May 22, 2020 | David F. Coppedge

Positive Selection Is a Myth

Evolutionists have been bluffing with math about signals of positive natural selection in the genes. They were wrong.

According to six Chinese researchers publishing in the biological preprint server bioRxiv, Darwinists have been using broken tools to measure positive natural selection (i.e., increases in fitness due to natural selection of beneficial mutations). And they have been using these broken methods for 20 years! Look what they say in “Two decades of suspect evidence for adaptive DNA-sequence evolution – Failure in consistent detection of positive selection” –

A recent study suggests that the evidence of adaptive DNA sequence evolution accumulated in the last 20 years may be suspect. The suspicion thus calls for a re-examination of the reported evidence. The two main lines of evidence are from the McDonald-Kreitman (MK) test, which compares divergence and polymorphism data, and the PAML test, which analyzes multi-species divergence data. Here, we apply these two tests concurrently on the genomic data of Drosophila [fruit flies] and Arabidopsis [a flowering plant]. To our surprise, the >100 genes identified by the two tests do not overlap beyond random expectations. The results could mean i) high false positives by either test or ii) high false-negatives by both tests due to low powers.

This cannot be true, they thought. They tried another method:

To rule out the latter, we merge every 20 – 30 genes into a “supergene”. At the supergene level, the power of detection is high, with 8% – 56% yielding adaptive signals. Nevertheless, the calls still do not overlap. Since it is unlikely that one test is largely correct and the other is mostly wrong (see Discussion), the total evidence of adaptive DNA sequence evolution should be deemed unreliable. As suggested by Chen et al., the reported evidence for positive selection may in fact be signals of fluctuating negative selection, which are handled differently by the two tests.

Proteins are coded by triplet codons of DNA “letters” A, C, T, and G.  (Illustra Media)

Surprising Results

It’s important to note that evolutionists do not usually find positive selection by looking at an organism, to see if it developed some new innovative feature, like an eye or a wing. What they do, rather, is use mathematical methods, like the ratio of non-synonymous mutations to synonymous mutations (dN/dS), to infer the action of natural selection. The thinking is that a synonymous mutation substitutes one codon for another like it, resulting in the same amino acid being coded in the translation. If there are more non-synonymous mutations (higher number in the numerator, or dN/dS > 1), they think it means that natural selection favored the new mutation by keeping it around. This gives them false comfort of providing mathematical support for natural selection. Unfortunately for evolutionists, that test and another one fail to really provide evidence for positive, progressive evolution. The tests are indistinguishable from chance – the Stuff Happens Law!

You can read the open-access paper. The authors were clearly surprised by what they found. They tried this way and that to fix the problems. They could not. They conclude that the tests are unreliable, and should no longer be trusted.

This may be the first study that compares the MK and PAML tests for the inferences of adaptive evolution on the same set of genes along the same phylogenetic branch. Many previous studies have also employed the two tests, albeit for different purposes (see Supplementary Information). It is surprising that the two widely used tests are so poorly concordant in detecting adaptively evolving genes. We examine possible explanations below.

Darwinian evolution relies on random mutations as the raw material for positive selection.  (Illustra Media)

They were surprised not only that both widely-used tests fail, but that nobody ever checked this before! As evolutionists themselves, not wanting to leave neo-Darwinist theory in tatters, they promised, “Possible paths forward on this central evolutionary issue are discussed.” So did they find any way forward? In the Discussion section, they considered four excuses for the failures. Some of the excuses are weaker than others, but none of the excuses stand up. One of the main faulty assumptions is that the rate of negative selection (i.e., elimination of deleterious genes) remains constant. That proves to be another case of a widely-used method relying on assumptions later shown to be flawed!

In the search for the signals of positive selection, the extensive literature of the last two decades has neglected the continual changes in negative selection, which often overwhelm the adaptive signals. To gauge the strength of negative selection will entail the use of polymorphism data from multiple species. Finally, an expanded framework that permits the simultaneous analyses of positive and negative selection will be necessary.

But they did not run any of these tests themselves; nor did they suggest a way to disentangle the signals of positive and negative selection. It may not be possible to do it. What do they mean by an “expanded framework”? Who knows? One thing is certain: as Zymurgy’s Law of Evolving Systems Dynamics quips, “Once you open a can of worms, the only way to re-can them is to get a bigger can.”

Bad News Overkill

This sorry conclusion needs to be added to other indications that genetics does not support neo-Darwinist theory:

  • Our Archive reprint posted 14 May 2020 reported experiments showing that epistatic interactions between mutations were always deleterious, even between two “beneficial” mutations.
  • Our Archive reprint posted 13 May 2020 reported that even if an organism adapts to higher fitness, it faces a changed environment that causes “slippage on the treadmill,” negating any progress made (like getting off the treadmill where you got on: a lot of sweat but no progress up the hill).
  • Evolution News reported another recent paper that showed how beneficial mutations cause collateral damage elsewhere. Published in PNAS, the paper by Jacob Mehlhoff et al. warned that mutations cannot be studied in isolation, but must be considered within the live organism. Every effect of collateral damage they measured—even with beneficial mutations—caused major problems, reducing the fitness of the organism.
  • Now, this new paper reported here says that even the mathematical tools used to measure “positive selection” are unreliable.

Any one of these findings considered separately is devastating to neo-Darwinian theory. Together, they cause overkill.

Antiwar activists used to say that after a point in an all-out thermonuclear war, any further explosions just make the rubble bounce. That proverb seems appropriate here after these four falsifications of neo-Darwinism. Who needs another falsification? How many show-stoppers does it take to stop a show? Just one will suffice. Take four.

Wouldn’t you love to see the look on Richard Dawkins’ face reading this headline after finishing his tea and crumpets? Smug in his easy chair, with sunshine coming through the window, he grins, having just reflected once more on what an elegant theory evolution is, allowing the gradual accumulation of favorable variations to allow organisms to climb Mt Improbable. Then he opens the morning paper and reads this article. Read this entry again while imagining his reaction.  Oh, the joy. Wouldn’t it be loverly?

Climbing Mt Improbable by slow and gradual steps, only to find that it’s not a stairway but a down escalator. (Credit: Illustra Media, Darwin’s Dilemma.)

Sadly, the global censorship of articles by Darwin skeptics ensures Dawkins will keep grinning, even though the FACTS of nature undermine his worldview. We must get the word out.


Exercise: Think of other widely-used methods in science used to draw inferences about the past, that could later prove to rest on faulty assumptions. Here’s one for starters: oxygen ratios in stalactite layers used to infer past climates.

 

 

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