Evolution in action: new plant species

I believe it's time for a refresher course in Scientific Method.

The following are the main steps in the scientific method: Observe nature, formulate a hypothesis about nature, design an experiment to test this hypothesis, perform this experiment, compare the results with the hypothesis, refine the hypothesis as necessary, and repeat. Once a variety of different experiments have been performed, all confirming that the hypothesis is true, then the hypothesis is considered to be a "theory," the pinnical of scientific advancement. While theories are occationally disproven, it always happens that the new theory will incorporate elements of the old one (often, it will arise that the old theory was in fact a "special case" of the new theory). For example, Netwon's theories of gravity were eventually disproven by Einstein, but Einsteinian physics still incorporates much of Newton's ideas, and in the "special case" of non-reletivistic speeds, Netwon's physics arises as a result of Einstein's. This is the life cycle of a scientific theory.

You may have noted that the words "absolute proof" were not in the above discussion. That is because in science, there is no "absolute proof." We always are working on the basis of incomplete evidence. After all, for all we know we could be living in the Matrix, and all the science we think is true is nothing more than a line of code in a computer. However, the evidence does not suggest that theory, and therefore we conclude that our existant theories of science are true. All science is provisional; everything can be disproven, given appropriate quantity and quality of evidence. There is no "absolutely true theory;" just "the best theory we currently have."

Any true scientist would agree to this discussion. I ask you which "materialists/atheists" you have met who do otherwise. To take any scientific proof as absolutely conclusive is not the mark of the skeptic; it is the mark of a believer. But to deny that science is true in most cases and about most things is the mark of one who would deny the very nature of our reality.
 
rwald said:
....to deny that science is true in most cases and about most things is the mark of one who would deny the very nature of our reality.
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And would you aver with 100% certainty you know "the very nature of our reality"?

That, you see, is the axiom problem.
 
Frankly, I put that line in mainly to keep people from quoting me out of context with the previous line. Yes, all science we currently know of could be wrong. Everything could be run by a race of pink bunny rabbits living inside of atoms. The point is, science is the only way to approximate an understanding of the true nature of reality. And I feel free in saying that without reservation, because I have seen no method other than the scientific method which can hope to arrive at a reasonably accurate model of reality.
 
rwald said:
...I have seen no method other than the scientific method which can hope to arrive at a reasonably accurate model of reality.
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See, we agree 100% with that statement. Just don't confuse the map for the territory.

Would you aver with equal certainty you know "the very nature of our reality" with the certainty you have that your bowling ball will not "tunnel" through the bag & land on the floor?

Long odds are still odds, not certainty. ;)

For me, I will note that I am at least that certain that no human will ever understand "the very nature of our reality".
 
Everything is possible. There are, however, varying degrees of probability. I'm not sure what the odds are of all the atoms in a bowling ball quantum-tunneling through a bag at the same time, but I suspect that you would have to wait for a time much longer than the universe's lifetime for this to happen. But I agree, in theory it can happen.

And if you really want me to, I'll state that science may very well never completely describe the "Theory of Everything." One key concept of science is that theories are only a model of reality. They reflect on the nature of reality, but may leave out some level of detail. For example, the Standard Model of particle physics is an OK model of reality; it describes all particles as being infinitely small points, states that there are only 12 basic particles, and asserts that neutrinos are massless. For most things, this model of reality is sufficient. However, when probing deeper into the nature of reality, it has become apparent that this model is not a completely accurate description of reality. New theories, such as supersting theory and quantum loop gravity, have been advanced to account for these flaws. Are any of these a "complete understanding of reality"? Probably not. They are merely models which more accurately reflect the true nature of reality.

Do I think that science can ever create a theory which, far from being a mere model of reality, is actually a full and complete description of reality? I'm not sure. This challenge may well be beyond the reach of science. Strictly speaking, our current understanding of science is "good enough" for most purposes; I think Stephen Hawking once said, "It is a mark of how advanced we are in our understanding of physics that it now takes vast, complex machines and great deals of money to conduct experiments the outcomes of which are not already known." The absolute, final, true nature of reality may never be fully understood -- but the scientific models thereof should be good enough for essentially any purpose.

Again, I ask: do you know of a better way for exploring the true nature of reality than science?
 
Hijacking a Thread at Warp Speed

rwald said:
... I suspect that you would have to wait for a time much longer than the universe's lifetime for this to happen. But I agree, in theory it can happen.
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Maybe tomorrow too; we shouldn't just ignore it.

the scientific models thereof should be good enough for essentially any purpose.

...do you know of a better way for exploring the true nature of reality than science?
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If you want to use machines to put men in orbit & sometimes bring them back alive ...

If you want medicine that saves one child (talk about winning the lotto) at a cost that would save thousands ...

If you want 100+ megaton explosions (last I heard it's open ended -- build 'em as big as you want to) ....

well, you get the idea ...

are you *sure* an Aborigine in Dreamtime is not closer to IT .... ;)
 
Do you really want me to list the advances that science has made possible?

And I've yet to see any evidence suggesting that Aboriginial Dreamtime, or any other religious myth, has much relation to the true nature of reality. Science may not be perfect, but it is close.
 
Final Hijack

rwald said:
Do you really want me to list the advances that science has made possible?
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No. Enough for me, here. (MORE than enough for most.)

Time to agree to disagree. :)
 
I think I understand your representation in the main!

TO BILLY HOYT

You wrote on page 3, 02-24-2003 11:56 AM: Your explanation is what is usually presented at a non-theoretical level. The underlying theory of population genetics is where you need to go to get this information. The differential equation describing directional selection shows a rate of decline that itself declines as the alleles are pulled out of the genome.
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Soderqvist: If stronger legs are favored in foxes, and rabbits by natural selection, why must this selection pressure decline because of alleles are pulled out of the genome?

That is, as fewer of the less fit alleles are left, the rate of selection drops. On the other side of the equation, mutation is replacing those alleles at a certain rate. The unfit alleles keep getting inserted back into the population. The net effect is that the two forces reach the mutation-selection equilibrium.
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Soderqvist1: Mutation is random regarding bodily features, it means that they are unbiased regarding bodily fitness. These hypothetical unfit mutated genes, its probability is infinitesimal that they will have the same nucleotide sequences!

In small populations, a third force often takes over. This force is random drift, sometimes called random genetic drift or genetic drift. These are fluctuations in allele frequencies unrelated to fitness. Only this drift can take an allele frequency to 0 (or, conversely, to 1). Over time, however, mutation will again replace it.
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Soderqvist1: I seriously doubt that mutation will end up with the same permutation configuration!

Bill Hoyt wrote 02-24-2003 02:40 PM: The phrase you're searching for is "punctuated equilibrium." But no, a Pekinese "shouldn't" turn back into a wolf again. A Pekinese, allowed to mate freely with a large number of other breeds, would become more wolf-like over time, however. Dogs and wolves are the same species (Canis lupus familiaris = dog; Canis lupus = wolf)
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Soderqvist1: A Pekinese is artificially selected and will probably not survive in nature!
But let's say; some other little creature will probably be genetically adjusted to other breeds just as you have pointed out!
 
Re: I think I understand your representation in the main!

Peter Soderqvist said:
TO BILLY HOYT
Soderqvist: If stronger legs are favored in foxes, and rabbits by natural selection, why must this selection pressure decline because of alleles are pulled out of the genome?
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The "pressure" is the s in the equation. It does not decline. The rate of decline is a function of the current allele frequency, however. That rate falls off as the allele frequency falls off. Go through the equation a bit, and you will prove it to yourself.
Soderqvist1: Mutation is random regarding bodily features, it means that they are unbiased regarding bodily fitness. These hypothetical unfit mutated genes, its probability is infinitesimal that they will have the same nucleotide sequences!
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This is the same mistake made by fundamentalists, Peter. There are several types of mutation. For now, we'll stick with point mutation, the substitution of one nucleotide for another. It represents a bidirectional chemical error rate. There is a rate of forward mutation (moving toward nucleotide X) and a rate of reverse mutation (moving away from nucleotide X)

These rates are typically on the order of 10<sup>-4</sup> to 10<sup>-6</sup>
Soderqvist1: I seriously doubt that mutation will end up with the same permutation configuration!
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What do you mean by "permutation configuration"?

Cheers,
 
Permutation configuration?

I mean that the mutation will not give us the same allele as before. Point mutation will give us a new configuration of nucleotides; it is in general a slight copy error, which will give us a new type of competitor!
 
Re: Permutation configuration?

Peter Soderqvist said:
I mean that the mutation will not give us the same allele as before. Point mutation will give us a new configuration of nucleotides; it is in general a slight copy error, which will give us a new type of competitor!
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In fact, point mutation does give us exactly the same allele as before. Let's say the codon involved is "normally" TTT. That codes for phenylalanine. A single mutation to TAT now changes this to code for tyrosine. The protein is now different in this new organism and somehow changes the phenotype. A point mutation at this same codon happens in around 10<sup>-4</sup> copies. That means that that is the probability with which we will see TAT become TTT once again.

That is the definition of point mutation: the replacement of one nucleotide by another.

Cheers,
 
Correction:
The "pressure" is the s in the equation. It does not decline.
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That's not quite correct. The "s" is the selection coefficient. The "pressure" is the final rate. The "s" doesn't change, but the "pressure" does, in fact, decline. I'm sorry for any confusion.

Cheers,
 
Dynamic said:
"Life doesn't strive toward consciousness. It strives to continue to exist and to reproduce."

Isn't it going a bit too far to say even that?
Organisms certainly strive to live and breed; explanations for this can be sought in their genetic makeup and the way it plays out on their cellular chemistry as they interact with their environment.
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I don't see the difference between "strive to continue to exist and to reproduce" and "strive to live and breed." ??

But are we to suppose that genes really care whether or not their hosts prosper, or whether they (the genes) become widespread in a population of organisms?
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The genes don't "care," but the organisms certainly do.

And:Isn't there still considerable debate over the importance of drift?
Somebody...I wish I could remember...was it Kimura?... who postulated that random drift was the most significant factor in evolutionary change?
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Yes, the debate on the importance of drift is considerable. Nobody, however, disputes that drift is the force responsible for fixation of alleles. The central debate is whether or not drift is the principal cause of the great molecular diversity in each genome. Darwin's natural selection should have resulted in great homogeneity in each genome; one allele should dominate at each locus. When we began looking directly at the genome, we were shocked to find incredible diversity. Before that shock, however, population geneticists had already worked out the equations describing disruptive and balancing selection. Those already gave a clue that Darwin's natural selection (now more formally known as directional selection) wasn't the whole story.

In the 60s, several population geneticists began proposing that most alleles were far more neutral than we had originally thought and that this similarity in selection coefficients might explain why we saw such allelic diversity. Kimura's 1971 paper put the theory forth in a formal way, and tied drift to this concept of neutral alleles. He demonstrated that, in the absence of strong selection coefficients, the relative force of random drift becomes the dominant factor and that the allele frequencies basically follow random walks.

But the random nature of the environment has been looked at more recently and Gillespie's 1991 theory of selection in a random environment is gaining acceptance as it becomes clearer that selection coefficients are actually not coefficients but functions of the total environmental context. A randomly shifting context could result in changes in s, and therefore, a great mix of alleles.

There is a third component, too, and that is the suggestion that the chromosomal linkage between genes causes a "hitch-hiking" effect. A strongly favored (disfavored) allele will always increase (decrease) the frequencies of its neighbors because the allele because selection must act on the entire chromosome. Only recombination breaks the hitch-hikers away from the favored (disfavored) allele.

Cheers,
 
I don't see the difference between "strive to continue to exist and to reproduce" and "strive to live and breed." ??

I didn't intend any difference; I was just trying to save a little typing.

The genes don't "care," but the organisms certainly do.

I seem to have adopted the "Dawkinsinian" perspective to the extent that I automatically look to the gene level for understanding. I was saying that organisms care about whatever their genes tell them to care about. But genes don't tell organisms to care about things because they care what the organisms care about, it's just that whatever works out well for the organisms causes the genes to become more populous as well. It's all just dumb, blind luck. For me, that's the beauty of it.

There must be a term for that hitch-hiking effect that ends with an "oid" or an "ism"? (I love those).
 
DNA is. It does it very well. No why required.

We're just the by-products of DNA doing its thing.

And yes, it is beautiful. :)
 
rwald said:
I belive the term is "linked genes" or "indirect selection."
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I've seen all three used, although "hitch-hiking" seems to be more popular.

Cheers,
 
rwald, do current results in genetics have examples of species "de-evolving", that is losing overall complexness?

I admit I'm uncertain how to define "overall complexness"; chromosome level, gene level, dna level, maybe? If an obvious central nervous system existed, a decrease in that complexness would I'd think be it.

Can you recall something in the fossil record that could be used to demonstrate de-evolution?
 
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