Tag Archives: Naturalism

Stephen C. Meyer and Doug Axe discuss 5 major problems with macro-evolution

Undeniable: How Biology Confirms Our Intuition That Life Is Designed
Undeniable: How Biology Confirms Our Intuition That Life Is Designed

The host of the Cross Examined radio show Dr. Frank Turek talks with Stephen C. Meyer and Doug Axe about a recent conference of Royal Society scientists discussing the problems with the theory of macro-evolution.

The MP3 file is here.

Summary:

  • about the Royal Society conference
  • the main topic was whether naturalistic mechanisms can produce new body plans and new organ types
  • no one disputes micro-evolution: beaks changing size, antibiotic resistance
  • many of the naturalistic scientists admitted the problems with current naturalistic theories, but they don’t want to embrace the need for a designer
  • none of the proposals that were debated solved the real problems with macro-evolution
  • Problem #1: the sudden origin of body plans in the fossil record
  • Problem #2: the origin of information (e.g. – in protein molecule)
  • Problem #3: need for favorable early mutations (for body plans)
  • Problem #4: the problem of epigenetics
  • Problem #5: the universality of the design intuition

Some of these problems have actually gotten worse for naturalistic evolution as our scientific knowledge has grown.

If you want the two best books on intelligent design, get Dr. Meyer’s “Signature in the Cell” and “Darwin’s Doubt”. I should note that Dr. Meyer is not a young Earth creationist, and has defended the Big Bang cosmology as a solid evidence for a Creator of the universe. Being in favor of an old universe and an old Earth is compatible with being opposed to evolution – because of scientific reasons.

Gary Habermas and James Crossley discuss the minimal facts case for the resurrection

Two ninjas face off at sundown
Two ninjas face off at sundown

James Crossley is my favorite atheist ancient historian, such a straight shooter. He’s on the skeptical left, but he has a no-baloney way of talking that I really like. I was so excited to summarize this, and there’s not a speck of snark in this summary. Crossley dates the gospel of Mark 37-43 A.D., far earlier than most scholars. Justin Brierley does a great job as moderator. Gary Habermas is OK, but he is not familiar with any useful arguments for God’s existence, (kalam, fine-tuning, origin of life, Cambrian explosion, etc.), and that is a problem in this debate.

Here are the details of the debate:

Christian Bible scholar Gary Habermas and agnostic New Testament scholar James Crossley return to answer questions sent in by Unbelievable? listeners.

They answer your questions on the Jewishness of Jesus, the dating of the New Testament documents and much more!

Note: this is the first of two shows they are doing together!!

The MP3 file is here. (If this disappears, tell me, I have a copy)

This non-snarky summary starts at 10:52.

Summary:

  • Habermas: the minimal facts are the facts that even the majority of skeptical scholars will accept

Habermas list of minimal facts: (near universal acceptance)

  1. Jesus died by Roman crucifixion
  2. After his death, his disciples had experiences that they believed were appearances of the risen Jesus
  3. The disciples were transformed by their experiences and proclaimed his resurrection and were willing to die for their belief in the resurrection
  4. The proclamation of his resurrection was early
  5. James was converted by a post-mortem experience
  6. Paul was converted by a post-mortem experience

Habermas list of widely-accepted facts:

  1. Burial for Jesus in a private tomb
  2. The private tomb found empty
  3. The disciples despaired after Jesus was crucified
  4. The proclamation of the resurrection started in Jerusalem
  5. Changing the worship day from Saturday to Sunday

Crossley’s views on the minimal and widely-accepted facts:

  • Crossley: I am in broad agreement with what Gary said
  • Crossley: “the resurrection appearances are some of the hardest, best evidence we have” because it’s in early 1 Cor 15:3-8 creed
  • Crossley: people were convinced that they had seen the risen Christ

The burial in a private tomb:

  • Crossley: I have my doubts about the private tomb burial and the empty tomb
  • Crossley: Mark’s gospel has the burial in a private tomb by Joseph of Arimethea, and Mark is the earliest gospel
  • Crossley: I don’t have a doubt, it’s just that there are other possible alternatives, and then the tradition was invented later – but that’s just a possibility
  • Crossley: there is not enough evidence to make a decision either way on the burial

The empty tomb:

  • Habermas: there are multiple lines of evidence for the empty tomb
  • Habermas: the reason it’s not one of my minimal facts is because a quarter to a third of skeptical scholars reject it

The transformation of the followers of Jesus:

  • Crossley: “yes, clearly, I don’t think you can argue with that, it’s fairly obvious”

The conversions of James and Paul:

  • Crossley: “yes, because it’s based on 1 Corinthians 15:3-8, that report, that was handed on to him”

Where Habermas and Crossley agree:

  • Habermas: you agree with the 6 facts in the minimal facts list, and you have problems with 2 of 5 facts from the widely accepted list
  • Crossley: Yes

The empty tomb:

  • Crossley: Two problems: first, 1 Corinthians 15:3-8 doesn’t mention it, but it “probably assumes the idea that Jesus left behind an empty tomb when resurrected, I am convinced by some of the conservative arguments on that one, but it’s not hard evidence for there actually being an empty tomb”
  • Crossley: Second, “the other early source we have ends with no resurrection appearances”, it makes him a bit skeptical of the empty tomb
  • Habermas: the empty tomb is not a minimal fact, I want 90% agreement by skeptical scholars for it to be a minimal fact
  • Habermas: I have never included the empty tomb in my list of minimal facts
  • Brierley: William Lane Craig puts it in his list of minimal facts
  • Habermas: It is very well attested, so if that’s what you mean, then it’s a minimal fact, but it doesn’t have the 90% agreement like the other minimal facts
  • Habermas: I have 21 arguments for the empty tomb, and none of them require early dating of sources or traditional authorship of the gospels, e.g. – the women discovered the empty tomb, the pre-Markan source, the implications of 1 Cor 15 has some force, the sermons summary in Acts 13 which Bart Ehrman dates to 31 or 32 A.D. has putting a body down and a body coming up without being corrupted

Why is 1 Corinthians 15:3-8 more respected as a source than the gospels?

  • Habermas: There is a unanimous New Testament conclusion, across the board, from conservative to liberal, that in 1 Cor 15:3-8 Paul is presenting creedal data, Richard Bauckham says that this goes back to the early 30s A.D., Paul got this from the eyewitnesses he mentions in Galatians 1 and 2
  • Crossley: [reads 1 Corinthians:3-8 out loud], now that’s a tradition that’s handed on, this is Paul, we know this is Paul, writing mid-50s, this is kind of gold, this is the evidence I wish we had across the board

Why doesn’t James accept the resurrection:

  • Crossley: Historians should not conclude that the supernatural is real, concluding the supernatural is outside of history
  • Crossley: I am more interested in what people believed at that time
  • Brierley: as a historian, are you required to give an explanation of the commonly-accepted facts
  • Crossley: yes, historians must give their explanation for the facts
  • Crossley: we know people have visions, and how the cultural context determines the content of visions, e.g. – the background of martyrdom
  • Brierley: so you would go for the hallucination hypothesis?
  • Crossley: yes, but I prefer not to use that word

Should historians rule out the supernatural?

  • Habermas: let’s not ask what caused the event, let’s just see if the disciples thought they saw him before he died, that he died on the cross, and then believed they saw him after he died, like you might see someone in the supermarket
  • Habermas: I’m not asking whether a miracle occurred, I just want to know whether Jesus was seen after he died on the cross
  • Crossley: that sounds like the angle I’m coming at this from
  • Crossley: the problem is that there is a supernatural element to some of the appearances, so it’s not a supermarket appearances
  • Brierley: it’s not angels and hallelujah in the sky
  • Habermas: nothing like that, no light in the early accounts, fairly mundane

Does James agree that people believed they saw Jesus after his death?

  • Crossley: yes,I think that’s fairly clear that we do
  • Crossley: but historians cannot prove claims that what happened to Jesus was supernatural
  • Brierley: your view is so far from what I see on Internet atheists sites, where they say it’s all legendary accumulation, fairy tales
  • Crossley: I’m perfect comfortable with the idea – and I think it happened – that people created stories, invented stories
  • Crossley: there are too many cases where people are sincerely professing that they thought they saw Jesus after his death

Would you expect the disciples to have visions of a resurrected Jesus if nothing happened to him?

  • Habermas: the dividing line is: did something happen to Jesus, or did something happen to his disciples?
  • Habermas: the view that people were seeing a kind of ghostly Jesus (non-bodily) – a Jedi Jesus – after his death is a resurrection view, but I hold to a bodily resurrection view
  • Brierley: N.T. Wright says a resurrected Jesus was contrary to expectations – should we expect the disciples to have a vision of Jesus as resurrected?
  • Crossley: Wright generalizes too much thinking that there was a single view of the resurrection (the general resurrection at the end of the age), there are a variety of views, some are contradictory
  • Crossley: Herod Antipas thought that Jesus might be John the Baptist returned from the dead, and he knew Jesus was flesh and blood, there is the story of the dead rising in the earthquake in Matthew, there are stories of the resurrection in Maccabees, and this would influence what people expected
  • Habermas: the earliest Christian view was *bodily* resurrection
  • Crossley: yes, I think that’s right
  • Crossley: In Mark 6, they thought Jesus was a ghost, so there is room for disagreement

Why should a historian not rule out a supernatural explanation?

  • Habermas: to get to supernatural, you have to go to philosophy – it’s a worldview problem
  • Habermas: he predicted his own death and resurrection
  • Habermas: one factor is the uniqueness of Jesus
  • Habermas: the early church had belief in the bodily resurrection, and a high Christology out of the gate
  • Habermas: you might look at evidence for corroborated near-death experiences that raise the possibility of an afterlife
  • Crossley: I’m content to leave it at the level of what people believe and not draw any larger conclusions
  • Crossley: regarding the predicting his own death, the gospels are written after, so it’s not clear that these predictions predate Jesus’ death
  • Crossley: it’s not surprising that Jesus would have predicted his own death, and that he might have foreseen God vindicating him

If you admit to the possibility of miracles, is the data sufficient to conclude that the best explanation of the facts is resurrection?

  • Crossley: If we assume that God exists, and that God intervenes in history, and that this was obvious to everyone, then “of course”
  • Brierley: Are you committed to a naturalistic view of history?
  • Crossley: Not quite, broadly, yes, I am saying this all I can do
  • Brierley: should James be open to a supernatural explanation?
  • Habermas: if you adopt methodological naturalism,it colors how look at the data is seen, just like supernaturalism does

Mike Licona debates Bart Ehrman on the reliability of the gospels

Two horses fight it out, may the best horse win!
Two horses fight it out, may the best horse win!

From the Unbelievable radio show.

Details:

Bart Ehrman is well known as a US New Testament Scholar who lost his Christian faith and now questions many core precepts of Christianity, including the Resurrection of Jesus.  When Mike Licona had doubts he devoted himself to investigating the evidence and became convinced that Jesus resurrection is the only rational explanation for the facts.

They debate key historical facts about the resurrection – are the letters of Paul that report the resurrection and the Gospel accounts trustworthy or theologised and changed with time?  What about apparent contradictions between the Gospels? Does the consensus of scholars count as evidence, or is there a Christian bias?  Can a miracle count as an explanation for historical data?

The MP3 file is here. (Note: this link works)

Snarky summary of the radio debate: (items with * are my made-up paraphrases/clarifications)

Ehrman:
– Bart’s new book is about forgeries in the ancient world
– some books were falsely attributed to prominent Christian figures
– there are mistakes in the Bible
– there are mistakes in the resurrection narratives
– the defeat of inerrancy led to his conversion to liberal Christianity
– the problem of evil and suffering caused him to become a non-Christian

Licona:
– there are minimal facts that are agreed to by a broad spectrum of scholars
– the minimal facts are accepted because they pass standard historical criteria
– Fact 1: Jesus died by crucifixion
– Fact 2: Individuals and groups had visions of Jesus after his death
– Fact 3: Paul, a skeptic and an enemy, had an appearance of Jesus that converted him
– these facts are agreed to atheist scholars, liberal scholars, etc.
– virtually 100% of scholars agree with these three facts
– there is no naturalistic explanation of these three facts
– therefore, the best explanation of these three facts is that God raised Jesus from the dead

Ehrman:
– all historians would accept these three facts, except for maybe the group appearances
– the death of Jesus is irrelevant to the resurrection
– the second and third point can be collapsed together
– so really there is only one fact

Moderator:
– the crucifixion is relevant because Muslims don’t admit that fact
– the crucifixion important because it establishes a resurrection, not a resuscitation

Ehrman:
– well, if the point is that he died, then yes, this does require a resurrection

Licona:
– the crucifixion refutes Muslims who deny that Jesus died
– the crucifixion refutes the apparent death theory (swoon theory)
– the death is required for a bodily resurrection
– it’s important to know what facts most scholars, regardless of worldview, agree on
– it’s important to emphasize that Licona is working from historical bedrock facts
– the resurrection is the best explanation for the historical bedrock facts

Ehrman:
– you are trying to list 3 things, but really it is just one thing – the appearances
– and not ALL scholars agree that the group visions occurred

Licona:
– name one prominent scholar who denies the group appearances

Ehrman:
– the radically leftist atheist nutcase John Dominic Crossan denies the group appearances
* Crossan is so far on the left that I look like a nutcase for even citing him
* Crossan believes in the Secret Gospel of Mark, which is a hoax – but I still cite Crossan
* Crossan believes that the synoptics are LATER than gnostic forged gospels – but I still cite Crossan
* Crossan presupposes atheism, so he cannot admit to miracle stories as a pre-supposition – but I still cite Crossan
* Crossan pre-supposes religious pluralism, so he cannot allow any exclusive claims Christians make – but I still cite Crossan
* Crossan is a good historian, it’s just that he is so far to the left that no one – NO ONE – agrees with his all of crazy theories
* I think it is a good idea to cite historians who pre-suppose atheism and political correctness before they sit down to do history

Licona:
– let me explain why most scholars accept the individual and group post-mortem appearances
– the best source for the appearances is the early creed recorded by Paul in 1 Cor 15:3-8
– Paul himself had an appearance of Jesus after Jesus’ death
– Paul received this material from a source very soon after the appearances – within 1-3 years
– we know that Paul met with Jesus disciples multiple times prior to writing
– Paul probably received it from Peter and James, who were themselves eyewitnesses

Moderator:
– this early dating presumably rules out legend

Licona:
– well legends CAN start quickly
– it does show that Paul was an eyewitness
– it does show that Paul was in contact with reliable eyewitnesses

Ehrman:
– 1 Corinthians is written around 55 AD, twenty-five years after Jesus died
– it is not implausible that Paul got the creed from the disciples, who were eyewitnesses
– but you don’t need a long time for legends to emerge, so that is a possibility

Licona:
– only about 3% of people could read and write back them
– instead, people had enormous capacity for memorization
– the Pharisees were particularly good at memorization
– Jews were very serious about passing along traditions accurately
– Paul, a prominent Pharisee, would have been capable of passing on early creeds accurately
– Paul, in 1 Cor 7, shows that he is willing to separate his opinions from authentic tradition
– Paul had an opportunity in 1 Cor 7 to put words into Jesus’ mouth, but he wouldn’t do it

Ehrman:
– cultural anthropologists show that things do get changed in some oral cultures
– in these oral cultures, it is assumed that the story teller will change the story
– only in written cultures are they careful to avoid changing the story
– in the New Testament, you can compare the same story in two different gospels, there are differences

Licona:
– Ehrman is right that the gospel writers pick and choose things from the oral tradition that they want to include in their gospels
– different oral tradition transmission schemes have more or less embellishment
– african tribes embellish more, rabbinic teaching embellishes less
* Jesus’ followers would have viewed him as a rabbi, and been careful about adding to his teachings
– Paul, an eyewitness, probably received the creed in 1 Cor 15 from other eyewitnesses
– Paul speaks about going twice to Jerusalem in Galatians
– he is meeting with Peter and James to check his facts

Ehrman:
– when you look at Mark and John, there are lots of differences in the narrative

Licona:
– I agree that the gospels have differences, but the oral tradition is likely fixed

Ehrman:
– but Mark and John have different sayings
– why doesn’t Mark have the same explicit high Christology that John has?

Licona:
– first, John is trying to weave the oral tradition into a compelling story
– and second, when you look in Mark, the high Christology is there in the Son of Man sayings
– the apocalyptic Son of Man is in Mark, and everywhere in the New Testament

Ehrman:
– the “apocalyptic Son of Man” isn’t in John

Licona:
– what about in John 9 with the man who was born blind

Ehrman:
– where is the apocalyptic part?

Licona:
– the healed man worships Jesus because he is the Son of Man
– that links to the apocalypic passages in the Old Testament

Moderator:
– what about the differences between the gospels?

Ehrman:
* well, now is the time for me to set up an inerrantist straw man and then knock it down!
* who was at the empty tomb: one angel or two angels? we don’t know, so the whole Bible is false!
* I used to be an inerrantist, so one minor difference is enough for me to dump the whole Bible
* I’ll kill you, you stupid straw man! I hate you, Moody Bible Institute! You lied to me!

Licona:
– many of these problems can be solved by realizing that the gospel writers compress time
– the stories don’t have to list ALL the characters in every scene
– you don’t have to force the Bible to meet some sort of wooden chronology
– the main thing is that the events happened, not that the descriptions match word for word across sources

Ehrman:
– you can’t infer a miracle from history, David Hume says so
* extraordinary claims require extraordinary evidence, David Hume says so
* no I don’t know what begging the question is, I’m not a philosopher
* no I don’t remember when Bill Craig kicked my ass on this Hume objection in our debate
– the New Testament gospels contradict each other at every point, they are not reliable at all!
* they cannot even agree what Jesus’ name is! There are 1 trillion variants of Jesus’ name!
* “one angel vs two angels” proves that the gospels contradict each other at every point
* my expansive list of FOUR theologically insignificant variants proves that the gospels contradict each other at every point

Licona:
– um, the gospels agree on the central narrative and disagree on the peripherals
– and they agree on the minimal facts I presented, even if they disagree about the number of angels

Ehrman:
* they have to agree on everything and be inerrant! The Moody Straw Man Bible Institute says so!
* I really really really need to have the number of angels be the same, or Jesus didn’t die on the cross

Licona:
– but you don’t deny any of the three minimal facts I presented (crucifixion, appearances, Paul)

Ehrman:
– well, I don’t know if the group appearances occurred – maybe they did
– i think Jesus died on the cross, and I think that people said they saw him alive afterward

Licona:
– if you deny the minimal facts, then you are outside the majority of scholars

Ehrman:
– the majority of scholars who agree to the minimal facts you presented are Christians
* Gerd Ludemann is an atheist Christian
* James Crossley is an atheist Christian
* Hector Avalos is an atheist Christian
* the majority of the atheist scholars are all Christians!
– VIRTUALLY EVERYBODY IN THE SOCIETY OF BIBLICAL LITERATURE IS A CHRISTIAN!!! (Yes, he said that)

Licona:
– you really think so?

Ehrman
– you name one non-Christian in the SBL

Licona:
– (incredulous) um, John Dominic Crossan is an atheist

Ehrman:
– but he CLAIMS TO BE A CHRISTIAN so that means HE IS A CHRISTIAN
* all you have to do to be a Christian is claim to be one
* you can even deny the existence of God and the divinity of Christ and still be one, you bigot!

Licona:
– would Jesus or the apostles recognize a Christian as being someone who doubts God’s existence

Ehrman:
– my view is that Jesus and the apostles would not recognize evangelical Christians as Christians
* a non-theist can be a Christian just by claiming to be one, but evangelical Christians are not Christians even if they claim to be Christians
– Christians can’t record accurate history about the resurrection because they are biased

Licona:
– on your view, if a person is a Christian then he can’t write about the evidence for the resurrection
– so then similarly, you would not allow Jews to write about the historicity of the Holocaust
– because you think that if people have an interest in what they are recording then they can’t be objective
– but you have to consider the evidence we have, taking the biases of the sources into account

Ehrman:
– but the only people who believe in the resurrection are Christians!

Licona:
– well, people can consider the evidence for the resurrection as non-Christians
– and then if they accept it they can become Christians

Moderator:
– what about your bias? you don’t believe in God – doesn’t that pre-supposition affect how you do history?

Ehrman:
– well, I presuppose naturalism, so I can’t admit to anything in history that implicates supernatural causes
* no I have never heard of the arguments for the Big Bang, fine-tuning, origin of life, Cambrian explosion, irreducible complexity, limits on mutations creating information, habitability and so on – I never heard about that stuff from my atheist university professors and even if I had I would have been expelled for talking about it because that would make people feel bad about their sinning

Licona:
– so it’s not bias you are concerned about, it’s that you don’t want history to contradict your untested religion of naturalism?
– why not just do the history without pre-suppositions to gather the minimal facts and then see what the best explanation is?

Ehrman:
* well God is out of bounds as an explanation because I could not have got my PhD if I mentioned God
* I really needed my smart atheist professors to like me and give me good grades so God is RIGHT OUT
* ideas like a real God and moral laws and Hell makes my atheist professors uncomfortable and that means low grades for me
* I’m not really interested in butting heads with professors – it’s easier to just agree with them and move on to selling books to the gullible
* My books are much more sensational than Dan Brown books, so please buy lots of them!

Licona:
– what if the historical evidence is good enough to show that Jesus rose from the dead?

Ehrman:
– well I would not call someone rising from the dead a miracle – I would call it weird
* I also think that the Big Bang is “weird” but that doesn’t prove that God created the universe out of nothing
* if it’s a miracle then I’m going to have to not sin, and maybe even go to Hell, and we can’t have that

Licona:
– well, you accept the three minimal facts
– what if we try all the naturalistic explanations for those three facts and there are problems with all of them?
– what if the resurrection is the best explanation for the three minimal facts?

Ehrman:
– but I want to arbitrarily rule God put because I want to pre-suppose naturalism
– there is not historical reason I have to rule put supernatural explanations a priori

Licona:
– I think you are struggling with the theological implications of a historical conclusion

Ehrman:
– well when you do theology, you have to avoid grounding your theology on science or history
– theology has to be completely made up or it’s not good theology

Licona:
– I think you are letting your dislike of the implications of the resurrection determine your historical conclusions
– you have to use historical methods to gather the minimal facts that every scholar accepts, regardless of worldview
– then you weigh ALL the hypotheses, natural and supernatural, that could account for these minimal facts
– then you choose the hypothesis that best explains the minimal facts

Information Enigma: 21-minute video explains intelligent design

Can random mutation and natural selection create new functional information?
Can random mutation and natural selection create new functional information?

The video is here:

I have read and listened and watched a lot of material on intelligent design, but I have never seen so much value packed into such a short lecture. I really hope you’ll watch this and that it’s helpful to you.

Summary:

  • the big question when discussing the origin of life: where did the information in living systems come from?
  • Until 530 million years ago, the oceans were largely devoid of life
  • In a 10 million year period, many new forms of animal life emerged
  • New biological forms of life require new information
  • the discovery of DNA shows that living systems work because cells have information that allows them to build the components of molecular machines: cell types, proteins, etc.
  • can random mutation and natural selection create new functional information?
  • normally, random mutations tend to degrade the functionality of information, e.g. – randomly changing symbols in an applications code does not usually introduce useful new functions, it usually renders what is there non-functional
  • the majority of possible sequences will NOT have functions, so random mutations will more likely give you non-functional code, rather than functional code
  • example: a bicycle lock  with 4 numbers has many possible sequences for the 4 numbers, and only one of them has unlock functionality, the rest have no functionality
  • if you have lots of time, then you might be able to guess the combination, but if the lock as has 10 billion numbers, and only one combination that unlocks, you can spend your whole life trying to unlock it and won’t succeed
  • how likely is it to arrive at a functional protein or gene by chance? Is it more like the 4-dial lock (can be done with lots of time) or the 10 billion dial lock (amount of time required exceeds the time available)?
  • the probability is LOW because there is only one sequence of numbers that has unlock function
  • consider a short protein of 150 amino acids has 10 to the 195th power possible sequences
  • if many of these sequences of amino acides had biological function, then it might be easier to get to one by random mutation and selection than it is with a lock that only unlocks for ONE sequence
  • how many of the possible sequences have biological function?
  • Thanks to research done by Douglas Axe, we now know that the number of functional amino acid sequences for even a short protein is incredibly small…
  • Axe found that the odds of getting a functional sequence of amino acids that will fold and have biological function is 1 in 10 to the 77th power
  • Is that number too improbable to reach by chance? well, there are 10 to 65th atoms in the entire Milky Way galaxy… so yes, this is a very improbable outcome
  • can random genetic mutations search through all the sequences in order to find the one in 10 to the 77th power one that has biological function? It depends on how much guessers we have and how many guesses we get in the time available
  • even with the entire 3.5 billion year history of life on Earth, only about 10 to the 40th organisms have ever lived, which far smaller fraction of the 10 to the 77th total sequences
  • even with a very fast mutation rate, you would not be able to reach a functional protein even with all that time, and even with all those organisms

I was once having a discussion with a woman about the research that Axe did at the Cambridge University lab. He published four articles in the Journal of Molecular Biology. I held out one of the papers to her and showed her the numbers. She said over and over “I hate the Discovery Institute! I hate the Discovery Institute!” Well, yeah, but you can’t make the Journal of Molecular Biology go away with hating the Discovery Institute. JMB is peer-reviewed, and this was experimental evidence – not a theory, not a hypothesis.

We have been blessed by the Creator and Designer of the universe in this time and place with overwhelming evidence – an abundance of riches. For those who have an open mind, this is what you’ve been waiting for to make your decision. For the naturalists who struggle so mightily to block out the progress of experimental science, they’ll need to shout louder and shut their eyes tighter and push harder to block their ears. Maybe if they keep screaming “Star Trek” and “Star Wars” over and over to themselves, they will be able to ignore the real science a little longer.

Are endogenous virus genes evidence for common descent?

Investigation in progress
Investigation in progress

This is a guest post by JoeCoder.

It’s often argued that when two or more organisms share viral genes in the same place, it is evidence those organisms evolved from a common ancestor.  Wikipedia’s Evidence for Common Descent page frames it as follows:

Endogenous retroviruses (or ERVs) are remnant sequences in the genome left from ancient viral infections in an organism. The retroviruses (or virogenes) are always passed on to the next generation of that organism that received the infection. This leaves the virogene left in the genome. Because this event is rare and random, finding identical chromosomal positions of a virogene in two different species suggests common ancestry.

This argument presupposes that the viruses inserted themselves into genomes randomly and stick around as junk DNA baggage, rather than genomes originally being designed with viral-like genes that perform useful functions.  However this argument has unraveled as we’ve discovered useful functions for many viral-like genes, including functions that specifically require a viral-like sequence.  Some examples among many:

  1. ERV sequences protect against viral infection through interference–a matching-but-opposite strand of RNA is created to bind to and disable RNA from a virus.
  2. Likewise, ERV’s seem to function “during embryo implantation to help prevent immune recognition by the mother’s immune system”
  3. In worms, an ERV has been observed to create actual viruses that transfer DNA from somatic cells (skin/brain/heart/etc.) to germline (sperm/egg) cells whenever the worm is exposed to too much heat, allowing them to rewrite their own DNA for future generations.
  4. Viral envelopes from ERV transcripts attach to cell membranes in the placenta and causes them to fuse as a normal part of development: “The HERV-W [a human ERV] envelope glycoprotein named syncytin 1 is expressed in all trophoblastic [part of the placenta] cells and directly involved in human trophoblast fusion and differentiation [cells taking on specialized roles]”

These aren’t isolated cases of function.   Phys.org interviewed one researcher:  “When we investigated public data from embryonic cells, we found that many RNAs originated from regions in the human genome that are ERVs.  We did not only observe isolated events, but systematic activation of these ERVs. Every cell type showed transcription of specific classes, something that is very unlikely to occur by chance”.

Those cases all involve RNA viruses and that’s old news.  But two weeks ago, a single-celled eukaryote called Cafeteria roenbergensis was found to harbor maviruses within its own DNA that remain dormant until it is attacked by a large virus known as CroV.  When this happens the maviruses activate to form an attack fleet, as NewScientist reports:

A voracious marine predator plagued by a giant virus has a defence system we’ve never seen before – it fights back by making its very own virus… Rather than waiting for maviruses to arrive by chance when CroVs attack, it actually carries the genes that code for mavirus inside its own genome.  These genes are usually dormant, but they get turned on when Cafeteria is invaded by CroV. “It acts as an inducible antiviral defence system,” write Fischer and his colleague Thomas Hackl in a new preprint paper.

This process kills the Cafeteria roenbergensis cell, but is useful in defending other members of its own species.  In this experiment maviruses were deliberately inserted into the Cafeteria roenbergensis genome (see the original paper), but more interestingly, sequences similar to the Cafeteria roenbergensis viral genes have been found in a wide range of animals:

A wide range of animals, from sea anemones to crocodiles, harbour genetic elements called Maverick transposons that closely resemble the mavirus genes. It’s possible that some of these organisms can also unleash viruses that attack giant viruses.

In spite of this, New Scientist still argues “our genomes are littered with the mutant remains of viruses and genetic parasites.”  But these discoveries reveal this as a rapidly-shrinking argument of the gaps. 

Save this for the next time someone insists that viral genes are useless junk DNA and therefore evidence of common descent.