first- do you have a reference dennis? (i have not found one. even the scientists who check this case are confuse)
secondly- if its true then its mean that from a total 20^392 combinations about 20^380 can code for a functional nylonase enzyme. its mean that nylonase isnt complex at all but very common in the sequence space. if its so easy to get a nylonase several times, why we never see any scientists who get a functional globin or even a functional insulin (very short protein- about50 amino acid long)from a random sequence?
as far as i can remember the simplest blood clothing need about 10 genes. lets say that it may even function with only about 4-5. do you realy think there is a step wise way to get 5 genes in the right sequence order?
I confess I have no idea what youâre talking about here - 20^380 possible nylonases? What?
The papers that discuss the nylonase frameshift to produce the 392 amino acid open reading frame and the later crystal structure of the enzyme are linked at the end of the nylonase post. The scientists are not confused about this.
Also, it does not follow from observing a structure in the present day that it simply must have appeared all at once. Biochemical pathways and structures are built through a process like this: add a component, then later changes make it essential. Repeat. If youâre interested (or, if other onlookers want to learn more) look for the series Iâve done on irreducible complexity here on BioLogos.
Sooo⌠Dennis is being asked to prove that 3D structure and folding is necessary for function? Isnât that a pretty standard observation that applies to enzymes in general? The key interactions within an active site may involve relatively few amino acids, but the relative positions and distances of these amino acids, the accessibility and dimensions of the active site, etc are all related to overall protein folding and 3D structure, and are important for enzymatic activity. Not sure youâve put your finger on any meaningful problem here. If you arenât sure how enzymes work in general, it would have looked better if you asked for some clarification instead of jumping to conclusions that might just showcase how unfamiliar you are with the topic, though I realize itâs a bit late for this suggestion.
What a truly bizarre conclusion to come to.
The simplest blood clotting system in existence today, however many steps are involved, may be a good clue in looking for possible earlier stages in the development of more complex systems, but we would be left without knowledge about how these earlier systems evolved. It seems extremely odd for anyone to look for the simplest system they can find, and them somehow jump to the conclusion that it must be the simplest possible system and that there is no way to get to it. You seem to be working your way to discussing the weirdly narrow-minded, unreflective and uninformed logic of irreducible complexity, based on the unrealistic premise that every system develops in the direct manner that you happen to be picturing and that there were never other components involved at earlier stages. Not only would this be unrealistic and impossible to establish, but this kind of thinking is totally in opposition to what we have discovered for known evolutionary pathways, which depend on exaptation, redundancy (like simultaneous dual systems) and the scaffolding of earlier systems (any of this sound familiar?). irreducible complexity is a really cool term underwritten by a very bad idea, and I would advise against going down that road.
if we get this function in about one in any million random mutations (scientsts get this function several times with several different sequences as starting point) then we can calculate that from a 20^392 different combinations about 20^386 are for nylonase alone.
i look at those (interesting) articles but the main argument remain. for example: scientists claiming that the flagellum evolve from the ttss (or share a commondescent). the ttss share some parts with the flagellum. therefore they are claiming that itâs possible to evolve a flagellum from a ttss. but they never prove that there is indeed a step wise way to get a flagellum from a ttss. we can compare this transition with a transition between a cell-phone and a digital watch. can an intelligent designer change a digital watch step wise into a cell-phone when any step is functional during this transition? if not- its also impossible to do that during a natural process like evolution. and remember that a cell-phone and a digital watch also shared parts like a battery and a digital screen.
prof richard dawkins do that when he claimimg that the first step during eye evolution is an eyespot. but actually an eyespot contain about 200 different proteins.
we can actually know that the first step in any complex trait need at least 3-4 parts. so it doesnt matter what is the simplest system that we have found.
Youâre not listening DC; the simplest known system does not reasonably reflect the simplest possible and advantageous system (whatever the advantage that any simpler system may be said to confer), and the direct stepwise buildup of current pathways is not only not a reasonable assumption, but it has repeatedly proven to be incorrect. Your premises turn out to simply be wrong, which either means that you are trying hard to build a strawman to knock down, or you simply donât understand what you are criticizing. Based on your question about the importance of folding and 3D structure for enzymatic activity, I am strongly leaning toward the second option:-).
I should add that there is some reason to take the âbuilding up a strawmanâ option seriously, since in spite of my pointing to the indirect pathways that evolution apparently takes and even in spite of your apparent knowledge of âdual modeâ lizards etc that you discuss above, and in spite of previous discussions you have had here, you seem to be carefully ignoring this and coming across as though you thought that every system needs to be built up stepwise in a direct manner. We are once again forced to come to the conclusion that you know better, yet you keep on keeping on as though youâd never heard a term like âexaptationâ in your life or as though you have some mental aversion to it whenever it comes up. You are a very interesting study DCâŚ
this is actually what i said. again: take for example a minimal vision system. how many parts do you think it need for a minimal function?
i dont think you understand what i ask for. i have claimed that this trait may not need a complex fold but a simple one. and because of that its very common. another possibility is that this is indeed a complex fold that do something very close to digest a nylon.
Why would I answer that? I could guess or look it up or take your word for it and it would still be irrelevant to the purpose of the discussion. [Correction: Iâve realized I misread your question, and that you are asking about a theoretically minimal system. I think my below points are relevant since you keep pointing to the simplest extant systems, but when it comes to the theoretical minimum; I donât know. Do you? And honestly, given what I have tried to explain, could it possibly matter to anyone who doesnât confine their thinking to your idiosyncratic direct stepwise buildup model of evolution?]
What I said responds clearly to the point you think you are making, not to some not very helpful question about how many parts something has. You search the natural world for the simplest system in an apparent series and then saying; âbut see, itâs still complicated!â. Should I conclude that the simplest but still complicated system you pointed to could not possibly have precursors? Why? I could say the same for the more complex systems, observing that if you remove one component, they donât work, but this turns out to be rather awful reasoning, especially since we do actually have simpler systems and we do have good indications of the progression from these simpler systems. Why should we presuppose the impossible scenario that all possible precursors of every complex system have survived to the present day? Instead of asking an irrelevant question, please make your real point and Iâll see how well the response fits it.
This is not the claim that you made; you were asking a question, and it was a strange one, since what Dennis was saying was fairly straightforward. You tend to often make claims like: âonly one or two amino acids are necessary for this enzyme to workâ, and you did the same here. Its an encouraging sign that youâve retreated from the claim that new information canât arise through mutation and natural selection. Dennis was pointing out that this is nonsense (very politely of course) since the overall string of amino acids contributes to exact folding that is necessary for activity. Thatâs not controversial, and as I pointed out, you donât seem to understand this, as demonstrated by your statement about one or two amino acids (you do realize that your statements are actually available above right? That you canât convincingly say that you were talking about something different like, for example, âa simple foldâ?). Just take the correction DC and move on. Not every amino acid has an equal impact on the activity, but the overall folding that is dictated by the sequence of amino acids is critical, and âone or two amino acidsâ is simply an error in your understanding of how enzymes work. Can you accept that your observation about one or two amino acids was a mistake on your part and can you begin to see that the development of a working enzyme from scratch in a very short timeframe is a very big challenge to the creationist position? And your newly revised discussion of âa simple foldâ is not helpful until you explain what you are talking about.
again: think about this example: lets say that you are an engineer that try to made the simplest video camera ever. do you think its possible to made a one or two part camera that may function as a minimal camera?
we know about exmaples that only one or two amino acid can do some functions. so its possible that even one or two (or 3) amino acid change can make this fold to digest a nylon. the rest of the fold may not need to this function.
You are still not listening: if the purpose is exactly the same (i.e. a video camera with all of the current functions) then yes, there may be a theoretical minimum number of parts, but at no point since 1859 has this been a part of the evolutionary thinking! The question is whether precursors may have some theoretical advantage of some kind, not whether they work as a video camera or even just a simple camera. And that function could be anything, from a bottle opener to a pair of binoculars. And that functional unit or a duplication of that functional unit (being therefore redundant), or some subsection of that functional unit may be used as a modular component for a more complex device that does something different (etc). You are asking the wrong question and using a demonstrably incorrect model of how evolution must happen in order to say; âAha, see! I canât get a video camera using only 2 partsâ â good for you, but since you arenât paying attention whenever I say that you shouldnât be expecting to find a video camera, and you donât seem to realize that you are working with a model that no one has considered viable in 150 years, I canât think of any better ways of explaining the same point. Please pay closer attention to the words that people are using here and do yourself a favor; look up exaptation and meditate on the word for a bit. The more carefully you read what people say, the less weâll have to repeat it.
Then you did not understand the references you were reading. You still arenât paying attention; please go back and read what I mentioned about relative positions, orientation in the active site, accessibility (an active site that is buried in the protein because of the overall folding is not useful for example) etc, not to mention allosteric interactions, hydrophobic transmembrane regions etc, all of which are important components relating to overall amino acid sequence and folding. Or just sign up for local or online biochemistry courses.
DC, did you really just respond by explaining that dipeptides exist?! I really donât know how to answer that. Yes they do, granted. I think you are confused about something here, so I would suggest (again) that you do a bit of background reading on enzymes (5 minutes on wikipedia may help) so that you can offer an answer that makes more sense, and we can pretend that this never happened;-)âŚ
so can you how me how a camera can evolve step wise from other thing when every step is functional for something?
the fact that this protein have a complex fold doesnt mean that it need it to digest a nylon. unless the paper (that i have not read yet) prove its not true. and in this case there is other possibilitys. one evidence against it is the fact that scientists evolve this traits also in another protein (with another fold). so it may mean that most of the fold doesnt need for this function.
DC, since this obviously wasnât as obvious to you as I thought it would be, Iâll point out that I was speaking about cameras in order to stick with the analogy. No I donât think cameraâs can evolve and no, I am not going to think up, just for your personal edification, an imaginative scenario about how different steps in a progression might be used for different purposes. If you are particularly creative and can somehow picture accurate and ever changing fitness landscapes, feel free to try out the exercise yourself.
This is a particularly incomprehensible paragraph (you might want to edit it for clarity), but based on the little I can interpret, all it really does is highlight misunderstandings about enzymes. Yes, different proteins are used in different evolutionary scenarios, which is fascinating, but the lessons you draw from this are unintelligible. I canât imagine why a different protein using a different active site and different amino acids in different arrangements would somehow need to the exact same fold to work. Oh, and I love that you stubbornly persist in using âfoldâ in the singular! I appreciate that you are trying, but if you have a point here, which Iâm sure you do, youâll have to work quite a bit harder to make it.
we can say the same as for an eye. if your claim is true then you can try to remove parts from a video camera and check if you will get a new function. what do you think the result will be?
this is actually what i have said before. if different folds evolve the same trait separately. its only prove that a nylon digestion is very common in the sequence space.
Ok DC, so please; whatâs your point here? Since cameraâs didnât evolve (we know their history because we made them, unlike organic beings), no I donât think we will find important uses for all the rigid and unchanging components in a camera or for collections of those components (although Iâm sure many of them are useful for other devices). You donât seem to be clear on the obvious limits of the analogy which you introduced in the first place. I will help: cameras are not organic, they do not reproduce, their parts are rigid, we know exactly how they are made, they do not have system redundancy, their parts do not mutate, duplicate or change. I can keep going, but this should be enough to establish that your Quixotic quest for a simpler camera is silly and that it has nothing to do with evolution. I was simply pointing out that your model of evolution is completely wrong. You seem to have read that and decided that it was a claim about cameras and camera manufacturers. Which is why I keep insisting that you read more carefully or more slowly, you just seem to get sidetracked so easily.