Uncommon Descent Serving The Intelligent Design Community

From Protein Science, “The Levinthal Paradox of the Interactome”

Share
Facebook
Twitter
LinkedIn
Flipboard
Print
Email

Paul Nelson highlights an interesting paper that appeared relatively recently in the journal Protein Science entitled “The Levinthal Paradox of the Interactome.” The paper’s abstract reads,

The central biological question of the 21st century is: how does a viable cell emerge from the bewildering combinatorial complexity of its molecular components? Here, we estimate the combinatorics of self-assembling the protein constituents of a yeast cell, a number so vast that the functional interactome could only have emerged by iterative hierarchic assembly of its component sub-assemblies. A protein can undergo both reversible denaturation and hierarchic self-assembly spontaneously, but a functioning interactome must expend energy to achieve viability. Consequently, it is implausible that a completely “denatured” cell could be reversibly renatured spontaneously, like a protein. Instead, new cells are generated by the division of pre-existing cells, an unbroken chain of renewal tracking back through contingent conditions and evolving responses to the origin of life on the prebiotic earth. We surmise that this non-deterministic temporal continuum could not be reconstructed de novo under present conditions.

Download the full paper here.

Comments
p.s. case in point: punctuated equilibrium that's not to say that gradualism is not necessary, but that given non-gradualistic data, the contradictory data can be circumvented.JGuy
October 29, 2012
October
10
Oct
29
29
2012
12:28 PM
12
12
28
PM
PDT
Joe@7:
To provide evidence in favor of common descent you need patterns of nested hierarchy.
Where is *nested* hierarchy predicted by common descent? or even necessitated by common descent? Give different data (not nested and/or not hierarchical data), a narrative could be constructed by evolutionist to accommodate it. JGuyJGuy
October 29, 2012
October
10
Oct
29
29
2012
12:25 PM
12
12
25
PM
PDT
1) We look at the complex machinery in the cell, and we conclude that it could not have come to exist merely by fixing random molecular events that happened to confer incremental advantage to the reproducing organism. The space of probabilities is too huge and the required events too constrained for this to be possible, even given more than the time available since the beginning of the universe. 2) We look at the complex 3D conformation of proteins, and we conclude that they could not fold merely by random molecular actions. The space of possible conformations is too huge and the space of functional conformations is too constrained for this to be possible, given the time we observe (from fractions of a a second to a few minutes). Now, in the first case, we conclude that intelligent agency must have designed and assembled the first cell, because the probability of cells forming otherwise is too small in the time available. But although the probability of proteins folding correctly is likewise too small in the time available, we do not conclude that intelligent agency is involved in each folding event. Rather, we conclude that something is guiding the proteins to fold correctly, and we do not (yet) understand the mechanism involved. We conclude that this mechanism was itself originally designed in order to make the proteins functional, but then the mechanism operates within our bodies without further intelligent intervention. So the question is this: By what principle do we conclude that the first cell was assembled by an intelligent agent, but proteins are not folded by intelligent agents? In other words, why don't we conclude that intelligent agency is required for each folding event, or conversely, why do we believe that we will eventually explain folding in terms of physical chemistry, but we will never understand origin of life that way?dogdoc
October 29, 2012
October
10
Oct
29
29
2012
10:07 AM
10
10
07
AM
PDT
Instead, new cells are generated by the division of pre-existing cells, an unbroken chain of renewal tracking back through contingent conditions
By the same logic, the development of every human from single cell to adult is makes a very interesting and compelling case for universal common ancestry.Mung
October 28, 2012
October
10
Oct
28
28
2012
06:10 PM
6
06
10
PM
PDT
@Arthur
Instead, new cells are generated by the division of pre-existing cells, an unbroken chain of renewal tracking back through contingent conditions
How is this any more than repeating the party line? To provide evidence in favor of common descent you need patterns of nested hierarchy. But they can't be found in either genetics* or morphology. *The one exception may be the patterns of broken genes, such as vitamin C, primate olfactory, and the mammalian yolk gene (vitellogenin). But in the same vein I've seen others cite patterns of broken genes that break phylogeny, making me wonder if convergent forces may be at play. And for the latter, I know bees also use vitellogenin for an entirely different purpose. Many other pseudogenes have later been found to have function, and I remember one 2011 paper in RNA that even argued the term "pseudogene" was a misnomer. Still, this is an area I hope to study more in the future.JoeCoder
October 27, 2012
October
10
Oct
27
27
2012
09:17 AM
9
09
17
AM
PDT
The paper makes a very interesting and compelling case for universal common design.Joe
October 27, 2012
October
10
Oct
27
27
2012
07:03 AM
7
07
03
AM
PDT
JoeCoder, A sentence in the quoted snippet above conveys the message: Instead, new cells are generated by the division of pre-existing cells, an unbroken chain of renewal tracking back through contingent conditions The cited paper doesn't really say much, contrary to Paul's claims in the linked EN&V piece. We've known for, like, forever that equilibrium chemistry isn't the usual condition for living cells; the paper merely re-states this in terms of the myriad protein-protein interactions that have been identified. The exponents bandied about are pretty irrelevant to real-life biology and biochemistry, and it seems almost silly to me to get worked up about them.Arthur Hunt
October 26, 2012
October
10
Oct
26
26
2012
07:44 PM
7
07
44
PM
PDT
@KF Thanks for the detailed reply. I had no idea that admission on the peer reviewed record is a major step forward." I hadn't seen anyone disagree that the space of possible interactions was anything less than 10^huge. @Arthur Hunt I haven't read it. How so?JoeCoder
October 26, 2012
October
10
Oct
26
26
2012
07:52 AM
7
07
52
AM
PDT
The paper makes a very interesting and compelling case for universal common ancestry.Arthur Hunt
October 26, 2012
October
10
Oct
26
26
2012
05:56 AM
5
05
56
AM
PDT
JC: What happens is that first, the paper admits -- on the peer reviewed journal record -- that the issue of vast config spaces is real. That is, there is an obvious challenge that for things that are complex and multipart, depending on proper arrangement for function, there are a great many more ways to get it wrong than to get it right. Dawkins' admission is going to be news for many of the objectors to this pattern of thought we see here at UD and in the penumbra of critic sites:
It is true that there are quite a number of ways of making a living -- flying, swimming, swinging through the trees, and so on. But, however many ways there may be of being alive, it is certain that there are vastly more ways of being dead, or rather not alive. You may throw cells together at random, over and over again for a billion years, and not once will you get a conglomeration that flies or swims or burrows or runs, or does anything, even badly, that could remotely be construed as working to keep itself alive. (The Blind Watchmaker, 1987, p. 9)
Sadly, that admission on the peer reviewed record is a major step forward. For, there has long been a reluctance to admit the patently plain, due to its implications and tensions with the picture of an easy path from Darwin's warm little pond or the like to life forms and onward to body plans. Next, look on how Dawkins tries to work its way out of the underlying challenge:
You may throw cells together at random, over and over again for a billion years, and not once will you get a conglomeration that flies or swims or burrows or runs
In short, he is going to try to present the alleged magic of chance variation plus DETERMINISTIC natural selection as the wonderful key to progress. But to see the first holes in that, all it requires is peeling back a few years to get this damaging admission in a moment of unfortunately uncharacteristic honesty on this general topic from Wiki's article on Natural Selection (the hero of the Darwinist plot-line . . . ), which of course has been patched up with a party line talking point more recently:
Natural selection is the process by which favorable heritable traits become more common in successive generations of a population of reproducing organisms, and unfavorable heritable traits become less common. Natural selection acts on the phenotype, or the observable characteristics of an organism, such that individuals with favorable phenotypes are more likely to survive and reproduce than those with less favorable phenotypes. The phenotype's genetic basis . . . will increase in frequency over the following generations. Over time, this process can result in adaptations that specialize organisms for particular ecological niches and may eventually result in the emergence of new species. In other words, natural selection is the mechanism by which evolution may take place in a population of a specific organism.
In short, there is actually every good reason to see that NS is a weak force, and one that is fundamentally stochastic. Chance based, in short. Differential reproductive success of varieties in environments is not necessarily a positively adaptive trait at all. In fact, since we are looking at relative success in particular environments, an overall deterioration and loss of functional capacity is quite consistent with such forces -- as a simple example think about insects losing their wings on islands, or Tom Cod surviving in polluted waters but which are not able to out-compete their neighbours in less messed up waters nearby. As is simple drifting if pop sizes, mut rates etc are not adequate. And for something like a whale body plan, that is blatant. (Notice how objectors recently studiously tiptoed around the pop scale and time to fix muts challenges posed by Sternberg and also by Berlinsky.) If that is bad enough to seriously question the dominant growing tree of life narrative, think about the problem at its root. For, here we do not have reproductive capacity based on von Neumann, code based self replication, to call upon. We have chemicals in ponds etc, which have only the usual statistical forces and factors, plus some hugely endothermic reaction patterns to address, as well as the challenge of homochirality in observed life. (This last means that at every stage, the odds are only 50:50 or so that the next monomer added will have the right geometrical handedness, which can play havoc with key-lock fitting requisites of cellular nanomachines, and with protein folding in particular. That's one yes/no question -- one additional bit of info -- per monomer in the chain, save for one or two of the input monomers that are too simple to be chiral. On balance, that adds a lot more complexity and tosses a huge puzzle on how do we end up with the sort of dominant handedness that observed lie forms have. So, OOL is at the root of the claimed growing tree of life, and it poses the island of function challenge. As the saga of the 6,000 word essay offer shows, consistently ducked and diverted from. Look [smell], a squirrel [red herring] over there! Look, another one! And, another! Where those red herrings are being led away to repeated strawman caricatures, many of which are already soaked with ad hominems and just wait for the right incendiary rhetoric to burst into confusing, issue-clouding, polarising, atmosphere poisoning flame. So, the importance of the article is not to be underestimated. Never mind, that islands of function are an obvious and abundantly empirically confirmed result of multipart functionality depending on specific arrangement of parts. Never mind that the implied easy incremental path from chemistry etc in a pond to a gated, encapsulated, metabolic automaton with a vNSR has yet to be empirically warranted enough to move out of the just so story territory. Never mind that he powers of differential reproductive success resulting from chance variation in reasonable environments have not been empirically shown as capable of generating novel body plans and never mind that there are serious questions on the pop genetics etc to get there as the whale etc show. Nope, we "know" that to be properly "scientific," accounts of origins MUST only explain on blind chance and necessity. And we "know" that the overwhelming "consensus" of the experts is that there is a successful account. And, we can dismiss such things as challenges on history and phil of sci or the logic of that materialistic a priorism. In short, there are some serious questions that are definitively on the table and need some serious, empirically well-warranted answers. One of those is most unwelcome in the School of Darwin: design. KFkairosfocus
October 25, 2012
October
10
Oct
25
25
2012
10:46 PM
10
10
46
PM
PDT
I was hoping this would get posted here so I could comment (UD really needs a forum!). The paper is closed and I haven't yet sought alternative means to get it, so I can share my thoughts on that. But I honestly don't understand what the big deal is. Haven't we always known that there's nearly 10^huge possible configurations for molecules in a cell, as well as the number of possible interactions between protein surfaces? The important question is: Are there gradual paths (originating from a simple molecule) across this ridiculously sparse landscape? I've long said "no", but I don't understand how this paper advances this idea. Maybe I've missed the big idea?JoeCoder
October 25, 2012
October
10
Oct
25
25
2012
05:16 PM
5
05
16
PM
PDT

Leave a Reply