Duda Jarek

Notice you can get all these protein by just copying DNA ... for minimal cells we are talking about hundreds of genes: https://www.nature.com/articles/s41586-023-06288-x - e.g. "493 genes, JCVI-syn3B". Synthesizing the central dogma + DNA, all these proteins will be created themselves ... e.g. enzymes for basic metabolism ... the hard part seem membrane structure, cytoskeleton, replication - which do you think will be technically impossible to recreate in a lab? It is said there are ~10x more bactoriophages than bacteria, coming from infected bacteria ... and this is only one of bacteria natural enemies, preventing exponential growth through e.g. Lotka–Volterra predator-prey cohabitation ... mirror bacteria will have nearly no natural enemies, with exponential growth limited nearly only by resources - taking it from other organisms, dominating succeeding ecological niches ... replacing especially higher organisms: with much slower evolution.

Mirror dogma as complete transcription/translation machinery - just chemistry, done everyday in labs, no problem to enclose it into a membrane ... so where are technical impossibilities for adding further functions like basic metabolism ... finally cell replication? The report is very detailed - if you have lots of concerns, maybe gather more skeptical biochemists and write some detailed critical answer to this report? (would gladly read) It needs sources of energy and materials, natural bacteria has adapted to mirror e.g. sugars so mirror bacteria should adapt to consume e.g. D-sugars ... but there are also lots of achiral molecules both chirality bacteria can directly consume - Table 1.1 of report: Citrate, fumarate, glycolate, glyoxylate, ɑ-ketoglutarate, pyruvate, succinate, Acetate, acetoacetate, butyrate, propionate, valerate, Medium-chain (C6–C10) fatty acids, Long-chain (≥C12) fatty acids, Butanol, ethanol, propanol, Dihydroxyacetone, ethylene glycol, galactitol, glycerol, mucate, Benzoate, m-coumarate, 2-furoate, 3-hydroxyphenylacetate, phenylacetate, phenylpropionate, phenylethylamine, γ-aminobutyrate, putrescine, γ-hydroxybutyric acid, methyl pyruvate, m-tartaric acid, Glycine, Agmatine, γ-aminobutyrate, dopamine, phenylethylamine, putrescine, spermidine, tyramine, Adenine, cytidine, thymine, uracil, Allantoin, urate. One basic question is immune response, and most of its mechanisms are chirality dependent, the report cites lots of research for various types of interactions between natural biology and enantiomers of natural biomolecules ... even if some of them would still work (the report distinguishes certain and unknown), many won't - this would be situation as in immunodeficiencies. Natural bacteria has lots of enemies starting with bacteriophages - mirror bacteria will not have. Also being different many new ecological niches will open for it - what through evolution could drastically change the ecosystem. Regarding Fermi paradox, sure there many dangers coming especially with new technologies - is there a hope our civilization will pass them for the next 10, 30, 100, 1000 years? Very serious question: how to make it more likely? If scientists will not have answers to such question, who to ask?

Like GMO? So you accept synthesizing mirror dogma is reachable (?) and further steps toward mirror bacteria (?), and now say consequences won't be that bad? (otherwise please define your uncrossable barrier on the way) So imagine such mirror bacteria got into the environment, if prepared by malicious player being able to feed on e.g. D-glucose, otherwise still consuming achiral molecules ... not having natural enemies like bacteriphages, being ignored by most immune systems, potentially toxic if consumed ... taking available ecological niches, evolving, spreading ... how do you think it would end? And we are still very early in synthetic life, which will lead to many further organisms relatively easy to create ... then practically impossible to stop spreading, evolving ... you don't see serious dangers to our civilization there? Can they be realistically overcomed? How? And what do you think about Fermi paradox: why, against statistics, we don't see advanced civilizations ... could synthetic life e.g. mirror be the reason?

From Craig Venture Institute, anyway 10-30 years could be also overstatement, and there could be e.g. malicious players paying to quickly get there ... for me it sounds very serious and dangerous, not some abstract SF story, but something really coming and nearly unavoidable (?) ... Can our civilization prevent such fate ? ("Fermi paradox explanation" in 10, 30, 100, 1000 years?) I am thinking about this question since 2007 and the most realistic way I see is another SF sounding technology - from articles observing response before impulse like https://www.scientificamerican.com/article/evidence-of-negative-time-found-in-quantum-physics-experiment/ ... as a physicists I believe in CPT theorem, which also says that causality should work in both time directions, e.g. in the action optimization or Feynman ensembles - in theory allowing for wormholes, but maybe also much more accessible ways to send just information back in time (e.g. using lasers https://arxiv.org/pdf/2409.15399 ) - if getting there, we could send back details about e.g. escaped mirror bacteria, hence physics should action optimize history of the Universe to one without such catastrophe.

I am just listening to discussion about this mirror bacteria report, somebody very serious just claimed that they are planning complete bottom-up synthesis of natural cell in a year(!), they are wondering if there should be moratorium already on mirror ribosome ... very serious, will respond later.

I have some experience in chemoinformatics (e.g. https://link.springer.com/article/10.1007/s11030-022-10589-0 predicting probability distributions of ADMET properties like cardiotoxicity) and yes - excluding various toxicities is extremely crucial and difficult part of drug design, from virtual screening to clinical trials. Some mechanisms should still work (e.g. achiral) and Chapter 5: Medical Countermeasures of the report discusses some approaches like achiral antibiotics, producing mirror antibiotics, or releasing mirror bacteriophages ... but many would not - as in immunodeficient persons we should compare with. From the other side, mirror bacteria would indeed have crippled mechanisms like adhesion, also feeding with natural components - but there are also many achiral sources (Table 1.1: Achiral organic molecules that can be utilized by wild-type or mutant E. coli K-12), and bacteria can adapt to feed on mirror sugars ... the question is if it can get into the bloodstream, e.g. through injuries, if so it could rather easily exponentially grow in population leading to e.g. sepsis for example from released mirror proteins in necrosis. And getting mirror bacteria, it would evolve, take new ecological niches having practically no natural enemies ... also malicious players could easily modify them to become more dangerous.

Sure one can synthesize proteins from single amino acids, but comparing with its production by bacteria, what would be the difference in cost and volume? A thousand? A million? My point is that there will be large financial incentives for such cost reductions and scaling up, and there is a quickly growing number of potential applications, e.g. from the report: > Are you also worried about naturally occurring mirror molecules? For naturally appearing around us, evolution should generally prepare us for. But for others it did not, what does not automatically mean toxicity, but that there is a probability of various toxicities due to looking random interactions (again thalidomide example) ... and the number of potential interactions grows with the square of number of chiral biomolecules, so multiply this probability by millions e.g. for necrosis of mirror bacteria in human bloodstream - for me it sounds worrying.

Sure a company could now produce mirror protein drug for maybe thousans of customers ... but what if millions would like to buy it? If we agree synthetic central dogma is doable, why they couldn't build on it adding further features? Where exactly is your boundary you believe they will not be able to cross?

Just watching a week old presented by Yutetsu Kuruma from Japan Agency for Marine-Earth Science and Technology: Design and construction of artificial cells based on cell-free system - mentions the most difficult is cell replication, where I completely agree ... but just recreating (mirror) central dogma looks doable (?) - and might be sufficient for safe mass production of mirror biomolecules (?) ... or will become the first step toward replicating mirror cells ... George Church Synthetic genomes & tRNAs in vitro & vivo (Nov 2024):

While as a physicists I can say FTL is forbidden by special relativity (but in theory allowed by general relativity) ... I honestly cannot imagine obstacles for recreating cell chemistry - generally easily made outside cell ... so recreating original cytosol composition of some minimal cell, why wouldn't it work? Which chemical processes? They would work individually, but couldn't synchronize like in a living cell? Anyway, looks like these are your words against their. Searching for "boot synthetic cell" I see lots of positive examples. Could you support your view with some references? ps. Lots of talks from Build-a-Cell seminar (tomorrow about mirror bacteria I plan to visit): https://www.youtube.com/playlist?list=PLb2LmjoxZO-gKWXZZadcko8tHHkPuEeJT E.g. 2020 John Glass from J. Craig Venter Institute (e.g. minimal genome: 483 kbp, 432 proteins, 39 RNAs):

Yes, they use this vague "boot" verb for kind of bringing life to a synthetic cell - but what exactly is it? Naively there is just chemistry - statistical reactions in cytosol as a dense soup of biomolecules ... recreating composition of this soup (for some minimal cell with just central dogma), what more is needed to make it alive?

There are programs searching for minimal cell (e.g. https://www.nature.com/articles/s41586-023-06288-x ) but for full synthesis it is not needed. Being able to synthesize mirror ribosome and DNA/RNA, they could get all required enzymes - then enclose it into a membrane ... and why wouldn't such minimal cell work? (to be further extended with more functions) From fig 2.4 of the report: This is bottom-up approach, but the report also discusses top-down: trying to stepwise convert natural cell into mirror one through various approaches, e.g. genetic code reprogramming like replacing tRNA with carrying mirror amino acids. Section 2.3 of report: "1. Production of mirror-image proteins in vivo by creating a crossover pathway made of natural-chirality components. 2. Production of mirror-image proteins in vivo by creating an entirely mirror-image central dogma. 3. Delivery or assembly of a full mirror-image DNA genome in vivo, and removal of the natural-chirality genome, to create a mirror bacterium."

> We have been just a few years away from synthetic life for a few decades now There is continuous progress (timeline from 2019 https://elifesciences.org/articles/45379 ), synthetic cells are created since 2010 ... where do you think will be the main difficulty for complete synthesis of natural minimal cell? I completely agree interactions between both chiralities are very complex, recommend in the report: "Table 1.1: Achiral organic molecules that can be utilized by wild-type or mutant E. coli K-12", "Table 1.2: Utilization of ʟ- and ᴅ-amino acids by E. coli", "Table 1.3: Utilization of the enantiomers of common monosaccharides by E. coli". And reminded thalidomide example - toxicity from basically random interactions, there would be a huge number of them e.g. from necrosis of mirror bacteria in human bloodstream - there is a large chance for various toxicities.

For me Chapter 2 is quite detailed, bottom-up, top-down and other approaches. If reaching first synthetic cell, what seems a matter of a decade, mirror one would just need to use enantiomers - and their synthesis is quickly developing, especially that there are financial motivations, like mass production of mirror proteins, DNA/RNA ... and there could be some malicious players, like nihilist terrorists, or AGI wanting to get rid of humans ... Chapter 4 is indeed extremely detailed, and difficult without immunology background, but basic scenario is such mirror bacteria getting into the bloodstream, and freely multiply being nearly invisible for immune system - reaching sepsis or different problems. Anyway, I agree this is still early (10-30 years away) - good time to discuss, understand, try to find protections if possible.

This is entire Chapter 4: Risks to Human Health of https://purl.stanford.edu/cv716pj4036, maybe take a look there. For example for macrophages looks like nearly nothing would work:

Below Table of Contents of https://purl.stanford.edu/cv716pj4036 itself allows to imagine our situation in ~20 years, when such synthesis should be relatively simple ... and deadly - how to prevent it? Chapter 2: Pathways to Mirror Life 26 2.1 Advances in chemistry permit the synthesis of mirror biomolecules with diverse applications 28 2.2 Progress in synthetic biology could allow the assembly of a mirror bacterium from non-living mirror components 33 2.3 A natural-chirality bacterium might be converted into a mirror bacterium in a stepwise fashion 41 2.4 Other approaches to creating mirror bacteria are plausible 50 2.5 The feasibility of mirror life will increase as related technologies advance 51 Chapter 3: Engineering, Biosafety, and Biosecurity of Mirror Bacteria 54 3.1 The creation of any mirror bacterium could enable the generation of diverse mirror bacterial strains and species and their modification by routine genetic engineering 55 3.2 Biocontainment approaches might reduce accident risk, but they would face challenges 60 3.3 Creating robustly biosecure mirror bacteria is not feasible 62 Chapter 4: Risks to Human Health 65 4.1 Innate immune detection of mirror bacteria could be significantly impaired 67 4.2 Mirror bacteria would likely be resistant to most innate immune responses 72 4.3 Adaptive immunity to mirror bacteria would likely be impaired 81 4.4 Mirror bacteria could plausibly pass barrier surfaces and translocate into the bloodstream and tissues 91 4.5 Mirror bacteria could plausibly replicate in blood and cause lethal systemic infection 98 Chapter 5: Medical Countermeasures 107 5.1 New antimirror compounds could be developed to target mirror bacteria, but most existing antibiotics would not function 108 5.2 Conjugate vaccines could plausibly be developed against mirror bacteria 113 5.3 The efficacy of other countermeasures against mirror bacterial infection is unclear 116 Chapter 6: Animal Infection 119 6.1 Vertebrate susceptibility to mirror bacterial infection would likely be similar to that of humans 120 6.2 Many invertebrates would likely be susceptible to mirror bacteria 123 Chapter 7: Plant Infection 134 7.1 Mirror bacteria are likely to evade plant innate immunity 135 7.2 Mirror bacteria could plausibly establish chronic local infections within leaves and roots 138 7.3 The extent to which mirror bacteria could spread through and colonize plant vascular tissue is unclear 145 7.4 Countermeasures for agricultural plants 151 Chapter 8: Environmental Survival and Spread 156 8.1 Mirror bacteria would be inherently resistant to many biological controls 157 8.2 Mirror bacteria could colonize natural environments outside of multicellular hosts 165 8.3 Invasive mirror bacteria could rapidly disperse through the environment 175 8.4 Invasive mirror bacteria could rapidly evolve and diversify 178 8.5 Invasive mirror bacteria could cause irreversible ecological harm 181 8.6 Countermeasures to invasive mirror bacteria might lessen but would not halt the ecological damage 187

Regarding time estimates, the report says: "We estimate that if substantial resources were invested in a concerted effort, the creation of a mirror bacterium might still be 10 years away; and if research continues on its current trajectory, mirror bacteria might be created in the next 15 to 30 years." Regarding dangers, basically mirror bacteria could be able to adapt to our e.g. sugars, especially thanks to very fast evolution, and immune system of standard life could be nearly defenseless - from the report: "In addition to functioning as a dangerous “accidental pathogen” to a wide range of natural-chirality species, mirror bacteria could persist within and potentially colonize external environments. Unlike their natural chirality counterparts, mirror bacteria would be completely resistant to all bacteriophages, partially evasive of and largely indigestible to predators, and largely resistant to antimicrobial compounds released by competing microbial species. These potentially decisive competitive advantages could allow sufficiently robust mirror bacteria to successfully invade many ecological niches despite lacking specific adaptations for them. Because predators would not be able to digest most mirror macromolecules, a growing mirror bacterial population would not be controlled by any commensurate increase in predation, which could allow populations to reach high abundance." It is hard to find better sources than this report now - I am slowly reading. It is around the Build-a-Cell community, but I got disclaimer "This Science paper does not represent any official position of the Build-a-Cell community", also with "Mirror Biology Dialogues Fund": https://www.mbdialogues.org/ and information about open discussion this Thursday.

Synthesis of artificial cells is already being made - nice summary graphics from 2022 https://pubs.acs.org/doi/10.1021/acsnano.2c06104 While it is much more difficult for higher organisms, bacteria often can use L-sugars (and quickly evolve) - e.g. from https://asu.elsevierpure.com/en/publications/bacterial-utilization-of-l-sugars-and-d-amino-acids "In our laboratory, we have investigated several anaerobic bacterial strains, and have found that some of these bacteria are capable of using D-amino acids and L-sugars. Strain BK1 is capable of growth on D-arginine, but its growth characteristics on L-arginine are approximately twice as high. Another alkaliphilic strain SCAT (= ATCC BAA-1084T = JCM 12857T = DSM 17722T = CIP 107910T) was found to be capable of growth on L-ribose and L-arabinose. It is interesting that this strain was incapable of growth on D-arabinose, which suggests the involvement of some alternative mechanism of enzyme activity" However, it might require special enzymes, e.g. from: https://pmc.ncbi.nlm.nih.gov/articles/PMC3504760/ "An l-glucose-utilizing bacterium, Paracoccus sp. 43P, was isolated from soil by enrichment cultivation in a minimal medium containing l-glucose as the sole carbon source. In cell-free extracts from this bacterium, NAD+-dependent l-glucose dehydrogenase was detected as having sole activity toward l-glucose. This enzyme, LgdA, was purified, and the lgdA gene was found to be located in a cluster of putative inositol catabolic genes. LgdA showed similar dehydrogenase activity toward scyllo- and myo-inositols. l-Gluconate dehydrogenase activity was also detected in cell-free extracts, which represents the reaction product of LgdA activity toward l-glucose. Enzyme purification and gene cloning revealed that the corresponding gene resides in a nine-gene cluster, the lgn cluster, which may participate in aldonate incorporation and assimilation. Kinetic and reaction product analysis of each gene product in the cluster indicated that they sequentially metabolize l-gluconate to glycolytic intermediates, d-glyceraldehyde-3-phosphate, and pyruvate through reactions of C-5 epimerization by dehydrogenase/reductase, dehydration, phosphorylation, and aldolase reaction, using a pathway similar to l-galactonate catabolism in Escherichia coli. Gene disruption studies indicated that the identified genes are responsible for l-glucose catabolism." From the report: "Mirror bacteria could evade many aspects of human immunity and potentially cause life-threatening infection Most immunological mechanisms rely on precise stereospecific interactions between host and pathogen macromolecules. The mirror-image macromolecules of mirror bacteria would likely not properly bind to host receptors, enzymes, or other host effectors, as they would have the “wrong” chirality. This could grant mirror bacteria a degree of intrinsic immune evasion well beyond any known natural pathogen. The immune system could be compromised in three key ways. First, the innate immune response relies upon initial detection of conserved microbial biomolecules, such as bacterial lipopolysaccharides and peptidoglycans, by host pattern recognition receptors. Because these molecules are almost exclusively chiral, immune recognition of mirror bacteria could be substantially impaired. Second, many innate immune mechanisms of pathogen control could be directly compromised; for example, phagocytosis, antimicrobial enzymes, and several complement system pathways rely on stereospecific protein interactions. Finally, mirror proteins would resist degradation and other stereospecific mechanisms necessary for antigen processing and presentation by innate immune cells, which would impair the activation of adaptive T and B immune cells and antibody production. "

Indeed, and looks the discussion has started in this thread in 2007: 17 years ago ... for ANS it took me ~8, I have more waiting 15 - science needs patience I have created "Chiral life concept" Wikipedia article in 2007 ( https://en.wikipedia.org/w/index.php?title=Mirror_life&action=history&dir=prev ), but it was quickly deleted as SciFi ... then I have recreated it in 2017. My original motivation here was becoming incompatible with pathogens as in the title - previous idea was by changing codon language: replace tRNA and rewrite DNA - I wonder if it could work? Probably there would be lots of issues with gene regulation ...

But for mass production of larger mirror proteins you need mirror ribosomes (they work on), preferably in mirror at least bacteria ... 2022: https://www.science.org/content/article/mirror-image-protein-factories-one-day-make-durable-drugs-body-cant-break Being able to synthesize mirror RNA and ribosomes, getting the rest is relatively simple ... then there are lots of successes for building artificial cells: https://en.wikipedia.org/wiki/Artificial_cell If such mirror organisms find some ecological niches (and evolve) due unprepared natural enemies, remind the thalidomide story ... now imagine consuming entire mirror organisms - there could be thousands of new interactions evolution did not prepared us for - some of them might be toxic.

I am starting reading the report above and e.g. "Mirror-image enzymes have recently been used to construct kilobase-length mirror RNA and DNA, and research is progressing toward building a mirror ribosome" suggests mirror bacteria could be made in a few years, and there are financial incentives - they are needed for mass production of especially mirror proteins, which could find lots of applications especially in medicine. From the other side, I remember some articles that bacteria could easily adapt to consumption of mirror sugars - such mirror bacteria escaping the lab, not having natural enemies, could find ecological niches, evolve ... often being toxic if consumed - could turn out extremely dangerous for Earth ecosystem. Anyway, mirror life is both great possibilities, but also dangers - needs wide discussion before it is too late ... I am repeating since 2007, glad it has finally reached the mainstream.

‘Unprecedented risk’ to life on Earth: Scientists call for halt on ‘mirror life’ microbe research "Experts warn that mirror bacteria, constructed from mirror images of molecules found in nature, could put humans, animals and plants at risk of lethal infections" 299 page "Technical Report on Mirror Bacteria Feasibility and Risks.pdf": Technical Report on Mirror Bacteria: Feasibility and Risks

Indeed "baryons -> black hole -> massless Hawking radiation" could be one way to realize stimulated proton decay ... but if this one is possible, there might be also other e.g. more direct ways, like using sequence of laser pulses to directly "swing out" proton from local minimum field configuration.

I was thinking about even more SF ultimate power source: stimulated proton decay - nearly complete matter -> energy transition, ~100x higher energy density than fusion from any matter. While they search for proton decay in room temperature water pools, it is hypothesized e.g. for baryongenesis (more matter than antimatter just after Big Bang), or Hawking radiation (baryons -> black hole -> massless radiation) - situations with extreme conditions, so I would search for it e.g. in the centers of neutron stars just before collapse to black hole, colliders like LHC (to test if it happens would need a dedicated experiment). E.g. to explain orders of magnitudes brighter objects than allowed by standard explanations like "Bizarre object 10 million times brighter than the sun defies physics, NASA says" from https://www.space.com/bizare-object-10-times-brighter-than-sun If possible, it would mean proton is a very deep but local minimum of field configuration - maybe it could be "swing out" of this minimum e.g. with some precise sequence of laser pulses?

In halo nuclei there are stably (milliseconds) bind neutrons/protons in much larger distances ... but we are still talking about a few femtometers. https://en.wikipedia.org/wiki/Halo_nucleus http://theor.jinr.ru/~ntaa/17/files/lectures/Ershov.pdf