Would intelligent aliens present a problem for Christianity?

Posted on 02/27/12 98 Comments

Jeff commented on my recent article “Should you call out Gouranga?” and in doing so offered a helpful basis to kickstart our discussion of exotheology. He is of the opinion that it is a problem to Christian theology if there are ”intelligent species in the cosmos other than humans” for as he says “then we’re left with several options for salvaging Christian orthodoxy, none of which appear to be very good options”. He then lists four possibilities.

1) The second person of the Trinity has been frantically zipping around the cosmos (and even other universes?) on one rescue mission after another, after another, after another, perhaps having visited and incarnated as billions or trillions of different species, in order to atone for each. (I suppose that “frantic” isn’t quite the right description, but this scenario certainly seems very messy, to say the least. It would certainly put a fantastic new spin on Galatians 4:4-5.)

2) The Son’s incarnation as the human Jesus was the only such incarnation, effecting atonement for all intelligent species throughout the cosmos. This scenario seems absurdly geocentric.

3) Humans are the only (or one of relatively few) species for whom God effected atonement. Perhaps Calvinist theology could accommodate this scenario, but I would think this would give pause to all but the most hardened Calvinists.

4) Humans are the only (or one of relatively few) species for whom atonement is necessary/possible. Other intelligent species differ fundamentally from humans in terms of agency and moral responsibility and therefore do not require atonement or are not capable of atonement. But why think such a thing? Why think that humans are so highly unique in this regard?

Jeff then draws his depressing conclusion:

All of these scenarios seem very implausible to me. Are there other, more plausible scenarios that I’m forgetting? Since there don’t seem to be any good reasons to think that humans are the only intelligent species (on the contrary, it seems most reasonable to think that there are many billions or trillions of intelligent species), it looks to me as if Christian orthodoxy is very implausible.

I’ll now turn to offer some reflections on Jeff’s thoughts because I don’t share his concerns.

Option 1: Multiple Incarnations?

Jeff seems to conceive of this possibility as one where the second person of the Trinity can be self-identical with only one incarnate creature at a time. Hence the reference to “zipping” around from incarnation to incarnation. But there are models of incarnation which would allow God the Son to be self-identical with more than one incarnate being simultaneously. (For example, Thomas Aquinas contemplated this very possiiblity of multiple incarnations.) And you thought it was a brain bender in Back to the Future to see Marty McFly having to avoid running into himself. In this case multiple individuals could simultaneously be God the Son.

Option 2: Absurdly geocentric?

The New Testament writers seem to be of the opinion that whatever the extent of the heavens and earth is, Christ’s atoning work is effectual for all of it. Is this really ”absurdly geocentric” as Jeff worries? Really I take his problem to be one more instance of the scandal of particularity. In other words, it is absurdly particularist that God would reveal himself uniquely through a particular people in history. And it is absurdly particularist that God would be incarnated as one individual. If Jeff has gotten over these scandals of particularity I’m not sure why the discovery of ETI would suddenly present an absurd geocentrism.

Option 3: An exclusivism too far?

Jeff thinks this option “would give pause to all but the most hardened Calvinists.” The prejudicial language is slightly bothersome. Why “hardened”? Anyway, the real issue is not Calvinism per se but rather exclusivism. And I don’t know why exclusivists would have a problem here. If, for example, an exclusivist is happy to accept that every aboriginal who lived and died in Australia for the forty thousand years prior to the arrival of Christian missionaries in the eighteenth century was lost, why would they have a problem with ETI on another planet? Perhaps, as William Lane Craig argued, God guarantees through his middle knowledge that all who would respond favorably to the gospel will have an opportunity to hear it. This means that on Craig’s view no aboriginal in Australia for the thousands of years prior to the eighteenth century would have responded favorably to the gospel and so none heard it. If you can believe that then presumably you can believe the same thing about a planet teeming with ETI.

Option 4: Does E.T. need atonement?

Would all ETI need salvation? Not according to C.S. Lewis or Walker Percy, who both addressed this question. But why think this might be the case? Because historic Christian orthodoxy already accepts the existence of intelligent creatures that are not in need of atonement: angels. Could there be other intelligent agents in the universe that are unfallen? It would seem that this is an empirical question rather than one to be satisfied by conceptual fiat.

More radically, is it possible that unfallen ETI could be the very things we call angels? Given that the definitions of what an angel is and what an ETI might be are sufficiently broad, this is a possible if not prima facie plausible hypothesis. Indeed, some alien visitations could plausibly be interpreted from a Christian perspective as demonic in nature. Could others be angelic? Who’s to say? (Don’t forget, Spielberg’s “E.T.” is one of the most obvious Christ figures in cinematic history with everything from miraculous healings to a Garden of Gethsemane phoning home, a death, resurrection and ascension!)

Conclusion

Just to be clear, I have no idea if ETI exists in the universe. I don’t share the confidence of the Drake equation and SETI researchers that they do exist, but neither do I share the skepticism of many biologists that they don’t. I certainly don’t believe that it is likely any aliens have visited earth. But I do know that if tomorrow they land on the White House lawn (because where else would they possibly land?) that Christianity will survive just fine.

Walter

I am sure that most of the world’s religions will evolve and adapt to incorporate the new view of reality, much the same way that they currently continue to adapt to the changing view of the world brought about by scientific progress.
- Beetle
  
  Right, as Randal observes, Christianity will survive just fine. Religion in general, and Christianity in particular, seems quite adaptable. If heliocentrism and evolution where not enough to demonstrate the practical limits of biblical wisdom, an ETI won’t be much challenge to religious faith! I don’t expect that humanity will encounter ETI in my lifetime, but discover of life on other planets and great strides in abiogenesis seem possible if not probable. I don’t expect either of those to have much of an effect on the number of people who self-identify as Christian (at least not compared to the popularity lost to sex scandals and resistance to gay rights).
  
  Randal (or anyone else): Please tell mere where I can learn more about the skepticism of many biologists with regard to ETI. I had not read of that before!
  - Beetle
    
    While looking for explainations why biologists would be skeptical of ETI, I came accross this article which I think you might appreciate (even though it did not answer my question). From Reasons To Belive: Is Astrobiology Research Based on a Mistake?
http://twitter.com/davidstarlingm davidstarlingm

Even numbers are generally better, and this post is no exception. Options #2 and #4 (or a combination thereof) seem the most plausible to me.

You say that both the “angel” category and the “ETI” category are sufficiently broad to allow overlap. What, do you think, are the boundaries of the intersection of these two categories?
- randal
  
  Even numbers are better? That’s an odd thing to say.
  Let me say that odd numbers are better just to even things out.
http://www.retheology.net Jared

I mentioned it before, but suggesting that humanity is the locus of a salvific message that we are to take to the stars does seem to smack of hubris, but that doesn’t mean it’s not true. So, I think option 2 is the most concrete response.

In my reading, this is in keeping with John’s view of the atonement as universal (John 3:16 mentions kosmos .. and the declaration is repeatedly not that Jesus came to eliminate sins, but to eliminate sin.) By my count, this lends itself to a universal hermeneutic.
- randal
  
  Hubris = extreme pride or arrogance.
  
  There is nothing necessarily prideful or arrogant about a person believing that God has acted definitively to save human beings in the universe. You certainly could argue that it is naive or provincial to think in that way, but I don’t think it looks even remotely hubristic, especially when we’re talking about God bestowing grace on unworthy sinners.
- pete
  
  Or maybe there is something to be said about our God who creates the whole universe, and chooses to focus on his people alone.
  
  “To the LORD your God belong the heavens, even the highest heavens, the earth and everything in it. Yet the LORD set his affection on your ancestors and loved them, and he chose you, their descendants, above all the nations—as it is today.” (Deut. 10:14-15)
  - http://www.retheology.net Jared
    
    That would actually be a cohesive hermeneutic I think – that as you read through the Hebrew Bible you see an increasing emphasis on the Jewish people, God’s chosen nation, being a light to the nations. Paul took this a step further.
    
    Maybe the church’s mission is to make disciples of all the cosmos.
pete

The only biblical possibility that allows for an “alien visitation” is that of an end time deception/great persecution before the Return of Christ.

Marginal Christians would fall away, and true Christians would be persecuted for failing to follow the tide of the ensuing idolatry.

And then Jesus will put a stop to it forever.
- randal
  
  I’m not sure what you mean when you say “biblical possibility”. ETI wasn’t on the radar screen at all of the biblical writers. But then neither was Copernicanism, Newtonianism, the germ theory of disease, relativity theory, and quantum mechanics and those all turned out to be true.
  - pete
    
    “But then neither was Copernicanism, Newtonianism, the germ theory of disease, relativity theory, and quantum mechanics and those all turned out to be true.”
    
    And none of those things were in anyway related to the redemptive history of God’s people.
    
    “I’m not sure what you mean when you say “biblical possibility”. ETI wasn’t on the radar screen at all of the biblical writers.”
    
    And neither was the carpenter from Nazareth in the Old Testament.
    
    But as for ETI:
    
    “After that, in my vision at night I looked, and there before me was a fourth beast–terrifying and frightening and very powerful. It had large iron teeth; it crushed and devoured its victims and trampled underfoot whatever was left. It was different from all the former beasts, and it had ten horns.” (Daniel 7:7)
    
    “He gave me this explanation: ‘The fourth beast is a fourth kingdom that will appear on earth. It will be different from all the other kingdoms and will devour the whole earth, trampling it down and crushing it.” (Daniel 7:23)
    
    While I’m not looking to go into a whole exegetical monologue, the point is that the Bible isn’t so much a science lesson, as it is a redemptive message concerning the people of God.
    
    And as such, if ETI makes contact with us on earth, biblically speaking we are dealing with an end-time deception, or the Bible is not a divinely inspired document.
    
    The failure of the Bible to predict such a major event, that would undoubteldy be a world-wide faith-changer, would render the critics credible.
    
    However, I think I have pointed to an area of scripture which at least allow for such an event. However, it is set in the context of an end-time deception.
pete

Before we develop theologies around a ETI potentiality, I think we should first look to Scripture to see how it would account for such a monumental event, and go out from there.
- http://www.retheology.net Jared
  
  I guess I don’t see why it would be such a monumental event. For 1500 years, the church believed that Euro-Asian life was the only life there was, and that converting the whole world meant Spain-China.
  I guess, I’m not really sure how to look at it Biblically. As far as I can tell there seem to be 3 issues.
  
  1. Adam as the progenitor of the human race and the doctrine of original sin means that in a literalist reading ETI is exempt(ed) from the fall.
  We do see, in scripture even, humans who are not descendants of Adam (Genesis 4) – but we do not assume that they are ou of scope of salvation. As I see, there are two possibilities:(granted, a third possibility is that somehow these other people are connected to Adam, but there is no textual evidence to support that, and I’m not interested in hermeneutical yoga…) So, 1) Adam’s sin affected the entire created order, like ripples in a pond, infesting the entire created order. This makes sense, as I mentioned above with a Johanine atonement as restorative for the created order or 2) the story of Adam and Eve is not, in fact, literal vis a vis it’s impact on the doctrine of original sin. That is, though Adam could well have been a real person, the story is more allegorically descriptive of our state of enmity from God. This point could be pushed further, but from past discussions we’ve had, Pete, I don’t think that would be a valuable use of time.
  
  2. You mentioned Daniel.
  It’s only in the past hundred years or so that Daniel has even been treated as a prophetic work. The Hebrew Scriptures are broken into three parts: Torah (Law) Neviim (Prophets) Ketuvim (Writings) – TaNaK. Daniel is actually in the writings part of the Hebrew Bible, but was moved by the reformers to be included alongside the other minor prophets. When viewing it as writing or, more broadly, wisdom literature, there are two ways that scholars tend to read it: The early reading, that it was actually written during the Babylonian exile and treating it as such; or the late reading, that it was written during the conquest of Antiochus Epiphanes and the desecration of the temple in the same vein that Revelation speaks of Babylon, when what it really means is Rome. Most scholars tend to side with the later reading, seeing it much more polemically driven.
  Another issue is understanding prophecy. Even if Daniel were to be lumped in with the prophets (which it is not) – to prophecy (Heb: nabi) means, literally, to speak on behalf of. Aaron is called the Nabi of Moses, and it gets translated usually as spokesperson. It comes from the Akkadian word ‘to Bubble forth’ – and is categorically distinct from an idea of seerism or sooth-saying. Prophets in the Old Testament tradition are more akin to preachers by today’s standards, people who are convicted of a truth and deliver it clearly and compellingly.
  
  3. I mentioned kosmos (John 3:16 in particular)
  The word is used 186 times in the New Testament – and always translated world, but almost always signifying a non-literal world (of the world, worldly). I’ve mentioned before that this implies a boundaryless concept.But the verse I want to look at specifically is Colossians 1:15 – [Jesus Christ] is the image of the invisible God.” This is a hugely significant phrase in a Greco-Roman context, because from Aristotle onward, the idea of a single ontological God was gaining ground. Greeks saw that everything they could qualify or quantify was God – and that kind of thinking already extended beyond the earth (The moon sun and stars were all God). And so for Paul to come along and declare that Jesus Christ is the visible image of this invisible God was a declaration of his supremacy over the whole universe, not just Earth.
  
  ——-
  
  You said:
  
  the point is that the Bible isn’t so much a science lesson, as it is a redemptive message concerning the people of God.
  Absolutely. I’d push it a step further though. It is a redemptive message for the whole created order. Remember Jesus’ warning, that if people stopped praising that even the rocks would cry out? Or Psalm 96 – Let all creation rejoice before the LORD. Or Romans 8:19-23.
  
  And as such, if ETI makes contact with us on earth, biblically speaking we are dealing with an end-time deception, or the Bible is not a divinely inspired document.
  You might have set up a false dichotomy based on a faulty premise. You’re hinging on a premise that a) Daniel is an end times Frommer’s Book; (I don’t think that’s the case) that b) ETI would be the fulfillment of that prophecy; (we’ve been told the same thing since Hal Lindsey wrote ‘The Late Great Planet Earth, or ’88 reasons the world will end in 1988′. Pointing to events as fulfillment of prophecy is tricky business.)
  
  The failure of the Bible to predict such a major event, that would undoubtedly be a world-wide faith-changer, would render the critics credible.
  The Bible hasn’t predicted lots of things. It didn’t predict any of the above things that Randal mentioned, or any of our technological advances (though I suppose there are ways to read those onto the Bible). It didn’t predict the end of slavery in the Christian world; or the economic practices we use today. Just because the Bible didn’t predict something doesn’t mean it’s not the case.
  Also, I’m not so sure it would be a real faith changer. Sure, there would be some churches that would have to tinker their theology, but the largest church in the world (Roman Catholics) have already made allowances for such an occurrence. And as the tide of Christianity continues to slide away from the Western World, that predominant theology will play an increasingly significant role in shaping orthodoxy.
  
  Cheers!
  - http://twitter.com/davidstarlingm davidstarlingm
    
    “For 1500 years, the church believed that Euro-Asian life was the only life there was, and that converting the whole world meant Spain-China.”
    
    This has been pointed out several times now, but I think it’s missing the point. There was nothing revolutionary about finding people in the Americas; the revolutionary thing was actually finding the new continent. I guess I’d need to see examples in historical literature that talk about the inhabitants of America in a different way than, say, the inhabitants of Australia….otherwise it just doesn’t make sense.
    
    “We do see, in scripture even, humans who are not descendants of Adam (Genesis 4) – but we do not assume that they are [out] of scope of salvation. a [....] possibility is that somehow these other people are connected to Adam, but there is no textual evidence to support that.”
    
    Just read the chapter. What people?
    
    “Greeks saw that everything they could qualify or quantify was God – and that kind of thinking already extended beyond the earth (The moon sun and stars were all God). And so for Paul to come along and declare that Jesus Christ is the visible image of this invisible God was a declaration of his supremacy over the whole universe, not just Earth.”
    
    Which raises another interesting point: unless the aliens have been hiding on the dark side of Uranus, there is no conceivable way for them to interact with us in any sustainable fashion. The nearest potentially habitable exoplanet, Gliese 581 g, is 110,000 billion miles away. Our fastest space probe, New Horizon, would take fifteen thousand years to get there. The fastest macroscopic objects in the galaxy, hypervelocity stars, have enough speed to escape the gravitational pull of the galaxy, but they would still take over 6,000 years to reach us from Gliese 581 g. So our chances of interacting with real aliens are quite low.
    
    “The Bible hasn’t predicted lots of things. It didn’t predict any of the above things that Randal mentioned, or any of our technological advances. It didn’t predict the end of slavery in the Christian world; or the economic practices we use today. Just because the Bible didn’t predict something doesn’t mean it’s not the case.”
    
    There wouldn’t be any reason for God to provide information about technological advances that wouldn’t be useful to anyone for centuries. Forgetting to us know that we are not alone in the universe (and not giving us instructions on how to interact with alien life), on the other hand, would be a pretty significant oversight.
    - http://www.retheology.net Jared
      
      Just read the chapter. What people?
      Either the people who would kill Cain, the people in the land of Nod, or the people that Cain marries. Admittedly, these are all inferred references, but I think there’s a strong case for their presence. A) God’s no kill order would have stood with Adam’s family, thus the mark of Cain would be unnecessary. B) There is no mention of Cain taking a wife until he is in the land of Nod, and the story of cain and abel very much reads as a youthful narrative C) “Away from the presence of God” connotes a anthropic context in the ANE – God’s people had God’s presence, everyone else was outside of God’s presence. Hence, the argument can be made that Cain was with everyone else.
      
      but they would still take over 6,000 years to reach us from Gliese 581 g. So our chances of interacting with real aliens are quite low.
      Well if you’re just going to be realistic, that’s no fun.
      
      and not giving us instructions on how to interact with alien life), on the other hand, would be a pretty significant oversight.
      I’d argue that he did. He didn’t give us guidance for living in a democratic or a post-modern society, but he gave us minds to read and apply his living and active word in a host of situations. I see no problem applying that same cultural hermeneutic to a truly alien species.
      
      …
      
      The issue of the native people in the new continent is actually a bit of a red herring. The real issue, it seems is whether the native persons of the Americas could be descendants from Adam. I’ve heard the YEC approaches to this issue, but I haven’t heard any convincing way to account for the fact that there is generally accepted evidence of civilization in North America as early as 10000 BCE. So the real issue is that these are a people, who all the evidence suggests, are not descendants of Adam, but are eligible for salvation.
      - pete
        
        “I’d argue that he did. He didn’t give us guidance for living in a democratic or a post-modern society, but he gave us minds to read and apply his living and active word in a host of situations. I see no problem applying that same cultural hermeneutic to a truly alien species.”
        
        One thing that is missed: Imagining that aliens make contact on earth. They would obviously be more advanced than us, and may already have an understanding of our world’s religious composition.
        
        What happens if these aliens are Muslim, Buddhist or Hindu? What happens if these aliens infact preach to us a gospel different from our own (cf. Galatians 1:8)
        
        Do you think humanity would have questions for them with respect to origins and God? Do you think they would give us an answer?
        
        Unless they are going to be God’s elect angels who rapture his elect people, I see them as flying in the face of scripture and the Gospel.
        
        I think we would all do well to see the same.
        
        http://www.retheology.net Jared
        
        I’m not sure how this changes anything. If they’re Muslim / Buddhist / Hindu, what have you, then our obligation is no less to point to the eternity in their hearts than it is to anyone else.
        
        I think if they are more advanced then us, the questions they point us to would be more advanced. But that’s a gnosis question, not a pistis one. They are presumably smarter than us with a deeper understanding of the laws of the universe, but that’s a separate question from the question of faith. Their questions and answers about faith would come out of their own context, the same as any other religion – and the goal of the missionary is to translate the gospel into that culture.
  - pete
    
    I don’t think that Daniel’s inclusion in “the writings” has any significance. Joshua and Kings happen to be included in the “Prophets”.
    
    As far as earlier vs. later dating goes, Daniel is cited by Macabees, whereas Daniel notes the rise of “violent men from among your people” and brushes it off. As such Daniel is in most likelihood an earlier Babylonian work.
    
    And as far as “kosmos” goes, it is plausible, but in now way supported by the “rocks cry out” citing of Hebrew Poetry…. it was poetry citing the greatness of God.
    
    I was thinking about any other possible citation allowing for alien visitation, and John 17 (“there are sheep of another pen”) as being inclusive of Gentiles and ETI… but the “Great Commission” only includes the “ends of the earth”… not the kosmos.
    - http://twitter.com/davidstarlingm davidstarlingm
      
      Yeah, it wouldn’t have been hard for the Great Commission to have included “and beyond the heavens” if ETI evangelism was intended.
    - http://www.retheology.net Jared
      
      Those are good points. I hadn’t considered a lot of that, and never noticed that the great commission does end with gys – not kosmos.
      
      Thanks for pointing that out.
http://twitter.com/davidstarlingm davidstarlingm

Taking a straightforward approach….

“Either the people who would kill Cain….”

Who would be more likely to kill Cain than Abel’s blood relatives? This was a very premodern culture; blood feuds were quite common.

“….the people in the land of Nod….”

There is no reference to anyone living in the land of Nod; in fact, verse 17 states that Cain founded the only known city in Nod. “Settled in the land of Nod” could be better read, “settled in the place now known as Nod.” Remember, this part of Genesis is an origin story; the author is presenting the origins of Nod to his readers who would likely be familiar with the region.

“….or the people that Cain marries [....] There is no mention of Cain taking a wife until he is in the land of Nod.”

There is no mention of Cain taking a wife in the land of Nod, either. The other sons and daughters of Adam and Eve are explicitly mentioned in Genesis 5:4.

If you want to find evidence of people who came from some line other than Adam’s, try Genesis 6:1-5. What that’s referring to is anybody’s guess.

“Well if you’re just going to be realistic, that’s no fun.”

Yeah, it sucks, I know. I’m just saying: if you the Bible to be true, then any apparently-alien life is vastly more likely to be demonic than exobiological.

“The real issue, it seems is whether the native persons of the Americas could be descendants from Adam. I’ve heard the YEC approaches to this issue, but I haven’t heard any convincing way to account for the fact that there is generally accepted evidence of civilization in North America as early as 10000 BCE.”

Dating of the Clovis culture sites, as well as the earlier Pedra Furada sites, is accomplished primarily by radiocarbon dating. YECs allege that radiocarbon dating calibration curves are uniformly distorted by the failure to account for dramatic changes in radiocarbon levels as a result of the Noahic flood. If one rejects the notion of a global flood (textually difficult but academically attractive), then there is no reason to think that the patriarchs in Adam’s line were direct year-by-year descendants; Adam could still predate Clovis.
pete

Bracketing my views on Genesis (mythical/legendary explanation of Israel’s theological/national history and origins), how does any exotheology positively include an alien visitation within canonical eschatology?
- http://www.retheology.net Jared
  
  I think placing it within the realm of eschatology exclusively is troublesome. Though, I suppose that would signify the end of an era if ever there were one…
  - pete
    
    The thing about aliens is that many people expect them, and many people want futher reasons to reject God, Jesus, the Holy Spirit, Church, and Scripture.
    
    If it happened, and Aliens gave the secular or non-Christian world what they were looking for, I humbly think that Christian Scripture has already predicted the consequence, even if the medium itself was not revealed.
    
    Note Daniel’s interpretation of Nebuchadnezzar’s dream of the statue (Daniel 2) and Daniel’s own vision of Beasts (Daniel 7) correspond to a certain reality, without so much as explicitly defining the medium, as it does the consequence.
    
    The consequence of all of these kingdoms (and most notably the kingdom of clay/iron in Chapter 2 and the Fourth Beast in Chapter 7), is that these kingdoms persecute the people of God.
    
    The final kingdom I have cited (clay/iron = fourth beast) is the final one to persecute God’s people before his return and judgement.
    
    Now if aliens were to land, in the grand scheme of history, would they be more or less notable than the kingdoms of Babylon (head of gold/first beast); Medo-Persia (chest of silver/second beast); Greece (3rd beast/arms and thighs of bronze); Rome (legs of iron…. I think it is wrong to see them as the fourth beast)?
    
    For a Bible which predicted those historical realities, do you think that it would fail to account for ETI, if that was a reality to be realized?
    
    I don’t think so
    - pete
      
      (and with reference to my last post)
      
      David is right. If aliens landed, and weren’t accounted for in scripture, it would lead us to reject the authority of scripture and Christian faith…
      
      A consequence that is precisely predicted by Jesus, Paul, Peter, and John.
      
      So if aliens do land, it means one of two things:
      
      1) The Christian faith is a sham, or subordinate to a “higher reality”…. check out theosophy for yourself
      
      or
      
      2) The end is very near, and Jesus is coming back very soon. Be prepared to die for your faithful allegiance to our LORD and Saviour Jesus Christ, because it is gonna be rough sledding until he returns.
      
      I stake my life and soul on #2
      - http://www.retheology.net Jared
        
        Again, I think that’s a false dichotomy. If aliens landed, and it weren’t accounted for in scripture, the living word and the spirit of god with us would adapt.
        
        3) There is more to God’s infinite wisdom than we know or understand, and he is revealing more of himself and his word and truth every minute of every day. The Bible is still the word of God, and the Church still has work to do.
        
        pete
        
        or what if it is accord with God’s plan for the culmination and fulfillment of time?
        
        And it is not a false dichotomy… however, you are welcome to provide a consistent hermeneutical understanding of scripture that would allow for ETI
    - http://www.retheology.net Jared
      
      For the record, I don’t think it is a reality to be recognized, as David pointed out above. The distances are too great.
      
      Secondly, now we’re getting into the meat of the argument. And we’re all making assumptions about something we can’t possibly know. So let’s assume the converse. What if the Aliens did have advanced knowledge of our theologies and accepted Christianity as the most cohesive? What if they were to correct some error that has crept into our doctrine? What if they were a tool that God is using to bring us back to him? It’s easy to make doom and gloom assumptions because we’re programmed to fear anything ‘alien’, but it’s just as probable that the converse is true.
      - http://twitter.com/davidstarlingm davidstarlingm
        
        “I don’t think it is a reality to be recognized, as David pointed out above. The distances are too great.”
        
        Considering the vastness of the distances and obvious improbability of an actual exobiological encounter, wouldn’t it be reasonable to assume that any supposed alien manifestation was more likely to be demonic in origin?
        
        In other words, which do you think is more likely: an actual alien envoy, or some sort of angelic beings posing as aliens?
        
        pete
        
        if the aliens came, it would be extra-dimensional, and thus demonic/satanic.
        
        The “extra-dimensional” or “other world” is exactly what the apocalyptic genre, including the latter portion of Daniel (Daniel 7-12), and Revelation (4-22) entail
      - pete
        
        correcting doctrine, based upon scriptural revelation is one thing.
        
        Preaching a new gospel is quite another (cf. Galatians 1:8)
        
        I remain agnostic about whether God chooses to have time end, in part, through alien encounter.
        
        I just want Christians to be prepared if it does happen.
jeremy

I always find posts like this interesting in that they always seem to miss the obvious. The basis of our faith is a God that is everywhere at all times. A God who is not bound by the same physical laws we bound by or the same sense of time and space, but we then limit His power to what we can understand. If Jesus was the Son of God, why must there be one incarnation of this part of the trinity? Is God or the Holy Spirit bound by the same limitation of being in one time or place at a time? Generally, the answer is no. So why do we assign those restrictions to one-third of the trinity?
- pete
  
  “If Jesus was the Son of God, why must there be one incarnation of this part of the trinity? Is God or the Holy Spirit bound by the same limitation of being in one time or place at a time?”
  
  Jeremy:
  
  I don’t think anyone here is denying that God/Jesus/Holy Spirit could have created countless fallen peoples on countless fallen planets; countless incarnations in countless universes; or countless Gospels within countless universes.
  
  As far as this universe is concerned, according to the gospel that this fallen people was given, there is no room for alien visitation unless it is part and parcel with an end time deception.
  
  I challenge anyone to take our Gospel (Old and New Testament) and find a place which allows for a peaceful alien visitation.
  
  The apocalyptic literature is the best place to start the search, and I respectfully submit that it does not allow for such a peaceful visit. Neither does the rest of the canon.
- randal
  
  Jeremy, I must admit I don’t really understand your comments. You say the article “seem[s] to miss the obvious”. You then go on to describe the divine transcendence and a rudimentary understanding of omnipresence. (It is rudimentary because we must define what we mean when we say God “is everywhere at all times”. People are liable to think it means God is spatially present everywhere. It most emphatically doesn’t mean that. Rather, omnipresence as an attribute is derivative of the divine omnipotence and omniscience. In virtue of God having all knowledge of all true facts about the world at any given time and having power over the states of affairs that those facts describe so far as those facts relate to a spatially extended material creation, we say God is omnipresent.) I am not sure why you think the divine transcendence was “missed”. The primary topic never was the divine transcendence but rather the divine immanence, specifically the issue of God the Son (or any person of the Trinity, or all persons of the Trinity) being self-identical with a particular material creature. The “restrictions” assigned when we talk about the concept of incarnation are simply the restrictions entailed by the very concept.
pete

and another question…

why do Christians see Christ’s return as “doom and gloom”?

I say “Maranatha!”
http://leadme.org Jeff

Hah, I’ll agree with Walter and Beetle that Christian orthodoxy would no doubt keep cruising along.

First, I just wanna note that I don’t see anything “depressing” about the conclusion I’ve come to. Anyway, to the four scenarios:

1) The simultaneous incarnations idea is interesting and something I’d never considered before. Still strikes me as having “a rather absurd aspect,” though, to use the Paul Davies quote you gave in the other article. Seems an awfully messy undertaking. In any event, no one here appears to be that hot on this possibility, including you Randal. To quote you from before: “[other incarnations] on other planets I think probably not, and on our planet I think definitely not.” So, moving along…

2) About the scandal of particularity, I do not believe that God chose to “reveal himself uniquely through a particular people in history,” so I’m not sure I’ve gotten past the scandal of that scenario. As for God incarnating as one individual, I’m not quite seeing the potential scandal in that if that individual was miraculously conceived. If on the other hand, that individual was the product of normal sexual intercourse and could have existed quite apart from a divine incarnation, then this might seem to be more of a scandal. At the end of the day, all I can say here is that if indeed there are many millions/billions/trillions of intelligent species, it strikes me as spectacularly implausible that humans would just so have happened to have been the sole direct recipients of divine incarnation.

3) Scratch “hardened” and replace it with “determined.” My bad. I don’t see, though, how a W. L. Craig best-of-all-possible-worlds argument can work here. It’s one thing if the problem is only that some relatively large percentage of humans are un-savable, but it seems to be almost a qualitatively different problem if very nearly 100% of the intelligent creatures in the cosmos are un-savable. Best of all possible worlds? No, it seems to me that only Calvinism could hope to address this scenario, though it still seems to fall woefully short (if not for reasons of highly questionable divine mercy, at least for the reason that we run into another spectacularly scandalous particularity–i.e., why humans rather than some other species?).

4) I don’t know that invoking the example of angels helps that much here. As the product of evolutionary processes, it seems inevitable to me that humans should be “fallen” (however you want to define that). And so why wouldn’t other species, most (all?) of whom are products of similar processes, be fallen as well? Even if there are some creatures (such as angels) who differ fundamentally from humans on this point, it would certainly seem to me that fallenness is the rule rather than the exception.

Keep in mind with all of this that I’m not trying to disprove orthodoxy so much as to demonstrate one of the sets of arguments that renders it very implausible to an outsider such as myself.
- pete
  
  “Keep in mind with all of this that I’m not trying to disprove orthodoxy so much as to demonstrate one of the sets of arguments that renders it very implausible to an outsider such as myself.”
  
  Forgive me Jeff if I’m asking questions that you have already answered before, but as you admit that you are an outsider to orthodoxy, I have a couple of questions for you:
  
  What is logically incompatible about a locus of authority (the Triune God of Christian Theism) creating a universe in which humanity is the focus?
  
  Secondly, what is logically incompatible about this God being the “good guy” of the story?
  
  Thirdly, what is logically incompatible about there being a “bad guy” (Satan) in the story, who seeks to undermine God, steal worship for himself, and drag his beloved image bearers off to Hell with him?
  
  And fourthly, what is logically incompatible about this “bad guy” tricking the world into following ETI’s away from God?
  
  As I know you have answers for all of the above, it will be your answer to the 4th question that piques my curiosity…
  
  Namely, as you have never seen an ETI, or these “trillions of intelligent beings”, why do you have more faith in ETIs than the God of Christian Orthodoxy?
  
  If I have misrepresented/misunderstood what you have written, my apologies.
  - pete
    
    it should have read “humanity is a focus”… and by that I mean that we are created alone in this universe
    
    clearly no devout believer would think that “we” are the focus over and above God.
  - http://leadme.org Jeff
    
    Pete, I don’t see anything logically impossible about any of that, but I do think that Christian orthodoxy is rendered highly implausible by these considerations (and by many other considerations as well). I’m not quite sure what you mean about Satan tricking people into following ETI’s away from God. I’m just considering probabilities here. Assume there’s just one intelligent species, on average, per galaxy (which would seem to be a very conservative estimate–the Milky Way, for example, contains several hundred billion stars). Since there are estimated to be several hundred billion galaxies in the visible universe, well, you can do the math.
    
    This has nothing to do with me refusing to trust God or anything like that. It is simply that I consider Christian orthodoxy to suffer from insurmountable implausibilities, and so I don’t see Christian dogma to have been shaped by the divine hand.
    - pete
      
      Jeff,
      
      To clarify, I’m not talking about Satan tricking people to follow ETIs
      
      Im talking about Satan and his band of merry demons masqeurading as ETIs
      - http://leadme.org Jeff
        
        Sure, Pete, that’s a logical possibility. But I’m still not sure what you’re getting at. Are you arguing that humans are the only non-angelic/non-demonic intelligent creatures in the cosmos?
        
        pete
        
        Yes I am.
        
        I am basing that on my acceptance of Christian canonical scripture.
        
        And that is what it boils down to. There is no room in the Bible for a peaceful visitation.
        
        And I recognize that the arguments for the validity of the Bible are way too long to exposit here.
        
        So I humbly submit that people who accept the canonical Bible as authoritative should not expect a peaceful close encounter from ETI.
        
        http://leadme.org Jeff
        
        Maybe I should ask this question:
        
        If I remember correctly, you do accept a broadly evolutionary model of origins, correct? If that’s the case, why would you think that earth is the only corner of the cosmos in which intelligent life has evolved? Would you say that evolutionary processes require direct divine intervention in order to produce intelligent life (or even to get going in the first place)? And so earth is the only planet on which God has guided evolutionary processes in order to produce intelligent life?
        
        If you believe that humans are the only intelligent non-angelic/demonic creatures in the cosmos, then maybe you and I are at a dead-end with this conversation.
        
        http://leadme.org Jeff
        
        But I’m not talking about potential visitations from other intelligent species. I’m simply running the numbers and saying that it seems most reasonable to me to think that there are many millions/billions/trillions of other intelligent species out there, whether or not we humans ever come into contact with any of them. And if indeed there are a large number of intelligent species out there, then Christian orthodoxy is rendered highly implausible, it seems to me, for reasons I’ve outlined. Again, alien visitation doesn’t have anything to do with my argument.
        
        Am I making sense? I feel like we’re misunderstanding each other.
        
        pete
        
        Okay… I guess because you are using probability theory as your starting point, and I am using scripture and statistics that David has already pointed out above.
        
        I’m not trying to talk past you. However, I believe that a maximally perfect transcendent agent caused this universe and all that is in it. I also believe this agent to have designed the universe to include one planet, according to his sovereign purposes, which sustains intelligent life.
        
        You may not agree with my worldview, but I hope you can see why someone who holds my view would logically have no reason to expectat there to be any other intelligent life in this universe.
        
        http://leadme.org Jeff
        
        Pete, does your view (that humans are the only intelligent species in the cosmos; that humans are the primary focus of the created physical order) strike you as perhaps being naively human-centric? It certainly strikes me as being that way. If your view is correct, I find it very hard to imagine why God would create such a staggeringly immense universe containing such an unfathomable number of worlds. If God is a being greater than which nothing can be conceived, then surely God’s resources and capacity for love are not strained no matter how many intelligent species there are.
        
        As for your biblical argument, I just don’t see the relevance. I’ll quote Randal from earlier in this comment thread: “ETI wasn’t on the radar screen at all of the biblical writers. But then neither was Copernicanism, Newtonianism, the germ theory of disease, relativity theory, and quantum mechanics and those all turned out to be true.”
        
        http://twitter.com/davidstarlingm davidstarlingm
        
        “Pete, does your view (that humans are the only intelligent species in the cosmos; that humans are the primary focus of the created physical order) strike you as perhaps being naively human-centric? It certainly strikes me as being that way.”
        
        As has been pointed out previously, this is the same essential objection that has been posed many times regarding Christianity — is the idea that God chose a particular group of people with whom and through whom he chose to interact. There are a great many possible reasons why operating through a particular time and place was be more in line with God’s purposes than the various alternatives.
        
        “I find it very hard to imagine why God would create such a staggeringly immense universe containing such an unfathomable number of worlds.”
        
        I find it rather awe-inspiring and humbling that God would create a universe with so many trillions of trillions of galaxies and yet choose to reveal his glory specifically through one tiny, 6e24 kg ball of rock orbiting a fairly small, stable sun in a nondescript arm of an average-sized galaxy.
        
        “If God is a being greater than which nothing can be conceived, then surely God’s resources and capacity for love are not strained no matter how many intelligent species there are.”
        
        Quality over quantity, I suppose….
        
        “I’ll quote Randal from earlier in this comment thread: ‘ETI wasn’t on the radar screen at all of the biblical writers. But then neither was Copernicanism, Newtonianism, the germ theory of disease, relativity theory, and quantum mechanics and those all turned out to be true.’”
        
        As was pointed out, Copernicanism, Newtonianism, germ theory, relativity, and QM have no direct impact on soteriology. The Bible asserts to contain “all things necessary for life and godliness,” not all details of science. Dealing with extraterrestrial intelligence certainly has significant implications for life and godliness (unlike, for example), relativity theory.
        
        http://leadme.org Jeff
        
        “There are a great many possible reasons why operating through a particular time and place was be more in line with God’s purposes than the various alternatives.”
        
        It’s one thing to hold that God’s purposes for humans were best accomplished by choosing one specific group of humans (i.e., the Israelites) amongst whom to accomplish those purposes. But would you concede that it’s an altogether different problem to think that God’s purposes for all intelligent creatures would have been accomplished directly amongst us humans? In the former case, it could be argued that God had to choose (for whatever reason) one specific group of humans, and that group just happened to be the Israelites (though it could easily have been the Canaanites, or the Egyptians, or the Greeks…). In the latter case, one could again argue that God had to choose one specific species, but now in this case it would appear to be just a stupendous coincidence that that species happened to be us humans, rather than one of the other millions/billions/trillions of intelligent species out there. This latter case presents a qualitatively different problem than the former case, and I don’t see how it can be brushed off so quickly.
        
        “I find it rather awe-inspiring and humbling that God would create a universe with so many trillions of trillions of galaxies and yet choose to reveal his glory specifically through one tiny, 6e24 kg ball of rock orbiting a fairly small, stable sun in a nondescript arm of an average-sized galaxy.”
        
        I find it instead to be incredibly implausible, and yet another example of us humans being remarkably short-sighted and self-centered.
        
        “The Bible asserts to contain ‘all things necessary for life and godliness.’” Does it? Or is that rather a bit of external theology that has been imposed upon the Bible? There isn’t any relevant biblical reference that comes to my mind.
        
        I think you might be downplaying the difficulty with which the Christian church finally adopted Copernicanism. And surely evolutionary theory has significant implications for life and godliness (which is, I think, the primary reason why there is still so much resistance to it from many conservative Christians), and yet one finds no mention of it anywhere in the Bible. Nor should one expect to find mention of it.
        
        http://leadme.org Jeff
        
        To clarify on the “all things necessary for life and godliness” point, I take it that you’re referring to 2 Peter 1:3? But I don’t read that as saying that the Bible, specifically, includes all such necessary things.
        
        http://leadme.org Jeff
        
        I want to note, too, that I’m certainly not hoping to see Christianity destroyed or anything like that. But I do think that the thick fog of myth that has encrusted Jesus for nearly 2000 years ultimately disrespects him and obscures his message and example and importance.
        
        http://twitter.com/davidstarlingm davidstarlingm
        
        Why do you think it is a thick fog? Why do you think the past 2000 years have obscured his message? What about Christianity do you believe most misrepresents Jesus?
        
        http://leadme.org Jeff
        
        John MacArthur has said that “the only reason Jesus came was to save people from hell.” Granted, his position is an extreme one, but it seems to me that orthodoxy necessarily privileges a cosmic, mythic, otherworldly view of Jesus over a view that sees his importance primarily in terms of the right here and right now.
        
        pete
        
        Im a conservative Christian.
        
        However, there is a common flawed hermeneutic with respect to Genesis.
        
        A comparison against other ancient near east cosmogenies reveals that the Creation account in Genesis has a polemic to it.
        
        However, much like Marcion’s prompting Christians to define their canon, atheistic brandishing of evolution has actually forced us to read the text in its correct light.
http://twitter.com/davidstarlingm davidstarlingm

Jeff said….

“….one could again argue that God had to choose one specific species, but now in this case it would appear to be just a stupendous coincidence that that species happened to be us humans, rather than one of the other millions/billions/trillions of intelligent species out there.”

Which is why other intelligent species in the universe would cast significant doubt on Biblical Christianity.

“….you might be downplaying the difficulty with which the Christian church finally adopted Copernicanism.”

The difficulty with adopting Copernicanism was actually a scientific one. If the earth really moved around the sun, then we would see parallax in the stars. This is the reason that heliocentrism was rejected when it was first proposed by Aristarchus in the third century BCE. This lack of parallax was the primary objection to heliocentrism for most of history; actual stellar parallax was not observed (providing definitive evidence of heliocentrism) until the 18th century.

The Church actually encouraged discussion and debate between geocentric and heliocentric models. Galileo’s infamous Dialogue concerning the two chief world systems was actually the result of a request by Pope Urban VIII who was an astronomer himself. However, Galileo sorely insulted Urban, declaring him a simpleton for denying that the motion of the tides proved earth’s movement (a claim we know to be false; the moon causes tides). Urban had a fit and pulled rank on Galileo….but that was a spat between astronomers, not a faith-based determination.
- http://leadme.org Jeff
  
  So David, am I understanding correctly that your position is that humans are the only intelligent species in the cosmos? Is your commitment to Christian orthodoxy your main reason for holding that position? Put another way, can you give any reason why someone such as myself (who is not committed to Christian orthodoxy) should think that humans are the only intelligent species in the cosmos? Also, do you see your position as being required by orthodoxy, or is it rather a position you hold in order to preserve the plausibility of orthodoxy in your eyes?
  
  My understanding of the church’s Copernican dilemma is that it was primarily a theological dilemma (interpretation of scripture, and humanity’s place in the universe), but I could certainly be misinformed on that. But anyway, I’d be more interested in your thoughts on evolutionary theory and it’s implications for life and godliness.
  - pete
    
    “So David, am I understanding correctly that your position is that humans are the only intelligent species in the cosmos? Is your commitment to Christian orthodoxy your main reason for holding that position? Put another way, can you give any reason why someone such as myself (who is not committed to Christian orthodoxy) should think that humans are the only intelligent species in the cosmos?”
    
    Questions over orthodoxy should be bracketed, as ETI was never an issue discussed at the great ecumenical councils of the 1st five centuries of the church.
    
    However, believeing the collective truth of the Biblical text, in its entirety, does require me to believe that an alien visitation is demonic.
    
    It sort of goes like this:
    
    Approximately 99% of the biblical prophecies have been fulfilled. The two main ones we are waiting for is the revelation of the “Man of Lawlessness” (2 Thess. 2) and the Return of Christ (Synoptics, Paul, Peter, John, Revelation)
    
    With respect to the prophecy surrounding the man of lawlessness:
    
    “For this reason God sends them a powerful delusion so that they will believe the lie” (2 Thess 2:11)
    
    Here Paul is referring to unbelievers and false Christians.
    
    I’m not saying God will choose to send aliens, but you can reasonably see how a Bible-based believer will view these things.
    
    As David already mentioned, ETI will present a strong defeater to Biblical Witness ….. IF…. it is not the same deception that Paul warned us all about.
    - http://leadme.org Jeff
      
      Pete, I still think you’re muddying the issue here. My argument has nothing to do with an alien visitation. I’m just looking at the probability that there is other intelligent life out there, whether or not we humans ever encounter any of it. I think you’ll have to go the route that David is going, and present a case for why you consider it unlikely that there is any other intelligent life in the universe.
  - http://twitter.com/davidstarlingm davidstarlingm
    
    “….your position is that humans are the only intelligent species in the cosmos? Is your commitment to Christian orthodoxy your main reason for holding that position?”
    
    Correct: I don’t think there are any self-aware species elsewhere in the cosmos. If self-awareness is not something specifically created by God, then it is an incredibly unique and improbable accident of evolution. There is no reason for us to expect that it should have happened here, much less elsewhere.
    
    Also, aliens aren’t consistent with Scripture. But neither are magical unicorns, and I don’t think those are very probable either.
    
    “….is it a position you hold in order to preserve the plausibility of orthodoxy in your eyes?”
    
    The discovery of sentient biological life elsewhere in the universe would, in my view, render orthodoxy highly improbable.
    
    “Can you give any reason why someone such as myself should think that humans are the only intelligent species in the cosmos?”
    
    I can’t think of any reason why someone such as yourself should think that humans aren’t the only intelligent species in the cosmos. The only reason I can think of would be wishful thinking, and you don’t seem particularly susceptible to that.
    
    “My understanding of the church’s Copernican dilemma is that it was primarily a theological dilemma…. “
    
    It’s a common misconception. There were a few religious leaders here and there who declared heliocentrism to be foolish on religious grounds, but the Church itself encouraged discussion on the issue. The Galileo ordeal was a debate between scientists that got political because Galileo was an arrogant ass.
    
    “I’d be more interested in your thoughts on evolutionary theory and its implications for life and godliness.”
    
    Universal common descent by natural selection is a perfectly viable (no pun intended) explanation for the diversity of life on earth. It is fairly internally consistent. However, in my experience (and again, I’m a physicist, so I probably over-simplify things), it doesn’t seem to lend itself to falsifiability. There aren’t really any potential discoveries which couldn’t be shoved into the existing framework fairly seamlessly.
    
    It’s possible that the mainstream view on evolution is fairly accurate, and Genesis 1-11 is a highly complex and unique form of myth. It’s also possible that the evolutionary model is the result of a whole bunch of intertwined question-begging, and the fossil record is the result of a global flood, leaving Genesis 2-11 as actual history and Genesis 1 up for grabs. I don’t really think that I can say definitively one way or another.
    - pete
      
      its pretty tough to call Genesis 2-11 actual history, once we see the ancient near eastern pagan text that the Genesis account was responding to.
      
      However, I don’t think anyone needs to be dogmatic one way or the other.
      - http://twitter.com/davidstarlingm davidstarlingm
        
        “its pretty tough to call Genesis 2-11 actual history, once we see the ancient near eastern pagan text that the Genesis account was responding to.”
        
        Which would be?
        
        All the ancient near eastern pagan origin texts I have seen are more likely to be derivatives of Genesis than the other way around.
    - http://leadme.org Jeff
      
      “I can’t think of any reason why someone such as yourself should think that humans aren’t the only intelligent species in the cosmos.”
      
      Really? We’re talking about hundreds of billions of galaxies, each containing tens/hundreds of billions of stars, and, most likely, an even greater number of planets. And that’s to say nothing of the possibility that there is more to the universe than that portion of it which is visible to us, or the possibility that there are other universes. I’m certainly no ETI researcher, but it seems to me that the odds are in favor of ETI.
      
      And even if you think that self-aware life is only possible as a special creation of God, why insist that earth is the only planet on which God chose to create self-aware life? Because the Bible would/should have mentioned it?
      
      Well, again, I’ll ask: if you think the Bible would/should have mentioned ETI, why doesn’t it mention evolution? If you’re not convinced of universal common descent, I’d be more than happy to do what I can to convince you of it. The genetic evidence alone is absolutely overwhelming (e.g., humans share a large number of precisely-matching genetic maladaptions with chimps and other primates).
      - http://leadme.org Jeff
        
        And as for self-awareness being an incredibly unique and improbably accident of evolution, what’s your expertise to make such a claim? For all we know, the descendants of modern-day chimps or dolphins (to use a few examples) might well develop self-awareness. Evolutionary convergence is the process I’m alluding to here.
        
        http://twitter.com/davidstarlingm davidstarlingm
        
        Such a development would invalidate a great deal of our assertions about the nature of consciousness, yes.
        
        http://leadme.org Jeff
        
        “Such a development would invalidate a great deal of our assertions about the nature of consciousness, yes.”
        
        Can you elaborate on that a bit for me?
        
        http://twitter.com/davidstarlingm davidstarlingm
        
        All of our legal systems are based around the idea that self-awareness is a necessary component of culpability. Self-awareness, or the capacity for self-awareness, is the determiner for human rights. You can own a dog, because a dog doesn’t know that it exists. Humans, on the other hand, are a different matter altogether.
        
        If chimps or dolphins developed and expressed self-awareness and an understanding of the conscious mind (i.e. the capacity to identify others as minds rather than just objects), we would have to completely reform our understanding of how rights are allocated and interpreted. Moreover, the religious notion that self-awareness and its commensurate rights are endowments from God would be invalidated.
        
        Those are just a few of the many considerations of such a development.
        
        http://leadme.org Jeff
        
        Not sure that I’m following you here. If chimps or dolphins developed self-awareness, then yes, that certainly would entail a restructuring of our legal framework. But I don’t see how that would invalidate any of our assertions about the nature of consciousness. It would only mean that we would have to recognize that humans are no longer the only self-aware species on earth.
        
        As for self-awareness being an endowment from God, again, why couldn’t God simply decide to endow chimps and dolphins with self-awareness?
        
        Again, I’m not seeing what you’re getting at here. And none of this has anything to do–so far as I can see–with your earlier statement that self-awareness is an incredibly unique and improbable accident of evolution.
      - http://twitter.com/davidstarlingm davidstarlingm
        
        Had such a nice response typed up, and then the browser crashed. Well, suck.
        
        “We’re talking about hundreds of billions of galaxies, each containing tens/hundreds of billions of stars, and, most likely, an even greater number of planets. I’m certainly no ETI researcher, but it seems to me that the odds are in favor of ETI.”
        
        The problem is that it hasn’t yet been demonstrated that increasing the number of planets increases the odds of getting an ETI. Thus this is just an argument from incredulity.
        
        “….if you think that self-aware life is only possible as a special creation of God, why insist that earth is the only planet on which God chose to create self-aware life? Because the Bible would/should have mentioned it?”
        
        That’s one of the contributing points, yes. But moreso because we have no evidence for any other self-aware life. One might as well posit that God created a wormhole machine under the pyramids that can be used for transport to a space station at the Galactic Core….but with no evidence, it’s just speculation.
        
        “….if you think the Bible would/should have mentioned ETI, why doesn’t it mention evolution?”
        
        Evolution bears nowhere near the social, theological, soteriological, and cultural implications of an ETI.
        
        “If you’re not convinced of universal common descent, I’d be more than happy to do what I can to convince you of it.”
        
        Feel free. If you’d like to email me, just follow me on twitter and I’ll DM you my email address.
        
        To be fair, though, I should probably say that I’m a physicist, in this vein and in this one. That’s not to say that I’m not open to learning new things — quite the opposite — but I tend to assume I can work out all the intricacies of any argument in one of the more applied fields. So I ask a lot of questions.
        
        “The genetic evidence alone is absolutely overwhelming….”
        
        I find the genetic and paleontological evidence to be quite compelling, actually. Universal common descent is consistent with itself and with the available evidence to a very high degree. In the absence of better explanations, it presents a highly likely model.
        
        Showing that evolution could have happened isn’t enough; though: I can’t unreservedly assent to the proposition unless it can be shown that evolution is more likely than any other explanation. And that’s what hasn’t been done, IMHO.
        
        “….(e.g., humans share a large number of precisely-matching genetic maladaptions with chimps and other primates).”
        
        I presume that you’re referencing the similarities between humanity’s fused 2 chromosome and apes’ 12 and 13 chromosomes, popularized by Dr. Ken Miller in this video. It’s definitely an interesting video.
        
        The problem is twofold: first, centric fusions don’t automatically precipitate speciation and don’t necessarily result in any phenotypic expression at all. Such fusions happen all the time without altering the genetic code in any way. Miller seems to imply that this fusion was the point of divergence between humans and apes, but any phenotypic alteration significant enough to precipitate speciation would have prevented reproduction. Thus, it is unlikely that this particular event had any consequences for the organism, thus raising the question of why there are no human genomes without this fusion. How could a fusion with no phenotypical expression propagate to the entire species?
        
        Second and more importantly: yes, the 2-chromosome is evidence of a genetic event. At some point, the human population was small enough that one Robertsonian-level mutation spread to the entire species. However, this is not evidence of common ancestry: this event clearly happened after human beings were a distinct species. We already know that humans and apes share common genetic material.
        
        For this to be actual evidence of common ancestry, we would need to find an ape that shares the same genetic event.
        
        Brap Gronk
        
        “I can’t unreservedly assent to the proposition unless it can be shown that evolution is more likely than any other explanation. And that’s what hasn’t been done, IMHO.”
        
        What other explanation(s) are more likely, in your opinion?
        
        http://twitter.com/davidstarlingm davidstarlingm
        
        Absent an internally consistent model for creation, universal common descent is the logical and likely explanation for the diversity of life. However, I’ve found that universal common descent and special creation are both broadly consistent with the available evidence; there are few pieces of evidence that do not fit within both explanations easily.
        
        http://leadme.org Jeff
        
        “Had such a nice response typed up, and then the browser crashed. Well, suck.”
        
        Doh! I feel your pain on that one.
        
        “One might as well posit that God created a wormhole machine under the pyramids that can be used for transport to a space station at the Galactic Core….but with no evidence, it’s just speculation.”
        
        That made me chuckle! But really? Come on David! I’ll grant you that I’m engaging in speculation. Of course. But I’m inclined to think the mediocrity principle ought to inform our speculations on this issue. Heck, even if the rare earth hypothesis is preferable, I’ve never seen anyone outside of conservative Christian circles advocate a unique earth hypothesis.
        
        And honestly, I’m a bit confused. You said earlier that we shouldn’t expect any genuine alien encounters, because of the massive distances involved. Tracking with you so far. [My own (layman's) thoughts on the Fermi paradox are that we probably just haven't yet developed the technological capability sufficient to detect evidence of distant ETI.] But now you’re saying that the lack of such encounters means that I’m engaging in rampant speculation and an argument from incredulity?
        
        Anyway, moving along, because we might be at the end of that particular strand of the conversation…
        
        As for the genetic evidence, I actually had in mind several other pieces of evidence. The Vitamin C/GULO issue is one. Perhaps even more striking is the issue of endogenous retroviruses shared by humans, chimps, and other primates.
        
        “Evolution bears nowhere near the social, theological, soteriological, and cultural implications of an ETI.”
        
        Perhaps. I suppose it depends on who you ask (cough, Al Mohler, cough). But even if that is true, I would think you would still agree that evolution does have significant implications for life and godliness. And yet mention of it is nowhere to be found in the Bible.
        
        http://twitter.com/davidstarlingm davidstarlingm
        
        I’ll respond to these three points separately.
        
        “I’m inclined to think the mediocrity principle ought to inform our speculations on this issue. Heck, even if the rare earth hypothesis is preferable, I’ve never seen anyone outside of conservative Christian circles advocate a unique earth hypothesis.”
        
        From a galactic perspective….sure, our planet is fairly unremarkable, despite its rather extensive temperateness. But unless it can be shown that intelligent life is likely to arise given a temperate environment, the near-certain existence of other habitable earths doesn’t add to the probability of extraterrestrial life.
        
        We have no reason to think our planet is unique. We have every reason to think that life is unique. And if life is unique, then how much more so intelligent life!
        
        “You said earlier that we shouldn’t expect any genuine alien encounters, because of the massive distances involved. But now you’re saying that the lack of such encounters means that I’m engaging in rampant speculation and an argument from incredulity?”
        
        Certainly it is encouraging for the ETI case that the enormous distances involved in interstellar communication would lead us to expect a lack of such encounters. I guess I’m just questioning the f_l factor of the Drake Equation.
        
        http://leadme.org Jeff
        
        “But unless it can be shown that intelligent life is likely to arise given a temperate environment, the near-certain existence of other habitable earths doesn’t add to the probability of extraterrestrial life.”
        
        If intelligent life is unlikely even given a temperate environment, there are still (presumably) so many trillions+ of temperate worlds in the universe that it would seem that the odds would still be in favor of the presence of ETI, on at least a small percentage of those worlds.
        
        “We have every reason to think that life is unique. And if life is unique, then how much more so intelligent life!”
        
        Why do we have every reason to think that? My understanding is that although scientists haven’t yet found any conclusive evidence of current/former life on Mars, there nevertheless are a number of solid leads. And that’s just the planet right next door to us. If such conclusive evidence is found, so much for the idea that abiogenesis is highly unlikely. As for it being highly unlikely that intelligent life would develop from lower forms of life: that would seem to be speculation either way, whether one considers it likely or unlikely. Can you give any specific argument as to why you consider this to be so highly unlikely?
        
        Furthermore, how about the possibility that other life forms need not be carbon-based? How about the possibility that other life forms might be able to thrive in environments we would think to be uninhabitable? (e.g., multicellular animals which do not require any access to oxygen have recently been found in a hypersaline basin at the bottom of the Mediterranean Sea). If anything, I’ve most often heard that the rare earth/rare life hypothesis relies on arguments from incredulity.
        
        http://twitter.com/davidstarlingm davidstarlingm
        
        “I actually had in mind several other pieces of evidence. The Vitamin C/GULO issue is one.
        
        The GULO gene is actually one of the reasons I tend to question universal common descent — not because GULO doesn’t fit UCD, but because it is such an obvious example of the confirmation bias pervasive in evolutionary research.
        
        Yes, rats, guinea pigs, prosimians, apes, and humans all share a similar GULO gene for ascorbic acid synthesis. Yes, this gene is active in prosimians and rats but inactive in guinea pigs, apes, and humans. Yes, humans and apes have the same deactivation point different from the guinea pig deactivation point. Undeniable evidence for common ancestry, right?
        
        Actually, it’s confirmation bias. The only reason this particular substitution error is considered evidence for common ancestry is because it matches the already-assumed evolutionary tree. But what are the actual facts? There are 129 substitution errors in the human GULO gene. There are 96 substitution errors in the guinea pig GULO gene. Of these, 47 are shared identically between humans and guinea pigs, (citation here at page 316), but are not shared with prosimians or rats.
        
        When genetic markers match between species thought to have a recent common ancestor, it is evidence of ancestry; when the markers match between species without a recent ancestor, it’s coincidence. Confirmation bias at its best.
        
        The matches between the guinea pig gene and the human gene make it obvious that these mutations are nonrandom; there must be certain points in the gene where environmentally-stimulated mutagenesis is more likely. It seems probable that the tendency for certain mutations are hard-coded into the genome, almost like the way vehicles are designed with crumple zones to protect the occupant cabin in case of accident.
        
        In any case, the matching error in ape & human genes could be the result of common ancestry, but it doesn’t prove common ancestry any more than the 47 matching errors between guinea pigs and humans prove their common ancestry.
        
        http://leadme.org Jeff
        
        I’ll grant you that the mutations may be nonrandom. And in the case of ERVs, I’ll grant that the points of ERV insertion may be nonrandom (and hence, the probabilities given in the ERV video I linked to may be significantly inaccurate). But even granting that, I don’t see what could be a better explanation for the data than common ancestry.
        
        Is it merely a coincidence that the higher primates share a nonfunctional GULO gene? Is it merely a coincidence that humans share so many ERV matches with chimps and higher primates. Is it merely a coincidence that the more closely-related to humans (according to the accepted evolutionary tree) a particular primate species is, the more ERV matches is shares with humans?
        
        You said earlier that evolution is non-falsifiable, or at least very difficult to conclusively falsify. But it’s very easy to imagine any number of genetic findings which would falsify it, or at the very least, which would rock our current evolutionary tree model.
        
        http://twitter.com/davidstarlingm davidstarlingm
        
        “I’ll grant that the points of ERV insertion may be nonrandom. But even granting that, I don’t see what could be a better explanation for the data than common ancestry.”
        
        Better? Maybe not. Equally consistent? I think so.
        
        The ERV argument depends on two premises: first, that retrovirus insertions are random, and second, that ERV sequences serve no genetic purpose.
        
        With respect to the first premise, I would predict that similar ERV matches will be found in species not thought to share a common ancestor. However (and this covers the second premise), it’s not necessarily the case that these sequences even represent genetic events. ERVs have been shown to play several essential roles, including dynamic protein coding and gene regulation. If the majority of ERVs were original to the genetic code, they would have served the same functions in primates as in humans.
        
        “Is it merely a coincidence that the higher primates share a nonfunctional GULO gene?”
        
        Not any more than it’s a coincidence that humans share 47 of the same GULO gene errors that guinea pigs have.
        
        The only possible explanation for the convergent error set between guinea pigs and humans (a set not shared by rats or prosimians) is that genes like GULO are designed to “break” at certain genetic “crumple zones” when environmental stress or radiation damage stimulates mutation. There’s a very good reason that the gene would be designed in this way; Vitamin C is an essential antioxidant. If the GULO gene were to become damaged but still function, it could produce an altered form of the L-gulonolactone oxidase enzyme that could be toxic. The GULO gene, then, is designed in such a way that errors will completely prevent gene expression by breaking in certain predetermined places, rather than allowing a more dangerous result.
        
        Here’s a short paper that goes over some of these arguments.
        
        “….it’s very easy to imagine any number of genetic findings which would falsify it, or at the very least, which would rock our current evolutionary tree model.”
        
        Like matching GULO errors between guinea pigs and humans?
        
        http://leadme.org Jeff
        
        Alright, did a bit more digging on the GULO issue. Apparently Nishikimi himself has admitted (privately, at least) that the relevant conclusions of the paper you referenced were mistaken. The similarities between the guinea pig and human sequences do trace back to a common ancestor, and it is the rat sequence which has undergone significant mutation, hence the dis-similarity between the rat and guinea pig sequences. In other words, the mistake made by Nishikimi, et al. was to compare the guinea pig and human sequences to the rat sequence, rather than to a sequence more representative of the ancestral sequence. Even creationist Paul Nelson has more or less conceded this (see the last paragraph of his first comment, which is the eighth comment listed under the comments section of this article).
        
        As for ERVs, the claim that they are functional is a claim commonly made by YEC and ID advocates, but it’s an incorrect claim. It is true that there are certain ERV components that have been co-opted into functional roles, but fully functional (or at least, adequately functional) ERVs=disease. As for whether the points of insertion are random, I did a bit of digging there as well. My understanding is that certain retroviruses exhibit very broad preferences for insertion (e.g., in genes vs. in promoters), but that the specific insertion sites appear to be random.
        
        http://leadme.org Jeff
        
        Whoops, somehow messed up that ERV link. I’ll try that again.
        
        http://twitter.com/davidstarlingm davidstarlingm
        
        Hadn’t actually seen either of those papers, but interesting link nonetheless.
        
        ERV insertion could still be random even if mutations like the GULO errors aren’t, and vice versa. They are unrelated genetic processes.
        
        ERV insertion may or may not be random, but that’s the less important part of the argument. The more important observation is that ERVs have been proven to play essential cellular functions and thus could well be original to the genome.
        
        The bottom line: like any good program, genomes have multiple layers of redundancy and a wide variety of self-repair provisions, many of which are still poorly understood. Such systems provide ample opportunity for evolutionary geneticists to locate genetic sequences that seem to reflect common ancestry, but this is just cherry-picking and confirmation bias.
        
        http://leadme.org Jeff
        
        David, can you provide me with a reference demonstrating that entire ERV sequences are functional? I’ve only ever heard that there is some small percentage of ERV components that have been co-opted into functional roles. And in any event, my understanding is that ERV sequences exhibit clear characteristics of insertion, such as duplication and displacement of the neighboring DNA. In other words, ERV sequences are clearly not part of the original genetic sequence, and so it’s not possible to argue that they are part of God’s original design. This article has a ton of helpful info and references.
        
        http://www.evolutionarymodel.com/ Evolutionary Model
        
        Hello, davidstarlingm and Jeff. I was made aware of this page when my site was viewed as a result of the link to my ERV page being clicked. I think I can add to this discussion.
        
        David, you said that the ERV argument for common ancestry depends on the premises that retroviral insertion is random, and that ERVs are nonfunctional. But neither are actually premises of the argument.
        
        Insertion:
        
        As for insertion, it need only be rare that insertion occur at the same loci twice (i.e. that integrase reuse base pairs twice) for orthologous ERV distribution between chimpanzees and humans to necessitate common ancestry. This is because of the ~201 thousand insertions in the human genome, ~0.1% are lineage specific; the remainder (~99.9%) are orthologous (IHGS Consortium, 2001; CSA Consortium, 2005).
        
        And all that is required for the hierarchical distribution of ERVs among catarrhines to necessitate common ancestry is for it to be rare that integrase reuses base pairs many times (4+), since there are numerous ERVs at orthologous loci in all catarrhines (Lebedev et al., 2000; Hughes & Coffin, 2005).
        
        But how rare is retroviral base pair reuse? The most charitable study I am aware of is Wang et al. (2007), which found that of 40,569 insertions, only 41 were in the same spot twice (i.e. reused a base pair twice), and none reused a base pair three or more times.
        
        So even with this generous figure of 0.1% 2x reuse rate, chimpanzee-human orthology should be 0.1%. But remember, it’s actually ~99.9%. And there should be no 3x+ reuse, yet there are many.
        
        Simply put, retroviruses very rarely insert in the same place twice, yet almost all of the tens of thousands of human ERVs are in the exact same spot. And (even in a huge sample of 40 thousand+) retroviruses don’t insert in the same place three or more times, yet there are many ERVs in the same spot in lots of different primates (including humans).
        
        Functionality:
        
        So the next question becomes; are retroviruses really insertions, or could they have been ‘designed in from the beginning’?
        
        (This question is crucial for understanding the functionality counterargument, so please bear with me.)
        
        The answer is yes, we know that ERVs are proviral insertions that have been endogenized and fixed in populations. We know this because the hallmark of an insertion is a displacement of chromosomal DNA, and the hallmark of insertion by integrase is the presents of target site duplication, due to the way it attacks the 5′ and 3′ phosphodiester bonds with an offset of a few base pairs.
        
        Since ERVs are accompanied by target site duplications and DNA displacement, they are necessarily endogenized/fixed insertions. Combine that with a full-length configuration of U3rU5-(pbs)-gag-pol-env-(ppt)-U3rU5, and it is undeniable that the insertions are proviral.
        
        This more than falsifies the idea that ERVs were designed in, since the fact that they are insertion means that there was a time when the organism existed in some form without them, prior to their insertion.
        
        Any functional components are necessarily post-insertion exaptations, and any currently necessary functions are scaffolds. Thus they cannot be part of any ‘original design.’
        
        Lastly…
        
        All that relates specifically to the distribution of ERVs, but to both summarize and expand on this, I’ll concisely state how transposable elements in general falsify uncommon ancestry (the foundation of special creation):
        
        Target site duplication, DNA displacement, and sequence identity show that TEs result from wide-spread physical bombardment of the genome, rather than preexisting genomic components that could have been “designed in” by a designer. Thus, their highly orthologous distribution (IHGS Consortium, 2001; CSA Consortium, 2005: orthology humans have with chimpanzees = 99.9% of 201,000 ERVs — 99.4% of 1,090,000 Alus — 99.6% of 516,000 LINE[1]s), and—in the case of ERVs—the presence/pattern of LTR-LTR discontinuity and shared SNPs, are extremely strong evidences that humans share common ancestry with the other primates.
        
        For more information, refer to my ERV page, as well as my response to the Discovery Institute’s rebuttal of my argument on said page.
        
        -Jon
        
        http://leadme.org Jeff
        
        Thanks for stopping by, Jon! I’ll be the first to admit that some of that terminology is over my head, but I followed most of what you said and found it to be very helpful.
http://twitter.com/davidstarlingm davidstarlingm

Jeff said:

“The similarities between the guinea pig and human sequences do trace back to a common ancestor, and it is the rat sequence which has undergone significant mutation, hence the dis-similarity between the rat and guinea pig sequences.”

Using just the alignment provided by Musgrave, several interesting observations can be made which reinforce the notion of mutational hotspots or genetic crumple zones. At bps 75, 85, and 95, chimps and humans share the same divergence from the “original”, consistent with evolutionary predictions, but at 96 and 132, orangutans and macaques share a divergence from the “original” that is not reflected in chimps and humans. This is troublesome because orangutans and macaques aren’t supposed to have a common ancestor more recent than the one they share with chimps and humans. Either the chimp-human common ancestor reverse-mutated to match the “original”, or orangutans and macaques had identical, independent mutations. Mutational hotspotting is a much better explanation, especially around the infamous 97 codon.

More obvious anomalies including matching divergence between cows and macaques (bp 13), cows and the chimp-human set (bp 85), simians and cows (131), dogs and guinea pigs (bp 76), chimps and non-simians (55), and cows and dogs (97). At bp 103, the “original” is uncertain; guinea pigs and livestock share one bp value while mice, rats, dogs, and primates share a different one. Either all these matches are coincidence (an 0.89% chance), or these represent consistent mutational hotspots. In fact, of the fifteen divergences shared by primates (used to support the evolutionary model), 67% have one of the previously mentioned unexpected convergences within one base pair.

In the post you linked to, Musgrave says,

What gets me is that creationists could have done this analysis of GULO genes themselves (like the other analysis I have reported on). I used entirely public databases and web-based programs to do the trees and alignments. The Creationists did nothing, and are propagating an error.

This post was from 2008. If Musgrave had bothered to do a little bit of research, he would have found this paper published by Truman and Borger in 2007 that exhaustively examines the very sequence he is discussing. Their phylogenetic tree findings are particularly illuminating. I don’t know which PHYLIP alignment protocol Musgrave used, but Truman and Borger used two, dnaml and dnapars. Dnaml, which aligns sequences in PHYLIP based on maximum DNA likelihood, produced this tree, showing a common ancestor between pigs and chickens and a more recent ancestor between cows and guinea pigs than guinea pigs and other rodents. Dnapars, which uses DNA parsimony (least evolutionary change), produced this tree, displaying dog-chicken and pig-guinea pig common ancestors.

The fact that evolutionary phylogenetic trees cannot be independently confirmed testifies to the way in which evidence is inadvertently but inevitably cherry-picked. As Truman and Borger state:

If these sets of [convergent mutations] had conformed to an obvious evolutionary phylogenetic interpretation, no one would have questioned the strength of this “pro-evolutionism” evidence. The fact is that sequence databases are full of the right patterns associated with the wrong evolutionary trees. Are we obliged to believe that random and yet somehow identical mutations occur again and again whenever evolutionary inconsistencies are found?

The human genome has three billion base pairs — that’s a lot of potential for pattern-matching. It’s like the Bible Code silliness; you can find any pattern you want if you have enough data to sort through.

Anyhow, enough about the GULO gene. How about the acidic ribosomal phosphoprotein P2 pseudogene? This gene is shared by many organisms, including humans and sheep. Both humans and sheep have a premature stop codon at the exact same place, just like humans and apes. Coincidence? Sure, only because we’re not looking for a common ancestor for sheep and humans.

Jeff’s other question:

“David, can you provide me with a reference demonstrating that entire ERV sequences are functional? I’ve only ever heard that there is some small percentage of ERV components that have been co-opted into functional roles.”

I don’t think I have enough experience in this area to provide exactly what you’re looking for, but I could point you to a few examples. The ERV-WE1 retroviral locus is a functional gene present in both apes and humans that is absolutely essential for placental development. This paper describes the proposed evolutionary history of the gene, although I would tend to predict that this is common in any mammals with basically human fetal development. This gene has a lot of transposable elements so I’m not sure how much the original ERV has changed, but its function is uniform in all known instances.
- http://leadme.org Jeff
  
  David, we could probably go back and forth on this forever, and in any event, I’m happy to admit that I’m certainly not a specialist in the field. I do know that other knowledgeable-in-the-field Christians–whose Christian beliefs are much more “orthodox” than mine–appear to be very unimpressed by Peter Borger, Reasons to Believe, etc. (including young earth creationist Todd Wood).
  
  The 47 guinea pig/primate matches argument having failed (and I’m not sure how much it would really help the YEC/ID case even if it were a valid argument), it looks to me like you’re now trying to cling to any little detail you can find, all the while ignoring the elephant in the room–namely, that the higher primates all share an identical point mutation rendering their GULO gene nonfunctional. And that’s not even to mention the behemoth in the room–namely, the issue of ERVs.
  
  In short, I just can’t see how you consider common descent and YEC/ID to be equally plausible. And I’m having a very hard time imagining what kinds of evidence you would admit as truly favoring common descent over and above YEC/ID.
  - http://twitter.com/davidstarlingm davidstarlingm
    
    “The 47 guinea pig/primate matches argument having failed (and I’m not sure how much it would really help the YEC/ID case even if it were a valid argument)….”
    
    If it were a valid argument, it would demonstrate that homoplasy is likely to be the result of mutational hotspots — genetic crumple zones designed to allow genes to break without causing fatal errors.
    
    And it didn’t actually fail. When I actually examined the gene, I noted a great many instances of homoplasy. 66% of the hominid homoplasy was clustered around the other instances, lending further support to my model.
    
    Moreover, the cited studies showed that phylogenetic tree analysis failed to consistently produce the expected evolutionary pattern, reinforcing the idea that evolutionary pattern-matching is fueled by unintentional cherry-picking and confirmation bias.
    
    “[You're] ignoring the elephant in the room–namely, that the higher primates all share an identical point mutation rendering their GULO gene nonfunctional.”
    
    Except that I just demonstrated that the greatest homoplasy surrounds that particular base pair. Clearly, that was one of the most vulnerable crumple zones of the gene — obviously vulnerable, because that point mutation rendered GULO immediately nonfunctional.
    
    “I’m having a very hard time imagining what kinds of evidence you would admit as truly favoring common descent over and above YEC/ID.”
    
    So am I.
    
    I don’t have nearly enough experience with genetics to say what kind of observations would absolutely rule out uncommon descent. I just have enough experience dealing with statistics to recognize confirmation bias in action.
    
    Like I said originally, I don’t assert that either position is impossible or even extremely unlikely. Absent a model for uncommon descent, UCA seems quite likely. But I have a fairly consistent model for uncommon descent, so….
    - http://leadme.org Jeff
      
      But David, you don’t have a working model for uncommon descent, so far as I can see. You’ve simply combed the data pulling whatever isolated data points you can find that might seem to lend support to your hot spot model. But given a large data set such as this, one should expect to find some isolated instances of convergence, simply due to chance, correct? If it were true that the guinea pig and primate sequences shared 47 instances of convergence, then your hot spot model would have some serious support. But that isn’t the case. In any event, even if your hot spot model is correct, this still doesn’t come close to being a working model for uncommon descent. The fact remains that all of the higher primates share an identical point mutation that none of the other mammals on this list share.
      
      One need not consider uncommon descent to be “absolutely ruled out” to nevertheless consider it to be far less plausible than common descent.
      - http://leadme.org Jeff
        
        Put another way, if that site is such a hotspot tthat all primates share an identical mutation there, we should expect that at least some of the other mammals under consideration would share that mutation as well. But they don’t.
        
        http://twitter.com/davidstarlingm davidstarlingm
        
        I wish I could post images into here, but I assume I can’t. So here’s a link to the mutation/homoplasy hotspot analysis I just threw together based on the GULO gene.
        
        I don’t have time to do a formal statistical analysis of this sequencing, but you can see how the mutations and homoplasies all cluster. I estimate that anything over 2 events is statistically significant.
        
        The human-primate homoplasies almost all occur at other hotspots. Note particularly the most significant cluster both in terms of mutation and homoplasy: the one surrounding the 97 codon. This is the “loudest” hotspot; it makes sense that one would find the most dramatic homoplasies here. Dogs and cows share an identical mutation here just like humans and primates; that doesn’t mean that dogs and cows have a more recent common ancestor than, say, cows and horses.
        
        I would hypothesize that these apparent hotspots occur at locations that would nullify the original gene rather than causing harmful protein synthesis. I’m not a PhD biologist, though, so I can’t say for sure whether that would work.
        
        http://twitter.com/davidstarlingm davidstarlingm
        
        A statistical analysis would rank all sites based on mutation activity, giving appropriate weight to both gross mutation count and mutation/homoplasy proximity. I would hypothesize that such an analysis would show 6 distinct “crumple zones” at 12-13, 55-56, 75-76, 94-100, 103, and 140, and the highest-probability mutation sites at 55, 76, 97, and 103. Small wonder, then, that that’s where the most significant human-primate similarities occur.
      - http://twitter.com/davidstarlingm davidstarlingm
        
        “But David, you don’t have a working model for uncommon descent, so far as I can see.”
        
        You haven’t seen it? Sorry, I must not have been clear enough.
        
        Model for Uncommon Descent: The original genomes of the various original species contained in situ individual copies of endogenous retroviruses intended to allow rapid adaptation. The genome as a whole contained preferred insertion loci designed to accommodate properly functioning exogenized retroviruses. Additionally, individual genes contained genetic “crumple zones” that would cause mutations to immediately disable the gene rather than preserving a dangerous functional copy. More similar creatures were given more homologous retroviruses, preferred insertion points, and crumple zones in anticipation of expected convergent adaptation.
        
        As the genomes evolved, their initial design slowly degraded, with two results. First, the preferred insertion loci were lost or moved. Second, the retroviruses mutated outside of their original function. These gradual changes resulted in the present functions of endogenous and exogenous retroviruses with respect to the genome; most of the original programmed adaptation has been exhausted.
        
        Predictions of this model: mutational homoplasy will be found in clustered hostpots in genes shared by species lacking a recent common ancestor. Phylogenetic analysis focusing on these sequences will produce wildly divergent trees in statistically significant contradiction to evolutionary predictions. Exogenous retroviruses will target specific insertion zones, even finding identical insertion loci in less degraded sequences. Genetic evidence will show the same sort of retroviruses (or even the exact same retroviral sequences) being used to effect the same kinds of adaptation across unrelated species.
        
        Not bad for a physicist, eh?
        
        “Put another way, if that site is such a hotspot that all primates share an identical mutation there, we should expect that at least some of the other mammals under consideration would share that mutation as well. But they don’t.”
        
        First — I would consider most of the higher primates to share a common ancestor. So the identical mutation is only shared between humans and that common ancestor, not all higher primates independently.
        
        Second — the other mammals under consideration do share homoplasic mutation clustered around that site; cows and dogs have the same matching mutation at that site and the mouse/rat group has an additional mutation at that site. There are 4 homoplasies and a total of 16 mutations within 3 base pairs of that site.
        
        http://twitter.com/davidstarlingm davidstarlingm
        
        Actually, I miscounted — 17-18 mutations and 5 or 6 homoplasies, depending on whether macaques share the same common ancestor as gorillas and chimpanzees.
        
        http://leadme.org Jeff
        
        David, is this your own original model? If so, I’m simultaneously impressed and incredulous. Can you point me toward something in the peer-reviewed scientific literature substantiating your model? Or if not, are you going to try to get this published in the scientific literature?
        
        At the end of the day, it all comes down to this: “I would consider most of the higher primates to share a common ancestor.” Do you have scientific reasons to believe that humans are a special creation, whereas most of the higher primates (which ones, specifically?) share a common ancestor? Is there biological or genetic evidence that convinces you of primate common ancestry? If so, why doesn’t that evidence work in favor of human common ancestry with other primates? For clarification, do you hold to a young earth or an old earth?
        
        http://twitter.com/davidstarlingm davidstarlingm
        
        Yes, this is my own model, just based off of the research I’ve done in the past few days.
        
        One of the previously referenced creationist papers hinted at the possibility of mutational hotspots, but it was the Wang et al paper that made me investigate the idea of preferred sites within preferred zones. I don’t know of any existing research that uses homoplasy to locate mutational hotspots, if that’s what you’re wondering.
        
        I would certainly want to publish it, but it would be tricky. For one thing, I’m not sure that I could make the case without ever referencing uncommon descent….and there’s no way any journal is going to publish a paper criticizing common ancestry on genetic grounds, not when it’s written by a guy with nothing but a B.S. in physics. I would want to consult with someone who has a PhD in biochem or genetics, but few evolutionary biologists would be willing to consult on something like this. I suppose I could publish it in creationist research. What would you think of that?
        
        Do you have scientific reasons to believe that humans are a special creation, whereas most of the higher primates (which ones, specifically?) share a common ancestor?
        
        Depends on what you mean by “scientific”. The purely morphological distinctions would lead me to group humans in one clade, higher primates in another, and so on, but I’m not sure. I don’t like baraminology — mostly because the name is rather humorous — but I’d probably end up with divisions like that. Most importantly, though, I’d want to come up with a consistent way to distinguish between homoplasy and inherited mutation. I’d need a better understanding of genetic statistics in order to do that.
        
        “For clarification, do you hold to a young earth or an old earth?”
        
        Like I said before, evolution has a great deal of evidence and appears very likely in the absence of other explanations. Same thing with the young/old earth thing. I do, however, link the two; progressive creationism is uncommonly silly, so it’s either a young earth and uncommon descent or an old earth and common descent. I can’t say which, but I can say that I don’t think there is warrant to be dogmatic in either direction on purely evidential grounds.
        
        http://leadme.org Jeff
        
        And what I’m asking for is something in the scientific literature that hypothesizes mutational hotspots at the sites you’ve identified.
http://twitter.com/davidstarlingm davidstarlingm

Jon,

Thanks for your comment! Wow. Mind = blown. You have thoroughly and completed surpassed my level of familiarity with genetics. Lots of information.

I freely admit that I don’t have nearly the experience to address most of what you’ve provided, although I did try to look up some of the studies you cited. I found Wanget al, and looked for the discussion of identical base pair substitutions.

One of the things that the article definitely established is that retroviral endogenization (at least for HIV) is decidedly nonrandom; the retrovirus targets certain types of sequences with a great deal of consistency. HIV shows a particular affinity for nucleosome-bound DNA.

The discussion of the 41 identical base pair insertions was quite interesting:

We found 41 sites that hosted two independent integration events at exactly the same base pair in the human genome. Sites were only included in the analysis if the proviruses integrated at a single site were in opposite orientations, indicating independent events. Alignment of the primary sequences surrounding these highly favored sites shows much closer matches to the consensus palindrome than in the HIV-Avr and HIV-Mse data sets as a whole. Analysis of these sites in the context of a comprehensive statistical model for integration intensity showed that highly favored integration at these sites was explained both by the favorable local DNA sequence and a globally favorable chromosomal environment.

Several observations can be made. First, these 41 sites represented only a very small subset of all identical insertions; these were merely the only points where the integration was reversed and thus was known to be an identical insertion (as opposed to just another copy of the same insertion event). So the actual percentage you cited is not at all useful.

Second, the study indicated that these identical insertions were definitively nonrandom; these were preferred sites selected for based on local sequences and overall chromosome position.

“This more than falsifies the idea that ERVs were designed in, since the fact that they are insertion means that there was a time when the organism existed in some form without them, prior to their insertion.

“Any functional components are necessarily post-insertion exaptations, and any currently necessary functions are scaffolds. Thus they cannot be part of any ‘original design.’”

Based on my examination of the Wang paper, I would suggest the opposite: that single copies of endogenous retroviruses were created in situ along with preferred reinsertion sites throughout the genome. This design allowed for exogenization and reinsertion upon environmental stimulus, evincing a mechanism of rapid adaptation. The prevalence of solo LTRs indicates a complementary mechanism for deletion, thus completing the cycle of adaptation.

The modern genome would be far degraded from the original, and thus most of the exact insertion sites would have been lost or modified, preventing identical insertion. Also, HIV isn’t exactly a nice fellow; it has clearly mutated past any initially beneficial function it may have had, so it may not be able to match the original insertion sites.

“Any functional components are necessarily post-insertion exaptations, and any currently necessary functions are scaffolds. Thus they cannot be part of any ‘original design.’”

A few other observations I made during research would tend to cast doubt on this bit as well. In my last comment, I mentioned the ERV-WE1 retrovirus and its role in the regulation of placental syncytiotrophoblast production. I predicted that this process ought to be found in other mammals.

Sure enough, further research confirms this. Hominids, sheep, and mice all have retroviral loci that regulate syncytin production in placental development. This isn’t the case their common evolutionary “ancestors”. What’s more, all three groups have a different endogenous retrovirus doing the same basic job. In at least one (or maybe it was two) of the studies, suppression of that gene prevented placental development completely, indicating that this role was absolutely necessary.

The common ancestry model would have us believe that mice, hominids, and sheep all had working placental systems, then acquired different retroviruses and all independently replaced portions of their existing placental systems with three different repurposed retroviri. Frankly, that’s a little hard to swallow. Convergence between two organisms in this fashion would be extraordinary enough; that three different independent species all show the same process speaks volumes for a common designer. I would suggest that all three species were created with the retrovirus either in place or with a preferred retroviral insertion point; the specific data allowing the expression of a species-tailored syncytin gene was programmed into each genome intentionally.
- http://www.evolutionarymodel.com/ Evolutionary Model
  
  Sorry for the late response, David, but I’ve only had time to work on writing it in small bursts over the past 5-6 days. The following is my response to most of what you addressed to me. The post below this one pertains to your proposed model of ERVs given uncommon decent. Also, I noticed that you explained it more formally and in greater detail to Jeff, so I will respond to that better version in a post I will place after the other one.
  
  I should also make sure I’m getting the html code right, so Test:
  
  Quote L1
  Quote L2
  Quote L3
  
  Test Link
  
  Assuming that test went well, here goes:
- http://www.evolutionarymodel.com/ Evolutionary Model
  
  Several observations can be made. First, these 41 sites represented only a very small subset of all identical insertions; these were merely the only points where the integration was reversed and thus was known to be an identical insertion (as opposed to just another copy of the same insertion event). So the actual percentage you cited is not at all useful.
  
  Good catch! I had completely overlooked this fact. However, their measurement of 0.1% 2x base pair reuse is far from useless. In fact, it only means that half of all events were observed. This is because retroviruses insert in either direction (sense or antisense) in equal proportion and without bias (Zhang et al. 2008; Brady et al. 2009).
  
  This means that the rate measurement of 0.1% corresponds to an actual rate of 0.2%; still extremely low and far from the ~99.9% chimpanzee-human ERV orthology. It also doesn’t change the fact that no 3x or greater base pair reuse was reported, and that many more genera than just two share ERVs in orthologous loci.
  
  That acts as a good transition to your next point; but first, an aside:
  
  Although this point doesn’t affect my argument, I want to thank you for noticing it. This is what makes discussion so valuable. I should have caught that myself and it is definitely something worth mentioning.
  
  Now, back to it:
  
  One of the things that the article definitely established is that retroviral endogenization (at least for HIV) is decidedly nonrandom; the retrovirus targets certain types of sequences with a great deal of consistency. HIV shows a particular affinity for nucleosome-bound DNA.
  […]
  Second, the study indicated that these identical insertions were definitively nonrandom; these were preferred sites selected for based on local sequences and overall chromosome position.
  
  You are quite right in saying that retroviral site selection isn’t the same as rolling a die or flipping a coin, i.e. it isn’t simply random. But it is important to understand what is meant by non-random, here. The following is a quote from the paper we are discussing, as well as one of its references relevant to site selection:
  
  The host cell DNA sequences hosting integration events show detectable but modest similarity to one another—thus retroviral DNA integration is not tightly sequence-specific (Stevens and Griffith 1996; Carteau et al. 1998; Holman and Coffin 2005; Wu et al. 2005; Berry et al. 2006). However, integration site selection in vivo is not random (Wang et al. 2007).
  
  Our results suggest that the observed statistical palindromic primary sequence might reflect the influences of integrase on site selection at target sites. The symmetry of the target site sequence might reflect that the integrase complex works in symmetrical dimers, tetramers, or oligomers at the integration sites, such that each half-complex would have a similar preference for target DNA structure. Our results also imply that it may not be appropriate to think of the consensus sequences as the most favorite sequence at each base. It might be better to think of certain bases being excluded at certain positions to meet the spatial or energy requirements of the integration complexes (Wu et al. 2005).
  
  The way I describe it is; relative to pure randomness, retroviral insertion is non-random, but relative to locus specificity, it is highly random, i.e. randomized.
  
  To put another way; compared to a truly random distribution, retroviral insertion significantly deviates from it in many genomic regions, i.e. isn’t random. However, compared to a locus specificity, it also significantly deviates, as retroviruses can and do insert virtually everywhere in the genome (just in higher or lower frequencies than a random distribution in various genomic regions).
  
  This is why target site preference does not account for ERV distribution given a lack of common ancestry. It simply cannot account for ~99.9% chimpanzee-human ERV orthology or multiple genera with ERVs in orthologous loci.
  
  The common ancestry model would have us believe that mice, hominids, and sheep all had working placental systems, then acquired different retroviruses and all independently replaced portions of their existing placental systems with three different repurposed retroviri. Frankly, that’s a little hard to swallow. Convergence between two organisms in this fashion would be extraordinary enough; that three different independent species all show the same process speaks volumes for a common designer. I would suggest that all three species were created with the retrovirus either in place or with a preferred retroviral insertion point; the specific data allowing the expression of a species-tailored syncytin gene was programmed into each genome intentionally.
  
  Firstly, the idea that placental systems don’t require syncytin from a retrovirus is not a stretch at all, since Old World monkeys have the same HERV-W insertion as hominids, yet their placental systems of work fine, despite env gene inactivation.
  
  Secondly, the idea that different retroviral env genes were co-opted for the same function is also not a stretch, since retroviral envelope proteins are already adapted for plasma membrane fusion, and since retroviruses are rather plentiful sources of such genes.
  
  Further, Syncytin-1 is an excellent case of clear co-option, as discussed in Cáceres et al. (2006):
  
  1) Old World monkeys also possess the Syncytin-1 progenitor HERV-W element.
  2) As with hominoids, the HERV-W element contains mutated, inactive gag and pol genes.
  3) The flanking regulatory sequences involved in Syncytin-1 expression are conserved in New World monkeys, which lack its progenitor HERV-W insertion.
  4) Phylogenetic analysis of HERV-W element forms a well-defined tree.
  5) The deactivation of OWM env was caused by a nonsense mutation (Cys -> Opal) which was later reversed in hominoids (Opal -> Arg).
  6) OWM inactive env contains more substitutions than hominoid active env.
  7) Ka/Ks ratios of OWM Syncytin-1 are uniformly distributed and show neutrality, whereas hominoid ratios form a gradient (5’ to 3’) and indicate constrained conserved sites.
  
  The progenitor HERV-W inserted, was deactivated, and was then reactivated in hominoids. With the help of the preexisting regulatory sequences, functional modification of the already-capable env gene conferred a selective advantage by aiding in membrane fusion. With multiple env genes throughout vertebrate genomes, similar co-option events occurred in rodents and sheep.
  
  It remains true that target site duplication, DNA displacement, and sequence identity show ERVs to be endogenized/fixed proviral insertions.
  
  -Jon
http://www.evolutionarymodel.com/ Evolutionary Model

Model for Uncommon Descent: The original genomes of the various original species contained in situ individual copies of endogenous retroviruses intended to allow rapid adaptation. The genome as a whole contained preferred insertion loci designed to accommodate properly functioning exogenized retroviruses. Additionally, individual genes contained genetic “crumple zones” that would cause mutations to immediately disable the gene rather than preserving a dangerous functional copy. More similar creatures were given more homologous retroviruses, preferred insertion points, and crumple zones in anticipation of expected convergent adaptation.

As the genomes evolved, their initial design slowly degraded, with two results. First, the preferred insertion loci were lost or moved. Second, the retroviruses mutated outside of their original function. These gradual changes resulted in the present functions of endogenous and exogenous retroviruses with respect to the genome; most of the original programmed adaptation has been exhausted.

I can think of several problems with this model:

1) Any hierarchically distributed original ERVs would not form the observed pattern of increasing LTR-LTR divergence with increasing number of distantly related lineages that share it, since they would all be equally old. And the correspondingly hierarchically grouped ‘preferred insertion points’ would cause any subsequent reinfection by these ERVs to also lack the observed LTR-LTR divergence pattern, since they would constantly be hierarchically inserting.

2) Any sets of original ERVs with hierarchically grouped ‘preferred insertion points’ would have to be likewise hierarchically different in composition to form it, yet many similar sequences themselves form hierarchical patterns.

Common ancestry better explains the hierarchical distribution of ERVs and LTR-LTR divergence ratios.

3) The hypothesized “crumple zones” encoded into ERVs would result in the same ERVs crumpling in similar ways, yet the mutations in identical orthologous insertions (including 5’ LTRs vs 3’ LTRs, which are identical upon insertion) form hierarchical patterns.

Common ancestry better explains the hierarchical distribution of LTR mutations.

4) If the infectious products of the original ERVs were locus-specific, and only now (after much time to degrade) they have broadened their genomic access to virtually all of the genome (with patterns of higher or lower insertion frequency from random, i.e. patterns of preference), then reconstructed inactive ERVs from consensus sequences should be far more locus specific. Actual measurements of such reconstructed retroviruses show no such thing. Quite the contrary; they show the exact same characteristics as modern ones, in that they show patterns of higher or lower insertion frequency from random, with some sites being used not far from random Brady et al. 2009). Modern MLV even shows stronger preference.

5) The presence of target site duplication (the observed result of insertion by integrase) is better explained by the hypothesis that they really are endogenized, fixed insertions.

Predictions of this model: mutational homoplasy will be found in clustered hostpots in genes shared by species lacking a recent common ancestor. Phylogenetic analysis focusing on these sequences will produce wildly divergent trees in statistically significant contradiction to evolutionary predictions. Exogenous retroviruses will target specific insertion zones, even finding identical insertion loci in less degraded sequences. Genetic evidence will show the same sort of retroviruses (or even the exact same retroviral sequences) being used to effect the same kinds of adaptation across unrelated species.

As contrast, here are predictions I have made given the model of common ancestry for ERVs (I’ve been meaning to put them on my website… perhaps I’ll get around to it one of these days):

As primate genomes continue to be sequenced in full, and compared to the human genome, it will be found that as the degree of taxonomic separation of the compared lineages increase:

1) The ratios of non-orthologous to orthologous ERVs, Alus, and other transposable elements will gradually increase—from the current human to chimpanzee ratio ~0.1% (IHGS Consortium, 2001; CSA Consortium, 2005).
Explanation: The older the divergence between the compared lineages, the more time each has had as a distinct lineage; thus the more independent insertions each should have accumulated.

2) The solo-LTR to full-length element ratio of the orthologous ERVs will rapidly increase.
Explanation: Insertions tend to rapidly undergo homologous recombination, but as soon as it begins accumulating mutations, its chance of recombination rapidly decreases (Belshaw et al. 2006). Thus there are very old full-length ERVs, but their numbers fall off quickly with age.
.
3) Orthologous transposable elements will largely be arranged in accordance with the current nested hierarchy of examined elements, but between insertion symplesiomorphy caused by incomplete lineage sorting (i.e. allelic segregation), and insertion homoplasy caused by target site preference, the amount of pattern deviation from will increase beyond the current solitary case of HERV-K-GC1. The majority of this increase will involve the deviation of only one lineage per deviant orthologous ERV.
Explanation: A site being used twice is quite rare, and a site being used three times is not observed; even in a sample of 40,528 HIV insertions (Wang et al. 2007). This—in addition to tendency towards allelic fixation—indicates that insertion symplesiomorphy/homoplasy will likely be limited to only one point of deviation at a time; as is the case with HERV-K-GC1 (Barbulescu et al. 2001).

We shall have to wait and see which set of predictions is better fulfilled, down the line.

-Jon