shoulders.