hrun:Is there any scenario you can imagine, where some aspect of a process occurring in organisms that are thriving on this planet, that do not show 'optimality' in some way or another and thus would indicate 'non-design'?

In The Design Matrix Mike scores four biological features: Pseudogenes, with an overall score of -4.5,
The PCP degradation pathway, with an overall score of -2,
The vertebrate eye, with an overall score of 0,
And the Genetic Code, with an overall score of +3.

None of them score a perfect +5 in Rationality or Foresight, where optimality would be considered.

Are you happy?

Original: hrun
There are many different 'types' or RNA around in the cell.

I know

As I said, it serves as a scaffold to onto which ribosomal proteins assemble to form the ribosome.

I was just wondering what you meant by the word "scaffold."

So, given these facts, why do you believe that the primary function of RNA is carrying information and not acting as a scaffold?

It carries the information required to form a ribosome.

So realizing the difficulty in even figuring out the 'primary purpose' of RNA, how can you conceivably make any reasonable hypothesis about what the goal of an unknown designer was to figure out if the materials used were optimal to achieve his/her goals?

Like I said, we can try to infer the purpose based on function (again, a heuristic, not an algorithm) and then we try to infer optimality based on purpose.

I bet that for every theory on goals of the designer that were optimized, I can give you ten theories on goals of the designer that were not.

Which is why I said it's more of a heuristic than an algorithm. Trying to infer purpose based on function tends to yield the correct answer, but doesn't necessarily do so.

How do you think in the end, this type of argument could strengthen the design inference is absolutely beyond my understanding.

I think that to some degree we can infer purpose based on function. If an alien were to see one of our space telescopes (ie: the Hubble) and they study it and infer how it functions (what it does) they can infer the purpose of it based on the function (and the alien, if they have superior technology, may know of a more optimal way of designing such a space telescope and determine that our telescope is non - optimal based on inferred purpose. Or they may determine that it is optimal based on inferred purpose. Optimality is not something required to infer design). If you were to see a space ship on mars, you can infer purpose based on function. One can also infer the purpose of a computer, boat, car, etc… based on function. Again, it's not full proof (it's not an algorithm) but it tends to yield the right answer (it's a heuristic) and we can often make reasonable inferences from it.

RNA doesn't sound like a failed experiment to me. In fact, based on what you just said, it seems like RNA is not non - optimal for the survival of life.

It all depends on what the intention of the designer was, doesn't it?

Here is my hypothesis: The designers goal was to utilize evolution to obtain organisms that grow ever smaller and have ever faster rates of reproduction. One quick look at nature shows us that biological structures are not optimal to achieve this goal. Thus, the design inference is weakened.

I bet that for every theory on goals of the designer that were optimized, I can give you ten theories on goals of the designer that were not. How do you think in the end, this type of argument could strengthen the design inference is absolutely beyond my understanding.

Original: hrun
Sure. Unless evolution was "experimenting" in parallel and the failed experiments didn't leave remnants. But fortunately, we have such examples: the rather non-diverse catalytic functions or RNA and the excellent catalytic functions of proteins. Or the poor stability of RNA and the high stability of DNA.

…

Yes, for the cell as we know it. In fact, if you were to replace ribose with any other sugar, then no polymerase would be able to interact with DNA anymore. Done. Ribose must be optimal. Indication of design.

RNA doesn't sound like a failed experiment to me. In fact, based on what you just said, it seems like RNA is not non - optimal for the survival of life.

I'm not exactly sure what you mean by a, "scaffold in ribosomes." A very important function RNA serves is that it takes DNA information to ribosomes so that the ribosomes know what proteins to make.

Ok. Very slowly, with some background information. There are many different 'types' or RNA around in the cell. You are focusing on mRNA (messenger RNA) which carries information from the genome to ribosomes.

The bulk of RNA found in cells is not mRNA but rRNA (ribosomal RNA). As I said, it serves as a scaffold to onto which ribosomal proteins assemble to form the ribosome. Without rRNA there is no ribosome and without ribosomes the mRNAs are completely useless.

So, given these facts, why do you believe that the primary function of RNA is carrying information and not acting as a scaffold?

So realizing the difficulty in even figuring out the 'primary purpose' of RNA, how can you conceivably make any reasonable hypothesis about what the goal of an unknown designer was to figure out if the materials used were optimal to achieve his/her goals?

Do you not get the point that I am making? The bulk of RNA has a different function, namely as scaffold in ribosomes. Without that function all life would be as dead as a doornail. So, again, why do you believe that carrying information is RNAs primary purpose?

I'm not exactly sure what you mean by a, "scaffold in ribosomes." A very important function RNA serves is that it takes DNA information to ribosomes so that the ribosomes know what proteins to make.

It carries information from DNA to ribosomes and if you didn't have it (and you didn't have a replacement) then the cell couldn't function very long under any circumstances. I am basing it on the vitality of the function.

Do you not get the point that I am making? The bulk of RNA has a different function, namely as scaffold in ribosomes. Without that function all life would be as dead as a doornail. So, again, why do you believe that carrying information is RNAs primary purpose?

I hope you are aware that IDists and their opponents agree on 99%+ of matters related to science. Issues like the anthropic principle and FLE do not take issue with any processes of which I am aware. Life's origin is a different kettle of fish but a relatively fringe area of science. That's one reason why the hysteria over the "ID movement" is more about politics than anything else.

This whole thread is not an argument about scientific facts. I think if one defines the constraints, it is perfectly reasonable to look for sugars that may perform better or worse than ribose. But the constraints have to be defined.

What I object to is the argument that one can just fish a 'goal' out of thin air, claim that something that we find in nature is optimal to attain this 'goal' and then claim that the design inference was strengthened.

Lets see how it goes:

1) I hypothesize that the goal of the designer was XYZ.
2) I look if structures found in nature are optimal to attain XYZ.
3) I find that indeed structures are optimal to attain XYZ and thus I infer design.

The question remains: How in the world would you verify (or even rationalize) your hypothesis unless you know something about the designer?

Just look at what Bilbo writes:

Mike takes as his starting point that Darwinian evolution is true. Then he hypothesizes that the designer would have used optimal designs and foresight, and exploited evolution to achieve further designs, possible even humans.

Hypothesis 1) just happens to be: The goal of the designer was to achieve exactly what we find today. How can you possibly know that this was the goal of the designer? And without knowing the goal of the designer, you have no way to argue about whether or not any known structure is optimal for its intended purpose.

But this is all getting old very rapidly and I don't think that I will make any headway in this thread.

The bulk of all RNA produced in a cell works as a scaffold. And it does so very efficiently? Why do you argue that the RNAs primary role is as information carrier?

It carries information from DNA to ribosomes and if you didn't have it (and you don't have a replacement) then the cell couldn't function very long under any circumstances. I am basing it on the vitality of the function.

So as cells are right now, there is no molecule that we can design that would replace RNA and would improve the overall functionality of the cell? That's your argument to indicate design?

This is not necessarily a position I take (though I think it's an interesting one), just trying to clarify the argument being made. I think that more research would have to be done to determine anything at the moment (to first determine if A: such is a characteristic only seen in designed objects of known origin (the whole more optimal framework relative to that which is less of a framework) and B: if life contains such characteristics).

Yes, for the cell as we know it. In fact, if you were to replace ribose with any other sugar, then no polymerase would be able to interact with DNA anymore. Done. Ribose must be optimal. Indication of design.

Assuming this is true, for me, criteria A would still have to be satisfied.

And I asked the follow-up question for this already. How do you propose to do that if you have only two categories of objects: Known to be designed by humans (and maybe by some animals depending on your definition of design) and origins unknown?

I already answered this.

Ok. You claim its not circular. The purpose of living things is to live. Since organisms live, and their purpose is living, the goal of the designer must have been to make living things. Everything within a cell is set up to optimize living. Thus design is inferred. How is this not circular?

This is not the argument being made. The function of living systems is to live. So we infer that it is their purpose and then we try to asses optimality. Not circular, but like I said, it's more of a heuristic than an algorithm.

You can leave this whole chain of arguments about purpose and optimal design out and just say: The designer wanted living things. Because we see living things, design is inferred.

Again, not the argument being made. The argument being made is that, it is unlikely that nature would choose an optimal pathway (at a more basic level) for living just because organisms live. It is more likely for a designer to do so, so we infer design. Not necessarily a position I subscribe to at the moment (I think more research is called for), but it is an interesting one nonetheless (and definitely worthy of consideration).