p-value testing will never be the same again

[shunyadragon]

Are you saying there are no such things as statistically independent events in nature? Coin flips are one example.

No.

I'm not sure what you are saying, but the probability of a given snowflake pattern forming is not 100%.

Your English is deficient. I did not say that.

The fallacy here is miscalculating P(A|A), which is 100%.

Blessings,
Lee

No, you apparently do not understand the reference.

[lee_merrill]

Building an arch using scaffolding is a well-known counter-example.

So then the problem becomes that of generating a structure more complex than (say) a flagellum, and yet being functional. This is unlikely.

The NFL theorem is about search functions, not fitness functions.

Well, search algorithms, in the case of evolution, fitness functions.

… the probability of a coin flip coming up heads is 50% if you view the coin flip before the event occurs. Viewing the event after the coin flip, the probability is 100% that it came up the way it did. So you can view an event such as protein production before the event occurred, and ask what that probability would be.

That would be "viewing the probability of a random arrangement after the fact" - which you just cautioned against for snowflakes, which you don't think are designed, but are content to do for proteins, which you want to show were designed.

No, before the fact, and if you were to show me a snowflake pattern, and then you were able to generate such a snowflake, I would attribute that to design, because that is so improbable to happen by natural processes.

You're even content to 'calculate' the probability using a completely different production method than the one found in nature, making your supposed probabilities not just irrelevant but deliberately so.

But we're talking about the first proteins, which presumably had to be assembled randomly.

Blessings,
Lee

[shunyadragon]

But you just said that if one part is removed, at times the organism does not survive.

Correct that is how natural selection works in evolution.

[quote]
So what is the evolutionary path to development of the flagellum? [quote]

So? So what? The evolutionary path of the flagellum is natural selection.

Source: http://www.sci-news.com/biology/bacterial-flagellar-motors-05612.html

Biologists Trace Evolution of Bacterial Flagellar Motors

Bacteria use molecular motors just tens of nanometers wide to spin a tail (flagellum) that pushes them through their habitat.

Like human-made motors, these nanoscale machines have distinct ‘stator’ and ‘rotor’ components that spin against each other. The structure of these motors determines their power and the bacteria’s swimming ability.

Previously, Imperial College researcher Morgan Beeby and co-authors looked at these motors and discovered a key factor that determined how strongly bacteria could swim.

They found that the more stator structures the bacterial motor possessed, the larger its turning force, and the stronger the bacterium swam.

Despite these differences, DNA sequence analysis shows that the core motors are ancestrally related. This led the team to question how structure and swimming diversity evolved from the same core design.

Now, in new research published in the journal Scientific Reports, Dr. Beeby’s team was able to build a ‘family tree’ of bacterial motors by combining 3D imaging with DNA analysis.

This allowed them to understand what ancestral motors may have looked like, and how they could have evolved into the sophisticated motors seen today.

The scientists found a clear difference between the motors of primitive and sophisticated bacterial species. While many primitive species had around 12 stators, more sophisticated species had around 17 stators. This, together with DNA analysis, suggested that ancient motors may also have only had 12 stators.

“This clear separation between primitive and sophisticated species represents a ‘quantum leap’ in evolution,” the authors said.

“Our study reveals that the increase in motor power capacity is likely the result of existing structures fusing. This forms a structural scaffold to incorporate more stators, which combine to drive rotation with higher force.”

© Copyright Original Source

Read on . . .

Actually, the NFL theorem does apply to evolution, and a changing fitness function is not a problem, it has to do with all fitness functions.

No it does not as described and cited concerning your bogus misuse of probability and science.

[Roy]

So with irreducibly complex objects, they do have to appear all at once in order to be functional.

Building an arch using scaffolding is a well-known counter-example.

So then the problem becomes that of generating a structure more complex than (say) a flagellum, and yet being functional.

No, the problem becomes your attempt to back-pedal and goalpost-shift rather than taking responsibility for your uncritical repetition of ID clap-trap. Irreducibly complex objects do not have to appear all at once in order to be functional.

This is unlikely.

You seem to think your uninformed opinion has some persuasive value. It doesn't.

The NFL theorem is about search functions, not fitness functions.

Well, search algorithms, in the case of evolution, fitness functions.

Fitness functions are not search algorithms. Once again you are uncritically repeating ID clap-trap.

That would be "viewing the probability of a random arrangement after the fact" - which you just cautioned against for snowflakes, which you don't think are designed, but are content to do for proteins, which you want to show were designed.

No, before the fact, and if you were to show me a snowflake pattern, and then you were able to generate such a snowflake, I would attribute that to design, because that is so improbable to happen by natural processes.
...
But we're talking about the first proteins,

We clearly aren't talking about the first proteins, because
- no-one has previously mentioned "first proteins";
- you keep claiming you're discussing "protein production before the event occurred".

Either you're talking about the first proteins after the fact, or you're not talking about the first proteins, or (most likely) you're spewing random claims without bothering with such minor matters such as truth or consistency.

...which presumably had to be assembled randomly.

Your ignorance is not an argument.

[lee_merrill]

Correct that is how natural selection works in evolution.

So then an irreducibly complex structure must appear all at once.

So what is the evolutionary path to development of the flagellum?

Source: http://www.sci-news.com/biology/bacterial-flagellar-motors-05612.html

Biologists Trace Evolution of Bacterial Flagellar Motors

… This, together with DNA analysis, suggested that ancient motors may also have only had 12 stators.

“This clear separation between primitive and sophisticated species represents a ‘quantum leap’ in evolution,” the authors said.

“Our study reveals that the increase in motor power capacity is likely the result of existing structures fusing. This forms a structural scaffold to incorporate more stators, which combine to drive rotation with higher force.”

© Copyright Original Source

But varying the number of stators does not describe the evolution of the flagellum! And stators could conceivably vary within the framework of evolution, that aspect is not irreducibly complex.

No it does not as described and cited concerning your bogus misuse of probability and science.

Well it does, actually, this part should not be in dispute.

Blessings,
Lee

[lee_merrill]

So then the problem becomes that of generating a structure more complex than (say) a flagellum, and yet being functional.

No, the problem becomes your attempt to back-pedal and goalpost-shift rather than taking responsibility for your uncritical repetition of ID clap-trap. Irreducibly complex objects do not have to appear all at once in order to be functional.

Well, you need to tell me why scaffolding does not require generating a structure more complex than (say) a flagellum!

Fitness functions are not search algorithms.

Sure they are, in evolution. The fitness function defines possible search paths.

Either you're talking about the first proteins after the fact, or you're not talking about the first proteins, or (most likely) you're spewing random claims without bothering with such minor matters such as truth or consistency.

No, I'm talking about generating a given first protein viewing the event before the fact, as in the article shunyadragon posted.

Blessings,
Lee

[shunyadragon]

Well, you need to tell me why scaffolding does not require generating a structure more complex than (say) a flagellum!

The purpose of the evolution of the scaffolding of the flagellum. There was no need to evolve a more complex structure with a different purpose. The same is true for the eye. It evolved from the very simple to the complex eye through different pathways of evolution, but once the complex eye evolved to serve its purpose it evolved no further.

Sure they are, in evolution. The fitness function defines possible search paths.

Evolution defines the fitness paths as steps constrained by the laws of nature and natural processes.

No, I'm talking about generating a given first protein viewing the event before the fact, as in the article shunyadragon posted.

Blessings,
Lee

Misrepresentation of the reference. Please explain. The article you cite does not support your assertions. In fact it refutes them completely.

[shunyadragon]

So then an irreducibly complex structure must appear all at once.

No, that is a foolish assumption of Intelligent Design based on a religious agenda.

But varying the number of stators does not describe the evolution of the flagellum! And stators could conceivably vary within the framework of evolution, that aspect is not irreducibly complex.

Of course, over millions of years stators do likely vary within the framework of evolution, but those that are successfully adapted to to contribute to the survival of the organism, and therefore, the evolution of the flagellum as described by the scientific reference. Natural selection rules.

Well it does, actually, this part should not be in dispute.

Blessings,
Lee

As cited in the references the use of those in the Discovery Institute misuse, science, probability and statistics to justify their religious agenda.

[Roy]

Well, you need to tell me why scaffolding does not require generating a structure more complex than (say) a flagellum!

I don't need to do any such thing.

I only need to point out that irreducibly complex objects do not have to appear all at once in order to be functional, and that you are trying to avoid responsibility for uncritically posting ID clap-trap.

Sure they are, in evolution. The fitness function defines possible search paths.

That's meaningless drivel.

Either you're talking about the first proteins after the fact, or you're not talking about the first proteins, or (most likely) you're spewing random claims without bothering with such minor matters such as truth or consistency.

No, I'm talking about generating a given first protein viewing the event before the fact, as in the article shunyadragon posted.

Since that article
- doesn't say anything about the first proteins, only about current ones
- not only doesn't do what you're doing but describes your approach as a "fallacy" and a "misuse of probability"
you're spewing random claims without regard for truth or consistency.

[Roy]

So with irreducibly complex objects, they do have to appear all at once in order to be functional.

Building an arch using scaffolding is a well-known counter-example.

So then the problem becomes that of generating a structure more complex than (say) a flagellum, and yet being functional.

So then an irreducibly complex structure must appear all at once.

"I forget things almost instantly. It runs in my family… well, at least I think it does..."

Just keep swimming, Lee, just keep swimming.

[rogue06]

The evolution of the flagellum has been well understood for some time now and perhaps we can credit ID for that since they in effect issued a challenge when they claimed it was irreducibly complex.

Source: Stepwise formation of the bacterial flagellar system

Abstract

Elucidating the origins of complex biological structures has been one of the major challenges of evolutionary studies. The bacterial flagellum is a primary example of a complex apparatus whose origins and evolutionary history have proven difficult to reconstruct. The gene clusters encoding the components of the flagellum can include >50 genes, but these clusters vary greatly in their numbers and contents among bacterial phyla. To investigate how this diversity arose, we identified all homologs of all flagellar proteins encoded in the complete genome sequences of 41 flagellated species from 11 bacterial phyla. Based on the phylogenetic occurrence and histories of each of these proteins, we could distinguish an ancient core set of 24 structural genes that were present in the common ancestor to all Bacteria. Within a genome, many of these core genes show sequence similarity only to other flagellar core genes, indicating that they were derived from one another, and the relationships among these genes suggest the probable order in which the structural components of the bacterial flagellum arose. These results show that core components of the bacterial flagellum originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene.

Source

© Copyright Original Source

The full paper is available at the link above.

The flagellum evolved from the Type III Secretory System (a.k.a. TTSS or T3SS). Notice the similarities, especially in the base structure.

00000000000000ab0.0003.jpg

As Kenneth R. Miller put it in his The Flagellum Unspun

At first glance, the existence of the TTSS, a nasty little device that allows bacteria to inject these toxins through the cell membranes of its unsuspecting hosts, would seem to have little to do with the flagellum. However, molecular studies of proteins in the TTSS have revealed a surprising fact – the proteins of the TTSS are directly homologous to the proteins in the basal portion of the bacterial flagellum. As figure 2 (Heuck 1998) shows, these homologies extend to a cluster of closely-associated proteins found in both of these molecular "machines." On the basis of these homologies, McNab (McNab 1999) has argued that the flagellum itself should be regarded as a type III secretory system. Extending such studies with a detailed comparison of the proteins associated with both systems, Aizawa has seconded this suggestion, noting that the two systems "consist of homologous component proteins with common physico-chemical properties" (Aizawa 2001, 163). It is now clear, therefore, that a smaller subset of the full complement of proteins in the flagellum makes up the functional transmembrane portion of the TTSS.

IOW, one way to evolve a complex mechanism is to start with a less complex mechanism and observe how over time it evolves to become more complex.


Another good article I'd recommend reading is Evolution myths: The bacterial flagellum is irreducibly complex.

Hope this helps.

[rogue06]

But we do validly infer design, with the process that Dembski outlines, this is not arguing from ignorance, it is based on knowledge of design.

Source: NFL page

Dembski's argument suffers from the same fundamental flaw as Behe's: he fails to allow for changes in the function of a biological system as it evolves.

© Copyright Original Source

But that is considered in the argument of irreducible complexity, the object of interest is non-functional if one part is removed.

Behe argued that bacterial flagellum was irreducible complexity (IC), because he claimed that eliminating one part causes the mechanism to fail. Since that assertion scientists have produced several examples of a bacteria with an operational flagellum that had less parts than Behe’s example.

Further, while Behe may be correct concerning IC not being able to evolve by a direct route, the fact is that it can most certainly evolve by indirect routes.

Are you aware of Behe's paper from 2004, Simulating evolution by gene duplication of protein features that require multiple amino acid residues where Behe and David Snoke calculated the chances of simple IC systems evolving in small populations of bacteria? Behe's own figures showed that such simple IC systems can evolve in about 20,000 years. This was Behe's attempt to determine just how unlikely it is for IC systems to evolve and he discovered that is wasn't all that difficult.

[TheLurch]

Further, while Behe may be correct concerning IC not being able to evolve by a direct route, the fact is that it can most certainly evolve by indirect routes.

The thing is, Behe's argument isn't data driven; it's fundamentally a logic-based argument. If a system is irreducibly complex, then it cannot possibly have evolved. As such, it can be taken apart simply using logic: show a means for an irreducibly complex system to evolve, and the argument becomes invalid - you don't even need data.

This has been done - the two examples i know of are use of a scaffolding protein to build a large complex, followed by its loss, and the duplication and diversification of a single gene that forms a polymeric complex. Yet people are still treating irreducible complexity as if it's meaningful in some way.

The data's nice, since it tells us something about the biology of these complex systems. But it's not needed to know that the whole argument should have been over long ago.

[lee_merrill]

The evolution of the flagellum has been well understood for some time now and perhaps we can credit ID for that since they in effect issued a challenge when they claimed it was irreducibly complex.

Source: Stepwise formation of the bacterial flagellar system

Abstract

Elucidating the origins of complex biological structures has been one of the major challenges of evolutionary studies. The bacterial flagellum is a primary example of a complex apparatus whose origins and evolutionary history have proven difficult to reconstruct. The gene clusters encoding the components of the flagellum can include >50 genes, but these clusters vary greatly in their numbers and contents among bacterial phyla. To investigate how this diversity arose, we identified all homologs of all flagellar proteins encoded in the complete genome sequences of 41 flagellated species from 11 bacterial phyla. Based on the phylogenetic occurrence and histories of each of these proteins, we could distinguish an ancient core set of 24 structural genes that were present in the common ancestor to all Bacteria. Within a genome, many of these core genes show sequence similarity only to other flagellar core genes, indicating that they were derived from one another, and the relationships among these genes suggest the probable order in which the structural components of the bacterial flagellum arose. These results show that core components of the bacterial flagellum originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene.

Source

© Copyright Original Source

The full paper is available at the link above.

Well, their conclusion is in some dispute, even in evolutionary circles.

The flagellum evolved from the Type III Secretory System (a.k.a. TTSS or T3SS). Notice the similarities, especially in the base structure.

Now I wonder why Liu and Ochman above didn't make this point. And a homologous structure does not demonstrate how one might change into the other, through selectable steps.

Blessings,
Lee

[lee_merrill]

Behe argued that bacterial flagellum was irreducible complexity (IC), because he claimed that eliminating one part causes the mechanism to fail. Since that assertion scientists have produced several examples of a bacteria with an operational flagellum that had less parts than Behe’s example.

Further, while Behe may be correct concerning IC not being able to evolve by a direct route, the fact is that it can most certainly evolve by indirect routes.

Are you aware of Behe's paper from 2004, Simulating evolution by gene duplication of protein features that require multiple amino acid residues where Behe and David Snoke calculated the chances of simple IC systems evolving in small populations of bacteria? Behe's own figures showed that such simple IC systems can evolve in about 20,000 years. This was Behe's attempt to determine just how unlikely it is for IC systems to evolve and he discovered that is wasn't all that difficult.

Well, as far as I understand this, the systems were for evolution of multiple amino acid residues, which would be the simplest IC systems. More complicated IC systems would then require (exponentially?) more time.

Blessings,
Lee