Biological Information and Intelligent Design: evolving new protein folds

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.

Why? You plan on running this experiment? You can’t have a target, as you might end up with something else/new if successful. I don’t know how different these two are, but if you start with one baseline E.coli bacteria and end up with salmonella (w/o contamination), then the Evolution experiment might be successful.

Hi Nonlin -

You think that speciation hasn’t been observed yet, and thus you propose that biologists must conduct experiments to see if they can induce speciation.

However, numerous instances of speciation have already been observed. You will recall the mice of Madeira. This webpage cites at least eight more, although it’s a bit of a stew. It’s the best I am able to find for now.

We don’t insist on conducting experiments to observe gravity, hinking that we won’t believe in gravity in the absence of experimental results. We already know gravity exists because we see it around us. The experiments that physicists conduct aren’t designed to prove the existence of gravity; instead, they are designed to refine our understanding of a universally acknowledged phenomenon.

In the same way, there is no need to conduct experiments to observe evolutionary speciation. It has already been observed many times over! Like experiments on gravity, the E. Coli experiments aren’t trying to prove the existence of something; they’re designed to refine our understanding of a phenomenon universally acknowledged among biologists.

Does that make sense?

In addition, experiments have been conducted on pseudogenes in primates (as I already linked to elsewhere). The pseudogenes demonstrate a nested hierarchy that exactly matches the nested hierarchy derived from other characteristics. Several nested hierarchies based on several sets of characteristics have all been derived, and the results all match.

In fact, you could even go to Oxford’s “Clade Genomics of Primates” site and perform your own cladistics. Best part: it’s free! Tell us what you find, if you care to explore for yourself.

Is this remarkable confluence of primate clade analyses just a coincidence? Or could it be that it is the product of an underlying reality?

Best,
Chris

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Hi Chris,

Just one comment on this - many experiments have been conducted to show what gravity is through the behaviour of objects - falling, rotating, plants in orbits etc. with a great deal of maths to quantify such matters. I think your approach is a bit difficult to accept, although I think you may be referring to some type of direct experiment that defines gravity per se.

It is ironic that within the context of my comment, ToE ends up been very speculative - a touch of humorous irony I think. :relaxed:

Saying you can’t have a target is true in one sense, but also points to the problem with your entire proposal: it is not that easy to define what is one species and what is another. Some scientists spend their entire careers refining classification schemes. Evolutionist are absolutely fine with — and even expect — a percentage of border cases. In fact, if there were clear, definable boundaries between all living things, that would be extremely strong evidence for non-evolutionary creationism!

But there are not. Efforts to create a systematic classification system which is not evolutionary tree-shaped have never been successful. They do not explain the data very well, if at all. Baraminology tries hard, but it does not find clear and unambiguous divisions between categories of living things, no matter if they are looking at the species level, or genus, family, order, or any other level.

If the underlying reality of the world was that there were finite, easily divisible varieties of organisms, they should have been sorted centuries ago. Biologists today should not still be debating or reclassifying anything except new discoveries, certainly not based on genetic evidence indicating that something is a little more or less closely related to something else than had been thought based purely on morphology, which happens all the time.

You may be interested in the methods described here, which are interesting especially for how thoroughly they fail.

https://ncse.com/library-resource/baraminology

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