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:
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.
