Here’s a simple experiment one can actually try. Take a bag of M&M’s, and without peeking reach in and grab one. Eat it. Then grab another and return it to the bag with another one, from a separate bag, of the same colour. Give it a shake. I guarantee (and if you tell me how big your bag is I’ll have a bet on how long it’ll take) that your bag will end up containing only one colour. Every time. I can’t tell you which colour it will be, but fixation will happen.
This models the simple population process of Neutral Drift. Eating is death, duplication is reproduction, and the result is invariably a change in frequencies, right through to extinction of all but one type. You don’t have to alternate death and birth; choose any scheme you like short of peeking in the bag and being influenced by residual frequencies (ie: frequency-dependent Selection), and you will end up with all one colour.
Is Chance a cause here? Well … yes, in a sense it is, in the form of sample error. Survival and reproduction are basically a matter of sampling the genes of the previous generation. More random samples are a distortion of the larger population than aren’t, so, inexorably, your future populations will move away from any prior makeup, increasing some at the expense of others till only one variant remains.
Selection is a consistent bias upon this basic process. If different colours also differed a little in weight, say, more of some would be at the bottom of the bag than others, so you’d be more likely to pick one type than another. In more trials, the type more likely to be picked would be picked more often, to express it somewhat tautologously. You’d get a sampling bias.
Both of these processes are random – or stochastic, to use the preferred term. In reality, they are variations of the same process, with continuously varying degrees of bias from zero upwards. It makes no sense to call selection nonrandom, unless by ‘random’ you mean unbiased. Where there is no bias, all is Drift. But turning up the selective heat does not eliminate drift – sample error – and so does not eliminate stochasticity.
With a source of new variation, these processes render evolution inevitable. Even with a brand new mutation, with no selective advantage whatsoever, 1/Nth of the time (where N is the population size) it will become the sole survivor. That’s the baseline. If there is a selective advantage, it will be more likely and quicker to fix, on the average. If at a selective disadvantage, it will be less likely and slower.
Conversely, without a source of new variation, all existing variation would be squeezed out of the population, and evolution would stop.
Shapiro explicitly states that mutation does not and cannot anticipate need.
That would be location 2675 in the Kindle edition. Feel free to find a place where Shapiro says mutation can anticipate need.
It’s not about anticipating need, but responding to present conditions.
There may be a tendency in some bacteria to increase mutation rate under stress.
This seems like an insane attempt to completely confuse the situation. Let’s get back to what were are talking about.
What does ONE removing of one M&M, and ONE doubling of another M&M represent? Does that represent ONE generation?
Your revierwer says Shapiro makes a case that mutations ” (arising irrespective of potential need) ” are insufficient. He is wrong about biology and wrong about what Shapiro says.
Piltdown2,
I would submit to you that most of the responses you are getting are either complete misrepresentations of truth, or just plain hand waving disguised as a response.
Shapiro does not think Darwinian evolution can explain what happens in nature, but he is forced by the nature of his position at a prestigious university, to refrain from completely rejecting materialism, because he simply likes his job too much, and he is well aware of what being called an IDst would do to his career. So he kind of knows the truth, and only admits it in as vague of language as possible.
His theories are clear ID theories when you get down to it.
I think the reviewer has either misunderstood Shapiro, or has misunderstood how the expression “random mutation” is used in biology.
When biologists say that mutations are random, they do not mean that they occur at the same rate at every location in the genome. That is, they do not claim a uniform distribution. There are some locations in the genome where any mutation is likely to be fatal. There are other locations where a mutation is likely to affect fitness, either for the better or the worse. It is in that latter case, where mutations are more likely to occur. And I think that is all that Shapiro is saying. It does not disagree with the standard view.
That is mostly false.
Shapiro does criticize natural selection, so is non-Darwinian in that respect. But his differences with the biological community are relatively minor.
As far as I know, Shapiro has a tenured position at U. of Chicago. There is no threat that he will be fired. He has been criticized by Jerry Coyne, also at U. of Chicago, and does not appear to be afraid of generating criticism.
The ID community likes to point to Shapiro, because he disagrees the neo-Darwinian account. But, when all is boiled down, Shapiro’s view does not support ID. Shapiro talks of being favorable toward ID, but Shapiro is talking about what he calls the intelligence in the cell. He is not talking about an external designer. Rather, he is talking about biological systems re-engineering themselves.
Mostly he argues that the mutation system is a bit like the immune system — optimized to produce mutations that are statistically more likely to be useful than random point mutations.
He does not say that mutations are produced by an intelligence that knows their effect or their value.
You almost had this right earlier, when you said that a generation is after all the original population is dead, replaced by new births.
In the experiment, a trial is just one death and one birth. For a population of size 10, you need 10 deaths and 10 births to completely replace the population by the next generation.
I am sorry, phoodoo, but it does not get any simpler than this. I gave you a clear example of what one generation means: a cycle of replacing the population. If you refuse to work through this simple example (just a few lines), there is no point for you in participating. You cannot learn anything without flexing your brain.
No, it does not. If you have 1000 M&Ms, this step removes one member of the old generation and adds one member of the new generation. At the end of this step, you have the old generation practically intact: 999 original M&Ms.
So one death and one birth is not one generation by any stretch, phoodoo. This is why you need about 1000 steps to replace the old ones.
phoodoo,
When people discuss Generation X, do you think they are talking about a single person? A couple?
Piltdown2,
You misread my question. Option B is that the designer mimics macroevolution, not that macroevolution mimics a designer:
Remember, a designer can take many, many paths that aren’t open to unguided evolution. Hence my other questions:
I’m part of a different generation, not Gen X. In regards to “my generation” discussing a single person would be off by a factor of, oh, say 400,000,000.
Of course, olegt, and myself, and others, have tried different ways to get through to phoodoo on this problem before without success. I don’t know what the barrier is to getting through to phoodoo — it’s obvious that a “generation” can never be defined as merely one birth and one death. It’s obvious even within one lineage, one human family: one mother can reproduce herself a dozen times before she dies. They cannot possibly be defined as a dozen “generations”.
How many generations does phoodoo think those dozen children are? Who knows. ”m not sure even phoodoo knows what xe thinks, because – except for the “4 isn’t 1” screech – xis answers have been all over the map and never seem to coalesce on any repeatable arithmetic.
Olegt,
Really? You are still going to deny this? I just explained to you that the whole generation of 10 M&M’s is replaced. 8 are replaced by blue still being blue, two are replaced by black being the lucky one to be doubled, and one blue has no offspring. Ten births, ten deaths, ONE GENERATION!
In fact, Olegt you thinking is so wrong, that you actually need to adjust your whole concept of the drawing of the M&M’s, Since you are not willing to realize that this is one whole generation, you need to actually pull the ONE who has had the doubled black OUT OF YOUR NEXT DRAWING, because they are part of the same generation and thus can not give another birth immediately after they just had one. Its completely faulty logic. You can’t keep choosing the one who just had an offspring as one of the potentials to have another offspring, ten times in a row.
One individual can have ten offspring in your scenario, all during the SAME generation of your population? If your population is 100, that means that you are allowing that one individual to have 100 potential births during that generation! If your population is 1000 you are allowing that individual to have 1000 births during that ONE GENERATION! If the population is 10,000 now that individual could have 10,000 births during that generation!!!
Do you still want to insist your definition of a generation is correct????
Are we finally making progress? Do you agree that in a population with N M&Ms 1 generation = N deaths?
You seem to be saying exactly that in this comment. I can’t tell that because you seem to have changed your mind in the next comment.
Do tell.
hotshoe,
Hotshoe,
Are you sure you still want to stick with Olegt on this one?
I better warn you first, his King is already in checkmate, but he just doesn’t realize it yet.
His pawns are all going to be abandoning him soon. Are you going to continue to stick by him?
Olget, are you still going to refuse to believe that one round of eating one M&M and replacing one M&M equals one generation, but instead in a population of ten you need to do this ten times to equal one generation?
My contention is that one round=one generation. Its your move now, be careful, your King is in trouble. Which is it?
phoodoo, this argument seems to irrelevant to the point of the OP.
It doesn’t matter especially how you count generations – the point of the experiment is that even without selection, as long as some M&Ms die (are eaten) and others are born to replace them (some are randomly drawn and duplicated), over time, one colour will become dominant.
Do you dispute this?
If not, cool 🙂
You are not making any sense, phoodoo. In the first paragraph you are urging me to agree with you that 1 generation = N deaths. In the second, you state that 1 generation = 1 death.
Don’t worry about my king, try speaking coherently.
No, Lizzie, I think it matters. It becomes the question of timescale. If we (collectively) are right then fixation of an allele happens in N generations in a population of N organisms. If phoodoo is right then it happens in N^2 generations.
But I agree with you that counting generations has become a major distraction in this thread. Maybe I should open one specifically about that.
Its very relevant Lizzie, you will see soon enough why, if you don’t now. What is your contention, in this little model, how many generations does the event of pulling out one M&M and eating one represent? Its either, as I have contended all along, representing one generation of the population, or it is as Olegt contends, in a population of ten, one round is only equal to one tenth of a generation, because he says this is only one death, so you need to do it ten times to equal one generation.
Who do you agree with?
Which is it Olegt, does one round of eating one M&M and replacing one M&M (just like your programmed your computer) equal to 1/10 of a generation in a population of ten, or does it equal one generation? Let’s get a straight answer.
You know my straight answer, phoodoo. I have been giving so many times that a child of five would know this. Send someone to fetch a child of five.
Removing 1 M&M out of N and replacing it with a new one does not equal 1 generation. It is completely bonkers to claim that it does. N−1 members of the original generation (the vast majority) remain intact. How can you contend that this tiny change in the population = 1 generation? It makes no sense whatsoever.
Olegt. (edited – I misread his post at first).
In a real population of living things, individuals are dying and reproducing all the time, so to get a generation time you have to take some kind of average – what is the average time between generations averaged across lineages?
If you set up an artificial population, but only have one death and one birth per iteration, you will have to calculate that average generation difference.
If you kill off a set proportion per iteration and breed from the rest, then you can count each iteration as a generation.
Either way, you need to estimate the generation rate, and obviously if it is slow, and the population is large, then fixation will take forever. But if you increase the generation rate and/or reduce the population, then it will happen quite quickly.
@ phoodoo
In a static population where births and deaths are equal, generation interval is a statistical measure of the “turnover” of individuals. In a population of (hypothetical) parthenogenetically reproducing females that each produce one daughter, this is simply the average age of the mothers when giving birth. Add in multiple offspring and you just use the mean of the mother’s age at those births.
In the case of humans we could say
And so on for larger groups and populations. As Allan Miller remarked, individuals and small groups will show wider (lumpier) variations than statistical averages of larger populations
If you look at the link there is a visual explanation of how to derive generation number too.
Hope this helps and any input from anyone to correct egregious error or gross misunderstanding much appreciated.
Ok, well I will answer you in a few minutes, but first to be fair, I should give Lizzie and Hotshoe a chance to join your sinking ship if they choose. You believe Lizzie agrees with you, so lets see if she wants to stand by that. If she doesn’t answer, I will assume that she agrees with you and continue on in a little while.
Take your time, phoodoo.
I might post a separate thread that deals with counting generations of M&Ms in our little model. We will pay no attention to their colors as generation count has nothing to do with that. Which is why this question does not belong in this thread.
Alan Fox,
I want to keep this simple Allan, so there is no confusion. Olegt contends that each round of the M&M game where you eat one, and then double another represents 1/N of a generation. If there are ten in the population, you need to do this ten times to equal one generation on average.
Do you agree with that concept, or do you agree with my concept that one drawing of the M&M’s has to equal one generation?
The first rule of holes: if you find yourself in a hole, stop digging.
Look at it this way, Phoodoo. Every quarter second of each day, someone is born and someone dies.
Would you say that there is a new human generation four times per second?
(In fact, of course, today, deaths are a little less frequent than births, but that’s because the human population is expanding – in our bag of M&Ms the two rates are kept constant)
Oh, I have tried this argument with phoodoo, Lizzie. And not once but maybe three times. It still didn’t help. He has no concept of scaling.
I am not clear on your answer, who do you feel is more correct, Olegt or I?
Olegt is more correct.
You are confusing the iteration of the model with generation rate.
That’s why I selected a link from a popular source that seemed to give a clear, simple explanation of the concept of generations and how generation interval and generation number is independent of population size as it is an average.
Dr. Miller is Allan, BTW, I’m Alan.
I am not confusing anything. So you think it is reasonable to allow ten draws from the bag to equal one generation in a population of ten? Just want to be sure.
Ok, so you also want to stay in Olegt’s camp, right?
*jumps in*
Well, of course. Generation number is the turnover of the population, every time the whole population is replaced (statistically – on average) counts one generation.
phoodoo
I think you can conclude that from my previous comment.
I can just see phoodoo living in a town where, on average, one woman per week goes to the local hospital and gives birth. phoodoo concludes that the human generation time is one week.
Astonishingly, he does.
Ok great. Now let me show you why you, Olegt, Hotshoe Lizzie, and Thorton are all wrong. After you spend time thinking about this, I think you will see the error of your ways:
My contention all along has been that the drawing of the M&M’s has to represnt one turnover of the population, where in each of the ten M&M’s is replaced by a duplicate, except for one which looses a replacement, and one which gains two replacements. This is a completed generation!
Now, in Olegts (and yours who agree with him) you can start with 9 blues and one black. You then draw a blue to eat (the one who doesn’t get to replicate with one offspring) and you choose one who gets to double its offspring. let’s say the one that doubles is a black. So you end up with 2 black and 8 blue. Ah, but according to Olegt the generation isn’t over, we get to keep drawing. Hm.
So in round two, we draw one blue, eat it, and we draw one to double, and guess what its another black, the the one who was the result of the doubling. In fact if we were to number her she is number two black, because she is the offspring of number one black.
So now we have 3 black, and 7 blue. Now at this point we know that the blacks are all related, we have a grandmother, a daughter and a granddaughter as it were.
Draw again. A blue gets eaten. And what do you know, another black gets drawn, its the granddaughter. She has an offspring, so now we have a great grandmother, a grand mother a grand daughter, and a great grand daughter. But guess what the generation is still not over. Because you see in Olegts mind, we still include them in the first generation, so all are available to be chosen to duplicate. Nobody is eliminated from reproducing. 6 blues, and 4 blacks, and we still aren’t finished with this generation yet.
Draw again, a blue gets eaten, another black is drawn, what do you know, its the great grand daughter! 5 blues and 5 blacks. The great great grandmother, and the great granddaughter are in the same population as the original population, still able to be selected for breeding. And we are not even halfway finished with this generation yet!!
But its gets better, much better. With Olegts way of thinking, in a population of 100 we can have the 95th descendant of a chain of blacks, still in the same generation as the original first generation. How about a population of 1000? great question. The 900th descendant is still among those we choose from each time we reach into the bag!
Now why does this happen? Well, there are a few reason’s but the most obvious is because you all don’t understand the premise at all. The premise is that EACH TIME YOU DRAW, you are looking at the next generation of the population. All the blues have been replaced and all the blacks have been replaced Sometimes the blacks have gained a slight edge, and sometimes the blues have. If we allow everyone to have a roughly equal shot at reproduction, then by averages someone is going to get a slight edge. It could be black and it could be blue. In a population of 9 blues and one black, the black has about a 1 in ten chance of gaining an edge in THAT generation. In the next generation, if it got the advantage, it now has a 2 in ten chance of gaining an edge, in THAT generation.
The descendants are a line of genealogy. We are NOT playing a totally rigged game where we get to say, well, ONE person in the population can have all the babies for the entire next generation, and nobody else gets any. That silly distortion becomes even more ridiculous the higher the population. In one hundred we are going to say that ONE sires every offspring, and everyone else gets none. In a thousand? Please.
I don’t care if ten of you want to disagree with me, I don’t care if 20 of you do. You are logically totally and completely incorrect. We allow a small shifting of the alleles per generation, not an entire turnover of the entire populations genes in one generation.
You are incorrect, I am sorry to tell you. But from what I have seen here, I don’t expect many of you to be willing to admit it.
And you are a great mathematician, right Joe?
So, phoodoo, before we get to the rest of your comment, can you clearly define what you understand by one generation? You seem to contradict yourself.
In the above passage you define a generation as “one turnover of the population, where in each of the ten M&M’s is replaced by a duplicate.” This suggests that we need at least ten deaths to occur to declare that a generation has passed. Or with N M&Ms, at least N deaths.
But then you turn around and say that one death has to equal one generation.
These two statements are mutually exclusive. It’s either 1 death per generation or at least N deaths per generation. Not both.
Can you tell us more clearly what your position is?
Another case of violent agreement?
Apparently not. The average turnover for any population size is the total of individual generation times divided by the total population number. To me this seems a very simple idea. Individual variations (age on giving birth, number of live births) are used to compute an individual’s generation time and average of a population (or a representative sample) is independent of population size.
Am I missing something?
Right, this is my understanding of his position, but I haven’t read the book, just reviews. And there are also may be some hereditable features that are not included in the genome – like the strengthening of the immune system by breast feeding.
Everyone reproduced once in each drawing, and all ten of the ancestors are dead. The eating of the one is simply to represent the one randomly chosen who reproduced slightly less descendants (in this case one) and the one who was doubled represents the one who reproduced slightly more (also in this case 1) . 10 births, 10 deaths, one generation. I told you this from the very beginning.
phoodoo,
What, that I understand the issue? 😉
There were no numbers in my argument. If the probability of fixation of a neutral allele is 1/N, that is true whether the allele is regarded as a ‘mutation’ or is not. You introduced the black allele; that is therefore a mutation that has happened. Its chance to fix, having happened, is 1/N. While you are sitting waiting for ONE PARTICULAR mutation to arise and fix, the population has nonetheless evolved by virtue of all the others!
Phoodoo-generations or everyone-else generations? 😉 For small N (in the hundreds), it takes about N2 replacements (I call that N generations on average). For increasing N it converges on 2N ‘true’, or mean, generations (in accord with another result from population genetics). I’ll post the code later – I’d like to try and speed it up.