More Biological Fine Tuning
Protein-coding genes provide a sequence of nucleotides that is read three nucleotides at a time. Each triplet is translated into a particular type of amino acid. So a sequence of 300 nucleotides codes for 100 amino acids, which are attached to each other to make a protein. But what if you started not with the first nucleotide in the sequence, but with the second one? You would have a different sequence of nucleotide triplets, and so a different sequence of amino acids. This is also true if you started with the third nucleotide. In fact you could switch over to the opposing DNA strand (the other half of the double helix) and again you would have the choice between three different “frames,” resulting in three different sequences of amino acids. So in all you can choose between six different reading frames. So any given gene has the theoretical possibility of containing different genetic messages, in the different reading frames. And indeed, years ago it was discovered that genes are overlapping—portions of their nucleotide sequence exist on the same segment of DNA, just in a different reading frame. But an even more bizarre theoretical possibility is that the reading frame could shift while the sequence of nucleotides is being read. In that case you are mixing and matching partial sequences from different reading frames. Now, a
new study has investigated this capability and discovered a fascinating mechanism that apparently enables the real-time frame shifting.
Nucleotide sequences are translated into amino acid sequences at the cell’s ribosome structures and the new study found that this translation process can be programmed to skip a nucleotide, and so switch to another reading frame, attaching two short snippets of nucleotide segments, known as microRNAs, to the main nucleotide sequence at certain locations. The study suggests that a pseudoknot, or triplex, RNA structure is formed causing the skip to occur. Of course the right nucleotide sequence is required, and the right microRNA sequences are required. It was not easy to solve this complicated puzzle, as one researcher
explained:
These are really complex RNA structures. It takes a lot of computer memory to search for them in human cells. It wasn’t until the past decade that computers were fast and powerful enough to find these signals.
It is yet another “novel mode” of realtime biological response resulting in “fine-tuned” cell performance. It all just smacks of random mutations.
As I pointed out over at Uncommon Descent, in this case the frameshifted version of the gene is nonsense. From the article:
ReplyDelete"In the case of CCR5 [the human gene found to have a programmed frameshift -GD], the frameshift changes the codons behind it into nonsense RNA. Since the ribosome can’t read them, other components of the cell step in and destroy the messenger RNA and its associated proteins."
"This might seem like a bad thing. But symptoms like fever are caused by our bodies’ immune response, not the underlying illness. And the immune response occasionally gets out of control, causing serious, sometimes fatal side effects."
"Dinman believes that by killing the messenger RNA and its array of immune system proteins, frameshifting acts like a dimmer switch, lowering the immune response to a safe level."
So it's not "fine-tuned", at least in that sense.
Thank you Gordon for the comment. I think it is clear that the authors were not referring to that when they referred to the design as "fine-tuned."
DeleteCornelius Hunter: It all just smacks of random mutations.
ReplyDeleteIt smacks of evolution.
Fascinating...!
ReplyDeleteThe overlapping nucleotide sequences remind me of programmer's "subroutines"--portions of code that are used over and over when called by higher level routines. Or the compression algorithms used by image processing systems.
"Finely tuned" begins to describe it. But the process described in the article you referenced sounds masterfully designed for conserving energy, time and spacial resources. I don't know how anyone can consider a functional wonder like this to be the "genius of blind, purposeless chance." While the "genius of evolution" is an oxymoron--there's no genius in purposelessness--the "genius of an intelligent designer" makes sense because it is simply far more logical.
When networks evolve by preferential attachment, it tends to result in scale invariance. That's a much closer match to biology than design.
Deletehttp://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001381
DeleteIf if's and but's were candy and nuts...
''When networks evolve by preferential attachment, it tends to result in scale invariance.''
ReplyDeleteDemonstration please.
bpragmatic: Demonstration please.
DeleteHere's a simple applet of a network evolving by preferential attachment, called the Barabási-Albert model.
http://mokslasplius.lt/rizikos-fizika/en/barabasi-albert-model
See Barabási & Oltvai, Network biology: understanding the cell's functional organiziation, Nature Reviews Genetics 2004. Also Zhu et al., Getting connected: analysis and principles of biological networks, Genes & Development 2007: "Assembly of interactions into networks reveals that current versions of biological networks are not randomly organized but rather have a 'scale-free' format containing hubs with many connections and a large number of nodes that have one or a small number of connections."
(Biological networks resemble scale free networks, but vary somewhat, possibly due to the prominence of drift.)
Hmmm, or possibly because there has to be a command chain to develop the whole thing from the same stretch of DNA. Maybe you should just wait until they decode more of the spliceosome code and see if there are any other gene segments that are used in 17 different ways throughout development. Data compression of this magnitude would be worshiped by programmers. The idea that it can exist in the real set is almost unbelievable given the constraints each schema imposes on the next and the new context provided with each instance. The idea that it could be found without intention is laughable. In other conversations, the whole idea of specifying a pattern to match in advance is anathema to evolutionists. But here, well it's just preferential attachment, it's what exists, so it's obviously what evolution must have done. What a joke.
DeleteJohn: The idea that it could be found without intention is laughable.
ReplyDeleteNot an argument. We can study evolutionary algorithms, and see that they can create just these sorts of intertwined structures.
John: But here, well it's just preferential attachment, it's what exists, so it's obviously what evolution must have done.
Biological networks have the characteristics of a process of cobbling things together without an overarching plan.
Zachriel: "Not an argument."
ReplyDeleteThat was just the result of the argument that preceded it that you did not respond to.
Zachriel: "We can study evolutionary algorithms, and see that they can create just these sorts of intertwined structures."
They create nothing of the sort. They create in kind models of hubs and lines.
Zachriel: "Biological networks have the characteristics of a process of cobbling things together without an overarching plan."
A rotary engine with the associated machinery to build itself is a perfect example of an overarching plan. If you reduce the relationships to hubs and lines, the only thing "cobbled together" is your model.
Zachriel: We can study evolutionary algorithms, and see that they can create just these sorts of intertwined structures.
ReplyDeleteJohn: They create nothing of the sort.
They don't create intertwined structures? Really?
John: They create in kind models of hubs and lines.
No more so than the result of biological evolution is an "in kind model". The result of an evolutionary algorithm maps the *relationship* between the phenotype and the environment.
John: A rotary engine with the associated machinery to build itself is a perfect example of an overarching plan.
Yes, and biological networks look nothing like a rotary engine.
Zachriel: "They don't create intertwined structures? Really?"
ReplyDeleteYou left out the word "these".
Zachriel: [They create in kind models of hubs and lines...]"...No more so than the result of biological evolution is an "in kind model".
Your continuation of my comment is incoherent. My original point was that the network would appear scale free because of the program an organism follows as it develops (and this is just one possible example). It may look so scale invariant because if you had to design so much to come from so little, you would be so constrained. You then could reduce your claim to saying basically, "we don't see any designs with this level of orchestration, this number of plans within plans", but that's really begging the question then because at the level we are capable of, we do create scale invariant contraptions. A Mazda would be a good example. Saying this requires more intelligence, so it can't be designed seems counter intuitive.
Zachriel: "Yes, and biological networks look nothing like a rotary engine."
I was talking about ATP synthase. It would look about as opposite of "cobbled together" as is possible to imagine.
John: You left out the word "these".
DeleteThey're not exactly the same. However, they are intertwined in a fashion expected of an evolving network.
John: My original point was that the network would appear scale free because of the program an organism follows as it develops (and this is just one possible example).
Sure, assuming it builds the network without regard to an overarching plan.
John: "we don't see any designs with this level of orchestration, this number of plans within plans"
The scale invariance is characteristic of preferential attachment, not planning.
John: I was talking about ATP synthase.
ATP synthase is not a network. Glenn J had introduced the analogy to computer programs.
Zachriel: "They're not exactly the same. However, they are intertwined in a fashion expected of an evolving network."
ReplyDeleteNow you're just restricting your comment to the network topology itself. I'm fine with that.
Zachriel: "Sure, assuming it builds the network without regard to an overarching plan."
but it does follow an overarching plan. You can debate about whether evolution wrote it or an intelligent agent, but it's clearly a plan. We even call them body plans.
Zachriel: "The scale invariance is characteristic of preferential attachment, not planning."
An engine is reused in a different context. The lines from the module to the new context will be fewer on average than the lines within. The new context may also be used as a module as part of a greater application - perhaps an optical drive in a computer. It does not follow that the motor was not planned simply because a pattern that mimics preferential attachement was followed. Therefore your dichotomy is an illusion.
Zachriel: "ATP synthase is not a network."
One of the four maps in the paper you cited was protein-protein interactions. ATP synthase is a protein complex. It's components interact. They would have lines drawn between them. You seem to be looking at networks more narrowly than the authors you cited.
John: Now you're just restricting your comment to the network topology itself. I'm fine with that.
ReplyDeleteOkay.
John: but it does follow an overarching plan. You can debate about whether evolution wrote it or an intelligent agent, but it's clearly a plan. We even call them body plans.
You're conflating meanings of plan. As we were referring to the evolution of the network over time, the plan refers to whether a specific network structure was planned for early in the evolution of the network, which it was not.
John: An engine is reused in a different context. The lines from the module to the new context will be fewer on average than the lines within.
Does it follow a power-law distribution?
This comment has been removed by the author.
ReplyDeleteZachriel: "You're conflating meanings of plan. As we were referring to the evolution of the network over time,..."
ReplyDeleteI wasn't. I was referring to what might be a necessary topology to unpack compressed data during embryonic developement and you responded to that.
Zachriel: "planned for early in the evolution of the network"
did you get mixed up while trying to create a little heads I win tails you lose scenario?
Zachriel: "Does it follow a power-law distribution?"
In a car there is probably one engine with many parts attached to it. There are more belt buckles with fewer parts. Ditto for simple fasteners.
John: I was referring to what might be a necessary topology to unpack compressed data during embryonic developement and you responded to that.
ReplyDeleteThis is the first mention of embryo on the thread. In any case, scale-free isn't the usual way known planners create plan.
John: did you get mixed up
Not at all. Scale free is a characteristics of a tinkering process, not a process leading to a specific end.
John: In a car there is probably one engine with many parts attached to it.
That doesn't make it a power-law distribution, though there may be some of that, especially in experimental models, which are more likely to develop by tinkering. Have you looked at a schematic of an automobile? They don't look much like a power-law distribution.
Zachriel: "This is the first mention of embryo on the thread."
ReplyDeleteof the word per se yes, but all the talk of development and body plans largely overlaps the concept.
Zachriel: "In any case, scale-free isn't the usual way known planners create plan."
I think the more advanced designs are more scale free within limits, perhaps one or two orders of magnitude more constrained than in biological networks. Perhaps a matter of degree is what you are focusing on?
Zachriel: "Scale free is a characteristics of a tinkering process, not a process leading to a specific end."
One possible reason we see this in designed things may be due to constraints of space.
Zachriel: "That doesn't make it a power-law distribution, though there may be some of that, especially in experimental models, which are more likely to develop by tinkering"
It seems you started out contrasting signals from evolutionary tinkering and human design, but now you are maybe trying to show that all human designs came from tinkering and so maybe that's why we see similar signals.
Zachriel: "Have you looked at a schematic of an automobile? They don't look much like a power-law distribution."
Maybe you have to translate it to hubs and edges before the clear evidence of tinkering can be seen.
John: One possible reason we see this in designed things may be due to constraints of space.
DeleteDon't see it. We'd be happy to review any study you provide.
You didn't comment on the first one which is far more compelling. The longer a species remains in existence, the more chances it should have to undergoe speciation events on average. We should expect to see the results of preferential attachement. We don't.
DeleteI'm not sure why anyone would study human designs to see if they follow power laws at the few levels of scale they might be represented by. I don't see why you wouldn't find hosts of examples of theme reuse at different levels that would closely resemble it though. But no, I'm not going to look for a study for something that intuitive especially when you still haven't responded to the first one.
John: The longer a species remains in existence, the more chances it should have to undergoe speciation events on average.
DeleteThat's not necessarily the case. There are a lot of factors in rates of speciation.
John: We should expect to see the results of preferential attachement.
We see evidence of power law distributions in ecosystems.
John: But no, I'm not going to look for a study for something that intuitive especially when you still haven't responded to the first one.
In other words, you have no support.
Zachriel: "That's not necessarily the case. There are a lot of factors in rates of speciation."
ReplyDelete"on average"... that's why they sampled more than one clade. There sample size was pretty impressive I thought
Zachriel: "We see evidence of power law distributions in ecosystems."
I'm sure you see things approximating it everywhere. We don't see them in rates of speciation over time however. Unfortunately for the theory of common descent, this is what we should see as new protiens can only attach to those that already exist.
Zachriel: "In other words, you have no support."
In other words, things that obvious don't need extra support. I already gave you great examples - an engine, a computer and an automobile. I already gave you two different plausible reasons to explain why we see it - space constraints and theme reuse. You just claimed you don't see it. I'm sorry if you need more. I don't because I don't really consider the criteria very strict. There's not really that much difference in scale to measure any strict adherence to a power law anyway. I don't really find it compelling and I think it's a pretty good indication of the type of arguments evolutionists resort to.
John: We don't see them in rates of speciation over time however. Unfortunately for the theory of common descent, this is what we should see as new protiens can only attach to those that already exist.
ReplyDeleteThis seems very confused. Why does a power law in proteins imply that rates of speciation must follow a power law? Or what are you saying?
John: In other words, things that obvious don't need extra support.
Of course it needs support. A power law distribution is a very specific mathematical pattern.
Zachriel: "Why does a power law in proteins imply that rates of speciation must follow a power law?"
ReplyDeleteOne would seem to affect the other. Originally I cited it as a description of a biological network where preferential attachement was directly theorized to occur, but yes, the one should be the macroscopic result of the other.
Zachriel: "A power law distribution is a very specific mathematical pattern."
But we're talking about the approximation of that pattern and the difficulty of a small scale over which to test it, not the fact that you can graph it as a line.
John: But we're talking about the approximation of that pattern and the difficulty of a small scale over which to test it, not the fact that you can graph it as a line.
DeleteYou made a specific claim, that the parts of an automobile follow a power-law distribution. You haven't been able to support the claim, and now seem to be retreating from it.
We can continue.. how many frames does a car have? Do few things attach to it or many? More or less than the engine? Is it just a few more things, or is it related to scale?
DeleteYou see that they roughly do within the constraints space obviously has on scale. I assumed you would understand this. I don't feel I've lost the point simply because we don't build machines the size of the sun.
Even the original paper you cited shows that hierarchical, modular networks can also be scale free (re my comments about module reuse, and programming).
But as I said, the point is almost moot to me. I was not sure how tightly you assumed biological networks followed these patterns. Here are some articles which echo many of my concerns. The first answered two of my questions, 1.) how different would the data be if plotted on the same axes, and 2.) what would happen if we compared "modern" proteins with more "ancient" ones.
http://pubs.rsc.org/en/content/articlehtml/2009/mb/b908681a#cit19
The second contains data sets cited by the first. Before this, I was going to propose to you that proteins only have so much space to bind to at any one time and that your theory ought to propose a certain amount of what these authors call "anti-preferential attachment". These authors developed what they call the CG method, which is a modified anti-preferential growth model and it matches yeast almost perfectly. The interesting design aspect is that if one node is connected to an existing node, it is more likely to be connected to other nodes in that neighborhood. Now from a design perspective this makes sense for parts in the same machine, as multiple faces would need to match in order to fit. But from an evolutionary perspective, why would not all manner of protein sub-units be randomly sticking to protein complexes until some of their other sides got "reworked" to also fit in and form some new "active site". I was going to ask about where all the "in the works" proteins were earlier. Just think about all those useless sticky boogers hanging on to everything waiting to become part of the next big protein complex! I mean, how many tries do you propose are needed and would be lingering around before you get things as elegant and efficient? But I wanted to focus on one thing at a time, so you could say this fell into my lap.
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000232