Front Loading with Ribosomes
by BilboMike Gene has written an intriguing post, at his blog, on front loading with ribosomes. From the post:
This assembly maps involves 15 universal small subunit ribosomal proteins, and of these 15, ten have a moonlighting role (we shall explore several of these functions at a future date). What’s striking is that all proteins involved in binding to the 3’ domain of the rRNA are not only universal proteins, but also have moonlighting functions.
In other words 2/3 of the proteins have moonlighting roles. Quite a large percentage. Darwinian evolution predicts that some ancient proteins will be coopted for future uses, but 2/3 of them? What is even more intriguing about Mike's post is his prediction:
Those universal ribosomal proteins that don’t seem to have a moonlighting role are s17, s5, s8, s11, and s15.
Thus, the front-loading hypothesis further predicts these too will eventually be discovered to have moonlighting functions.
Anyone care to predict that he's wrong?
June 27th, 2009 at 5:34 pm
I care to predict that this is not a prediction that follows from a front loading hypothesis.
What do you think biologists would guess if they see that 2/3 of such proteins have a moonlighting role? And why would front loading predict cooption of 100% of the proteins and not of 66% or 33% or 42%?
Supposedly, multifunction 'serves the need' for front loading. However, that does not make the case about how many proteins in the ribosome should have multiple functions. What I would guess happened here is that somebody is making an educated guess and claims it is a front loading prediction.
Comment by hrun — June 27, 2009 @ 5:34 pm
June 27th, 2009 at 6:17 pm
Hi hrun. Consider two polar opposite circumstances. In the first we see a cellular world in which every new innovation is the consequence of spontaneous events causally unconnected to any precursor function. The alternative indicates that every biological novelty flows from an existing entity and that feedback adaptive mechanisms, indicating unexpected "foresight," were present in the most ancient cells. A good basis for suspicion of front loading in my view. Closeness to either extreme could indicate the strength of evidence for or against FL.
Comment by Bradford — June 27, 2009 @ 6:17 pm
June 27th, 2009 at 6:44 pm
Your representation of polar opposites does not make sense. Both front loading and non-front loading make room for multifunctionality, the cooption of old structures and for the creation of new structures. Neither makes any logical predications about how many of the ribosomal proteins have multifunctionality.
Comment by hrun — June 27, 2009 @ 6:44 pm
June 27th, 2009 at 7:12 pm
You could conclude that current explanations are inherently front loaded processes.
Comment by Bradford — June 27, 2009 @ 7:12 pm
June 27th, 2009 at 7:20 pm
And thus this whole exercise becomes completely meaningless. The point remains, there is nothing in front loading theory that suggests that all proteins of the ribosomes should be multifunctional. If it turns out to be the case, front loading has not been supported one bit. And if it turns out not to be the case, front loading has not been invalidated one bit.
That's the differences between predictions made based on a theory and guesses made based on a hunch.
Comment by hrun — June 27, 2009 @ 7:20 pm
June 27th, 2009 at 7:39 pm
As I see it, to "make room for" and to "predict" are two different things. Does the currently held theory of evolution "predict" that all ribosomal proteins would be multifunctional or does it simply "make room for" that possibility? Mike Gene's specific hypothesis does predict this.
Also, are you basing your contention that it shouldn't make such a prediction on some generic front-loading hypothesis or do you have specific knowledge of Mr. Gene's?
Comment by Daniel Smith — June 27, 2009 @ 7:39 pm
June 27th, 2009 at 7:52 pm
How does Mike Gene's specific hypothesis predict this? Show me the underlying tenets of front loading that lead you to the logical conclusion that all ribosomal proteins are multifunctional.
I am basing my contention on the simple fact that in the linked article, Mike simply makes his prediction, much like I can make the prediction that it will rain tomorrow. Nowhere does he show that this is, in fact, a prediction that follows directly from his front loading hypothesis.
Comment by hrun — June 27, 2009 @ 7:52 pm
June 28th, 2009 at 12:07 pm
I can understand where evolution might predict that older components of the cell would be more likely to be coopted. Thus a protein that is so old as to be universal to all remaining life would be more likely to be coopted than other proteins. All Front-loading seems to do is take this naturalistic prediction and assume purpose. How exactly would Front Loading show that the naturalistic explanation is insufficient and purpose must have been involved? Both "theories" seem to predict the same outcome (once again, I'm shocked I tell you, shocked!) but one theory adds a vague and undefined concept of purpose being required. Nothing in this latest "prediction" speaks to this extraneous factor or why it's required.
Comment by Todd Berkebile — June 28, 2009 @ 12:07 pm
June 28th, 2009 at 2:04 pm
Hrun:
Indeed. It follows from the logic of front-loading as laid out in TDM.
Fair criticism. The logic of front-loading allowed me to predict that ribosomal proteins would moonlight. Admittedly, it is more like an expectation than a precise prediction, but what matters is that the hypothesis directed my attention with subsequent payoff. After determining that about 2/3 of the universal SSU ribosomal proteins appear to moonlight, the criterion of Rationality kicks in. If the ribosome was front-loaded where two out of three ribosomal proteins were preadapted, why not 100%? Of course, there could very well be design reasons that might explain why s5, for example, is not co-optable. Clearly then, the FLE perspective calls for a very close look at these proteins.
Bad guess.
Todd:
Does it? Where?
So, wouldn’t this mean that a) all proteins are equally cooptable? And thus, b) the older the protein, the more moonlighting roles it should have acquired? Long ago, I suggested the need for a metric to determine the frequency of cooption across time. Non-teleologists scoffed and said it was a stupid idea.
That’s just your spin. I laid out my reasoning TDM and the blog.
You have never grasped the significance of Duck/Rabbit, have you? FLE does not require that I prove “naturalistic explanation is insufficient” so that “purpose must have been involved.” Or are you just saying that you require the ‘god-of-the-gaps’ approach?
Where does evolutionary theory predict that ribosomal proteins would moonlight?
Irrelevant. FLE does not need to prove that purpose is required. It simply helped me to predict that ribosomal proteins would moonlight.
We can make this whole topic a lot more juicy and ask what the Duck predicts about the origin of the universal ribosomal proteins.
[BTW, since I dropped by because of the track-back on my blog, I may as well advertise some more evidence for the plausibility of front-loading while I am here. ]
Comment by MikeGene — June 28, 2009 @ 2:04 pm
June 28th, 2009 at 3:06 pm
I think that one of the problems are that while you know that none of the predictions or hypothesis you propose will allow to distinguish between classical evolution or front-loading, this fact is lost on some of the posters here on TT.
And I do like the fact that you agree it is not an actual prediction.
These are the only points I wanted to make in this regard.
Comment by hrun — June 28, 2009 @ 3:06 pm
June 28th, 2009 at 6:54 pm
I've said this before, if all you are claiming is "it is possible live was designed" then there is absolutely no one who is disagreeing with you. Lots of things are possible, but you have yet to show any evidence that fits a FLE theory better than mainstream theories. You have yet to even show how evidence could be used to choose between these theories. No amount of "maybe" or "could be" or "doesn't contradict" moves a person from "possible" to "probable".
Comment by Todd Berkebile — June 28, 2009 @ 6:54 pm
June 28th, 2009 at 8:54 pm
Talk of "co-optation" immediately leads me to think about Gould and Vrba's concept of "exaptation"; that is, the "co-optation" of one trait for another as the result of shifting selective pressures. It seems perfectly reasonable to me that the older a trait is (and a protein can certainly be considered a "trait", especially if it has a biological function, such as participating in the structure and function of ribosomes), the more likely it is that selection could have shifted and co-opted it for some other "moonlighting" function.
Ribosomes are universal in living cells. Ergo, by standard evolutionary (i.e. cladistic) logic, riobosomes are among the very oldest functional structures in biology. Given their age, it seems quite likely to me that one or more of the proteins that participate in the structure and functions of ribosomes might have been co-opted via a shift in selection. Indeed, since ribosomes are so ancient, it surprises me that only two-thirds of the proteins in ribosomes have been "co-opted" in this way.
In other words, there is no contradiction whatsoever between this finding and macroevolutionary theory as a whole. On the contrary, discovering that few (or, worse, none) of the proteins in ribosomes have "moonlighting" functions would suggest that there is something wrong with our current understanding of evolutionary cladogenesis. In the same way, discovering that relatively new proteins (i.e. proteins that have not been around very long in evolutionary time, as indicated by a relatively dearth of synapomorphies) have a higher rather than lower rate of exaptive co-optation would seem to indicate that such proteins were "designed" for rapid exaptation.
Comment by Allen_MacNeill — June 28, 2009 @ 8:54 pm
June 28th, 2009 at 8:57 pm
And I strongly agree with Todd B's objection that the fact that FLE and NFLE both predict the same observations is an indication that FLE has no real epistemological leg to stand on. Metaphysical legs may be interesting, but they can't get you where you want to go…
Comment by Allen_MacNeill — June 28, 2009 @ 8:57 pm
June 28th, 2009 at 9:26 pm
I have the feeling that this is a distinction that is clear to Mike, but not his followers.
Comment by hrun — June 28, 2009 @ 9:26 pm
June 28th, 2009 at 10:02 pm
As usual a critic assumes the worse possible interpretation. Mike once commented that some things are too important to be left to science (paraphrasing). Choosing between multiple interpretations, not contradicted by science, is philosophically sound. The choice would be the one that aligned with one's metaphysics. There is no Occam's razor applicable to metaphysical values. We are aware of this even if those, whose allegiance is to scientism, are blinded to it.
Comment by Bradford — June 28, 2009 @ 10:02 pm
June 28th, 2009 at 11:54 pm
How is this choosing the worst possible interpretation?
Certainly so. But if one ones to base the choice on scientific inquiry then there has to be a scientific way to distinguish the two. Thus far, neither Mike, nor anybody else has put forward a way how one could directly distinguish FLE from 'classic' evolution. Mike has stated that he (at least for now) has no intention of developing FLE to the point where this could be done. However, others on this blog appear to think that FLE is indeed a scientific hypothesis.
Maybe not, though. I might, as always, be wrong. If so, then we ALL agree that FLE is no scientific theory.
Comment by hrun — June 28, 2009 @ 11:54 pm
June 29th, 2009 at 12:38 am
hrun:
It's been clear for quite some time that neither Mike or anyone else at TT is claiming a scientific descriptor for front loading. Whether or not that changes in the future is an open question. Speaking only for myself, I believe front loading occurred at life's origin i.e. the origin of a viable cell able to evolve and adapt. I also note that there is no scientific data excluding that possibility from consideration. Indeed there is little data allowing for a coherent account of cellular origins consistent with any particular theory.
Comment by Bradford — June 29, 2009 @ 12:38 am
June 29th, 2009 at 7:13 am
So then why is this stuff called 'prediction' by Bilbo? Like Mike admitted, it is not actually a prediction. It is what he expected, a hunch, an educated guess, a speculation about what he thinks a front loader would have done. Somebody else will come to a completely different hunch about what a front loader might have done. If it turns out to be true or false, it can't verify or falsify FLE.
And Bilbo's attempt to contrast the predictions made by 'Darwinian evolution' and by Mike does not seem to me like he actually internalized that fact.
Comment by hrun — June 29, 2009 @ 7:13 am
June 29th, 2009 at 12:17 pm
Since Professor MacNeill has chosen to enter this debate, I'll ask the same questions of him that Mike asked of Todd.
It's true that I didn't understand why Mike was making the prediction of all the ribosomal proteins would have moonlighting roles. Now that Mike has explained himself — "the criterion of Rationality" kicked in — I understand why the prediction follows from FLE. So I've "internalized" why FLE predicts that 100% of the proteins will moonlight. I do not yet understand why Darwinian evolution predicts that 100% of the proteins will moonlight.
Comment by Bilbo — June 29, 2009 @ 12:17 pm
June 29th, 2009 at 12:29 pm
Have you also internalized that Mike did not in actuality made a prediction?
Comment by hrun — June 29, 2009 @ 12:29 pm
June 29th, 2009 at 4:18 pm
He already discussed this and is far more qualified than I to answer. Then again, I find it interesting that this seems obvious to a lay person such as myself but is apparently incomprehensible to the telic mind.
Comment by Todd Berkebile — June 29, 2009 @ 4:18 pm
June 29th, 2009 at 4:21 pm
According to Mike himself he did not make a prediction. Beware of confirmation bias causing you to read more into this than what he said.
Comment by Todd Berkebile — June 29, 2009 @ 4:21 pm
June 29th, 2009 at 9:40 pm
Hrun:
I’ve always made it clear that this is not about “distinguishing” between ‘classical evolution’ or front-loading. This is about exploring the plausibility of using evolution to carry out design objectives. That is, the whole idea of front-loading needs to be fleshed out so that it stands on its own before we can ever hope to do a meaningful comparison. In addition to making this clear with countless arguments, I even have a handy metaphor to drive the point home. Or did you think those bunny pictures are just fuzzy mascots?
Look at it this way. It is commonly believed that natural selection is too blind and contingency is too great for evolution to even approach as a teleological process. That’s the position FLE distinguishes itself from, as I am slowly chipping away at that common belief and establishing the plausibility of front-loading. Nothing less, nothing more. The only argument that would truly counter my case is one that attempted to argue that front-loading is implausible.
It depends on what you mean by prediction. What I said was “it is more like an expectation than a precise prediction, but what matters is that the hypothesis directed my attention with subsequent payoff.” I can see that you want to skip over the point that matters and focus on semantics. Very well. You write:
Since I have made it clear, many times over, that TDM is not science, but instead an investigative approach more akin to a police investigation, a prediction is likely to come in the form of expectations, hunches, and educated guesses guided by the logic of the hypothesis. What matters is not the semantics, but that the prediction/expectation/whatever paid off and provide continued guidance for investigative focus.
Yet if semantics are crucial here, you should provide the definition of ‘prediction’ so it can be applied consistently across the board.
Todd:
If all I was saying is that it is possible life was designed, then this position would not have been able to predict things like ribosomal proteins that moonlight (or deep homology). Clearly, that is not all I am saying.
Are you willing to agree that the hypothesis of life’s design, followed by the front-loading of subsequent evolution, is both a reasonable and plausible hypothesis?
So what would count as something that fits FLE theory better than mainstream theories? I predict you need a fantastic gap.
Anyway, has it occurred to you that you have yet to show any evidence that fits mainstream theories better than FLE?
Since you acknowledge that FLE is as well supported as mainstream theories, you choose against FLE simply because it is teleological, right?
In TDM, I devote a whole chapter to explaining there is room between the possible and the probable.
Allen:
This is the Duck. Yes, one can choose to interpret these phenomenon and data through this non-teleological filter. I see what you see.
Is this an actual prediction or an educated guess that a layman might come up with? If it is an actual prediction, where was it made and why was it not used to discover the moonlighting properties of ribosomal proteins?
In other words, since no contradiction was claimed, you are knocking down a straw man argument.
So the only thing we risk falsifying is our “current understanding.” Interesting.
Long ago, I suggested the need for a metric to determine the frequency of cooption across time. Non-teleologists scoffed and said it was a stupid idea.
FLE has a real epistemological leg to stand on, as demonstrated by its growing plausibility and investigative pay-offs, and by the logic I laid out in TDM. What’s more, you are acknowledging it is as well supported as NFLE, except, I suspect, that you don’t like the teleological aspects. To this we could add the other clues I have been discussing – a consilience of clues.
Back to hrun:
I don’t think scientific inquiry can resolve this difference in perspective.
Which means that FLE is as well supported as non-teleological evolution. I have no problem with people interpreting evolution through the non-teleological prism. The problem, as I see it, comes when folks expect the non-teleological perspective to be embraced by all despite the fact that they cannot distinguish their non-teleological views from FLE.
It’s not a matter of intention; it’s a matter of ability. One person, with limited time and knowledge, can only do so much, especially with a topic as ambiguous as this. Fleshing out the plausibility of front-loading is by far a hefty enough challenge in of itself.
You are the one who introduced the word “scientific” into the thread (use the Find function on your browser to confirm). It is not found in my blog entry or Bilbo’s blog entry.
Yes, I have always made this clear. It is an investigative hypothesis that employs teleological thinking. And it is slowly developing a modest track record of success.
I don’t expect those viewing things from within the confines of the Traditional Template to grasp what I am saying. So instead, perhaps it would help to focus on something everyone should be able to grasp.
According to hrun, the problem is that I made no prediction (“it is not an actual prediction.”)
According to Todd/Allen, the problem is that my prediction is also made by mainstream evolutionary theory (“FLE and NFLE both predict the same observations”).
So which is it?
I’d love to hang around, but I can’t. So it would seem this is a great chance for y’all to hash out your disagreement among yourselves and perhaps come up with a consensus on what constitutes a prediction. In the past, critics have come at me with all sorts of contradictory criticisms, but they were never willing to address the contradictory nature of their criticisms. Perhaps this time can be different. If so, I’ll look in and try to squeeze in another reply some time later.
Comment by MikeGene — June 29, 2009 @ 9:40 pm
June 29th, 2009 at 9:55 pm
Mike, I used the term 'scientific prediction' since prediction by itself can be understood as 'Something foretold or predicted; a prophecy'. Which is most likely not the context in which Bilbo wanted it understood. So I went with a scientific prediction which is commonly understood to take the form:
'If X is true then it follows that Y is also true.'
I think I have internalized your position on this. I don't think Bilbo or Bradford have. Unless Bilbo was actually thinking of your prediction as a 'prophecy'. And I don't know which is worse.
Yes, an expectation, not a prediction (neither something foretold, nor something following the 'if X is true then it follows that Y is also true' kind) but simply something you expect.
The reason why I skipped over the 'subsequent payoff' part is because I don't see the 'subsequent payoff'. What I see is confusion by a person like Bilbo who takes your expectation to be an actual prediction.
Oddly enough, I still don't believe it has sunk in for everybody.
I did.
Comment by hrun — June 29, 2009 @ 9:55 pm
June 29th, 2009 at 10:15 pm
Hi hrun,
Your quick reply allows me the opportunity to squeeze off another. So the definition is:
'If X is true then it follows that Y is also true.'
Yet if we turn our attention to Todd and Allen’s response, it would go like this:
If non-teleological evolution is true it follows that ribosomal proteins will moonlight.
Is this a prediction?
Comment by MikeGene — June 29, 2009 @ 10:15 pm
June 29th, 2009 at 10:20 pm
I don't know. One would have to ask Todd and Allen if they can show that one follows logically from the other, wouldn't one? My guess would be that they are actually a hypothesis.
You might note, for example, that Allen (at least in his first and in depth response) did not use the term predict/prediction. Strikes me that he might be a scientist.
Comment by hrun — June 29, 2009 @ 10:20 pm
June 29th, 2009 at 10:42 pm
Well, I'm still withholding judgement about whether or not front-loading is possible until an advocate rustles up a mathematical model demonstrating how data could be compressed into a usable form which then uncompresses itself over time. Given the noise inherent in evolution I can't see how coherent information could be transmitted in this way. Certainly life could have been designed since we can nearly design life ourselves.
I don't know, FLE seems too vague to me to be distinguishable. I'd suggest an advocate should figure out an answer to that question post-haste though if they want to be taken seriously.
I agree, therefore I choose the more reductionist theory and dismiss the other as extraneous.
No, because it adds unjustified complexities (like an uber mind more complicated than the created result the mind is meant to explain).
Yes, that's exactly what I was alluding to. And my response is that no amount of "maybes" moves a person along your proposed route. At best you are saying, "If you didn't know about all this other stuff, then FLE might seem reasonable, right?" But I do know about all that other stuff so its impossible not to judge the relative merits. Infinite evidence would NOT lead to all positions being "plausible".
Comment by Todd Berkebile — June 29, 2009 @ 10:42 pm
June 30th, 2009 at 12:30 am
One plausible way is that it could be designed so that if any of the front loaded information became corrupted, other fail-safe watchdog mechanisms would prevent replication. This technique is easy to demonstrate with software or hardware.
Comment by kornbelt888 — June 30, 2009 @ 12:30 am
June 30th, 2009 at 1:00 am
The counterpart to this is an overly simplistic break in causality. It just is becomes an ultimate explanation for a self-generated or always was universe.
Comment by Bradford — June 30, 2009 @ 1:00 am
June 30th, 2009 at 1:10 pm
Who are you talking about?
Comment by chunkdz — June 30, 2009 @ 1:10 pm
June 30th, 2009 at 1:10 pm
I do not yet understand why Darwinian evolution predicts that 100% of the ribosomal proteins will moonlight. Darwinian evolution depends upon co-optation. And given the number of ribosomal proteins, and how long they have been around, it stands to reason that some of them would be co-opted for other functions. But that most or all of them would be co-opted? Oh come on. That strikes me as a very iffy proposition. Show me some calculations that would back it up. Or at least show me that NFLE people used their hypothesis to investigate ribosomal proteins for moonlighting.
Meanwhile, FLE would begin with the hypothesis that the ribosomal proteins were going to endure for a very long time, so that it would be advantageous to design them so that they could moonlight. This hypothesis guided Mike to search for moonlighting properties of ribosomal proteins. He was rewarded by finding that at least 2/3 of them do moonlight. Then using his design hypothesis that the designers were Rational, he predicts that we will find out that the other 1/3 moonlight as well. He may be proven wrong about that, and the explanation would be that the remaining proteins aren't able to moonlight.
Is it a strict prediction? Perhaps not, but for a historical science (which is what ID is), it's close enough.
Comment by Bilbo — June 30, 2009 @ 1:10 pm
June 30th, 2009 at 1:30 pm
It doesn't. It's simply a testable hypothesis. If it is confirmed it does not mean that evolution (or FLE) is validated, nor does it mean that if it is disconfimred that evolution (or FLE) is invalidated.
Sorry Bilbo, but you must be joking, right? If it is an evolution prediction you want some calculations, but if it is a FLE prediction you simply take Mike's word for it? Talk about a double standard.
Oh really? So Mike found that out, now did he? So if we look up who actually found and published this information we can figure out who is hiding behind the Mike Gene pseudonym? Again, you must be joking.
So do you now use the term prediction in the sense of 'being foretold' by Mike or are you claiming that it is a scientific prediction of the structure 'If X is true then Y also must be true'?
Comment by hrun — June 30, 2009 @ 1:30 pm
June 30th, 2009 at 1:55 pm
hrun:
Is hrun your real name or a pseudonym?
Comment by Bradford — June 30, 2009 @ 1:55 pm
June 30th, 2009 at 2:49 pm
Of course it is a pseudonym. What kind of a question is that?
Comment by hrun — June 30, 2009 @ 2:49 pm
June 30th, 2009 at 2:57 pm
Are you hiding behind your pseudonym or was that your way of sending a friendly message?
Comment by Bradford — June 30, 2009 @ 2:57 pm
June 30th, 2009 at 2:57 pm
Is that one plausible way? I guess it might be, but where's the model? You are correct that such a model, if plausible, would be easy to demonstrate in software. So why hasn't any FLE supporter worked on such a program to develop this model? By your own admission it should be easy to demonstrate and yet FLE supporters can't even accomplish that much. The devil is in the details (maybe that's why theistic supporters don't develop a real model, they are afraid of contact with Satan!
), just saying it should be possible doesn't impress me.
Comment by Todd Berkebile — June 30, 2009 @ 2:57 pm
June 30th, 2009 at 2:59 pm
In evolution? In the origin of life? How so? Please explain.
Comment by Todd Berkebile — June 30, 2009 @ 2:59 pm
June 30th, 2009 at 3:03 pm
You don't need software. Apoptosis is a mechanism which induces cellular suicide when cellular functions become irreperably corrupted.
Comment by Bradford — June 30, 2009 @ 3:03 pm
June 30th, 2009 at 4:06 pm
It was neither. It was my way of pointing out that maybe other researchers than Mike (researchers who were not relying on FLE) discovered that 2/3 of ribosomal proteins have a moonlighting function.
Comment by hrun — June 30, 2009 @ 4:06 pm
June 30th, 2009 at 4:07 pm
I didn't mean to say that it's easy to show in a genome at present. It's easy to demonstrate as a technique for ensuring system integrity for computer processes and mechanical process control.
To borrow from the Zachriel school of thought, given that DNA and cells exhibit process control features due to the nature of the protein "machines" and programmable DNA, we can extrapolate that to a plausible recoding of the "software" in the DNA to achieve this. Are you aware of what some of the processes within cells now are acheiving? Of course, nobody is doing this in a cell yet. But given what we know already about cells and DNA, there doesn't seem to be any reason why it couldn't. At any rate, I appreciate your "show me" attitude!
Comment by kornbelt888 — June 30, 2009 @ 4:07 pm
June 30th, 2009 at 4:12 pm
True. That's one approach to certain kinds of problems. I was thinking more along the lines of preserving yet-to-be-functional genes thru deep. Co-opting existing functional genes is an interesting idea, but if we found dormant genes preserved thru deep time that would all but seal the deal when it comes to evidence of front loading, IMO.
Comment by kornbelt888 — June 30, 2009 @ 4:12 pm
June 30th, 2009 at 6:00 pm
And how exactly does that prove that Front-Loading is possible? In the case you mention there is code for a function that simply runs. How does this demonstrate that this code could have auto-unpacked from a smaller amount of front loaded data?
Yes, either preserving or uncompressing or decrypting, something along these lines that resists random noise would need to be demonstrated as even being possible in order to take FLE seriously.
It might be interesting, but it fails to demonstrate FLE. There needs to be a mechanism beyond "random chance" that causes the future cooption to be inevitable or at least highly likely.
Comment by Todd Berkebile — June 30, 2009 @ 6:00 pm
June 30th, 2009 at 6:04 pm
I'm sorry, I'm not following what you asking. Can you please restate the question?
Comment by Todd Berkebile — June 30, 2009 @ 6:04 pm
June 30th, 2009 at 6:11 pm
So if it were demonstrated that the genetic code was optimized for error minimization, that might lead you to take FLE seriously?
Comment by chunkdz — June 30, 2009 @ 6:11 pm
June 30th, 2009 at 6:46 pm
The point of the comment was to show that a computer simulation is not needed to establish the point made by kornbelt888. An "anti-corruption" cellular mechanism already exists.
That's a good question for ID critics as well. It's been my position that cellular functions are irreducibly complex with respect to both the minimal number of genes needed for cellular viability and the level of efficiency of their encoded proteins. If that is so then a design inference follows.
Comment by Bradford — June 30, 2009 @ 6:46 pm
June 30th, 2009 at 6:47 pm
Minimizing error is not a mechanism for unfolding new data. You cannot create a new novel gene simply by not losing existing information. If that was the only avilable mechanism then the first life would need to have every single bit of front loaded information and "evolution" would only be a slow decay of information. This is not what we see in nature, we see new and novel data unfolding and we see FLE advocates claiming this new information was somehow there all along in a frontloaded form but they cannot explain how it was stored or how it unfolded.
Comment by Todd Berkebile — June 30, 2009 @ 6:47 pm
June 30th, 2009 at 6:53 pm
So? This does nothing to indicate that FLE is possible.
Why? The critics are not claiming this is possible, so why would you want them to explain how it is possible?
Unrelated. Even if that was true that does not demonstrate that FLE is possible. Life may have been designed and FLE still might be impossible. The point of my request is to demonstrate that there is even a theoretically possible model for "unpacking" front loaded data through evolution. This model doesn't care how complicated the initial conditions are, I only ask that you demonstrate a model for FLE of data.
Comment by Todd Berkebile — June 30, 2009 @ 6:53 pm
June 30th, 2009 at 7:00 pm
It's clear that you have no idea what FLE is.
Comment by chunkdz — June 30, 2009 @ 7:00 pm
June 30th, 2009 at 7:07 pm
Critics are claiming that a tiny genome evolved to produce descendents with ever increasing complexity. They just don't have the empirical data to back the claim.
Comment by Bradford — June 30, 2009 @ 7:07 pm
June 30th, 2009 at 7:14 pm
Here is one possible method for unpacking data through evolution: Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequence
Notice that the "392-amino acid-residue-long bacterial enzyme 6-aminohexanoic acid linear oligomer hydrolase involved in degradation of nylon oligomers is specified by an alternative open reading frame of the preexisted coding sequence that originally specified a 472-residue-long arginine-rich protein." So the coding sequence was in use until a time came when an alternative open reading frame proved beneficial – thus ensuring the integrity of the "front-loaded" enzyme (if that's what it was).
Comment by Daniel Smith — June 30, 2009 @ 7:14 pm
June 30th, 2009 at 7:57 pm
Todd, who are these FLE advocates that you speak of? Names, please.
Comment by chunkdz — June 30, 2009 @ 7:57 pm
July 1st, 2009 at 9:32 am
I see, you can't answer my inquiry so obviously that means I'm dumb.
Unfortunately its equally clear that the advocates have no idea what it is either seeing as how they cannot even provide a mathematical model suggesting how information was front-loaded and how that front-loaded information unfolds at a later time.
Comment by Todd Berkebile — July 1, 2009 @ 9:32 am
July 1st, 2009 at 9:41 am
You mean empirical data like the fully sequenced genomes of multiple species which supports this claim? Oh yeah, they don't have any data alright.
As you are fully into your typically "change the subject" routine I guess this means you won't be proving even a simple example program showing that FLE is even theoretically possible. All you need is a program that evolves some front-loaded data to reach a desired future outcome. At this stage you can assume anything you want about how the data is stored, how complex the initial data is, what entails an "evolutionary process", how the data is validated, etc etc. Once even the most primitive example exists then you have a starting point to compare against actual evolutionary processes. Its hard to take FLE seriously when they apparently don't even understand the implications of their own theory well enough to make a primitive model of it.
Comment by Todd Berkebile — July 1, 2009 @ 9:41 am
July 1st, 2009 at 9:51 am
Daniel,
The link you provided takes me to a Verizon sign-in page so I cannot read the details. From your quote it seems you are suggesting that the "front loaded" information must be used in it's "unfolded" state in order to preserve it. I agree that would be required to survive the noise of evolutionary process. This should be accounted for when the FLE supporters make a model of a proposed theoretical mechanism for FLE. But knowing we must account for that factor in the model does not provide us with the model for how the final form was predestined or encouraged or front loaded to emerge. I suspect what we have in the example is random variation leading to cooption, but the random variation is an input of new information not originally present in the front loaded organism.
Comment by Todd Berkebile — July 1, 2009 @ 9:51 am
July 1st, 2009 at 9:54 am
No Todd. I mean empirical data specifying the conditions in which RNA arises with a functionally sequenced genome able to evolve and pass on biologically useful information.
Comment by Bradford — July 1, 2009 @ 9:54 am
July 1st, 2009 at 11:31 am
I disagree. If we found that no or very few ribosomal proteins were co-opted for future functions, this would count strongly against the FLE hypothesis. It would not count against the NFLE hypothesis.
It was Todd B.'s and Prof. MacNeill's assertion that given the number of ribosomal proteins and the length of time that they have been around, that it was inevitable that most or all of them would be co-opted for other uses. I say that this is mere bluffing, and that it would take a high degree of luck for most or all of the proteins in one system to be usable in other systems. If they want to present some sort of counter-argument, it will need mathematical calculations.
Meanwhile, the FLE hypothesis assumes that the designers, knowing that the ribosome will be around for a long time, would design their proteins for use in other systems. If we could not find any or very few that had other uses, we would have good reason for doubting FLE.
We don't know if someone discovered if the ribosomal proteins moonlighted before Mike did. It could be that there was a catalog of the various proteins and their functions, and no one had bothered to make a correlation between the ribosomal proteins and their moonlighting role before Mike did. It would be interesting to find out. Perhaps Mike could answer that question.
I claim that if Mike had found that few or no ribosomal proteins had been found that moonlighted, it would count strongly against FLE. Likewise, I claim that finding that most of them do moonlight counts strongly for FLE, since NFLE can't really explain why so many of them would be able to have moonlighting roles, except by luck. As to the further prediction that 100% of them moonlight, it is a weaker prediction, based on the Rationality of the designers. If we find out that it is less than 100%, we can conclude that it was because they couldn't find other uses for them.
Comment by Bilbo — July 1, 2009 @ 11:31 am
July 1st, 2009 at 11:48 am
Why? Are multifunctional proteins the only way FLE could be implemented?
If we don't know, then why do assert it to be so.
Yes Bilbo. I know that those are your claims or assertions. However, just claiming it, doesn't make it so.
I claim that there are other ways how an intelligent designer could have implemented FLE. In fact, I claim that an intelligent designer would think it is much to complicated to have multifunctional proteins. So there. Now what do we do? We have two assertions.
Comment by hrun — July 1, 2009 @ 11:48 am
July 1st, 2009 at 11:57 am
You are mistaken, this is not what we said. We said that the older a component is the more likely it is to have been coopted. No one said cooption was "inevitable." The assumed model is that there is some chance of cooption per unit of time or per exposure to new environmental conditions. From this model the older something it the more likely it would be to have been coopted but such a model would never predict a 100% cooption probability.
Comment by Todd Berkebile — July 1, 2009 @ 11:57 am
July 1st, 2009 at 12:02 pm
I see, you are trying to change the subject to move the conversation into a knowledge gap. The origin of life is not the topic, we are talking about theoretical models showing how information could be front-loaded. For the purpose of this discussion I will agree that God poofed life into existence, now please demonstrate a model for how he might have front loaded some future outcome into that original life.
Comment by Todd Berkebile — July 1, 2009 @ 12:02 pm
July 1st, 2009 at 1:12 pm
Any biological mechanisms allowing for change and adaptation are mechanisms that front load future outcomes into origin. Specified future outcomes require specific guiding mechanisms. What they might be is speculative but looking for processes that induce biased outcomes with respect to protein properties might serve the purpose.
Comment by Bradford — July 1, 2009 @ 1:12 pm
July 1st, 2009 at 1:13 pm
Todd:
I didn't say you were dumb. I said you don't know what FLE is.
For instance, you said:
This is not FLE as I have ever heard it put forth. Please tell us which FLE advocate is saying this.
Comment by chunkdz — July 1, 2009 @ 1:13 pm
July 1st, 2009 at 1:35 pm
Then obviously there is a communication failure somewhere along the way. I considered the statement Bradford just made in the previous post to fit what I am saying. So within this very thread is an example of an advocate claiming what I am suggesting they claim. Honestly I wasn't trying to make a controversial statement and if you are reading it as such then feel free to suggest a better wording.
Comment by Todd Berkebile — July 1, 2009 @ 1:35 pm
July 1st, 2009 at 1:46 pm
So the very fact that DNA is able to mutate is an example of "front loading" even though this ability does not favor any specific future outcome? You are claiming that FLE does NOT guide towards a preferred outcome? But you leave open the option of later discovering some guiding mechanism which would favor a specific outcome?
Wow, that is one pointlessly weak statement. Basically it boils down to "only what is possible is possible" or perhaps "life was front loaded to only do the possible, not the impossible." You have effectively admitted that FLE cannot move towards a specific desired outcome (or at least you can't conceive of even a mathematical model for how such a thing might even be theoretically possible).
Your new version of FLE sounds exactly like the "random outcome" and the "different results if you replay the tape" that mainstream theories suggest. Interesting. I guess God does play dice with the universe after all.
Comment by Todd Berkebile — July 1, 2009 @ 1:46 pm
July 1st, 2009 at 1:48 pm
Bradford did not say that new information was "there all along". Please just give us a name, a cite, a web address so that we can evaluate your claim. Who is saying that the information was "there all along"?
Comment by chunkdz — July 1, 2009 @ 1:48 pm
July 1st, 2009 at 2:30 pm
It's not an example of front loading anything specific other than a capacity for adaptive change which is of no minor consequence. A process like directed mutations would provide a more specific rudder directing outcomes.
Comment by Bradford — July 1, 2009 @ 2:30 pm
July 1st, 2009 at 3:19 pm
Ok, now we are getting someplace. Now your model needs to have the information describing this directional rudder built in. The rudder imparts a vector that constrains future "random" changes so they are more likely to move towards a desired outcome. Of course, this sounds exactly like Natural Selection, so to distinguish FLE we also need the information that describes this rudder to be stored along with the information that it is guiding (otherwise the "guidance" would be a purely external factor and not front-loaded into the organism). We have some more pieces of data that need to be built into your FLE model, all you need to do is follow through on the ideas and develop the proof of concept model. Then you can compare your actual model against actual data and see if it can make better predictions than real theories. You are so close to performing actual science.
Comment by Todd Berkebile — July 1, 2009 @ 3:19 pm
July 1st, 2009 at 4:10 pm
Todd, you've got your relevant points backwards:
1. Evolutionary algorithms are the proof of concept model for FLE. EAs operate on highly improbable configurations based on characteristics of the future problem to be solved. The evolution seen in EAs is front loaded to solve specific problems.
2. No one has yet provided any evidence that law and chance absent any "front loading" can even cause evolution in the first place. Take a program based on arbitrarily chosen laws and initial and boundary conditions based on random inputs (obtained from atmospheric noise) and see if evolution will result.
"Non-front loaded evolution" proponents probably won't ever get to the point where they are actually doing science, since they think that they are already doing science without addressing #2. Todd, your side is so close to performing actual science, yet so far away.
Comment by CJYman — July 1, 2009 @ 4:10 pm
July 1st, 2009 at 4:12 pm
Um, everyone who advocates the FLE theory believes that information from the early state guided or constrained or created the information that unfolded into the later state. Some advocates say things like, "random mutation can only destroy information, it cannot create new information." Do you honestly think front-loading can be done without putting any information into the precursor state? Are you sure I'm the one who doesn't know what FLE means? Why don't you provide a definition of front loading since I am obviously so ignorant.
Comment by Todd Berkebile — July 1, 2009 @ 4:12 pm
July 1st, 2009 at 4:35 pm
Please be more precise, I'm not seeing how this follows.
An EA can operate on any type of information, it could be a random string or a human genome. It just needs variation and a fitness function. Besides, we agreed above that for the purpose of demonstrating FLE God poofed life into existence so we are agreeing that the initial conditions are complex.
Please show how this follows? Are you claiming that evolution couldn't work unless there was a specific problem to solve?
Sure thing, pretty much every evolution simulation out there starts with a random initial condition for the genome and a specified fitness function. In these examples the environment is information rich but the organisms are initially random. Fitness effectively transfers new information from that environment into the organism slowly over time. That's basically what Natural Selection is, after all, a slow accumulation of information about how to survive in a given environment.
For another example, how about the cellular automata demonstrated by Stephen Wolfram wherein certain random patterns combined with trivial cellular automata "laws" often generate stable repeating patterns? Or those that show "growing" sub-features? These system seem to create order from chaotic information with only extremely trivial "laws" being applied.
Comment by Todd Berkebile — July 1, 2009 @ 4:35 pm
July 1st, 2009 at 4:38 pm
Why don't you simply answer the question, Todd? Which FLE advocate said that new information "was there all along"? What is his/her name?
Comment by chunkdz — July 1, 2009 @ 4:38 pm
July 1st, 2009 at 4:42 pm
You seem to be claiming that unless the origin of life is known, evolution could not possibly be "science"? I must have misunderstood because that's an obviously nonsensical position. The origin of life is irrelevant to providing a model of how FLE or traditional evolution would work. This is as silly as Ben Stein saying evolution must be wrong because it doesn't explain physics.
Comment by Todd Berkebile — July 1, 2009 @ 4:42 pm
July 1st, 2009 at 4:57 pm
My answer was "all of them," so simply name any FLE advocate. I already mentioned Bradford as an example of matching what I said. Others who have attempted to claim an information theory barrier to evolution include William Dembski, Werner Gitt, and Lee Spetner. The whole concept of specified complexity is that evolution cannot create the information inherent in life, that information must have been injected in some form by a mind. As Dembski has claimed to believe in common descent it follows that all the information we see in modern organisms was "there all along" in some form or another. The fact that you continue to think this is an odd or controversial statement implies to me that you simply aren't understanding what I am trying to say. I guess I am not being clear, but I don't know what term I'm using that you find confusing.
So how about my counter-question, are you claiming that front-loading does NOT require pre-existing information that is "unfolded"? Can you show me a single FLE advocate who denies that information was front-loaded into the prior states and unfolded into the later states? In other words, can you show me a single FLE advocate who thinks FLE doesn't require information? What exactly IS it that is "front loaded" if it is not information?
Comment by Todd Berkebile — July 1, 2009 @ 4:57 pm
July 1st, 2009 at 5:13 pm
Since this thread is about an article by Mike Gene, I'll pick him.
Can you show me where Mike Gene said that novel information "was there all along"?
Comment by chunkdz — July 1, 2009 @ 5:13 pm
July 1st, 2009 at 5:22 pm
Is your complaint about that exact quote? Are you deliberately using that exact quote out of context with the list of options I provided? What I am saying is that all FLE advocates think information was front loaded, I find it hard to fathom that you actually disagree with that. I'm not sure if Mike has ever used those exact words in that order, but I am quite sure that "front loading" is meant to imply that "information" was placed into early life so that it could be used/coopted/unfolded in later life. This information was "there all along" even though it was not being used for its final purpose. Do you understand that this is what I am claiming? If you demonstrate that you understand what I am claiming and you STILL doubt that Mike fits the description then I will take the time to look up a supporting quote or two from the DM.
Comment by Todd Berkebile — July 1, 2009 @ 5:22 pm
July 1st, 2009 at 5:47 pm
No Todd. Your words were clear to all of your fellow TT members.
Please tell me where Mike Gene or any other FLE advocate said anything resembling this. If you continue to dodge the question, then I can only conclude that you have been arguing for years against a concept which you haven't even rudimentally understood.
Comment by chunkdz — July 1, 2009 @ 5:47 pm
July 1st, 2009 at 6:01 pm
You have still not done anything to indicate that you understand what I am claiming, but I'll bite. When I get some free time I'll dig through posts available right here on TT that are examples of what I'm saying. I am still baffled that you apparently deny that any FLE supporters believe in front loading information. I'd love for you to answer my question of what exactly you think it was that is front loaded if it isn't information?
Comment by Todd Berkebile — July 1, 2009 @ 6:01 pm
July 1st, 2009 at 6:04 pm
That's the nifty thing, Todd. I suspect that simply setting up a system in which things can (or are likely) to evolve is considered FLE already– which, of course makes it even harder to ever attempt to distinguish FLE from non-FLE.
Comment by hrun — July 1, 2009 @ 6:04 pm
July 1st, 2009 at 6:05 pm
But after several posts, you have added no light whatsoever.
Well, it is a common view.
So some information was front-loaded according to MikeGene, and all of it was front-loaded according to others. That's why people speculate about mechanisms required to protect this vital information. Note that MikeGene rejects fundamental ID arguments about evolution.
Comment by Zachriel — July 1, 2009 @ 6:05 pm
July 1st, 2009 at 6:21 pm
Zachriel:
So Todd says "All" FLE advocates, including Mike Gene, support his statement. But Zachriel says that Mike Gene reject's Todd's statement, but some [unnamed] others support it.
Do you guys want to get your story straight before we go any further?
Comment by chunkdz — July 1, 2009 @ 6:21 pm
July 1st, 2009 at 6:28 pm
Thanks for the links Zachriel, that saves me some time. I also found a tread right here where Krauze offers this definition:
He says, "the original design influenced the course" whereas I said, "FLE theory [claims] that information from the early state guided or constrained or created the information that unfolded into the later state. " Boy, these sure seem to be saying the same thing to me. And that was just the first google result I got.
Comment by Todd Berkebile — July 1, 2009 @ 6:28 pm
July 1st, 2009 at 6:33 pm
What? Mike's statement completely agrees with what I am saying. This sentence completely matches what I am claiming above:
There is information front loaded into the organism (original front-loaded state) that unfolds (in this example by biasing future evolutionary outcomes, similar to the directional mutation example Bradford just used above) to result in the final state (multi-cellular life, in this example).
If you think this is different than what I am saying then I can assure you you are not understanding what I am claiming.
Comment by Todd Berkebile — July 1, 2009 @ 6:33 pm
July 1st, 2009 at 6:40 pm
You may be right, but since this would exactly match the description of Natural Selection I'm going out on a limb and assuming something additional is required.
Comment by Todd Berkebile — July 1, 2009 @ 6:40 pm
July 1st, 2009 at 6:41 pm
Todd:
Ahem… the quote that I asked you to substantiate was the following:
Please do so with no further obfuscation.
Comment by chunkdz — July 1, 2009 @ 6:41 pm
July 1st, 2009 at 6:48 pm
Read it again, Todd. Mike is not agreeing with you. He's describing a common misunderstanding about FLE, so it would actually be safe to say that he DIS-agrees with you.
Comment by chunkdz — July 1, 2009 @ 6:48 pm
July 1st, 2009 at 6:56 pm
The common misunderstanding is that 100% of all possible future information was in the first organism. Mike agrees with me that some people hold this view ("those who think that evolution is incapable of generating new “information.”") but he points out that this view is incorrect. Instead, he says the better claim is that the original information simply guided the development of future information. By acting as a limiter of viable options the original information unfolded into a limited/constrained set of final information states (which is also one of the options I offered). I understand what Mike is saying and I am telling you this is also precisely what I am saying. If you think they are different then you are not understanding what I am saying.
Comment by Todd Berkebile — July 1, 2009 @ 6:56 pm
July 1st, 2009 at 7:15 pm
There are at least two known error correcting mechanisms for DNA transcription. Moreover, DNA and it's "decoders" appear to be a versatile, re-programmable system. It seems plausible to me that such a system could be programmed with dormant genes, preserved thru deep time, with fail safe integrity control. It's done in other systems all the time, computers and mechanics.
Comment by kornbelt888 — July 1, 2009 @ 7:15 pm
July 1st, 2009 at 7:22 pm
Ok, if that is a plausible mechanism then it should be easy to create a program that demonstrates this mechanism. This is the idea that the front loaded data is somehow compressed into the initial state, preserved via error correction mechanism and then unfolded somehow once adequate conditions exist. Still some details to work out, but I'm sure you could build a program to demonstrate this; go for it!
PS: chunkdz, korn's statement is yet another example that conforms to the claim I made above, so we can add him to the list.
Comment by Todd Berkebile — July 1, 2009 @ 7:22 pm
July 1st, 2009 at 7:30 pm
You didn't say some people hold this view, Todd. When asked for a name of someone who holds this view you said "All of them".
But now you have changed your answer to "some others", yet you stubbornly refuse to name a single one.
So who is it Todd that you are talking about? Is it now "All of them – except Mike Gene?"
Comment by chunkdz — July 1, 2009 @ 7:30 pm
July 1st, 2009 at 7:33 pm
Actually, there may very well be some middle ground front loading where a cellular "tool kit" exists to be exploited within much narrowly defined search spaces than purely random searches. Life as we know it may be a combination of that, and "hard" front loading were certain characteristics are guaranteed, like say mammalian body plans, along with drift and other well understood sources of variation.
Comment by kornbelt888 — July 1, 2009 @ 7:33 pm
July 1st, 2009 at 7:47 pm
Sorry about that, here's the correct link
It's a shift in reading frame. There's no "new" information as far as I can tell, both genes are still "there", occupying the same genomic space (albeit slightly shifted). One is expressed, the other is not.
What everyone needs to understand is that those who posit front-loading will use the same evidence as those who don't – they'll just interpret it from the perspective of front-loading. Things like whole genome duplication, gene duplication, and shifts in reading frame (as the above paper describes), will be examined from a front-loading perspective and predictions (or expectations) will be elucidated. There's no reason to constantly compare those expectations to those of the currently held theory. This is not an attack on that theory, it's an attempt at a different idea. Let those that want to flesh out a different theory flesh it out. If you want to interpret the evidence from the perspective of the currently held theory, no one is arguing that you shouldn't. If you think the evidence fits that theory better, you're free to continue to believe that. If you're really interested in front-loading, try interpreting the evidence from that perspective without constantly comparing it to the currently held theory.
Comment by Daniel Smith — July 1, 2009 @ 7:47 pm
July 1st, 2009 at 7:54 pm
What are you asking for? A computer program that shows how integrity control work that precisely mimics cellular processes? Or a computer program, simply?
This is the idea that the front loaded data is somehow compressed into the initial state, preserved via error correction mechanism and then unfolded somehow once adequate conditions exist. Still some details to work out, but I'm sure you could build a program to demonstrate this; go for it!
I can create a program, simply, to demonstrate such a mechanism (although compression is not a necessary feature, and would seem to require more computational resources than necessary.) But to precisely mimic the cellular processes at present would require more understanding than I have at present of building protein nano machines. The concept seems plausible given what is already known, but I, like you, would like to see a proof of concept implementation.
Comment by kornbelt888 — July 1, 2009 @ 7:54 pm
July 1st, 2009 at 7:56 pm
Yes, all FLE supporters believe some information was generated up front in order to unfold later on. I'm still saying that. The quotes from Mike show that he fits this view. The post from kornbelt shows he fits this view. You have not shown anyone who supports FLE and denies this view. I've made my case, you have offered no counter example.
If you think my statements have changed you are reading something wrong. I offered many examples of potential ways to unfold the front loaded data. One of the examples is the view that evolution cannot create ANY new information. Some, but not all, FLE supporters hold this view. Yet ALL FLE supporters agree that FLE involves the front loading of information that unfolds to affect future states, which is exactly what I claimed all along. Far from "stubbornly refusing" I have offered multiple names of people with views that conform to my statement.
Sigh, I've said this multiple times now, the statements from Mike are a perfect example of what I was saying. Please, at this point you are embarrassing yourself by persisting. Clearly you failed to understand what I was saying, tried to twist my statement into an exaggerated "absolute" claim in order to show that some exception exists, you failed because my statement is not controversial and in fact matches the definition of front-loading, and now you stubbornly refuse to acknowledge your mistake.
Comment by Todd Berkebile — July 1, 2009 @ 7:56 pm
July 1st, 2009 at 8:17 pm
Here's the point, the program forces the implementer to generate some assumptions about their model. It eliminates the hand-waving "what-ifs" and "maybes" and "could-bes." The resulting fully specified model will imply specific predictions. Those predictions can be compared against empirical data to refine the model. With this model you can study questions such as: how much mutation can be sustained while maintaining data integrity? Do real cells see more or less mutation than what your model can withstand? What percentage of the information is required just to preserve the front loaded information? Is it conceivable that an equivalent percentage of information in real cells serves a similar purpose? I'm sure the list goes on and on. Your model could be refined and tweaked as new data is available. If in the end you can create input data (be a front-loading designer) that yields desired outcomes (use evolution as a tool) after undergoing a process that mimics a real world scenario then you can claim with confidence that FLE is an idea that deserves to be considered. And these are steps any lay-person should be able to take.
What I suspect is that if someone made such a model there would be fairly harsh criticisms about the first few revisions concerning whether they have any connection to reality (similar to the criticisms of Dembski's CSI). You must refine and improve the model in response to this peer review (don’t just cash in the book royalties and abandon the idea like Dembski). If the model can survive these criticisms and improves in its complexity and predictive power then you will have proved that there's something to FLE after all.
Comment by Todd Berkebile — July 1, 2009 @ 8:17 pm
July 1st, 2009 at 8:30 pm
I agree, and well put.
Comment by kornbelt888 — July 1, 2009 @ 8:30 pm
July 1st, 2009 at 8:52 pm
That's what I would have thought, too, but so far I have not gotten a good description of what this extra needs to be.
It is this 'extra' that would distinguish FLE from non-FLE.
Comment by hrun — July 1, 2009 @ 8:52 pm
July 1st, 2009 at 9:02 pm
Todd,
A little reminder. All that goalpost moving has made you tired.
Really, Todd? All FLE advocates say that novel information "was there all along"?
Oops!
Clearly Mike Gene does not fit your stereotype because he thinks it is the blind watchmaker who creates the new information, not that the information was "there all along".
So in effect, you came to a blogpost about Mike Gene to complain that Mike Gene does not fit the stereotype that you like to paint FLE'ers with!
Culture warriors are a funny bunch, people. They don't often make a lot of sense, but they are extremely entertaining to watch!
Comment by chunkdz — July 1, 2009 @ 9:02 pm
July 1st, 2009 at 10:41 pm
I see you are sticking to the classics! Throw out enough cliches and maybe you'll get luck and find one that fits some day.
I already showed how Mike's statement fit with what I was saying, now you're just going in circles. The front loaded information was clearly there all along, that's what it means to have been front loaded. Neither Mike nor I have claimed that 100% of the final information was front-loaded although we both pointed out that some people hold that view. You obviously have no concern for the ideas being expressed, you are simply looking for sound bites that you can twist out of context. And in your view this makes me a culture warrior. Interesting. Well I'm done with you, fell free to sling some more poo and claim victory when I ignore you.
Comment by Todd Berkebile — July 1, 2009 @ 10:41 pm
July 1st, 2009 at 11:12 pm
Ho hum. Once again you ignore your own words:
Nowhere does Mike Gene suggest that the new, novel information that we see unfolding in nature was "there all along". In fact, he considers this to be a common misconception of FLE. A common misconception that you seem determined to perpetuate.
To the contrary, I think clearing up misconceptions is a great foundation for critical thinking to begin.
Well, at first I was willing to give you the benefit of the doubt and suggest that you simply didn't know what you were talking about. It's now clear that you do have some understanding of it, yet you still wish to spread misconceptions about it. So yeah, that's the M.O. for a culture warrior. You'll just have to live with that.
I'm sorry that we couldn't get past the stereotyping and misconceptions. It's actually an interesting subject if you approach it with an open mind.
Comment by chunkdz — July 1, 2009 @ 11:12 pm
July 2nd, 2009 at 7:38 am
According to his statement cited above, MikeGene considers it a *different* and flawed view, not a misconception. For comparision, here is a speculative scenario proposed by Behe in Darwin's Black Box:
Perhaps Todd Berkebile didn't initially express his views perfectly, but his position seems clear at this point. But it is clear that Front-Loading proposes that essential information already exists in the original organism.
Comment by Zachriel — July 2, 2009 @ 7:38 am
July 2nd, 2009 at 9:30 am
Chunkdz asks, "Can you show me where Mike Gene said that novel information "was there all along"?"
JJS P.Eng. quotes the DM
Mike Gene
My italics and bold. The italics says that the blind watchmaker isn't enough. The bold says that the design information is carried through deep time by a front-loaded vehicle. The last sentence really brings it home for you.
Comment by JAllen — July 2, 2009 @ 9:30 am
July 2nd, 2009 at 9:38 am
Personally I agree that these factors will make it very difficult to write a program that even demonstrates the theoretical possibility of front loading, but supporters ensure us it will be easy. The reason I suggest they make a program to model a theoretical FLE mechanism is precisely so they will encounter these obstacles and thus come to understand some of the fundamental problems with FLE. There is no amount of us pointing out these problems that will convince them, they would have to do the work to learn it for themselves. But who wants to do a bunch of hard work just to prove themselves wrong? Well, other than scientists I mean.
Comment by Todd Berkebile — July 2, 2009 @ 9:38 am
July 2nd, 2009 at 11:14 am
Dembski wrote:
"The Front Loading Fiction"
Comment by Bradford — July 2, 2009 @ 11:14 am
July 2nd, 2009 at 11:21 am
Raevmo:
Mutations may disable genes within a particular individual but the species as a whole is a different matter. Some genes and functions are virtually ubiquitous. They tend to be those essential to life. Accounting for their origin goes to the heart of the matter.
Comment by Bradford — July 2, 2009 @ 11:21 am
July 2nd, 2009 at 11:26 am
Zachriel:
And this is news? Todd was not talking about the novel information built into the first cells. He was talking about the new and novel genes that we see unfolding in nature.
Mike Gene never suggested that these novel genes were "there all along".
This is just another ruse from Todd, Zach. You are smart enough to see it.
Comment by chunkdz — July 2, 2009 @ 11:26 am
July 2nd, 2009 at 11:39 am
If an original organism had essential functions how could essential information not exist in such an organism?
Comment by Bradford — July 2, 2009 @ 11:39 am
July 2nd, 2009 at 11:54 am
Exactly. The LUCA was front-loaded one way or another. The question that is intriguing to me is "how good was the front-loading"?
Was it "blind kludge-happy moron watchmaker" good?
Or was it "highly advanced technology" good?
Comment by chunkdz — July 2, 2009 @ 11:54 am
July 2nd, 2009 at 1:09 pm
chunkdz:
That is a distinguishing question. The former comporting to the mainstream view and the latter indicating design. Was an initial organism in possession of a tiny but viable replicating genome encoding suboptimal end products? If not design is indicated.
Comment by Bradford — July 2, 2009 @ 1:09 pm
July 2nd, 2009 at 6:01 pm
No, Mike lists a number of different ways to implement FLE. But using multifunctional proteins is certainly one of them. And using a protein machine that one can expect to be around for a few billion years is an ideal opportunity to use multifunctional proteins. So had Mike looked and found few or no moonlighting proteins, he should have seriously questioned his hypothesis, as should anyone.
So let's get it from the rabbit's mouth:
You're right about your statements, Todd, but Prof. MacNeill's statement was a little stronger:
He doesn't use the word "inevitable," but it comes to the same thing. He's "surprised" that "only two-thirds of the proteins in ribosomes have been "co-opted" in this way."
Further, if there had been only a few or none, this would have suggested there was something wrong with our current understanding of evolutionary cladogenesis."
Oh my! So naturally, evolutionary biologists have been desperately looking for co-opted ribosomal proteins, fearing the worst. And Oh! the sigh of relief that has spread throughout the scientific community now that Mike Gene has confirmed their expectations!
Baloney. No one was desperately looking to see if ribosomal proteins had moonlighting roles. If no co-option of ribosomal proteins had been found, the scientific community would have shrugged its shoulders and said, "So what? No big thing."
But Mike Gene looked. Why? Because his theory predicted it. And it paid off big time. And you critics don't have the balls to admit it.
Comment by Bilbo — July 2, 2009 @ 6:01 pm
July 2nd, 2009 at 8:39 pm
Bilbo, I am really struggling to follow you here.
First you say: "If we found that no or very few ribosomal proteins were co-opted for future functions, this would count strongly against the FLE hypothesis.
I ask: "Why? Are multifunctional proteins the only way FLE could be implemented?"
The you say:"No, Mike lists a number of different ways to implement FLE. But using multifunctional proteins is certainly one of them. "
So if using multifunctional proteins are only one of many ways to implement, then why in the world would finding no multifunctional proteins (or just some) count strongly against FLE. This doesn't make any logical sense.
Let's move on.
At least you know realize that Mike's way to 'discover' that ribosomal proteins have moonlighting function was by reading multiple reviews that summarized primary literature that pointed out that many ribosomal proteins have moonlighting function.
Now, you can say the the FLE hypothesis guided him to this, but of course the non-FLE hypothesis discovered this fact just fine.
Let's move on some more.
Again, I am glad to see that you now realize that the only people who claim to be making predictions are you and Mike). Thankfully you both realized that it was actually not a 'precise' or 'strict' prediction, but still, a prediction.
Finally this: "nd Oh! the sigh of relief that has spread throughout the scientific community now that Mike Gene has confirmed their expectations!"
Bilbo, you are seriously confused about who confirmed what. Let's look again what Mike wrote: "Eventually, I ran across a review that did list many of moonlighting roles. I recently found another review paper that added to the list published a year or so ago. And a few days ago, I found a paper that shows a moonlighting role for s5…"
So Mike has 'confirmed' the expectation by taking "a review" that listed many of the moonlighting roles and by taking "another review" that added to that list and by taking a very recent paper that added yet another one. So by reading two review papers that listed that 14 ribosomal proteins have moonlighting function and one primary paper that show that one additional ribosomal protein has moonlighting function Mike 'has confirmed' the expectation.
Again, I have a lot of trouble following your logic.
Comment by hrun — July 2, 2009 @ 8:39 pm
July 2nd, 2009 at 8:44 pm
Oh my, I missed this one:
Bilbo, who do you think wrote those review papers that Mike read. Just as an explanation: Review papers are summaries of primary literature written by scientists. The two reviews that Mike lists covered 14/15 of those moonlighting functions. Now, I would be willing to be a nickel against a crisp one hundred dollar bill that you have not actually read those reviews (and certainly not the primary literature that these reviews were based on).
How exactly do you imagine were those review papers written that listed 14 out of 15 (or 93%) of the moolighting ribosomal proteins?
Comment by hrun — July 2, 2009 @ 8:44 pm
July 2nd, 2009 at 9:06 pm
Well, if the chance of cooption was one in a million per year and the protein is 4 billion years old the odds of it not being coopted would only be 0.003992. Given a limited set of 15 proteins and those assumed rates the most likely outcome is that they would have all been coopted by now. Of course rather than simply guess at a cooption rate scientists would instead try to compute the real rate from examining the data.
No one was looking for this data? They just accidentally did the research that discovered it? Scientist: "Damn it, I was trying to make a creamy ravioli sauce and I accidentally discovered cooption! Now what will I have for dinner?"
Why do I suspect that in your mind Mike is wearing a lab coat and slaving over brightly colored test tubes.
Even though Mike himself pointed out he didn't predict this, rather it simply matched his intuition? It matches my intuition based on natural theories too, yet this fact fails to equally impress you.
It did? How exactly did it pay off? Mike has now had a peer reviewed article published? He now has a research grant to study his theory? This is far from the first time Mike has claimed that various research matches his telic instincts, I'm sure its just a coincident that in ~100% of those cases the results also match naturalistic predictions.
Maybe all the various different authors of all those papers are all actually Mike! He does use a pseudonym after all.
Or perhaps just in Bilbo's world Mike did all the original research for those papers himself.
Comment by Todd Berkebile — July 2, 2009 @ 9:06 pm
July 2nd, 2009 at 9:22 pm
Todd writes:
Hrun wrote (a few days back):
See, I thought the same thing. Bradford did not see the humor in my remark and asked me (rather needlesly) if hrun is a pseudonym. Maybe next time I will employ the use of those things that are supposed to help convey my emotions in written text.
Comment by hrun — July 2, 2009 @ 9:22 pm
July 2nd, 2009 at 9:50 pm
"hrun",
Oh see, that's why I don't use a alias, so I mock those who do with impunity.
Comment by Todd Berkebile — July 2, 2009 @ 9:50 pm
July 3rd, 2009 at 4:42 pm
Because moonlighting would be one of the more obvious ways to front-load proteins for the future, and using protein machines that will be around for billions of years, such as the ribosome, would be one of the more obvious places to have them. Finding few or none would be a strong indication that front-loading wasn't being considered.
Exactly. Evolutionary biologists did not predict that many ribosomal proteins would have moonlighting roles. Mike Gene did.
Well finally an attempt at some calculations. I image we could be more precise, if we knew how often gene duplication occurs. And if we knew how often a duplicated protein can have some beneficial interaction with other proteins. I'm not saying you're wrong, Todd. You might be right. If Mike is right, though, scientists found moonlighting roles for the ribosomal proteins by serendipity, not because they had done some kind of calculation that led them to expect to find those roles.
If you had told me about your intuition before we found out about how many ribosomal proteins have moonlighting roles, I would be impressed. Mike did tell us about expecting to find lots more moonlighting proteins in his book.
Comment by Bilbo — July 3, 2009 @ 4:42 pm
July 3rd, 2009 at 5:30 pm
But you said that there are many ways to implement front loading. How is 'not using the obvious way' a strike against FLE? It just doesn't make any sense.
Did you even read what Mike wrote? He got the information that ribosomal proteins have moonlighting function from a review– written not by Mike but by evolutionary biologists.
Bilbo, just listen for one second: Mike was told by review papers, written by scientists, that 14 out of the 15 ribosomal Mike lists in his book have moonlighting function. You quoted that paragraph out of the book yourself. Did you now read it? So why are you impressed by Mike and not by Todd? Both simply got the information from a source and then used their intuition to posit that more ribosomal proteins will be found to be multifunctional.
And hey, if you were to actually look at the review, maybe you'd find that the scientists who wrote them also expect to find more multifunctional ribosomal proteins.
Comment by hrun — July 3, 2009 @ 5:30 pm
July 4th, 2009 at 9:40 am
Cooption as a component of evolutionary theory is as old as Origin of Species. Frankly, that's one of the most important of Darwin's insights: fins to legs to arms to wings to fins.
Comment by Zachriel — July 4, 2009 @ 9:40 am
July 5th, 2009 at 9:02 pm
Todd B.:
Zachriel quoting MG:
… further, from MG:
This may have already been added (I haven't made my way through all the comments yet. Seems these 10 (or so) subunit ribosomal proteins could be the "consequence of carefully chosen initial states". It, atleast (imo), seems reasonable for a "nascent proto-science" styled investigation into origins. Seems to have surprised the researchers or, as MG already pointed out in the comments here: I should point out these moonlighting roles are usually discovered through serendipity, as no one was looking for them on the basis of any evolutionary prediction.
Sounds reasonable. *shrug*
Hrun:
Most of us are pretty dumb. You're doing good work here keeping the rubes in line. Thanks so much. You're a real peach.
Comment by Rob R. — July 5, 2009 @ 9:02 pm
July 6th, 2009 at 8:16 pm
We weren't debating cooption. We were debating the amount of cooption.
Comment by Bilbo — July 6, 2009 @ 8:16 pm
July 6th, 2009 at 9:21 pm
You are welcome.
In any case, it is not a commentary on your mental capacity. It is simply an observation: compare Bradford's view of ID or FLE with Mike's.
Comment by hrun — July 6, 2009 @ 9:21 pm
July 7th, 2009 at 2:17 pm
Lol! Your intuition is based on natural theories? It's like you are saying "It looks like a duck to me, because ducks look like ducks."
Is this supposed to impress us?
Comment by chunkdz — July 7, 2009 @ 2:17 pm
July 7th, 2009 at 4:02 pm
Sorry, hrun, somehow I didn't see your reply until today:
The problem that a designer who wants to front-load information faces is how to preserve that information into the future, which might be serveral billion years. Moonlighting proteins in systems that are essential to a cell is a way that would guarantee that the exact information is preserved, since the very same protein in the orignal system is used in a different system. No need to depend upon chance mutations "discovering" embedded information, by somehow mutating one protein into a different protein.
But now, say we looked at ribosomal proteins and found that very few or none of them moonlighted. If the designer failed to use a method that would guarantee that the exact same information was used, what confidence would we have that the other ways of front-loading information really were meant to be ways of front-loading, instead of simply luck?
Yes I read it. According to Mike, they weren't looking to fulfill a prediction, but finding them by serendipity.
Mike first read about moonlighting proteins, then in his book made the prediction that lots more would be found. Then he used his FLE hypothesis and went looking to see how many ribosomal proteins moonlight. So far he has found — is it 11 now? Todd has attempted to explain why so many ribosomal proteins moonlight, after the fact. Had he made the prediction before knowing so many moonlighted, I would be impressed. But leaving that aside, if Todd's calculation turns out to be correct, I will still be impressed with Todd's explanation. But I strongly suspect it's not correct, based on Behe's and Doug Axe's work.
Maybe I would. Another good question for Mike.
Comment by hrun — July 3, 2009 @ 5:30 pm
Comment by Bilbo — July 7, 2009 @ 4:02 pm
July 7th, 2009 at 10:42 pm
You know what, I actually discovered America. I predicted that there would be a large landmass west of Europe. And then I researched the matter, found an atlas and confirmed that indeed there is. Huzza!
Comment by hrun — July 7, 2009 @ 10:42 pm
July 8th, 2009 at 2:32 pm
That makes you smarter than Columbus. He thought he was going to find China, not a new continent. Most educated people thought the distance across the Atlantic Ocean, from Europe to China, was too far to make it by ship, before they ran out of supplies. Columbus thought the circumference of the Earth was a lot smaller than it actually was.
By the way, what exactly was the basis for your prediction?
Comment by Bilbo — July 8, 2009 @ 2:32 pm
July 8th, 2009 at 3:09 pm
Mike Gene's reply:
Mike's question for hrun:
Comment by Bilbo — July 8, 2009 @ 3:09 pm
July 8th, 2009 at 4:08 pm
It actually wasn't really a 'strict' or 'scientific' prediction.
Comment by hrun — July 8, 2009 @ 4:08 pm
July 8th, 2009 at 4:35 pm
I did not call them whimsical guesses, nor did I say they were akin to whimsical guesses. But expectations are not predictions. The reason why I used 'expected' was because I would presume that the scientists are careful enough in their language to distinguish the fact that even though they might expect other proteins to be multifunctional, they would recognize that evolution does not predict them to be multifunctional.
Was I not clear and consistent in how I applied the terms? Just as an example of how scientists use the word 'expectation' I quote this passage from a review on extraribosomal functions (PMID: 19362532):
Guess how they title the section this paragraph is found in? They title it 'Speculations' and not predictions.
Comment by hrun — July 8, 2009 @ 4:35 pm
July 8th, 2009 at 5:13 pm
Odd. When I looked at the Lindström review I found this:
So are you suggesting that Lindström tells people to look for more extraribosomal functions without the expectation that people will find such functions?
And as for the talking point by Ira Wool, I wonder if you looked at the book chapters Ira was referencing:
Since the talking point is quite short, one would suspect that speculations about extraribosomal functions would rather be found in the 10 page paper or book chapter he is referencing.
Comment by hrun — July 8, 2009 @ 5:13 pm
July 9th, 2009 at 6:13 pm
Hi hrun, I passed your questions onto Mike. Meanwhile, back to your analogous prediction:
When I asked what your basis for a prediction was, you replied:
But you see, it doesn't really matter whether or not it was "strict" or "scientific," or an expectation, or a speculation. If you based it upon some independent information or hypothesis, then went looking to see if we had evidence that the landmass was there, and found it, that would be very impressive, even if it had already been discovered by others.
Comment by Bilbo — July 9, 2009 @ 6:13 pm
July 10th, 2009 at 11:25 am
Ah. Now you are actually using the correct term: a hypothesis. That took quite long, but we are finally getting somewhere. And of course people might think what I am doing is simply nit-picking, however, the term prediction (used in a scientific context) has a clear definition—and this was no prediction. Mike had a hypothesis and looked for confirmation in published papers on pubmed using research papers and reviews. Finally, we can put the term prediction to rest and use the accurate term of expectation, speculation or hypothesis.
So based on Mikes intuition he came up with the hypothesis that ribosomal proteins are multifunctional. Interestingly, the review that Mike cites as a major source for the multifunctionality of ribosomal proteins ALSO shares this hypothesis. (Remember, otherwise the author would like not suggest that people search for more multifunctional ribosomal proteins).
So, how does this support the distinction that Mike apparently is trying to draw between him (FLE adherent) vs. the scientists who write the reviews on Pubmed (not FLE adherent)?
Comment by hrun — July 10, 2009 @ 11:25 am
July 11th, 2009 at 4:33 pm
Hi hrun,
Since I never figured out how to communicate with the other members of TT, I can't verify that you are banned from TT. In case you're not, I'll post my reply here and at The Design Matrix.
Mike went looking for moonlighting roles for ribosomal proteins, based on his hypothesis, which predicts it.
It's not clear whether other scientists are expecting moonlighting roles for ribosomal proteins, and if they are, why they are expecting them.
Comment by Bilbo — July 11, 2009 @ 4:33 pm