“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
For the same reason people can walk on a roof without falling off.
Possibly the most inapt analogy ever.
Do you mean specific alleles exist by design? And if evolution has a target, what would be the target allele to determine, say, skin color? If one allele ever disappears, is part of the design lost? And if one new allele emerges, was that the designer in action again?
You seem to be saying that new alleles are extremely rare in sequence space so the “Designer” is needed to find them. Is that right?
I dunno. Seems apt to me. What Mung might be saying (and I admit it can be hard to tell) is that islands of function can be isolated without having a size of 1. A big, flat roof has room to walk around on, even if it’s separated from all other roofs by many miles. Similarly, an island of function could be quite large in sequence space, i.e. could have hundreds or thousands of synonymous or near-synonymous sequences, without affecting the IDiots’ point. (There are reasons the point is bogus, but that isn’t one of them.)
Mung, how about answering the question?
If function is so sparse in sequence space, why is it almost always possible to find a synonymous sequence just on mutation away from any given working sequence?
Not observed by Thornton.
Here’s the point: two proteins can be widely separated, but still reachable from a common ancestor via single steps. That’s Wagner’s claim, and he is not alone in making it. No one, including Axe, has really disputed it.
Agreed, but not relevant to my point or, apparently, to Mung’s analogy. You will recall the analogy was a response to mentions of synonymous substitutions. Mung was correct in pointing out that all that didn’t matter. You’re talking about non-synonymous substitutions. And I would go so far as to say that any non-synonymous substitution that makes no change to protein function is still irrelevant. It’s clear that you can do a lot to cytochrome c, for example, and still leave it cytochrome c. That’s why researchers concentrate on gene families with divergent functions. Pay attention to that and forget the synonymous or near-synonymous substitutions.
But Thornton looks at sequences that support multiple bindings.
Mung’s analogy might be a bit more relevant if genes couldn’t be duplicated and couldn’t do more than one thing.
I might point out that Behe sees no barrier to the evolution of new proteins.
Allan Miller,
You are right here that I think the architecture of the genome being a sequence is a show stopper for modern evolutionary theory and I believe that Meyer has a strong argument. I thought the OP you wrote on the subject was excellent yet the problem you are facing trying to say sequences can be found from random change is beyond the reach of a good argument. Joe Thornton did great work showing ancestral relationships of proteins, but you know as well as I do that showing that an enzyme surface evolving to catalyze a new molecule is very different then the emergence of a motor protein or a protein that is part of a spliceosome. The origin of new sequences is a big challenge for science and I don’t believe the current paradigm is going to solve it. I am willing to explore any good idea that overcomes the difficulty of sequences being explored by stochastic processes.
But not beyond the reach of empirical research it seems.
http://www.nature.com/nature/journal/v410/n6829/full/410715a0.html
But that’s from 2001.
OMagain,
Thanks for the paper.
Very true, OMagain,
IDists hate Keefe & Szostak, 2001, with a vengeance. It pretty much sinks the “islands of function” argument. They don’t understand how McLaughin et al. 2012 destroys Axe’s Quixotic quest, showing that even optimized proteins have many, many somewhat functional neighbours, and they hopelessly misinterpret Hayashi et al. 2006 , which shows that the lower slopes are far more tolerant than the peaks.
colewd keeps claiming that X (or Y or Z, it keeps changing…) is “too unlikely” to have arisen via stochastic processes, while simultaneously claiming that he is not making a probability argument (wtf?), and studiously declining to try an actually model such a stochastic process.
Would any of the IDists care to engage these data, or can we expect more this-is-complicated-therefore-designed Gish-galloping hand-waving?
The combination lock analogy is the tornado-in-a-junkyard fallacy.
Huh? You say that as if you haven’t already read Keefe & Szostak 2001. Surely you read it before you responded to Rumraket’s citation here?
Or not.
ET fix link
DNA_Jock,
Yes, I had read the abstract. I was thanking him for citing evidence with his argument. Thank you for the papers you cited. I have briefly looked through them and need to spend more time to understand what they add to the argument. I think the Szostak data is similar to the low end probability data in of Hunt’s paper so I am not sure it helps the argument for stochastic processes. If you could explain how the paper you cited changes Axe’s argument that would help. How do we build a flagellar motor through stochastic processes when you need organization of 4^400000 of DNA sequential space so a motor can build itself in the proper order and build a new one every time a bacteria divides?
You might note that every structure evolution produces is fantastically improbable, like a specific bridge hand on steroids. You continue to ask “How can we deal THIS PARTICULAR SPECIFIC bridge hand if the deck is properly shuffled?” And as usual, you imply that after a proper shuffle, NO bridge hand can possibly be dealt, because the process of dealing it (with odds of 51-1 against every single card is simply not plausible to you.
Since nothing anyone has said has penetrated at all, you are at least providing a Free Home Demonstration of why creationists never learn anything.
I would be interested in seeing an OP with a full description of your argument. It sounds like you have potentially testable claims. I’d like to hear what exactly you are claiming is a “show stopper for modern evolutionary theory” and what evidence you would accept as disconfirming that claim, if it were found.
Would it be too much to ask you all to make up your minds? They are improbable or they are not improbable, which is it? They are rare they are not rare, which is it? Protein folds are a dime a dozen, protein folds are worth their weight in gold, which is it?
woah, are you stupid or what. smfh
Yes.
You really don’t get it, in spite of all of the attempts to explain.
A specific bridge hand is highly improbable. Yet it is highly probably that you well get a bridge hand.
Organisms are extremely complicated and sensitively adjusted pieces of machinery. If you take a complicated piece of machinery, even one which is not working all that well, and make a very large, random alteration to its insides, the chances that you will improve it is very low indeed.
– Richard Dawkins
Would it be too much to ask you to address the actual point? SOME bridge hand is guaranteed, any SPECIFIC hand is very unlikely. Bridge hands are common. Specific hands (that is, specified in advance) are very rare. Protein folds are a dime a dozen, but any SPECIFIC fold is highly unlikely. The bullet fired into the air is sure to land somewhere. The chances of it landing in any specific place are very tiny. Is this really beyond your ability to comprehend?
Flint, to Mung:
I’m betting on ‘yes’.
Mung, after all, is the person who wrote this — and meant it:
When you think about it, this is how Mung’s god physically exists. And nowhere else.
Selection is more like a particularly subtle demon that has operated on the different steps up to life, and operates today at the different levels of life, with a set of highly original tricks. Above all, it is highly active, driven by an internal feedback mechanism that searches in a very discriminating manner for the best route to optimal performance, not because it possesses an inherent drive towards any predestined goal, but simply by virtue of its inherent non-linear mechanism, which gives the appearance of goal-directedness.
– Manfred Eigen, Steps Towards Life
Manfred Eigen must be an IDiot.
And you cannot change your spots.
Guess what the first hit for that particular quote is?
http://www.evolutionnews.org/2016/03/randomness_in_n102731.html
And do you know what the rest of the quote says?
Seem to me you are deliberately trying to restart the quote-mine accusations, for whatever perverse reasons you are driven by.
Quote mine alert! The DI sliced and diced several paragraphs together. You are no better.
Can’t you READ? Or do you just stop reading when you get to the bit you want to mine?
Again, why don’t you just leave the site?
I’ll tell ya, this particular instance of Mung behavior is personally offensive to me.
I care that I spent hours doing the research — then Mung just comes along and spends seconds making a dumbass remark about it.
I care that I spent hours selecting what I hoped were the important points out of a densely-written chapter (not wanting to use the whole chapter but concerned about leaving out the logical connections between parts of Dennett’s argument) then fixing the formatting so the pdf would display correctly when excerpted for this site.
I care that when I posted the result of my effort last night, I specifically bolded that same phrase — then Mung just choses to ignore in order to make his fake point.
Goddamn.
Just goddamn.
ID arguments appear to be restricted to a fairly limited set of fallacies, repeated (quite literally) ad nauseam.
Imagine a large number of ping-ping balls were dropped on a glacier. An IDist comes along later and remarks:
Finally, the conclusion “This is so unlikely, therefore it must have occurred by magic” represents the mis-application of Fisher to a Bayesian problem…
And if they are provided with an explanation for how the ping-pong ball got there, the responses are “Can you prove that that is the exact path taken?” and “Whatever, take a look at that ping-pong ball!”
Lather. Rinse. Repeat.
ETA: In case the analogy is unclear to anyone, Axe’s work consists of “See these two ping-pong balls? There’s ice between them.”
No shit, Doogie!
Aside from the implications of the full sentence in the Manfred Eigen quote, there is the issue of the word “search”. Just recently Mung was being very picky and saying that what mattered when we use the word “search” was whether the process satisfies Dembski, Ewert, and Marks’s definition of “search”. Suddenly Manfred Eigen is dragged in, and I’m pretty sure neither Mung nor Eigen has checked whether what Eigen means by “search” is what DEM mean.
For the DEM “search” Tom English and I proved that, if one starts from a reproducing organism which has genotypes and fitnesses, the result of the “search” is that one does far, far, better than a blind search. DEM did not take that into account. Active Information can be acquired, contrary to the conclusion that DEM would like to draw from their theorems.
That is important for anyone who is trying to use DEM’s theorems to argue for ineffectiveness of evolutionary processes. Do you agree with our argument, Mung?
colewd,
There are issues besides the quality of the argument. There is a need for data relevant to the space, and an understanding in the person with whom one is arguing of the mechanisms by which space is … uh … explored.
Each sequence space of any given size is different internally, and any movement through such a space crucially dependent on the nature of modification processes available, the distribution of critical positions along the string, and where you start.
In short, size of sequence space is neither here nor there. The local characteristics of the space are vastly more important than the global.
By repeating some huge combinatorial number, you are starting from a position that
– all spaces of a given size have the same characteristics
– the only parameter that matters is this total number of permutations
– only one exact function will work, with each amino acid exactly the same ‘distance’, in chemical property, from all others
– there is no opportunity to get to a higher-dimensioned space by way of a lower.
None of these is the case in biology.
For example, there is a vast number of amino acid sequences that will fold into an alpha helix. I might, indeed, place a small bet that any alpha helix can be turned into any other of the same length, without going through any intermediate which is not an alpha helix, by simple point mutation, much like those word ladder games. You might struggle to get a random helix, but having got one, you can wander around to your heart’s content. Structural constraint limits sequence, but does not destroy connectedness.
Now consider two spaces, x unique strings of length N and y unique strings of length N/2. Space x has vastly more members – y^2 times more – than y. Landing on an alpha helix is much less likely in x, so conversely, the probability of an alpha helix in space y is greater than that in space x – the shorter the string, the more likely a random sequence of acids of that length will give a turn or so of alpha helix. This is simply your contention in reverse.
So, as a final exercise, estimate the probability of arriving at a 20-acid alpha helix, when one is allowed to include shorter spaces. For example, by duplicating and end-joining a 10.
When one is wedded to digital metaphors, and considers each ‘letter’ independent of the others, one may fall prey to an illusory conception. In the alpha helix, it is not simply that the acid at a position can be substituted, but that the acids either side affect the constraint. Because (FFS!) this is chemistry.
We are getting folding – functional strings – precisely because the digits are not binary bits or Scrabble tiles. Ignoring interaction for a function that fundamentally depends on interaction is silly.
Or he understands when he’s speaking metaphorically.
Or, Eigen is using his terms literally in one sense, but not in the sense which gets IDists salivating all over their keyboards when they automatically respond to the word “search” or “design” as if that proves there’s a “searcher” or a “designer”.
IDists are Pavlovian idiots. They can’t help themselves.
No, Joe, that wasn’t my point. You and Tom were critiquing the DEM paper. My point was that if you are going to do so you need to be talking about the same thing they are talking about. If in their paper “search” means one thing but you and Tom mean something else by “search” then you are obviously not talking about the same thing as DEM. What matters when being critical of the DEM paper is not whether evolution is a search according to how you and Tom define a search, but whether evolution is a search according to how DEM define a search in their paper. That should be non-controversial.
Who cares. It’s irrelevant. See above.
He should have used scare quotes.
So? I actually have the book. I also have the Eigen book. So I don’t have to rely on “creationist web sites” for my quotes.
Allan Miller,
My frame of reference is Art Hunts paper. This study goes over the probability of protein folds and I assume that Alpha helixes are part of this discussion. This paper gives a range of probabilities and is a panda thumb response to Axe’s paper.http://aghunt.wordpress.com/
In addition Michael Lynch wrote a two papers on the possibility of complex adaptions.http://mbe.oxfordjournals.org/content/27/6/1404.full While limited adaptions look doable like in Thornton’s work. The resources of time and population become too large to support large evolutionary change with the current mechanisms.
You remind me of that old story of the scientist who calculated that the bumblebee can’t fly. Except you have extended that story, by asserting that THEREFORE bumblebees must use some as-yet-undetected method, since they are observed to fly.
If your observations do not fit your calculations, you choose to reject the observations in favor of the calculations. Actual scientists are more likely to suspect some incorrect assumptions in their calculations. Yes, it’s always possible that mechanisms exist that haven’t yet been identified. But according to your calculations, these missing mechanisms must be far more influential than all other identified mechanisms combined. Which would make them blazingly obvious, yet many many careers have been spent studying this without noticing them. Odd, don’t you think?
Show your math.
I admire Professor Hunt particularly for his incisive but restrained contributions at ARN (R. I. P.) I haven’t seen him around the blogosphere lately apart from, I seem to recall, a couple of comments at UD. I wonder if someone were to email him, he might find time to weigh in.
You remind me of the person who can’t address the post so they engage in ad hominem instead.
Ah, so Mung’s point was that in the post by Tom and me, we might not have been careful to use the same definition of “search” that Dembski, Ewert, and Marks used in their theorems. And if we didn’t our argument would not be valid.
Actually, we were aware of that issue, so we made sure that our GUC Model did satisfy DEM’s definitions of “search”. So our conclusions were valid. We thank Mung for worrying, but everything is in fact fine.
So Mung can now indicate that Mung agrees that our argument in that post is correct. Or point out a mistake in our argument — something in our GUC Model that violates DEM’s definition of “search”.
(An issue that has nothing to do with Manfred Eigen).
It’s funny how you think that’s somehow a rebuttal to me adding If, on the other hand, you make a very small random alteration to it’s insides, you may improve it
to the quote, thereby entirely changing its perceived meaning. That somehow where you got a quote is relevant to how you use it.
Reading comprehension issues? From Lynch’s paper:
The point of the use of the quote had to do with organisms as machines. We were talking about engineering, after all. Your failure to be able to follow a line of thought doesn’t make me a quote-miner.
What makes you a quote-miner is the obvious quote-mine. How is the part that you intentionally left out not relevant to the part you quoted, whatever you were trying to convey? Quote-mining is about attempting to make it look like the author of the quote is saying something he or her is not saying and that’s exactly what you did there. It’s not your opinion or your position what matters when you use a quote, it’s the author’s. It’s not that hard to grasp
colewd,
You. Are. Just. Guessing. See, a problem that is handwaved in is just as readily handwaved away again.
Oh, really?
Let’s recap.
That’s the original post, by you, consisting of nothing except that quote.
And now you add that the use of the quote had to do with organisms as machines. You might want to consider adding your commentary in the same comment as the quote next time. As other people might consider you did that just so you could say
You want to be accused!
If that’s true you can point to where you talk about that.
If that’s true you can point to where you talk about that.
colewd,
What, noted ID proponent Art Hunt?
What, noted ID proponent Michael Lynch?
These people do not support your contention that evolution of present forms is impossible due to the nature of the combinatorial space. Nor are they here, you are just doing that tedious ID thang of bringing someone else along for interlocutors to shadow box with. It sticks out a mile – evolutionists argue almost exclusively in their own words, IDists rely on mountains of other people’s thoughts – largely people who do not actually agree with them.
Care to bring them along to actually say something, or are you just going to use them as talismen because you don’t know how to address in your own words THE ACTUAL POINTS that I spent some time typing out (to say nothing of the 4000 word OP you claim to have read).
You just repeat the same vague assertions, and don’t go within a mile of understanding the issues I raised. You assume that alpha helixes are covered? What can I do against such scholarship?