[_ Old Earth _] Permutation Problem for Evolution

[Barbarian]

All scientific methods like geological columns which can be tested and calibrated using fossil evidences and radiometric dating can be used and are allowed. Observed and documented evolution in short run can also be used in calculations.

Let's tighten this up a bit. Let's limit evidence to verifiable data obtained by experimentation and observation of the physical universe. Let's make a distinction between data, which is information obtained by scientific inquiry, hypotheses, which are used to propose meaning of the data, and theories, which are ideas that have been tested and confirmed by investigation.

Non-scientific methods or any scientist’s opinions are not allowed.

Shall we allow Popper's and Kuhn's concepts of what is scientific, be the standard? How will you define what is "scientific?"

There are strict rules on what contributes an evidences and explanation. Fossils are observations. However, these fossils are not evidences for Evolution but rather, evolution is an explanation for those fossils.

That's a bit too circular to be used. Of course all data, including fossils, are evidence. They are evidence for evolution. However, I'd be willing to go back and re-establish the fact for you. What would you reasonably expect to be in the fossil record, if our present understanding of the way speciation works is true?

Any evidence that support evolution using random mutations and natural selection, must also not be an evidence for other methods like artificial selection that can produce the same results.

Why do you think there's a difference between natural selection and artificial selection? In the past, unethical creationists have defined "artificial selection" to be anything involving the investigation of a scientist. Obviously, we can go no further if that's what you mean. I assume you don't mean that.

This is to make sure the evidence is strictly for evolution and to rule out other possibilities.

Some things in evolution could be interpreted in religious ways to mean other things. That being so, we will only concern ourselves with the question of whether or not it is evidence for evolution.

The scientific process must be able to be simulated using a computer model to confirm if the explanation provided is indeed correct.

Not all scientific investigation can be reduced to a simulation. Further, such simulations depend on models that must be something less than a perfectly accurate depiction of the modeled process. We need to note the limitations of such models.

Since evolution including the natural selection entirely depends on mutations which are random, the number of possible mutations required in each generation and the number of times the mutations had to be naturally selected by the environment and how they agree with fossil evidence in order to prove evolution must be clearly explained.

If you want to know this, you will have to learn about population genetics, which is highly mathematical. But I'm willing to show you. Do you understand why the vast majority of possible mutations will not be preserved in a specific environment, greatly reducing the effective scope of evolutionary change?

Unexplained repeated favorable-ness from randomness is strictly not allowed. While random events are allowed, repeated random events that are favorable for a particular event to occur which is artificially simulated, will be declared artificial and not random.

This is not a matter of opinion. We should go with likelihoods, say to the 90% confidence level. Is that acceptable?

The level of random occurrences must be in agreement with all laws of Mathematics including probability, and permutations and combinations.

Explain what a random event is. I'm puzzled as to why you think permutations and combinations are an issue.

The below permutation problem for evolution must be addressed properly and scientifically.

The randomness used to prove evolution using “random mutations†will be tested against Kolmogorov randomness (or algorithmic randomness) which states, a string (usually of bits) as being random if and only if it is shorter than any computer program that can produce that string.

Won't work. "Random mutations" aren't random in that sense. Some sites on the genome are more prone to mutations than others, depending on the particular genome. "Random", in the sense that it's used in population genetics, means that the particular mutations that appear are not predictable for any given organism.

Randomness of mutations was verified independently by Luria and Delbruck, who showed that mutations did not appear in response to environmental pressures. (for which they were awarded a Nobel) We'll have to use that measure if you want to talk about genetics.

The properties of randomness like uniformity (i.e. equally probable every where) and independence (i.e. current value of a random variable has no relation with the previous value), will be tested where ever random events/values are used in proving evolution.

Unfortunately, that's not strictly true in genetics, either. A given change to a genome may alter the likelihood of a different mutation. I'm thinking you're probably getting into things that you don't have the ability to test.

Show me a problem, and we'll take a look at it.

 

[Barbarian]

Take any two genomes of single celled organisms (the lowest single celled genome is half-a-million base-pairs)

Let's make this a bit more accurate. Since a change to any base pair in a gene mutates that gene, you can use genes, thus at once making the process simpler and more accurate.

in which one must be an ancestor of another. You must be able to explain how evolution was able to defy permutations (possible mutations from one species) using random mutations and natural selection.

Let's take a look at that. Suppose we know the genomes of your great, great, great, grandparents. If you descended from them, your genome would be some combination of those (we can ignore permutations, since the order of those genes on a chromosome does not normally affect the expression of those genes). There would be 656 chromosomes from which you'd get 46 The possible permutations of those chromosomes (assuming no crossovers, or other unusual effects) would be 1.1448954580977759379278948070893e+1507 . A huge number. But since the order in which you get those chromosomes doesn't matter, we can use combinations, instead. Here we will get 7.5154665846200250738198335347286e+128 possible combinations. As you see, the "problem" is that the likelihood of you actually descending from those people is so unlikely as to be effectively impossible. Yet you got here. In some cases, it was by natural selection; some of those genes from some of those people were harmful enough to be removed. Other times, it was just a random event that gave rise to some part of your genome. The "permutation problem" doesn't exist for this.

Now, let's consider the case of a population, a small portion of which becomes geographically isolated. Over 20 thousand years, the isolated population has (let's say) three mutations that when all present in the genome, makes it impossible for the new population to successfully breed with the old population.

Given that there were billions of possible combinations of mutations, is it impossible for this particular combination to have formed? If so, explain how. If not, there "permutation problem" doesn't exist.

Feel free to take this to the base pair level. But the result will be the same.

The actual level of possible mutations that can occur (that is, if 2 values Adenine-Thymine and Guanine-Cytosine – AT, GC for each base-pair it is 2^5000000) and how natural selection was able to pick a needle in a haystack from that massive data-set must be properly explained.

Simple. It didn't. It just happened to have those particular mutations. It could have gone otherwise; there were lots of other possible favorable combinations. As you see, it's not random, since all the unfavorable combinations were eliminated, and only favorable ones retained.

If natural selection which is non-random depends on mutations which are random, and considering the evidences for observable natural selection, why is the timescale used for “observable natural selection” does not fit the “non-observable grand-scale evolution”.

As you learned earlier, it does fit nicely. Gould did a nice analysis on the growth of hominid brains, showing that it wasn't particularly fast, given the number of mutations that would be possible in a few million years.

To explain better, humans differ by 0.1% of genome with each other which is 3 million base-pairs. However, chimpanzees differ by 5% which is 150 million base-pairs. If we had a common ancestor with Chimpanzee 8 million years back, that is around 400000 generations back (20 years/generation), you must explain how the 150 million base-pairs (or half of it say, 75 million base-pairs considering that we don’t have the exact genome of common ancestor but have the closest relative) got themselves in order to form the human species in just 400000 generations, yet the permutations for it (that is, if 2 values Adenine-Thymine and Guanine-Cytosine – AT, GC for each base-pair it is 2^150000000).

I think you are able now to realize why this is no problem. You found an arrow stuck in a tree, and drew a bulls-eye around it. Barry Hall, in his classic work on evolution in E. Coli, documented the evolution of a new, irreducibly complex enzyme system in a very short time. The mutations were, of course, random, but the gradual evolution of a new enzyme happened by the population retaining those mutations that made the enzyme better and better over time.

The "permutations" of base pairs that didn't improve (or actually degraded) the enzyme's specificity, were lost as the bacteria with more efficient enzymes quickly overgrew the rest. And that's all it takes.

 

[felix]

All scientific methods like geological columns which can be tested and calibrated using fossil evidences and radiometric dating can be used and are allowed. Observed and documented evolution in short run can also be used in calculations.

Let's tighten this up a bit. Let's limit evidence to verifiable data obtained by experimentation and observation of the physical universe. Let's make a distinction between data, which is information obtained by scientific inquiry, hypotheses, which are used to propose meaning of the data, and theories, which are ideas that have been tested and confirmed by investigation.

sure.

Non-scientific methods or any scientist’s opinions are not allowed.

Shall we allow Popper's and Kuhn's concepts of what is scientific, be the standard? How will you define what is "scientific?"

No. We are not living in 70s and 80s where computer wasn't there and Popper and Kuhn would have no idea "computational approach" of "scientific inquiry" .
We will use "computational approach". Today, we have cloud with power to simulate rocket launches, planetary motions, and several other things. So, let's use "computational approach".

There are strict rules on what contributes an evidences and explanation. Fossils are observations. However, these fossils are not evidences for Evolution but rather, evolution is an explanation for those fossils.

That's a bit too circular to be used. Of course all data, including fossils, are evidence. They are evidence for evolution. However, I'd be willing to go back and re-establish the fact for you. What would you reasonably expect to be in the fossil record, if our present understanding of the way speciation works is true?

No. All data, including fossils are "observations".

E.g.,
A apple falling down is an evidence for gravity: The observation of falling apple can be successfully explained by newton's theory of gravitation and can be reproduced by repeating the experiment.

Evidence constitutes observations and experimental results which must be reproducible which makes it a fact. Anything that cannot be experimented and results reproduced are still an observation and not an evidence.

Any evidence that support evolution using random mutations and natural selection, must also not be an evidence for other methods like artificial selection that can produce the same results.

Why do you think there's a difference between natural selection and artificial selection? In the past, unethical creationists have defined "artificial selection" to be anything involving the investigation of a scientist. Obviously, we can go no further if that's what you mean. I assume you don't mean that.

This is to make sure the evidence is strictly for evolution and to rule out other possibilities.

Some things in evolution could be interpreted in religious ways to mean other things. That being so, we will only concern ourselves with the question of whether or not it is evidence for evolution.

Because, natural selection is random and randomness governs and creates new species. However, artificial selection is non-random an intelligent being artificially selects it.

The scientific process must be able to be simulated using a computer model to confirm if the explanation provided is indeed correct.

Not all scientific investigation can be reduced to a simulation. Further, such simulations depend on models that must be something less than a perfectly accurate depiction of the modeled process. We need to note the limitations of such models.

Yes, I found a page that refers to it:

http://ethics.csc.ncsu.edu/old/04_97/f97/13.html#Limitations

• Processing and storage capabilities of modern computers are not limitless. (Ans: we have cloud today)
• Models only represent aspects of systems which we can both understand and quantify. (Ans: Yes, what we understand and quantify in evolution)
• Models always involve assumptions. (Ans: yes, same assumptions of evolution)
• Models are only as good as their creators. (Ans: That's you. I can build the model one a model is proposed)
• Simulations, like any other programs, are subject to bugs. (Ans: That you or me)

So, I don't see a problem.

Since evolution including the natural selection entirely depends on mutations which are random, the number of possible mutations required in each generation and the number of times the mutations had to be naturally selected by the environment and how they agree with fossil evidence in order to prove evolution must be clearly explained.

If you want to know this, you will have to learn about population genetics, which is highly mathematical. But I'm willing to show you. Do you understand why the vast majority of possible mutations will not be preserved in a specific environment, greatly reducing the effective scope of evolutionary change?

Yes, please who how population genetics explain permutation problem for evolution.

Unexplained repeated favorable-ness from randomness is strictly not allowed. While random events are allowed, repeated random events that are favorable for a particular event to occur which is artificially simulated, will be declared artificial and not random.

This is not a matter of opinion. We should go with likelihoods, say to the 90% confidence level. Is that acceptable?

The level of random occurrences must be in agreement with all laws of Mathematics including probability, and permutations and combinations.

Explain what a random event is. I'm puzzled as to why you think permutations and combinations are an issue.

A random event is equally probable with other random events and independent with each other. This means, if you have 10 possible random events occurring sequentially for 4 consecutive times, then the total possible events from which this particular sequence of random events is selected is 1 in a 10^4 (permutation and combinations). Which means, the probability such a sequence of events occurring is 0.0001. The first event with such a low probability can occur. However, the next event with such a low probability favoring a particular target will be deemed artificial.

The randomness used to prove evolution using “random mutations” will be tested against Kolmogorov randomness (or algorithmic randomness) which states, a string (usually of bits) as being random if and only if it is shorter than any computer program that can produce that string.

Won't work. "Random mutations" aren't random in that sense. Some sites on the genome are more prone to mutations than others, depending on the particular genome. "Random", in the sense that it's used in population genetics, means that the particular mutations that appear are not predictable for any given organism.

Randomness of mutations was verified independently by Luria and Delbruck, who showed that mutations did not appear in response to environmental pressures. (for which they were awarded a Nobel) We'll have to use that measure if you want to talk about genetics.

The properties of randomness like uniformity (i.e. equally probable every where) and independence (i.e. current value of a random variable has no relation with the previous value), will be tested where ever random events/values are used in proving evolution.

Unfortunately, that's not strictly true in genetics, either. A given change to a genome may alter the likelihood of a different mutation. I'm thinking you're probably getting into things that you don't have the ability to test.

Show me a problem, and we'll take a look at it.

If random mutations aren't random then you shouldn't be calling it 'random' mutations. Sites on a genome which are more prone to mutations are only "observations" because mutations on coding regions will have drastic effect and will die soon and most die even before birth leaving the observations only on healthy living .

Cyclopia for example occurs 1 in 16,000 in born animals, and 1 in 250 in embryos, one in 2,500 that end in miscarriage - which means, 320000 embryos every year. Cyclopia is just one such genetic mutations causing death at birth.

 

[Vaccine]

Hello Felix! I think you raise a valid point. The more science learns the more we see how inadequate Darwin's theory is to explain the origin of species.

Hi barbarian! I see you point out creationists admit speciation. There are always exceptions to the rule. As a rule "most" dont change (Gould).

 

[felix]

Take any two genomes of single celled organisms (the lowest single celled genome is half-a-million base-pairs)

Let's make this a bit more accurate. Since a change to any base pair in a gene mutates that gene, you can use genes, thus at once making the process simpler and more accurate.

That's wrong. Genes contribute to only 1.5% of DNA and the rest which has biochemical functions are omitted. You can't omit a biochemical function in evolution when you assume a common ancestor is evolving.

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions (Ref: https://www.ncbi.nlm.nih.gov/pubmed/22955616).

in which one must be an ancestor of another. You must be able to explain how evolution was able to defy permutations (possible mutations from one species) using random mutations and natural selection.

Let's take a look at that. Suppose we know the genomes of your great, great, great, grandparents. If you descended from them, your genome would be some combination of those (we can ignore permutations, since the order of those genes on a chromosome does not normally affect the expression of those genes). There would be 656 chromosomes from which you'd get 46 The possible permutations of those chromosomes (assuming no crossovers, or other unusual effects) would be 1.1448954580977759379278948070893e+1507 . A huge number. But since the order in which you get those chromosomes doesn't matter, we can use combinations, instead. Here we will get 7.5154665846200250738198335347286e+128 possible combinations. As you see, the "problem" is that the likelihood of you actually descending from those people is so unlikely as to be effectively impossible. Yet you got here. In some cases, it was by natural selection; some of those genes from some of those people were harmful enough to be removed. Other times, it was just a random event that gave rise to some part of your genome. The "permutation problem" doesn't exist for this.

Now, let's consider the case of a population, a small portion of which becomes geographically isolated. Over 20 thousand years, the isolated population has (let's say) three mutations that when all present in the genome, makes it impossible for the new population to successfully breed with the old population.

Given that there were billions of possible combinations of mutations, is it impossible for this particular combination to have formed? If so, explain how. If not, there "permutation problem" doesn't exist.

Feel free to take this to the base pair level. But the result will be the same.

If we have the genome of ggg-grandparents (2^5 ancestors * 46), there would be 736 pairs of chromosomes or 1472. Not sure how you got 656.

Each chromosome is cut into 4 on small and/or 6 times on larger chromosomes through recombination. If you start cutting the chromosomes randomly 4 times and the longer pieces for 5 generations you will have around 1 cM to 10 cM left still uniquely matching that ancestor. The possible combinations you mentioned are actually the possible "descendants" that can come out of those ancestors thus, "confirming' a relationship.

The actual level of possible mutations that can occur (that is, if 2 values Adenine-Thymine and Guanine-Cytosine – AT, GC for each base-pair it is 2^5000000) and how natural selection was able to pick a needle in a haystack from that massive data-set must be properly explained.

Simple. It didn't. It just happened to have those particular mutations. It could have gone otherwise; there were lots of other possible favorable combinations. As you see, it's not random, since all the unfavorable combinations were eliminated, and only favorable ones retained.

Mutations are random "mistakes".

If natural selection which is non-random depends on mutations which are random, and considering the evidences for observable natural selection, why is the timescale used for “observable natural selection” does not fit the “non-observable grand-scale evolution”.

As you learned earlier, it does fit nicely. Gould did a nice analysis on the growth of hominid brains, showing that it wasn't particularly fast, given the number of mutations that would be possible in a few million years.

No, you are ignoring the fact that mutations are random "mistakes" and repeated randomness favoring a particular phenotype change is not random.

To explain better, humans differ by 0.1% of genome with each other which is 3 million base-pairs. However, chimpanzees differ by 5% which is 150 million base-pairs. If we had a common ancestor with Chimpanzee 8 million years back, that is around 400000 generations back (20 years/generation), you must explain how the 150 million base-pairs (or half of it say, 75 million base-pairs considering that we don’t have the exact genome of common ancestor but have the closest relative) got themselves in order to form the human species in just 400000 generations, yet the permutations for it (that is, if 2 values Adenine-Thymine and Guanine-Cytosine – AT, GC for each base-pair it is 2^150000000).

I think you are able now to realize why this is no problem. You found an arrow stuck in a tree, and drew a bulls-eye around it. Barry Hall, in his classic work on evolution in E. Coli, documented the evolution of a new, irreducibly complex enzyme system in a very short time. The mutations were, of course, random, but the gradual evolution of a new enzyme happened by the population retaining those mutations that made the enzyme better and better over time.

The "permutations" of base pairs that didn't improve (or actually degraded) the enzyme's specificity, were lost as the bacteria with more efficient enzymes quickly overgrew the rest. And that's all it takes.

Evolution in E. Coli by Barry Hall is artificial modification on DNA nothing natural. The questions are for "permutation problem for evolution" - not artificially designing/modifying stuff in DNA. It takes just 1 try to artificially arrange 10 balls from 1 to 10 but requires a billion tries randomly.

 

[Barbarian]

No. We are not living in 70s and 80s where computer wasn't there and Popper and Kuhn would have no idea "computational approach" of "scientific inquiry" .

I got my master's in systems and biological systems at USC in 1978. I used computers to build simulations for "scientific inquiry." I happened to run across what was later recognized as the Feigenbaum number, while running simulations on the Lotke-Volterra predator/prey models. You've been misled on that point.

There are strict rules on what contributes an evidences and explanation. Fossils are observations. However, these fossils are not evidences for Evolution but rather, evolution is an explanation for those fossils.

That's a bit too circular to be used. Of course all data, including fossils, are evidence. They are evidence for evolution. However, I'd be willing to go back and re-establish the fact for you. What would you reasonably expect to be in the fossil record, if our present understanding of the way speciation works is true?

I notice you forgot to answer the question. We'll need to have that.

A apple falling down is an evidence for gravity: The observation of falling apple can be successfully explained by newton's theory of gravitation and can be reproduced by repeating the experiment.

As undergraduate students reproduce Mendel's and Darwin's work on evolution.

Evidence constitutes observations and experimental results which must be reproducible which makes it a fact. Anything that cannot be experimented and results reproduced are still an observation and not an evidence.

No, that's wrong. If you were right, astronomy would not be a science. Let's stick with science and what it does.

Any evidence that support evolution using random mutations and natural selection, must also not be an evidence for other methods like artificial selection that can produce the same results.

Why do you think there's a difference between natural selection and artificial selection? In the past, unethical creationists have defined "artificial selection" to be anything involving the investigation of a scientist. Obviously, we can go no further if that's what you mean. I assume you don't mean that.

Because, natural selection is random

As you learned earlier, natural selection is the antithesis of randomness. It is as predictable as gravity.

and randomness governs and creates new species.

As you learned from the penny example, any random process, like mutations, acted upon by a non-random process, like natural selection, produces a non-random result. Would you like to see the math, again?

However, artificial selection is non-random an intelligent being artificially selects it.

Sorry, that is not what "non-random" means. We'll use the definition from statistics:
Statistics. of or characterizing a process of selection in which each item of a set has an equal probability of being chosen.

Non-random is where this does not hold.

The scientific process must be able to be simulated using a computer model to confirm if the explanation provided is indeed correct.

I showed you a good simulation to demonstrate how it works mathematically. It has the virtue of the "code" being directly implemented so you can see that it applies.

When you get that finished, let us know how it worked out.

Since evolution including the natural selection entirely depends on mutations which are random, the number of possible mutations required in each generation and the number of times the mutations had to be naturally selected by the environment and how they agree with fossil evidence in order to prove evolution must be clearly explained.

If you want to know this, you will have to learn about population genetics, which is highly mathematical. But I'm willing to show you. Do you understand why the vast majority of possible mutations will not be preserved in a specific environment, greatly reducing the effective scope of evolutionary change?

Yes, please who how population genetics explain permutation problem for evolution.

As you learned earlier, there is no "permutation problem" for evolution. It's based on a misconception about the mathematics involved.

Explain what a random event is. I'm puzzled as to why you think permutations and combinations are an issue.

A random event is equally probable with other random events and independent with each other.

You used the term you proposed to define, as a definition. You're going to have to tighten that up a little. Let's use the mathematical definition above.

using “random mutations†will be tested against Kolmogorov randomness (or algorithmic randomness) which states, a string (usually of bits) as being random if and only if it is shorter than any computer program that can produce that string.

Won't work. "Random mutations" aren't random in that sense. Some sites on the genome are more prone to mutations than others, depending on the particular genome. "Random", in the sense that it's used in population genetics, means that the particular mutations that appear are not predictable for any given organism.

Randomness of mutations was verified independently by Luria and Delbruck, who showed that mutations did not appear in response to environmental pressures. (for which they were awarded a Nobel) We'll have to use that measure if you want to talk about genetics.

The properties of randomness like uniformity (i.e. equally probable every where) and independence (i.e. current value of a random variable has no relation with the previous value), will be tested where ever random events/values are used in proving evolution.

Unfortunately, that's not strictly true in genetics, either. A given change to a genome may alter the likelihood of a different mutation. I'm thinking you're probably getting into things that you don't have the ability to test.

Show me a problem, and we'll take a look at it.

I notice you forgot to show me such a problem. When do you think you can do that?

If random mutations aren't random then you shouldn't be calling it 'random' mutations.

You're dealing with the real world here. Mutations are random with respect to when they appear. In reality, flipping a coin isn't truly random, either.

Sites on a genome which are more prone to mutations are only "observations" because mutations on coding regions will have drastic effect and will die soon and most die even before birth leaving the observations only on healthy living .

Could you repeat that in English? That makes no sense at all. For some organisms, we have well-documented mutation and back-mutation rates.

Cyclopia for example occurs 1 in 16,000 in born animals, and 1 in 250 in embryos, one in 2,500 that end in miscarriage - which means, 320000 embryos every year.

No. That's just a rate, not a sum.

 

[Barbarian]

Evolution in E. Coli by Barry Hall is artificial modification on DNA nothing natural.

No, that excuse won't work for you. The bacteria were simply given an environment that challenged their ability to use a specific substrate. Their subsequent evolution was merely observed as mutations occurred and were preserved or removed by natural selection. Hall did nothing to chose any pathway or any mutations. As I suspected, any observation of the process, you'll call "artificial", which means that you'll only accept evidence from processes that are not observed. Nice try.

The questions are for "permutation problem for evolution"

As you learned, the "permutation problem" doesn't exist. If it did, you wouldn't be possible, since the likelihood of your particular genome is even more improbable than the likelihood of a new species evolving.

not artificially designing/modifying stuff in DNA.

Show us where Hall artificially designed some change in the DNA. You already know he didn't do that, don't you?

It takes just 1 try to artificially arrange 10 balls from 1 to 10 but requires a billion tries randomly.

Here's your chance; show us how Hall designed those changes artificially. Prediction: No such evidence will be presented.

 

[felix]

I got my master's in systems and biological systems at USC in 1978. I used computers to build simulations for "scientific inquiry." I happened to run across what was later recognized as the Feigenbaum number, while running simulations on the Lotke-Volterra predator/prey models. You've been misled on that point.

Was that in 1978?
With "Feigenbaum constants" recognized, what's the problem? How does that relate to evolution anywhay?

I notice you forgot to answer the question. We'll need to have that.

As undergraduate students reproduce Mendel's and Darwin's work on evolution.

Please let me know the reference.

No, that's wrong. If you were right, astronomy would not be a science. Let's stick with science and what it does.

Astronomy is observable and reproducible (although not all). Do you know that we have many satellites and the properties they use to revolve? GPS is a good example. Other observations are not evidences for suggested astronomical theories.

As you learned earlier, natural selection is the antithesis of randomness. It is as predictable as gravity.

Gravity does not have any random parameters. As i already mentioned, even the environment favoring natural selection itself is random.

We'll use the definition from statistics:
Statistics. of or characterizing a process of selection in which each item of a set has an equal probability of being chosen.

That is the 1st property of randomness... so what?

I showed you a good simulation to demonstrate how it works mathematically. It has the virtue of the "code" being directly implemented so you can see that it applies.

When you get that finished, let us know how it worked out.

If you want to know this, you will have to learn about population genetics, which is highly mathematical. But I'm willing to show you. Do you understand why the vast majority of possible mutations will not be preserved in a specific environment, greatly reducing the effective scope of evolutionary change?

You seem to say the same thing again and again about randomness, so I ignored the rest. Instead of me typing a lot or copy/paste, I will provide you a link

http://bioinfo.med.utoronto.ca/Evolution_by_Accident/Evolution_by_Accident.html

Evolution is "fundamentally random". Also, keen to see what undergraduate students we able to reproduce using evolution.

 

[felix]

No, that excuse won't work for you. The bacteria were simply given an environment that challenged their ability to use a specific substrate. Their subsequent evolution was merely observed as mutations occurred and were preserved or removed by natural selection. Hall did nothing to chose any pathway or any mutations. As I suspected, any observation of the process, you'll call "artificial", which means that you'll only accept evidence from processes that are not observed. Nice try.

Hall removed and changed DNA (genome) manually. That is neither artificial nor natural selection.

Show us where Hall artificially designed some change in the DNA. You already know he didn't do that, don't you?

It takes just 1 try to artificially arrange 10 balls from 1 to 10 but requires a billion tries randomly.

Here's your chance; show us how Hall designed those changes artificially. Prediction: No such evidence will be presented.

Hall's
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1213848/pdf/453.pdf

Anyone can alter it:
http://www.funakoshi.co.jp/data/datasheet/GBR/K006.pdf

Let's hear from Hall himself:

Given a gene of 1000 base pairs there are over 1034 sequences that differ from the wild-type sequence by 10 or fewer mutations. Not only can we not explore all of those possible variants, life itself has barely had sufficient time to explore all of those possibilities. The mass of the earth's oceans is about 1.4×1024 g. Even if living cells constituted 10−4 of the mass of the oceans, given about 1012 bacterial cells per gram, a reproduction rate of about 1 cell generation per day and a mutation rate of about 10−9 per cell generation and 4 billion years of life there has been sufficient time to explore only 1.6×1034 variants of a single 1000-bp sequence. However, evolution does not proceed by exploring all possible variants but by incorporating single mutations, selecting the fittest of those variants, expanding the population of the fittest variants, and incorporating additional single changes.

Hall, B. G. (1999), Toward an understanding of evolutionary potential. FEMS Microbiology Letters, 178: 1–6. doi: 10.1111/j.1574-6968.1999.tb13751.x[/QUOTE]

What Hall did not explain in the above passage is the "permutation problem for evolution".

 

[Barbarian]

Hall removed and changed DNA (genome) manually. That is neither artificial nor natural selection.

Barbarian suggests:
Show us where Hall artificially designed some change in the DNA. You already know he didn't do that, don't you?

It takes just 1 try to artificially arrange 10 balls from 1 to 10 but requires a billion tries randomly.

But as you learned, natural selection can do it without any intervention at all. That's what happened in Hall's bacteria. He merely selected a strain that could not metabolize a particular substrate. But he didn't design any of the changes that evolved over time. I notice you declined to show us that he did.

Barbarian oberves:
Here's your chance; show us how Hall designed those changes artificially. Prediction: No such evidence will be presented.

Hall's
http://www.ncbi.nlm.nih.gov/pmc/arti...48/pdf/453.pdf

Prediction verified. Nowhere in that document does it say Hall did anything to cause any of the changes that evolved.

Let's hear from Hall himself:
Given a gene of 1000 base pairs there are over 1034 sequences that differ from the wild-type sequence by 10 or fewer mutations. Not only can we not explore all of those possible variants, life itself has barely had sufficient time to explore all of those possibilities. The mass of the earth's oceans is about 1.4×1024 g. Even if living cells constituted 10−4 of the mass of the oceans, given about 1012 bacterial cells per gram, a reproduction rate of about 1 cell generation per day and a mutation rate of about 10−9 per cell generation and 4 billion years of life there has been sufficient time to explore only 1.6×1034 variants of a single 1000-bp sequence. However, evolution does not proceed by exploring all possible variants but by incorporating single mutations, selecting the fittest of those variants, expanding the population of the fittest variants, and incorporating additional single changes.
Hall, B. G. (1999), Toward an understanding of evolutionary potential. FEMS Microbiology Letters, 178: 1–6. doi: 10.1111/j.1574-6968.1999.tb13751.x[/QUOTE]

What Hall did not explain in the above passage is the "permutation problem for evolution".

I highlighted it in red for you. As you see, the "permutation problem" would exist only if natural selection did not exist.

 

[Barbarian]

Barbarian observes:
I got my master's in systems and biological systems at USC in 1978. I used computers to build simulations for "scientific inquiry." I happened to run across what was later recognized as the Feigenbaum number, while running simulations on the Lotke-Volterra predator/prey models. You've been misled on that point.

Was that in 1978?

1976-1978.

With "Feigenbaum constants" recognized, what's the problem? How does that relate to evolution anywhay?

Just pointing out that you were completely wrong about computer use by biologists in the 70s. My work was poorly funded, but I had access to computer time.

Barbarian obeserves:
I notice you forgot to answer the question. We'll need to have that.

I notice you didn't answer it again. I'll be putting questions like that in green, so you won't forget them. What would you reasonably expect to be in the fossil record, if our present understanding of the way speciation works is true?

Barbarian observes:
As undergraduate students reproduce Mendel's and Darwin's work on evolution.

Please let me know the reference.

www.erin.utoronto.ca/.../lab_files/lab_02_bacteria.pdf

Barbarian, regarding the claim that only experimentation can be science:
No, that's wrong. If you were right, astronomy would not be a science. Let's stick with science and what it does.

Astronomy is observable and reproducible (although not all).

Show me a reproducible event in astronomy. Would you say the observation and data collection from a supernova would be science, even though we can't reproduce such an event?

If not, explain why your definition differs from that of science, If so, explain why you think biology should not have the same standard of science.

Barbarian observes:
As you learned earlier, natural selection is the antithesis of randomness. It is as predictable as gravity.

Gravity does not have any random parameters.

So, if there's a rockfall down a mountain, you could calculate the position and path of every bit of rock falling? No, I don't think so. Randomness works that way in gravity, too.

As i already mentioned, even the environment favoring natural selection itself is random.

As is the surface of the mountain down which the rock falls. Again, you seem to have a double standard going here.

Barbarian observes:
I showed you a good simulation to demonstrate how it works mathematically. It has the virtue of the "code" being directly implemented so you can see that it applies.

When you get that finished, let us know how it worked out.

The simulation you requested, you still haven't done.

Barbarian asks:
If you want to know this, you will have to learn about population genetics, which is highly mathematical. But I'm willing to show you. Do you understand why the vast majority of possible mutations will not be preserved in a specific environment, greatly reducing the effective scope of evolutionary change?

Again, no answer.

Evolution is "fundamentally random".

We know you want us to believe that. But the fact that you keep dodging the simulation, tells us that you aren't so sure of that, yourself.

Gave you a link to one such exercise. Now, do you think you might be willing to answer some of my questions that you've been dodging? j (see above in green)

 

[felix]

Barbarian suggests:
Show us where Hall artificially designed some change in the DNA. You already know he didn't do that, don't you?



But as you learned, natural selection can do it without any intervention at all. That's what happened in Hall's bacteria. He merely selected a strain that could not metabolize a particular substrate. But he didn't design any of the changes that evolved over time. I notice you declined to show us that he did.

Barbarian oberves:
Here's your chance; show us how Hall designed those changes artificially. Prediction: No such evidence will be presented.



Prediction verified. Nowhere in that document does it say Hall did anything to cause any of the changes that evolved.

In Hall's experiment, what does that anything to do with speciation?

Let's hear from Hall himself:
Given a gene of 1000 base pairs there are over 1034 sequences that differ from the wild-type sequence by 10 or fewer mutations. Not only can we not explore all of those possible variants, life itself has barely had sufficient time to explore all of those possibilities. The mass of the earth's oceans is about 1.4×1024 g. Even if living cells constituted 10−4 of the mass of the oceans, given about 1012 bacterial cells per gram, a reproduction rate of about 1 cell generation per day and a mutation rate of about 10−9 per cell generation and 4 billion years of life there has been sufficient time to explore only 1.6×1034 variants of a single 1000-bp sequence. However, evolution does not proceed by exploring all possible variants but by incorporating single mutations, selecting the fittest of those variants, expanding the population of the fittest variants, and incorporating additional single changes.
Hall, B. G. (1999), Toward an understanding of evolutionary potential. FEMS Microbiology Letters, 178: 1–6. doi: 10.1111/j.1574-6968.1999.tb13751.x

What Hall did not explain in the above passage is the "permutation problem for evolution".

I highlighted it in red for you. As you see, the "permutation problem" would exist only if natural selection did not exist.[/QUOTE]

Yes, that was his opinion. What he didn't mention is, the "fittest" for a environment, for which natural selection can even proceed, itself random.

 

[Barbarian]

In Hall's experiment, what does that anything to do with speciation?

You were confused about how natural selection eliminates the "permutation problem." This is how.

Let's hear from Hall himself:
However, evolution does not proceed by exploring all possible variants but by incorporating single mutations, selecting the fittest of those variants, expanding the population of the fittest variants, and incorporating additional single changes.
Hall, B. G. (1999), Toward an understanding of evolutionary potential. FEMS Microbiology Letters, 178: 1–6. doi: 10.1111/j.1574-6968.1999.tb13751.x

What Hall did not explain in the above passage is the "permutation problem for evolution".

I highlighted it in red for you. As you see, the "permutation problem" would exist only if natural selection did not exist.

Yes, that was his opinion.

No. That's what the experiment shows. Instead of trying every possible permutation, natural selection merely picked out the best mutations each generation, and so bypassed all the inefficient choices. No permutation problem. BTW, engineers have noticed that evolution works more efficiently than design. They're using natural selection to handle problems too complicated for design. They're called "genetic algorithms."

The cool thing is, often the engineers don't even know why they work better. They just do. Natural selection just picks whatever works best at each iteration, and that's all it needs.

What he didn't mention is, the "fittest" for a environment, for which natural selection can even proceed, itself random.

Turns out that natural selection can adjust to whatever environment. Your argument is like saying all salesmen will average the same number of sales, because customers appear randomly.

 

[felix]

Turns out that natural selection can adjust to whatever environment.

Oh really? So, why is it not adjusting now?
Actually, that's "the assumption" which invalidates all your other replies.

 

[Barbarian]

Barbarian observes:
Turns out that natural selection can adjust to whatever environment.

Oh really? So, why is it not adjusting now?

It is. Every day. The Beak of the Finch documents how that works. And as the environment shifts, alleles and phenotypes change with it. That's how it works.

Actually, that's "the assumption" which invalidates all your other replies.

Surprise. If you had done the simulation I gave to you, your next adventure would be to change the environment a bit, and see how natural selection would respond to restore fitness in the new environment.

 

[felix]

Barbarian observes:
Turns out that natural selection can adjust to whatever environment.

Oh really? So, why is it not adjusting now?

It is. Every day. The Beak of the Finch documents how that works. And as the environment shifts, alleles and phenotypes change with it. That's how it works.

Actually, that's "the assumption" which invalidates all your other replies.

Surprise. If you had done the simulation I gave to you, your next adventure would be to change the environment a bit, and see how natural selection would respond to restore fitness in the new environment.

The question is with respect to speciation and the permutation problem which evolution has.

 

[Barbarian]

The question is with respect to speciation and the permutation problem which evolution has.

As you learned, the "problem" doesn't exist. Hall explains:
However, evolution does not proceed by exploring all possible variants but by incorporating single mutations, selecting the fittest of those variants, expanding the population of the fittest variants, and incorporating additional single changes.
Hall, B. G. (1999), Toward an understanding of evolutionary potential. FEMS Microbiology Letters, 178: 1–6. doi: 10.1111/j.1574-6968.1999.tb13751.x

Simple as that. Natural selection doesn't work the way you seem to think it does.

 

[felix]

The question is with respect to speciation and the permutation problem which evolution has.

As you learned, the "problem" doesn't exist. Hall explains:
However, evolution does not proceed by exploring all possible variants but by incorporating single mutations, selecting the fittest of those variants, expanding the population of the fittest variants, and incorporating additional single changes.
Hall, B. G. (1999), Toward an understanding of evolutionary potential. FEMS Microbiology Letters, 178: 1–6. doi: 10.1111/j.1574-6968.1999.tb13751.x

Simple as that. Natural selection doesn't work the way you seem to think it does.

You seem to contradict on both threads. You seem to say that God USED nature and then disagree that is "not artificial". If God can pick a needle in a haystack, yes He can and that is "artificial" because there is no random in it. Just like you (or any one) can breed a particular type of dog (which is already there and proved) and there is no permutation problem for it - straight forward and simple, "because" it is artificial and not random.

 

[Barbarian]

You seem to contradict on both threads. You seem to say that God USED nature and then disagree that is "not artificial".

By definition, nature is natural. If you don't use words as they are used by others, you will be continually misunderstood.

If God can pick a needle in a haystack, yes He can and that is "artificial" because there is no random in it.

As you learned, there is no "needle in the haystack" problem. As Hall remarked:

However, evolution does not proceed by exploring all possible variants but by incorporating single mutations, selecting the fittest of those variants, expanding the population of the fittest variants, and incorporating additional single changes.

BTW, it's an error to think that God can only work by necessity. As St. Thomas Aquinas wrote:
The effect of divine providence is not only that things should happen somehow; but that they should happen either by necessity or by contingency. Therefore whatsoever divine providence ordains to happen infallibly and of necessity happens infallibly and of necessity; and that happens from contingency, which the plan of divine providence conceives to happen from contingency.
St. Thomas Aquinas, Summa Theologica, The Providence of God, Article 4, Reply 1

Just like you (or any one) can breed a particular type of dog (which is already there and proved) and there is no permutation problem for it - straight forward and simple, "because" it is artificial and not random.

If you think so, you don't know anything about breeding animals. You can aim for something, but just like natural selection, you're limited to what mutations will provide. You can only select those that make the animal more fit, according to your intentions.

Natural selection works that way, too. As Barry Hall said.

 

[felix]

You seem to contradict on both threads. You seem to say that God USED nature and then disagree that is "not artificial".

By definition, nature is natural. If you don't use words as they are used by others, you will be continually misunderstood.

Let me correct you:

If you don't use words as they are used by (non Christian who don't believe in God)

Since you say "others": Do these "others" also believe that someone is USING nature for evolution? By the way, theory of evolution does not even remotely include any higher intelligent beings using nature to "design" new creatures.