Common Descent: Humans and Chimps / Mice and Rats

Sorry @scd. You are missing the point entirely.

That paper is doing something different. It is looking at naive estimates (e.g. assuming constant mutation rate) over a much larger timeline (e.g. 50 mya), where we have much less information in the fossil record, and we have no direct measure of actual mutation rate, neither do we have full genomes on most these plants. All these things work together to make the molecular clock really bad in these cases. We are not troubled, because there are just to many unknowns to make a confident calculation.

In contrast, human/chimp evolution is about 6 million years, we have a much stronger fossil record, and we can and have directly measured mutation rates, and we have full genomes now too.

We found out a long time ago from studies like this that mutation rate varies a great deal. However, we did not know how to directly measure mutation rate till the last decade. That is what provides the independent verification.

@scd, you do not have to agree, but you have an opportunity to understand the thing you reject. Give that a shot.

Earlier, we looked at different parts of the genome (Y-chromosome vs. the rest), and compare their rates and divergences to test of common ancestry. That comparative work removes a great deal of uncertainty and the unknowns, and makes the results much more accurate. It is a very well controlled experiment.

Very closely related to this conversation is some work that Stephen Shaffner did. His angle uses the same formula (T = MR), but focuses on different types of mutations, and the relative differences in rates. He looks at the very tight correlation between the variation among humans, and the differences between chimps/humans, and other species too.

The key point about this analysis is that it does a much better job controlling for uncertainties in T and R. We know T is hard to tell from the fossil record. We know that R varies by type of mutation (we can measure this in the lab). So instead of trying to infer T, we can just see if the relative rates ® match up with the relative differences (D) for different classes of mutations. That is why the fit is so tight on these graphs. It is a much better controlled experiment.

From here, we can see that there are several lines of converging evidence, that are all correlated with each other.

  1. Mutation rate (the rate of change)
  2. Variation (difference between genomes of the same species)
  3. Divergence (difference between genomes of different species)

All these things are tightly correlated. Without common ancestry, there is no reason divergence should be correlated with these things.

Human variation, which is the cumulation of a lot of mutations, looks just like divergence (human with other species) as if it is the cumulation of a lot of mutations too. That is the key point. It just looks like the differences are the result of the cumulation of a lot of mutations by the same process.

See the data below…

This carries over to other species divergences too.

This statement sounds like there is a relationship between the amount of mutations as a whole and the functional mutations. That is, where there is a lot of “noise” there are more functional or “target” mutations.

Then when I pointed out that a comparison of rat/mice to human/chimp genomes shows that though the former has more “noise” the later seems to have more functional genetic differences you write…

So that statement seems to say (correctly I think) that there is no strong positive correlation between the amount of “noise” (mutations that are not important functionally) and the number/magnitude of functional differences. Chimps and humans don’t have as much noise as rats/mice, but clearly are much more different than rats/mice. Not sure that fits with your first statement. There are more differences in function than expected given the low amount of “noise” given your first statement.

To me, that is the fingerprint of God. There are more functional changes in less amount of time than is typical with what we typically see in other parts of nature. To you, the environment just drove the changes faster. No problem. Me, I wonder if the fast changes really happened by the same process as the slow changes. Sort of like @Jongarvey 's latest post at the Hump of the Camel. Or as I was pointing out on the whale evolution thread between the very slow changes in roquoral whales compared to what we know about Pakecitus to Rodhocetus.

I see it as a problem, if common descent with special creation at least of specific genes and proteins is automatically excluded from consideration, as it is by others not you. If they can’t make verifiable predictions yet about how fast nature can create observed change in function then its not even a theory yet, maybe not even a hypothesis unless it can be tested without numbers. They can’t rule out the finger of God until they are able to quantify what can be expected from the “natural” universe alone, quotes around that in a tip of the hat to JG.

Not just quantity, but quality too. That is, how big a jump in say…protein fold changes can “nature” make by processes we know about. If those changes can’t accomplish the changes they think happened, then they are missing something.

I know you have a broader view of “common descent” than your more secular colleagues. Maybe I should focus more on the theology. I am not sure there is any real resolution to this issue with our present level of knowledge. I just don’t want naturalists in the name of science attempting to impose a resolution before we truly have one by sweeping these sorts of incongruities under the rug.

I hate all this what do you mean by evolution stuff. Then people will list off 5 definitions for evolution. Just stop. Everyone knows what is meant. When talking biology you can understand evolution in two ways. 1. The thesis of common ancestry. Or the process by which new species emerge as the modified descendants of pre-existing ones. 2. It can be understood as evolutionary theory. Or the tgeory that explains how evolution has taken and still takes place on earth, with reference to particular, old and current, aspects of life on Earth and to particular episodes of its history. Simple as that.

1 Like

We will never be able to rule in or rule out the finger of God.

It is not a problem to exclude God’s action from the outset because the purpose of science is not to determine God’s action. Rather it is to understand creation, the way nature works. To understand God’s action, we look to Scripture.

Science, at absolute best, only gives us partial accounts of the world. Never complete descriptions or entirely sufficient explanations. This is transparently obvious to most people who actually work as scientists.

I see your frustration, but it is helpful to focus it in on common descent, of which the common descent of man is the most important example. All the conflict has, historically, centered on the evolution of man. That, also, is where the evidence for evolution is the strongest. When we see the evidence for the evolution of man, and theologically come to terms with that, there is no reason to hold out on all the rest.

hi prof swamidass.

but this is a problem for several reasons:

  1. it means that evolution cant predict what will be the difference among species. and therefore evolution cant be test at this point.
  2. we can claim such a thing to any such contradiction we will find.
  3. this evidence fit naturally with special creation but not with a common descent. so the best (and simplest) explanation will be creation in this case.

how we can know it for sure? for instance: if we have T in human, how do we know that the original base was A?

This is a complete non-starter for me, @anon46279830.

If the natural universe couldn’t pull it off, there would be no need for God to hide this fact.

@scd,

Common descent is a default logic. If the earth is 5 billion years, common descent is unavoidable… because nothing can stop DNA and RNA from changing and evolving.

Rejecting common descent is like rejecting the age of the earth.

Now, if you insist the Earth is 10,000 years old or less, then you are not just making a religious avowal, you are also opposing the eye witness of nature . . . and to no avail! Why? Because if think most of the fossils are from the flood, you still end up with the inexplicable:

  1. where are all the human fossils that should be in the same layers as the dinosaur fossils?

  2. to end up with the 1.5+ million species of terrestrial creatures that we see in the modern world, you still have to conclude there was hyper-evolution in the animals released from the Ark.

None of these conclusions can be sustained!

I am sorry you feel that way. I don’t see that He is “hiding” anything. We just don’t have the ability to see everything, along with extreme personal bias when examining the evidence.

@anon46279830

I do not accept the position that God was “compelled” to do things in a way to that fools humanity into concluding what would otherwise be a common-sense conclusion.

The default position satisfies Occam’s Razor better than any other position.

Nor do I. He is not “compelled” to do anything but tell the truth since His Word is Truth. Your basis for the assumption that He is “fooling” us is based on the idea that we should be able to detect His intervention at our current level of knowledge. That is, that He forced big dramatic instantaneous changes that made a lot of “noise”. But if He has perfect knowledge why does He need tremendous force of intervention? Think of the “butterfly effect”. If He knows that a butterfly flapping its wings and time and place “X” will cause a hurricane 1,000 miles away next week, why does He need to get a big spoon and stir up a hurricane?

That’s not Him “hiding” anything. Maybe inside a certain window of knowledge we can’t see it but when we press on it is even more sublime than His getting a big spoon and intervening with a lot of force later rather than use a maximum amount of wisdom and foreknowledge to do the same things with minimal force.

In your view the conclusion is “common sense”, but I and others on this board have pointed out situations where some things happened that are not “common sense”. Again, you have to be able to see things from outside your own skin. Pakicetus to Rohocetus in 200K years coming from the same processes which took blue whales and finbacks 3 million to split up is not “common sense”. It is something a reasonable person should be able to question.

So much of the “noise” being generated by the debate of “creation versus evolution” comes from a fundamental misunderstanding of the Hebrew term translated by the English word “create.” The Hebrew verb “bara” carries with it no connotation of how, or even how quickly, something was done.
Let me illustrate, because not even the word “create” in English does so.
Starting from a huge slab of marble, Michelangelo masterfully and painstakingly, over a long period of time, carved out a sculpture called “The Pieta,” a masterpiece of art. Were we to have asked him at the time whether he was the one who made the carving, he might have said (in Italian) “yes; I created it.”
He would not thereby have communicated any information whatsoever about HOW he did it, nor of HOW LONG it took.
Similarly, when confronted the biblical statements regarding God having “created” something, we have to look deeper into the context for any such information, since the phrase itself is not specific.
So, please, please, please stop hearing “all of a sudden, out of thin air” when you come across this word in the Bible. Instead, you can focus on the de novo nature of what was accomplished, when this phrase is used.
'Nuff said. Cheers!

1 Like

@anon46279830

No. The basis for my assumption is that the natural evidence that God has led for us can only be humanly interpreted to support evolution. There can be no expectation that humans should be able to see that Evolution is not true. The evidence is so compelling (compelling enough for you to be an Old Earther when so many YEC’s are not) - - there is really only one way to conclude the age of the Earth.

Common descent with modification is in the very same category.

12 posts were merged into an existing topic: Cars, Biology and Evolution

Which is the other side of the same coin I described, but once again you fail to see that because you are extremely locked into your own perspective. My guess is that your are in a field or situation where everyone you work with has views very similar to your own in anything which matters to your work, or there is ongoing conflict. This has nothing to do with intelligence per se. Or maybe it is some specialized form of intelligence, but you simply cannot engage in productive dialogue “to understand and be understood” as it says in the blog intro, without making a far greater effort than you have managed to this point, to be able to understand and entertain thoughts with which you do not agree.

Wow. Plenty of people with doctorates doubt that it is true as a total explanation for life on earth. I don’t think anyone here argues that it does not happen. The debate is over how it happens and whether known evolutionary processes can reasonably be considered responsible for all of the changes in life observed in Earth’s history.

I agree the evidence is overwhelming for the age of the earth. I disagree that evolution by known natural processes as a total explanation for life on earth has anything like that level of certainty going for it. In addition, I am still able to dialogue with a YEC and address the things they consider as evidence on their own merit rather than immediately recoil and tell them that there is no debate and the evidence is so overwhelming that I don’t even need to consider or address (for example) an intact protein found in a dinosaur fossil. I can still consider their evidence even if I reject their overall conclusion about what it means. Because I can do that, I can comprehend how statements about their model fit into their framework and discuss it with them, even though I do not accept the framework.

My model is not a simple question of ‘evolution’ or ‘no evolution’. Creation is occurring in High Heaven and the Natural universe in parallel in Genesis chapter 1. There is a “land above” and a “land below”. In the land above, it is a lot like TE. God speaks, and the earth brings forth living creatures. He doesn’t have to do anything else. It just responds to His word. This realm is the place where His will is NOT done quickly, automatically, and perfectly. It may try, but it can’t do God’s will without God’s help anymore than we can. It is a place suitable for creatures like us, and a good place for deciding if we want to be where His will is always done or our unregenerated will is done.

Some ways this may have occurred also meet the bare definition of “evolution”, though avowed naturalists would object. Consider if you are able the following scenarios which I repeat from above…

For example “Descent with modification” is one definition of evolution, I guess a preferred one around here. To me it could also be a form of creationism or at least intelligent design, depending on how the modifications occur. For example, farmers breed animals for certain traits and get them through descent with modification. They select far more powerfully for desired traits than nature does. So that fits this definition of evolution, but surely it is intelligent design as well.

Let’s have a thought experiment: Now suppose instead of farmers who went around selecting for traits, God Himself did so. If a certain group got a rate mutation that would produce a benefit if paired with another mutation which existed only in a second isolated group He would know it and be able to put those two populations together so that they would have the suite of mutations that, when combined with yet another rare mutation four generations from now, would result in a new function. So He is using Divine knowledge to leverage natural processes to produce something new. I would say that is evolution (descent through modification), intelligent design (intent drives the changes not natural selection) and “soft-touch” creationism (He intervened in the natural world to produce outcomes even if He never touched the genomes directly, He merely guided natural events in a way that nature would not in herself at anything like the same rate).

Now suppose that instead of taking the role of a selective breeder (with perfect knowledge) only, He also assumed the role of Genetic Engineer. That is, instead of strictly waiting for Nature to come up with mutations which could be combined to create new function, He did just what our engineers do. He made cuts and inserts in genetic code. Maybe nature would never get a particular protein to fold just right waiting for chance or mutation so He inserted a gene which would. So when our scientists make mice which glow because jellyfish genes have been inserted in them, and this population breeds, is this “descent with modification”? Well maybe, but the modification did not come wholly by NATURAL descent. It is doubtless intelligent design and specialcreation, and questionably evolution as well.

That said, such a situation could still involve natural descent, but that would not be where the modification would come from. Take the gap between a fish and an amphibian. What if over the course of thirty or forty generations He put just enough changes in each generation that they would still be able to be birthed and bred by natural means but each generation would also be further toward the amphibian end of things. This so that even though no amphibian was created out of thin air, or clay, one still had a very different creature through only forty generations removed from the fish, thanks to genetic engineering moving things a bit further along each generation. That is “descent with modification” but the modification is via genetic engineering. So is that evolution, special creation and intelligent design all rolled up into one?

Like Jon, I don’t think “natural selection” or any of the natural means we have discovered could have on its own produced the vast diversity we see today or in the fossil record. I think nature had help. And I think some of this arguing we are doing over it is because we are talking past one another on terms.

1 Like

Well, looks like I had explained this wrong in the past. Sorry. It really should have read:

Sorry if that had confused anyone. It is supposed to read 10x more different, not 10x more similar.

@swamidass,

Generally speaking, a working hypothesis for this difference on differences would look at how many “changes” and/or the “depth of changes” chimpanzee populations have experienced compared to human populations.

Chimpanzees are not known for their robust ability to live in any part of the planet. While, in contrast, this is a hallmark of human populations.

While chimpanzees thoroughly exploit trees and forest canopies, at some point humans started to stake out the savanna biomes … learning how to “farm” all sorts of ecological niches, and becoming master generalists.

How we “quantize” environmental changes would be helpful in attempting to measure such things… but at least the concept offers some insights into what might encourage increasing genetic differences in one branch of the mammal tree, compared to rats and mice which may thrive to similar extent no matter what niche is occupied by either rats or mice.

@anon46279830

Oh for goodness sake… I’m a Unitarian Universalist. I’m about as “locked in” as an angel’s 2 year old toddler would be.

But this could still be the reason I react to your scenario the way I do. The one thing you encounter in the U.U. denomination is lots and lots of “what ifs” about religion, history, history of religion and the afterlife.

You have as much right as anyone to cook up your own recipe. But my study into the history of Yahweh-ism has put me in a rather archaeological/literary mode, where I take just as much input (if not more) from information outside the Bible.

You, on the other hand, have to keep linking up with the Bible’s plot structure. I think that’s unwise. And here’s where I think the problem starts - - with pond ripples proceeding outwards from there:

Exodus. Exodus could not happen before the arrival and consolidation of the Pelest/Philistines. This was accomplished around 1130 BCE. Before 1130 BCE, all the way back to the Hysksos, the Egyptian hegemony over the Levant and Southern Syria was incredibly consistent. It wasn’t perfectly consistent, but it would not be wrong to say that every 50 years or so, the Egyptians were crawling all over the highlands, past Jerusalem to Beth Sheehan, collecting tribute, farm products, and re-asserting their rule. That was 400 years or so where there is no way an Exodus group could have sat at the edge of the Sinai wilderness (for 40 years) and not have been wiped out by the Egyptians.

Once the Philistines consolidated, the Egyptians were barred from accessing the Sinai for a few centuries.

If your scenario can still function with an 1130 BCE Exodus, I’ll listen to you some more. But I don’t believe many Evangelicals are willing to accept the time frame.