A computer programmer noticed that he was not able to type very much in a single day. But he mused that if there were a large number of software bots working on his code, then they might be able to proceed via totally blind trial and error. So he decided to try an experiment.
In the initial version of his experiment, he established the following process.
1. The software was reproduced by an imperfect method of replication, such that it was possible for random copying errors to sometimes occur. This was used to create new generations of the software with variations.
2. The new instances of the software were subjected to a rigorous test suite to determine which copies of the software performed the best. The worst performers were weeded out, and the process was repeated by replicating the best performers.
The initial results were dismal. The programmer noticed that changes to a working module tended to quickly impair function, since the software lost the existing function long before it gained any new function. So, the programmer added another aspect to his system — duplication.
3. Rather than have the code’s only copy of a function be jeopardized by the random changes, he made copies of the content from functional modules and added these duplicated copies to other parts of the code. In order to not immediately impair function due to the inserted new code, the programmer decided to try placing the duplicates within comments in the software. (Perhaps later, the transformed duplicates with changes might be applied to serve new purposes.)
Since the software was not depending on the duplicates for its current functioning, this made the duplicates completely free to mutate due to the random copying errors without causing the program to fail the selection process. Changes to the duplicated code could not harm the functionality of the software and thereby cause that version to be eliminated. Thus, in this revised approach with duplicates, the mutations to the duplicated code were neutral with regard to the selection process.
The programmer dubbed this version of his system N.E.C.R.O. (Neutral Errors in Copying, Randomly Occurring). He realized that even with these changes, his system would not yet fulfill his hopes. Nevertheless, he looked upon it as another step of exploration. In that respect it was worthwhile and more revealing than he had anticipated, leading the programmer to several observations as he reflected on the nature of its behavior.
Under these conditions of freedom to change without being selected out for loss or impairment of current function, what should we expect to happen to the duplicated code sequences over time and over many generations of copying?
And why?
[p.s. Sincere thanks to real computer programmer OMagain for providing the original seed of the idea for this tale, which serves as a context for the questions about Neutral Errors in Copying, Randomly Occurring.]
Eric,
The reason we can design buildings and airplanes is the properties of construction materials can be abstracted. We can abstract the strength of stee and plastic and concrete and glass. We can predict the strength of a cantilever without building it because the properties of materials can be abstracted.
We cannot abstract the properties of novel organic molecules. We can make guesses about changes to existing proteins, but we cannot really abstract anything useful, such as how the change will affect and organism in its environment.
It gets more complex with regulatory networks and development. The number of dimensions affected by any change is beyond computation.
Oddly enough, differential reproductive success integrates all these dimensions. Feel free to propose an alternative.
It’s just as well that ericB, like most ID/creationist leader wannabes, gets his chance to be a “lecturer” here rather than in a classroom.
Any poor students being subjected to his “argument” would be well-advised to run. None of ericB’s misconceptions and misrepresentations appears to be correctable; he doesn’t even appear to be able to comprehend when his mindless imitations of probability calculations are meaningless.
EricB doesn’t know it, but his misconceptions and beliefs about “degradation” of the gene go all the way back to Henry Morris and Duane Gish; as this sneering catechism from the ICR by Thomas Kindell illustrates. This is also the source of Sanford’s “genetic entropy.”
A number of commenters seem to have missed that my latest post was explicitly directed toward origin of life issues, especially the origin of new molecular machines, rather than the biological evolution of cells as we know them.
So, the question at hand is not…
That is an inappropriate understanding of the issue because it assumes as a starting point that the molecular machinery in question already exists, is already operating, and is already selected due to the significant benefit that it is providing.
Instead, the question is of this kind…
In short, it is a question about molecular machine origins. Is it reasonable to think the processes described by variation and selection (or its absence) provide the explanation for the origin of such machines?
About the word “error”, I use it exactly in the sense that of an error in copying / replicating a sequence. Perfect copying would eliminate variation, which would be an obvious dead end, as I’ve already pointed out. Therefore, to have any hope of a helpful variation, there must necessarily be Errors in Copying that are at least Neutral.
I’ve never assumed that all such errors are “bad”, and I’ve explicitly stated otherwise, including emphasizing this in my very first Observation.
What I do point out is that when this process of random copying errors accumulates randomly over time in a sequence, this does degrade the sequence integrity with regard to any former function that the sequence had (e.g. the sequences supporting the vision system degrade to the point where fish become blind). Notice that is not a claim that reproductive success has degraded, or that the “genome” has degraded. It is a statement about the integrity of the content of the sequence in question with regard to its former expressed function.
Here is an example where you are considering an experiment in the biological evolution of cellular organisms, not the origin of life question I am raising.
Is there any result in the Lensky experiment that showed the origin of an entirely new molecular machine composed of multiple coordinated parts? If so, please elaborate, but I would guess not, since you earlier wrote:
“Exploring all the possibilities in near space” might serve well for enhancing the fitness of organisms with existing function, but it doesn’t answer the question of how such a process creates a first molecular machine that is not in the near space of any similar but prior molecular machine of its kind.
About the word “errors”, see above. Also regarding “how evolution works”, see above. The issue is origin of life and of the first instances of molecular machines, not biological evolution of cells as we know them.
Are you referring to the scientific literature regarding biological evolution? If so, see above. Are you referring to the scientific literature regarding the origin of molecular machines? If so, see my next comment.
Life’s Ratchet: How Molecular Machines Extract Order from Chaos
Physicist Peter M. Hoffmann is an expert on the topic of how molecular machines operate. He describes his own research in this way: “My research I consider nano mechanics, so I like the mechanical idea of it …” He has written a book relating to this topic titled Life’s Ratchet: How Molecular Machines Extract Order from Chaos. See also this video.
video of lecture followed by questions and answers
However, extracting “order” has never been the problem with explaining the origin of the molecular machines and the systems of molecular machines, such as the translation system. At 45:22 in the video, a question is asked that is the most relevant to the origin of molecular machines.
We can make multiple observations from Hoffman’s answer.
1. He is commendably honest and forthright about his summary of the current state regarding the origin of the machines, i.e. “… scientists don’t have a good answer”, and “… we have no idea at this point”, and “…nobody has an answer for that”, and that the research results so far provide “… nothing that approaches like a molecular machine.”
2. Our lack of an answer at this point is so complete that he is not able to tell whether it might be solved by a “genius” in another 10 years or if we will still be waiting for an answer through the next one thousand years.
3. Nevertheless, he has faith that we will find an answer someday. It is not based on seeing the answer, but a belief in a future answer that will be found someday. “I think we will figure it eventually out …”.
4. To the extent that he dares to guess about the general nature of what an answer may look like, he appeals to replication, variation and accidentally hitting on such a machine: “so there has to be some way of initially creating a replicator, something that can replicate itself, like an RNA molecule that then eventually hit on these molecular machines, but that’s… [pause] um… [pause]”
5. To consider whether such a scenario is reasonable in principle, it is necessary to apply the principles concerning the behavior of imperfect copying, selection (or the lack thereof), and the accumulation of random copying errors in sequences that do not yet provide any selectable reproductive benefit. Hence the direct relevance of N.E.C.R.O..
I see ericB still can’t or won’t learn even the basics of the science he’s attacking.
As noted before, it’s impossible to have an intelligent discussion with someone who insists on making up his own cartoon versions of evolution as he goes.
I’m watching the video right now. It’s pretty good thus far.
I think most participants at TSZ and most scientists would say something similar. I don’t recall ever hearing someone claim that OOL is a solved problem, and I don’t recall anyone suggesting that it will be an easy problem to solve.
I’m not sure where you are getting that “he has faith” bit. To me, “I think we will figure it eventually out” sounds rather weak. I don’t hear church folk saying “I think I am saved” or “I think there is a God”. If they said that, you would be questioning their faith.
In truth, most scientists don’t spend a lot of time worrying about OOL. Science is predominately concerned with the world as we find it, rather than with its history. Evolutionary biology is far more concerned with ongoing processes than with the detailed history of species.
Let’s be very clear about this: NO; YOU cannot make ANY observations about Hoffmann’s comments.
Here are some direct facts which you are incapable of addressing:
#1: Hoffmann knows the relevant science far above the high school level. YOU, on the other hand, can’t even grasp simple science and mathematics at the high school level.
#2: There is no way you can even speculate about the context in which Hoffmann is making his remarks. YOU haven’t even read Hoffmann’s book; and even if you tried to read it, you wouldn’t understand it.
#3: Your comments are totally irrelevant because: (a) They don’t address anything Hoffmann has done in his research, his book, or his talk, (b) your comments are complete gibberish made up on the spot and, ( c) your comments have nothing to do with any real science.
You don’t have the slightest inkling of what Hoffmann was saying. What you did was quote-mine part of the Q&A after Hoffmann’s talk. You don’t understand the quote-mine. That is what ID/creationists do; scan for quote mines, NEVER listen or read for comprehension.
You deliberately and repeatedly avoid direct questions about basic concepts in science.
You keep repeating your misconceptions and misrepresentations.
You not only cannot do elementary mathematics calculations correctly, you have no clue whatsoever if your “calculations” apply to anything.
You are in no position to pontificate about anything.
Do you really think other people who know the relevant science are this stupid?
There aren’t a large percentage of scientists in the scientific community who are working on the problem; but I know some of the people who are. It is an extremely interesting research problem for which there isn’t a lot of funding available relative to other research needs. And the current political climate and gridlock in Washington DC is not favorable for research of any kind.
It’s a challenging problem; but it is also a very tantalizing problem because there are no physics or chemistry issues standing in the way. The challenge lies in the vast number of paths that one can think of and for which one must try to reproduce the sequences of events. The problem is in the vastness of the search, not in the basic chemistry and physics.
It has only been in recent years that the technology for probing the physics and chemistry of living systems without destroying them has become available; and many new techniques are currently being developed.
But the point is – and Hoffmann also makes this point as well – the answers are in that nanoworld of soft matter; matter that is near its melting point and is comprised of flexible, self-coiling, and thermally driven assemblies. The energy cascades that lead to the evolution of these molecules are unknown at the moment; but there is little doubt that they exist, and they may be right under our noses (or in our noses, as one physicist has opined).
Hold it. You’re interested in Origin Of Life issues—you just said so yourself, in so many words—so why the heck are you mumbling about this Triplet-Reading System whatzit in the first place? Do you really think that this Triplet-Reading whatzit was generated by whatever processes were involved with Origin Of Life? If so, on what grounds do you reject the hypothesis that the ur-Life produced by OOL did not have a Triplet-Reading System, and said T-RS arose at some later time, however-many centuries (millennia? megayears?) after the Origin of Life?
cubist, please take another look at Hoffmann’s answer (bolding added).
I am using the same distinction between evolution and origin of life. The issue of accounting for the origin of the molecular machines that support the cellular life we now see is reasonably categorized as an issue within the origin of life.
If you want to use terms differently, that’s fine (just so long as you communicate that clearly without creating confusion).
I know you followed the other thread on the origin of the translation system. (This thread branched off of that one.) Both here and there, it is taken for granted that if there is an unguided natural process explanation, then something without a Triplet-Reading System would have had to come before, and also there would need to have been many developments afterward, including those that involve the creation and use of proteins.
The focus here is upon the impact of the Observations concerning Neutral Errors in Copying, Randomly Occurring upon whether it is reasonable to expect such a process to produce molecular machinery such as for the Triplet-Reading System.
As I pointed out, even Hoffmann’s expectation is that this would need to be a result of replication, variation, and hitting upon a selectable machine. But is this reasonable or not, given what happens prior to having sequences for a working system that is producing a selectable contribution to reproductive success? If that is reasonable, I am still waiting to here from those who can reconcile such a claim with the random accumulation of neutral copying errors.
I’m looking forward to the comments from all who engage with the subject matter of the topic in a meaningful and constructive way. There have been many good comments so far in the discussion.
I agree. The whole presentation is quite well done.
Whether one considers his faith weak or strong may depend on whether one is asking about his confidence in our finding the answer he expects, or instead about his confidence that the true answer is the kind of answer he expects (whether we can figure it out or not).
The point I find commendable about his frankness is that he is willing to put it on the table that no one has a good idea right now (which is much different than saying we have some many good possibilities the problem is just figuring out which one is the right one).
A straight shooting person will be frank about issues that present serious problems and for which there are no good answers. I’ve raised some issues about what I see as serious problems for all unguided scenarios to create molecular machines. What remains to be seen is how the commenters at TSZ deal with the substance of those issues.
BTW, you are a moderator, correct? Does TSZ still follow this policy?
No it’s not. Not even close.
If all you’re going to do is bounce back and forth and play Creationist whack-a-mole at least edit the thread and retitle it accordingly.
Actually no, all you’ve presented is argument from poor analogy along with a boatload of personal incredulity.
I’m sure that works fine in your usual ID-Creationist circles. Not so much when there are scientifically literate people present.
Yes, that is still the policy. But it mostly relies on self-policing.
No, you have not raised any “issues;” you are simply making up pseudoscience and brashly trying to pass it off as a “barrier” to abiogenesis. There is no such physics and chemistry in the real sciences. You aren’t in any position to assess Hoffmann’s comments; but those of us who know the science are.
And it is not off-topic to point out your attempts to fake knowledge that you obviously do not have. You are insulting the intelligence of the people here; and that is just plain arrogant rudeness on your part.
Hoffmann believes – just as do other people working in this area, as well as those of us who have worked in the areas of condensed matter physics – that the molecules of life evolved. Given the environment in which they exist, this is the most likely mechanism.
Are you getting any of this?
Do you have any clue about the energetics of molecular formation? Can you even imagine which kinds of molecular assembly are formed in which kinds of environment? Can you even suggest a process? Your mindless use of ID/creationist calculations is pretty convincing evidence that you do not and cannot.
The reason you aren’t getting any “takers” for your “theory” is that your ignorance of basic high school level science is glaringly evident. Apparently that isn’t a clue for you; so you just continue to plunge ahead trying to fake it. I am asserting that you don’t really know science and that you are just practicing ID/creationist debating tactics.
Hold it. Of those “molecular machines that support the cellular life we now see” (emphasis added), the only ones that can be “reasonably categorized as an issue within the origin of life” (emphasis added, again) are those which were found in whatever ur-Life was a product of the Origin of Life. I mean, surely you don’t think that “accounting for the origin of”, say, the human appendix, “is reasonably categorized as an issue within the origin of life”… do you, ericB?
What’s the deal, ericB? Do you think that every post-OOL development in biology “is reasonably categorized as an issue within the origin of life”? Do you think there are any post-OOL developments in biology which can be “reasonably categorized as an issue within the origin of life”? Do you have any reason to think that the Triplet-Reading System found in contemporary cells was, equally, found in whatever ur-Life was produced by Origin Of Life, as opposed to this T-RS thingie being a later development that didn’t even exist until N millennia after Origin Of Life?
Mike Elzinga,
that is just plain argument from authority….
absolutely no substance to declaring because you work in the field of physics, we should accept your proclamation that molecules ‘evolved’….
fyi, replicating molecules is a far cry from bridging the gap to multiple, simultaneous, coordinated replications of numerous molecular configurations….
you haven’t the fainest idea how molecules ‘evolved’…
…your assertion that you do is cheap, chunky costume jewelry
I’d be interested to hear how “Intelligent Design” bridges that gap.
Could you explain?
You seem to be implying that if ID can’t bridge the gap, then we must except Mike Elzinga’s assertion that since physicists and chemists know a lot about molecules, we’ll just have to take their word for it that the physical properties of molecules account for their complexification into the myriad systems we observe today.
….thats kinda like the Ayatolla(sp) telling us that he is God’s prophet and we’ll just have to take his word for it….after all, the prophet has studied the Koran for a long, long, time and can recite it by heart…he knows it like the back of his hand…he prays five times a day……he fasts at Ramadan……he smites the infidels….who are we to argue that he doesn’t have a direct line to God….
What’s a better explanation than emergence? how about programming?
evidence collected in the last 20 years tells us this is a viable explanation…remember out of sight is not out of mind….we know gravity from its effects…we are now in an exciting scientific time….having the opportunity to study the programmed characteristics of molecules….so we’ll know the programming of complex molecules by their effects.
…..you know this is gonna take place in our lifetimes…the programming of molecules…we can already store huge amounts of date in the form of DNA already….so actual science is taking us head on into ID territory…..
….Mike Elzinga’s old school attitude does dilly squat to advance biology…repeating ad nauseum that there is nothing other than physics and chemistry at play is counter- productive…we should be asking how molecules were programmed….not whether programming did in fact take place.
You could always try learning the science.
Mike is not insisting that you take his word for it. He is insisting that you learn the science first, before coming to conclusions.
Eric,
You seem to be deeply confused.
In your original thread, you posed a challenge:
Noting “For the purposes of the challenge, all questions about the chemical feasibility of creating DNA or RNA as a material that could serve as a potential medium are waved[sic]”, and also that by “unguided chemicals” you meant simply “no intelligent intervention”.
Allan Miller answered it
here and
here
You repeated ” I’ve explicitly allowed one could assume the presence of DNA and RNA as a given”
Allan provides more detail.
Allan notes that you appear to have reneged on your concession
Then on this thread, you introduce a terrible analogy, and proceed to argue from analogy.
Many posters point out fatal flaws in the analogy, and ask, “So what?”
To summarize:
You asked about the origin of the triplet reading system (TRS). Allan answered on the previous thread. On this thread, you introduce a VLFLA for ‘drift’, then conflate the origin of the TRS with OOL, and decide to ignore responses that contain the word ‘evolution’, trying to claim that evolution is not relevant to your challenge.
You do understand that RNA replicators evolve, surely?
You would be able to communicate your ideas far better if you wrote fewer words, but were much, much more precise and clear in how you used those words.
Of course, one man’s bug is another man’s feature.
It’s interesting that ID advocated cite archaeology and criminology as examples of design detection, and yet they never put forth supernatural causes for pottery or crimes.
Ad with few exceptions, they don’t suggest aliens as the source of historical artifacts. Not seriously.
Why is that. Why isn’t the possibility of alien abduction ever cited as the cause of unsolved disappearances? Or ghosts as the cause of unsolved murders? If we can’t find a natural cause, why isn’t supernatural design the best explanation?
You ID-pushers like to make noise about how ID is better than evolution. In support of your ID-is-better position, you cite various things which (you claim) evolution is unable to explain. Fine—but if ID really is better than evolution, shouldn’t ID be able to explain some things evolution can’t? And if ID can’t explain some particular Thing X which evolution also fails to explain, wouldn’t that support the proposition that ID is, in fact, not any better than evolution?
So… how does ID bridge this “gap” you speak of? If ID doesn’t actually bridge this “gap”, doesn’t that mean ID is no better than, and perhaps worse than, any real-science theory which also can’t bridge this “gap”?
Part of what bothers the stubbornly self-uneducated people like Steve Proulx and other ID/creationists is that they absolutely despise anyone who has actually applied the necessary time an effort to understand real science. They especially despise anyone who insists that ID/creationists actually know something basic about the science they presume to criticize.
It is easy for ID/creationists to quote-mine the writings of others and then jerk any discussion into an endless labyrinth of word-gaming and “citing of authorities” about who said what and what the meanings of their meanings mean.
This game has become the standard “debating” tactic that ID/creationists use as they try to portray themselves as being learned; but they are faking it. They hate being called out on their fakery, and they viciously attack anyone who calls their bluff. That is what happened to Elizabeth over at UD, that is what Steve P is miffed about, and that is why ericB is not responding to questions about basic high school level science.
If ID/creationists want to be taken seriously, they need to demonstrate that they can address specific concepts in science and explain why such concepts are wrong. They also need to do what everyone in the science community is required to do; namely, to generate specific research proposals on how their ID/creationist “theories” are to be tested in the lab and in nature. That includes research techniques, equipment, number of workers, and a budget.
This is why I insist that ID/creationists demonstrate at least a thorough understanding of basic scientific concepts before they launch into their “critiques” of science at any level. In every case I have observed over the last 50 years, ID/creationists cannot pass even basic concept tests at the high school level; they fail with a resounding thud every time. Their fakery has been exposed. If that upsets them; well that is just tough. If that is the game they choose to play, then they deserve to be laughed at; even by children.
But we will NOT have ID/creationist crap in the school classroom.
Scientists actually do research rather than just hang around on the Internet and word-game everything to death. All ID/creationists ever do is make up stuff and play word games. The contrast between working scientists and ID/creationists couldn’t be starker.
There is a reason that science advances and ID/creationism goes nowhere. Scientists actually know the science; ID/creationists don’t have a clue.
Mike Elzinga,
Same o, same o from Elzinga.
He attacks what he views as the weakest link, and holds on like a pit bull. He continually makes the silly arguments from authority, labor, and utility. He believes you have to have a degree in science to understand it.
Bullshit Mike. Plenty of people have logical brains but no scientific training. You need to speak to that. Stop trying to hide behind your priestly scientism. There is nothing holy about the scientific method. To point that out is not a hatred of science, but an understanding of its limitations.
What is peculiar is that you didn’t even address the point….it was asked how ID bridged the gap that IMO evolution could not….from simple replication to multiple, coordinated replications of numerous molecular configurations…..I said programming…and I said that science is showing the viability of such a hypothesis…that molecules can be programmed….we know now how to utilize DNA as a superior storage mechanism…..we will figure out how molecules can be programmed and we will discover that is how molecules change…not by some silly, simplistic, archaic notion of random mutation acting on heritable variation…
Oh, I like science alright Mike… its moving head on in ID’s direction….that’s why we didn’t hear a peep from you….you wont even go there….to your detriment….
….I’ll take 21st century science over your 20th century science any day Mike….its an exciting time….but if you are not willing to make the change, then so be it….fade away into the mechanical moonlight….
I like how cubist uses that phrase ID pusher….reminds me of Steppenwolf’s The Pusher……
….goddamn the pusher man…..he’s got tombstones in his eyes…..he’ll sell you lots of sweet dreams….
ah,ah, ah…the “ID’ pusherman…..
LOL at “programming”. Another classic one word non-answer from a clueless IDiot bullshit artist. Kinda reminds me when Joe G use to answer “frontloading!!” as his stock non-answer for any question about ID asked of him.
Why didn’t you just say “MAGIC!!”? It has just as much explanatory power as your lame excuse.
Except science = racecar windshield, ID = bug. It ain’t gonna be pretty.
Well, Mike Elzinga describes perfectly the tactics of the “ID Skeptics” over at UD, except they just make up the “quotes” because they can’t even be bothered enough to quote mine.
Back on another thread, ericB made this assertion about how to calculate the probability of molecular assemblies such as RNA sequences.
I asked ericB the following questions, which he has scrupulously avoided answering.
EricB has no clue about the answers to these questions; he just mimics ID/creationist pseudomath and drones on. EricB also doesn’t know if anyone in the ID/creationist movement understands the second law of thermodynamics.
So taunting Steve P is now also on the hook to answer these questions. He has failed basic science and math concept tests repeatedly in the past over on Panda’s Thumb. Let’s see if anything has changed.
I am still insisting on some evidence that ericB – or ANY ID/creationist for that matter – really understands high school level science and any other level of science they pretend to critique.
And, by the way; Mung is still on the hook to answer all these questions he has also scrupulously refused to answer. His usual feces hurling is not an answer.
What I see: Lots of fuss and commotion.
But what I notice most about the emotional comments is what is missing. No one seems to want to try to address the issues that have been raised. No one is dealing with the issue of how to get the origin of molecular machines (e.g. the T-R S) out of the random accumulation of neutral copying errors prior to being able to provide selectable reproductive advantage.
If you think I am wrong, where is the explanation on how this is supposed to work, e.g. for the origin of the first Triplet-Reading System?
Mostly it seems that people want to shift the conversation to talk about anything else, such as to dwell on a question of terminology that — either way — doesn’t resolve the issue.
Example: I agree with Hoffmann that the question of the origin of the molecular machines is in the realm of the origin of life. Read his statement. If you think Hoffmann is wrong to say so, you are welcome to your opinion. Just communicate clearly. I’ve said clearly that I am using the distinction of terminology that Hoffmann makes.
Key point #1: However, you choose to label it, even though Hoffmann is an expert on the operation of molecular machines, he is clear about the fact that the origin of the molecular machines is a problem where no one has a good answer. Change the label all you want — his statement is still true.
Key point #2: Calling it one thing or another doesn’t make the origin of the molecular machines (e.g. the Triplet-Reading System) any easier. You still need to contend with the reality that the future benefit of future output of any system cannot grant natural selection during construction for its origin. That’s not an opinion. That is the reality of the nature of natural selection. It is blind to future benefit. Even functional systems that do not provide selectable reproductive benefit are not protected by selection. Cave fish go blind.
So far, everyone seems intent on talking about anything other than to face that issue. There was no serious objection to its truth when considered earlier. Now, no one seems prepared to consider the consequences of its application.
So far, the silence on this question says much.
But someone may yet have a way of resolving this problem. So it just may be too early to assess.
Key rebuttal #1. Saying “we don’t know yet” isn’t evidence for “it must be impossible”.
Key rebuttal #2: that matters not one iota. There will always be some variations in a population that are better than others. Those variations will outcompete their neighbors and have a higher chance to survive and reproduce.. It’s differential reproductive success that counts, not striving towards some unspecified “goal”.
After all this time you still haven’t grasped that what’s “beneficial” can change every time the environment changes. Are you ever going to pick up a beginning biology book and learn at least the basics? Your continued major misunderstandings are embarrassing.
This is what is so “interesting” about your so-called “argument.” The rebuttals have been right in front of you the entire time, but you just refuse to look. Instead you are now trying to pretend the subject has been changed.
ID/creationism deserves people like you. You are easy to shoot down; and it is completely painless for you. It makes it so easy on everyone.
Did you even go to high school?
I’m glad you appreciate my wordsmithery, Steve. I also note that you didn’t bother to address the substance of the comment you responded to. So here it is again, giving you another opportunity to engage in substantive discussion regarding ID:
You ID-pushers like to make noise about how ID is better than evolution. In support of your ID-is-better position, you cite various things which (you claim) evolution is unable to explain. Fine—but if ID really is better than evolution, shouldn’t ID be able to explain some things evolution can’t? And if ID can’t explain some particular Thing X which evolution also fails to explain, wouldn’t that support the proposition that ID is, in fact, not any better than evolution?
So… how does ID bridge this “gap” you speak of? If ID doesn’t actually bridge this “gap”, doesn’t that mean ID is no better than, and perhaps worse than, any real-science theory which also can’t bridge this “gap”?
Speaking of avoidance, ericB, I can’t help but notice that you have avoided addressing my response to an earlier comment of yours. Here it is again, for your convenience:
Of those “molecular machines that support the cellular life we now see” (emphasis added), the only ones that can be “reasonably categorized as an issue within the origin of life” (emphasis added, again) are those which were found in whatever ur-Life was a product of the Origin of Life. I mean, surely you don’t think that “accounting for the origin of”, say, the human appendix, “is reasonably categorized as an issue within the origin of life”… do you, ericB?
What’s the deal, ericB? Do you think that every post-OOL development in biology “is reasonably categorized as an issue within the origin of life”? Do you think there are any post-OOL developments in biology which can be “reasonably categorized as an issue within the origin of life”? Do you have any reason to think that the Triplet-Reading System found in contemporary cells was, equally, found in whatever ur-Life was produced by Origin Of Life, as opposed to this T-RS thingie being a later development that didn’t even exist until N millennia after Origin of Life?
You are asserting, without support, that the TRS must have arisen via NECRO (i.e. “drift”)
See the links to the previous thread within this post for a detailed explanation of your error.
Additionally, Cubist has asked you if you realize that you are conflating TRS with OOL.
And, Mike has asked you about probabilities, trying to lead you to realize that your math is wrong.
Well, “questions” plural, asked multiple times; but I have to agree here. Your failure to engage is noted.
ericB,
Eric:
C’mon, Eric, I did have a stab. My scenario in the prior thread postulated an organism with transcription but not translation. The primary transcript is the functional product in such an organism (and still is in the case of functional RNAs – tRNA, rRNA, etc). I consider it likely that a ‘TRS’ can only arise in such an organism, and cannot arise in an OoL scenario. Such an organism would be a replicator, and would therefore be an arena in which selectable reproductive benefit can arise. One potential benefit is the production of uncoded peptides, by a peptidyl transferase ribozyme. Peptidyl transferase remains almost entirely an RNA function today. The number of functions that such peptides could perform is significant, but I cannot give you a definitive one. I suggest that peptidyl tranferase activity is enhanced by aminoacylating short ‘carrier’ RNAs (the precursor of tRNA), which transfers ATP energy to drive the reaction (the peptide bond will not form spontaneously). I suggest that such a primitive system can be further stabilised and segmented by associating the attachment of carriers with docking against a strand of RNA (the precursor of mRNA). This binding energy helps drive peptidyl transfer. Initially, this does not have to be as specific as it is today. Binding energy alone is insufficient to account for the discrimination of the system. There are other interactions that determine the tighter specificity of the modern ribosome; these did not have to be operational on Day 1.
I would suggest that a triplet is the optimal reading frame for stereochemical and energetic reasons, not because it permits a >15-acid code. A singlet or doublet would be difficult to present proud of the tRNA backbone, and hard to orient correctly. A quadruplet may bind too strongly, and is additionally more difficult to hold straight in a folded RNA. Even a triplet starts to bend away in the 3rd position, hence the ‘wobble’ rules.
As to the capacity of such amendments to come from a succession of copying errors (including duplications) and fixation of selectable benefit … well, why not? tRNAs and the two classes of aaRS have probably come from duplication events, for example, carrying extensive evidence of homology.
I’m aware that you don’t buy any of it, which is why I abandoned the effort – ultimately, it’s no skin off my nose.
Allan, glad to see you are commenting.
Not only did you have a stab in the prior thread, but no one else attempted it to the degree that you did (though there was one other more limited contribution).
When I referred above to “No one is dealing with the issue …” (note tense) I was referring to the immediate response to the application of the principles of Neutral Errors in Copying, Randomly Occurring to the proposed origin of the Triplet-Reading System.
“Why not?” is a great question.
“… and fixation of selectable benefit”
1. As I mentioned, according to your own description, that fixation of selectable benefit only comes sometime after operation and production has begun.
2. Natural selection cannot consider future benefits.
3. Therefore, prior to that hypothetical “one accidental success to fix the basic system”, natural selection cannot consider its future benefit. Even if operational, the system is no more protected against dysfunctional degradation from random copying errors than would be the vision system of cave fish.
“As to the capacity of such amendments to come from a succession of copying errors (including duplications) … well, why not?”
4. Errors the eliminate the function of systems that don’t currently contribute to reproductive success are the easiest for a blind process to create. There are typically a great many ways to break a system through blind changes.
5. Everything stated above about the vulnerability of the system while operational is at least as true, if not more so, before it becomes operational.
6. For any possibility of change to occur, the relevant sequences must be impacted by random copying errors (else no change). Yet, those same neutral random copying errors are guaranteed to have the long term net effect of randomizing the content of those sequences. It is a necessary consequence of random neutral change to random locations over time for any sequence not protected from change by natural selection. Though freedom from the restrictions of natural selection means freedom to change, it also means freedom from the conservation of natural selection and its protection against randomizing change from random copying errors.
7. The net result of the above points is that the sequences that are proposed to provide the first Triplet-Reading System are essentially taking a blind random walk through sequence space and through configuration space, since multiple components are involved.
8. Hoffmann referred to the idea of “an RNA molecule that then eventually hit on these molecular machines”. It is important to note that to achieve a successful end to the blind random walk, the randomizing blind random walk is not terminated by achieving function. It is not enough to “hit upon” a working molecular machine. It is only terminated successfully by achieving a contribution to reproductive benefit. Achieving the former without the latter does not stop the process or random walking. The blind random walk would just keep walking blindly through and past mere function back into dysfunction — unless it happens to accidentally “hit on” real selectable reproductive benefit.
9. Sequence space is vast and configuration space even more so, and it is sparse when comparing functional configurations to all nonfunctional configurations. See, for example, The Triplet-Reading System and the Exponential Space of Interacting Parts and especially the points therein about The Levinthal paradox of the interactome.
10. The prospect that a blind random walk through sequence space and configuration space will “hit on” not only a working Triplet-Reading System, but one that is producing a selectable reproductive benefit is exponentially bleak.
EricB still can’t be bothered to learn the basics of evolutionary biology I see. Still pitching the dumb strawman argument that evolution is a blind walk through configuration space instead of a feedback driven process that works to maximize survival potential. Still can’t grasp that evolution doesn’t have to search the entire sequence space, it just searches the space in the immediate vicinity of an already viable form. Still thinks that any change to a copied existing genetic sequence must be a degrading “error” instead of a potentially useful variation.
You should realize by now that your severe mangling of the science hasn’t managed to sway a single person. That should tell you something about the quality of your argument, but it probably won’t.
This one statement contains the entire set of Fundamental Misconceptions of the ID/creationists in a single sentence.
It is all in there; from Henry Morris, to William Dembski, to David L. Abel, to John Sanford, and Granville Sewell. It displays a complete lack of understanding of the fundamentals of biology, chemistry, physics, and mathematics at even the high school level.
As ericB has been demonstrating very clearly, there is no remedy for this in the case of an ID/creationist; and it shows why ID/creationists should be studied for their misconceptions and misrepresentations rather than debated.
I agree. In one brief paragraph it sums up a complete disregard for 150 years of science. Back to Paley.
Eric wrote
And from this you infer what, precisely?
Allan is being too modest: it was a very good stab. When I saw it, I sat back with my bowl of popcorn. I suspect others did too.
Well, the issue has been dealt with (note tense). Fairly conclusively.
Eric, you may believe that you are cogently rebutting Allan’s scenario, but you are merely demonstrating ignorance and/or a lack of reading comprehension. By way of illustration, in your most recent 10-point rebuttal I notice two correct statements:
“2. Natural selection cannot consider future benefits”
and
“9. Sequence space is vast and configuration space even more so, and it is sparse when comparing functional configurations to all nonfunctional configurations. ”
#2 is not the powerful restriction that you seem to think it is.
As thorton points out, #9 is completely irrelevant.
The rest makes no sense.
Eric, please try the following: re-read both threads, working under the assumptions that most of your critics a) have, in fact, understood your argument and b) do, by and large, know what they are talking about.
Then answer the questions posed.
Can you describe what you envisage as the step immediately before the “working Triplet-Reading System”?
Would it be a “working Triplet-Reading System” with the switch set to “off”?
In any case, for the sake of argument, it’s impossible. Or exponentially bleak if you prefer.
How do you explain it? Was it 99% evolution with 1% design intervention? 100% design? 100% evolution but built in at the start of the universe to turn out like that?
Don’t be coy. Please share! We’ve identified how something did not happen, great, now let’s move onto the far more interesting what did do it. Got anything there? Or is identifying what did not happen (hint: there are a lot of ways it did not happen) as far as we go on this journey?
In sentence one, you speak of “random copying errors”. In sentence two, you add the qualifier “neutral”, as in “neutral random copying errors”. What about “random copying error”s that are not “neutral”—are those things as nonexistent as unicorns, or what?
I can see that “random copying errors” in the absence of selection must, eventually, lead to randomization. Why is this a problem for the Triplet-Reading System? Are you arguing that the T-RS must necessarily have arisen at some point in time before selection got up & running? If so, on what grounds do you reject the hypothesis that the T-RS did show up at a time when selection was up & running?
ericB,
Perhaps I threw you a curve by mentioning ‘fixation’. Really, it only needs to occur to be of immediate advantage to its possessors and their descendants, and to be available for subsequent amendment. If it is reproductively advantageous, it will likely spread through the broader collection within which the lineage will compete, ultimately to fixation in that population. This simply buys more tickets. The change already occurred, and now a population of descendants is building up. More organisms have Change A, which increases the chance that Change B will occur to make organisms with A + B. This is not a ‘target’ – AC, AD, AE […] are equally likely products given that A has occurred. But the more individuals you have, the more the space is being probed (blindly, non-intentionally, randomly, etc).
Read and digest the above. 😉 Any ‘dysfunctional degradation’ renders the allele less fit. The population contains descendants of the original mutation that have NOT undergone ‘dysfunctional degradation’. They are fitter (capable of producing greater numbers of offspring on average) than the degraded version, and therefore that will tend to be lost from the population. The ‘selectable amendment’ doesn’t have to wait for anything to be fixed (in the population) in order to be fitter. It already is. There is a brief window when drift will dominate for statistical reasons – when numbers are small, accidental elimination is more likely. But the advantage is there on Day 1; the change has happened and it is merely a matter of it catching on.
Much harder if the system is replicated, has a large number of instances and ‘broken’ versions are outcompeted by ‘unbroken’ ones. Since I have offered a potential selective advantage for all steps, the acknowledged ability of random factors to change sequence when there is no relative advantage/disadvantage is not an issue (not, at least, a negative one).
The entire system never ‘becomes’ operational. At each stage, there is an operational system to which another amendment may be made, and which is protected against degradation by Natural Selection – by benefits accruing to the current system, I shouldn’t have to make clear but feel I must.
I missed the bit where I said it was all down to A random walk! Of course such a complex system must arrive serially. Each small step includes a local random walk. From any given genomic sequence the ‘process’ of variation hits nearby space, randomly, and may hit a beneficial sequence if such is to be had from there. This creates a new circumstance (with immediate, not future, benefit). This amended genome hits its neighbourhood. Same again. The upshot is the TRS, which seems, with the benefit of hindsight, exactly what was needed, and where we were headed all along as if by magic.
Define ‘function’. And see this and this.
Bleak to the power x? Good thing that is not what I propose, then! I don’t suggest a single beneficial target in an otherwise flat adaptive landscape. Replicator populations can stick to the viable ground in a sequence space, random-walking locally but being channelled by local adaptive benefit – in the first instance, the ability to produce a simple dipeptide could easily have a benefit. This changes the landscape, and other functions could be reached from there that would be unavailable to a one-step or an entirely random walk from the original start point.
Mike Elzinga:
Conspicuously absent from Mike’s rant is anything at all resembling an argument.
Skeptical much?
Mike Elzinga:
Pretty sure you’re lying. But I don’t track all the crap you write that I respond to (or chose to ignore due to the infantile content).
So just in case I didn’t say it earlier, but I probably did:
mike elzinga:
Who knows? What is the source and what is the probability of each symbol in the sequence? If you’re talking about biology, I suggest you read Information Theory and Molecular Biology.
mike elzinga:
It depends. You managed to type them up and post them online. Did you manage that without the behaviors of atoms and molecules? How so?
Is there something about atoms and molecules that forced you to post those exact sequences rather than some other sequences?
Good old truth lover Mung.
Always time to do a drive-by poo flinging.
Never time to answer questions about his ID claims.
The more direct the questions about basic, high school level science ID/creationists are asked to address, the more we see avoidance tactics like this. And then they project their internal anger and hatred onto those who expose them.
I have watched this behavior for nearly 50 years now; and it never changes. For example, recall Behe’s sneering at the literature he didn’t have a clue about during the Dover trial. And who can forget the famous “fart video” that Dembski posted on line after they lost at Dover? Duane Gish used to get visibly angry when he was called out on his misrepresentations of basic science; at which point he would launch into his thermodynamics argument and end up just looking even stupider.
It’s real, visceral hatred these people have. Their dear leaders have hung their followers out to be slaughtered. The memorized “debating” tactics they spent so much time practicing aren’t working for them, and these followers don’t understand what is happening.
I want to apologize that work deadlines and my limited time availability can delay responses longer than would be ideal, and limit my ability to respond to many other posts. Sorry about that. I will be trying to get back to some other posts later, as my time for this allows. Know in advance, however, that I will obviously prioritize for comments that are on the topic of this thread, not off-topic digressions.