"Representation of Darwin's idea as having been of gradual change. Large parts of the argument is based on this; it's wrong."
Without gradual change, Darwin's argument becomes more difficult.
"Misrepresentation of "information creating itself" by disregarding the action of natural selection. Natural selection does the weeding. I have actually tested the use of this (again with simulations)"
I don't disregard it at all. The problem is that in order for something to be remain semantically valid, often times multiple changes have to be made in multiple places simultaneously to preserve coherency. Natural selection would act _against_ such changes, unless there were switching mechanisms where the information was pre-coded. This is exactly what I was arguing in my article.
"Misrepresentation of "information creating itself" by attacking a straw man. The argument of random monkeys isn't usually used to illustrate this, instead it is used to illustrate the opposite: Combinatorics increase complexity FAST, so pure random chance will not reach this."
You should tell this to Huxley. The debate that solidified Darwinism in biology was done so entirely based on this idea.
"Misrepresentation of "reactions are reversable"."
There was no misrepresentation here. Without enzymes to control the process, how are long genes supposed to build up?
"Misrepresentation of the set of computational systems, in that the system of a living being has a multitude of different pathways for most reactions."
This is fairly irrelevant. And it's not actually any different from computers. The actual difference is in parallelism. Computers are not as parallel as organisms. This actually makes _more_ problems for organisms, not fewer.
"Also, we are able to effectively write programs using genetic algorithms (search for genetic programming), so the argument would seem to be irrelevant even if it wasn't fundamenally attacking a bad analogy."
Genetic algorithms are just another name for non-deterministic algorithms. They take quite a bit of intelligent design to get right. See the second quote on this page. Genetic algorithms have to take into account the semantics of the system just as much as any other type of algorithm.
"Misrepresentation: The talk of chaos as connected to computer programs (as per above.) Quantum mechanics aren't chaotic, and as a such this falls down."
I think you are misunderstanding what I was saying.
""not dying" is a very strong selector"
It is a very strong selector. And in such an early biotic system as you propose, it would simply select out.... everything.
"However, random mutation work in combination with natural selection, and it is NOT exploring the full search space."
This is part of the problem -- if anything requires a "leap" to get across, Darwinian mechanisms could not do it, because natural selection would select out the intermediates. This is the premise of irreducible complexity.
"These fit well with neoDarwinism - the system is a feedback loop, and better ways of handling mutations has been selected. That is a natural consequence - these would be the best things that could happen to a reproducing machine, OF COURSE they will be selected for."
Of course they would get selected for, but it is not an "of course" that they would have originated to begin with.
"You mention Scott Gilbert and genetic assimilation. Gilbert considers this to fit under Darwinism"
The problem is that the facts do not bear it out. In order for genetic assimilation to be Darwinian, the internalization would have to occur without the external inducers at the same rate that it does with the inducers, but in fact, the assimilation is favored with the presence of the external inducers.
"What we know is that all the evidence we have point at it all being connected *as far back as we get data*."
Actually, there is quite a lot of discontinuity in both the fossil record and among current organisms. There is no plausible mechanism for phylum-level diversification, and it proceeds _opposite_ what Darwin suggested. Darwin's theory says that diversity precedes disparity, but the fossil record shows the opposite -- disparity at the earliest levels.
Even up until the family level of organisms there is huge discontinuity across-the-board. It is an article of neo-Darwinistic faith, not evidence, that such discontinuities can be jumped via neo-Darwinism.
"Look at how we get species specialization when we isolate things (there was a large system of carp-related fishes that demonstrated this, can't remember exactly where, and I've no time for looking up references right now."
Again, you are pointing to _change_ without demonstrating that the change is random. Change is not incompatible with any system of origins, be it YEC, OEC, Prescribed/Front-Loaded Evolution, or neo-Darwinism (in fact, YEC posits that change happens much faster than any of the other systems).
"Life could originate from clay crystals"
Not really. The problem with the crystal view is that crystals don't actually reproduce themselves. The pattern is determined by law. On the other hand, the cell is a fully functioning Shannon communication system, where the pattern is _copied_, with the sequence not being determinable by law, but open to variations, which are copied reliably.
"There's evidence that RNA functions in this kind of replication"
The evidence is very small, and even smaller that it could do so without getting completely destroyed before it is actually a cell. The papers I've seen on RNA acting as a replicator only actually allow it to replicate its complementary strand. Even then, there is the problem of actually getting the food. The full cellular function is required -- the ability to find food, keep the local environment stablle, and recover from destabilizations -- without these, the pre-organisms would be completely destroyed before making any significant number of copies.
"If nothing prevents them, then beneficial changes have to occur"
I agree that beneficial changes occur. The difference is that they are cell-directed, not happenstance.
"pretty much demolishing the "mutations are degenerative" argument."
You miss the point. The search space is so large and the targets so few, that, if the mutations were non-directional (and non-directional mutation is the fundamental teaching of neo-Darwinism) then beneficial mutations would be so rare that there would hardly even be one in the history of the universe.
If, however, there are a class of mutations that are directional, then you would avoid the problems of neo-Darwinism. However, this would mean that the organism was adapting itself, and provide an ultimately teleological origin to change.
You do realize that removing choice from the equation also means that we have no choice as to what we believe. This means that whatever you think about the scientific arguments about evolution and creation you think simply because you could not do anything else, and likewise the same for me.
Thus, having an argument on any issue is fairly pointless, since we have no control.
"I can see the factors - and I could override them with other factors"
If you can, then its choice -- something make the choice outside of the material influencers.
If you can't, then don't pretend that anything you are doing is anything but what has been predetermined by physics, or, at best, a randomized path constrained by physics (if you take quantum indeterminancy to be truly random).
"The fact that living things can be put into categories that share characteristics, including arbitrary ones, is strong evidence that they share some ancestors."
Not really. You can categorize anything. In fact, the human mind is built to categorize. The existance of categories is more an effect of the human mind than "real".
"It's "simply involked" because evolution explains so much about the world."
I think it "explains so much" because it has been simply invoked so many times. Gone is the necessity of making plausible explanations, evolutionists can just say "evolution did it!", come up with a good story, and be done.
"Natural selection can't produce anything new by itself, it needs the variation and replication components as well. As for the search space, noone is suggesting that the search is exhaustive, it just has to occationally find improvements"
In a large enough search space, this simply won't happen. For an examination on the difficulties involved, you should take a look at Behe's paper in protein science. Also note that Behe is simply looking at changes involving a few amino acids.
"Evolution is clearly sufficient to explain breeding done by humans and the development of creatures in recorded history."
How is it "clearly sufficient"? It is clearly sufficient for the former, but not the latter. Darwinism has never shown how it can be the origin of complex systems or traits. Even simple ones it has problems with. Much less the de novo development of multiprotein cascades.
"More importantly, there's no scientific explanation out there right now for the origin of life other than ones that include abiogenesis."
I think that's because your definition of "science" rules them out a priori. Why cannot intelligent causes be considered in the origin of life?
"Now you've switched from science to philosophy."
The two are intimately intertwined. The original name for science was "natural philosophy". To say that you are doing one or the other only is essentially making an arbitrary demarcation.
"If you don't think a physical mechanism could possibly work, just let me know how a non-physical one would."
The same way it works in every day life. I create all sorts of things in my job. My creative acts are not predetermined by physics, but arise out of my own intelligent causation. It is _limitted_ by physics, but not determined by it.
"A change is neither degenerative nor beneficial. It is just a change."
This is from the strange world of Darwinian genomics, which seeks to remove the idea of function from biology.
"Whether it is disadvantageous or beneficial depends upon environmental context, and the same alteration may be disadvantageous in one context and advantageous in another."
This is true to a degree. However, it also depends on whether or not the change makes sense in the context of the cell's own system. i.e. a change, in order to be beneficial, must maintain a semantic unity with the rest of the cell system.
The idea of directed mutation is that the class of changes which are most likely to generate beneficial mutations are directed by the cell itself in order to be adaptive. Darwinism holds that changes within the genome are not based on the needs of the organism, but just happenstance, and merely the good ones selected out. This has both experimental and theoretical problems.
Experimentally, more and more data is coming out showing that organisms _do_ change in specific ways in order to be more adaptive.
Theoretically, the search space for beneficial changes is so large, that without direction there would be no possibility of it occurring. See Dembski's Searching Large Spaces. And Dembski is not the only person to recognize the problem. This problem is also referenced in A Biochemical Mechanism for Nonrandom Mutations and Evolution.
"All of the difference between species observed to date are the result of multiple changes of the sort that arise by mutation."
You are confusing "mutation" with "random mutation". Also, this is not entirely true, as species can actually diverge without mutation just through mendellian mechanisms.
"There is no known or imaginable mechanism to prevent mutations from producing the kinds of genomic changes from occurring that have been shown to underlie all species differences"
I'm not sure what you are saying. I'm not saying that any specific mutation is _prevented_. However, many mutations are prevented from surviving, because, well, they would die.
The generative mechanism is cell-directed transcription (as shown in the paper linked above). Mobile elements also seem to be involved, although the exact mechanism triggering and placing them is not known. But, contrary to the neo-Darwinian view of "parasitic elements", mobile elements are highly adaptive in helping organisms cope with stress in specific ways, and can even help restructure genomes.
"They're variant amino acid sequences for antibiotic targets that produce slightly different proteins."
Contingency loci. This is not random change.
"Or community plasmids or viral sequences that don't have any advantage normally, but the bacterial community keeps around because those that don't are periodically wiped out."
Another adaptive response.
"But if you think about it as a random genetic mutation in the structure of a blood protein that, in its heterozygous state, confers great resistance to a lethal disease"
I do think about it that way. Note that your only example thus far of an actual random mutation has been degenerative. And yes, people who die from this don't reproduce much afterwards.
"How about cystic fibrosis? If "sick things don't reproduce well", cystic fibrosis should have been history long before modern medicine got around to diagnosing it."
????
So you are saying that natural selection doesn't work?
"Try looking up "ribosomal RNA sequencing" sometime, since you say you're big on scientific papers."
rRNA sequencing conflicts with the morphological data in many cases.
"How could life arise from non-life? The Wiki entry on "origin of life" has a good summary of the theories on how that could happen. As well as the experimental proof behind them."
Yes, there's many theories. But the "proof"s simply aren't there. Try checking out:
Also there's the little problem that, before enzymes, the reaction rate would be way too slow to do anything of interest before being totally destroyed.
You also seem to be misunderstanding the idea of Intelligent Design (and even creationism). First of all, ID is compatible with (but does not require) common descent. Neither creationism nor intelligent design require a designer to be continually tinkering throughout natural history. The point is that the processes in the cell are ultimately _telic_ processes. They are informational processes, guided by the information that was originally coded. The Darwinian idea is that information can generate itself. Demski has handily refuted such idea using basic math (any search space involving more than 500 bits to achieve the next fitness level is basically impossible).
The quintessential ID hypothesis is probably Davison's Prescribed Evolutionary Hypothesis (previously called the Semi-Meiotic Theory) which says that phylogeny follows a semi-directed path just like ontogeny does.
The quintessential Creationary hypothesis is probably Todd Wood's Altruistic Genetic Element hypothesis.
Also, if you're interested, two good examinations of neo-Darwinism are:
"Mendelian inheritance is incapable of generating variation, it merely reshuffles the variation that already exists."
Yes and no. Heterozygous fractionation can cause phenotypic variation.
"Variation arises by mutation."
Yes, I have no doubt that this is one of the mechanisms. The question is, are the mutations with regard to the needs of the organism or not?
"Many species genomes have been sequenced, confirming the prediction of evolutionary theory that all differences between species are due to an accumulation of small changes at the genetic level"
The idea that these differences are the results of accumulation of small changes is a presumption, not a result.
"changes identical to those that have been demonstrated to arise by random mutation"
The changes that result from random mutations are degenerative, while adaptive mutations are beneficial. Yet Darwinists want to cling to the former and pretend that the latter are somehow the former in disguise.
"that the similarity of sequences reflects a relatively recent common ancestral sequence, more recent than other genes of the bacteria in question"
Actually, they assumed that, simply because the sequences were similar. However, that is a presumption, not the result of analysis. I think others disagree, as it has been shown to have come into both populations independently.
"Look up the recent publications about alcohol dehydrogenases."
I will!
"What you now mention is a good example of convergent evolution, where the needs of function impose structure."
Note that you have just undermined your entire argument for homology being evidence of common ancestry. Now, how does convergent evolution occur quickly? If evolution proceeds via random mutations which are selected, convergent evolution should not be able to occur quickly. However, if genomic change is a result of an algorithm followed by the organism, it can occur quickly. And, in fact, it does! This is evidence that change occurs according to in-built plans, not according to happenstance mutations.
"If you are a believer in intelligent design, please admit to it."
I've never hidden it.
"But do not bother us here with its flawed arguments."
Yes, just ignore the message before listening. My guess is that you've never bothered to understand what it actually is.
"For further discussion everybody is better off reading the judge's dissection of intelligent design in the recent Kansas ruling."
Yes, scientists should just appeal to authority so they don't have to actually deal with the arguments. They can just call foul from the sideline and hope it goes away.
Why is that? Design patterns do not use the same code every time. If they did, they would just be library routines, not design patterns.
"If you like I can show you some sequence alignments, for example between human and fly Eya/PAX6 (= Eyes absent) and other species in between that show quite astonishingly how these species are related."
You can find the same kind of homologies in 6-aminohexanoate-cyclic-dimer hydrolase in Flavobacterium and Psedomonas, despite the fact that we have _observed_ their appearance as separate occurrences. In fact, I believe in the case of Pseudomonas, the gene appeared de novo after 9 days.
So, if you can have a gene that appears _separately_ in two different lineages, with that gene appearing within days and exhibitting high homology, what does that do to the rest of the molecular arguments from homology?
"Aren't you actually grossly violating that by attempting to bring forth an untruth because you're too lazy to check the evidence?"
I have checked the evidence.
"Evolution and natural selection is the cause of most, if not all, variation in the biological world."
This is simply false. Natural selection has not been able to explain hardly anything. It is simply invoked. Read some biological papers. Whenever something new is found, it is simply listed as "having evolved" without any discussion about how the evolution could even have taken place.
_Most_ of the variation that takes place is the result of Mendellian inheritance, which, by the way, was discovered by a creationist (who used it to argue _against_ transformism).
The environment induces a large part of variance. Scott Gilbert has written about many of these, include variance resulting from an animal sensing predatory animals in the environment, and specifically changing their morphology to account for it. The process of genetic assimilation will make these changes the default morphology even in absence of the predator after a certain number of generations.
Natural selection explains almost nothing. All natural selection means is that dead things don't reproduce, and sick things don't reproduce well. This is a conservative, not a creative process. And random mutation has too big of a search space to do anything productive. Perhaps you should take a 21st century view of evolution rather than the 1950's version of it you are looking at now.
Please tell me what the evidence is that (a) everything shares a common ancestor, and that (b) random mutation + natural selection is sufficient for creating the diversity that exists today from that common ancestor. If you want to be really adventurous, you can also show how (c) life could have proceeded from non-life.
Also, while we're at it, you could try showing how choice can arise through material mechanisms. If choice can't arise through material mechanisms, then either (a) choice as a real entity doesn't exist, or (b) a material view of origins is insufficient.
This is incorrect. It has been disputed, but that isn't the same as being debunked.
"The claim of "many" is overblown. There are a very very few, compared to the overall number of people that study this."
Are you sure, or are others just maintaining a low cover? Just look at the Sternberg mess. Sternberg got his whole reputation thrown out the window just for allowing an Intelligent Design article to be published.
"Almost all of them have the distinction of being a member of some religion that have their belief."
If you found evidence of a creator, would not the next logical step be to find out who it is? Note that not all agree on the conception of a creator. Some are agnostics such as Denton, secular Jews such as Berlinski, and also Hindus and Buddhists.
"And few of them seem to even be against evolution per se - they just try to insert other factors *too*"
There are exactly zero people who disagree with evolution in its entirety.
""There is evolution BUT specication comes from God". And there is no significant rationale for doing so."
There is abundant reason for doing so. First, let's get rid of the word "speciation", as there are 20 different meanings of speciation, and none of them is really what creationists are talking about. Creationists are saying that there are semantic barriers to change. This is realized at the molecular level, where transposons (which are essentially semantic toolkits) are very specific taxonomically, with no evidence that they arise from anywhere else.
"That's what a scientific theory is, BTW - a cathedral of knowledge that explains variance."
There is noone who disputes variance.
An interesting article you might be interested in is here.
"Shared genetic material, shared aspects of biochemistry that could be different, shared morphology, etc."
Aren't those the same kinds of similarities between cars that have vastly different designers and designs? You're not proposing that cars are not the product of separate creations just because they have a lot of similarities are you?
"Nature abounds with examples where very remotely related genera will use very similar genes to specify tissues with similar functions but very dissimilar compositions. The same gene that specifies eyes in the fruit fly for instance specifies eyes in us humans. Yet our eyes are not like those of a fly at all."
Isn't this more of an argument for common design (design patterns, etc.) than for common descent?
"Each of those entries is not unique to Perl (applying as well to other common languages like C++ or sh), straight-out false, or just as prevalent in "math geek" writings as standard speech."
Not really. While some individual ones are available elsewhere, Perl's combination is fairly unique, with some of them being really unique. For example, the sections "Disambiguation by number, case and word order", "Topicalization", ""Inevitable" Divergence", and "Pronominalization" are fairly perl-specific.
"That's a myth- a retroactive redefinition of the origin. Perl's design was taken as a union of the styles of sh, C, and awk."
That's just surface structure. Perl doesn't seek to be a natural language processing platform. But it does intend to bring human language characteristics to programming. See here:
Re:Humans linguists should stick to human language
on
Torvalds Says 'Use KDE'
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· Score: 2, Insightful
"Do you think that the "modelling after human languages" thing was a success?"
Yes, but not in the way that you are thinking. It was a success, not because it is easier or harder to learn, but because I can be more expressive in Perl than in other languages.
One of the great things that I love about Perl is that you can rearrange statements. I can say:
if($x) {
blahblahblah() }
or I can say
blahblahblah() if $x;
In the former, I am emphasizing (to myself and other programmers after me) that the condition is more important, while in the latter I am emphasizing the action as having the importance.
Likewise, moving often-used idioms into the core language is a feature of human languages that he imported into Perl. While most programming languages would opt for several features of Perl to be libraries (like RegEx), Perl has it as a part of the syntax of the language itself. Importing the core idioms of a population into a language is something that real languages do.
Having both "if" and "unless" is a very human-language thing to do, and it makes it more obvious what you are trying to do in your program than a bunch of "if(! )"s.
The beauty of Perl is that programming in Perl is much more expressive than programming in other languages. The point is not to be "easier for noobs", but for the meaning in the program to be better conveyed to other programmers who are fluent in the language.
Having a pronoun is also very linguistic.
A more specific list of human-language features of Perl is here:
"If anything, it's the opposite: they ought to stay away from it, and learn a language with a halfway sane syntax and semantics, as opposed to a warmed-over Unixy shell scripting language that went through a brief period of overuse during the dotcom bubble."
Them are fightin words.
Whether you enjoy Perl or not, Perl is interesting because it was developed by a linguist and modelled after human languages, rather than by a Math geek modelled after a strict theoretical model. It's fairly unique in that perspective.
Even more, you can actually configure Perl to be an interpretted Latin:
Slashdot Mirror
"Representation of Darwin's idea as having been of gradual change. Large parts of the argument is based on this; it's wrong."
Without gradual change, Darwin's argument becomes more difficult.
"Misrepresentation of "information creating itself" by disregarding the action of natural selection. Natural selection does the weeding. I have actually tested the use of this (again with simulations)"
I don't disregard it at all. The problem is that in order for something to be remain semantically valid, often times multiple changes have to be made in multiple places simultaneously to preserve coherency. Natural selection would act _against_ such changes, unless there were switching mechanisms where the information was pre-coded. This is exactly what I was arguing in my article.
"Misrepresentation of "information creating itself" by attacking a straw man. The argument of random monkeys isn't usually used to illustrate this, instead it is used to illustrate the opposite: Combinatorics increase complexity FAST, so pure random chance will not reach this."
You should tell this to Huxley. The debate that solidified Darwinism in biology was done so entirely based on this idea.
"Misrepresentation of "reactions are reversable"."
There was no misrepresentation here. Without enzymes to control the process, how are long genes supposed to build up?
"Misrepresentation of the set of computational systems, in that the system of a living being has a multitude of different pathways for most reactions."
This is fairly irrelevant. And it's not actually any different from computers. The actual difference is in parallelism. Computers are not as parallel as organisms. This actually makes _more_ problems for organisms, not fewer.
"Also, we are able to effectively write programs using genetic algorithms (search for genetic programming), so the argument would seem to be irrelevant even if it wasn't fundamenally attacking a bad analogy."
Genetic algorithms are just another name for non-deterministic algorithms. They take quite a bit of intelligent design to get right. See the second quote on this page. Genetic algorithms have to take into account the semantics of the system just as much as any other type of algorithm.
"Misrepresentation: The talk of chaos as connected to computer programs (as per above.) Quantum mechanics aren't chaotic, and as a such this falls down."
I think you are misunderstanding what I was saying.
""not dying" is a very strong selector"
It is a very strong selector. And in such an early biotic system as you propose, it would simply select out.... everything.
"However, random mutation work in combination with natural selection, and it is NOT exploring the full search space."
This is part of the problem -- if anything requires a "leap" to get across, Darwinian mechanisms could not do it, because natural selection would select out the intermediates. This is the premise of irreducible complexity.
"These fit well with neoDarwinism - the system is a feedback loop, and better ways of handling mutations has been selected. That is a natural consequence - these would be the best things that could happen to a reproducing machine, OF COURSE they will be selected for."
Of course they would get selected for, but it is not an "of course" that they would have originated to begin with.
"You mention Scott Gilbert and genetic assimilation. Gilbert considers this to fit under Darwinism"
The problem is that the facts do not bear it out. In order for genetic assimilation to be Darwinian, the internalization would have to occur without the external inducers at the same rate that it does with the inducers, but in fact, the assimilation is favored with the presence of the external inducers.
"What we know is that all the evidence we have point at it all being connected *as far back as we get data*."
Actually, there is quite a lot of discontinuity in both the fossil record and among current organisms. There is no plausible mechanism for phylum-level diversification, and it proceeds _opposite_ what Darwin suggested. Darwin's theory says that diversity precedes disparity, but the fossil record shows the opposite -- disparity at the earliest levels.
Even up until the family level of organisms there is huge discontinuity across-the-board. It is an article of neo-Darwinistic faith, not evidence, that such discontinuities can be jumped via neo-Darwinism.
"Look at how we get species specialization when we isolate things (there was a large system of carp-related fishes that demonstrated this, can't remember exactly where, and I've no time for looking up references right now."
Again, you are pointing to _change_ without demonstrating that the change is random. Change is not incompatible with any system of origins, be it YEC, OEC, Prescribed/Front-Loaded Evolution, or neo-Darwinism (in fact, YEC posits that change happens much faster than any of the other systems).
"Life could originate from clay crystals"
Not really. The problem with the crystal view is that crystals don't actually reproduce themselves. The pattern is determined by law. On the other hand, the cell is a fully functioning Shannon communication system, where the pattern is _copied_, with the sequence not being determinable by law, but open to variations, which are copied reliably.
"There's evidence that RNA functions in this kind of replication"
The evidence is very small, and even smaller that it could do so without getting completely destroyed before it is actually a cell. The papers I've seen on RNA acting as a replicator only actually allow it to replicate its complementary strand. Even then, there is the problem of actually getting the food. The full cellular function is required -- the ability to find food, keep the local environment stablle, and recover from destabilizations -- without these, the pre-organisms would be completely destroyed before making any significant number of copies.
Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequence says that the gene was generated by Flavobacterium.
Emergence of Nylon Oligomer Degradation Enzymes in Pseudomonas aeruginosa PAO through Experimental Evolution says that the gene was generated by Pseudomonas.
"If nothing prevents them, then beneficial changes have to occur"
I agree that beneficial changes occur. The difference is that they are cell-directed, not happenstance.
"pretty much demolishing the "mutations are degenerative" argument."
You miss the point. The search space is so large and the targets so few, that, if the mutations were non-directional (and non-directional mutation is the fundamental teaching of neo-Darwinism) then beneficial mutations would be so rare that there would hardly even be one in the history of the universe.
If, however, there are a class of mutations that are directional, then you would avoid the problems of neo-Darwinism. However, this would mean that the organism was adapting itself, and provide an ultimately teleological origin to change.
You do realize that removing choice from the equation also means that we have no choice as to what we believe. This means that whatever you think about the scientific arguments about evolution and creation you think simply because you could not do anything else, and likewise the same for me.
Thus, having an argument on any issue is fairly pointless, since we have no control.
"I can see the factors - and I could override them with other factors"
If you can, then its choice -- something make the choice outside of the material influencers.
If you can't, then don't pretend that anything you are doing is anything but what has been predetermined by physics, or, at best, a randomized path constrained by physics (if you take quantum indeterminancy to be truly random).
"The fact that living things can be put into categories that share characteristics, including arbitrary ones, is strong evidence that they share some ancestors."
Not really. You can categorize anything. In fact, the human mind is built to categorize. The existance of categories is more an effect of the human mind than "real".
"It's "simply involked" because evolution explains so much about the world."
I think it "explains so much" because it has been simply invoked so many times. Gone is the necessity of making plausible explanations, evolutionists can just say "evolution did it!", come up with a good story, and be done.
"Natural selection can't produce anything new by itself, it needs the variation and replication components as well. As for the search space, noone is suggesting that the search is exhaustive, it just has to occationally find improvements"
In a large enough search space, this simply won't happen. For an examination on the difficulties involved, you should take a look at Behe's paper in protein science. Also note that Behe is simply looking at changes involving a few amino acids.
"Evolution is clearly sufficient to explain breeding done by humans and the development of creatures in recorded history."
How is it "clearly sufficient"? It is clearly sufficient for the former, but not the latter. Darwinism has never shown how it can be the origin of complex systems or traits. Even simple ones it has problems with. Much less the de novo development of multiprotein cascades.
"More importantly, there's no scientific explanation out there right now for the origin of life other than ones that include abiogenesis."
I think that's because your definition of "science" rules them out a priori. Why cannot intelligent causes be considered in the origin of life?
"Now you've switched from science to philosophy."
The two are intimately intertwined. The original name for science was "natural philosophy". To say that you are doing one or the other only is essentially making an arbitrary demarcation.
"If you don't think a physical mechanism could possibly work, just let me know how a non-physical one would."
The same way it works in every day life. I create all sorts of things in my job. My creative acts are not predetermined by physics, but arise out of my own intelligent causation. It is _limitted_ by physics, but not determined by it.
"A change is neither degenerative nor beneficial. It is just a change."
This is from the strange world of Darwinian genomics, which seeks to remove the idea of function from biology.
"Whether it is disadvantageous or beneficial depends upon environmental context, and the same alteration may be disadvantageous in one context and advantageous in another."
This is true to a degree. However, it also depends on whether or not the change makes sense in the context of the cell's own system. i.e. a change, in order to be beneficial, must maintain a semantic unity with the rest of the cell system.
The idea of directed mutation is that the class of changes which are most likely to generate beneficial mutations are directed by the cell itself in order to be adaptive. Darwinism holds that changes within the genome are not based on the needs of the organism, but just happenstance, and merely the good ones selected out. This has both experimental and theoretical problems.
Experimentally, more and more data is coming out showing that organisms _do_ change in specific ways in order to be more adaptive.
Theoretically, the search space for beneficial changes is so large, that without direction there would be no possibility of it occurring. See Dembski's Searching Large Spaces. And Dembski is not the only person to recognize the problem. This problem is also referenced in A Biochemical Mechanism for Nonrandom Mutations and Evolution.
"All of the difference between species observed to date are the result of multiple changes of the sort that arise by mutation."
You are confusing "mutation" with "random mutation". Also, this is not entirely true, as species can actually diverge without mutation just through mendellian mechanisms.
"There is no known or imaginable mechanism to prevent mutations from producing the kinds of genomic changes from occurring that have been shown to underlie all species differences"
I'm not sure what you are saying. I'm not saying that any specific mutation is _prevented_. However, many mutations are prevented from surviving, because, well, they would die.
The generative mechanism is cell-directed transcription (as shown in the paper linked above). Mobile elements also seem to be involved, although the exact mechanism triggering and placing them is not known. But, contrary to the neo-Darwinian view of "parasitic elements", mobile elements are highly adaptive in helping organisms cope with stress in specific ways, and can even help restructure genomes.
I've got about 4 papers on this, and I'll try to look through them and see exactly what they say about it.
"What do you think antibiotic resistance is?"
A genetic adaptive response.
"They're variant amino acid sequences for antibiotic targets that produce slightly different proteins."
Contingency loci. This is not random change.
"Or community plasmids or viral sequences that don't have any advantage normally, but the bacterial community keeps around because those that don't are periodically wiped out."
Another adaptive response.
"But if you think about it as a random genetic mutation in the structure of a blood protein that, in its heterozygous state, confers great resistance to a lethal disease"
I do think about it that way. Note that your only example thus far of an actual random mutation has been degenerative. And yes, people who die from this don't reproduce much afterwards.
"How about cystic fibrosis? If "sick things don't reproduce well", cystic fibrosis should have been history long before modern medicine got around to diagnosing it."
????
So you are saying that natural selection doesn't work?
"Try looking up "ribosomal RNA sequencing" sometime, since you say you're big on scientific papers."
rRNA sequencing conflicts with the morphological data in many cases.
"How could life arise from non-life? The Wiki entry on "origin of life" has a good summary of the theories on how that could happen. As well as the experimental proof behind them."
Yes, there's many theories. But the "proof"s simply aren't there. Try checking out:
Chance and Necessity Do Not Explain the Origin of Life
Origin of life on earth and Shannon's theory of communication.
You also have the problem that before DNA-editting enzymes, the error rate would be too high to support life, but the enzymes are encoded by DNA.
Also there's the little problem that, before enzymes, the reaction rate would be way too slow to do anything of interest before being totally destroyed.
You also seem to be misunderstanding the idea of Intelligent Design (and even creationism). First of all, ID is compatible with (but does not require) common descent. Neither creationism nor intelligent design require a designer to be continually tinkering throughout natural history. The point is that the processes in the cell are ultimately _telic_ processes. They are informational processes, guided by the information that was originally coded. The Darwinian idea is that information can generate itself. Demski has handily refuted such idea using basic math (any search space involving more than 500 bits to achieve the next fitness level is basically impossible).
The quintessential ID hypothesis is probably Davison's Prescribed Evolutionary Hypothesis (previously called the Semi-Meiotic Theory) which says that phylogeny follows a semi-directed path just like ontogeny does.
The quintessential Creationary hypothesis is probably Todd Wood's Altruistic Genetic Element hypothesis.
Also, if you're interested, two good examinations of neo-Darwinism are:
A Biochemical Mechanism for Nonrandom Mutations and Evolution
and
"Mendelian inheritance is incapable of generating variation, it merely reshuffles the variation that already exists."
Yes and no. Heterozygous fractionation can cause phenotypic variation.
"Variation arises by mutation."
Yes, I have no doubt that this is one of the mechanisms. The question is, are the mutations with regard to the needs of the organism or not?
"Many species genomes have been sequenced, confirming the prediction of evolutionary theory that all differences between species are due to an accumulation of small changes at the genetic level"
The idea that these differences are the results of accumulation of small changes is a presumption, not a result.
"changes identical to those that have been demonstrated to arise by random mutation"
The changes that result from random mutations are degenerative, while adaptive mutations are beneficial. Yet Darwinists want to cling to the former and pretend that the latter are somehow the former in disguise.
"that the similarity of sequences reflects a relatively recent common ancestral sequence, more recent than other genes of the bacteria in question"
Actually, they assumed that, simply because the sequences were similar. However, that is a presumption, not the result of analysis. I think others disagree, as it has been shown to have come into both populations independently.
"Look up the recent publications about alcohol dehydrogenases."
I will!
"What you now mention is a good example of convergent evolution, where the needs of function impose structure."
Note that you have just undermined your entire argument for homology being evidence of common ancestry. Now, how does convergent evolution occur quickly? If evolution proceeds via random mutations which are selected, convergent evolution should not be able to occur quickly. However, if genomic change is a result of an algorithm followed by the organism, it can occur quickly. And, in fact, it does! This is evidence that change occurs according to in-built plans, not according to happenstance mutations.
"If you are a believer in intelligent design, please admit to it."
I've never hidden it.
"But do not bother us here with its flawed arguments."
Yes, just ignore the message before listening. My guess is that you've never bothered to understand what it actually is.
"For further discussion everybody is better off reading the judge's dissection of intelligent design in the recent Kansas ruling."
Yes, scientists should just appeal to authority so they don't have to actually deal with the arguments. They can just call foul from the sideline and hope it goes away.
"It would if the genes were exactly identical. "
Why is that? Design patterns do not use the same code every time. If they did, they would just be library routines, not design patterns.
"If you like I can show you some sequence alignments, for example between human and fly Eya/PAX6 (= Eyes absent) and other species in between that show quite astonishingly how these species are related."
You can find the same kind of homologies in 6-aminohexanoate-cyclic-dimer hydrolase in Flavobacterium and Psedomonas, despite the fact that we have _observed_ their appearance as separate occurrences. In fact, I believe in the case of Pseudomonas, the gene appeared de novo after 9 days.
So, if you can have a gene that appears _separately_ in two different lineages, with that gene appearing within days and exhibitting high homology, what does that do to the rest of the molecular arguments from homology?
"Aren't you actually grossly violating that by attempting to bring forth an untruth because you're too lazy to check the evidence?"
I have checked the evidence.
"Evolution and natural selection is the cause of most, if not all, variation in the biological world."
This is simply false. Natural selection has not been able to explain hardly anything. It is simply invoked. Read some biological papers. Whenever something new is found, it is simply listed as "having evolved" without any discussion about how the evolution could even have taken place.
_Most_ of the variation that takes place is the result of Mendellian inheritance, which, by the way, was discovered by a creationist (who used it to argue _against_ transformism).
The environment induces a large part of variance. Scott Gilbert has written about many of these, include variance resulting from an animal sensing predatory animals in the environment, and specifically changing their morphology to account for it. The process of genetic assimilation will make these changes the default morphology even in absence of the predator after a certain number of generations.
Likewise, microbes can change their genome in response to the environment. They can use transposons to activate latent genes, they can induce a highly regulated mutagenesis which produces almost entirely beneficial mutations.
Natural selection explains almost nothing. All natural selection means is that dead things don't reproduce, and sick things don't reproduce well. This is a conservative, not a creative process. And random mutation has too big of a search space to do anything productive. Perhaps you should take a 21st century view of evolution rather than the 1950's version of it you are looking at now.
Please tell me what the evidence is that (a) everything shares a common ancestor, and that (b) random mutation + natural selection is sufficient for creating the diversity that exists today from that common ancestor. If you want to be really adventurous, you can also show how (c) life could have proceeded from non-life.
Also, while we're at it, you could try showing how choice can arise through material mechanisms. If choice can't arise through material mechanisms, then either (a) choice as a real entity doesn't exist, or (b) a material view of origins is insufficient.
"Behe's books has repeatedly been debunked."
This is incorrect. It has been disputed, but that isn't the same as being debunked.
"The claim of "many" is overblown. There are a very very few, compared to the overall number of people that study this."
Are you sure, or are others just maintaining a low cover? Just look at the Sternberg mess. Sternberg got his whole reputation thrown out the window just for allowing an Intelligent Design article to be published.
"Almost all of them have the distinction of being a member of some religion that have their belief."
If you found evidence of a creator, would not the next logical step be to find out who it is? Note that not all agree on the conception of a creator. Some are agnostics such as Denton, secular Jews such as Berlinski, and also Hindus and Buddhists.
"And few of them seem to even be against evolution per se - they just try to insert other factors *too*"
There are exactly zero people who disagree with evolution in its entirety.
""There is evolution BUT specication comes from God". And there is no significant rationale for doing so."
There is abundant reason for doing so. First, let's get rid of the word "speciation", as there are 20 different meanings of speciation, and none of them is really what creationists are talking about. Creationists are saying that there are semantic barriers to change. This is realized at the molecular level, where transposons (which are essentially semantic toolkits) are very specific taxonomically, with no evidence that they arise from anywhere else.
"That's what a scientific theory is, BTW - a cathedral of knowledge that explains variance."
There is noone who disputes variance.
An interesting article you might be interested in is here.
"Shared genetic material, shared aspects of biochemistry that could be different, shared morphology, etc."
Aren't those the same kinds of similarities between cars that have vastly different designers and designs? You're not proposing that cars are not the product of separate creations just because they have a lot of similarities are you?
"Nature abounds with examples where very remotely related genera will use very similar genes to specify tissues with similar functions but very dissimilar compositions. The same gene that specifies eyes in the fruit fly for instance specifies eyes in us humans. Yet our eyes are not like those of a fly at all."
Isn't this more of an argument for common design (design patterns, etc.) than for common descent?
Wherever it has the best/most cheese. Therefore, if the astronauts get stranded, they won't go hungry.
On a related note, if anyone is curious how memory management library calls such as "malloc" work, you might check out my article on the subject.
"Each of those entries is not unique to Perl (applying as well to other common languages like C++ or sh), straight-out false, or just as prevalent in "math geek" writings as standard speech."
Not really. While some individual ones are available elsewhere, Perl's combination is fairly unique, with some of them being really unique. For example, the sections "Disambiguation by number, case and word order", "Topicalization", ""Inevitable" Divergence", and "Pronominalization" are fairly perl-specific.
"That's a myth- a retroactive redefinition of the origin. Perl's design was taken as a union of the styles of sh, C, and awk."
c s.html
That's just surface structure. Perl doesn't seek to be a natural language processing platform. But it does intend to bring human language characteristics to programming. See here:
http://world.std.com/~swmcd/steven/perl/linguisti
"Do you think that the "modelling after human languages" thing was a success?"
c s.html
Yes, but not in the way that you are thinking. It was a success, not because it is easier or harder to learn, but because I can be more expressive in Perl than in other languages.
One of the great things that I love about Perl is that you can rearrange statements. I can say:
if($x) {
blahblahblah()
}
or I can say
blahblahblah() if $x;
In the former, I am emphasizing (to myself and other programmers after me) that the condition is more important, while in the latter I am emphasizing the action as having the importance.
Likewise, moving often-used idioms into the core language is a feature of human languages that he imported into Perl. While most programming languages would opt for several features of Perl to be libraries (like RegEx), Perl has it as a part of the syntax of the language itself. Importing the core idioms of a population into a language is something that real languages do.
Having both "if" and "unless" is a very human-language thing to do, and it makes it more obvious what you are trying to do in your program than a bunch of "if(! )"s.
The beauty of Perl is that programming in Perl is much more expressive than programming in other languages. The point is not to be "easier for noobs", but for the meaning in the program to be better conveyed to other programmers who are fluent in the language.
Having a pronoun is also very linguistic.
A more specific list of human-language features of Perl is here:
http://world.std.com/~swmcd/steven/perl/linguisti
"If anything, it's the opposite: they ought to stay away from it, and learn a language with a halfway sane syntax and semantics, as opposed to a warmed-over Unixy shell scripting language that went through a brief period of overuse during the dotcom bubble."
/ Perligata.html :)
Them are fightin words.
Whether you enjoy Perl or not, Perl is interesting because it was developed by a linguist and modelled after human languages, rather than by a Math geek modelled after a strict theoretical model. It's fairly unique in that perspective.
Even more, you can actually configure Perl to be an interpretted Latin:
http://www.csse.monash.edu.au/~damian/papers/HTML
"That's unreasonable. I use the CLI every day, and a GUI multiplies my productivity by allowing me to have multiple terminals open simultaneously."
You need to learn to use "screen".