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Does Genetics Point to a Single Primal Couple?

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April 5, 2010 Tags: Human Origins

Today's entry was written by Dennis Venema and Darrel Falk. You can read more about what we believe here.

Does Genetics Point to a Single Primal Couple?

A Single Primal Couple?

Most Christians who have grappled with the science of genomics (the branch of biology that compares the DNA sequences of different organisms to one another) have done so with the question of common ancestry in mind: do humans share an ancestor with other forms of life, such as chimpanzees?

Here the evidence is very compelling, and reasonably accessible to non-specialists. For example, the human genome has numerous defective genes embedded it, and the vast majority of these defective genes are also present in the chimpanzee genome in the same relative positions with identical mutations. This sort of evidence is easily understood due to its qualitative nature.

A second question, and one that is less frequently explored even by Christians who accept common ancestry, is the issue of human/hominid population sizes during our evolutionary history. Specifically, is the human race descended from one ancestral pair in the recent past? Are we, as C.S. Lewis puts it in his Chronicles of Narnia, the “sons of Adam and daughters of Eve”? Is there genomic evidence to suggest that the human race is genetically derived from a primal pair? Here the evidence is more difficult for non-specialists to appreciate, because it is quantitative in nature.

Genomics can be used as an estimate of population sizes in the past by measuring genetic variation in the present. Genes come in different forms, or alleles: for example, the human ABO blood types are determined by three alleles of one gene. Some genes in human populations exist in hundreds of forms.

The catch, however, is that any individual person can only carry at most two different varieties of any one gene: one from mom, the other from dad. It therefore follows that a large population can pass on a large number of gene forms (alleles), but a population that passes through a population “bottleneck”—where only a small number individuals survive—will fail to pass on most of its genetic variation to future generations.

Attempting to square the Genesis account and common ancestry by positing a literal Adam and Eve who were the progenitors of the entire human race is, biologically speaking, looking for the most extreme population bottleneck a sexually reproducing species can experience: a reduction to one breeding pair.

Is there evidence that such a bottleneck has ever occurred? Dr. Peter Enns has been exploring whether this is even the right question to be asking from a biblical perspective (here, here, here, and here). Here we explore three independent ways of answering the question, this time from a biological point of view.

Method I:

The genetic consequences of a bottleneck required by a literal reading of Genesis 2-3 would be severe: at maximum, four gene-forms (two from each parent) would be passed on by Adam and Eve. Interbreeding in the (necessarily 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.

We can use this information, 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.

Method II:

In earlier posts, we have discussed the fact that DNA segments known as Alu repeats, can insert themselves at various locations the genome. It turns out that the Alu sequence comes in various forms, like different makes of cars—Fords, Toyota, etc. There are several thousand families of Alu.

Consider just one family, which we will call Ya5. Members of this family have been inserted into human chromosomes at 57 mapped locations. If all humans descended from a single pair of individuals, all humans would have each of the 57 elements in pretty much the same locations, since individual members of the family almost never move. However, the human population consists of groups of people who share some insertion points but not others. The multiple shared categories make it clear that although a human population bottleneck occurred, it was definitely never as small as two. In fact, this line of evidence also indicates that there were at least several thousand people when the population was at its smallest.

This method is much different than Method I since it does not depend upon mutation rate, but the answer is similar.

Method III:

A third independent estimate makes use of a concerted research effort called the HapMap project. Humans have 3 billion bits of information in their genomes. (The official term for one bit is a “nucleotide.”) The bits between any two individuals differ at many sites, which is, of course, why we don’t all look the same.

In the HapMap project, one million of these differences have been analyzed by examining something called linkage disequilibrium The technical details are beyond the scope of our discussion, but to give you a feeling for how it works, imagine that you have a gene for blue eyes and a gene for a bent finger, both of which you inherited from your dad. Assume these genes reside in the same “neighborhood” on chromosome 2. Because these genes are close to one another, chances are that if your brother got the blue eye allele from your dad, he would have received the bent finger allele as well. After all they are neighboring genes, both on chromosome 2. Why? Blocks of genes in the same neighborhood on a chromosome are usually inherited together. Alleles that are very close together on chromosomes tend to stay together for many generations before they are “mixed and matched” through a process called recombination.

Now pretend that someone analyzes both your DNA and that of your brother in a double blind experiment. The investigator would, upon examining the results, be able to say, “I’ll bet these two people are related to each other.” And he would be right.

Now picture being able to do this, not for two differences, but for a million differences all at once and not just for two people, but for many people from all over the world. Using this approach, it is possible to tell how many people gave rise to all the prevalent combinations of differences. In short, we can tell if everyone came from just two people at any time in the last 200,000 years. So did we?

No.

This third independent method tells us that everyone alive today is related, but not to a single pair of people. We are related to a population that consisted of several thousand people with their several thousand combinations of these million genetic differences.

Here’s the real point of this. When you have one way of doing a calculation and you get a certain answer, perhaps you are justified in being a little skeptical. Perhaps you made a mathematical mistake, or maybe you made a faulty assumption. However, when you do your calculation using two totally different approaches, using methods with completely different assumptions, and each method gives you the same answer, you become convinced it is correct. Three, of course is just icing on the cake.

So that’s the situation we are in with regard to the human population size in ancient history. There was a bottleneck. There were likely fewer people alive during that time than the number of fans attending a typical NHL hockey game. (We don’t know if they were all together in one village, of course, but the total was small.) However, it was not two people. Our species diverged as a population. The data are absolutely clear about that.

References:

  1. Relethford, JH. 1998. Genetics of modern human origins and diversity. Annu. Rev. Anthropol. 27: 1-23.
  2. Tenesa A, Navarro P, Hayes BJ, Duffy DL, Clarke GM, Goddard ME, Visscher PM. 2007. Recent human effective population size estimated from linkage disequilibrium. Genome Res. 17:520–526. (available free here)
  3. Sherry ST, Harpending HC, Batzer MA, Stoneking M. 1997. Alu evolution in human populations: using the coalescent to estimate effective population size. Genetics 147:1977-1982. (available free here)
  4. http://hapmap.ncbi.nlm.nih.gov/index.html.en

 

 


Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.
Darrel Falk is former president of BioLogos and currently serves as BioLogos' Senior Advisor for Dialog. He is Professor of Biology, Emeritus at Point Loma Nazarene University and serves as Senior Fellow at The Colossian Forum. Falk is the author of Coming to Peace with Science.

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Dennis Venema - #8925

April 6th 2010

Hi Martin,

(Dennis is fine, BTW).

I’m glad you found Todd’s paper helpful. It’s a shame that this paper is not more widely known - it has never been linked to or openly discussed by any YEC ministry as far as I know (e.g. ICR, AiG).

I too admire Todd’s theological commitment, but (obviously) I don’t agree that his approach to Genesis is the only acceptable Christian one.

Best,

Dennis


Gregory - #8932

April 6th 2010

Just a very short note to say that ‘Christian’ and ‘secular’ are not very good ‘opposites’ to apply in most cases. C. Taylor’s recent massive book “A Secular Age” shows this quite clearly. Almost without exception when I read the word ‘secular’ on discussion boards these days it refers *only* to types 1) and 2) but not to the more important type 3) of ‘secular’, as Canadian Catholic Taylor, following the work of Brit Protestant David Martin (see “A General Theory of Secularization”, 1978), indicates.


pds - #8933

April 6th 2010

Dennis,

The article simply shows that we cannot be certain about using molecular evidence to extrapolate back in history.  I had no special point about vertebrate phylogenies.  That is just one of problems I see in Darrel’s assertion:

“We do take a firm position on the scientific fact that two people could not have been the genetic progenitors of all humankind.”

I see this as overly dogmatic and not established by the evidence presented.

Thanks for your comments here.


Dennis Venema - #8936

April 6th 2010

Hi pds,

Thanks for the clarification. Does it not strike you odd that the authors of the article in question do not draw the same conclusion you do? Scientists like nothing better than to start a controversy if they think they have evidence to warrant same.

I agree that horizontal gene transfer (HGT) in single-celled organisms makes for interesting challenges in deducing phylogenies for them. I still don’t see how this applies to vertebrates, like humans, unless you’re positing that we also have HGT! The tree of life may be a mangrove, but we’re a well defined branch well above the waterline.

Best,

Dennis


Martin Rizley - #8944

April 6th 2010

Dr. Venema,
Regarding the human/chimp genetic similarities, are you familiar with a recent article published in the journal Nature entitled “Chimpanzee and Human Y Chromosomes are Remarkably Divergent in Structure and Gene Content.”  Apparently, the main thrust of the article is that recent research shows that human and chimp DNA is more divergent than was previously thought.  Apparently, according to the article, the human Y chromosome looks just as different from a chimp as the other human chromosomes do from a chicken.  The ICR website has a recent article that summarizes these recent findings.  You can read it at the following website:  http://www.icr.org/article/5292/


Harry - #8946

April 6th 2010

Martin,

Todd Wood has already made a blog post on that article some time ago, and even predicted how deniers of evolution would attempt to portray it. ICR is not a reliable source for information on genomic research.

http://toddcwood.blogspot.com/2010/01/chimp-and-human-y-chromosomes-radically.html


Harry - #8947

April 6th 2010

Just thought I’d add that Wood also explained in his paper that attempting to emphasize differences between the genomes (something done by groups such as Reasons To Believe, and now increasingly by other groups) does basically nothing to the overwhelming appearance of common descent. No matter how many differences can be pointed out, or how many studies show certain regions that are quite divergent, it is a fact that the human genome (taken as a whole) more closely resembles the chimp genome than the gorilla genome does (assuming the same methods for comparison). There is no way around this.


DWDMD - #8973

April 7th 2010

What continues to strike me through all the Biologos blogs is how so many writers assume that interpretating Genesis 1-2 literally is more biblically faithful than interpreting it as ancient myth through which God the Creator told us what we need to know about who God is and who we are. It seems very egocentric to me that a person may rate his literal interpretation (which IS an interpretation, BTW) of Creation stories as truer than than the metaphorical interpretations of Christian Old Testament scholars as well as traditional theologians throughout history - especially those theologians closest to the time of Christ himself! (cont.)


DWDMD - #8974

April 7th 2010

I am sure Augustine’s quote must have posted on this site before, but here he is again:

Usually even a non-Christian knows something about the earth, the heavens, and the other elements of the world…and this is knowledge he holds to as being certain from reason and experience.  Now, it is a disgraceful and dangerous thing for an unbeliever to hear a Christian presumably, giving the meaning of Holy Scripture, talking nonsense on these topics, and we should take all measures to prevent such an embarrassing situation, in which people show up vast ignorance in a Christian and laugh it to scorn (Augustine The Literal Meaning of Genesis.i.19)
By denying well-founded science on a supposed biblical basis, we are hurting our witness for Christ in the world! We are making God too small, as Peterson says. Jesus is the Word and it is in cooperation with his active, living presence that we interpret the Bible.
Diane


Bilbo - #9003

April 7th 2010

HI Dennis,

I’m curious about the bottleneck.  So we are all descended from “several thousand” humans.  Who were they descended from?  Let’s say that at 150,000 years ago there were 5,000 humans that we are all descended from.  How many humans were there 151,000 years ago?  More or fewer?


John VanZwieten - #9009

April 7th 2010

Bilbo,

If there were fewer before the bottleneck, then the bottleneck would be pushed further back in time.  That logically leaves “more” or “the same” as possible answers.


Bilbo - #9027

April 7th 2010

John: If there were fewer before the bottleneck, then the bottleneck would be pushed further back in time.  That logically leaves “more” or “the same” as possible answers.

Should we extrapolate from this and say that at some point in the past there were 6 billion humans?


Bilbo - #9028

April 7th 2010

Or if it’s the “same,” are we saying that several thousand humans just poofed into existence at the same time?


unapologetic catholic - #9031

April 7th 2010

Bilbo at 9027 and 9028.  Neither.  Extrapolaiton quickly leads to absurd results   You can’t assume anythign close to unique ancestors for every person at any oen time. Just look at extrapolating today’s six billion human population back to the time of Christ and you’ll see the difficulty.

And nobody I am aware of claims poofery.

Populaitons of humans could have remained fairly stable for hundreds of thousands, or even for millions of year,s fluctuating in the 100,000 +/- indivudual range as they slowly evolved from pre-human ancestors.


Bilbo - #9034

April 7th 2010

Hi UC,

I assume there was some point at which there was a clear genetic difference between homo sapiens and their ancestors.  How many homo sapiens would have been the first generation?  “Several thousand”?


unaplogetic catholic - #9036

April 7th 2010

“I assume there was some point at which there was a clear genetic difference between homo sapiens and their ancestors.”

You assumption is completely incorrect.  There was never such a point.


Bilbo - #9047

April 7th 2010

Hi UC,

And we know there was a never a clear genetic distinction ...how, exactly?


Argon - #9064

April 7th 2010

Bilbo, I think the problem is that such a distinction is a subjective construct, an attempt to place a line precisely between “grey” and “light grey”. I think the best one could hope for, from the standpoint of genetics is the population at the time when the last interbreeding population was reproductively isolated. Note that at that particular point in the past, members in the population still shared the overwhelming majority of genes with their cousins.

Try Ernst Mayr’s book “The Growth of Biological Thought: Diversity, Evolution, and Inheritance”. Look in the index for “typological vs. population thinking”. That may help clarify species concepts and evolution of populations.


Bilbo - #9067

April 8th 2010

Hi Argon,

Yes, I think it is generally accepted that for speciation to occur, a population usually must be reproductively isolated, allowing enough mutations to occur until it is reproductively distinct from the original group.  It just seems to me that would mean there was a point in time when that one extra mutation made the difference.


Bilbo - #9074

April 8th 2010

Anyway, if my reasoning is sound, here is a possible scenario:  Adam (and Eve?) are born with that one extra mutation that makes them the first couple of a new species.  They are endowed with unfallen consciousness of God, but fall.  Their descendants intermarry with the rest of the isolated population, passing on their mutation, and so eventually the entire group becomes a new species.


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