Biological Information and Intelligent Design: evolving new protein folds

Humans and squid have the “same eyes” in the same way bats and birds have the “same wings”.

Which is to say, that they (eyes and wings) are superficial similar and make use of the same physical principles, but the details of their execution (e.g. anatomy and DNA) are very different. There are similarities, but the differences are nearly innumerable.

Now finding a bird wing on a bat (not just superficially, but in the details too) would be a surprise. Finding a human eye in an octopus (not just superficially, but in the details too) would be a surprise too. That, however, is not what we see.

This is a fun change of roles too. Usually I am explaining how similar humans and chimps are. They really do have the nearly the same eyes, for example. Now, you are trying to argue that octopi and humans eyes are the “same.” Putting these questions together serves as a good control…

  1. In what ways are octopi eyes different than mamalian (whales, human, chimp) eyes?

  2. Why are those differences there?

  3. Is there any feature for which octopi are more similar to humans than chimps, or whales? If they really are the same design, why not?

I think it hard not recognize that octopi eyes are just like the wings of bats and birds. Somewhat similar on the outside, and little on the inside (e.g. Pax), but fundamentally different designs. The similarities makes sense in the light of common history and the constraints of physics, and the differences make sense in light of divergent history.

Whales and fish are a great control here too. Their eyes are much closer to the design of humans, even though they function in the same environment as as octopi. Why is that? Once again, this make sense in light of the increased amount of common history.

Any how, I’m looking forward to you wowing us by listing of the many differences between cephalopod and human eyes. Go for it.

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[quote=“Cornelius_Hunter, post:81, topic:34703”]
It is ironic because you don’t have a testable hypothesis.[/quote]
It isn’t because I do, as Chris noted below.

What’s amazing is that you write hundreds of words, none of which include a testable hypothesis. Therefore, you are agreeing with my noting that you don’t have one.

Evolution is a phenomenon. Evolutionary theory is about mechanisms underlying the phenomenon. Why don’t you seem to grasp this basic distinction? Who are “they” and what were they counting and when?

No, there are plenty of testable hypotheses. You’re the one limiting yourself to explanations, because you have zero confidence that a design hypothesis will hold up to testing.

What does that even mean? In the real scientific world, we talk about experiments being repeatable, not theories.

So you don’t have a testable hypothesis.

We test it every time we sequence and BLAST a new gene, Cornelius, and you know it. Given all the words you produce, have you ever done a BLAST yourself?

Not the same design.

Utterly false.

[quote]But this “testability requirement” is an old trick that has been used by religious people for a long time to get God out of the picture.
[/quote]It’s fundamental science, a practice that you reject.

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No, I didn’t know that. So please tell us, how did evolution fare on the salamander specific genes I mentioned above? What was the outcome of that test?

How about instead of dropping my question to you when you quote, you answer it?

Given all the words you produce, have you ever done a BLAST yourself? Why don’t you BLAST the salamander genes for yourself?

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You left out the the very next sentence after the passage you quoted. Why? That sentence drastically changes the conclusions a reader would draw from the article. It is 100% contrary to your conclusion, so I cite it in full:

The findings suggest that the ancestral animal genome was quite complex, and fly and worm genomes lost some of that intricacy as they evolved.

Anemones didn’t gain those complex genes, they inherited them from the common ancestor of anemones and vertebrates: I see exactly zero problems with that conclusion.

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That and present-day anemones are not “basal”. This is an example of the platypus fallacy.

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Priceless. Utterly priceless.

Especially the attempted diversion about “have you ever done a BLAST yourself?” Next you can ask me if I’ve ever used a computer.

Because then you would not have had anything to complain about.

Um, no, it 100% supports my conclusion. Trying reading it again.

Oh, well that changes everything.

This has nothing to do with the platypus fallacy.

[quote=“Cornelius_Hunter, post:91, topic:34703”]
Priceless. Utterly priceless. [/quote]I agree.

[quote]Especially the attempted diversion about “have you ever done a BLAST yourself?” Next you can ask me if I’ve ever used a computer.
[/quote]It’s not a diversion, and I’ll take your bluster as a “no.”

If you can’t even be bothered to do any analyses for yourself, and your bluster suggests that you don’t even know how, why should anyone take your criticism of those who do the analyses seriously?

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“Next you can ask me if I’ve ever used a computer.”

You know, Cornelius, I actually put effort into following your links, reading and analyzing the originals, and writing as thoughtful a response as I can.

And in return, all you wrote is playground taunts?!

Time to take a break.

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@Cornelius_Hunter,

I believe you misinterpret my position. I am not one of those BioLogos supporters who proposes that God guides for a little while … and then looks away for a little while.

I believe he guides the whole picture! And I use the same explanation as apparently you do … which is that even the parts that seem less obvious, or even counter-obvious, are all part of the master plan.

Where I differ is that you think the results are so amazing… it Must be produced by God. I don’t find that a very convincing position … . since what we actually see is kind of a pretty mixed bag.

And it seems that a mixed bag is the worst testimony to the position of I.D.

But then there is the ‘coup de gras’ - if Genesis is to be taken literally, and vast continents of terrestrial animals (including birds) were wiped out in a global flood - - how do we end up with up to a million or more terrestrial species and kinds in the present world … if the animals were released only a few thousand years ago from the Ark?

Either Speciation is possible or not possible. And if it is possible, it seems very unlikely that it would happen in just a few dozen centuries… but would require the millions of years that a God who relies on Evolutionary methods would use.

Why not actually test Evolution in the lab - the only way to make sure? Here is a proposal:

How could we actually test Evolution? Lab observation of genetic changes over a number of generations is the ideal experiment, and this has been done many times, but not as a pass-fail test of the Evolution hypothesis. To confirm Evolution and separate it from mere adaptation or genetic drift, a Baseline and a Minimum Threshold have to be established before the actual experiment is conducted. The ideal organism to be tested is very small and is rapidly reproducing. The Baseline would be a fully documented single organism from which all subsequent generations descend while the Threshold for success would be a descendant that under no circumstance would be classified same as the Baseline organism. This may be contentious as biological classifications such as Population, Strain, Species, Genus, etc. are all subjective.

How long should the experiment last? If E.coli is the test organism (10^9 organisms/ml and 20 min/generation), it takes only 1 (one) liter of E.coli saturated solution and 1 (one) hour to obtain as many individuals as were needed for human evolution from ape (5 Mil years, 10 Mil/generation and 20 yrs. /generation). E.coli are not humans indeed, but neither are the laboratory conditions same as natural ones as the main advantage of the laboratory is to accelerate testing in a controlled environment by introducing specific inputs at a much faster rate than in nature, and by monitoring their effects to adjust these inputs.

Other test considerations include: What exactly cause the transformations observed? Do the new strains have to trade off new features for old ones or are they overall better off? What are the limits of transformation? What happens with the new population if the stimulus is removed? Do the various strains turn into a homogenous population? Does that population retain its transformations or does it revert to the Baseline?

Remember that E. coli is also the end result of a few billion years of evolution in a planet sized lab. To expect it to turn into something else in a lab in a few years would not be an expected result.

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You don’t know how long it took. But regardless, unless you’re saying Evolution stopped, we should get something new from E.coli or the Baseline organism of your choice. The trick is to agree on a good Threshold.

As mentioned, the role of the lab is to accelerate testing in a controlled environment by introducing specific inputs at a much faster rate than in nature. Are you arguing against lab testing?

Do you think we should read anything first? Say, the scientific literature?

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Both mere adaptation and mere genetic drift are evolution.

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Oh, so for example, the ability to digest nylon should count as “something new?”

That threshold was crossed decades ago by any reasonable meter. What are you hoping to accomplish by repeating the exact same suggestion here that I responded to a few days ago at length? If you’ve modified your post at all, I’ve missed it.

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Hi Nonlin - Hope you’re enjoying God’s blessings today. That’s a good point. Unlike humans, they do not reproduce sexually. That could make direct comparisons just a little difficult.

And that could make direct comparisons just a bit difficult, too. You see, our population has plenty of variation in our genome going back hundreds of thousands of years.

And now you have identified another problem: under natural conditions E Coli can and do use lateral transfer that crosses species boundaries, quite unlike humans.

Many of these questions are answerable in an E Coli experiment like the one you described. It turns out Lenski and Mittler, among others, have already answered a whole lotta interesting questions about mutation rates and genetic drift and what happens to a bacteria population’s genome when you introduce a stressor such as antibiotic agents.

Like this?
Richard Lenski at MSU did not obtain anything other than his baseline E.coli, Barry Hall at U. Rochester and Paul Rainey at Oxford only confirmed adaptation, Miller Urey did not demonstrate abiogenesis without which Common Descent is a nonstarter.