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| Fig. 1 Editor at MyMachine Dot Org |
I. Background
A little over a decade ago in the "Weekend Rebel Science Excursion" series on Dredd Blog, the following was pointed out:
That is because, in today's post, I am going to talk about Abiology, a subject that is not yet in some of our parent's dictionaries.
Abiology is an area of science that is like Rodney "I don't get no respect" Dangerfield when it comes to the entirety of evolution.
Regular readers know that in various and sundry posts on the Dredd Blog System we have bemoaned the dearth of research within evolutionary circles concerning the subject of abiotic evolution or Abiology."
(Weekend Rebel Science Excursion - 27, Jan 2014). That subject matter was followed up by The New Paradigm: The Physical Universe Is Mostly Machine, 2, 3 , and Did Abiotic Intelligence Precede Biotic Intelligence? and many others ... but the one to "take the cake" was probably Small Brains Considered - 7.
II. Foreground
Since we can't have our cake and eat it too, what about "word salads"?
There has been a big bang of evidence that is knocking a lot of "word salad" dishes off the table:
"The contradictions between Big Bang theory predictions and observations are not at all limited to those that have been widely dubbed a “Crisis in Cosmology”. Despite the continuing popularity of the theory, essentially every prediction of the Big Bang theory has been increasingly contradicted by better and better data, as shown by many teams of researchers. The observations are, on the other hand, consistent with a non-expanding universe with no Big Bang. The real crisis in cosmology is that the Big Bang never happened."
(The Scientific Evidence Against The Big Bang). Both commercial science and commercial religion are like commercial storms on the stock market, which makes big bangs a 'regular' thing.
III. It's The Economy Evidence Stupid
The origin of a lot of these problems has one origin: insufficient, erroneous, or misused evidence.
Let's consider a fundamental example of conflict due to interpretation of evidence:
"I'LL BEGIN with an interesting debate that took place some years ago between Carl Sagan, the well-known astrophysicist, and Ernst Mayr, thegrand old man of American biology. They were debating the possibility of finding intelligent life elsewhere in the universe. And Sagan, speaking from the point of view of an astrophysicist, pointed out that there are innumerable planets just like ours. There is no reason they shouldn't have developed intelligent life. Mayr, from the point of view of a biologist, argued that it's very unlikely that we'll find any. And his reason was, he said, we have exactly one example: Earth. So let's take a look at Earth. And what he basically argued is that intelligence is a kind of lethal mutation ... you're just not going to find intelligent life elsewhere, and you probably won't find it here for very long either because it's just a lethal mutation ... With the environmental crisis, we're now in a situation where we can decide whether Mayr was right or not. If nothing significant is done about it, and pretty quickly, then he will have been correct: human intelligence is indeed a lethal mutation. Maybe some humans will survive, but it will be scattered and nothing like a decent existence, and we'll take a lot of the rest of the living world along with us."
Fig. 2 Word Salad: 'Parts is Parts'
(What Kind of Intelligence Is A Lethal Mutation?, religion touches upon this?). For another example, once upon a time genes were "selfish" and so that is why "people are selfish", then that idea was struck by an enlightenment bolt during an idea storm:
"Since the discovery that DNA encodes genetic information, research on the evolution of life has focused on its genetic origins. Following this “genes-first” approach, Oxford University evolutionary biologist Richard Dawkins has argued in his book The Selfish Gene that cells and organisms evolved simply as packages to ever-more efficiently protect and transmit genes.
But this genes-first point of view ignores much. All cells share three organelles, or internal structures, besides gene-containing chromosomes: ribosomes which contain the machinery for translating genetic information into the proteins that perform the cell’s work; a cell membrane that selectively permits materials in and out; and acidocalcisomes, which store and regulate the ions that drive the chemical reactions of life.
We challenge the “selfish gene” concept, proposing instead that if a cellular component is “selfish” it must be ribosomes. Cells – and DNA itself – evolved, we argue, to optimise the functioning of ribosomes. That upends everything we think we know about the evolution of cellular life and ribosomes themselves."
(Nevermind the selfish gene ribosomes are the missing link). So, on to the gene evidence and the ribosome evidence, eh?
IV. Fundamental Evidence
Both the ribosomes and genes have been considered in many posts within series here on Dredd Blog (e.g. Small Brains Considered - 11).
But the basic evidence comes from discussion and speculation about the genome sequences themselves.
So, with insufficient quality control in the processes of gathering and detailing those genome sequences, problems can spread:
"Another reason is because DNA collection and sequencing per se is not an exact discipline even in human DNA forensics.
And human DNA forensics is most demanding because it can be used to execute or imprison humans in court cases.
Notice:
'But just how accurate is DNA sequencing and its data storage techniques? What effect do these inaccuracies have on genomics and their use in pharmacogenetics?
...
Regardless of how accurate this process of sequencing may seem, through the sequencimg of the entire human genome, this yields a total of approximately 300,000 base pair errors.'
(The Ethics of Genomics, cf. Sequencing 101: understanding accuracy in DNA sequencing, Bridging the gaps in DNA sequencing)."
(On The Origin Of A Genetic Constant - 12). Today's appendices contain evidence of genome sequence accuracy and/or the lack thereof.
V. The Appendices
The vast information (I kid you not) contained in today's five appendices includes an analysis of genome sequences based on 'Abiology' mentioned in section I. Foreward above.
Those appendices contain atom counts for each organism's genome sequence.
Those five appendices are (ABC, DEFGHIJ, KLMNO, PQR, and STUVWXYZ).
The organism data in them are alphabetically listed according to the first character of the organism's name (if you want to search, use the first letter of an organism to determine the appendix to search in).
For example, the very first organism is "Abditibacteriota bacterium" appearing in the "ABC" appendix, and the very last organism is "Zymomonas mobilis" appearing in the "STUVWXYZ" appendix.
Some genomes are so large that the initial loading of the GBFF files does not contain the nucleoties (the ACGT's at the bottom of the page) so you can load them by clicking on the yellow FASTA button near the top left of the page.
VI. Table Notes: About Atoms In Nucleotides
The HTML tables in the appendices contain the following:
Link: an URL to the organism's GenBank data
Organism: The name of the organism
Nucleotide Count: the quantity of nucleotides in the sequence
'A' count: the quantity of 'A' nucleotides
'C' count: the quantity of 'C' nucleotides
'G' count: the quantity of 'G' nucleotides
'T' count: the quantity of 'T' nucleotides (DNA)
'U' count: the quantity of 'U' nucleotides (RNA)
Table Column Names:
Atom Type (carbon, hydrogen, nitrogen, or oxygen)
Atom Count quantity of each atom type
Atom Percent percent of each atom type
(Atom type Count divided by total atom count)
DNA/RNA Const the genetic constant value
Variation From Const (Atom % compared to genetic constant)
Atom Count Variation (number of atoms outside the valid number)
The analysis of each genome sequence is based on how many atoms of carbon, hydrogen, nitrogen, and oxygen is contained in a valid genome sequence of each organism featured.
That valid atom count is based on the accurate method of genetic constant calculations (Genetic Constants In DNA and RNA).
VII. Closing Comments
This discussion presents an easy-by-comparison method for a researcher or other interested person to decide if a genome sequence is valid enough to use for the particular endeavor which that researcher or other interested person is engaged in.
If the sequence is not accurate enough for that purpose, ask for a more recent/better sequence from your sources.
But, note that any inaccuracies found during the atom counts analysis can mean that the gene or protein sequences may likewise be suspect:
"The proteome is a constantly changing entity, with complexity generated at many levels. It is essential that signatures are verified as being disease related, rather than as a result of the background noise inherent in any complex system, further adding to the challenge of biomarker identification. Indeed, due to the heterogeneous nature of human beings and their diseases, a panel of biomarkers rather than a single marker may be required to achieve the high sensitivity and specificity required for clinical applications. With particular regard to oncology, most studies to date have involved patients with advanced disease, and given that genomic studies indicate that the molecular composition of early and late stage tumours can be different, the hope that these signatures will translate to early stage pre-invasive lesions where there are no reliable diagnostic tools may prove to be too simplistic".
(Proteome). The sequencing gathering techniques are improving but are not yet perfect.
Just sayin' ...
The next post in this series is here.
