Organization of life

Darwin’s theory of gradual change (gradualism) can account for new forms and functions. In other words, a complex structure evolves from a similar structure or is refined. The same idea can be applied to organisation. The eye of mammals and the eye of insects do the same thing, but since mammals are more complex than insects, their eyes are generally more complex as well.

Note that as the animal becomes more complex overall, its features collectively become more complex as well. The statement is kind of obvious but it should be pointed out.


 

Thank you for the reply, I was starting to think I won't get any.
I was asking about something else however. When the mind organizes objects one attributes the organization to a specific conceptual scheme. On the opposite, when biology looks at the living things in the world it discovers self-organizing things independent of concepts. My question is what is the organizing principle? How does an individuality, like a chemical element, reach towards a more complex organization (DNA for example) when it could as well exist on its own? Why does the tree come to exist as organized material together instead of staying a disorganized mass?
One can point at how this happens, I ask however about why it happens, and where the necessity for forming complex individualities comes from. I also urge anyone to answer, even if their answers are just personal, even random ideas. It's interesting to know about this.

In 1953, Harold Urey and Stanley Miller set up an experiment to reproduce early chemical conditions of the Earth and added “lightning” to jump-start the process of forming amino acids, the building blocks of life. They achieved some success, but there were problems. The strongest objections, perhaps, is that amino acids aren’t all that difficult to produce — so what they achieved is perhaps not so remarkable.

Creationists like to argue that life couldn't have naturally developed from non-life because of entropy. Essentially, they claim that order and complexity, the reduction of entropy, cannot occur naturally — but this argument simply doesn’t work.

First, the Second Law of Thermodynamics, which limits the ability of a natural system to have a decrease of entropy, only applies to closed systems. When a system is open and can exchange energy with the outside, then that open system can have a decrease in entropy and an increase in order. The most obvious example of this is, coincidentally, a living organism. All organisms run the risk of approaching maximum entropy, or death. But they manage to avoid this by drawing in energy from the world: eating, drinking, and assimilating.

Second, whenever a system experiences a decrease in entropy, a wider price must be paid. When a biological organism absorbs energy and grows — thus increasing in complexity — work is done. When work is done, it is not done with 100% efficiency. Some energy is always wasted and some given off as heat — this means that in the larger context, overall entropy is increased even as entropy decreases locally within an organism. Thus, the Second Law is not violated.

We can see how organization can arise out of entropy by looking at the example of gas clouds — and the key to it all is gravity. If we examine a small amount of gas in an enclosed space and at uniform temperature, we find that it does absolutely nothing. The system is at its state of maximum entropy and we’d have no reason to expect anything to happen.

But if the mass of the gas cloud is large enough, then gravity will begin to play a significant role. Over time, pockets will start to contract, exerting even higher gravitational forces on the rest of the mass. The clumping centers will contract further, beginning to heat up and give off radiation, thus allowing for temperature gradients to form and heat convection to take place.

Thus, a system which was supposed to exist in thermodynamic equilibrium and maximum entropy has moved on its own to a system with less entropy, but more organization and activity. Clearly, gravity changes the “rules” of a system in important ways, allowing for events which might seem to be excluded by thermodynamics.

The problem is that appearances can deceive, and the system described above must not have been in true thermodynamic equilibrium. Although a uniform gas cloud should stay as it is, it still seems to “go the wrong way” in terms of organization and complexity. Life works the same way, appearing to “go the wrong way” with complexity increasing and entropy decreasing. In reality, though, it’s all part of a very long and complicated process whereby entropy is eventually increased, even if it appears to decrease locally for (relatively) brief periods.

Is it possible that simple organic molecules could self-organize into a living, reproducing organism?

Given our current scientific understanding, it is far too premature to definitely answer either yes or no.  There are many hypotheses for how first life might self-assemble on the early earth.  All of these hypotheses are still speculative.  The most widely accepted hypothesis is a multistep process something like this:  First, in the right environment (hypotheses include underwater thermal vents, shallow surface ponds, sandy beaches, volcanic craters, clay deposits, and weathered feldspar), simple organic molecules concentrated and self-assembled into strings of nucleic and amino acids (RNA and proteins).  Second, when enough of these molecules were concentrated together, they formed an interacting auto-catalytic system that jointly catalyzed their mutual reproduction.  Third, these RNA-and-protein catalytic systems evolved, with RNA and eventually DNA taking on the role of information storage, which we see in all living cells today. .....
      Life is a complex web of interactions where proteins are required for nucleic acid synthesis and nucleic acids are required for protein synthesis.  Similarly, the metabolites that fuel it are the synthetic precursors for protein and nucleic acid synthesis, yet they require proteins for their own synthesis.  Origin of life investigators have had a difficult time envisioning a proteins-only solution.  The RNA world scenario has fared somewhat better, but it is not clear how proteins get integrated.  The replicating closed auto-catalytic system described by Stuart A. Kaufmann has the advantage that the complex web of interactions is built in from the outset.  In essence this view acknowledges irreducible complexity, that is, the system has to be sufficiently complex in order for auto-catalytic behavior to emerge.  There is no stepwise evolution of this emergent property; it suddenly appears (as with all emergent properties) once the polymer complexity has achieved the threshold level.  Thus, the system is complex and whole from the start.  Indeed, this is what living systems appear to be.

I think the posters above are on to something. To understand the organization of molecules into larger molecules like amino acids or DNA, you need an understanding/appreciation of widely accepted abiogenesis theories and Harold Urey and Stanley Miller's experiment.

I read all of your answers and they come close to my question but still circulate around it. I think the problem is in how to explain the question itself, I'll try again.
In philosophical tradition there are two simple concepts of substance and aggregate; for Leibniz substance is organized (the human body) while an aggregate is the result of a very immediate form of perception which passes through reality by seeing connections without particular order in them by similarity (here a couple of rocks, I turn around to see an aggregate of twenty ants moving around, one ant disappears from my sight soon but the aggregate is still there). In my previous examples, in the first two posts, the working of those concepts can be seen: books put together to form a library are an aggregate by virtue of the lack of immanent connection between them in a physical sense (they don't come close or relate to each other), however they form a conceptual substance, which have pushed me to organize them. On the other hand my body is a physical substance, as its elements relate to each other organically.
Leibniz talks about monads - non-physical entities which are the substances. In the physical world an organism's parts relate to each other by virtue of the existence of the monad, which holds them together - the meaning of this is that the concept is alive in the organism and not just part of the mind. I ask about something very similar to this: what holds things together?
One of the traps of this question is you would have to go a little beyond a description of how they are held together by conducting experiments or observing processes. It's more a matter of a hole which appears in the knowledge while learning about the descriptions, asking for the thing at work behind it. A description would be: "one element connects to the other because they are attracted by certain immanent to them forces". In this case I would be asking about why they are attracted to each other to begin with, about an inner immanent principle. Neither of the elements know of the other in a conceptual sense, yet they seem to know of the other in a physical sense, they sense each other, etc.

Entropy decreases as atoms form more stable compounds, don't they? There is less disorder when two atoms come together then when they repel one another, and that's what nature always prefer as far as thermodynamics goes.

I think I understand this, the question is why it happens that this is the case.