No Junk DNA vs. Rarity of Function

[Agauger (Ann Gauger)]

@swamidass

@agauger, that is not accurate. It is a system designed to mimic an undesigned process. This is necessary because it is exceedingly difficult to to select for enzyme activity in an in vitro system,

@swamidass
I don’t know much about this field. It’s an interesting thing to follow up, and may be significant. But antibody production has some aspects that resemble random mutation and selection, for example the binding of a selection of primary antibodies, and some aspects, like serial clonal amplification and selection, that are perhaps more directed and focussed than an actual evolutionary search. I don’t know. Are the profile of mutations similar? What is the effective size of the population being searched?

The protocol matters. In directed evolution, the precise reaction conditions help determine the profile of mutations that can be expected, as well as the completeness of sampling of sequence space. There are tricks used to allow continued mutagenesis, long after most proteins would be completely destabilized. After several rounds, the investigator may do a round of selection at a higher temperature to select for increased stability, then proceed again.

Finally, I fully acknowledge the difficulty of selecting for a enzyme activity in vitro, having done so myself.

@swamidass

All in vitro in lab experiments involve human intelligence. If this is a valid objection, than it is disengenuous, or at least self-contradictory, to demand in vitro evidence of the evolution of new enzymes.

As you say, every in vitro experiment is designed. My own in vitro experiments were designed. I am sorry if you thought I was invalidating in vitro experiments in general. I just want to know more about the dynamics of this one, and the kind of results that are possible. Experimental protocols do matter as to the validity of results, however.

[AllenWitmerMiller (Semi-Expired Professor & Minister.)]

@Agauger

As for the last, I would be performing these experiments myself, except I have developed an essential tremor, that gives me shaky hands.

So sorry to hear that. I too deal with that to varying degrees depending on the day, though mostly in just one hand when attempting particular kinds of task. Very unnerving.

As of recent weeks I can still type (because deliberate “stabbing” motions of individual fingers are involved, I suppose)—yet I am unable to pour a graduated cylinder’s contents without the shaking spilling the contents.

[Agauger (Ann Gauger)]

Touch screens are my bane. And pouring from heavy jugs. The amount of effort involved seems to matter. So does the state of my nerves.

[Mung]

@swamidass

I’m pretty sure that is Axe’s and @Agauger’s argument. That is exactly what they have been arguing.

Now that @Agauger has spoken, have you changed your mind? My reading is that she quite distinctly validated my own take on her position.

[Mung]

@swamidass

@agauger, that is not accurate. It is a system designed to mimic an undesigned process.

Interesting statement @swamidass. Are you suggesting that we can know what an undesigned process looks like such that we can design our experiments to mimic one? Unintelligent undesigned detection?

[swamidass (S. Joshua Swamidass)]

@Mung

I’m pretty sure that is Axe’s and @Agauger’s argument. That is exactly what they have been arguing.

Now that @Agauger has spoken, have you changed your mind? My reading is that she quite distinctly validated my own take on her position.

This has been a helpful thread. The most valuable bit was that quote that @colewd gave from Behe. Yes, @Agauger has said her argument is focused on proteins, because that is where ID feels they can prove sequences are designed. However, many of them think this is also true of non-coding regions. It appears that there are different opinions about the validity of the non-coding region claim within ID. The differences are not visible.

It will be helpful for the IDists here to draw those distinctions out. Who thinks what about this in the ID camp? I’m not sure we know yet.

@Mung

My reading is that she quite distinctly validated my own take on her position.

It appears you maybe right about @Agauger . You seem likely to be correct about Behe (but he has seemed to argue the opposite in other cases). I know for certain that many in ID you would be wrong about. That is partly why these conversations are good. It is also why I ask IDists to explain where they are personally on these matters, and ask them to articulate their disagreements. It helps get this all stratight.

You were not entirely correct, but neither was I.

@Mung

@agauger, that is not accurate. It is a system designed to mimic an undesigned process.

Interesting statement @swamidass. Are you suggesting that we can know what an undesigned process looks like such that we can design our experiments to mimic one? Unintelligent undesigned detection?

Nope.

A more precise sentence would be: It is a system designed to mimic a process in nature. As should be well known, God can use natural processes to design things including evolution. I’m usually good about using neutral language, but sometimes I slip, especially when others are not being clear, but there is another topic beign discussed.

[Mercer (John Mercer)]

@Agauger

That’s an interesting example. Using the power of the immune system to search for a protein that binds to a hapten that resembles the transition state of the reaction desired is pretty ingenious. I’d have to read some papers to see how the work was done.

Indeed it is. It’s disturbing though, because someone who makes global claims about the rarity of function in protein sequence space should have already read the papers in detail.

Especially someone who discounts evidence by retroactively applying the standard of “genuinely new” to enzymatic activities, because these are genuinely new.

@Agauger

But that’s a designed system, making use of an elegant system to target a desired reaction and refine its specificity over time.

That preobjection is unfounded, as Swamidass noted.

Note also that to use this as a test of your hypothesis, you’d disregard any refinement stages and take the frequency that gives the first hint of measurable enzymatic activity.

Then you’d be sure to regard that frequency as a rock-bottom minimum, as catalytic antibodies are constrained to fit inside IgG variable regions, while most proteins in vivo are much larger.

@Agauger

As for the last, I would be performing these experiments myself, except I have developed an essential tremor, that gives me shaky hands.

I’m sorry to hear that. Does that mean that no one is doing bench work there any more?

[Mung]

@swamidass

You were not entirely correct, but neither was I.

You’ve stated that I was not “entirely correct”. You’ve stated that you were not “entirely correct.” What you have not done,is provide specifics.

I was not “entirely correct” because …

You were not “entirely correct” because …

[Mercer (John Mercer)]

@Agauger

That’s an interesting example. Using the power of the immune system to search for a protein that binds to a hapten that resembles the transition state of the reaction desired is pretty ingenious.

The first high-profile paper was published 32 years ago and thousands have been published since. How can you not know about this?

@Agauger

I’d have to read some papers to see how the work was done.

So have you?

For me, the more interesting question is, why haven’t you ever read any of these papers in the past 32 years?

Do you really not see the bubble you’re in?