Uncommon Descent Serving The Intelligent Design Community

Mitochondrial ribosomes — Define “match”


Nick Matzke at PT describes a poster waved in protest at the recent Darwin vs. Design conference at Southern Methodist University. The poster read “Why do the ribosomes (protein synthesizing machinery) in our mitochondria match those of bacteria?” The intent behind this question was to suggest that we evolved from bacterial ancestors, whose remnants in us are the mitochondria and, presumably, their ribosomes, which the poster asserts “match” those of bacteria.

Since I’m happy for the sake of argument to allow common descent, the more interesting question for me is what causal powers were required to produce ribosomes in the first place. But the poster, even taken on its own terms, is problematic. Eukaryotic, prokaryotic, and mitochondrial ribosomes are all quite different (see here), and it’s not clear whether mitoribosomes, as they’re called, are closer to prokaryotic than to eukaryotic ribosomes by any reasonable metric. In any case, to say that bacterial (prokaryotic) ribosomes “match” mitoribosomes seems false on any reasonable construal of the term.

Designed Jacob re library code The first 13 years (~1980-1993) of my professional programming career was almost entirely assembly language and not much of it reusable. Millions of lines. The only programming I'd done in higher level languages was either in college (Basic, Pascal, Fortran) or one outlier project for a gameboy predecessor in FIG Forth at the very beginning of that time. Finally about 1994 I set aside the "real men use assembly language" credo and tried using C as by that time memory size and CPU speed constraints had become less critical in the PC world than the need to get large programming projects done quickly. Since I always had the option of dropping to inline assembly or linking with modules written in assembly it was relatively painless with little actual sacrifice. I soon discovered that I could get things done an awful lot faster so for the next 7 years I pretty much used C and C++ for everything and leveraged libraries of all kinds as much as possible. One problem I found with libraries though, especially more obscure ones written for specific tasks, is they have bugs in them and often the length of time it takes to work around or fix the bugs is greater than the time it would take to write the portion of the library needed yourself. DaveScot
Speaking of ribosomes, on "Intelligently Sequenced" (a very interesting ID blog, with emphasis on molecular biology) I found a link to this very, very interesting article: http://pubs.acs.org/cen/coverstory/85/8508cover.html I cite here a couple of passages which are very significant, but the whole article is full of astounding information, and confirms my idea that biophysics and bioengineering are our only hope to deppen our understanding of life: ""The view accepted by most people now is that the active-site nucleotide does not play a dramatic role in peptidyl transfer," Green says. The general consensus, she says, is that orientation and positioning of substrates by the ribosome structure accelerates ribosome catalysis much more than any specific chemical effect." "Although the ribosome per se may not promote peptidyl transfer in a very active chemical manner, it's possible that the P-site tRNA substrate does catalyze the reaction-a proposed case of substrate-assisted catalysis. The growing protein chain is attached by an ester to a 3′-hydroxyl on one of the P-site tRNA nucleotide residues. In 2004, Strobel, Green, and coworkers confirmed earlier hints that peptidyl transfer is accelerated by a neighboring 2′-hydroxyl group on the same nucleotide. They found that deleting that 2′-hydroxyl causes a millionfold reduction in ribosome catalytic activity." "Such revelations notwithstanding, the ribosome continues to hold onto a few secrets. "There have always been researchers who think that we understand how the ribosome works," Noller says. However, "at this point, in spite of high-resolution crystal structures and decades of biochemical, genetic, and biophysical studies, I don't think we understand the fundamental mechanisms at all," he says, "How do tRNAs and mRNA move during translocation, a process that involves molecular movements of many tens of angstroms every 50 milliseconds or so?" Noller asks. "What is the role of EF-G in that process? How does EF-Tu speed up binding of aminoacyl-tRNA to the A site by several thousandfold? The ribosome is enormous and tremendously conserved phylogenetically, yet the things we claim to understand at this point involve only a handful of nucleotides." "The questions are getting finer, and they're also getting harder to ask," Strobel notes. "Where one person says we have the answers, the next person says we have the questions."" Well, as this kind of knowledge increases, what need is there to still fight about ID? It will soon be absolute, spontaneous evidence to everybody. If "deleting that 2′-hydroxyl causes a millionfold reduction in ribosome catalytic activity", is anybody doubting the absolute specificity of such an information? gpuccio
Rude - it is beautiful. That's why the only code I ever really write is libraries: nothing but reusable code. Designed Jacob
Nick Matzke wrote: "Well, after holding up these signs for a while, the men on stage noticed and decided to answer one of them. They chose the last one, regarding ribosomes. Immediately, the only person on stage with any knowledge of biology, Michael Behe, took up the question. His answer was that ID theory does not allow for explanations regarding interspecies commonalities such as those implied in the question." Given that Behe accepts common descent, I find it difficult that this is the full answer that he gave to the audience. I hate to accuse Nick of dishonesty. Let's just say that I think he forgot everything Behe had to say about this example. Bilbo I
Rude, Plato destroyed the post-modernist argument 2400 years ago which is why few read or learn about his ideas anymore. Michael Sugrue has the greatest analysis of post-modernism I have heard. He calls it an intellectual cul-de-sac. On your comment: "each side is equally guilty of feigning and dodging" I am just suggesting that ID recognize the problems, address them as best they can as part of their presentation and move on to discussing the science. jerry
Jerry: “Each of the two sides tends to focus on what supports their side, which for each is what mainly undermines the other side.” Good point for introspection. However if we assume that the truth is not really our goal because it is not obtainable, and that each side is equally guilty of feigning and dodging, then we ought to just quit the pretense and join the postmodernists. Philosophers dispute endlessly the methodology of science and all too often forget that the real key is honesty—brutal honesty. Science is about really wanting to know. For the postmodernist there is nothing left but politics. Rude
People usually ask questions for two reasons. The obvious reason is that people ask questions to get answers. The other reason is that some people throw out questions, not really wanting an answer, but to highlight that there are questions to be asked. The more difficult to answer, the better. I think the sign protestors fall into category number 2. They were presenting questions that the theory of evolution explains easily and they wanted to highlight the lack of explanatory power of the ID position on those issues. While I think the posters were kind of funny, I wouldn't have bothered showing them. ID can explain everything. The designer has/had absolutely no limits. Things can be in common descent patterns, or not. They can be great designs, or poor. The designs can re-use pieces of other designs, or they can use new designs to accomplish the same function. That's just the nature of ID, and like Dembski said, ID doesn't need to match the level of detail that evolution theories have. Fross
As a sidebar to my previous post. My wife's company over the past 20 years was involved in sales force organization and communication. One of the fundamental things every salesman must learn is how to handle objections and anticipate what the objections will be beforehand and make answers to the objections part of the presentation. One of the things ID proponents should be trained to do when making presentations is to answer all the common objections as part of their presentation. It would undermine all the hecklers or sign waivers and marginalize their comments. jerry
Rude - yes, modularity and reusability are core programming principals. It is what separates a novice from someone who actually knows what they are doing. Atom
Each of the two sides tends to focus on what supports their side, which for each is what mainly undermines the other side. There is no mechanism that explains the changes in species or the construction of complex systems or proteins that have formed as sub-systems of organisms and the cell. Any random process that would lead to this complexity seems to defy belief. So ID emphasizes this. There a lot of anomalies in the actual species, which do not seem to make sense if someone was directing their construction. And why did it take such a long time to get to where we are if any intelligence was directing the process. And why did a benevolent God create such misery along the way. This is what the materialists focus on. Actually common descent could be logically part of each side and is a weak argument for either against the other. I know we have answers for their objections but they have answers for our objections. They are not equally persuasive but it seems the focus of each side's argument is on the weaknesses of the other side. jerry
A programmer once described for me some of the principles of beauty in programming, and one thing in particular I remember was—don’t remember the term—might have been “reusability”—anyway (and I’m no programmer) it is apparently beautiful when the same lines of text can be reused over and over—wonder if we see some of this in nature? Rude
The poster read “Why do the ribosomes (protein synthesizing machinery) in our mitochondria match those of bacteria?” The intent behind this question was to suggest that we evolved from bacterial ancestors, whose remnants in us are the mitochondria and, presumably, their ribosomes, which the poster asserts “match” those of bacteria.
Yes, that is their intent. But if their fact claim were true, isn't there a problem with assuming that it would be clear to assume the thing they are asserting? Why not common designer? They could have as well said, why do chimps and man have five digits? or Why do men and apes have four limbs, a torso and a head? Do those things neccessarily assert the idea of common descent? No. So, why is it even an argument for assertion? The default to materialism is why the assertion is assumed to point to common descent. So, in effect, he/she that held the poster was thinking.. since we default to materialism.. materialism is the correct origin/cause. JGuy
You could be a mutant- (think Jeff Foxworthy's "You could be a redneck") If your jaw is too small to accomodate all of your teeth, you could be a mutant. Thank you. Thank you very much. I'll be here all week... Joseph
If a feature is the same it's evidence for a blindwatchmaker. But if a feature is different it's also evidence for a blindwatchmaker. You can't win an argument with an idealogue. mike1962
LoL! If those were the "best protest signs ever" then ID isn't being intelligently protested against.
“Why do we have wisdom teeth if they do not fit our jaws?”
My wisdom teeth came in fine. Also no one said the design had to be perfect and even if it started out perfect no one said it had to remain that way. What we see now is after many gnerations of genetic accidents caused by pollutants.
“Why did it take 20 species of elephant to go extinct to get two species that survived?”
It didn't. That is just the way it worked out.
“Why do the ribosomes (protein synthesizing machinery) in our mitochondria match those of bacteria?”
They don't! Now we know why evolutionists don't want to debate in a public forum. I couldn't imagine being told I was that stupid in front of an audience. Where's DaveScot when you need him? Joseph
As usual, when we look at the true facts, without any ideological filter, we can see a fascinating scenario, and a lot of very interesting questions arise. We should love questions. They are our hope and challenge. The only stupid questions are those which are spoken with a pre-ordained answer in mind, and not out of a sincere love for truth. On the interesting web page linked in this thread, I have counted at least 13 questions, all of them very good, arising from a simple analysis of what is truly known about mitoribosomes. Each of them could be the cause of interesting hypotheses and of precious inquiry. But if we pretend that we already know the answer (let's say that everything must be explainable in terms of RM + NS), then the access to truth is denied. False reasoning always bears a cost, and in this case the cost is very heavy. So, the precious knowledge we already have about ribosomes reinforces one of my basic convictions: that all research is ID research, in the sense that any research gives us facts, and as ID is true, facts are always ID friendly. But, obviously, somebody must have the honesty to look at facts for what they are, and proceed from them toward further knowledge. gpuccio
[...] William Dembski wrote a blog entry related to ribosomes and the implicit argument that an evolutionary process, indicating common descent, would be counter evidence to intelligent design. Dembski writes: "the more interesting question for me is what causal powers were required to produce ribosomes in the first place." Indeed. Why begin and end a causal trail with the existence of ribosomes themselves? Since ribosomes have specified functions, it makes a great deal more sense to evaluate the causal trail to protein synthesis when evaluating whether ribosomes are evidence against ID. How would the capacity to synthesize proteins evolve from the point in time where ribosomes had not yet come into existence? The synthesis of proteins is an irreducibly complex mechanism. Where are the pathways to the evolution of ribosomes in particular and more generally to protein synthesis itself? How can ribosomes be counted as evidence against ID unless pathways to them are first secured on a sound evidentiary footing? These icons link to social bookmarking sites where readers can share and discover new web pages. [...] Ribosomes - Telic Thoughts
idnet.com.au wrote: "I think Nick laid his hand down prematurely." Think about baseball, NIck. Think about baseball. TRoutMac
I have eukaryote and prokaryote reversed in the previous post. It should be "eukaryotes formed from one prokaryote absorbing/combining with another to form mitochondria." I said I wasn't a micro-biologist jerry
All life uses DNA and similar replication processes. Couldn't you use the same argument based on this fact that there must be common descent? I am certainly not a micro-biologist but are there other proteins or RNA that are also in common. If there are not then could you use that as proof that there isn't common descent. Either way there will be some of each so what does each imply. Wouldn't this be more of an argument that would support the proposition that prokaryotes formed from one eukaryote absorbing/combining with another to form mitochondria. The whole argument seems specious even if they were similar. jerry
There certainly seem to be more questions than answers about the evolution of mitoribosomes. I think Nick laid his hand down prematurely. idnet.com.au
Would we not expect some commonality if there were a common designer? Robo

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