Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 120 (8763 total)
Current session began: 
Page Loaded: 06-23-2017 4:31 PM
397 online now:
caffeine, Coyote, DrJones*, PaulK, Taq (5 members, 392 visitors)
Chatting now:  Chat room empty
Newest Member: aristotle
Post Volume:
Total: 811,942 Year: 16,548/21,208 Month: 2,437/3,593 Week: 550/882 Day: 68/103 Hour: 1/3

Announcements: Reporting debate problems OR discussing moderation actions/inactions


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
1
23456
...
31NextFF
Author Topic:   Molecular Population Genetics and Diversity through Mutation
Genomicus
Member
Posts: 844
Joined: 02-15-2012
Member Rating: 3.4


(3)
Message 1 of 455 (784814)
05-23-2016 7:59 PM


Originally, as I was mulling over a new topic for EvC, I was going to offer a rebuttal to Faithís argument that creationism can indeed work as an explanatory model for horizontal gene transfer and phylogenetic incongruences.

However, Iíve decided to instead tackle Faithís argument in the ďThe Science in CreationismĒ thread that evolution ďalways reduces genetic variability, which is the opposite of what evolution needs.Ē This argument seems to have been floated by Faith way back in 2005 (and earlier), in the thread titled ďNatural Limitation to Evolutionary Processes.Ē

I wasnít around EvC at that time, but the argument presented by Faith seems come back again and again, most lately in ďThe Science in CreationismĒ thread. I believe that thread has mostly outlived its usefulness, so I will just propose a new topic. It also seems that thereís been some difficulty coming up with a viable mathematical approach to understanding the subject.

Thus, my refutation of Faithís argument here will take a molecular population genetics approach. Most of the material discussed below is pretty standard introductory content in evolutionary biology courses, and can be found online, as well. Only high school algebra, high school probability theory, and a smattering of Mendelian genetics should be needed to grasp the basis of my argument.

I will begin by noting that genetic drift eliminates diversity in a population. Genetic drift, of course, is basically a sampling error -- there are a number of cool images on the web that can help you visualize why genetic drift, by itself, removes genetic diversity in a population.

So both genetic drift and selection eliminate diversity in a population; both of these processes weed out alleles at a given locus. As both of these processes remove genetic diversity in a population of organisms, I will focus on genetic drift. Note that my argument holds perfectly well for selection; however, the mathematics for selection are slightly more intricate, so I will go there only if necessary.

Now comes the math. Why does genetic drift weed out diversity? For starters, let G = the probability that 2 alleles (from the same locus) randomly chosen from the population are identical.

Thus, G = how much genetic variation there is in the population. If G = 1, then there is absolutely no variation at that locus; all the alleles are the same. When G = 0, every single allele (from that locus) in the population is different. Perhaps they differ by a few nucleotides here, and a few there -- but they are all different if G = 0.

So far so good. A quick side note: from now on, whenever I say ď2 allelesĒ or ď2 identical allelesĒ or ďthe 2 alleles are different,Ē or whatever, I mean 2 alleles of the same loci. And by ďlocus,Ē of course, I mean the chromosomal location of the allele under consideration, or ďWhere in the genome you can find this allele.Ē

Now, then, let Gí = the probability of randomly picking 2 identical alleles from the population after one generation, or one round of more-or-less random mating.

The value of Gí = 1/2N + (1-1/2N)*G.

You might think ďWhere the actual freak did that come from?Ē

So let me explain.

There are basically only two ways for 2 alleles picked at random to be identical. First, 2 alleles could be identical because they share an immediate ancestor -- a parent -- in the previous generation. The probability of 2 randomly picked alleles being identical because of this is 1/2N.

Here, N = the size of the mating population. But 2N is used because we are dealing with diploid organisms, so there are 2 allele copies per organism. So when you think about it -- yes, if Iím looking at one allele, and I want to randomly find an identical allele that has the same parent, then the probability of doing that successfully is 1/2N.

The other way for 2 alleles to be identical is if they do not share a parent, but if the immediate ancestors of each allele have identical alleles. So, for example, letís say A and B are two identical alleles, with different parents. A and B can be identical if the parent allele of A is identical to the parent allele of B. Think through it and it will make sense.

So whatís the probability of 2 alleles being identical through this way? Itís (1-1/2N)*G. Why 1-1/2N?

Well, say you have 2 identical alleles. The probability that they are identical is 100%, or 1. There are two basic ways for them to be identical: they share the same immediate ancestor in the prior generation (1/2N), or they are identical because both their parents were identical. These must add up to 1, so the probability of the alleles being identical because their parent alleles were identical must be 1-1/2N. But 1-1/2N must be multiplied by G to get the actual probability of the alleles being identical because their parent alleles were identical; this is because G = the probability that 2 alleles randomly chosen from the population are identical.

G is independent from 1-1/2N, so the two are multiplied together to get the actual probability of 2 alleles (picked randomly from the population) being identical because their parent alleles were identical.

Then we add 1/2N to (1-1/2N)*G to get the value for Gí, which is the probability of randomly picking 2 identical alleles from the population after one generation. This brings us to the equation above:

Gí = 1/2N + (1-1/2N)*G

Now, letís take this equation out for a test drive.

Suppose N = 100, and the initial probability of two alleles being identical = 50%. After 1 generation, Gí = 1/200 + (1-1/200)*.5 = 50.25%. In other words, the probability that the two alleles, drawn at random from the population, will be identical has increased. We can carry this on through for several generations.

G2 = 1/200 + (1-1/200)*.5025 = 50.5%. The probability keeps increasing, inching the population towards homozygosity. After 10 generations, weíre at 52.6%. Eventually, it will reach 100% in a real population. In other words, all the alleles will be identical -- so there is no genetic diversity in the population.

But now letís take a look at the role of mutation in this.

Mutation puts variation into a population at the rate 2Nu, where u = the mutation rate for selectively neutral alleles. Why 2Nu? Well, there are 2N gene copies per generation, and u = mutation rate, so these are multiplied together to get the overall ďrate at which variation enters the population.Ē

More precisely, u = the mutation probability for a given allele. So u = the probability that an allele in a given locus of a gamete will have a mutation. When mutation rate is taken into consideration, then, we must revise the equation for Gí. Remember, Gí is the probability of 2 alleles picked at random from the population will be identical after one generation; if G = 1, all alleles are the same; if G = 0, no alleles are the same.

So the new equation, taking mutation into consideration, is this:

Gí = (1-u)^2 * [1/2N + (1-1/2N)*G]

What is 1-u? The factor 1-u is the probability that a mutation did not occur in one allele. But remember these are diploid organisms (2 allele copies), so the probability that a mutation didnít take place in either allele is (1-u)^2 -- it is multiplied by itself (the two events are independent, so a la basic probability theory, they are multiplied instead of added). Why 1-u? Well, u = the probability that a mutation does happen; u must necessarily be less than 1, so 1-u is the probability of the allele not having a mutation.

Okay, now letís plug in some numbers. Say the mating population size is 100 and G = 50%. Letís say the mutation rate is 10^-5 (pretty standard mutation rate for a number of diploid organisms). That means thereís a 1 in 100,000 chance that a given allele will mutate. After one generation, Gí, the probability of 2 alleles being identical (picked randomly from given loci) is: 50.248995%, which is extremely close to the 50.25% reported above, where mutation was NOT taken into consideration. However, what happens when the population size is increased?

When the population size is 100,000 (instead of a mere 100), the probability of randomly picking 2 identical alleles begins decreasing. After one generation, itís 49.99925%. Each generation, the probability inches closer to 0. In other words, because of mutation, the probability of randomly picking out 2 identical alleles increasingly becomes 0. This, in turn, means that thereís an enormous amount of genetic diversity in the population. In short, mutation has an effect that can and does counter both genetic drift and the forces of selection.

The challenge is for Faith to show that:

(1) The mathematics undergirding these processes become irrelevant in isolated founding populations, which represent a sampling of the allele frequency of the ancestor population. Clearly, if founding populations are quite small and geographically isolated, then genetic drift and selection will work to eliminate genetic diversity. Often, the result will be extinction. But if the founding population is sufficiently large, then mutation will be enough to continue adding diversity to the gene pool, generation after generation -- despite selection and genetic drift.

(2) Most mutations are too detrimental for any of this to be of real meaning in biology, or beneficial mutations too rare for positive selection to have something to work on.

(3) While mutation can overcome the reduced diversity wrought by genetic drift, selection is necessarily always strong enough that mutation cannot overcome its reductive effects.

Any questions, just ask!

Note: when I say "parent" in the above piece, I mean "parent allele," of course.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : Clearing up typos n' stuff.


Replies to this message:
 Message 4 by Faith, posted 05-24-2016 6:04 AM Genomicus has responded
 Message 11 by caffeine, posted 05-24-2016 4:56 PM Genomicus has responded
 Message 151 by RAZD, posted 06-05-2016 11:49 AM Genomicus has acknowledged this reply

  
AdminAsgara
Administrator
Posts: 2072
From: The Universe
Joined: 10-11-2003


Message 2 of 455 (784816)
05-23-2016 8:39 PM


Thread Copied from Proposed New Topics Forum
Thread copied here from the Molecular Population Genetics and Diversity through Mutation thread in the Proposed New Topics forum.
    
Coyote
Member
Posts: 5861
Joined: 01-12-2008
Member Rating: 4.0


Message 3 of 455 (784817)
05-23-2016 9:32 PM


Genetic corruption/reduction
From reading (sometimes between the lines) it seems that the whole idea of reduction of genetic diversity comes from the religious idea of "the fall."

It is believed by some that Adam originally had perfect DNA, and sin (original sin) introduced corruption, reduction, or some such defects. As a result succeeding generations had less perfect DNA. This seems to be at least a part of what Faith is relying on for her posts about reduced genetic diversity.

That this is believed to have been going on only for some 6,000 years explains why that continual reduction has not resulted in the extinction of mankind.

I think this also explains Faith's reluctance to accept increased diversity through mutations, particularly beneficial mutations.

Given all of this, I fearlessly predict that your efforts to include numerical analyses and rational explanations will fail, as you are using evidence and logic to try and change a religious belief.

We'll see if, after a few hundred posts, this fearless prediction comes to pass...


Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.

Belief gets in the way of learning--Robert A. Heinlein

In the name of diversity, college student demands to be kept in ignorance of the culture that made diversity a value--StultisTheFool

It's not what we don't know that hurts, it's what we know that ain't so--Will Rogers

If I am entitled to something, someone else is obliged to pay--Jerry Pournelle

If a religion's teachings are true, then it should have nothing to fear from science...--dwise1

"Multiculturalism" demands that the US be tolerant of everything except its own past, culture, traditions, and identity.


  
Faith
Member
Posts: 25264
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 4 of 455 (784832)
05-24-2016 6:04 AM
Reply to: Message 1 by Genomicus
05-23-2016 7:59 PM


But I'm just as mathematically challenged as ever
Although I appreciate that you want to keep the math to a simple level, even that's probably going to be too much for me, sad to say. And I didn't have probability theory in high school either. I'd like to be able to think in terms of math about these things but it isn't happening. (I comfort myself with the thought that Darwin also admitted to being mathematically challenged.) So I may not be able to stick it out on this thread very long.

I will begin by noting that genetic drift eliminates diversity in a population. Genetic drift, of course, is basically a sampling error -- there are a number of cool images on the web that can help you visualize why genetic drift, by itself, removes genetic diversity in a population. So both genetic drift and selection eliminate diversity in a population; both of these processes weed out alleles at a given locus.

Yes, thank you, good place to start, with processes that do eliminate genetic diversity. I have to admit that the term "sampling error" has always escaped my understanding despite many efforts to make sense of it, but nevertheless I think I have a visual grasp of what drift actually does.

But if you are answering my argument it needs to be kept in mind that what Iím focused on is the phenotypic changes that are considered to be evolution, those which accumulate in a population to the point of defining a new subspecies, changes which require the loss of genetic diversity you are discussing. If this isnít kept in mind it starts to sound like I have some interest in loss of genetic diversity as such, for no good reason. But again, the point is that it must accompany the phenotypic changes we identify as evolution. While I include selection as one of the processes that brings about these changes, I think the more powerful mechanism of change is geographic isolation / reproductive isolation of a subpopulation, which is why that is the example I usually use, and ring species are my favorite example of how the changes occur from daughter population to daughter population. I can only predict that loss of genetic diversity must accompany each new subpopulation of course, and Iím aware that hybrid zones may occur and that gene flow may not completely cease between some subpopulations, but since selection and drift lose genetic diversity, it seems to be a good general prediction for this situation too. Ring species get some dramatic new phenotypic variations. What Iíd like to see set up as a lab experiment is basically a ring species, daughter population to daughter population changes monitored for gemetic diversity.

If evolution, meaning the production of a population-wide change in phenotypic presentation (black wildebeests to blue wildebeests, normal lizards to large-headed lizards, Darwinís finches and so on, all changes normally called evolution) always requires a reduction in genetic diversity, that is obviously contrary to what evolution needs in order to do what the ToE says it does. (Yes, Iíll get to the claim that mutations counteract this). As I understand it, genetic drift may or may not involve phenotypic changes. The Wikipedia article on drift says that, and also says there is an ongoing debate about whether drift or selection is the real cause of evolution. I have in mind that wherever you have phenotypic changes that become characteristic of a population you also have loss of genetic diversity because you canít get those changes without removing the genetic diversity.

As both of these processes remove genetic diversity in a population of organisms, I will focus on genetic drift. Note that my argument holds perfectly well for selection; however, the mathematics for selection are slightly more intricate, so I will go there only if necessary.

Now comes the math. Why does genetic drift weed out diversity? For starters, let G = the probability that 2 alleles (from the same locus) randomly chosen from the population are identical.

Thus, G = how much genetic variation there is in the population. Ö

Well, I was going to make a big effort to follow the math but Iím already at sea. I give up on the math already. Sorry. There is probably no way Iím going to be able to participate on this thread. Iím going to continue far enough to get a sense of the logic of it at least, and comment on that, but that may mean Iím hopelessly off topic.

First observation: all your description of the math is hypothetical, ďif this then thatÖĒ so that I have no idea what actual facts, if any, are described by these calculations.

But now letís take a look at the role of mutation in this.

Mutation puts variation into a population at the rate 2Nu, where u = the mutation rate for selectively neutral alleles. Why 2Nu? Well, there are 2N gene copies per generation, and u = mutation rate, so these are multiplied together to get the overall ďrate at which variation enters the population.Ē

More precisely, u = the mutation probability for a given allele. So u = the probability that an allele in a given locus of a gamete will have a mutation. When mutation rate is taken into consideration, then, we must revise the equation for Gí. Remember, Gí is the probability of 2 alleles picked at random from the population will be identical after one generation; if G = 1, all alleles are the same; if G = 0, no alleles are the same.

So the new equation, taking mutation into consideration, is this:

Gí = (1-u)^2 * [1/2N + (1-1/2N)*G]

What is 1-u? The factor 1-u is the probability that a mutation did not occur in one allele. But remember these are diploid organisms (2 allele copies), so the probability that a mutation didnít take place in either allele is (1-u)^2 -- it is multiplied by itself (the two events are independent, so a la basic probability theory, they are multiplied instead of added). Why 1-u? Well, u = the probability that a mutation does happen; u must necessarily be less than 1, so 1-u is the probability of the allele not having a mutation.

Okay, now letís plug in some numbers. Say the mating population size is 100 and G = 50%. Letís say the mutation rate is 10^-5 (pretty standard mutation rate for a number of diploid organisms). That means thereís a 1 in 100,000 chance that a given allele will mutate. After one generation, Gí, the probability of 2 alleles being identical (picked randomly from given loci) is: 50.248995%, which is extremely close to the 50.25% reported above, where mutation was NOT taken into consideration. However, what happens when the population size is increased?

When the population size is 100,000 (instead of a mere 100), the probability of randomly picking 2 identical alleles begins decreasing. After one generation, itís 49.99925%. Each generation, the probability inches closer to 0. In other words, because of mutation, the probability of randomly picking out 2 identical alleles increasingly becomes 0. This, in turn, means that thereís an enormous amount of genetic diversity in the population. In short, mutation has an effect that can and does counter both genetic drift and the forces of selection.

I donít see anything in all of that to tell me about the actual rate of mutations, but isnít that what we need to know?

The challenge is for Faith to show that:

(1) The mathematics undergirding these processes become irrelevant in isolated founding populations, which represent a sampling of the allele frequency of the ancestor population. Clearly, if founding populations are quite small and geographically isolated, then genetic drift and selection will work to eliminate genetic diversity. Often, the result will be extinction. But if the founding population is sufficiently large, then mutation will be enough to continue adding diversity to the gene pool, generation after generation -- despite selection and genetic drift.

Well, now I see that you are saying the same thing Iíve answered many times in this argument already: it doesnít matter how much new genetic variability you can put into, or put back into, a population, when it is evolving a new population of new phenotypes, a new look, the trend is going to be to loss of genetic diversity, no matter how much new diversity may have been added. As I put it above, you can't get the phenotypic changes without removing the genetic diversity. So if you are adding genetic diversity, you are obviously not removing genetic diversity.

The processes that bring about the new phenotypes, that is, that are actively evolving the population, have to get rid of whatever genetic diversity doesnít support the new phenotypes, and the end is going to be the same no matter how much diversity is added: a subspecies with reduced genetic diversity, and if many daughter populations succeed one another eventually the loss of genetic diversity should be quite dramatic. And if during all these evolutionary changes new genetic diversity is added, all that can do is interfere with the formation of the phenotypes that is underway. It can happen, of course, but then it isnít evolution.

(2) Most mutations are too detrimental for any of this to be of real meaning in biology, or beneficial mutations too rare for positive selection to have something to work on.

Well, thatís information I get from evolutionists, I donít make it up. Of course I draw conclusions from it they donít draw.

(3) While mutation can overcome the reduced diversity wrought by genetic drift, selection is necessarily always strong enough that mutation cannot overcome its reductive effects.

But I think you are making the common mistake of thinking of this as a simple process of addition and subtraction, but itís not. The selective or subtractive processes that bring about the new phenotypes toward a new subspecies HAVE to get rid of the genetic diversity that doesnít support them. It isnít just a matter of more or less, itís a matter of REQUIRING loss of genetic diversity in order to get the phenotypic changes which are normally identified with evolution. True, as Iím often reminded, nature couldnít care less about preserving emerging phenotypes, but the point Iím making is that the ToE DOES care and is always describing the production of new phenotypes a la microevolution as an open-ended process that just keeps on going making endless new variations. But if selection eliminates genetic diversity youíd think that would be a caution right there. Additions CANíT overcome this effect because subtraction is REQUIRED if evolution is occurring. Breeding by artificial selection should get this across, and Darwin was right to apply that method to nature. He just didnít recognize the necessity of the loss of genetic diversity, and that lack of recognition continues today.

So Iím probably way off topic since I canít deal with the math. And as so often happens when I spell out all this I've probably left out necessary information or garbled something important. Oh well.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 1 by Genomicus, posted 05-23-2016 7:59 PM Genomicus has responded

Replies to this message:
 Message 5 by Modulous, posted 05-24-2016 7:41 AM Faith has not yet responded
 Message 6 by PaulK, posted 05-24-2016 7:55 AM Faith has responded
 Message 7 by Modulous, posted 05-24-2016 11:59 AM Faith has responded
 Message 18 by Genomicus, posted 05-24-2016 7:51 PM Faith has responded

    
Modulous
Member
Posts: 7407
From: Manchester, UK
Joined: 05-01-2005
Member Rating: 3.0


(1)
Message 5 of 455 (784833)
05-24-2016 7:41 AM
Reply to: Message 4 by Faith
05-24-2016 6:04 AM


Re: But I'm just as mathematically challenged as ever
. The selective or subtractive processes that bring about the new phenotypes toward a new subspecies HAVE to get rid of the genetic diversity that doesnít support them.

This isn't quite true for a few reasons which reveal quite fundamental misunderstandings about what is happening.

So let's consider a foundation population on an island that is smaller than the parent population but all the alleles are represented in the foundation population. The environment is different on the island so the selective pressure is different. With the classic finches, there might be a pressure towards certain shapes of beaks, for example. So alleles which stand in the way of the trait we are looking at, reduce in frequency in the genepool. This is fine, it may result in the extinction of all of the involved alleles but harmful alleles can hang around.

On the whole though, let's agree there is some loss of alleles.

But while this is going on, and after the population beak size has stabilized, mutations are occurring. Other genes, less constrained than beak related ones mutate as normal, and the beak ones are still mutating during the selection process, so there were lots of alleles for medium sized beaks, now there are lots of alleles for thin sized beaks.

Let's say they grow to a reasonable size a new population splits off from them back to their homeland, where the original population lived, but is now extinct for convenience of this example. Medium sized are needed and there are no medium beak alleles!

Well it's not quite that simple, for a number of reasons but let's just suppose a small number of ideas that might give us reason to rethink the certainty of your position

a) The new population may survive with their less than optimal beaks for mutations to give rise to alleles that cause medium sized beaks. We know there is a mutational pathway that will allow it.
b) The new population may have broken copies of the medium beak allele which may allow for the re-emergence of the medium beak allele
c) The new population may, because of the mutations and variety building up back on the island and in the time before that when they were in the original parent population, have other strategies for survival open to them. Perhaps a shift to a heavier insect diet and away from crustaceans etc. While they are heading in that direction, maybe medium sized beaks won't even be advantageous anymore, even though the external environment is the same as with the parent population - the internal environment (ie the genotype) differs from the parent population.

But if selection eliminates genetic diversity youíd think that would be a caution right there. Additions CANíT overcome this effect because subtraction is REQUIRED if evolution is occurring.

This presupposes that additions can't occur after subtraction when in fact they happen all the time. Each generation is an addition of mutational variety. Some varieties reproduce more than others. Some don't reproduce at all. Of those that do, their reproductive efforts are an addition of mutational variety, those that don't may represent a loss of variety. You can't just focus on where the water is leaking from and conclude it'll stop on its own soon enough if you don't note that there is more water entering the system from elsewhere.

There is no one selective pressure. You seem to be of the mind that 'evolution' starts with the culling out disadvantageous traits. There is no start point to evolution. We can draw arbitrary lines to discuss a narrative which helps us understand what is happening to varying degrees of depth, but evolution is happening all the time. Constantly. Every organism is a test, every birth a new trial run.

It's just interesting to us when the environment changes resulting in the population's phenotype changing. That environmental change can be changes in the environment or changes within the genepool (if allele X for gene 1 is lethal if in the presence of allele Y for gene 2, then how common allele Y is going to impact how common allele X can feasibly exist within the population. If something causes allele Y to become uncommon, then allele X may now increase in frequency without that impediment)

But evolution is about changes in the genepool, not the phenopool. The changes to the phenopool are caused by changes to the genepool (ie., an organisms physical traits are caused, in part, by the genes), but to understand evolution we need consider the genepool only. How advantageous or disadvantageous an allele is can then be abstracted from the question as to WHY it is advantageous (or not).

If you don't do this, you are right, it all looks a bit mysterious. But only looking at the general outcome is missing what's going on under the hood. Genotype and phenotype are loosely connected through an interaction with the environment. It's a chaotic system with chaotic outcomes.

You simply can't look at it with a non-mathematical eye and make reasonable predictions as you claim to do.


This message is a reply to:
 Message 4 by Faith, posted 05-24-2016 6:04 AM Faith has not yet responded

    
PaulK
Member
Posts: 12759
Joined: 01-10-2003
Member Rating: 3.0


Message 6 of 455 (784835)
05-24-2016 7:55 AM
Reply to: Message 4 by Faith
05-24-2016 6:04 AM


Re: But I'm just as mathematically challenged as ever
quote:

Well, now I see that you are saying the same thing Iíve answered many times in this argument already: it doesnít matter how much new genetic variability you can put into, or put back into, a population, when it is evolving a new population of new phenotypes, a new look, the trend is going to be to loss of genetic diversity, no matter how much new diversity may have been added.

As Modulous has pointed out this is a bad argument for reasons that have been pointed out before - and which are implicit in the post you are answering. The times when a new species is forming is just a fraction of the lifetime of a successful species - and the rest of that time is when we expect the increases to occur.
(For good reason. Losses should slow when a species is increasing in population, and the number of mutations appearing is proportional to population size.)

And, of course, this is one of the points that you haven't been able to refute.


This message is a reply to:
 Message 4 by Faith, posted 05-24-2016 6:04 AM Faith has responded

Replies to this message:
 Message 10 by Faith, posted 05-24-2016 4:52 PM PaulK has responded

    
Modulous
Member
Posts: 7407
From: Manchester, UK
Joined: 05-01-2005
Member Rating: 3.0


(1)
Message 7 of 455 (784843)
05-24-2016 11:59 AM
Reply to: Message 4 by Faith
05-24-2016 6:04 AM


Re: But I'm just as mathematically challenged as ever
Since maths is too much, maybe a graphical visualisation may help understand the same principles in a more intuitive fashion:

So the whole 3 minutes is interesting (the last is very interesting, but its less obvious why - sometimes less optimal solutions are what evolve), but the dynamic fitness landscape with three peaks is interesting as the species influence one another and seperate out into three groups on 3 peaks (aka speciation). So that's how it might work in simple terms, the question is about diversity.

In this 2d space, phenotypic diversity is a function of the area described by the creatures on the edge (that is to say, draw a line around all the creatures and calculate the area of the shape drawn). phenotypic diversity is a function of geneotypic diversity. So we can see that diversity may change depending on the landscape, but it can move from one peak to another with little drop in diversity anywhere.

In that final example, there wasn't much diversity. There was a very fit phenotype, but anything slightly different is worse (ie any mutation is a harmful mutation), but nearby there was a way to be slightly fitter than terrible and the population stabilized to the more diver solution as it was more stable and that's how the maths work out. They cluster to average fitness not optimal fitness, that way, mutations are less likely to be so regularly harmful.

Hardy-Weinberg

So let's consider a population that is static from generation to the next. Or a single generation if that's easier. Let's talk about beaks too for fun. 1 gene with two alleles. One allele is F and is dominant. Another is f and is recessive. The real world is more complex, but then maths has to come in so I'm trying to avoid that.

Because of the rules of Mendellian genetics, you can test the phenotypic frequencies and infer the genotypic frequencies. Unfortunately as I say, real life is more complex as traits don't typically have a single gene controlling them. But that's not too important.

In this static population there is nothing that affects allele frequency so once we have worked it out we're done. So what if something were to start affecting things, then what?

1. Natural selection

Natural selection will cause alleles that are 'fit' to increase in frequency and the less fit to decrease in frequency. If the reason the gene is 'fit' is because it helps to build a certain phenotypic trait, such as F and f, then we may see beak size frequency to also change.

It might turn out that if F is less fit, it goes extinct because it always gets expressed and so it is always 'exposed' to natural selection acting because of the phenotype. If f is less fit instead, it only gets 'exposed' when the organism has ff, so extinction is less certain. But it is possible that because of natural selection we lose F or f entirely.

This is represented by the peaks in the 2D diagram.

2. Sexual selection

Another selective force that can apply in some cases where mating is non-random, and allele that create sexy phenomes or phenomes that find other phenomes sexy may change the frequencies around. Again an allele could be lost.

3. Drift

Can only act to reduce allele frequencies to extinction as described in OP

4. Gene Flow

Alleles sporadically popping into or out of the population, such as when one population becomes physically isolated or when a previously isolated group's isolation ends such as with immigration.

For a given population this can add or remove alleles.

5. Mutation

Everytime a mutation happens to an allele it creates a new allele unless it happens to mutate the allele in such a way so as to be the same as an already existant allele. How often an allele mutates varies based on a number of factors but reasonable estimates can be made based on observation and mathematics.

Each offspring in the 2d landscape video is slightly different from its parent. This allows for the population as a whole to take random walks towards stable peaks in the landscape. Without the mutation there is no searching through possible trait combination and no adaptation.

In your version of evolution a new peak emerges and if it somewhere near where the population is in this abstract space, everything not on the peak is killed off and lost forever. With mutation, we can see it isn't so obvious from a casual inspection of life.

The Fitness landscape

The 3 minute video just looks at mutation and selection of two traits, which allows for a 2d shape or 'landscape' to created visually for what combination of those traits is most 'fit' and to see that because new variations are mutating, the population can move from peak to peak in certain circumstances. It's a random search through a 2d space. But if we're doing this by traits, then there are a lot more than two traits, so the reality is that we're looking at a several-thousand-dimensional landscape, which shifts and change dependent on what's going on within it. As I said, it's complex and chaotic, but it's a chaotic system searching (through logical necessity) for some kind of optimal stable equilibrium and if the circumstances stop changing life might find itself in equilibrium for a long time, before getting knocked out of it again by a changing landscape.

The question you raise is, is there enough mutation to overcome the selection process? Well it's a good question, and it's not a trivial one too. All I can tell you from here is that it is a mathematical and empirical question. The pros tell me it can work and here's how. You tell me it can't because it can't. I'm not a scientist, but those guys seem to have better reasons for saying what they do than you do.

I see no reason a population cannot bounce between two peaks forever as long as the peak changes are slow enough compared to the mutation rate to allow for 'tracking the peak'. You think they'll run out, but slow the selection pressure changes and they just keep getting more and more. So unless someone has done the maths that says otherwise, you have no basis to intuit that it must result in long term depletion of diversity.

I will grant you this though, most species are extinct. Some extinctions had survivors in the form of daughter species, many did not. Those that left nothing downstream were not adapting to the changes in their fitness peaks fast enough. They lacked a pathway through the space to get to a new peak before all of their genes were selected out in total loss of diversity mode.


This message is a reply to:
 Message 4 by Faith, posted 05-24-2016 6:04 AM Faith has responded

Replies to this message:
 Message 8 by Faith, posted 05-24-2016 4:29 PM Modulous has responded

    
Faith
Member
Posts: 25264
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 8 of 455 (784847)
05-24-2016 4:29 PM
Reply to: Message 7 by Modulous
05-24-2016 11:59 AM


Fitness graphic
HBD posted that graphic quite a while ago and it's just as mystifying to me now as it was then, as mystifying as math.

Of course reality is messy, a lot messier than the descriptions I'm giving which are an attempt to streamline things down to essentials. There are conditions in which populations are stable, that is, NOT EVOLVING, which is what Hardy-Weinberg is describing. It is actually described AS not evolving. Gene flow of any sort also reverses the evolution I'm talking about, any addition of genetic diversity reverses it, but I've already said that.

Again, what I am focusing on is what happens when you are getting the active production of new phenotypes in reproductive isolation, because that is the clearest expression of evolution, usually believed to be THE way all life evolved from former life. But the fact is that this leads ultimately to genetic depletion, yes even with all the additions you can throw at it -- as long as new phenotypes are being produced you are getting a loss of genetic diversity.

What that graphic is designed to show I really have no idea, however.

I can agree that natural selection is one way genetic diversity is reduced as new phenotypes are expressed, making it one version of what I'm arguing. I just think it's clearer to emphasize the factor of reproductive isolation of a subpopulation, which is also brought about by natural selection but can be seen a lot more clearly in the example of geographic isolation.


This message is a reply to:
 Message 7 by Modulous, posted 05-24-2016 11:59 AM Modulous has responded

Replies to this message:
 Message 9 by PaulK, posted 05-24-2016 4:45 PM Faith has not yet responded
 Message 13 by Modulous, posted 05-24-2016 5:14 PM Faith has responded
 Message 23 by herebedragons, posted 05-24-2016 11:08 PM Faith has responded

    
PaulK
Member
Posts: 12759
Joined: 01-10-2003
Member Rating: 3.0


Message 9 of 455 (784848)
05-24-2016 4:45 PM
Reply to: Message 8 by Faith
05-24-2016 4:29 PM


Re: Fitness graphic
quote:

Again, what I am focusing on is what happens when you are getting the active production of new phenotypes in reproductive isolation, because that is the clearest expression of evolution, usually believed to be THE way all life evolved from former life. But the fact is that this leads ultimately to genetic depletion, yes even with all the additions you can throw at it -- as long as new phenotypes are being produced you are getting a loss of genetic diversity.

But it does not lead to "genetic depletion" because variation IS added. if you insist on only looking at the - relatively short - periods when diversity is declining you will not see the increases - but that doesn't mean they don't happen.

You have yet to offer any valid reason why diversity cannot be restored between speciation events. So what if it contradicts your ideas about evolution - I'll stick with the evidence that says that your ideas are wrong.


This message is a reply to:
 Message 8 by Faith, posted 05-24-2016 4:29 PM Faith has not yet responded

    
Faith
Member
Posts: 25264
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 10 of 455 (784849)
05-24-2016 4:52 PM
Reply to: Message 6 by PaulK
05-24-2016 7:55 AM


The endless dance of the wishful refutation
As Modulous has pointed out this is a bad argument for reasons that have been pointed out before - and which are implicit in the post you are answering. The times when a new species is forming is just a fraction of the lifetime of a successful species - and the rest of that time is when we expect the increases to occur.

And I've answered that I don't know how many times. You can get all the increases you want, taking all the time you want, it makes no difference to the point I'm making. There are certainly periods when active evolution is not occurring, most of the time no doubt.

But when evolution does occur, when new phenotypes are being formed out of all that increase, selected out of it, isolated out of it, then you are also getting the loss of genetic diversity I'm talking about, in the population that is evolving. The parent population may remain stable, not evolving, accumulating increase. I'm only talking about where evolution is occurring. The increases contribute only to a static condition of a population, you are only getting evolution when particular phenotypes are selected out to become the new characteristic of a new subpopulation, which can form in many ways, sometimes even within the parent population, but is most clearly seen when geographically isolated from the parent population.

(For good reason. Losses should slow when a species is increasing in population, and the number of mutations appearing is proportional to population size.)

Leaving aside the crucial question of just what sort of mutations are appearing in just what proportions to just what purpose, losses will slow when a population is genetically STABLE, increasing in numbers or not. If it's an evolving subpopulation, with new gene frequencies that have yet to be reproductively worked through the whole population, then the population will be increasing while the losses may be increasing at the same time by drift.

And, of course, this is one of the points that you haven't been able to refute.

You keep saying that and I keep saying you're wrong. I guess we can do this little dance endlessly. The last time I said it was in post 903 on the Science in Creationism thread.

ABE: I see you repeated your point in messager 9:

You have yet to offer any valid reason why diversity cannot be restored between speciation events.

I never said it couldn't be restored. What I'm saying is that it makes no difference because when the population is actively evolving all that increase gets pared down to favor a few phenotypes with the concomitant loss of genetic diversity. Even if you have a new trait all it can do is contribute to a new subspecies with reduced genetic diversity. The hopeful belief of the ToE that further variation is endless is brought to a halt at that point no matter what traits are involved.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 6 by PaulK, posted 05-24-2016 7:55 AM PaulK has responded

Replies to this message:
 Message 12 by PaulK, posted 05-24-2016 5:13 PM Faith has responded

    
caffeine
Member
Posts: 1283
From: Prague, Czech Republic
Joined: 10-22-2008
Member Rating: 5.7


Message 11 of 455 (784850)
05-24-2016 4:56 PM
Reply to: Message 1 by Genomicus
05-23-2016 7:59 PM


Nitpick alert
So both genetic drift and selection eliminate diversity in a population; both of these processes weed out alleles at a given locus.

Certain types of selection can work to maintain diversity, such as in cases of heterozygote advantage.

Not that this affects any of your argument, but I can't resist a good nitpick.


This message is a reply to:
 Message 1 by Genomicus, posted 05-23-2016 7:59 PM Genomicus has responded

Replies to this message:
 Message 17 by Genomicus, posted 05-24-2016 6:41 PM caffeine has acknowledged this reply

  
PaulK
Member
Posts: 12759
Joined: 01-10-2003
Member Rating: 3.0


(1)
Message 12 of 455 (784851)
05-24-2016 5:13 PM
Reply to: Message 10 by Faith
05-24-2016 4:52 PM


Re: The endless dance of the wishful refutation
quote:

And I've answered that I don't know how many times. You can get all the increases you want, taking all the time you want, it makes no difference to the point I'm making.

Simply stating your opinion is hardly sufficient - especially when that opinion seems to be obviously wrong. And refusing to consider the problems in your argument helps nobody (well it helps us win the argument but only because you disqualify yourself, which isn't really what I want)

quote:

Leaving aside the crucial question of just what sort of mutations are appearing in just what proportions to just what purpose, losses will slow when a population is genetically STABLE, increasing in numbers or not. If it's an evolving subpopulation, with new gene frequencies that have yet to be reproductively worked through the whole population, then the population will be increasing while the losses may be increasing at the same time by drift.

And there is a failure to think things through. In an increasing population a larger proportion of the offspring survive. That will reduce losses from drift and selection.

quote:

You keep saying that and I keep saying you're wrong.

You can keep saying it as long as you like, but that won't make it true. An opinion held against the evidence is not and never will be a successful refutation.

quote:

I never said it couldn't be restored. What I'm saying is that it makes no difference because when the population is actively evolving all that increase gets pared down to favor a few phenotypes with the concomitant loss of genetic diversity

Except that it does make a difference. Obviously it does. If genetic diversity is restored between speciation events we have no continuous decline in diversity, just a cycle between higher and lower levels of diversity.

Edited by PaulK, : Added a response to Faith's addition


This message is a reply to:
 Message 10 by Faith, posted 05-24-2016 4:52 PM Faith has responded

Replies to this message:
 Message 15 by Faith, posted 05-24-2016 5:34 PM PaulK has responded

    
Modulous
Member
Posts: 7407
From: Manchester, UK
Joined: 05-01-2005
Member Rating: 3.0


(1)
Message 13 of 455 (784852)
05-24-2016 5:14 PM
Reply to: Message 8 by Faith
05-24-2016 4:29 PM


Re: Fitness graphic
HBD posted that graphic quite a while ago and it's just as mystifying to me now as it was then, as mystifying as math.

It measures two traits that result in either faster speed or larger size. The further North a creature is in this place the faster it is. The further east it is the larger it is. A creature in the North East corner is very fast and very large. In the South West corner they are slow and small.

It's just a graph. But each point on the graph has a 'fitness' This is represented as height to create a landscape of peaks and valleys. Peaks are high fitness areas of the graph. Valleys are low fitness areas.

. There are conditions in which populations are stable, that is, NOT EVOLVING, which is what Hardy-Weinberg is describing.

No such conditions exist in reality. Instead the population reaches an evolutionary stable state. Drift and mutation are still happening and selection ensures any mutations that push organisms too far away from the peak will decrease in frequency relative to those closer.

It's not Hardy-Weinberg.

It is actually described AS not evolving.

Maybe, but its still part of evolution whether the phenotypes are changing or not.

Again, what I am focusing on is what happens when you are getting the active production of new phenotypes in reproductive isolation, because that is the clearest expression of evolution, usually believed to be THE way all life evolved from former life.

And this is shown in the video. It shows a species at minimal fitness with three different 'niches' or peaks in fitness open to them, they split into 3 groups and the variety of traits is not impacted for very long.

But the fact is that this leads ultimately to genetic depletion, yes even with all the additions you can throw at it -- as long as new phenotypes are being produced you are getting a loss of genetic diversity.

Addition followed by subtraction followed by addition....

I'm telling you that people that know the maths say you are wrong, you can't understand the maths.
I give you a video that explains the concept in terms of two traits using a visualisation rather than raw maths you say

What that graphic is designed to show I really have no idea, however.

It shows how a population's traits can change without losing genetic variabiality. Ie., it shows your intuitions on this subject are not to be trusted as it is as a fact, possible for a populations traits to evolve without losing genetic variability.

Whatever else you say, some of the evidence that you always beg for is being presented. As ever you claim not to understand it. But at the same time you claim to know better, without providing any reason.

I can agree that natural selection is one way genetic diversity is reduced as new phenotypes are expressed, making it one version of what I'm arguing. I just think it's clearer to emphasize the factor of reproductive isolation of a subpopulation, which is also brought about by natural selection but can be seen a lot more clearly in the example of geographic isolation.

That's fine, but it's important not to lose sight of the big picture by focussing only on a part of it. The visualisation in the video can be seen in terms of this. Look at the dynamic 3 peak example, the west most peak is the fittest way to be while living in the home area and the other two peaks represent other, isolated areas. That way the parent population is seen to evolve towards fitness, and the two daughter species evolve towards the other peaks - simulating the example you suggest. And as the visualisation of the mathematics shows, diversity is not lost intrinsically lost.

Look at the last example, not only is diversity not lost, it's gained. Diversity is represented by the area of the population in the graph.


This message is a reply to:
 Message 8 by Faith, posted 05-24-2016 4:29 PM Faith has responded

Replies to this message:
 Message 14 by Faith, posted 05-24-2016 5:23 PM Modulous has responded

    
Faith
Member
Posts: 25264
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 14 of 455 (784853)
05-24-2016 5:23 PM
Reply to: Message 13 by Modulous
05-24-2016 5:14 PM


Re: Fitness graphic
I'm telling you that people that know the maths say you are wrong, you can't understand the maths.

Actually, what I've seen of Dr. A's and Genomicus' math shows me that math is only as good as the person's conceptualization of the actual situation. If it's not conceptualized correctly then the best mathematical expression is nothing but garbage in garbage out. That's how increases in genetic diversity are proved by math, by simply assuming it's possible when it's not. The graphic in your post is no doubt a case of the same error.


It is actually described AS not evolving.

Maybe, but its still part of evolution whether the phenotypes are changing or not.

Oh yeah yeab yeah, EVERYTHING is evolution, yeah yeah, but that's why I keep saying ACTIVE evolution, because I'm describing the specific process where you are getting new characteristic phenotypes and ultimately a new subspecies based on those phenotypes. That is NOT happening in your stable population. And Hardy-Weinberg DOES describe a stable population that is NOT EVOLVING, showing that I'm using the term correctly and you are not.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 13 by Modulous, posted 05-24-2016 5:14 PM Modulous has responded

Replies to this message:
 Message 16 by Modulous, posted 05-24-2016 6:28 PM Faith has not yet responded
 Message 19 by Dr Adequate, posted 05-24-2016 9:15 PM Faith has not yet responded

    
Faith
Member
Posts: 25264
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 15 of 455 (784854)
05-24-2016 5:34 PM
Reply to: Message 12 by PaulK
05-24-2016 5:13 PM


Re: The endless dance of the wishful refutation
And there is a failure to think things through. In an increasing population a larger proportion of the offspring survive. That will reduce losses from drift and selection

But it can't reduce the original loss of genetic diversity from the new gene frequencies caused by the formation of the new subpopulation in the first place.


This message is a reply to:
 Message 12 by PaulK, posted 05-24-2016 5:13 PM PaulK has responded

Replies to this message:
 Message 28 by PaulK, posted 05-25-2016 12:55 AM Faith has responded

    
1
23456
...
31NextFF
Newer Topic | Older Topic
Jump to:


Copyright 2001-2015 by EvC Forum, All Rights Reserved

™ Version 4.0 Beta
Innovative software from Qwixotic © 2017