Adam and the Genome 5: Chapter 3- Adam’s Last Stand? (Part 1)

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 1

And now we get to main event.  What does genetics say about the human race descending from one and only one pair?  Dennis recounts the controversy following the June 3, 2011 Christianity Today article, “The Search for the Historical Adam”, and the resulting NPR interview in which he was quoted saying:

“But now some conservative scholars are saying publicly that they can no longer believe the Genesis account.  Asked how likely it is that we all descended from Adam and Eve, Dennis Venema, a biologist at Trinity Western University, replies: ‘That would be against all the genomic evidence that we’ve assembled over the last 20 years, so not likely at all.’”

Did I say controversy? — raging furor would be more like it.  Trinity Western administrators fielding angry calls.  It is a wonder Dennis didn’t lose his job for no longer believing the Genesis account (and I imagine that a few of you reading this blog post think he should have).  We will delve into what it means to “believe the Genesis account” when we get to Scot’s section of the book.  For right now, let’s try to stay focused on the science.  Dennis was naïve to assume that people understood that evolution was a population-level phenomenon.  If humans evolved, then they evolved as a population; he thought everyone knew that.  But he was to learn that saying the population genetics data indicates we descend from a group of about 10,000 individuals was more controversial than the data supporting common ancestry that we covered in the last chapter.

The brilliant analogy of Anglo-Saxon changing over time to Modern English shows how speciation occurs.  It is the incremental change of average population characteristics after two populations separate.  No one expects a new language to start with two speakers suddenly speaking in ways radically different than the population it arose from.  Yet many people think this how speciation occurs.  They assume all species are founded by an ancestral breeding pair that is suddenly markedly different from the population it arose from.  He says:

“Thus, I’ve encountered many folks who, upon understanding the evidence that humans and other apes share common ancestors, assume that humans—like all other species in their thinking—got their start when a founding couple “mutated away” in tandem from their ape-like ancestors.  These folks then wonder if the Genesis narratives may be portraying this radical shift, with perhaps God intervening to create the necessary, large-scale mutations that made us a biologically distinct species.”

But that is not how speciation works.  The populations are genetically separated in some way, usually physical isolation (although not always) and no longer breed together.  When mutations occur they are no longer shared across the divide.  Now the two populations begin to drift apart in their average characteristics.  Trying to draw a sharp dividing line on this biological gradient is as useless as deciding what day Anglo-Saxon became Modern English.  Dennis uses an example from his teaching.  He will ask the class to spell “lose”.  Usually, a number of students will spell it as “loose” which is becoming more common, especially on social media.  So the ability of a language to hold variant spellings or grammatical variants is dependent on the number of speakers in the language.  Dying languages have no variation at all since they have so few speakers (like some Native American languages).  Modern English, as it has become a world-wide language can support a large number of variants.  The same occurs with species; a large population size allows for maintaining a large number of variants, since each member of the species is able to hold up to two distinct variants (alleles) of any given DNA sequence in its genome.  Therefore, there is a connection between the number of variants in a population and the size of that population.  Scientists can use that connection to estimate the size of the population from the number of variants.  And since the rate of change over time is slow, it is straightforward to extrapolate backward from the present to the past.

It is technically possible that a species could be founded by a single breeding pair, just as it is technically possible a new language could be founded by two speakers.  However, that would be highly unusual and, with respect to the genetics anyway, there would be a tell-tale mark on the genome that would persist for hundreds of thousands of years—a severe reduction in genetic variability for the species as a whole.

For an example of a species with a lack of genetic variability, Dennis cites the case of the Tasmanian devils.

The carnivorous marsupial once roamed over all of Australia, but now only exists on the island of Tasmania.  Tasmanian devils have so little genetic variability that for the last hundred or so years they have exactly the same alleles with only rare differences.  This indicates a “bottleneck” event occurring in which there was a severe reduction in the population with the resulting loss of genetic variability.  The problem for the devils is that there is a form of cancer transmitted by bites that is threatening their complete extinction.  Normally, a recipient animal could fight off the cancerous cells but the devils are all so genetically similar that the cancer cells do not trigger an immune response.

In humans, by contrast, there is much genetic variability.  That is why there can be such a problem with donor organs; a close match has to be found.  For the Tasmanian devils any one could be an organ donor for another (or, sadly, a tumor donor).  This example also illustrates how long it takes a population to rebuild its genetic diversity—many thousands of generations.  The implications are clear; Tasmanian devils experienced a severe bottleneck in the distant past, humans did not.

There have been some theories that have proposed bottleneck events for humans.  The controversial Toba catastrophe theory, presented in the late 1990s to early 2000s, suggested that a bottleneck of the human population occurred about 70,000 years ago, proposing that the human population was reduced to perhaps 10,000–30,000 individuals when the Toba supervolcano in Indonesia erupted and triggered a major environmental change. Parallel bottlenecks were proposed to exist among chimpanzees, gorillas, rhesus macaques, orangutans and tigers. The hypothesis was based on geological evidence of sudden climate change and on coalescence evidence of some genes (including mitochondrial DNA, Y-chromosome DNA and some nuclear genes).  However, subsequent research, especially in the 2010s, appeared to refute both the climate argument and the genetic argument. Recent research shows the extent of climate change was much smaller than believed by proponents of the theory. In addition, coalescence times for Y-chromosomal and mitochondrial DNA have been revised to well above 100,000 years since 2011.

Since the question of estimating population size from genetic diversity is the key question that determines the geneticist’s claim humans could not originate from just two people, Dennis takes some time to sketch out the methods used that support that conclusion.  One simple way is to select a few genes and see how many alleles of that gene are in the present day population.  Taking into account the mutation rate and the mathematical probability of new mutations spreading in a population or being lost, computer calculations indicate an ancestral population of right around 10,000.  In fact, to generate the number of alleles we see in the present day from a starting point of just two individuals, the mutation rate would have to be far in excess of what we observe for any animal.

The astute skeptic could point out the assumption is that the mutation rate has remained constant; but what if it was higher in the distant past?  However, we have other ways to measure ancestral population sizes that do not depend on mutation frequency.  These methods provide an independent check on results using allele diversity.  One such method is known as “linkage disequilibrium”.  The basic idea is that if two genes are located close to each other on the same chromosome, the alleles present at both locations tend to be inherited together. 

(Note: the following discussion is taken pretty much straight from the book– I just couldn’t figure out how to condense it.  But I’m not going to block quote it for readability.)  In Figure 3-1, the long line represents a chromosome, and the hash marks across it show us where the two genes in question are located.  Geneticists even us the Latin word for location (locus, pronounced “low-cuss”) as a synonym for ‘gene’.  (Latin makes us sound smarter, I guess).  If we could zoom in on the diagram, we would see a long DNA molecule with two regions that are translated into proteins (the two genes).  The different alleles at either locus would have slight sequence differences, giving us four possible combinations for these two loci (plural for locus, pronounce “low-sigh”).  The four possible combinations are “AB”, “Ab”, “aB”, and “ab”.

During cell divisions that make gametes (i.e. eggs or sperm), there is a process of mixing and matching of alleles to make new combinations.  For example, suppose an individual had one chromosome with the A and B alleles and another with the a and b.  During gamete formation, it is possible to produce gametes that are “recombinant”—in this case, ones that have either and “Ab” or “aB” combination.  Recombination requires a process of precise chromosome breakage and rejoining called “crossing over”—something you might recall from high school biology (Figure 3-2)

The key point to understand is that the closer together two loci are on a chromosome, the less likely it is that a crossover event will happen between them.  The further apart two are loci are, the more likely it is that a crossover will recombine them.  What this means is that alleles of loci close together tend to be inherited as sets.

Let’s work through an example of how this plays out in practice.  Consider an extended family represented by a pedigree.   This is the type of diagram geneticists use to trace alleles through large families.  Females are represented by circles and males by squares.  Connecting horizontal lines indicate parents, vertical lines are offspring. Generations are labeled with Roman numerals and individual are labeled with Arabic numerals.  In this way we can refer to any individual in the pedigree (Figure 3-3).

Now consider a large pedigree where we know the allele combinations of everyone represented (Figure 3-4).  For example, individual I-4 has one chromosome with the “AB” alleles linked together, and one chromosome with the “ab” as a set.  We can represent her chromosome set, then, as “AB/ab” – the shorthand geneticists’ use.  We can then use this convention or other individuals in the pedigree.  For example, the daughter of I-1 and I-2 might have an “AB/ab” combination.  If these two loci are very closely linked together, it is highly unlikely that crossing over will occur.  Thus she would have inherited her “aB” set from her mother, and “AB” set from her father.

Likewise, her husband, II-3, would have inherited “Ab” from his dad, and “ab” from his mom.  Their children (generation III) similarly would inherit these sets without crossing over.  Looking at the combinations carried by these children then allows us to infer things about their ancestors.  If these two loci are very close to each other, we might not expect them to recombine over hundreds of generations or more.  Thus it’s reasonable to infer that these four combinations come from four distant ancestors.

The trick is that we can now do this for tens of thousands of loci across the whole human genome.  As we have sequenced the DNA of more and more individuals in different people groups around the globe, we’ve simply been asking the questions: 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.  We’ve now done this sort of analysis for millions of pairs of loci (you read that right—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.

• • •

Other posts in the series:

• Adam and the Genome, part 1
• Adam and the Genome, part 2
• Adam and the Genome, part 3
• Adam and the Genome, part 4

Adam and the Genome 4: Chapter 2- Genomes as Language, Genomes as Books (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 2- Part 2

Chapter 2 begins with a brilliant analogy of how evolution works by comparing how Modern English evolved from ancient Anglo-Saxon.  The major points of the analogy were:

• The various examples from the fossil record are not instantaneous changes from one to the next.
• They are samples drawn at intervals from a continuous process.
• Over time, however, changes accumulated that gradually shifted the average characteristics of the language / population as a whole.
• Given enough time, it becomes more and more of a stretch to say the language or the organisms are the same.
• Despite the striking differences we see now, the process that produced them was gradual.
• There is no convenient point where we can say Anglo-Saxon “became” Modern English or apes “became” humans; the process was a continuum.”

Dennis then talked about how DNA is composed of 4 “letters” and how those “letters” are used to replicate and code for proteins that do the “heavy lifting” work of the cells/organism, and how redundancy was built into that process.  He then gave the example of the insulin protein and how knowing how DNA sequences code for that protein allows us to compare one organism’s sequence to another, in the first case dog to human.  Then in his second example, comparing human, apes, and dog insulin.  Based on anatomical characteristics, evolutionary theory predicts that these ape species share a more recent common ancestral population with humans than non-primate species such as dogs, do.  If that is so, then their gene sequences should be a closer match to human sequences than what we observe in dogs.  And that is, in fact, what we observe, and this level of identity far exceeds what is needed for functional insulin.  We have failed to reject the hypothesis that humans share a common ancestral population with apes.

The pattern that was observed in the insulin gene sequence has now been confirmed to exist across numerous other gene sequences of humans and great apes.  Beyond genes, our entire genomes are either around 95% or around 98% identical, depending on how one counts the effect of deletions of small blocks of DNA.  And not only nearly identical, but organized in the same spatial pattern.  In the book analogy, at the sentence, paragraph, and chapter level, our two “books” are organized in the same way.

The next example Dennis gives for shared ancestry are the olfactory receptor genes, or simply put, our sense of smell.  Mammals on the average have about 1,000 genes devoted to the sense of smell, out of a total gene count of 25,000; which means a significant proportion dedicated to this purpose.  Mammals that hunt (like wolves) have very keen senses of smell because their olfactory genes are kept in good repair—deleterious mutations are weeded out through selection.   Humans have a diminished capacity for smell; and the reason became apparent after the human genome was sequenced.  Many of our olfactory receptor genes are damaged (mutated) but they persist because the mutations are replicated once they are “locked” in.  As a result these genes persist as genetic “fossils” in our DNA.  They are known as “pseudogenes” (false genes) because they have many of the features of genes but cannot translate as a gene should to produce a useful protein product.  Now, not only do other primates have mutations in their olfactory receptor genes, but the same genes are lost and often the exact same mutation event, down to the exact DNA letter change, is seen in more than one species.

So in the first example from Figure 2-7, the gene 5AK4p is shared among all 4 species.  It has a “stop” mutation at DNA letter 236, which is a mutation that “stops” the gene from coding for the amino acids necessary to do its job.  So what is the reason all 4 species share the same mutation?  It could be coincidence that the same mutation occurred 4 times independently in different species.  A second possibility is that the mutation occurred once in a common ancestral population to all 4 species, and subsequently inherited by all 4 species.  The paper Dennis is citing also observes that several mutated genes fit this pattern.  Even if one gene might have this pattern by chance, it is extremely unlikely that numerous genes would have this same pattern by change alone.  Heredity is the more parsimonious explanation and, again, we have failed to reject the hypothesis that humans share a common ancestral population with apes.

A second pattern we observe is shown by gene 2; in this case, a deletion mutation (i.e. one DNA letter missing) at position 212 in humans, chimps, and gorillas, but not orangutans.  Deletions mess up the code so that the mutated codon will code for the wrong amino acid—that ruins the protein’s function.  Again, the simplest explanation is that this mutation occurred once in the population ancestral to humans, chimps, and gorillas and that the ancestral lineage for orangutans had already separated by this time.  Once again the researchers found many examples that fit this pattern.

A third pattern in gene 3 shows a mutation shared only by humans and chimps.  Again, the simplest explanation is that this mutation occurred once in the population ancestral to humans and chimps, and that the ancestral lineage for orangutans and gorillas had already separated by this time.

Finally, we see mutations unique to a single species (genes 4-7).  Such mutations are expected, since each species also has a period of unique history after its lineage separates from all the others.

Note, however, what we DON’T see: mutations shared by gorillas and chimps, but not seen in the other species, for example; or mutations shared by humans and orangutans that are not also seen in gorillas and chimps.

Why don’t we see these categories?  Because the species are related in the manner suggested by the patterns we do see, therefore, we would not expect them. The data form a pattern called a “nested hierarchy”, which is a fancy name for a family tree.  While this was worked out on the basis of partial genome sequencing, we now have full genome sequencing for all 4 species, and the genome-wide identity between humans and other apes follows the same pattern.  Again, we have failed to reject the hypothesis that humans share a common ancestral population with apes.

Now the astute observer might ask; if this is true for humans and primates, then it must also be true if whales descended from land-based artiodactyls.  Dennis answers that:

“In fact, DNA evidence comparing a modern artiodactyl (hippos) and modern cetaceans was the first evidence that these species share a common ancestral population, before the key diagnostic fossilized ankle bones were found in ancient whales.  Not surprisingly, paleontologists doubted the new DNA science until they found the fossils that confirmed its predictions.  DNA and fossils tell the same story; they are converging lines of evidence.”

Dennis then discusses the case of vitellogenin pseudogenes in placental mammals.  (Note: I am borrowing language from Dennis’ articles at Biologos to save me time hand typing from the book.  Dennis’ discussion in this book is a condensed version of the 5 articles he posted at Biologos on the Vitellogenin issue. See http://biologos.org/blogs/dennis-venema-letters-to-the-duchess/vitellogenin-and-common-ancestry-understanding-synteny.)  Vitellogenins are large proteins used by egg-laying organisms to provide a store of nutrition to their embryos in egg yolk.  Evolution would predict that all placental mammals once had vitellogenin genes in their genome, even if those genes would no longer be useful, if they did indeed shared a common ancestor in the past.

Modern birds (such as chickens) have three vitellogenin genes: VIT1, VIT2, and VIT3. The latter ones sit side by side in the chicken genome, with VIT1 in a different location. The three VIT genes sit next to other genes in the chicken genome: VIT1 sits next to a gene called “ELTD1”, and VIT2 and VIT3 sit between genes named “SSX2IP” and “CTBS”. These genes are not involved in making egg yolk – they just happen to be the closest neighbors of the VIT genes.  With these data in hand, the researchers then searched the human genome for the genes near to the chicken VIT genes. These three genes (ELTD1, SSX2IP, and CTBS) are also found as functional genes in humans – and as expected, these genes have the same spatial arrangement in the human genome as they do in chickens.

Figure 2-9:  The VIT1 and VIT2, VIT3 regions in the chicken and human genomes.  White boxes indicate functional genes.  Black boxes indicate sequence matches between the two genomes.  The ELTD1, SSX2IP, and CTBS genes in humans and chickens are highly similar and line up with one another when comparing these regions.  Small fragments of matching sequence can be seen covering both regions, including fragments matching portions of the chicken VIT1, VIT2, and VIT3 genes, though the most extensive matching is see in the fragmentary human VIT1 pseudogene.

To put it simply: we have a gene (no longer working) for making egg yolk.  Why?  WHY would God create us de novo with a gene for making egg yolk in our DNA?  It makes perfect sense if God created us through a natural biologic process of descent with modification.

Dennis notes that given the abundant lines of DNA evidence that support the hypothesis that humans are the result of a natural biologic process, it is no exaggeration to say that very, very, few trained biologists reject common ancestry for any other reason than prior religious conviction. Dennis is friends with Todd Wood, who holds to a young earth creation position, but is one of the very few YECs who will engage the science honestly.  Dennis quotes from an article on Todd’s blog from 2009:

Evolution is not a theory in crisis. It is not teetering on the verge of collapse. It has not failed as a scientific explanation. There is evidence for evolution, gobs and gobs of it. It is not just speculation or a faith choice or an assumption or a religion. It is a productive framework for lots of biological research, and it has amazing explanatory power. There is no conspiracy to hide the truth about the failure of evolution. There has really been no failure of evolution as a scientific theory. It works, and it works well.

I say these things not because I’m crazy or because I’ve “converted” to evolution. I say these things because they are true. I’m motivated this morning by reading yet another clueless, well-meaning person pompously declaring that evolution is a failure. People who say that are either unacquainted with the inner workings of science or unacquainted with the evidence for evolution. (Technically, they could also be deluded or lying, but that seems rather uncharitable to say. Oops.)

Creationist students, listen to me very carefully: There is evidence for evolution, and evolution is an extremely successful scientific theory. That doesn’t make it ultimately true, and it doesn’t mean that there could not possibly be viable alternatives. It is my own faith choice to reject evolution, because I believe the Bible reveals true information about the history of the earth that is fundamentally incompatible with evolution. I am motivated to understand God’s creation from what I believe to be a biblical, creationist perspective. Evolution itself is not flawed or without evidence. Please don’t be duped into thinking that somehow evolution itself is a failure. Please don’t idolize your own ability to reason. Faith is enough. If God said it, that should settle it. Maybe that’s not enough for your scoffing professor or your non-Christian friends, but it should be enough for you.

Todd took a lot of grief from the YEC community which goes to show their disingenuous attitude.  I don’t how else to say it.  He wasn’t being a “closet evolutionist” as he was called, he was being honest about the state of the evidence.  It reminds me of the Glenn Morton story .

The thing is that Darwin nor any of his contemporaries, except maybe Gregor Mendel, could have imagined that organisms would retain a text-like record of their evolutionary past in their hereditary material.  Genetics and the DNA evidence could have overturned the whole evolution theory.  Genome sequencing could have rejected the hypothesis of common ancestry.   In actuality, these new technologies have provided some of the most detailed and convincing evidence of descent with modification i.e. EVOLUTION.

Humans do share common ancestors with other apes; apes share common ancestors with other mammals; mammals share ancestors with other tetrapod vertebrates; tetrapod vertebrates, as we have seen, share ancestors wit fish; and ultimately all life on earth shares common ancestors dating back over 3 billion years.