April 24, 2017

Adam and the Genome 6: Chapter 3- Adam’s Last Stand? (Part 2)

strong>Adam and the Genome 6: Chapter 3- Adam’s Last Stand? (Part 2)

We continue our review of the book, Adam and the Genome: Reading Scripture after Genetic Science, by Dennis Venema and Scot McKnight. Today, Chapter 3- Part 2

In Part 1 of Chapter 3- Adam’s Last Stand?, Dennis summarized two methods of estimating the size of ancestral populations based on the present characteristics of that populations genome.  If there was a “bottleneck” of only two people then the genetic consequences would be severe: at maximum, four gene-forms (two from each parent) would be passed on by Adam and Eve. Interbreeding in the very small population after the bottleneck would result in the further loss of some alleles due to chance alone. In short, the genetic impact of such an event would leave a stamp on the genome of that species that would persist for tens of thousands of generations as mutations slowly generated genetic diversity.

This information can be used, then, to estimate the minimum number of people that could have existed at any point in time. First we ask how many different alleles there are for a number of genes within the current population. Correcting for the rate at which we know new forms of genes appear (mutation), we can calculate the minimum number of people needed to generate the current amount of diversity. Numerous studies analyzing many different genes all point to a bottleneck. However, these studies are all clear: during the bottleneck, there were several thousand individuals, not two.

The second method, independent of the first, is called “linkage disequilibrium”.  In population genetics, linkage disequilibrium is the non-random association of alleles at different loci (i.e. where on the chromosome the genes are located). Loci are said to be in linkage disequilibrium when the frequency of association of their different alleles is higher or lower than what would be expected if the loci were independent and associated randomly.  Based on the number of allele combinations that we observe in this population, how many ancestors do we need to invoke in order to explain what we observe?  In this case, rather than estimating mutation frequency, the calculations require knowing how often crossing over happens between two loci.  This is also something we can measure directly in humans and other animals, and there is a well-characterized relationship between chromosome distance between two loci and crossing over frequency.  As Dennis says:

“We’ve now done this sort of analysis for millions of pairs of loci (yes—millions) for each chromosome pair in our genome (all 23 pairs).  And what is the final tally after crunching all that data and counting up ancestors.  The results indicate that we come from an ancestral population of about 10,000 individuals—the same result we obtained when using allele diversity alone.”

The third and last method that Dennis outlines is called “incomplete lineage sorting” or ILS.  This method, like disequilibrium analysis, is virtually unaffected by varying estimations of mutation rates.

  • While humans and chimpanzees are the closet living relatives as species, we expect that some human genes will be closer matches to other apes such as gorillas.
  • When a population undergoes a speciation event some genes will have two or more alleles within the population as a whole.
  • As populations separate, they will both inherit that diversity. The two alleles are represented as shaded boxes on a phylogeny or “family tree” in Figure 3-5
  • The common ancestral population of gorillas, chimps, and humans has two alleles of one gene (“A” and “a”) within the population.
  • As the population separates into 1) human-chimp and 2) gorilla, both populations inherit both alleles.
  • In the gorilla lineage “a” is lost, leaving only variant “A”.
  • As chimps and humans split, “A” is lost and “a” is retained in the chimp lineage while in the human lineage “a” is lost and “A” is retained down to the present day.
  • The final pattern is:
    • Humans and gorillas have “A”
    • Chimps have “a”
  • Gorillas and humans now have more closely related alleles than either does with chimps.
  • This pattern lets us know that the common ancestral population of humans and chimps had both “A” and “a”
  • Also the common ancestral population of gorillas, humans and chimps had both “A” and “a”.
  • If you have a way to infer what genetic variants were present in a population, you have a way to estimate its population size.
  • Scientists predicted in advance of sequencing the gorilla genome, an ILS of 25%.
  • When gorilla genome was sequenced the observed rate was 30%.
  • Scientists predicted in advance of sequencing the orangutan genome, an ILS of 1%.
  • When the orangutan genome was sequenced the observed rate was 0.8%.
  • Those results indicated that the estimation of ancestral population size leading eventually to humans was accurate.

Dennis concludes:

“Put most simply, DNA evidence indicates that humans descend from a large population because we, as a species, are so genetically diverse in the present day that a large ancestral population is needed to transmit that diversity to us.  To date, every genetic analysis analyses estimating ancestral population sizes has agreed that we descend from a population of thousands, not a single ancestral couple.  Even though many of these methods are independent of one another, all methods employed to date agree that the human lineage has not dipped below several thousand individuals for the last 3 million years or more—long before our lineage was even remotely close to what we would call “human”.  Thus the hypothesis that humans descend solely from one ancestral couple has not yet found any experimental support, and it is therefore not one that geneticists view as viable.”

In the next section, Dennis addresses the question that genetics can’t answer: what did we look like and how did we behave?  That question can only be answered by the fossil record, which because of its nature cannot conclusively reveal who our direct ancestors might be; it can only show remains that would be those of close relatives.  At the time of publication of Origin of the Species by Darwin there were no known fossils that seemed to be intermediate between apes and humans.  A few Neanderthal remains weren’t well understood and were also very similar to modern humans.  At the time, there was a widespread expectation within the scientific community that an evolutionary lineage would be a ladder-like progression from one species to the next culminating in modern man.  You know the one I’m talking about; that looks like a police lineup (that has been endlessly parodied).

From Darwin’s ideas, scientists and the public expected there to be a series of “missing links” connecting humans to apes that could be found in the fossil record and that any such species would be direct ancestors of humans.  Since brain size was the obvious difference; scientist expected that “ladder” to show increasing cranial capacity i.e. evolution from the chin up and only then from the chin down.  This expectation would hamper research into human evolution for many decades.  One result of that false expectation was the fraudulent “Piltdown Man” with a human skull and an orangutan jaw with the teeth filed to shape them to the expected form.   As the paleontological data continued to accumulate the data increasingly showed that Piltdown man did not fit the pattern; that the pattern was indeed evolution from the chin down first.  Scientific suspicion of Piltdown man grew until the teeth filing was uncovered.  It should be noted for the record, that careful scientific investigation by evolutionary anthropologists eventually uncovered the fraud, not creation scientists doing “creation research”; although the creationist literature loves to cite Piltdown man as an example of how “science gets it wrong” and how we should “doubt science rather than the Bible when they conflict”.  It was “science” that eventually uncovered the fraud, but, as I’ve said before, the YEC are an irony-free community.

As we have seen for cetaceans, eventually a picture emerged that gives us a reasonable idea of how possibly our lineage changed as we parted ways with the lineage leading to chimpanzees.  Though chimps are our closest living relatives, there are a number of species in the fossil record known as “hominins” that are more closely related to us than to chimps.

“Probable hominins” like Ardipithecus ramidus, a species that lived in Africa about 4 million years ago (mya) had skeletal characteristics intermediate between upright walking and the climbing of trees, and a small cranial capacity of 300-350 cubic centimeters (cc) (modern humans are about 1,300-1,400 cubic centimeters).  Australopithecus afarensis (aka Lucy) about 3-4 million years ago shows further shifts toward walking and a cranial capacity of 400-550 cc.  Later still we see pre-modern Homo erectus (“Upright Man”) dating to about 1.8 mya with full bi-pedalism and a cranial capacity of 700 cc.

The Smithsonian has an insightful illustration with careful artist renderings:

In Dennis’ words:

“Similar to what we discussed regarding whales, we cannot be certain that any of these species is in fact a direct ancestor of present-day humans.  What these species show us is the probable path of our actual lineage, since these species are at least close relatives of our ancestral line.  The evidence thus suggests that our lineage over the past 4 million years passed through an Ardipithecine-like species, on to an Australopithecine-like species, and then through various shades of Homo until our species is first preserved in the fossil record 200,000 thousand years ago.  And as we have seen for languages, the process was a continuous one of average change within a population over time.  What we see in the fossil record matches up with what we see in our DNA.”

In other words, we have failed to reject the hypothesis that humans share a common ancestral population with apes.

• • •

Other posts in the series:

Comments

  1. So where did the ‘original’ genetic diversity come from?

    • Great question! My understanding is that the genetic diversity of the common ancestors are essentially unbroken back to LUCA (last universal common ancestor due to mutations always occuring. Also there was a major leap forward in maintaining diversity when sex was invented, or discovered, or just happened– they couldn’t help it – they were young and in love– the sun was setting– the tide pool was warm and inviting… and then LIGHTNING. Of course I am given to understand that for a billion years or so she wasn’t in the mood… so we had to self… um… um self… um … self-replicate. Okay, I’m clearly in over my head… DENNIS!!! DENNIS!! ARE YOU OUT THERE!!!

      • …on the other hand, maybe there’s something to be said for a 10k-young universe after all. 😉

    • Adam Tauno Williams says:

      My understanding – which is very limited – is that this question is a very different one as it predates the question of human origins by unimaginable periods of time – and that the answers are much more speculative. Likely as soon as you had something like genetic encoding of information you would have had mutation; possibly at higher rates than ‘modern’ life, as genetic systems optimized themselves to be more stable.

      If you find ‘standard’ genetics crazy complex take a look at the ribosomal DNA – there is a rabbit hole! 🙂 We’ve got nuclear DNA, mitochondrial DNA, ribosomal DNA…. everything they taught me in junior high was rubbish! Having, at least attempted, to read some literature on the Ribosome when I see descriptions like “the ribosome is a complex molecular machine” I want to laugh out loud. A lawn mower is a complex machine… the ribosome is a locomotive.

      And we haven’t even mentioned the archaea with their single circular chromosomes!

      • Adam Tauno Williams says:

        Meant to be a reply to Ben’s “So where did the ‘original’ genetic diversity come from?”

  2. Mike the G, I don’t get who the target audience is for this book. I’m skimming your review enough to see that it is much like an undergraduate college course. I’m confidant that if it was important to do for some reason, I could study it and comprehend enough to pass a test, but it would be of absolutely no use to me in real life unless, God forbid, I had to have passably intelligent conversation with scientific evolutionists. I consider both young earth creationism and scientific evolutionism to be equally silly, and realize that both factions would consider me and my views as even more silly. At the end of the day, none of this affects me one way or another, but I can’t imagine your average independent fundamentalist baptist buying the book, poring thru it over countless hours, and becoming convinced of its truth in some great epiphany. Who do you see reading this book other than a few believer scientists such as yourself or a few Bible college professors such as Scot McKnight? The book is cheap enough, but so far it would be even cheaper just to hit myself in the head with a hammer. However thanks for making this effort, which I realize is considerable. I’m following along, sort of, and expect the conversation to get even more interesting to me when Scot joins in later.

    • I think, Charles, that books like these are most useful for those who have already started their journey away from YEC and literalism. My hope is that will be more and more evangelical Christians as time goes on.

    • The problem is that anti- science types make claims about science which can only be refuted fairly by understanding the science to some degree. This inherently gives the anti- science crowd an advantage, because when it comes to arguing with rhetorical ploys, appeals to emotion and preconceived ideologies– basically the usual modes of discussion you find in politics– creationists will ” win” with their target audience and the New Atheists will ” win” with theirs. I lump the New Atheists in with the creationists not because they are anti – science, but because they argue in a similar rhetorical appeal to emotions style against religion ( and I am definitely not saying all atheists do this, because they don’t).

      Anyway, if you actually want to explain the case for evolution in a way that refutes creationist claims, on some portions of the science you have no choice but to get somewhat technical. If people don’t want to follow along, that’s fine, but they should also admit they are incapable of judging the science until they do the necessary work and stop using the folksy cow manure arguments against evolution.

      • Adam Tauno Williams says:

        I understand what Charles is saying – but to people who have been indoctrinated that this is a critical issue upon which all things hang it is a critical issue; it has enormous existential implications. I know people who would have read this book if it existed at the time.

        I have personally never felt biological evolution had enormous existential implications . . . . but I was not raised in a YEC household. But I have witnessed people twisted into painful knots where letting go of YEC was an agonizing processes – or at least who have to deal with aggressive YECists in their day to day lives [family?].

        Isn’t it natural that when one comes to the point of realizing one thing is not true to ask what the alternative(s) are? That is healthy curiosity.

        • >> . . . people who have been indoctrinated that this is a critical issue upon which all things hang . . .

          Adam, I understand that this point is considered the main point by some, but it really isn’t. The main point concerns the Bible understood by the letter rather than by spirit as the foundation of our reality and our salvation. And I consider that belief as no skin off my nose anymore than the belief in Darwinian evolution. They are simply different stages in the growth of consciousness. At one stage you learn your ABC’s and your 2 plus 2’s. At another you learn how to calculate square roots, tho I doubt if that is taught anymore. At another you can learn Calculus if you are so inclined, which I have not been as of yet.

          What makes this of any importance is the obvious presence of those with skinned noses that won’t heal. I have been so determined not to be bamboozled for so long that I have trouble understanding people who refuse to walk out the open door in front of them, or rather refuse to put down the big sack of baggage too large to fit thru the door. At the same time, part of that sack of baggage is often the fierce determination not to be bamboozled.

          How to deal with this is simply a problem to be solved as best possible in my view, and I don’t think the best way is to focus on peripheral issues, tho that may help. I tend to let sleeping dogs lie. Where it gets thorny in my view is in people who have been raised in lower consciousness beliefs and who appear to be permanently indoctrinated and injured. Do we call this child abuse and take such children away from their parents? That’s a two-way street that I don’t want to see heavy traffic on. Does StuartB wish he had been put into foster care as a child? I can’t answer for him, but if he would say no, or even yes for that matter, how then can we best help bring about healing and wholeness for Stuart? Is this book we are studying helpful to him? Is it helpful to Mike the G other than as a Darwin for Dummies so he can drink beer with his scientist friends without looking stupid? I’m not speaking against the book, just trying to understand who here is being helped escape by it and how.

          • Klasie Kraalogies says:

            Charles, truth matters. Obviously at some point Mike and I diverge at some point as to what the truth is, but for both of us, truth matters. We cannot assume it doesn’t matter in this or that aspect of reality. Furthermore, and this is an argument I have often made, if we cannot trust our senses by and large, we cannot trust any information- and that would include the very Scripture you base your beliefs on.

            If we can treat reality in a cavalier fashion, then well, nothing matters for nothing is true or real – and by extension, beautiful or good. All would be a postmodern mishmash…

            • >> that would include the very Scripture you base your beliefs on.

              Klasie, that is the whole point of young earthers. They base their beliefs on Scripture, as do most Evangelicals, and they fiercely resist any information, such as this book, which threatens their understanding of Scripture. I would say that their understanding of the truth of Scripture differs from mine, as does mine from yours, and yours from Mike’s, and so on. At some point it should become obvious that there is no claim to absolute truth in a relative world, and that nothing can be held “true” outside of a specific context, and this is what separates postmoderns from moderns. In that you describe what seems obvious and a done deal to postmoderns as a mishmash, you evidently reject this whole evolutionary turning of the world. Perhaps you reject quantum physics or metaphysics as well.

              I agree with you that truth matters. I consider myself a truth seeker, and long ago decided to follow truth wherever it led. When I speak of truth, I always try to put it in a particular context because otherwise claims of absolute truth are ridiculous in a world of relativity and only lead to futile argument and worse. I do not trust my senses to be absolutely accurate, nor do I trust any given information to be completely accurate. Indeed both senses and information can be wildly inaccurate. I proceed on the basis of probability. Experience tells me it is highly probable that when I get out of bed in the morning, the floor is going to support me and I do not have to grasp a rope hanging from the ceiling. That doesn’t mean the floor can’t collapse under me or even the solid earth, but this is so unlikely I don’t have to think about it. It is also possible that my solid experience of God could collapse, but so far it’s more solid than the earth we walk around on.

              I expect your idea of “reality” is very much different than mine, and that’s okay with me. I can say the same about most people’s idea of reality and it doesn’t stop me from living in my reality or from interacting with people who live in a much different world. It is not required that you think like me or believe what I find probable. I have no reason to try to persuade you to think like me, nor do I have any reason to try persuading young earthers or flat earthers or anyone else set in their beliefs. On the other hand, I do like to let people know there are options. My beliefs are a lot more fluid and expansive and subject to revision as I learn more along the way. If you want to call that “cavalier” it’s not going to change my ongoing quest in the slightest.

              • Klasie Kraalogies says:

                I think you misunderstand me completely regarding my poibt about scripture. The fault the YEC’ists make is one of interpretation. If we cannot trust our sense we cannot absorb any information – by text or any other way. Basically, not to be too simplistic, you cannot assume the words “For God so loved the world…” don’t actually say “I want a pb&j sandwich”. You destroy all epistemology, all language, and therefore all religion and faith. It is the ultimate (extreme) post-modern trap. However, if things mean things, if symbols can be set to impart information, if logic is true (and yes, without logic there is no langauge), then science comes into play. How you interpret it is not something I can dictate to you- you can listen to the wise words of Mike, or the foolish nonsense of Ken Ham, or even my own babblings, but you pushing your head deeper into the sand is a particularly unique brand of foolishness. And I say that as a friend (I hope).

                • Robert F says:

                  Without objective truth that doesn’t depend on interpretation (which is not the same as uninterpreted truth; all truth is interpreted, it’s just that there are correct and true interpretations, and incorrect and untrue ones as well) for its meaningfulness, no correct information could be transmitted by language or any other means. The problem is that the YECists are incorrectly interpreting scripture, and as a result are arriving at incorrect understanding about human origins and other matters too. When post-modernism asserts that no meta-narrative is true for everyone, it is actually asserting its own meta-narrative, and thereby contradicting itself.

      • Well put, Donald and Adam.

      • Headless Unicorn Guy says:

        The problem is that anti- science types make claims about science which can only be refuted fairly by understanding the science to some degree.

        And in the time it takes to start giving that understanding, a saturation barrage of more Bible Bullets are incoming, Fire For Effect. (“SCRIPTURE! SCRIPTURE! SCRIPTURE! SCRIPTURE! SCRIPTURE! SCRIPTURE! SCRIPTURE! SCRIPTURE! …”)

  3. I wasn’t intending my remark to be criticizing Charles for rejecting evolution. I was just pushing back on his implied criticism of the book. There is a need for books like this for anyone who really wants to understand some of the science without becoming a biologist. You could read some population genetics texts, but they aren’t written for the specific purpose of refuting creationist arguments. You can also stick to the easier material already available, but then you won’t know why scientists think there were never just two humans alive at one time. Books like this bridge the gap for people who aren’t going to read population genetics texts, but want to understand the arguments to some degree.

    • Well, that appeared in the wrong place. I meant it to be a reply to Adam replying to me replying to Charles.

  4. Headless Unicorn Guy says:

    At the time, there was a widespread expectation within the scientific community that an evolutionary lineage would be a ladder-like progression from one species to the next culminating in modern man.

    The Victorian-era baggage of evolution (the word) as Linear UPWARD Progress, not the branching bush with no intrinsic direction. That’s why Darwin himself preferred the term “Descent with Modification”.

    “The Victorians thought that history ended well because it ended with the Victorians.”
    — G.K.Chesterton

    You know the one I’m talking about; that looks like a police lineup (that has been endlessly parodied).

    i.e. The Sixties-vintage Time-Life Books “March of Evolution” graphic.

  5. Robert F says:

    I have no skin in this game. I accept the truth of evolution, and have since I was a kid. Dinosaurs and Neanderthals captured my imagination while Adam and Eve didn’t, and my public school education left no room for creationism. But anyway you cut it, I’m still lost in the cosmos.

  6. Not sure exactly where to place this comment because it fits as a reply to several items posted here already. To those who don’t see the big deal about human origins– the audience of this book is the same audience that Rachel Held Evans and Peter Enns are reaching. For the half billion members or so, at least the time I looked it up, of denominations and groups who subscribe to inerrancy and literal interpretation, human origins is a big deal. Why? because for THAT camp, it’s all tied together–literal interpretation, sotierology, original sin, YEC, dispensational eschatology, inspiration, etc, etc. For them, it is all tied together, you take one thing away, it all falls apart. All of it. That is why they fight so hard, despite all the evidence to the contrary. If you haven’t been a part of that scene, you probably just won’t get it. It’s hard to explain to someone who wasn’t there. For example, when I first read Evans’s “Monkeytown” it had a huge impact on my life, because I share her experiences. I had a friend read it, and she didn’t get it, but she grew up Lutheran. For so so so many, taking away Adam and Eve as the singular parents of the whole human race, well, it just unravels everything.

  7. >> For so so so many, taking away Adam and Eve as the singular parents of the whole human race, well, it just unravels everything.

    Joe, why in the world would you or any professing Christian want to bring this level of sudden angst and devastation to anyone on purpose? You seem to take great pleasure in it. I can see the benefit of someone who has begun to doubt their upbringing reading this book and the others you mention, but why do you think any of your half billion who subscribe to inerrancy and literal interpretation would even consider reading something which would make their whole world fall apart? Rather than pulling out the cornerstone and having the whole edifice collapse and bury someone, it seems to me there must be better, gentler ways of helping someone think outside their box. Maybe not as easy to come up with as smiting, and probably not as satisfying to the ego.

    • I really don’t know how you could take that I would get pleasure in it. If that is what I implied, I am sorry. That is not what I am saying. I am not saying the intended audience is the half billion members of said denominations who buy the whole she-bang. You’re right, they wouldn’t pick it up. I am just trying to explain why they would not pick it up, and why to them this is a big issue. I am not saying it is a big issue to me. I myself am in recovery from an upbringing in that camp. Unless you’re ready for this information (“already begun to doubt their upbringing” as you say), it won’t find a place to grow in your mind. You really can’t win the argument with that crowd. They won’t really engage in honest, open debate, at least in my experience. They dig deep and double down when confronted, because they know it will all unravel if they give any ground.

  8. >> You really can’t win the argument with that crowd.

    Absolutely, Joe. That doesn’t seem to stop folks from trying, and I consider it a complete waste of time. Even worse, as you say, it just causes a double down and heels dug in. Doesn’t mean there aren’t ways of reaching folks at that level, but coming up with that is a lot more difficult than arguing and lawyering and apologetics, which I think too often is just done to make the arguer feel self-righteous. As has been pointed out by a lot of smart people, you can’t solve a problem with solutions from inside the box that made the problem. I think the best approach would be to educate the pastors first, but in order to educate someone you have to understand what it is you’re trying to overcome, and I don’t think people with “higher” education are very good at that. And of course some pastors are just plain unreachable. Another approach would be trying to reach young people. And sometimes you just have to let folks be.