doggoes kitties open thread

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

Hope you all are having a lovely day today, whatever this day means to you (or doesn’t). Consider this an open thread, to discuss whatever, from presents to politics to cats to whatever holiday stress you might be feeling.

And here’s some stuff I found on the Twitter.

— David, who is hanging in there

2,118 replies on “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.

Dunno about the wingnuts, but really do NOT go over to the incels place. They are doing their usual (had a hell of a lot of guests there too – over 1200 when I peaked and puked).

The sheriff in the press conference said to report it if someone is posting disturbing and violent things on social media as Cruz supposedly had a number of red flaggy posts. I just had to bitterly laugh. How many times to the subjects of harassment campaigns try to report threats only to be brushed off and dismissed by law enforcement? It’s all well and good to ask the public to report, but the police have to stop writing this stuff off as trolling and only online, not real.

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.

I’m sorry to hear about the most recent school shooting. When will people let go of their love of guns? When will America toughen up its gun laws? Every time this happen my first thought is “Not another one!” and then I feel guilty for thinking it. But it keeps happening and innocent people keep dying. 🙁

My good news is old news, but I finally found a video of Mirai Nagasu’s free skate in the team figure skating competition where she became the 1st US woman and 3rd woman ever to land a triple axle in the Olympics.

I’m mostly just noting it here because although Mirai herself is not an immigrant, her parents are. So she’s one of those “chain immigration” people the right is crowing about these days. Clearly her presence here is an asset and not a harm to this country and she’s a major part of why the US team won a medal in the team event.

Snowboarding gold medalist Chloe Kim is also the daughter of immigrants.

Maybe that Fox News asshole shouldn’t have whined about the US Olympians being too gay and/or dark?

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.

You’re ahead of me. The only woodcarver I’ve ever heard of is Gepeto.

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

Tony Hunt, Sr. I went to school with one of his sons.

(If you go to the longhouse exhibit at the Royal B.C. Museum, and look in the concave section behind one of the two poles to either side of the main house, there’s a plaque or something there with his name on it. He did a lot of the work for that exhibit.)

*checks Wikipedia page* Oh, wow, didn’t realize he died just a couple of months ago.

Redsilkphoenix: Jetpack Vixen, Agent of the FemiNest Collective; Keeper of a Hell Toupee, and all-around Intergalactic Meaniesays:

Gonna leave this here, since it’s relevant to an earlier part of the thread. SF/Fantasy writer Peter David once referred to the phenomenon of entering a room and promptly forgetting why you’re there as ‘time burps’. A fuller explanation can be found in this old movie review he did ages ago for The Comic Buyer’s Guide:

@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?
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.
(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. (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.

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.
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.

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).

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.

I can’t really think of a whole lot to say here. A lot I agree with. Particularly, the penchant for evolution to layer on what it already built, without ground-up redesigns, and to “kludge” something that (often barely) works. (You don’t have to be perfect, just better than the next replicator, to outcompete it.)

One note, regarding complexity measurements: a case could likely be made that the complexity of the genome correlates with the complexity of everything else, well enough that log(total complexity) can be approximated by log(genome complexity) + constant. I don’t know if anyone explicitly made such a case, however.

Also interesting is the notion that inosine and uracil, bases found only in RNAs, might be “basal” to the other bases. Might the first replicating RNA have been binary instead of quaternary, with IU instead of ACGU, waaay back? Or perhaps it was more complex instead, hexary with ACGTUI all used…the presence of “living fossil RNAs” like rRNAs that use five of the six (ACGUI) could be evidence in favor of the latter.

On the “metabolism-first” front there is an issue: until RNA, there was no mechanism for heredity. Evolution, and arguably therefore being fully alive, couldn’t have operated yet. Autocatalytic patterns of chemical reactions taking place in some porous rock would be hard to call any more “alive” than fire is, even though (like fire) a portion could be split off and both halves grow. But without real memory. That such might have existed first, and RNA been generated as a side effect, and by random changes have come to influence the reaction cycles in turn, becoming coupled and eventually a full participant, is not implausible. Only once the RNA could be said to code for a phenotype, though, would the process cease to be a semi-random ferment and begin to show iterative selective change.

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.