Abiogenesis

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I'll agree with you there. Context, grammar, and knowledge of the author are all important hermeneutical elements.

With regard to the percentages of similarity being thrown about, I did look into it.

What I wrote seems to be correct.

You only get >95% between Humans and Chimps if you first filter out about 98.5% of our DNA that doesn't code for any protein, then only count the occurrence of genes that produce identical proteins (ignoring the frequency of these genes) in the remaining 1.5%.

Depending on how you preselect what to compare, and what not, you can go at least as high as 99.9%; It's all in the definition, it has nothing to do with reality. Another definition and it goes down, way down. There are only ca 23000 genes in those 1.5 %. (Just for context: 1.5% is about 45 million base pairs)

All you are really comparing are the building blocks. It's however not the proteins used to build a body that makes the difference, it's the way they are put together and are regulated. So what you're really comparing is the bill of materials; ignoring all other things.

"The beauty of a living thing is not the atoms that go into it. But the way those atoms are put together."

So by ignoring 98.5% of the DNA you find that the remaining 1.5% contains many similar genes? And humans still have more then 600 genes which have no equivalent among chimps? So we're not even using the same basic building blocks to build our bodies?

More then 80% of the whole DNA is being transcribed into RNA. Can we really just ignore it? This non-coding DNA (please remember it's ca. 98.5% of the genome) must have a function, we just haven't figured out what it is. Until we do, we can't really compare anything in any meaningful way.

I would also like to point out that there are a lot of epi-genetic differences which aren't even being addressed here? It very doubtful that the DNA would actually contain a blueprint of a cell, because the cell is a given in the context of life. DNA alone is useless, it needs a suitable cell to interpret and execute the software encoded in it. Take the same DNA, use a different kind of cell [a different context] and you will get a (slightly to extreemly) different interpretation and execution. The DNA will therefor most likely contain only an essential bill of materials, maintenance plans and external behavioral patterns which are interlinked with developmental development plans in multicellular life.

Last edited by Meta on 21 Dec 2009, 6:43 am, edited 1 time in total.

What you are claiming is not consistent with the facts presented on the page that you are linking to. It claims that The chimpanzee genome is 95% identical to the human genome.
A genome is not just the genes and introgenic (aka non-coding) DNA is included in genome sequencing.

What does this 95% identical really mean?

Why "identical" and not "similar"?
How "identical" are the following strings?

S1: ABCDEFGHIJ
S2: ABBBBCDEFGHIK
S3: ABCDDEFFFGHIJ
S4: JIHGFEDBCA
S5: ABCDE00000FGHIJ

Last edited by Meta on 21 Dec 2009, 3:00 pm, edited 1 time in total.

Would this help:
http://en.wikipedia.org/wiki/Computatio ... logenetics

Previously, you defined self-organization to be something that can only be created by an intelligent agent. This leads to circular reasoning if you insist you insist that abiogenesis cannot occur because of self-organisation. It is consistent with the laws of physics to have a processes on the microscopic level that lead to emergent properties on the macroscopic level but don't have meaning in the constituents. Temperature, for example, is an emergent property of a material on the macroscopic level that is derived from interactions of the constituent atoms and molecules but those constituents themselves don't have temperature. Also, if you make a distinction between self-organization and self-ordering then there is nothing to suggest that abiogenesis was not a result of self-ordering rather than self-organization.

I did not. I said that the only know source of organization is an intelligence. (Self-organization might be possible if the "self" was intelligent enough? Maybe, I doubt it, but it could)
Well, I would not have a problem with abiogenesis if an intelligence would be there to design, build and in general organize it. I can't proof it yet but it seems logical enough that self-organization (without intelligence) would require that P=NP. Based on observations I don't think thats acceptable, e.g. writing a program just isn't as easy as executing it.
Yes and No? Yes, an intelligence can organize somethings into a system which is more then the sum of its parts. No, such a system will not just casually appear without someone organized it, unless we are talking about stochastic or ordering phenomena... Like...
Temperature, pressure, etc are human made statistical abstractions. We have build devices which translate the reality into this abstraction. It's a very good abstraction, very few edge cases where it is leaking (e.g. How cold is it in outer space? Space doesn't have a temperature.); None the less, it's us who give a measurement we designed its meaning.

Maybe this is the case whenever we talk about emergent properties of systems?
There is a clear difference when one looks at the information required.

Last edited by Meta on 22 Dec 2009, 9:25 am, edited 1 time in total.

Epistemologically, you have the only sound position currently available. Time and new facts will shed further light on the question. Perhaps more may have been folded up in the Singularity than we have supposed. Or maybe not. Work and research will clarify the matter.

ruveyn

In a reply to one of my previous posts, you said that things can only be natural if they are trivial. Then in a later post, you said this:



So by this, organization is something that cannot appear from the from the less organized system and therefore requires an intelligence. Therefore, self-organization is something that can only be created by an intelligent agent by definition. At least if that is what self organization is. You haven't given a definition of self organization. At any rate, a system with less information to start with can end in more information at the end of the process if that process is not reversible. Entropy is a measure of information in physics. An adiabatic process is a process that is reversible, for instance an adiabatic gas is a gas that can expand to one state with low pressure but return to the previous state when the pressure is increased again, (it obeys a conservation of entropy). If the there is transfer of heat to or from the gas, then there the process is not reversible and the amount of entropy (i.e. information) increases from a state of low entropy. So here we have a case where a system of low information becomes a system of high information. In the case of abiogenesis, under the current hypothesis, we have a some organic chemicals in a pond of water. In the daytime, the sun heats the pond. The UV radiation from the sun breaks some bonds in these chemicals. At night the chemicals recombine in a chemical equilibrium. This happens repeatedly. Since the part of the reaction where the bonds are broken by the UV rays are not reversible, there is nothing in the laws of physics, chemistry or even from information theory that says the molecules of the organic compounds in each successive equilibrium configuration will not have more information or be more complex than the previous ones. In fact they probably will be. These successively increasingly complex compounds could eventually lead to the first protocells. The evolution of life by natural selection after that does require a decrease in entropy but this is compensated by an increase in entropy in its surroundings, so this is not violation of the increasing entropy law because it only applies to closed systems.



You cannot know if something would require an intelligence or not without knowing the processes involved. So the above statement is not true. As explained above, a system with low information can give rise to a system with high information and it is explained how this could occur in the context of abiogenesis.



Systems can organize themselves into systems that are more than the sum of their parts provided that the system is not reversible. Or if you mean something that requires less disorder then this can also happen provided that the system is open and gets information from outside itself. This does not necessarily mean that it comes from an intelligence. Natural selection is a process where information is passed from the environment to the organism, thats the alternative. Temperature and pressure are actually properties that can be measured. Temperatures of objects in space can still be measured by the blackbody radiation it emits. If there are was nothing in space, then it would not have a temperature because that's why temperature is an emergent property. Object in space can still lose heat to space because the lose energy due to the radiation. Abiogensis as described above can also be the result of ordering and stochastic processes.



Temperature is an example of an emergent property, yes.



You still have not given a clear definition of what self-organization is. What is this "clear difference" you are talking about? Information can increase from systems of lower information.

I have already indicated that the term trivial is a difficult term to define.

E.g. Given a pre-condition and a post-condition its not trivial to invent a confirming algorithm and its proof of correctness. Once one has such an algorithm and its proof it is trivial to execute or verify the correctness of the proof. Execution and verification are in fact so trivial that it can be automated. You can't automate inventing an algorithm and its proof.

I hope this makes it clear?
It does seem that way.
Now you switch from organization to self-orgnization... The only way that might work is if the "self" is sufficiently intelligent. I don't know how intelligent, I don't know the relationship between current level of organization and sufficiently intelligent in this case. It does seem doubtful if you ask me.
I don't have to. See the papers I referred to or just read some of the literature on abiogenesis. Self-organization is the overriding principle under nearly all abiogenesis and some evolutionary thinking.
Not so. If I take a pile of bricks, lift it up and let it fall there will be a new pile of bricks. This process if irreversible. It will not have anymore organizational information (the special kind of information we are interested in) then before.
You do realize that you are now talking about very simple statistical abstractions? The ordering or organization of the gas molecules may not be relevant if we are speaking of the macroscopic abstraction "pressure". This example is in no way relevant to the issue.
Having more bonds will give larger molecules a much greater chance of being broken up. Depending on the amount of UV radiation it will reach a point of equilibrium with all molecules having a normal distribution around a certain length.

It also seems likely that there will be processes which form unbreakable (at least by UV) bounds? So reactants are being lost in the process, if the rate of this loss is too great the pond will contain only this unbreakable bounds. In fact this is the most likely outcome: See the UV from the sun as a (natural) selection criteria? Only UV insensitive bounds are not broken, so in the end this will be the kind of bounds which become the most abundant.
I disagree.
Well, that's wrong. You do remember that the universe is assumed to be a closed system? The same law also applies to "open" systems, being an open system means only that there is some way to transport entropy. e.g. Imagine a room with a closed door, a table and a window. All the parts that make up a computer are spread out on the table in the sun in from of the window.

No amount of sun light will make this a computer. The only thing that the sunlight will accelerate is decomposition of the parts. Sunlight tends to accelerate processes which make things less organized, not more.

Now we open the door.

I could now walk in and assemble the computer without breaking any physical law.

I could also walk in with an already assembled computer and take the parts on the table with me when I walk out again. This is all consistent with the laws which control entropy.

So an open system can transport entropy and order (note: all organization uses orderings, but not all orderings are organizational; there is no equivalence!). Order (and organization) can walk in through the door so to speak. (more)
How so? I do think that the MacMini here on my desk would require an intelligence to construct even though I don't know how Apple constructed it. So at least in some cases we can see from the result that things require an intelligence to construct them.

I remain unconvinced?
Assuming for a moment that this is true. Will this result in the same systems which an intelligence would design and build?
Technically you are correct. It doesn't help much however if the environment does not contain much organizational information in a suitable form.
No. Life is organized, so abiogenesis (without an intelligence doing the organization) require self-organization, not just self-ordering. And all you have shown is that self-ordering is possible.

And here we come to the problem at hand.

From Self-organization vs. self-ordering events in life-origin models:

There is a difference. When you assume descent from a common ancestor, with modification, then you must expect that the more closely related two species are, the more similar will be the genetic basis of similar functions. If two species are only remotely related, they may achieve the same function through very different mechanisms with different genetic background. The simplest prediction from ID would be that the designer reuses whatever the best solution is that is already available. That prediction contradicts the data. ID allows you to make additional assumptions to fit the data, but that is itself a problem.

I have asked Meta several times whether he believes that a theory that can be adjusted to be consistent with any evidence is a better theory than one that can only be consistent with a small sub set of all conceivable data. He has never answered. It's really weird that he ignores it, because if he doesn't know how important that question is, he can't claim to be competent to enter any scientific discussion and expect to be taken seriously. You may appreciate the point more.

A relatively simple way to think about the issue is to look at the six possible combinations of what a theory says should or should not happen, what the theory can't decide, and what things really can or can't happen:
a) Theory says X should happen and it does and so X or its consequences are potentially observable.
b) Theory says X should not happen, and it does not and so X or its consequences are not observable.
c) Theory says X should happen but it does not and so X or its consequences are not observable.
d) Theory says X should not happen, but it does and so X or its consequences are potentially observable.
e) Theory can't say whether X should happen and it does not and so X or its consequences are not observable.
f) Theory can't say whether X should happen, and it does and so X or its consequences are potentially observable.

To keep things simple, I ignore measurement errors.

A good scientific theory must discriminate between things that do happen and things that do not happen. Categories a) and b) in the list are correct predictions, c) and d) are errors. The more often a theory falls into categories e) and f), the less useful it is.

I can appear to increase correct predictions in category a) by making a theory vague, allowing it to be consistent with lots of conceivable things. This "improvement" is an illusion if my theory then really falls into categories e) and f).

A demonstration: I have a theory of everything that is consistent with all conceivable events. It is short enough to be written on a T-shirt. The theory is Stuff Happens, Or Not. Give me any data at all, and I say "See? That fits my theory perfectly! Stuff happens!" If you tell me something has never been seen, I can say some stuff doesn't happen.

You can see why I will not win next year's physics Nobel. My theory is completely useless. I have traded everything in categories a) and b), those that matter, for categories e) and f), those that don't matter.

That is exactly what happens with intelligent reuse. If you add in the assumption that we don't understand the criteria of the designer, you can make it fit absolutely any pattern of similarity and differences of genotype and phenotype. Evolutionary theory is far more constrained.

You asked recently whether evolutionary theory is falsifiable. That shows appreciation of this important principle. Now apply it to ID. I think if you try to keep ID constrained, its predictions are falsified. If you extend ID to make it fit available data, then extended ID can be made to fit so many conceivable data patterns that it becomes useless.

I have tried to get Meta to prove me wrong on this, but he hasn't tried. Would you have a go?


So marsupials and placental mammals with similar ecological niches should have DNA more similar than mammals with different ecological niches or marsupials with different ecological niches. That would happen if only function determined genetic similarity. And it is not true. You can posit unknown design constraints or aesthetic principles to make ID fit the data, but then ID no longer makes predictions. Then it can't decide.

Even if you are not a strict Popperian, the more useful you try to make your theory, the more falsifiable it becomes. If you try to rescue a theory from conflicting data by making it vague, eventually your theory simply becomes useless. That is my view of ID. Where it is specific, it is wrong. It only manages not to be wrong, by being too vague to be be wrong, and then it is useless.

How do you know two species are closely related? Without referring to genetic similarities, because that would make this argument circular. How do you even define "similar"? On what level? Nucleotide? Genetic? (limited to the 2% used to make proteins?), Genomic? Proteomic? Cellular? Organs? Bodies? Behavior? Algorithmic? Whatever fit best with the hypothesis of universal common ancestry?
That makes a solution "best available"? How do you measure that? What about side effects?
Does it?
Maybe it's just a particular interpretation of the ID hypotheses that is the problem?

For one, ID could perfectly happy accept common ancestry, either in limited form (Lions and tigers share a common ancestor?) or even universal common ancestor through front-loading?

Even with only limited common ancestry we would expect related, however diverging, populations to share very similar genetic codes, similar to their original ancestors. Non-directly related organism will share only basic biochemical toolkits and a general framework, while diverging significantly with regard to the parts which need to be different.

Or maybe there is another solution we haven't thought about, neither abiogenesis nor ID.
Every "good" scientific theory is a prohibition: it forbids certain things to happen. The more a theory forbids, the better it is. (keyword: Karl Popper)

For example: ID forbids (physical) self-organization?
Maybe I did not ignore it as much as not give it as much weight as you seem to do.

Very good explanation.

You know what? You have actually convinced me that intelligent reuse is not going to be a fruitful approach.

Combining what Sand said and your arguments in this post, then a small, simple, succinct hypotheses which actually forbids something is better then any broad, wide, overarching hypothesis?
Let's try this then later today.

We have already one hypothesis:

H1: Physical laws and stochastic processes cannot cause (cybernetic) organization.

Where (cybernetic) organization is defined as containing prescriptive information. A organized system is governed by rules ("algorithms") which are (incl. any data required) encoded in tokens which can be read, interpreted and executed by the system. The system is cybernetic controlled. The encoded sequence of tokens is physically arbitrary: The sequence cannot be derived from any physical properties of the medium used to encode the tokens. The encoded information is meaningful: It has either a symbolic meaning: A sequence of tokens prescribe something physical or there is an executable interpretation. There is no physical path to derive the encoding sequences from either something physically or the executional interpretation. Any physical relationships are one-way, irreversible: From encoded, trough interpretation, over into either physical realization or execution. If execution results in a modification or transformation of a sequence of tokens of the encoded information ("self modifying code") then this is an algorithmic relation, not a physical relation.

H1 is a strictly, very narrow, falsifiable hypotheses, not an overly broad explanatory theory or model. H1 can be falsified by an empirical demonstration that a strictly natural, physical system can self-organize. Logical deduction based on assumptions which require self-organization to be possible do not falsify it. H1 is intentionally very limited and very narrow.

Is it better to not understand something true, than to understand something false?

OK. So trivial means the simplest in form. In that case, then as I've said before, everything in nature is certainly not trivial. Consider turbulence. Turbulence happens in fluids despite them being made up of the same atoms and molecules that makes up all matter. Yet, to build models of turbulent flow requires some knowledge of chaos theory. Scientists still do not understand turbulence fully.



If something seems a particular way, that does not make it so. At the beginning of the 20th century, Newton's laws seemed to be the correct description of motion according to our daily experience but motion at high velocity close to the speed of light is outside our daily experience. Consequently, special relativity seems contrary to common sense. Motion as described by Aristotle also seemed correct prior to Galileo.



I don't think it's relevant since we're arguing about whether intelligence is even necessary.



Can you give links to papers actually written by evolutionary scientists or people proposing theories of abiogenesis? I have never heard of them mentioning self-organization or, if they have, making a distinction between self-organization and self-ordering.



Actually, you do have more information in that example. The new shards of the broken bricks and the rearrangement of molecules at the edges of the shards due to the bonds in the lattice being broken all constitute new information. By distinguishing between "organizational" information and other kinds of information, you are looking for information that has some kind of meaning. Meaning has nothing to do with it. Meaning is just something that humans attach to information. It's all about how much information a system contains. It has nothing to do with meaning because meaning doesn't exist fundamentally without humans giving it meaning.



I'm afraid it is relevant. Compress a gas in a container and the gas molecules more vigorously hit against the walls of the container resulting in pressure (pressure = force/area). Also, I was trying to point out that more information is created. To further understand what I was getting at, look up the Gibbs paradox:

http://en.wikipedia.org/wiki/Gibbs_paradox



Actually, no. The broken bonds are then available to connect with other broken bonds in other molecules creating more complex molecules in reactions. Breaking bonds only frees them up and the UV radiation actually facilitates the formation of more complex molecules. Basic chemistry.



Remember that the molecules recombine at night when there is no UV radiation. During the daytime, a few more bonds will be broken and the process repeats itself. Remember also that breaking bonds requires energy. So no, the likelyhood of molecules completely breaking down will not increase because there are more bonds to break.



You can disagree if you like but in the meantime will you look up organic chemistry to see how it works?



Yes, the universe as a whole is a closed system. So the point is that entropy in a particular place can decrease as long as it increases as a whole. How does a refrigerator work? It cools down from being hot indicating a decrease in entropy. However, heat is expelled out the back so entropy is increased as a whole.



We weren't talking about sunlight re-arranging the components of computer were we? We were talking about the formation of a membrane and some ribonucleotides.



Why was the door closed again? By closed system, I didn't mean a locked room. By closed system, I meant a system where all physical processes are contained with nowhere for information to escape to.



Which takes energy doesn't it? Just like organization in living things require energy but they feed off the energy in their surroundings.



Yes, that is what I was trying to say. But creationists as far as I know don't take living systems and their environment into account.



Except that you already knew that your Apple Mac was made by someone. To look for something that's artificial you have to look for something that people make and even then you can't be sure that a natural process wasn't involved. Maybe that process is unknown.



Well, I hope I cleared it up.



Does that matter? I don't think you can recognize if something is made by an intelleigence or not unless you've ruled out all natural processes.



Except that it does. That's why organisms are adapted to the environment. They can't survive in environment that doesn't allow them to.



There's no distinction. Organization is only something we give meaning.



That still doesn't provide a clear definition of self-organization. Algorithms can occur in nature.

No, that has nothing to do with it. It's trivial to make an unordered pile of books, but its also trivial to make an ordered pile of books. What's not trivial is writing a pile of books.
True. By the same argument therefor it may have seemed simple enough at the time that Darwin thought about it that life would be able to self-organize by trail and error (natural occurring variation and selection), it now seems to be rather hard based on what we know now about these kind of things?

Well, I have already pointed to some papers in this regard in previous posts. Next you could look up someone like Stuart Kaufmann. Also, its often just assumed implicitly without actually saying it.

Your question seems to poses somewhat of a catch-22, doesn't it?

Anyone who sees the distinction between self-organization and self-ordering will have inherently a problem with abiogenesis and some aspects of modern evolutionary hypothesis. So they are not very likely to propose theories of abiogenesis...

On the other hand someone who is ignorant of the difference will not make the distinction in a paper they would write and might even fall for equivocation in some cases. This is not because they are stupid, but because they are for example zoologist and therefor assume (based of the modern framework) that self-organization just happens, what the hell?

It takes a lot more knowledge of algorithms, complexity, automata theory, etc and trying to figure out how to make self-organization work before you even begin to see the difference between the self-organization and self-ordering.

And once you do, its impossible not to see it.

However, it proves to be very hard to explain to someone who has not seen it. Someone who does not notice the difference will see self-ordering as a valid simplification of self-organization. Because actual self-organization is much to hard to think about... To even ask the question what self-organizion would actually look like, what it would actuarially require and what the consequences would be of it actually being plausible seems to be something people only start doing after they have started seeing the difference...

And once you do, its impossible not to see it. But you can't tell anyone because most people haven't noticed it yet.

Also, once you do see the difference you start to get a real problem with abiogenesis and some small aspects of the modern hypothesis with regard to evolution. Any you can't tell anyone because most people don't understand what the fuss is all about.

Well, it's a start.
Meaning has everything to do with it. We just don't have a full understanding how and what meaning really means.
No, actually, you don't really need humans at all. Meaning only requires that there is an encoding of a symbolic message and an interpreter which can read and execute the symbolic message. The relationship is algorithmic, not physical.

Meaning, as an emergent property, in life is based on the rules with are embedded in the interpreter and those encoded (data) in the sequences of DNA. This is how it's different from stochastic properties like pressure and temperature which are follow from physical laws, not arbitrary rules. Again: The rules work within the laws, but there is no way to derive the rules from the laws or from any other physical relationship.
Well, its both actually, at the same time. Meaning is kind of like this emergent property which can only exist in the whole, but cannot be pin pointed in any part. Like how each of the static loads in the chips are meaningless at that level, but taken as a whole they make that the computer can execute programs and you can read this message.
That's simply not true. When you have a particular engine some kinds of matter become fuel? If you only have a coal furnace, then plutonium isn't a fuel. The moment you have a particular cell capable of interpreting DNA, some DNA sequences become meaningful; Change the cells interpretation and the meaning of the DNA sequences changes (might even disappear). Different DNA sequences will have meaning.

All life as we know it requires an interpreter with really specific abilities and very specific message; Taken as a whole the information in the DNA sequences is meaningful, not to humans, but to the system itself. The meaning is a prescription of the parts of the system and the way to put them together where needed. It also prescribes behavior and communication protocols between cells. The meaning is a multipart algorithm.
Yes it will. A molecule with 20 bounds will have a twice as large a chance to have any bond broken somewhere then a molecule with only 10 bounds. Assuming that each bond has any equal chance of breaking.
Have you? Your argument just isn't there.

I'm pointing out that not everything is possible in an open system. If you want prove that something it possible you will need to come with real evidence. And the fact that something exists isn't evidence of how it came to exist.

But where do the instructions come from?
I don't really care about that creationist do or think. (No offense intended)

No really. The only thing that became clear that the misunderstanding lays much deeper then I until now thought possible.

To rule out all natural processes is impossible; Someone could always argue that you just haven't found the right one. This argument is equivalent to saying that there is an invisible creator somewhere and then expect someone to prove that he doesn't exist.

I was very careful with my hypotheses from my previous post to avoid this particular fallacy.

The hypothesis that self-organisation exists is not scientific: You can't falsify it.
The hypothesis that self-organisation does not exist is scientific. A clear empirical demonstration would be enough to falsify it.

No, it does not. There is no physical path running in that direction.
Then they just die. The most do anyway. To know that you have a problem does not tell you what the problem is, nor does it give you a suitable solution for this problem. This is not an episode of Star Trek! Any realistic population can't try everything and see what sticks to be wall. Only a very small subset can be realized and such a small subset would be limiting the process such that it can't explain what we see anymore. This is the problem we've discovered in the computer simulations.

The funny thing is, we can get those computer simulation to perform in a way that would follow the pattern of evolution we see in fossils. It would however mean that we need to begin with a reasonable population (of designed individuals) and to introduce new forms and new meaningful genetic messages from time to time. Then you get this burst mode pattern of suddenly new forms, mass extinction of existing older life, followed by a period of intense increase of variation based on the new forms and new information until this is also exhausted and then we enter a period of mostly stagnation. So we get the results we expected to see, but only it we move away from any darwinian notion of self-organization. (see also evolutionprize.net, Hillis on panspermia.org)
And Denial is not just a river in Egypt.

Clearer then ever given by those who assume that it is possible.
Could you give an example?

Seen my hypothesis (H1) in my previous post? Any ideas about that one?

You'll get a shorter answer because WP has just lost over an hour's typing by telling me it's too busy just after I clicked "Submit" and not going back to my message after.

People were doing taxonomy long before molecular genetics. Even if you stick to genetics only, you can avoid circularity by judging the phylogenetic relationship using genes independent from those related to the phenotype you study.


If you are asking about the similarity of the phenotype, you look at the level that defines your phenotype. If I ask whether a species is a cursorial hunter,or an ambush predator, I don't look at nucleotides. If you are asking about the similarity of the genetic basis of the phenotype, you should look at the developmental processes and the genes that influence them. I don't know what you are asking because you offer so many criteria, many of them irrelevant to one or the other similarity relevant to the point.


Correlate variation with fitness, work out the variables relevant to function, compare different solutions, either found in nature or designed by humans. You don't need to know the best possible solution to refute reuse of the best available solution, you only need to show that a species uses a worse solution than one already used by an older species. Or you show that a better solution could be designed.


Give me an example, so that I know what you are asking.


We already had that discussion. Look back on Unintelligent Design and what came from that.


Then offer a version of ID that is better.


Or it could not. This is an example of making ID worse by making it fit a wider variety of data.


I don't think so. If the alien designers of life on Earth that you talk about themselves had a spontaneous origin through self-organization, then ID would be true for Earth even though self-organization is possible. The impossibility of self-organization is not a prediction that follows from ID. If self-organization were impossible, that would make ID more probable simply by excluding many other theories, but it is not a prediction from ID.

If you can work out a way to avoid that problem, you also need to decide whether embryonic development is self-organization. It appears to fit your definition, but embryonic development does happen. If you want to avoid having been falsified before you were born, you need a definition of self-organization that excludes development.

It eat three of my posts as well.

I see a few problems with that idea. For one, the interdependence of genes is very difficult to assess, how can you be sure that there is not dependency? Secondly, we find that the genes of one individual or population tend to have wildly independent and often conflicting phylogenetic relationships. Especially if the evidence that horizontal gene transfer has occurred in all forms of life (not just bacteria) is true then we'll be unable to apply the phylogenetic relationship based on one set of genes on another independent set of genes.

My point is that the term "similar" is underdefined; Additionally types of relatedness are assumed and consistency is lost.
Fitness is not an attribute of genes, in many ways there is not "best available". In many cases you will find that it would be similar to working out "the best available" from rock, paper, scissors, lizard, Spock. (Four complications in understanding the evolutionary process)
I will try to find an easy example.
Good idea, better yet. Why couldn't I just ignore alternatives and point out the flaw in current dogma? Hence, the H1 hypotheses in my pervious post. (I don't really care about ID all that much, I do care about combating the non-sense of self-organization of cybernetic systems).
I see it more as a way to find out which aspects are fundamental and which aspects are strictly auxiliary.
Which in turn resulted in my reaching the point where I don't really have any particular need of ID at all to make the critical points that I think need to be made.
Why do you think that? I have never understood this argument. Can you explain why you think embryonic development looks like an example of self-organization?

The information required for embryonic development is already embedded in and available to the system from the start. Without the right information not much embryonic development will take place. No new meaningful information is created in the process; Only copied, transformed, and expressed. It's a process of realization, not of original creation.

Notice how reading is similar to copying, but very unlike (original) writing? How reading is similar to execution or evaluation, but very unlike programming?

Embryonic development can be compared to executing an already written program. Any process of variation and selection can similarly be seen as ordering and configuring a set of already written programs (and maybe it does so because it is programmed to do so, it hard to see any of this being caused by physical laws alone, not requiring at least some rules?). The few cases where representation or encoding of the information gets slightly altered is at best an example of configuration and at worst a copy error (which is often corrected).

Self-organization however would require writing an origional program from scrap. Programming is a process which can't be expressed in a finite set of rules. [That is not to say that AI is not possible, I take our presence as evidence that it is. It will however require a different approach then we have been taking until now.]