What is the genetic evidence for human evolution? | The BioLogos Forum

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In the last couple of decades, our understanding of genetics has grown dramatically, providing overwhelming evidence that humans share common ancestors with all life on earth. Here are some of the main types of genetic evidence for common ancestry.

Read more here.

This is a companion discussion topic for the original entry at https://biologos.org/blog/what-is-the-genetic-evidence-for-human

I don’t know what frustrates me more… the different numbers I constantly hear ( I never know if a number I hear is going to last until the next time someone makes a similar proposition about something), or the seeming lack of critical analysis. So in this article, point one:

"The rate of change has been measured precisely to an average of 70 bases (out of our 6 billion total) per generation. "

I have been hearing 100 mutations per generation for quite some time… now this?

If we have the same scar as chimpanzees and orangutans, then the deletion or insertion must have occurred before these species diverged

Or… they got their own scars, just as they got their own nutrients to form their own proteins. The thing is, we would expect similarities in DNA for functional reasons, even without inheritance. Insertions and deletions are called such because of the assumption that it “must” have happened, ie. something must have been inserted or deleted because the genomes are different. I’m not sure about that logic. It would be like saying that a five petalled flower experienced an insertion of a petal, or the four petaled experienced a deletion. Or… one could simply say they are different… or, one could say that the five-petaled gained four from one, and the four petaled gained three from one, or the one-petaled lost two from three. We know there are differences, but the genome itself doesn’t tell us whether something was gained or lost, just that they are different. Our naming of insertion or deletion is dependant on our presumptions, and not self-evident. I’m just following the logic. You may differ.

we would expect the synonymous changes to be passed on much more effectively than non-synonymous changes.

Yes, of course…a non-synonomous difference would often be fatal, since the protein would cease. But again, under what assumptions would we presume that which one was first? Especially when it comes to synonomous differences in different species. If they do the same job, one is not worse than or better than the other, so they both work.

That is exactly what we find among the DNA of humans and chimpanzees: there are many more synonymous differences between the two species than non-synonymous ones.

The synonymous differences would indicate a difference between species, not a similarity between species. With a similar ancestor we would expect fewer differences, not more synonymous differences. It is an ironic difference, since the same function is still happening, just like both a human and a chimp each eating bananas. (But not the same banana.)

Hi johnZ -

If we think of DNA as a form of information, then perhaps a more fruitful metaphor than scars is typographical errors.

Suppose that you are a teacher and one of your students turns in a 3000 word essay. You notice that it has 53 typographical errors. Using internet search and text tools, you discover that each paragraph of the student’s essay has appeared in various blog posts, with a few words rearranged here or there. Moreover, each and every one of the student’s typographical errors is identical to a typographical error in one of the blog posts.

What would you assume about the origin of the student’s essay? Would you assume that the student wrote the essay especially for the assignment, and the fact that it has 53 typographical errors that are identical to those appearing in blog posts arose independently, from the student’s own imperfect editing ability? Or would you assume that the student’s essay and the blog posts have a common origin (i.e., that the student copied and plagiarized)?

Just as most people would confidently infer a common origin from identical typos in corresponding text, scientists confidently infer a common origin from identical “scars” in corresponding genes.

Does this explanation help?

I know they infer a common origin. That’s not something you have to educate me about.

John, are you in physics or engineering or some other field which deals in very precise measurements? Biology just doesn’t yield that kind of thing. Mutation rates vary widely according to the type of mutation, less so but still substantially in different parts of genome. In recent years they can measure these “genealogical” mutation rates based on sequencing families or sequencing cousins with a defined common ancestor of known age in years and generations, but before that mutation rates in humans were measured by connecting an archeological date with a intra or inter species divergence and counting mutations to get an “evolutionary” mutation rate. Until genome sequencing this was necessarily based on sequences of limited orthologous regions of the genome. Mutation rates are low enough that often the actual count of mutations detected was pretty small.

Mutation rates vary for a variety of reasons. Mutations are occurring in DNA in chromatin, a very complex structure of DNA wound around histone octamers, with many other low and high abundance proteins bound. The local chromatin structure affects observed mutation rates, which are the output of DNA replication errors, chemically damaged or light damaged bases, single and double stranded breaks that occur during the unwinding that is required for transcription and replication, and the processing of all these errors and damage by a number of different DNA repair systems, some of which include error prone polymerases. The few mutations that happen to be in the few sperm or eggs that make the next generation are what we see in the short term. In the long term mutations have to be fixed by drift or selection in order to affect the whole species. When we measure an average apparent mutation rate, we’re measuring the output of this highly complicated system. Variants in the polymerase genes and DNA repair genes can cause small or large differences in observed mutation rate, although if the effect is large the individual is likely to die young of cancer. Observed mutation rates can be somewhat different between species and over time as well, for some combination of all these reasons.

With model species, you can use a single well characterized strain, inbred for animals like mice, and you still see a surprising amount of variation between individuals in whatever you measure. When I was in grad school I studied the mitotic cycle in a single strain of slime mould. It was kept frozen at -80 deg C. and a small amount thawed and grown for each experiment. No matter how carefully I ran the same procedure the measured intermitotic time (of giant syncytial cells with 10^8 nuclei in the same cytoplasm) varied from 7.5 to 9 hours in different experiments. With purified enzymes you can get quite reproducible measurements with low variance, but if it’s alive, it varies substantially, no matter what you do. With measurements in humans you are dealing with an outbred population. If you look at those papers on family sequencing you will see substantial variations in the number of mutations, even between siblings. Monozygotic twins would probably be more reproducible, but I haven’t seen that done yet. The numbers you are being given are averages. The variances would shock a physicist. :slight_smile:

Agronomy, the science of combining chemistry, physics, engineering, biology and economics to grow crops. In the last 30 years, crop yields have about doubled in our area. This is not by any single factor, but combines the benefits of plant breeding, gmo crops, improved fertility practices, soil structure, soil moisture conservation, improved herbicides, improved machinery for seeding and harvesting, gps for steering and fertility management, disease management, livestock management. Most of these things are highly variable, especially soil management and fertility management, so I understand high variances. In fact, sometimes recommendations are made for some plant nutrients, when less than half of the land requires it, because those areas that do require it provide a big enough benefit to cover the cost.

So I understand high variances.

But regardless of variances, a reported average should not vary much, unless the work was not done well (too few samples to be statistically reliable). So a difference between 100 mutations and 70 bp changes per generation is HUGE, especially since some mutations can result in multiple bp changes. I would also assume that there are potentially “hidden” mutations, where a bp change is more likely to experience another mutation in the future, again exchanging a bp to something else, or where an insertion is later deleted.

While it makes sense that within a species, genetic similarities will indicate common ancestry, it is an item of faith that genetic similarities indicate common ancestry among different species, orders, and families.

I really have to stop responding to these comments… I have too many other things to do.

No. It is not just a “matter of faith”. It is based on evidence. The Theory of Evolution is not based on something as vague as “similarities”, genetic or otherwise, but on the NESTED HIERARCHIES, the phylogenetic trees at not only the morphological level but the molecular level. (That is why genomic mapping was such a slam-dunk for evolution theory.) This also explains why Common Design doesn’t look anything at all like Common Descent. (They are NOT equal explanations for the evidence.)

The two possible hierarchies, one formed by comparing morphology (the physical appearance of the organisms) and the other formed by comparing molecular data (genotype of the organisms), would be expected to be congruent if all life had originated via evolution from a common ancestor. While there are certainly discrepancies between the two nested hierarchies, the two trees certainly show an amazing degree of similarity.
Of course, based upon the fact that the genes of an organism determines the morphology of the organism, one may expect the two trees would share a certain degree of resemblance. However, the biochemical analyses can also look at things that have very little or no influence on morphology, such as non-functional DNA or the sequence of metabolic enzymes, and end up with the same results. Also, there is no reason to assume that similar morphology demands similar genetics, as convergent evolution of marsupials and eutherian mammals will attest. Creatures such as the marsupial mouse and the eutherian mouse look very similar, but they differ a great deal in their genetics and biochemistry. This is because there are many ways for DNA to encode for the same proteins or the same regulatory elements, thus resulting the same morphology with different genetics. Therefore while common design would not predict such a congruence between trees, common descent would. Thus, common descent is greatly corroborated by such congruence.http://evolutionwiki.org/wiki/Nested_Hierarchy

Above is a quote from evolution wiki. This directly contradicts Tertius assertion that evolution is not based on “similarities”, since even the nested hierarchies are based on similarities. Interestingly, the similarities chosen for the nested hierarchies tend to be fewer for the families and more for the species. This would be essential in order to develop a nested hierarchy. Using an analogy, we would see that we could divide things into buildings and vehicles. Buildings then would be divided into houses, offices, factories and churches. Vehicles could be divided into wheeled and non-wheeled, and wheeled divided into two-wheeled and more than two wheeled, and more-than-twowheeled into trucks, trains, cars, tractors. We have a type of morphological and functional hierarchy. This obviously does not show evolution, except for an evolution of design.

However, does the examination of the genomes show this self-evolution required for evolutionary theory? It seems to, but does it not depend primarily on the assumptions made?

Common design not does prevent a similarity between genomes for similar morphologies. Nor does it prevent using dissimilar genome for similar morphologies. I do not really see a limitation for common design in this way. However, the common similarities do support a common design, but not that common design is limited by limitations that we might impose. We might one day build a bicycle out of steel, and another day out of wood or titanium. The design is common, but the materials are different. The design might even be different somewhat, but not so different that we would not call them all bicycles. Thus there is no justification for saying that Common design would be invalid under the present evaluation of genetics.

Does common descent provide a better explanation than common design? Keeping in mind that common descent is somewhat speculative; in other words, beyond observing actual instances of genome changes in the present, and observing the potential to interfere in natural selection based on random mutations, we are speculating that our definition of nested hierarchies relates to a progression in time over millenia. Simple genetics does not seem to provide this progression intuitively. In other words, I wonder what we see as viable forward progression, could genetically be just as viable in reverse.

In addition, I see some problems with nested hierarchies in this: If we divide everything into single cells and multi-celled organisms, we have separated and divided organisms into “nests”. What justification do we use to assume that single celled organisms caused multi-celled organisms outside of their “nest”? Or the reverse… that multi-celled did not devolve into single celled? And if both happened, then how does that justify the validity of using nested hierarchies in this way?

“This directly contradicts Tertius assertion that evolution is not based on “similarities”, since even the nested hierarchies are based on similarities.”

No. I re-read what he wrote and the professor made clear that it is not a matter of just vague similarities. The similarities appear in patterns known as phylogenetic trees. The anti-evolution spin rarely talks about the hierarchical patterns and pretends that evolution theory is about nothing but similarities. If it was that vague then the point might be well taken. But it is not a matter of vague similarities.

Common descent and common design do not look at all alike. Did power-steering appear in one car model in one car factory and then other cars in the same factor? No, when a new feature protected by patent is licensed out to multiple car manufacturers, it may appear in many different makes and models of vehicles. We would expect that of Common Design----not Common Descent.

Pretending that Common Descent and Common Design look the same and are just a matter of “same data, different interpretations” is only convincing to an audience that has no awareness of the obvious differences between them.

John, I don’t see that you understand the concept of a nested hierarchy.

A nested hierarchy is nothing more than a well defined(super) set which contains and consists of other specified (sub)sets.

This definition from Nested Hierarchies for Dummies is one I accept. It is not a difficult concept, and the idea behind it is what guides keying books for botany. Nested hierarchies do not always have to be genetic; they can be morphological. and of course they can apply to non biological things as well.

I didn’t say whether the similarities were vague or obvious. Of course they appear in patterns; this is what defines the nesting hierarchy. It is a bit of a circular argument however… we can put things into similar categories, with ever increasing amounts of similarity, and thus can show a pattern of small similarity to greater similarity, which we call evolution from great similarity to small similarity. No one doubts our ability to do this, to create these nested hierarchies. The question is only whether they were created that way, or whether they gradually developed through random mutations and preferential or adaptive selection.

Again, your lack of understanding is showing. The source of the differences and whether they were fixed by drift or selection is completely irrelevant to whether the hypothesis of common descent is making incredibly strong predictions about these data. You’re just handwaving.

Now, let’s look at cars. We can easily make a nested hierarchy of Ford vehicles. What’s the relationship between that hierarchy and a hierarchy we derive from the engines of those same vehicles? The hierarchy we derive from head bolts from those engines? From lug nuts from their wheels? Can we make any predictions for homologous parts before we do the analysis? How is this even remotely close to the relationships between hierarchies of organisms and their characteristics?

To modify what OldTimer wrote, pretending that Common Descent and Common Design look the same and are just a matter of “same data, different interpretations” can only be done by someone who hasn’t even bothered to examine the data and is only convincing to an audience that has no intention of examining any data.

You are right, Joao, I do not understand alpha tubulin sequences, nor N-acetyl transferase sequences. But I find the proposed sequences that I do somewhat understand, very amusing. The development of fish into land animals, and then the development of land animals into mammal fish, ie. whales or some such. Very amusing. Especially the raionale for it. And the lack of intermediate fossils.

Since I do not understand the two chemical sequences you are mentioning, I cannot make statements about it, but I suspect that any hierarchy developed will have a corresponding dna and hormonal and endocrine similarity of difference most of the time.

In other words, I do not think it is irrelevant, if it also fits with a common design approach.

[quote=“johnZ, post:18, topic:455”]
You are right, Joao, I do not understand alpha tubulin sequences, nor N-acetyl transferase sequences.[/quote]
I didn’t ask if you “understood sequences,” John. I asked:

"What does common descent predict about the tree from physical characteristics of whole organisms? The tree from mathematical analysis of alpha-tubulin sequences? The tree from mathematical analysis of N-acetyl transferase sequences? What do those three trees look like relative to each other?

“Even more importantly, what do these trees predict about a tree derived from mathematical analysis of the sequence of a third protein, utterly unknown to the observer? This ability to predict future data is where your claim that this is a mere matter of faith is demolished as wishful thinking.”

That doesn’t require understanding sequences, it requires understanding nested hierarchies and the enormous restrictions placed upon the relationships between them by common descent.

Um, John, I’m talking about nested hierarchies derived from amino acid sequences, not “chemical sequences.”

Remember–the mathematical relationship you were pretending to understand? How did you get from that to misrepresenting evolution of organisms as a linear process?

[quote]Very amusing. Especially the raionale for it. And the lack of intermediate fossils.
[/quote]How many intermediate fossils for cetacean lineages have been published in the last 10 years, John?

[quote=“johnZ, post:18, topic:455”]
In other words, I do not think it is irrelevant, if it also fits with a common design approach.
[/quote]“IF”? Weren’t you just claiming to know that it does? You don’t have any idea whether it does or not!

Didn’t realize you could publish a fossil…

That’s probably why you don’t realize that there’s no lack of intermediate ones…

I always thought you had to publish your findings about a fossil. Fossils are not paper; they are real. Ciao, Joao.

Style points for @johnZ for playing the ever popular “I’m going to point out that the exact words you used could have been worded better” game in an entertaining way (for me at least) and with an amazingly low character count! If only this could catch on…

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Are you truly unaware of all the intermediate fossils for cetaceans there are?

Yes, I am truly unaware. Amazing isn’t it. This is why, while Chris pointed out my attack on grammar or syntax or whatever was sort of cute, yet it had a serious point to it. A fossil does not have a label called “intermediate” or “transitional” attached to it. There have been all kinds of problems with trying to identify a fossil as intermediate, such as archeoraptor, piltdown man, etc. Just because it is claimed in a paper, doesn’t make it so. And the other problem is that by the theory, almost every other animal becomes an intermediate in some type of hierarchy. Think of the nautilaus, fish, coelecanth, ape ancestor, ecoli, dinosaur, etc., etc.

Of course there are intermediates, animals similar to two or more other types, having characteristics that are halfway between two others, etc., etc. But does intermediacy mean that they were transitional? When this topic has come up before, I was informed that transitionals are such, not because the organisms were transitional, but because they had transitional characteristics. So the argument about transitionals tires me out. It is primarily based on the belief that there are transitionals, and that transitionals exist between every single species, whether we know what they are or not.