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.
Well, I beg to differ, Joe. I think it is you who has misunderstood.
You can simply check, for example, that AVIDA does not reward every step. You are simply wrong. Most mutations are neutral and some deleterious.
Read it and weep:
Must the are result be foreordained before you can call it a target?
Zac spit out your point if you have one.
peace
Even if it doesn’t reqard every step it still does not represent Darwinian evolution. Read the peer-reviewed paper I posted. It explains it.
Patrick- Genetic drift is evolutions sans selection.
Well what the word really means is heritable difference in reproductive success. If a variant does better than its peers it will become more prevalent. If it does worse, it will become less prevalent.
Yes, it’s differential reproductive success that is not linked to heritability, just to luck.
That doesn’t refute my point.
No, it isn’t. Branching processes lead to nested hierarchies. Unless the branching process is instantaneous, it will give rise to fuzzy category boundaries between the bifurcating lineages until the branching process is complete.
You keep saying that. What you don’t seem to get is that how “you see things” is immaterial to reality. Repeatedly stating your ideological position does not constitute a discussion.
Frankie,
So you’re a glass half empty kind of guy? Selection refers to the fact that more fit phenotypes, and therefor their underlying genotypes, tend to be selected for reproduction more often.
Evolution explains developmental pathways just fine. What it does poorly is to predict specific future traits. Evolution is a process analysis, not a targeting strategy.
The paper you posted does not explain that AVIDA does not represent Darwinian evolution.
At any rate, if it does, perhaps you could point out where.
BTW, while I think the paper is very good, it is not correct to describe it as peer-reviewed. It is a commentary “Dispatches” article. They are only edited, not peer-reviewed.
The Lenski paper on AVIDA, was, however, peer-reviewed.
Frankie,
Indeed. That does not address any of the flaws I pointed out in the piece you quoted. When they get simple things wrong, it doesn’t make sense to give their conclusions much weight.
Looks like all the fun has moved over to this thread.
The kind of “fixity” of species that Darwin argued against is perhaps more Aristotelian than Platonic. In an event, what we’re really talking here is the old metaphysical distinction between particular and kinds.
The key idea there was that what made a whole bunch of lions all lions was that they all exemplified lionhood, and that what God did was He created lionhood. The whole life-activity of lions — feeding, fighting, fleeing, and reproducing — is how lionhood persists in exemplifying itself.
(Imagine multiple copies of the same book, for example).
If we reject that ontology in favor of an anti-essentialism about species, then what exactly is a species? Consider a community, or even a sports-team. New members are added, old members drop out, and yet the team persists. It’s not that there is no team, but that the team itself is a particular rather than a kind. It’s a particular that exists in space and in time, and it is made of parts such as players, coaches, etc.
On the Aristotelian view, individual organisms are particulars but the species is a kind. On the Darwinian view, the species is also a particular, in just the same way that a community is a particular.
No. Someone can aim at a target and miss; but from your own citation, they were using a standard growth medium.
With regards to rates of evolution, the question was whether evolution will stop after the organism reaches an adaptive maximum. It turns out that evolution continues, generally slowing down; but, as with the case of citrate utilization, sometimes that equilibrium is punctuated by a burst of evolution.
With regards to repeatability, it’s a long-standing question as to whether evolution inevitably tends towards certain solutions, or whether it is contingent on previous pathways. The experiment shows that evolution is, at least some of the time, contingent.
Your thinking is medieval at best. “Color” is a perception that’s created by the interaction of different wavelengths of light on the different cone receptors of the eye. These cones have frequency sensitivities that peak at different wavelengths, but also overlap. The cones are biological structures and somewhat variable in their implementation and density within the retina, so each individual detects color slightly differently. You can’t say what colors “God” has mandated, unless you select one individual cone arrangement as “God”, and all the others as “non-God”.
Does your color perception define God’s to the rest of us?
Of course, different species have different light detection structures in their eyes, some with more cones, some with more rods, some with different cone structures that peak at different wavelengths than ours, some with only two cone types, some with three like most of us, some with four.
The nerve structures to the back of the brain that connect to the vision centers are different in every individual as well, as are the neuronal patterns within the vision centers themselves.
So you can’t claim there are any “objective” colors, because the entire concept is inherently variable between each individual, and the only way for anyone to learn a color is by example. A person identifies “red” as the color that they were told was “red” when they were small children, and that identification is carried into adulthood. As they see other shades, but have no name for each tiny variation, and as they interact with other individuals, and learn that others have a slightly different standard of “red” than they do, they get to understand the idea of broad categories of color.
It’s sad that your upbringing was so impoverished in the introduction of such basic concepts.
It’s obvious that God uses King James English. Always has, always will.
If it was good enough for Moses, then it should be good enough for you.
evolutionary algorithms don’t prove natural evolution.
they may support it, but that doesn’t mean it occurred that way.
I can see why variation as a mechanism for adaptation could be beneficial from an engineering point of view in order for organisms to have a better chance of survival, and I can see how evolutionary algorithms can support that scenario.
but if members of this forum think it proves anything beyond that, they’re simply confused. it’s not so simple and clear cut as wishful thinkers here claim.
I have written dozens of evolutionary algorithms and they do not support your case. avida is no exception.
all the evo-babble is useless, IMHO.
I have explained in a previous comment the fundamental core of evo algorithms based on merely two principles.
you have to believe that those two principles are enough for everything we see in biology.
if you have even a moment/seconds hesitation, you’re not an evolutionist.
and you can start thinking beyond the blind-watchmaker.
you’re free from that point.
tbh this seems like babble to me.
Elizabeth,
but it’s not evo-babble, big plus
free yourself TSZ from the shackles of the blind-watchmaker!!!
You should get that on a T-shirt!
Iced,
It’s important to distinguish between the fact of evolution and modern evolutionary theory. Evolution occurred. That’s a fact. It’s been observed
How it occurred is the interesting question. Software simulations can, as you note, support some theories and potentially discredit others. Some like Schneider’s ev can even support specific theories about biological evolution.
Do you have links to any of these dozens of evolutionary algorithms you have written?
I have some, I left them under the demonstration of the calculation of FIASCO…
God is an individual and his perspective is objective
Even if you were unable to “learn” the identity of a discrete color it does not follow that objective discrete color does not exist. it’s not all about you
However I would disagree that the only way for anyone to learn a color is by example
peace
and
I did not ask about questions I asked about hypothesis.
strike two
Peace
Exactly, evolution is great at explaining fuzzy things like “developmental pathways” and not so good with discrete things like traits and structures and species.
peace
Just like meteorology is great at explaining fuzzy things like anticyclones and depressions and not so good with discrete things like where and the next hurricane will make landfall.
Chaotic systems are like that, fifth. The principles are simple, but the actual predictions are not. What the principles predict is the pattern, not the specifics.
I don’t have links on Github or anything like that.
they’re simply pet projects of mine I tested many years ago one of my local computers.
i utilized them in a couple of ways and many of which had no target. but terminated at the point where optimal results were given. so one could say the target was to look for optimal results, but from the programs point of view there was no “specific” end-target. another was to “evolve” code translated from binary to ASCII text to executable code translation, other were targeted weasel-like implementations. the results show variation is powerful tool once you have defined specific parameters at both local and global contexts. these parameters while they’re no so obvious at first, are very much present, and while they’re not themselves a target, are very specific.
and no it isn’t important distinguish between any of that.
Right and when we want to understand an especially unlikely weather event we do not appeal to meteorology.
Why do we appeal to “evolution” to explain things like structures and traits and species?
peace
Who is this “we” you speak of?
We don’t?
What, don’t we all turn to neuroscience to understand especially unlikely weather events? Or was ID? I forget.
I mean, why use meteorology for understanding weather, of all things? Clearly it’s for meteorites.
Glen Davidson
Huh? It seemed clear enough.
With regards to the rate of evolution, one hypothesis is that, in a stable environment, adaptation will reach a local maximum, and then stop. A contrary hypothesis is that adaptation will continue at a slower rate, punctuated with periods of more rapid evolution. The latter was observed.
With regards to repeatability, one hypothesis is that given the same situation, evolution will follow the same pathway. A contrary hypothesis is that evolution may follow different paths. The latter was observed.
Evolution proceeds at a fairly constant rate. What changes rate is obvious, visible changes in morphology.
But molecular change proceeds regardless of need or selective pressure.
Nice point, petrushka.
fifthmonarchyman,
No he didn’t. He used citrate as a buffer. You calling me a liar?
fifthmonarchyman,
In your everyday usage you can call a banana a faucet for all anyone cares. We are talking of technical usages of the term ‘species’. There are several, and the appropriate choice depends on what purpose it is to serve. If you wish to deny evolution by restricting the definition to only everyday usage … well, go for it. Why should anyone else care?
You completely agree, and yet you insisted in the comment to which I was responding that the only reason to apply the BSC was to shore up ‘Darwinism’. It is not necessary to redefine species, it is simply necessary to understand what one is referring to. Call it what you like. If you are ‘interested in species and how they came to be’, how can you then simply dismiss common ancestry as an irrelevance? Do you think every single morphological type was created separately?
You experience the current forms of divergently morphing lineages. They appear discrete and ‘essential’ because of the limited time frame of observation.
And you know what he knows, right?
And he has, and therefore you are one step up the ladder of Perfect Knowledge from me, right?
fifthmonarchyman,
It’s not that objective, when you get down to the nitty-gritty. How do you quantify morphological difference? Is an extra vertebra in a snake a morphological difference sufficient to distinguish one ‘Platonic’ species from another? How about two? Or one plus a different-coloured stripe? Or one, a stripe and an extra pair of teeth? One, a stripe, an extra set of teeth plus a tendency to take a certain type of prey? And so on. I’d suggest you haven’t spent as much time as you might actually observing natural gradations, rather than pontificating about essences. Continuums abound.
Frankie,
Yes, of course it does, Joe. Spetner, Knox, Provine, a bit of Mayr. Seen it all, a thousand times.
Frankie,
Joe is correct.
llanitedave,
Verily.
Allan Miller,
I thought I was talking with Frankie….
Anyway, his statement is correct. I wrote hurriedly and poorly.
I now await his response to the substantive problems with what he quoted.
What an incredible refutation in the OP!
“Have at it guys.”
Is that all it takes to be “skeptical”?
Is this a lame attempt at outing?
Technically the very first post, not the op itself, is a refutation.
Mung, you seem a little butthurt today. Not slept well?