Abiogenesis

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Sorry that I was slow to reply but I haven't had much chance. Despite logging on twice since Saturday to do so.

Every example you've given, including the above one about the books, suggests that definition which is similar to the second one in Wiktionary. I said simplest because of a comparison with the meaning of the word used in mathematics. It could also probably be the first one. With either of those definitions, I've already said why I don't think everything in nature is trivial. Here's the quote:






The basic premise of evolution which is the survival of the fittest by means of natural selection has never been disproven. Until it is, it will remain the dominant mainstream theory. Most academics working in that area believe that evolution has been pretty much proven with the overwhelming evidence there is.



Stuart Kaufman talks about self-organization but also doesn't seem to make a distinction between self-organization and self-ordering like you have done:

http://www.iscid.org/stuartkauffman-chat.php.

At least according to your definition. Every other example I've given, including crystal growth and spontaneous magnetization, you've said is self-ordering. A few of the examples of self-organization is given here:

http://en.wikipedia.org/wiki/Self-organization.

The self-ordering of organic molecules to form more complex molecules as proposed in abiogenesis is similar to any of these things. If you look at that thread where people chat to Stuart Kaufman, he actually replies to one person that you would not need an intelligent agent according to Shannon because if one is present it would be hidden in the decoding. If this is what you've been referring to in requiring an intelligent agent due to the complexity of life then I personally do not see how this follows. Certain processes may imitate what an intelligence might do but that does not mean that one was present. Furthermore, abiogenesis is just one theory of how life started. You don't need to know how it started in order to understand how it diversifies and proliferates. Evolution and abiogenesis are two separate ideas.



It's information about the state of a system.



It's a word.



The temperature and pressure were given as examples of emergent properties occurring in nature. They are not analogs of processes that occur in cells. Those rules don't immediately have to be derived. They were built up over time via mutation and natural selection.



And the words on your screen are nothing but small dots of colour called pixels. It's only when you look at them as a whole that they have meaning and you can read them. Meaning requires an interpreter, without one there is no meaning. The logic gates and tiny circuit components on a computer chip are just organized in a way by us that makes it useful like any other machine humans have built.



Fuel, or any power source, does not contain instructions about how to operate a machine. It contains energy. We have just been clever enough to utilize that energy to be useful to us. That's right about the utilization of DNA by different cells. However, even the instructions about how to build the cell itself is encoded in the DNA. Those genes transform the original basic cell into the required cell and they are activated during the initial embryonic development of the organism. It's all just chemical interactions. No, the algorithm is a process that interprets the instructions encoded in the DNA, in a sense, but they are really cyclic chemical processes.



Then each the two resulting molecules will have a bond available to combine with bonds of other molecules. The process will end in a situation where the compounds would be resistant to UV radiation because the only bonds left will be the ones that aren't vulnerable to the radiation. However, there is nothing to suggest that those molecules won't be larger and more complex than the ones that we started off with because they recombine at the night time. It has been shown empirically that when organic compounds are in a concentrated pool, the UV radiation will actually enhance the formation of more complex compounds. There is empirical evidence for it.



Some sources then? I don't have access to the paper in the first one but abstract is there. Here are the references:

http://www.sciencemag.org/cgi/content/abstract/sci;283/5405/1135

http://www.biomedcentral.com/content/pdf/1471-2148-3-12.pdf

http://www.astrobio.net/exclusive/492/shining-light-on-lifes-origin#



Look at the references above.



That depends on what you're talking about. If you're talking about certain biological systems then each organ functions like part of a machine. If you're talking about the instructions about how to build an organism then that comes from the DNA. You don't seem to like the idea that the information contained in the DNA could of been built up over time.



ID was proposed by creationists in order to sneak an religion into the science classroom. It was never meant to be scientific.



Maybe.



Saying that there is an invisible creator is exactly what you've been doing and that was my main point. You just called it a designer. The fact that you can't rule out all natural processes is the reason why ID is unscientific. It also has no explanatory power either. No, just because it can accommodate everything does not mean it explains anything. An explanation of anything has to explain why things are the way they are and not any other. Why did the intelligent designer not give us three eyes etc..?



Multiple mutations in the genes happening in different individuals at once and then selection by what can survive long enough to reproduce.



They would die anyway but at least they would live long enough to reproduce and pass on their genes. What does Star Trek have to do with it? The stagnation, where things don't change much anymore, that happens in the end happens in nature as well. When you get to a point where one organism dominates and others can't evolve fast enough to adapt either they go extinct. That dominant species will remain dominant until some catastrophe wipes them out (like whatever killed the dinosaurs) or the environment changes. Evolution is not directed to some goal like what you do in evolutionary programming. It just adapts according to the environment. When the environment changes life then has to adapt to the new environment. There is no intelligence directing it, it just changes direction as climate resources and other things change.



Those simulations seem to simulate evolution not how life started. As I've said, the period of stagnation happens to life in reality as well. Then the environment changes and mutation and selection process would result in new forms of life yet again. As for the seeding, I don't know what the algorithms were that were used in the programs that are referenced in those links but new information would come through as organisms adapt to a new environment when it changes. Also, another thing that is referenced there is that there are rapid as well as gradual changes that occur in nature. This is true but the rapid changes can be explained by things like genetic bottlenecks due to a very small population (like what happened with humans some 600 000 when modern Homo Sapien Sapiens emerged from the Homo Sapien Idultu subspecies) and also other things. The Cosmic Ancestry theory was proposed by Fred Hoyle as an alternative to abiogenesis that stated that life doesn't have an origin. That theory was inspired by his Steady State model of cosmology which stated that the universe didn't have a beginning. Since the big bang model has been proven, that theory is no longer viable because the universe had a beginning.



I don't know what that means.



Show the sentence in that paragraph that says what self-organization actually is. All processing of information is algorithmic in some way.



How about black hole entropy. The resolution of the black hole information loss paradox showed that the information coming out of a black hole via Hawking radiation is related to the information going in with whatever has fallen in. That information that comes out is also somewhat mangled and the process that transforms the information is algorithmic even though it's random in a sense. Evolution does not violate that H1 hypothesis because it's not completely random.

You do the maths. Geneticists inferred the existence of genes and worked out how they were ordered on the chromosomes long before sequencing was possible. That was all done by long tedious breeding and counting of phenotypes. You can use the same method to find out whether two genes contribute to the same phenotype. Then they are not independent. You can use genes that are no longer functional. If you can work out that they have been non-functional since before the branch in the phylogenetic tree that interests you, you can use them. Or, as I mentioned, you don't use molecular genetics to construct a phylogenetic tree. I only made the point about genes to correct the misconception that use of genetic information here has to lead to a circular argument.


That's why you don't use a single gene.


It works well enough to test the prediction. And I wonder why you used similarity earlier to argue for ID when you think it an underdefined concept.


I never said it was. Whatever gave you that idea?


Then the prediction from ID doesn't apply, and you test the prediction where your data indicate there is a single peak to the fitness function. But you said you don't care about ID all that much.
So let's forget ID and discuss self-organization.


First look again at my answer a month ago when I commented on Abel & Trevors, so that I don't have to repeat that. Is your definition of self-organization very different from theirs?


Much of it. Not all of it.


Think about the number of genes in the human genome and the number of neurons and connections in the human brain. There aren't enough genes to encode the connection pattern of the human brain. It works for C. elegans, but you are already in trouble with a bee. Or do you think the information that goes into forming a functioning brain is not meaningful?

You also wrote this:
Is self modifying code an example of self-organization? Then how do you exclude development?


OK, maybe that is different from Abel & Trevors. Then only the origin of life would be self-organization, and nothing that followed after, because none of it involves making programs from scrap, only modifying them.

You object to underdefined concepts. Is your take on self-organization defined well enough to apply to some real world examples? What you said about hierarchical modular organization made me think everything on this list (with perhaps one exception) involved an addition of at least one extra layer in the hierarchy and, according to your ideas, should be impossible to evolve. But if self-organization is "writing an origional program from scrap" then only the first two things on this list should need self-organization:
1 the first cell
2 genetic information in RNA
3 genetic information in DNA
4 cell organelles
5 bacterial communities and the associated signalling (biofilms etc)
6 cell nucleus
7 colonies of eukaryotes with identifiably different roles
8 multicellularity without identifiable organs (think sponges)
9 multicellularity with identifiable organs (think jellyfish)
10 nerve cells
11 hormones
12 mesoderm
13 skeleton
14 lungs
15 wings in vertebrates
16 going from light sensitive spot to camera eye with lens

If it is true that most of the things on the list add new levels of hierarchical modular organization, but only the first two need self-organization, then of course adding a new level would not depend on self-organization as you define it.

We still have some unresolved issues about the evolution or organs and the genotype-phenotype relationship. I think they are relevant to where you are taking the discussion now. Would you answer my questions?