On irreducible complexity - Otangelo ("Rationalist") is clueless on the Falsification Principle

[Nesslig20]

So yeah, recently Otangelo had conversations with Dan (Creation myths) and Dapper Dino (and after show) on Irreducible complexity and how to scientifically test it. Not surprisingly, he is completely off the mark on nearly everything.

And explaining why this is the case to Otangelo often goes like this


He doesn't know how to test scientific hypothesis by falsification, he doesn't understand basic logic to recognize why defining Irreducible complexity to mean "cannot evolve" is problematic to the argument.

Well, here is the explanation to him, in power point slide format, so hopefully it will help. I don't think it does to Otangelo, but at least it can provide a reference for others to say "HERE is where you went wrong again".






See MORE on the Vpu protein, watch Dan's (Creation Myths) presentation.

 

[Desertphile]

The cultists who claim ID-IC applies to reality have yet to try disproving themselves and their occult superstitions--- even though it is their duty to present avidence for their claims as well as evidence against their claims: they do neither.

 

[rationalist]

I just saw this post today.

HIV comes from SIV. Some forms of SIV also has a VPU protein that counteracts tetherin. So this isn't the evolution of a new function. It's regaining an existing function. Although it regained the function through a different mutational pathway.
"Vpu protein of SIVgsn [SIV in Greater Spot-nosed Monkeys] has been shown to counteract greater spot-nosed monkey tetherin."[2]
For more info, see the VPU section of my HIV evolution article.[1]

1. http://bereanarchive.org/articles/biology/hiv-evolution#vpu
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935100/


I will come with a more throughout reply later.

 

[rationalist]

Claim: The VPu protein has evolved a novel function
Vpu tetherin antagonism:
https://jvi.asm.org/content/91/6/e02177-16#:~:text=To promote virus release from,region adjacent to this deletion.

Reply: HIV comes from SIV. Some forms of SIV also has a VPU protein that counteracts tetherin. So this isn't the evolution of a new function. It's regaining an existing function. Although it regained the function through a different mutational pathway.
"Vpu protein of SIVgsn [SIV in Greater Spot-nosed Monkeys] has been shown to counteract greater spot-nosed monkey tetherin."[2]
For more info, see the VPU section of my HIV evolution article.[1]

1. http://bereanarchive.org/articles/biology/hiv-evolution#vpu
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935100/

Dr.Dan Cardinale: It’s 100% a new function. The hiv-1 group m together in antagonism is via a completely new mechanism. All the siv forms of the tetherin antagonism, via NEF or VPU, involve targeting the intracellular domain of tetherin, and human tetherin is missing most of this domain, so none of those mechanisms work. It’s completely new. I'll also note that this is a good example of "you need to read the whole paper". They've done the experimental work on this. SIV VPU *that antagonizes tetherin in other apes* fails in humans, because our tetherin is shorter. Also, HIV-1 group M evolved from SIV-cpz, not SIV-gsn.

Reply: The scientists use language indicating it got back its function rather than acquired a new function:
"the vpu gene did not diverge to the extent that the activity could not be RESCUED."
"When SIVcpz crossed the species barrier to infect humans... Vpu subsequently REGAINED its tetherin-antagonizing function."
If you want to call it a new function, ok. It all depends on how different something has to be before you call it "new." In the article
http://bereanarchive.org/articles/biology/hiv-evolution#vpu
it can be seen in the diagram that shows what changed, and a description below that about the three amino acids that changed for the anti-tetherin function.
If you take an irreducibly complex mousetrap and replace the metal hammer with a metal spike, does that disprove irreducible complexity?

Dr.Dan Cardinale: Look, this is cut and dry. I’m right about this and I’m not gonna waste more time pretending there’s a debate here. You can either do your homework and see that I’m right, or read just enough to tell yourself I’m wrong. If you want to be taken seriously, pick a better hill to die on.

Claim: https://onlinelibrary.wiley.com/doi/abs/10.1002/jmor.11011
Reply: In this paper they found a lizard that uses placenta, and assumed it evolved. There was no evolution observed. This is evidence against Darwin's tree of life because only eutherian mammals should have placenta.

So IC has not bee falsified yet.

 

[rationalist]

Claim:


Reply: There are basically just two worldviews

(a) time, chance, and the natural properties of matter; or
(b) design, creation, and the undeniable properties of organization and mind.

There are following possible causing agents of origins and the universe as a whole:

There are 4 possibilities we are faced with regarding the beginning of the universe:

1. The universe is an illusion and none of this exists
2. The universe is "self-created"
3. The universe is "self-existent/eternal"
4. The universe was created by someone who is "self-existent/eternal"

1. The universe and the physical laws: an intelligent creator, or random unguided natural events
2. The fine-tuning of the universe and the origin of life: an intelligent creator, random natural events, and physical necessity


The origin of life can be explained by just TWO possible mechanisms:

The origin of life
Either life emerged by a fortuitous accident, spontaneously through self-organization by unguided stochastic coincidence, natural events that turned into self-organization in an orderly manner without external direction, chemical non-biological, purely physico-dynamic kinetic processes and reactions influenced by environmental parameters, or through the direct intervention, creative force and activity of an intelligent cognitive agency, a powerful creator.

Biodiversity:
above three, and evolution


Claim: you are OBVIOUSLY making a false dichotomy - that is, you are considering ONLY TWO options - namely, random chance, or a god. Have you considered that there may be OTHER explanations?
Reply: Extraordinary claims require extraordinary evidence. If the claim is that other worldviews exist, the claimer must be able to back up the claim, otherwise, it can be dismissed without evidence.

Claim: Argument from incredulity
Reply: "Incredulous" basically means "I don't believe it". Well, why should someone believe a "just so" story about HOW reality came to exist? That is the THING that we are incredulous about - a *certain scenario* ( naturalism, cosmological, chemical, and biological evolution, abiogenesis, and Neo-Darwinism, and that irreducibly complex biological system, coded, instructed or specified complex information, and entire factory complexes composed of myriads of interconnected factories, full of computers and robotic production lines could emerge naturally ) that's only *imagined* about how various amazing abilities of animals and plants happened all by themselves, defying known and reasonable principles of the limited range of chance, physical necessity, mutations, and Natural selection. There are busy little molecular machines that let it untangle, replicate, and build according to plan. A large cadre of researchers continues to make new discoveries on a regular basis. Our mythology is that it explains life, but the system is far, far too complex to occur by accident, and requires that features to support many processes are required, making a path for its evolution very hard to surmise. DNA isn't the secret to life. It's a whole bunch of puzzles we don't have answers for. The proponent of naturalism is "incredulous" that an intelligent creator/designer could exist, beyond and behind our entire space-time continuum, who is our Creator. But there is nothing ridiculous about that - especially if you can't personally examine reality to that depth - how do you know nature is all that exists? What IS ridiculous (IMO) is trying to imagine a *naturalistic origin* of these things. What we need, is giving a *plausible* account of how it came about to be in the first place, and the " No-God hypothesis" simply doesn't cut the cake.



Claim: Once IC has been falsified with one example, one can use inductive reasoning and generalize, and the hypothesis has to be modified.
Reply: I cane see your point. In the meantime, I do not acknowledge that IC has been falsified.



Claim: If ONE system claimed to be IC has been observed to evolve, then the hypothesis has been falsified.
Reply: Ok. I will agree with that point.



Claim: The VPu protein has evolved a novel function
Vpu tetherin antagonism:
https://jvi.asm.org/content/91/6/e02177-16#:~:text=To promote virus release from,region adjacent to this deletion.

Reply: HIV comes from SIV. Some forms of SIV also has a VPU protein that counteracts tetherin. So this isn't the evolution of a new function. It's regaining an existing function. Although it regained the function through a different mutational pathway.
"Vpu protein of SIVgsn [SIV in Greater Spot-nosed Monkeys] has been shown to counteract greater spot-nosed monkey tetherin."[2]
For more info, see the VPU section of my HIV evolution article.[1]

1. http://bereanarchive.org/articles/biology/hiv-evolution#vpu
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935100/

Dr.Dan Cardinale: It’s 100% a new function. The hiv-1 group m together in antagonism is via a completely new mechanism. All the siv forms of the tetherin antagonism, via NEF or VPU, involve targeting the intracellular domain of tetherin, and human tetherin is missing most of this domain, so none of those mechanisms work. It’s completely new. I'll also note that this is a good example of "you need to read the whole paper". They've done the experimental work on this. SIV VPU *that antagonizes tetherin in other apes* fails in humans, because our tetherin is shorter. Also, HIV-1 group M evolved from SIV-cpz, not SIV-gsn.

Reply: The scientists use language indicating it got back its function rather than acquired a new function:
"the vpu gene did not diverge to the extent that the activity could not be RESCUED."
"When SIVcpz crossed the species barrier to infect humans... Vpu subsequently REGAINED its tetherin-antagonizing function."
If you want to call it a new function, ok. It all depends on how different something has to be before you call it "new." In the article
http://bereanarchive.org/articles/biology/hiv-evolution#vpu
it can be seen in the diagram that shows what changed, and a description below that about the three amino acids that changed for the anti-tetherin function.
If you take an irreducibly complex mousetrap and replace the metal hammer with a metal spike, does that disprove irreducible complexity?

Dr.Dan Cardinale: Look, this is cut and dry. I’m right about this and I’m not gonna waste more time pretending there’s a debate here. You can either do your homework and see that I’m right, or read just enough to tell yourself I’m wrong. If you want to be taken seriously, pick a better hill to die on.

Claim: https://onlinelibrary.wiley.com/doi/abs/10.1002/jmor.11011
Reply: In this paper they found a lizard that uses placenta, and assumed it evolved. There was no evolution observed. This is evidence against Darwin's tree of life because only eutherian mammals should have placenta.



Claim: If we move the goalpost to A, B, C, etc. the claim becomes unfalsifiable.
Reply: Agreed. But permit me the Tu Quoque here.

Falsification of evolution is impossible

https://******************************/t1713-the-theory-of-evolution-cannot-be-falsified

The great problem with evolution theory, as many writers have pointed out, is that it cannot be falsified. Nothing can falsify it, and that makes it an article of faith. It also puts it on a par with faith in God. Now that I regard as serious.

I say that it cannot be falsified for the following reasons:

1 If it has been seen to occur (it never has, as far as I know) that's proof of evolution(see, it happened!)
2 If it has not been seen to occur, that's proof too. (Never mind, we know it did, pat pat).
3 If it can account for the origin of anything, that's proof. (see, that's proof!)
4 If it can't, then that's proof too. (Ah the evidence hasn't emerged as yet).

It simply cannot be falsified and therefore it is not a scientific theory. Popper says so.

One patronising criticism one hears is 'that's found on a creationist site' as if that invalidates a fact! If one were to say, it's found on talkorigins, and is therefore invalidated, then who knows what wrath will descend? There's a double standard here.

 

[Sparhafoc]

When you 'reply' to what a scientist said, but you're not actually replying to them, just writing some words they'll never see - it is functionally equivalent to going and shaking your fists at the clouds because you don't like the rain.

And I do like your circular reasoning statement that accidentally acknowledges the paucity of Creationist argumentation. If a system was not irreducibly complex to begin with, then ID got it wrong by claiming it was. Of course, ID proponents never actually do the work to establish whether their claims are falsifiable, they merely declare things couldn't have evolved because of their incredulity. As usual with religious claims attempting to project their beliefs into the universe, when shown wrong, they simply shuffle along to the next claim. ID exists only in ignorance.

 

[rationalist]

When you 'reply' to what a scientist said, but you're not actually replying to them, just writing some words they'll never see - it is functionally equivalent to going and shaking your fists at the clouds because you don't like the rain.

And I do like your circular reasoning statement that accidentally acknowledges the paucity of Creationist argumentation. If a system was not irreducibly complex to begin with, then ID got it wrong by claiming it was. Of course, ID proponents never actually do the work to establish whether their claims are falsifiable, they merely declare things couldn't have evolved because of their incredulity. As usual with religious claims attempting to project their beliefs into the universe, when shown wrong, they simply shuffle along to the next claim. ID exists only in ignorance.

Natural selection preserves or "selects" functional advantages. If a random mutation helps an organism survive, it can be preserved and passed on to the next generation. Yet, the flagellar motor has no function until after all of its 30 parts have been assembled. The 29 and 28-part versions of this motor do not work. Thus, natural selection can "select" or preserve the motor once it has arisen as a functioning whole, but it can do nothing to help build the motor in the first place. 1

Knockout experiments and tests provide empirical evidence that the flagellum is irreducibly complex, as Scott Minnich testified at the Dover process:

Kitzmiller Transcript of Testimony of Scott Minnich pgs. 99-108, Nov. 3, 2005, emphasis added

We have a mutation in a drive shaft protein or the U joint, and they can't swim. Now, to confirm that that's the only part that we've affected, you know, is that we can identify this mutation, clone the gene from the wild-type and reintroduce it by the mechanism of genetic complementation. So this is, these cells up here are derived from this mutant where we have complemented with a good copy of the gene. One mutation, one part knock out, it can't swim. Put that single gene back in we restore motility. Same thing over here. We put, knock out one part, put a good copy of the gene back in, and they can swim. By definition, the system is irreducibly complex. We've done that with all 35 components of the flagellum, and we get the same effect.
(Kitzmiller Transcript of Testimony of Scott Minnich pgs. 99-108, Nov. 3, 2005, emphasis added)

ABOUT INCREDULITY.
"Incredulous" basically means "I don't believe it". Well, why should someone believe a "just so" story about HOW reality came to exist? That is the THING that we are incredulous about - a *certain scenario* ( naturalism, cosmological, chemical, and biological evolution, abiogenesis, and Neo-Darwinism, and that irreducibly complex biological system, coded, instructed or specified complex information, and entire factory complexes composed of myriads of interconnected factories, full of computers and robotic production lines could emerge naturally ) that's only *imagined* about how various amazing abilities of animals and plants happened all by themselves, defying known and reasonable principles of the limited range of chance, physical necessity, mutations, and Natural selection. There are busy little molecular machines that let it untangle, replicate, and build according to plan. A large cadre of researchers continues to make new discoveries on a regular basis. Our mythology is that it explains life, but the system is far, far too complex to occur by accident, and requires that features to support many processes are required, making a path for its evolution very hard to surmise. DNA isn't the secret to life. It's a whole bunch of puzzles we don't have answers for. The proponent of naturalism is "incredulous" that an intelligent creator/designer could exist, beyond and behind our entire space-time continuum, who is our Creator. But there is nothing ridiculous about that - especially if you can't personally examine reality to that depth - how do you know nature is all that exists? What IS ridiculous (IMO) is trying to imagine a *naturalistic origin* of these things. What we need, is giving a *plausible* account of how it came about to be in the first place, and the " No-God hypothesis" simply doesn't cut the cake.

As usual with religious claims:

Ahm, no. Intelligent design is NOT a religious claim, as you very well know. It does not resort to particular God(s). Its claim is restricted to say that intelligent agents are a better, more plausible explanation for the biocomplexity seen in nature. No more.

when shown wrong, they simply shuffle along to the next claim. ID exists only in ignorance.

ID has not shown to be wrong in the first place. A prime example we have just here and now. The two examples are given by Dan Cardinale and Dapper Dino do NOT refute the IC claim, despite their loud vocalization during my debate with them. As I expected, once given a closer look at their claims, they fall down like a card house. Dan Cardinale replies after I refuted his claims was precious.....you would not have been snarkier. LOL.

You take your mouth full. Full with confidence, where there is no reason to be so. Abiogenesis is a FAILED hypothesis. So is the endosymbiosis claim. The origin of eukaryotes is an enigma. So is the origin of the genetic code, information directing the making of cell factories, computers, circuits, energy turbines, energy plants etc. We only know of intelligence being able to make such things with specific functions. Random non-intelligent mechanisms have NEVER been shown even in principle to bring forward these things.

I am a fully intellectually satisfied theist. The cognitive dissonance is all yours. Even if you don't admit it.

 

[Sparhafoc]

Ahm, no. Intelligent design is NOT a religious claim, as you very well know

I'll come back to deal with the rest of your outrageous bullshit tomorrow, but I have to point and laugh at this. Everyone knows it's entirely religious - it's just Creationism repackaged, the wedge strategy, cdesign proponentsists (sic), with the preponderance of its proponents associated with the Discovery Institute, a Christian propaganda outlet who have spent millions of dollars on risible attempts to undermine science as if that would then make their antiquated beliefs true... and even you - good little propaganda warrior that you are...

Life depends on matter, energy, and information

Have you got anything in your rhetorical arsenal aside from quote-mining and Gish Gallops? Paradoxes in the origin of life. 2015 Jan 22 Benner SA1. http://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/25608919 Steve Benner is the founder and president of the Westheimer Corporation, a private...

leagueofreason.org.uk

In a thread where you pretend to be interested in science, where you pretend that evidence points towards design, you then not only leap to provide a religious argument when challenged to discuss evidence, but you go a step further and show that it's not just religious, and it's not just about theism, but it's also expressly about your Christian belief.

You can cut the bullshit as not one person here is going to be fooled by any blathering that the entire motivation of I.D. is religious.

I am a fully intellectually satisfied theist.

And if I had a thimble-sized stomach, I could be fully sated by an ounce of water.

 

[rationalist]

I'll come back to deal with the rest of your outrageous bullshit tomorrow, but I have to point and laugh at this. Everyone knows it's entirely religious - it's just Creationism repackaged, the wedge strategy, cdesign proponentsists (sic), with the preponderance of its proponents associated with the Discovery Institute, a Christian propaganda outlet who have spent millions of dollars on risible attempts to undermine science as if that would then make their antiquated beliefs true... and even you - good little propaganda warrior that you are...

Life depends on matter, energy, and information

Have you got anything in your rhetorical arsenal aside from quote-mining and Gish Gallops? Paradoxes in the origin of life. 2015 Jan 22 Benner SA1. http://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/25608919 Steve Benner is the founder and president of the Westheimer Corporation, a private...

leagueofreason.org.uk

In a thread where you pretend to be interested in science, where you pretend that evidence points towards design, you then not only leap to provide a religious argument when challenged to discuss evidence, but you go a step further and show that it's not just religious, and it's not just about theism, but it's also expressly about your Christian belief.

You can cut the bullshit as not one person here is going to be fooled by any blathering that the entire motivation of I.D. is religious.




And if I had a thimble-sized stomach, I could be fully sated by an ounce of water.

I make a clear distinction between intelligent design and my personal religious beliefs. if you can't grasp this, it is your problem. Attempting to refute my views based on strawman arguments is the ultimate sign of defeat.

 

[Sparhafoc]

Flagellum, Collapse of Irreducible Complexity

Ken Miller, a cellular Biologist and a Christian, summarizes the destruction of I.D.'s appeals to incredulity with respect to the bacterial flagellum.

Not religious, my dangly bits.

 

[Sparhafoc]

I make a clear distinction between intelligent design and my personal religious beliefs. if you can't grasp this, it is your problem. Attempting to refute my views based on strawman arguments is the ultimate sign of defeat.

Caught with your pants down tugging furiously. Everyone can see the context of that thread - you pretended to be talking about science, you contended that design was a necessary inference from the evidence, then you leapt into full on Aquinas Christian Apologetics mode.

Lie all you like, chap. It doesn't harm my case at all.

 

[Sparhafoc]

An IC system cannot evolve by definition, so if evidence shows that a previously asserted IC system did evolve, then Creationists will prevaricate and perform, lie and spout bullshit... then pretend they never claimed it was IC... well it couldn't have been, because IC systems cannot evolve by definition, amirite?

I'll have my cake AND I'll eat it thank you very much.

 

[Nesslig20]

Claim: If we move the goalpost to A, B, C, etc. the claim becomes unfalsifiable.
Reply: Agreed. But permit me the Tu Quoque here.

 

[rationalist]

View attachment 180

ROFL....

Ok. Just one example falsified is fine with me and I grant that the concept and hypothesis of IC would have to be reformulated . Those two showed by Dan Cardinale and Dapper Dino did not cut the cake.

An irreducibly complex system is characterized by five points:
1. a single system composed of several well-matched, interacting parts
2. that contribute to the basic function
3. the removal of any one of the parts causes the system to effectively cease functioning
4. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system
5. any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.

To No.3
The principle of evolutionary continuity, succinctly formulated by Albert Lehninger in his Biochemistry textbook. An adaptation that does not increase the fitness is no longer selected for and eventually gets lost in the evolution (in the current view, only those adaptations that effectively decrease the fitness end up getting lost). Hence, any evolutionary scenario has to invoke – at each and every step – only such intermediate states that are functionally useful (or at least not harmful).
https://onlinelibrary.wiley.com/doi/abs/10.1002/cbdv.200790167

 

[rationalist]

Flagellum, Collapse of Irreducible Complexity

Ken Miller, a cellular Biologist and a Christian, summarizes the destruction of I.D.'s appeals to incredulity with respect to the bacterial flagellum.

Not religious, my dangly bits.

Maybe you should ask Ken Miller, why he did stop to reply to me at his Facebook timeline, when i challenged him not only on the Flagellum, but also on the locomotion mechanism of the Mycoplasma mobile....

The extraordinary cellular propulsion system of Mycoplasma mobile - faster than Usain Bolt



https://***************************...m-of-mycoplasma-mobile-faster-than-usain-bolt

 

[rationalist]

Caught with your pants down tugging furiously. Everyone can see the context of that thread - you pretended to be talking about science, you contended that design was a necessary inference from the evidence, then you leapt into full on Aquinas Christian Apologetics mode.

Lie all you like, chap. It doesn't harm my case at all.

Yes, you got me...... i did not make the distinction in that case. My fault. Acknowledged.
But that does not mean that the framework of the ID hypothesis is not to draw a line. It does, and any inference to the nature of the designer is prohibited.

Once, a step further is done, it does not belong anymore to ID, but theology, religion, and philosophy.

 

[Nesslig20]

Claim: The VPu protein has evolved a novel function
Vpu tetherin antagonism:
https://jvi.asm.org/content/91/6/e02177-16#:~:text=To promote virus release from,region adjacent to this deletion.

Reply: HIV comes from SIV. Some forms of SIV also has a VPU protein that counteracts tetherin.
So this isn't the evolution of a new function. It's regaining an existing function. Although it regained the function through a different mutational pathway.
"Vpu protein of SIVgsn [SIV in Greater Spot-nosed Monkeys] has been shown to counteract greater spot-nosed monkey tetherin."[2]
For more info, see the VPU section of my HIV evolution article.[1]
1. http://bereanarchive.org/articles/biology/hiv-evolution#vpu
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935100/

As Dr. Dan pointed out in your quote, the Vpu protein in some SIVs can only antagonize tetherin of non-human primates by interacting with certain domains that are missing in the human version of tetherin. Hence, the Vpu protein of HIV-1 group M antagonizes human tetherin in a specific way, completely different to how SIV Vpu/Nef proteins antagonise tetherin in non-human primates. Not only that, the Vpu's of SIV strains from which HIV-1 goup M evolved do not antagonize tetherin. Their Vpu's only antagonise CD4, and use the other protein (Nef) to antagonise non-human primate tetherin instead. And, again, these Nef also cannot antagonize human tetherin.

So, it is a fact that the function of *HIV-1 group M* Vpu to antagonize *HUMAN* tetherin is completely novel.

Dr.Dan Cardinale: It’s 100% a new function. The hiv-1 group m together in antagonism is via a completely new mechanism. All the siv forms of the tetherin antagonism, via NEF or VPU, involve targeting the intracellular domain of tetherin, and human tetherin is missing most of this domain, so none of those mechanisms work. It’s completely new. I'll also note that this is a good example of "you need to read the whole paper". They've done the experimental work on this. SIV VPU *that antagonizes tetherin in other apes* fails in humans, because our tetherin is shorter. Also, HIV-1 group M evolved from SIV-cpz, not SIV-gsn.

Reply: The scientists use language indicating it got back its function rather than acquired a new function:
"the vpu gene did not diverge to the extent that the activity could not be RESCUED."
"When SIVcpz crossed the species barrier to infect humans... Vpu subsequently REGAINED its tetherin-antagonizing function."

Full quote from the paper:

Since SIVcpz uses the Nef protein to counteract tetherin, it is surprising that HIV-1 uses Vpu. However, human tetherin has diverged from the chimpanzee protein, most notably owing to a deletion of a pentamer within the CT. As a consequence, the SIVcpz Nef protein is not active against human tetherin (Sauter et al. 2009). Clearly, this would have placed strong selection pressure on HIV-1, and this has resulted in the reacquisition of an anti-tetherin activity by Vpu. Perhaps the surprising aspect of this is that, while the Vpu protein of SIVcpz was not being constrained to retain anti-tetherin activity, nevertheless the vpu gene did not diverge to the extent that the activity could not be rescued.

It is clear that they don't say that "it got back its function" with "it" being the Vpu protein. What they meant is that the virus managed to regain the ability to antagonize tetherin, although in a different host and using a different protein instead.

This doesn't disagree with what I nor Dan are saying.
We aren't saying that tetherin antagonism (in general, in any host species) by SIV/HIV viruses (using any protein) is novel.
We ARE saying that the function the HIV-1 group M Vpu protein to antagonize human tetherin is novel, particularly in the specific way this Vpu interacts with tetherin in humans. That is what we are referring to as novel.

Also, the second quote:

Interestingly, Vpu does not seem to have impacted on tetherin evolution in Old World monkeys or hominids, but this might be due to the short period of time since the gain-of-function evolution in Vpu (Lim et al. 2010).

HIV-1 was originated by cross-species transmission of SIV from chimpanzees to humans (Gao et al. 1999). SIVcpz is considered to have evolved from a recombination of two SIV strains, SIVgsn and SIVrcm. SIVgsn but not SIVrcm encodes Vpu (Courgnaud et al. 2002, 2003; Dazza et al. 2005). SIVcpz obtained Vpu from SIVgsn and Nef from SIVrcm. It is speculated that, in the original SIVcpz, Vpu and Nef proteins had only little antitetherin capacity (Sauter et al. 2009; Yang et al. 2010b). Over time, SIVcpz Nef evolved to become the primary tetherin antagonist, while Vpu maintained the capacity to downmodulate CD4 from the cell surface (Sauter et al. 2009; Yang et al. 2010b). When SIVcpz crossed the species barrier to infect humans, Nef was unable to antagonize human tetherin due to the lack of the Nef-sensitive 14DDIWK18 site. Vpu subsequently (re)gained its tetherin-antagonizing function (Sauter et al. 2009; Zhang et al. 2009; Lim et al. 2010). However, only the Vpu of pandemic HIV-1 group M efficiently antagonizes human tetherin whereas Vpu of group N and O is a poor tetherin antagonist (Sauter et al. 2009). This suggests that the extent of Vpu adaptation to antagonize human tetherin influences the pathogenicity of HIV-1.

Similar to the previous quote, it does not go against what we are saying about the interaction between human tetherin and HIV-1 group M Vpu.

Also Note: Earlier in the paper where it described the tetherin antagonism of Vpu in humans as a "gain-of-function", but more importantly, how the original article writes "(re)gained". See the brackets ( ) ? I looked even at the secondary source from which you copy pasted this quoted that contained the text break denoted by the triple dots (...), even that also wrote "(re)gained".

Since this cannot be attributed to innocent misunderstanding, I can only come to conclusion that you have intentionally and deliberately removed the brackets in order to twist the words from the paper as much as you can to make it align with your narrative. This does not make you look good Otangelo. This is severely dishonest. In fact, this is so dishonest, I am even beginning to wonder wether this counts a as a violation of the rules on this forum, but I am not moderator of this forum. Although, if I were one, I wouldn't let this fly Otangelo. This is outright despicable. Shame on you.

If you want to call it a new function, ok. It all depends on how different something has to be before you call it "new." In the article
http://bereanarchive.org/articles/biology/hiv-evolution#vpu
it can be seen in the diagram that shows what changed, and a description below that about the three amino acids that changed for the anti-tetherin function.
If you take an irreducibly complex mousetrap and replace the metal hammer with a metal spike, does that disprove irreducible complexity?

I call something "new" if it wasn't present before. Here, this something is the specific way the Vpu protein of HIV-1 group M interacts with human tetherin, which is dependent on the residues (amino acids) that you mentioned. That is new. The mousetrap question is not analogous at all to this situation.

So IC has not bee falsified yet.

What is maddening about this first comment is that this debacle has NOTHING to do with the IC argument. I could, for the sake of argument, say that this particular interaction was REGAINED. Let's say that the old Vpu did had this interaction, but that the interaction was lost and later evolved again. It wouldn't change the fact that this interaction is irreducibly complex, according to Behe's defintion, and that this interaction evolved from a state where it didnt exist. Whether or not this interaction did exist even further back, or whether or not the same funciton was previously performed by a different protein in a different way such that the general function itself may not be "novel", is utterly irrelevant to this point. Not only have you been wrong, missing the point of what we are saying, and dishonest - all you have been doing is waving around a red herring.

Reply: There are basically just two worldviews
(a) time, chance, and the natural properties of matter; or
(b) design, creation, and the undeniable properties of organization and mind.

[skipped some rambling about the origin of the universe, since it was incoherent and irrelevant to the topic]

The origin of life can be explained by just TWO possible mechanisms:

Claim: you are OBVIOUSLY making a false dichotomy - that is, you are considering ONLY TWO options - namely, random chance, or a god. Have you considered that there may be OTHER explanations?
Reply: Extraordinary claims require extraordinary evidence. If the claim is that other worldviews exist, the claimer must be able to back up the claim, otherwise, it can be dismissed without evidence.

What you are doing here is shifting the burden of proof. I am not claiming there are other world views. I am pointing out that YOUR dichotomy relies on the unsupported claim that no other options exists. Hence, it is NOT up to me to show there are other options (although it wouldn't be difficult to imagine several), it is up to YOU to demonstrate your claim that there are none.

Claim: Argument from incredulity
Reply: "Incredulous" basically means "I don't believe it". Well, why should someone believe a "just so" story about HOW reality came to exist? That is the THING that we are incredulous about - a *certain scenario* ( naturalism, cosmological, chemical, and biological evolution, abiogenesis, and Neo-Darwinism, and that irreducibly complex biological system, coded, instructed or specified complex information, and entire factory complexes composed of myriads of interconnected factories, full of computers and robotic production lines could emerge naturally ) that's only *imagined* about how various amazing abilities of animals and plants happened all by themselves, defying known and reasonable principles of the limited range of chance, physical necessity, mutations, and Natural selection. There are busy little molecular machines that let it untangle, replicate, and build according to plan. A large cadre of researchers continues to make new discoveries on a regular basis. Our mythology is that it explains life, but the system is far, far too complex to occur by accident, and requires that features to support many processes are required, making a path for its evolution very hard to surmise. DNA isn't the secret to life. It's a whole bunch of puzzles we don't have answers for. The proponent of naturalism is "incredulous" that an intelligent creator/designer could exist, beyond and behind our entire space-time continuum, who is our Creator. But there is nothing ridiculous about that - especially if you can't personally examine reality to that depth - how do you know nature is all that exists? What IS ridiculous (IMO) is trying to imagine a *naturalistic origin* of these things. What we need, is giving a *plausible* account of how it came about to be in the first place, and the " No-God hypothesis" simply doesn't cut the cake.

Me pointing out your increduclity is NOT about you not accepting "darwinism". It was referrig to your incredulity about more options than you lay out in your dichotomy. The implicit assumption in that dichotomy is that, because you cant think of other options, there are none. Hence, the reply is just another instance of you missing the entire point. Not to mention that what you wrote in your reply is utter nonsense...but it is nonsense that is not relevant to what I was saying in my slides, so luckily I don't have to bother explain why it is nonsense.

Claim: Once IC has been falsified with one example, one can use inductive reasoning and generalize, and the hypothesis has to be modified.
Reply: I cane see your point. In the meantime, I do not acknowledge that IC has been falsified.

To modify the claim: Behe's hypothes is that if something is IC it cannot evolve, thus IC systems pose a problem to evolution. If you can show one example of an IC system that did evolve, it shows that IC is NOT a barrier to evoluton. Hence, IC system do not pose a problem for evolution.

You can modify the hypothesis all you like, but the problem is that many of your modifications makes it unfalsifiable, e.g. your redefinition of IC to mean "cannot evolve" by definition. You can also say that you do not acknowledge that IC has been falsified, but until you provide a falsifiable hypothesis, this statement is meaningless.

Claim: If ONE system claimed to be IC has been observed to evolve, then the hypothesis has been falsified.
Reply: Ok. I will agree with that point.

Again, I have to adjust the claim that I am actually saying: If one system that is IC (according to Behe's definition) has been observed to evolve, then the hypothesis that IC systems cannot evolve has been falsified.

Not just "claimed" to be IC, it is IC by the definition according to Behe.

Claim: If we move the goalpost to A, B, C, etc. the claim becomes unfalsifiable.
Reply: Agreed. But permit me the Tu Quoque here.

Aside from the previous meme, I was serious. NO, I won't permit it. It is a blatant dodge of the challenge. Even if I were to grant you that evolution is UNfalsifiable (which I certainly do not), it doesn't disprove the point I was making here.

You seem to have missed this slide, as you didn't make any comments on this. Do you understand now that to redefine IC to mean "cannot evolve" would be problematic?

 

[rationalist]

As Dr. Dan pointed out in your quote, the Vpu protein in some SIVs can only antagonize tetherin of non-human primates by interacting with certain domains that are missing in the human version of tetherin. Hence, the Vpu protein of HIV-1 group M antagonizes human tetherin in a specific way, completely different to how SIV Vpu/Nef proteins antagonise tetherin in non-human primates. Not only that, the Vpu's of SIV strains from which HIV-1 goup M evolved do not antagonize tetherin. Their Vpu's only antagonise CD4, and use the other protein (Nef) to antagonise non-human primate tetherin instead. And, again, these Nef also cannot antagonize human tetherin.

So, it is a fact that the function of *HIV-1 group M* Vpu to antagonize *HUMAN* tetherin is completely novel.


Full quote from the paper:

It is clear that they don't say that "it got back its function" with "it" being the Vpu protein. What they meant is that the virus managed to regain the ability to antagonize tetherin, although in a different host and using a different protein instead.

This doesn't disagree with what I nor Dan are saying.
We aren't saying that tetherin antagonism (in general, in any host species) by SIV/HIV viruses (using any protein) is novel.
We ARE saying that the function the HIV-1 group M Vpu protein to antagonize human tetherin is novel, particularly in the specific way this Vpu interacts with tetherin in humans. That is what we are referring to as novel.

Also, the second quote:

Similar to the previous quote, it does not go against what we are saying about the interaction between human tetherin and HIV-1 group M Vpu.

Also Note: Earlier in the paper where it described the tetherin antagonism of Vpu in humans as a "gain-of-function", but more importantly, how the original article writes "(re)gained". See the brackets ( ) ? I looked even at the secondary source from which you copy pasted this quoted that contained the text break denoted by the triple dots (...), even that also wrote "(re)gained".

Since this cannot be attributed to innocent misunderstanding, I can only come to conclusion that you have intentionally and deliberately removed the brackets in order to twist the words from the paper as much as you can to make it align with your narrative. This does not make you look good Otangelo. This is severely dishonest. In fact, this is so dishonest, I am even beginning to wonder wether this counts a as a violation of the rules on this forum, but I am not moderator of this forum. Although, if I were one, I wouldn't let this fly Otangelo. This is outright despicable. Shame on you.


I call something "new" if it wasn't present before. Here, this something is the specific way the Vpu protein of HIV-1 group M interacts with human tetherin, which is dependent on the residues (amino acids) that you mentioned. That is new. The mousetrap question is not analogous at all to this situation.


What is maddening about this first comment is that this debacle has NOTHING to do with the IC argument. I could, for the sake of argument, say that this particular interaction was REGAINED. Let's say that the old Vpu did had this interaction, but that the interaction was lost and later evolved again. It wouldn't change the fact that this interaction is irreducibly complex, according to Behe's defintion, and that this interaction evolved from a state where it didnt exist. Whether or not this interaction did exist even further back, or whether or not the same funciton was previously performed by a different protein in a different way such that the general function itself may not be "novel", is utterly irrelevant to this point. Not only have you been wrong, missing the point of what we are saying, and dishonest - all you have been doing is waving around a red herring.


View attachment 181


What you are doing here is shifting the burden of proof. I am not claiming there are other world views. I am pointing out that YOUR dichotomy relies on the unsupported claim that no other options exists. Hence, it is NOT up to me to show there are other options (although it wouldn't be difficult to imagine several), it is up to YOU to demonstrate your claim that there are none.


Me pointing out your increduclity is NOT about you not accepting "darwinism". It was referrig to your incredulity about more options than you lay out in your dichotomy. The implicit assumption in that dichotomy is that, because you cant think of other options, there are none. Hence, the reply is just another instance of you missing the entire point. Not to mention that what you wrote in your reply is utter nonsense...but it is nonsense that is not relevant to what I was saying in my slides, so luckily I don't have to bother explain why it is nonsense.


To modify the claim: Behe's hypothes is that if something is IC it cannot evolve, thus IC systems pose a problem to evolution. If you can show one example of an IC system that did evolve, it shows that IC is NOT a barrier to evoluton. Hence, IC system do not pose a problem for evolution.

You can modify the hypothesis all you like, but the problem is that many of your modifications makes it unfalsifiable, e.g. your redefinition of IC to mean "cannot evolve" by definition. You can also say that you do not acknowledge that IC has been falsified, but until you provide a falsifiable hypothesis, this statement is meaningless.


Again, I have to adjust the claim that I am actually saying: If one system that is IC (according to Behe's definition) has been observed to evolve, then the hypothesis that IC systems cannot evolve has been falsified.

Not just "claimed" to be IC, it is IC by the definition according to Behe.


Aside from the previous meme, I was serious. NO, I won't permit it. It is a blatant dodge of the challenge. Even if I were to grant you that evolution is falsifiable (which I certainly do not), it doesn't disprove the point I was making here.


You seem to have missed this slide, as you didn't make any comments on this. Do you understand now that to redefine IC to mean "cannot evolve" would be problematic?

Everything is ok until the part where you call me dishonest.

Claim: " If you can show one example of an IC system that did evolve, it shows that IC is NOT a barrier to evoluton. Hence, IC system do not pose a problem for evolution."

Reply: That's not true. It depends on population size and how many simultaneous changes one needs.

So if someone replaces the hammer on a mousetrap with a spike, now it can also kill animals with shells.
I don't know if tetherin antagonism is irreducibly complex. But if it is, the act of swapping one part for another in an IC system doesn't disprove IC.

(re)gained vs regained seems like a trivial point.

What you are doing here is shifting the burden of proof. I am not claiming there are other world views. I am pointing out that YOUR dichotomy relies on the unsupported claim that no other options exists. Hence, it is NOT up to me to show there are other options (although it wouldn't be difficult to imagine several), it is up to YOU to demonstrate your claim that there are none.

Either there is a God, or there is not a God. I wonder, why are you even disputing this? It is self-evident.

Comparing worldviews - there are basically just two
https://***************************...-are-basically-just-two-in-regards-of-origins

Even if I were to grant you that evolution is falsifiable (which I certainly do not),

Evolution is not falsifiable ?

 

[Nesslig20]

Everything is ok until the part where you call me dishonest.

Everything whent OK until the part where YOU did something dishonest. And that is the only conclusion I can reach (see next).

(re)gained vs regained seems like a trivial point.

It is not. Why did you remove the brackets from "(re)gained" in the original quote? Why not just copy paste it and leave it as it was. Why go out of your way to remove those brackets deliberately? It's obvious. You edited it to make it fit your narrative as best as you could. That's dishonest. Plain and simple.

Claim: " If you can show one example of an IC system that did evolve, it shows that IC is NOT a barrier to evoluton. Hence, IC system do not pose a problem for evolution."
Reply: That's not true. It depends on population size and how many simultaneous changes one needs.

Wait, hold up. You admit that IC can evolve, depending on the population size and how many simultaneoius changes one needs. Hence, IC...in and of itself...is not a barrier to evolution by your admission. Of course, you will say that you think that IC cannot evolve under some unspecified circumstances. But that is a different argument from the original IC argument, that being that IF something is IC it cannot evolve...period...now you have moved the goal post to a different argument that says...sometimes IC can evolve, but sometimes ("IC-plus") it can't. Which is an unfalsifiable hypothesis as it stands due to its vagueness, but it also makes the tacit admission that IC specifically is not a barrier to evolution.

So if someone replaces the hammer on a mousetrap with a spike, now it can also kill animals with shells.

This is not analogous to the tetherin situation in any way (see next).

I don't know if tetherin antagonism is irreducibly complex. But if it is, the act of swapping one part for another in an IC system doesn't disprove IC.

It is not swapping parts. The interaction of HIV-1 group M Vpu with Human tetherin is dependend on several well-matching parts (several amino acid substitutions). That interaction is IC according to Behe's definition (previously explained several times)

Either there is a God, or there is not a God. I wonder, why are you even disputing this? It is self-evident..

That is a true dichotomy (A and not A), but this does not translate to the "worldviews" that you previously claimed. There are various world views that include God(s) and various ones that don't. Furthermore, whether there is a God or not is irrelevant to the topic of this discussion. That being: whether IC is a barrier to evolution. If there is a God or not, it wouldn't matter to whether IC is a barrier to evolution. If IC is not a barreir to evolution, it wouldn't mean God doesn't exist or that God didn't had an invisible "hand" in evolution (theistic evolutionary worldview). And if IC is a barrier to evolution, it wouldn't automatically mean that Goddidit. Try to focus.

Evolution is not falsifiable ?

That was a typo. I meant to say:
"Even if I were to grant you that evolution is UNfalsifiable (which I certainly do not)"

 

[rationalist]

Everything whent OK until the part where YOU did something dishonest. And that is the only conclusion I can reach (see next).

It is not. Why did you remove the brackets from "(re)gained" in the original quote? Why not just copy paste it and leave it as it was. Why go out of your way to remove those brackets deliberately? It's obvious. You edited it to make it fit your narrative as best as you could. That's dishonest. Plain and simple.

Wait, hold up. You admit that IC can evolve, depending on the population size and how many simultaneoius changes one needs. Hence, IC...in and of itself...is not a barrier to evolution by your admission. Of course, you will say that you think that IC cannot evolve under some unspecified circumstances. But that is a different argument from the original IC argument, that being that IF something is IC it cannot evolve...period...now you have moved the goal post to a different argument that says...sometimes IC can evolve, but sometimes ("IC-plus") it can't. Which is an unfalsifiable hypothesis as it stands due to its vagueness, but it also makes the tacit admission that IC specifically is not a barrier to evolution.

This is not analogous to the tetherin situation in any way (see next).

It is not swapping parts. The interaction of HIV-1 group M Vpu with Human tetherin is dependend on several well-matching parts (several amino acid substitutions). That interaction is IC according to Behe's definition (previously explained several times)

That is a true dichotomy (A and not A), but this does not translate to the "worldviews" that you previously claimed. There are various world views that include God(s) and various ones that don't. Furthermore, whether there is a God or not is irrelevant to the topic of this discussion. That being: whether IC is a barrier to evolution. If there is a God or not, it wouldn't matter to whether IC is a barrier to evolution. If IC is not a barreir to evolution, it wouldn't mean God doesn't exist or that God didn't had an invisible "hand" in evolution (theistic evolutionary worldview). And if IC is a barrier to evolution, it wouldn't automatically mean that Goddidit. Try to focus.

That was a typo. I meant to say:
"Even if I were to grant you that evolution is UNfalsifiable (which I certainly do not)"

HIV has undergone every possible combination of 4 mutations, so it's not surprising that it could find gains that require 2, 3, or 4 amino acids at the same time, if each amino acid change doesn't require too many mutations. But probably you don't even need to have them all at the same time though.

"HIV's acquisition of its ability to counteract human tetherin appears to be a stepwise evolutionary gain where mutations gradually improved the ability, since "chimeras within each region yielded intermediate phenotypes. In other words, each mutation made HIV increasingly better at counteracting tetherin. How can it be IC if it's a gradual path?

In other words, each step was advantageous to improve the mechanism.....

The principle of evolutionary continuity, succinctly formulated by Albert Lehninger in his Biochemistry textbook. An adaptation that does not increase the fitness is no longer selected for and eventually gets lost in the evolution (in the current view, only those adaptations that effectively decrease the fitness end up getting lost). Hence, any evolutionary scenario has to invoke – at each and every step – only such intermediate states that are functionally useful (or at least not harmful).

https://onlinelibrary.wiley.com/doi/abs/10.1002/cbdv.200790167

In the end, this is NOT an example of an irreducibly complex system at all as said before. The system lost, and then (re)gained its function.

From pages 55-56 in chapter 3 of Edge of Evolution:
Suppose that P. falciparum needed several separate mutations just to deal with one antimalarial drug. Suppose that changing one amino acid wasn’t enough. Suppose that two different amino acids had to be changed before a beneficial effect for the parasite showed up. In that case, we would have a situation very much like a combination-drug cocktail, but with just one drug. That is, the likelihood of a particular P. falciparum cell having the several necessary changes would be much, much less than the case where it needed to change only one amino acid. That factor seems to be the secret of why chloroquine was an effective drug for decades. How much more difficult is it for malaria to develop resistance to chloroquine than to some other drugs? We can get a good handle on the answer by reversing the logic and counting up the number of malarial cells needed in order to find one that is immune to the drug. For instance, in the case of atovaquone, a clinical study showed that about one in a trillion cells had spontaneous resistance. In another experiment, it was shown that a single amino acid mutation, causing a change at position number 268 in a single protein, was enough to make P. falciparum resistant to the drug. So we can deduce that the odds of getting that single mutation are roughly one in a trillion. On the other hand, resistance to chloroquine has appeared fewer than ten times in the whole world in the past half-century. Nicholas White of Mahidol University in Thailand points out that if you multiply the number of parasites in a person who is very ill with malaria times the number of people who get malaria per year times the number of years since the introduction of chloroquine, then you can estimate that the odds of a parasite developing resistance to chloroquine is roughly one in a hundred billion billion. In shorthand scientific notation, that’s one in 10^20.

page 60: "Recall that the odds against getting two necessary, independent mutations are the multiplied odds for getting each mutation individually. What if a problem arose during the course of life on earth that required a cluster of mutations that was twice as complex as a CCC? (Let’s call it a double CCC.) For example, what if instead of the several amino acid changes needed for chloroquine resistance in malaria, twice that number were needed? In that case the odds would be that for a CCC times itself. Instead of 10^20 cells to solve the evolutionary problem, we would need 10^40 cells."

A "CCC" is Behe's own term. "chloroquine-complexity cluster"
it's what he calls the two simultaneous mutations needed for p. falciparum (the parasite that causes malaria) to evolve resistence to the drug chloroquine.

Can Random Mutations Create New Complex Features?

http://www.evolutionnews.org/2012/06/can_random_muta061221.html

the data suggest many structures might in fact not be evolvable by Darwinian evolution--especially when multiple mutations are needed to convey any advantage on an organism.

In 2004, Michael Behe co-published a study in Protein Science with physicist David Snoke showing that if multiple mutations were required to produce a functional bond between two proteins, then "the mechanism of gene duplication and point mutation alone would be ineffective because few multicellular species reach the required population sizes."

In 2008, Behe and Snoke's critics tried to refute them in the journal Genetics, but failed. The critics found that, in a human population, to obtain only two simultaneous mutations via Darwinian evolution "would take > 100 million years," which they admitted was "very unlikely to occur on a reasonable timescale.

Douglas Axe demonstrated the inability of Darwinian evolution to produce multi-mutation features in a 2010 peer-reviewed study. Axe calculated that when a "multi-mutation feature" requires more than six mutations before giving any benefit, it is unlikely to arise even in the whole history of the Earth.

protein folds in general are multi-mutation features, requiring many amino acids to be fixed before the assembly provides any functional advantage.

Another study by Axe and Ann Gauger found that merely converting one enzyme into a closely related enzyme -- the kind of conversion that evolutionists claim can easily happen -- would require a minimum of seven simultaneous changes,6exceeding the probabilistic resources available for evolution over the Earth's history. This data implies that many biochemical features are so complex that they would require many mutations before providing any advantage to an organism, and would thus be beyond the "edge" of what Darwinian evolution can do.

An empirical study by Gauger and biologist Ralph Seelke similarly found that when merely two mutations along a stepwise pathway were required to restore function to a bacterial gene, even then the Darwinian mechanism failed.7 The reason the gene could not be fixed was because it got stuck on a local fitness maxima, where it was more advantageous to delete a weakly functional gene than to continue to express it in the hope that it would "find" the mutations that fixed the gene.