The Problem with the ID Argument

[Mercer (John Mercer)]

@colewd

All these subunits are dedicated to the splicing function as far as I know.

As far as the origin I don’t know of any pre cursor to prp8 we have observed.

Have you considered learning more before presenting this as a challenge to evolutionary theory?

[Mercer (John Mercer)]

@Jordan

These seem like you’ve slipped into arguing for your position rather than defining the mechanism. I think it would be very valuable and helpful if you can separate defining your theory/mechanism from defending it. Typically in science we start our explanations with very careful setting up of the problem and proposed mechanism before we move on to showing how our mechanism better explains the data than competing mechanisms and discussing the strengths and limitations of the mechanism.

That’s what I’m trying to get to here, we need to define the mechanism well enough that we can distinguish it from competing mechanisms. The mechanism doesn’t have to be precise, it just needs to be precise enough to to be able to distinguish between the options.

It doesn’t even need to be correct, but it has to be mechanistic. This is why ID has to be limited to pseudoscience and design. As soon as there is a mechanism, it fails.

[Jordan (Jordan Mantha)]

@colewd

If we are talking about the mechanisms we can observe prp8 is a sub unit of U5 which is a sub unit of the spliceosome containing U1, U2, U4,U5,U6 for the main spliceosome. There are also U11 and U12 for the smaller version. All these subunits are dedicated to the splicing function as far as I know.

As far as the origin I don’t know of any pre cursor to prp8 we have observed.

I guess I’m confused a little here. I thought we were talking about theories about the origin of Prp8. I’m fine with expanding that out to the whole spliceosome if you think that it orginated as a unit. The fact remains, you are only describing the what, the mechanism is the how and that still seems to be missing. Can you tell us how, in your model, the spliceosome originated? I’m not asking you to defend it, just to describe it.

@colewd

Universal common ancestry has evolutionary mechanisms, ID would need to come up with better ones in order to get scientists to reject UCA as their working model.

How is it a working model without a mechanism that you can model?

So I think of a model as a mathematical or conceptual analogy. It’s an approximate representation of reality put in a way that we can understand. It’s also a way to describe things that aren’t direct observations.

Universal Common Decent is a model in the sense that scientists can use it as a way of thinking about the relationship between all living things. Since it’ a model, it could have some limitations or exceptions without making it invalid. I would consider the “Universal” part of UCD to be a fuzzy area. Does it really have to be 100% universal to be useful as a model? Not at all. I think a person could affirm universal common ancestry and de novo creation of Adam & Eve, for instance. If you wanted to have the first eukaryote be generated de novo I don’t think that rules out UCD as a model either.

UCD doesn’t exist in a vacuum though, if we want to understand the “how” to UCD’s “what”, you need to look at evolution. This is where the theory (with a mechanism) comes in, to explain how our model of UCD works.

Also note, I’m not a biologist so I could be wrong in my particular conception of UCD and evolution. I’m just trying to match them up with how I use the theory/model terms in my area.

[colewd (Bill Cole)]

@Jordan

Can you tell us how , in your model, the spliceosome originated? I’m not asking you to defend it, just to describe it.

I would say the process that produced prp8 and ultimately the spliceosome is similar to the process that produced the 64 bit microprocessor. The microprocessor is in itself very complex but does not function on it own as it is a piece of a functioning system. What we are discussing is beyond ID at this point but I am trying to offer some additional ideas.

@Jordan

So I think of a model as a mathematical or conceptual analogy. It’s an approximate representation of reality put in a way that we can understand. It’s also a way to describe things that aren’t direct observations.

Universal Common Decent is a model in the sense that scientists can use it as a way of thinking about the relationship between all living things.

I agree.

The big weakness in the theory is finding lines of demarkation of species that share a common ancestor and those that don’t if indeed there are multiple origins.

[Mercer (John Mercer)]

@colewd

I would say the process that produced prp8 and ultimately the spliceosome is similar to the process that produced the 64 bit microprocessor.

I wouldn’t, but I’m a biologist.

[Timothy_Horton]

@colewd

I would say the process that produced prp8 and ultimately the spliceosome is similar to the process that produced the 64 bit microprocessor.

The process which produces microprocessors involves lots of discrete manufacturing steps including making a silicon wafer, using UV light to etch the circuitry onto the wafer, doping the wafer with SiO2 to produce transistors, then cutting the wafer into individual pieces which are then installed in the final physical package.

How did you determine proteins are produced with the same process?

[Timothy_Horton]

@colewd

The big weakness in the theory is finding lines of demarkation of species that share a common ancestor and those that don’t if indeed there are multiple origins.

Funny then that geneticists and evolutionary biologists have no problems finding evidence of demarcation from the common ancestor of most species.

Bill do lions and tigers share a common ancestor? How about tigers and domestic cats? Yes or no and how can we tell?

Do the canindae and ursidae (bears) share a common ancestor? Yes or no and how can we tell?

[John_Harshman]

@Timothy_Horton

Bill do lions and tigers share a common ancestor? How about tigers and domestic cats? Yes or no and how can we tell?

Do the canindae and ursidae (bears) share a common ancestor? Yes or no and how can we tell?

These are not questions that, in my experience, Bill is willing to discuss.

[Timothy_Horton]

@John_Harshman

These are not questions that, in my experience, Bill is willing to discuss.

I know but by dodging them (and he will) he still makes a statement about how much he values scientific integrity.

[colewd (Bill Cole)]

@John_Harshman

Bill do lions and tigers share a common ancestor? How about tigers and domestic cats? Yes or no and how can we tell?

I have no idea other than a guess. Do you now have a method to make a informed decision on whether common ancestry exists? Maybe Jordan can participate with you guys.

[davecarlson]

@colewd

Do you now have a method to make a informed decision on whether common ancestry exists?

Sigh.

(Please note that the above comment is the only one that I can think of that doesn’t violate the spirit of “peaceful science”.)

[Timothy_Horton]

@colewd

I have no idea other than a guess.

OK, then we’re justified in ignoring you every time you start carping about the evidence for universal common descent.

Do you now have a method to make a informed decision on whether common ancestry exists?

The same one science has been using for more than half a century. Genetic distance combined with the phylogenetic tree of the fossil record. But you just admitted you have no idea how those work so I trust you’ll not whine about UCD anymore.

[John_Harshman]

@colewd

I have no idea other than a guess.

You could always consult the literature. Try “Felidae phylogeny” and let me know if you find anything. Perhaps it would be better than a guess.

@colewd

Do you now have a method to make a informed decision on whether common ancestry exists?

Always have. We’ve discussed it several times, using examples pulled from my own publications. Are you sure you don’t remember any of that?

[John_Harshman]

@Timothy_Horton

Genetic distance combined with the phylogenetic tree of the fossil record.

This is a garbled description of the actual science. But it hardly matters if you’re talking to Bill.

[colewd (Bill Cole)]

@John_Harshman

This is a garbled description of the actual science. But it hardly matters if you’re talking to Bill.

If you have a clear way to determine ancestry between species then explain it. @Jordan what are your thoughts? Let’s see if @Jordan believes you have a clear hypothesis.

[Timothy_Horton]

@John_Harshman

This is a garbled description of the actual science. But it hardly matters if you’re talking to Bill.

I was trying to really really dumb it down but you’re right, it won’t matter.

[John_Harshman]

@colewd

If you have a clear way to determine ancestry between species then explain it.

Again, did you actually read either of the articles I pointed you at? Did you check out the thread on crocodylian phylogeny here? I see no reason to repeat myself for the nth time when you don’t seem to remember any of it.

[Timothy_Horton]

@John_Harshman

Again, did you actually read either of the articles I pointed you at? Did you check out the thread on crocodylian phylogeny here? I see no reason to repeat myself for the nth time when you don’t seem to remember any of it.

Whatever you do don’t mention a blue fish from a Pixar movie. That will get you a time out.

[Greg]

@Timothy_Horton

Yes the phylogenetic tree created from the genetic record is an empirically observable indication of UCD.

Then call it what it is-an indication based on dozens of preconceived notions and assumptions. We have obviously not literally observed anything close to proof that we all evolved from some common descent. We observe species changing in real time. But in a world that is designed and created by God there will be dozens if not hundreds if not thousands of assumptions that must be made in order to arrogantly declare that (especially naturalistic) UCD is true. These assumptions are guided by Darwinianism and i hear through the grapevine that this is a devolving theory driving towards the cliffs of extinction.

I as a builder see commonalities in construction of various structures all of the time, but i never go out on a limb and assume that this must mean the same builder, or the same lumber company sourced the builds etc. You may take your “indications” and happily have show and tell with like minded naturalists loaded within our universities today. But i find a much wiser crowd in a place called the church that already stands upon what is true and this templeton endorsed contest to marry naturalism which science can become bedfellows with quite easily and Christianity where revelation tells us of a God who transcends the natural is tantamount, is not welcommed. Therefore common descent in your mind as an evolutionist runs contrary to common design in my mind as a creationist. Taking the mysterious, powerful, transcendent God and fitting Him into a box of manmade figments of imagination is just not right and is in no way complementary to texts in God’s revelation starting in Genesis.

[Jordan (Jordan Mantha)]

@colewd

I would say the process that produced prp8 and ultimately the spliceosome is similar to the process that produced the 64 bit microprocessor. The microprocessor is in itself very complex but does not function on it own as it is a piece of a functioning system.

I think I agree with @Timothy_Horton on this part:

@Timothy_Horton

The process which produces microprocessors involves lots of discrete manufacturing steps including making a silicon wafer, using UV light to etch the circuitry onto the wafer, doping the wafer with SiO2 to produce transistors, then cutting the wafer into individual pieces which are then installed in the final physical package.

How did you determine proteins are produced with the same process?

The similarities between the spliceosome and a microprocessor seem to be superficial, at most. The only thing I can see is that they are both a complex assemblies. But on the other hand, they are made of completely different materials and in completely different ways (manufacturing plants vs. cells). If a model is an analogy, then the power of the model is in its clarity and correspondence to the reality it models.

@colewd

What we are discussing is beyond ID at this point but I am trying to offer some additional ideas.

How can that be? I thought ID was supposed to be a competing theory for the origin of living organisms. Do you mean that ID doesn’t have a specific mechanism for the spliceosome in particular? That’s OK, but is there a general mechanism by which ID proposes that new biological assemblies are generated? I’m assuming there is something beyond “an intelligence did it”, but perhaps not. If not, I think that is problematic for ID as a scientific pursuit.

That doesn’t mean it couldn’t be a valid philosophical or theological pursuit, but I think it loses credibility as a scientific theory without some sort of specified mechanism.

@colewd

Bill do lions and tigers share a common ancestor? How about tigers and domestic cats? Yes or no and how can we tell?

I have no idea other than a guess. Do you now have a method to make a informed decision on whether common ancestry exists? Maybe Jordan can participate with you guys.

Well, I know not everybody can be expected to be a biologist or to recreate research papers, but I did participate in @John_Harshman’s excellent office hour: John Harshman: The Phylogeny of Crocodiles . I read a lot of Wikipedia articles and some papers, I installed phylogenetic software and learned a bit about the algorithms it uses. I made lots of mistakes but @John_Harshman, @davecarlson, @Rumraket, and @swamidass helped me understand it much better.

@colewd

If you have a clear way to determine ancestry between species then explain it. @Jordan what are your thoughts? Let’s see if @Jordan believes you have a clear hypothesis.

Well, I certainly don’t know a lot about this area. One of the things that I’ve learned is that scientists know their work very well. They are still human and may have a tendency to overreach at times when it comes to interpretation of the science, but they are mostly people passionate about getting to the truth of the what’s and how’s of the universe. So, all that to say, I generally defer to my colleagues.

Here’s how I understand the ancestry question. A phylogenetic tree shows hypothesized relationships between organisms. The interesting part to me is that computational phylogenetics uses very little in the way of biology. Very generally, you can put a set of protein/DNA sequences in and apply various statistical algorithms (which are similar to those used outside of biology) to generate a tree. I took a class on machine learning and statistical inference that included clustering techniques similar to those used in phylogenetics. One of the most startling things to me is how grounded in statistics evolutionary biology is. Look at the founders of population genetics, for instance.

Of course a phylogenetic tree is just a hypothesis of relationships based on statistics, so you want to compare it to other data. You could compare a tree with a known ancestry (if we have a record), a phylogenetic tree built from morphology, or to the fossil record. If common decent is a generalizable model, we should be able to have close matches between trees created from different data (DNA, morphology, fossil record, for instance) across many examples. This, according to my colleagues, is what we see.

So, I’ve had a peak at the methodology (which is grounded in statistical techniques used outside biology) and I’ve played with the software a little bit to see how it works myself. I see no reason to reject the common descent model. It fits the data.

Is it universal? I don’t know. I don’t know that anybody knows it’s 100% universal. I would suppose that those who have no mechanisms outside nature would merely assume it’s 100% universal. Those of us who allow for agents outside nature may wonder if it’s not quite absolutely universal but that does not invalidate the model or mean we can toss it aside for one we just happen to like more.

As Christians we have a ready example of this kind of thinking. Think of the Resurrection. “Dead people stay dead” is still a good and useful model for understanding the world, even though we affirm that there was an exception. I think it’s plausible that God was involved in the first cell, or maybe made a tweak here or there to steer things in the right direction, but I have yet to see clear/convincing evidence that it was anything detectable by science.