[Stripe]

Originally Posted by Alate_One

Average can be a rather useless statistic depending on the distribution of your sample. Since there's really not enough data to determine the distribution of "changes for a new feature", stating an average is nothing more than a wild guess and useless to the discussion.

We know. You do not want there to be this discussion...

[The Barbarian]

Since we've established that only one nucleotide substitution is necessary for a new trait, the point is moot.

[Yorzhik]

Originally Posted by The Barbarian

One substitution can make a new trait.

Ignoring substitutions for a moment, one bp can't make a trait.

Alate_One, if you are reading this, are you going to engage in the kind of game Barbie is playing now?

[Yorzhik]

Originally Posted by Alate_One

It depends. Sometimes it may only take one, other times more than one, other times whole genes.

And the average is?

If I remember correctly the seven came from the alignment of the two opsin genes within humans.

That may have been an example, but seven came from a guess at the average.

Seven was the number of non-similar amino acid differences between the opsin gene that responds to middle wavelengths (green) and the one that responds to long wavelengths (red). However, on looking through the literature a bit more I found this quote in a paper discussing the evolution of color vision.




Source

Nearly all mammals, save the old world monkeys, apes and humans are dichromats, that is essentially red-green color blind. Virtually all other vertebrates are tetrachromats and have color vision. Mammals presumably lost theirs during the time they were strictly nocturnal and small during the age of dinosaurs.

The middle wavelength receptor appears to have evolved from the long wavelength receptor, probably by gene duplication due to the strong selective advantage for primates to be able to spot red and orange colored fruits in a sea of green leaves.
We can see species of monkeys today where not every individual in the population has trichromat vision (the trait is not fixed).

This is very interesting, but has little to do with the topic at hand.

So if you'd like to look at this specific instance that's fine,but generalizing is a bad idea.

To answer the question of what is the main driver of evolution, one must find out what is the "main", or "most used" example.

Then you'd count the mouse's coat color?

Sure. Whatever helps us arrive at the average.

Yes, but you're harping on single nucleotide changes because you want to say it takes too many single changes to make a new trait so that it can't be selected for. Since we really don't know what kinds of mechanisms are common. There's tons of genome data but we don't know what all of it actually does.

We do know a few things. And the more we know the more it looks like mutation+NS is not the main driver of evolution.

They appear to be errors since there isn't a consistent response at the DNA level to particular changes in the environment. Instead we see lots of different changes that give a similar phenotype i.e. Convergent evolution.

If you'd like, I'm perfectly willing to extend my claim to include errors, as well as mutations. The difference is this: an error is when DNA to the next generation a deletion, duplication, or inversion occurs. A mutation is where a nucleotide is incorrectly copied.

Yes I am. You already asserted that regulatory regions AND protein coding regions have to be changed for a new feature to be created,

Find a quote where I claimed this or you're a liar.

But the overall picture of how regulation makes new traits in the evolutionary sense is very fuzzy.

Since your whole theory rides on avoiding the stepping stone problem, and it looks like the stepping stone problem is very likely, you don't have a theory until you show how the theory avoids it.

[Alate_One]

Originally Posted by Yorzhik

Ignoring substitutions for a moment, one bp can't make a trait.

Alate_One, if you are reading this, are you going to engage in the kind of game Barbie is playing now?

Ignoring substitutions? Um why would you want to do that? (other than to further some kind of mathematical game you want to play) Evolution by definition is tinkering with what came before. So basically you don't actually want to discuss this case study do you?

One BP = the ability to tell the difference between green and red. That's a new trait isn't it?

Now you might say, hey you need to have the old version as well to be able to have both pigments so you can discriminate. Well the amazing thing is most animals are diploid, meaning they have at least two copies of every gene one from mom and one from dad. So change one amino acid in one copy and one of them now reacts to a slightly different wavelength than the other. Bam instant new feature.

Now the interesting thing about the opsin gene in question is it's carried on the X chromosome meaning that with a single mutation, only females will actually exhibit the new feature. We see this in quite a number of species of monkeys where the males are all dichromats, but many (though not all) females are trichromats (like humans). This also means that humans (nearly always females) carrying altered versions of a opsin gene as well as the normal version can have enhanced color discrimination ability.

Test to see if you are a tetrachromat - most likely (still extremely rare) if you are female.

[Alate_One]

Originally Posted by Yorzhik

And the average is?

Average would assume we had a reasonable sample size. Biology is a collection of special cases, the very idea of average number of changes for a new feature is questionable at best.

That may have been an example, but seven came from a guess at the average.

No, it came from that example.

This is very interesting, but has little to do with the topic at hand.

It has everything to do with the topic at hand. It's a case study of the evolution of a new feature. Or do you want to keep arguing in the abstract and unknown?

To answer the question of what is the main driver of evolution, one must find out what is the "main", or "most used" example.

Again, biology is a collection of special cases, while selection is clearly important, generalizing overly is only going to get you in trouble.

We do know a few things. And the more we know the more it looks like mutation+NS is not the main driver of evolution.

Because you say so, right. Did you miss the parts of that lecture that talked about genetic signatures of positive and purifying selection?

You making this baseless claim, is like me going to my favorite auto mechanic and insisting that gasoline is not the "main driver" of a car's forward motion.

If you'd like, I'm perfectly willing to extend my claim to include errors, as well as mutations. The difference is this: an error is when DNA to the next generation a deletion, duplication, or inversion occurs. A mutation is where a nucleotide is incorrectly copied.

Not a biological definition. A mutation is simply a change in DNA. A nucleotide being incorrectly copied or repaired for that matter is still an error.

Find a quote where I claimed this or you're a liar.

Originally Posted by Yorzhik

I've always tried to get the evolutionists to think in terms of the regulatory regions included with the protein coding regions because mutations must happen in both places.

Since your whole theory rides on avoiding the stepping stone problem, and it looks like the stepping stone problem is very likely, you don't have a theory until you show how the theory avoids it.

You have it backwards. Your whole angle rides on there being a huge stepping stone problem. I've yet to see evidence of this problem. So I'd suggest YOU produce it.

You can assert the theory rests on YOU being persuaded but it doesn't. I find it interesting to look at the mechanics of evolution, but to claim that everything must be 100% clear or XYZ scientific theory is bunk, is just plain stupid. No other scientific theory is subjected to this level of idiocy, and this is purely because it conflicts with your interpretation of scripture.

[Yorzhik]

Originally Posted by Alate_One

Ignoring substitutions? Um why would you want to do that?

Substitutions is what the thread is all about. The reason I had to add "ignoring substitutions for the moment" was because Barbie can't have an honest conversation.

If you understand that traits are made from a lot of bp, that would imply that making a new feature could very well require more than one mutation before it is positively selectable.

[Yorzhik]

Originally Posted by Alate_One

Average would assume we had a reasonable sample size.

You don't? Then you don't have a theory.

Biology is a collection of special cases,

You don't understand the concept of "special case". A sample size you can be confident in is required before you know you have a "special case."

the very idea of average number of changes for a new feature is questionable at best.

Your theory rides on it. If the average is greater than 1, you have a stepping stone problem.

No, it came from that example.

So you are confident the average is 1?

It has everything to do with the topic at hand. It's a case study of the evolution of a new feature. Or do you want to keep arguing in the abstract and unknown?

If you don't know, you don't have a theory.

Barbie has about 40 or so examples where 1 mutation created a positively selectable feature. How many new features have been created in all organisms in all time? If you add Barbie's and your examples together are you confident you have enough?

Again, biology is a collection of special cases, while selection is clearly important, generalizing overly is only going to get you in trouble.

Generalizing might be trouble. But you need to know if you have a stepping stone problem or not. Since every trait takes a great number of bp to be expressed, it is unlikely that a single mutation can create a new feature most of the time.

Because you say so, right. Did you miss the parts of that lecture that talked about genetic signatures of positive and purifying selection?

I didn't miss any parts. They simply didn't answer the problem.

You making this baseless claim, is like me going to my favorite auto mechanic and insisting that gasoline is not the "main driver" of a car's forward motion.

The difference is that the mechanic can show you how gasoline is the main driver. You've been insisting that you don't need to show anything.

Not a biological definition. A mutation is simply a change in DNA. A nucleotide being incorrectly copied or repaired for that matter is still an error.

Great. Then I don't have to extend anything. Point mutations, duplications, inversions, and deletions. It is most likely to take more than 1, on average, to create a new feature.

Originally Posted by Yorzhik

I've always tried to get the evolutionists to think in terms of the regulatory regions included with the protein coding regions because mutations must happen in both places.

Wow. Talk about uncharitable. To claim that I asserted that regulatory regions AND protein coding regions have to be changed for a new feature to be created from this quote is weak - because I've agreed that your sight color, and Barbie's 40 or so other examples are fair game to add to the average.

Or did you not realize I agreed those were valid? Those examples that didn't have a change in both regulatory and protein coding regions?

You have it backwards. Your whole angle rides on there being a huge stepping stone problem. I've yet to see evidence of this problem. So I'd suggest YOU produce it.

It's your theory. Since traits take a great number of bp to be expressed, it is likely that creating a new feature will require more than 1 mutation, on average, to be positively selectable.

Do we have an example? We do.

In 2010, research published by molecular biologist Ann Gauger of the Biologic Institute, Ralph Seelke at the University of Wisconsin–Superior, and two other biologists provided empirical backing to the claims of Axe and Behe.2 Their team started by breaking a gene in the bacterium Escherichia coli required for synthesizing the amino acid tryptophan. When broken in just one place, random mutations in the bacteria's genome were capable of "fixing" the gene. But when two mutations were required to restore function, Darwinian evolution could not do the job.

You can assert the theory rests on YOU being persuaded but it doesn't. I find it interesting to look at the mechanics of evolution, but to claim that everything must be 100% clear or XYZ scientific theory is bunk, is just plain stupid. No other scientific theory is subjected to this level of idiocy, and this is purely because it conflicts with your interpretation of scripture.

It only relies on me being persuaded if the stepping stone problem relies on me. It doesn't. It's a real problem evolution has to show is wrong in order to be a theory.

[The Barbarian]

Now the interesting thing about the opsin gene in question is it's carried on the X chromosome meaning that with a single mutation, only females will actually exhibit the new feature. We see this in quite a number of species of monkeys where the males are all dichromats, but many (though not all) females are trichromats (like humans). This also means that humans (nearly always females) carrying altered versions of a opsin gene as well as the normal version can have enhanced color discrimination ability.

That would explain it. Guys are CGA; only 16 colors. You ask them what color something is, and it's "light purple." A female says "medium orchid."

[The Barbarian]

(Yorzhik asks how many bp substitutions it takes to make a new trait)

(Barbarian cites numerous examples where it takes 1)

(Sound of goal posts being frantically repositioned)

Either a single bp makes a trait, or it takes more than 1 to make a trait. You're inferring it takes more than 1 bp to make a trait (not change a trait).

As you learned earlier, evolution always works by modifying something already there. So it's changes to existing alleles or duplicating alleles and then modifying them.

[noguru]

Originally Posted by Stripe

We know. You do not want there to be this discussion...

You are a complete idiot.

[The Barbarian]

Alate_One writes:
Average would assume we had a reasonable sample size.

You don't? Then you don't have a theory.

Wrong again. The theory doesn't require any particular number of substitutions to make a new trait. So far, all we know is that new traits caused by a single substitution are quite common.

The lack of a large body of evidence for your assumption means you don't have a theory.

Alate_one writes:
the very idea of average number of changes for a new feature is questionable at best.

Yorzhik tries again:

Your theory rides on it.

Nope. Your assumption rides on it. Unless you get some data, you're just making up fairy tales.

Alate_one writes:
You making this baseless claim, is like me going to my favorite auto mechanic and insisting that gasoline is not the "main driver" of a car's forward motion.

Yorzhik tries again:

The difference is that the mechanic can show you how gasoline is the main driver.

As you learned, random mutation and natural selection is the driver of evolution.

It is most likely to take more than 1, on average, to create a new feature.

So far, all the ones in evidence required one. So you're just blowing smoke here.

Since traits take a great number of bp to be expressed, it is likely that creating a new feature will require more than 1 mutation, on average, to be positively selectable.

Do we have an example? We do.
In 2010, research published by molecular biologist Ann Gauger of the Biologic Institute, Ralph Seelke at the University of Wisconsin–Superior, and two other biologists provided empirical backing to the claims of Axe and Behe.2 Their team started by breaking a gene in the bacterium Escherichia coli required for synthesizing the amino acid tryptophan. When broken in just one place, random mutations in the bacteria's genome were capable of "fixing" the gene. But when two mutations were required to restore function, Darwinian evolution could not do the job.

But this isn't a new trait. It's about repairing a damaged one, which requires very specific steps. If you feel the need to be deceptive to make your point, isn't that a significant clue about the value of your belief?

Yorzhik, you can't trick science out of existence. You have to do the grunt work of finding real evidence. Stamping your foot and insisting that science has to do it your way to be valid just makes you look foolish.

[noguru]

Originally Posted by The Barbarian

Yorzhik, you can't trick science out of existence. You have to do the grunt work of finding real evidence. Stamping your foot and insisting that science has to do it your way to be valid just makes you look foolish.

You don't say.

[Alate_One]

Originally Posted by Yorzhik

You don't? Then you don't have a theory.

I don't have a large sample size where we know the specific molecular basis of the formation of new traits, though more are being added every day. You know that molecular genetics is an ADDITION to evolutionary theory.

Your theory rides on it. If the average is greater than 1, you have a stepping stone problem.

Greater than one does not necessarily equal a stepping stone problem. While one mutation might not always be a new feature, it might offer enough benefit to be selectable.

Other mutations are thought to be neutral but potentiating mutations for something else. Since there isn't a set goal as to what the new feature would be or how any particular genetic sequence will get there, there is no need for a "stepping stone" problem at all.

Since the picture of stepping stones you are using, assumes you must have a specific stone before another, the flexibility of proteins and regulatory sequences and evolutionary changes we have looked at indicate there are many paths to any one particular outcome.

If you don't know, you don't have a theory.

Your assertion, not reality. If we used this kind of logic, we should start jumping off of cliffs because gravitation is not fully understood (arguably less understood than evolution).

Generalizing might be trouble. But you need to know if you have a stepping stone problem or not. Since every trait takes a great number of bp to be expressed, it is unlikely that a single mutation can create a new feature most of the time.

Since every new trait builds on something that's already there, there's no reason your assertion has any basis at all.

I didn't miss any parts. They simply didn't answer the problem.

That's the fun part of being a YEC, you get to keep moving to goal posts so nothing is ever enough.

The difference is that the mechanic can show you how gasoline is the main driver. You've been insisting that you don't need to show anything.

I've showed you plenty of instances of mutation and selection in the past. Do you really want me to waste my time and look them all up again? Or maybe you could just read a biology or evolution textbook and we could discuss specific examples.

Do we have an example? We do.

Barb has already tackled this bit quite well. I'd be curious as to how many generations were used and how their "selection" was performed (since you didn't provide a source).

That said, evolution isn't about repairing something that's broken to a specific outcome. Indeed when we look around the genomes of most organisms we find lots of broken genes and unused bits. Instead evolution frequently repurposes genes sometimes even nonfunctional ones into something else. The experiment you describe looks for only one particular outcome, effectively FORCING a stepping stone problem.

All you've been doing in every post is setting up the same straw man over and over and insisting I put a hat on it and give it my blessing. Not going to happen since it's based on a misunderstanding of both genetics and evolution.

[Yorzhik]

Originally Posted by Alate_One

I don't have a large sample size where we know the specific molecular basis of the formation of new traits, though more are being added every day. You know that molecular genetics is an ADDITION to evolutionary theory.

That's why this is technically a problem for what is proposed as the main driver of evolution, and not evolution itself per se. That main driver being mutation + NS.

Greater than one does not necessarily equal a stepping stone problem. While one mutation might not always be a new feature, it might offer enough benefit to be selectable.

If it offers enough benefit to be selectable, it is a new feature. Thus, greater than one does necessarily mean a stepping stone problem.

Other mutations are thought to be neutral but potentiating mutations for something else. Since there isn't a set goal as to what the new feature would be or how any particular genetic sequence will get there, there is no need for a "stepping stone" problem at all.

Apparently you don't know what the stepping stone problem is. It takes all paths into account.

Since the picture of stepping stones you are using, assumes you must have a specific stone before another, the flexibility of proteins and regulatory sequences and evolutionary changes we have looked at indicate there are many paths to any one particular outcome.

No. Apparently you don't know what the stepping stone problem is. It assumes there is another stone. Any stone. Near enough to get to.

Your assertion, not reality. If we used this kind of logic, we should start jumping off of cliffs because gravitation is not fully understood (arguably less understood than evolution).

It is scientific reality. If you don't have the evidence required to show your theory is likely, you don't have a theory. One way to show the evidence would be to get the average and show how evolution achieves this average. Thus, it's your fight against finding the average that is more damning than your lack of evidence itself.

And thanks for proving my point. Gravity, unlike evolution, does not say the science is settled on the mechanism. Instead of fighting the science, you should admit the stepping stone problem is real and look for another mechanism besides mutation + NS.

Since every new trait builds on something that's already there, there's no reason your assertion has any basis at all.

Sure it builds on something else. But here is your problem:

If something were simple to change, let's say a three letter word to other 3 letter words, we can predict that the changes could very likely be a single letter here and there could create a whole new group of valid 3 letter words.

But now let's say we have a sonnet by Shakespeare. If we change that sonnet into another one, even a similar one, we can predict that the changes would likely require more than a single letter here and there can create valid English between the original sonnet and a new one.

That's the fun part of being a YEC, you get to keep moving to goal posts so nothing is ever enough.

Now that's not very nice. If you think they addressed the stepping stone problem, the same goal post as I've asserted from the beginning, please give me the time stamp where they did so.

[qutoe]I've showed you plenty of instances of mutation and selection in the past. Do you really want me to waste my time and look them all up again? Or maybe you could just read a biology or evolution textbook and we could discuss specific examples.[/quote]
So you gave me the average in the past? You don't have to dig up all your examples, just let us know what it is.

Barb has already tackled this bit quite well. I'd be curious as to how many generations were used and how their "selection" was performed (since you didn't provide a source).

http://bio-complexity.org/ojs/index....w/BIO-C.2010.2

Please let us know.

That said, evolution isn't about repairing something that's broken to a specific outcome.

Of course it should. Or are you now suggesting that evolution knows the difference between fixing something and gaining new features by the exact same process?!

Indeed when we look around the genomes of most organisms we find lots of broken genes and unused bits. Instead evolution frequently repurposes genes sometimes even nonfunctional ones into something else. The experiment you describe looks for only one particular outcome, effectively FORCING a stepping stone problem.

Of course it is forcing a stepping stone problem! I'm shocked a person who is a scientist doesn't know as much as a layman, that science isolates specific problems to test a theory.

All you've been doing in every post is setting up the same straw man over and over and insisting I put a hat on it and give it my blessing. Not going to happen since it's based on a misunderstanding of both genetics and evolution.

Since you are showing a lack of understanding the basic problem, I'm not so sure you should be so quick to accuse me of setting up a straw man.