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.
Rumraket,
Fair enough; I was being rather casual. If only sexually reproducing species can even have a micro/macro distinction, then obviously it isn’t. But it is an example of small genetic changes coming to dominate a population, which accords reasonably closely with ‘within-species’ dynamics in a sexual milieu. Iterative ‘micro’ changes can sum to be ‘macro’ changes, though I am aware that a lot of people prefer the more dichotomous definition which depends on gene flow, and cannot apply to prokaryotes.
I understand and hadn’t even considered the nonapplicability of speciation in terms of asexual reproduction. I was more curious to see if, following some proposed definition of prokaryotic speciation, the evolution haven taken place in the Lenski experiment would qualify.
Would some of the proposed phylogenetic tests for delineating species for prokaryotes actually classify any of the extant running popluations in the experiment, as another species of E coli, compared to the founding species? For example (picking a paper out of a hat), would this proposed methodology score them as distinct?: Defining natural species of bacteria: clear-cut genomic boundaries revealed by a turning point in nucleotide sequence divergence.
See Vulić et al., Mutation, recombination, and incipient speciation of bacteria in the laboratory, Proceeding of the National Academy of Sciences 1999: “These results demonstrate the establishment of an incipient genetic barrier between formerly identical lines”
That was very interesting, thank you. I wonder what the result would be now, 16 years and another 45.000 generations down the line, if 20.000 generations are enough to qualify as incipient speciation in bacteria.
Yes it does.
I think I missed the Nature paper that demonstrated how organisms control their own genomes. Can you elaborate?
Sure. I think they call it tunnel vision.
So that’s a no, then. You can’t elaborate.
According to your book of morals, liars get the sword.
While the psychoanalysis is amusing, what I was actually suggesting was that you elaborate on your claim that organisms control their own genomes. Care to do that?
I’d also be interested in Mung supporting that claim in light of the observed results from Lenski’s study.
But I’m sure all we’ll get is another OP about the bible instead.
Rumraket,
Yes, that would be an interesting test, to see if Lenski’s bacteria (or even lab strains in general) are sufficiently diverged from ‘wild type’ to be partitioned by this particular almost-dichotomous ‘species’ boundary.
Sure if you define species in just the right way and squint real hard any difference at all would qualify as speciation. The problem with that is that such a definition is vacuous.
peace
fifthmonarchyman,
No, people are looking at ways to divide the continuum in as objective a way as possible. Of course, one could debate the existence of a continuum … but given that there IS, because all species concepts fail somewhere due to it, we just have to look for ways of dealing with it – for classification purposes, which hardly trouble the natural world much (they prefer the Food/Mate/Rival/Predator system).
You seem to want your cake and eat it – deny the continuum, then criticise species concepts because they have to deal with it. Is there a Platonic version of E. coli? How far are Lenski’s flasks from this essence? Wild Type E coli can’t utilise citrate, for example, and this fact is actually diagnostic – it is used to distinguish them.
Citrate Test
please define species.
Please give a non vacuous definition of species.
If you can’t do either of those things, on what basis do you offer this objection? Seems to me you want to define species as “what evolution cannot create”.
You seem to want to define speciation as:
On the same UD thread you also said
So again it seems to me that you define speciation as what evolution cannot do.
You then say:
So, a few questions.
Is there only one “species” of bacteria then?
If not, how do you separate one from another? How do you draw those lines?
That is the working method of creationism and ID.
Control the definitions so that evolution is impossible.
I feel an OP coming on….
hey ffm,
You going to provide your definition of species or what?
Or do you just want to point out what you perceive as problems without caring if they are really problems, as long as those “problems” fit your agenda?
So you’re willing to drop your snark about not finding anything in Nature?
What I want to know is why none of you registered “skeptics” had a word to say when Neil made his stupid statement but all of a sudden when I tell him he’s wrong you all come out of your holes.
Have you ever heard of DNA repair? Of course you have. And that would be just a single example of an organism controlling it’s genome and ought to suffice on its own to settle the matter.
Repair isn’t control.
I repair computers. That isn’t the same as operating them or programming them. When you’ve lost the argument, equivocate.
In the context of evolution, controlling a genome implies changing it to effect some new function.
The context that the word “control” was being used is this statement from Frankie:
“If an organism controls its genome then the changes are not accidents, errors nor mistakes.”
Neil’s statement was not stupid. Yours was incorrect.
Hey Mung,
I’m an organism. My DNA repairs itself. Is it under my control? No, I don’t think so or I’d get it to repair it better then it is.
Fail.
I think Mung has been taking lessons from wjm.
Perhaps you would be better trying to expain it using terms Mung understands.
Repair: Using redundant information within the cell to correct replication errors in such a way that the correct Complex Specified Information is once again available to the cell’s metabolism
Control: Analysing replication errors and evaluating whether any such error has added worthwhile extra CSI before deciding if correction is required.
I take it your an authority on the matter then. Well, that settles it!
Do please tell us what control is, then.
You’re probably actually serious too. But changing it to maintain current function isn’t control. I can’t argue with that logic, nor do I care to.
Mung,
Frankie: “If an organism controls its genome then the changes are not accidents, errors nor mistakes.”
NR: “An organism does not control its genome”
Mung: “Yes it does. Repair pathways”
ie, if it repairs errors, then any errors that are not correctly repaired are deemed ‘controlled’?
Patrick, All one has to do is show that natural selection and drift can produce what ID says is designed and ID falls.
Also Intelligent Design Creationism only exists in the minds of the willfully ignorant. So thank you for proving you do not want an honest discussion. ID is not and has never been about the designer. And it does not matter to science if God was the designer.
Why should the entailments of the dsign need anything about the designer?
According to the scientific evidence they do. See James Shapiro and Barbara McClintok (sp)
The Evolving Complex Features thread discussed this very topic.In this comment Lizzie addressed Behe’s IC claims:
There’s more in that thread.
Patrick, I showed that Elizabeth was wrong.
LoL! You have no idea what the experiment demonstrates. By your “logic” school kids are not taught the same thing in the same class because not all of them get the same answers on the tests.
Shapiro makes claims that are far too strong.
McClintock’s work was on the genome of the next generation, which is not the same as the organism’s own genome.
Is the organism controlling the state of it’s own genome by repairing errors or not?
The terms error and error correction ought to provide some clue.
And I’m not even getting into Shapiro.
The Evolution of the Genome
The Origins of Genome Architecture
Both Stern’s new perspective on development and his reassessment of the role of populations leads to the surprising conclusion that the evolution of genomes appears to be predictable. Stern argues that developmental biology and evolutionary biology are intertwined: it is impossible to understand one of them fully without understanding the other.
Evolution, Development, and the Predictable Genome
Neil, are you going to tell us what you mean by control?
I am an organism. Am I controlling the state of my own genome by repairing errors or not?
Shapiro’s claim are based on observations and research. The claims of evolutionism are based on ignorance.
And you are also wrong about McClintock as she observed maize actively repairing damaged chromosomes.
Oh? What are those claims, as you see them?
Frankie,
ID(creationism) fails because it has no hypothesis with testable entailments. Modern evolutionary theory could be disproved tomorrow and IDC would still be vacuous nonsense.
Your sectarian beliefs are not the default.
I collected some choice quotes from founders and leaders of the intelligent design creationism movement here that demonstrate quite the opposite. The clincher comes from the National Center for Science Education during the Dover trial. Without change to the rest of the book, the term “creationist” was replaced with “intelligent design proponent” (and the artifact “cdesign proponentsists” was left in as a bonus).
That kind of cut-and-paste clearly demonstrates that the two terms are synonyms. At least, it does to anyone not foolish and uneducated enough to be a cdesign proponentsist.
Frankie,
Already explained. The constraints of the designer constrain that which is designed. A designer without constraints could produce literally anything, and therefore explains absolutely nothing.
Frankie,
You had not even registered on this site at the time of that thread.
There were a few bloviating, willfully ignorant intelligent design creationists posting on that thread, but no one who did participate refuted anything Lizzie said.
4 on the standard scale.
ID has said exactly what the testable entailments are and there isn’t any modern evolutionary theory.
The only connection between ID and Creation is that Creation is a specific subset of ID.
Wrong- we just need entailments of the design. The designer comes after design is determined.
You had not even registered on this site at the time of that thread.
There were a few bloviating, willfully ignorant intelligent design creationists posting on that thread, but no one who did participate refuted anything Lizzie said.
She doesn’t even understand Behe’s claims and no one has shown that undirected processes can produce IC