Biological Information and Intelligent Design: Signature in the Ribosome

[benkirk (Benjamin Kirk)]

@Cornelius_Hunter

There is, and always has been, a tendency for proponents to view contradictory evidence as non normative and anomalous.[/quote]
And there’s no such tendency for denialists like yourself to do the same?

[quote]And to be clear, good theories do often have such anomalous data which at some point become resolved. So it is very tempting to apply this remedy to every problem. But when we see the ship disappearing over the horizon, our first reaction should not be to ignore it because we’ve reduced the variance, or it is not random, etc. The problems with common descent are of this nature, and they are everywhere in biology. These are not minor, and they are not rare.

So what’s the evidence? Can you present even a single datum instead of resorting to quote mining?

[Casper_Hesp]

Thanks for your reply.

@Cornelius_Hunter

Hi Casper:

I did not mean to suggest that. That is not my position, but it is of many evolutionists.

I’m happy to hear that. What is, in your view, the relationship between design and evolution? If you are open to the idea that evolution is involved in design, what would that look like? I’m trying to find some common ground here.

@Cornelius_Hunter

No, I’m not saying that. That’s why I put the “~” in front of it.

If you’re talking only about local optimality then your argument of the astronomical search space does not really matter that much. Also, I noticed you did not respond yet to my question: [quote=“Casper_Hesp, post:114, topic:5974”]
Do you completely reject the possibility that a sufficient code occupying a local optimum in the search space was arrived at through some early form of variation and natural selection?
[/quote]
I’m still interested in hearing your answer there, if you find the time.

@Cornelius_Hunter

No, I don’t think that is fair. There is very little reason to belief, from molecular biology, that the DNA code would self assemble somehow (i.e., be biochemically determined).

You puzzle me… I pointed out that your arguments are mostly based on incredulity. Then you express your disagreement with my statement by asserting again that you don’t believe self-assembly could happen?

[Cornelius_Hunter]

@Casper_Hesp

If you’re talking only about local optimality then your argument of the astronomical search space does not really matter that much

No, the problem of evolving the DNA code in general, and the search for the canonical code in particular, is an enormous problem. Don’t be fooled by the mere fact that it might be a local optimum. (btw, given that the code has several different functions, layers of information coding, and so forth, it is tricky to judge just how “optimal” it is–it might be a global optimum). Even if a local optimum, it is a very rare local optimum, and the search space is a very inhospitable desert that evolution would have great difficulty traversing (as I explained). This is an enormous problem, and why some people are trying to explain it as biochemically determined, and so didn’t really have to evolve, as such. That explanation not only is unlikely given what we know, but if true would confirm design.

[Billcole]

@benkirk

You’re also very mistaken about binding specificities. They are almost always quite broad.

Hi Ben
This is fundamental to our disagreement is contrary to the vast biochemical evidence. If you can make a supported argument here I am interested but short of that your claim is not consistent with what we are observing.

If binding specificities were broad how would the cell cycle work?

Why would single mutations be implied in cancer?

How would enzymes discriminate small molecules?

Ask yourself honestly, are you making this claim because without it stochastic evolution is highly unlikely?

[Billcole]

@Lynn_Munter

t seems to me all that would tell you is the probability of a particular form of DNA occurring, which is not what we are after at all. It goes back to results vs. possibilities. How many other ways of building a similar capability—in simpler or more complex form—are there? How many of the pieces can be based off each other with only slight modifications?

Hi Lynn
Again, when you come up with a sequence and it successfully folds you may have much more freedom of sequence if your requirement is simply to fold.

If your requirement is to bind ATP then this becomes more difficult but within the resources of evolution.

If your requirement is to bind with an existing protein then the requirement starts to go beyond the resources of evolution (populations and time) There currently are several experiments that explore this.

[Billcole]

@gbrooks9

I don’t understand your line of reasoning?

Are you saying that Evolution is not true because God would never have thought of this when he designed Evolutionary processes that shaped Earth’s life forms

Hi George
The argument is that specific binding requires specific sequences. The more specific the sequence, the more unlikely that a stochastic search can find it.

[gbrooks9 (George Brooks)]

@Billcole… which is why some BioLogos supporters, no doubt, may consider God a logical requirement to Evolutionary progress.

[Lynn_Munter]

@Billcole

If your requirement is to bind with an existing protein then the requirement starts to go beyond the resources of evolution (populations and time) There currently are several experiments that explore this.

@Lynn_Munter

How do you define required protein function? I would argue that virtually no proteins are ‘required’ when they are first generated. The organism’s ancestors all got along perfectly fine without that protein, even if subsequent generations gradually adapt around its function until it becomes indispensable to them. Again we see, in the nature of your question, a results-focused evaluation that ignores the real variety of possibility in favor of looking for a particular outcome.

Is the “requirement” you keep talking about one to bind with a specific protein in the body, or will any protein in the body do? This is an important question.

[benkirk (Benjamin Kirk)]

[quote=“Billcole, post:129, topic:5974”]
Hi Ben
This is fundamental to our disagreement is contrary to the vast biochemical evidence.[/quote]
Really? Yet you haven’t offered a speck of evidence to support your claim!!!

If you can make a supported argument here I am interested but short of that your claim is not consistent with what we are observing.

What have you observed, Bill? I’m still waiting for you to support your claim about the evidence:

@Billcole

If it is missing just one OH molecule it will not bind to the VDR.

So, show me the data. I took a break from revising the paper we’ve submitted to the Journal of Biological Chemistry (loaded with binding assays, btw) and I can’t find anything to support your claim.

If binding specificities were broad how would the cell cycle work?

It’s relative affinity that matters, Bill. There’s no real black/white. It’s the sort of complexity we expect from evolution.

Why would single mutations be implied in cancer?

First, not all are in binding sites. Second, the ones that are change relative affinities, not off/on. And it’s “implicated,” not “implied.”

How would enzymes discriminate small molecules?

It’s virtually all relative, not absolute.

[quote]Ask yourself honestly, are you making this claim because without it stochastic evolution is highly unlikely?
[/quote]I’m making my claim because it reflects reality.

Honestly, Bill, why are you making direct claims about the evidence, then trying to shift the burden of support when challenged?

Do you realize that you have inadvertently tested a hypothesis about how biochemistry should work if it were intelligently designed?

@Billcole

If it is missing just one OH molecule it will not bind to the VDR.

Please show me the binding assays that support your claim, Bill.

[benkirk (Benjamin Kirk)]

@Billcole

The argument is that specific binding requires specific sequences. The more specific the sequence, the more unlikely that a stochastic search can find it.

Yet your immune system does precisely that every day.

And, btw, the high-affinity binding proteins that bind specific sequences are definitely NOT required to have specific sequences themselves.

Have you bothered to look at the evidence?

[benkirk (Benjamin Kirk)]

@Casper_Hesp

If you’re talking only about local optimality then your argument of the astronomical search space does not really matter that much.

…but I suspect that won’t prevent him from continuing to use it…

[Cornelius_Hunter]

@Casper_Hesp

Do you completely reject the possibility that a sufficient code occupying a local optimum in the search space was arrived at through some early form of variation and natural selection?

I’m still interested in hearing your answer there, if you find the time.

The problem here is that “sufficient code occupying a local optimum” could mean a lot of things. No one really knows what is sufficient. It could be that our rarefied, canonical, code iis sufficient, but nothing less. What I can say is that evolving something like our code requires traversing an enormous distannce in the design space, passinng through an enormous nnumber of codes, in a rugged fitness landscape full of local minima. Not going to happen.

[gbrooks9 (George Brooks)]

@Cornelius_Hunter

The problem here is that “sufficient code occupying a local optimum” could mean a lot of things. No one really knows what is sufficient. It could be that our rarefied, canonical, code iis sufficient, but nothing less. What I can say is that evolving something like our code requires traversing an enormous distannce in the design space, passinng through an enormous nnumber of codes, in a rugged fitness landscape full of local minima. Not going to happen.

@Cornelius_Hunter

And yet we have millions of species in existence on Earth today.

https://www.washingtonpost.com/national/health-science/87-million-species-exist-on-earth-study-estimates/2011/08/22/gIQAE7aZZJ_story.html

Were all of them saved by Noah, less than 4000 years ago? Or did he only save relatively Fewer Kinds?

If the latter, then the explosion of these kinds into multiple different species had to have been a virtual speedway of evolution within categories of kinds …

Or God created all these individual species after the Ark landed on dry ground.

Which do you think makes the most sense. Frankly, I think the Third option makes the most sense – that all these millions of forms took millions of years to slowly develop.

George Brooks

[Cornelius_Hunter]

@gbrooks9

Which do you think makes the most sense.

Well as I said, I think design is a better explanation (i.e., ID), but beyond that, neither general or special revelation give us all the details, so it is speculation.

[gbrooks9 (George Brooks)]

@Cornelius_Hunter

Well I think design is a better explanation (i.e., ID), but beyond that, neither general or special revelation give us all the details, so it is speculation.

@Cornelius_Hunter

You have side-stepped the very heart of the issue … how long it took to generate those multiple species!

Geology gives us plenty of details… and the Bible gives us plenty of alternative details regarding Chronology.

How long ago do you think Noah’s ark floated on the Earth’s waters?

[Billcole]

@gbrooks9

You have side-stepped the very heart of the issue … how long it took to generate those multiple species!

Geology gives us plenty of details… and the Bible gives us plenty of alternative details regarding Chronology.

How long ago do you think Noah’s ark floated on the Earth’s waters?

Hi George
These are interesting questions.

We know that common descent occurs but if the design hypothesis is true, what can we attribute to design intervention and what to simple descent with modification. How would we perform an experiment to determine this? My guess is when we see new proteins that bind with other proteins to perform a specific new function then the likely hood is that some type of design intervention occurred. In the paper Joshua cited on the universal common descent thread that shows significant alternative splicing code differences between chimps and man, I think it is a reasonable hypothesis that some type of design intervention was required to generate these alternative splicing codes.

[gbrooks9 (George Brooks)]

@Billcole

We know that common descent occurs but if the design hypothesis is true, what can we attribute to design intervention and what to simple descent with modification. How would we perform an experiment to determine this? My guess is when we see new proteins that bind with other proteins to perform a specific new function then the likely hood is that some type of design intervention occurred.

@Billcole…

When a jet pilot fixes on a point in front of him too much… his plane collides and is destroyed.

Your “guess” at what is Design and is not is completely arbitrary and frankly, irrelevant.

If you cannot explain where all the millions of species came from … then your “guesstimate hypothesis” is a failure.

Just trying to save you some time…

George

[Billcole]

@gbrooks9

If you cannot explain where all the millions of species came from … then your “guesstimate hypothesis” is a failure.

How do you know the guesstimate hypothesis is a failure? Do you consider universal common descent a failed hypothesis?

[benkirk (Benjamin Kirk)]

[quote=“Billcole, post:141, topic:5974”]
We know that common descent occurs but if the design hypothesis is true, what can we attribute to design intervention and what to simple descent with modification. How would we perform an experiment to determine this?[/quote]
We look at inconsequential differences.

[quote]My guess is when we see new proteins that bind with other proteins to perform a specific new function then the likely hood is that some type of design intervention occurred.
[/quote]So every time your body makes a new antibody (a new protein that binds with other proteins to perform a specific function), a design intervention occurred?

You might want to note that there are very few new functions involved in the sort of evolution you are trying to argue against.

[gbrooks9 (George Brooks)]

@Billcole

How do you know the guesstimate hypothesis is a failure? Do you consider universal common descent a failed hypothesis?

@Billcole

Any hypothesis that doesn’t explain where millions of species comes from in 5000 years is a failure.

I do not consider Universal Common Descent a failure because Old Earth scenarios provide enough time for just about anything to happen.