Intelligent Design and Common Descent


(Ann Gauger) #269


That’s a valid point. But I still want to know how likely random sequence is to produce function.

(S. Joshua Swamidass) #270

@Agauger if the experiment you proposed worked, and produced a functional protein under the constraints you proscribed, how would you rule out God’s action in the experiment? How do you know God didn’t design that protein?

(Dr. Patrick Trischitta) #271

(Arthur Hunt) #272

More frequently than you would like, I expect. That’s one example. The larger field of cytoplasmic male sterility in plants is littered with similar instances of random sequences, isolated or fused with other proteins, acquiring function.

(George) #273

@Agauger ( @swamidass ):

I read your article, and found it extremely well written. I am glad i dont have to develop a concise defense against that particular piece!

And it raises the point i have brought up before: the way a “Designer” would immediately resolve the questions you raise in the article should not be in dispute. God may or may not use a Purgatory or a Limbo, but as a creator God certainly create endless strings of improbable DNA or improbable proteins - as often as he needs to!

And so you and Joshua could agree on these questions sooner


… IF the issue of Science confirming God’s involvement wasnt mixed up in the whole quedtion as well.

[ [ In the future, I will be checking that ID discussions that erupt in the middle of threads are moved to the ID thread category; and that Godless-Evolution discussions get moved into the CHATTER category. ] ]

(Ann Gauger) #274


I want to know how likely random sequence is to produce function. That’s not a sharpshooter fallacy. It’s a legitimate question, of which you have one fixed opinion, and I just want to know. I just want to know by direct demonstration, not inference.

You will not see my point. I see your point, but it doesn’t answer my question. How likely are random sequences to produce function?

Maybe you are right. The genome shows a lot of apparent new genes. Therefore it’s easy to get new function from random non-coding DNA. That’s the inference.

How about a demonstration? If this was easy to do it would have been done already.

(T J Runyon) #275

And that’s a good question to ask. But when I see something that looks like we would expect it to look if it did evolve I’m more likely to come to the conclusion that it did evolve because either (1) we are wrong about the rarity of such event or (2) there is something we just Don’t know yet. And I come to this conclusion based on the poor track record of supernatural explanations and the excellent track record of natural ones. Natural explanations are more likely to be correct. I’m not taking design off the table though. @T_aquaticus seems to think (1) and he may be right. This is a little outside my knowledge base so I’m withholding judgement. My reason for accepting it evolved in this case is more philosophical.

(S. Joshua Swamidass) #276

By these standards I’m not sure direct demonstration is humanly possible. I’m still curious about this:

It seems that we are always making an inference in biology. I can’t even imagine a scenario that would count as direct inference. Apparently Behe agrees. When shown evidence of T-urf13, he was convinced it was a designed protein, even though @art showed the step by step process by which it arose.

[Note add later: in this case, I am using “designed” to mean not by natural processes alone. I should clarify that I also believe God created T-urf13, by an evolutionary process. In that sense, God did design it, by a natural process that might have been guided, but it is not apparent whether or not he did.]

(Ann Gauger) #277


Ah, a metaphysical question. If the experiment worked and a random sequence evolved a functional protein, then I would say yes, apparently natural processes can generate a functional protein from random sequence.

Did God guide the process? We can’t tell through science. This moves into the realm of theology.

(S. Joshua Swamidass) #278

I don’t disagree with this.

The bigger problem, however, @Agauger is that we have already shown you clear evidence of function arising from non-coding regions. This is as clear as we can reasonably expect. You are asking for a “direct” demonstration that just doesn’t exist. If we were to produce examples, as we have already done, it would just be an example of design, wouldn’t it?

The issue here is not the failure to directly demonstrate this. We have directly demonstrated it. Rather it is that “direct” is a relative term and biology always relies on inferences. There is no way to rule out God’s interference in an experiment. By pressing for a direct demonstration, you are appealing to God’s action having confounded all the demonstrations we have already made. However, there is no way to rule that out in any demonstration, so it doesn’t seem fair to press this in this way.


Apparently, quite likely given all of the examples of random intergenic sequence acquiring function.

That’s exactly what you have in species with non-functional DNA and species that have functional DNA derived from that non-functional DNA through the addition of the mutations evidenced by the differences in their DNA sequence.

(Dr. Patrick Trischitta) #280

Let’s keep to methodological naturalism here. Those are the rules here at PS when discussing science.


As others have noted, God could still be acting through nature in some undetectable way which could be considered intelligent design in some sense. This is more of a metaphysical question than a scientific one. What I am speaking to is the claim that the known natural mechanisms of evolution are incapable of producing these features. If I am guilty of anything it is falling for a God of the Gaps fallacy.


A paper worth noting:

The authors found that 25% of random sequences conferred increased fitness in a competition assay in an E. coli model.

(Ann Gauger) #283

By pressing for a direct demonstration, I am saying God’s action could be responsible for what you see, not mutation and selection.

What you have shown actually is words and assertions and inferences and arguments. No data. I brought the references.

Some demonstrations are pretty clear by evidence and repeated experience. Pasteur, Koch, Avery. Some inferences are very well substantiated by evidence and repeated experience. The sequence hypothesis. But those things all took time and verification. But some things still need more evidence, (if you don’t like demonstration), especially given the fact that it overthrows prior theory. This is one of them in my opinion.

PS I know how to keep my metaphysics and science in the right order.

(S. Joshua Swamidass) #284

A post was merged into an existing topic: Side Comments on Gauger and Mercer

(S. Joshua Swamidass) #285

A post was merged into an existing topic: Side Comments on Gauger and Mercer

(Ann Gauger) #286


Yeah, that was the paper I was thinking of. There are technical problems there. But I don’t have time now to address this.

I’ll try to return to it tomorrow. Thanks for citing it though.


Your reference lists naturally occurring indel mutations as a mechanism for producing orphan genes (i.e. nondeleterious frame shifts). They have the data to back it up.

The Lenski experiment is a perfect example. In that experiment there was a recombination event that moved a promoter in front of another stretch of DNA. It demonstrates how recombination events can result in previously non-coding DNA being transcribed.

(Arthur Hunt) #288

I want to make sure I am reading this correctly - Ann, are you claiming that God in essence created T-urf13 apart from known, well-established mechanisms, that the functions possessed by T-urf13 are God-inspired or -directed and not borne of the accessibility of these functions in sequence space? Are you really going down that rabbit hole?

I want to make absolutely sure, since there are some themes intertwined here and you are making this apparent claim in response to an example that Josh pointed out.