A revolution for evolution - Intelligent design must not replace hard science in classrooms.

But the points at which the recombination take place are not.

Sure they are. Recombination varies linearly with distance. The further apart two genes are, the more likely a recombination will occur between them, because crossing over is random.

I noticed you also ignored the point that chromosome segregation is random. Convenient.

What you seem to be saying here is that neo-Darwinism is untestable. However, there are ways to speed up frequency of mutations in the lab, without affecting their distribution.

No, I'm saying that what we've observed is consistent with evolutionary theory.

We understand _some_ of it very well. But, for instance, it seems that E. Coli can actually regulate how well DNA polymerase operates, based on stress conditions:

First of all, it's DNA Poly III, not IV or V, that performs large-scale replications in E.Coli.

Second of all, this doesn't change the fact that random errors are introduced by all polymerases; regulating the activity of an error-prone polymerase does not change the random nature of the mutagenesis. It's just another way that prokaryotes can encourage diversity, which is necessary for survival by natural selection - which is consistent with evolutionary theory.

Finally, I notice you didn't answer my question about complexity, which is at the heart of the issue here. You want to see a complex adaptation, but you refuse to precisely define it.

How many base pairs are required to make an adapatation complex?

Can a prokaryote even show a complex adapatation that would satisfy your criteria?

"Second of all, this doesn't change the fact that random errors are introduced by all polymerases; regulating the activity of an error-prone polymerase does not change the random nature of the mutagenesis."

It points mutation to certain times and places. That is non-Darwinian, and is more inline with designed mechanisms than atelic processes.

"I noticed you also ignored the point that chromosome segregation is random. Convenient."

It's irrelevant.

"No, I'm saying that what we've observed is consistent with evolutionary theory."

It's more consistent with creationism. We keep on running into teleology in biochemistry.

"First of all, it's DNA Poly III, not IV or V, that performs large-scale replications in E.Coli."

That's precisely the point. Poly IV comes in when and (and possibly where) the organism needs modification. This is a purposeful, planned process.

"Finally, I notice you didn't answer my question about complexity, which is at the heart of the issue here. You want to see a complex adaptation, but you refuse to precisely define it."

Well-matched parts, multiple amino acid changes across multiple genes.

"How many base pairs are required to make an adapatation complex?"

If you are in the hundreds, I would count that as complex.

"Can a prokaryote even show a complex adapatation that would satisfy your criteria?"

There are many complex adaptations. The point is that none of them occur by Darwinian mechanisms. Take for instance Pseudomonas. It can adapt to new food sources within 9 days, by putting together pairs of entirely new genes. Now, if the mutational rate which produced the genes were present throughout the entire genome, error catastrophe would quickly occur. This indicates that the mutation was directed onto a single gene. In fact, the cell even knows to put the new gene on a plasmid to ship it to the rest of the colony that hasn't discovered it yet. I discuss it here:

http://crevo.blogspot.com/2005/06/evolution-chance-and-design-to-cb940.html

Likewise, Behe shows just how slow the Darwinian mechanism is in doing a change of only a few amino acids, if it is even possible at all:

http://www.proteinscience.org/cgi/content/abstract/ps.04802904v1

Our observations of beneficial change in organisms is almost entirely driven by mechanisms of purpose, not happenstance. The idea of Darwinism is almost completely foreign to everything that happens in biochemistry. Are there completely random mutations? Sure, they exist. But they aren't playing a major role in adaptation.

If you are in the hundreds, I would count that as complex.

So in other words, your argument against evolution is based on some arbitrary criteria and has nothing to do with evolutionary theory. Thanks, that's what I thought.

Pseudomonas / DNA Poly IV,V

Restricting mutagenesis (by whatever mechanism) to a specific part of the genome would give the organism a selective advantage and is consistent with natural selection. Hint: This is why sexual recombination is favorable. Even flu viruses show this pattern of having some parts of the genome more mutagenic than others, because natural selection favours it.

Also, note that it's very intellectually dishonest to use phrases like, "the cell even knows that" since you're implying higher order intellegence where none has been shown to exist, i.e. at the cellular level.

Our observations of beneficial change in organisms is almost entirely driven by mechanisms of purpose, not happenstance.

And yet every example of genetic change we've covered is effectively random. Even if an organism restricts mutation to a single gene, the mutated sequence will be randomly determined because of the fundamental biochemical mechanisms. Natural selection acts on those random mutations.

Forensic science is empirical.

Forensic science makes use of empirical science. Thus when when an investigator uses ballistics to determine the path of a bullet he is using an empirical science. When he collects his evidence and says that Dillinger fired the shot he is making a forensic, non-empirical, conclusion. When Evolution studies the human genome it is engaging in an empirical science. When it concludes that random mutations and natural selection over a long period of time accounts for the variety of life it is making a forensic conclusion that is only conjecture. The confidence that we can place in such forensic conclusion is variable. Thus in court we see the need for "preponderance of the evidence" in civil court and "beyond a reasonable doubt" in criminal court.

What about the theory that an invisible supernatural weathermaker causes many of the rain storms around the world? Is that deserving as a competing theory to Natural Meteorology? Should it be taught in schools as a rival theory?

Now you are being insulting as well as silly. This is based on the assumption that faith must be irrational and purely a matter of fideism. Anyone with a familiarity with philosophy would know that there are rational proofs for a belief in God in general and in the Christian revelation in particular. Inasmuch as human testimony is open to scientific study so is the witness of the Apostles. If the possibility of falsification by a random fossil find is enough to qualify Evolution as an empirical science then the same could be said of the Christian faith. The discovery of the tomb of Jesus with his bones intact would falsify it. Thus either both Evolution and Christianity are empirical sciences or neither is.

"Restricting mutagenesis (by whatever mechanism) to a specific part of the genome would give the organism a selective advantage and is consistent with natural selection."

It is not consistent with natural selection being able to _build_ such a restricting mechanism. As Dembski showed in Searching Large Spaces, building such a second-order mechanism is an order of magnitude harder than building a first-order system.

"Even flu viruses show this pattern of having some parts of the genome more mutagenic than others, because natural selection favours it."

Where do you base the idea that this pattern _originates_ from natural selection? What data, specifically, supports that natural selection _originated_ this selective mutagenesis?

"And yet every example of genetic change we've covered is effectively random."

Incorrect. It would be random if it were evenly distributed. All that has been shown is that it is a non-deterministic algorithm. That is not the same as randomness or haphazardness. It simply means that the algorithm employed has multiple search options to try next. Neo-Darwinism suggested the notion of a wholly unoptimized search. If a search is optimized, it had to be optimized for a particular purpose. Which, of course, negates Dawkins suggestion that they only appear to have a purpose. If you want to say that it is these purposeful change mechanisms which have originated by purposeless processes, it is up to you to provide the evidence, since all of the evidence of complex adaptation in genomic change is purposeful, directed change.

"Also, note that it's very intellectually dishonest to use phrases like, "the cell even knows that" since you're implying higher order intellegence where none has been shown to exist, i.e. at the cellular level."

The point is to show that the genomic change is directed from the cell -- it is not a passive process, it is the cell actively reconfiguring itself.

"Even if an organism restricts mutation to a single gene, the mutated sequence will be randomly determined because of the fundamental biochemical mechanisms."

If the organism restricts itself to a single gene, then it is NO LONGER RANDOM. You no longer have the purposeless notion of change -- instead it appears that the change is quite purposeful! The cell even has instructions as to which gene needs changing! That is a completely different paradigm of change as is taught in standard school texts. It is one totally consistent with ID and Creationism, but one which has no merit in atelic notions of origins.

To expand a bit on the "no longer random" part:

Let's say I need a new gene. There are several possibilities:

1) I have no idea I need something to change. If a cosmic ray or copying error causes something to change, and its beneficial, great. However, if the change is detrimental or doesn't fix my situation, I'm toast.
2) I know I need something to change, but have NO IDEA what. Therefore, I can cause increased mutations to occur randomly throughout my genome, and hopefully something good happens before I suffer from error catastrophe.
3) I know I need something to change, and I know it is this, specific gene. Therefore, I can put my resources to bear on changing this gene until I can sense that I am no longer in need.
4) I know I need something to change, and I have this part list of things that I know works to make specific things happen. I'm going to rearrange re-usable parts until I get something working.
5) I know I need something to change, I know what it is that needs changing, and I know exactly what I need to do to change it.

1 & 2 are Darwinism. 3-5 are ID and Creationism. Darwinists like to claim that 3-5 can be the result of 1 & 2. However, Dembski's No Free Lunch and Searching Large Spaces show why complex adaptations cannot occur through blind searches. Intelligence _must_ be put into the equation, or the blind search makes error catastrophe a certainty LONG before adaptations can occur.

If you have _data_ on how 3-5 can come into being as the result of 1 & 2, I'd sure be interested in seeing it. Until then, I think that biochemistry pretty clearly shows that teleology is quite well at play in biochemistry.

It would be random if it were evenly distributed.

... If the organism restricts itself to a single gene, then it is NO LONGER RANDOM.

So your definition of random is exclusive to a uniform distribution over the entire genome? I can't have random numbers with a normal distribution? Or a Poisson distribution?

Congratulations on redefining 'random' in order to better your own argument. This is getting to be a common trend with you. Yeesh. Have you even read a single biology/math textbook?

For the lurkers, here's a simple example. If I have the numbers [1][2][3][4][5] and I flip a coin randomly to change number 4 to either 6 or 8, guess what? The new sequence is random. It may have a narrow distribution, but because the new sequence isn't deterministic (i.e. you can't predict what it will be), it's random.

Where do you base the idea that this pattern _originates_ from natural selection? ... It is not consistent with natural selection being able to _build_ such a restricting mechanism.

Natural selection does not originate or build anything. It acts on existing diversity. You're clearly showing your unfamiliarity with evolutionary theory.

it is the cell actively reconfiguring itself ... Let's say I need a new gene

This implies intelligence (as does the entirety of the rest of your ridiculous post). This has not been demonstrated and should not be a part of your assertions.

Cells do not have an 'idea' about how they want to change. They do not 'plan' new phenotypes.

Genomic change is random through recombination or mutation. Natural selection acts on those changes. It is observed that nature is reactive, not proactive. This is consistent with evolutionary theory.

Really, why am I bothering to discuss this at all with you? If you're willing to redefine "random" to suit your purposes, there doesn't seem much hope in expecting a rational criticism of evolution from you.

Also, Dembski? No.

Forensic science makes use of empirical science. Thus when when an investigator uses ballistics to determine the path of a bullet he is using an empirical science.

When a paleontologist compares hominid skulls he is using emprical science. When geneticists compare DNA of species to test evolutionary hypothese they are using empirical science. Evolution is grounded in empirical science.

When he collects his evidence and says that Dillinger fired the shot he is making a forensic, non-empirical, conclusion.

I don't see how a conclusion can be either un-empirical or empirical. A conclusion can be based on empirical evidence or not.

If all emprical evidence points at Dillenger firing the shot then the conclusion in this case is based on empirical evidence.

Equally the existance of the dinosaurs is based on empirical evidence. Noone was around to witness the dinosaurs existing, but empirical observation of fossils supports that conclusion.

When it concludes that random mutations and natural selection over a long period of time accounts for the variety of life it is making a forensic conclusion that is only conjecture. The confidence that we can place in such forensic conclusion is variable. Thus in court we see the need for "preponderance of the evidence" in civil court and "beyond a reasonable doubt" in criminal court.

Sure I agree that theories in science have variable confidence and are not proven. I just disagree that they are merely guesses/conjecture.

Now you are being insulting as well as silly. This is based on the assumption that faith must be irrational and purely a matter of fideism.

I wasn't being insulting. I was looking at the matter objectively. I was not assuming the Intelligent Designer of life was God, but a generic designer.

What I don't understand now is why you think an invisible intelligent creator of species isn't silly and is science but an invisible intelligent creator of rainclouds *is* silly and isn't science. This has nothing to do with religion, but how to determine whether explainations are scientific explainations, or not. I don't see how you can allow one as science, but not the other.

Anyone with a familiarity with philosophy would know that there are rational proofs for a belief in God in general and in the Christian revelation in particular.

Officially, Intelligent Design does not say the designer is God. It could be aliens or whatever. The general explaination is simply that an unknown designer created species over time.

If the possibility of falsification by a random fossil find is enough to qualify Evolution as an empirical science then the same could be said of the Christian faith. The discovery of the tomb of Jesus with his bones intact would falsify it. Thus either both Evolution and Christianity are empirical sciences or neither is.

if falsification was the only criteria for a scientific explaination then it would be.

Evolution is grounded in empirical science.

I never said otherwise.

Sure I agree that theories in science have variable confidence and are not proven. I just disagree that they are merely guesses/conjecture.

Here we are getting to the heart of the matter. First, conjecture is not the same as a guess; it can be based on solid evidence. Conjecture is a logical conclusion that is not testable. In the case of Dillinger we are questioning a particular crime and is thus unrepeatable and untestable. The empirical evidence might be quite compelling so that we can reach the threshold of "beyond a reasonable doubt" that is required in a criminal court. Likewise, although all the evidence might point to Dillinger, it might be incomplete and not meet that threshold. We might have to settle for the threshold of "the preponderance of the evidence" and seek redress in civil court. A third possibility is that, although the evidence might produce a strong suspicion, nothing could be proved in any court.

If we agree that theories in science have variable confidence then it should be proper to discuss what confidence that should be given to the theory of Evolution. Umbrage should not be taken if some find evidence for Evolution to be incomplete and less than compelling.

The difference is that there is an adequate explanation for the formation of rainclouds whereas many people think that the gaps in the theory of Evolution are still too great to rule out a non-natural explanation. Occam's razor suffices for the first; it is not yet sharp enough for the latter.

Officially, Intelligent Design does not say the designer is God. It could be aliens or whatever. The general explaination is simply that an unknown designer created species over time.

I was not presenting an explanation of Intelligent Design but rather responding to your attempt at ridicule by the introduction of the unnecessary "invisible supernatural weathermaker". It is very popular to present supporters of Intelligent Design as nothing more that a bunch of twelve-toed flat earthers who have no rational reasons for their beliefs. The conclusions that would allow a supernatural explanation for life are just as rational as those that lead to the belief in Evolution.

if falsification was the only criteria for a scientific explaination then it [Christianity] would be.

I was specifically responding to your earlier statement that Evolution was an empirical science because if was falsifiable:

It is testable and therefore is empirical science. For example a human skeleton found in the cambrian would falsify the explaination that humans arose through minor variations over millions of years.

What other criteria would qualify Evolution as an empirical science that would rule out the acceptance of the Apostolic witness to the Resurrection? (Remember that I am speaking here of an empirical science, not a natural one.)

"So your definition of random is exclusive to a uniform distribution over the entire genome? I can't have random numbers with a normal distribution? Or a Poisson distribution?"

The distribution is not as important as the lack of teleology involved. If the cell is _directing_ the mutation it is no longer random, it is _directed_.

"Congratulations on redefining 'random' in order to better your own argument. This is getting to be a common trend with you. Yeesh. Have you even read a single biology/math textbook?"

I'm not redefining random. There is nothing random about changing a specific gene, even if there is randomness within the change. For example, if I have a search algorithm, there is no algorithmic difference between searching through an unordered 10-item list sequentially and searching through it randomly. The difference is that, in biology, randomizing it makes it more likely that one of the organisms will make the right choice. However, there is a big difference between searching a specific list in a random order, and searching a random area of memory in a random order to do a random change. The former is a part of a programmed algorithm, the latter is what Darwinists say is going on. Note that it is just as algorithmic to search non-deterministically as it is to do so deterministically. That is different from a completely random change.

"Natural selection does not originate or build anything. It acts on existing diversity. You're clearly showing your unfamiliarity with evolutionary theory."

Then you should alter your wording to reflect that.

"This implies intelligence"

No, it doesn't. It simply implies programming.

"Cells do not have an 'idea' about how they want to change. They do not 'plan' new phenotypes."

The evidence indicates otherwise. As I pointed out in the article, in specific stresses, E. Coli switches on a mutagenic form of DNA polymerase to modify specific genes. That's "having an idea".

"Genomic change is random through recombination or mutation."

It's amazing you keep this up in the face of evidence otherwise.

Conjecture is a logical conclusion that is not testable

In which case evolution isn't conjecture. Observations can be made that could potentially disprove evolution, so it is testable. It doesn't have to be reproduced in a lab to be testable.

Natural explainations cannot rule out non-natural explainations. Non-natural explainations always remain possible. Just because rain can form due to a natural process doesn't mean it always does. If you are going to use Occam's razor, then surely it's the intelligent design explaination which is simpler. It is afterall just "an unknown designer made rainclouds using an unknown method". That's it.

I was not presenting an explanation of Intelligent Design but rather responding to your attempt at ridicule by the introduction of the unnecessary "invisible supernatural weathermaker".

I wasn't attempting ridicule. I was pointing out that if you change the rules of science to allow ID to be a scientific theory then you implicitly allow other supernatural explainations to become scientific theories as well, even ones you don't think are rational.

An Intelligent Designer of life is not a ridiculous idea, and it is not an irrational idea. It makes a lot of sense and it might very well be true. But as it is not testable and so is not a scientific explaination.

The conclusions that would allow a supernatural explanation for life are just as rational as those that lead to the belief in Evolution.

A supernatural explaination for meteorology is also rational but also untestable. Weather is pretty complex and unpredictable, therefore what is irrational with an explaination for weather that involves the supernatural? One example would be some geia theory that says the earth is a concious living supernatural being and it controls the weather systems as part of some higher unknown plan. Is the only reason you think such a theory doesn't deserve to be science because you think it is irrational? Why is it irrational? It might be true afterall. The real reason it isn't science is that it is untestable.

People use the scientific method everyday unknowingly on a lot of things that aren't thought of as a science. For example I can make a hypothesis about where my lost car keys might be and test predictions based on that hypothesis. But while that might follow scientific methodology it isn't part of a scientific field so I wouldn't call it a science. But of course that doesn't make it any less credible or useful.

Evolution is a theory within the field of biology, because it seeks to explain the diversity of life, so it is thought of as a scientific theory. ID is an explaination which is within the field of biology, although I do not see it as a science because it cannot be tested and therefore verified in any way.

I suppose some theories in economics might be testable using the scientific method, but unless economics is considered a science (some people say it is, others disagree), then a theory in economics won't be called a scientific theory.

Generally religions are not sciences, because a lot of it is based on non-empirical evidence, such as divine texts. That's why religious faith exists. But that doesn't mean science cannot be applied to some of it.

Creation Science is a science because it is a broad explaination that falls within verious fields like biology and geology.

The acceptance of the Apostolic witness to the Resurrection might be testable using the scientific method, but I really do not know how broad an explaination it is, or what scientific field it would fall under.

In which case evolution isn't conjecture. Observations can be made that could potentially disprove evolution, so it is testable. It doesn't have to be reproduced in a lab to be testable.

While the observations are testable, the conclusion that they were the result of random mutation and natural selection is not.

Exactly which rule of science rules out Intelligent Design; falsifiability? Intelligent Design is making its claim on specific conclusions that the observed variety of life forms cannot be explained by natural means. Each of these individual claims can be falsified by showing a specific natural cause. Likewise, Intelligent Design is attempting to use the scientific method to disprove Evolution by falsifying specific jumps in the evolutionary record as being impossible by natural means.

I would like to point out here that neither Evolution nor Intelligent Design need, or should, be taken as a whole rather than in their parts. Each could be true in explaining specific changes in the evolutionary order. Thus some jumps in the evolutionary record could be by natural causes and some not. It is the individual claims that need to be judged. The evidence for Natural Evolution is much too weak to assume that it must cover all the changes that we observe. Perhaps it may in time, but that has yet to be shown.

To continue from your above statement, since Intelligent Design claims that its conclusions are based on reason, why would its acceptance have to admit irrational theories?

Weather is pretty complex and unpredictable, therefore what is irrational with an explaination for weather that involves the supernatural?

Unpredictability, as you know, does not rule out natural explanations. Therefore there is no need to appeal to the supernatural. Intelligent Design's objection to Evolution is not that it is unpredictable but that it is impossible.

ID is an explaination which is within the field of biology, although I do not see it as a science because it cannot be tested and therefore verified in any way.

Its individual claims that specific evolutionary changes are impossible by natural means are testable because they could be falsified by identifying the particular natural cause.

Personally I hold that economics is a science. It is a social science, not a natural one. Although generally accepted in popular speech, it is a conceit of the natural sciences to appropriate the term "science" to themselves alone. There are true sciences outside the natural fields.

I was not claiming that the acceptance of the Apostolic witness to the Resurrection was a natural science, only that it is an empirical as Evolution; either both are or neither are. For the record I do not think that the conclusion of either is empirical.

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