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,
Again, Dr Behe used the second to clarify the first.
IC has always been about the degree. Even Dembski says that. Behe makes it very clear in the responses to critics:
.
And one more thing- Behe’s claim pertains to biology and AVIDA has nothing to do with biology. It has nothing to do with Darwinian evolution so it cannot show that Darwinian evolution can produce IC. Just read the first reference I provided.
The number of components has always been the key
What? Why isn’t a hybrid a species? Read “On The Origins of Species..” Darwin talks about it.
Frankie,
What do you think the definition of species is?
Is it an article of faith that God cared whether mankind would take the form of an ape or a bird?
There are plenty of perfectly orthodox Christian theologies that assume that God used natural processes to achieve his/her creative will.
I think there is confusion of terms here. I think that there are many possible sequences that could produce, say, human intelligence, and indeed, there are lots of variants of those sequences even within the human species. We are each, of course, unique genetically. So there isn’t a single sequence that produced human-level intelligence, and no other that will do so.
I think that was what Neil was partly getting at (I could be wrong). Lots of sequences can produce a single function.
It’s worth finding out 🙂
It’s rather more than that.
And what else do you have? Anti-biotic resistance doesn’t help. Finch beaks don’t help. So what do you have besides Lenski and all the other experiments that show evolution is very limited?
The same as biologists use. Look it up.
fifthmonarchyman,
You keep saying this, but it isn’t true. Inability to grow on citrate is a defining characteristic of E. coli. Therefore it made for an appropriate buffer, being a substance that could not be used as a nutrient. The evolution of citrate transport was a surprise, not a target.
Frankie,
Oh so now it is, but you’d like to move the goalposts.
Thanks – have a donut. 😉
Frankie,
There are about 30 species concepts used by biologists for various purposes. Which one should we be looking up?
I know as with everything in your worldview it is a continuum. You have no way of saying why or even if two populations are different species. For the Darwinist all life just morphs into an nondifferentiated blob species don’t need explaining because they don’t really exist
That seems to be a fatal flaw of your view IMHO and quite a let down.
I’m interested in the origin of species. If I want an explanation for that I guess I need to go else where
peace
How is that “moving the goalposts”? Don’t blame me just because all experiments show that evolution is very limited.
Do you think biologists have just one definition? Point me to it, If you can. It looks like you’re dodging. Clarify terms and we can continue.
You don’t have to tell me that the concept is ambiguous. “Species are separate if they cannot interbreed, except when they can”
fifthmonarchyman,
I think you’ll find it is more general than that. If the criticism of Lenski is that he did not demonstrate evolution in n different organisms, where n is a number you are going to tell us is the threshold for a valid evolutionary demonstration, then yeah, epic fail.
It already had the ability to digest citrate. The transport protein’s gene was turned off in the presence of O2. The organism duplicated the gene and put it under the control of a different, existing, promoter.
I know there are several definitions of species. It is an ambiguous concept. It doesn’t have any mathematical rigor behind it.
Frankie,
The concept is not ambiguous, there are simply numerous ways of defining it, because real biology is continuous and the category dichotomous. You have simply mangled two different definitions and thought yourself clever.
Frankie,
You’ve failed to show that. “experiments show that evolution is very limited” in fact given the time and populations of the Lenski experiment it shows anything but. So then you move the goalposts to wanting other studies.
Some continuums have steeper slopes than others.
That is false. I hereby define a species as every member of the population that can interbreed. This satisfies both the why and the if. Why – because I define the term as such. If they can interbreed, then they are the same species.
They clearly don’t. I’m demonstrably different from the plants in my window, and the Budgies on the peg hanging from my ceiling. For example, I don’t have green leaves, or feathers.
Species clearly exist and we are explaining how they come about.
It seems you need a break, perhaps a good night’s sleep, because you’re reduced to mindlessly regurgitating trivially demonstrable falsehoods.
Species emerge when subpopulations diverge so much genetically and/or phenotypically that gene-flow is no longer possible between them.
There you go.
I wish you a good night’s sleep.
Yet you say you are apposed to even looking for an alternate sequence. Why??
I would say there is a single ideal sequence and the variants are simply physical approximations of this idea “Form”. Just like a circle in the phyiscal world is an approximation to the Ideal circle.
peace
Frankie,
I know. That’s why I said ‘citrate transport’, not ‘citrate metabolism’.
Frankie thinks there is “one”, Seems to be tainted by YEC thinking. He should come back after reading some basic biology books.
Dembski on IC:
Moderators please take notice of Richard’s lie. Thank you.
Creationists have one construct of species, “Kinds”. But we both know that’s unscientific gibberish, right?
Lenski’s experiment shows that evolution is very limited. All other studies support my claim about evolution being very limited.
You have an example?
What? And who said that “Kinds” = “species”? And what do you know about science?
How is it limited?
Frankie,
No they don’t. repeating something clearly refuted (the small population and timeframe) that is clearly untrue.
The concept is ambiguous. The fact that no one can nail it down is evidence for that. The fact that definitions are violated is more evidence of that.
You are the one repeating something clearly refuted. Hiding behind time just proves you are outside of science
That doesn’t make the two definitions not separate. But it doesn’t matter, because by either EQU is IC, and evolves by high-degree IC pathways. So IC is not a bar to evolution. Drift is the answer – it carries the population across the “canyons” in the fitness landscape that Behe thought would prevent such features from evolving.
Behe’s paradigm case was a mousetrap. And AVIDA has to do with biology in that it consists of virtual organisms adapting to a virtual environment in just the way that Behe claimed they couldn’t. EQU is the equivalent of the mousetrap that Behe said couldn’t evolve. But it does, and by IC pathways too.
It is an in silico instantiation of the mechanism that Darwin proposed, and which Behe claimed could not result in an IC structure via an IC pathway. It turns out Behe was wrong.
The number of unselected steps is part of Behe’s second definition. The number of components isn’t – his first definition refers to what happens if any one component is removed. So there has to be at least two, but apart from that, there are no constraints.
Elizabeth,
One definition, Elizabeth. The second just CLARIFIED the first. AVIDA doesn’t have anything to do with Darwinian evolution. It has nothing to do with biology. You could never get away with what you are saying in an open and honest forum.
Yes, Dembski’s definition is more robust.
He was smart enough to see that Behe’s was refutable, and indeed is refuted by AVIDA.
Dembski’s has its own problems though:
Again, AVIDA shows that “one fell swoop” isn’t even necessary. The key is drift.
Wow that certainly reduces the number of species in the world
wolves and coyotes
Cattle and bison
Lepomis macrochirus and Lepomis cyanellus
Lions and Tigers
etc etc
Each can interbreed and as EL points out interbreeding does not even make sense for bacteria and similar organisms.
peace
It seems that with GMO we can “interbreed” any organism with any other. Not sure how you can say species clearly exist in your worldview.
With horizontal gene transfer there is never a threshold so wide that gene-flow is no longer possible. So no species exist in your worldview
well there you go
peace
Sure. Here’s the creationist take, Kinds. We both know its gibberish, right? https://answersingenesis.org/creation-science/baraminology/created-kinds-and-essential-natures-bible-and-philosophy/
What is the “waiting problem”?
Seriously.
Does any ID advocate have an example of a history of sequence changes and the time involved that violates any statistical expectations?
How is this not open and honest? All can reply apart from one ‘troubled’ individual who is banned for posting porn. That’s more open than *any* ID venue.
Why is this a problem?
Two definitions, Joe. One refers to properties of the function; the second to properties of the minimum pathway necessary to reach the function. The two definitions are not the same. It doesn’t matter, but there’s no point in saying one is a clarification of the second when the two describe different things.
Of course it does. It’s an instantiation. in a computer environment, of precisely the mechanism that Darwin proposed. You may not think that Darwin’s system works in biology, but it works in silico – AVIDA demonstrates that it does.
Well, that’s another question – would the same mechanism work in biology? That’s why Lenski also works in biology. But it certainly has the key features: a population of virtual organisms that have a genome, phenotypic features, and can reproduce with variance. It’s a toy model of biology, but that doesn’t make it not-a-model.
Perhaps you’d like to re-read the rules?
I don’t care how many they are, the fact that it is possible to give a definition demonstrates my point. You may not LIKE this definition, too bad. Give a better one and explain why it’s superior.
So we make a different definition and use it for bacteria.
We just exclude GMO. There, done. Why is this so hard for you? It is simply a matter of definition.
We just clarify that gene-flow has to take place via sex. Clearly species then still exists.
Sleep tight.
It’s a concept with fuzzy boundaries. The idea of “species” (literally “kinds”) preceded the concept that of common descent. And near the nodes of the branchings, the boundaries are fuzzy.
Conventionally, species are defined as populations that do not generally interbreed, rather than populations that cannot interbreed. Lions do no generally breed with tigers, for instance, and hybrids when they occur in nature are less common than within-population matings.
But it’s fuzzy, and indeed, speciation may begin and then the lineages merge again.
Check out ring species
Species as a process rather than as a set of categories makes sense under common descent, but common descent came after the concept of species, historically.
Suppose you have an evolutionary algorithm that generates code.
Suppose that the fitness test is whether the code is executable.
Suppose that you then look at the code, what will you see?
This? http://www.genetic-programming.com/gpflowchart.html
Lots of “new” posters today..
Well, it’s good to see some lively discussion 🙂
YOUR POSITION CANT EXPLAIN LIVELY DISCUSSION.
Exactly, in your worldview species don’t really exist so there is noting to explain. It’s all one fuzzy landscape each population bleeding into all the others.
I just don’t see things that way
peace
fifthmonarchyman,
How you define things is arbitrary. How genetic material moves, isn’t.