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.
Your position can’t account for sock puppets constrained by the very limited vocabularies of their owners.
why do I get green flying spaghetti monster as avatar?
And so are other, more advanced approaches — which weren’t available to your hero Linnaeus (no fault of his, of course, and he would adopt all modern science practices if he could come to life nowadays) — which aren’t limited to your childish preference for “morphological differences” being the only way to categorize species.
So, you’re still wrong in your ideological preference for Linnaean “purity”. Do feel free to join the 21st century any time soon.
Richardthughes,
Despite the fake moustache and toupee, I have a pretty good idea what Frankie’s reading list consists of.
fifthmonarchyman,
The fact that one is (if evolution is true) dealing with plastic ever morphing lineages, definitions accommodating that fact would seem preferable. You sneer at the evolutionist ‘worldview’ because it does not conform to the static definition of some long-dead Greek?
Species are like languages. Unless you think they too have some definitional stasis in the mind of God.
fifthmonarchyman,
The Biological Species Concept is objective and accounts for all we see with no additional qualifications necessary (if that is the acme of utility for a definition!). It does have the character of not mapping precisely upon, say, morphological species, but then if they were the same thing there wouldn’t be two, would there?
fifthmonarchyman,
God uses the Biological Species Concept.
you say that but we still when looking at the species level look mostly at morphological differences. It still works it is more objective and straight forward.
The “more advanced” approaches you speak of are the reason there is a species problem today they are the reason the tree gets shook up and scrambled every time a new discovery is made close to the base and they are unable to account for things like HGT.
newer does not always mean better
peace
I don’t see why the concept of species should be tied to lineage at all. What a thing is and how it got here are two different subjects
There is no compelling reason to link them other than to support Darwinism that I can tell.
well I sort of do 😉
check it out
https://en.wikipedia.org/wiki/Species_problem
Are you saying God doesn’t know the boundaries of a species and he does not know exactly when a new species arises?
I’m pretty sure omniscience is a definitional attribute of who God is
peace
It’s the opposite. Darwin’s insight, i.e. the one that led him to the model of Common Descent, was that they were linked.
Not the other way round. The model fits the data.
fifthmonarchyman,
There is no ‘should’. If you are looking at two morphologically distinct types, it may or may not matter that they had a common ancestor. It really depends on what you are using your species concept for.
But when we are talking of gene flow (ignoring LGT), reproductive isolation is the key. Morphological distinction may or may not be an isolating mechanism, and isolation may or not lead to distinction, so there is some cross-talk between the two approaches.
That’s not the right way round. Given ‘Darwinism’ (FFS!), we need to refine our species concept. We don’t need to do so in order to make ‘Darwinism’ (FFS!) more correct. If ‘Darwinism’ (FFS!) is the case, then species on which both morphology and isolating mechanisms would agree on their distinctness must be linked by a path of descent to a common ancestor. So we have in there 3 things: morphological species, isolated species and ‘chronospecies’ – organisms that did not exist at the same time, but display sufficient morphological distinction on the broad scale to warrant naming.
Yes, I’m sure you do. Tower of Babel and all that. Contrary to all evidence. Given that Babel was intended to confuse the peoples of the world, is Google Translate the work of the devil?
I don’t need lessons in species concepts from Wikipedia. I am fully aware of the issues. Say something about my paragraph you quoted in your own words. Is the BSC invalid because there are others?
God knows that the concept “when a new species arises” itself betrays a shaky grasp of species concepts – that it is an artefact of ill-informed puny-human thought which takes concurrent distinctness as meaning that there must have been a single point in the past when one or both popped into existence. Most apologists don’t think that, unless they think that the Ark held (say) both the lesser spotted and greater spotted woodpeckers, and 300,000 species of beetle.
And you know what an omiscient being does or does not think, right?
fmm,
You mentioned that Lenski had in mind a specific target when he ran his experement. Could you provide a citation? I believe it’s possible you are in error here, and I’m sure you’d like to know the real truth of the matter. If you are correct, you can provide a citation. if you are not, well, you’ve just learnt something no?
When I first started to write EA/GAs I was very surprised to find that even the very simplest, bare model converges on solutions very quickly. Solutions that may not be optimal but are certainly far far better then you would expect by chance.
It’s as if once the code has the bare minimum of connections for a complete cycle the fact that it can be run many millions of times a second then multiplies that power into something surprisingly powerful for a minimal implementation.
I agree, we should burn the libraries post haste! And be very suspicious of anyone wearing eye-glasses!
To call what Lenski did an experiment is to acknowledge he had a target. If he had not target it would be called an observation not an experiment
We can know his target by looking at the environment he chose to run his experiment in.
check it out
http://myxo.css.msu.edu/ecoli/dm25liquid.html
He did not choose a neutral environment but one that was rich in citrate. Therefore we can infer that he wanted to see if ecoli would evolve in such a way as to more efficiently metabolize citrate.
peace
So no, you can’t provide a citation. And you provide an inference instead.
Is this inference of yours revelation with no possibility of error, or just mere knowledge?
Right and I see no compelling reason in everyday usage to shoehorn questions of ancestry into our understanding of species. If I’m looking at two populations of tree and I want to know if they are different species I really don’t care if they share a common ancestor
I completely agree here. I’m just not sure why it’s relevant. I’m interested in species and how they came to be. I’m not too interested redefining what a species is.
I’m looking for an explanation of species and you are telling me that species as I understand them do not actually exist. But that is a cop out I know that species exist because I experience them directly everyday and that is the question that brought me to you in the first place.
1) omniscience is not about what God thinks but what he knows. (Hint he knows everything)
2) I can know what God thinks (or knows) if he reveals himself to me
peace
I provided a citation did you miss it?
peace
No, you did not provide a citation. But regarding what you did provide, did you actually read what it said?
As that page says:
Which seems to contradict what you said:
Any thoughts on that? Or are you sticking to your original answer?
By “citation” I was looking for a link to where it is stated that the purpose of the experiment is as you claim. Not to something that you interpret into support for your claim.
Are you saying that the only way you can know if something is a target is if it is explicitly noted as such beforehand?
peace
Heh. No, you can simply draw the target around the place where it landed. Bullseye guaranteed every time!
Yes the statement seems to support what I said. At the beginning citrate was not seen as a food source for bacteria.
peace
you are again confusing experiment with observation.
peace
It’s randomly assigned. You can change it via your personal profile.
A peer-reviewed paper states and demonstrates that AVIDA does not simulate nor instantiate Darwinian evolution:
(Nick Barton and Willem Zuidema, “Evolution: The Erratic Path Towards Complexity,” Current Biology, Vol. 13, R649–R651, August 19, 2003)
With real biological evolution not all genetic changes are going to provide some advantage. With AVIDA that is what happens.
Also, from IDEA Center:
Elizabeth holds a cartoon version of ID and IC AND she doesn’t understand Darwinian evolution. Not a very god starting place for a discussion.
It’s so objective that there is a pronounced “species problem”. Look it up.
But EAs and GAs use a targeted search. That is evolution by intelligent design.
I bet it consists of more evolutionary thought and insight than yours does.
The fact that the boundaries are fuzzy is evidence against the claim that evolution expects a nested hierarchy. Nested hierarchies require distinct and pristine categories.
Let’s start with the common notion of species. Indeed, we recognize distinctions between organisms based on their characteristics regardless of any biological theory. So, one definition of species is a population that exhibits distinguishing and persistent characteristics.
Now, let’s look more closely. We will notice that species generally do not interbreed outside their group. This might be due to physical barriers, behavioral differences, or some other incompatibility. Maybe this is how they maintain their distinctiveness.
Let’s look even more closely. Variations will sometimes seem to be significant, but not persistent, or are subtle enough that one observer will group two populations into a single species, another observer splitting them into two species. We will also notice that fertility can vary by degrees. Species we thought were distinct will sometimes interbreed. And we will notice that varieties will grade in their fertility (such as tobacco plants).
Turns out that, as Darwin showed, this grading of fertility is evidence for reproductive divergence from a common ancestor. There is usually no distinct dividing line between closely related species, but a process occurs whereby populations will become more distinct or less distinct, depending on environmental conditions.
This doesn’t mean species don’t exist. Clearly lions and tigers are distinct species. Varieties and species can be thought of as a clumping of populations based on trait characters.
Reading you own link, “Note also that E. coli cannot use citrate to support growth; it serves only as a chelating agent in this medium.”
Again, reading your link, “Reproductive isolation evolved more rapidly between some lineages than between others, irrespective of their genetic distance.”
correct, I predict (based on my evolutionary models of mind) 98% must be junk thought, therefore junk books.
Hey Zac
Thanks for the lesson too bad it is completely beside the point. Which was that it is not necessary to know ancestry in our common every day experience with species.
I hope you will understand if I don’t respond to you again for a while
Peace
We directly supported your point, then asked you to look more closely.
So what do you conclude from that? That given a novel environment, bacteria can evolve to make use if it?
correct the environment had citrate and E coli did not use citrate to support growth
I think I pointed this out all ready.
Repetition and irrelevant condescending rabbit chases are not something I normally enjoy. So if you have a point make it if not Good day
peace
yes.
Just how novel an environment and just how extensive the evolution was not established by the experiment.
peace
No, it isn’t. In AVIDA most genetic changes do nothing, and some are deleterious.
I understand IC very well – I have read most of Behe’s writing. I do not “understand” ID, because I find it internally contradictory. I don’t think it makes sense.
I understand Darwinian evolution very well, and AVIDA is an instantiation of Darwinian evolution. It’s not particularly like biology in details (mutation rates, size of population, reproductive apparatus, phenotypes, etc), although it resembles it more closely in many ways than MA, but it implements the Darwinian proposal in silico.
You can certainly take issue with it as a model of biology. It is not a model of biology. Nor is Behe’s mousetrap. It’s a model of Darwinian evolution, and it disproves the contention that a “mousetrap” i.e. a function that can only function if all its parts are present cannot evolve by Darwinian means, and it also disproves the contention that a function cannot evolve by pathways that include many neutral or deleterious steps.
I’m not sure why you keep asserting that all changes in AVIDA are advantageous. They are not. That is WHY it falsifies Behe’s claim.
But you would surely agree, then, that to get adaptive evolution you do not need to specify the sequences required to adapt, nor to tinker with the genome, merely to change the environment, right?
Which is precisely what Darwin proposed.
You are mistaking a targeted problem for a targeted solution.
It is perfectly possible to write an EA in which the problem is itself randomly drawn – you just let the fitness function vary randomly. Consistently, the population of virtual organism will adapt to the current environment, even though you have targetted nothing, merely let the environment change as the real one does.
An experiment has a hypothesis, not a target. Among their goals was testing how rates of evolution vary over time, and the repeatability of evolution given identical environments.
So we are in agreement. Lenski’s experiment used a standard growth medium. They may have had an inkling the bacteria would evolve the ability to utilize citrate, but it certainly wasn’t foreordained, as was clear from the experimental results.
No, they don’t, Joe.
Well, they do stop working after a certain number of bacterial generations.
Frankie,
The critique you quote misses quite a bit about the Avida research.
The logic operations are not included in the base Avida language, they must evolve before they can be used as building blocks for more complex operations. In the case of EQU, at least five instances of simpler logic operations must be present in the genome.
The logic functions rewarded are NOT (2), NAND (2), AND (4), OR_NOT (4), OR (8), AND_NOT (8), NOR (16), XOR (16), and EQU (32). Only the first instance of each operation was rewarded, not “every single addition.”
This is completely inaccurate. Mutations did not always add functional code. In fact, as Elizabeth has pointed out a number of times, some mutations were deleterious.
EQU evolved in only about a third of the runs, which hardly makes it “inevitable.”
The pathways that led to EQU included non-selective components. See the paper just referenced.
That’s simply nonsense. Without selection, there is no evolution.
Coincidently I’m in the process of writing an evolutionary algorithm that will take over the world. It will be totally over for humanity once I’m finished.
Of course they do. That is the whole point of nested hierarchies- separate and distinct categories.
What? There is a targeted search. Natural selection is not a search. Also AVIDA is not a GA or an EA
What was the hypothesis if not that bacteria can evolve in response to a novel environment (that included citrate) ?
peace
You don’t understand IC. You don’t understand Darwinian evolution. AVIDA is not an instantiation of Darwinian evolution. Even peer-review goes over that.
Natural selection is actually just a process of elimination. There isn’t any selecting going on.