Response to Dr. Zach Hancock
by Donny Budinsky
This is a reply to several comments (the relevant ones) made by Population Geneticist Dr. Zach Hancock to my article (1) on mutation rates and fixation.
The Response
Zach says:
“This first article is remarkably bad.”
My response:
Thanks Zach. How sweet of you. But from my experience, when a proponent of common descent calls a creationist article bad, it’s usually a reliable sign it’s a great article! We’ll see if you can back up your opinion of the article.
Zach says:
“We have direct evidence of strong purifying selection on mitochondrial genomes. I’m a little baffled, anyone would say otherwise.”
My response:
Zach, there is selection in mitochondrial genomes. But the selection that takes place does not work to change the mutation and fixation rate by any significant degree. It is a fact that the entirety of the mtDNA is functional—and it is also a fact that the great majority of mutations arising in this small, circular chromosome are neutral. Since this mtDNA is functional, the mutations happening in it are essentially nearly neutral. They are faintly deleterious. What this means is most mutations occurring in the mtDNA are collected in a ratchet-like manner. They build up over time unchecked by selection since selection is restricted in what it can do.
Yes, you can provide some evidence of selection, but this is mainly for detrimental mutations (those damaging enough for selection to see). The rule for selection is constraint. The exceptions don’t overturn the rule. Selection is constrained in its authority to act on the mitochondrial chromosome for many reasons. Its unique pattern of inheritance (maternal line only) is one key reason. Additional reasons include its lack of recombination, a high mutation rate, limited DNA repair enzymes, and high copy number within a cell (allowing for heteroplasmy) Selection pressure is essentially directed towards sustaining function. Since most mutations are effectively neutral, they won’t be damaging enough to adversely impact reproduction. All these reasons combined means harmful mutations will still be passed on regardless of selection tensions doing their best to eliminate them.
I am baffled that you don’t understand this. I believe it is because you have potent evolutionary presuppositions going into your interpretation of the data. Don’t misunderstand me. I am not saying there is no selection on mtDNA. It is true that overall selection on this unique part of the genome is weak, it does not mean there is no selection at all. If mutations arise in specific genes that encode essential proteins for the function of the mitochondrial DNA, and these mutations are high-impact, these areas of the genome are likely to experience robust purifying selection. You require strong selection, or unrealistic amounts of selection, to get what you need from the data to sustain your evolutionary fable.
Zach says:
“The mitochondrial genome is almost entirely functional (most of it protein-coding), and it performs one of the most important functions for the cell (respiration), if there were no purifying selection we would all be dead already.
My response:
I expect better from you, a PhD Population Geneticist. You are demonstrating my point exactly! The fullness of the mitochondrial genome is functional. It is also a fact that the majority of mutations occurring in this uni-parentally inherited genome are neutral. By neutral, we mean these mutations don’t have considerable enough of an effect on the overall function of the mitochondria for selection to see. This means selection won’t be capable of dealing with them—until it’s too late. You’re right about the “we would all be dead already”. This is exactly where our species is heading. Let’s explore this.
Mutation accumulation in both the autosomal nuclear DNA and haploid chromosomes put shelf lives on genomes. The mtDNA also experiences a much faster mutation rate than the nuclear DNA. This rate is about 100-fold higher! It is also a much smaller chromosome (16,569 base pairs). The reason we aren’t actually “dead already” is because we haven’t been accumulating mutations for 10s of thousands of years. There should be much more diversity in this chromosome if it were as old as apologists of evolution assert (2, 3).
The mitochondrial chromosome is not as old as evolutionary scientists would have us believe. We’ve only been storing mutations for 4500 years since the Flood Bottleneck. Individual rust spots on a car are not fatal to the car but over time, they damage the car to the point where the car is no longer practical. An alternative example is a book. A book undergoing single typographical errors over time will still be legible. It will still serve its intention. But after enough spelling mistakes amass, the book will descend into nonsense and will no longer be useable. This is what we see in genomes. Therefore, a mutation can be nearly neutral (slightly deleterious) in the mitochondrial chromosome and yet remain unselectable.
Zach says:
“Two lines of evidence for purifying selection in the mitochondria: 1) inferential, based on patterns of nonsynonymous to synonymous substitutions; 2) direct, observational evidence of the purging of a harmful allele introduced into a mitochondria experimentally over ~generations.
My response:
Zach, you are again missing the point. The responses we are receiving from the most accomplished the evolutionist camp has to offer (PhD Biologists and Geneticists) are truly a gift to Creation Science. Yes—even considering the reality that most mutations occurring in mitochondrial DNA are considered neutral or nearly neutral (not enough of an effect on the function of the mitochondria to activate the effects of selection), there are some mutations (an insignificant amount) that are harmful enough to not be considered effectively neutral and will be removed by selection. And even that is determined upon several factors (their location and level of heteroplasmy within a cell).
As I stated earlier, and will restate due to its importance, selection is much more constrained than evolutionary scientists such as Dr. Hancock want to acknowledge. For instance, selection on the mitochondrial chromosome is particularly restrained because of its distinctive inheritance (maternal only) but also the incidence of various copies of mtDNA within a cell. This leads to a phenomenon called heteroplasmy (just mentioned above). Heteroplasmy decreases the efficiency of cleansing selection (which Zach needs a sizable amount of) against negative mutations. This means harmful mutations will endure within mitochondrial genomes to an even greater extent than what we see in nuclear DNA.
I can only hope the rest of your lengthy comment deals with my article.
Zach says:
“if there were no selection,”
My response:
I never said there was no selection.
Zach says:
“, then the ratio of nonsynonymous (mutations that alter the amino acid that is coded for, which is almost always harmful) to synonymous (mutations that don’t alter the amino acid due to the redundancy of the genetic code) should be ~1. In fact, it should be slightly above 1, since there are more ways to have a nonsynonymous substitution than a synonymous one.”
My response:
Thanks for all that Zach. I’ll say it again: you are confirming my point exactly. The amount of selection in the mitochondrial genome is trivial. This is why even considering the trivial amount of selection taking place (large mutations), mutations are still accruing in the Y and mitochondrial chromosomes in a ratchet-like style. The rare exemptions don’t overturn the rule. You can point to the uncommon exceptions all day and all it does is reinforce my points.
You require much more selection to get evolutionary time. The no selection zone is significantly expanded when you consider realistic boundaries. There are mutations in even the most conserved protein coding regions of the mtDNA. Mutations still gather in highly functional territories of genomes. It’s not that selection sees every mutation accumulating in the mtDNA. No—selection is very constrained.
Purifying selection is still not powerful enough to remove the compulsory number of mutations for evolution to be true. You want your cake and eat it too. You want to invoke strong purifying selection and admit the majority of mutations in the mtDNA are neutral. Seemingly, those mutations need to be strictly neutral. But the idea that most mutations are exactly neutral doesn’t fit reality. Just because they aren’t harmful enough for selection to see doesn’t mean they aren’t somewhat deleterious. We also see genetic diversity expanding today—but with the amount of diversity being right in line with Creationist expectations. Apparently, selection isn’t working too well.
Final Comments
Zach has a few more things to say but simply continues along the same lines as his preceding remarks. He cites a 2014 paper (Ma et al.) where they inserted fruit fly embryos with various mitochondria, some of which had mutations that made them vulnerable to temperature.
Zach says:
“Almost all of the temperature-sensitive mitochondria were purged from the population in only ~10 generations. That’s direct evidence of purifying selection.”
My response:
This is desperate. It reveals the powerful evolutionary based presuppositions these evolutionary scientists have going into any counter to Biblical Creationists. We aren’t saying there is no selection taking place in the mtDNA. The question is: how much selection is taking place? Its not much. Selection removes the most harmful mutations and does nothing to prevent the accumulation of effectively neutral mutations. Biblical Creationists can account for some selection while maintaining a realistic view of how limited selection is. It is largely powerless to stop the neutral mutations accumulating in the highly functional mitochondrial chromosome.
The Biblical model of ancestry we defend also has a Flood Bottleneck 4500 years ago where the earth restarts with 8 people, and 3 reproducing couples. People don’t actually spread out until the tower of Babel event, which could have been 300-500 years after the Flood. This means we would have a period of time before people spread out into all parts of the globe and rapidly expand in population numbers where fixation rates were much faster. This is one of the reasons why the Biblical Creation model also has a balancing out effect of the mutation to fixation rates. I could go into much more detail on this important point, but that is not the focus of this article.
Zach ends by saying:
“Bacteria get along just fine, after all, and I start every popgen course by walking through the math of selection on haploid genomes since it’s simpler than the diploid case.”
My response:
Zach is wrong. Bacteria do not “get along just fine”. Lenski’s Long-Term evolutionary experiment demonstrated that even bacteria are subject to reductive evolution. But to compare bacteria to what we are talking about in highly complex organisms, such as humans, is apples and oranges. For those who want a detailed examination of bacteria and genetics, please see my article on the topic (4).
Conclusion
What we have here is another professional evolutionist who has demonstrated the difficulty of defending the evolutionary model of human origins when the data so powerfully confirms Biblical history.
Comments from Matt Nailor:
Let’s not forget that they have already assumed purifying selection in germline mutation rate studies and found it has no effect on the massive differences between the evolutionary phylogenetic mutation rate and the germline rate obtained in pedigree studies.
What about in highly considered regions of the mtDNA like Cytochrome C? We find the same thing. Mutations are still building up as diversity increases. We can see it across all species and you will notice that not a single species is mutation free.
(The highlighted areas show the lowest diversity in mutations found in the species.)
This information was taken from the DNA barcoding website.
So what do we know?
The mutation burden problem has existed over many decades and they have not solved it. There are many names for this problem in the published literature. Feel free to email me at healthfiirst@gmail.com for an abundance of links on this.
References
1. Is This Biologist Right About Mutation & Fixation Rates? | Standing For Truth. Patreon. Published 2025. Accessed February 12, 2025. https://www.patreon.com/posts/is-this-right-121898013
2. Carter RW. Mitochondrial diversity within modern human populations. Nucleic Acids Research. 2007;35(9):3039-3045. doi:https://doi.org/10.1093/nar/gkm207
3. Standing For Truth. Did Adam and Eve Exist? This Scientific Evidence Will Blow Your Mind! The Debate Has Been SETTLED. YouTube. Published January 12, 2025. Accessed February 12, 2025. https://www.youtube.com/watch?v=Fmdb2bdxVIg
4. Refuting Arguments Against Genetic Entropy | Standing For Truth. Patreon. Published online 2016. doi:https://doi.org/10.1534/genetics.115.1804712
A Population Geneticist Attempts to Save the Day for Evolution
Response to Dr. Zach Hancock
by Donny Budinsky
This is a reply to several comments (the relevant ones) made by Population Geneticist Dr. Zach Hancock to my article (1) on mutation rates and fixation.
The Response
Zach says:
“This first article is remarkably bad.”
My response:
Thanks Zach. How sweet of you. But from my experience, when a proponent of common descent calls a creationist article bad, it’s usually a reliable sign it’s a great article! We’ll see if you can back up your opinion of the article.
Zach says:
“We have direct evidence of strong purifying selection on mitochondrial genomes. I’m a little baffled, anyone would say otherwise.”
My response:
Zach, there is selection in mitochondrial genomes. But the selection that takes place does not work to change the mutation and fixation rate by any significant degree. It is a fact that the entirety of the mtDNA is functional—and it is also a fact that the great majority of mutations arising in this small, circular chromosome are neutral. Since this mtDNA is functional, the mutations happening in it are essentially nearly neutral. They are faintly deleterious. What this means is most mutations occurring in the mtDNA are collected in a ratchet-like manner. They build up over time unchecked by selection since selection is restricted in what it can do.
Yes, you can provide some evidence of selection, but this is mainly for detrimental mutations (those damaging enough for selection to see). The rule for selection is constraint. The exceptions don’t overturn the rule. Selection is constrained in its authority to act on the mitochondrial chromosome for many reasons. Its unique pattern of inheritance (maternal line only) is one key reason. Additional reasons include its lack of recombination, a high mutation rate, limited DNA repair enzymes, and high copy number within a cell (allowing for heteroplasmy) Selection pressure is essentially directed towards sustaining function. Since most mutations are effectively neutral, they won’t be damaging enough to adversely impact reproduction. All these reasons combined means harmful mutations will still be passed on regardless of selection tensions doing their best to eliminate them.
I am baffled that you don’t understand this. I believe it is because you have potent evolutionary presuppositions going into your interpretation of the data. Don’t misunderstand me. I am not saying there is no selection on mtDNA. It is true that overall selection on this unique part of the genome is weak, it does not mean there is no selection at all. If mutations arise in specific genes that encode essential proteins for the function of the mitochondrial DNA, and these mutations are high-impact, these areas of the genome are likely to experience robust purifying selection. You require strong selection, or unrealistic amounts of selection, to get what you need from the data to sustain your evolutionary fable.
Zach says:
“The mitochondrial genome is almost entirely functional (most of it protein-coding), and it performs one of the most important functions for the cell (respiration), if there were no purifying selection we would all be dead already.
My response:
I expect better from you, a PhD Population Geneticist. You are demonstrating my point exactly! The fullness of the mitochondrial genome is functional. It is also a fact that the majority of mutations occurring in this uni-parentally inherited genome are neutral. By neutral, we mean these mutations don’t have considerable enough of an effect on the overall function of the mitochondria for selection to see. This means selection won’t be capable of dealing with them—until it’s too late. You’re right about the “we would all be dead already”. This is exactly where our species is heading. Let’s explore this.
Mutation accumulation in both the autosomal nuclear DNA and haploid chromosomes put shelf lives on genomes. The mtDNA also experiences a much faster mutation rate than the nuclear DNA. This rate is about 100-fold higher! It is also a much smaller chromosome (16,569 base pairs). The reason we aren’t actually “dead already” is because we haven’t been accumulating mutations for 10s of thousands of years. There should be much more diversity in this chromosome if it were as old as apologists of evolution assert (2, 3).
The mitochondrial chromosome is not as old as evolutionary scientists would have us believe. We’ve only been storing mutations for 4500 years since the Flood Bottleneck. Individual rust spots on a car are not fatal to the car but over time, they damage the car to the point where the car is no longer practical. An alternative example is a book. A book undergoing single typographical errors over time will still be legible. It will still serve its intention. But after enough spelling mistakes amass, the book will descend into nonsense and will no longer be useable. This is what we see in genomes. Therefore, a mutation can be nearly neutral (slightly deleterious) in the mitochondrial chromosome and yet remain unselectable.
Zach says:
“Two lines of evidence for purifying selection in the mitochondria: 1) inferential, based on patterns of nonsynonymous to synonymous substitutions; 2) direct, observational evidence of the purging of a harmful allele introduced into a mitochondria experimentally over ~generations.
My response:
Zach, you are again missing the point. The responses we are receiving from the most accomplished the evolutionist camp has to offer (PhD Biologists and Geneticists) are truly a gift to Creation Science. Yes—even considering the reality that most mutations occurring in mitochondrial DNA are considered neutral or nearly neutral (not enough of an effect on the function of the mitochondria to activate the effects of selection), there are some mutations (an insignificant amount) that are harmful enough to not be considered effectively neutral and will be removed by selection. And even that is determined upon several factors (their location and level of heteroplasmy within a cell).
As I stated earlier, and will restate due to its importance, selection is much more constrained than evolutionary scientists such as Dr. Hancock want to acknowledge. For instance, selection on the mitochondrial chromosome is particularly restrained because of its distinctive inheritance (maternal only) but also the incidence of various copies of mtDNA within a cell. This leads to a phenomenon called heteroplasmy (just mentioned above). Heteroplasmy decreases the efficiency of cleansing selection (which Zach needs a sizable amount of) against negative mutations. This means harmful mutations will endure within mitochondrial genomes to an even greater extent than what we see in nuclear DNA.
I can only hope the rest of your lengthy comment deals with my article.
Zach says:
“if there were no selection,”
My response:
I never said there was no selection.
Zach says:
“, then the ratio of nonsynonymous (mutations that alter the amino acid that is coded for, which is almost always harmful) to synonymous (mutations that don’t alter the amino acid due to the redundancy of the genetic code) should be ~1. In fact, it should be slightly above 1, since there are more ways to have a nonsynonymous substitution than a synonymous one.”
My response:
Thanks for all that Zach. I’ll say it again: you are confirming my point exactly. The amount of selection in the mitochondrial genome is trivial. This is why even considering the trivial amount of selection taking place (large mutations), mutations are still accruing in the Y and mitochondrial chromosomes in a ratchet-like style. The rare exemptions don’t overturn the rule. You can point to the uncommon exceptions all day and all it does is reinforce my points.
You require much more selection to get evolutionary time. The no selection zone is significantly expanded when you consider realistic boundaries. There are mutations in even the most conserved protein coding regions of the mtDNA. Mutations still gather in highly functional territories of genomes. It’s not that selection sees every mutation accumulating in the mtDNA. No—selection is very constrained.
Purifying selection is still not powerful enough to remove the compulsory number of mutations for evolution to be true. You want your cake and eat it too. You want to invoke strong purifying selection and admit the majority of mutations in the mtDNA are neutral. Seemingly, those mutations need to be strictly neutral. But the idea that most mutations are exactly neutral doesn’t fit reality. Just because they aren’t harmful enough for selection to see doesn’t mean they aren’t somewhat deleterious. We also see genetic diversity expanding today—but with the amount of diversity being right in line with Creationist expectations. Apparently, selection isn’t working too well.
Final Comments
Zach has a few more things to say but simply continues along the same lines as his preceding remarks. He cites a 2014 paper (Ma et al.) where they inserted fruit fly embryos with various mitochondria, some of which had mutations that made them vulnerable to temperature.
Zach says:
“Almost all of the temperature-sensitive mitochondria were purged from the population in only ~10 generations. That’s direct evidence of purifying selection.”
My response:
This is desperate. It reveals the powerful evolutionary based presuppositions these evolutionary scientists have going into any counter to Biblical Creationists. We aren’t saying there is no selection taking place in the mtDNA. The question is: how much selection is taking place? Its not much. Selection removes the most harmful mutations and does nothing to prevent the accumulation of effectively neutral mutations. Biblical Creationists can account for some selection while maintaining a realistic view of how limited selection is. It is largely powerless to stop the neutral mutations accumulating in the highly functional mitochondrial chromosome.
The Biblical model of ancestry we defend also has a Flood Bottleneck 4500 years ago where the earth restarts with 8 people, and 3 reproducing couples. People don’t actually spread out until the tower of Babel event, which could have been 300-500 years after the Flood. This means we would have a period of time before people spread out into all parts of the globe and rapidly expand in population numbers where fixation rates were much faster. This is one of the reasons why the Biblical Creation model also has a balancing out effect of the mutation to fixation rates. I could go into much more detail on this important point, but that is not the focus of this article.
Zach ends by saying:
“Bacteria get along just fine, after all, and I start every popgen course by walking through the math of selection on haploid genomes since it’s simpler than the diploid case.”
My response:
Zach is wrong. Bacteria do not “get along just fine”. Lenski’s Long-Term evolutionary experiment demonstrated that even bacteria are subject to reductive evolution. But to compare bacteria to what we are talking about in highly complex organisms, such as humans, is apples and oranges. For those who want a detailed examination of bacteria and genetics, please see my article on the topic (4).
Conclusion
What we have here is another professional evolutionist who has demonstrated the difficulty of defending the evolutionary model of human origins when the data so powerfully confirms Biblical history.
Comments from Matt Nailor:
References
1. Is This Biologist Right About Mutation & Fixation Rates? | Standing For Truth. Patreon. Published 2025. Accessed February 12, 2025. https://www.patreon.com/posts/is-this-right-121898013
2. Carter RW. Mitochondrial diversity within modern human populations. Nucleic Acids Research. 2007;35(9):3039-3045. doi:https://doi.org/10.1093/nar/gkm207
3. Standing For Truth. Did Adam and Eve Exist? This Scientific Evidence Will Blow Your Mind! The Debate Has Been SETTLED. YouTube. Published January 12, 2025. Accessed February 12, 2025. https://www.youtube.com/watch?v=Fmdb2bdxVIg
4. Refuting Arguments Against Genetic Entropy | Standing For Truth. Patreon. Published online 2016. doi:https://doi.org/10.1534/genetics.115.1804712
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