It’s a little on the vague side, but I don’t have a fundamental problem with it. In our case the “effect” we’re looking for is the generation of the Prp8 gene/protein, correct? So the mechanism is the set of processes and parts (I would use steps and states, but I think they’d mean the same thing here) that accomplish our task (generation of Prp8), right?
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prp8 is a large protein that is part of the U5 protein machine which is part of the spliceosome. The mechanisms that generate Prp8 are different then the mechanism responsible for the origin of prp8 U5 and ultimately the spliceosome.
First I will answer your questions the best I can regarding the cellular mechanisms tomorrow.
ID is not a theory about mechanism, so it doesn’t make sense to ask it to provide one.
I guess you would agree that the human mind is able to actualize things in the world. But do we have a mechanism for this?
Yes. For instance, I had a thought in my mind regarding what I wanted to say here. And in explaining how you are now able to read the words I have typed on your computer monitor, we can describe every step of the process in purely mechanical terms, from the electrical impulses in my brain, to how these are communicated to my fingers, to how the keystrokes are translated thru the computer into an image on my screen, and how that information is transmitted thru the internet to your screen.
To just say “Faizal’s mind made it happen” is not even the barest beginning of an explanatory mechanism.
I note that you have offered possible mechanisms from electrical impulses in your brain through my screen. Ok. But what about the initial mechanism from your thoughts to the electrical impulses in your brain ? How mind interact with matter is the thing to be explained and materialists are silent about the underlying mechanism of this interaction.
Yet another reason ID is 100% worthless as a scientific explanation.
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@Giltil, the problem is that mechanism is what makes a scientific theory a scientific theory. I just got done teaching this to my General Chemistry and Physics I students Wednesday. You may have a hypothesis, a conjecture, an observation, it could even be a Law, but without a mechanism it’s really not a theory.
One of the major reasons we require a mechanism is that it allows us to test and distinguish between competing theories. Without the mechanism, it’s really just a (personal) interpretation of a particular set of data. We can’t apply such an interpretation widely (which is the purpose of a theory) without a mechanism.
For instance, Alfred Wegener developed Continental Drift, but without a mechanism it was not widely accepted within the scientific community until the mechanism (plate tectonics) was developed.
No, but that’s why the mind is not scientifically accessible, only the brain (if you go with a dualist approach). Theory of mind would be appropriately belong to a philosophical or theological discussion.
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The amino acids come from food outside or metabolic systems inside the cell. Since eukaryotic proteins contain introns prp8 is required to make the amino acids for the enzymes in the metabolic systems.
From a paper I found on U6 the entire protein suite is transcribed together. I have no reason to believe that U5 is any different.
The specific position is next to other U5 genes. I think our understanding is limited here awaiting further research.
Every protein that is manufactured in the eukaryotic cell requires prp8. There are restricted portions of DNA in differentiated cells. Differentiated cells must express prp8. Multiple copies exist in the genome.
prp8 is unique to eukaryotic cells. All eukaryotic cells have some isoform of this protein and will not function without it. The protein is highly mutation sensitive.
Since prp8 has nuclear introns you need prp8 to make prp8.
Let’s remember that some eukaryotic genes do not have introns and that some introns are self-splicing.
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This is true but self splice introns do not work in the nucleus due to its low magnesium content.
Then it’s fortunate that many mRNA’s make it out of the nucleus. What’s your point? Is this an objection to something?
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If I might say so (not to be promoting any one person’s ideas 
), the discussion in that thread about the shared ancestry of spliceosomal introns with group II introns, and the ability of proteins quite different from PRP8 (and the rest of the suite of nuclear spliceosomeal proteins) to facilitate intron splicing, may be of interest here.
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Based on this what is your opinion regarding calling universal common descent a theory?
UCD by itself isn’t a theory Bill. It’s an empirical observation, the result of natural physical processes explained by Evolutionary Theory. Evolutionary theory explains the mechanisms involved.
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I guess you’d have to ask a materialist about that.
You seem to have missed the point, which was to contrast an account that actually provides mechanisms, even if not absolutely complete, with @colewd incredibly lame and inept effort to provide an account for how a mind created Prp8, which was basically “A mind did it, with its mind.”
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UCD is a process before human history yet is an “empirical observation” observed by humankind.?? Brilliant. This whole level of aptitude in thinking on UCD is on almost the same level of aptitude of proposing running nations upon principles, politics and economics that are known to be historical failures. This is university level intelligencia today. Its like we are doing the same as species-devolving towards extinction.
Yes the phylogenetic tree created from the genetic record is an empirically observable indication of UCD.
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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.
So in your theory Prp8 originated as a part of the whole U5 unit? Or is it the whole spliceosome that is generated? Is the generation de novo or seeded in some way?
I would probably not call universal common descent a theory. I might disagree with @Timothy_Horton a little bit too in that I wouldn’t call it an empirical observation. I would probably call it an inferred observation (i.e. coming from empirical data, but not directly observed).
In particular, common decent seems to be readily shown from phylogenetics and direct observations of speciation. The inference is that if you carry common decent back in time, you arrive at a singular, universal common ancestor.
I don’t know if any scientist would say that with 100% certainty we can prove universal common descent. That’s just not how science works. I think what the scientist would (or should) say is that it is currently the best supported scientific model for understanding the origins of all living organisms. To displace it as the reining paradigm you need to have a model that explains the data better than universal common descent, and you need to have some sort of mechanism to explain how it happened. 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.
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No, you routinely ignore most of the evidence that is relevant to the claims you make.
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Good advise. Thanks.
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.
How is it a working model without a mechanism that you can model?