Merry Christmas, if you’re into that sort of thing!

CNN is saying 16 dead. The arrested suspect is one Nikolas Cruz, 19 years old. He was reportedly banned from the school last year for making threats, and seemed to be obsessed with guns.

@weirwood: Well, that didn’t take long. Are there wingnuts claiming it’s fake yet?

And I bet Wayne La Pierre could drive a railroad spike through a 2×4 with his erection right now.

Alex Jones (may something karmically appropriate happen to him soon) is reportedly shouting his usual drivel.’

ETA: Link that doesn’t give Alex Jones any hits:

https://www.mediamatters.org/video/2018/02/14/alex-jones-florida-high-school-shooting-it-may-be-false-flag-and-democrats-are-suspects/219370

Ugh. Just… Ugh. -_-

Well, uhm, if anybody wants some good (or at least distracting) news… Pixar’s finally released a trailer for Incredibles 2, and it’s looking to play with gender roles the way the original played with superhero tropes. Needless to say, the babymen have already broken out the pitchforks and I’ve already broken out the popcorn.

@SFHC

The Incredibles is close to my heart, being the second film I really got into (after Star Wars). To date, it is the only work of media for which I have ever drawn fanart.

one of the people I went to school with was a son of one of the hereditary chiefs, who was also a fairly famous woodcarver and associated with the Royal B.C. Museum.

Ooh, who? I’m afraid the only West coast woodcarvers I know anything about are Bill Reid and Charles Edenshaw.

@WWTH: that video link does not work. Please reupload, or find another copy whose uploader isn’t pulling stupid geo-blocking shenanigans.

Would a big reply to Surplus to Requirements about the Life Before Earth paper be better later? I’m unsure of the contrast with the discussion about the shooting. No particular reason I just feel like I should check.

@Surplus to Requirements
My apologies for how long this took. My head has been a mess. It helps to be able to explain what I’m studying though. It forces me to put it into a solid form.

Re: “Life Before Earth”
Full disclosure, in the “sides” present in the field of abiogenesis of life I am “metabolism first” with respect to that or genomes coming first, and “RNA first” with respect to that or DNA genomes. I love that they had the guts to be so objective, but they need to add a lot of features to their definition of genetic and biological complexity. They omit all of biochemistry, molecular biology, and cellular biology except for the length genomic storage molecule. The overall logical structure is fine, I give them credit for having a tool with potential use. Now they need to add the rest of the mess, which has an order.

From the paper.
Function: “Function can be defined as a reproducible sequence of actions of organisms that satisfies specific
needs or helps to achieve vital goals (e.g., capturing a resource or reproduction)”.

Ok. I can work with that.

Genetic complexity:”the length of functional and non-
redundant DNA sequence”

No. This is only a part of an organism. A part that society likes to grab onto since it’s so easy to objectify and hyper-focus on DNA.
This is only the size of a part of cellular life as we know it. It includes nothing of the organism expressed from that DNA but “functional” as a placeholder and I’m comfortable suggesting that length of genome is than 1 percent of the functions that can be usefully described. I will not trust their time estimates based on overall numbers of nucleotides. (I will admit that I forgot about the millions of years old bacterial spores though, whatever a spore is has something worth investigating with respect to genome integrity. The interstellar journey would involve different conditions and longer times).

They can add to it, otherwise panspermia is still hypothesis in a general sense of not being disproven. A concept that challenges their definitions and shows the assumptions is selective pressure on genome size. Why are genomes as big as they are?
http://jvi.asm.org/content/74/6/2647/F3.large.jpg
Was the viroid only a hydrogen atom back then? I’m joking but the fact remains that there is a whole library of chemistry to measure against time.

We don’t need everything to start finding useful patterns that are suggestive of the nature of the past, but we do need more than their hypothesis and framework currently accounts for.

With respect to your previous comments when it comes to the existing evidence I have to emphasize that the evidence is samples of debris collected by zircons condensing out of cooling magma. In that evidence we are only talking about carbon C12/C13 isotope proportions and the fact that biological processes that fix carbon have a bias for the C12 over the C13. We can say that we see isotope ratios consistent with biological carbon fixation. But life is doing more than taking inorganic carbon (CO2, CH4, CO, HCO3…) and using it to make things.
https://en.wikipedia.org/wiki/Isotopic_signature#Carbon_isotopes
https://en.wikipedia.org/wiki/Carbon_fixation
(I’m investigating the reverse TCA cycle as an ancient carbon fixation mechanism re:LUCA)
EC numbers scattered in Wikipedia’s pages refer to the “Enzyme Commission number”, in a system that attempts to organize enzyme chemistry rationally. A system very useful to us here.
https://en.wikipedia.org/wiki/Enzyme_Commission_number (This is data for a definition of functional biological complexity and the rest of my comment will hopefully show how).

I point out that the bond formed between the deoxyribonucleotide-triphosphates in DNA is between the 5’C of Ribose and an O bound to phosphorus (phosphate, PO4). A distinct chemistry than the one picked up by the zircons. Polymerized nucleic acid can’t be placed by that evidence. I can offer you something interesting in the way that DNA is made because it’s older than the polymerase and that whole metabolism had to be there along with the finished product. The history is written in the pathways, we just need to find the connections and recognize related chemistries. Life is a kludge all the way down and you can see the layers.

A kludge or kluge (/klʌdʒ, kluːdʒ/) is a workaround or quick-and-dirty solution that is clumsy, inelegant, inefficient, difficult to extend and hard to maintain.

The evidence trail that I am following involves asking where the DNA comes from in terms of metabolism, which means asking where the RNA came from because DNA is made from RNA. The bases are synthesized on a phospho-ribose, not a deoxy-ribose (the removed -OH is used in RNA self-splicing). That’s a reason why I’m “RNA first”. Not only are proteins kludges but metabolic pathways are too. Evolution takes advantage of what is present, likely chemistry. Ribose, Purines, Pyrimidines and Phosphate were all present before a replicator was useful. I believe that the story of RNA is also in the two pathways that make it (purine and pyrimidine bases). Why poly-ribose-phosphate? Why poly-ribose-purine-phosphate? Why poly-ribose-pyrimidine phosphate? Maybe genomes started as a mechanism to accumulate phosphate from seawater as life crawled from the vent? I’m investigating the “Iron-Sulfur World” hypothesis and a recent paper (linked in the news article) that argues for an ancient phosphate free core to metabolism.
http://www.cell.com/cms/attachment/2118887101/2086319312/gr1.jpg

The phosphate group, diphosphate, or triphosphate is common to nearly all of the universal pathway but a bit of de novo (“from new”, but so-called “recovery pathways” will likely be informative) pyrimidine biosynthesis, an aminated (had an -NH2 attached) bicarbonate ion (carbamate). I’m imagining a hypothetical metabolic shift from hydrothermal vent inspired sulfur chemistry to a phosphate based one with respect to nucleotide biosynthesis and lots of other carbon metabolism (pentose phosphate pathway, glycolysis…not TCA cycle). The “buisness end” of fatty-acid synthesis (-coenzyme-a), reductive (NAD) and other coenzyme chemistries inherent to these pathways is in sulfur chemistry.
Hydrothermal vents are coated in sulfur among other things as the vent systems begin and evolve.

Ribose is in that previous set as a part of the pentose phosphate pathway in metabolism. The story of ribose metabolism includes not only genome construction, but nucleotide-phosphates attached to cofactors involved in metabolic cycles across a large part of the rest of metabolism. (I see them as nucleotide-phosphate handles for simpler cofactors constructed from amino acid skeletons). For example coenzyme-a which is involved in fatty acid synthesis among other things.
https://en.wikipedia.org/wiki/File:Coenzym_A.svg
It’s made from three amino acids attached to an adenosine-diphosphate. The cysteine and it’s sulfur is the “business end”.

The bases are related to ribose and perhaps phosphate differently. Phosphoribose has purine built on it bit by bit, while pyrimidine is added as an orotate ring made from bicarbonate and aspartate.
https://en.wikipedia.org/wiki/Nucleotide#Synthesis

For Purines ribose-phosphate is first aminated (from glutamine, replacing an O), attaches a glycine, adds a formyl (HC=O), is aminated again (from glutamine replacing O again), the chain is closed into a ring, a bicarbonate is added (another C=O), an aspartate is added and fumerated is removed resulting in amination, another formyl (HC=O) is added, and then the chain is closed into a ring resulting in IMP (IMP>AMP, GMP).

https://upload.wikimedia.org/wikipedia/commons/2/25/Nucleotides_syn1.svg

Glutamine is a hypothetical cofactor for me here and in other eras simple NH2 or other source of N may have been involved since the repetition suggests evolved modularity (glutamine was abundant or synthesized). These steps may be functionally compressible into simpler pathways depending on the enzyme families (in fact some of those enzymes take glycine N/C, aspartate folic acid…), . The same goes for HC=O addition via 10F-THF where an aminated phenylalanine intermediate (pABA) grabs onto the formyl by the N contributed by glutamine which might connect single carbon and glutamine metabolism. I’m still thinking about larger meanings for ring closures and that two step amination using aspartate and making a TCA cycle intermediate fumerate. The bicarbonate may be a environmental or produced since it’s common to purine and pyrimidine pathways (bases as bicarbonate scavengers?).

For pyrimidines I previously mentioned bicarbonate as the beginning of pyrimidines that is aminated, phosphorylated, combined with aspartate, which is then closed into a ring, and oxided into orotate (C-C>C=C). Orotate is then added to ribose-phosphate to make OMP (OMP>UMP>CMP,TMP).
So purines began potentially ribose dependant and pyrimidines ribose independent. Orotate could have had a separate job prior to purines. I’m still thinking about the aspartate which also connects the two pathways as an N donor in purines and a backbone in pyrimidines the way glycine is in purines. That oxidation is also interesting as it involved a bunch of cofactors one of which uses riboflavin (GTP+ribulose-phosphate).

I believe that the order of synthesis is significant as uridine comes first and is turned into cytosine and thymidine. Perhaps the genetic code involves the evolution of this pathway beyond U to C/T and maybe beyond I to A/G since you can find I in rRNA and other RNA.
The ribose may have come first followed by orotate binding which gave Inosine and purines the chance to evolve. Finally at this point we have the start of a path that would allow for double stranded DNA (the modifications that follow OMP and IMP). Evolution and phosphate accumulation may have been related, or not as I’m still unsure where to place a putative phosphate metabolic shift relative to this whole process.
There’s a story here that looks like it involves layers of metabolic chemistry being added over time. Functional complexity that happened regardless of planet of origin.

I hope this has been informative.