This is quite a lot to respond to, so let's take it one step at a time.
A change in genetic information does not mean that new information has been created. For an analogy, if you are programming a code and you make a syntax mistake, the code is different, but the vast majority of the time the mistake will lead to negative errors. Basically, functional information is lost, degraded. Even if you grant that some mistakes will lead to positive changes (which is debatable), it is a huge leap of the imagination to declare that successive, accumulating beneficial mutations could produce the vast amount of new information required for evolution to occure. It simply defies the laws of mathematical improbability. For every one beneficial mutation there are 999 harmful ones. Even if you ignore that fact, you've got a long way to go to prove that each mutation in a series that creates a new feature in an organism can provide a positive effect, when it is obvious that thousands of positive mutations would be required for even the simplist of the changes that evolution claims have happened to every single species in the world. You cannot possibly bridge that gap, or at least, logically bridge that gap.
Ok, let's refine what I said. If a mutation degrades information, in that the mutations causes the genetic information to lose a function it once had, I would not refer to that mutations as adding new, functional information. I would say that genetic information has been negatively corrupted. If a mutation in a fly's genetic structure causes it to grow four wings, yet it cannot fly anymore, I would call that an information-degrading mutation, for the simply reason that the fly has lost its ability to fly, and has not gained a more-complicated ability at the same time.
I think you are forgetting what exactly a negative mutation is. If the mutation is indeed negative, the organism's defective mutation will not propogate throughout the gene pool of that species. It will be less fit, and therefore, less able to pass along its gene.
Mating is indeed not random, which is why truly negative mutations will not propogate.
The negative or positive orientation of a mutation is determined by natural selection. If the organism can't run away from its predator, it doesn't matter if it is more attractive to a mate. Still, natural selection decides it pretty much automatically.
My reference to mutations being negative or positive was for simplicity's sake, but it is quite obvious that the majority of mutations have a profoundly negative effect on an organism while offering no positive effects to outweigh it.
There are mutations which have little to no effect on reproduction, which means that they play no role in natural selection. Other factors may propagate a mutation, but unless the mutation is positive it will not benefit the organism and cause the mutation to be propogated, and thus, successive mutations cannot accumulate and then benefit the organism. The idea of a "long chain of successive, beneficial mutations" that slowly accumulates is simple wrong. It is indefensible unless the vast majority of the mutations in that sequence can be shown to create a positive or neutral effect, without causing a severe negative effect. As you should already know, that is a huge difficutly to prove plausible.
We have never seen a mutation create a completely new gene; it has never happened as far as we know. To argue otherwise is simple speculative. You cannot say that a gene is altered and thus a new gene has been created, when in fact the first gene's function has been lost or degraded. At some point, new genes must be added, and old ones simply cannot be slowly reconfigured, with many harmful consequences. Unfortunately for evolution, this is consistently what we see happening.
Sure, so the mutation has little effect, and thus there is no reason to believe that the mutation has any reason to propogate among the entire species. You cannot argue that it simply will propogate, when natural selection says that there is no reason for it to.
Sure.
Your previous statement "There won't be a noticeable phenotype to affect reproduction, despite the genetic difference" is a perfect example of a "neutral" mutation. Obviously, the mutation is not 100% neutral, but it can be said to be basically neutral since the effect is non-noticeable, and non-contributing to natural selection.
Not all genes are on the same chromosome and linked in this way. My point is simple: mutations that cause positive effects are extremely rare. Much more often is harmful mutations that cause an organism to be less fit, or mutations with small effects that make no noticeable change in an organism's fitness. With either of the latter two, that mutation by itself has no reason to propogate, and cannot accumulate.
So, with what you said about mutations affecting and being affected by other genes. Yes, that is true, BUT it still does not change the fact that in order for a series of positive mutations to be responsible for ultimately creating new genes, the mutations must provide positive benefits along the way. It is a blind leap of faith to argue that all the mutations will be neutral or non-damaging, AND also linked to other desireable genes, up until the point where a new gene is created and becomes desireable by itself.
I never argued against the fact that mutations with slight effects would not show increases in frequency, but you must know that eventually the mutations must have a positive effect or else they will simply not be responsible for an organism's evolution.
The number of mutations in order for the gaps to be filled in are in the thousands... the facts are that each one of them could simply not be non-damaging, and the statistics show that the much much greater probability would be that the series of mutations would never occur because of the damage that would be done in each successive mutation.
This chain of positive mutations is imaginary, and the suggested chain of non-effecting mutations that eventually lead to steps forward in evolution is implausible.
That is quite a lot of information to respond to. I finally managed to find sources that discussed the experiments you are referring to.
I was a little dismayed to find out that you failed to point out the alternative hypothesis that still exists:
The natural substrate for phosphotriesterase will have structural similarity to these phosphotriesters when it is discovered.
So basically, because they don't know the natural substrate, the additional hypothesis is that the enzyme evolved over the past 50 years. I wonder why you failed to mention this.
I'm saying that the evidence to support your view does not exist. It is speculation.
New, functional information. A mistake in copy may change the order of the sequence in a gene, but that is not the same as new, functional information being created.
The functionality is on the level of a changing identifier, defined only by the proteins themselves. Once again, the reshuffling of genetic information is not the creation of new information, it is an organization of preexisting information. HIV is indeed unique in many of its properties, an amazing virus. But to extrapolate the mutation of HIV, like the aspect of multiple antibiotic resistance, and say that it is evidence for mutations leading to evolution, is simply not true. The change has a great effect, but that does not mean that the change itself is large or significant in terms of information or complexity increase, but rather that our body's reaction to is significant. It is, by comparison, a shuffling of the genetic information that does not increase information, but just simplpy change it. There is no added functionality. The functional change is only on the side of our immune defenses, and the drugs that are designed to destroy the virus.
Two points:
1) There is no increase in functional complexity with the mutation. It is not the type of change, in quality or direction, which would cause the virus to become a more complex type of living organism.
2) The virus has no evolutionary relationship to any other form, so the changes with it cannot be transferred or used as examples for evolutionary history of truly living organisms.
I don't assume that fossils have a high rate of preservation during normal passing of time. But the total absence of any fossil showing a transition between the major changes that are proposed to have occurred is astounding. Combine that with the fact that there are supposedly millions of years of time while these changes were to occur, and you can see why there are so many objections to the "conclusions" evolutionary biologists are so eager to jump to.
Here's what's happening. I'm challenging the proposed evidence for evolution, and you are saying that I must also challenge these other things science holds to be true. The reality is, I'm not questioning these other things, because the evidence for them is strong, and I do not have reasons to doubt the conclusions that others have reached based on that evidence.
However, I see the same evidence you see for evolution, but I also see how the conclusions are drawn that do not match with the factual data that has been collected. When that happens, I have to ask myself what other motives could possibly exist besides the desire to know the truth about the history of life. This I have done. Upon digging deeper into the question, I have found more uncertainty about evolution, not less. I have read the objections, and looked for the answers, but the answers are not there, and I am not willing to throw reason and science out the window to believe something that has been handed to me by others with false assumptions, false motives, and questionable evidence.
I'm not sure why you think we can't test gravity, but I assure you there are ways. The history of life is just that: history. It happened one way, and just one way. In that respect, we cannot test it, we can only construct a plausible scenario based on the evidence we have. My arguement is that evolution's scenario is neither plausible, nor based on the evidence we have.
You see, most people will not question something that scienctists support, unless there is a compelling reason to do so. I have compelling reasons to question evolution.
There are other explanations, also plausible, that are supported by the data we have. For instance, anatomic homology supports the Creation model as much as it supports evolution. It is not direct evidence for evolution, as some would lead you to believe.
Science does work by proposing alternative theories to present questions. I believe the evidence greatly favors the Creation model. Many scientists are also naturalists, and cannot accept the idea of God participating in physical reality. For that reason alone, many refuse to dismiss evolution, or accept the Creation model, regardless of how improbable evolution becomes.
But if science does not lead us to the truth about the history of life, then where is its value? I would rather accept Creation and dismiss evolution than believe a lie due to my philosophical belief in naturalism.
Irreducible complexity is a good one. A lot of problems there. How about the nonsupportive fossil record, or the discrepancies in the dating methods? Or biogenesis? Or what about the geological layers that misrepresent the proposed timeline of evolution?
I could go on...
Indeed, the species are united quite remarkably, each well suited for their role. The problem is not that gaps exist, but that the gaps are incredible in their magnitude. For instance, no fossils exist to connect the supposed transition from reptile to bird. None. How many millions and millions of years do you imagine that transition taking? Do you not find it strange that not a single fossil can be found during that time period?
This is but one example. Read Michael Denton for some more... the examples abound.
Originally posted by: abj13
Then what are you defining as "information?" A mutation by itself changes the genetic information, therefore changes the genetic sequence and creates new genetic information (in comparison to the wildtype genotype). Are you trying to say that information must be phenotypically represented?
A change in genetic information does not mean that new information has been created. For an analogy, if you are programming a code and you make a syntax mistake, the code is different, but the vast majority of the time the mistake will lead to negative errors. Basically, functional information is lost, degraded. Even if you grant that some mistakes will lead to positive changes (which is debatable), it is a huge leap of the imagination to declare that successive, accumulating beneficial mutations could produce the vast amount of new information required for evolution to occure. It simply defies the laws of mathematical improbability. For every one beneficial mutation there are 999 harmful ones. Even if you ignore that fact, you've got a long way to go to prove that each mutation in a series that creates a new feature in an organism can provide a positive effect, when it is obvious that thousands of positive mutations would be required for even the simplist of the changes that evolution claims have happened to every single species in the world. You cannot possibly bridge that gap, or at least, logically bridge that gap.
Originally posted by: abj13
I don't understand what you are getting at with that statement. A simple statement falsifies what you said: A negative mutation that is inheritable affects an organism to enact the laws of natural selection, but that is creating "new information."
Ok, let's refine what I said. If a mutation degrades information, in that the mutations causes the genetic information to lose a function it once had, I would not refer to that mutations as adding new, functional information. I would say that genetic information has been negatively corrupted. If a mutation in a fly's genetic structure causes it to grow four wings, yet it cannot fly anymore, I would call that an information-degrading mutation, for the simply reason that the fly has lost its ability to fly, and has not gained a more-complicated ability at the same time.
Originally posted by: abj13
Now understand what I said with the previous statement, a negative mutation does not necessarily mean it will be "selected out of the population" or remain at a low frequency. That allele will remain, because populations are not always in Hardy-Weinberg equilibrium. Mating is not random. Population size is not always sufficiently large. There is emmigration and immigration. This will enable a negative mutation to remain in the population and/or propegate.
I think you are forgetting what exactly a negative mutation is. If the mutation is indeed negative, the organism's defective mutation will not propogate throughout the gene pool of that species. It will be less fit, and therefore, less able to pass along its gene.
Mating is indeed not random, which is why truly negative mutations will not propogate.
Originally posted by: abj13
Another thought-provoking example is this: A negative mutation could affect the running ability of a organism, but may make that organism more attractive. Is that negative or positive?
The negative or positive orientation of a mutation is determined by natural selection. If the organism can't run away from its predator, it doesn't matter if it is more attractive to a mate. Still, natural selection decides it pretty much automatically.
Originally posted by: abj13
Your characterization of mutations is way too black and white. You assume a "negative" mutation will not be passed onto further generations. However, not all negative mutations impact reproduction to sufficiently inhibit it. Mutations have a wide spread in their effects, because of aspects like redundancy and degeneratcy. Mutations are not always "on and off" switches for genes.
My reference to mutations being negative or positive was for simplicity's sake, but it is quite obvious that the majority of mutations have a profoundly negative effect on an organism while offering no positive effects to outweigh it.
There are mutations which have little to no effect on reproduction, which means that they play no role in natural selection. Other factors may propagate a mutation, but unless the mutation is positive it will not benefit the organism and cause the mutation to be propogated, and thus, successive mutations cannot accumulate and then benefit the organism. The idea of a "long chain of successive, beneficial mutations" that slowly accumulates is simple wrong. It is indefensible unless the vast majority of the mutations in that sequence can be shown to create a positive or neutral effect, without causing a severe negative effect. As you should already know, that is a huge difficutly to prove plausible.
We have never seen a mutation create a completely new gene; it has never happened as far as we know. To argue otherwise is simple speculative. You cannot say that a gene is altered and thus a new gene has been created, when in fact the first gene's function has been lost or degraded. At some point, new genes must be added, and old ones simply cannot be slowly reconfigured, with many harmful consequences. Unfortunately for evolution, this is consistently what we see happening.
Originally posted by: abj13
A mutation could also cause an increase or decreased amount of protein production. This should be obvious when looking at regulatory proteins like transcription factors. What is the difference in a person who has 100mg/dl of glucose in their blood, versus a person with 95 mg/dl of glucose? There won't be a noticeable phenotype to affect reproduction, despite the genetic difference.
Sure, so the mutation has little effect, and thus there is no reason to believe that the mutation has any reason to propogate among the entire species. You cannot argue that it simply will propogate, when natural selection says that there is no reason for it to.
Originally posted by: abj13
Genotype does not always equal phenotype.
Sure.
Originally posted by: abj13
Furthermore, your concepts of netural mutations is incorrect. Genes are linked. They are linked on strands of DNA and the lengths of chromosomes. The natural selection of one gene on part of a chromosome will also influence the allelic frequency of other genes, since they are linked on the same chromosome.
Your previous statement "There won't be a noticeable phenotype to affect reproduction, despite the genetic difference" is a perfect example of a "neutral" mutation. Obviously, the mutation is not 100% neutral, but it can be said to be basically neutral since the effect is non-noticeable, and non-contributing to natural selection.
Not all genes are on the same chromosome and linked in this way. My point is simple: mutations that cause positive effects are extremely rare. Much more often is harmful mutations that cause an organism to be less fit, or mutations with small effects that make no noticeable change in an organism's fitness. With either of the latter two, that mutation by itself has no reason to propogate, and cannot accumulate.
So, with what you said about mutations affecting and being affected by other genes. Yes, that is true, BUT it still does not change the fact that in order for a series of positive mutations to be responsible for ultimately creating new genes, the mutations must provide positive benefits along the way. It is a blind leap of faith to argue that all the mutations will be neutral or non-damaging, AND also linked to other desireable genes, up until the point where a new gene is created and becomes desireable by itself.
Originally posted by: abj13
Think about it. If a organism with a high level of fitness and reproductive potential suddenly gains a "neutral" mutation, what will happen to the neutral mutation's allelic frequency? Before the mutation, its frequency (for the sake of simplicity) was zero. But after organism reproduces, that neutral mutation's frequency is greater than zero. Since most of the offspring will likely have a high level of fitness and reproductive potential, the "neutral" mutation will propegate in each subsequent generation, creating a new form of genetic information. The accumulation of this neutral mutation is not random. It is inherently coupled to the rest of the genome, and the other aspects of evolution.
I never argued against the fact that mutations with slight effects would not show increases in frequency, but you must know that eventually the mutations must have a positive effect or else they will simply not be responsible for an organism's evolution.
The number of mutations in order for the gaps to be filled in are in the thousands... the facts are that each one of them could simply not be non-damaging, and the statistics show that the much much greater probability would be that the series of mutations would never occur because of the damage that would be done in each successive mutation.
This chain of positive mutations is imaginary, and the suggested chain of non-effecting mutations that eventually lead to steps forward in evolution is implausible.
Originally posted by: abj13
NO!
That is not even close to what I was saying. The chemicals provided an environmental selective pressure to promote the selection of the phosphotriesterase protein with a high affinity for phosphotriester bonds. The allele would have never been propegated and refined if there was not the chemical selective pressure. The mutation, though, is random, but must have been recent, because A)no other bacteria show phophotriesterase activity, B)phosphotriesterases have only been "abundant" in the past 50 years. But read my next part of my response:
That conclusion doesn't take the final step, when I posed the question: "How could an enzyme arise that could catalyze chemicals never seen by bacteria?" Now let me frame that question. Since bacteria have never been exposed to phosphotriester pesticides, phosphotriesterase should be a "neutral" gene and protein. Now, if we assume what you said, that phosphotriesterase is already present in bacteria, it should be seen in other bacteria with zero effect on their fitness. Yet, we've got a problem.
...
So where did phosphotriesterase arise? If it was already present, it should be present in other populations of bacteria, only as a neutral affect on those species. But that isn't the observation. Therefore, pinning that phosphotriesterase has always existed is a badly sinking ship.
The conclusions we can draw is that a mutation had to result in the new enzymatic activity. This mutation must have occured very recently, because of the activity is not seen in other bacteria, nor is it seen in other populations of bacteria that have been exposed to the chemicals. Further selection and mutation would refine the enzymatic site, to promote the high affinity phosphotriesterase has for human chemicals.
New genetic and phenotypic information arose.
That is quite a lot of information to respond to. I finally managed to find sources that discussed the experiments you are referring to.
I was a little dismayed to find out that you failed to point out the alternative hypothesis that still exists:
The natural substrate for phosphotriesterase will have structural similarity to these phosphotriesters when it is discovered.
So basically, because they don't know the natural substrate, the additional hypothesis is that the enzyme evolved over the past 50 years. I wonder why you failed to mention this.
Originally posted by: abj13
Originally posted by: Trevelyan
Your example of the yeast cell is merely a speculation, without concrete evidence to support it.
And how? You statement is at the level of saying "no you are wrong."
I'm saying that the evidence to support your view does not exist. It is speculation.
Originally posted by: abj13
Originally posted by: Trevelyan
but the fact that it changes does not mean new information is being created. (Read: new, functional, information.)
LOL, what are you defining as "new?" Seems like you are dancing around the issue by demanding something has to have a new "use."
New, functional information. A mistake in copy may change the order of the sequence in a gene, but that is not the same as new, functional information being created.
Originally posted by: abj13
Protein coat A is not genetically or phenotypically the same as protein coat B. That is completely new information, because the genetic information changed, and the functionality has changed (now it can avoid the previous generation of anti-bodies).
The functionality is on the level of a changing identifier, defined only by the proteins themselves. Once again, the reshuffling of genetic information is not the creation of new information, it is an organization of preexisting information. HIV is indeed unique in many of its properties, an amazing virus. But to extrapolate the mutation of HIV, like the aspect of multiple antibiotic resistance, and say that it is evidence for mutations leading to evolution, is simply not true. The change has a great effect, but that does not mean that the change itself is large or significant in terms of information or complexity increase, but rather that our body's reaction to is significant. It is, by comparison, a shuffling of the genetic information that does not increase information, but just simplpy change it. There is no added functionality. The functional change is only on the side of our immune defenses, and the drugs that are designed to destroy the virus.
Two points:
1) There is no increase in functional complexity with the mutation. It is not the type of change, in quality or direction, which would cause the virus to become a more complex type of living organism.
2) The virus has no evolutionary relationship to any other form, so the changes with it cannot be transferred or used as examples for evolutionary history of truly living organisms.
Originally posted by: abj13
Actually no. Unless you make absurd claims abou the fossil record, ie like others assume that fossils have a high frequency of being preserved.
I don't assume that fossils have a high rate of preservation during normal passing of time. But the total absence of any fossil showing a transition between the major changes that are proposed to have occurred is astounding. Combine that with the fact that there are supposedly millions of years of time while these changes were to occur, and you can see why there are so many objections to the "conclusions" evolutionary biologists are so eager to jump to.
Originally posted by: abj13
So, an experiment with the manipulation of variables is required for it to be "non-speculative?" That's more specious reasoning. By your own logic, our ideas of gravity in the solar system are purely speculative, since we cannot "test and experiment" with them. Heisenberg's Uncertainty principle should throw a wrench into quantom theory. If we cannot have a clue about the electron, how in the world can we assume there are distinct energy levels. The evidence of light emission is then purely speculative, since we are not directly manipulating the electron.
Here's what's happening. I'm challenging the proposed evidence for evolution, and you are saying that I must also challenge these other things science holds to be true. The reality is, I'm not questioning these other things, because the evidence for them is strong, and I do not have reasons to doubt the conclusions that others have reached based on that evidence.
However, I see the same evidence you see for evolution, but I also see how the conclusions are drawn that do not match with the factual data that has been collected. When that happens, I have to ask myself what other motives could possibly exist besides the desire to know the truth about the history of life. This I have done. Upon digging deeper into the question, I have found more uncertainty about evolution, not less. I have read the objections, and looked for the answers, but the answers are not there, and I am not willing to throw reason and science out the window to believe something that has been handed to me by others with false assumptions, false motives, and questionable evidence.
Originally posted by: abj13
These aspects of science are directly comparable to evolution. You argue against evolution since doesn't have "test and experimentation," but that is exactly the issue with quantum theory and other aspects like gravity on the macro-scale.
I'm not sure why you think we can't test gravity, but I assure you there are ways. The history of life is just that: history. It happened one way, and just one way. In that respect, we cannot test it, we can only construct a plausible scenario based on the evidence we have. My arguement is that evolution's scenario is neither plausible, nor based on the evidence we have.
You see, most people will not question something that scienctists support, unless there is a compelling reason to do so. I have compelling reasons to question evolution.
Originally posted by: abj13
The point of variable experimentation is to obtain data. We already have data for the solar system or for evolution, through observation and analysis. Science is about testable hypotheses, not adhereing to a specific dogma of data collection. I don't know where you get the idea that data collection must involve the manipulation of variables. Evolution predicts X, Y, Z. Well, we can go to the fossil record, genomes, current species analysis, and well, this all supports predictions X, Y, Z.
There are other explanations, also plausible, that are supported by the data we have. For instance, anatomic homology supports the Creation model as much as it supports evolution. It is not direct evidence for evolution, as some would lead you to believe.
Originally posted by: abj13
The problem others have though, if evolution is false, then what hypothesis does the data fit?
Science does work by proposing alternative theories to present questions. I believe the evidence greatly favors the Creation model. Many scientists are also naturalists, and cannot accept the idea of God participating in physical reality. For that reason alone, many refuse to dismiss evolution, or accept the Creation model, regardless of how improbable evolution becomes.
But if science does not lead us to the truth about the history of life, then where is its value? I would rather accept Creation and dismiss evolution than believe a lie due to my philosophical belief in naturalism.
Originally posted by: abj13
Originally posted by: Trevelyan
There is an ample supply of unanswered questions that continue to be unanswered. The criticisms are mounting, but no one seems to have the time or ability to settle them.
Such as?
Irreducible complexity is a good one. A lot of problems there. How about the nonsupportive fossil record, or the discrepancies in the dating methods? Or biogenesis? Or what about the geological layers that misrepresent the proposed timeline of evolution?
I could go on...
Originally posted by: abj13
The usage of "transitionary fossils" always ends up being butchered by people when they challenge it. A scientist may find that organism B is "transitionary" to organisms A and C. The only problem is that some people will demand "Well, what is transitionary to A and B?" This logic, though, completely ignores the initial statement that B is "transitionary" to A and C. Its funny sometimes, if one takes a step back from the evolutionary tree and look at it as a whole, its incredibly surprising how well united the species are.
Indeed, the species are united quite remarkably, each well suited for their role. The problem is not that gaps exist, but that the gaps are incredible in their magnitude. For instance, no fossils exist to connect the supposed transition from reptile to bird. None. How many millions and millions of years do you imagine that transition taking? Do you not find it strange that not a single fossil can be found during that time period?
This is but one example. Read Michael Denton for some more... the examples abound.