The Current Status of Ewert's Dependency Graph of Life

[John_Harshman]

@Meerkat_SK5

Instead, the question is whether evolution was a guided ( universal common design) process by a Divine mind or unguided ( universal common descent) process by natural selection. That being said, my model does accept a limited form of common ancestry.

That’s you making up your own definitions of terms. Universal common design is not guided evolution. Separate creation is not guided evolution. And common ancestry does not preclude guided evolution.

@Meerkat_SK5

Now, here are some of my model’s differences from Universal common descent:

(A) Functional/sequence convergence (i.e. dependecy graph)

(B) Widespread examples of convergent evolution

(C) Functional pseudogenes and ERV’s

The dependency graph doesn’t represent functional sequence convergence. And functional sequence convergence is quite rare. Examples of convergent evolution are plentiful, but are a small proportion of the total, and examples of convergent molecular evolution are few. A few pseudogenes and ERVs are functional, but most are junk. Nor is that a prediction of common design.

Nothing you say makes sense.

[Meerkat_SK5]

@John_Harshman

That’s you making up your own definitions of terms.

Correct. This is what new models do.

@John_Harshman

Nothing you say makes sense.

And almost everything you said is not true…

@John_Harshman

The dependency graph doesn’t represent functional sequence convergence.

From Winston’s model:

"They explain similarities among species by appealing to functional constraints or common design instead of common
descent [17, 22].

Many species face similar functional constraints and thus must solve some problems in similar ways. Common design leads to similarity because designers frequently reuse components, modules, and solutions leading to similarity. "

@John_Harshman

And functional sequence convergence is quite rare.

Convergent evolution seen in hundreds of genes | Nature

@John_Harshman

A few pseudogenes and ERVs are functional, but most are junk. Nor is that a prediction of common design.

Overcoming challenges and dogmas to understand the functions of pseudogenes | Nature Reviews Genetics

@John_Harshman

If you really look at it, this scenario doesn’t hold up. So what you would say is not compatible with the data.

How so?

@John_Harshman

What basic types does Bechly identify? How? Did you even watch the video?

How many times do I have to explain this. Basic types are created kinds, which means they represent the sudden appearance of organisms that have no precursor ancestors in the fossil record.

@John_Harshman

No. I’m telling you that pseudogenes don’t result from horizontal transfer and neither do ERVs.

So what then? I don’t get your point. These are the differences between models as I mentioned.

@John_Harshman

So? Nothing to do with horizontal transfer. Nothing, in fact, to do with how gene regulation works in chordates. You persist in citing articles that don’t say what you think they do. And this has nothing to do with phylogeny either.

My point is that viruses can be manipulated to produce more than one process for more than one motive.

For instance, HGT is what explains the biochemical similarities and the phylogenetic patterns from distant relatives. The ceRNA hypothesis explains why we have psuedogenes. Both involve RNA or viruses to facilitate the process.

[Chris_Falter]

@colewd

I don’t see how the model gets from non coding NC DNA to a functional gene through reproduction and natural variation.

The paper explains this in exquisite detail.

@colewd

Without this the reasoning is based on historical extrapolation appealing to similar sequences in NC DNA.

This statement is diametrically opposed to the methods and conclusion of the paper.

My conclusion is that you did not understand it.

I suggest that you re-read the paper, and if you still do not understand it, that you bring specific questions back to this audience. There are many biologists who understand these things far better than you or I, and they are willing to converse. Why not take advantage of the opportunity?

Best,
Chris Falter

[Rumraket (Mikkel R.)]

@Meerkat_SK5

Well yeah, making scientific predictions are a matter of faith. So what’s your point?

You didn’t make any predictions, you just expressed hope for a future development.

@Meerkat_SK5

I agree, it’s the universal common design model as a whole that explains all the data. HGT and the dependency graph are just aspects of that overall model to make it robust and better than common descent because HGT does not go far enough to explain the phylogenetic patterns.

These are all just assertions and you have done no work to try to fit any model to the data.

@Meerkat_SK5

All organism appear to be related phylogenetically according to the Universal common design model. Again, we can explain it a different way based on what I presented in the Origin of life model we discussed before.

You have given no such explanation, only waved your hands in the direction of your hope for a future development of the dependency graph, and biased HGT, neither of which have explained anything about the match between phylogeny and the geological/fossil record.

It also doesn’t make any sense I have to say. We simply don’t see life being “universally commonly designed”, nor undergoing biased HGT to any noteworthy extent anywhere. We do however see life actually evolving and diverging from common ancestors. There is not any need for you to even try to provide an alternative explanation for the history of life on Earth.
There is something fundamentally misguided about trying to replace an already extremely successful theory with such an incoherent and unevidenced mix of ideas and concepts.

@Meerkat_SK5

No, I have never presented my argument in the same fashion as ID theorists, which is what I think is the reason for this disconnect.

Instead, the question is whether evolution was a guided ( universal common design) process by a Divine mind or unguided ( universal common descent) process by natural selection.

Guided evolution is still evolution and is entirely compatible with common descent. And neither the dependency graph nor biased HGT is evidence favoring guided evolution.

@Meerkat_SK5

That being said, my model does accept a limited form of common ancestry

If you’re only advocating for guided evolution, your “model” should in principle be compatible with universal common descent, and you have no need to invoke neither a dependency graph nor biased HGT to explain anything.

It’s impossible to have a sensible exchange of ideas and arguments with a person who hasn’t thought through what he is really trying to argue, and it’s made all the worse by your strange private vocabulary. If all you want to argue for is that evolution is guided, stop calling it something else than that. Just use the most descriptive and simple title possible, it massively aids comprehension and simplifies all debate: Guided evolution. Not universal common design, not Old-Earth creationist baraminology, or whatever else. Just guided evolution.

Look at all the confusion you’ve created so far.

@Meerkat_SK5

BUT I can’t tell you yet which groups of organisms share designs versus share ancestry because an OEC version of Baraminology has not been fully developed yet .

It seems it has not been developed at all. It exist only as a sort of vague idea in name only about unspecified independently created clades of organisms.

@Meerkat_SK5

Now, here are some of my model’s differences from Universal common descent:

(A) Functional/sequence convergence (i.e. dependecy graph)
(B) Widespread examples of convergent evolution
(C) Functional pseudogenes and ERV’s

What @John_Harshman said. None of this makes any sense.

[colewd (Bill Cole)]

@Chris_Falter

I suggest that you re-read the paper

Hi Chris
I will when I have a chance over the next few days.
Best
Bill

[John_Harshman]

@Meerkat_SK5

This is what new models do.

That isn’t at all what new models do. You can’t make up your own definitions if you want anyone to know what you’re talking about, especially if you don’t actually define your terms. Common descent has a meaning. Guided evolution has a meaning. Separate creation has a meaning. The only two that are compatible are common descent and guided evolution. Common descent assumes neither unguided evolution nor natural selection.

@Meerkat_SK5

From Winston’s model

Convergence has a meaning too, and it doesn’t mean functional constraints. And in fact Ewert is contrasting convergence due to functional constrant with similarity due to re-use of components.

@Meerkat_SK5

Convergent evolution seen in hundreds of genes | Nature

From the article (not primary literature, even) that you cite: “Different organisms often independently evolve similar observable traits such as anatomical or functional features, but the genetic changes underpinning such ‘convergent evolution’ are usually different.” Note that these are a couple of hundred genes out of around 20,000, i.e. 1%. I’d call that rare. And even this is an unusually high number.

@Meerkat_SK5

Overcoming challenges and dogmas to understand the functions of pseudogenes | Nature Reviews Genetics

Since that’s paywalled, I can’t tell what it actually says. What percentage of pseudogenes did the authors find to have function?

@Meerkat_SK5

@John_Harshman

If you really look at it, this scenario doesn’t hold up. So what you would say is not compatible with the data.

How so?

HGT does not produce a consistent nested hierarchy. That’s why basal relationships within Eubacteria are hard to discover.

@Meerkat_SK5

How many times do I have to explain this. Basic types are created kinds, which means they represent the sudden appearance of organisms that have no precursor ancestors in the fossil record.

You have to explain it until it makes any sort of sense. You haven’t answered the question either. What basic types are there? Try again.

@Meerkat_SK5

So what then? I don’t get your point.

My point is that you claimed that pseudogenes and ERVs result from horizontal transfer, but they don’t.

@Meerkat_SK5

My point is that viruses can be manipulated to produce more than one process for more than one motive.

How is that evidence for your claims?

@Meerkat_SK5

For instance, HGT is what explains the biochemical similarities and the phylogenetic patterns from distant relatives.

But it doesn’t. HGT is expected to destroy nested hierarchy, not produce it.

[Meerkat_SK5]

@Rumraket

You didn’t make any predictions, you just expressed hope for a future development.

@Rumraket

These are all just assertions and you have done no work to try to fit any model to the data.

This is technically true. LOL. I am simply taking the work that has been done from other experts and putting the pieces together to provide a robust theory, such as the Orch-OR theory, common design model and Winston’s model (OEC version. The only thing that could be considered my idea is the merging of all three origin of viruses models into one.

@Rumraket

It also doesn’t make any sense I have to say. We simply don’t see life being “universally commonly designed”, nor undergoing biased HGT to any noteworthy extent anywhere.

Again, that’s not what the studies suggest:

“Although observed rates of acquisition of horizontally transferred genes in eukaryotes are generally lower than in prokaryotes, it appears that, far from being a rare occurrence, HGT has contributed to the evolution of many, perhaps all, animals and that the process is ongoing in most lineages . Between tens and hundreds of foreign genes are expressed in all the animals we surveyed, including humans. The majority of these genes are concerned with metabolism, suggesting that HGT contributes to biochemical diversification during animal evolution.”

From the second study:

“We have shown three lines of evidence for preferential gene transfer having the potential to create phylogenetic patterns comparable with those generated by shared ancestry. These transfers are characterized by the preference of taxa to exchange genes with partners more similar to themselves rather than rare HGTs that may occur randomly and indiscriminately.”

@Rumraket

There is not any need for you to even try to provide an alternative explanation for the history of life on Earth.
There is something fundamentally misguided about trying to replace an already extremely successful theory with such an incoherent and unevidenced mix of ideas and concepts.

Universal common descent does NOT explain the state of the fossil record or origin of life/viruses

@Rumraket

Guided evolution is still evolution and is entirely compatible with common descent.

Nope, Universal common design and common descent are mutually exclusive because Universal common descent does not explain the fossil record and the origin of life/viruses.

@Rumraket

And neither the dependency graph nor biased HGT is evidence favoring guided evolution.

Well, its supposed to be evidence specifically favoring common design NOT guided evolution.

[John_Harshman]

@Meerkat_SK5

Between tens and hundreds of foreign genes are expressed in all the animals we surveyed, including humans.

Tens and hundreds out of how many, total? Have you considered that?

@Meerkat_SK5

lines of evidence for preferential gene transfer having the potential to create phylogenetic patterns comparable with those generated by shared ancestry. These transfers are characterized by the preference of taxa to exchange genes with partners more similar to themselves rather than rare HGTs that may occur randomly and indiscriminately.

As I’ve told you before, this is talking about horizontal transfer being most likely between close relatives, thus largely matching the real phylogeny. This is no comfort for your theories.

@Meerkat_SK5

Universal common descent does NOT explain the state of the fossil record or origin of life/viruses

True. Then again it isn’t intended to. However, the fossil record is consistent with common descent but inconsistent with separate creation. If it were consistent with separate creation you would be able to identify the basic types, which you haven’t managed in even a single case. Nobody else has either.

@Meerkat_SK5

@Rumraket

Guided evolution is still evolution and is entirely compatible with common descent.

Nope, Universal common design and common descent are mutually exclusive because Universal common descent does not explain the fossil record and the origin of life/viruses.

“Universal common design” is nearly meaningless except as a synonym for “god did it”. But how did god do it? It could have been through guided evolution and common descent. They’re fully compatible. Both Michael Behe and Michael Denton agree with that.

@Meerkat_SK5

Well, its supposed to be evidence specifically favoring common design NOT guided evolution.

Then you shouldn’t have equated common design with guided evolution. See how your shifting personal definitions cause confusion?

[Meerkat_SK5]

@John_Harshman

Since that’s paywalled, I can’t tell what it actually says. What percentage of pseudogenes did the authors find to have function?

I don’t know since I am relying on secondary sources. Here is a snippet of the article though…
“However, with a growing number of instances of pseudogene-annotated regions later found to exhibit biological function, there is an emerging risk that these regions of the genome are prematurely dismissed as pseudogenic and therefore regarded as void of function.”

@John_Harshman

Convergence has a meaning too, and it doesn’t mean functional constraints. And in fact Ewert is contrasting convergence due to functional constrant with similarity due to re-use of components.

There are different types of convergence and I was specifically referring to functional convergence, which involves what Winston has suggested in his model.

@John_Harshman

You have to explain it until it makes any sort of sense. You haven’t answered the question either. What basic types are there? Try again.

I cannot provide a detailed account of those examples because Old earth Baraminology has not been fully developed yet. But, here is an idea of what those examples might be for now:

The sudden appearances of Avalon, Cambrian fauna, Ordovician, Nekton animals, Odontodes vertebrates, Land vertebrates, Insects, Dinosaurs/birds, placental mammals, Genus Homo, and Humans

@John_Harshman

@Meerkat_SK5

My point is that viruses can be manipulated to produce more than one process for more than one motive.

How is that evidence for your claims?

Because it is consistent with the origin of life model that I showcased in a recent topic.

@John_Harshman

But it doesn’t. HGT is expected to destroy nested hierarchy, not produce it.

Well, HGT does two things to phylogenetic patterns from the study I showed you before:

“We conclude that the observed phylogenetic pattern reflects both vertical inheritance and biased HGT and that the signal caused by common organismal descent is difficult to distinguish from the signal due to biased gene transfer.”

@John_Harshman

Tens and hundreds out of how many, total? Have you considered that?

Sure, but why is this a point of contention?

@John_Harshman

this is talking about horizontal transfer being most likely between close relatives, thus largely matching the real phylogeny. This is no comfort for your theories.

I think you meant to say this is NOT talking about…If so, I have already conceded this, which is why I am invoking Winston’s model to explain the rest of the data.

@John_Harshman

“Universal common design” is nearly meaningless except as a synonym for “god did it”. But how did god do it? It could have been through guided evolution and common descent. They’re fully compatible.

Quantum tunneling is how he did it. Here is a snippet of an article you should read:

"In summary tunnelling has guided us via prominent examples to biochemistry where quantum tunnels are important infrastructures in the world of functional molecules: spontaneous mutations in DNA, enzymatic reactions and especially energy transduction pathways are highly influenced, supported and even enabled by quantum tunnelling. The transition probability of the tunnelling concept from the field of organic chemistry [123] to biochemistry [124] has significantly increased within the past years while, at the same time, the conceptual barrier between chemistry and biology has become smaller and has begun to disappear [125] (see also Pross, 2013, in this issue).

Quantum Tunnelling to the Origin and Evolution of Life (nih.gov)

I bolded that part to illustrate why you cannot separate the origin of life from evolution, which is also why Universal common design and descent have to be mutually exclusive models. (ex. General relativity and Newton mechanics)

[John_Harshman]

@Meerkat_SK5

I don’t know since I am relying on secondary sources.

You have to stop citing papers you haven’t read. It’s just rude. I refuse to discuss a claim based on your poor scholarship.

@Meerkat_SK5

There are different types of convergence and I was specifically referring to functional convergence, which involves what Winston has suggested in his model.

No, he’s not talking about convergence of any sort. Separate creation is not compatible with convergence, which is a feature of common descent.

@Meerkat_SK5

I cannot provide a detailed account of those examples because Old earth Baraminology has not been fully developed yet.

Exactly. You can’t provide an account at all. And it will never be fully developed. This is you once again relying on hypothetical future information to support your argument. That isn’t cricket.

@Meerkat_SK5

The sudden appearances of Avalon, Cambrian fauna, Ordovician, Nekton animals, Odontodes vertebrates, Land vertebrates, Insects, Dinosaurs/birds, placental mammals, Genus Homo, and Humans

I have pointed out previously that none of these are identified as basic types. I have also pointed out previously that Avalon isn’t even a taxon; it’s a location. Similarly, Ordovician is a time period, Odontodes are teeth, and none of them is a family, which you have previously said is what basic types are. And I have further pointed out that many of these supposed basic types are nested within each other, so at most one of those nested groups can be a basic type. This is you once again reposting an incoherent claim without ever addressing previous criticisms.

@Meerkat_SK5

Because it is consistent with the origin of life model that I showcased in a recent topic.

It’s also consistent with many other irrelevant notions. Consistency is not a good guide to relevance.

@Meerkat_SK5

“We conclude that the observed phylogenetic pattern reflects both vertical inheritance and biased HGT and that the signal caused by common organismal descent is difficult to distinguish from the signal due to biased gene transfer.”

Yes, that’s because the HGT they observe largely follows the true phylogeny. This is not useful to your claims.

@Meerkat_SK5

Sure, but why is this a point of contention?

Because I said that horizontal transfer is rare in eukaryotes, and tens to hundreds of genes out of roughly 20,000 would be considered rare. In other words, that paper supports my claim, not yours.

@Meerkat_SK5

I think you meant to say this is NOT talking about…If so, I have already conceded this, which is why I am invoking Winston’s model to explain the rest of the data.

No, I said what I meant. What?

@Meerkat_SK5

I bolded that part to illustrate why you cannot separate the origin of life from evolution

But that’s not what it means. You must try harder not to be incoherent.

[Roy (34-year veteran)]

@Meerkat_SK5

@John_Harshman

That’s you making up your own definitions of terms.

Correct. This is what new models do.

Completely wrong.

New models may include new terms, or they may use existing terms to describe a novel idea or process. They rarely reuse existing terms while meaning something different, because that can make it harder to understand. They especially don’t reuse existing terms from the same field to mean something other that the usual meaning in a context where the usual meaning could also apply, because that leads to total confusion. They should never reuse existing terms without explicitly stating that they are doing so and including the new definition. Doing so guarantees that a model will be misunderstood.

[Faizal_Ali]

@colewd

The issue may be what you mean by falsification . To you it may simply mean someone like @John_Harshman said there are problems with the theory.

No, that is not the meaning of falsification.

[colewd (Bill Cole)]

Hi Chris
I re read the paper this morning and don’t think this model is very different than prior models as it is based on Fisher/Wrights work.

It is different from other work that involves gene duplication as it uses NC regions as the point of origin for de novo genes. These models are very difficult to test as they predict results in greater than 100k years for quickly replicating organisms.

The other issue with models like this is figuring out the real correlation between fitness and new function. Behe’s work showed that blunting of genes can improve fitness.

@Chris_Falter

The paper explains this in exquisite detail.

What exquisite detail in this paper do you think predicts the origin of new functional sequences?

Best
Bill

[Rumraket (Mikkel R.)]

@colewd

These models are very difficult to test as they predict results in greater than 100k years for quickly replicating organisms.

You test models against data when the timescales are greater than can be experimentally assessed. That’s how they test models in geology and astronomy.

The model in that paper is consistent with rates of gene gain on geological timescales inferred from comparative genetics.

@colewd

Behe’s work showed that blunting of genes can improve fitness.

Behe has done no work to show this, it was already known. Behe has instead used this already established knowledge (gained from other people’s work) as a premise in his attempt to argue that this is effectively the only mode of evolution.

[colewd (Bill Cole)]

Are these the species they used to generate the model? How many mutations do you think they allotted for discovery of a new gene? How would these estimates translate to what we see in the Howe diagram?

[Faizal_Ali]

@colewd

Are these the species they used to generate the model? How many mutations do you think they allotted for discovery of a new gene? How would these estimates translate to what we see in the Howe diagram?

Unbelievable.

[Rumraket (Mikkel R.)]

@colewd

Are these the species they used to generate the model? How many mutations do you think they allotted for discovery of a new gene?

That’s in the paper, Bill.

@colewd

How would these estimates translate to what we see in the Howe diagram?

Very well. Taking the slowest rate among those numbers (4.6 * 10⁵ years), and extremely conservatively(and totally unrealistically) assuming sequential evolution of each new gene (meaning for each additional new gene, the previous one has to evolve first, so half-way through the establishment of one gene another can’t start evolving from another locus), that still gives us ~889 new genes in 400 million years.

[John_Harshman]

@Rumraket

that still gives us ~889 new genes in 400 million years.

That’s per lineage, of course. Counting all lineages, the diagram encompasses around 1.3 billion years. Say 2600 new genes. And that’s just from non-functional sequences, and doesn’t count the genes arising from duplication.

[colewd (Bill Cole)]

The model time-step calculated in column 3 is the time it takes for 1 mutation to occur in a locus of 100 bp

From the paper.

Are you claiming new genes form from a single mutation in 100 BP of DNA?

[Chris_Falter]

@Meerkat_SK5

I cannot provide a detailed account of those examples because Old earth Baraminology has not been fully developed yet.

Here, let me correct this sentence for you.

I cannot provide a detailed account of those examples because Old earth Baraminology has not been fully developed yet don’t have a theory yet, just a few vague ideas that are not falsifiable.

Maybe this will help you understand why scientists, members of a community built on the foundation of falsifiability, are skeptical of your “theory.”

HTH,
Chris