Biological Information and Intelligent Design: evolving new protein folds

From what I see, the study shows compatibility with the phylogeny model and a better algorithm to predict protein function. This is great, so congratulations! I don’t see any new fundamental data, so I wouldn’t call this “direct testing” of anything. In other words, when phylogeny assumes Evolution, any such study will be compatible with Evolution.

With regards to the experimental approach:

How convenient - please link to supporting research. And if so, what business has Lenski “evolving” E.coli since 24 February 1988? And how about hacking the DNA into a new organism? That would still be a very good first step.

Not so if we pre-define success. You said it yourself: “We can make things more objective and precise”.

I do not predict that, and do not reject your belief in Evolution. All I am seeking is the proper evidence.

Are you saying Relativity is incompatible with the Observations?!? I think you mean the initial interpretation of the observed orbit was wrong. Happens all the time.

I am not, but theory has to match the observation or else the theory goes. There’s no two ways about this. Even Relativity is being tested continuously and will be adjusted when/if will fail - like Newtonian Mechanics was: http://nonlin.org/hard-science-is-soft-science/

@NonlinOrg,

I’m waiting for you to say, with exclamation points, “I never ever make sweeping generalities…”

@NonlinOrg

What’s the point of trying to watch speciation in a bacterium . . . when we don’t even have a template for the kinds of environmental stressors we need to accomplish it?

Below is a video on the 3 Rabbits problem . . . the foundation of the problem is laid by a Creationist who saves everyone a l ot of time by telling his audience about the facts he already acknowledges regarding an Alaskan rabbit population that cannot breed with a Florida rabbit population, but both of these populations can breed with a Minnesota breed.

In the video link below, science journalist Peter Hadfield (aka: Potholer) discusses the views of Creationist Kent Hovind, and in particular the existence of a strange “wabbit” situation !
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@NonlinOrg, Do you agree that the three populations came from the same original population? If you do, then is it clear that what has developed amongst these populations is at the very core of the Speciation discussion?

George

I generally try to adjust the tone to match the other party - maybe not always perfectly. That can be improved. However, some of your perception might be amplified by the “strong disagreement”. I joined this blog to improve or abandon my ideas based on discussions with those that disagree. That’s the only way to learn. Unfortunately, everyone is way too emotional when it comes to these topics. Why?

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Do you disagree with those two statements?

What’s your point (sorry, won’t watch random videos)? Assuming you refer to my Testing Evolution proposal, this is what I said: …the Threshold for success would be a descendent 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. If you ask, I would put all cute wabbits in the same category, but that’s just me. Fine, the ugly ones too.

Among mammals, the fastest speciation observed that I am aware of is the mice of Madeira. I am using my phone now, so I apologize for not providing a link.

Also, someone who like @Swamidass who has a ph.d in a particular domain can probably be thought of as an authoritative source of info. You might consider “dialing down” your tone (a great Californiaism) by formulating a request: “that topic is interesting, would you mind sharing some links so I could do some background reading?”

“Then, like, I’ll be in the green room, like, du-u-ude!”

My apologies to all Californian readers for the lame imitation of your marvelous patois.

We seem to be close to agreement here. A key consideration is that biological processes are far more stochastic than relativistic processes, so biological predictions are inherently probabilistic and biological inferences are inherently Bayesian. OTOH, if you have mastered quantum physics, you and stochastic processes (and Bayesian inference) are already BFFs.

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I have already discussed the goals of the Lenski experiment, which you still seem not to understand. @Swamidass has also discussed the goals of such experiments, and you haven’t understood him, either.

I think you are defining evolution differently than the scientific community defines it. Until you start using the same definition, this discussion will probably bear little fruit. And you definitely won’t understand the research the scientific community has been performing until the definition is clarified.

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@NonlinOrg

Excuse me, whoever you are… but the video is not random. It demonstrates the reality of your bacteria test… by fast-forwarding us to a point where we have 3 subpopulations - - and instead of bacteria we have rabbits.

If you won’t watch an evidentiary video for 15 minutes … why should I believe you will watch a bacteria experiment that should take centuries to accomplish anything important?

You are way too flip and dismissive for my personal tolerances …

You are quite bold to complain you don’t get my point While telling me you wont watch the relevant video that does a great job of establishing some common parameters between Evolutionists and YECs:

If you watched the video, you would Get my point… Do you actually want me to type a transcription of half the video? Sorry … I don’t type things for people who make random objections …

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That’s fine, but would the six species be characterized as anything else other than mice? BTW, Madeira mice look like regular mice to me. Here is the link you wanted: SPECIATION? - - One Species turns into Six Chromosomal Races (amended)

That’s fine. We’ll set up several experiments with different Baseline bacteria. One should pan out eventually …or else.

There are several definitions indeed, but referring to “Common descent”, how would you directly test this other than by obtaining a Threshold organism descended in the lab from a Baseline organism, yet different enough to not be classified as a Baseline organism?

Hang loose, dude!

@NonlinOrg,

You can’ expect to see speciation That Includes radically different appearance in one lifetime.

A Genetic scientist would explain to you that once you have lost the reproductive bridge between two populations, there is nothing keeping the two populations “in sync” any more.

So one population can get bigger, and another population can get fur-ier. Over time… the different directions the populations take (in the genetic sense) is inclined to become more and more obvious. But First! … you have to separate the groups from a reproductive viewpoint.

Do you follow this, @NonlinOrg? If you don’t … then there is nothing about Evolution that you will understand.

In the example of the 3 populations of rabbits … the Alaska rabbit can live in the very deep cold, while the Florida rabbit can live in the very high heat. And their coloration is different. YEC’s themselves constantly refer to the dramatic changes in shape and size in domesticated dogs - - that are inheritable!

Each of these examples is a sample of what can happen with genetic change: different appearances that can be inherited … or incompatible genetics in the reproductive sense - - which are Also inheritable.

Hi NonLin -

Thanks for the link! The 6 different populations on Madeira are well on their way to no longer being Portuguese brown mice, as their common ancestors were 500 years ago. They are becoming other species of mice.

You were looking for observations of a transition from one species to another. The evidence you were looking for has been delivered!

It’s worth noting that even this transition, over 1500 generations of mice, required 500 years. It’s hard to fund science projects that require 500 years. Many funding sources are patient, but none are that patient.

Many are the phenomena that can only be tested indirectly. You can’t directly test the Big Bang, for example. However, you can predict that it would generate cosmic microwave background radiation, and then set up the equipment to look for the CMBR. Or you could hope that a couple of Bell Labs technicians would stumble into microwave interference from every direction in the sky. Either will suffice to win a Nobel Prize.

Like the Big Bang, common descent via nested hierarchies can’t be directly tested–it simply takes too long. However, you can predict that you will find a nested hierarchy of pseudogene mutations among primates that corresponds to the nested hierarchy produced by evaluating other empirical characteristics. And voila!

This is just one example of how you would conduct empirical research that attempts to falsify common descent.

Later days, Nonlin!

OK, you made me watch. Happy?

Now, all I am saying is “Show me”! And by “Show me”, I mean a real-life experiment. Is that too much to ask for?

But why do I insist? Do you know ‘Toy Story’, the movie? Some kids might insist that’s all a live recording of a real event. But we, the adults, know that it was in fact created in the studio by a team that labored over each individual frame.

For starters, a DNA hacking experiment will do, as long as the new organism is different enough (tbd) and not a degraded version of the original. That’s going well beyond the “Common Descent” promise.

Let’s just do it and close this issue!

@NonlinOrg,

I cannot show you a fish population growing into a tetrapod population in a single lifetime.

I cannot show you a bacteria population turning into non-bacteria in a single lifetime.

But, I can offer you this:

I think we can show, over time, two groups of bacteria (both coming from the same source), can be made incompatible with each other by exposing them to different ecological factors.

How does that sound, @NonlinOrg ?!?!?

“Incompatible” is not the same as “Common Descent” so no, that’s not sufficient but…
a) I am part of a very tiny minority that thinks something’s fishy on a scientific method basis
b) We don’t have to solve this today - let’s ponder some more

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@NonlinOrg,

Wha? If we take two cups of bacteria from a single bucket of bacteria … and then raise the two populations under contrary conditions… and at the end of the study we find that no bacteria from Cup A can breed with bacteria from Cup B …

There’s not much doubt that the two Cups represent common descent.

The question is how to define reproductive incompatibility.

For you to write what you wrote suggests to me you are not qualified to even discuss these issues. Why would anyone design an experiment to your liking when you don’t even recognize when 2 cups of bacteria have the same origin?

I’m not even going to touch the sentence where you make vague charges that scientists are falsifying their work …

There is nothing left to ponder if I describe exactly the experiment you want to have performed … and you conclude that it doesn’t represent Common Descent … How could someone say these things as a byproduct of being confused … they sound willfully intended to undermine the discussion …

You keep going in circles. The point is ‘Evolution as Common Descent of different organisms’. ‘Lack of sexual reproduction’ or ‘incompatible’ is not sufficient to qualify the two populations as different enough. Why is this hard to understand? Think human vs. chimp: no one even cares to mention the ‘lack of sexual reproduction’ when it comes to the difference between these two.

Touch it, please. Yes, something is very fishy when people are religiously fanatic about Evolution but cannot show a shred of experimental proof. We are supposed to separate our religious views from science, but of course that NEVER happens: Philosophy, Religion, and Science – NonLin . And the least credible are those that deny this and those that never have any doubts (there’s a high correlation between the two populations).

I’m still waiting for details from you about what kind of traits would make E. Coli different enough to qualify as a demonstration of evolution in your experiment…?

I replied to you above: “Maybe it’s easier to see what other known bacteria are related to E.coli, yet clearly different and to analyze what makes them different. Then to look for a combination of those factors.”

Oh, did you want someone else to do that analysis for you? I suggested salmonella:[quote=“Lynn_Munter, post:134, topic:34703”]
You mean known, related bacteria like salmonella? Ok. So what makes salmonella (or a different bacteria of your choice) different from E. coli?
[/quote]

You never answered this question, so I figured you weren’t interested anymore.