Mutations Made Easy

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We can watch gametogenesis and meiosis in vivo under a microscope, and we have direct lab and field observations of the action of random mutation and natural selection. No inference required. “Evolutionists” don’t need to be adamant about anything - their understanding of these two elements is based on direct observation of fact; not inference.

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No one is contesting that mutations occur, especially during meiosis and mitosis. I'm not following how this presents a strong argument on your side in how it propagates a macroevolutionary progress.

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Morowitz is a respected origin-of-life researcher.

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I wasn't making inferring that Morowitz and I share commonality. He isn't a creationist. But I see him as somebody that simply reports the facts without an agenda -something quite rare in the scientific community, IMO. I know who he is and what he does. One of his peeves is for people to assert that life originated at random. For starters, my reason for mentioning him has to do with two premises.
1. Impossibility of abiogenesis (which he dispells)
2. Thermodynamics in living systems (which he agrees with)I was flamed for mentioning abiogenesis as being OT. And I was flamed for asserting that thermodynamic principles don't only apply to closed systems.The author of several books, Morowitz has written extensively on the thermodynamics of living systems, as well as on popular science topics. In his current research, he is investigating the interface of biology and information sciences and continues the exploration of the origins of life.Since neither of these two things are relevant to our current topic, I'll let this one alone.

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you are gravely mistaken on both what constitutes a mutation and how the cellular machinery acts to minimize and/or repair mutation. Perhaps a brief primer is in order.

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All that I mentioned was that most mutations are benign (which they are), or that they cause serious adverse effects (which they do). But the clincher is, a beneficial mutation is so rare, and so sparingly understood, that the liklihood of it propagating a mcaroevolutionary method is extremely unlikely even in one population, let alone, all of them. I then went on to say that all mutations are deemed 'harmful' to the body and that the body treats all mutations as detrimental. DNA repair exists for a reason. I'm not sure what you are even arguing against.

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Obviously, free radicals are highly volatile because they are able to bind with other atoms fairly easily.

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What don't you understand about my reasoning for mentioning it? There are several methods the body uses to repair damaged cells, and free radicals disrupt normal, healthy cellular activity. We have nucleotid repair, base pair repair, mismatched repair, all of which excises mutated gametes.

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I think you may possibly be confusing prions with mutations.

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No, I'm not talking about prions, because prions come from the outside in, instead of the inner-components of the cell mutating. Prions deal with how diseases from an outside source effect the body, like Mad Cow disease. I'm talking about free radicals and how the body combats it.

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The language analogy can be a very useful explanatory tool

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I never meant for it to be more than an analogy.

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given the fact that multiple protein configurations can perform the exact same function, arriving at a functional protein gets a lot easier.

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Assuming that a series of recombinations and deletions within the genome or even its base pairs could increase in complexity, is like saying if we copied the first page of the Dictionary, we'd somehow arrive at a complete Dictionary and in sequential order. Life doesn't organize itself in this way.

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I do disagree that “a very large percentage is devastatingly harmful.” You seem to be contradicting your previous statements concerning the neutrality of most mutations.

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Most mutations are silent. A large percentage of the total sum is detrimental. There is no contradiction. And we shouldn't forget that the only reason some mutations aren't harmful is because the of cell repair.

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I’m not sure I’m following you. Why would a beneficial mutation not be advantageous?

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Effects of Redundancy on Mutation Rates

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As I just explained above, the trait is maintained in the population. The disease itself is a byproduct of this polymorphism. You are confusing genetic disease with parasitical/bacterial/viral disease, I think.

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That's interesting because I thought that's what you were doing when you introduced prions into the equation, instead of taking what I said about Free Radicals for face value.

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The example you cited, sickle cell anemia, doesn’t cause changes in immunity to malaria. Possession of the trait in a heterozygous condition does.

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If two people with the Sickle Cell gene procreate, then the progeny will be affected by the full blown disease. Therefore, the immunity will be bred out of existence when more, and more people populate. Where's the ambiguity in that?

You stated, as if I was differing in my statements:

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Good thing you weren't trying to compare the two of you. However, let me refresh your memory of what you stated:

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I said:

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One of his peeves is for people to assert that life originated at random.

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That's just to arrive at any lifeforms at all.

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I'm not seeing the apparent contradiction. I even went on to say that its in referrence to abiogenesis and that I was specifically barred from mentioning it because the Admins said I was OT.

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Unfortunately for your argument on Chiro's thread, both of these two points completely refute your arguments using them on that thread.

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How does it refute my argument when everyone in here mentions that entropy only exists in closed systems? Is the principle of entropy existent in open systems as well, or not?

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The fact is most mutations are silent. They are mostly benign deletions from copying errors in the genes (FALSE: There are multiple types of mutation, from frame shift to substitution).

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The fact is, most mutations are silent. That's true. I never said there weren't multiple types of mutations or that there weren't multiple causes for it. I didn't even go into that. How you arrived at that conclusion is anyone's guess. I didn't even infer it. I did, however, reference three types of repair on the cellular level. From this I'm assuming that you think most mutations are either harmful or beneficial. If so, is that your official stance?

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Its important to note, however, that the only reason most mutations are benign is because of specific cells that serve to repair mutations.(FALSE: Enzymes are the repair mechanisms. They are found within the cell. They are not cells.) In fact, it is their only function.

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Okay, my apologies. You're right. Its specific enzymes which is the vehicle behind the cell in its repair mechanism. I can split hairs down to nanoparticles if you need me to.

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The "false" statements are what I addressed with my "mini primer". Do you understand the 2 points I raised? If not, I'll be happy to explain them further.

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I'm actually lost as to what we are even arguing about.

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In the first place, "free radicals" aren't mutations.

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No, but they [free radicals] are the cause of some mutation, which left unchecked, can lead to more mutations. Nonetheless, I don't see the problem with my statement. Its almost as if you're stating that free radicals have nothing to do with mutations. I guess I'm asking you: What are you even arguing about? Free radicals can cause mutation. True or false?

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You're again contradicting yourself in the same way. Either mutations are mostly neutral, or they're mostly detrimental.

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I said the majority of mutations are benign. Out of the total sum of mutations, a large (not majority) are detrimental. I didn't give two majorities. If, say, 68% of mutations are benign, and 31.5% are detrimental, and .5% are beneficial, then once again, there is no contradiction. 68% would be the majority figure. 31.5% would be a large figure of the overall summation of 100%, but it isn't the majority. And for the record, no, that isn't an official figure. I'm just using it to get my point across.

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This is a response to my question? For future reference, I never debate websites.

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Okay, so on that note I'm assuming that I'm not required to respond to your websites in order to clarify your answers. Is that a good assumption?

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Plaisted is wrong. His spurious equations and hypothetical population show absolutely nothing. He neglects the action of purifying selection on mutation, neglects the fact not all of his "mutant" offspring will reproduce thus reducing the population's overall mutational load, and he fails to take into consideration gene flow from other populations. In other words, he plays mathematical games to buffalo the incredulous. Sort of like his partner in crime Dembski.

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His thesis was very clear and eloquent. I suspect that you simply disagree with him on grounds that his cohort is William Dembski or that you don't like the implications of his thesis. In either case, your incredulity is suspect.

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A lot of other people have already picked up on this. Saves me from trying to draw a Venn diagram on a message board. Any part of their responses you didn't understand?

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If anyone likes one in four odds, that's on them. Those are horrible odds. Its miraculous that anyone would scoff at such a figure. If I presented a 4 prospective wives to you, but told you that one of them has AIDS, would you choose wisely or opt not to choose at all?"When both parents have the genetic defect that causes sickle cell disease, there's a 25% chance that a child will be born with the disease. Children who inherit the defective gene from only one parent run a 50% chance of carrying the sickle cell trait. People who just carry the sickle cell trait usually don't get the disease, but they can pass the defective gene on to their children."Not Found | Medical College of WisconsinSo, if more and more carriers of the trait procreate, the frequency increases and the odds of developing said Anemia will become more likely. In any case, my original point has been completely undermined. Many evolutionists assert that Sickle Cell Anemia developed in the malaria stricken continent of Africa to combat malaria. So, why are we detracting from the initial argument?

This brings me back to the two reasons why I mentioned Morowitz. He says it does and apparently a large numer of reputable scientists agree. Its our definition of 'entropy,' that is causing this ambiguity. There is more than one kind of entropy. Classical entropy deals with 2LoT. That's unquestionable. This is one objections to the Big Bang that I have. But I won't go into that because its OT. But there are also theorems on logical entropy. To clarify what I'm referring to, let me pull up the Dictionary version. The definitions are as follows:1. Symbol S For a closed thermodynamic system, a quantitative measure of the amount of thermal energy not available to do work.
2. A measure of the disorder or randomness in a closed system.
3. A measure of the loss of information in a transmitted message.
4. The tendency for all matter and energy in the universe to evolve toward a state of inert uniformity.
5. Inevitable and steady deterioration of a system or society1 and 2 deal with classical entropy as they relate to 2LoT. 3-5 deal with something closely related with 2LoT, but recognizes that all systems, whether open or closed, will always tend toward disorder w/o the intervention of newly introduced energy. Hot things become cold things with no intervention, but cold things never become hot for no apparent reason. Living things become dead things, always, but dead things never become living things. That is simplistic as I could put it. As it relates to biology, the constant transferring of genes would not lead to an upgrade of information, but a steady, gradual decline. I believe we are becoming less and less pure, genetically speaking, which is clearly the opposite. Does natural selection exist? Yes. And it does help in slowing this inevitable process down. But nonetheless, ultimate corruption is an inevitable outcome. Do you understand now my mentioning for entropy? What's wrong with that? Copying errors occur that lead to the steady degradation of information. Seriously, what's unfactual about that? I gave you three referrences to what mechanisms correct mutations. It happens all the time in our body, unbeknownst to us. And if these enzymes didn't do their job, we'd succomb to cancer at a much more prevelant rate than we do.DNA repair - WikipediaThis site even provides on information of nucleotide, base pair, and mismatch repair. I'm not suggesting that mutations are always fixed. That's so blatantly obvious that's not even worth mentioning, being that cancer and Down Syndrome. How could you think that I was saying anything counter to that? Severely incorrect statements? Lets not get carried away. I've already conceded that I should have said enzymes. The point was clear, however, that these enzymes aid in the repair of certain mutations. Without certain enzymes, free radicals can affect cellular activity. They can corrupt the integrity of any cell by carcinogenesis if left to proliferate. They can and do accumulate when left unchecked. You keep breaking things down to subatomc particles when it isn't necessary to do so. We might just as well speak about quarks if we were going to reduce things into nanoparticles. Well, then I should thank you on clarifying the ettiquate of EvC. Thank you. I will make a mental note of that.
1. I'm not sure what you mean by 'purifying' selection on mutation. Can you elaborate?
2. Not all organisms live until the chance for reproduction, this is true. However, he obviously is speaking about the ones that do survive in a population. Therefore, there is no need to distinguish the ones that do not survive because they bear no relevance to his equation.
3. What do you mean by 'gene flow from other populations'? By population, do you mean a specific specie or a specific classification? IOW, lets take Darwins classic Finches as an example. Do you mean how one specie of Finches can effect another? Or do you mean how one type of bird can corrupt or benefit another? I disagree. The majority of affected people come from African decent. Lets say we have 100 carriers, 50 male, 50 female. Then we have 100 with full-blown SCA, 50 male, 50 female. All it takes is for these people to get it is to procreate in order for it to proliferate in their progeny. Heterozygous becomes homozygous in the offspring and that's when people start dying. I'm not saying its a pandemic, I'm just saying that if people from African, Hispanic, and certain Meditteranean decent continue to procreate in that specific group, it has a much greater chance of at least bcoming a significant problem.

I'm aware that Morowitz is an RNA-frist proponent, which admittedly makes the only quasi-reasonbale approach to abiogenesis. Morowitz postulates that RNA predates DNA and protein and that RNA acts as the catalyst for self-replication. But even this has the chicken-egg problem attached to it. In other words, which came first, the chicken or the egg? How would ever really know? But this is detracting from my premise. My sole purpose for mentioning Morowitz is that he provides a basis for the 2nd law to exist in open systems and that he provides an astronomical figure for the commencement of abiogenesis - both of which has been argued against me since the beginning of the thread by multiple people. Whatever other conclusions have arose in your mind are inconsequential. I don't think we can say that with any measure of truth. The earth is using up energy provided by the sun which follows the 1st law that energy isn't created or destroyed, but rather transmitted. But the suns energy is becoming less available with time. The influx of energy into an open system would not decrease entropy. Actually, the added heat energy would increase the rate at which things deteriorate. The classic pro-evolution stance on it is that it takes energy to work, which we gather from food, which directly comes from photosynthesis from the suns energry. But this does nothing to explain how we should increase in complexity and autonomy and moreover, how the sun should be used to maintain it. Evolutionary theory tacitly asserts that life increases in complexity. Therefore, that defies the second law."The contribution of thermodynamics to theoretical biology is absolute negation of automatic commencement or automatic maitenance of life." -Lord Kelvin Okay, so your objection lies with my not mentioning transpositions and insertions aiding in mutation? Okay. Not a problem.

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Without certain enzymes, free radicals can affect cellular activity. They can corrupt the integrity of any cell by carcinogenesis if left to proliferate. They can and do accumulate when left unchecked. You keep breaking things down to subatomc particles when it isn't necessary to do so. We might just as well speak about quarks if we were going to reduce things into nanoparticles.

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I didn't acknowledge it??? That was my only point. Free Radicals effect cellular activity and aid in the causation and proliferation of many mutations. That's all I've said, that's all I've ever meant; any guesstimate on your part beyond that is of your own devise. Plaisted gives several referrences to overall population. I'm not sure what you mean. I thought it was very clear and concise:"Suppose a population has an average of n harmful mutations per individual. Suppose N is the total number of base pairs. Assume N >> n (N is much larger than n). Then the probability of a harmful mutation at a particular base pair will be n/N and the chance of no harmful mutation will be 1 - n/N, which is nearly 1. Now, the number of mutations per individual will be a binomial distribution. Let p be n/N and q be 1 - n/N; then the mean is Np which is n, and the standard deviation is sqrt(Npq) which is about sqrt(n).""Suppose that an individual survives if at least 439 copies of this gene are uncorrupted, but if all 440 copies have a harmful mutation, the individual will die. Then about 1/40 of the population will die, and each such individual has 40 extra harmful mutations. In this way, the death of one individual removes an excess of 40 harmful mutations from the population. This means that the population can endure one mutation per generation at equilibrium with only 1/40 of the zygotes dying due to harmful mutations. So we obtain a considerable improvement in this way. In fact, it may be that organisms in harsh environments make use of this mechanism to improve their ability to endure harmful mutations.""We now consider whether beneficial mutations can counteract the decline of a population due to high rates of harmful mutation. In the first place, it is not reasonable to expect a beneficial mutation to cancel out the loss of function of more than one gene (and even this is unlikely). Suppose a beneficial mutation occurs in about 10^-9 of the gametes. Suppose the fraction of the population having the gene knocked out is 10^-6. Then the selective advantage of this mutation is at most 10^-6, so its equilibrium frequency will be 10^-3. This means that only one in a thousand individuals with this gene knocked out will be helped by the beneficial mutation. Thus its effect is essentially zero. In fact, the situation is much worse. The selective advantage is so small that it will take nearly 10^-6 generations for the frequency of this beneficial mutation to double, to 2*10^-9. By this time the population will long since have died out due to error catastrophe.""genes have other functions, too, the loss of X, Y, or Z by itself will have a significant selective disadvantage, so the fraction of the population with X, Y, or Z knocked out will be kept small. This means that the fraction of the population with all 3 knocked out is essentially zero. This is a way of insuring that the function F is always performed, and that certain defects never occur. Such a mechanism might prevent gross physical abnormalities or other conditions that could cause great suffering. If such a mechanism is in operation, it could be seen as an evidence of design in creation."There is no omission. In fact, he clarifies his intent by giving subdivisions of mutation rates per population and per chance mutation. There is no need to further discuss the lost population because they have no bearing on the rest of the equation or the existing population. He isn't speaking on an individual basis, but of the mutation rates in any given populace. "Let us consider the possible values for Q(n), where n is the average number of harmful mutations per individual in the population. If Q(n) is about 1/2, then the slope at n is at most 1/2n and we can expect about half of all individuals to die. There will not be much difference in the death rate for individuals in the population, since most of them will have a number of mutations differing from n by at most one or two times sqrt(n). A detailed calculation shows that the population can tolerate at most about Q(n)/(1 - Q(n)) mutations per generation. If Q(n) is 1/2, then this is at most one mutation per generation. If Q(n) is 3/4, then this is three mutations per generation. So we see that a large mutation rate will imply that most of the zygotes die and the species will be at a terrible handicap of fitness. This calculation assumes that the derivative of Q(x) with respect to x is constant up to about n; in fact, it will probably decrease, making the slope much smaller at n. This would mean that the population could tolerate only a much smaller rate of mutation."There is no omission. He's not speaking soley of individual mutation, but how individual mutation can or cannot affect a population. No, he's agreeing with the fact that isolation and mutation can cause subspecies, which can be exemplified in Darwin's finches. He's explaining how mutations cannot propagate a significant taxonomical change from mutations, but rather can and do cause subspecies. And if that was the case it would be painfully evident by now. If all that is needed is two heterozygous carriers to mate in order to create a homozygous trait in the offspring, how could the immunity proliferate and not the disease?

And haven't I explained that there are several differences in the meaning of entropy? We have the classical approach of thermodynamics which deals with the dynamics of heat, heat transfer, and heat loss. This is what you and everyone else has been pointing out. You aren't wrong, you're just giving partial credit to such a vast and unavoidable proprty of physics. What you describe is exactly what 2LoT is, and 2LoT says that in closed systems where an exchange of energy could not be transfered, entropy is inevitability. Point taken. I've never contended with that. However, I've gone over that there are at least two other equivalences that hold fast to observation. We have entropy in statistical theory, which culminates the equivalence of entropy and disorder. We also have entropy in relation to the passing of information.If you remember me pointing out Boltzmann's theory, this summarizes exactly what I'm talking about. This is what I've always been referring to and it makes no difference what kind of system you're in. Boltzmann argued that the second law was a consequence that distribution of information or energy would become increasingly disordered. And the aggregate of the final condition is of macroscopic uniformity and microscopic disorder, not a continual motion of more and more complexity. Boltzmann concluded that there are so many more possible disordered states than ordered ones. Therefore, a system, open or closed will always be found either in the state of maximum disorder or moving in that genral direction.Essentially, what I'm arriving at, is, entropy affects everything, even in abstract principles. If you built a house 70 years ago and no one applies any maitenance on it (work, energy, force) it will always tend towards disorder. The same principle applies to us. Everyday of our lives, we become less and less perfect, less and less viable. To somehow think that just because we have the sun, the molecules that compose the house and us is somehow going to stay the same forever or increase is proposterous. In the same way, a car derrives its energy from fossil fuels that are in a finite amount. It takes alot of work for the car to move forward. Eventually that available energy is going to decrease, until new energy is introduced. This principle is undeniably serious. And if you say that has nothing to do with entropy, then someone should come up with a damn good name for this principle. Everything deteriorating with time is absolutely obvious that if its not called entropy, then it at least is deserving of a name. Its as blatantly obvious as "what goes up must come down.And to further elucidate my point, I have used this site before. The reason I use it is because, one, it is factually correct, and two, the writers are neither creationists nor evolutionists. They are in my mind, unbiased individuals that have simply arrived at their conclusions based on observation. In other words, there is no hidden agenda that anyone could claim about creationists and evolutionists:The rule that things never organize themselves is also upheld in our everyday experience. Without someone to fix it, a broken glass never mends. Without maintenance, a house deteriorates. Without management, a business fails. Without new software, a computer never acquires new capabilities. Never.

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Charles Darwin understood this universal principle. It's common sense. That's why he once made a note to himself pertaining to evolution, "Never use the words higher or lower" (9). (However, the word "higher" in this forbidden sense appears half a dozen times in the first edition of Darwin's Origin of Species (10).)

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Even today, if you assert that a human is more highly evolved than a flatworm or an amoeba, there are darwinists who'll want to fight about it. They take the position, apparently, that evolution has not necessarily shown a trend toward more highly organized forms of life, just different forms:

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* All extant species are equally evolved. ” Lynn Margulis and Dorion Sagan, 1995 (11)
* There is no progress in evolution. ” Stephen Jay Gould, 1995 (12)
* We all agree that there's no progress. ” Richard Dawkins, 1995 (13)
* The fallacy of progress ” John Maynard Smith and Ers Szathmáry, 1995 (14)

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But this ignores the plain facts about life and evolution.

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Life is Organization
Seen in retrospect, evolution as a whole doubtless had a general direction, from simple to complex, from dependence on to relative independence of the environment, to greater and greater autonomy of individuals, greater and greater development of sense organs and nervous systems conveying and processing information about the state of the organism's surroundings, and finally greater and greater consciousness. You can call this direction progress or by some other name. ” Theodosius Dobzhansky (15)

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Progress, then, is a property of the evolution of life as a whole by almost any conceivable intuitive standard.... Let us not pretend to deny in our philosophy what we know in our hearts to be true. ” Edward O. Wilson (16)

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Life is organization. From prokaryotic cells, eukaryotic cells, tissues, and organs, to plants and animals, families, communities, ecosystems, and living planets, life is organization, at every scale. The evolution of life is the increase of biological organization, if it is anything. Clearly, if life originates and makes evolutionary progress without organizing input from outside, then something has organized itself. Logical entropy in a closed system has decreased. This is the violation that people are getting at, when they say that life violates the second law of thermodynamics. This violation, the decrease of logical entropy in a closed system, must happen continually in the darwinian account of evolutionary progress.

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Most darwinists just ignore this staggering problem. When confronted with it, they seek refuge in the confusion between the two kinds of entropy. Entropy [logical] has not decreased, they say, because the system is not closed. Energy such as sunlight is constantly supplied to the system. If you consider the larger system that includes the sun, entropy [thermodynamic] has increased, as required.The Second Law of Thermodynamics: Entropy and Evolution. by Brig KlyceDo you now understand why evolution is an apparent violation of the second law? Do understand my objection?To add: I've got a pretty busy day ahead of me Quetzal, but when I get a chance I will respond to your post.

I agree that we are not in any immediate danger of the sun running out of enough energy to sustain us. This is to say, everything is affected by 2LoT, including the very source where we obtain our energy.The influx of energy into an open system would not decrease entropy. Actually, the added heat energy would increase the rate at which things deteriorate. All I'm pointing out is that there is a fine balance in nature; so finely tuned in fact that its miraculous to me how people can essentially say that it was one coincidence after another. Too little heat will not sustain organisms on earth, too much will scortch them. If you have a home out in the middle of Death Valley, the beating sun wears it down at a much quicker rate than someone living in a much more temperate enviornment. There is nothing revolutionary about it. What's revolutionary is the apparent conclusion that many have come to, that somehow, the introduction of energy will completely negate deterioration. That obviously isn't the case, because too much energy will also speed up these processes. And when left to themselves, all things degrade with time, even in spite of a constant influx of energy. Does the energy slow the process down in manageable amounts? Of course it does. That would be silly to say otherwise. But this does not overcome the fact that the general flow is still from more ordered to more disordered. I've read up on Schroeder, Shannon, Bohr, Kauffman and all the others theory on it. Here is what I don't understand: In one instance, evolutionary biologists say that life isn't really increasing in complexity, just changing in a non-specific motion, but in the next instant, they can't get around the fact that if transspecific evolution exists, that everything is increasing in complexity. And then in one instance we have people say that 2LoT doesn't and can't occur in open systems. It is this unclear representation of its own theory that piques my interest. Because of the principles summarized by the Second Law, an actual and functional state of complexity still has the tendency to break down and not to exhibit this creative power necessary to compel an amoeba to a man.As far as the non-equilibrium dissipation, it sounds alot like the 4th law, or at least, a spin-off of the proposed 4th law of Thermodynamics which is thus far, theoretical. In an attempt to account for the inevitable and sudden formation of autocatalytic sets of molecules, a hypothesis had to be formulated. The basic premise is that there is a law which directs the diversity and complexity in the universe in an ever-increasing display, so long as plently of sustained energy is introduced. But this can't be the case because it runs counter to the 2nd law, which is so exhaustively confirmed by physics that it should be used as a screening device for any proposed theory. Okay, my wording of certain actions concerning mechanisms in the future will leave no doubt as to what I'm speaking about. I understand his premise just fine. Its yours that I'm a little hazy, only because it seems like to me that you are factoring in organisms that no longer bear any relevance to the equation. The equation represents the overall population of whatever organism. And the only reason why they are of no consequence is because they have ceased to exist. I could agree with that, but if people with homozygous traits mate, then shouldn't that start the increase by selection and drift?