Testing YEC Hyper-Evolution from Common Ancestors: Comparisons of mtDNA Genome Diversity in Mammals

Ken Ham’s Ark Encounter will vividly display what many young earth creationists believe the common ancestors of today’s species of animals may have looked like as they rode out a global flood 4350 years ago.   After disembarking from the ark, young earth creationists have proposed that these common ancestors experienced a burst of adaptive radiation into new  environments leading to the creation of thousands of new species.   If this prediction is accurate then I would expect there to be a very close genetic relationship between those organisms that have shared a common ancestor less than 5000 years ago.  On the other hand while Ken Ham and others believe in common descent for some species they deny common descent between somewhat ill-defined “kinds.”  Kinds, therefore do not share a common ancestor and therefore should not show the same sort of genetic relationships as do those that do share common ancestors.   I have argued that creationists are ill-advised to believe that the genetic data support their hyper-evolution/sparate kinds hypothesis.

This is revised article that I published a few years ago as a follow-up to a post I called "How similar is similar? Baramins, species and common ancestors"

This is revised article that I published a few years ago as a follow-up to a post I called “How similar is similar? Baramins, species and common ancestors”

To test my observations about YE creationist’ genetics, I made some predictions about the genetic similarities of some species of mammals (See: How Similar is Similar: Barmins, species and common ancestors).  I didn’t make my predictions in a vacuum but rather personal experience with comparing DNA sequences of numerous individual genes in many of these species.  However, I had never compared complete mitochondrial genomes before undertaking this exercise. Below I present some background about what I did and then I show you actual data that I collected to test the predictions that I have made.   I make no claim that the data I present are convincing evidence of common ancestry or a lack of common ancestry. My point is not to prove or disprove common ancestry but to provide some provocative data that all who wish to understand the relationships of organisms and their origins must account for.

What is the Mitochondrial Genome and Why Compare these Sequences?

The "Other" human genome. The mitochondrial genome is found in your mitochondria and is only inherited from your mother. So with respect to the genes of your mitochondria you are 100% like your mom.

The “Other” human genome. The mitochondrial genome is found in your mitochondria and is only inherited from your mother. So with respect to the genes of your mitochondria you are 100% like your mom.

The nuclear genome is very complex, very large, and not all species have been completely sequenced and so careful apples-to-apples comparisons would be difficult.  I have chosen a simpler system to compare genetic differences among species: The mitochondrial genome.

The human mitochondria (power plant of the cell) has its own genome of 16,569 base pairs.  Each one of us has multiple copies of this genome in every cell and you inherited this small genome from your mother.   What makes this genome very useful for comparing individuals and species is that it is passed down generation to generation and when there is a mutation that mutation will be passed to the next generation.  There is virtually no opportunity for lineages of mitochondrial genomes to get mixed or have genetic exchange.  Hence you can trace your mtDNA lineage back down your material lineage theoretically to the first human female.  This is were the idea of “mitochondrial eve” comes from.

Eve would have had one particular version of a mtDNA genome and then passed it to all her offspring.   If any of her daughters experienced a mutation in the mtDNA genome of their eggs, they would pass those variants to their children and so on. Thus if you and I differ at 100 locations among our 16,569 base pair then I would know that at least 100 mutations had occurred in mine and your lineages combined since we shared a common mother  – our common ancestor.  In the present day human populations one recent study (http://genome.cshlp.org/content/early/2016/02/16/gr.198754.115.full.pdf) reported that from comparisons of just 320 complete human mtDNA genomes there were 1156 locations in the mtDNA genome which vary in the population.  This  tells us that there are a minimum of 1156 unique mutations in the human mtDNA genome since mitochondrial Eve. Another analysis has identified more than 10,000 separate mutational events in the mtDNA genome in human history (see reference below for an explanation).

So these properties of the mtDNA genome of animals are useful for comparing time of divergence for species from an ancestor because if you have one species that splits into two species the differences in their mitochondrial genomes will generally represent the number of changes since there was an ancestral population (see footnote for caveats to this).  For the young earth creaitonists we could call this the mitochondrial eve for each “kind.”  For example, the ancestor of wolves (and domestic dogs) and coyotes had a mitochondrial genome sequence or some set of variant genomes in the population but when the population diverged and then became coyotes and wolves as separate species the time that they have been breeding separately will result in an accumulation of unique changes to each of their mitochondrial genomes.

A typical mitochondrial DNA genome showing the order of genes found in almost all animals.

The Human mitochondrial DNA genome showing the order of genes found in almost all mammals.

How does all this relate to the question of genetic similarity between species that I have talked about previous (see: How Similar is Similar)?   The 70% genetic similarity of the human and chimpanzee genome according to Tomkins (update: he now has recalculated and say is more like 88%) is a difficult number to understand because it has no context.  I asked, what if we were to compare other genomes, how much difference would we see using the same criteria for estimating similarity?  Because Tomkins examined many types of changes to the nuclear genome it is hard to assess his values. I have chosen to look at much simpler system. The mtDNA genome is nearly the same size in all land animals. It has the same complement of genes and those genes are always in the same order.  This means that anyone can take the DNA strand from one species and just line it up with another species and ask – how many differences are their in their DNA code – The As,Ts,C,s and Gs?  For example we can line up a human mtDNA and chimpanzee code and see that each of us has on average has about 1450 differences between our genomes of nearly identical size.

With this simple system we can then ask, how different are the mtDNA genomes of some representative species of various mammals.  Or, put another way, how much variation is actually observed between species that young earth creationists believe are in the same “kind” (ie. have the same common ancestor).

I’ve made some comparisons of those species and here is how I did it.   It is very simple and you can do it yourself.  Go to this site: http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome  and type in this code EF667005.1 for the Black bear mtDNA genome in the Query search window and then go to the bottom of the page and click on “BLAST”.  In a few seconds to minutes you will have comparisons and alignments of that genome with other bears and organisms that have similar sequences.   Scrolling down through the results you will be able to see the total number of differences between the “query” sequence and other species or individuals of the same species.   What I am not reporting in the table below are the number of small insertions or gaps that in the genome. They are not a significant number in most cases.

Finally – The Results!

Ok, lets get to the results.  Below is an image of the table of my results. Click for a larger and more legible version.  You can also download a PDF version by clicking here: mtDNA-genome-mammals-comparison-naturalis-historia.

mtDNA-genome-mammals-comparison-thenaturalhistorian

Let’s make some observations: 

While mtDNA differences are not always going to reflect a 1-to-1 relationship with the differences we would see in the nuclear genome or the morphology (ie. what it looks like) of an organism what we see here is a good proxy for the relative differences we would see.   If two species have more mtDNA differences they probably also will have more total genetic differences than two species that have fewer mitochondrial differences.*  What can we infer from the data then?

1)  All members of the human race are very similar with respect to their mtDNA genomes.  There is remarkably little variation among humans (probably not much more than 100 differences among any two individuals).  Compare this to populations of chimpanzees which show over 300 variants among populations.   Chimpanzee individuals are therefore more variable than humans (BTW, sequences of nuclear DNA genome also confirm that chimpanzees have more total genetic variation than humans).  This might not seem intuitive since most people think that chimpanzees all look the same and humans seem to have many differences in appearance but appearances can be deceiving when assessing overall genetic diversity.   We will see this with dog breeds as well which are more similar to each other and to wolves than humans are to each other.

The global distribution of mtDNA haplotypes in the 1500s. The haplotypes here recognized mutations that are found in large numbers of individuals. There are many subdivisons of these based on other mutations associated with the group. For example I have a mtDNA haplotype of D4e1 which is in the D-group haplotype. I have a very unusual mtDNA genome version given my western European ancestry. My mtDNA is more related to native americans. The pie charts show the proportions of people that have particular mtDNA genomes.

The global distribution of mtDNA haplotypes in the 1500s. The haplotypes here recognized mutations that are found in large numbers of individuals. There are many subdivisions of these based on other mutations associated with the group. For example I have a mtDNA haplotype of D4e1 which is in the D-group haplotype (found in northeast Asia and  South America. I have a very unusual mtDNA genome version given my western European ancestry. My mtDNA is more related to native Americans. The pie charts show the proportions of people form the 1500s that had particular mtDNA genomes.

2) The Neanderthal and Denisovan sequences are more different from any living human than any living human is from one another.  However, even this amount of difference is less than is found in other closely related species or even among chimpanzees of the same species.  This is why Neanderthals are considered to be a separate branch and yet still very closely related to modern man (sometimes considered a subspecies or variety).  See the graphic below to get some sense of the differences of these hominid and modern human sequences.  This shows that Neanderthals and any person alive today will have about 200 differences in their mtDNA genomes whereas any two humans alive today only differ by a maximum of 100 differences.

Pairwise nucleotide differences from all pairs of complete mtDNAs from 54 present-day and one Pleistocene modern human, six Neanderthals and the Denisova hominin are shown. Graph reprinted by permission from Macmillan Publishers Ltd: Nature, Krause, J., Fu, Q., Good, J. M., Viola, B., Shunkov, M. V., Derevianko, A. P., and Pääbo, S. (2010). The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature. 464: 894-897., copyright 2010.

Pairwise nucleotide differences from all pairs of complete mtDNAs from 54 present-day and one Pleistocene modern human, six Neanderthals and the Denisova hominin are shown. Graph reprinted by permission from Macmillan Publishers Ltd: Nature, Krause, J., Fu, Q., Good, J. M., Viola, B., Shunkov, M. V., Derevianko, A. P., and Pääbo, S. (2010). The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature. 464: 894-897., copyright 2010.

3) The average human has 1462 differences with that of a typical chimpanzee.  That sounds like a lot of differences. This is 8.8%.  Notice that for Tomkins  (see previous article) he claims only 70% similarity  between humans and chimps but this was only for the nuclear genomes. Had he applied his algorithm to the mtDNA genome I am quite confident he would come up with nearly the same 8.8% difference or 91.2% similarity because this genome is simple and it is just a matter of looking at simple sequence differences. Everything else about the chimp and human mtDNA genome is the same.   But what does this 8.8% mean. We see above that human are less than 1% different so let me be clear that there is a very real difference between these genomes.   But lets look at some other genomes and see if this 8.8% is as much as it sounds.

4) I didn’t show the numbers for chimps compared to great apes and orangutans but the differences (<2000 differences) are much greater than the differences between humans and chimps. However, creationists who study “kinds” have placed all the great apes in a single “holobaramin” implying that all apes came from a common ancestor just 4320 years ago.   By putting apes, orangutans and chimps together they are saying that they believe that the great genetic distances between these groups could have formed by evolutionary processes since God created the original “ape” ancestor.  At the same time they are claiming that humans could not have evolved from apes because they so genetically distinct!?  Do you see why I have been saying that creationists should be careful about proclaiming genetic differences as proof of no common ancestor.  There is a severe double standard in interpretation going on here.

5) Let look at the canine sequences next.  Domesticated dogs and wolves are more similar than humans are to each other. Despite the obvious morphological differences in dog breeds they are genetically almost identical both in the mtDNA and nuclear genomes and they are barely different from wolves.   Look at the coyote and dog comparison.  There is an average of 700 differences.  Coyotes and dogs can interbreed and so this amount of difference is no big deal.    But look at the red fox and dog/wolf comparison. Here we see a whopping 2269 differences.  This is close to double the differences that we find between chimps and human mtDNA genomes.   Remember that many creationists wish to claim that foxes and wolves are part of the same holobaramin which means they all share a common ancestor.  They posit this likely ancestor to be a pair of canines that were on Noah’s ark.  If this is the case that pair would have contained  single (in the female remember) mtDNA genome which then would have had to have been copied into all of the descendant species of dogs including coyotes, wolves and the foxes.  Just between these two we would have to hypothesize that there have been 2269 mutations between these lineages.  Does this reflect how different the nuclear genomes are?  I would bet that it does.  I would be quite shocked if the red fox and wolf genomes were not more different from each other than a chimpanzee and humans  genomes are using Tomkins methods because there are differences in chromosome number and genome size in addition to high rates of sequence divergence and probably even novel gene differences between the two.

6) Now look at the “cat” family members.  The lion and tiger, which are poster species for creationists who say that evolution has happened within kinds, have 1373 differences.  This is almost the same as the number of differences between humans and chimpanzees and I think reflect some very real differences between lions and tigers. Once again, if their entire nuclear genomes were compared I am sure we would find very similar differences (ie. 70% overall similarity by Tomkins calculation method) between these two “closely” related big cats. But what of the other cats species.  Look at the domesticated cat and cheetah – 1765 differences.  Can creationists really claim that all these cats are actually related to a single common ancestor and probably had a single mtDNA sequence just 4000 years ago but then claim that the genetic difference between chimps and humans is so vast that it is ridiculous to think they had a common ancestor?

7) The rest of the chart starts to be a bit redundant if not even more extreme.  Look at the bears.  Brown bears and polar bears are clearly quite similar and have a common ancestor by everyone’s (creationists or not) estimation.  They differ by only 295 base pairs which is similar to the difference among chimpanzees or difference between humans and Neanderthals.  But look at the other bear species, especially, the Panda comparisons.  Some are far more different from one another than the chimp and human sequences.    Lastly, I threw in some ungulate samples here including sheep and goats.  Sheep and goats are almost universally proclaimed by creationists to represent the same “kind” and yet again we see again that these two taxa have as many differences as humans and chimps.  Again, I would say that I am fairly sure that when the entire genomes of these organisms are finally sequenced we will find that they will have as many significant differences as humans and chimps.

Summary

I expect that these data will be very surprising to some people. However, there really isn’t anything new here. These data have been around for quite a while even while hundreds of new genomes are becoming available every month.  I was not at all surprised by these numbers which is why I’ve been telling my creationists friends that they shouldn’t get excited about these percentage similarity numbers that they hear.   Of course there are many aspects of genomes that are much harder to compare.  Simple sequence similarity doesn’t tell the whole story (see footnote below for more details).  I do think that chimps are significantly different from humans but neither do I believe they are any more different, with respect to overall genetic similarity, than foxes and wolves or even sheep and goats.  It isn’t our code that makes us special!  If am am right it makes no sense for creationists to strenuously argue that humans and chimps are not related by common descent but then promote a view of rapid radical evolution of kinds into thousands of species many of which are as distinct as we are from primates.

Extra notes:

Comparing genomes is very complex because there are so many different way to look at the genome.   There is total genome size, number of chromosomes, amount of repetitive DNA, overall sequence similarity, coding vs non-coding (ie. genes vs non-genic regions) sequence similarity, DNA hybridization, etc..   Even genetic codes that are very similar can be read (translated) into profoundly different phenotypes (physical manifestations of the code). For example, single differences in important genes can result in huge differences even among individual humans but some genes could have many sequences differences and yet result in little difference to the organisms.  For example,the hormone leptin is very similar in structure among mammals despite many individual differences.  A human and a whale have many differences at the level of the DNA sequence  but you could effectively swap the whale gene for your gene and probably be fine.

Because of these complexities the mtDNA genome is a more elegant system to look at differences because it is much easier to compare. However, I am not unaware of some real and potential problems with such comparisons. First, mtDNA genomes don’t all “evolve” at the same rate. The mutation rate in some lineages is known to be a bit faster than others. I could have shown rat/mouse differences but it is known that they have a faster rate of mutation accumulation and so their differences are exaggerated   I do believe that the comparison of fairly similar species that I have done above reflects lineages that have similar mutation rates and thus the numbers really have meaning in relationship to one another.  Second, you have to remember that the actual number of differences is probably greater than you are seeing.  Some mutations that happened in the past could have back mutated to appear exactly like another lineage even though they way they both arrived at a T at a particular position was different and thus that two Ts are not the same.

Another complication is lineage sorting as a result of having a starting population with multiple versions of mtDNA.  Over time if a population gives rise to new species the individuals of that new species will have varying amounts of differences between them because they both started with multiple copies of the mtDNA genomes.  However, for creationists the assumption set is much simpler and lineage sorting doesn’t present as much of a problem.  If all “kinds” were reduced to a single pair in Noah’s ark, then no matter how much variation there was before the flood that variation will go through an extreme bottleneck probably being reduced to a single or several very closely related mtDNA genomes.  Thus all new species formed after the flood in the creation model of fast evolution start from a single version of mtDNA and any variation we see today in populations or between species must be the result of mutation to that initial genome.

I didn’t want to get into functional constraints and directional selection because these are not important factors in these comparisons (another reason that comparing mtDNA genomes is nice).  Someone might say that God might have started with a mtDNA genome from a primate model because it best fit the needs of a human physiology and this account for the similarity.  However, that person would also have to believe that large differences in sheep and goats was created naturally.  Why are these genomes SO different if these species are so similar and obviously share a huge amount of their physiology?   Any argument for the similarity of one set of genomes can’t be divorced from application to another set of genomes.

Below is an example of what a sequence search result looks like in BLAST.  In this case this is a pair of sequences of a gene from pacific oysters.

Alignment of two sequences of the same gene from two species of oysters. Notice the

Alignment of two sequences of the same gene from two species of oysters. Notice the identities of the two sequences. There are also two “gaps” that  you can find if you look closely.

*This does not hold true when one starts to look at differences between more distantly related animals. For example, the differences between a fish and reptile are about the same as a fish and a human and a butterfly and a human. This is because the genome is so small that many changes are redundant and thus the genome become saturated with changes and for every new change another site in the genome will have converged on the same sequence as something it is not related to.

References:

Soares, P; Ermini, L; Thomson, N; Mormina, M; Rito, T; Röhl, A; Salas, A; Oppenheimer, S; Macaulay, V; Richards, MB (June 2009), “Correcting for purifying selection: an improved human mitochondrial molecular clock”, American Journal of Human Genetics 84 (6): 740–59,doi:10.1016/j.ajhg.2009.05.001PMC 2694979PMID 19500773   Comment: in this paper Soares et. al. compared just 2196 complete human mtDNA genomes and from those identify 10,683 separate mutation events.  This includes mutations that have occurred multiple time at the same location in the genome. For example, I might have a mutation of an A to a T at position #1000 in my mtDNA genome.  Another person for whom I have no common ancestor for at least 1000 years might also have the exact same mutation.  Because our common ancestor did not have this mutation we both gained this mutation independently.

Comments

  1. I confess I’ve only skimmed this blog post, but some strident comments by Ken Ham on his Facebook page today might be of interest (in case any of his followers stumble upon your blog though I suspect Ham is targeting a recent Kenneth Keathley blog that AiG were unhappy about):
    “Evolutionists call natural selection/speciation “evolution,” and call molecules-to-man “evolution.” It’s a bait and switch to indoctrinate!
    And just because evolutionists call natural selection/speciation evolution doesn’t mean those who talk about natural selection are evolutionists. Natural selection/speciation is observable science and has nothing to do with molecules-to-man evolution–in fact, they show the opposite.
    You see, creation scientists show that natural selection/speciation are not evolution — just changes within a KIND reflecting the genetic variability. Natural Selection/speciation involves loss and new combinations and conserving of information–NOT new information as needed for evolution.
    So creation scientists observe natural selection/speciation but just because evolutionists call this evolution doesn’t make it evolution! Natural Selection/speciation is observational science opposite of evolution; molecules-to-man evolution is historical science (belief).
    Evolutionists think they own natural selection/speciation, as they claim it’s evidence for molecules-to-man evolution — but it’s not! The small changes that occur in natural selection/speciation have ZERO to do with big changes necessary for evolution of one KIND to another.”

    NONE of which has ANYTHING to do with any specific Bible teaching. Such as Genesis 8:17 (New International Version) which reads “Bring out every kind of living creature that is with you—the birds, the animals, and all the creatures that move along the ground—so they can multiply on the earth and be fruitful and increase in number on it.” Which indicates a big increase in number of individuals following reproduction but says nothing whatsoever about speciation/radiation either ‘within a kind’ or more generally. (A minority of YECs eg David Tee and possibly Ray Comfort still deny that speciation or natural selection or perhaps both really occur.)

    Ham also conveniently fails to mention mutations or gene duplication or genetic drift or how it has proven difficult to determine whether some fossils are of ‘primitive’ birds or feathered dinosaurs even though the Bible suggests they were separately created on different ‘days’ (these fossils are ones which AiG would insist are ‘younger’ than Noah’s Flood and died – and went extinct as species – less than 5,000 years ago).

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  2. Christine Janis says:

    This is brilliant. Thanks so much for taking the time to document this.

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  3. Caleb G. says:

    If this Hyper-speciation model promoted by Ken Ham and company takes off among YECers, then perhaps one day YECers will admit that chimpanzees and humans are part of the same “kind.” :-) If you continue to insist that lions and tigers are part of the same “kind” and that foxes and dogs are part of the same “kind”, then wouldn’t humans and chimpanzees also need to be considered part of the same “kind,” since they are closer genetically to each other than lions vs. tigers and foxes vs. dogs?

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  4. wowfunny251 says:

    I think a problem with this is that the “limit” to evolution (from a creationist perspective) is not a limit on how many mutations can occur, it’s a limit on what natural mutations can do. So given enough time, two members of the same “kind” (though I detest using that term because of Ken Ham’s abuse of it) may become more genetically dissimilar than two distinctly created kinds.

    From my perspective, an example of this would be the variation in living chimpanzees (which would all be one created species) and the variation between humans and neanderthals (which I consider to be distinct “kinds”).

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    • Yes, this is a good point. Very true that just knowing number of differences is a long way from explain the “real” differences between two organisms. The mtDNA differences are generally considered to be at synonymous/neutral sites and thus what we are looking at here is essentially neutral evolution/genetic drift. The advantage of looking at neutral sites is that the molecular clock comes into play. The greater distance within chimps than humans is a piece of evidence that their populations are older than human populations. But mtDNA mutations have little to do with morphological change and they only track specialization rather than being any cause of it. Another problem I didn’t mention is that because of the size of the genome once two genomes become more than 20% dissimilar they won’t really get any more different over time because back mutations cause some sites to become identical to another species again (ie. A becomes T and then later it can go back to being an A and the two sites look like they are homologous (have the same history) but they are what we would call homoplasious sites.

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      • wowfunny251 says:

        True, what you say is a problem for YEC. But not Old-earth creationism, because as an OEC, I believe the chimp “kind” was created long prior to the human kind. In Genesis one, humans are the last thing created before the day of rest begins. And because of the complexity of genetics, and the dispute over molecular-clock dating, I greatly prefer arguments from the phenotype than from the genotype. And phenotypically, say humans and neanderthals, are far more dissimilar than any different human populations are from one another.

        Though unlike YEC’s, I consider Tigers and Lions, Donkeys and Horses, etc. to be distinctly created kinds. And the similarity between them is mere common design. I see exquisite design of the ecosystems these creatures are built into, and the distinct behaviors and relational qualities of these creatures appears to me to be something directly done by the creator.

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  5. The genomic similarity between chimps and humans is pretty fascinating, but we shouldn’t lose sight of just how different these species are morphologically, physiologically, behaviorally and intellectually. In fact it seems like missing the forest for the trees to ignore all of the variation detectable on the macro scale simply because you can’t see much difference in the genomes. Something has to explain the variation, and DNA sequence (whether nuclear or mitochondrial) is not the whole story.

    Its actually not all that surprising that we don’t find the expected variation at the DNA sequence level given how uninformative the naked DNA sequence has proven to be in many circumstances. For example, genome wide association studies are now notorious for identifying only fractions of the heritability of any given trait. Also even if you put a fully intact human genome with all the organelles and proteins necessary for life inside a human, lipid bilayer, I don’t expect you would get a functional human cell. These two realities taken together suggest that DNA sequence is only a part of the picture. The rest of the picture (or at least other aspects of the picture) resides in how the DNA is read. As such, fully understanding all of the differences between humans and chimps, etc will require a great deal more research into topics like histone modifications, DNA methylation, alternative splicing, chromatin conformation and proteomics. These are additional layers of complexity where non-DNA-sequence variability can reside that may show us how two very similar genomes can create such phenotypic differences.

    At this point, I don’t see any reason to jump to the conclusion that chimps and humans are the same kind or have a common ancestor simply because their naked DNA looks similar. I’m also not sure that percent identity of multi-billion base pair genomes really does the extant dissimilarity justice. 1.5% difference between nuclear genomes gives you around 45 million nucleotide differences; that seems like a lot of potentially explanatory variation.

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    • Hi Trevor, my point is really the opposite and I think you have helped me make it. Humans and chimps are quite different but look at the differences between species of other kinds. They are just as different. They should not be considered the same kind.I didn’t have chimp/gorilla or gorilla orangutan comparisions but they are far more different than chimp human and the also have very different morphologies, behaviors. Their nuclear genomes and especially their Y chromosomes are much more different from each other than chimps/humans and so it seems pretty clear that AiG is saying something very radical by suggesting they all have a common ancestor.

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      • I see. Looking at the naked DNA, your relative comparisons are probably correct. What I was trying to point out, though, is that the naked DNA is not the whole picture. If we were able to compare their proteomes, methylomes, transcriptomes, histone codes, etc, (all in one model) we may be able to make a more informed comparison, and we may very well see our categories change dramatically. I think that the human/chimp comparison (high genome similarity but low phenotypic correspondence) highlights the need to consider these other characteristics in our assessment of similarity and, for YECs, our concept of kinds.

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  6. Thanks for this fine article.
    As a reader using Kindle I would like to inform, that the print option on this site gives problem. The print includes the right colomn (blogroll and categories links etc.).
    This makes it almost useless to read on Kindle. Wouldbe good to have a clean print of only the article.

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    • Thanks for info. I hadn’t thought to look at it on Kindle. I’m disappointed that it doesn’t format well since it deal fairly well on cell phones. I have the option to use a single column format for the articles, I will start doing that more to help. Just wondering if the font is readable? Some have told me that the font is too light for them? I can purchase an upgrade to change the fonts but haven’t gotten around to that yet.

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  7. This blog post is sort of relevant. I can’t help wondering whether Ham and co (with their post-flood hyper-evolution though of course they won’t call it that) are doing some ‘historical’ science – or rather historical ‘science’ in their case.
    http://theness.com/neurologicablog/index.php/answering-creationists-unanswerable-questions/#more-8951

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    • I saw that article as well. They are most definitely doing lots of “historical” science but as long as it doesn’t contradict the answers they expect they are fine with it. That was the gist of my How do we know T. rex had short arms posts.

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  8. Just spotted that it’s a Ray Comfort video (I think I watched it some months/years ago).

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  9. On neanderthals (I’ve now worked my way through the blog and see that you mention them) you are probably aware of this story (NB the researchers were looking at father to son rather than mother to daughter genetic inheritance ie the Y chromosome in, I assume, nuclear rather than mitochondrial DNA): http://www.bbc.co.uk/news/science-environment-35992612

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  10. hi. what about those articles?:

    https://www.icr.org/article/8017/

    http://www.icr.org/article/genetic-clocks-verify-recent-creation/

    they give some interesting data.

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    • Those data would be interesting if they had any basis in reality but there are a lot of assumptions and liberties taken by Tomkins and Jeanson to get those results. Jeanson’s estimates of how much mtDNA should have diverged are really meaningless since he assumes neutrality of all the sites in the mtDNA genome and he does not consider purifying selection on deleterious mutations. He shows more mutations happening than there are actual sites in the mtDNA genome and never seems to realize that this suggests his model is completely unrealistic. Tomkins uses references to extreme values to make his calculations which make his conclusions suspect too. His model is far too simple since he doesn’t include extinction of alleles thus requiring many more mutations than those just observed today. Overall, both of these authors are using some sophisticated sounding words but its mostly sophisticated nonesense when one looks at the details and considers all the parts of the stories that they are leaving out. Here is one article that explore a bit of the problem: https://eyeonicr.wordpress.com/2013/12/13/nathaniel-jeansons-null-hypothesis/

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      • deuteroKJ says:

        This may be worth a separate blog post. I have a feeling Jeanson, due to his credentials and more pleasant demeanor, will become more of a player in YECism. He comes across as more serious and less strident, and therefore may gain a broader hearing from uncommitted.

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    • One more thing about Tomkins and Jeanson, even if we grant the accuracy of their numbers, which is not a safe assumption, they don’t really squeeze the variation into the right time frame. They talk about 10,000 years but because of the genetic bottleneck of the Flood they need to get all the variation into less than half of that time. To make things worse neither of them mention that neanderthals and denisovans and Sima de los Huesos individuals really are 200 to 400 differences from other humans rather than the 22 that Tomkins quote. So if they can’t their low numbers to work in 4350 years how are they going to squeeze in the other hominids that they say are descendants of Noah? In addition, the point of my article is that there are far more differences between “species” of kinds and so working really hard to show that humans aren’t that different and even their variation is hard to explain hardly helps the case of showing that a lion and tiger which are far more different could have easily have been derived from the same genetic stock.

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  11. Hi NH

    Thanks for the fascinating post. Why do you think there are far more mitochondrial differences (per base) between humans and chimpanzees than there are nuclear differences?

    Forget what Tomkins has written, if you take just about any nuclear sequence and compare it between humans and chimpanzees, you should come up with a difference of about 2%. I realise that indels might inflate that number a little, but even if we were to include structural changes over the entire genome we would come up with a difference of about 3%.

    This is a long way off from the differences in the mitochondrial genome which you have found to be 8.8%. Why such a large difference?

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    • He, that is a good observation and question. The mtDNA does show much greater divergence than the nuclear genome. This is the result of how the mtDNA genome is inherited and results in the faster incorporation of mutations. We can observe – not infer – real rates of mutation accumulation in mtDNA and see that these genome evolve faster. Each generation the mtDNA genome gets bottlenecked down to a few or a single copy of the genome as it is passed on in the egg and thus mutation can become fixed in the mtDNA genome. Also, the mtDNA genome gets copies more often than the nuclear genome between generation and thus it has an increased chance of picking up new mutations. The overall effect is that that this genome changes at a faster pace. This is seen in all animal lineages that I know of.

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  12. This is great!, my eyes have been opened! Some how i totally forgot about mtdna. Excited to research more genomes. My theory is the species with shorter times to reproductive maturaty will have greater variation, i shall begin by checking the fox and the wolf as they seem good canidates.

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Trackbacks

  1. […] “Natural Historian” has written about this extensively as well. In this post, “Testing YEC Hyper-Evolution from Common Ancestors,” he addresses this very thing. He has written numerous other posts in the same […]

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