# What is the Plan?

A prominent ID supporter at UD, gpuccio, has this to say:

My simple point is: reasoning in terms of design, intention and plans is a true science promoter which can help give new perspective to our approach to biology. Questions simply change. The question is no more:

how did this sequence evolve by some non existent neo darwinian mechanism giving reproductive advantage?

but rather:

why was this functional information introduced at this stage? what is the plan? what functions (even completely unrelated to sheer survival and reproduction) are being engineered here?

Gpuccio references actual biology in his writings and is one of the few at UD that do, and as such I’m prepared to take him at his word that the ID project is now ready to move from simply determining design to answering the questions he posed:

• what is the plan?
• what functions (even completely unrelated to sheer survival and reproduction) are being engineered here?

If any ID supporter would like to provide a specific example with answers for those 3 points for discussion that would be perfect.

Gpuccio’s OP concludes:

The transition to vertebrates was a highly engineered process. The necessary functional information was added by design.

In response I simply repeat back the question what is the plan?

## 328 thoughts on “What is the Plan?”

1. colewd: If we roll the dice and a very improbable outcome came up 10 times in a row, at the time we observed it the probability of the out come is indeed 100%.

The next question might be, what is the chance the result we are observing is the result of a stochastic process?

What is the probability of another sequence of 10 particular but dissimilar rolls, coming up? The same as 10 of the same in a row.

2. colewd: The next question might be, what is the chance the result we are observing is the result of a stochastic process?

Indeed. Do you believe there is such a thing as truly random dice?

3. Rumraket: What is the probability of another sequence of 10 particular but dissimilar rolls, coming up? The same as 10 of the same in a row.

This always seems to confuse some people. If the dice are fair, then ANY sequence of 10 rolls is going to be highly improbable, and all will be equally improbable. I think people tend to find ordered sequences (according to some ordering scheme in their minds) as being somehow inherently less likely. For example, they might consider a lottery number selection of 1-2-3-4-5-6 as being less likely than a more “random-looking” sequence.

What would be suspicious is if the same sequence were rolled twice.

4. Hey colewd, what kind of nuclear proteins do you study and how do you study them?
I’m interested and curious

5. Yeah I’d like to hear more about those supposedly harder to evolve nuclear proteins too.

6. gpuccio @UD

I have discussed Keefe and Szostak’s paper ad nauseam. I cannot always repeat the same things.

Yeah, I’ve discussed protein sequence space ad nauseam too. But up it crops, over and over and over.

7. gpuccio@UD

Neither the weakly binding proteins, nor the artificially engineered final protein, have been shown to be even vaguely naturally selectable, Indeed, the final protein has been shown to be deleterious, in the right environment.

Hahaha! This is funny. I’m quite sure gpuccio will not appreciate how funny that is. ‘Deleterious in the right environment’ indeed.

8. Pooch is counting on God to provide the ‘deleterious’ environment when needed.

9. I would note that intelligently designed proteins that are ‘naturally selectable’ appear to be a bit thin on the ground. Unless one simply declares all functional proteins to be designed.

Random peptides have, incidentally, been shown to successfully replace knockouts for multiple functions in vivo, with absolutely no connection between the algorithm used to subset peptide space and the peptide replaced. But I guess, unless one releases them into the wild and gets a brand new pathogenic strain out of it, it’s inconclusive on the ‘selectable’ question!

10. If we roll the dice and a very improbable outcome came up 10 times in a row, at the time we observed it the probability of the out come is indeed 100%.

The next question might be, what is the chance the result we are observing is the result of a stochastic process?

Could you relate this to biology in some way? While you are doing so, don’t forget the possibility that the first ‘improbable’ result was copied, loads.

11. Since I typically disagree with gpuccio, it’s good when I occasionally find something to agree with him about.

I think his criticism of Flint’s statement is valid. He writes:

Flint, why would that be suspicious? According to your reasoning, the first occurrence has the same probability as any other sequence. Correct.

Well, but after the sequence has occurred, what is its probability of occurring a second time? The answer is simple: exactly the same.

So, what is the probability of having the same sequence occurring twice in a row? Exactly the same as the probability of having any couple of sequences occur (the product of the individual probabilities).

Pooch is right, and another way to see that is to recognize that a sequence repeated twice consecutively is equivalent to a single sequence of twice the length. All such sequences are equiprobable under a uniform distribution.

What makes certain results suspicious is something other than their improbability as individual sequences. I addressed this topic in the following OP:

12. gpuccio destroys the core of his own argument and does not seem to notice:

I think we can find some sequence with a weak affinity for anything, in a modestly big library [Szostak’s] like that.

http://www.uncommondescent.com/intelligent-design/the-highly-engineered-transition-to-vertebrates-an-example-of-functional-information-analysis/#comment-614206

He re-emphasizes the point that the result was generated by ’rounds of intelligent selection’. It’s almost as if he’s ignored every post made on this thread.

gpuccio, you obviously have the time to comment on my posts rather than the more specific more technical rebuttals others have made. Why is that?

For example, are all functional proteins designed?

14. Yes, gpuccio, rounds of intelligent selection are only possible in a peptide space that is connected – where weak function can be tuned by [some kind of] selection to improve. Why is this possible in an experimental setup, yet not in nature? It’s not as if the people are picking the sequences most likely to improve. They are simply assaying for the chosen function, then subsetting the peptide library on that basis, mutating and repeating.

This, further, has medical application. By applying the thing-that-doesn’t-work-in-nature, by a remarkable stroke of luck it does work in other arenas.

15. Allan Miller: Why is this possible in an experimental setup, yet not in nature?

Perhaps it’ll help if I ask

Why is this possible in an experimental setup, yet not in nature?

as gpuccio seems keen to talk to me. Not sufficiently keen to talk here, but keen nonetheless.

16. I will repeat myself.

Having a human person stand next to the test tube isn’t going to make function magically more prevalent in amino acid sequence space. There does not emanate magical function-creating beams from human bodies into test-tubes such that the proteins inside can suddenly do things they are not supposed to.

It doesn’t matter at all whether humans are doing the selecting. The function is there regardless of who or what is selecting it. The fact that the function is there to select means sequence space is largely connected by functions.

A human being being within a few meters of the test tube isn’t going to make ATP binding suddenly appear where it would not be if the human stepped further away. Gpuccio’s excuse couldn’t be any more ridiculous even if he tried.

17. Rumraket
It doesn’t matter at all whether humans are doing the selecting. The function is there regardless of who or what is selecting it. The fact that the function is there to select means sequence space is largely connected by functions.

gpuccio?

18. Rumraket: It doesn’t matter at all whether humans are doing the selecting.

Similar objections were raised against Lenski’s LTEE. As if researchers were picking the winners!

19. This is gpuccio’s summary of what gpuccio asked me to read:
http://www.uncommondescent.com/intelligent-design/natural-selection-vs-artificial-selection/

So, to sum up, the main differences between NS and AS are:

1) AS can define any function, and select for it. NS works only on one function: reproductive success.

2) In NS, the coupling between function and selection is direct: it’s the function itself which confers the reproductive advantage, which is the reason for the selection itself. In AS, the coupling between the defined function and the selection process is indirect and symbolic: the connection is established by the designer, by definite procedures designed by him.

3) NS has a definite threshold of measurement: it can only act if enough reproductive success is present as to ensure the fixation of the trait. AS can measure and select any desired level of the defined function.

4) In NS, the only selecting procedure is tied to the reproductive success, and is in essence differential reproduction. In AS, any intelligent procedure can be used to isolate, expand and fix the desired function.

It seems that proteins don’t reproduce like organisms do, therefore all experiments are invalid.

20. This is just absurd:

the connection is established by the designer, by definite procedures designed by him.

21. Remaining in a pool drawn from a wider protein library is reproductive success [eta – given that these pools form the next generation, mutated]. The distinctions between artificial and natural scenarios are … artificial. All that is fundamentally required for selection is heritable variation. The medium of inheritance is immaterial.

22. OMagain:… asking me to read his OP on natural vs unnatural selection.

23. gpuccio also said,

Maybe I should remind OMagain that, in his theory (neo darwinism), naturally slectable functions are the only functions that count. Any other “function” is insignificant, because it cannot be “seen” by the NS process.

IOWs, any function which does not confer any reproductive advantage is not a function, in a neo darwinian context.

Is that so difficult to understand? I suppose that one who embraces a scientific theory should at least try to understand it.

And that seems to be the heart of it for him.
http://www.uncommondescent.com/intelligent-design/the-highly-engineered-transition-to-vertebrates-an-example-of-functional-information-analysis/#comment-614206

24. ATP binding is a naturally selectable function. Countless critical regulatory elements and core metabolic enzymes have ATP binding pockets necessary for their current function. If tomorrow all the ATP binding capacity of Gpuccio’s cells disappeared, he’d die in less than a minute (and if he doesn’t have children already, his reproductive success would go to zero).

But as I wrote already earlier, we can forget about Keefe and Szostak if it makes Gpuccio feel better, and start talking about other similar types of experiments, such as Hayashi et al 2006, where the selection criterion was the capacity of a bacteriophage to infect a bacterium, using a randomized ~140 amino acid protein subdomain. So the reproductive success here was that of a bacteriophage. That’s textbook natural selection. What’s Gpuccio’s excuse going to be now?

25. So the peptide space is grudgingly accepted to be rich in ‘function’ – defined as showing up in some assay for that function – but poor in ‘naturally selectable function’? How has that been determined? You can’t just look at the space and declare it so. It renders all the ooga-booga probability calculations (and all effort spent addressing them) a waste of time, since selection is entirely context dependent. There is no information regarding it anywhere in protein space.

26. Hi Patrick
He is managing his very active op right now which is consuming his spare time.Hopefully he can join us sometime in the future.If you have commented with a minority view on a blog you know how time consuming it is.

Since it seems that UD is a safe haven for gpuccio’s ideas and most of the discussion is taking place here, I encourage you to again invite him to join us.

Many of the participants here are banned at UD and still others are unwilling to participate in a forum where their comments may be edited or deleted at the whim of the site’s owner. TSZ does not alter or delete comments nor does it ban people arbitrarily. If gpuccio really wants an open discussion of his ideas, TSZ is a far superior venue.

27. gpuccio,

“For example, are all functional proteins designed?”

OK. I tend to believe that they are, but what I believe is of no importance.

The correct question is: for what functional proteins can we reasonably infer design?

And I have given the answer many times:

For all proteins which exhibit a total functional information (or an informational transition) higher than an appropriate threshold (150 bits are good, for me), and for which there is no trace of a detailed naturally selectable pathway that can lower the probabilistic barriers (that is easy: there is no such trace at all for any complex protein).

It appears to be simply the lack of any step by step pathway that is detailed enough for gpuccio that determines if a protein is designed. Presumably were such a pathway provided to his satisfaction it would only render that particular protein available to natural selection without intelligent design. The rest would remain designed.

Presumably he also asserts that arches are not possible due to the lack of a now-gone support structure.

28. gpuccio, 259

Rumracket at TSZ reaches new peaks of his favourite quality:

“A human being being within a few meters of the test tube isn’t going to make ATP binding suddenly appear where it would not be if the human stepped further away. Gpuccio’s excuse couldn’t be any more ridiculous even if he tried.”

Obviously, the fact that the human being has set up columns which can bind proteins with ATP affinity, and performs mutational PCR followed by further column selection, is not relevant. The important thing is that the human being is within a few meters of the test tube. This is magic, after all.

And of course nature is completely able to do the same. As OMagain has demonstrated many times, we can believe anything, if we try hard.

260,

Rumracket tries again:

(we can criticize these guys as much as we like, but they are really obstinate!).

“ATP binding is a naturally selectable function. Countless critical regulatory elements and core metabolic enzymes have ATP binding pockets necessary for their current function. If tomorrow all the ATP binding capacity of Gpuccio’s cells disappeared, he’d die in less than a minute (and if he doesn’t have children already, his reproductive success would go to zero).”

It is tiresome to explain neo darwinism to neo darwinists, but OK:

The problem is simply: is the weak ATP binding in the protein which was present in the original library naturally selectable?

IOWs (please, put your full attention on it, maybe you will understand): if such a sequence arose by chance in some living being, did it give some reproductive advantage, which allowed for its selection and fixation?

If the answer is no, then the sequence is not naturally selectable.

As I have said, there is no trace of demonstration the either the original sequence or the final engineered protein can confer some reproductive advantage in a living system.

Are you aware of any evidence that I am not aware of?

261

“But as I wrote already earlier, we can forget about Keefe and Szostak if it makes Gpuccio feel better, and start talking about other similar types of experiments, such as Hayashi et al 2006, where the selection criterion was the capacity of a bacteriophage to infect a bacterium, using a randomized ~140 amino acid protein subdomain. So the reproductive success here was that of a bacteriophage. That’s textbook natural selection. What’s Gpuccio’s excuse going to be now?”

No excuse. I am a great fan of the Ayashi paper, as everybody who reads my posts should know.

It is one of the few experiments which deal really with NS.

The result show clearly that, while some low level rescue of function (in a system where the function is already present and organized, but has been partially knocked out) is possible, but that the rugged nature of the functional landscape makes it practically impossible to reach the wildtype, or any comparable functionality: indeed, none of the selected sequences has any sequence homology with the wildtype. (So much for connected spaces!) And the authors compute that an initial library of 10^70 would be necessary to reach the wildtype.

You see, even if you darwinists seem not to understand it, the rugged landscape is the death of any possible connected space.

262,

http://www.uncommondescent.com…..n-defined/

you will see that “function” is a very generic concept, unless it is linked to precise definitions and context.

In ID, for example, function in itself is of no importance. What is important is only the quantity of information connected to some defined function. Complex functional information points to design, not function in itself.

In neo darwinisms, the only function that counts is naturally selectable function. So, it is the burden of neo darwinists to show that naturally selectable functions exist with some relevant frequency in random libraries.

That’s what Keefe and Szostak’s paper is supposed to do.

It’s not what it does. It simply uses a very generic concept of function, and then gives the illusion that the results can apply to naturally selectable function.

And you neo darwinists fall for it! So much for skepticism.

So your position becomes that NS of new complex functions arising from RV cannot be detected, but can exist, like the missing intermediates, and like all the myths of neo darwinism.

Have you ever thought that science should be based on facts, and not only on conjectures (and rather unreasonable conjectures, for that!)

29. OMagain: In neo darwinisms, the only function that counts is naturally selectable function. So, it is the burden of neo darwinists to show that naturally selectable functions exist with some relevant frequency in random libraries.

What relevant frequency demonstrates that Intelligent Design is the only possibility gpuccio? Is that a sufficiently technical question? Think carefully before you answer I would suggest.

30. Gpuccio@UD

Have you ever thought that science should be based on facts, and not only on conjectures

Good grief! ID of organismal proteins – how non-conjectural is that? Or is gpuccio of the “ID is not a science” school?

31. OMagain: For all proteins which exhibit a total functional information (or an informational transition) higher than an appropriate threshold (150 bits are good, for me), and for which there is no trace of a detailed naturally selectable pathway that can lower the probabilistic barriers (that is easy: there is no such trace at all for any complex protein)

This is hilarious. Gpuccio is making a designer of the gaps-argument. Where we lack a sufficiently detailed phylogeny, that’s where the designer acted.

32. Rumraket: Gpuccio is making a designer of the gaps-argument. Where we lack a sufficiently detailed phylogeny, that’s where the designer acted.

This is hilarious. That’s not his argument.

33. Gpuccio: Rumracket at TSZ reaches new peaks of his favourite quality:

“A human being being within a few meters of the test tube isn’t going to make ATP binding suddenly appear where it would not be if the human stepped further away. Gpuccio’s excuse couldn’t be any more ridiculous even if he tried.”

Obviously, the fact that the human being has set up columns which can bind proteins with ATP affinity, and performs mutational PCR followed by further column selection, is not relevant. The important thing is that the human being is within a few meters of the test tube. This is magic, after all.

Obviously doing a column extraction is the method by which ATP binding is detected. There’s zero grounds for a belief the protein in question can’t bind ATP in vivo.

What Gpuccio fails to address is why ATP binding even exists where he seems to insinuate it shouldn’t. That’s what he keep trying to argue, that something functional was found because the whole thing is “artificial”, rather than “natural”. A synthetic distinction in the first place, since the principles of intermolecular binding are the same everywhere: shape and electromagnetic attraction.

But Gpuccio needs keep the banner of a somehow invalidated experiment flying whatever it takes, rather than simply concede that his views of sequence space have been falsified. So if humans did the selecting by using some kind of human technology, the rules are suddenly different.

OMagain: And of course nature is completely able to do the same. As OMagain has demonstrated many times, we can believe anything, if we try hard.

Yes, ATP binding exists in natural proteins too. It operates on the same principle, an ATP binding motif that structurally fits the ATP molecule, and a mutual electromagnetic attraction between the atoms in the protein and the atoms in the ATP molecule.

There is no difference whatsoever between an artificially evolved ATP binding protein or a natural ATP binding protein. They both have an ATP binding motif. They may be different in sequence, but the method by which ATP binds is the same. No amount of obfuscation is going to make this go away.

If the capacity for binding ATP is tied to a key metabolic enzyme for example (and it is, in ATP synthase), then that enzyme, if mutated to a weak binding capacity, would have an impact of reproductive success, because the ATP synthase would be only weakly functional, if at all. So there’s clearly an in vivo selectable function in ATP binding.

Gpuccio: Rumracket tries again:(we can criticize these guys as much as we like, but they are really obstinate!).

“ATP binding is a naturally selectable function. Countless critical regulatory elements and core metabolic enzymes have ATP binding pockets necessary for their current function. If tomorrow all the ATP binding capacity of Gpuccio’s cells disappeared, he’d die in less than a minute (and if he doesn’t have children already, his reproductive success would go to zero).”

It is tiresome to explain neo darwinism to neo darwinists, but OK:

The problem is simply: is the weak ATP binding in the protein which was present in the original library naturally selectable?

Yes it is, the function is part of countless natural proteins. Lots of allosteric regulation is done by ATP binding.
A protein that has a binding pocket for ATP, changes it conformation and as a consequence it’s (for example) enzyme active site access is altered such that activity is reduced, or totally inhibited. Or the same thing happens to regulatory elements that bind DNA, they have a binding pocket for a key stretch of DNA and one for ATP. ATP binds the ATP binding motif and the protein changes conformation, such that it lets go of the DNA.

So yes, ATP binding is a naturally selectable function. It will remain a naturally selectable function no matter how many synthetic excuses and red herrings Gpuccio can invent to save his warm, abiding religious faith about protein sequence space, from falsification.

Gpuccio: IOWs (please, put your full attention on it, maybe you will understand): if such a sequence arose by chance in some living being, did it give some reproductive advantage, which allowed for its selection and fixation?

That is entirely possible, yes. Context dependent of course, as always. There is a context in which some organism could use an allostericly ATP regulated enzyme or genetic regulatory element, and there is some in which it could not. It doesn’t have to be universally beneficial in every and all biological contexts (in the same way the Polar bear’s fur isn’t universally beneficial in all biological contexts), to be a naturally selectabe function.

Gpuccio: If the answer is no, then the sequence is not naturally selectable.

Gpuccio: As I have said, there is no trace of demonstration the either the original sequence or the final engineered protein can confer some reproductive advantage in a living system.

Are you aware of any evidence that I am not aware of?

Yes, I’ve read basic biochemistry and molecular biology where evidently you have not. I know of how enzymes work and how gene regulation work. ATP binding motifs are ubiquitous in life for those purposes.

“But as I wrote already earlier, we can forget about Keefe and Szostak if it makes Gpuccio feel better, and start talking about other similar types of experiments, such as Hayashi et al 2006, where the selection criterion was the capacity of a bacteriophage to infect a bacterium, using a randomized ~140 amino acid protein subdomain. So the reproductive success here was that of a bacteriophage. That’s textbook natural selection. What’s Gpuccio’s excuse going to be now?”

No excuse. I am a great fan of the Ayashi paper, as everybody who reads my posts should know.

It is one of the few experiments which deal really with NS.

The result show clearly that, while some low level rescue of function (in a system where the function is already present and organized, but has been partially knocked out) is possible

Which is the key fact taht remains to be explained, if as Gpuccio insists, protein sequence space is largely void of function. If a random 140 amino acid peptide could be immediately mutated into orders of magnitude increased function, this implies both that there is function all around the initial peptide in sequences space, and that it is naturally selectable.

Indeed, the fact that a totally random 140 amino acid sequence, utterly unrelated to the deleted D2 domain, had a low level of infectivity to begin with, implies the infectivity function is extremely easy and almost ubiquitous in protein sequence space.

Gpuccio:but that the rugged nature of the functional landscape makes it practically impossible to reach the wildtype :or any comparable functionality:

With a sequence pool of between 10 and 10^6 sequences, only allowed to change by substitutions.
Which is irrelevant in the first place, because whether the function is lower than wild-type or not, the fact is the function is there and has a demonstrable effect on reproductive success.

Simply but, if Gpuccio is right, the function simply shouldn’t be there. Gpuccio’s main thesis has always been that sequences space is largely devoid of any functions and that most of it is straight up nonfunctional, such that one can’t move around in it and maintain any function, that it is basically some obscure, very far apart and small islands of isolated function.

The fact that there’s a long way to the wild type from here is immaterial. The function is good enough to allow the phage to infect E coli.

The fact that the very first pool of random sequences were immediately functional is a problem to explain for Gpuccio, if the sequence space should be mostly dead. What colossal luck the reasearchers must have had, to just so happen to start the experiment at a functional area in a largely dead sea, right? It’s funny how this is a consistent result with these kinds of experiments. It’s almost like sequence space is actually replete with function.

Gpuccio: indeed, none of the selected sequences has any sequence homology with the wildtype. (So much for connected spaces!)

It is utterly irrelevant that the seqeunce has no homology to the wild-type. The interconnectedness of sequence space does not mean all sequences should be homologous, obviously.

The important fact is that there is a selectabe function closeby, which means this area of sequence space isn’t lethally nonfunctional in a vast area. In fact this just argues that the same basic function exists in multiple locations in sequence space and with relatively few mutations, something that functions well enough to allow reproduction to continue can be reached.

Gpuccio: And the authors compute that an initial library of 10^70 would be necessary to reach the wildtype. You see, even if you darwinists seem not to understand it, the rugged landscape is the death of any possible connected space.

You don’t seem to appreciate what is meant by sequence space being connected. It doesn’t mean you can move from any arbitrary point in the space to any other arbitrary point as if it is one long slope of selection, and end up with a homologous sequence to the wild-type in the end. Rather, what is meant is that there is usually always something functional nearby, not that the particular instance (such as the wild-type D2 domain) of the function in question can always be reached.

You know there are multiple different enzymes in life that catalyze the same reactions, yet are pretty much entirely unrelated as best we can tell?

Why WAS there a function there, for the synthetic sequence to improve? Shouldn’t it have been much, much more likely for the synthetic sequence to have landed in some vast desert of nonfunctionality that could not ever (within reasonable timeframes) have been mutated towards any appreciable level of function?

Gpuccio: In ID, for example, function in itself is of no importance. What is important is only the quantity of information connected to some defined function. Complex functional information points to design, not function in itself.

That’s so cool. In ID, what matters is some silly piece of rethoric with zero real-world application, designed to impress gullible, already convinced religionists, into being flabbergasted by how scientific it sounds to spray words like “information”, “complex” and “specificity” all over the place.

34. gpuccio,

What a pity. The comments at TSZ have gone completely wild.

No more arguments, no more reason.

I will just answer this brief question from Allan Miller, who remains after all one of the most “normal” people there:

“Good grief! ID of organismal proteins – how non-conjectural is that? Or is gpuccio of the “ID is not a science” school?”

ID explains facts, and is motivated by facts. Functional information in proteins is a fact. My OP here is about facts.

I copy here my question at #215. About a fact:

“Astrotactin 2 is a 1339 AAs protein. 889 of them are identical in sharks and humans.The positives are 1048.

On the other hand, missing intermediates, imaginary pathways, connections in proteins space, are all conjectures without a trace of support from facts, and against any rationale.

So yes, ID is not conjectural, and neo darwinism is.

And no, I am not of the “ID is not a science” school. ID is science. Completely empirical science.

heh

35. gpuccio,
I would remind you of you own claim regarding what questions ID should answer:

why was this functional information introduced at this stage? what is the plan? what functions (even completely unrelated to sheer survival and reproduction) are being engineered here?

36. OMagain:
gpuccio,
What ‘facts’ does ID explain?

All of them.

What we see is what the designer wanted. Done.

37. Mung: This is hilarious. That’s not his argument.

That’s what the section I quoted, which he wrote, means.

Gpuccio wrote: OK. I tend to believe that they are [Designed], but what I believe is of no importance.

The correct question is: for what functional proteins can we reasonably infer design?

And I have given the answer many times:

For all proteins which exhibit a total functional information (or an informational transition) higher than an appropriate threshold (150 bits are good, for me), and for which there is no trace of a detailed naturally selectable pathway that can lower the probabilistic barriers (that is easy: there is no such trace at all for any complex protein).

So there you go Mung, that is what he wrote. If we lack a highly fine-grained phylogeny of the protein in question, it was designed. That’s a textbook designer-of-the-gaps argument.

He does not have to explicitly say “we don’t know – therefore design” to be in effect arguing like that and thus be guilty of the fallacy.

38. OMagain: So yes, ID is not conjectural, and neo darwinism is.

And no, I am not of the “ID is not a science” school. ID is science. Completely empirical science.

Why doesn’t it, you know, actually predict what design does, like fitting the design to the function, rather than fitting inherited information to the function?

If design predictions (real ones) fit the evidence, we’d all* be IDists.

Glen Davidson

*Those of us here, at least, I’d wager. There could be some holdouts who really could never abide being wrong, but they’d be the counterparts of the IDists.

39. Rumraket: He does not have to explicitly say “we don’t know – therefore design” to be in effect arguing like that and thus be guilty of the fallacy.

There is much blather generated to avoid stating it that boldly, since it’s so obviously fallacious when written in that way. But make up a false means of design detection, like Dembski did, and many will think he’s right. Paley, of course, never went for such a false idea, rather he tried to (and failed to) demonstrate that life has the characteristics expected from architects and artificers.

The fact that Paley’s straightforward and intellectually honest (if on the fuzzy side) standard has been abandoned in favor of idiotic claims that design is (normally) detected by elimination of other causes* shows how it really is all designer of the gaps.

Glen Davidson

*I really don’t know if this has ever been done IRL by intellectually honest seekers. But perhaps it has been done in some cases, so long as the design didn’t have to be miraculously complex and beyond present human capabilities.

40. At UD, colewd complains about the “strawman” of designer of the gaps, then resorts to same in the next paragraph:

The TSZ guys are bringing designer of the gaps arguments out. The use of straw-man arguments appears to signal the end of a viable challenge to your arguments at this point.

The fact that the genome is a sequence appears to be a very difficult problem for Neo-darwinism and modern evolutionary theory including universal common descent.

Maybe. But that’s what real science does, finds actual problems based on actual constraints. Bogus crap like ID has no problems, as it has no solutions nor the means of getting to any. ID has yet to explain anything meaningfully. Evolutionary theory has problems because it has considerable explanatory resources, while not being able to actually go back and film the evolution of eukaryotes. Real histories of all kinds have problems of information lost to time. Fables, like ID, don’t.

41. The fact that the genome is a sequence appears to be a very difficult problem for Neo-darwinism and modern evolutionary theory including universal common descent

Yet Colewd is completely incapable of articulating why.

42. Rumraket: If we lack a highly fine-grained phylogeny of the protein in question, it was designed. That’s a textbook designer-of-the-gaps argument.

This is hilarious. That’s not his argument.

43. Mung: This is hilarious. That’s not his argument.

Please elucidate his argument then, Mung.

44. none of the selected sequences has any sequence homology with the wildtype

I think this illustrates pretty well why IDiots can’t wrap their heads around the card deck fallacy. Of all the sequences, the selected ones had to be homologous to something in the wild or else don’t count… because they’re not “part of the plan”.

I would say, starting from random sequences and then mutation+selection, getting something that has an homologous in the wild might have suggested teleology… too bad it falsified “islands of functions” instead

45. Mung: This is hilarious. That’s not his argument.

Thanks for that insightful clarification Mung. I’m going to go ahead and keep believing you are mistaken until actual clarification is served. If that’s not alright with you I couldn’t give any less of a fuck. You are welcome to start contributing substantially instead of just offering vapid commentary.

46. Rumraket: Thanks for that insightful clarification Mung. I’m going to go ahead and keep believing you are mistaken until actual clarification is served. If that’s not alright with you I couldn’t give any less of a fuck. You are welcome to start contributing substantially instead of just offering vapid commentary.

This. It’s all they know. You are wrong and that’s it. They never notice they are never right as that’s not what it’s about for them.

47. Richardthughes: Please elucidate his argument then, Mung.

Do you think Rumraket has provided an accurate portrayal of the argument?

Here’s gpuccio on the subject:

On the other hand, missing intermediates, imaginary pathways, connections in proteins space, are all conjectures without a trace of support from facts, and against any rationale.

He denies reasoning from missing data. So either he is contradicting himself or you and your pals here at TSZ are misrepresenting him.

gpuccio:

Well, they may think that they are open minded, skeptics, capable of respectful discussion.

Well, they are not.

Who do you suppose he is talking about?

Rumraket even quoted gpuccio as saying:

For all proteins which exhibit a total functional information (or an informational transition) higher than an appropriate threshold (150 bits are good, for me), and…

Then Rumraket went on to ignore everything before that and…

I am perfectly capable of “contributing substantially instead of just offering vapid commentary,” but have to ask myself why should I? Who here really wants honest respectful dialogue?

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