Does Jim Stump think PNAS supports geocentrism?

“He puzzled and puzzled ’till his puzzler was sore.”

Jim Stump, senior editor over at BioLogos, made some interesting claims on facebook this week. Trying to convince yet another ID proponent to fully commit to organic evolution,[1] he asserted that

“Common ancestry is a multiply confirmed theory that explains the observable data in detail. So asking what kind of evidence would contradict that is about like asking what kind of evidence would it take for you to accept geocentrism.”

While this makes for good rhetoric, you’ll struggle to find modern astronomers who publish on geocentrism. However, you will find a large and growing number of biologists who question universal common ancestry (UCA).

The idea that there may have been multiple origins of life was even offered by Darwin, when he wrote, “There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one…” And it hasn’t gone away. In 1983, in PNAS, Raup and Valentine published Multiple Origins of Life, and argued for just that. So apparently, these two biologists published something tantamount to geocentrism…in one of the biggest journals in the world. This should be the first indicator that Stump’s statement might be hyperbole.

But, Stump went on to double down on his allegiance to UCA, cavalierly offering,

“The fossil record continues to be uncovered, and continues to show more and more what you expect to see if common descent is true. At all of the major transitions, there are intermediates found in just the right places.”

This would be a surprise to most in the industry. For example, the man considered to be the 20th century’s Darwin (Ernst Mayr), in his 2002 book What Evolution Is, said of the Cambrian fauna, “Almost all of these phyla appeared seemingly full-fledged…No fossil intermediates between them have been found and no living intermediates are in existence.” Time has not relieved evolutionary theory of this burden, but has further substantiated it.

Haldane once said that, if you wanted to convince him that evolution (however we’re defining that) was wrong, show him a rabbit in the pre-Cambrian. We haven’t done that, but since his time, we have discovered several vertebrate forms from both the agnatha and the gnathastomes (primitive sharks) in the early Cambrian (alongside the first sea cucumbers, crustaceans and flatworms, to name a few). This likely wouldn’t persuade the loyalist. But the fact remains that we find 30 phyla and 50 classes of animals emerging on the scene in a narrow span of geologic time (Erwin and Valentine have pegged it at a 5-8 million year window). Hardly what you’d expect if common descent was true, and definitely not the plenitude of transitional fossils we’d anticipate.

It’s true that the prevailing theory has been UCA. It’s only been in the past 30-40 years that data have suggested otherwise, and change is slow. But, slow or not, change is coming.

Let’s return to the Cambrian discussion for a moment. The situation is so bad that, just this year, a large research team (33 researchers from 23 different labs around the world) published a paper in Progress in Biophysics and Molecular Biology. In it, they attempted to explain the Cambrian by cosmic panspermia:

“Life may have been seeded here on Earth … bacteria, viruses, more complex eukaryotic cells, fertilised ova and seeds have been continuously delivered ever since to Earth…”

By “ova” they’re actually talking about cephalopods. That’s interesting, because the phylum Mollusca (which contains the Cephalopoda) has long been problematic. In fact, clear back in Darwin’s day, Huxley suggested HAM (the Hypothetical Ancestral Mollusk), because no common ancestor to the mollusks was forthcoming. And it hasn’t come as of 2018. In fact, a recent study by Lindberg and Chiselin found that,

“Our best approximation of the phylogeny of HAM (based on known ancestor-descendant relationships and stratigraphy) requires 53 more steps than the most parsimonious tree found by cladistic analysis. The evolution of HAM exhibits all the typical process-es and developmental heterochronies thought to encompass organic morphological evolution, and both phenetic analysis and cladistic analyses have problems relating paedomorphic taxa. HAM has not aided evolutionary biologists or paleontologists in solving problems, but it has often had the opposite effect, by requiring that theories be treated within its framework… Unfortunately, these imaginary animals do not come clearly labeled with warnings about the harm that they might do if mistaken for real organisms.”

Again, contra Stump’s original claim, this is exactly what you wouldn’t expect if UCA was true.

Many scientists today doubt UCA.

Ford Doolittle (from the National Center for Biotechnology Information) has. Rokas and Carroll have as well. Craig Venter has probably sequenced more genomes than any man alive. At an origins of life panel discussion he recently said,

“I’m not so sanguine as some of my colleagues here, that there’s only one life form on this planet . . . The tree of life is an artifact of some early scientific studies that aren’t really holding up. . . . there may be a bush of life.”

The discussion got more lively when Paul Davies chirped up,

Davies: “Well, I’ve got the same genetic code, ‘We’ll have a common ancestor.’”

Venter: “You don’t have the same genetic code. In fact, the Mycoplasmas [a group of bacteria Venter and his team have used to engineer synthetic chromosomes] use a different genetic code that would not work in your cells. So there are a lot of variations on the theme…”

You see, the national database for genetic information (at NCBI) currently identifies more than 20 different DNA codes used by various organisms. Not what you’d expect on UCA.

Even as an atheist, I thought this might be the case. If life can evolve once, then we should expect it could evolve multiple times. If that’s true, why should we force the data to coalesce on one original life form? It’s just the way we rigged the game. (see also:…/mg20126921.600-why…/)

And fossils are not where they always ought to be. In fact, another little report from just this year (out of the Royal Society of London), found the so-called “walking dead” (accumulations of fossils in mixed groupings due to movement of rock and sediment post-mortem), sufficient to distort our understanding of extinctions events of the past! We still don’t know the relationships between the tetrapods for crying out loud!

Stump continued,

“And remember that fossils are just one piece of the puzzle. Now genetics allows us to construct family trees of species in remarkable detail. That genetic evidence could have contradicted common ancestry, but it absolutely confirms it. Again, you can always say God created things separately but made them look like they were related… but how long can you keep that argument up?”[2]

ORLY? Again, that’s news to many in the field.

To quote Dávalos et al.,

“Incongruence among phylogenies estimated from different sets of characters is pervasive. Phylogenetic conflict has become a more acute problem with the advent of genome-scale data sets. These large data sets have confirmed that phylogenetic conflict is common, and frequently the norm rather than the exception.”

Antonis Rokas has been deeply involved in the study genes and phylogenies. In a 2005, he and his colleagues admitted, even “a 50-gene data matrix does not resolve relationships among most metazoan phyla.” The metazoans are all multicellular animals (save for sponges). The more genetic code we look at, the worse things get. Point-and-case, in a recent meta-analysis dealing with “bushes” in our tree of life, Rokas and Carroll (2006) decided to omit 35 percent of the single genes from the data matrix because, “those genes produced phylogenies at odds with conventional wisdom.” (see also and, as two more examples.)

While this post isn’t about the monkeys to man hypothesis, Stump did bring that up as well. It’s very important that our primate ancestors don’t get triggered by the blasphemy of suggesting we may not have descended from them after all. Founder of BioLogos (and renown scientist), Francis Collins, put his foot down back in 2006, writing,

“Darwin’s theory predicts that mutations that do not affect function (namely, those located in ‘junk DNA’) will accumulate steadily over time… That is exactly what is observed…If, as some might argue, these genomes were created by individual acts of creation, why would this particular feature appear?”

In other words, if evolution and UCA was true, our genome should be littered with the remnants of failed and derelict DNA, no longer serving any function. So called “junk DNA” was thought to make up about 97% of our genome at that time. Collins made it clear that this was a very testable prediction. If junk is plentiful, it supports evolutionary theory. If it is not, it would be a strong support of ID theory.

Six years later, a massive (and I mean massive) consortium of researchers from around the world published their work on the ENCODE project in the journal Nature.

Their major finding?

“These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions.”

This shook everyone. Famed molecular biologist Dan Graur wrote,

“If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome… If ENCODE is right, then evolution is wrong.”

He then promptly walked it back, first suggesting that we might be able to accommodate up to 10% functionality in the genome while retaining the basic evolutionary model, and then 25%.

Unfortunately for Graur, the needle has kept moving. A study from this year now suggests that 95% of the human genome is under selection (meaning it has some functional role in fitness).

Meanwhile, if Stump actually reads the scientific literature he touts, he must have been shocked earlier this year, when biologists completed a full re-work of several great ape genomes. This was important for many reasons. First, as the authors conceded, the first chimp genome project was heavily biased. There was actually human DNA contamination in roughly 40% of the labs doing the work. Additionally, the human genome was used as a scaffold for assembling the chimp genome (i.e., they were literally matching DNA segments from the chimp genome to the existing human genome sequences). In this new attempt, the controls were much better, and there was no explicit comparison of the primate genomes to any existing human genomes. As such, Richard Bugg, professor of evolutionary genomics at the University of London, decided to do the comparison, and found that, “The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 84.38%” (a far cry from the presumed 98% similarity between chimps and humans). What’s really scary is that this is almost exactly the degree of similarity predicted by Jeffrey Tomkins, a young earth creationist scientist! BioLogians may have to lay down for that one. Again, clearly not what we would predict under Darwinian evolution and UCA.

So, in the holiday spirit, and lift a quote from Dr. Seuss, “He puzzled and puzzled ’till his puzzler was sore. Then the theistic evolutionist thought of something he hadn’t before. What if evolution, he thought, was a little bit more.”

[1] This is an unsettling pattern with BioLogos. (see here for an example:

[2] Note that Stump equates the scientific hypothesis of multiple origins to some kind of god-of-the-gaps argument, and this shows his true fear, which is not scientific, but theological


9 thoughts on “Does Jim Stump think PNAS supports geocentrism?”

  1. Been a while Wayne. Your quote about Buggs and Thomkins is disturbingly inaccurate. You know that these were flawed analyses right? You are a biologist. You should know better there. Ever thought about doing the analysis yourself? We can show you how.


  2. Do you accept the rest of my post? That is, that the first primate genome contained both human contamination, and was built using the human genome as a scaffold? What do you think of ENCODE, and the more recent papers suggesting that selection is working on most of the genome?


    1. The first primate genome did contain human contamination, and was built using the human genome as a scaffold. The current genomes are not. We can test the effect of this, and it is tiny. That is just a red herring.

      The interpretation of ENCODE does not match that of most biologists I know, those of us that are doing scientific work on a regular basis. I’m sure you know that too. I wonder if it you know why.


      1. Joshua, I just want to point out a few things. First, I want to point out that you haven’t really engaged the bulk of this post. The major (MAJOR) point was that Jim Stump was trying to bully a high school physics teacher, and suggested that anyone questioning universal common descent was equivalent to a geocentrist. I provided reputable scientists, writing in reputable journals, questioning this assumption. His broad and sanguine claim regarding the fossil record was also false. And pretty much everybody in the field knows it. Note, this does not mean that macroevolutionary processes have not been at work. Just that Stump was very lazy and frankly incorrect in his rendering of the situation. You’ve decided not to engage about 90% of my post. Instead, you focused on the very end, in which I deal with human genomes. My point there (and you seem to side with evolutionists on this) is that, if ENCODE is remotely close to true, evolutionary theory falls apart. The junk DNA story NEEDS to be true on current evolutionary theory. I don’t know exactly who you are referring to when you say, “ENCODE does not match that of most biologists I know.” I don’t doubt that. Nonetheless, you must agree that the general trend over the past 15 years or so has been to find functionality where it wasn’t thought to exist. Here are few quick examples, broadly supporting the ENCODE view:

        Again, with the elucidation of Gene Regulatory Networks, and the vast assemblages of non-coding genome features that play into expression, editing and post-translational modification, you must admit, the move has been towards increased functionality. Even Collins has backtracked from his statements about junk DNA.

        As for the ape-human genome comparisons, I contacted Dr. Buggs about his analysis. Remember, his 84.3% value is a simple nucleotide-to-nucleotide comparison. Still, he has gone round and round with BioLogos people about it, and people can track that down here (I know you have Joshua):

        It’s also worth mentioning that Buggs fully admits that his analysis doesn’t involved genomic structure and higher-order organization (which he believes would create further distance between the primate and human genomes). Now, you jumped to the idea that I’m arguing for a non-primate (de novo) origin of Homo sapiens. I never said that. I simply said that the data have pushed us further away than classical (Darwinian) models of evolution can accept, given only 3 million years of divergence time.


      2. I’m not here to defend Jim. I don’t know that situation, and wouldn’t be surprised one way or another. So yes, I did not engage that part of the post. No endorsement or dispute from me there. Regarding the genome similarity, there have been many revisions of the number, and Dr. Bugg’s estimate I’m familiar with, and followed that exchange. His esitmate lacked proper controls and wildly under estimates similarity. That fact still remains.


      3. Im not jumping to an idea of de Novo ceeation. I’m just surprised that a biologist such as yourself would accept extraordinary claims about chimp-human similarity, without verifying them yourself or asking for appropriate controls. If we aren’t working from the same set of facts, with they are this straight forward, conversation will be…difficult?


      4. On last point. ENCODE isn’t remotely true, it is totally true. It is good data, being badly misinterpreted by people that forgot about neutral theory. It challenges Darwinism, sure, but it doesn’t challenge neutral or near neutral theory.


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