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.
yes, under evolution there is no such thing as a species.
under evolution you can only ask what is the parent and what is the child.
you can also infer the child is a bit like the parent, and the parent is a bit like the child.
that’s all.
But it’s what is there. How do you explain ring species if species boundaries aren’t fuzzy where species are closely related?
lcer,
Not at all. You can ask, Can two organisms mate? will their offspring be fertile?
Have you thought about this much?
What there is instead are clades.
OK
An individual species is defined by a unique ideal platonic Form existing in the mind of God. It’s superior in that it is totally objective, species actually exist and their boundaries are fixed.
Always making new definitions because the old ones don’t quite do what they were supposed to do. That is a curse for your worldview and Oceania circa 1984.
Except your definition seems never to be complete.
Instead of a matter of definition it seems to be a matter of personal preference masquerading as a plastic ever morphing definition. If a definition can’t be stipulated and expressed before the fact you have defined nothing.
Except for things like bacteria etc etc etc
It seems like the death of a thousand qualifications to me
peace
Analogies are dangerous but here is a not-bad one:
Colours aren’t discrete categories. Red shades into orange, which shades into yellow which shades into green, to cyan, to blue, to violet and even round via magenta to red again.
To say that there are some pairs of colours that may or may not both be “red” (may be “red” and “orange” is not to deny that colours exist, or even to deny that it’s possible to categorise them. It’s just that the boundaries in some cases are not clear. But it’s pretty clear that red and blue are different colours, or even red and yellow.
Same with species – whether the different population of herring gulls that surround the North Pole are different species or merely different breeding groups is not clear. And even lions and tigers, as fifth points out, can breed viable, if odd, offspring, under non-natural conditions. That doesn’t mean that they aren’t different species, and it certainly doesn’t mean that species don’t exist. It just means that some species are more closely related than others, some so closely it’s hard to say whether they are different species or not.
That’s because they nest as a tree structure – like a family tree, which is why common descent is a very good explanation for the pattern. Lions and tigers are more alike than cats and dogs. Cats and snakes are more alike than cats and starfish. Norwegian herring gulls and Scottish ones are more alike than any of those, and maybe so closely related you’d say they were the same species.
It’s still a valid concept, but makes most sense of the data when considered as a hierarchy resulting from a branching process. rather than as a series of discrete categories.
I just don’t define species as interbreeding populations. So whether a population can interbreed is beside the point from my perspective.
This seems to be a better approach than defining species as interbreeding populations (sort of).
peace
Well, the definition is usually “non-interbreeding populations”.
But define it how you like. You ought at least to know how biologists define it, though, when evaluating biological theories about speciation. Otherwise you won’t know what they are talking about.
This is a major misunderstanding shared by a lot of ID proponents, I’ve noticed – that changing definitions is somehow cheating.
Definitions are simply descriptions of what is meant by a word. If it turns out that the way we used to describe something is no longer very apt, we either change the definitions, or find new words. So “elements” no longer mean the four elements that the Greeks believed were fundamental, even though the concept has been retained. Conversely, we no longer talk of “humours” – they no longer have a useful descriptive function in physiology.
Same with “species”. It was a useful term when people thought that species were discrete. Now we know they are not. We do still use the term, but it has to be redefined to reflect that some species boundaries are fuzzier than others – some populations interbreed more readily than others, and that this reflects a nearer common ancestor.
That’s not cheating – it’s updating language to reflect better descriptive and explanatory models. It is not a weakness of science that it is always changing, and being refined – it is a strength. Unlike some forms of religion, it is constantly tested against reality, and reality always trumps the theory. We fit models to data, not the other way round – when the data show that species are not always discrete, it’s the model that has to change.
What does the subjective quality of “interesting to a biased observer” have to do with the topic under discussion?
No, it’s that reality is complicated. Bacteria don’t reproduce sexually, so lineages have a different pattern, and the gene flow pattern is different.
This is your opinion. I would disagree
No red is a discrete point on the wheel as is orange etc. The shades you speak of are simply points on the wheel to the left or right of red
Except it’s not like a family tree at all because you can’t identify the actual discrete branching points. It’s more one fuzzy amorphous blob that flows in an out of different populations.
Therefore there is nothing to explain because species don’t really exist
peace
My definition of species is not complicated it’s objective and it accounts for all we see with no additional qualifications necessary.
peace
Well, that’s odd. What do you think the discrete categories are? Do you dispute that visible light contains a continuous range of frequencies, rather than discrete bands? Do you dispute that when we see colours, our colour receptors fire in different proportions, along a continuous distribution?
It seems odd to me that anyone could dispute this. Can I ask you to elaborate?
So would you say that only one frequency is “red” and one is “orange” and all the others in between aren’t actually colours at all? Or that every frequency is as different colour? If so, how do you define the band widths?
You can infer the branching points pretty well. That’s what cladistics is about.
Not sure what your last sentence means. Gene flow is a useful concept but it has fairly well defined patterns of flow. Mostly longitidunal.
How does it account for herring gulls?
Because if you aren’t trying to explain anything specific evolution works just fine as an explanation.
It’s only when you decide that a particular feature is interesting and therefore merits an explanation that you run up against problems like the one explored in the paper.
As rumracket points out “Evolution does not work that way”
peace
Please elaborate. Are you asking me to explain how hearing gulls arise or are you asking me how to account for the various plumage in herring gulls?
By the way, check it out
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1691675/
peace
I would say that all the other colors in between are colors in their own right. They exist as platonic Forms in the mind of God.
As far as how we experience color that is a different matter entirely. What we experience is not the standard by which color is ultimately judged what God experiences is. Our goal should be to define color (and species) the same way God does.
peace
Sorry, you’re wrong.
God told me.
God told me your goal should be to define color and species the same way Elizabeth does. He also told me that he’s been trying to get that message through to you without having to resort to smiting you with a lightning bolt to get your attention. That’s why, in my usual chat with god today, it asked me to do the unusual favor of telling you to shut up and listen to Elizabeth for a change.
Hope that helps!
Richardthughes,
…has nothing to do with whether evolution can or even should infer species.
even Elizabeth seems to agree. ie: not species, clades
so under evolution, there is no such thing as “species”
So, to be clear, you find reproductive compatibility orthogonal to species?
Richardthughes,
reproductive compatibility has nothing to do with it.
if x is a child of y, already implies there is reproductive compatibility.
No. There is such a thing (just as there is such a thing as colours) but as speciation is seen as a non-instantaneous and even reversible (in the early stages) process, the resulting “species” will sometimes still be so close as to defy clear categorisation.
The point, though (because we seem to have been derailed somewhat) is that speciation is not the same as adaptive evolution, and the paper in the OP is about adaptive evolution. Speciation can occur without adaptive evolution and adaptive evolution can occur without speciation. They are different concepts. Darwin’s concept of common descent was about speciation; his concept of modification through heritable variation and “natural selection” was about adaptation.
To that we can now add drift, a concept that was not readily available to Darwin, who preceded what we now know about genetics.
species is looking at populations.
there is nothing objective under evolution as it’s just variations.
No, I’m asking how your concept of species as discrete entities maps on to the phenomenon of “ring species” such as herring gulls.
You’re confused. You’re a direct descendent of your father, ergo, there’s “reproductive compatibility”. You’re also a direct descendent of your great-grandfather. But there is no reproductive compatibility. Because the old guy is dead. No longer any gene flow from that direction (and hopefully no longer any flow from you to dead old -great-grandad, either.)
I’m not making much sense of this, I’m afraid.
hotshoe_,
all you have is parent child relationships, which renders a tree.
each node connects to the parent hierarchically except the first one (whichever you start with).
Yes. That’s the principle of common descent.
color is a property in and of itself regardless of how we interpret it. so it’s still objective.
even though there is an infinite (or may as well be) possible shades of colors, color is still color.
Elizabeth,
random variations make the concept of species subjective.
there is no point to say species under evolution.
color is not not color
“random variations make the concept of species subjective.
there is no point to say species under evolution.”
That’s pretty odd, given that evolutionary biologists have a long and storied history of saying LOTS about species. Perhaps they’re all just deeply confused.
“Perhaps they’re all just deeply confused.”
yes, under continuous process run by random variation as opposed to discrete cannot say “species”.
Whereas designs are finite and discrete. Unlike life.
it’s constructs, just brainstorming activity evolutionary biologists perform and write it down on napkins which for reasons including lack of content is added to textbook anyways.
Richardthughes,
designs probably infinite as well but discrete.
The Book of Evolution
evolution = parent -> child variation, life and death, that’s all.
whatever subset of words/mechanisms you describe “variation” is still variation.
blind at that.
Wavelength is objective; color is not. Color can be a blend of wavelengths or cn be induced by flicker and movement.
The names of colors and the demarcation of color based on wavelength is subjective. The spectrum is continuous, just as variation is continuous. there is never an individual that is a different species than its parent.
How many types of car are there? Hair dryer? CPU?
all evolutionary algorithms work on just two principles:
1) random variation
2) life or death
a)
parent
|
varied child
if produces child, implies life. variation continues.
if not produces child, implies death. variation continues somewhere else (if somewhere else itself exists).
absolutely nothing more to evolution and evolutionary algorithms.
the rest is just abstractions/constructs for “variation”. duplications, blah blah blah…more words added, bigger textbook, more money, more funding, more scam.
I’m not sure that the ring species hypothesis is valid at all and herring gulls are probably not ring species as per the paper I linked.
With that stated this phenomena is categorically irrelevant to species seen as discrete entities. Species are not defined by sexual compatibility so sexual compatibility or lack thereof is beside the point entirely when discussing species in this framework.
Different populations of herring gulls may or may not be the same species regardless of whether or not they can interbreed. My approach would basically follow the traditional Linnaeuun pattern of cataloging species based on morphological differences
peace
lcer,
that glossed over stage 2, what’s the probability distribution for that and what is it contingent on?
Just how high are you?
Good thing we’ve advanced a bit since the 1700s then, isn’t it. We’ve learned a bit more than superficial “morphological differences” (or similarities, either).
Too bad for you, personally, that you can’t get in the time machine and go back. And stay there, happy as a clam.
Disagree wavelength is objective and color is as well. God knows what red looks like whether we do or not.
Again I disagree. An individual could be a different species than it’s parent if it approximates a a different form than it’s parent.
I realize that this is a different way of looking at the world than you are used to. The question I have is how do you would know that your perspective is the correct one?
Peace
from here
https://en.wikipedia.org/wiki/Phenetics
quote:
Many systematists continue to use phenetic methods, particularly in addressing species-level questions. While a major goal of taxonomy remains describing the ‘tree of life’ – the evolutionary path connecting all species – in fieldwork one needs to be able to separate one taxon from another. Classifying diverse groups of closely related organisms that differ by very subtle differences is difficult using a cladistic approach. Phenetics provides numerical tools for examining overall patterns of variation, allowing researchers to identify discrete groups that can be classified as species.
end quote:
peace
No peace.
Do you ever bother to pay attention to what you link which supposedly supports your foolish ideas?
Here’s the part which directly supports what I already said (we’ve advanced a bit since your beloved 1700s):
You should be embarrassed of your ignorance, not showing it off in public like you do.
I’ll grant we no longer use phenetic methods when looking at evolutionary relationships but we were talking about species.
I’m not sure I’d call the abandonment of phenetics in the deeper orders an advancement as witnessed by the never ending controversy with the make up of the tree of life but that is a discussion for another time.
Today we are discussing how to identify species and when it comes to species phenetics is still very much a valid approach
peace
and we have no clue whether variations can account for all of biology.