Well it surprises me to hear you say so. Especially since when we met on BioLogos I was dragged into a discussion on human evolution when I really wanted to talk about theology, much like this situation, and it was you who convinced me that even though these gene differences existed they were not remarkable given modern calculations of human mutation rates. I was assuming rates based on data from around the time I quit teaching public school science and was asking “how could this amount of change occur in the time they say it did?” You never challenged the idea that humans have hundreds of genes chimps don’t have and vice versa. Just that it was problematic for human evolution.
The new research takes into account the possibility for multiple copies of genes and that the number of copies can differ between species, even though the gene itself is the same or nearly so. “You have to pay attention to more than just the genes that are shared,” says geneticist Matthew Hahn of Indiana University, Bloomington, lead author of the new report. Researchers believe that additional copies of the same gene allow evolution to experiment, so to speak, finding new functions for old genes.
And…
The group estimated that humans have acquired 689 new gene duplicates and lost 86 since diverging from our common ancestor with chimps six million years ago. Similarly, they reckoned that chimps have lost 729 gene copies that humans still have.
Exactly. The longer clips are just statements about the number of copies of each gene. From parents to children there is high variability in copy number already. CNVs expand and shrink all the time. They technically are increases of information too, and a very easy way to change function.
If what they are calling duplicates were still exactly the same as the original I would agree with you. But is that what they are saying? They either are made or become, different genes with different functions. It says as much at the end of my first quotes. The article cites an example of a “gene family” where humans have 15 genes “duplicates” and chimps only six. It is not like you are going to find a group of humans with six and a tribe of chimps with 15. And those genes are called “duplicates” but you know they are not identical, just in the same family. Like it says in this one….
Modern measurements by direct sequencing indicate a divergence due solely to base substitution in single-copy DNA of 1.25% (4, 5). Part of the reason our estimate of 1.4% is larger is because repeated sequences are included, and they diverge somewhat more than typical single-copy sequences (4). Some of this difference is due to the CpGs present in Alu repeats, which are mutated at 10 times the rate of other nucleotides.
When they do, they would be represented by the blue line moving up from old form to the new on my graph. But I still maintain they represent a different process than changing the frequency of existing alleles and that therefore rates of change calculated based on the first kind of event should not be used to suggest a rate of change possible by adding novel new information to the genome.
@gbrooks9 I should have tagged you in my post above. I think you are seeing duplicates as “exact duplicates” when I think the papers are talking about something else going on- the extra genes being a natural lab for the organism to try new things. My point is that this is a different process than changing the frequency of existing alleles of already present genes in a population and that rates of evolution inferred from that process should not be a valid way of calculating a possible rate of change for a process whereby truly novel info is introduced. And notice I am not even saying that it doesn’t happen. I am saying what is gleaned about the first process is not evidence for the power of the second.
Functional genes only have a limited number of alleles in any given population, right? Take a sample of 1,000 people in London, or Paris. How many alleles will there be in the average functional gene? Way less than 1,000 right? Even if my kids get some mutations in my set, they are not unique mutations. Someone else has the same point mutation. That’s not adding new genetic info to the population. It is still dealing a card that was already in the deck.
In a six sentence statement in which two of the sentences were questions and the last four were leading to the same single point “quite a bit” was incorrect? Look I think we have wasted enough of each others time on this. I still think I have a point, you don’t see it and think I have it all wrong but are vague about why. I’m not going to take a course in genetics, I read the text book on it years ago just fine and I am citing studies from people who probably teach it. If someone on this board wants to go to the trouble to really explain why I have it wrong I’ll listen. Otherwise let’s just move on to something more productive.
A gene is a locus or factor… which can have just one allele or a hundred.
But there is usually only one allele in 23 chromosomes… with another allele expressed in the other set of 23 chromosomes.
So I think you meant how many alleles are there for the average gene.
If there are additional copies of genes in a chromosome… there could be additional alleles not being expressed.
The amount of information all this represents is almost impossible to determine… since you never know which string of genetic molecules will suddenly produce an effect!
I do. Say that a trait, eye color perhaps, is determined by three genes. In a population of 10,000 how many different alleles are floating around for those three loci? What if the first of the three genes has five different alleles, the second 7 and the third 6. That’s 126 possible combinations. Even if my genetic info does not copy correctly so that one of my children gets a point mutation, some mutations tend to crop up more often than others. Perhaps the rest just ruin the function of the gene so that even though there are 100 ways to turn it off, functionally it is the same, the gene is turned off. So there are only so many possibilities. If the change that my kid gets is just another one of those seven alleles already in locus #2 then it is not adding information to the genome of the population.
If there is gene duplication with a new gene that changes function, that would not be a part of the red wave or zone. That would be a movement on the blue line in my graph. It is something different than what is measured on the red line or zone which represents all the “hands” or phenotypes that can be dealt with existing genetic “cards”. The blue line would represent “new cards” being added or removed from the “deck” of genetic information in that population. All I am trying to point out is that there are TWO kinds of change going on here. One is the expression from reshuffling of existing alleles and the other is novel alleles or new genes being added/lost. I am baffled and frustrated that I can’t seem to make that nuanced but well-within-the-capabilities of the minds-we-have-here principle understood.
If there are 3 active gene sites… it is quite likely that there is a unique set of alleles (or just one allele) PER GENE.
Your hypothetical example sounds more like 2 active genes with 1 gene an inactive copy.
Because gene behavior is so varied and at times baffling… it is usually better to provide a REAL example… so that real world consequences can be analysed.
In one person yes, but not in the whole population. There may be a number, let’s say seven, different alleles floating around for that locus in that population. Are you saying that in a population of 10,000 individuals at each given locus each member of the population would likely have an allele whose sequences are not shared by any other member of the population? I think that’s way overstating typical diversity especially in humans.
You just can’t make hypothetical rules for Genes. As it is … a real world situation can have ONE RULE… and then a second situation with exactly the same circumstances can BREAK the rule.
So… generally speaking… until you find an exception… 3 active gene sites in 23 human chromosomes are most likely going to have THREE different sets of alleles… with only one set working at only one gene.
I’m not sure what you think you can establish if it is some other way… no doubt somewhere, for some species, for some trait… it is as you say it could be.
I am not making rules. I am giving an example using what I think are reasonable numbers. And your statement makes no sense to me. We are talking past one another.
On any one person yes, but I kept trying to get someone, anyone, to see, with a marked lack of success, that in a given population of humans (or any animal really) you are going to have multiple alleles floating around for the same site. I may only have 2 of the seven which exist in the population in my DNA, or maybe even just one if I am homozygous for that locus, but the others will be present in other members of my community.
It is pointless to again explain what I am saying means if you do not grasp what I am saying. And I can tell from your statements that you do not. I wish some other member of this board could come on here and see if I am really just not communicating well or if you two are just really really really locked into a certain way of interpreting what I am saying so strongly that you cannot comprehend what I am actually trying to say. Who shall we ask to come look at it?
They have already had a go at it. How about @Zachary_Ardern and @AJRoberts and @Ashwin_s ? If none of those three can make heads or tails of what I am trying to say, then I must concede the problem is mine.
@anon46279830 you are trying to make a fine distinction with fuzzy language and a tenuous grasp on what you are describing. We can’t read your mind, and you don’t have the language or understanding to communicate clearly. Your time is better spent trying to understand what biologists are saying instead of asking us to make sense of what you are saying.