From albinism.org: "The word "albinism" refers to a group of inherited conditions...." "For nearly all types of albinism both parents must carry an albinism gene to have a child with albinism." Stop gainsaying without support.
Your wolf analogy is the direct opposite of natural selection. There's nothing random about it. But let's get to the core issue.
Your point about the stages of color change is well taken. And some traits do confer a higher survivability rate, but since the rate of change starts small and changes slowly (as you say), so does the survivability advantage of the change. So let's say it's a hundred stage process from say a green (normal) salamander to a bright yellow one. Each iteration improves it's chances of survivability, as you say. Lets say, with birth and death rates, that there are ten million of these salamanders around at any one time. We'll use our previous numbers, and head to a new generation. 95% of the new ones aren't going to mutate at all, so we're down to 50,000. 95% of mutations are meaningless, so only 250 (1 in 4000) get a mutation that does anything at all. But did it occur on your gene? The are 10,000 of them, so your group of 250 has a one in 10,000 chance of getting the "one hundredth closer to bright yellow" gene. Meaning each one has only a 1 in 40 chance of getting to step one. Dice have no memory, so the next generation doesn't help you. In the next generation, one salamander out of ten million still only has a 1 in 40 chance of of getting one one-hundredth of the way to bright yellow. Go a hundred thousand generations, and the next one still rolls the same odds.
But let's say you get your guy. His dad gets naturally selected, he gets the trait, and he's produced. He's 1/100th less green than his buddies, he has a 1/100th better chance for survival than his compatriots. His generation, however, faces the same long odds at the genetic level. There's only a 1 in 4000 chance that he'll get a mutation at all, etc etc. It's only when we talk about this guy surviving to give offspring that the improvement kicks in and natural selection gets to play a part again. It's exponentially, astronomically unlikely that we get to step one hundred. Genetic drift will help a little, but not at first. Genetic drift is somewhat logarithmic, and the impact of it on early genetic mutation approaches zero.
And I've drastically oversimplified the problem. You've got millions of salamanders over millions of generations. Fine. It's a huge number. I'm trying to show you that the problem is exponentially greater.
Albinos do not prove your contention. Albinism a recessive, inherited genetic defect, not a randomly generated mutation that will get selected for. Albinism does not occur spontaneously, and when it does it is not selected as a trait to pass to future generations.
Genetic change in fact happens very, very minutely. In humans (I don't have the numbers for slalmanders) the rate of mutation in the human genome is 4.2 per generation. And remember that the vast majority of genetic mutations have no physical effect at all, regardless of the species. So while genetic mutations do occur, those that manifest themselves as evolutionarily significant are (in proportion to the population) quite rare.
But let's return to the salamanders, and grant your posit. You say that the color change happens all at once, as a genetic accident. Fine. A salamander, as a result of a random genetic mutation, turns (slightly) yellow. He's the only one, though, because the one to his immediate left has a random genetic mutation that has turned him (slightly) red. The genetic mutations that you say happen 'all the time' are present in our population. Since they're accidental, they all have an equal chance of occurring. Our yellow salamander might mate, might not. If he does, he passes the trait. Now we have two yellow ones at the next generation, along with two red ones. Or maybe a two yelows, a red, and one with bigger eyes. In your world of genetic mutation happening all the time, how do any traits get selected for at all?
At the root, though, we still have an information theory problem, a numbers problem. Let's assume a salamander has 10,000 genes (humans have beteen 20k-40k, depending on who's answering), and only one needs the tiniest change to turn color, as you say. There's a 5% chance for any genetic change at all to occur in a given salamander in a given generation, and 95% of the changes, when they occur, are meaningless. Let's say 90% of all the salamanders of a given generation live to reproduce. This is all speculation, but you begin to see the problem. Given this scenario, how many salamanders must we have, for how many generations, to arrive at a bright yellow subspecies? And we haven't even thrown in alternate mutations that are competing for the same genetic real estate.
And yet, after all this, we still find yellow salamanders, and in a relatively small population. I say, again, that the populations are too small, and the generations are too infrequent, to support natural selection as described.
Genetic variation does occur. Not all zebra stripes or leopard spots are the same. These are not the 'mutations' that you speak of. There still just aren't enough iterations for natural selection, as described, to account for what actually takes place.
Cool article, but we're talking about slightly different aspects of the same thing. I'm asking how the flashlight works, and you're telling me 'You push the button and light comes out.' My question concerns the batteries.
Once again, I agree that evolution occurs. Genetic information mutates. Natural selection, however, does not explain how we proceed from genetic variation in one generation to a new genetically based trait in some future generation.
Take the salamanders. You're using it to support your argument by saying that the new sub-species is (in effect) the genetic trait, while we can trace the divergent species back to the original and see all the intermediate steps that led up to it. I would argue that the intermediate steps themselves are too complex to be explained through natural selection.
The article talks about how one group of salamanders developed 'cryptic coloration' while the other developed bright colors. Fine. How complex was the change in the genetic code necessary to develop either of those characteristics? Over how many generations did these changes occur? And by extrapolation, what was the total population (over time) necessary to achieve that change?
This is the crux of my argument. The entire problem of the salamanders, and every other species or trait we could discuss, is based on information theory. All we're ever talking about is randomly and incrementally changing one string of data (ACTGTGACCAGACTCA) to another (ACTGTGCAACGACTCA) within a defined set. We know (or can find out) how long the genetic code for a salamander is, what sequence needs to be changed (Where the color information lies), and what it needs to be changed into (to get a trait such as bright yellow). We know that a portion of the evolutionary process is random (since you can't select for genetic code that doesn't do anything, and changing colors doesn't happen all at once), so we can sit in the lab and simulate the population needed to arrive at the sort of things we see in nature, like bright yellow salamanders.
We can then go out and count salamanders. We can date the original salamander fossils. We can study their territorial and migratory habits. We can then make a guess (but honestly, a pretty good one) about how many generations of salamanders, and how many total salamanders, there have been.
I bet the first number, the one that tests natural selection, is frikkin' huge. I bet it's amazingly, startlingly smaller than the second number, the one that examines the actual process without describing it.
This sort of experiment has been done before, as you've read above. Natural selection theory is based on steps that do not result in the observable world.
I'm not asking it to explain evolution. I've already granted that evolution occurs. We're talking about the mechanism by which evolution takes place. And it doesn't have to explain where the variation takes place, or where it originates. And it's not the basis for evolution, it's a step within it.
The origin of evolution seems to be genetic mutation, or more simply an alteration of the genetic code that makes an organism what it is. The mutation can be the result of the environment (radiation, organic chlorine, certain viruses, whatever) or the process (errors in the DNA duplication process).
These mutations occur, and the vast majority are either corrected back to the original code, or remain but have no impact. It's the small remainder that we're concerned with. What I'm saying is that natural selection, the reinforcement of random, advantageous genetic traits through reproduction, is not a theory that actually leads us from whatever-was-here-before to whatever-is-here-now.
You've got a false assumption here. While genetic mutation does take place when even a single cell divides, that code (and the beginnings of the trait that it might lead to) won't pass the 'fitness test' until the organism itself reporduces. If the organism is itself the single cell, then fine. But just because a single bone cell in my body is suddenly 0.00001% less succeptible to cancer at some time in my life is not enough to pass the trait on to all the bone cells of my children. It's the organism's reproduction that matters. Your numbers are more demonstratably false than the GA model.
As to the aphids, it seems to me that those species that use such spamming methods to reproduce do it as a species defense mechanism. A species that lays a million eggs at a time will assume that 990,000 will die prior to reproduction. So the evolutionarily-effective numbers are probably, again, much smaller than you assert. Also, assuming that the aphids do reproduce as you say, wouldn't they display a proportionally large variation from their genetic code of just a few decades ago? And don't tell me they've reach evolutionary Nirvana. No honest theory of natural selection talks about it stopping. It is more reasonable to assume that their slower evolutionary pace is evidence of a lower effective reproduction rate.
Which leads us back to the original post, that the population set just isn't big enough.
Scroll back up and read some of the arguments about intermediacy and population sets, and you'll see the holes in your statements.
We agree that DNA does not reproduce with complete fidelity. Mutations, genarations, successful traits get passed, I agree with it all. The problem rises when we agree that any physical trait that helps an organism reproduce (or survive, or attract a mate, or whatever) must be the result of a significant genetic transformation that cannot occur within just a few generations. Or even a few hundred generations.
The likelihood of successfully completeing a desired DNA sequence disappears exponentially. Each incremental step has no bearing on reproduction or survivability, and thus has (at the very, very best) a 50/50 chance of being passed on. This chance gets cut in half on the next generation. And so on. And we haven't even taken into account competing traits, or traits that must be selected for as a group, or the fact the vast majority of mutations have no evolutionary impact, or a dozen other complications.
I submit (and others have argued better than I ) that the population set for any species and genetic trait you care to mention is both too small in size and too short in duration. For your statement to be true, a species would have to recognize the intermediate steps toward a favorable trait, and pass that along as if it were the trait itself. That's a risky proposition.
And those are just the traits that improve survivability. Natural selection must also account for the traits that are purely social. Google the Frigate Bird. Look at that crazy thing (It's called the gular sac, apparently). It has nothing to do with the physical survival of the species. It's just used to attract mates.
We can assume that the sac evolved, that it wasn't there to begin with. So how did the incremental steps, the steps that don't result in the beginnings of a red sac, get reinforced. And most importantly, how did the genetic trait in the female, the trait that causes the female to find red sacs attractive, get reinforced before the red sacs were even there?
Did the red sac come first? If so, why were all those intermediate steps reinforced without the female's participation? Your random natural selection cannot result in this.
You misidentified the trivially simple in your last line. DNA mutation is a simple mechanism. Natural selection is an extremely complicated process.
How about an alternate question. Can I propose that natural selection (as a subset of evolutionary theory) has some pretty monstrous holes in it, without being labelled an anti-intellectual zealot?
I'm serious. I challenge someone to give a succinct definition of natural selection that can stand up to intellectually honest scrutiny. I think I can prove you wrong, and I won't once mention God.
Evolution certainly occurs. The evidence is irrefutable. It is my position that natural selection is not up to the task of explaining how it occurs.
We did exactly the same thing at a small-town local museum. Here's our recipe for each station:
1.) Set of powered speakers. We're using the Edirol MA-10's because everything is self contained. There's no AC brick, and they come with all the necessary cables. Very good audio quality.
2.) CD Drive in an external case. The simpler the case, the better. It's only job is to supply power to the drive. If you can get one that has its own power socket, so much the better. You can just plug the speakers into it, and plug the drive into the wall. The important part is, the drive MUST HAVE A PLAY BUTTON, not just an eject button. Only drives with a play button will work.
3.) CD with audio. Record your message, burn it as an audio CD. One track only.
4.) Solder, wire, and a switch. Take apart the front plastic on the CD drive, and see where the play button is soldered in. A little experimenting will show you where to solder the wire in. The switch should be of the momentary contact sort, like a doorbell switch, not the push-on, push-off kind.
That's it. Plug the audio-jack from the CD drive into the speakers, insert the CD, hit the switch, and adjust your audio using both the volume at the drive and at the speakers. We liked this solution because it was cheap, it was low maintenance, and it was distribution-tolerant. The only system-wide failure could be the power.
People here are desperately trying to force the movie to work by injecting their own motivations and explanations, by making their own constructions in which the characters' actions and dialog make sense. This is the sign of bad design. If they'd kept the dialog to a Terminator level, I'd honestly have enjoyed it more. Yes, it would have been a more shallow trilogy, but shallow is better than broken. I've read Descartes, I've read 'The Machine in the Garden', I know my way around Zen Koans, and I'm telling you there ain't nothing here. The major points:
1. They violated the initial premise of the movie. Morpheus told us that the Matrix was a prison meant to keep humans occupied while machines used their bioelectric energy to power themselves. Fine. It's your movie. But in the end, no humans got saved. There's a truce, and therefore the machines get to keep their batteries. Sure, we could discuss the dilemmas inherent in jacking folks out of a happy illusion and into a tragic reality (sort of an anti-Plato's cave), but there's the problem: This would have been a MUCH more satisfying discussion.
2. Neo gets to take his superpowers with him. He's the One because he can violate the rules imposed by the Matrix. Fine. It's your movie. But in the end, he gets to control the machines from -reality-. Problem is, we've been led to believe that the Matrix is just a giant UPS system connected to a much larger complex. The Architect is not the thing Neo speaks to at the end. And yet, he still gets to blow Real machines up and see fictional Matrix characters when looking at real poeple with his inner sight (Anyone read Dune Messiah?) This means that there is a God, he's interested in humans, has taken a fancy to Neo, and wants a big machine to understand what's going on. There's no other explanation, unless I was getting popcorn when Trinity found an 802.11x antenna in Neo's ear.
3. The Architect has problems he shouldn't have. If I were building a Matrix and I didn't want people to reject it, I'd fake a new reality just like I faked the old one. The idea that Zion is just another part of the Matrix has been rejected in other threads, but too hastily IMHO. In other movies it would be a copout, but here it would be central to the Matrix premise. What better way to imprison minds than an illusionary escape? What better way to explain Smith's presence in Bane? What better way to explain Neo's powers?
4. Smith, Smith, Smith. We are led to believe that Smith has (or shortly will) overwritten himself onto every human in the Matrix. Jeez, the problems with that one. Are the original personalities lost? If so, why didn't the Architect do something like that himself a long time ago, and solve his problems that way? And just what exactly how did Neo defeat Smith? 'He let Smith win' isn't Eastern philosophy, or Karma, or Christ. The architect tells us that the Matrix has been done before, but this Smith thing is new to this cycle. Every other time, the Matrix has either ended with the One's cooperation or without. Zion is destroyed. This time, Smith is here, and this time Neo is fighting in part on 01's behalf. So this the fight itself is entirely new, no matter how it ends. There's no Karmic wheel to get off of, or if there is it's way, way before the Smith/Neo fight. So with Smith gone, where are the Matrix humans? If they're dead, what did the 01 Nation gain by letting Neo fight?
So, they could have gone Schwartzennegar simple, but didn't. They could have gone for good, meaty morale dilemmas, but didn't. They went for tea-party philosophy, and succeeded.
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Your wolf analogy is the direct opposite of natural selection. There's nothing random about it. But let's get to the core issue.
Your point about the stages of color change is well taken. And some traits do confer a higher survivability rate, but since the rate of change starts small and changes slowly (as you say), so does the survivability advantage of the change. So let's say it's a hundred stage process from say a green (normal) salamander to a bright yellow one. Each iteration improves it's chances of survivability, as you say. Lets say, with birth and death rates, that there are ten million of these salamanders around at any one time. We'll use our previous numbers, and head to a new generation. 95% of the new ones aren't going to mutate at all, so we're down to 50,000. 95% of mutations are meaningless, so only 250 (1 in 4000) get a mutation that does anything at all. But did it occur on your gene? The are 10,000 of them, so your group of 250 has a one in 10,000 chance of getting the "one hundredth closer to bright yellow" gene. Meaning each one has only a 1 in 40 chance of getting to step one. Dice have no memory, so the next generation doesn't help you. In the next generation, one salamander out of ten million still only has a 1 in 40 chance of of getting one one-hundredth of the way to bright yellow. Go a hundred thousand generations, and the next one still rolls the same odds.
But let's say you get your guy. His dad gets naturally selected, he gets the trait, and he's produced. He's 1/100th less green than his buddies, he has a 1/100th better chance for survival than his compatriots. His generation, however, faces the same long odds at the genetic level. There's only a 1 in 4000 chance that he'll get a mutation at all, etc etc. It's only when we talk about this guy surviving to give offspring that the improvement kicks in and natural selection gets to play a part again. It's exponentially, astronomically unlikely that we get to step one hundred. Genetic drift will help a little, but not at first. Genetic drift is somewhat logarithmic, and the impact of it on early genetic mutation approaches zero.
And I've drastically oversimplified the problem. You've got millions of salamanders over millions of generations. Fine. It's a huge number. I'm trying to show you that the problem is exponentially greater.
Genetic change in fact happens very, very minutely. In humans (I don't have the numbers for slalmanders) the rate of mutation in the human genome is 4.2 per generation. And remember that the vast majority of genetic mutations have no physical effect at all, regardless of the species. So while genetic mutations do occur, those that manifest themselves as evolutionarily significant are (in proportion to the population) quite rare.
But let's return to the salamanders, and grant your posit. You say that the color change happens all at once, as a genetic accident. Fine. A salamander, as a result of a random genetic mutation, turns (slightly) yellow. He's the only one, though, because the one to his immediate left has a random genetic mutation that has turned him (slightly) red. The genetic mutations that you say happen 'all the time' are present in our population. Since they're accidental, they all have an equal chance of occurring. Our yellow salamander might mate, might not. If he does, he passes the trait. Now we have two yellow ones at the next generation, along with two red ones. Or maybe a two yelows, a red, and one with bigger eyes. In your world of genetic mutation happening all the time, how do any traits get selected for at all?
At the root, though, we still have an information theory problem, a numbers problem. Let's assume a salamander has 10,000 genes (humans have beteen 20k-40k, depending on who's answering), and only one needs the tiniest change to turn color, as you say. There's a 5% chance for any genetic change at all to occur in a given salamander in a given generation, and 95% of the changes, when they occur, are meaningless. Let's say 90% of all the salamanders of a given generation live to reproduce. This is all speculation, but you begin to see the problem. Given this scenario, how many salamanders must we have, for how many generations, to arrive at a bright yellow subspecies? And we haven't even thrown in alternate mutations that are competing for the same genetic real estate.
And yet, after all this, we still find yellow salamanders, and in a relatively small population. I say, again, that the populations are too small, and the generations are too infrequent, to support natural selection as described.
Genetic variation does occur. Not all zebra stripes or leopard spots are the same. These are not the 'mutations' that you speak of. There still just aren't enough iterations for natural selection, as described, to account for what actually takes place.
Once again, I agree that evolution occurs. Genetic information mutates. Natural selection, however, does not explain how we proceed from genetic variation in one generation to a new genetically based trait in some future generation.
Take the salamanders. You're using it to support your argument by saying that the new sub-species is (in effect) the genetic trait, while we can trace the divergent species back to the original and see all the intermediate steps that led up to it. I would argue that the intermediate steps themselves are too complex to be explained through natural selection.
The article talks about how one group of salamanders developed 'cryptic coloration' while the other developed bright colors. Fine. How complex was the change in the genetic code necessary to develop either of those characteristics? Over how many generations did these changes occur? And by extrapolation, what was the total population (over time) necessary to achieve that change?
This is the crux of my argument. The entire problem of the salamanders, and every other species or trait we could discuss, is based on information theory. All we're ever talking about is randomly and incrementally changing one string of data (ACTGTGACCAGACTCA) to another (ACTGTGCAACGACTCA) within a defined set. We know (or can find out) how long the genetic code for a salamander is, what sequence needs to be changed (Where the color information lies), and what it needs to be changed into (to get a trait such as bright yellow). We know that a portion of the evolutionary process is random (since you can't select for genetic code that doesn't do anything, and changing colors doesn't happen all at once), so we can sit in the lab and simulate the population needed to arrive at the sort of things we see in nature, like bright yellow salamanders.
We can then go out and count salamanders. We can date the original salamander fossils. We can study their territorial and migratory habits. We can then make a guess (but honestly, a pretty good one) about how many generations of salamanders, and how many total salamanders, there have been.
I bet the first number, the one that tests natural selection, is frikkin' huge. I bet it's amazingly, startlingly smaller than the second number, the one that examines the actual process without describing it.
This sort of experiment has been done before, as you've read above. Natural selection theory is based on steps that do not result in the observable world.
The origin of evolution seems to be genetic mutation, or more simply an alteration of the genetic code that makes an organism what it is. The mutation can be the result of the environment (radiation, organic chlorine, certain viruses, whatever) or the process (errors in the DNA duplication process).
These mutations occur, and the vast majority are either corrected back to the original code, or remain but have no impact. It's the small remainder that we're concerned with. What I'm saying is that natural selection, the reinforcement of random, advantageous genetic traits through reproduction, is not a theory that actually leads us from whatever-was-here-before to whatever-is-here-now.
As to the aphids, it seems to me that those species that use such spamming methods to reproduce do it as a species defense mechanism. A species that lays a million eggs at a time will assume that 990,000 will die prior to reproduction. So the evolutionarily-effective numbers are probably, again, much smaller than you assert. Also, assuming that the aphids do reproduce as you say, wouldn't they display a proportionally large variation from their genetic code of just a few decades ago? And don't tell me they've reach evolutionary Nirvana. No honest theory of natural selection talks about it stopping. It is more reasonable to assume that their slower evolutionary pace is evidence of a lower effective reproduction rate.
Which leads us back to the original post, that the population set just isn't big enough.
We agree that DNA does not reproduce with complete fidelity. Mutations, genarations, successful traits get passed, I agree with it all. The problem rises when we agree that any physical trait that helps an organism reproduce (or survive, or attract a mate, or whatever) must be the result of a significant genetic transformation that cannot occur within just a few generations. Or even a few hundred generations.
The likelihood of successfully completeing a desired DNA sequence disappears exponentially. Each incremental step has no bearing on reproduction or survivability, and thus has (at the very, very best) a 50/50 chance of being passed on. This chance gets cut in half on the next generation. And so on. And we haven't even taken into account competing traits, or traits that must be selected for as a group, or the fact the vast majority of mutations have no evolutionary impact, or a dozen other complications.
I submit (and others have argued better than I ) that the population set for any species and genetic trait you care to mention is both too small in size and too short in duration. For your statement to be true, a species would have to recognize the intermediate steps toward a favorable trait, and pass that along as if it were the trait itself. That's a risky proposition.
And those are just the traits that improve survivability. Natural selection must also account for the traits that are purely social. Google the Frigate Bird. Look at that crazy thing (It's called the gular sac, apparently). It has nothing to do with the physical survival of the species. It's just used to attract mates.
We can assume that the sac evolved, that it wasn't there to begin with. So how did the incremental steps, the steps that don't result in the beginnings of a red sac, get reinforced. And most importantly, how did the genetic trait in the female, the trait that causes the female to find red sacs attractive, get reinforced before the red sacs were even there?
Did the red sac come first? If so, why were all those intermediate steps reinforced without the female's participation? Your random natural selection cannot result in this.
You misidentified the trivially simple in your last line. DNA mutation is a simple mechanism. Natural selection is an extremely complicated process.
I'm serious. I challenge someone to give a succinct definition of natural selection that can stand up to intellectually honest scrutiny. I think I can prove you wrong, and I won't once mention God.
Evolution certainly occurs. The evidence is irrefutable. It is my position that natural selection is not up to the task of explaining how it occurs.
1.) Set of powered speakers. We're using the Edirol MA-10's because everything is self contained. There's no AC brick, and they come with all the necessary cables. Very good audio quality.
2.) CD Drive in an external case. The simpler the case, the better. It's only job is to supply power to the drive. If you can get one that has its own power socket, so much the better. You can just plug the speakers into it, and plug the drive into the wall. The important part is, the drive MUST HAVE A PLAY BUTTON, not just an eject button. Only drives with a play button will work.
3.) CD with audio. Record your message, burn it as an audio CD. One track only.
4.) Solder, wire, and a switch. Take apart the front plastic on the CD drive, and see where the play button is soldered in. A little experimenting will show you where to solder the wire in. The switch should be of the momentary contact sort, like a doorbell switch, not the push-on, push-off kind.
That's it. Plug the audio-jack from the CD drive into the speakers, insert the CD, hit the switch, and adjust your audio using both the volume at the drive and at the speakers. We liked this solution because it was cheap, it was low maintenance, and it was distribution-tolerant. The only system-wide failure could be the power.
People here are desperately trying to force the movie to work by injecting their own motivations and explanations, by making their own constructions in which the characters' actions and dialog make sense. This is the sign of bad design. If they'd kept the dialog to a Terminator level, I'd honestly have enjoyed it more. Yes, it would have been a more shallow trilogy, but shallow is better than broken. I've read Descartes, I've read 'The Machine in the Garden', I know my way around Zen Koans, and I'm telling you there ain't nothing here. The major points:
1. They violated the initial premise of the movie. Morpheus told us that the Matrix was a prison meant to keep humans occupied while machines used their bioelectric energy to power themselves. Fine. It's your movie. But in the end, no humans got saved. There's a truce, and therefore the machines get to keep their batteries. Sure, we could discuss the dilemmas inherent in jacking folks out of a happy illusion and into a tragic reality (sort of an anti-Plato's cave), but there's the problem: This would have been a MUCH more satisfying discussion.
2. Neo gets to take his superpowers with him. He's the One because he can violate the rules imposed by the Matrix. Fine. It's your movie. But in the end, he gets to control the machines from -reality-. Problem is, we've been led to believe that the Matrix is just a giant UPS system connected to a much larger complex. The Architect is not the thing Neo speaks to at the end. And yet, he still gets to blow Real machines up and see fictional Matrix characters when looking at real poeple with his inner sight (Anyone read Dune Messiah?) This means that there is a God, he's interested in humans, has taken a fancy to Neo, and wants a big machine to understand what's going on. There's no other explanation, unless I was getting popcorn when Trinity found an 802.11x antenna in Neo's ear.
3. The Architect has problems he shouldn't have. If I were building a Matrix and I didn't want people to reject it, I'd fake a new reality just like I faked the old one. The idea that Zion is just another part of the Matrix has been rejected in other threads, but too hastily IMHO. In other movies it would be a copout, but here it would be central to the Matrix premise. What better way to imprison minds than an illusionary escape? What better way to explain Smith's presence in Bane? What better way to explain Neo's powers?
4. Smith, Smith, Smith. We are led to believe that Smith has (or shortly will) overwritten himself onto every human in the Matrix. Jeez, the problems with that one. Are the original personalities lost? If so, why didn't the Architect do something like that himself a long time ago, and solve his problems that way? And just what exactly how did Neo defeat Smith? 'He let Smith win' isn't Eastern philosophy, or Karma, or Christ. The architect tells us that the Matrix has been done before, but this Smith thing is new to this cycle. Every other time, the Matrix has either ended with the One's cooperation or without. Zion is destroyed. This time, Smith is here, and this time Neo is fighting in part on 01's behalf. So this the fight itself is entirely new, no matter how it ends. There's no Karmic wheel to get off of, or if there is it's way, way before the Smith/Neo fight. So with Smith gone, where are the Matrix humans? If they're dead, what did the 01 Nation gain by letting Neo fight?
So, they could have gone Schwartzennegar simple, but didn't. They could have gone for good, meaty morale dilemmas, but didn't. They went for tea-party philosophy, and succeeded.