Common Ancestry Study Examined, Part 2

This is the second part, of an examination of a 'study', purported to be 'Proof of Common Ancestry!'

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2993666/

We devised a computational experiment on a concatenated alignment of universally conserved proteins which shows that the purported demonstration of the universal common ancestry is a trivial consequence of significant sequence similarity between the analyzed proteins.

Ok.  So this is a computer model, comparing similarity of proteins.  The data is from somewhere else, and is just protein building blocks from the genomes used.  They seem to think that 'common ancestry', is a 'trivial consequence'.  Everything factual and logical seems to defy a conclusion of 'common ancestry!,' yet the conflicts are swept aside, and the mantra is merely rechanted by the True Believers.

This conclusion and assumption is unwarranted by the facts.  Any similarities of proteins, as building blocks, ARE 'trivial', and does not indicate common ancestry any more than intelligent design.

The nature and origin of this similarity are irrelevant for the prediction of "common ancestry" of by the model-comparison approach. Thus, homology (common origin) of the compared proteins remains an inference from sequence similarity rather than an independent property demonstrated by the likelihood analysis.

This is a rational conclusion, that flies in the face of the intent of the study.  The 'homologies' of the proteins..  that is, the VISUAL  similarities are merely the age old fallacy of 'Looks Like!' belief.  They reject a purely homology based 'proof', and admit that even a 'sequence similarity', is an inference for common ancestry,  based on perceptions of 'likelihood', and plausibility. 

How this is seen as 'Proof!', of common ancestry,  when they expose the flaws in 'seeing!' homology as evidence, remains a mystery of progressive Indoctrination. 

A formal demonstration of the Universal Common Ancestry hypothesis has not been achieved and is unlikely to be feasible in principle. Nevertheless, the evidence in support of this hypothesis provided by comparative genomics is overwhelming.

Amazing.  They state clearly and openly that there is NO DEMONSTRATION  of common ancestry in this study, but go on to glibly assert it as 'supported!'  The facts of homologous similarity of proteins do not compel a conclusion of common ancestry,  yet they will reaffirm belief, to fool the gullible into thinking they have 'Proved!' it with this study.

Why is 'demonstrating the universal common ancestry hypothesis,' 'unlikely to be feasable?'  Because it has been tried for over a century with no success?  Because it is a religious/philosophical BELIEF, with no corroborating scientific evidence? 

If common ancestry is a natural process,  why is demonstrating it unfeasable?  It should be easy to demonstrate the transition between organisms, the mechanism for increasing complexity,  and the abundance of transitional forms, that would indicate this constant 'evolving' of living things.

In a recent, remarkable Letter to Nature, Theobald applied an information-theoretical approach to offer just that: a formal, homology-independent test for the hypothesis of the common ancestry of the extant cellular life forms [4], a claim that is further reaffirmed in the accompanying News and Views article by Steel and Penny [5]. Following the general information theoretical framework for statistical tests of common ancestry laid out previously by Sober and Steel [6], Theobald reports a likelihood ratio test of the common ancestry hypothesis for genes represented by orthologs in the three domains of life. According to Theobald, "...when comparing a common-ancestry model to a multiple-ancestry model, the large test scores are a direct measure of the increase in our ability to accurately predict the sequence of a genealogically related protein relative to an unrelated protein." [4]. It is interesting to note that this "formal demonstration of the common ancestry of life" seems to quickly gain quite some following. Thus, the Wikipedia article on the Last Universal Ancestor quotes Theobald's study as the principal argument in support of the UCA [7].

Here the authors criticize another study, and their conclusions, that garnered much attention, and was even used in wiki to support belief in UCA (universal common ancestry).  They note, with interest, that the assertions from this study 'quickly gained quite some following,' which they would like to replace, it seems, with their own study.


We maintain, however, that the purported formal demonstration of the Universal Common Ancestry of all known cellular life forms is illusory. Indeed, in the quoted key sentence, the claim that the sequence of one of the universal proteins (e.g., a bacterial version) predicts another (e.g., the corresponding archaeal version) is simply a restatement of the fact that these proteins display a highly statistically significant sequence similarity.

So this other, more popular study, that gained quite a following, is disputed, as being just another 'similarity!' of homology proof.  Theobald's study only restated 'sequence similarity!', that these authors found 'illusory'.  But THEIR study, another computer model, will actually prove common ancestry by showing a more compelling likelihood from statistical analysis.  I hope to examine that claim next.

I realize that studies like this are difficult to wade through, to see what is actually being said.  Masked in techno babble,  and constant asserted, dogmatic 'conclusions', with no clear cut compulsion from the evidence (which is vague and often undefined), the reader can be bluffed to think, 'How sciency that sounds!  They must really be smart!'

But if you can sift through the BS, all you find are assertions and beliefs, that the facts do not compel.  Only low information bobbleheads are fooled by these bluffs.