January 5, 2018 | David F. Coppedge

Visualize Darwin Before Looking at Data

When the evidence doesn’t fit evolutionary theory, guess what has to change?


The king is dead. Long live the king!

This contradictory set of sentences could be used to describe King Charles (Darwin). Whenever he dies, he lives long—his theory does, at least. We’ve seen Darwinism falsified so many times, it’s become routine (e.g., 11/24/12). Now, evolutionists at the University of Texas would like to forestall any upcoming falsifications that might make young trainees’ minds wander. Their method: always force-fit genetic evidence that contradicts evolutionary expectations into a “phylogenetic context.” Evolution first! That’s the new strategy, according to their paper in PNAS:

Comparisons of genome function between species are providing important insight into the evolutionary origins of diversity. Here, we show that comparative functional genomics studies can come to the wrong conclusions if they do not take the relationships of species into account and instead rely on pairwise comparisons between species, as is common practice. We reexamined two previously published studies and found problems with pairwise comparisons that draw both their original conclusions into question. One study found support for the ortholog conjecture, and the other concluded that evolution of gene expression differed in pattern and process between animal phyla vs. within animal phyla. Our results show that, to answer evolutionary questions about genome function, it is critical to consider evolutionary relationships.

By this strategy, evolution can never be falsified, because it is a given. It takes priority over data. If you just look at the data (in this case, pairwise comparisons), you might come to the mistaken conclusion that neo-Darwinism is wrong. This cannot be. The evidence must be mistaken. You see five fingers, not four.

That’s what the “Significance” paragraph of this paper seems to propose. Does it hold true in the rest of the open-access paper, “Pairwise comparisons across species are problematic when analyzing functional genomic data” by Dunn, Zapata, Munro, Siebert and Hejnol? Seems so. Look at the Abstract’s opening lines:

There is considerable interest in comparing functional genomic data across species. One goal of such work is to provide an integrated understanding of genome and phenotype evolution. Most comparative functional genomic studies have relied on multiple pairwise comparisons between species, an approach that does not incorporate information about the evolutionary relationships among species. The statistical problems that arise from not considering these relationships can lead pairwise approaches to the wrong conclusions and are a missed opportunity to learn about biology that can only be understood in an explicit phylogenetic context.

Dunn et al chastise authors of two papers for not first thinking properly about evolution, as if they had failed to recite their morning prayers. Even though those papers resulted in evolutionary conclusions, they must have been guilty of independent thinking when they used the evidence outside of the proper phylogenetic (evolutionary) context. “It will be critical to adopt phylogenetic comparative methods in future functional genomic work,” they say with a gesture of finger-wagging. Like medieval inquisitors, they admonish the questioning that only Pope Darwin, who is both Pontifex Maximus and Emperor, is capable of interpreting mysterious data rightly and without contradiction. For both papers, Dunn et al show that the proper phylogenetic methodology resolves the contradictions and rescues King Charles (blessed be he).

Phylogenetic comparative methods account for evolutionary history and explicitly model trait change along the branches of evolutionary trees. The value of these methods relative to pairwise comparisons has been repeatedly shown in analyses of other types of character data. One reason that comparative functional genomic studies have not embraced phylogenetic approaches is that there has not yet been a concrete demonstration that pairwise and phylogenetic comparative methods can lead to different results when considering functional genomic data.

Biologists must not look at evidence alone. Only by visualizing Darwin’s tree can one avoid possible semi-heretical or “potentially idiosyncratic” views, like the ortholog hypothesis. The morning ritual must include tree meditation before coming into the science lab. Then, the evolutionist is prepared to operate within “an explicit phylogenetic framework.” Dunn et al advise the cardinals to more tightly regulate what is being taught in the monasteries:

The problems that we identify with pairwise comparisons in two recent functional genomics studies indicate that there are likely to be similar problems in other studies that use these methods. Future studies that compare functional genomic data across species will be compromised if they continue to use pairwise methods. Studies of evolutionary functional genomics should not be focused on the tips of the tree using pairwise comparisons. They should explicitly delve into the tree with phylogenetic comparative methods.

Proper Tree-Thinking Illustrated

Darwin propagandist Laura Geggel of Live Science shows how to think properly about evidence. When a well-preserved fossil shark was found, she first visualized Darwin’s tree and the countless eons of time over which it developed. This sensitized her imagination so as to reach the proper state of euphoria, so that she could proclaim, “Common Ancestor of Sharks and Humans Lived 440 Million Years Ago.

Humans and sharks are incredibly different creatures, but the two shared a common ancestor 440 million years ago, a new study finds.

Researchers made the discovery by studying the fossilized bones of a shark that lived during the Devonian, a period lasting from 416 million to 358 million years ago, when four-legged animals first started colonizing land.

The evidence is beside the point. It doesn’t really matter that the shark was found with an “articulated skeleton” that was “squashed flat” and had specializations for filter feeding, including multiple kinds of teeth, similar to those in a modern basking shark. Darwinists can deal with all these details properly once they have faithfully performed the morning tree meditation exercises.  Her adviser, Michael Coates at the University of Chicago, assists her in the use of phylogenetic thinking for keeping contradictory evidence in line. “Several lineages of the earliest sharks converged on what we now recognize as classic shark-like features, such as having a long throat with multiple gill slits,” he says. Continuing, he reinforces the ancient teaching that convergence can work evolutionary miracles.

Scientists used to think that multiple gill slits were primitive, but G. adentatus shows they aren’t, he said. “These serial gill slits represent an early specialization, and, we argue, this specialization is for filter feeding, somewhat like a modern basking shark,” Coates noted.

Published with the imprimatur of Pope Charles, this article will warn readers not to just look at the evidence by itself. That might lead to a Reformation or something.

Tom Bethell, Darwin's House of Cards (2017)Recommended Resource: Tom Bethell’s myth-busting book, Darwin’s House of Cards.

When I was learning science, journal papers used to intimidate me. They were so full of incomprehensible jargon and math, they had an aura of invincibility about them. Who could penetrate the highfalutin pronouncements emanating from the towering heights of university science departments? Who could take on the National Academy of Sciences? Those huge tomes lining row after row of stacks in university libraries—how dare the common man question them?

Later, as I began to see what the Darwinians were up to, that fear turned to anger. This entry is a case in point. Sure, you have to learn a few unfamiliar words. You have to learn some philosophy of science, and reconsider what that fine word ‘evidence’ means, and what constitutes ‘scientific explanation.’ A little background in Kuhn, Feyerabend and C. S. Lewis helps. Also beneficial in your deprogramming is some study into how often scientists have been wrong and continue to be wrong. Visualizing them as ordinary fallible people and not wizards is a must. But perhaps most of all, when you understand how utterly impossible it is to explain life from chemicals and to evolve humans from bacteria, you are armed for battle. These propagandists for Darwin deserve all the reproach that truth-loving people can throw at them, because, as you have just seen, they refuse to follow evidence where it leads, but insist on force-fitting everything into their religious worldview. Richard Lewontin‘s famous faux pas is worth repeating:

It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door.

You’ve just watched an example of this in action. Are you going to join the reformation, or let this totalitarian, irrational, anti-knowledge system continue without a fight? Don’t leave for the battlefield without one of your most effective weapons: laughter. They hate that.


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