NIH: 100M Years to Change a Binding Site

[Stripe]

If we're comparing the DNA of two critters, each one of those sets of DNA is what we're trying to read - each is the "gold standard" in my example. In an ideal world, we can read each perfectly. In the real world, we can make the error rate as low as desired, as Tom Schneider said in the very next sentence after the snippet you quoted.

Yep, but we need the genomes of two critters that have descended one from the other. And we don't have the standard to tell entirely what data is correct and what data is in error.

 

[Frayed Knot]

Yep, but we need the genomes of two critters that have descended one from the other. And we don't have the standard to tell entirely what data is correct and what data is in error.

Each one has exactly correct data, for that critter.

The original question was whether it's possible for evolution to account for the complexity, the information content, of the genome of current species. Given an ancient species with a certain set of DNA, could that lead to a descendant species whose DNA has more complexity, more information, than the one we started with, using only evolution's tools of gene duplications and other transcription errors.

And the answer that everyone has seen, in some painstaking detail, is "yes."

 

[Stripe]

Each one has exactly correct data, for that critter.

Sure. But there is a standard that they do not adhere to perfectly, right?

the answer that everyone has seen, in some painstaking detail, is "yes."

Oh, I don't know about that.

 

[Yorzhik]

Then your application of information theory is inappropriate. If there is no message, from the perspective of the method of quantification you are using, then anything you say about it has little relevance.

Corpses do bleed!

I'd love to keep conversing with you, but my time will be short for a while again and I need to focus on people that make sense.

 

[Jukia]

Sure. But there is a standard that they do not adhere to perfectly, right?

Maybe that is the whole point of evolution---there is no "gold standard". If you have 2 living things, one which descended from the other, and which are both capable of living and reproducing, it matters not which is the standard, both work. For evolution, that is all that matters.

 

[Yorzhik]

That's not what we're talking about here. We're talking about taking a strand of DNA, and getting the sequence of its bases into our heads, or onto a sheet of paper.

That would make no sense at all. Why would we care to measure information in a system where the decoder can't hardly do any decoding at all? A better measure would be from a decoder that understands the information, and which, literally, it's life depends on correct decoding.

A pattern with more randomness results in more information.

You're joking with me. And by joking I mean, "It is thus clear where the joker is in saying that the received signal has more information. Some of this information is spurious and undesirable and has been introduced via the noise. To get the useful information in the received signal we must subtract out this spurious portion."

 

[Alate_One]

Maybe that is the whole point of evolution---there is no "gold standard". If you have 2 living things, one which descended from the other, and which are both capable of living and reproducing, it matters not which is the standard, both work. For evolution, that is all that matters.

Even more to the point, in a sexual organism, new species don't arise from individuals but from populations and every individual has a slightly different genome, so there is no "gold standard" anywhere except for a particular individual. Even then, there can be variation between patches of cells in a single individual!

 

[Stripe]

Maybe that is the whole point of evolution---there is no "gold standard". If you have 2 living things, one which descended from the other, and which are both capable of living and reproducing, it matters not which is the standard, both work. For evolution, that is all that matters.

We know. Evolution relies upon the overturning of common sense.

Even more to the point, in a sexual organism, new species don't arise from individuals but from populations and every individual has a slightly different genome, so there is no "gold standard" anywhere except for a particular individual. Even then, there can be variation between patches of cells in a single individual!

Except that there is degradation apparent in every population. If it needs be that we determine the gold standard as that belonging to a population then so be it. But be the standard found in an original individual or a population the fact remains there must be one!

 

[Alate_One]

Except that there is degradation apparent in every population.

You're calling it degradation because you are assuming the truth of your supposition, which has not been demonstrated. Do you not believe there are variations that are not harmful? Or is a human with blue eyes "worse" than one with brown?

If it needs be that we determine the gold standard as that belonging to a population then so be it. But be the standard found in an original individual or a population the fact remains there must be one!

Why must there be one? A sexual species survives because there is variation. If there is no variation, that species will die very quickly. See the Irish Potato famine.

Even if you believe every species descended from two individuals, do you think they were clones of one another? There can be no "gold standard" no matter how you look at it. Any standard you set would be arbitrary.

 

[Stripe]

You're calling it degradation because you are assuming the truth of your supposition, which has not been demonstrated.

Yes, it has. Name any process .. introduce random changes to that process .. watch it fail.

Random changes always degrade Do you not believe there are variations that are not harmful? Or is a human with blue eyes "worse" than one with brown?

You're gnoring the facts and focusing on things that do not look bad.

Why must there be one? A sexual species survives because there is variation. If there is no variation, that species will die very quickly. See the Irish Potato famine.

Variation is not the same as randomisation.

Even if you believe every species descended from two individuals, do you think they were clones of one another? There can be no "gold standard" no matter how you look at it. Any standard you set would be arbitrary.

No, it wouldn't. You can have a standard and have numerous individuals that match up to that standard.

 

[Jukia]

We await some science behind your positive statements, Stripe. Stripe says so does not count as science.

 

[Stripe]

We await some science behind your positive statements, Stripe. Stripe says so does not count as science.

Random changes to credit card numbers make credit card numbers that do not work.

 

[Alate_One]

Yes, it has. Name any process .. introduce random changes to that process .. watch it fail.

Gee, tell that to your own B memory cells. :chuckle:

Is that why NASA uses evolutionary design?

Variation is not the same as randomisation.

Randomization can create variation. Ask mutation breeders.

No, it wouldn't. You can have a standard and have numerous individuals that match up to that standard.

Then you don't have ONE standard, you have many.

 

[Alate_One]

Random changes to credit card numbers make credit card numbers that do not work.

Credit card numbers require an EXACT set of numbers to function at all. DNA doesn't require such precision to be functional.

And honestly you think credit card numbers are a good analogy for biology? :rotfl: You're ridiculous.

 

[Stripe]

Then you don't have ONE standard, you have many.

No, you don't. And if you could understand this then you'd be able to understand the challenge to evolution. You'd also understand how your examples of random changes are not actually random.

 

[Yorzhik]

Gee, tell that to your own B memory cells. :chuckle:

Keep laughing. Have you asked a programmer about programmed variation?

Is that why NASA uses evolutionary design?

Oh, great, here's one now. The secret in the sauce is a goal the program is designed to achieve. In fact, it's identical in principle to the B memory cells.

So, yes, there is a time when random is good. It's when an umbrella program has control. Like b memory cells and "evolutionary" algorithms.

Randomization can create variation. Ask mutation breeders.

Right, it's good as long as the breeder is in control.

 

[Alate_One]

Keep laughing. Have you asked a programmer about programmed variation?


Oh, great, here's one now. The secret in the sauce is a goal the program is designed to achieve. In fact, it's identical in principle to the B memory cells.

So, yes, there is a time when random is good. It's when an umbrella program has control. Like b memory cells and "evolutionary" algorithms.

:rotfl: so you just contradicted Stripe! (That ws the point of my reply, silly) He says "random changes are always bad". But you're talking about selection, be it carried out by a program, affinity maturation, etc. We know that selection does not require a "program" to be in control. It could be as simple as the two mouse proteins I linked earlier (actual mice shown below). It's so obvious a guy back in the 1800s thought of it.

 

[Stripe]

so you just contradicted Stripe!

Atheists love to point at disagreement in the opposition as if it were evidence for their own story.

We know that selection does not require a "program" to be in control.

Not unless we assume the truth of evolutionary theory. If you want a program to work with random numbers well, then you have to well design the program. And it does your case no good at all to say that the random part is controlled by a well designed program.

 

[Yorzhik]

:rotfl: so you just contradicted Stripe! (That ws the point of my reply, silly) He says "random changes are always bad".

They are if a program doesn't intend them. That's no contradiction of Stripe, it's your inability to discuss this topic honestly.

But you're talking about selection, be it carried out by a program, affinity maturation, etc. We know that selection does not require a "program" to be in control. It could be as simple as the two mouse proteins I linked earlier (actual mice shown below). It's so obvious a guy back in the 1800s thought of it.

This is where you are wrong (bolded section). If there is no program in control to keep the random in check and guide it toward a goal, it will always be harmful.

 

[Alate_One]

They are if a program doesn't intend them. That's no contradiction of Stripe, it's your inability to discuss this topic honestly.

Um, random is random "intentional" or not. The point is is there screening of what comes out. There is screening in natural selection as well as the other processes I mentioned.

This is where you are wrong (bolded section). If there is no program in control to keep the random in check and guide it toward a goal, it will always be harmful.

As long as there is some kind of screening to throw out the nonfunctional from the functional, random changes are fine. That's what evolution does.