The Argument Clinic

[Meerkat_SK5]

@John_Harshman

Notice that the self-replicating machine you quote about below isn’t actually a machine but an imaginary, 2-dimensional system resembling Conway’s game of life.

Not quite, it is a quantum machine or computer, but it is abstract not imaginary. More importantly, its a proven model for biological and artificial life:

“The fundamental details of the machine were published in von Neumann’s book Theory of Self-Reproducing Automata , completed in 1966 by Arthur W. Burks after von Neumann’s death.[2] While typically not as well known as von Neumann’s other work, it is regarded as foundational for automata theory, complex systems, and artificial life.[3][4] Indeed, Nobel Laureate Sydney Brenner considered Von Neumann’s work on self-reproducing automata (together with Turing’s work on computing machines) central to biological theory as well, allowing us to “discipline our thoughts about machines, both natural and artificial.”[5]”

@John_Harshman

Microtubules don’t produce those three things. Your reference mentions one of those things but the notion is entirely speculative and there is zero evidence for the idea.

False on both claims. Take a look:

“Ironically, Dawkins lists the origin of sex as one of three remaining mysteries in evolution, along with consciousness, and differentiation, the mechanism by which “genes influence bodies.” All three mysteries can be explained through microtubules.”

"…Tubulin proteins comprising microtubules (discussed later in Section: Microtubules and Sex in the Primordial Soup) each have eight tryptophan indole rings arrayed in a geometry strikingly similar to that in FMO photosynthesis proteins. Using molecular modeling, Craddock et al. (2014, 2015) showed FRET-like excitons passing through tubulin among eight tryptophan pi resonance clouds, driven by ambient energy, and blocked by anesthetics which bind naturally in nonpolar regions. …*Compelling evidence from anesthesia research directly links consciousness to this quantum underground.

@John_Harshman

Sorry, but that’s just insane. And it wouldn’t result in a nested hierarchy among basic types.

Not true again. Microtubules operates the same way as cellular automata, which produces nested patterns:

“Descriptions of MTs as computer-like devices (Hameroff and Watt, 1982; Hameroff, 1987; Rasmussen et al., 1990) viewed individual tubulins as bit-like information units in Boolean switching matrices, or cellular (molecular) automata played on microtubule lattices. Simulation of tubulin dipoles interacting with neighbor dipoles and synchronized by Fröhlich coherence showed rapid information integration and learning (microtubule automata; Smith et al., 1984; Rasmussen et al., 1990; Fig. 20.10).”

I also want to clarify that I am not suggesting Equidae sprang fully formed like magic. I am suggesting they rapidly formed over millions of years by microtubules rather than natural selection. It is like someone who puts cookie dough in the oven and then it turns into hard cookies.

@John_Harshman

It may suggest, by analogy, how the evolution of multicellularity might have begun in various taxa. But that’s another thing entirely.

Yes, this is what I meant from the study.

@John_Harshman

No, your conclusion, as usual, doesn’t follow from your premise. Note also that every new transitional fossil fills what was previously a gap. If your notion were true, that would never happen.

I agree. Let me change it up.

If this is true, closely related families or basic types will reveal convergent evolution when their common features are applied to different situations.

@John_Harshman

Of course there were. And note that your “basic type” isn’t perissodactyla; it’s Equidae, and presumably Rhinoceratidae and Tapiridae too. Probably various extinct perissodactyl groups too.

Yes, that is what I was going to put: Equidae

@John_Harshman

And there are most certainly intermediates between these groups.

That is not what this study suggests

"preliminary results from the analyses of two new equid datasets (Froelich 2002; Rose et al. 2014) indicated, in general, that equids shared continuity with one another (sometimes with other perissodactyls – especially non-equid equoids – as well) and displayed discontinuity with various perissodactyl and non-perissodactyl outgroups. These patterns were strongest in the Froelich (2002) dataset, especially when various subsets of the data were analyzed alone (equids vs. tapiromorphs only, equids vs. all other perissodactyls, and equids vs. non-perissodactyls). "

New Baraminological Methods Confirm Monobaraminic Status of the Horses (Perissodactyla: Equidae) and Preliminary Analyses of New Datasets Suggest the Possibility of Discontinuity between Horses and Various Outgroup Taxa (liberty.edu)

@John_Harshman

Once more, your conclusion doesn’t follow from your premise. Why do you bother?

I agree, let’s change it again. We can conclude that Equidae is a legitimate basic type that shares a common design feature with the Tapir and Rhino based on these lines of evidence

Fossil discontinuities between Equidae and other Perissodactyls

Hybridization within Equidae were successful

A clear cut fossil lineage within the Equidae family

Ecology criteria shows common design features of Odd-toed group rather than common ancestor

@John_Harshman

That was a fine bit of word salad. Universal constructor theory does not simulate natural selection. Natural selection does not produce nested hierarchies. Again, who can possibly know what you were trying to say?

@T_aquaticus and @misterme987 disagree with you:

"The key phrase here is “a complete self-replicating automaton”. That’s common ancestry. It is the process of replication that produces the nested hierarchy.

If the automatons were separately created then there is no reason why we should see a nested hierarchy."

Consensus should determine what's taught in science classes. Why?

The key phrase here is “a complete self-replicating automaton”. That’s common ancestry. It is the process of replication that produces the nested hierarchy. If the automatons were separately created then there is no reason why we should see a nested hierarchy. The sources are saying that the nested hierarchy is produced by replication and common ancestry. Nothing on that page describes a nested hierarchy of features or sequence. For example, I can imbed the same “for loop” in many different places within a larger nested subroutine. This would violate a nested hierarchy. I do it all of the time when I am writing Python scripts. This also doesn’t relate to physical structures. Vehicles do not fall into a nested hierarchy. They do not fall into a tree. There is no reason why a creator would need to use a tree to design organisms. Everything. Vehicles do not fall into a nested hierarchy. Vehicles are separately created, and there is absolutely no reason why separate cre…

“A simple search on Wikipedia shows that von Neumann’s universal constructor model is the same as common ancestry, just applied to mechanical rather than biological systems. The “universal constructor” isn’t a reference to some ‘universal common designer,’ it’s von Neumann’s name for the mechanical ‘universal common ancestor’ which self-replicates. So the fact that von Neumann’s model shows the same nested hierarchy pattern as biological lifeforms doesn’t help your case, it hurts it.”

Common Ancestry and Nested Hierarchy

Before moving on in this discussion, let’s just all try to agree on one simple fact: that nested hierarchies are far more complex and robust than creationists often make them out to be. All three of the major creationist organizations claim that nested hierarchies are merely different levels of similarity between extant organisms. But biological nested hierarchies are much more than this. Biological phylogenies have: Nested hierarchy in sequences where function does not change between organisms. For example, in the OP, I constructed a phylogeny based on CYT B, CYT C, and COX1 proteins. These are all proteins that operate in the electron transport chain, and so they do the exact same thing in all of the taxa from that phylogeny. In fact, life quite literally depends on them doing the exact same thing in every organism; if they did not, then our mitochondria could no longer make ATP. Nested hierarchy in unconstrained sequences. There are certain places in the genome (including func…

@Mercer can you please tell me if you disagree with @John_Harshman as well or not?

@John_Harshman

I acknowledged no such prediction. I said something quite different, that from common design we might expect that re-used parts (including DNA sequences) should be identical in separate taxa. I also said that we don’t find that. But of course you don’t read.

Nope, wrong again:

“…creation would predict that “convergent” features would be absolutely identical and would appear in the species as if from nowhere, with no relationships to features in related taxa. Of course we see the former, not the latter, in almost every case”

You acknowledged exceptions and I provided many examples of systemic convergence.

@John_Harshman

What does “animal-like ancestors” mean? What does any of this mean?

Sorry, I just meant animals.

@misterme987

The discontinuities of ‘baraminology’ are only apparent. As you zoom out, so to speak, and look at more and more organisms, ‘baraminology’ finds less and less discontinuities, as Phil Senter showed . The fact that ‘baraminology’ shows any discontinuities at all is an artifact of the incomplete fossil record, so this is just yet another fallacious argument from an incomplete fossil record.

Yeah and Todd Wood has refuted what Phil Senter has argued:
Using creation science to demonstrate evolution? Senter’s strategy revisited - WOOD - 2011 - Journal of Evolutionary Biology - Wiley Online Library

@misterme987

Just to be clear, you believe that horses were created by consciousness from inside the Earth using microtubules? And you think that common ancestry is an “extraordinary claim” compared to that? This is pure nonsense.

I think John clarified my point quite nicely.

@misterme987

Sounds like quantum woo. Besides, microtubules aren’t what you evidently think they are. They aren’t some mysterious force that ‘consciousness’ uses to create horses de novo, they are complexes of tubulin proteins that provide structural support to eukaryotic cells.

Not quite accurate. Take a look:

"Interiors of all animal cells are organized and shaped by the cytoskeleton, a dynamic scaffolding of protein lattice polymers. These self-organizing structures include microtubules, microtubule-associated proteins (MAPs), actin, and intermediate filaments, all anchored by the centriole, a pair of microtubule-based mega-cylinders in the cell center (centrosome), just outside the nucleus. Plant cells also have microtubules and centrioles, and prokaryotes and archaebacteria have similar, but slightly different protein structures. All living cells are organized by microtubules or closely related structures. "

@Dan_Eastwood

You ask for sincere criticism and you have gotten it, but you aren’t taking it seriously.

I am taking it seriously. I just think we are talking pass each other on your point. I am asking you now to help me understand what you are trying to convey to me.

@Dan_Eastwood

AND you still have no test for distinguishing design from evolution. All you are doing is dancing around the problem without ever addressing it.

Did you read this part of what I said about how we can distinguish the two:

To be clear, confirmation for this model has been primarily based on the prediction entailed by the teleological hypothesis that life is ultimately rational; if life was designed, then there is a reason behind its architecture and composition.

In this case, since there must be teleological reasons the designer used these mechanisms for design, such as HGT and Cytosine deamination. Then, those reasons can be tested and if confirmed, it produces evidence for the theory as Fuz Rana and Mike Gene have argued [15][16].

Thus, this model can be used to make meaningful predictions that were not expected from Darwinian evolution (ex. Alleged design flaws found to be optimal)

If you did and still feel the same way, @John_Harshman would disagree with you on this point as well:

“Non-frontloading is anything that isn’t frontloading. Frontloading supposes that the ancestors of some taxa were created with genes that would be useful to those taxa in the future, with the explicit intention of having them become useful. (Note that this requires common descent of such taxa, which you deny.) Note that this requires prior intention, which preadaptation and exaptation and cooption do not.”

@Dan_Eastwood

If you ever attempt to publish, I promise you those reviewers will give you far less consideration than you receive here.

Yeah. Been there and done that. The reviewers said very similar things that you said. But, this was a long time ago and my paper was almost totally different. I am not seeing how your objection or the reviewers’ objections still hold to today with the current version of my article. BTW, If you want to see what those reviewers said for yourself, I can send it via private message. Maybe you can highlight what you feel is still unaddressed and then I can potentially understand your objection better. It is your call.