Stairway to Understanding Hypothesis vs. Common Descent, my presentation to science students and church groups

There are numerous absurdities if one assumes common descent with no miracles, most prominent is the emergence of eukaryotes, emergence of features shared only by Eukaryotes and Archaea (a prokaryote), emergence of features shared only by Archaea and Bacteria, and features shared only between Eukaryotes and Bacteria (a prokaryote). Common descent is analogous to geocentrism of old or the pre-Snells-law problem of bent sticks in water. Ideas may look superficially right until one is confronted with multiple anomalies requiring epicycles.



For example Archaea have a different chirality in their membrane phospholipids that is different than the one shared by Eukaryotes and bacteria, the metabolic pathways for achieving this are different too. Such Taxonomically Restricted features don’t agree with common descent unless one invokes statistical miracles.

From :Structure of Prokaryotes: Bacteria and Archaea | OpenStax Biology 2e

Figure 7. Bacterial and archaeal phospholipids. Archaeal phospholipids differ from those found in Bacteria and Eukarya in two ways. First, they have branched phytanyl sidechains instead of linear ones. Second, an ether bond instead of an ester bond connects the lipid to the glycerol.

Archaea and Eukaryotes implement machinery to load and position and direct the motion of helicases in the 3’-5’ direction, wherease bacteria in the 5’-3’ direction.


Since helicase is critical to replication, monkeying with this should be selected AGAINST rather than by natural Selection (NS).

Real NS, rather than the one fantasized by Darwin, is a mechanism against evolution, not for it. This fact is belied by the fact that even evolutionary biologists claim such architectures are ancient and conserved (by natural selection!) – which means natural selection would select against deviation from a functional pattern. This relates to the problem of fitness peaks in evolutionary computing. As usual, evolutionary theory has logical incoherencies that are rarely acknowledged. There are huge laundry lists of problems that could be developed to highlight problems with common descent, and I’ve only given a couple examples.

Perhaps I’ll mention a few more. Membrane bound organelles in Eukaryotes such as Golgi and ER. Shared proteins across all domains of life would required a total reformatting and implementation of localization signals (like nuclear localization signals) to ensure the proper transport of proteins to the right location, not to mention having processing systems involving appropriate TransLOCONs to achieve this.

Or how about the problem of evolving DNA Double Strand break repair in Chromatin-based architectures from non-chromatin based architectures – the complexity boggles the mind.


It’s just nuts to represent that “phylogenetic methods” as give a statisfying mechanistic explanation for how the process of transitioning from one species to another wasn’t lethal. This is analogous to asking someone to believe a Tornado passing through a junkyard would create a functioning 747 jetliner.

I’ll be making presentations at church, internet, and various other venues regarding the topic of common descent and the patterns of similarity and diversity in biology.
The question arises why there is an approximate nested-hierarchy (actually there are overlapping nested hierarchieS that are taxonomic rather than phylogenetic) and why there are creatures like chimps that are so similar to humans. Why would God make this pattern when God could, hypothetically make humans only and no other creatures. In such a hypothetical “humans only world” one might presume there was no common descent, but an act of special creation. Of course, in such a scenario, someone could claim there were transitionals that just got erased, just like evolutionists pretty much do today!

The answer I suggest for the nested and other patterns in biology is that there is biology is designed to provide a stairway, a means for understanding biology. The first part of this is showing common descent is infeasible mechanically, and would require miracles to make it feasible – at such point, it is little different than creationist theory, except evolutionary bioloigsts insist (by using non-sequitur illogic) that their phylogenetic methods prove common descent happens naturally, when in fact it takes just as many if not more miracles to make common descent happen.

The second part is considering how hard it would be to do biology if there were only humans and no other creatures that had shared features like the same genetic code.

Consider what we would have to do if there were no other creatures than humans. We would have to dissect each other to understand the operation of our own organs. Instead we can dissect pigs because we share similarity with pigs:

We can study invertebrates like C. Elegans and Drosophilla to study vertebrates like humans. We can study yeast to understand the chromatin/histone code of humans. We can study simpler transcription and translation and regulatory systems in bacteria that make it possible to understand far mor complex systems in humans that involve layers of complexity, especially in cell-specific regulation. We can study the giant axon in squid neurons to understand the function of human neurons. So in practice, to study humans, we actually study creatures NOT on the direct line (or even close to it) of supposed ancestry.

In practice, UNwittingly, the scientific community uses the Stariway of Understanding to understand human biology rather than common descent. And there are also practical problems where we have to bypass common descent anyway because of the problem illustrated in this pan-genome diagram:

Finally, it appears we are getting to the point cross-species gene/proteing sequence comparisons are making it possible facilitate structural biology.

Think about how much harder it would be, for example, if there were no patterns of sequence diversity among the same basic protein – it would be hard to identify catalytic or other structurally important residues using alignment techniques such as CLUSTAL and MUSCLE such as the catalytic motif of Serine-X-X-Lysine motif in this paper I co-authored with John Sanford regarding the beta-lactamase NylB family of nylonases.


And there are more bioinformatic tools on the horizon…such as this one by Kirk Durston:

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring

As hinted above with Eukaryotes, Archaea, and Bacteria, one could actually make overlapping nested hierarchies. For example we could divide the groups according to helicase processing rather than the traditional categorizations. From a design perspective, to the extent it helps us carry out investigations in the lab, this perfectly fine and may lead to better understanding of structure and function in the end.

The idea of designed paralogs becomes more inviting as well. We can take Topoisomerase II-alpha and II-beta from humans and put them in yeast, and the yeast are ok, but the reverse will fail based on the paralog knockout experiments on human cells. This pattern of a Stairway of understanding from simple to complex make sense of the data, but doesn’t make sense in terms of natural selection. Same for the evolution of microubules involving at least 3 major paralogs. Evolutionary biologists had to invoke absurd epicycles of miraculous simultatneous gene-fusion and co-evolution to account of the pattern. Similar absurdities emerge with patterns involving zinc finger proteins and assuming phylogeny based on duplication mechanisms.

That is a logical fallacy known as the argument from incredulity.

You haven’t shown that there has been a deviation from a functional pattern.

When you make a claim, produce some evidence to back it.

How is that a problem? Do you have anything else other than incredulity?

The problem is your denial of the transitionals we have found:

There is no problem. Lineage specific gene loss is expected. Noise is expected. What you ignore is the signal.

Argument from incredulity.


Pure cargo-cult science on display here. Lots of vacuous claims, lots of pretty graphics, almost no sense made. Almost every sentence in the OP is either somehow confused or misleading.

Take this very first section as an example:

Hey, I wonder why biologists think eukaryotes are the result of endosymbiosis between an archaeon and a bacterium. That would explain the archaeal and bacterial attributes. And then the merger of the two led to the selective pressures that drove the evolution of eukaryotic features such as the nucleus. But, you know, one would have to read books to learn more. I highly recommend Nick Lane’s The Vital Question on endosymbiosis and the evolution of eukaryotes.

Sal is looking at a node in a phylogenetic tree, and then declaring that the fact that attribute X is shared by all members on one side of the bifurcation, while all members on the other side share attribute Y, is somehow evidence against their being related. That’s like saying I can’t be related to a person with brown eyes because you’ve found a heritable attribute we don’t have in common. Obviously, obviously that doesn’t follow.

I don’t have the patience to sit through the rest of that laughable nonsense.


On bacterial vs archaeal phospholipid evolution:


You wouldn’t know a transitional if it hit you in the face

Thanks @stcordova for sharing. Even in the face of so much opposition it is important to keep educating those who have ears to hear.

I think you are reinforcing Sal’s point here. When the argument arrives at incredulity, we all know that your paradigm has already failed and it is time to invoke the proper start to all of this anyway - God.

Actually we would. But how about hitting us with about 1 million of those transitionals. Until you do that, you don’t really have a leg to stand on.

That would be a God of the Gaps fallacy. In case you forgot, an argument from incredulity is a logical fallacy. If I say I can’t believe the Sun is 93 million miles away, does the Sun suddenly get closer to Earth? Reality doesn’t conform to what we can or can’t believe.

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Your God of the gaps fallacy is a humanly devised fallacy. It only exists in your mind and in the world of logic, which is also human-based. In truth, God not only fills every gap in our knowledge, he is very source of knowledge itself. You can take your god of the gaps fallacy and go somewhere else with it.

What are we looking at here?

Oh wow are you actually starting to build your leg to stand on? What is 1 million minus 8?

I’m asking you to identify this specimen. Species? Genus? Family? Anything.

It occurs to me that the reasons you give for God to design creatures in such a way that we have apparent common descent are equally valid as reasons for God to create via actual common descent. Two comments on that: first, that those reasons don’t extend far enough to cover evidence for common descent that isn’t related to functional physiology (e.g. pseudogenes with the same mutation); and second, that real common descent actually accomplishes those goals better than merely designing in such a way that we have apparent common descent. So God actually has better reasons for creating via common descent than he does for direct creation with common-descent-like design.


Not interested. Why don’t go ahead and identify it for us since is seems to be in your private bank of knowledge and interests you far more than some of us here.

When you have to throw logic out the window, you have a problem.

Oh? Because God has to first be logical to exist?

If an argument commits fallacies then the argument is not logical. It’s a simple concept. If I said that it requires a miracle for protons and neutrons to form an atomic nucleus that is not a valid falsification of Atom theory.

Sorry, but what you describe is a scala naturae, not a tree. You have falsified your own hypothesis just by stating it.

You know that we in fact do that, right? It’s standard in medical schools, at least.

You have never responded to criticisms of your understanding of that diagram, which fits common descent much better than it fits any other hypothesis. Have you forgotten all that prior discussion, or did you just never read any of it?


Oh, one more thing. Notice how the first sentence talks about common descent without miracles and everything else removes the qualification? That’s you tacitly assuming that if there are miracles there is no common descent. Why are you allowed to do that?


Not a problem at all, and certainly not requiring of a “statistical miracle”.


Given the evidence we have, that is certainly true. It would make no sense for a designer to use a process that merely gives the appearance of evidence for common descent while actually doing independent direct creation. Given the scope and nature of that evidence, one could even say that God would have had to go out of his way to fake the evidence for common descent. I take that to be in conflict with how most theists think of God’s character.