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Proteins, Warrants, and Design Inferences

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At the request of others I’m reproducing a recent comment as an article.

UD member Fross writes:

I understand that the ID position is that the protein itself had to have been designed, not the variations that can occur through mutation.

DaveScot replies:

Proteins don’t automatically warrant a design inference. It depends on the function of the protein and interdependencies on other proteins. A signalling protein could easily get a random mutation that slightly modifies a biologically active site making it more or less able to bind with a target and that can change a whole downstream cascade of events with large scale ramifications. I think I read recently that such a site has been implicated in whether a dog turns out to be a large or small breed, for example, as the cascade result is how much growth hormone is produced. It’s not the sole determinant though as you can cross a large breed sire with a small breed bitch and the puppies never turn out so large the mother can’t bear them.

On the other hand some proteins that are components in intricate molecular machines and because their shape must critically match the shapes of other components for the machine to function variations that change the shape would cause the machine to not work without simultaneous variations that change the shape in other proteins. These simultaneous changes seem to go far beyond any reasonable odds of happening together. Click on the “Categories” sidebar Molecular Animations to see some examples of this type of molecular machinery. People have found this one particularly compelling for its simplicity, ease of understanding, and difficulty in imagining how it could have evolved ex nihilo. The problem it solves is DNA supercoiling which must have been a problem from the very first DNA molecule, all forms of life have one or both these machines in them, so it presents a classic chicken/egg problem with only one protein involved. What came first, the DNA molecule that has to have a topoisomerase family enzyme in order to be unwound for replication and reading or the DNA molecule that carries the information required to construct a topoisomerase enzyme? And this is a very very simple machine made of a single protein unlike many others you’ll see in that animation series in which the machines are formed of multiple proteins. A ribosome in particular is composed of many different proteins and ribonucleic acids working together. The whole machine must be assembled and working in order produce the parts that make the up machine that makes the parts! This particular machine is also present in every form of life and is so basic (it’s the machine that reads the coded information in a gene and builds a protein according to the coded assembly sequence) no life as we know it is possible at all without it. How’d that happen without a designer envisioning the entire machine in abstract then building all the hundreds of interlocking pieces that make it up simultaneously? It’s like proposing that you can build an automobile by starting off with randomly shaped chunks of metal and just randomly changing the shapes until they all fit together into a working automobile. To compound the problem you need a fully working automobile to gather the parts together to make an automobile. This is the story the chance & necessity pundits ask you to accept and take as a matter of materialistic faith that, impossible as it sounds, eventually science will reveal how it was done without intelligent agency.

And speaking of dogs, that brings up what appear to be fundamental limits on variation that mutation and selection can produce. Dogs are possibly the most widely varying species on the planet while still remaining a single species. In 20,000 years of artificial selection and preservation of variants that never would have survived in the wild there hasn’t been a single variant with an anatomical feature not characteristic of canines nor has a new species of dog emerged. Not even something as simple as a retractable claw. The variations are entirely limited to the deleterious (dogs are predisposed to a large litany of genetic disorders) and the cosmetic. You can get big dogs and small dogs (change in scale) you can get wide variation in ratio of body part size (change in aspect), you can get broadly different coloration, patterning, coat length and thickness, and that’s about it. What artificial selection and preservation can’t accomplish seems to be even farther beyond the scope of natural selection and preservation which is restricted in that any variation must be either nearly neutral or decidedly beneficial in order to have the selection value required to fix the variation within the population.

Island species are another good example of these limits. Isolation on an island for millions of years and the quite different environmental pressures (or lack thereof) drives selection at an accelerated rate for island species. The result is often dwarfism or gigantism but never any variation on the level required for evolution writ large like the appearance of a novel cell type, tissue type, organ, or body plan. In short, the observed limits of highly accelerated natural selection over millions of years are same kind of limits in variation you see in dogs through thousands of years of artificial selection but nothing beyond that. It appears there is something other than random mutation and natural selection that produces the fundamental differences between the higher taxonomic categories.

Intelligent agency solves all these problems. We already know for a fact that intelligent agency with the capability or near capability of building or modifying complex organic machines in defiance of impossible odds of random assembly is extant in the present universe. That agency is us. The question then becomes one of how many such agencies exist in the universe, what forms they can take, did any of those possible forms predate humanity, and did they have the physical means, motive, and opportunity to accomplish the things we see here without violation of any known laws of physics. For example any agency in a remote galaxy would be prohibited from influencing anything in this galaxy because of the limitation imposed by the speed of light barrier. Given that normal matter and energy compose only a small fraction (5%) of what makes up the universe it seems premature to rule out exotic forms of intelligent agency that could very well be composed of non-baryonic matter that we only suspect exists through indirect observation of its gravitational effects on normal matter. In fact what we consider normal matter and energy may be the minority component and thus really an atypical form in the big picture – the froth on the top of an unplumbed ocean. Hubris is rampant in the halls of science today. Of course that’s nothing new. The history of science is littered with disgarded theories that were once thought to be writ in granite. Thinking we have a fundamental understanding of nature where that understanding is lacking only in the fine details is something that has plagued inquiry since the getgo.

gpuccio, enjoyed your comments yet again... with this complexity on the molecular level, it is hard to fathom that RM&NS & whatever new version "EvoDevo" account for the building blocks of life combinatory processes, much less being conserved, repaired and simultaneously supplying the "builders" of those blocks in the first place. It is like magically seeing a church appear one step at a time, with one step of a human at a time. The wood for the floor appears, the nails appear, the hammer appears, the hand to hammer the nail appears, the eyes appear to guide the hammer, but with all of this coordination, there is no mind to guide the eyes, the hand, and the hammer onto the preprocessed nails into the wood floor. Oversimplified, but obvious point. As Dave states, it is the proverbial chicken/egg conundrum. Michaels7
"the puppies never turn out so large the mother can’t bear them." Uhoh - evidence of a benevolent designer! (Or a malevolent designer that was not all-powerful?) Designed Jacob
Davescot: "For me the real clincher is not individual proteins but assemblages of proteins. There’s more complexity in the assembly instructions IMO than in the individual proteins. " While I wholeheartedly agree with you about the unfathomable complexity of assemblages, I think you are too optimistc about single protein engineering. I think that both single proteins and their assemblages are incredibly and irreducibly complex. About proteins, we have to remember a few things: a) Any configuration of a 120 aminoacid protein (a small one, indeed) has already a higher complexity than the order of magnitude of Dembski's UPB (1:10^150). Let's remember that that's a very high limit, and that Dembski has really been fair and generous towards our opponents in fixing it so high (or so low, if you prefer). A realistic limit, appropriate for our planet and reasonable assumptions about the origin of life in it, should be of many, many orders of magnitude lower. b) It is certainly true that not all the parts of a protein have the same functional importance, and that some domains are functionally critical, but still the whole configuration of the molecule, the assemblage of its subunits, the polimerazition of the final molecules, the addition of other biochemical groups (carbohydrates or else), are all important and relevant steps to both function and stability of the protein. That leaves us with a potential search space for configurations which is really unimaginable and uncomputable. c) Proteins have both a structural and a functional role. While structural proteins can sometimes be simpler, functional proteins are usually enzymes. The role of an enzyme is to incredibly accelerate a biochemical reaction which would practically not take place in absence of the enzime itself. Enzymes are wonderful molecular machines, whose mechanism of action still defies our understanding. Usually, the current model for an enzymatic function is that the enzyme must very specifically bind the molecules which have to react, and "force" them to react by creating a perfect context, both spacial and biochemical, of interaction between its substrates. So, in my opinion, any enzyme (and we have lots of them) is a very irreducibly complex machine: it has to bind the substrate, and to do so in ideal conditions so that the molecular reaction (an absolutely improbable molecular reaction, of itself) can take place, and at a very high rate. Moreover, any enzyme is usually precisely regulated, at various levels, in different cells and in different functional moments in the same type of cell. That's why I do think that the design of an enzyme has to be a very intelligent task. The relationship between primary structure and 3D folding is still a mystery, as you correctly point out. The richness and specificity of biological enzymatic proteins demonstrate that passing from one enzyme to another one is not a simple task, neither for blind evolution (absolutely impossible) nor for a human designer (at present, practically impossible). Obviously, it is possible to pass from one molecule to very similar ones, through small, one bit variations, and it is true that some mutations keep the function, others only determine a slight loss, while others cause a more or less complete loss of function. To my knowledge, it is still to demonstrate that casual mutations may cause an increase in function in a preexisting protein, although such a concept, at least for small quantitative variations, is not totally impossible. What is impossible is that an enzyme targeted for a specific reaction can become "another" enzyme, targeted for another function, by simple casual mutations. Equally impossible is that a great number of such simple casual mutations can transform an enzyme into another through a more or less comtinuous path of minimal mutations, each of which must represent a new, different, selectable function (or increase of preexisting function). Everybody should see the utter impossibility of that concept (which, indeed, is what classical darwinists believe!), but if you can't see it, you are invited for the nth time to suggest any step by step path of selectable mutations at the molecular level from one enzyme to another. Any. d) The immune system, again, is a good model of that all. In the immune system, the problem is simpler, because it is limited to recognition of form, without immediate functional connection. Indeed, antibodies recognize the specific form of an antigen, while the functional reaction that follows is in some way stereotyped according to few possibilities. Remember that, in order to create the basic repertoire necessary to recognize (weakly) most epitopes, the organism has to use a battery of very specifically concieved raw genes (V,D,J), and rearrange them very creatively to "cover" in some way, and with much approximation, the search space of epitopes. And epitopes are small peptidic sequences, usually 3-20 aminoacids long, and therefore the search space is not so huge. But, after the immune response, the organism has still to enact the wonderful mechanism of hypermutation and intelligent selection (based on the memorized information of antigen conformation) to produce specific, higly reactive antibodies. That model should show us how difficult it is to create a specific receptor even for a small proteic sequence (an epitope), using a highly specialized and complex molecular machine such as the immune system and its coding DNA, and various specialized cell types such as antigen presenting cells, B and T lymphocytes, etc. Therefore, I really believe that the engineering even of a single functional protein, appropriate for a specific functional context, is always an extremely high level design program. gpuccio
Imagine polypeptides in "a layer 1 meter thick covering the surface of the entire earth." "If these polypeptides reformed with new sequences at the maximum rate at which chemical reactions may occur" for 5 billion years, then even under those conditions... "...we find the probability of producing one protein of 101 amino acids in five billion years is only 1/10^45. Using somewhat different illustrations, Steinman and Cairns-Smith also came to the conclusion that chance is insufficient." "It is apparent that "chance" should be abandoned as an acceptable model for coding of the macromolecules essential in living systems. In fact, it has been, except in introductory texts and popularizations." Excerpts from The Mystery of Life's Origin, p. 146, by Thaxton, Bradley, and Olsen, 1984. It should be apparent that even if one invoked a miraculous degree of "luck" to produce a protein, one protein cannot a cell make. Clearly something other than amino acids mixing in the mythical prebiotic soup is needed to account for proteins. For more, see the Steven Meyer origin of life articles at the previously provided link. ericB
I believe there is a small communication difference here. If we are starting from an organism with DNA and proteins, and then observe the making of one more protein that is merely a slightly mutated variation on another existing protein, then DaveScott is right to say this isolated protein does not warrant a design inference. On the other hand, I had the impression that UD member Fross was alluding to something quite different when he said "I understand that the ID position is that the protein itself had to have been designed, not the variations that can occur through mutation." Stephen Meyer has written a number of times about the problem of the origin of life. http://www.arn.org/authors/meyer.html The fact that there should be proteins at all is highly improbable -- so much so that origin of life researchers have given up on the idea of life starting from proteins. Neither chance nor laws can account for the existence of proteins, nor have any other routes to life found a soft, gentle path up the mountainside to proteins. ericB
Possibly but that's still qualified with "most" proteins leaving an opening for some not being designed. Moreover, I don't think there is currently enough evidence to support the conclusion that functional proteins are quite so isolated in sequence space. There may very well turn out to be a set of building blocks of which most or all proteins are constructed. We don't have a handle on protein folding yet (prediction of protein folding is a Holy Grail in biochemistry). Families of proteins with similar construction are common and cooption for functions not shared by other family members is also common. Gene duplication is common and provides a mechanism for moving through sequence space from one island of functionality to another. There may be paths from one island to another which make sequence space more navigable than one might otherwise think. For me the real clincher is not individual proteins but assemblages of proteins. There's more complexity in the assembly instructions IMO than in the individual proteins. You can look at a pile of auto parts and while each part might be rather unique it's the assembly instructions that are really hard to come by without forethought. DaveScot
Didn't Stephen Meyer's paper "The Origin of Biological Information..." (Proceedings of the BSW), claim that amino acid sequences that consistently fold up into a unique, stable, 3D shape, are highly isolated in amino acid sequence space? If so, that might extend the irreducible complexity argument to most proteins, irrespective of their ability to work with other proteins in a functional, subcellular machine. DarelRex

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