Posted on 06/15/2003 10:36:08 AM PDT by Alamo-Girl
I think I get the point of evolutionary pathways, however it seems you missed my point. Evolution theory does not determine how nature behaves. Nature behaves according to its own 'logic'. A theory needs to be in accord with the 'logic' of nature, not the other way around.
I think we are pretty much in agreement that to change a protein into a better one there are very few combinations which will be successful (else you would not need supercomputers to do your work). I also would agree that in a situation where several steps are necessary, the successful outcome of the last phase is constrained by the steps leading to it. Where we disagree is that you seem to think that because the last phase constrains what will be successful, that it pre-determines how the prior steps will take place. Mutations are not constrained by the possible outcome. That is why there are so many bad mutations. While the chances of an outcome being selected may be constrained at each successive change, the number of attempts needed to achieve each step are still determined by the whole phase space of random chances possible in achieving the change. Therefore, increased constraints on what will be a successful change decrease the chances of its being achieved.
I figure you probably know a lot about Avida (the software) and don't want to engage two complicated threads simultaneously, so I'd like to ask you a few questions. (I can't tell how dated my web research is and perhaps you have the latest information.)
Does the Avida software still require an initial parameter for genome length? If so, what was used in this simulation?
Does it still use an inventory of code from which the virtual organism can select? If so, how large was the inventory in this simulation?
What would be the Avida parameter setup for bootstrap abiogenesis - genome length of zero?
Yockey tackled several reviews on a single message much like Penrose did on Shadows. In his latest book on the subject, Penrose actually includes the rebuttals in separate sections. I like that a lot!!!
Call it empirical zeal. ;-`
If not, "Vas you der, Charlie?" then at least, "Vhat can you brrring, herrre?"
It certainly looks like that. Also, I failed to give the link to the article I quoted University of Edinburgh .
Are the Hox genes conserved across phyla like the eyeness gene, i.e. between human and mouse,
Have not seen percentages, but many of the Hox genes in drosophyla are quite close to those in vertebrates. So much so that:
Functional similarity between Hox genes of different organisms demonstrated by gene swapping experiments: e.g. expression of human Hoxb4 in flies causes the same phenotype as overexpression of the fly homologue Deformed (Dfd).
From: University of Toronto.
Fascinating. Looks to me that either it is creation, intelligent design or that common ancestor which predated the Cambrian Explosion in evolution theory was astonishingly programmed - by random happenstance - for adaptation.
Sorry milady, but I don't really know anything about it. I've never really been very interested in Alife -- while it may be entertaining, I don't think it is a particularly useful pursuit. My expertise is generally in computational theory and information theory at large. I have a background in chemistry, but even that isn't something I keep up with.
What would be the Avida parameter setup for bootstrap abiogenesis - genome length of zero?
Genes are very coarse functional units; you would actually bootstrap from much finer functional units than genes. For real-world simulation purposes, you might be able to start with amino acids using precomputed phase spaces and then do as-needed computation beyond that (taking advantage of the fact that higher-order combinations aren't as common as lower order combinations).
I think the Avida software is an engine for modeling the system dynamics, not real biological systems. This is plenty useful though. The real argument about evolution is whether or not that particular mathematical model of system dynamics leads to interesting results, which can be demonstrated in painstaking detail using this modeling system. If the system dynamics model works, then so does biological evolution (ignoring whether or not evolution is actually responsible for speciation).
My personal theory is actually a bit different than conventional doctrines. I'm more inclined to say that variation and complexification is caused by automata mechanisms, with a fair bit of selection pruning the automata process. To my own mathematical mind, this is the fastest and simplest bootstrap pathway to very high-order complex biologies, NOT textbook evolution. My apparent defense of evolution is primarily that the mechanism is definitely valid, not because I think that is best theory for speciation mechanisms. It irritates me that people constantly argue that it is an invalid mechanism (which is an argument from ignorance), and yet choose to ignore the fact that it is a weak argument from a systems dynamics theory standpoint. To me it says that most of the detractors are not educated on the topic enough to formulate a reasonable and coherent argument.
I'm not defending evolution per se, I'm attacking the egregiously poor arguments against it (though most people apparently have a hard time seeing the difference).
Moreover, even if all of these were discovered - it would nevertheless require a bootstrap on the front end to initiate the process. And the existence of such a bootstrap, if algorithmic, would point directly to intelligent design.
I agree and think this would fall into the realm of unspun's Theory of Relationality mentioned a few threads ago.
When considering theistic evolution it is my opinion that man began to evolve (devolve?) by God's design at the moment of original sin. Man changed from a state of perfection (in communion with God) having a very long life span to a flawed, willful being consigned to Earth with an ever decreasing average lifespan. Obviously the lifespan thing has recently been increasing so would this indicate we have passed a nadir of sorts and are continuing the plan of evolution to bring us back to fullness? That God designed a way for man to be redeemed again (through Christ) shows His love for us and that a plan has been set in motion. We experience the part of this plan specific to our own time continuum. Just a few things that popped into my thoughts while reading the thread and some posts.
One other observation. G3K has taken a remarkable turn in civility and calmness. My congratulations to all involved. I have always marvelled at the depth of his knowledge and now that he is not attacking it is a pleasure to read his postings. Thank you G3K, I knew you could it.:-)
Anyway I will keep reading more of the previous postings tomorrow. It is getting late so I will hug you and bid you a fine Good night. Love.
And there is also tremendous waste.
For example, when the genome project was done, scientists were surprised that there were only some 30,000 odd thousand genes in humans because they had already identified some 100,000 different proteins used in human organisms.
Please support your statement that they were "surprised".
The reason is that genes can be made to make more than one protein by using very sophisticated code reuse.
That's *not* the primary source of the multiplicity of proteins in relation to the number of genes.
Instead, many protein "variations on a theme" are created via alternative splicing, and post-translation modifications. In other words, proteins often get changed via their interaction with other proteins and the rest of the "cellular machinery", not through "very sophisticated code reuse".
Some genes can make more than 50-60 proteins!
Please give a specific example so that we can see whether this supports the claim of "very sophisticated code reuse", or whether it's due to the much more mundane post-translation changes.
One of the most sophisticated examples of "complexity explosion" in the human body is the immune system, which works by generating around a trillion unique antibodies through combinatorial combinations of proteins and then "weeding" or "cultivating" them appropriately in response to infection. Even this works by post-translation recombination instead of "code reuse".
Code reuse is definitely a sign of intelligence.
No, it is not "definitely" a sign of intelligence. I've seen many examples of code reuse arise spontaneously via evolution (e.g., through the "Tierra" model of evolving computer programs).
Words like "definitely" are very absolute. Make sure that they are warranted before you employ them.
It takes hard thinking to figure out how to take code from here and there to make it do something else you need done. This cannot be done by dumb luck.
I don't know whether it can be done by "dumb luck", but it can certainly happen by evolution -- I've personally seen it done.
Intelligent people do not believe in evolution
This has been a remarkably civil thread for this topic on FreeRepublic, and I would suggest that your insulting tagline is out of place here. It's also transparently false: Millions of intelligent people do, indeed, believe in evolution.
I know of no evolutionist, nor any evolutionary theory, which relies in any way on "the future predicting the past". If someone's argument appears that way to you, I submit that you've misunderstood what they're actually saying and you should give it another look.
When put this way it is obvious nonsense.
Yes, that *would* be nonsense. But that's not what he's saying.
When put as 'pathways' determine the outcome, it does not sound as silly but it is the same logic - that what will be successful in the future is the cause for the events in the past.
I find no statement in any of his posts which can fairly summarized in the way that you have. Could you quote the portion of his post(s) which you feel rely on the "future" being the "cause" of events in the past?
[In short: difficult to compute is utterly unrelated to probability. We aren't just analyzing what happens from a specific known starting point, we are reverse engineering the entire phase space of possible starting points and possible end points.]
You are again giving support to my statement above. What you are speaking of is the reverse of how things actually happen. The future does not determine the past (except in the Terminator movies!).
He most certainly is not. Computing an entire phase space is in no way an exercise in "the future determining the past".
You've obviously spent a great deal of effort on this, and I'll try to give it the thoroough treatment it deserves.
However, given the size of your post, that's going to take some time, so bear with me as I tackle parts of it at a time over the next few days/weeks.
In fact, that might have been a better way to have it critiqued in the first place -- post it serially a portion at a time, so that any weaknesses in part X could be identified and repaired before you went on to attempt to build anything further on its foundation.
On the meta level, however, my first impression is that you're all over the map, and you might benefit from paring things down to the bare essentials -- only those which directly support your conclusion. Speaking of which, what *is* your conclusion? You cover a lot of ground, but never really clearly state where your journey has supposedly led you.
You seem to end up just saying, "the battle rages on and it may not matter who wins". If so, you've spent a great deal of time writing about nothing of consequence.
So as my first critique, I'd advise you to more clearly summarize your position at the end. Or if you don't have a position, at least state why a travelogue-with-no-destination was worth the reader's time.
In short, halfway through most readers will be asking themselves, "okay, where is this leading?" Make sure that by the end they aren't still asking the same question.
Next, a lot of it seems like unfocused armchair philosophical musings. That's a great way to while away some spare time and to explore the mental envelope, but it's also a great way to end up reinforcing one's own conceptual predispositions, regardless of whether it may bear any resemblance to reality. For excellent examples, consult any summary of ancient philosophizings about medicine, the nature of matter or the universe, etc. It may have been philosophically "reasonable" to conclude that the planets and stars rode on hard crystalline spheres which rotated about the Earth, but that didn't make it *so*.
The enormous success of science as a method for discovering truths about the universe is primarily due to one key concept: While it's all well and good to develop philosophical views about what may be or what may have happened or why things act as they do, it's all just mental masturbation unless you get around to doing *reality checks* on your ideas. It is no exaggeration to say that the whole practice of science and the scientific method is a formalization of how to do dependable reality checks.
There's a lot of philosophizing in your article, but precious little reality-checking. Your article would benefit immensely from some reality-checking (i.e., reference to real-world evidence or experiment) which bolsters your premises and your philosophical stopovers. Otherwise, you risk arriving at a worldview consisting of conceptually beautiful but false crystalline spheres, instead of the less elegant but more correct inverse-square law of gravitational force and its consequences on orbital motion.
No matter how clean and graceful and philosophicaly satisfying the intelligent design hypothesis might be, eventually it's going to have to deal in some fashion with the very messy state of the biological evidence (e.g., fossil whales with legs, chickens with suppressed genes for reptilian teeth, shared SINEs, etc.) which far better fits an evolutionary scenario than a creationist one.
One can philosophize for days or years on end, but the nagging question will always remain: What does the evidence actually indicate, and does it truly support your view or not? Sooner or later, it's reality-check time.
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