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.
That could burn.
1- That natural selection can produce the appearance of design
2- That natural selection can produce IC
Patrick doesn’t understand that Lizzie has made the same claims in this thread.
No it doesn’t, an unknown designer with unknown abilities can never be ruled out.
The appearance of design is design if you use the ID definition of design, a pattern of elements of a thing. ID says nothing about the mechanisms of design
Where?
Mung,
The organism is a product of the genome. Repair enzymes are produced by the genome, as is everything else. If you think ‘the organism’ has any control beyond genome products, let me know how you think that executive control is implemented (ignoring brains, for the present).
None of this, in any case, addresses the issue which I illustrated above. I’ll repeat it, just once: Frankie said that, since the organism ‘controls’ the genome, mutations are not accidents. You insisted that the organism does control the genome, but your example is completely orthogonal to the production of ‘non-accidental’ change, because you chose the very mechanism that prevents change! Bong! You lose.
Frankie,
Then it should be no problem for you to state here the scientific hypothesis proposed by IDC proponents and the testable entailments thereof. Please do so — you’d be the first.
Look up “Rabbits in the Pre-Cambrian” and do try to learn a bit about the topic before opining.
Frankie,
You cannot make claims that an artifact is designed without some knowledge of the capabilities of the putative designer. That’s why CSI and other IDC metrics have proven useless.
Frankie,
Please then clearly state Behe’s claims and explain how Lizzie’s statements of them were inaccurate.
As with presenting a scientific hypothesis of IDC, you’d be the first.
Frankie,
That’s incorrect. If one showed that water could produce a convincingly ‘designed-looking’ arrowhead, this would not thereby prove that all arrowheads were produced in that manner. You can’t eliminate a possible cause just by finding another.
Additionally: All ID has to do is show that ID can produce what ID says is designed and … well, it would look a hell of a lot less like cargo cult pseudoscience. You demand a standard of others you cannot/will not meet, because of some binding-on-no-one bullshit that Design is the backstop when all else fails (neatly saving your mob from doing any actual positive work on it).
Patrick,
ID is based on three premises and the inference that follows (DeWolf et al., Darwinism, Design and Public Education, pg. 92):
1) High information content (or specified complexity) and irreducible complexity constitute strong indicators or hallmarks of (past) intelligent design.
2) Biological systems have a high information content (or specified complexity) and utilize subsystems that manifest irreducible complexity.
3) Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity.
4) Therefore, intelligent design constitutes the best explanations for the origin of information and irreducible complexity in biological systems.
The criteria for inferring design in biology is, as Michael J. Behe, Professor of Biochemistry at Leheigh University, puts it in his book Darwin ‘ s Black Box: “Our ability to be confident of the design of the cilium or intracellular transport rests on the same principles to be confident of the design of anything: the ordering of separate components to achieve an identifiable function that depends sharply on the components.”
He goes on to say:
” Might there be some as-yet-undiscovered natural process that would explain biochemical complexity? No one would be foolish enough to categorically deny the possibility. Nonetheless, we can say that if there is such a process, no one has a clue how it would work. Further, it would go against all human experience, like postulating that a natural process might explain computers.”
Then there is the explanatory filter. If it is shown that nature can produce it then we never get to the design inference box.
More from Behe:
There you have it. And that is just a start
I quoted Behe and Lenski- Lenski saying that EQU did not evolve unless the previous steps were selectable and Behe saying that is what IC is all about. Elizabeth tried to say that is something new Behe added but it is all in “Darwin’s Black Box”.
Umm, evolutionism can’t explain rabbits. I have looked for the modern theory of evolution and all I get is people like you who just bluff and stall. I find people talking about it. I found that the “modern synthesis” was first the name of a book and then the name given to what was gleaned from a collection of books, but that doesn’t make it a scientific theory.
Biological reproduction is irreducibly complex. There isn’t any path from molecular replicators to biological reproduction. You guys have quite a bit of faith in undirected processes. Strange that we need engineers to pull of the marvels nature does by itself.
OK:
the Lenski paper:
Frankie,
Assertion without evidence.
IDCists have never clearly defined terms like “information”, “information content”, “specified complexity”, or any other metric that supposedly indicates design. None of those, as used by IDCists, can be objectively measured.
Again, this depends on the definitions of “information”, “information content”, “specified complexity”, and “irreducible complexity.” IDCists have thus far provided no such operational definitions.
Baseless assertion.
“Intelligent design” is not an explanation. It is utterly vacuous and unsupported by any objective, empirical evidence.
Frankie,
It would do no such thing. Since IDCists refuse to discuss the nature of their supposed designer (PBUH), there is no way to tell that, should some type of increased motility result, the invisible, undetectable designer hadn’t reached her finger into the flask.
More importantly, this argument assumes that “design” (and let’s be frank, IDCists mean the Abrahamic god) is the default explanation. That’s ridiculous. As I said before, if modern evolutionary theory were disproved tomorrow, ID(creationism) would still be vacuous, unscientific nonsense.
Patrick, Kindly stuff it. IDists have said exactly what would falsify ID and you aren’t in any position to say otherwise. The DESIGN comes first, Pat. We don’t even ask about the designer until after we have determined DESIGN exists.
There isn’t any modern evolutionary theory and ID would have a great impact on biology. For one we would know that most mutations are most likely the product of the organism’s control. For another we would also infer there was an immaterial aspect to life- immaterial information guiding the processes.
Crick defined information as it pertains to biology. ID is OK with that- ie sequence specificity. Meyer talks about that quite a bit.
And point 3 isn’t a bald assertion but an observation based on years of experiments. That is the whole point. Step up and support your position and ID falls. You have failed at doing that and ID thrives because of that and our growing knowledge of cause and effect relationships.
For example the genetic code is a real code. It isn’t a metaphor nor an analogy. It’s as real of a code as any we use. It is not reducible to physics and chemistry nor can it be explained by physics and chemistry. There is only one known source for codes.;
Wow Joe. A whole decade after you ID-Creationists got destroyed in Dover and you’re still repeating the same loser talking points. Since that stupidity hasn’t worked in ten years maybe it’s time to try a new tactic?
You take a completely different view of creationism in the Varieties of Religious Language thread. Why the change?
Actually that’s not true.
Glad to see that you realize that. Please spread the word.
You appear desperate Allan. Grasping at straws to “save the skeptic.”
Actually, Neil claimed that organisms do not control their own genomes and I responded to Neil. Here it is for you again:
Maybe Neil didn’t mean what he said. I asked him to clarify what he meant. So far he’s declined to say what he meant by “control.”
But your attempt to say the organism does control it’s genome, but in such a way as to prevent change, therefore it’s irrelevant, is just lame.
Repair enzymes are not produced by the genome. The genome doesn’t produce anything. The genome is a repository.
And we should ignore brains because?
Frankie,
Prove it.
Frankie,
If information is merely sequence, and sequences can clearly be extended and amended by biological processes, why do so many IDists insist that information cannot be created by evolution?
Mung,
Please yourself. If you think ‘the organism’ sits above its genome in some way, and that prevention of evolution is evolutionarily relevant, get yourself some gold paper and cut a big star out of it.
Cobblers. All enzymes are produced by the genome, including those enzymes that produce enzymes. Is there some non-DNA-produced part of an organism I should be aware of?
Because only certain organisms have them, and very few of those that have can use them to ‘control their genome’. I was anticipating a ‘gotcha’. Clearly, an organism with a brain could direct its own evolution.
Sorry, been in Sweden for the last week, without much opportunity to catch up. Catching up now.
Of course – and this very week (while I was in Stockholm no less!) the Nobel was awareded to the researchers involved.
There is a language issue here, I think.
The systems that result in successful reproduction are complex. I think it is not terribly helpful to split them into aspect that are “controlled by the organism” and ones that are not. The entire system is a control system.
With respect, Joe, I don’t think you did.
Behe gave two clear definitions of IC – one describing a functional entity, one describing an evolutionary process, and indeed you quoted at least one of them.
By both those definitions, EQU, in AVIDA is IC – all the version of EQU that have evolved are IC functions (take a way one part and it ceases ot perform its function), and in all runs it evolves by deeply IC pathways, involving not only many neutral steps but some apparently necessary deleterious steps. Interestingly, in none of the runs reported did it it evolve by the shortest possible pathway.
So the basic principle that Behe laid out is falsified by AVIDA.
A different principle might still stand: that in biology there are things that could not have evolved by evolutionary means. But IC is no longer the determining criterion for such things, because we know, from AVIDA, that being IC, alone, or being only evolvable by a deeply IC pathway, alone, is not a bar to evolution.
The reason is drift. In a narrow sense, Behe is vindicated, because it turns out that Darwin’s idea that for something to evolve an adaptation to an environment, each incremental step had to confer some advantage in reproductive success in that envirionment turns out not to be true.
But that’s OK, because it simply means that Darwin was too stringent. Adaptive evolution turns out to be easier than he envisaged.
Moved a comment to Moderation Issues.
Elizabeth,
Let’s not concede too much to Behe. The problem of incremental advantage had been advanced and solved well before he started on it.
Behe has made and continues to make the incorrect assumption that there is only one path to any genetic sequence. He makes a second incorrect assumption that a mutation that is detrimental in one context is irredeemable detrimental. In short, he makes the assumptions that are necessary to make evolution impossible, and he simply ignores evidence that evolution continues anyway.
He never seems to notice this or wonder how it happens.
The claim is that undirected evolution cannot produce CSI from scratch. ID is OK with directed evolution. Directed evolution can actually be modeled.
Science already has:
The cell division processes required for bacterial life Proof provided. Have fun choking on it
True.
Frankie, read the rules please.
Elizabeth,
Read Darwin’s Black Box- Behe says that the pathway is the key in that book. That means you are wrong, as usual. Not only that EQU only requires 5 precursor “components”. They aren’t even mechanical parts as Behe describes. So you lose there too.
You read the rules. You and yours are the ones disregarding them. There is no way you are debating in good faith. Either that or you just don’t understand ID and its claims.
Behe never makes the claim petrushk stated. How can anyone take you guys seriously?
Fine.
No, because EQU always evolves via a high-degree IC pathway.
huh? What are you calling “components” here?
A bit of goal-post moving here, I think, Frankie.
Everytime someone claims ID is falsifiable.
EQU only evolved when the parameters are ridiculous and don’t match reality. EQU never evolves once Behe’s criteria is set.
It is falsifiable and we have said how to do so.
Let me put that more accurately:
What evolves is the lineage of organisms, and their ability to perform logic functions. The first organisms in an AVIDA run to be able to perform EQU usually comes from a parent that can already perform several other functions, and often gains the ability to perform EQU at the expense of one of those. Its evolutionary descendents often regain the lost function.
It is not the case that only five “components” are required to “EQU”. Many components are normally required. What is true is that some of these are conserved by being required to perform precursor functions, and that conservation of these components increases the probability that a descendent will undergo a mutation that enables it to perform EQU.
What parameters are you referring to?
Behe’s criteria for IC were:
Won’t work if one component is removed
Evolves via a long series of non-advantageous steps.
Both these criteria are fulfilled in examples of EQU evolution in AVIDA.
Ok Frankie, what are the limitations of an unknown designer with unknown abilities? Name one to start.
ID is about the DESIGN. You can falsify ID by showing us undirected processes can produce what we say is DESIGNED.
Frankie,
This does not prove IC any more than removing your heart or a major artery proves that the circulation system is IC.
Moved post to guano. Address the comment, not the commenter!
Either:
1. The hypothesis of ID is that no ‘non intelligent’ causation can create the pattern of elements in question
Or :
2. The hypothesis of ID is the pattern of elements in question was caused by intelligence.
2 is unfalsifiable, an unknown designer with unknown abilities can create any pattern of elements , agree?
So that leaves 1 by which by your method of falsification seems to be the hypothesis that you are working with,correct? If so how do you determine any process is undirected when dealing with an unknown designer with unknown abilities ?
Second, falsification requires you to admit your hypothesis is wrong to your satisfaction, unfalsifiable