Article on statistical homology review

https://www.scientificamerican.com/article/universal-common-ancestor/

i will examine this article, based on statistical analysis.

From the article:

In the 19th century, Charles Darwin went beyond others, who had proposed that there might be a common ancestor for all mammals or animals, and suggested that there was likely a common ancestor for all life on the planet—plant, animal and bacterial.
A new statistical analysis takes this assumption to the bench and finds that it not only holds water but indeed is overwhelmingly sound.
This is an article in a magazine about a statistical study of dna. It is a computer analysis, set up to measure probability based on assumptions of common descent.

Theobald was able to run rigorous statistical analyses on the amino acid sequences in 23 universally conserved proteins across the three major divisions of life (eukaryotes, bacteria and archaea). By plugging these sequences into various relational and evolutionary models,

What is being done here, is entering data from amino acid sequences into a computer model.. a program based on the assumption of descent. They project evolutionary sequences, to draw a conclusion of probability.

he found that a universal common ancestor is at least 10^2,860 more likely to have produced the modern-day protein sequence variances

Probability cannot be measured, statistically, unless you have assumptions about the data. By assuming common descent, and projecting from the simplest sequences (assumed to be the earliest in the tree of life) to the later, more complex ones, a figure can be calculated, to project probability. Details about the data and calculations are omitted.

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.

Points about this article:
1. The data, parameters, and assumptions for each computer model are not revealed or defined.

2. Conclusions ABOUT the study are trumpeted, but not the actual data and methods of calculations.

3. Flawed assumptions, that apply circular reasoning, using the premise to prove the conclusion, are present.
From the journalist:

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

This is asserted, but is an assumption that contradicts itself.. the vagaries of 'amorphous transfer of genes', is not established, is unevidenced, and assumed.

With horizontal gene transfers, genetic signatures can move swiftly between branches, quickly turning a traditional tree into a tangled web.

This is assumed and unevidenced. It is a conjecture based on the assumption of common descent. No actual data or studies have DEMONSTRATED the belief in 'horizontal gene transfer', which insinuates the 'tangled web', i.e., that genes flow easily between phylogenetic types, plugging into any organism equally. Attempts have been made for over a century, to show, by experimentation, that organisms can move from one genotype to another, without sucess.

4. The flawed conclusions by journalists, and those promoting the belief in common descent override any scrutiny as to what this study actually shows.

5. Computer models can be programmed to generate a desired outcome, and are not empirical, especially when dealing with something as vague as 'probability!'

6. The article is a cheerleading piece, singing the praises for common descent, and glossing over what was actually done, leaving it to the imagination and wishful thinking of True Believers to see, 'Evidence!', in a contrived computer model that shows probability, if you assume common descent.

7. The desperation of the True Believers, to see this as 'Evidence!', is a tragic commentary on the decline of critical thinking and skepticism. This is not evidence of anything, except the creative ability of man to deceive himself, with smoke and mirrors. There is NO EVIDENCE of 'new!' genes, chromosomes, genomic structures, or anything resembling common descent. It is conjecture and assumptions, trumpeted as 'proof!'

How is this evidence of common descent? Did anyone actually read it, with scientific scrutiny? Is confirmation bias the only thing needed to see 'proof!', in these studies?