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.
wtf?
Mung is listening to the voices in his head again.
I sometimes wonder if you all really are just trying to keep things stirred up for the sport of it.
The environment contained citrate
Lenski wanted to see if bacteria would evolve to better utilize it’s environment. Therefore the better utilization of citrate was an target. It’s really that simple
The fact that citrate is a buffer and that it is part of the standard mixture is completely beside the point.
E coli in nature does not inhabit an environment like Lenski provided. If he wanted to just observe the evolution of bacteriea his chosen environment would be a farm pond not a petri dish that contained citrate.
All of this should be obvious to anyone but when I simply point it out to you I am accused of questioning your integrity.
I fully expect you guys to start the cursing and mocking anytime now,
Oh wait you already did.
peace
No. A farm pond is heterogeneous and dynamic. The experiment required a constant well-understood environment. See the discussion of the experimental hypotheses above, and this interview of Lenski below.
Only if he had a target. If he did not care about his results his environment would make no difference.
The natural environment of E coli is not constant and unchanging, His chosen environment was not the natural one
Your inability to acknowledge even the most obvious and uncontroversial things is a big part of why I can’t have a discussion with you Zac
I hope you understand
peace
You should try reading Lenski’s own words in the interview Zachriel links to. You might find some of your concerns addressed.
It was essential to the experiment that the evolutionary dynamics were repeatable. That required a constant and well-known environment. For instance, one of the questions was whether different populations would evolve in different directions. If divergence was observed, but the environment was variable, then you would not be able to determine whether the divergence was due to the environment, or to historical contingency.
I give up It has again been demonstrated that for some reason we are unable to communicate. From my perspective It’s like you don’t even read what I post
If I had to guess this has something to do with the fact that you think of yourself as a collective instead of as an individual.
Collectives can’t participate in conversations. To do that requires a unitary consciousness.
Good day, I hope you understand this
peace
We provided a general and a specific reason why pond water wouldn’t work. We provided an extended interview with Lenski concerning the hypotheses that guided and extended the experiment.
We’ll try again.
The “targets” are the hypotheses that are being tested by the experiment. It’s typical in an experiment to have control variables, which, in this case, includes the environment.
right it would decreased the likelihood that the target would be realized
In the interview Lenski confirmed that he had to have a simple medium in order to minimize “complications”. What are complications? Of course they are things that keep you from achieving your target.
correct and the hypothesis was?,
If you can’t even address my posts don’t bother.
peace
.
E coli lives in the mammalian gut, not farm ponds. There is citrate there too, and many many other things.
In science, when you do experiments, you want to control the amount of factors that can influence the outcome. That’s one of many reasons why you’d start with an experiment that uses a constant environment.
No, complications are the number of factors that can influence the outcome such that you don’t know which of the many influencing factors that actually resulted in the outcome you got.
If your experiment contains 30 influencing factors and you get a result, you will have a very hard time figuring out which of them caused your result. That’s why in experiments you want to keep things simple and ideally, only have one thing at a time that can vary so you can be sure what that one thing is the cause of.
“The first set of questions, about the dynamics of adaptation, had clear expectations that were testable in a fairly standard hypothesis-driven framework. For example, I was pretty sure we would see the rate of fitness improvement decelerate over time, and it has [2]; and I was also pretty sure we’d see a quasi-step-like dynamic to the early fitness increases, and we did [3]. Nonetheless, these analyses have yielded surprises as well, including evidence that fitness can increase indefinitely, and essentially without limit, even in a constant environment [2]. In re- gard to the second set of questions, about the dynamics of genome evolution and their coupling to phenotypic changes—I’m sure these were part of my original thinking, but I admit that I had almost no idea how I would answer them. Hope sprung eternal, I guess; fortunately, wonderful collaborators, like the molecular microbiologist Dom Schneider, and new technologies—wow, sequencing entire genomes—saved the LTEE.”
No, complications are the number of factors that can influence the outcome such that you don’t know which of the many influencing factors that actually resulted in the outcome you got.
Lenski: “Before we get to hypotheses, though, I like to begin with general questions about how and why things are the way they are. The LTEE originally set out to answer three sets of questions. First, concerning the dynamics of adaptation by natural selection: is improvement invariably slow and gradual? Or are there periods of rapid change and stasis, even in a constant environment? How long can fitness continue to increase in an unchanging environment?”
There were many other questions too that the experiment was designed to address. Read the link Zachariel gave you.
And sometimes in a discussion one person is just incorrect.
Are you totally sure you are not wrong about this? As when you said what you said, I was sure that was not the case.
Oh I understand it. And I’ve actually seen it many many times. Zachriel will deconstruct your arguments until their lack of support is eventually made clear. And then you can either acknowledge that or…
No, rather it’s the patient, methodical nature of the procedure that unnerves you.
And when you say your inability to acknowledge even the most obvious and uncontroversial things you are really just saying that your interpretation is the obvious one and it should stand by default. But as you’ve seen, that is dealt with deftly. And so now what?
And good day to you! But consider the lily. No, wait. Consider the fact that you are leaving yet there are so many unanswered questions. Questions like:
Well, according to you it was to see ecoli it could start to live off citrate and as a citation you provided me page about the experimental materials used. So, um, perhaps you should be the person to answer your own question? You might even learn something (and unlearn something too!) in the process.
Elizabeth,
It’s a crap-shoot. Whatever is good enough now may not be tomorrow. Then there are competing benefits- does better sight trump better hearing? Is faster better than slower? Is taller better than shorter? It all depends. With Darwin it’s all contingent serendipity.
fifthmonarchyman,
Here is the post to which I was responding.
You are simply wrong. He assumed it would not utilise the citrate, which is why it was added to the medium. He used 139 um glucose as a nutrient to create a ‘minimal medium’. There was 12 times as much citrate in there, to act as chelating agent (not strictly a buffer as I previously stated). If it could utilise citrate, that would not be a minimal medium, and he’d have to use something else. Can you back your assertion up with a reference that, at any point, Lenski’s intent was to evolve citrate metabolism? Or that the evolution he was looking for was specifically adaptive – ‘better utilisation’ of any particular environment provided?
Patrick,
It didn’t say that every mutation added code. Please learn how to read.
Frankie,
And is any of that a problem?
Where do you get your information? Nested hierarchies can be depicted as a branching process but branching processes do not produce nested hierarchies. Nested hierarchies depend on definitions and only we can provide that.
Also Linnaean taxonomy, a nested hierarchy, was not produced by a branching process. The US Army, another nested hierarchy, was not produced by a branching process.
Yes, it is if you are concerned with science. Contingent serendipity isn’t science.
Lenski has no idea if natural selection produced the changes in his E coli. That is because he has no idea if the mutations were happenstance, ie accidents, mistakes or errors. As far as he knows the E coli changed their own genome- Shapiro’s natural genetic engineering.
Of course it does. It says that evolution does not produce nested hierarchies.
Fitness is an after-the-fact assessment. And it could be just about anything- faster, slower, fatter, skinnier- whatever it is!
There is a huge difference between elimination and selection.
Is that your reading list? Mine is much more vast than that- Darwin, Jones (Darwin’s Ghost), Mayr- a lot of Mayr- Simpson, Gould, Dawkins, Coyne, Shubin, Wagner, Huxley, Dennett, Schwartz, – I could go on and on.
so ronery
I quoted the part where it explains that, Elizabeth.
Frankie,
What a meaningless response! If selective advantage changes according to circumstance, this is less ‘science’ than if something were equally advantageous in all circumstances and all environments? Science is only about the deterministic? What a laugh.
Let’s sweep it all away and replace it with the science of “whatever the Designer felt like doing” then, shall we?
And out of that list, can you point to any evidence that those people agree with you that evolution does not produce nested hierarchies?
Please link to this alleged modern evolutionary theory. Also EV has been refuted as having anything to do with biological evolution.
Frankie,
Indeed, and frequently do. While you may claim to have read those books, your cut-and-paste activity is mostly restricted to the same tired quotes from Provine, Mayr, Knox and Spetner, on an interminable loop.
Darwin, Mayr and Wagner- I quoted Wagner. Transitional forms would ruin a nested hierarchy which requires clear and distinct categories.
LoL! It all depends on the CONTEXT of the discussion.
We can actually test for intelligent design. We have a methodology- you do not.
Frankie,
Sure. 31,000 generations later, they decided to get on with this potentiating mutation, so that 5,000 generations later they could start to ultilise this food source that had been around since Gen 1.
Frankie,
Of course you do. Give us a link to it, then.
Frankie,
That’s right! You have – ooh! – a dozen quotes ready to roll for any anticipated context. Shame you can’t use your own words, and have to resort to quote mining.
Elizabeth says that she understands IC. However in “Darwin’s Black Box” Behe makes it very clear that he is talking about a Darwinian pathway to produce IC. Even evolutionary biologists knew this as in 2000 two wrote a paper trying to debunk that claim about the pathways.
IC was a response to Darwin:
IC has always been about the evolutionary pathways. And Lenski proved that when Behe’s conditions are met no IC evolves.
I didn’t quote- mine. Obviously you are just a pathetic little baby.
Frankie,
Unevolvable structures are not claimed to have evolved in the Lenski experiment.
How many times do you have to shown the methodology? It is basically the same as forensic science and archaeology- eliminate lesser explanations and then see if the design criteria is met. Science 101- that’s is why you are at a loss.
Frankie,
So we can look forward to a mature discussion in your own words then? Excellent. A New Dawn.
Clueless and proud of it- EQU doesn’t evolve unless the previous steps are selectable.
You are a joke. I quote the experts to support my claims- claims I made in my own words.
Umm they were surviving just fine for 31,000 generations., Then finally one came along and found a new way to survive even better.
Frankie,
How have you eliminated the ‘lesser explanations’ – as a methodology? Is there anything in biology you have conclusively shown to be designed?
Frankie,
EQU is not part of the Lenski experiment.
Frankie,
The Gen 31,000 mutation was selectively neutral, or nearly so – it did not generate the cit+ phenotype. That happened at Gen 36,000. Reconstituting populations prior to Gen 31,000 does not yield either mutation. Reconstituting 31,000 – 36,000 can regenerate cit+. None of this is supportive of Shapiro, unless genomes can detect the future, but only sometimes.
Frankie,
Here’s what you quoted:
And here’s what I said about it (do keep context in, deleting it makes you look like you’re trying to hide something):
My rebuttal of the assertion is correct.
Creationist heal thyself.