(Note: my recent interview with Edouard Tahmizian of Internet Infidels is at the end of this post.)
Christian apologist Dr. Jeremiah Johnston, a New Testament Baptist scholar, pastor and author who ministers internationally as president of Christian Thinkers Society, was recently interviewed by Ruth Jackson on the show, Unapologetic, from Premium Unbelievable about his latest book, Body of Proof: The 7 Best Reasons to Believe in the Resurrection of Jesus–and Why It Matters Today (Bethany House Publishers, 2023). Dr. Johnston wrote a 93,000-word dissertation while he was studying at Oxford on the physical, bodily resurrection of Jesus, concluding that the resurrection was the best explanation for what happened. In his interview, he makes an even stronger claim (13:11): “We can prove the resurrection of Jesus really happened.” That’s a very tall claim, to put it mildly. As Scripture testifies, “Pride goes before destruction, a haughty spirit before a fall.”
The “meat” of Dr. Johnston’s 30-minute interview starts at (13:55) and ends at (29:12). My overwhelming impression, after listening to the interview, was that Dr. Johnston’s reasons would not impress an unbeliever. I’d now like to explain why, by briefly commenting on each of Dr. Johnston’s seven reasons. The quotes are from Dr. Johnston’s interview.
1. Christianity created a better world
“Number one is: it’s the only way you can explain that everywhere the Christian movement goes, society has improved for the better.”
My comment: You have got to be kidding me. Does “everywhere” include pre-Columbian America, where tens of millions of native Americans died from wars, genocidal violence, enslavement, oppression and above all, diseases (such as smallpox, measles and influenza), after coming into contact with European Christians in 1492? And what about the Atlantic slave trade, which imposed hellish conditions on Africans and their slave descendants in the New World, over a period of several centuries, resulting in tens of millions of deaths? (If Dr. Johnston doesn’t think that Christianity was responsible for these crimes against humanity, then I’d suggest that he read All Oppression Shall Cease (Maryknoll, NY: Orbis, 2022), a highly acclaimed history of slavery and the Catholic Church by Jesuit priest Fr. Christopher Kellerman.) To convincingly counterbalance these appalling numbers, one would have to demonstrate that Christianity saved hundreds of millions of lives, in other ways. So, where are the stats? I don’t see any.
Dr. Johnston also mentions hospitals and health care, and he does have a valid point here, as atheist scholar Professor Bart Ehrman himself acknowledges:
“Hospitals – defined as buildings or building complexes that provided both outpatient and inpatient health care by professionally trained doctors and nurses based on the most advanced medical knowledge of the day — were a Christian invention. The services they provided were free of charge.”
Dr. Ehrman, who is currently working on a book tentatively titled, The Invention of Charity: How Christianity Transformed the Western World, notes that “in the Roman world at large, those with wealth showed almost no concern for those in need, even desperate need.” When they did give to the poor, it was usually out of a desire for self-improvement, rather than concern for the suffering of the poor. However, as Ehrman points out, the Christian concept of charity ultimately derives from Judaism. Christianity served as the vehicle to universalize this notion throughout the Roman empire.
It is not that Christians invented the idea of “charity”: they inherited a concern for the needy from their Jewish forebears. But they, not the Jews, converted the Roman world, and, in the end, universalized and, to some extent, institutionalized the imperatives, incentives, and practices of charity… Prior to the Christian conquest of the Empire, the Western world knew of no such things as hospitals, orphanages, private charities, or governmental assistance to the poor. These are Christian innovations.
So while Christianity has done a ton of good in the world, it has also done a lot of harm. Which is greater, the good or the harm? It’s really hard to say. And while the tireless labor of Christian medical missionaries may have saved a great many lives in Third World countries during the 20th century, one could fairly argue that modern science, rather than religion, deserves much of the credit here.
2. Jesus predicted his own resurrection
“Number two: Jesus called it. If the Church had a hash tag, it would be: on the third day… Jesus called his resurrection. He predicted his violent death and resurrection in Mark 8:31, Mark 9:31, and Mark 10:33-34. He quotes Hosea 6:2-3 – ‘After two days he will revive us. On the third day [he will restore us.]'”
My comment: If Jesus actually predicted his own resurrection, then he created an expectation in the minds of his disciples that he would rise. And if that’s the case, then the popular apologetic argument, that the disciples couldn’t have hallucinated the risen Jesus because they were beaten men whose hopes had been dashed by seeing him crucified, is rendered invalid. On the contrary, the disciples were primed to expect a resurrection. And we know for a fact that three of them (Peter, James and John) were prone to seeing visions: Mark 9:2-13 explicitly tells us that even before Jesus’ death, they’d seen him arrayed in clothes of dazzling white, accompanied by Moses and Elijah, and that they’d heard the voice of God speaking from a cloud, on a mountain. A skeptic might say that these were highly imaginative and impressionable witnesses.
But did Jesus really predict his own resurrection? The vast majority of critical Biblical scholars would say that he did not. Let’s not forget: the Gospels were written decades after Jesus’ alleged resurrection, by people who were already committed Christians. Certainly, Jesus may have expected some last-minute miraculous vindication from God, immediately before his death, which would account for his cry of desolation on the cross when none eventuated. Alternatively, he may have been resigned to his crucifixion at the hands of the Romans, but looked forward to being vindicated at some future point in history, when he would return at God’s right hand to judge the living and the dead. But the prophecies of the resurrection found in Mark’s Gospel are generally regarded by scholars as theologically motivated: if God actually raised Jesus from the dead, then He must have told Jesus in advance, and of course, Jesus must have told his disciples. At any rate, when Dr. Johnston claims that Jesus predicted his own resurrection, he is going against the consensus of New Testament scholars. That doesn’t make him wrong, but it does make his argument questionable.
3. Jesus was able to raise the dead
“Three: Jesus performed. He demonstrated resurrection power… He raised Jairus’s daughter from the dead. That’s Mark, chapter 5. Luke 7: the widow of Nain’s son. He stops a funeral procession. The boy would have died that day. He said, ‘He’s not dead; he’s sleeping.’ Jesus raised him up. And of course, John 11: Lazarus, where he brings Lazarus forth from the dead, after being dead four days. So Jesus showed that he did indeed have power over death… Jesus is the first-fruits [of the] resurrection, never to die again. We will have ‘un-dieable’ bodies in the resurrection. They will never need to be upgraded… They will always be in perfect condition. And Jesus’ resurrection body is a model of that. What’s fascinating to me is: I also talk about those who had to die twice – these individuals who were not the first fruit of the resurrection like Jesus. They would have died twice. We actually have two different burial spots for Lazarus: Bethany and on the island of Cyprus, where he was buried a second time, which is really cool.”
My comment: The resurrection miracles described by Dr. Johnston were written down by the Gospel writers at least three decades after they actually happened, at a time when many (and perhaps all) of the original witnesses would have been dead. Would Dr. Johnston believe a claim that a Hindu healer had worked such a miracle three decades earlier, if he were unable to interview the witnesses? I doubt it.
Another point that needs to be considered is that Jesus himself declared that Jairus’ daughter (whom he healed) wasn’t dead, but asleep. What if he was right, and the girl was actually in a deep coma? The same applies to the widow of Nain’s son. Even in today’s world, people can be mistakenly pronounced dead, and there have been tragic cases of people buried alive. So, were the people Jesus raised really dead? Maybe not. To be sure, the story of Lazarus being raised four days after his death cannot be explained away in this fashion, but despite allegedly happening right before Palm Sunday, it is found only in John (which is generally thought to be a late Gospel): Matthew, Mark and Luke don’t mention it at all.
But even if the narratives were all true, and Jesus actually had the power to raise the dead, the point is that they died again, as Dr. Johnston rightly points out. Such narratives fail to establish that Jesus was able to raise himself to life (or be raised back to life) in an immortal, indestructible, “un-dieable” body (to use Dr. Johnston’s term). That’s a much taller claim.
4. There was no motivation for the disciples to invent the story of Jesus’ resurrection.
“We [previously] talked about number four: there was no motivation to invent a resurrection narrative. That’s the original contribution to knowledge in Body of Proof.” Earlier on in the interview (10:12), Dr. Johnston declared, “I’ve talked to a lot of marketing people, and if you were trying to market a new religion, … you talk about a tone-deaf way to start a new religion. Female witnesses, your Messiah is killed by Roman crucifixion, your Messiah is resurrected from the dead. Nobody believed in resurrection outside Judaism in the Roman Empire. You could not have started with worse talking points than what the new Christian movement started with, if you wanted to draw a following. The only reason it did, in spite of the marketing bias, … is that’s what actually happened… It was what they experienced, and it was true… There is no psychological motivation to invent an early resurrection narrative about Jesus, if it didn’t happen… Judaism is a coherent religion. They believe that there will be a resurrection at the end of days, a general resurrection… There was no reason to claim that Jesus rose from the dead. You could have honored him as a great prophet, a great thinker, a moral teacher. You had no reason, there was no psychological motivation to go out and about and say, ‘Hey, he really rose from the dead.'”
My comment: What the above argument demonstrates is that the resurrection narrative wasn’t invented out of whole cloth, as there would have been no religious motive for such a fabrication. What the argument fails to establish is that the resurrection narrative is actually historical. Other explanations for the disciples’ belief in Jesus’ resurrection are possible: perhaps the unexpected discovery of the empty tomb (after the body had been stolen by grave robbers), coupled with Jesus’ repeated predictions (assuming he made them) that he would be raised back to life, was enough to trigger spontaneous, post-mortem visual and tactile apparitions of Jesus among Peter, James and John, and later the other disciples, causing them to believe that he had indeed risen. (In this connection, see Dale Allison’s discussion of the best skeptical scenario here, at 55:42.) I’m not claiming that this scenario is a likely one; I’ll leave that for others to judge. My point is that belief in Jesus’ resurrection didn’t need a motivation. All it needed was a sufficiently powerful cause.
5. Archaeology supports the reliability of the Gospel accounts
“Number five: … it’s the truth that written and archaeological sources overwhelmingly support the Gospel resurrection narratives, which are embedded in Matthew, Mark, Luke and John. When we study the material culture, we see that archaeology is Christianity’s closest cousin. We see that unlike any other faith [or] belief system in the world, Christianity puts itself to the historical test, and says, ‘Hey! Test us!’ … I go into depth [in my book] about Jewish burial traditions… No Jew would lose track of their loved one… Scholars have sold lots of books by saying that Jesus’ body was likely eaten by stray dogs, that his body was never buried [in a tomb]; it was buried in a mass criminal pit… When we acquaint ourselves with Jewish burial tradition, we understand that you would not lose sight of your brother, even if he was an executed criminal. Even if he died as a crucified criminal, you would not lose track of his bones. We have this from Jehohanan, who was discovered during the reign (sic) of Pontius Pilate. Crucified, had to be buried before nightfall, in accordance with Jewish burial traditions. He was buried with a crucifixion spike stuck through his heel. When you look at the archaeology, I quote Jodi Magness from the University of North Carolina. She’s an atheist archaeologist, but she says, ‘When you look at the Jewish juridical procedure, as presented in the Gospels, … the Gospels get it right.’ And that’s from an archaeologist… We have to appeal to Roman emperors for the same level of textual attestation as Jesus of Nazareth.”
My comment: Dr. Magness’s conclusion is a fairly modest one: “Although archaeology does not prove there was a follower of Jesus named Joseph of Arimathea or that Pontius Pilate granted his request for Jesus’ body, the Gospel accounts describing Jesus’ removal from the cross and burial are consistent with archaeological evidence and with Jewish law.” Moreover, Dr. Magness’s proposal differs from the Gospels in a key respect. In her article, What did Jesus’ Tomb Look Like? (Biblical Archaeology Review, 32:1, January/February 2006; reprinted in The Burial of Jesus, Biblical Archaeology Society, Washington DC, 2007), Dr. Magness puts forward her own novel interpretation of statements found in the Gospels, that Jesus was laid in a new tomb where no-one had ever been laid (Matthew 27:60, Luke 23:53, John 19:41). She thinks they simply mean that Jesus’ body was laid in a new burial niche in the wall (or loculus) inside Joseph of Arimathea’s family rock tomb:
Joseph’s tomb must have belonged to his family because by definition rock-cut tombs in Jerusalem were family tombs… The Gospel accounts apparently describe Joseph placing Jesus’ body in one of the loculi in his family’s tomb. The “new” tomb mentioned by Matthew probably refers to a previously unused loculus. (2007, p. 8)
However, the Gospels speak of Jesus being laid in “a tomb cut in stone, where no one had ever yet been laid” (Luke 23:53). That’s completely different from a new niche in the wall of an existing tomb, where many bodies have already been laid. Thus even Dr. Magness doesn’t think the Gospel accounts of Jesus’ burial are completely accurate.
I might add that I don’t know of any critical Biblical scholar who believes that Jesus was buried with 100 Roman pounds of myrrh and aloes (or 75 of our pounds), as John 19:39 informs us – an amount literally fit for a king!
But here’s the thing: even if the Gospel accounts of Jesus’ burial were accurate in all details, how on earth would that establish the truth of Jesus’ resurrection? Burial is a completely natural event; resurrection, a supernatural one. To infer the latter from the former is to make an invalid inference.
Finally, although the textual evidence for Jesus’ existence compares favorably with the textual evidence for the Roman emperors, Dr. Johnston overlooks the fact that we have coins commemorating the Roman emperors. We don’t have any such coins for Jesus.
6. The conversion of two prominent skeptics: Paul and Jesus’ brother James
“Number six is really key, because Jesus appeared to those who believed in him, Jesus appeared to those who doubted him, Jesus appeared to those who opposed him… I talked in detail in [my] chapter about the apostle Paul, and how radical his conversion was, but also, I want to talk about the Lord’s brother, James. When Paul is converted in A.D. 31 or 32, … Paul goes into Arabia, and then after Arabia, he goes to Jerusalem… Paul goes and he spends fifteen days, according to Galatians 1 and 2, with Peter and with James, in the city… And they talk all about the Gospel. Paul wants to make sure he [has] … the Gospel right. And so, here’s the fascinating thing: James did not believe that his brother was the Jewish Messiah until the Resurrection… What would it take for you to die, believing and proclaiming your brother was the Son of God? We know that … Jesus appears to James. That’s 1 Corinthians 15:7… Hyper-critical scholars acknowledge Paul wrote 1 Corinthians [15] verse 7: ‘And he appeared to James.’ What’s fascinating, James then becomes a pillar of the Church. He then dies in A.D. 62. According to Josephus, he is stoned to death, proclaiming that his brother is the resurrected Son of God, the Messiah. So, wow! So when you look at the ‘hostiles’ that came to Christ – those that doubted him, those that opposed him – it’s compelling evidence.”
My comment: Two quick points. Regarding Paul, we don’t know exactly what he saw when he encountered Jesus on the road to Damascus, but judging from the descriptions in Acts 9:1-9, Acts 22:1-11 and Acts 26:9-18, he seems not to have seen a flesh-and-blood Jesus but a blindingly luminous being of light, as well as hearing a voice from the sky. In other words, whatever he encountered, it was not Jesus’ resurrected body, but an apparition. Therefore it cannot count as evidence for Jesus’ bodily resurrection.
Regarding James, Paul’s mention of him in 1 Corinthians 15:7 is indeed authentic, as scholars of all stripes acknowledge. However, as Christian apologist Ryan Turner acknowledges in his online article, An Analysis of the Pre-Pauline Creed in 1 Corinthians 15:1-11 (October 1, 2009), verse 7 (which refers to Jesus appearing to James) is most likely not part of the original creed: it was appended by Paul. In any case, as Professor Dale C. Allison points out in his widely acclaimed book, The Resurrection of Jesus: Apologetics, Polemics, History (T & T Clark, 2021), we do not know if James’ conversion came before or after Jesus’ resurrection appearances. Perhaps he was already a believer by the time he encountered Jesus. Or perhaps he was only half-hearted in his opposition to Jesus, or possibly, he vacillated back and forth between supporting and opposing Jesus. Professor Allison concludes that “‘conversion’ might be too strong a word for what happened to him” (2021, p. 79). What’s more, details of Jesus’ resurrection appearance to James are scant: we don’t know where or when it happened, what Jesus looked like when he appeared to James, what (if anything) Jesus said to James, or how James felt when he saw Jesus. Finally, Josephus’ narrative of the death of James in A.D. 62 (Antiquities 20, chapter 9) does not say that he was martyred for his faith in Jesus’ resurrection, but rather, for being a breaker of the law.
7. Jesus’ resurrection is the only reason why we are able to make sense of suffering
“Number seven … Jesus’ resurrection is the only reason we can make sense of the suffering in our lives. When we look at Romans 8:18, the apostle Paul said, ‘I don’t count these sufferings worthy to be compared with the glory that I will receive some day, in heaven.’ Paul said …, ‘Better for me to die in Christ than to live.’ He was looking constantly to the hope of the resurrection as the answer to all the suffering… The resurrection is what ultimately makes sense of all the suffering.”
My comment: Here’s a question for Dr. Johnston. Suppose you were living in Judea before the time of Christ, but after the time when the Jewish Scriptures had been compiled. Do you really mean to tell me that you’d be utterly unable to make any sense of the suffering in the world, despite growing up in a society based on ethical monotheism? Or again: suppose you lived in fourth-century B.C. Athens, and you were listening to philosophers debate the existence of a supreme, benevolent God. Do you really mean to say that you think the atheists would have the better of the argument, prior to Jesus’ resurrection? I think not. In that case, all you can possibly mean is that you believe Christianity makes better sense of the suffering we see in the world than other religions (including Judaism and philosophical monotheism). But even if this is true, it, at best, a supplementary reason for believing in Jesus’ resurrection, and it’s a theological reason, not a historical one.
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And finally, ere’s a recent 42-minute interview I did with Edouard Tahmizian, Vice-President of Internet Infidels, about my recent article on The Skeptical Zone, Dr. Gavin Ortlund’s defense of C.S. Lewis’s “Liar, Lunatic or Lord” trichotomy, and Why I think it won’t work on skeptics. Most of my readers will already be familiar with this post. At about 24:00, when I conclude my presentation, the discussion gets more interesting, and you’ll see me looking up at the camera again, instead of looking down at my notes. Ed also raises some points relating to his Internet Infidels paper, The Origin of Evil (which he’s recently revised), and we talk about Jesus mythicists (whom Ed knows very well). Finally, around 30:30, I talk about life in Japan. Enjoy!
Behe 2004 Simulating evolution by gene duplication of protein features that require multiple amino acid residues
What differs in the 2009 version? Does it take on board Michael Lynch’s critique of 2005?
PS. This has been done to death in “Bill’s Math Class” at Peaceful Science.
But that isn’t what I asked. I asked whether the models had s as a function of the evolving population, not whether different s’s were tested.
It’s a really important point. The population itself is part of the environment that is doing the “selecting” i.e. the environment in which some variants offer an advantage and some a disadvantage. And that population is changing as variants drift through it. If nobody else has an extra-long tail, an extra-fine long may be greatly advantageous in attracting a mate. But once most of your peers have one, it might be of only marginal use in attracting a mate and a net disadvantage in terms of your ability to escape from predators.
My point being: that using a simplistic mathematical model and finding it doesn’t account for reality doesn’t mean that the theory that generated the model is wrong – it may mean that the model leaves important stuff out of the theory.
It’s hard to follow what your argument is when you don’t spell it out. Mechanism OF WHAT?
Limited in what way? WHAT is the “pattern” you think it does not explain?
I mean, I’m aware I’m coming into a long-running discussion that I haven’t been following, but I’m not getting from your posts what you think the problem is here – could you try to summarise your argument?
Changes in what? By what criteria are there “too many”?
Flint,
Hi Flint
This is the question that needs to be explored. Thanks. I think the Venn diagrams as they develop is a good place to start.
What makes you think a (single-root) tree pattern doesn’t fit?
Elizabeth,
The model does not as far as I can tell. I am not sure this is relevant as nothing happens in the model until the duplicated gene reaches some new function. This is the waiting time that needs to fit into evolutionary time frames.
Mechanism for generating new genes.
The pattern of similarity and differences in genes. Reproduction generates a new copy of the same genes from a combination of the mother and the father. What we see in the Venn diagrams is radically different than what we would expect from reproduction.
By the criteria of what we know reproduction produces. Populations mechanisms of change such as reproduction , natural variation and fixation limit variation yet what we observe in different vertebrate populations are lots of variation in gene types.
The single point of origin theory does not predict this. It predicts very small changes over long periods of time.
What the patterns do show supports Behe’s method of design detection. A purposeful arrangement of genes (parts) that build unique animals.
Elizabeth,
It does not explain the differences in gene and chromosome patterns and how reproduction could explain these patterns.
That most of what Bill writes in comments (supposedly arguing against evolutionary processes but it’s hard to tell) is hard to follow is a common complaint of those reading them.
Behe showed that it would take a long time to get a novel function via drift.
The Venn diagrams show lots of novel genes (gonna ignore the proportion that are losses)
Vertebrates have long generation times.
Therefore, there is insufficient time since the common ancestor to fix all these new novel genes.
</colewd>
AIUI that is the ‘argument’.
In addition to the failures pointed out above (TSS, ignores recombination, etc, etc), I will lay good money Bill expects the novel genes to fix sequentially, as in “if it takes 20,000 years to fix one, then it must take 2,000,000 years to fix 100”
that‘s why he’s so impressed with the large numbers outside of the center of the Venn, and he’s still not picked up on the improbable correlation between the Tree of Life and the pattern of values in the flower.
That it would take a long time to get a specific novel function in a specific set of duplicate genes, requiring 2 individually deleterious mutations. So, the Texas sharpshooter fallacy.
He conceded in his paper that the situation is entirely different if we are just waiting for any novel function in any gene.
Bill claims that when I say this I am strawmanning Behe. Am I? This is what Behe says in his paper:
Behe & Snoke 2004:
“Such numbers seem prohibitive. However, we must be cautious in interpreting the calculations. On the one hand, as discussed previously, these values can actually be considered underestimates because they neglect the time it would take a duplicated gene initially to spread in a population. On the other hand, because the simulation looks for the production of a particular MR feature in a particular gene, the values will be overestimates of the time necessary to produce some MR feature in some duplicated gene. In other words, the simulation takes a prospective stance, asking for a certain feature to be produced, but we look at modern proteins retrospectively. Although we see a particular disulfide bond or binding site in a particular protein, there may have been several sites in the protein that could have evolved into disulfide bonds or binding sites, or other proteins may have fulfilled the same role. For example, Matthews’ group engineered several nonnative disulfide bonds into lysozyme that permit function (Matsumura et al. 1989). We see the modern product but not the historical possibilities.”
Bill mostly refrains from spelling out his arguments because that would require he had arguments, instead of just vague ideas he can’t articulate.
But also because, were he to do so, it would become even more easy to see the errors in reasoning he makes, and that would just make it all the more embarrassing for him.
Bill knows of no example of any gene gained counted among those in the venn diagram that has a novel disulfide bond, for example. And even if there were such genes among them (there might be a few, who knows?) that doesn’t mean they would have to evolve in the manner Behe modeled, requiring 2 mutations being individually deleterious, in the absence of recombination, in a specific gene viewed retrospectively, etc.
There have been some enjoyable science fiction stories where some scientists have invented a device that sends some large object deep into the past, and it rebounds back to the present. The question they’re investigating is whether this interference in the deep past will alter the present. From the third person perspective, each time the object returns the scientists are drastically different, but from their viewpoint nothing has changed at all, because they are the product of an entirely different history each time. They conclude that that their form (whatever it might end up being) was inevitable, and evolution will produce the same organisms every time!
I picture Bill as one of these scientists.
Really helpful, thanks.
But what are the model criteria as to whether or not the duplicated gene has a function?
It seems you have a “god’s eye view” fallacy going on here (a common problem with models because the modeller is the model god!)
If the model specifies in advance what genetic change constitutes a “function” or not, then it will be GIGO. The fact is that we don’t KNOW whether a genetic change means a change in phenotypic function until we’ve actually observed the phenotypes interacting with their (changing, because the population is changing) environment.
I mean, obviously you can tell whether a genetic change specifies a different protein or not, but there’s a lot more to function than coding for a proteins.
Elizabeth,
The model estimates the time it takes to find two specific functions that are prevalent in cells. Disulfide bonds and ligand binding. The value of it is to show in detail all the steps necessary for a duplicated gene to evolve a new function.
If you study the model and then look at the large gene differences between species you realize that gene duplication and variation is very unlikely able to explain the pattern we are observing. Jock made this statement.
Some tree of life patterns may exist yet this is not the argument. The argument is that the single origin model is not supported by these Venn diagrams as 50% of the genes are not shared between 4 different vertebrates. Without a mechanistic explanation for how reproduction and natural variation caused these differences the best explanation is that we are observing the result of 4 different origin events.
Again the pattern fits Behe’s criteria for design detection. A purposeful arrangement of genes (parts) that build 4 distinct animals.
Contrast how Bill Cole characterizes Behe’s paper, with how Behe himself speaks of it:
Behe & Snoke 2004:
“Such numbers seem prohibitive. However, we must be cautious in interpreting the calculations. On the one hand, as discussed previously, these values can actually be considered underestimates because they neglect the time it would take a duplicated gene initially to spread in a population. On the other hand, because the simulation looks for the production of a particular MR feature in a particular gene, the values will be overestimates of the time necessary to produce some MR feature in some duplicated gene. In other words, the simulation takes a prospective stance, asking for a certain feature to be produced, but we look at modern proteins retrospectively. Although we see a particular disulfide bond or binding site in a particular protein, there may have been several sites in the protein that could have evolved into disulfide bonds or binding sites, or other proteins may have fulfilled the same role. For example, Matthews’ group engineered several nonnative disulfide bonds into lysozyme that permit function (Matsumura et al. 1989). We see the modern product but not the historical possibilities.”
colewd:
Those wondering what Bill is talking about regarding “4 distinct animals” can get a clue here. Human, mouse, chicken, zebrafish.
Alan Fox,
They are the product of 4 distinct separate origin events.
So you say, Bill. But the evidence of common descent is unequivocal.
You could both be right, depending on what you mean by “origin”. I think it’s reasonable, not too confusing, to consider every species as having an origin, roughly the time since it branched from an ancestor. If it were possible to trace the lineage of Bill’s 4 species in detail, I imagine you’d have to track back through quite a few “origins” to find common ancestors. My reading is, you’d find the common ancestor of human and mouse first (working back into the past), then the common ancestor of that species and chickens, and finally the common ancestor of all three with the ancestor of the fish.
All four fall into the phylum chordata, so the common ancestor would have an internal skeleton and a backbone or notochord. It likely lived about 375 million years ago, and likely most resembled the fish.
That’s a nice point. And of course one of the reasons why the single tree looks like an orchard in cross section is that branching is a much more rapid process than consolidation/optimisation.
It’s not so much that “punk eek” is an epicycle to fudge common descent. It’s that claiming that “punk eek” is an epicycle to fudge common descent is itself an epicycle to fudge the orchard.
If punk eek is true then common descent is no problem. And I go back to my point that watching any evolutionary algorithm shows you that punk eek is the way evolution works. It wouldn’t have been obvious to Darwin but it’s obvious to anyone with a computer and an evolutionary model.
Alan Fox,
Only when you ignore the genetic and chromosomal evidence against a single origin event. The contradictory evidence against a single origin event is unequivocal until a reproductive mechanism is discovered that can account for the patterns.
Common descent is part of the pattern. The question is how do we access its limits.
What? This doesn’t make any sense. The fact that all living organisms share the same genetic code (with a few interesting variations) is clear support for common descent.
There is no evidence suggesting separate origins for some organisms. Common descent fits the pattern we see.
For my amusement, can Bill cite contrary evidence?
What does that sentence even mean?
Alan Fox,
The Howe Venn and the chromosome patterns. How do some deer have 70 chromosomes and others have 7. How are there thousands of unique genes between humans and mice that are supposed to be close ancestrally related mammals?
There is no mechanism associated with reproduction that explains through any model these patterns yet it is an axiom of a current scientific theory with thousands of papers based on this axiom.
Alan the question you asked here shows me you cannot see the other side of the argument. I have provided the evidence countless times and it also was part of the longest discussion here. You do not provide arguments just repeated assertions and then forget evidence that contradicts those assertions.
They’re mostly duplicate(paralogous) genes Bill. Genes that got duplicated in either lineage, independently since the split from their common ancestor.
The mechanism is the ways in which gene duplications happen. The model is standard population genetics.
This is not the case. What you have provided many times is your misinterpretation of a diagram. And no matter how many people try to explain this to you, no matter what words or illustrations or examples they provide, you WILL not see it. All I can say is, yes, you are providing evidence, but it’s not evidence of what you think it is.
This, I think, is inherent in the religious approach. Scientists can, and often do, modify or discard theories that don’t explain some important data. But religious people can’t change their claims if those claims are not based on data, but on doctrine. Even the Pope accepts common descent.
Incidentally, I enjoyed Elizabeth’s notion of a cross section of a tree. Slice a tree horizontally, well up into the branches, and what you find at the slice is lots of what appear to be independent, stand-alone branches. Select four branches, say about 10 feet from one another, and it’s easy to miss the fact that they all connect to the same tree somewhere down below.
You are referring to muntjac deer, I suppose. Why do you believe this is evidence against common descent? It most certainly isn’t
Wow what a surprise. The deer with fewer chromosomes have undergone multiple consecutive chromosomal fusion events, and scientists have even been able to map every single event, the mechanism responsible, and put them on a phylogeny.
From the legend to Figure 1:
“a Maximum likelihood tree of muntjac and outgroup species with the respective sequencing technologies (red geometries), the divergence time (blue numbers) and number of chromosome fusion or fission events (red numbers) shown. Different combinations of black arrows represent different types of chromosome fusion and fission. The 31 fusion events leading to M. crinifrons are displayed in detail with the chromosome code (black numbers) of H. inermis, which are connected with the arrow mark on the phylogenic tree with dotted lines. Red hollow circles mark the nodes whose divergence times were used as calibration for estimating the divergence time among other species.”
Bill “Always Wrong” Cole strikes again!
Bill the question you asked here shows me you cannot see the other side of the argument. I have provided the evidence countless times and it also was part of the longest discussion here. You do not provide arguments just repeated assertions and then forget evidence that contradicts those assertions.
Alan Fox,
Because there is no mechanism that explains how these changed could happen and become fixed in the various populations. Chromosome mutation events are rare and most likely deleterious.
The paper that Rum cited like you assumes all deer share a common ancestor and then creates a marked up tree with various mutations. What Rum has not posted is a population genetics model that shows feasibility of all the changes in the various deer populations.
This is the problem with the theory as the assumptions until recently were never questioned.
Bill they are showing directly, in the paper, where the fusions occurred on the chromosomes. They leave the direct genetic analogoue to footprints in mud behind. This isn’t an “assumption.”
“We further identified the putative orientation of centromeres’ positions in the acrocentric chromosome preserved in H. inermis and M. reevesi (Supplementary Fig. 8). A fusion event was defined as tandem fusion if it connected the apical centromeres of one ancestral chromosomes and the distal telomere of another ancestral chromosome, and a fusion event was defined as Robertsonian fusion if it connected the apical centromeres of two ancestral chromosomes. Based on the centromeres’ position and chromosomal synteny, in the female M. crinifrons we identified 28 tandem fusion events and 3 Robertsonian fusion events derived from the 2n = 70 ancestral karyotype (Fig. 1a and Supplementary Table 7). Combined with published cytological results21,38,39, we determined occurrence order of the 31 fusion events along the phylogenetic tree from the common ancestor node of five muntjacs to the M. crinifrons (Supplementary Fig. 9), and estimated the rate of chromosome fusions as 8.20~8.52 events per million years among the M. muntjak vaginalis, M. gongshanensis and M. crinifrons after they diverged from M. reevesi (Fig. 1a and Supplementary Fig. 9).”
And then there’s the fact that the origins of these fusions coincides with a large drop in population size (reducing the effect of selection, which also means the effect of negative selection against putatively deleterious mutations) during a glaciation event:
“Demographic history of muntjac deer
We reconstructed the temporal changes of the historical population size of muntjac deer and related species. The results showed that the M. muntjak vaginalis, M. gongshanensis, and M. crinifrons with reduced chromosome number underwent a striking decline of population size about 1~2 Mya when they diverged with each other (Fig. 1b). However, such a population decline during this period was not detected in M. reevesi and two nonmuntjac deer species (Supplementary Fig. 7 and Supplementary Table 6), as well as in other previously investigated ruminants32. This time window overlaps with the Xixiabangma glaciation (XG) occurred 0.8-1.17 Mya in the area of the Hengduan mountain and its surroundings36, where M. reevesi, M. muntjak vaginalis and M. gongshanensis are now distributed (Fig. 1c). We proposed a hypothesis that genetic drift associated with the geographic isolation facilitated by XG might have facilitated the fixation of extensive chromosome fusions in M. muntjak vaginalis, M. crinifrons, and M. gongshanensis during or after their divergence from M. reevesi. It is noteworthy that this hypothesis still needs more data, such as more population data in the future, due to the reduced reliability of demographic inference of PSMC method at 1 Mya37.”
What I’d like to know is, where did Bill hear about these deer in the first place? I certainly had never heard of them, but I learned that they are small deer found in Southeast Asia. I have spent quite a bit of time in Southeast Asia, but was still not aware there were such animals, much less aware of their chromosomes!
I may be wrong, but it certainly smells like Bill is regurgitating stuff he has found on creationist sites, doesn’t understand what he reads, and certainly isn’t in danger of stumbling across a coherent biological explanation for anything like this (which would never be presented on creationist sites).
Bill’s grasp of biology seems essentially similar to the grasp of politics by people who listen to nothing but Fox News. All spin and lies all the time.
I knew of muntjac deer because they are an introduced species in UK and it was quite common to catch them in headlights crossing quiet roads at night. I didn’t know about the chromosome fusions (or that there were more than one species of muntjac) until Bill’s comment. Fact-checking Bill’s claims is a prerequisite to discussing them.
The iconic chromosome fusion event is coincident with speciation of humans from chimpanzees.
Unless you are Jeffrey Tompkins. 🧐🥴😄
I much appreciate your calm and detailed debunking of Bill’s claims. 👍
Might have known that this would have already come up at Peaceful Science.
In chapter 18 of “Organisms and their Evolution”, Teleology and Evolution, Stephen Talbott writes:
This way of considering evolution is consistent with the views of the likes of Blake, Goethe and others. and from whom I have learned to contemplate on the phrase I have oft repeated, “the whole reflected in the parts”.
I contend that the evolution of the animal kingdom is at the same time an evolution of consciousness. I see our development from egg to adult as an unfolding of consciousness at the level of the individual organism. And this I see happening at a higher level when viewing evolution as a whole. The parts are governed by the whole. Is this not at least worth considering?
CharlieM, Talbott (a third-wayer and computer engineer) gets more wrong than he gets right in that chapter. I found his polemic against Michael Ruse amusing.
Rumraket,
The paper is based on common descent as an axiom. This is assuming your conclusion. What is it about deer chromosomes that could create this much variation where we do not see it in other mammals?
Alan Fox,
So what claim specifically do you think was debunked? Do you see that the tree diagram was based on using common descent as an axiom?
Alan do you realize you are missing basic errors in logic on Rums part? You need to be careful when using the word debunked.
Do you define debunked is when Alan Fox believes some argument to be true?
Are you claiming to be the final judge of truth on this site?
Rumraket,
How would so many duplications get fixed in the population? How would thousands of duplicated genes find different function given reasonable population genetic models?
Nonsense. The hypothesis of common descent is supported by the evidence.
No. Science is about building and testing models. The model of common descent is a very good fit to the evidence. There’s no true or false, there’s just models that become less inaccurate.
Duplication events don’t appear to be rare when looked for. And in a population of sexually reproducing organisms, these events happen in parallel and come together in recombination.
Genes are not searching for anything. A particular genome will result in a phenotype that is either more or less successful in leaving progeny than its peers in the niche environment.
Alan Fox,
It is also contradicted by the evidence. Perhaps it exists to a limited extent inside certain populations. The paper is based on the assumption that all deer share a common ancestor. The large variation in chromosome counts is a powerful challenge to what we all considered true prior to this revelation.
Its important to keep an open mind given the quantity of data high frequency sequencing is bringing to the party.
Do you think it’s possible that you are mistaken? Others here accept common descent because it fits the evidence, and if something else fit better, others would accept that. They do not NEED common ancestry to be true, but you NEED it to be false. So others consider all the evidence to see where it leads, while you search for bits and pieces you can carefully misinterpret to support a doctrine you NEED to be true. And by now, you have made it undeniably clear that your need is based on religious requirements, not on science at all. But I wonder if you can even see this, even in the bowels of Christ.
Which is?
Chromosome fusion explains the variation in number and sequence comparison provides the evidence that the fused chromosomes are homologous.