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

That’s just self-serving nonsense.

No, same rules. Honesty, clarity. That’s it.

Yes, but you must understand you did at least two separate things wrong there. You failed to credit your real source and you failed to read the primary source. The demands aren’t inconistent.

How can interfering with the workings of the cell be considered a function? What is your definition of “function” exactly that makes this true? And it should be obvious that any such definition is not useful.

Conclude what you like. But none of this has anything to do with Owen.

Yes you did. You claimed that phylogenies are mistaken, i.e. that the relationships do not actually exist.

Why would we expect that? You will have to give some kind of reasoning here, because it’s not at all obvious.

Is it too much trouble to ask you to think before you post?

Not, I’m afraid, a nested hierarchy. It’s common for creationists to mistake similarity for nested hierarchy, so I’m not surprised. Re-use of features for particular engineering needs does not produce a nested hierarchy.

No, Owen’s theory of archetypes has nothing to do with any of that.

Go ahead, then. Use that “method” to delimit some basic types and we’ll see how it really does work.

Because there actually are justifications for phylogenetic methods and it’s clear what they’re measuring, and why.

Nope. “Silurian lobe-finned fish” is not a synonym for “vertebrate”. Try again.

Nope again. Owen offers no justification for nested hierarchy. He doesn’t even offer a real justification for homology, just “the creator chose to do it that way”. Useless.

I don’t believe you got any of that from Ernst Mayr. But quote it exactly and we’ll see what he really said. I’m pretty sure the fundamental incompetence will turn out to be yours. Again.

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The causal definition “ascribes function to sequences that play some observationally or experimentally determined role in genome structure and/or function.”

Since Fuz Rana is a biochemist, he is more than qualified to speak on such matter:

"The ENCODE Project focused on experimentally determining which sequences in the human genome displayed biochemical activity using assays that measured:

  • transcription,
  • binding of transcription factors to DNA,
  • histone binding to DNA,
  • DNA binding by modified histones,
  • DNA methylation, and
  • three-dimensional interactions between enhancer sequences and genes.

The implied assumption is that if a sequence is involved in any of these processes—all of which play well-established roles in gene regulation—then the sequences must have functional utility." [Emphasis added]

Now, going back to the study I referenced: “We identify two major consequences of nonfunctional protein-DNA binding. First, there are interference effects , where such binding can disrupt various molecular processes, including transcription, gene regulation, replication and mutational repair”

In their experiment, they determined function using in vitro measurements of
protein-DNA binding specificities. As a result of their experiment, they showed how "genomes have evolved to reduce the occurrence of weak binding motif. The distinct set of DNA binding
proteins coded in each species’ genome imposes a large set of global, evolutionary constraints that have ubiquitously shaped genome-wide motif statistics. " by LONG QIAN and EDO KUSSELL PHYS. REV. X 6, 041009 (2016)

I think Mattick and Dinger eloquently explains how and why the ENCODE results have everything to do with Owen’s theory:

"There may also be another factor motivating the Graur et al. and related articles…

…In essence, the argument posits that the presence of non-protein-coding or so-called ‘junk DNA’ that comprises >90% of the human genome is evidence for the accumulation of evolutionary debris by blind Darwinian evolution, and argues against intelligent design, as an intelligent designer would presumably not fill the human genetic instruction set with meaningless information (Dawkins 1986; Collins 2006).

This argument is threatened in the face of growing functional indices of noncoding regions of the genome, with the latter reciprocally used in support of the notion of intelligent design and to challenge the conception that natural selection accounts for the existence of complex organisms (Behe 2003; Wells 2011)."

Therefore, what you said is “more opinion than fact and difficult to reconcile with the exquisite precision of differential cell- and tissue-specific transcription in human cells”, as Mattick suggested in their article.

Johanthan Witt from the Discovery institute explains it like this:

" These results are unexpected, even bizarre, on the assumption that all life evolved from a single common ancestor through a long series of small, random genetic mutations over millions of years.

But if Darwinian evolution only explains modest differences among closely related species, and if the various similarities and differences across plants and animals of widely varying types are primarily due to an intelligent designer reusing genetic information for common purposes and fresh DNA sequences for innovations, the persistent failure of a single tree of life to emerge makes perfect sense: there is no evolutionary tree of life, because common descent isn’t the case. A common designer is. "

No, there is much more than similarity involved, as Fuz Rana suggested. For instance, in the very first automobiles, there is , of course, design features that all of those cars share. However, in future generations, there are new design features and functionality introduced in the automobile that becomes part of the its design.

Then, in future generations and beyond, we are going to have both of those design features as part of their design. Then, later on beyond that, when there is a third design element that is introduced and then becomes standard practice. As a result, we now have 3 design elements that if you looked at all the automobiles through the history of automobile design, you would then group those automobile designs within groups and so on in a nested hierarchical design.

This is what Owen has suggested within this theory:

" Now, however, the recognition of an ideal Exemplar for the Vertebrated animals proves that the knowledge of such a being as Man must have existed before Man appeared. For the Divine mind which planned the Archetype also foreknew all its modifications.

…To what natural laws or secondary causes the orderly succession and progression of such organic phænomena may have been committed we are as yet ignorant. But … we learn from the past history of our globe that she [i.e. nature] has advanced with slow and stately steps … from the first embodiment of the Vertebrate idea under its old Ichthyic vestment, until it became arrayed in the glorious garb of the Human form” (p.317). [emphasis added]

“There appears also to be in counter-operation during the building up of such bodies, a general polarising force, to the operation of which the similarity of forms, the repetition of parts, the signs of the unity of organisation may be mainly ascribed; the platonic or specific organising principle would seem, to be in antagonism with the general polarising force, and to subdue and mould it in subserviency to the exigencies of the resulting specific form.”

What do you mean by justification for it?

Yes, the same can be said about Baraminology methods. Here is a snippet of Todd and his partner’s research on mammals where they were able to use the method to recognize basic types:

" To expand the sample of statistical baraminology studies, we identified 80 datasets sampled from 29 mammalian orders, from which we performed 82 separate analyses. We analyzed each dataset with standard statistical baraminology techniques: baraminic distance correlation (BDC) and multidimensional scaling (MDS). We evaluated the BDC and MDS results from each character set for potential continuity and discontinuity.

We found evidence of holobaramins in 57 of the 82 analyses (69.5%). Of the remaining character sets, three showed evidence of monobaramins and 22 (26.8%) were inconclusive. These results are consistent with previous efforts to test the discontinuity hypothesis, which found that a majority of character sets showed evidence of holobaramins. Tentative holobaramins represent 57 taxonomic groups, many of which have not been previously analyzed by statistical baraminology. Together with previously identified holobaramins, this study increases the number of putative mammal holobaramins to 64."

Primary source: “A survey of Cenozoic mammal baramins” by C Thompson and Todd Charles Wood (cedarville.edu)

Secondary summary source: Cenozoic Mammals After Their Kinds • New Creation Blog

From his Book:

Estimated Time of Origin of Major Classes of Vertebrates

Vertebrate Class Period Time of Origin

Jawed fishes Ordovician 450 million years ago

Lobe-finned fishes Silurian 410 million years ago

Amphibians Upper Devonian 370 million years ago

Reptiles Upper Pennsylvanian 310 million years ago

Birds Upper Triassic 225 million years ago

Mammals Upper Triassic 225 million years ago

Golly, that wasn’t very surprising. Another prediction confirmed…

Clearly. But if you want to be taken more seriously by real scientists, you should be using the primary literature.

With real, professional scientists, whom you claim are wrong on very basic aspects of biology.

So I’m not sure why you quoted my question without addressing it. Here it is again:

Oh, and you are completely missing the “nested” part of nested hierarchies. Completely.

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It’s a very poor definition that uses the word it attempts to define. And isn’t “is replicated” an observationally or experimentally determined role? If so, then isn’t all of every genome functional by that definition?

That’s a poor assumption, since there’s no reason to suppose that those processes always play roles in gene regulation, just sometimes.

What part of “nonfunctional” was unclear in that quote? What that study shows is that junk sequences can undergo negative selection to dispose of deleterious sequences.

They didn’t even mention Owen’s theory, and their argument is pure speculation about motive.

You can only believe that if you don’t understand how transcription factor binding sites work. They can only have an effect if the transcription factor in question is being expressed in that cell, and of course that expression is the source of cell- and tissue-specific transcription. Functional and spurious binding sites are thus specific in the same way and for the same reason.

What results? Who is Johanthan Witt?

What persistent failure is he talking about? Why isn’t the supposedly re-used genetic information identical in the species it appears in rather than differing from species to species in a nested hierarchy, one shared (with well-explained exceptions) across genes?

That’s not about nested hierarchy in extant species (or current models of cars); it’s about the fossil record, so it’s irrelevant as well as absurd.

Doesn’t explain why those modifications follow a nested hierarchy.

Silly statement, assuming a scala naturae that isn’t in evidence. And still irrelevant to any point you thought you were making.

What does that even mean? Do you have any idea?

I mean a reason, given the theory, to expect there will be nested hierarchy and homology.

It can be said, but it wouldn’t be true. Again, there is not even an attempt to show that given the separate creation of basic types, the methods used would be expected to diagnose them. That’s what “justification” means. I doubt, incidentally, whether you have any notion of what those methods are or how they work.

Yep, nothing you quote says anything like your claim. Your fundamental incompetence is confirmed. Let me remind you of what you said:

Yes, it’s gibberish. No, it isn’t anything Mayr said.

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He is quoting from here:

The results in question seem to be those from these two papers:

  1. Liliana Dávalos et. al, “Understanding Phylogenetic Incongruence: Lessons from Phyllostomid Bats,” Biological Reviews of the Cambridge Philosophical Society 87 (2012), 991–1024, doi:10.1111/j.1469-185X.2012.00240.x.

  2. Leonidas Salichos and Antonis Rokas, “Inferring Ancient Divergences Requires Genes with Strong Phylogenetic Signals,” Nature 497 (May 16, 2013), 327–331.

Jonathan Witt, PhD, is Executive Editor of Discovery Institute Press and a senior fellow and senior project manager with Discovery Institute’s Center for Science and Culture. His latest book is Heretic: One Scientist’s Journey from Darwin to Design (DI Press, 2018) written with Finnish bioengineer Matti Leisola. Witt also authored Intelligent Design Uncensored (IVP, 2010) with William Dembski, and A Meaningful World: How the Arts and Sciences Reveal the Genius of Nature with Benjamin Wiker.

Witt previously served as a tenured professor of literature and writing at Lubbock Christian University. He has a Ph.D., with honors, in English and Literary Theory from the University of Kansas.

This of course makes him @Meerkat_SK5’s favorite type of source, yet another apologist with no expertise on the subject matter whatsoever!

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Why not both: secondary and primary?

Whoa, when did I ever claim this?

Keep in mind that I am not arguing for one defintion of function over another. I am saying all are important in understanding why the ENCODE project results support Owen’s Theory… This is because his theory involves both top-down and bottom-up processes, which would include mechanisms like natural selection. My point is that there is no basis to exclude any of these definitions of function when it comes to evaluating whether Owen’s theory is validated or not by the results.

What exactly do you mean by this?

Let me use Dan Graur’s description of it instead then:

“the “causal role” concept is ahistorical and nonevolutionary ([Cummins 1975](javascript:;); [Amundson and Lauder 1994](javascript:;)). That is, for a trait, Q , to have a “causal role” function, G , it is necessary and sufficient that Q performs G .”

On the Immortality of Television Sets: “Function” in the Human Genome According to the Evolution-Free Gospel of ENCODE | Genome Biology and Evolution | Oxford Academic (oup.com)

They didn’t simply identify a few examples of function and then concluded all of the junk DNA was functional. Instead, they systematically identified members of a sequence elements group that displayed function one by one. This objection also fails to take into account the competitive endogenous RNA hypothesis on pseudogenes, which provides an elegant framework to explain the function of all members of the category.

Yes, It’s non-functional according the selection-effect definition of function, but NOT according to the casual definition. For example, the study showed that high affinity non-functional binding sites are rare. This means that most of the binding that was measured by the ENCODE project was probably functional binding. This is because if most of the binding was random it would mess up the process of gene regulation because random interactions among genome components would potentially be very deleterious to the organism.

Thus, there are very good reasons to believe transcription factors do more than just make noise but display functionality.

You are being silly here John. Owen’s theory involves God as the final and primary cause for evolutionary change, which is what Mattick and Dinger were referring to here. So they don’t need to mention Owen’s theory. An argument from silence fallacy.

I am not sure what your overall point is supposed to be here.

Family trees based on anatomical features have frequently contradicted family trees based on molecular similarities, which the study I provided has revealed.

Tim has already provided you with the study I sent you regarding those results. So no need to give it to you again here.

No, I was referring to the abstract archetypical plan that humans would use to construct those cars, which would end up reflecting a nested pattern of automobiles. Thus, we can explain those nested patterns in biology from a common design perspective as well, which is what Owen’s theory has suggested.

For example, Owens describes three types of homologies evident in the
vertebrates:

I. Special homology: the “correspondency of a part or organ, determined by its
relative position and connections, with a part or organ of a different animal;
the determination of which homology indicates that such animals are constructed on a common type.”

II. General homology: where “a part or series of parts stands to the fundamental
or general type, and its enunciation involves and implies a knowledge ofthe
type on which a natural group of animals, the vertebrates for example, is
constructed. . . .”

III. Serial homohgy: where “as in the vertebra, any given part of one segment
may be repeated in the rest of the series in the same skeleton” [3, p. 7

I am going to have to rely on a secondary source to better describe Owen’s work here since you seemed to not understand some of what he has described in his work:

"Using these categories, Owen claimed to have discovered the basic plan of vetebrate anatomy. First, all vertebrae (among which he emphatically and unfortunately included the skull) of a given vertebrate body were all serially homologous to one another. That is, despite their modification into thoracic vertebrae, tail vertebrae, skull, etc., they are homotypically identical.

Second, each vertebra of every fish, amphibian, reptile, and mammal was seen to be a general homologue of each other. Moreover, since Owen was able to show the same relationships between the limbs of all vertebrates, the limb appendages being both serially homologous within individuals and generally homologous between all groups of vertebrates, he stated his third, and unifying, conclusion: The limbs were specially homologous to the diverging regions of the vertebra. The shoulder blade, for instance, was seen as a special homologue to the pleurapophysis protruberance of the vertebra (and therefore, a modification of the rib). By these three conclusions, Owen believed that he had demonstrated the common pattern to all vertebrate bones and felt that his research had uncovered the basic plan by which the Creator had formed this branch of the animal kingdom [3, p. 127]." [emphasis added]
Owen’s Vertebral Archetype And Evolutionary Genetics: A Platonic Appreciation (psu.edu)

I think the highlighted part is describing the biological version of automobiles that I just mentioned beforehand regarding nested patterns we see with automobiles from an abstract plan that humans devised. The difference is that God’s omniscience allows him to see all the future modifications beforehand that allows us to discover these nested patterns in the first place. On the other hand, humans could not construct an abstract common blueprint that included all the modifications they would be required to make in the future.

He does explain why actually and its to survive the environment:

“Owen had envisioned a unified plan of structure pervading the diversity of vertebrate organisms. All vertebrates were derived from a common archetype from which each species would be ideologically
modified in order to survive in its environment. He even reconstructed a probable Urbuild—called Archetypus—which he noted might have a structure similar to the contemporary lungfish, Lepidosiren [4, p. 5].”

This is one of the main reasons why Owen preferred the transcendental view of biological structures over the teleological view because it incorporated both function and commonality or unity, which explains much more:

“The satisfaction felt by the rightly constituted mind must ever be great in recognizing the fitness of parts for their appropriate function; but when this fitness is gained as in the great-toe of the foot of man and the ostrich, by a structure which at the same time betokens harmonious concord with a common type, the prescient operations of the One Cause of all organization becomes strikingly manifested to our limited intelligence.” [emphasis added]

Primary source: Owen, On the Nature of Limbs, 38.

Secondary source: Archetype or Ancestor? Sir Richard Owen and the Case for Design - Reasons to Believe

No again actually f. He did give a reason. I am going to use the secondary source again to make sure you understand his content:

"But Owen was not content merely to observe such great manifestations of order. He postulated a mechanism which could account for such unity among the diverse vertebrates. First, vertebrae were homotypic by virtue of some “vegetative repetition of a single vertebral element” [3, p. 87]. Each of these serially repetitive vertebral elements could then be teleologically modified independently of each other until it became evident only to the most trained observer that certain of the parts are homologous. " .

"…the more modified the organism from the archetype, the higher its position in the ranks of nature. Eventually, furthest removed from the archetype of any vertebrate, one finds Man, “the highest and most modified of all organic forms, in which the dominion of the controlling and specially-adapting force over the lower tendency to type and vegetative repetition is manifested in the strongest characters” [3, p. 132]. Yet even here, says Owen, “We find the vertebrate pattern so obviously retained.” [emphasis added]

I highlighted this part so you can see how his mechanism does provide justification for why we would expect nested patterns and homology.

Primary sources: .R. Owen. On the archetype and homologies of the vertebrate skeleton.
London, 1848

R. Owen. On the nature of limbs. London, 1849.

Rev. R. Owen. The life of Richard Owen, p. 387. New York: Appleton,
1894.

Secondary source: Owen’s Vertebral Archetype And Evolutionary Genetics: A Platonic Appreciation (psu.edu)

I am assuming you are referring to the BDIST method specifically because they use a variety of methods to establish baramins that evolutionists use as well.

What do you mean by “expected to diagnose”? Give me an example so I can properly address whether this method has shown to do this already or not.

If this is what you meant before about being “expected to diagnose”, then I do know. This article has described it as:

" a phenetics-based algorithm, which calculates the pairwise correlation and baraminic distance between all possible species pairs in a study, based on a set of input characters with discrete values. The algorithm then creates a statistical graph (called a baraminic distance correlation matrix, or BDC), which shows how individual species relate to each other. Optimally, species from a single baramin cluster together on the graph. The designer has refused to share the program with this author. However, it was possible to reconstruct several features of the algorithm from published descriptions of BDIST."

Refining baraminology methods - creation.com

I said “Lobbed-finned fishes from the Silurian era would be an example of an archetype because of the million-year gaps between these fishes and Jawed fishes and Amphibians.”:

Jawed fishes Ordovician 450 million years ago

Milion year gap

Lobe-finned fishes Silurian 410 million years ago

Million year gap

Amphibians Upper Devonian 370 million years ago

Have you forgotten how to read? :joy:

Use the secondary as an introduction. But when you are making a grand claim, only primary will do.

Exactly what I said. You don’t understand it at all. Please stop pontificating as though you do.

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Because the secondary literature may be misquoting or misunderstanding the primary literature.

That’s not, however, a definition of “causal role function” unless we know what the acceptable G are. I would suggest that a deleterious sequence does not perform an acceptable function G.

What are you talking about?

It doesn’t. It may explain a function of some members of the category, though I don’t recall any immediately.

Were most of the ENCODE sites high-affinity binding sites?

Of course they do, but that was never at issue.

I didn’t know that was the feature of Owen’s theory you were referring to. Note that Mattick and Dinger were not supporting any such idea.

My point is that tissue-specific binding is not an indicator of function.

So what? They agree more than they contradict. When there’s a contradiction, it’s worth a publication.

But it wouldn’t. There’s no reason it would. In your example, all the existing cars are identical in the features mentioned. No nested hierarchy at all.

That’s “Owen”, not Owens. I don’t understand what general homology is; do you? Of course special homology is just what we ordinarily think of as homology, and serial homology is just homology of different parts in the same organism. But what is this supposed to be an example of? Why should common design produce either of these sorts of homology, and why should homology follow a nested hierarchy?

Yeah, that part was one of Owen’s wrong ideas.

It doesn’t, and in fact you didn’t describe a nested pattern with automobiles, nor do we in fact see such a pattern.

What do you mean “modifications”? That sounds like you’re advocating common descent among vertebrates, which you have previously denied.

That explanation doesn’t work. As modifications to suit the environment would not be expected to follow a nested hierarchy unless the modifications happened in the course of common descent. What’s being modified? If you’re talking about independent modifications to the archetype, we would expect a star phylogeny, not a nested hierarchical tree.

Another bad guess on Owen’s part, since lungfish arrive in the fossil record much later than the first vertebrates do. Shouldn’t the archetypal species come first?

It doesn’t, though. From that we would expect a star phylogeny or, on a line leading to humans, a scala naturae.

I am referring to all their methods, and evolutionists don’t establish baramins, so any standard method would have to be misused for such a purpose.

I mean, by “diagnose”, determine how the biota is divided into basic types. Identify such types. What reason is given to suppose that their methods could actually identify basic types?

It’s not, and you don’t know. Just quoting doesn’t show understanding. Do you in fact know what a pairwise correlation is? A baraminic distance? How tight does a cluster have to be in order to show that all the species are of the same basic type? How separated do clusters have to be to show that they represent different basic types? Why should those values be accepted?

Again, you contradict Owen, who considers lobe-finned fishes, jawed fishes (and you don’t seem to know that lobe-finned fishes are a subset) and amphibians are all representatives of a single archetype. You don’t seem to realize that those dates are for the first examplars only, and there is no gap. It’s like saying that there’s a gap in Route 66 between St. Louis and Kansas City because the two cites are separated by some distance. Gibberish.

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@Meerkat_SK5, does this help?

The problem with this is not everybody on this forum would agree with this demand from you. I can’t please everybody’s demands or preferences.

I provided a better example down below.

This is not what the following studies on the ENCODE project results suggests in regards to functional RNA in the genome. Professor Alistair Forrest of the Harry Perkins Institute of Medical Research and his research team have found many more examples of function in the non-coding regions:

“There is strong debate in the scientific community on whether the thousands of long non-coding RNAs generated from our genomes are functional or simply byproducts of a noisy transcriptional machinery… we find compelling evidence that the majority of these long non-coding RNAs appear to be functional, and for nearly 2,000 of them we reveal their potential involvement in diseases and other genetic traits.”

Secondary source: Improved gene expression atlas shows that many human long non-coding RNAs may actually be functional – ScienceDaily

Primary source: An atlas of human long non-coding RNAs with accurate 5′ ends | Nature

In that case, what is the actual issue you are having when I argue that junk DNA has been shown to be functional under the casual role definition of function?

According to which definition of function because it certainly is when it comes to the causal role defintion.

I know and that was not the point of why I referenced what they said about it. But, no problem. I think we are on the same page here now.

Remember, the modifications Owen is referring to are abstract platonic forms that existed already in the mind of God where God foreknew all the changes that were going to happen from a universal common plan of organisms. For instance, Humans would the created modified form of Neanderthals that was previously created from a preexisting non-material common blueprint rather than a common ancestor. Neanderthals would be the created modified form of Homo heidelbergensis. Homo heidelbergensis would be the created modified form of mammals. Mammals would be the created modified form of vertebrates. As a result, we get back to a single common archetypical plan for all vertebrates showing a nested hierarchical pattern from a common design perspective (i.e. Design with slight modification). This is almost precisely what Owen’s theory suggests:

"…the more modified the organism from the archetype, the higher its position in the ranks of nature. Eventually, furthest removed from the archetype of any vertebrate, one finds Man, “the highest and most modified of all organic forms, in which the dominion of the controlling and specially-adapting force over the lower tendency to type and vegetative repetition is manifested in the strongest characters” [3, p. 132].

BTW, this is essentially no different when referring to cars. Sudan cars would the created modified form of vehicles with four wheels that was previously created from a preexisiting immaterial common blueprint rather than a common ancestor. Vehicles with four wheels would be the created modified form of land-based vehicles. Land-based vehicles would be the created modified form of Engine-powered vehicles. Engined-powered vehicles would be the created modified form of unpowered vehicles. As a result, we get a nested hierachical pattern from a common design perspective when it comes human designs.

I think the point you have just raised is exactly what the science of Baraminology is seeking to address.

Where do we draw the line between having a large kind with much variation and multiple kinds with a
common design element?

Or which organisms reflect a common descent versus a common design?

For example, most of marine fish life was previously constructed for an ocean environment from this preexisting immaterial common blueprint, as I mentioned before. But, there were other marine life that were adapted to fit a particular environment that gave rise to species within a created kind.

Well, this goes back to what I said earlier about Owen’s theory making different predictions in regard to phylogenetics from distant relatives.

I specifically said we would expect to find more examples of family trees based on anatomical features to contradict family trees based on molecular similarities.

This is because these results would be expected if Darwinian evolution only explains modest differences among closely related species. On the other hand, the various similarities and differences across plants and animals of widely varying types would be primarily due to a universal common designer reusing the universal common blueprint for common purposes and fresh DNA sequences for innovations.

In other words, “the persistent failure of a single tree of life to emerge makes perfect sense: there is no evolutionary tree of life, because common descent isn’t the case. A common designer is.”

Darwin has made bad guess as well, such as the fossil record.

Well, they improved on the method to make sure it does establish baramins as the article I gave suggested:

“A new algorithm was developed to filter out such low entropy characters, and species with a high proportion of missing characteristics. The algorithm was applied on several dinosaur and two cephalopod data sets. It significantly cleans up the data sets and increases the number of baramins reported in previous studies, but eliminates many of the species and characters. There is a trade-off between the amount of available data and data quality. This affects the outcome of morphological baraminology studies.”

Well, you made the claim that baraminology methods was cargo cult science. Therefore, you are obligated to support your assertion that these methods don’t meet the standards of science. If you can’t because you are not an expert , then don’t make the claim in the first place. It’s your burden of proof to meet.

Right, archetypes within archetypes within archetypes leading back to a single conceptional archetypical form for all life forms. I am failing to see a contradiction here.

Yes, they would.

Sure. Lots of functional sequences are in non-coding regions. No surprise. But the point is that these functional, non-coding regions only amount to around 8% of the genome. And that’s true even if every single LNCRNA turned out to be functional. Further, “potential involvement in diseases” is not good evidence of function, since deleterious mutations can happen in strict junk DNA.

Transcription factors aren’t junk DNA and nobody thinks so. But transcription factor binding sites (not at all the same thing) can easily be junk. Are you confused about the difference?

Is it? We still don’t know what the causal role definition actually means, because your definition was self-referential.

Why would god create what is, in effect, a simulation of common descent? And here you seem to be claiming that each and every species is its own basic type. Is it too much to ask for some degree of consistency and clarity from you? Apparently it is.

No mention whatsoever of nested hierarchy, which concept you appear not to understand. Owen is talking about a scala naturae, as I have pointed out before and you have ignored.

That’s a really silly and arbitrary nested hierarchy that it would be easy to punch holes in. For example, a four-wheeled, unpowered wagon doesn’t fit into your hierarchy at all, nor does an airplane. Not every binary division of the world is a true nested hierarchy.

You think wrong. The “science” of baraminology is seeking to mimic real science in order to support a preconceived conclusion.

More gibberish. And please try for consistent terminology. Above, you consistently say “kind” when you mean “basic type” according to your previous claims.

You have to provide a reason for that, which you don’t. Your attempt below is nonsensical.

Why would they be expected. This makes zero sense. And it does nothing to explain the nested hierarchy of DNA sequences.

Sorry, no. There is no single tree of life because of horizontal transfer, mostly in bacteria, and incomplete lineage sorting in eukaryotes. But there’s something quite close to a single tree, just minor variations here and there.

So what if he did? And “the fossil record” isn’t even a guess. You would have to be more specific. But of course it would still be irrelevant.

That does absolutely nothing to argue in favor of the method actually working.

As it happens, I am an expert. You, on the other hand, appear to know nothing of the methods you tout. The answer to all my questions is that the authors don’t know and never say.

Again, the question here is all about basic types. Archetypes are not the same at all. And you depart from Owen, who did not envision archetypes within archetypes. Why should archetypes be nested? Your only argument seems to be that God builds new species by modifying the plans for old species. But why should he do any such thing, simulating common descent?

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This claim that vehicles form a nested hierarchy is complete garbage, and will remain complete garbage because none of its proponents ever provide a vehicle nested hierarchy based on data[1], because many many counterexamples have been presented, but mainly because most of those claiming it make hilarious errors that show they simply don’t know what they’re talking about.

This time is no exception:

Most of the unpowered vehicles which were modified by the addition of engines were and still are four-wheeled land-based vehicles.

This is a “vehicle with four wheels” and a “land-based vehicle”, but it definitely isn’t a “created modified form of Engine-powered vehicles
coach


  1. Cartoon cladograms of cars, vans and trcuks [sic] don’t count. ↩︎

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Then suit yourself, but don’t expect any of the working scientists here (or anywhere else) to take you seriously.

Your example, as Roy noted, shows that you don’t understand what “nested” means in this context. Please learn it before writing any more.

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A defining feature of the nested hierarchy is that modifications at the tip of one branch can be passed downstream, but cannot be passed down to the trunk and back up to the tips of other independent branches. Just because birds get feathers does not allow the feature to be adopted by bats.

Vehicles are not subject to this limitation, and therefore are not in a nested hierarchy. Intermittent wipers appears on sedans, sports cars, and trucks well after these were independent branches. Fuel injection, back up cameras, cruise control, all appeared without respect to hierarchy. Nature cannot do this, but human design does so routinely. A genetic mutation at the tip of one branch cannot travel down to the trunk of the tree of life and back up to another. (putting aside the special case of HGT). Good luck If you wish to dispute that life is arranged in a nested hierarchy, but do not attempt to equate the nested hierarchy with human designs. That is trivially wrong.

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I have addressed this already so I am going to back track for a moment.

My response before was that “protein surfaces are carefully structured to allow strong interactions between protein pairs while minimizing the strength of the unwanted interactions between protein “strangers.” For instance, a study indicated that the concentration of PPI-participating proteins in the cell is also carefully designed where Protein structure and concentrations have to be precisely regulated to promote the PPIs critical for life…”

As Fuz Rana suggested, “high-precision structures and interactions, exemplified by PPIs, are hallmark features of biochemical systems and, by analogy to fine-tuned human designs, point to the work of a Creator.”

Your response to this was…

You specifically said:

Couldn’t natural selection produce the same sort of thing?

I am going to provide a different answer here this time. First off, why is this relevant to the response I gave. Secondly, Fuz Rana suggested in relation to this question that…

“Transcribing 60 percent of the genome when most of the transcripts serve no useful function would routinely waste a significant amount of the organism’s energy and material stores. If such an inefficient practice existed, surely natural selection would eliminate it and streamline transcription to produce transcripts that contribute to the organism’s fitness.”

So the point of this quote is to show that Transcription binding could NOT logically be a random process as I think you might have been suggesting or assuming. Instead, it is a highly precise finely tuned process that has to be this way or else the biochemical processes in the cell would grind to a halt.

As Fuz Rana mentioned, “three of the assays employed by the ENCODE consortium measure binding of proteins to the genome, with the assumption that binding of [transcription factors] to DNA indicated a functional role for the target sequences… Biochemists have known for some time that the biochemical activities cataloged by the ENCODE Consortium are important for gene regulation and gene expression.”

As I mentioned before, I gave you the study already that shows how protein binding in genomes is not random but highly specific and the human genome harbors very few nonfunctional protein-binding sites. Since non-functional binding sites are rare, their assumption was probably valid. The study also showed that modeling these nonfunctional binding sequences in genomes from an evolutionary process failed to account for them. They concluded that natural selection must have weeded out high affinity nonfunctional binding sites in genomes.

Thus, it is reasonable to conclude that they did discover function from these binding sites based on the Causal role definition of function.

Because that is his nature. If God is by nature a perfect human being, then we would expect him to operate in the same fashion as humans except for one important difference that I mentioned already.

The difference is that God’s omniscience allows him to see all the future modifications beforehand that allows us to discover these nested patterns in the first place. On the other hand, humans could not construct an abstract common blueprint that included all the future modifications that would be required to make in the future. Instead, humans make modifications to preexisting designs that are very similar to how natural selection works where there is no foreknowledge of future designs. Instead, humans have to work with the information they possess at that present time.

This leads me to address this objection…

Again, from the standpoint of unguided Universal common descent, I would agree. But, I was making the comparison of similar nested patterns between humans and nature from the standpoint of Owen’s model of nested patterns. According to Owen’s model, the nested hierarchy of vertebrates and cars would both exist in a platonic state NOT a materialistic one. This means that unless you are going to argue that it is a logical contradiction (not a physical one) to retro-fit cars in a nested pattern, the analogy stands correct.

Yes, it is expected if common descent is not universal because ,as I told you before, Common design theory does not negate common descent altogether but allows for a limited version of it.

Both claims here are false. Here is an article that shows how you can:

"The model of Britten and Kohne [21] is probably the most accepted hypothesis to account for the formation and divergence of homologous sequences of DNA. …Comparing it with Owen’s model (fig. 1), certain “temporal homologies” stand out. The first step in both systems in the tandem multiplication which Owen called “vegetative repetition” and which Britten and Kohne call “saltatory replication.” The end result in both cases is the formation of identical structural units. The next step in both these models is the independent divergence of the component members.

Owen’s repetitions of the archetypal vertebra become the skull bones, the thoracic vertebrae, etc.; Britten and Kohne’s repetitive sequences become a family of similar but by no means identical homologues. Hence, from an original unity of structure, a homologous group arises. Finally, both models postulate that the homologous elements may continue to diverge so greatly that they can hardly be recognized as homologous. "

"…To be sure, the archetype of the modern biologist is far different from Owen’s notions. Whereas Owen’s vertebral archetype was a Platonic ideal organism whose modifications were preordained by the Creator for its survival, the archetype of the molecular biologist is a sequence of nucleic acid from which other sequences evolved in a trial-and-error encounter with the changing milieu of both organism and environment "

Owen’s Vertebral Archetype And Evolutionary Genetics: A Platonic Appreciation (psu.edu)

What’s your point here? Are you allowing for a universal common design with limited common ancestry or conceding my overall point here?

What is an archetype ( i.e. common blueprint or design)?

An abstract conceptional framework described in the bible from which basic types were linked together and constructed from in a progressive sequence that ended with man. Basic types and Archetypes are NOT the same thing though. Instead, Archetypes are the conceptional framework described in the bible from which basic types were constructed from.

homological structures pointed back to a single conceptional design in the mind of God rather than a single ancestor. In other words, having different archetypes within archetypes is akin to having different ancestors within ancestors that lead back to a single universal archetype or ancestor. Examples would be…

Flowering Plant Archetype

Fern Archetype

Aquatic Invertebrate Archetype

Fish Archetype

Amphibian Archetype

Insect Archetype

Bird Archetype

Carnivore Mammal Archetype

Reptile archetype (which includes turtle and snake archetypes or archetypes within archetypes)

What is a basic type (or holobaramin)?

a created kind is the materialized form of archetypes that has similarity in form/ design due to similarity in function and common designer but no common or primitive ancestors.

What is a species (or monobaramin)?

a breed within a basic type with a specific set of reproductively connected characteristics that produce a recognizable pattern. It is able to reproduce with others of the same species and potentially able to hybridize with other breeds/species within a basic type. It focuses on the ability to breed, gives strong attention to form and morphology, and uses habitats and geography only as indicators of where species boundaries may occur.

This is not what they suggested:

"In the actual process of moving toward the goal of characterizing holobaramins, the taxonomist needs to identify apobaramins and partition them. Subtractive criteria need to be used in dividing the apobaramins into separate holobaramins. Then with the goal of characterizing holobaramins, the taxonomist focuses on the monobaramins, and additive criteria are employed to build these monobaramins.

An analogy for explaining this process has been proposed:

It is like there has been a huge snowfall covering the trees to the top, and we are digging down into the snow to identify the connections, the branches, limbs, and trunk. Is there one tree below? Or is it an orchard of separate distinct trees? As the data slowly come into view we will have arguments about what is connected to what, or whether there is discontinuity at a given place. Some researchers will mis-identify various branches as connected, when these later are seen as unconnected, and so forth. But this clears up as we dig. We are not “cutting and pruning” the data. Rather, we leave the data precisely where it is. We merely are cutting and pruning our perceptions–particularly our temporarily mistaken perceptions of the data (ReMine, 2000).

In other words the scientist is iterating tentative taxonomies by increasing or decreasing sizes of the branches to arrive at the best approximation of reality. This systematic procedure is driven by observed facts rather than some presupposed framework."

What are the Genesis “kinds”? - ChristianAnswers.Net

No, I do know most of them but just not all of them.

You haven’t, and nothing you say after that is relevant.

Turns out that isn’t true. The wastage is not significant.

The first part of that sentence is so ambiguous as to be either true or untrue depending on how it’s interpreted, and the study doesn’t say what you think it does.

You have not shown any of that to be true, and even if it were true you haven’t shown that it would produce a nested hierarchy. Humans do not produce nested hierarchies. Cars do not form a nested hierarchy. “Because it is his nature” could explain anything and therefore nothing.

Owen didn’t have a model of nested patterns, and humans don’t make nested patterns.

It means no such thing. You are making no sense here.

Unfortunately, the nested hierarchy extends way past anything you are willing to consider a basic type, so your explanation of “differences among closely related species” is not relevant.

How you can what? What you quote has nothing to do with refuting anything I said.

No, not at all. I merely point out that evolution of all life from a common ancestor is not completely treelike. My point is that your understanding of all this is just wrong.

Archetypes are not described in the bible, and we were supposedly talking about basic types, not archetypes. Do you remember?

In other words, archetypes within archetypes is nothing more than a simulation of common descent. But why should God want to simulate common descent?

The discussion is supposed to be about basic types, not archetypes, so all those examples are irrelevant. Nor do you have any reason to suppose that any of those examples should be considered archetypes.

If you would stop just repeating crap you have already posted and instead respond specifically and with relevant arguments, if in fact you would actually read what I say and follow it in some coherent fashion, we might be able to have a real discussion instead of me banging my head against a wall.

Gibberish intended to imitate the surface features of a scientific publication.

Sure, they can claim that. It just isn’t true. All those folks have a prior commitment to their personal interpretations of Genesis that can’t be altered. That’s why Genesis is considered the supreme evidence in baraminology.

That is not evident from what you have said. Why are we even bothering?

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Wear a helmet!

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