Register | Sign In


Understanding through Discussion


EvC Forum active members: 63 (9159 total)
5 online now:
Newest Member: K.Rose
Post Volume: Total: 914,745 Year: 2,002/9,624 Month: 1,435/567 Week: 43/338 Day: 2/41 Hour: 0/0


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   Mutations Confirm Common Descent
sensei
Member
Posts: 467
Joined: 01-24-2023


Message 76 of 106 (907150)
02-19-2023 11:11 AM
Reply to: Message 75 by Theodoric
02-19-2023 10:55 AM


Re: Hubris much
Why are you even talking when nothing but shit is coming out of your mouth?

This message is a reply to:
 Message 75 by Theodoric, posted 02-19-2023 10:55 AM Theodoric has replied

Replies to this message:
 Message 78 by Theodoric, posted 02-19-2023 1:00 PM sensei has replied

  
Dredge
Member
Posts: 2850
From: Australia
Joined: 09-06-2016


Message 77 of 106 (907160)
02-19-2023 12:03 PM
Reply to: Message 71 by AZPaul3
02-18-2023 5:00 PM


APauling666 writes:
If I recall the numbers right I think we share about 60% of our gene pool with onions and other plants. Give or take.
With me, that figure is considerably higher ... my DNA has been analysed as 85% potato and 14% banana.

This message is a reply to:
 Message 71 by AZPaul3, posted 02-18-2023 5:00 PM AZPaul3 has not replied

  
Theodoric
Member
Posts: 8926
From: Northwest, WI, USA
Joined: 08-15-2005
Member Rating: 3.4


Message 78 of 106 (907167)
02-19-2023 1:00 PM
Reply to: Message 76 by sensei
02-19-2023 11:11 AM


Re: Hubris much
So are you in middle school? Does your pastor and mom know you swear like that?

What can be asserted without evidence can also be dismissed without evidence. -Christopher Hitchens

Facts don't lie or have an agenda. Facts are just facts

"God did it" is not an argument. It is an excuse for intellectual laziness.

If your viewpoint has merits and facts to back it up why would you have to lie?


This message is a reply to:
 Message 76 by sensei, posted 02-19-2023 11:11 AM sensei has replied

Replies to this message:
 Message 79 by sensei, posted 02-20-2023 6:49 AM Theodoric has replied

  
sensei
Member
Posts: 467
Joined: 01-24-2023


Message 79 of 106 (907192)
02-20-2023 6:49 AM
Reply to: Message 78 by Theodoric
02-19-2023 1:00 PM


Re: Hubris much
All you do here is troll

This message is a reply to:
 Message 78 by Theodoric, posted 02-19-2023 1:00 PM Theodoric has replied

Replies to this message:
 Message 80 by Theodoric, posted 02-20-2023 8:11 AM sensei has replied

  
Theodoric
Member
Posts: 8926
From: Northwest, WI, USA
Joined: 08-15-2005
Member Rating: 3.4


(1)
Message 80 of 106 (907200)
02-20-2023 8:11 AM
Reply to: Message 79 by sensei
02-20-2023 6:49 AM


Re: Hubris much
What are your qualifications and credentials to think you can overthrow all of the scientific thought of the last 2 centuries? If you want to be taken seriously you need to show that you know what you are discussing. Why should the world's leading scientists listen to you?
Do you have the qualifications? Is it religious hubris? Did your mommy and pastor tell you that you could?

What can be asserted without evidence can also be dismissed without evidence. -Christopher Hitchens

Facts don't lie or have an agenda. Facts are just facts

"God did it" is not an argument. It is an excuse for intellectual laziness.

If your viewpoint has merits and facts to back it up why would you have to lie?


This message is a reply to:
 Message 79 by sensei, posted 02-20-2023 6:49 AM sensei has replied

Replies to this message:
 Message 83 by sensei, posted 02-21-2023 1:05 PM Theodoric has not replied

  
Taq
Member
Posts: 9840
Joined: 03-06-2009
Member Rating: 4.5


Message 81 of 106 (907252)
02-21-2023 11:21 AM
Reply to: Message 70 by sensei
02-18-2023 4:38 PM


sensei writes:
How much of our human DNA are shared among all people today?
I think the average is somewhere around 99.5%.
And how much of it is shared with other primates?
Depends on the primate. We share around 96.5% of our DNA with chimps if you factor in indels, and they are our closest relatives. Out of all primate species chimps share the most DNA with us. Conversely, chimps share more DNA with humans than they do any other primate species.
I know I can look it up, but I'm asking you, so we can be sure that there is no disagreement on the numbers and you cannot accuse me of making anything up.
Are you going to address the evidence in the beginning of the thread, or is this just a gotcha post?

This message is a reply to:
 Message 70 by sensei, posted 02-18-2023 4:38 PM sensei has not replied

  
Taq
Member
Posts: 9840
Joined: 03-06-2009
Member Rating: 4.5


Message 82 of 106 (907253)
02-21-2023 11:22 AM
Reply to: Message 74 by sensei
02-19-2023 5:57 AM


sensei writes:
I'm hoping to get a more accurate number and run different comparison methods.
Can you address the evidence presented at the beginning of this thread?

This message is a reply to:
 Message 74 by sensei, posted 02-19-2023 5:57 AM sensei has replied

Replies to this message:
 Message 84 by sensei, posted 02-21-2023 1:38 PM Taq has replied

  
sensei
Member
Posts: 467
Joined: 01-24-2023


(1)
Message 83 of 106 (907284)
02-21-2023 1:05 PM
Reply to: Message 80 by Theodoric
02-20-2023 8:11 AM


Re: Hubris much
Keep trolling. I do my research, I do not need your permission.

This message is a reply to:
 Message 80 by Theodoric, posted 02-20-2023 8:11 AM Theodoric has not replied

  
sensei
Member
Posts: 467
Joined: 01-24-2023


(1)
Message 84 of 106 (907295)
02-21-2023 1:38 PM
Reply to: Message 82 by Taq
02-21-2023 11:22 AM


It seems like a good argument for common ancestry of primates, ngl. Though I haven't looked at all of your sources yet, you made a convincing argument.
You got my attention, and if I can find data to verify independently as much as I can, we can discuss this further, if you wish.
Right now, what I was thinking, is if we look at humans only, for example, there is a percentage that is shared among all humans.
If we are in an ongoing evolution process, there is a portion of DNA in humans that is currently not shared among all individuals.
Depending on the part of DNA we are looking at, it can be anywhere between 0 and 1 fraction of total human population. For example DNA sequence for blue eyes may be around 8%, or perhaps more, as it may be present but not dominant.
Some of these varying DNA could reach 100% at some point and would promote to being fixed, shared in whole population.
From the data, we should be able to extract the rate of mutations and the fraction that fluctuate through the space between 0 and 1. We would need to make some assumptions on how much one sequence may have some beneficial advantages or not over other sequences. Then, hopefully, the model will give some predictions with margins of error, on how much different primate species should have in common. But I need to work out the model first and put in our data.

This message is a reply to:
 Message 82 by Taq, posted 02-21-2023 11:22 AM Taq has replied

Replies to this message:
 Message 85 by Taq, posted 02-21-2023 1:54 PM sensei has replied

  
Taq
Member
Posts: 9840
Joined: 03-06-2009
Member Rating: 4.5


(1)
Message 85 of 106 (907299)
02-21-2023 1:54 PM
Reply to: Message 84 by sensei
02-21-2023 1:38 PM


sensei writes:
If we are in an ongoing evolution process, there is a portion of DNA in humans that is currently not shared among all individuals.
With as many living humans as there are right now (~7 billion) it is almost guaranteed that every non-lethal mutation exists somewhere in the human population, even if it is just in a few individuals. Therefore, nearly all DNA is not shared amongst all humans. Only a tiny fraction of all bases in the human genome are going to be shared by all humans.
From the data, we should be able to extract the rate of mutations and the fraction that fluctuate through the space between 0 and 1.
I don't think it is that easy because you would need human populations that are not interbreeding with one another. However, the math does exist:
quote:
Each of the 2N genes in the original population has an equal chance of being the lucky one
Any one gene in the population, therefore, has a 1/( 2N ) chance of eventual fixation by random drift (and a ( 2N -1)/( 2N ) chance of being lost by it). Because the same argument applies to any gene in the population, it also applies to a new, unique, neutral mutation.
When the mutation arises, it will be one gene in a population of 2N genes at its locus (i.e., its frequency will be 1/(2/N )), and it has the same 1/(2N ) chance of eventual fixation as does every other gene in the population. It is therefore most likely that the mutation will be lost but it does have a small chance of success. The probability that a neutral mutation will eventually be fixed is 1/(2N ).
The rate of evolution equals the probability that a mutation is fixed, multiplied by the rate at which mutations appear. We define the rate at which neutral mutations arise as µ per gene per generation. (µ is the rate at which new selectively neutral mutations arise, not the total mutation rate. We are here considering only those mutations that are neutral.) At each locus, there are 2N genes in the population: the total number of neutral mutations arising in the population will be 2N µ per generation.
The rate of neutral evolution is 1/(2N ) x 2Nµ = µ. It is equal to the neutral mutation rate.
Evolution - Random events in population genetics
One of the difficulties could be the mutation rate which won't necessarily stay the same over a given period of time. Some papers suggest that the mutation rate in chimps is 50% higher than that in humans, as one example:
quote:
Mutations generate genetic variation and are a major driving force of evolution. Therefore, examining mutation rates and modes are essential for understanding the genetic basis of the physiology and evolution of organisms. Here, we aim to identify germline de novo mutations through the whole-genome surveyance of Mendelian inheritance error sites (MIEs), those not inherited through the Mendelian inheritance manner from either of the parents, using ultra-deep whole genome sequences (>150-fold) from a chimpanzee parent-offspring trio. We identified such 889 MIEs and classified them into four categories based on the pattern of inheritance and the sequence read depth: de novo single nucleotide variants (SNVs), [ii] copy number neutral inherited variants, [iii] hemizygous deletion inherited variants, and [iv] de novo copy number variants (CNVs). From de novo SNV candidates, we estimated a germline de novo SNV mutation rate as 1.48 × 10−8 per site per generation or 0.62 × 10−9 per site per year. In summary, this study demonstrates the significance of ultra-deep whole genome sequencing not only for the direct estimation of mutation rates but also for discerning various mutation modes including de novo allelic conversion and de novo CNVs by identifying MIEs through the transmission of genomes from parents to offspring.
Direct estimation of de novo mutation rates in a chimpanzee parent-offspring trio by ultra-deep whole genome sequencing | Scientific Reports

This message is a reply to:
 Message 84 by sensei, posted 02-21-2023 1:38 PM sensei has replied

Replies to this message:
 Message 86 by sensei, posted 02-21-2023 6:29 PM Taq has replied

  
sensei
Member
Posts: 467
Joined: 01-24-2023


Message 86 of 106 (907350)
02-21-2023 6:29 PM
Reply to: Message 85 by Taq
02-21-2023 1:54 PM


Well, I found sources from around 2018-2021, stating that 99.9% was shared among all humans. But you are suggesting it's lower, that in fact, for the vast majority of all DNA parts, if we'd pick one, there is likely to be one or a few individuals having a mutated sequence for that part?
Besides changes in mutation rates, population sizes are also changing. I hope I can find some rough estimates of population sizes throughout most of primate history.

This message is a reply to:
 Message 85 by Taq, posted 02-21-2023 1:54 PM Taq has replied

Replies to this message:
 Message 87 by Taq, posted 02-21-2023 6:33 PM sensei has replied
 Message 90 by Phat, posted 02-22-2023 10:47 AM sensei has replied

  
Taq
Member
Posts: 9840
Joined: 03-06-2009
Member Rating: 4.5


Message 87 of 106 (907352)
02-21-2023 6:33 PM
Reply to: Message 86 by sensei
02-21-2023 6:29 PM


sensei writes:
Well, I found sources from around 2018-2021, stating that 99.9% was shared among all humans.
I was going from memory, so if there are published papers with 99.9% then go with that.
for the vast majority of all DNA parts, if we'd pick one, there is likely to be one or a few individuals having a mutated sequence for that part?
Yes. If you pick a specific base from a specific person, there will be at least a handful of people with a different base at that position as long as it isn't a lethal mutation. This is because 7 billion births is enough to create every possible mutation in the human genome several times over.
Besides changes in mutation rates, population sizes are also changing.
For the idealized neutral mutation rate the size of the population doesn't matter. All that matters is the mutation rate. If you look at the equation the population size cancels out in the equation.

This message is a reply to:
 Message 86 by sensei, posted 02-21-2023 6:29 PM sensei has replied

Replies to this message:
 Message 88 by sensei, posted 02-22-2023 3:31 AM Taq has replied

  
sensei
Member
Posts: 467
Joined: 01-24-2023


(1)
Message 88 of 106 (907369)
02-22-2023 3:31 AM
Reply to: Message 87 by Taq
02-21-2023 6:33 PM


So the 99.9% is if we would pick two random and unrelated individuals, they would share about 99.9% of their genetic markup.
Population size does matter for fixation rate, I suppose.
Maybe it's easiest to start a model for fixed population size n and mutation rate mu. And even start with a population where all DNA is identical. Then one question would be, after m generations, how many mutated bases (or genes) would have spread through 0.1 and 0.2 fraction of the population? And then same for 0.2 and 0.3, or more generally, between p and q.
Should we only consider point mutations for simplification? As I don't think it would affect the results much. But there are several types of mutations, and model may get too complicated.

This message is a reply to:
 Message 87 by Taq, posted 02-21-2023 6:33 PM Taq has replied

Replies to this message:
 Message 89 by Taq, posted 02-22-2023 10:40 AM sensei has replied

  
Taq
Member
Posts: 9840
Joined: 03-06-2009
Member Rating: 4.5


Message 89 of 106 (907370)
02-22-2023 10:40 AM
Reply to: Message 88 by sensei
02-22-2023 3:31 AM


sensei writes:
So the 99.9% is if we would pick two random and unrelated individuals, they would share about 99.9% of their genetic markup.
It is an an average between any two human beings. Some will share more (such as close relatives) and some will share less.
Then one question would be, after m generations, how many mutated bases (or genes) would have spread through 0.1 and 0.2 fraction of the population? And then same for 0.2 and 0.3, or more generally, between p and q.
This article is probably right up your alley:
What Genetics Says About Adam and Eve - Article - BioLogos
It discusses the distribution of rare and common mutations and how they play out in a population over time.
Should we only consider point mutations for simplification?
That is a simplification that many use because it is difficult to calculate a meaningful indel or recombination rate. Substitutions are much more common and occur at a rate that is more clock like.

This message is a reply to:
 Message 88 by sensei, posted 02-22-2023 3:31 AM sensei has replied

Replies to this message:
 Message 91 by sensei, posted 02-23-2023 2:16 PM Taq has replied

  
Phat
Member
Posts: 18138
From: Denver,Colorado USA
Joined: 12-30-2003
Member Rating: 1.1


Message 90 of 106 (907372)
02-22-2023 10:47 AM
Reply to: Message 86 by sensei
02-21-2023 6:29 PM


Sensei seems sensible
I like you, Sensei. You seem to want to actually have a conversation and exchange ideas with people...at least you are so doing with Taq. Good job!

This message is a reply to:
 Message 86 by sensei, posted 02-21-2023 6:29 PM sensei has replied

Replies to this message:
 Message 93 by sensei, posted 02-24-2023 3:43 AM Phat has replied

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2023 by EvC Forum, All Rights Reserved

™ Version 4.2
Innovative software from Qwixotic © 2024