Design Framework for Evolution

For the last couple of years I try to apply design patterns mainly from software engineering to unravel evolution. This approach resulted in different scenario's for the origin of life and the first cells, based on design paradigms. I now created a website where I present a general design framework for evolution and where I explain how life originated, how the first genome and the first cell evolved and how the design patters can be used to explain evolution in general.-Life can be modelled on design patterns that are conceptually similar to iterative software development and using similar deisgn patterns such as encapsulation and object-orientation.
-Life evolved inside-out, meaning that we life originated by adding funcitonal layers on top of existing ones. For the eukaryotic cell this means first replicating DNA, then a nucleolus, then a nuclear lamina and the nuclear membrane before the evolution of the plasma membrane
-Ontogeny reflects the phylogeny. By looking at the dependencies between the different components of the cell and the way they are assembled during development, one can deduct the evolutionary steps. Thus, we can reverse engineer evolution and avoid irreducibly complex systems.The website is design4evolution.net. Would like to hear your opinions on the design approach, the molecular steps I propose and the general philosophical aspects of my approach and findings.

Pressie: Maybe you should try to define what you mean with the word 'life' before we can have a meaningful discussion?I use the word Life in a purely mechanistic way and I propose that a replicating genome can be considered the first life form. Replication of a genome is the common denominator of all life and the basis of its evolution. Basically I go back in evolution (I reverse engineer evolution) and peel away all the extras that were added in evolution until I end up with something that I consider the essence and beginning of Life. The alpha and the omega of Life so to say.Although prions and viruses at the basis of Life are very interesting to research, my work does not imply them directly. Proteins are derived from DNA, so DNA was first. Viruses are dependent on the cell machinery, so they evolved later. One could even argue that viruses are so intricately envolved in the cell's mechanisms that they have evolved as part of the cell and were never a seperate entity.

Hi genomicus. Yes, that is true, it does not directly invoke an intelligent designer, but also does not preclude it. Based on my reverse engineering, I propose a mechanistic scenario of how the eukaryotic cell was put together. However, when one arrives at the driving forces for this behavior, it gets a lot more difficult. Classical terms such as natural selection and random mutation seem irrelevant or useless at a macroevolutionary scale. For now, I assume that energy input in the form of day/night and seasonal changes can explain evolution, but at the moment we miss some parts of the equation.

Viruses have a seperate life cycle that is relatively independent from the life cycle of their hosts, but they are 100% dependent on the host itself.The problem is that we see viruses as a seperate entity able to infect cells and take cells hostage. I see them as extension of cells, pieces of DNA that have evolved to communicate pieces with other individual organism.On a microevolutionary scale, they may be infectious agents, but they may represent powerful evolutionary tools on a higher level. In the line of my 'design framework', viruses can maybe be seen as intelligent agents that increase evolvability

I do not see viruses as a seperate Life entity, but part of the Life cycle of other organisms. Just as I don't see a membrane transporter or a transposon as Life, but only part of it.

Pressie, I have described my definition of Life in mechanistic terms, and have described viruses as part as other life forms. I use a replicating genome as the definition of Life, so some may consider viruses to be a Life form because they have a genome. I don't see the relevance for the discussion.

Hi NoNukes, the terms random mutation and natural selection are irrelevant for macroevolution because they do not explain the origin of Life, the origin of the cell, the origin of multicellular organisms etc. They also have no mechanistic basis and are non-predictive.They could well be an important factor in evolution, but irrelevant at the macro level we are talking. In studying the working of an engine, we do not use nanophysics. In order to explain Microsoft XP, we do not use the 0s and 1s, but we talk about software modules and classes.

I consider macroevolution basically everything before the Cambrium. Microevolution is the small things in evolution, like beak size, different insect species, adaptation to enviroment. Microevolution is more adaptation than real evolution, which is for me the addition of new functions and the increase in complexity.The really big events in evolution are the origin of Life, the origin of the first cell, multicellularity, the origin of sex, origin of insect metamorphosis etc. Neodarwinism is rather useless here.

"So going from ocean dwelling vertebrate and invertebrate to dinos, from dinos to birds and from small mammals to homosapiens is what you consider microevolution? This all happened after the Cambrian period."My point is basically that I find it more relevant for evolution how cells and multicellular organisms originated in the first place, than how a four legged creature with a spine developed into a slight more complex four-legged creature with a spine.Once you have a cell, the rest is almost trivial. It is all more of the same, recombinations on common themes. Real macroevolution happened at the microlevel. How did cells evolve, that is the real question.I guess 99% of the gene families that are present now, originated before the Cambrian (or Cambrium in Dutch). Then the rest would be microevolution. Also, no real new system designs after the Cambrian.

AZPaul3. Thank you for your (albeit rather condescending ) post.1. You say that I bring nothing new. I propose a stepwise and detailed mechanistic scenario for the origin of Life based on well-defined design framework. I for instance propose, or rather deduce, that the nucleus was the first cellular entity. That is quite new, is it not? Have you even read my website?2. Of course I use different terms that do not coincide with the current definitions. It is a different framework that I use. A lot of people seem to define macroevolution based on macroscopic differences, but in engineering terms, that is a mistake. Evolutionary speaking, the effort is in the cell biology. From nothing to a eukaryotic cell, from a cell to multicellularity.3. Maybe mainstream evolutionary science is a better term than neodarwinism. I just use it as a general term for anything that has been brought up in the last decades. I do not see a coherent theory, no mechanistic scenario. To me it looks more like a religion than anything else.4. "Evolution says nothing about the origin of Life". Excuse me? As if the origin of Life is separated from its evolution. It sounds rather creationist to me. Anyway, genetic drift, neutral evolution, hopeless monsters, Margulis' fairy tales, thet all make no sense to me because they are non-mechanistic.You say that nothing in evolution has any predictive value. It makes your entire framework non-predictive and therefore non-scientific and trivial. At least my theory is based on a predictive framework and on my framework, you can predict evolutionary scenarios. You can also falsify the theory.

AZPaul3,I use a completely different framework from mainstream evolutionary science, that is why I use different terms. Mine is based on design paradigms and my definitions come from engineering. Microevolution and microevolutions are indeed different terms for me. They are worthless in another framework. The same as terms like genetic drift or neutral evolution are irrelevant for my research.For me, the origins discussion is essential in evolution. And as I explained on my website, the early stages in evolution will define the constraints and possibilities later in evolution. There are strict rules in evolution that determine the path of evolution. That's why the origins question equals macroevolution in my design framework.-Evolution: The stepwise additions of new functional modules over time (i.e. an increase in complexity)-Adaptation: The differential use of existing functionality to adapt to changes in the environment (i.e. no or minor change in complexity)I am interested in evolution (and I am quite satisfied with current population genetics to explain adaptation. A lot of people like me have come to the conclusion that current evolutionary theories do not explain evolution at all. As soon as you start to translate evolutionary scenario's into real mechanistic steps, you run into trouble. If you don't address the origins question, you cover only the last 1% of evolution, speaking in system terms.I am interested in the mechanistics of the evolution of the eukaryotic cell. Is current evolutionary science going to help me in this effort. No, because there is no real framework. Anything goes. Will population genetics tell me how the nucleus was assembled during evolution? I believe engineering science is giving me the answers.For instance, I give a rather detailed mechanistic explanation of the origin of the eukaryotic cell, indicating that the nucleus was the predecessor of our eukaryotic cell. That is quite a big difference from what you read in the textbook. How the eukaryotic cell was assembled during evolution matters enormously. Cancer is uncontrolled cell growth of eukaryotic cells, and the cell cycle regulators originated very early in evolution. Only if you understand the evolution of the eukaryotic cell, you will start to understand the cell cycle.

genomicus: "But what about the origin of molecular machines, like, say, the bacterial flagellum?I think that the way they are assembled in development could be exactly the way it was assembled in evolution. So basically, you start with either the stator or the rotor and keep adding extra modules to it. I am not sure, I haven't looked into it for a long time. What is important is that the previous stages in evolution should all be functional and preferably with the same functions as the end product. So, if that is movement, you would expect an early truncated flagellum or even the rotor/stator combination to already create movement."This brings me to a second question. Your scenario for the origin of the eukaryotic cell seems mechanistically plausible, but what kind of experiments could be done to test your hypothesis? "Experiments are difficult, but we should further analyze the components of the nucleus and eukaryotic cell and see if they fit. For instance if it was proven that essential nucleolar proteins originated after the nuclear lamina was formed.

NoNukes: "Why would I do such a thing? When would I be finished designing? Who am I?"What I am trying to do is reverse engineer the steps in evolution. The flagellum was assembled during evolution and there is a logical way of assembling it, giving the constraints of evolution.I consider Life an evolving molecular machine and metaphorically I speak from the point of view of an engineer. Seeing the flagellum/nucleus/cell as it is now, what would be the logical way to assemble it. How would you assemble it if you were an engineer, basically.The questions you ask are valid and represent the driving forces and goal-orientation of Evolution. I don't think that there was a conscious design or an active designer at work. For me, the driving forces are in the life cycle itself and an intrinsic active evolvability built into the genome.But once you have reversed engineer the steps in evolution (all the way thinking in terms of system designs and design patterns), we can deduce what actually happened and start thinking about the driving forces.The steps towards the eukaryotic cell that I propose, adding layer on top of layer of extra functionality are a lot easier current evolutionary theories. If you think that a eukaryotic cell with a plasma membrane can generate a nucleus, you will encounter tremendous physical problems. For instance, how would you evolve the essential nuclear pores when there was no nuclear membrane in the first place. This is what you call irreducibly complex. My solution is not reducibly complex.Imagine a baseball. It consists of several layers. It would be pretty difficult to start with the outside leather and stitching and to try to put in the cork ball in the end. The logical sequence would be from the inside to the outside. I can deduce that without knowing what the purpose of the baseball was, who assembled it or where the subparts came from.

NoNukes: "I want to pursue the 'driving forces' beyond mere hand waving because these are the forces that substitute for random variation and natural selection that predominate in natural evolution."See it as a software program that will create its own extra code with each software development cycle. You start it up, the program adds some extra code in the source code and compiles and sees whether it still works, i.e. whether the extended program can still add code and be complied into a working program that can add automatically to the source code and then compiles, etc.And testable, I guess. My next project maybe, although my Java skills are a bit rusty.

NoNukes: I don't want an analogy with programming. I want to know what in the real world corresponds to your "driving forces" such that no random addition processes are involved and such that natural selection is not a meaningful effect.I never said that no random addition processes are involved or that natural selection is not a meaningful effect. I expect them to be involved, but they do not explain evolution. Like gasoline is necessary to work an engine, but does not say anything about how the engine works.The driving forces I speak about can be built in into the genome. A random mutation process can be exploited to give direction. Mutation-sensitive parts of the DNA for instance.