Creation Mutation (of Mutation)

lucaspa · #11 14th January 2004, 10:06 AM

Originally Posted by judge

It does not automatically follow that because random (unpredictable to us) mutation and natural selection do in fact occur, therfore any kind of change is possible.

Let's remember what 'random' means here. Random means the variation is random in reference to the needs of the individual or the population. That is, in a climate growing colder, just as many deer with shorter fur will be born as deer with longer fur. It does not mean that any base sequence can change to any other base sequence in a single movement.

What natural selection does mean is that populations will be designed to fit the design problems posed by the environment. This means that populations will change over many generations and look very different from the starting population. It also means that natural selection has the potential to explore all possible genomes over time. Let's call the set of all possible genomes the Library of Mendel. In practice, some genomes in the Library will become inaccessible as traits are previously selected. This is the source of homologies. Once a trait is under selection by two or more positive selection pressures, it becomes unchangeable later.

Just because random mutation and natural selection do occur does not mean that microbes turned into men.
The onus is on you to demonstrate this happened not on creationists to demonstrate it cannot happen.

The first is true, but the data is there to back up the claim. The second is false because the creationist claim is exactly that: it cannot happen. Or, put another, more rigorous way: the hypothesis is that evolutionary processes will give the diversity of life from a common ancestor. It is the responsibility of everyone involved to try to show that this either did not or could not happen. That is the essence of how science works: it tries to show hypotheses to be false. Evolutionary biologists have done this. From Darwin on they have tried to show common ancestry and natural selection to be wrong. The data presented as support are the result of unsuccessful attempts to show the hypothesis to be wrong. So, if you can show us a successful attempt, then we can say evolution is falsified.

But as naturalism precludes creation as a legitimate theory it has no choice but to hypothesise that it did happen

There are several fallacies here.
1. There are two types of naturalism -- methodological and philosophical. Methodological says nothing about creation or a Creator. It simply is looking for the material method by which the Creator accomplished creation. This was Darwin's attidude and his quotes in Origin are at the end of the post. Darwin certainly didn't preclude a Creator or creation. Now, philosophical naturalism is a faith. And yes, philosophical naturalists (atheists) have to exclude creation. But philosophical naturalism is not part of science. It is a personal faith.
2. What you call "creation" is really creationism. Creation is simply a theological statement that God created. Science can't touch that one because methodological materialism won't let it. Science cannot deny that God created. (Science can't confirm it either. Science is agnostic.) Creationism is a how God created. Instantaneous formation in present form. But evolution is also a how God created. Again, see Darwin. Notice the phrase "secondary cause".
3. If the data had supported creationism rather than falsified it, we would indeed have concluded that God created according to creationism. In the period 1700-1831 science did think that. Creationism was the accepted scientific theory. But the scientists of the time -- all theists, nearly all Christians, and many of them ministers -- falsified creationism.

Random (unpredictable to us) mutation and natural selection are important parts of at least some special creationist paradigms.

Here is an example.
http://www.evolutionisdegeneration.com/

The site does not take into account
1. Observed mutations that increase the amount of DNA.
2. Observed mutations that yield new traits, increased enzyme activity, or new structures.
3. Observation that selection is a means of creating information.

So the site has got natural selection all wrong. And is falsified by observations.

lucaspa · #12 14th January 2004, 10:08 AM

Sorry, the Darwin quotes:

There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved." C. Darwin, On the Origin of Species, pg 450.

Also: "To my mind it accords better with what we know of the laws impressed on matter by the Creator, that the production and extinction of the past and present inhabitants of the world should have been due to secondary causes, like those determining the birth and death of the individual." pg. 449.

In the Fontispiece of Origin we have the following quotes. Notice that the second explicitly denies philosophical naturalism:

"But with regard to the material world, we can at least go so far as this -- we can perceive that events are brought about not by insulated interpositions of Divine power, exerted in each particular case, but by the establishment of general laws" Whewell: Bridgewater Treatise.

"The only distinct meaning of the word 'natural' is stated, fixed, or settled; since what is natural as much requires and presupposes an intelligent agent to render it so, i.e., to effect it continually or at stated times, as what is supernatural or miraculous does to effect it for once." Butler: Analogy of Revealed Religion.

]"To conclude, therefore, let no man out of a weak conceit of sobriety, or an ill-applied moderation, think or maintain, that a man can search too far or be too well studied in the book of God's word, or in the book of God's works; divinity or philosophy; but rather let men endeavour an endless progress or proficience in both." Bacon: Advancement of Learning

judge · #13 15th January 2004, 07:24 AM

Originally Posted by lucaspa

Let's remember what 'random' means here. Random means the variation is random in reference to the needs of the individual or the population. That is, in a climate growing colder, just as many deer with shorter fur will be born as deer with longer fur. It does not mean that any base sequence can change to any other base sequence in a single movement..

Thanks for the reply Luscapa. I think you have ststed the commonly accepted meaning of random WRT mutations very well here, but even amongst "evilutionists" there seems to be no full consensus. see here...
http://www.iidb.org/vbb/showthread.p...threadid=69103
And even so the definition you have provided is impossible to ever really confirm empirically IMHO.
.

What natural selection does mean is that populations will be designed to fit the design problems posed by the environment. This means that populations will change over many generations and look very different from the starting population. It also means that natural selection has the potential to explore all possible genomes over time. Let's call the set of all possible genomes the Library of Mendel. In practice, some genomes in the Library will become inaccessible as traits are previously selected. This is the source of homologies. Once a trait is under selection by two or more positive selection pressures, it becomes unchangeable later. .

Yes...but this is not so different to the ideas in the link I provided (at least it seems so to me)

.

The first is true, but the data is there to back up the claim. The second is false because the creationist claim is exactly that: it cannot happen. Or, put another, more rigorous way: the hypothesis is that evolutionary processes will give the diversity of life from a common ancestor. It is the responsibility of everyone involved to try to show that this either did not or could not happen. That is the essence of how science works: it tries to show hypotheses to be false. Evolutionary biologists have done this. From Darwin on they have tried to show common ancestry and natural selection to be wrong. The data presented as support are the result of unsuccessful attempts to show the hypothesis to be wrong. So, if you can show us a successful attempt, then we can say evolution is falsified..

some scientists would disagree.
Biological Reviews of the Cambridge Philosophical Society 2001 May;76(2):255-89.

Are ecological and evolutionary theories scientific?
Murray BG Jr.

Department of Ecology, Evolution, and Natural Resources, Rutger University, New Brunswick, New Jersey 08901-2882, USA. bmurray@rci.rutgers.edu

ABSTRACT: Scientists observe nature, search for generalizations, and provide explanations for why the world is as it is. Generalizations are of two kinds. The first are descriptive and inductive, such as Boyle's Law. They are derived from observations and therefore refer to observables (in this case, pressure and volume). The second are often imaginative and form the axioms of a deductive theory, such as Newton's Laws of Motion. They often refer to unobservables (e.g. inertia and gravitation). Biology has many inductive generalizations (e.g. Bergmann's Rule and 'all cells arise from preexisting cells') but few, if any, recognized universal laws and virtually no deductive theory. Many biologists and philosophers of biology have agreed that predictive theory is inappropriate in biology, which is said to be more complex than physics, and that one can have nonpredictive explanations, such as the neo-Darwinian Theory of Evolution by Natural Selection. Other philosophers dismiss nonpredictive, explanatory theories, including evolutionary 'theory', as metaphysics. Most biologists do not think of themselves as philosophers or give much thought to the philosophical basis of their research. Nevertheless, their philosophy shows in the way they do research. The plethora of ad hoc (i.e. not universal) hypotheses indicates that biologists are reluctant inductivists in that the search for generalization does not have a high priority. Biologists test their hypotheses by verification. Theoretical physicists, in contrast, are deductive unifiers and test their explanatory hypotheses by falsification. I argue that theoretical biology (concerned with unobservables, such as fitness and natural selection) is not scientific because it lacks universal laws and predictive theory. In order to make this argument, I review the differences between verificationism and falsificationism, induction and deduction, and descriptive and explanatory laws. I show how these differ with a specific example of a successful and still useful (even if now superseded as explanatory) deductive theory, Newton's Theory of Motion. I also review some of the philosophical views expressed on these topics because philosophers seem to be even more divided than biologists, which is not at all helpful. The fact that biology does not have predictive theories does not constitute irrefutable evidence that it cannot have them. The only way to falsify this philosophical hypothesis, however, is to produce a predictive theory with universal biological laws. I have proposed such a theory, but it has been presented piecemeal. At the end of this paper, I bring the pieces together into a deductive theory on the evolution of life history traits (e.g. clutch size, mating relationships, sexual size dimorphism).

.

(snip)
3. If the data had supported creationism rather than falsified it, we would indeed have concluded that God created according to creationism. In the period 1700-1831 science did think that. Creationism was the accepted scientific theory. But the scientists of the time -- all theists, nearly all Christians, and many of them ministers -- falsified creationism. .

See above..creationism has not been falsified.

.

The site does not take into account
1. Observed mutations that increase the amount of DNA..

Nitpick...this does not change the basic theory and may in fact be an argument over the meaning of "information"...

.

2. Observed mutations that yield new traits, increased enzyme activity, or new structures..

Again this does not change the basic structure of the arguments IMO. The book itself relates changes in pigment for example in various animals. This is certainly a different trait

.

3. Observation that selection is a means of creating information. .

Not sure what you mean here
.

So the site has got natural selection all wrong. And is falsified by observations.

It claims IIRC that natural selection removes degenerate organisms. Do you think this is wrong?

thanks for an interesting and thoughtful reply though. I hope I have understood you properly in all my replies

lucaspa · #14 15th January 2004, 10:55 PM

Originally Posted by judge

Thanks for the reply Luscapa. I think you have ststed the commonly accepted meaning of random WRT mutations very well here, but even amongst "evilutionists" there seems to be no full consensus. see here...
http://www.iidb.org/vbb/showthread.p...threadid=69103

Many "evolutionists" on debate boards on not totally familiar with the subject. So I am not surprised on a philosophy forum that you get several different opinions. What you need to do is comb the evolutionary biology literature, since it is in that specialty that you are talking.

And even so the definition you have provided is impossible to ever really confirm empirically IMHO.

It has been tested and supported. That is what population genetics did. You can measure traits of individuals born in the population and see that they are indeed a bell-shaped curve around a mean -- random with respect to the needs of the individual and population. Then over generations you can see the bell-shaped curve shift in one direction or another as a result of selection.

.Yes...but this is not so different to the ideas in the link I provided (at least it seems so to me)

Your link only has exploration in one "direction" -- degradation. However, the data indicate that genomes can also become more "complex" and that organisms can acquire new traits. The website states that organisms can only lose traits.

.some scientists would disagree.
Biological Reviews of the Cambridge Philosophical Society 2001 May;76(2):255-89.

Are ecological and evolutionary theories scientific?
Murray BG Jr.

Department of Ecology, Evolution, and Natural Resources, Rutger University, New Brunswick, New Jersey 08901-2882, USA. bmurray@rci.rutgers.edu

ABSTRACT: Scientists observe nature, search for generalizations, and provide explanations for why the world is as it is. Generalizations are of two kinds. The first are descriptive and inductive, such as Boyle's Law. They are derived from observations and therefore refer to observables (in this case, pressure and volume). The second are often imaginative and form the axioms of a deductive theory, such as Newton's Laws of Motion. They often refer to unobservables (e.g. inertia and gravitation). Biology has many inductive generalizations (e.g. Bergmann's Rule and 'all cells arise from preexisting cells') but few, if any, recognized universal laws and virtually no deductive theory. Many biologists and philosophers of biology have agreed that predictive theory is inappropriate in biology, which is said to be more complex than physics, and that one can have nonpredictive explanations, such as the neo-Darwinian Theory of Evolution by Natural Selection. Other philosophers dismiss nonpredictive, explanatory theories, including evolutionary 'theory', as metaphysics. Most biologists do not think of themselves as philosophers or give much thought to the philosophical basis of their research. Nevertheless, their philosophy shows in the way they do research. The plethora of ad hoc (i.e. not universal) hypotheses indicates that biologists are reluctant inductivists in that the search for generalization does not have a high priority. Biologists test their hypotheses by verification. Theoretical physicists, in contrast, are deductive unifiers and test their explanatory hypotheses by falsification. I argue that theoretical biology (concerned with unobservables, such as fitness and natural selection) is not scientific because it lacks universal laws and predictive theory. In order to make this argument, I review the differences between verificationism and falsificationism, induction and deduction, and descriptive and explanatory laws. I show how these differ with a specific example of a successful and still useful (even if now superseded as explanatory) deductive theory, Newton's Theory of Motion. I also review some of the philosophical views expressed on these topics because philosophers seem to be even more divided than biologists, which is not at all helpful. The fact that biology does not have predictive theories does not constitute irrefutable evidence that it cannot have them. The only way to falsify this philosophical hypothesis, however, is to produce a predictive theory with universal biological laws. I have proposed such a theory, but it has been presented piecemeal. At the end of this paper, I bring the pieces together into a deductive theory on the evolution of life history traits (e.g. clutch size, mating relationships, sexual size dimorphism).

This criticizer doesn't get a free ride. For instance, natural selection is completely deductive. Mendelian genetics is also universal. So two of Murray's claims about biology are falsified right there. Also, evolution is "predictive" in the scientific sense of predicting new knowledge to be found. Murray is using "predictive" in the physical sense of predicting future events. This is so because all conditions can be known. Predicting the future direction of designs/natural selection is tough because we have to completely know the environment, and that is so complex we rarely do. In that regard, evolution is more like Chaos Theory and not like Newtonian gravity -- change the initial conditions a little and the result is very different.

However, some experiments in limited environments are being able to predict natural selection in the future. Murray doesn't seem to be aware of them.
Evaluation of the rate of evolution in natural populations of guppies (Poecilia reticulata). Reznick, DN, Shaw, FH, Rodd, FH, and Shaw, RG. 275:1934-1937, 1997. The lay article is Predatory-free guppies take an evolutionary leap forward, pg 1880.

This is an excellent study of natural selection at work. Guppies are preyed upon by species that specialize in eating either the small, young guppies, or older, mature guppies. Eleven years ago the research team moved guppies from pools below some waterfalls that contained both types of predators to pools above the falls where only the predators that ate the small, young guppies live. Thus the selection pressure was changed. Eleven years later the guppies above the falls were larger, matured earlier, and had fewer young than the ones below the falls. The group then used standard quantitative morphology to quantify the rate of evolution.

So we have a study in the wild, not the lab, of natural selection and its results. The rate of evolution was *very* fast. In this study natural selection was measured quantitatvely, and even predicted since it was predicted that, in the absence of predators that fed on large guppies but in the presence of ones that fed on young guppies, the guppies would grow larger and mature earlier to avoid the predators. That is exactly what happened.

1. Case, TJ, Natural selection out on a limb. Nature, 387: 15-16, May 1, 1997. Original paper in the same issue, pp. 70-73 (below). Discusses natural selection in the wild where lizards were introduced to various islands in the Bahamas. Length of limbs varied according to the plant life present on the islands.
JB Losos, KI Warheit, TW Schoener, Adaptive differentiation following experimental island colonization in Anolis lizards. Nature, 387: 70-73,1997 (May 1)

See above..creationism has not been falsified.

I'm sorry, but it has. The Murray article isn't arguing for creationism, and the website simply ignores too much evidence -- evidence that does falsify creationism. Falsification does not depend on people admitting the theory is falsified. There were phlogiston chemists who went to their grave not admitting phlogiston was falsified. Didn't matter. Nor did it matter that Einstein never admitted that strict determinism was falsified.

BTW, not only is fitness observable but is mathematically calculable, just like Newtonian gravity is calculable. The formula for fitness is:

Fitness is the ratio of the progeny actually produced to the progeny expected from Mendelian inheritance (fitness = f(p)/f(0) ). Fitness is therefore always relative (Understanding Evolution, pp. 153-154.) We can also get a selection coefficient that measures the selective advantage, or disadvantage. S = 1.0 - fitness.

Nitpick...this does not change the basic theory and may in fact be an argument over the meaning of "information".

The site specifically says that no new traits or information evolve. In terms of "information", it has been shown that evolution increases the information of an enzyme -- its specificity for example.
Ohta T, J Theor Biol 1987 Jan 21;124(2):199-211 A model of evolution for accumulating genetic information.

National Institute of Genetics, Mishima, Japan.

"By taking into account recent knowledge of multigene families and other repetitive DNA sequences, a model of evolution by gene duplication for accumulating genetic information is studied. Genetic information is defined as the sum of distinct functions that the gene family can perform. A coefficient, "genetic diversity" is defined and used in this study, that is highly correlated with genetic information. Initially, a multigene family with a few gene copies is assumed, and natural selection starts to work on this gene family to increase genetic diversity contained in the gene family. As an important mechanism, unequal crossing-over is incorporated. Together with mutation, it is responsible for supplying genetic variability among individuals for selection to work. A specific model, in which individuals with less genetic diversity are selectively disadvantageous, has been studied in detail. Through approximate theoretical analysis and extensive Monte Carlo studies, it has been shown that the system is an extremely efficient way to accumulate genetic information."

45: Fukuchi S, Okayama T, Otsuka J. Evolution of genetic information flow from the viewpoint of protein sequence similarity. J Theor Biol. 1994 Nov 21;171(2):179-95.

Again this does not change the basic structure of the arguments IMO. The book itself relates changes in pigment for example in various animals. This is certainly a different trait

But not a "new" one according to the website. We are talking new traits that never existed before. Those observations contradict the statements in the website. Remember, Judge, it is not the supporting evidence that is most important. It is the observatiosn that can't be there if the theory is true. And that is what I am talking.

Not sure what you mean here

Read Dembski. I choose Dembski since he is an IDer/anti-evolutionist and therefore you can trust him.
"Suppose that an organism in reproducing generates N offspring, and that of these N offspring M succeed in reproducing. The amount of information introduced through selection is then -log2(M/N). Let me stress that this formula is not an case of misplaced mathematical exactness. This formula holds universally and is non-mysterious. Take a simple non-biological example. If I am sitting at a radio transmitter, and can transmit only zeros and ones, then every time I transmit a zero or one, I choose between two possibilities, selecting precisely one of them. Here N equals 2 and M equals 1. The information -log2(M/N) thus equals -log2(1/2) = 1, i.e., 1 bit of information n is introduced every time I transmit a zero or one. This is of course as things should be. Now this example from communication theory is mathematically isomorphic to the case of cell-division where only one of the daughter cells goes on to reproduce. On the other hand, if both daughter cells go on to reproduce, then N equals M equals 2, and thus -log2(M/N) = -log2(2/2) = 0, indicating that selection, by failing to eliminate any possibility failed also to introduce new information. "

Now, since natural selection always has more born than live, selection is going to increase information.

It claims IIRC that natural selection removes degenerate organisms. Do you think this is wrong?

Natural selection, if you read Darwin, is about preservation, not removal. "But if variations useful to any organic being do occur, assuredly individuals thus characterized will have the best chance of being preserved in the struggle for life; and from the strong principle of inheritance they will will tend to produce offspring similarly characterized. This principle of preservation, I have called, for the sake of brevity, Natural Selection." [Origin, p 127 6th ed.]

That the less fit individuals do not survive the "struggle for existence" is incidental. So yes, the site is wrong. The site also indicates that removal of "degenerate organisms" is the only function of natural selection. And that is clearly wrong. The site igores the propagation and retention of beneficial and innovative variations.

thanks for an interesting and thoughtful reply though. I hope I have understood you properly in all my replies

You're welcom. And yes, thank you for trying to understand what I have said. That always makes for a productive discussion. In turn, I hope I have addressed your new points.

judge · #15 16th January 2004, 12:01 AM

Originally Posted by lucaspa

Many "evolutionists" on debate boards on not totally familiar with the subject. So I am not surprised on a philosophy forum that you get several different opinions. What you need to do is comb the evolutionary biology literature, since it is in that specialty that you are talking.

Small nitpick, although the main section of forums is philosophy the specific subforum linked to is evolution/creation.
and the point is that even scientists even biologists such as Dr Caporale whoi is mentioned in the discussion do not limit themselves to the definition of random you provided.

lucaspa · #16 16th January 2004, 09:58 AM

Originally Posted by judge

.some scientists would disagree.

I just wanted to comment on the fallacy of the general argument being used.

The general argument is that, if someone has a contrary position, that position is automatically valid. But that is not so. Our prisons are full of people who have a contrary opionon about their guilt. We don't consider their opinion valid.

For a theory to be valid or falsified, it is not necessary to have everyone agree that it is valid or falsified. Ideas --and theories are ideas -- are independent of the people who advocate them. Therefore, objectively a theory can be valid or falsified whether everyone agrees or not. That's why we evaluate evidence and arguments.

Now, in the Abstract that you posted, Murray makes several erroneous statements:

Biology has many inductive generalizations (e.g. Bergmann's Rule and 'all cells arise from preexisting cells') but few, if any, recognized universal laws and virtually no deductive theory.

Hardy-Weinberg is a recognized universal law. So is Haldan's Rule and Cope's Rule. However, evolution is a recognized universal principle. As Theodosius Dobzhansky put it "Nothing in biology makes sense except in the light of evolution."

If you look at Darwin's summary of natural selection, it is deduction.

Many biologists and philosophers of biology have agreed that predictive theory is inappropriate in biology, which is said to be more complex than physics, and that one can have nonpredictive explanations, such as the neo-Darwinian Theory of Evolution by Natural Selection.

Here Murray is misuing the term "predictive". Evolution has been remarkably successful at predicting new knowledge to be found, and this is the general use of the term in science. But neo-Darwinism has also now been used to predict outcomes. For instance, the PBS show Evolution demonstrated how evolution by natural selection predicted the course of a treatment for AIDs. That the patients are still alive attests to the accuracy of the prediction.

Biologists test their hypotheses by verification.

Biologists test their hypotheses the same way every other scientist does -- by attempting to falsify them.

I argue that theoretical biology (concerned with unobservables, such as fitness and natural selection) is not scientific because it lacks universal laws and predictive theory.

Both fitness and natural selection are not only observable and have been observed, but are quantifiable and have been. Selection coefficients and fitness coefficients are routinely calculated. You only have to give the most cursory of glances at the population genetics literature to see this. How Murray missed this I have no idea. But I will order the paper and look. But with all the known errors in the Abstract, I don't have much hope for Murray's new theory. Any theory has to account for the known data and Murray doesn't seem to even be aware of that. Not a good sign.

lucaspa · #17 16th January 2004, 10:04 AM

Originally Posted by judge

Small nitpick, although the main section of forums is philosophy the specific subforum linked to is evolution/creation.

Right. Which title right there tells you that you have two opposing philosophies being debated. "Creation" is a theological concept. Creationism is the scientific theory. The overall board is Infidels.org. What you have here is a philosophical debate on atheism vs theism with evolution standing in for atheism and creation standing in for theism.

and the point is that even scientists even biologists such as Dr Caporale whoi is mentioned in the discussion do not limit themselves to the definition of random you provided.

Judge, I am not going to read the entire thread. Why don't you put the relevant objections here and I'll look at them.

"Darwinism is widely misunderstood as a theory of pure chance. Mustn't it have done something to provoke this canard? Well, yes, there is something behind the misunderstood rumour, a feeble basis to the distortion. One stage in the Darwinian process is indeed a chance process -- mutation. Mutation is the process by which fresh genetic variation is offered up for selection and it usually described as random. But Darwinians make the fuss that they do about the "randomness" of mutation only in order to contrast it to the non-randomness of selection, the other side of the process. It is not necessary that mutation should be random in order for natural selection to work. Selection can still do its work whether mutation is directed or not. Emphasizing that mutation can be random is our way of calling attention to the crucial fact that, by contrast, selection is sublimely and quintessentially non-random. It is ironic that this emphasis on the contrast between mutation and the non-randomness of selection has led people to think that the whole theory is a theory of chance." R Dawkins, Climbing Mt. Improbable, pp 80- 82.

There are several studies that show that mutations are not "random" with respect to the place on the genome where they occur. Some areas are "hotspots" for mutations and have a lot. Other areas are very much protected against mutations and have few.

All the evolutionary biology texts I have read (and I have read several) define "random" for mutations as I have given it.

Again, that Dr. Caporale disagrees does not automatically mean his position is valid.