I’ve expressed my appreciation before (here, here and here for example) of population geneticist David L Wilcox in his thoroughly orthodox integration of standard evolutionary theory with historic faith. Most recently I noted that James Stump at BioLogos flatly contradicted his statement that theistic evolution, by definition, meant guidance by God.
Well, now I’ve stumbled upon the notes he made for a talk for ASA this year called Updating our Genetic Prehistory which has given me some ideas for a useful new series on Adam.
It would have been a good session to get to for a number of reasons. Firstly, it is a great update on the state of knowledge about our genetic ancestry. Unfortunately that aspect of it is also quite technical and complex for the non-biologist, but that’s the nature of the beast. He covers, though, the recent discoveries about hybridisation between modern humans and Neanderthals and the lowdown on the so-called Denisovian remains. Up-to-date calculations regarding “Y-Adam” and “Mitochondrial Eve” and so on are quite instructive. But download and read the notes yourself – you can always skip any bits where your eyes glaze over.
A few scattered points that I found interesting. One is that he dealt respectfully and objectively with the Young Earth Creationist position of baraminology. He concluded that the data didn’t fit this pattern well – but he didn’t crow about it any more than he did over other hypotheses that proved mistaken. That’s refreshing.
Another plus was his understanding and embracing of the findings of ENCODE and the other new kids on the biological block. One might have been reading James Shapiro in the emphasis on “Alu sequences” not as irrelevant and undesigned parasites (as Ayala on BioLogos in 2011), but as some of the key elements involved in human evolution. Rather than parroting the old mantra of the similarity between the human and chimp genome, he dealt with the vast difference in the non-coding sequences, recognising their huge importance as genes involved with complex control networks – with at least one more entire level of organisation in humans than in apes.
Admittedly, the recent advances in science account for this emphasis – but in some quarters they seem to have gone almost unnoticed.
The notes seem to drop slight hints about the degree of randomness of these massive and rapid changes, and I would love to know if he said more at the session. He believes that God controls every stage in evolution, and that “chance is, in fact, the hand of God.” I’d love to know how he discusses such issues in the very detailed, and orthodox, population genetics he is covering.
Well, to the issue that I’d like to build into a series. Towards the end, Wilcox has a slide of the various positions that have been suggested in relation to a historic Adam and Eve. My impression is that he has none of the angst about accepting a historical basis than some other TEs, but doesn’t seem to have opted firmly for one model (though I could be wrong there). Yet it would be good for us to examine – with the range of academic and theological backgrounds available to us – the strengths and weaknesses of each model. So to end this, I’ll list them as described in Wilcox’s notes, and do a piece on each one for comment over the next little while. Please – no comments yet on the relative merits of these, until they are fleshed out. The next article will give the biblical background.
Models of Adam and the sin problem (and links to posts)
- Generic Head – Sin originated with Adam, and has been passed along to all his descendents (which is everybody) like a genetic inheritance. (? Does this mean Adam was the only ancestor for the race –or just a particular man who is in all our genealogies? – AKA, Y chromosome Adam).
- Federal Head – Sin originated with Adam. He was not the only man living, but God appointed him as representative and put him to the test. When he sinned, sin passed on to all men everywhere (and when) by divine fiat. I.E., there was a sudden transformation of human life.
- Tribal Head – Adam was the “head man” of a small tribe put in the garden. The tribe was put to the test, and they all followed Adam’s lead into sin. We are all descended from that tribe (alone?) and have inherited their sinful nature.
- Cultural Head – Adam was the appointed race representative in the garden. He sinned. Sin passed on from Adam to all other people then (and now) alive by communication between people – especially in families. Human society suffered a gradual transformation as sin spread like an infectious disease.
- Experimental Head – Sin was already there, but we don’t know how – that’s why the garden was needed, the perfect environment. Adam was the experimental proof of the human condition – he showed we humans are all sinners by nature – that it is not environmental.
- Symbolic Head – Adam was a character in a story told to illustrate the human dilemma – we are sinners for some reason or other. But the story does not represent the origin of that state, only its nature as rebellion against God.
Jon, I looked over the Wilcox notes, and they are interesting. I try to follow this stuff, so I have seen a good number of the papers he references, although I can’t claim to be capable of understanding some of the pop. genetics stuff in any detail. I would like to say something about Alu elements. I’ve followed the literature on human transposable elements off and on for near 20 years.
Genomic sequencing led to a very complete catalog of human TE insertion sites, and in the last few years methods have been developed to look on a large scale for polymorphic L1s and Alus. What I have gotten out of these papers is that less than 1% of the TEs in the human reference genome are human specific insertions. (About 3 million total and a few thousand are human specific.) What couldn’t be told at first was how many of the species specific insertions are fixed and how many are polymorphic. Of course, only insertions that are fixed in the population can possibly be determining species characteristics, and you can’t tell which insertions are fixed until you have analyzed many whole genomes from all over the world.
Various methods have been used to look at many individual genomes for polymorphic insertions, and something approaching 10,000 have been identified (L1s + Alus), but of course as you identify insertions at lower and lower allele frequencies, the number of polymorphic insertions you find is only limited by how big the population is.
I haven’t seen anyone commit to how many fixed insertions there are and which ones they are, although enough genomes have been analyzed now that they must have a good idea. I e-mailed the guy whose lab is supposed to be building the database of polymorphic insertions to ask if they planned to identify the set of fixed, species specific insertions, and he said they were, but they still haven’t done it over a year later. It is possible from some of the recent papers to make a guess as to the number of fixed insertions, and it looks like to me it’s no more than a few hundred. For that reason I’m skeptical that species specific Alu and L1 insertions will really account for a lot of human specific biology. I doubt that there are enough of them to fill that role.
PNGarrison
Thanks for sharing that work. It’s difficult to evaluate the significance of the numbers till you understand fully what the things do, I guess: even a few hundred decision nodes can matter a lot applied to complex mulitlevel subsystems. Certainly more than the equivalent number of coding genes, anyway.
Wilcox’s phrase “the new epigenetic world” still seems appropriate – though that wasn’t the main lesson I took from the notes.
Finally your struggling – as a geneticist – with the language of pop. gen. shows how much need there is for interdisciplinary contact in the faith-science area: and (as Peter Hickman says in a comment on the previous post) for people who can turn the important bits of science into strip-cartoon form for the rest of us to evaluate and appreciate.
Jon, after my last comment I decided I might as well go to an authoritative source to answer the question about human specific insertions. I e-mailed one of the more prominent researchers of primate transposable elements a quick question and his response revealed that my surmise about numbers of insertions was pretty far off. His numbers:
Human specific fixed Alu insertions – about 4000
” ” ” L1 insertions – about 500
Most of these would be expected, based on what is known, to be neutral, but as far as I’ve seen nothing is known about whether some contribute to human specific traits.
I should have added for comparison that there are 1.1 million Alus shared with chimps, many of those with gorillas and other primates as well, and about 500,000 L1s likewise shared with other species.
Sounds like we’ll have to wait a few more years for the final answers, then!
Noticed one little bit in PNAS just now:
Human-specific endogenous retroviral insert serves as an enhancer for the schizophrenia-linked gene PRODH
http://www.pnas.org/content/early/2013/11/07/1318172110.abstract
There are a lot fewer human-specific ERV insertions than other TEs (134 in one source,) but they contain potent regulatory sequences, especially in the long terminal repeats, so there might be others that are important.
Just one point Jon. I understand why people want to discuss Adam and Eve within the context of common descent, as this may cast Genesis as unscientific. But if we dismiss such a claim (and after all almost everyone agrees that there were other human beings, and all manner of animals, in the Genesis account), than what is served by considering a re-wording of the Genesis story?
This comment is not a criticism, but simply one of curiosity – by this I mean that any of the accounts/models you propose can be understood as compatible with the Biblical understanding – but what is the purpose for proposing these models?
GD
I think you’re assuming too much about the “almost everyone” who agree that others were around at the time of the Genesis account.
The reason why many quite thoughtful Christians hold to a Young Earth model against the evidence of the scientific data is that that the matter of the origin of human sin, whether in a framework deriving from Augustine, or from Irenaeus, seems to them to require Adam as our first biological precursor. The science appears not to allow that – hence arises mental conflict.
The models have, I guess, been proposed to deal with that and related issues, thus (a) enabling Christians to integrate their faith with the public story of human origins better, to help those tempted to ditch their beliefs to match the science, and of course to help in Christian apologetics.
They’re going to have relative strengths and weknesses, which will be good to discuss. Even if we end up concluding that they are all compatible with the faith, then we’ll have helped people breathe more easily and accept uncertainty.
Jon,
The origin of sin is a central doctrine, and it does require Adam to be the ‘first man’ and Eve who was tempted. The Law however, is also central to this, and I take Paul’s remark in Rom 6-7, esp the remark, “Rom 7:7-12 to indicate that a person may not have known the Law … thus Adam has a far bigger role ….. however I understand your remark concerning Young Earth teachings, although I have a cursory understanding of such. I am sure you will cover this, but I want to emphasise the importance of lineage, from Adam to Abraham, to Israel, and ultimately to Christ. This is where I think some confusion may arise, in that this is a biological re common ancestor/evolution from apes and so on …. just as a comment.
So I agree with the remark by Peter Hickman, that we should have a discussion of sin, and I also suggest that this includes that of the Law (as Romans also shows).
GD
All good – you’ll appreciate that I wanted in this post mainly to get people looking at the Scriptural sources in order to critique the “models” individually as they’re presented. Your thoughts about the importance of lineage are just the sort of thing that need to be front-of-mind.
I’m aware that since half the Bible is about sin (the other half being about salvation from it; OK I exaggerate) there’s a danger of trying to cover “life, the universe and everything” on this one thread!
Jon, given that sin is a fundamental part of this discussion it might be useful if you define what you mean by it, i.e. a definition of the Biblical meaning of the word. ‘Sin’ and ‘sins’ appear frequently throughout Scripture. I don’t think it is a given that all believers agree on exactly what it comprises.
As an aside, how, if at all, should the ‘law of first mention’ be applied to ‘Sin is crouching at the door’, etc?
I’ve always been puzzled by God saying, “… but you must master it” in the light of Paul’s teaching that the Law provokes sin and the implication that, without the Spirit at least, sin may not be mastered.
Peter
Good point. The New Bible Dictionary discusses sin’s definition and concludes that, in essence, it’s “contradicting God”.
It points out that God is always the one against whom sin is ultimately directed in the Bible. I think that’s important in the question of its origin, because many TEs, IDers and others cut to other ideas like “selfishness”: but “The common notion that sin is selfishness betrays a false assessment of its nature and gravity” (NBD).
Thus many modern TEs have argued like this: “Evolution is about the selfish struggle for your own survival (or about selfish genes). So it’s not surprising we’re selfish because evolution made us so. So rather than a fall from Adam’s perfection, we need to rise above how we were created.” Yeesh!
I’m dubious about the validity of “law of first mention” (I used to write for a magazine where another author cited it all the time, ignoring the fact that the Bible wasn’t written in the order it’s bound.) But in this case there has to be some significance that the first book of torah, though not using the word “sin” for the first act of sin, mentions it of Cain in the same vocabulary as that used in Gen 3.16.
The question of inability to master sin takes us back (a) to the nature of that inability and freedom of the will (remember that discussion?) and (b) to progessive revelation.
Re (a) people from Augustine onwards speak of a moral inability: we can’t obey because we won’t, not because it’s physically impossible – and that’s why we are culpable, and why God can still command. Re (b) it was the unfolding story of that moral inability – ultimately in the apostasy of Israel despite every advantage – that led to the announcent of the gospel of grace and the Spirit, which of course is Paul’s theme in what you cite.
pngarrison
I’ve run out of nested comment levels, so will have to reply here. I could add more in the editor, but we’d end up like BioLogos, with comments one-letter wide.
We still seem to be at the very early stages of evaluating even this small part of the story, so assessing the significance of those 134 unique insertions is a bit futile, I guess.
But if they were all (or largely) found to be major factors in the evolution of the human brain’s control systems, that is one heck of a collection of coordinated high-level modifications from our common ancestor with Mr Chimp.
As I’ve said before, at what point does one decide that retroviruses are evolutionary tools that occasionally go wild, rather than repetitive elements being parasites coopted to good use by chance?
Of course., one thing we do know for certain is the importance of even a single retrovirus in evolving wraiths into humans in Stargate Atlantis! 🙂
The evidence as it stands now is that the vast majority of TE insertions that have been around for a while evolve neutrally, which suggests no functional importance. And of course ERVs had a life as retroviruses before they were genomic residents. Most of them increased their copy number by being produced as viruses and reinfecting more germ cells, although some used intracellular transposition. I don’t see any evidence at this point for some kind of orchestrated functionality. The number of fixed new TE insertions is a very tiny fraction of all the genetic differences between us and chimps. That, together with the fact that within each class of new insertions all the elements are almost identical, as they come from only a few source elements and haven’t had time to diverge, I think it’s more likely that most of the functionally significant changes are from more typical types of mutation that occur in a large variety of forms. It’s hard to see how you can make a bunch of different phenotypic changes by sprinkling the genome with a bunch of nearly identical insertions.
Fair enough, pngarrison – but might that not to some extent be because we look for the functional as we do in protein-coding genes – complex sequences leading to individual complex components? If, for example, a control function resides in regulating the pace of transcriptions, then the right repetitive element in the right place might do the trick. Similarly I’ve read articles by computer engineers noting the similarily of repetitive elements to features in computer operating systems. And we have the whole developing understanding that the three-dimensional structure of DNA in cells is part of what determines relationships between functional elements.
If there’s any truth in all that, it wouldn’t be to do with “sprinkling” anything around the genome, but ensuring that the coding elements are in the right place at the right time.