In this article, I examine the question, “If the Last Universal Common Ancestor (LUCA) is a laundered idea, how could I discover that?”
Laundered Ideas, Predictions, and Disconfirmation Conditions
For disconfirmation conditions to be effective, one must determine and acknowledge the merit of the disconfirmation conditions, preferably before the conditions are met. If the conditions are eventually met before they are acknowledged as disconfirmation conditions, it may not be clear in that moment that one’s beliefs should be disconfirmed and the beliefs are not necessarily affected by the new evidence.
I have been talking about disconfirmation conditions because they are a powerful tool giving me a means to know the point at which I would be wrong. Since believing true ideas and not believing false ideas is a priority to me, knowing when I am wrong is a gift, because I can easily change the corresponding belief to coincide with reality. I believe if a false belief is disconfirmed, I should no longer hold that belief.
Predictions can play the role of a disconfirmation condition, yet the same problem arises if the predictions are not acknowledged as disconfirmation conditions before the predictions fail.
One makes a prediction by starting with a theory and combining it with an auxiliary theory to predict what one would expect to find or find to be true in the future, given both the theory and auxiliary theory are true. For example, one can combine the theory of Common Descent (existence of LUCA), with the auxiliary theory, that changing the genetic code is fatal. A prediction that follows is that the genetic code would not change and therefore there is a universal genetic code. If the prediction failed, meaning not all organisms use the same genetic code, it would mean the given, “both the theory and auxiliary theory are true”, is false. So predictions allow one to connect theory to disconfirmation conditions and this is why the theory of Common Descent is considered falsifiable and science.
Predictions and disconfirmation conditions can also be enumerated for laundered ideas, the difference arises in how proponents of a laundered idea respond when disconfirmation conditions are met, or predictions fail. The key to the continuity of a laundered idea is an appeal to scientific consensus rather than reason and evidence. If the laundered idea is considered scientific consensus and a prediction fails, the failed prediction combined with scientific consensus suggests the existence of an additional auxiliary theory to help explain the apparent contradiction.
Why is the hypothesis of an additional auxiliary theory problematic? It reduces the original argument to the following. Since one is not all-knowing, one cannot say that such an additional auxiliary theory does not exist, so one cannot say that the original theory and auxiliary theory are wrong. Why then, would one make the prediction in the first place? The purpose of the prediction is to allow reality to be included in the feedback loop in a method of inquiry we commonly refer to as the scientific method. How could this dismissal of a tried-and-true feedback loop persist within the scientific community, allowing a laundered idea to survive?
Perhaps the key is that a laundered idea is by definition considered scientific consensus from a variety of disciplines. Scientific consensus allows the dismissal of an intradisciplinary feedback loop, in favor of an interdisciplinary feedback loop, to appear to be the more reasonable conclusion. If one where to find a failed prediction in one’s own scientific discipline, since there is consensus between the other disciplines on the same idea, it is not unreasonable to consider one might be mistaken in some way or missing part of the bigger picture. Therefore, searching for an additional auxiliary theory to explain the apparent inconsistency would seem to be a reasonable and perhaps more reasonable course of action.
Identifying Laundered Ideas Using Intradisciplinary Disconfirmation Conditions
The broken intradisciplinary feedback loops will be the primary method of identifying laundered ideas. If the concept of scientific consensus allows laundered ideas to persist, despite continuous failed predictions, then one should be able to find examples of these contradictions or broken intradisciplinary feedback loops pervasive in the scholarly literature.
A broken intradisciplinary feedback loop can be defined as a broken feedback loop within a scientific discipline in which scientists are no longer receiving the feedback uniformly and can be classified into two groups, the deniers of the laundered idea, and the sanguine.
The denier can be defined as the scientist whose disconfirmation conditions have been acknowledged and met for the laundered idea. The denier is convinced the scientific consensus is wrong concerning the laundered idea, which is interpreted by the remaining scientists as a denial of scientific consensus.
The sanguine is defined as the scientist who agrees that the enigmatic intradisciplinary evidence against the laundered idea exists, however is optimistic or positive due to scientific consensus, that an additional auxiliary theory will be discovered to explain the enigma.
Let’s look at some concrete examples.
The primary goal of this article is to explore ways of detecting laundered ideas using LUCA as an example. The theory of Common Descent or the existence of LUCA is sometimes referred to as the tree of life concept, where all branches of the tree converge into the root of the tree, LUCA. If LUCA is a laundered idea, one can expect to find the LUCA deniers and sanguine in the scientific literature. A denier that values an extended career is unlikely to say outright that the universal tree of life is a fiction. Telling scientists in a wide variety of disciplines that their science is science fiction is a questionable career decision. Instead, deniers might opt for using softer words like “holdover” or “was far easier to envision and defend”.
"In the following we will consider this circumstance from philosophical, scientific, and epistemological perspectives, surmising that phylogeny opted for a single model as a holdover from the Modern Synthesis of evolution. It was far easier to envision and defend the concept of a universal tree of life before we had data from genomes." Prokaryotic evolution and the tree of life are two different things https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-4-34
Notice the deniers are encouraging their optimistic colleagues to give due consideration to the data itself. The denier’s need to appeal to epistemology to explain the disparity between belief and data provides further evidence that two methodological camps are emerging.
"The belief in the existence of a universal tree of life - inclusive of prokaryotes - is stronger than the evidence from genomes to support it." Prokaryotic evolution and the tree of life are two different things https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-4-34
We can also find deniers coining terms such as “tree-thinking” to refer to their sanguine colleague’s optimistic adherence to a belief in LUCA.
"Our phylogenetic analyses do not support tree-thinking. These results have important conceptual and practical implications. We argue that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading." Do orthologous gene phylogenies really support tree-thinking? https://bmcecolevol.biomedcentral.com/articles/10.1186/1471-2148-5-33
"So, are we close to having a microbial tree of life [9]? Or are we closer to rejecting a single tree as the null hypothesis for the process of microbial genome evolution [1,54]? All in all, the latter seems more likely, for if our search for the tree of life delivers the tree of one percent, then we should be searching for graphs and theories that fit the data better than a single bifurcating tree." The Tree of One Percent https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794558/
If the idea is truly laundered, the scientific discoveries contradicting the laundered idea will continue to accumulate and the expectations of the deniers and the sanguine will eventually become incompatible. At this point, the deniers will need to distinguish their methodology (the scientific method) from the sanguine (epistemology starting from scientific consensus). In microbiology, these methodologies regarding LUCA have been coined the “positivists” and “microbialists” camps, for the sanguine and deniers respectively.
“When it comes to the concept of a tree of life, there are currently two main camps. One camp, which we shall call the positivists, says that there is a tree of life, that microbial genomes are, in the main, related by a series of bifurcations, and that when we have sifted out a presumably small amount of annoying chaff (LGT), the wheat (the tree) will be there and will still our hunger for a grand and natural system [7-10]. The other camp, which we will call the microbialists, says that LGT is just as natural among prokaryotes as is point mutation, and that furthermore, it has occurred throughout microbial history.” The Tree of One Percent https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794558/
The authors highlight the problem of the data conflicting with a preconceived notion and points to an interdisciplinary feedback loop, specifically, as the reason for this separation into intradisciplinary conceptual camps.
“Evolutionary biologists like to think in terms of trees. Since Darwin, biologists have envisaged phylogeny as a tree-like process of lineage splittings. But Darwin was not concerned with the evolution of microbes, where lateral gene transfer (LGT; a distinctly non-treelike process) is an important mechanism of natural variation, as prokaryotic genome sequences attest [1-4].“ The Tree of One Percent https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794558/
This separation of individual scientific disciplines into distinct camps regarding LUCA specifically due to an interdisciplinary feedback loop, indicates a broken intradisciplinary feedback loop in relation to the concept of LUCA and suggests that LUCA is a laundered idea.
Identifying Laundered Ideas By Market Value
Once intradisciplinary camps have been established for and against an idea, the methodologies of the two camps will begin to produce different results, providing the most potent test for whether or not the idea is indeed a laundered idea, surviving on consensus alone. The results of the sanguine can be expected to reside exclusively within academia, while the results of the deniers will reside both within and outside academia, having market value to improve existing or produce new goods and services.
The strongest evidence that LUCA is a laundered idea is that the results of the sanguine are rejected in favor of the results of the deniers by the market. When the genetic mutation rates for humans are calculated assuming Common Descent, the rates cannot be used in forensics, instead they rely on the rates from the deniers.
“Therefore, Parsons and Holland, in their work identifying 220 soldiers' remains from World War II to the present, now have new guidelines--adopted by the FBI as well—to account for a faster mutation rate.” Calibrating the Mitochondrial Clock. Science 279: 28-29. https://www.science.org/doi/abs/10.1126/science.279.5347.28
Parsons and Holland paper referenced by FBI:
P.L. Ivanov, M.J. Wadhams, R.K. Roby, M.M. Holland, V.W. Weedn, V.W., and T.J. Parsons (1996) Mitochondrial DNA sequence heteroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authenticity of the remains of Tsar Nicholas II. Nature Genetics 12:417-420.
Until 1997, the FBI used the mutation rates assumed from including a chimpanzee genome in the data used to calculate the rate.
“Phylogenetic rate estimates have historically been based on a single, external human–chimpanzee divergence calibration point at the root of the tree (Ovchinnikov et al. 2000; Tang et al. 2002; Mishmar et al. 2003; Soares et al. 2009)” Improved calibration of the human mitochondrial clock using ancient genomes. 2014. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166928/
By excluding the chimpanzee, it was discovered that the actual mutation rate was faster by an order of magnitude and the FBI updated their guidelines accordingly.
Updated FBI interpretation guidelines for mitochondrial DNA sequencing referencing Parsons and Holland (Reference #7)
In other words, the FBI rejected the results calculated by the sanguine, and have been using the reproducible results of the deniers from that moment on. However, the slower rates rejected by the FBI are still scientific consensus.
The emergence of intradisciplinary epistemological camps regarding LUCA specifically due to an interdisciplinary feedback loop, suggests broken intradisciplinary feedback loops. The market is beginning to reject the results of the sanguine in favor of the deniers. These methods appear to be good candidates for helping one discover if LUCA and other ideas are indeed laundered ideas.