Register | Sign In


Understanding through Discussion


EvC Forum active members: 65 (9162 total)
1 online now:
Newest Member: popoi
Post Volume: Total: 915,818 Year: 3,075/9,624 Month: 920/1,588 Week: 103/223 Day: 1/13 Hour: 0/1


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   Extent of Mutational Capability
CRR
Member (Idle past 2243 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 192 of 279 (793896)
11-07-2016 2:38 AM
Reply to: Message 176 by Dr Adequate
11-02-2016 10:32 PM


Re: The Maths
Actually your (or sfs's) maths is wrong by several orders of magnitude.
By your argument the number of mutations in the human lineage should be 100 x average population size x 350,000. Say an average size of 1 million and you get ~3.5x10^13; which is larger than the size of the genome. If all those actually got fixed it would be error catastrophe!
But they don't all get fixed; only a very small proportion do. Genetic drift is far more likely to eliminate a neutral mutation than to fix it.
A large number of conceptions never even make it to birth if the mutations are lethal within the first 9 months so the a filter has already been applied to the types of mutations that appear in each succeeding generation. This is probably why so many of them appear to be near neutral.
A bit of thought should show you that the calculation is flawed. If we have fixed 18 million mutations in 350,000 generations that comes to 50 mutations being fixed per generation. The human genome is not varying at anything like this sort of rate. There are only a couple of mutations that are currently in the process of being fixed, one of which is adult lactose tolerance. It would also mean that there would be a great deal of variation in the human genome around the world, but it is actually notable for the low variation worldwide.
It appears you and sfs have been seduced by fortuitously good agreement between a wrong calculation and experimental results.

This message is a reply to:
 Message 176 by Dr Adequate, posted 11-02-2016 10:32 PM Dr Adequate has replied

Replies to this message:
 Message 195 by Dr Adequate, posted 11-07-2016 3:21 AM CRR has replied

  
CRR
Member (Idle past 2243 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 193 of 279 (793897)
11-07-2016 2:40 AM
Reply to: Message 186 by Dr Adequate
11-03-2016 9:37 AM


Re: The Maths
I have a real life so can't always respond immediately. That happened to be one I could tackle in some down time on the train. I have now responded to you so you don't need to feel left out.

This message is a reply to:
 Message 186 by Dr Adequate, posted 11-03-2016 9:37 AM Dr Adequate has not replied

  
CRR
Member (Idle past 2243 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 194 of 279 (793898)
11-07-2016 2:42 AM
Reply to: Message 190 by Pressie
11-04-2016 9:23 AM


Re: The Maths
Who has refuted ReMine's paper? No one that I know of.

This message is a reply to:
 Message 190 by Pressie, posted 11-04-2016 9:23 AM Pressie has replied

Replies to this message:
 Message 196 by Dr Adequate, posted 11-07-2016 3:22 AM CRR has not replied
 Message 198 by Pressie, posted 11-07-2016 6:18 AM CRR has replied

  
CRR
Member (Idle past 2243 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 199 of 279 (794234)
11-12-2016 1:50 AM
Reply to: Message 195 by Dr Adequate
11-07-2016 3:21 AM


Re: The Maths
Prematurely condescending? Quite possibly, but it is a good way to learn.
However there is still a hole in your argument. You calculation relies on the estimated number that would become fixed in infinite time, but we only have the supposed time since separation of the species.
The mean time to fixity is T(mean) ≈ 4 Ne generations, so for Ne>90,000 less than half of the potential would become fixed in 350,000 generations, and this number becomes progressively smaller with each generation. Conversely the population has generally increased over time. It is estimated that around 50—60 million people lived in the combined eastern and western Roman Empire in the 4th century AD and a similar number in China, plus the rest of the world. So no mutations occurring since 1AD would have been fixed in the human population.
Estimates of the population of the world at the time agriculture emerged in around 10,000 BCE have ranged between 1 million and 15 million so it is unlikely any of those have been fixed either.
So even neutral drift is is going to come up well short of the number of genetic differences between humans and chimps.
Do you have any evidence that a significant number of mutations are currently being fixed by genetic drift? Sufficient to be consistent with your proposition?
[edit]
According to ReMine "Using straightforward data and theory supplied by Motoo Kimura himself (the author of the neutral theory), this chapter shows that in ten million years a human-like population could, at best, substitute 25,000 expressed neutral mutations."
Edited by CRR, : as marked

This message is a reply to:
 Message 195 by Dr Adequate, posted 11-07-2016 3:21 AM Dr Adequate has replied

Replies to this message:
 Message 202 by Dr Adequate, posted 11-12-2016 11:32 AM CRR has replied
 Message 203 by Dr Adequate, posted 11-12-2016 1:21 PM CRR has replied
 Message 204 by caffeine, posted 11-12-2016 3:29 PM CRR has not replied

  
CRR
Member (Idle past 2243 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 200 of 279 (794235)
11-12-2016 2:09 AM
Reply to: Message 198 by Pressie
11-07-2016 6:18 AM


Re: The Maths
It was published in Journal of Creation, (Previously called TJ)
Volume 19, Issue 1, Published April 2005
The paper was submitted previously to the journal Theoretical Population Biology, where renowned evolutionary geneticists Warren J. Ewens and James F. Crow reviewed it, along with Alexey Kondrashov and John Sanford. They all acknowledged this paper is essentially correct in all matters of substance. However, Ewens and Crow rejected it from publication on the grounds that it is not sufficiently new or different from what was known by themselves and some of their colleagues in the 1970s.

This message is a reply to:
 Message 198 by Pressie, posted 11-07-2016 6:18 AM Pressie has replied

Replies to this message:
 Message 201 by Admin, posted 11-12-2016 7:22 AM CRR has not replied
 Message 208 by Pressie, posted 11-14-2016 5:42 AM CRR has not replied
 Message 209 by Pressie, posted 11-14-2016 5:51 AM CRR has not replied

  
CRR
Member (Idle past 2243 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 206 of 279 (794277)
11-13-2016 5:21 PM
Reply to: Message 202 by Dr Adequate
11-12-2016 11:32 AM


Re: The Maths
What in the world gave me that idea? Fixation - Wikipedia(population_genetics)
"Because the effect of natural selection is stipulated to be negligible, the probability at any given time that an allele will ultimately become fixed at its locus is simply its frequency {\displaystyle p} p in the population at that time. " Note ULTIMATELY.
Fixation - Wikipedia(population_genetics)#Probability_of_fixation
"Additionally, research has been done into the average time it takes for a neutral mutation to become fixed. Kimura and Ohta (1969) showed that a new mutation that eventually fixes will spend an average of 4Ne generations as a polymorphism in the population." Note AVERAGE.
Fixation - Wikipedia(population_genetics)#Time_to_fixation
At the time of separation when the clock is started much of the neutral mutation is already substantially established and you can't appeal to that to make up the gap.
I agree that population figures are not perfectly known, actually they are very rough estimates. However that works both ways since it also limits the precision of your calculations. To rescue your proposition you would have to assume that population numbers have been very small for most of the time to allow fixation to occur, and the evidence for that is scant.
A very rough estimate assuming an average population of 90,000 is that 1/2 of the first generation neutral mutations would have been fixed (T,mean=4Ne), and less in each succeeding generation so that perhaps 1/4 of potential mutations would have bee fixed in the 350,000 generations available.
Note that ReMine gave a much smaller figure than this. I'm not sufficiently across the maths of neutral theory to say if he is right or wrong.
Overall I believe you have failed to substantiate your claim that genetic drift alone is sufficient to explain the number of genetic differences between humans and chimps. Perhaps you can direct me to a published source to back up your position.

This message is a reply to:
 Message 202 by Dr Adequate, posted 11-12-2016 11:32 AM Dr Adequate has replied

Replies to this message:
 Message 207 by Dr Adequate, posted 11-13-2016 8:58 PM CRR has not replied

  
CRR
Member (Idle past 2243 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 220 of 279 (797469)
01-21-2017 8:40 PM
Reply to: Message 203 by Dr Adequate
11-12-2016 1:21 PM


Re: The Maths
Re Message 203 (I've been away for a while, had a hard disk fail, etc.)
That's an interesting example, and at first looks convincing.
Now in previous posts you were clearly talking about mutations that had been fixed in the population (# 195, 176) and I was arguing that there wasn't sufficient time to fix the required number.
In this example it is quite certain that the mutations I acquired independently will not be fixed in the population. It is equally certain that neither will the mutations independently acquired by my parents and passed on to me. Similarly with the from my grandparents (unless the population is extremely small). I can be pretty confident that until the number of my ancestors reaches at least the population size that none of them will have been fixed.
So on the basis of the example you have given I can conclude, as in #206, that only a portion of the potential mutations would have bee fixed in the 350,000 generations available. My ballpark estimate was but the actual portion would depend on the population history.

This message is a reply to:
 Message 203 by Dr Adequate, posted 11-12-2016 1:21 PM Dr Adequate has replied

Replies to this message:
 Message 224 by Dr Adequate, posted 01-21-2017 10:54 PM CRR has replied

  
CRR
Member (Idle past 2243 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 221 of 279 (797470)
01-21-2017 9:46 PM
Reply to: Message 217 by Taq
11-18-2016 11:12 AM


Look Sharp
I've seen the sharpshooter fallacy on Youtube where someone deals several cards then says "hey, I just achieved a 1/? event!"
We need to look not only at the probability of en event but also at the probabilistic resources available. The chance of a royal flush is small but enough people are playing poker that we can be sure it happens nearly every day.
On the other hand the chance of a bridge player getting dealt 13 cards of the same suit in order is so small (~1/10^60) it might never have happened, at least with a properly shuffled deck. (I hope I got my maths right)
Douglas Axe has estimated the chance of a chain of amino acids forming a functional protein is ~1 in 10^77. Denton estimates that no more than 10^40 proteins have ever existed on Earth. So even with those vast probabilistic resources the odds are fantastically small that a protein could have formed by chance. (obviously there are lots of assumptions and boundary conditions in any estimates of this kind). Pro-evolution researchers have done estimates and come up with the chance forming a functional protein as ~1 in 10^50. However that still leaves the chance at ~1/10^10 so it remains fantastically improbable. Note this avoids the sharpshooter fallacy because any functional protein would be success.
You can read more on this in Axe's "Undeniable".
Other work has been done on the evolvability of proteins and shows that even the probabilistic resources of the Earth and Billions of years are not enough. And that's assuming you have a heritable replicator to start with; otherwise you can't have evolution.

This message is a reply to:
 Message 217 by Taq, posted 11-18-2016 11:12 AM Taq has not replied

Replies to this message:
 Message 222 by Coyote, posted 01-21-2017 9:54 PM CRR has replied
 Message 225 by Dr Adequate, posted 01-21-2017 10:59 PM CRR has not replied
 Message 228 by caffeine, posted 01-22-2017 5:42 AM CRR has not replied
 Message 230 by Percy, posted 01-22-2017 10:02 AM CRR has not replied
 Message 231 by RAZD, posted 01-22-2017 10:36 AM CRR has not replied
 Message 232 by dwise1, posted 01-22-2017 4:30 PM CRR has not replied
 Message 233 by Coyote, posted 01-22-2017 4:52 PM CRR has not replied

  
CRR
Member (Idle past 2243 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 223 of 279 (797472)
01-21-2017 10:33 PM
Reply to: Message 222 by Coyote
01-21-2017 9:54 PM


Re: Look Sharp
Yes, if the cards can be in any order it changes the odds a lot. Bridge probably has a similar problem to whist in that you have to follow suit where possible and shuffling between hands might not be perfect.

This message is a reply to:
 Message 222 by Coyote, posted 01-21-2017 9:54 PM Coyote has not replied

Replies to this message:
 Message 229 by NoNukes, posted 01-22-2017 9:07 AM CRR has not replied

  
CRR
Member (Idle past 2243 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 226 of 279 (797475)
01-22-2017 12:24 AM
Reply to: Message 224 by Dr Adequate
01-21-2017 10:54 PM


Re: The Maths
Nevertheless Doc, you've managed to disprove your first position.

This message is a reply to:
 Message 224 by Dr Adequate, posted 01-21-2017 10:54 PM Dr Adequate has replied

Replies to this message:
 Message 227 by Dr Adequate, posted 01-22-2017 1:36 AM CRR has replied

  
CRR
Member (Idle past 2243 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 234 of 279 (797777)
01-27-2017 3:33 AM
Reply to: Message 227 by Dr Adequate
01-22-2017 1:36 AM


Re: The Maths
At Message 176 you posted a copy of sfs's post claiming that genetic drift could explain the difference between human and chimp genomes. At Message 195 you showed that you were talking about fixed mutations.
My argument was that taking mean time to fixity into account meant that less than half of the mutations could have been fixed in that time.
At Message 203 you presented what appeared to be the same argument from a different perspective. Once again I showed that not all of the mutations could possibly have been fixed by drift.
You are going to have to do a lot more to show that genetic drift is a plausible explanation for the genetic difference between humans and chimps.
Edited by Admin, : Replace message numbers with message links.

This message is a reply to:
 Message 227 by Dr Adequate, posted 01-22-2017 1:36 AM Dr Adequate has replied

Replies to this message:
 Message 235 by Dr Adequate, posted 01-27-2017 12:24 PM CRR has replied

  
CRR
Member (Idle past 2243 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 236 of 279 (798109)
01-31-2017 2:48 AM
Reply to: Message 235 by Dr Adequate
01-27-2017 12:24 PM


Re: The Maths
Well perhaps you will have to explain it again so that even I can understand it.

This message is a reply to:
 Message 235 by Dr Adequate, posted 01-27-2017 12:24 PM Dr Adequate has replied

Replies to this message:
 Message 237 by Pressie, posted 01-31-2017 7:12 AM CRR has not replied
 Message 238 by Dr Adequate, posted 01-31-2017 9:42 AM CRR has replied

  
CRR
Member (Idle past 2243 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 241 of 279 (798207)
02-01-2017 6:34 AM
Reply to: Message 238 by Dr Adequate
01-31-2017 9:42 AM


Re: The Maths
As you said Usually this will involve fixation in the two populations as a whole. We are talking about fixed mutations. What you haven't considered is population size and time to fixity.
So what would have been the population of chimps?
Millions of chimpanzees used to live throughout equatorial Africa from southern Senegal through Central Africa to western Tanzania. This is an area almost the size of the United States. Today, there are estimated to be merely 170,000-300,000 chimpanzees left in Africa, and their population is decreasing. rapidly.www.savethechimps.org/about-us/chimp-facts/
A female chimp will usually have her first child at around the age of 14 years old. A female chimp will not be fertile again until her child is fully weaned, so at most a female chimp will give birth every five years. She may have approximately 4-6 children in her lifetime. Chimp Life | Save the Chimps So the original estimate back at #176 of 20 years/generation is reasonable.
The average estimated population is ~235,000 so even today the mean time to fixity in chimps is 4Ne~=4*235,00=940,000 generations, or 18 million years.
In other words there has been time to accumulate the required number of mutations but not enough time to fix more than a small fraction.
How about the human population? Unless you assume dramatically small population sizes once again there has not been enough time to fix more than a small fraction. My previous estimate of ~25% was very generous; it would be much smaller.
So the conclusion is that the proposition that genetic differences between humans and chimps can be explained by genetic drift fails by at least an order of magnitude.

This message is a reply to:
 Message 238 by Dr Adequate, posted 01-31-2017 9:42 AM Dr Adequate has replied

Replies to this message:
 Message 243 by PaulK, posted 02-01-2017 7:00 AM CRR has replied
 Message 246 by Dr Adequate, posted 02-01-2017 9:58 AM CRR has replied

  
CRR
Member (Idle past 2243 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 242 of 279 (798208)
02-01-2017 6:35 AM
Reply to: Message 240 by Dr Adequate
01-31-2017 9:41 PM


Re: The Maths
btw. Thanks for what you've taught me.

This message is a reply to:
 Message 240 by Dr Adequate, posted 01-31-2017 9:41 PM Dr Adequate has not replied

  
CRR
Member (Idle past 2243 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 244 of 279 (798224)
02-01-2017 8:20 AM
Reply to: Message 243 by PaulK
02-01-2017 7:00 AM


Re: The Maths @PaulK
Taking into account the diversity which existed before the split is not going to save the situation. You would have to consider the amount that were "partially fixed" but common and the effect that would have. Then you have to consider minimum time to fixity and that the mean time to fixity can not be linearly extrapolated to 100% mutations fixed.
Of course you can make the proposition work if you make enough dubious assumptions along the way.
As well as the 35 million base pair differences there are also over 700 non-homologous genes to be explained, the increase in brain mass, as well as the obvious ability to walk on two feet and talk.

This message is a reply to:
 Message 243 by PaulK, posted 02-01-2017 7:00 AM PaulK has replied

Replies to this message:
 Message 245 by PaulK, posted 02-01-2017 8:45 AM CRR has not replied
 Message 247 by Dr Adequate, posted 02-01-2017 10:04 AM CRR has not replied

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2023 by EvC Forum, All Rights Reserved

™ Version 4.2
Innovative software from Qwixotic © 2024