The Genetic Code and Universal Common Ancestry

Then take two Latin speaking populations and put them on different planets. What are the chances that they will independently come up with the same English language after 2,000 years with no communication between them? In fact, why do we have different languages at all?

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This could be more like putting human populations in different planets and they come up with languages.

Eukaryote evolution is the evolution of a type of cell… not the same exact genetic material.
The raw materials are there already.
So why only in one occasion.

We can play this analogies game all day. It’s a waste of time.

The type of cell is determined by the genetic material. The reason a prokaryote is different from a eukaryote is their genetic material. The reason a lion is different from a tree is the differences in their genetic material.

I’m not playing games. Perhaps you are.

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Are you claiming that all eukaryotic cells have the same genetic materials?

I am not playing games. Just pointing out a fact.

@Krauze is sounds like you have a design intuition, with which I agree and believe is proper because God created us.

By saying it is no more than a hunch, doesn’t this take you outside the ID camp?

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They inherited the same genetic materials at some point in their ancestry.

When I said “any scenario” I was thinking of something other than just different codes or different origins of life. Suppose, for example, that different eukaryotes had completely different codes. Suppose that dogs and cats had completely different codes.

My hunch is really a form of conjecture, as described by the late, great philosopher Karl Popper:

“The way in which knowledge progresses, and especially our scientific knowledge, is by unjustified (and unjustifiable) anticipations, by guesses, by tentative solutions to our problems, by conjectures. These conjectures are controlled by criticism; that is, by attempted refutations, which include severely critical tests.” (Karl Popper, 1963, Conjectures and Refutations: The Growth of Scientific Knowledge, p. xi)

To Popper it didn’t matter what the source of a conjecture was. It could be a gut feeling or an idea that came to you in a dream. All that mattered was that your conjecture made contact with empirical reality in a way that allowed it to be subjected to attempted refutations, i.e. that it was falsifiable.

My design conjecture is motivated by the observation that at the cellular level, life looks more like engineering than it does the products of geochemical processes. Cells employ molecular machinery, information processing systems, software-hardware distinctions, etc. As for the genetic code, it’s one symbolic language translated into another through a sophistical molecular machinery. Codes are typically the product of intelligent agency - indeed, we have no other example of a code being produced by non-teleological processes.

If the genetic code was designed, several testable expectations flow from this, as I have described elsewhere.

My tentative approach to intelligent design may place me outside the ID Movement proper. But I agree with Behe, Dembski et al. on one crucial point: I do not rule out intelligent design as a possible scientific explanatory mode in principle.

For intelligent design to be considered science, it must be fleshed out theoretically to the point where testable models can be formulated in a systematic manner that generates avenues for research.

My disagreement with the ID Movement rests on whether intelligent design is at that stage today. My disagreement with 99 percent of the ID critics is whether that could in principle be the case one day.

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I looked but didn’t find the testable predictions. Could you be more specific?
I also want to repeat a question I have asked several times in different ways, but you seem not to have noticed each time: what is the nature of your hypothesized designer or designers?

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From my blog post:

This scenario generates predictions, potentials for falsification, and avenues for further research.

For example, Freeland et al. (2000) conclude that the standard genetic code can only be considered “the best of all possible codes” if the set under consideration is limited to those codes where amino acids from the same biosynthetic pathway are assigned to codons sharing the first base, for which the researchers give the historical explanation that the current code is expanded from a primordial code. If this pattern persists (i.e. it is not an artifact of the researchers only looking at robustness against substitution mutations) the teleological scenario would expect there to be good engineering reasons to group amino acids from the same biosynthetic pathway together like this. On the other hand, if more sophisticated models underscore the need for historical explanations and/or show the standard genetic code to be mediocre, the teleological scenario will be in trouble.

The teleological scenario also predicts that all organisms have the standard genetic code or derivatives thereof. Scientists estimate that Earth has about one trillion microbial species, with 98 percent yet to be discovered. If, as we start finding and studying those, we find variants that are precursors to the standard genetic code, the teleological scenario will once again be in trouble.

Thus, we see that teleological explanations, rather than being vacuous “the designer did it” proclamations, can generate testable insights about nature.

As I have written elsewhere, I consider myself a “methodological designist”. Just like the shell model of the atom doesn’t have to be “true” to generate insights, I’m less interested in the ontological nature of the designer (“Is it a god? Aliens? Just a useful heuristic?”) than in exploring the theoretical space opened by considering the possibility of design.

I don’t see a testable prediction in there. I pointed a fairly obvious one out to you above.

You said that you saw intelligence in the provision for having start codons that allow proteins to have any C-terminal amino-acid residue, no?

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The problem with your predictions is that they aren’t unique predictions. They aren’t things we would expect to be false given natural evolution. Thus they don’t make design testable.

I don’t think the possibility opens up any theoretical space. It doesn’t lead us to ask any questions we would not have asked otherwise. And since an unspecified designer could potentially design anything for any reason, your hypothesis is made much less useful when you specify nothing about its characteristics. But of course you do implicitly specify a few things when you talk about “engineering principles” and such. Your designer seems to be only a few steps above human abilities, concerned with economy of effort and avoidance of mistakes. It seems created in your image, a big engineer.

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Yes, Krauze stated that having stop codons that don’t specify amino acids made sense:

That makes a crystal-clear prediction.

Below human abilities, as I’m pointing out above…

What we would be interested in is predictions your model makes that are different from the predictions made by common descent and evolution. It would also be a good idea if these predictions dealt with the shared genetic code.

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@Krauze,

How will you test the difference in evolution between “God helps” vs. “God doesn’t help”? Will you strike a deal with the Great Almighty to cooperate with your testing methods?

Neither do any of us. Scientists infer design all the time. That does not place you in the ID camp.

@Krauze,

So you think Intelligent Design can be confirmed or identified by Scientific methods? How do you get God to cooperate with an experiment?

Response to various, rearranged into common topics.

On unique predictions
@John_Harshman and @T_aquaticus, you both claim that conventional evolutionary biology (or “natural evolution” and “common descent and evolution”) make the same predictions as those I’ve described. Of course, no support for these claims are actually given.

Just to repeat, the two predictions flowing from my scenario are:

  • Future analyses will underscore the optimality of the standard genetic code and obviate the need for a historical explanation
  • All organisms will turn out to have the standard genetic code or derivatives thereof. Precursors to the standard genetic code will not be found.

By what logic does the conventional view make these predictions? Have these predictions been published anywhere?

@John_Harshman, you even seems to want me to adopt an anti-evolutionary approach, predicting “things we would expect to be false given natural evolution”. I suppose I’m expected to scour the fossil record for a Precambrian rabbit before I’m allowed to speculate on intelligent design.

For the record, I’m fine with conventional evolutionary biology being able to put together competing explanations for the observations I point to. After all, conventional evolutionary biology is flexible and can even accomodate scenarios that never took place.

On “catching the designer in the act”
@gbrooks9, you want me to “strike a deal with the Great Almighty to cooperate with [my] testing methods” and “get God to cooperate with an experiment”.

Now, you’re free to identify the designer as “the great Almighty”. I don’t make that claim, however. Also, I don’t envision the designers as interfering following the seeding of the first life.

It’s a misunderstanding of science that it can only study phenomena that are taking place in a lab. If that was the case, historical science would be impossible. For example, scientists are happy to study hypothetical organisms like the Urmetazoan, even though its not available to “cooperate with their experiments”.

On the nature of the designer

I’m not sure how I’m supposed to respond to this. You start out talking about an “unspecified designer” but then you admit that I do in fact “implicitly specify a few things”.

For the record, I envision the designers as being human-like in their intelligence, acting in ways that are intelligible to us. If the designers “work in mysterious ways”, my approach will attribute their actions to natural causes.

On the state of design in science

Sure, scientists infer human design all the time. Not so with non-human design, which is what we’re discussing here.

On start codons
@Mercer believes my view “makes a crystal-clear prediction” about start codons that I for some reason don’t want to acknowledge. I’m afraid that the clearness of this prediction is subject-dependent, as I have no idea what prediction you’re talking about. You’re more than welcome to explain it and lay out the logic behind it, however.

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Correct. I’m trying to walk you through it, as you don’t seem to be thinking very critically.

You wrote:

Yes, I think the use of stop codons in the standard genetic code makes pretty good sense:

I agree that it makes design sense.

I asked:

Wouldn’t analogous start codons make just as much sense?

Are start codons analogous to stop codons?

Um, you just said you think the designer is human like. So how is this not human design?