Evolution of complexity/information

I had said in post#11BUT I AM NO LONGER LOOKING!My test will be that evos MUST be supposing the minimization of STEINER TREES rather than SPANNING trees as to any correlation between the Gibbs' minimzation and an induced biogeography that need no longer be "historical" in the c/e debate any longer. SO NOW I might be able to suppose not only that Croizat might INDEED have found diverse ecologies in SIMILAR geographic distributions but that reason minimizes the SPACE on earth not the clade differences between puntuated equilibriums and generalized punctuations! This will likely find that it was evolution theorists and not creationists that make prohibitive futher eduction of the dominion of this boundary of ecosystems!

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DNA doesn't build organisms .... it builds proteins.

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and, machine code doesn't draw pixels on a screen. Machine code puts command on a processor stack, and pops them off the stack, in a certain order. And those commands only direct the shuffling of bits which in turn shuffle electrons which eventually cause the cathode ray tube to fire yet another electron at a phosphor dot painted on the glass screen you actually look at.

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Chemical interactions in vast nested, cyclic, complex systems
result in organisms.

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Rather like nested procedures, eh?

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All analgies to communication systems are very poor in this context.

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Not on the basis you gave. Please note I have not asserted an exact identity between computer code and DNA, but it seems to me they are very very similar.

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Neat how computer code can physically affect the environment (RAM, I presume, I'm computer literate in a limited way). Thanks for pointing that out.

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Well, yes RAM but also all other forms of memory. That is, all memory appears as vast numbers of electric switches that can be on or off. But there is nothing essential about this mechanical structure except technical utility; in principle, you could build a functional computer out of a big enough network of canals and locks. Yes, out of mud and water. Because the key is not what the material substrate of the device is - but how it is organised. We only use silicon and electricity because a usable machine built out of canals would probably need more surface area than the planet has and would execute operations in decades not nanoseconds.

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I think computer code is not independent of the computer. It can certainly be formulated outside the computer, but it can work ONLY in the computer. But, I may have misunderstood happy on this point.

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I think thats perfectly valid to describe the present state of programming. But as above, the computer itself is just a mechanical medium on which the code executes. There is no reason in principle that it could not execute on a substrate that was essentially biological, even if this is beyond our means at present.

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...just seems to support ID all the more, to me. Just a thought there.

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Well, I sort of see where you are coming from, but it comes down to assumed premises. Because of course to me, if a human is "teaching" a computer, then this is really just one computer is teaching another.What I am getting at is that IMO we have enough knowledge now to draw direct analogies between information processing as we know it and some of the complex things that happen in biology. In 1950 what DNA did had little parallel in any scientific realm and was nearly magical. Now we can look at how a very small representation, organised in the right way, can create a cascade of cause and effect that quite independantly create complex outcomes. Having developed "instructional coding" outselves, we can make sense of DNA much more easily than we ever did before. Thus to me, it actually undermines ID, because one more element of the magic of biology is now understood. No divine instructor or blueprint is required after all.

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I quite agree. Computer code is hardly sufficient (in terms of wonderfulness), but I have little else in my experience to compare genetic code to for these particular aspects.

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As an analogy, the comparison of computer code and DNA is fine. The problem comes when the only line of argument is the analogy itself. For instance, some claim that since random computer code doesn't do anything in the computer then random DNA (ie abiogenesis) is impossible. In this case an analogy becomes a premise in the argument which is a fallacy. Analogies should only be used as a tool for helping people understand your point.

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Since the genetic code contains the information to make the cell, and since the cell cannot form without the genetic code, how did they come to be as a system that works in such a coordinated fashion?

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Life that is alive today requires DNA. However, this doesn't mean that life in the past required DNA. There is no scientific evidence that a supernatural creator made the first DNA requiring life, or that a supernatural creator even exists that would be capable of creating life. However, we do have evidence that random RNA sequences are capable of carrying out reactions similar to proteins, meaning that RNA alone could have been capable of being the first genetic code. We have evidence that amino acids and nucleic acids form abiotically. The scientific evidence is weighted towards abiogenesis.

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If DNA is nothing more than templates for protein shapes (which is tremendous in and of itself), what would a fertilized egg do if all the DNA were extracted upon the completion of the fertilization event?

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Strictly speaking, DNA is a template for protein and RNA interaction. The result of those interactions are more proteins.A fertilized egg would not replicate without DNA. But again, this does not mean that life requires DNA.

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You also appear to simply be assuming that the genetic code was not devised and implemented.

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And you are simply assuming that it was. There is not scientific evidence that the genetic code was either devised or implemented. If there is not evidence thus far, then why should it be considered to be a viable theory?

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I, of course, believe in a young Earth, but I think this is a fascinating puzzle for people who believe the Coelacanth has existed for 400 million years...how can DNA be THAT stable if its changing so much?

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Let's separate this quote from the coelocanth argument, which is dealt with in other threads. The DNA does change at the same rate as other organisms. However, the selective pressure on the organism do not allow it to change because it is already well adapted to it's environment. Therefore, most mutations that cause a change in the shape of the organism are selected against. Natural selection can preserve morphology as easily as it can change morphology.

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Not sure exactly what you are saying in regards to whether the complexity of info in living organisms supports evolution or creation, though. In case it isn't clear, I think it supports creation

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Complexity doesn't support creation.To discover what 'information' may or may not support we
need to understand the way in which the concept of information
can best be applied to organisms.I don't think looking at the DNA sequences does that.DNA sequences do not 'define' an organism ... the entire
genome does (maybe only part depends what we find out
in the future).The reason that we need the entire genome is that it is the
set (bag?) of proteins produced that interact to create
what we understand as an organism.

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To discover what 'information' may or may not support we
need to understand the way in which the concept of information
can best be applied to organisms.

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I don't think looking at the DNA sequences does that.

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Exactly. All of us (creo and evo alike) need to remember that the model (ie information theory) needs to describe reality, not the other way around.Personally, I think that information flows from the environment to the genome. Differential reproduction through natural selection is what creates information in the genome.

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DNA sequences do not 'define' an organism ... the entire
genome does (maybe only part depends what we find out
in the future).

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The reason that we need the entire genome is that it is the
set (bag?) of proteins produced that interact to create
what we understand as an organism.

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Again, totally agree. Although they are tightly connected, phenotype is more important than genotype when discussing biological information. That is, a simple DNA sequence does not contain information in the same was an an expressed DNA sequence. It may just be semantics, but I think it is an important distinction.

The genome is the entire set of DNA sequences, right? I thought, incorrectly perhaps, that phenotype is a result of genotype; or put another way, that phenotype depends directly upon genotype (though I understand that not all parts of the genotype may be expressed in the phenotype)...right? What sort of information flows from the environment to the genome? How does it flow? What is "differential reproduction" (sorry, I've never heard of that before) and what part of "differential reproduction" does natural selection affect? I wonder if you might be confusing complexity of structure with complexity of information. If the expression of a blueprint contains complex information, how can the blueprint contain less complex information ~ if that is what you're saying? But in all cases, the blueprint is structurally simpler than its expression. To me, it would seem the other way around ~ that is, that the expression of the blueprint is actually simpler than the blueprint itself as far as complexity of information is concerned.Consider the blueprint for a house. It is two-dimensional and small, a mere piece of paper. In this way, sure, the blueprint is simpler than the house that results from the blueprint. However, all the complexity of information and intelligence was in formulating and interpreting the blueprint. And the blueprint also contains written information that is expressed (but not written) in the house. Ultimately, the house has NO intelligence (though it does contain information). However the blueprint and the house are a result of intelligence at work. In the case of DNA, the blueprint directs the interpretion of itself, so it is all the more amazing. And the expressions of DNA contain varying degrees of intelligence...wow! Even the humble paramecium I saw under a microscope once seemed to be making some decisions (which way to go, what to eat) and without a brain of any sort. Perhaps some of my family and friends think I operate much like this paramecium .I may be wrong, but it would seem that any particular expression of my genetic code (my brain, for instance) will represent only a part of that code and, thus, be less complex than the code itself. (Of course, some might think MY brain is pretty simple, so that might be a bad example ).To see whether the information in DNA is less complex than the organism itself, we could just remove ALL the DNA from the organism at any point in time (from conception onwards) and see how the organism fares without it. If the DNA is not conducting any "directing" type functions (like which and how many proteins to make and when to make them or when to start mitosis etc.), then the organism might do fine, if the more complex information is in the products of the DNA (i.e., proteins) or in the environment.Are you guys saying DNA does not contain complex information even though the organism does? I am probably misunderstanding something.Here are some DNA questions I think are important:Is genetic code meaningful anywhere outside the cell environment?Does the cell environment exist because of DNA?Does DNA need cell structures in order to replicate?
Does the DNA code for any of the cell structures?Is the replication process simple?Why does DNA replicate at all, is there a "replicate now" sequence?Are proteins considered simple?What do proteins do?Is the process by which DNA makes proteins simple?Is making proteins a simple chemical reaction similar to mixing two chemicals in a jar and a third product is automatically made (for example, an acid and a base making a salt)?Could the cell make the proteins without the DNA?Well, for what it's worth...just some thoughts.This message has been edited by TheLiteralist, 12-07-2004 02:45 PMThis message has been edited by TheLiteralist, 12-07-2004 02:48 PM

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The genome is the entire set of DNA sequences, right?

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Yep, including non-coding DNA.

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I thought, incorrectly perhaps, that phenotype is a result of genotype; or put another way, that phenotype depends directly upon genotype (though I understand that not all parts of the genotype may be expressed in the phenotype)...right?

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Genotype and phenotype are intertwined. It is difficult to look just at the gene sequence and determine what the phenotype should be. As you have mentioned, there is also the question of gene expression which is, at times, separate from the gene itself. Expression is controlled by other genes, intergenetic sequences, environmental factors, etc. It may come down to a mere semantic argument, but I see a division between genotype and phenotype when dealing with "information" within biology.

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What sort of information flows from the environment to the genome? How does it flow? What is "differential reproduction" (sorry, I've never heard of that before) and what part of "differential reproduction" does natural selection affect?

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Excellent questions, I'll see if I can answer. I sometimes have a tough time communicating scientific ideas into lay language so let me know if it isn't clear.Firstly, mutations occur in the genome. Those mutations will have one of three consequences; either the organsism will be harmed, unharmed, or will benefit from that mutation (ie detrimental, neutral or beneficial mutations). It is not the mutation that determines how it will affect the organism. It is the environment that determines whether or not the mutations will hurt or help the organism. For instance, developing fins for a land locked organism is not beneficial, and in fact will harm them because it will slow them down. However, for an organism that lives near water it may be beneficial.So how do we determine if a mutation causes an "increase in information"? By how it affects the organism in an environment.This is where natural selection comes in. Natural selection does not cause certain mutations to occur, but it does amplify beneficial mutations through differential reproduction. Those organisms who are judged more fit by the mutations they carry will have more offspring, and hence pass that mutation down to more children (ie differential reproduction). When this process continues for many generations it becomes obvious that some mutations will dominate the population. All gene sequences we see today, and therefore all of the information we see in the gene sequences, are there because natural selection preserved those gene sequences and amplified their number over millions of generations. The environment is responsible for the information we see in the genetic sequences. That is why I say information flows from the environment to the genetic material.As an analogy, let's say you start dialing random phone numbers. The numbers themselves are not information. Some of those numbers you dial will ring certain people. You are then able to connect a random string of digits to a persons house. You have created information from a random string of digits. It is the same for genetic sequences. Some will be beneficial, or ring a house as in the analogy, and will be preserved. Natural selection gives meaning to random genetic sequences in the same way that recording a name to match a phone number gives meaning to the random phone number.

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To see whether the information in DNA is less complex than the organism itself, we could just remove ALL the DNA from the organism at any point in time (from conception onwards) and see how the organism fares without it.

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I don't know if this is a fair comparison. If we removed all food from (ie glucose) the organism it would die as well. Does glucose, a very simple sugar, contain a complex code? But yet glucose, just like DNA, is an important reactant in biological function. Are the reactions between glucose and the cell any different, at a chemical level, than the reactions between the cell and DNA? Nope. DNA is a center of chemical reaction, not a blueprint.

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Does DNA need cell structures in order to replicate? (Yes)

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Actually, it doesn't. DNA can be replicated using a single protein and free nucleotides. It is called Polymerase Chain Reaction, or PCR.

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Does the DNA code for any of the cell structures?

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All cell structures are a result of the chemical reactions that occur between DNA and other molecules. If you want to call this process "decoding", go for it.

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Is the replication process simple?

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As mentioned above, the replication of DNA can be very simple. However, DNA in living cells is quite complex. Does the replication process NEED to be complex? Nope.

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Why does DNA replicate at all, is there a "replicate now" sequence?

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DNA doesn't "need" to replicate. If it doesn't replicate then it disappears. If it does replicate then it's numbers increase. Life is a result of DNA sequences that replicate.The "replicate now" order is usually a result of various triggers, and varies greatly between cell types and organisms. In bacteria, the when food and a lack of metabolic waste is detected it sets off a trigger that causes replication. This is grossly oversimplified, but it is actually proteins and small chemicals that are responsible for starting replication in most cases.

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Are proteins considered simple?

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That is a very subjective question. To a mechanic, a car is not that complex but to the average driver looking under the hood the car is quite complex. I work with proteins all of the time, so I think they are very simple. You might have a different view.

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What do proteins do?

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Carry out chemical or physical reactions.

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Is the process by which DNA makes proteins simple?

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I think it's simple.

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Is making proteins a simple chemical reaction similar to mixing two chemicals in a jar and a third product is automatically made (for example, an acid and a base making a salt)?

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It is closer to the process of polymerization, such as nylon production. Specific protein sequences can be made without DNA through simple cookbook like reactions. It is difficult to make anything longer than 20 or so amino acids, but it can be done. It just happens to be easier to have bacteria make it for you.

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Could the cell make the proteins without the DNA?

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Yes. Just give it messenger RNA.

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To see whether the information in DNA is less complex than the organism itself, we could just remove ALL the DNA from the organism at any point in time (from conception onwards) and see how the organism fares without it. If the DNA is not conducting any "directing" type functions (like which and how many proteins to make and when to make them or when to start mitosis etc.), then the organism might do fine, if the more complex information is in the products of the DNA (i.e., proteins) or in the environment.

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If you want to look at it from a systems engineering PoV then you
start to see that the DNA is an implementation issue, not a
requirements issue.It's one of the fundamental functional elements of cells as
we know them, but it's not all there is in 'creating' the
organisms that we see wigling it's psuedopods under our microscopes.Specifically, when considering information in the context of
evolution the 'information' surrounds the relationship between
the environment and the organism. We will sometimes be able to trace
changes in that 'information' back to the DNA (maybe)but it
is not the changes in the DNA that are directly relevant to
the informational question with regard evolution.

Loudmouth and I perhaps do not agree on this, but I think a blueprint is a serviceable analogy for DNA. It depends upon the level of detail at which you're examining life's processes, but this analogy has been used plenty of times by scientists. There's even a book on my shelf titled Blueprints: Solving the Mystery of Evolution.But I think the comment you're responding to was trying to make the point that complexity of structure can be merely apparent and does not necessarily correlate with complexity of information. A good analogy is coordinate systems. In a cartesian coordinate system, x² + y² = 4 looks like it might represent a line with a fair amount of complexity. But in a polar coordinate system the same line is written r=2. It's just a circle.If I could modify your surmise slightly, I agree with you that genuine complexity of structure must spring from equivalent complexity in the original specification, with the qualifier that detecting the regularities in the structure that might point to simplicity of design is very difficult.--Percy

Some of the confusion seems to be that Dr. Gladsyhev's analysis of CHEMISTRY is not appreciated as much as I, BSM, promote it to be.I think Georgi is DEAD ON with his; This might be able to give you an idea as to where in the environment the info is coming from! The full text is linked here
EvC Forum: GP Gladyshev's paper (s)or mine?

Is your avatar genuine Bradscrawl? --Percy

Yes,
& as soon as I get an internet picture host, I will start using more legible versions with my posts. The picture is my blueprint for a means to experimentally determine theromostat parameters modifying current electrolytic reaction devices. The "scrawl" is not legible on this public commputer but with my laptop you can make it all out except for the comment that the diagram might need to be inserted into a centrifuge to actually apply ( I was uncertain if gravity needed to be taken into account). Regardless the top two figures are quick sketchs of Faraday's and Thompson's devices for measuring thermal currents and the increasing "white" area is a prediction of mine as to where in this apparatus (if working) coupling rather than oxidation and reducation rxns are most probably to occur.I dont think I am going to get into avatar switching but I will put out some more drawings. In particular I made a drawing of what I consider to be what Georgi DEMONSTRATED in his latest paper (monohierarchy within a biological polyheirarchy) and on reading his paper over, I began to wonder if limb buds might not be causal with this CLOSED materiality (my poly heirarchy was restricted to those that display a normal distribution).

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Loudmouth and I perhaps do not agree on this, but I think a blueprint is a serviceable analogy for DNA.

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My opinion is that it is the exact opposite end of the
spectrum.The DNA processing in the cell is the solution to a string of
increasingly higher level requirements.A higher level requirement would be the 'blueprint'.DNA processing is one of a set of potential solutions to
those organismal requirements.