“The reason a bike lock works,” explains Meyer, “is that there are vastly more ways of arranging those numeric characters that will keep the lock closed than there are that will open the lock.”
Most bicycle locks have four dials with ten digits. So for a thief to steal the bike, he would have to guess correctly from among 10,000 possible combinations. No easy task.
But what about DNA? Well, in experiments Axe conducted at Cambridge, he found that for a DNA sequence generating a short protein just 150 amino acids in length, for every 1 workable arrangement of amino acids, there are 10 to the 77th possible unworkable amino acid arrangements. Using the bicycle lock analogy, that’s a lock with 77 dials containing 10 digits.
http://www.evolutionnews.org/2015/10/eric_metaxas_on_1100261.html
I believe this is what Mung has been talking about. I asked Mung:
How many goes do you get? How many bacteria in the earth’s soil?
Mung replies:
Not nearly enough.
I feel this is interesting enough for an OP as it seems to finally touch upon what IDers think the designer actually does that can be investigated scientifically.
For example, if we find in a population a protein that is different to the version in an ancestral population but which still works, the by (their) definition, that is prima facie evidence of the designer at work.
Perhaps we can then take the population with the original protein, enclose it in our most sensitive equipment and attempt to detect the designers actions when it “solves the bike lock” and finds the new protein and somehow makes the required adjustment?
If I were an ID supporter these are exactly the sorts of experiments I’d be proposing, and with money on the table (Templeton) I continue to be surprised at the lack of such endeavours. At the very least they can rule out some levels of possible designer interaction at the macroscopic level.
And Mung, I’d be interested in knowing how many would be enough?
Earlier during his direct testimony, Behe had argued that a computer simulation of evolution he performed with Snoke shows that evolution is not likely to produce certain complex biochemical systems. Under cross examination however, Behe was forced to agree that “the number of prokaryotes in 1 ton of soil are 7 orders of magnitude higher than the population [it would take] to produce the disulfide bond” and that “it’s entirely possible that something that couldn’t be produced in the lab in two years… could be produced over three and half billion years.”
http://www.talkorigins.org/faqs/dover/day12am.html
And the biggest problem is that we simply have evidence of imperfect reproduction having occurred–apparently accounting for evolution thereby–and evidence for nothing else accounting for modification of organisms to fit niches. If there is something else, fine with me, but it’s rather presumptuous to assume that we have ample knowledge to recognize that known and documented processes are insufficient in the absence of evidence for anything else occurring.
Then too, why is it that evolution lacking complete explanations for everything a problem when there are other problems in science? Are dark matter and dark energy serious challenges to our physics, as far as it goes? Not really, physics is generally just considered to be incomplete. We don’t know why we sleep, with some known reasons quite probable, and the whole reason is still fairly nebulous. Should we suppose that it’s a result of paranormal forces, the Sandman or some such thing, or do we pretty much stick with known neuroscience unless and until some big discovery is made?
Most people think the latter, but because there are a bunch of people who have theologic problems with evolution who highlight any extant question about evolution, it is treated differently by many who should recognize that science is ongoing. The squeaky wheel and all of that. But there’s no good reason to suppose that evolution has any especial problems, merely questions that are quite difficult due to events that occurred very long ago and without leaving any record except for the modified structure itself, like the bacterial flagellum.
Does anyone demand that we know when and where plate tectonics began? No. Then why are we supposed to be able to explain the evolution of the bacterial flagellum, other than the noise made by those who have ulterior motives for making it?
Glen Davidson
hotshoe_,
Its an argument based on the rarity of protein folds in both the Hunt paper and Axe paper that are based on may other papers over the last 20 years. It is applying this probability to see if modern evolutionary mechanisms are likely causes of the emergence of the flagellar motor. I am certainly willing to change my mind if someone can come up with a reasonable counter argument of how 4^400000 of sequential genome space became organized enough to build this motor through a stochastic process. Joe Thornton’s work does not help explain it.
Sorry, no. Asking for the cause of some specific structure is exactly like asking for the cause of the bullet landing precisely HERE and nowhere else.
And here you go again, looking at the specific spot the bullet landed (the “rotary motor”), rather than the process of trial and error.
The “cause” of the flagellum is exactly like the “cause” of every other existing biological structure, and every structure not yet imagined, but guaranteed to occur in the future.
Despite several people pointing it out to you over and over, you apparently simply cannot grasp that your question assumes its own answer, and that no accurate answer to such a question is possible, because ANY accurate description cannot be a direct answer to a question with the WRONG answer built into it.
And once more for good luck. The probability of the flagellum is infinitesimal. So is the probability of ANY specific post hoc target. You repeatedly commit the Texas Sharpshooter fallacy – finding specific bulletholes, drawing circles around them, and demanding to know the mechanism for such uncanny accuracy!
Flint,
Again Flint I am arguing if a given cause is likely not arguing the probability of a specific event. When you change my cause argument to a probability argument you are creating a straw man.
colewd,
colewd,
Exactly.
That’s how it works in the world of real bacteria, not in the ID-fantasy world. Reality is sloppy, excessive, and uncoordinated, but since there’s nothing “better” the cells somehow carry on carrying on.
Yes, parts were “added gradually”. We’re certain about that from comparisons of homologous proteins in the flagella of different types of modern bacteria. I can’t find the article I was reading (just last night!) but I recollect that across different families they only share a half-dozen ancestral flagellar genes, and all the remaining genes — say, 40 in E coli — arose by duplications and diversification.
Now, someone might speculate that the designer-god twiddled its microscopic fingers to install each of those gene variations in succession over the millions of years. But there’s firm evidence that the entire flagella package was NOT designed once, installed once, hands dusted off, work complete once and for all.
Which “cell cycle” do you want to know about now?
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edit to fix blockquote failure
GlenDavidson,
I agree with this point. Evolution is based on inference arguments because it is difficult to understand causes of historical events. If you could test and validate the cause then the design inference would fade away.
hotshoe_,
http://www2.le.ac.uk/departments/genetics/vgec/diagrams/22-Cell-cycle.gif
colewd,
The fact that YOU do not understand the explanation does not mean that the explanation is not valid.
I don’t understand quantum mechanic explanations of gravity but I’m not self-centered enough to assume that means the explanations are not valid.
You don’t have to learn any actual biochemistry to learn a lesson from what I’ve just said.
So now you’ve switched what you were talking about — something about transcribing proteins (which have to be “coordinated” to be “assembled” in some sequence to fit each other physically, like in a car factory) — and now you suddenly want to talk about chromosome duplication?
Do you have a point to make here?
hotshoe_,
The challenge here is that these proteins need to fit together with charge, shape and function. The emergence of one through a stochastic process late in the evolution of this motor is unlikely. The more likely conclusion in my mind is that we have yet to identify the cause of historical evolutionary change.
There always will be believers motivated to glorify their designer-god. Although, as I said, why they are stupid enough to want their god to get all the blame for motile lethal E coli … who knows.
Therefore, god did it.
RIght-o.
Carry on carrying on, dude. Or dudette as the case may be.
hotshoe_,
Yes, the cell cycle is based on coordinated transcription. A flagellar motor is built as part of the cell cycle i.e. the cell division of a bacteria. I think it is fair to say that its transcription is coordinated since it is assembled protein by protein.
hotshoe_,
Is this the only idea you have? Could there be a mechanism in nature we have not thought of? Can cells do their own engineering?
OK, so may we presume that whether models of evolution do or do not satisfy DEM’s conditions for a “search” is what you wanted to establish?
In the post that Tom and I wrote, we showed that their theorems do not establish that an “evolutionary search” cannot cause the organism to have Active Information. Even if evolution is modeled as being a search, once there is a reproducing organism there at the start, the DEM theorems do not stop it from incorporating Active Information into the genome.
May I assume that this is the issue you meant to raise?
colewd:
No it’s not. Whatever gave you that idea?
Flagella extrusion is a separate concept from cell division. That should be obvious if you stop to think for a moment; the cell-division graphic you yourself linked to shows nothing about flagella.
What they do have in common is that both processes require transcribing various sections of DNA, and both processes require metabolizing ATP to push/pull various macromolecules into position.
Are those similarities what is confusing you here?
colewd:
What you think is “fair” is of no interest to anyone but you. A climax forest is assembled tree by tree. A logjam is assembled log by log. Oh, that’s coordinated, right? Umm, no.
Maybe the problem is just in how you’re using/misusing the word “coordinated”.
There are feedback loops in cellular chemistry where the sufficient/excess presence of one transcription product — say, a specific flagellar protein — blocks more transcription of that particular stretch of DNA. But it’s sloppy and not really coordinated; it’s predictable but only within a broad range; it’s not as if the cell has a foreman standing around counting the proteinsas they roll off the production line: 19998, 19999, 20,000 STOP!
Is that what you feel is “coordinated”?
Well, depends on what you mean by evidence right?
😛
Or, if nothing happens without the designers design, and bikes are stolen then the designer designed a bike theft. Ergo the designer is a bike thief! If design is a mechanism then designing is stealing!
I wonder does the theft itself have measureable FIASCO?
If I take a bike apart and put it in a box and shake it, will I get a fishing reel back when I open the box?
Which one?
Sure thing, boyo, but there’s no evidence that we need any other “mechanism” besides what we already understand of unguided evolution, random mutation, and biochemistry. Occam’s razor has something to say about not multiplying hypotheticals unnecessarily.
And what “mechanism” are YOU proposing besides I-don’t-accept-the-current-science-so-there-must-be-something-more-exotic-and-important ? You want to be taken seriously, you have to start doing some serious work.
Are you currently a biochemist? Are you currently studying to become a biochemist? Let us know when you have something beyond your mere imagination to put forward for testing.
Depends what you mean by “own engineering”.
There’s zero evidence that cells can cause mutations which will be favorable to their descendants/replicants in the future.
There’s zero evidence that designed/guided mutations have ever happened in the past.
We know that the multiple genes now used by modern bacteria in flagella assembly arose separately over hundreds of million years, not all at once. Whether you want to speculate that was guided by some designer-god, or “engineered” by the cells themselves, it was pretty goddamned slow process. But that kind of slow process of acquiring sifting and co-opting genes is exactly what our current science of evolution predicts.
Score another one for mainstream science: prediction tested and verified. Score nothing for nebulous speculation.
YOu continue to argue that a specific biological structure is “unlikely”. The cause (mutation, selection, drift) has been presented to you many times. You respond that these are “too unlikely”. If you are arguing if a given cause is likely, this is arguing a probability. It is a pure probability argument. Sheesh.
And you say, over and over, that in your opinion the identified causes are so unlikely to produce what they’ve produced, that there must be some missing mechanism to increase the likelihood. And you probably notice that nobody accepts “I don’t believe it, therefore it must be wrong” as an argument at all.
hotshoe_,
Do you want a do over on this one 🙂
Any and all or none of those things. And we’ve talked about most of them here already. If you’d like to start an OP I’m sure that would be fine.
For example, if cells do their own engineering then how does that help explain the results of the E. coli long-term evolution experiment? If cells can do their own engineering, then why did only some choose to engineer their way to a new food source and not others?
And by engineering presumably you mean something based on a pre-existing plan or based on some kind of cellular intelligence currently unknown? That sort of thing?
Sure, but the trouble is that ideas are easy. Look, I’ve just had loads!
But ok, define what you mean by engineering and perhaps we’ll get somewhere!
And I’m sure there are loads of mechanism in nature that we’ve not thought of!
But so what? When we find those mechanisms, will you point to them and say they are insufficient and there must be more mechanisms we’ve not thought of? It seems to me you would do that.
So sure, all of those things or none of them. I’m quite sure we don’t know everything there is to know. But what does vague “specific proteins are complex and unlikely to form in one go all at once at random” get us? Especially when nobody claims that’s what happens anyway, except you and you already had an entire thread about that and ignored it. So there’s no actual evidence you understand the mechanisms that have been found, you just don’t see your deity’s hand at play hence they are insufficient (don’t play coy).
etc etc.
No, of course I don’t want a “do-over”. I’m right.
Your cell-division graphic is not about flagella extrusion; they’re two separate processes.
You’re either confused or … something …
Which flagellum? 🙂
hotshoe_,
Do you agree that cells can repair mutations?
QFMFT
OMagain,
Not sure but the discussion of a sperms tail will be even better 🙂
What’s your point?
hotshoe_,
My graphic is of a Eukaryotic cell. Thought you could self correct of this one 🙂
What the fuck is that supposed to mean?
hotshoe_,
Repair is evidence of engineering. BTW: offline until tomorrow.
No, DNA repair is not evidence of “engineering”. Not as any rational person uses those words.
Don’t worry, no need to hurry back online.
Not as if you’ll be able to “engineer” anything useful to say unless you learn some science in the meantime.
Let’s try this again.
The work done by natural selection is R and D, so biology is fundamentally akin to engineering, a conclusion that has been deeply resisted out of misplaced fear for what it might imply.
– Daniel Dennett
Dennett also discusses what can be the outcomes of evolution and its probable implications when viewed as an engineering process.
Water finding a pattern of channels in a watershed is R and D as well. Clearly, watersheds are engineered. And anyone familiar with oxbow lakes understands that the River Designer is tinkering with his outcome all the time.
Dennett fears, quite rightly, that “engineered” will be equated with “planned”.
(Although a link to your quote, so that the rest of us can read the rest of it, would be polite.)
It’s from the book Darwin’s Dangerous Idea (1995). Mung isn’t quotemining, Dennett meant it the way it sounds — although not the way our boyo means it when boyo comments that
because Dennett is first and foremost a Darwinist, and would totally disagree with colewd’s baseless speculation that we need something more or better to explain adapted structures besides Darwinian evolution as understood by today’s science.
In the pdf copy I have, the full quote is bottom of page 185, a precis of the coming chapter 8:
Not surprisingly, Dennett’s book is lovely and readable, even if quite densely argued and very hard to summarize in soundbites.
Here’s a “brief” portion which gives a flavor of Dennett’s “engineering” analogy:
[bolding mine, to forestall IDists misuse of Dennett to support any of their ideas that his term “engineering” in biology means “planned or directed action by some intelligent designer (or by elves!). ]
[all excerpts from pages 190-195. Darwin’s Dangerous Idea ]
Dennett:
Mutate, schmutate. Too many children were living to adulthood, so the Designer stepped in and put a stop to the nonsense.
Pure Design.
Mung,
There are those who can multi task … after all, if Dennett is arguing evolution as algorithmic, what a happy confluence of concepts!
colewd,
I suspect that no-one’s work or efforts would help explain it – to you. I began to do so in another thread, but you soon descended into the sneering of ‘just-so-story’, even when all I was doing was explaining flaws in your naive “100-acids-in-a-blender” model. Your mind is already made up.
You are one of countless critics who has decided (erroneously) how evolution must work. You then roll up to a forum and demand, for reasons best known to yourself, that people enlighten you, on the strict understanding that you are not in the market for any of their bullshit.
colewd,
Calling Joe G.
I wonder if this would be a proper test for the “rare protein functionality in sequence space” hypothesis:
1. Take the mammals tree https://research.amnh.org/paleontology/perissodactyl/f/mammal_tree2.png
2. Pick a protein and run BLAST sequence comparisons for humans – chimps – gorillas – and down the tree (some dermoptera, chiroptera, then scadentia, rodentia… all the way to Monotremata)
3. Extend that to amphibians, fish…
If we can find that each step down the evolutionary tree differs by a small number of amino-acids for every protein, but folds are very different for species far departed in the tree, I would think this would count as strong evidence that the hypothesis in question is falsified.
Does that make any sense?
Alleles.
If functional space is so rarefied, why are there alleles?
If islands of function are isolated, why is it possible to have synonyms just one mutational step away from any working sequence?
And why can every human take a couple of mutations in protein coding regions if proteins are so “fine tuned”?
How can directed evolution (yes, it’s a thing) work if proteins are so isolated?
Good point! But what if the algorithm is simple hill climbing and evolution really is a search? We might have Tom and Joe arguing against Dennett!
Design, obviously. 🙂