Journal club time: paper by Sanford et al: The Waiting Time Problem in a Model Hominin Population. I’ve pasted the abstract below.
Have at it guys 🙂
Background
Functional information is normally communicated using specific, context-dependent strings of symbolic characters. This is true within the human realm (texts and computer programs), and also within the biological realm (nucleic acids and proteins). In biology, strings of nucleotides encode much of the information within living cells. How do such information-bearing nucleotide strings arise and become established?
Methods
This paper uses comprehensive numerical simulation to understand what types of nucleotide strings can realistically be established via the mutation/selection process, given a reasonable timeframe. The program Mendel’s Accountant realistically simulates the mutation/selection process, and was modified so that a starting string of nucleotides could be specified, and a corresponding target string of nucleotides could be specified. We simulated a classic pre-human hominin population of at least 10,000 individuals, with a generation time of 20 years, and with very strong selection (50 % selective elimination). Random point mutations were generated within the starting string. Whenever an instance of the target string arose, all individuals carrying the target string were assigned a specified reproductive advantage. When natural selection had successfully amplified an instance of the target string to the point of fixation, the experiment was halted, and the waiting time statistics were tabulated. Using this methodology we tested the effect of mutation rate, string length, fitness benefit, and population size on waiting time to fixation.
Results
Biologically realistic numerical simulations revealed that a population of this type required inordinately long waiting times to establish even the shortest nucleotide strings. To establish a string of two nucleotides required on average 84 million years. To establish a string of five nucleotides required on average 2 billion years. We found that waiting times were reduced by higher mutation rates, stronger fitness benefits, and larger population sizes. However, even using the most generous feasible parameters settings, the waiting time required to establish any specific nucleotide string within this type of population was consistently prohibitive.
Conclusion
We show that the waiting time problem is a significant constraint on the macroevolution of the classic hominin population. Routine establishment of specific beneficial strings of two or more nucleotides becomes very problematic.
Elizabeth- EQU does not evolve if there aren’t any selectable steps. That is what Lenski said, Deal with it.
“At the other extreme, 50 populations evolved in an environment where only EQU was rewarded, and no simpler function yielded energy. We expected that EQU would evolve much less often because selection would not preserve the simpler functions that provide foundations to build more complex features. Indeed, none of these populations evolved EQU, a highly significant difference from the fraction that did so in the reward-all environment (P ~= 4.3 x 10-9, Fisher’s exact test).” Lenski
EQU does not evolve with unelectable steps
Feel free to explain.
How many times does it have to be explained? 1 new protein binding site in the history of AIDS? That pretty much proves evolution is very limited.
EQU does not simply evolve via a “indirect, circuitous” route, though. Yes, some necessary steps produce something selectable (indirect, selected steps) but it also evolves via many necessary steps that do nothing at all (unselected steps, and even deleterious steps). Behe turns out to be wrong that “the likelihood of an indirect route drops precipitously” as the number of necessary interacting parts increases, because, as I keep saying, these parts do not have to occur simultaneously. This was Behe’s huge mistake, and it seems he still doesn’t get it. He forgot drift. He assumed that necessary unselected sequences would rapidly drop out of the population, and would not accumulate. It turns out they don’t. They hang around, hugely increasing the probability that another necessary but unselected step will occur in an individual that already possesses some of the other necessary (but still unselected) sequences, and thus that eventually, an organism with all the necessary, but unselected, sequences, will be born.
And I agree. So did Darwin.
One post moved to Guano. Read the rules, folks.
LoL! Your mistake is trying rewrite what IDists have written. Drift is nothing more than luck. And if luck is all you have then you don’t have any science.
Lenski said that EQU does nit evolve under Behe’s rules. That’s it, Elizabeth. All you are doing now is proving that you are a baby.
Then what is your issue? It seems that you agree with Behe now,
Read the rules and if you people are posting in good faith then good faith needs to be redefined.
Nice quote mine,m but you left out a bit from the same abstract.
If “Behe’s rules” are that you need some selectable steps for something to evolve, than nobody disagrees with Behe, and all he is saying is what Darwin proposed.
Of course that isn’t what Behe is saying, because if he was, nobody in ID would be paying any attention, because he’d just be saying what nobody disputes.
There wasn’t any quote-mine and your quote doesn’t refute mine. Also natural selection wasn’t involved.
Wow- you are hopeless. Now you want to put words in Behe’s mouth. Pathetic, even for you.
Behe was pointing out that there are many systems that do not have selectable steps. That was the point of the book, duh.
Seven mutations were required for AIDS to jump from Chimpanzee to humans.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2898239/
I agree with what you claim Behe is saying. but if that’s what he’s saying, he’s not saying anything that supports ID – merely that some necessary steps need to be advantageous if something complex is going to evolve.
We know that. Darwin thought that they ALL needed to confer some slight advantage, but studies like Lenski’s show that this is not the case, and that indeed, some steps can be quite markedly deleterious. This means that Darwin’s idea was actually too stringent. Adaptive evolution turns out to be even easier than he foresaw.
But of course this is NOT what Behe is saying – he’s saying that if a thing requires too many components that are not advantageous when they first appear (i.e. are not “selected”) then they are very unlikely ever to turn up in the same organism.
That’s why he thinks that evolution has an “Edge” – if a feature requires too many components, none of which individually confer an advantage, it can’t evolve. Another way of saying this is that if the shortest evolutionary pathway from the previous selected step involves too many unselected steps, the thing can’t evolve (the pathway is high-degree IC).
However, AVIDA shows that a pathway can be deeply IC (many many unselected but necessary steps) and the thing still evolves. Not only that, but in practice the actual pathway taken tends to be even more deeply IC than the shortest possible pathway. And not only that, but can even include necessary, but deleterious steps.
So either way, Behe is no use for ID.
If he’s saying what you think he is saying, he is simply saying: adaptive evolution requires some selected steps. Which is standard Darwinism.
If he’s saying what I think he is saying, he is wrong.
And the point of AVIDA is that such systems still evolve.
I haven’t seen you actually say anything that merits refutation.
Evolution proceeds by steps, some of which are neutral. Deleterious mutations are not insurmountable obstacles. Behe is simply wrong.
yes, it does. With a great many unselected steps. It has to – there is no available path that does not include many unselected steps, and in practice, it takes paths that have even more than the shortest.
Unless you really meant “unelectable”.
Except they do not evolve via undirected processes. THAT is the debate. And they do not evolve unless there are selectable steps
So what? 1 new protein binding site = impotence
You have serious issues. You don’t understand the claims of ID and IDists and you want to change what we say.
Undirected evolution cannot be modeled. It does not make any predictions. It is a useless research heuristic.
AVIDA is not a simulation or instantiation of biological evolution. It means nothing to the IC argument.
Lenski said EQU does not evolve with unselectable steps. Take it up with him.
You can say Behe is wrong but you cannot demonstrate it. Evidence rules, not your BS
No, they don’t. That is why Darwin proposed incremental evolution by steps that were slightly advantageous each time they appeared.
However, it turns out that between steps that are slightly advantageous you can have many steps that are not.
It also turns out that some complex features require many parts that are not advantageous at the time they appear.
Behe thought that this would be a bar to the evolution of features that required more than a few of such parts.
But EQU is feature that requires many parts that are not advantageous at the time they appear, and some that are even disadvantageous at the time they appear.
But it nonetheless frequently evolves, because it turns out that the requirement for steps that are not advantageous at the time they appear is not a bar to evolution at all.
This is because frequently neutral, and even deleterious, variants can still become quite common in the population, and so accumulate. When the one necessary to transform all these neutral or disadvantageous features into a useful complex feature turns up, bob’s yer uncle.
And it happens quite often, because of accumulation via drift.
He said it does not evolve if there are no NO SELECTED INTERMEDIATE steps.
Do you disagree?
Your propaganda is not evidence, Elizabeth. And your propaganda is all you have.
And AGAIN, Behe is talking about UNDIRECTED EVOLUTION- ID is OK with directed evolution.
You cannot model undirected evolution producing biological IC. The concept is vacuous.
And that is Behe says. There are plenty of selectable steps to EQU in AVIDA.
AND as Sanford pointed out, AVIDA uses unrealistic mutation rates to get EQU
But far more unselected ones. Behe said:
EQU evolves by pathways with a very large number of necessary-but-unselected mutations.
It is also IC by this definition, from Darwin’s Black Box:
By both these definitions (and I quote Behe verbatim) EQU is IC, and yet evolves, with high probability.
It also uses an unrealistically small population size. So, meh.
No, Elizabeth. Lenski said EQU does not evolve if Behe’s rules are met. And IC is not about mere evolution. You have some mental block there.
But undirected evolution cannot produce any populations so you lose.
I gave you “Behe’s rules” in his own words. Those are met by AVIDA’s organisms that can perform EQU.
Lenski didn’t say they didn’t, because they did.
If he said something else, he was referring to a different rule.
And if the “Behe’s rule” he was referring to was something like “complex features require SOME selected steps to evolve” then Behe wasn’t saying anything that anybody disagrees with.
That is true. For evolution to work you need starting population of self-replicators. Evolution can only explain how populations adapt and change once in existence, it cannot explain the origin of life.
But then nobody claims otherwise. OoL is still a mystery, although there are some interesting leads.
Why do you say that? How often do you think new protein bindings occur in the history of evolution?
They would have to occur quite often to get the molecular machines we observe.
Especially given the short amount of time we’ve actually been looking. If X is claimed to be impossible and yet we’ve seen X just one time in the short decades we’ve been looking then millions of years suddenly starts to seem like plenty of time for many X’s.
Exactly which step in OOL requires the intervention of a designer?
Without the OoL you cannot say anything about evolution as the two are directly linked. I quoted Lenski saying EQU did not evolve with unselected steps. The problem is you.
Behe pointed out many structures that require evolution via unselected steps. That was the whole point to “Darwin’s Black Box”.
Don’t blame us because your position makes untestable claims.
LoL! petrushka can’t support undirected evolution so it erects a strawman.
Then Frankie what is the OOL of the intelligent designer?
That’s a good question. If it’s invalid to talk about evolution without knowing the details of OOL then it’s just the same for the IDists claims about the designer. No knowledge of the designer and design, IDists can’t say anything about the design because they can’t say anything about the designer!
Nicely caught newton!
I have no idea what that means. Perhaps English isn’t your primary language.
Umm we can detect design without knowing anything about the designer. We don’t even ask about a designer until after we have determined design exists.
Do give us a call.
Lenski did not say that “EQU did not evolve with unselected steps”. It was only possible for EQU to evolve via a great many unselected steps. What he did say (and which is true) is that when there were NO selected steps, EQU never evolved.
No selected steps is not the same as with unselected steps. The vast majority of steps in AVIDA are unselected.
From the paper:
Note that the “reward-all environment” is NOT an environment in which all STEPS are rewarded. It is simply the environment in which all 10 logic functions were rewarded.
That may be the source of the confusion.
In AVIDA, the virtual organisms are rewarded by performing logic functions. There are 10 in all. You can set the environment so that some, or all, or none, are rewarded, and by amounts of your choosing.
That means that a virtual organism that can perform all 10 correctly gets the maximum possible reward.
However, to be able to perform these functions, they have to undergo mutations, and the vast majority of these mutated offspring are no more capable of performing logic functions than their parents, and some are less so (may perform fewer functions)
In addition, the ability to perform each of the logic functions requires lots of mutations before a new logic function is built, and some logic functions appear only to be constructable via a mutation that breaks some previously operable function (although the lineage will sometimes get the broken function back, later on).
So it’s a tough environment to evolve in – all the functions are IC (remove any part and it breaks), and not only that, but all the functions require many unrewarded steps to build. On top of all that, EQU, it turns out, actually requires that some prior function be broken in its forebears before the sequence that performs EQU can arise.
And, as Lenski says, when NO function other than EQU is rewarded, EQU doesn’t evolve. When only some are, it sometimes does (it did once anyway).
However, and this is the key point: in every run, the majority of steps were either neutral or disadvantageous i.e. unselected:
And here is the kicker:
So not did EQU require several mutations, none of which were advantageous at the time of appearance, one of the required mutations reduced fitness by 50%.
And this is why AVIDA is so much better a model of evolution than Mendel’s Accountant – in AVIDA, as in life, a mutation or variant’s selection coefficient varies according to the genetic context. That is not possible in MA, as far as I can see – instead of rewarding actual functions, MA simply assigns fixed selection coefficients to each variant, regardless of their genetic context.
Someone who knows MA better than I will put me right if I’ve got this wrong.
It’s quite simple. Just fill in the acronym; OOL = origin of life. Then the question becomes “what is the origin of life of the intelligent designer?” Of course, on previous form, I guess you will respond that this is something you don’t need to consider. Unfortunately for those wishing to promote ID as a scientific venture, failing to propose hypotheses about how, when and when the “intelligent designer” acts (entailments) means that ID can be asserted to fit any scenario, confirming it as scientifically vacuous.
Prediction confirmed! 🙂
Nice deflection Frankie.