Design Framework for Evolution

Catholic Scientist: What about when species evolve towards less complexity? Like those cave fish that lost their eyeballs, or birds that have vestigial wings?Interesting examples. I would consider those to be adaptations or maybe streamlining examples.

catholic scientist: No offense, but I'd expect an engineer to make a lousy biologist. Life is not a machine nor does it behave like one... it gets messy and illogical.""No offense at all, especially in the light of your comments. Life is a nanomachine and it behaves as one. It is as simple as that. It does nog get messy and illogical, only when you don't understand that it is a machine it gets messy and illogical.Catholic scientist: There is no logic when it comes to assembling parts of life. Basically, whatever is just good enough to make it so the animal doesn't die before it reproduces is what is going to get included in the selection process. That allows for all kinds of ridiculous bullshit.""This is exactly what I dispute (and explain on my website). There is logic in assembling the parts of Life. Of course there is logic, otherwise it would not work. There are only limited possibilities to assemble things in evolution. Many 'scientists'tend to forget the principles of functional continuity in Evolution. A major mistake.

Catholic scientists: "At its core, life is just chemistry. I wouldn't call spontaneous chemical reactions "machines", but I don't really care to argue the semantics."Again, this is what is disputed. But indeed, this is the basic premise of current evolutionary science. But evolution is not a chemostat, it is a molecular machine with molecules at its basis.Catholic scientist: "I don't see the design-by-contract approach being applicable to biology. There is no contract. Its whatever works goes, where working is reproducing before you die."Design-by-contract means that other components of the system can always rely on the interfaces that were initially used. For biology, it means that you can not change things that evolved earlier in evolution. Imagine you would change the genetic code. It would mean that all proteins (downstream) would change and nothing would work anymore. That is why the genetic code has never changed (or changed only within very limited effects). The genetic code has not adapted to become a perfect code, the rest of Life has adapted to the existing genetic code.

AZPaul3: "A kludge like the laryngeal nerve creating a god-awful design any engineer would run screaming out of the room over. Have we talked any of the intercellular signaling cascades? Talk about screwed up overly complex energy wasting kludges!"A basic misunderstanding in applying engineering and you seem to confuse engineering principles with a conscious designer. Evolution is not freeform and functionality was put on layer-by-layer. This puts many constraints on the ultimate outcome.Compare it to current computer legacy systems. The old systems at the core of many banking systems for instance do not conform to current design principles and we would find them now overly complex, but they work and we cannot change them easily. Still it is engineering and we have overcome the 'silly legacy systems' by encapsulating them so that we hide the complexity. And you can only understand how legacy systems work by applying engineering principles.

AZPaul3: "The point being that evolution works with what it has, layers new functionality onto the old and after several such events the result can be seen as overly complex, energy inefficient and wasteful ... but it works and that is the only reason such messes remain in the system."So we agree to a certain point.I do not like the terms overly complex or energy inefficient, because they imply a certain goal and the terms are quite anthropomorph (that is why you sound like Life has a designer). Also, you and others seem to use the words 'mess' and 'wasteful', as a way to show that Life is not designed by a designer. 'Mess' and 'wasteful' have no place in science.In software design, but also in other system designs, the layering is recognized as a design patterns. If you want the system to always work during evolution (the concept of functional continuity, it would imply that earlier layers must be kept intact. From this, you can deduce the actual path of evolution, by peeling of layer by layer and carefully look at the relation and dependencies between the layers. That process is called reverse engineering.If you look at the origin of the nucleus, I have deduced the steps. I see the dependencies between functional layers and previous layers. Has evolutionary science produced a framework that can predict (deduce) certain steps in evolution? I never saw one. Anything goes in evolutionary science as long as someone comes up with some sort of fitness goal. And hey, if things don't match up, you just terms like 'neutral evolution' and 'genetic drift' or 'hopeful monsters'.

NoNukes: "What you seem to be saying with your software analogy, is that evolution works on whatever is already designed. "Evolution works on whatever is already -implemented-. All the previous layers may have evolved by chance events and based on a selection process, but did thet did occurr according to specific rules. These rules that are implied in the design frmaework can be used to deduce the actual steps.I would not use the words random and natural, because they are difficult terms and are of no use in predicting the steps taken in evolution. Brownian motion is random, but can be used to give a direction to a molecule. I also assume a selection process, but they do not have to be natural.NoNukes: "Okay, but where? Give me an example of the genome itself giving direction for addition of improvement to spur on evolution."First, you have to be careful to use the word 'improvement', because improve implies that something was not good and that you know what would be better. I think more along the lines of a machine that increases in complexity without an external driving force (like environment). It is intrinsic.Some examples that would explain the 'self-evolving':-Telomerase is an enzyme that actively extends the chromosomes. Evolution-wise, this may create new virgin DNA that can be used for the creation of new genes.
-Active recombination and formation of new genes by randomly recombining exons and genes with the use of active cut-and-ligase enzymes.
-Crossing-over in sexual reproduction. Although the initial events leading to crossing over be be random, the result is an organism with an active recombination mechanism. Inequal crossing-over can drastiscally increase genome size.I know that these things are difficult to prove, but they must be seen in the context of the self-evolving molecular machine.Wings and fins would have evolved not because there was some fitness advantage, but due to an intrinsic recombination process in which all possible kinds of extremities (wings, fins, legs) are continuously explored. Viable new organism with rudimentary wings could then evolve into functional wings using RM+NS, but the origin of the wings would lie in another process.

Catholic scientist: "Then get to it. Go ahead and dispute it. Quote the relevant parts of your website here and lets debate them."I dispute that Life must be seen as a set of chemical reactions, but instead Life must be seen as a molecular machine that follows certain rules. I depict a new framework for evolution with different paradigms.New Paradigms1. Evolution can be modeled on a design framework
2. Life evolved inside-out
3. Ontology reflects PhylogenyEvolution can be modeled on a design framework
The design framework on which the new theory was built can be best described using the design-by-contract methodology from software development. It represents an object-oriented programming where systems can expand as long as existing interfaces must remain intact. Such a system can only expand by refining existing interfaces and implementing new interfaces. Dependencies in the system on interfaces prevents modification of functionality and lead to legacy systems. From the dependencies in the system, one can deduce the evolution of the system.Life evolved inside-out
It proposes that the first entity of Life was the replicating of DNA, representing also the first life cycle. This replicating (cycling) DNA that started to produce ribozymes including ribosomes subunits and later proteins organized in a nucleolus. The nucleosus wrapped itself in a protein matrix and was surrounded by the nuclear lamina. On this nuclear lamina, the nuclear envelope evolved giving rise to the nucleus as the first cell. Outside of the nucleus, again a protein matrix, the cytoskeleton was formed onto which an additional membrane fused, the plasma membrane.Ontology reflects phylogeny
The eukaryote cell acquired the capability to fuse with another cell which duplicated its DNA content, resulting in a life cycle that contained both a haploid and a diploid stage. In higher eukaryotes multicellularity evolves in the diploid stage by a progressive mitosis of the fertilized egg and a postponement of the sexual maturity of the germ cells. Early decisions in egg division decide the fate map of the mature organism and represent strong branching point in evolution. Overall, evolution is seen as the addition over time of extra functionality on top of the original life cycle of replicating DNA.

catholic scientist: "Why should I think that life should be seen that way and why should I think your paradigm is correct?"Because my framework gives actual molecular mechanisms for evolution and I guess we are both here to find out how Life evolved. It also makes sense (to me in any case) that Life is an evolving molecular machine and should be treated that way.My paradigms must of course be seen in the light of scientific advance. They can be tested. Because I present a concrete (design) framework, it is also up for discussion. For instance, people may argue that functional continuity may be reached by other mechanisms and scenario's.But test the framework yourself. Try to come up with a logical sequence of events that give rise to the eukaryotic cell. Then look at my explanation and you can decide for yourself which one is better.

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Taq: Quite frankly, software does not have a lot in common with DNA.

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Do not confuse the implementation of a design with the design itself. Like a blueprint is not a building and a model is not the real thing. Molecules are not balls with sticks and a 3D image of an animal on the screen is not the animal itself.Life is a molecular machine (or a system of machines if you like), and the entire system can be represented by a model or a design. The underlying design of both molecular machine (Life) and software (virtual machines) can still be the same.

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NoNukes: Brownian motion can give an unpredictable motion to a molecule. It would seem vain to me to reject Brownian motion or to call it unscientific on that basis. But it seems that you reject natural selection/random mutation on exactly that basis.

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What I try to say is that although random process may be involved, these would not help us to explain evolution. I do not reject NS+RM at all, but they cannot provide a framework for unraveling evolution. I know that an engine can run on gasoline as the enrgy source. It doesn't tell me however how the engine works or where the car is going. Same for evolution, RM+NS only says that Life evolved, but if you ask further they don't know say how evolution works or what path it has taken.

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NoNukes: You have some reason to believe that this cannot occur simply with a genome vulnerable to copying errors

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We need mechanisms beyond RM+NS to explain evolution. I think that in order to grow in complexity there needs to be an intrinsic driving force, not an extrinsic force.I do think that it is possible to create a genome that can actively recombine into a more complex genome (exon shuffling, crossing over etc.) by initial copying errors. But to understand the active 'recombination machine'that has evolved, you need to look at the functions of the machine. The function of a house is not explained by timber, nails and a hammer.