I’m aware of all but the first one. All of them are submitted as evidence to support universal common ancestry.
The articles are commended for adding the problems with their research.
The following are the problems.
" Here we present a simplified version of this same counterexample, which can be interpreted as a tree with arbitrarily long branches, and where the UCA test fails again. We also present another case whereby any sufficiently similar alignment will favour UCA irrespective of the true independent origins for the sequences. Finally, we present a class of frequentist tests that perform better than the purportedly formal UCA test.
Conclusion
Despite claims to the contrary, we show that the counterexamples successfully detected a drawback of the original UCA test, of relying on sequence similarity. In light of our own simulations, we therefore conclude that the UCA test as originally proposed should not be trusted unless convergence has already been ruled out a priori.
Source: Infinitely long branches and an informal test of common ancestry - PMC"
This states out and out the results could be misinterpreted.
It does state that a possible alternative answer for the findings could be caused by convergent evolution.
But, wait a minute.
" Convergent evolution is the fabricated conjecture evolutionists invoke to explain very similar characteristics between creatures that could not have been inherited from a common ancestor and that evolutionists will never accept as having been produced by an intelligently designed internal programming that is specified for common purposes.
Evolutionary literature often contracts convergent evolution down to its central idea and simply calls it convergence.
The Basic Notion of Convergence Is Imaginary
It is tempting to start an evaluation of convergent evolution by identifying all its problems. This is where a word of caution is necessary. Like other key elements of evolutionary theory, convergence is not an observable process but is rather “observed” only in someone’s mind as imaginary visualization. Convergence is another evolutionary mystical, mental construct.
We should not naively proceed into matter-of-fact discussions of convergence without questioning the basic premise that such a Darwinian process truly happened. If we don’t question it, we give convergence a life of its own—just like “Liz” got her investors to hand over their money for an imaginary product and thus perpetuated the misleading of other people. It is better to begin by rejecting the idea that convergence accurately explains any historical realities and then show that fanciful narratives about convergence amount to ad hoc, just-so stories."
Source: Major Evolutionary Blunders: Convergent Evolution Is a Seductive Intellectual Swindle | The Institute for Creation Research
Now, does this mean UCA is in the clear and should e accepted as scientifically sound?
Not for a long shot.
In fact the very reason why convergent evolution is stopped for running as a possible cause, is the same reason why UCA should not be.
Because considering it to have been the cause, gives it a life of its own, without subjecting it to the scientific method.
So, where are the tests for a UCA? The macro molecule test that are found among those organisms thought to have been related, have no evidence that they are there because of common ancestry.
There is another reason why they are there. HOX genes. HOX genes, form arms of the ape, and the arms of humans.
Those HOX genes, are programmed to form those similar parts of the anatomies, but, they are programmed to express them according to the kinds of organisms in question.
And there is no reason why those similarities of the macro molecule could be an expression of the DNA, to form them without there being a common ancestor.
" "To fill this gap, two recent papers have developed formal statistical arguments for CA (Theobald 2010a; W. Timothy J. White 2013). In the first of these papers, Theobald applied likelihood ratio tests (LRT), Bayes factors, and the Akaike information criterion (AIC) to the three domains of present-day life (Archaea, Bacteria, and Eukarya) and found overwhelming evidence for universal CA. While not questioning his conclusions, several papers subsequently raised objections to Theobald’s statistical methods (Yonezawa and Hasegawa 2010; Eugene V. Koonin 2010; Yonezawa and Hasegawa 2012; de Oliveira Martins and Posada 2014). The most compelling among these objections was that the results of the tests are a trivial consequence of significant similarity among the sequences.
There are at least two ways in which sequence similarity can mislead formal statistical tests and overstate the strength of evidence in favor of CA. First, the process of sequence alignment injects gaps into the sequences to account for an unknown history of insertions and deletions along different lineages. The gaps are selected so that the aligned sequences are maximally similar subject to some constraints. If the alignment process mistakenly separates bases in different species that should be directly compared, then the strength of evidence for CA could be overstated. However, this possible source of potential overconfidence is negligible when there is little alignment uncertainty and is easily handled by excluding regions where alignment uncertainty is relatively high. A second and more serious concern is if sequence similarity were due to a biological cause other than common ancestry. Yonezawa and Hasagawa demonstrated that Theobald’s methods favored CA over SA even when comparing unrelated mitochondrial genes (cytb and nd2 from cow, deer, and hippopotomous) that were aligned without gaps by simply truncating the end of the longer sequence (Yonezawa and Hasegawa 2010). In this instance, Theobald’s methods were misled by the distinct preferences in nucleotide base composition by codon position common to all protein-coding mitochondrial genes (Theobald 2010b). In particular, nonidentical base distributions at each site contradict a key assumption underlying the likelihood model used for SA by Theobald. One can also imagine when considering a hypothesis of SA that comparable genes with similar functions in separate species could have similar sequences due to functional constraints rather than to CA. In light of all of this criticism, the community remains without a thoroughly convincing statistical method to demonstrate universal CA, whether among all domains of life or for more specific sets of species."
Source: Statistical evidence for common ancestry: New tests of universal ancestry | bioRxiv
"But in the past couple decades, new doubt has emerged in some circles. Microbiologists have gained a better understanding of genetic behavior of simple life forms, which can be much more amorphous than the typical, vertical transfer of genes from one generation to the next. The ability of microbes such as bacteria and viruses to exchange genes laterally among individuals—and even among species—changes some of the basic structural understanding of the map of evolution. With horizontal gene transfers, genetic signatures can move swiftly between branches, quickly turning a traditional tree into a tangled web. This dynamic “throws doubt on this tree of life model,” Theobald says. And “once you throw doubt on that, it kind of throws doubt on common ancestry as well.”
With the discovery of archaea as the third major domain of life—in addition to bacteria and eukaryotes—many microbiologists became more dubious of a single common ancestor across the board."
“In the course of his research, Theobald had been bumping against a common but “almost intractable evolutionary problem” in molecular biology. Many macromolecules, such as proteins, have similar three-dimensional structures but vastly different genetic sequences. The question that plagued him was: Were these similar structures examples of convergent evolution or evidence of common ancestry?”
"“I really took a step back and tried to assume as little as possible in doing this analysis,” Theobald says. He ran various statistical evolutionary models, including ones that took horizontal gene transfer into consideration and others that did not. And the models that accounted for horizontal gene transfer ended up providing the most statistical support for a universal common ancestor.
Source: RTMCDGE and "Dissent from Darwin" Petition - #63 by rtmcdge"
These are other articles that list problems the researchers were confronted with.
In all of them, one must assume common ancestry is the cause. But, when they are looking for what would support the UCA, what ever is found, must be weighed against whether or not it can be proven that it was due to an evolutionary event of some UCA.
One did mention the fact the UCA has never been identified.
And this must be the case.
The evidence, the empirical evidence, what can be supported with fact, is that humans give birth to humans. This is what the science of biology must specify this. And only when the fake science of evolution is consulted is when the POSSIBILITY of there being a UCA brought into the picture.
But, there is no empirical evidence that humans ever shared a common ancestor with any other kind of life form.
And there is no evidence that any other kind of lifeforms shared a common ancestor.
Because what is observed, is contradicting UCA.