[R] Start around 10:28 PM EST, 2026-01-11.

[R] Start 8:57 PM EST, 2025-12-19.

[T] Define experimentation and oncology.

[>] How common is this practice? Is it more common among certain nationalities? What have been the predominant medical fields in which self-experimentation has occurred? How dangerous an act has this proved to be? What have been the trends over time? What is the future likely to bring?

[R] Regarding the previous questions, my guess is that (1) mostly European or European-descended individuals self-experiment, (2) that the incidence of serious harm or death is less than maybe 25% probably less than 10% per experiment, (3) that people in the 21st century, proportionally speaking, self-experiment less often, despite the total number of self-experimenters (probably mostly biohackers) increasing, and that (4) the future may involve an increase in the incidence of self-experiment as resource-abundance and outlets (drugs and other substances) expand.

[Q] Why did the peak of self-experimentation occur in the first half of the 20th century?

[Q] What forms of self-experimentation exists (imagine a typology)?

[Q] What arguments exist for curtailing differentially self-experimentation?

[E] What was Walter Reed’s Yellow Fever Commission in Cuba in 1900?

…plan to allow mosquitoes suspected of harboring the deadly disease to bite Commission members, thus to demonstrate the mode of transmission.

[Q] What percentage of self-experiments are registered somewhere? What percentage of self-experiments are group over individual efforts?

[T] Acquire a copy of the 2003 work by Arsen Fik, Self Experimenters: Sources for Study.

[Q] “I discarded the 49 examples antedating 1800 and divided, into 50-year time periods, the remaining 465 episodes that occurred over the next 2 centuries” Would any findings change if the author chose a 10 or 25 window instead of a 50 year window?

[Q] The six categories of self-experiment determined are “infectious disease (including vaccines), anesthesiology (general and local), physiology, pharmacology, radiology (including x-rays and other radiation sources), and oncology.” How would more modern self-experiments fall into these categories? Are any categories now present, only in modernity? There are probably many more self-experiments that remain unrecorded formally. One example that comes to mind are people’s attempts at inducing lucid dreams with light-flashes.

[T] Re-create figure 1 using Python.

[T] Re-create Table 1 as a line graph using Python.

[E] Which category of self-experimentation were most prevalent between 1800 and 1900?

Infectious diseases and vaccines.

[R] Of course it makes sense that only after a new technology is introduced can people begin to self-experiment using it. Less obvious is the notion that as a technology becomes better adopted by conventional outlets or institutions self-experimentation with these technologies seems to decrease.

[Q] “The nation most prominently represented was the United States (33% of the total), followed by Germany (15%), the United Kingdom (13%), Russia (11%), and France (8%), with lower representations among coun- tries in the remaining 20%.” What are the population-proportions here? I recall that, in the 21st century, a number of European countries have very high ratios of researchers and or research papers and or citations per capita; perhaps the same holds true for self-experimentation.

[E] What are some famous examples of self-experimentation between 1800-2000?

These were Ramsay, who exposed himself to various gases to determine their anesthetic properties; Metchnikoff, who injected himself with blood containing relapsing fever spirochetes; Lawrence, who drank a solution containing radioactive sodium; de Hevesy, who drank a solution containing heavy water to monitor its elimination from the body; and Schweitzer, who submitted himself to an unproven yel- low fever vaccine to determine any side effects.

[T] Define catheter, atrium, anachronistically.

[>] In Saul Benison’s oral-history memoir of the curmudgeonly Tom Rivers, a leading virologist at the Rockefeller Foundation from 1922 through 1955, I found the quotation I sought: “I know that if anyone ever came up to me and asked me to take an untried vaccine, I’d ask ‘Have you taken it?’ and, by God, if that person said ‘No,’ I’d tell him to go to hell.” To confirm the safety of their products, the develop- ers of vaccines were expected to subject not only them- selves to inoculation, but their immediate personal and professional families.

[>] Rivers5 has called this “gang or group research.” He goes on to say, “Great discoveries are not made by committees or groups of workers; they originate in the minds of single individuals . . . I know of no important discovery in medicine or biology in the last hundred years that evolved out of gang research. You can do a hell of a lot of scut work by gang research, but the ideas for discovery are still going to come from the ideas in one man’s mind. In other words, you can hire men but not ideas.”

[R] The previous quote reminders you of the counterarguments to the Ortega hypothesis.

[R] The author of this article does not seem to cover results from outside of academic publications or reports. Another survey of self-experimentation, with a typology for the level of formationalization in self-experimentation, seems due. The biohacking community seems not much represented.

[T] Find and download any interesting publications citing this work on Google Scholar.

[R] “Perhaps as we progress into a new era of molecular biology, which is characterized by the development of increasingly complex methods of research, the need for self-experimentation will vanish.” In scientific pursuits, self-experimentation is present at both the level of the researcher and the level potential beneficiary (once a technology or procedure has been developed). Historically, self-experimentation seems to have occurred more at the formal level and (perhaps) now self-experimentation is occurring more at the latter level.

[R] End 22:10 PM EST, 2025-12-19 (with break).

[R] Start at 23:12PM EST, 2025-12-19.

[R] Before beginning this work, I would define population ethics as something like “ethical frameworks which describe emergent dynamics in the welfare of groups of individuals.”

[R] Start at 7:17AM EST, 2025-12-26.

[E] What does population axiology concern?

…how to evaluate populations in regard to their goodness, that is, how to order populations by the relations “is better than” and “is as good as”.

[T] Proceed through the references and indicate which you desire to download and examine further.

[E] What is Derek Parfit’s Repugnant Conclusion?

For any perfectly equal population with very high positive welfare, there is a population with very low positive welfare which is better, other things being equal.

[Q] What does “are elliptical for” mean with respect to two statements?

[R] It is easy to imagine someone reading the definition for the Repugnant Conclusion and falling into the trap of the hypothetical at the remark “for any perfectly equal population”.

[R] The only knob to turn, to crank down or up, is the population, in the Repugnant Conclusion, correct? Population size and interconnectedness seem to have a dynamical effect on population welfare. Is population size included in the “…perfectly equal…” stipulation?

[R] If we accept the Repugnant Conclusion, then any population axiology that is proposed cannot avoid but address it, as a condition of adequacy? My attempt to interpret: “A few theorists have argued that we should accept the Repugnant Conclusion and hence that avoidance of this conclusion is not a convincing adequacy condition for a population axiology.”

[R] Summary so far: There are population axiologies that have impossible results which show beliefs differ according the the size of a population and differ population welfares. Our beliefs should be consistent across population size and welfare. Many axiologies with beliefs that are inconsistent in this manner rule out as a condition of adequacy the Repugnant Conclusion. Some argue that the Repugnant Conclusion should be accepted.

[E] What is Derek Parfit’s Very Repugnant Conclusion?

For any perfectly equal population with very high positive welfare, and for any number of lives with very negative welfare, there is a population consisting of the lives with negative welfare and lives with very low positive welfare which is better than the high welfare population, other things being equal.

[R] I do wonder what “better than” means in this context. Perhaps this means “total welfare”?

[R] End at 7:55AM EST, 2025-12-26.

[R] Start at 22:13 PM EST, 2025-12-19.

[T] Define mass extinction, iridium, clay, Cretaceous, Palogene, bolide impact, calcareous, foraminifera, plankton, glass, shocked quartz, Chicxulub crater.

[Q] What are all the mass extinctions which humanity knows to have occurred and what evidence exists for their occurrence?

[R] Let us see how the authors will (1) link iridium (Ir) anomalies in New Jersey to the mass extinction of marine plankton marking the Cretaceous-Paleogene (K-Pg) boundary.

[Q] What evidence do we have to support the hypothesis “that a large bolide impact caused the Cretaceous-Paleogene (K-Pg) boundary mass extinction”?

[E] What are some lines evidence to support the Alvarez hypothesis:

Iridium anomaly right at the level of mass extinction in planktonic foraminifera and calcareous nannoplankton; altered impact glass and impact-derived shocked quartz; and the finding and dating of the ~180-km-diameter Chicxulub crater.

[E] What is the leading counter-hypothesis to the Alvarez hypothesis?

…hotspot volcanism of the Deccan Traps in India.

[T] Define hotspot volcanism, Deccan Traps, chron C29r, Pinna, dinocyst zone, tsunamite …

[Q] Where was “India” during the Late Cretaceous and how do we know this?

[Q] What is the normal ppb of Iridium in different materials and how significant or unlikely would one expect ~0.5 ppb to be?

[Q] How can one ascertain whether an organism was “in life position”? Re: “A third hypothesis, that the Ir is in place but the Pinna layer is a reworked tsunamite, was rejected based on the observation of P. laqueata in life position (Landman et al., 2007).”

[Q] Is it even possible for the Iridium to be displaced 20cm? Through what geological mechanism would this occur? Re: “A modest Ir anomaly of ~0.5 ppb occurs at the base of the Pinna bed, suggesting two hypotheses (Landman et al., 2007): (1) the diverse Cretaceous fauna survived the impact; or (2) the Ir is displaced 20 cm down section.”

[T] Define bioturbation, glauconite, sand, indurated, isotope dilution, downdip, paleodepth, spherule, tektite, carbonate, lapilli, clasts, ballistic deposits, …

[Q] Why were these eight localities chosen? How many localities minimally would be needed to test the relationship? At what point in testing localities are the returns in information diminishing? Re: “To test the relationship between Ir and the mass extinction event, we conducted a campaign of shallow coring (<25 m) at eight New Jersey localities in 2008 and 2009 adjacent to outcrops of the K-Pg boundary.”

[Q] How does a NiS fire-assay work? Re: “This requires Ir analysis on small samples (1 g), which we accomplished using a NiS fire-assay technique modified after Ravizza and Pyle (1997).”

[T] Have LLMs explain this to you in more detail: “Low procedural blanks (7 pg g–1) combined with high-sensitivity sector field inductively coupled plasma–mass spectrometry provide the detection limits (10 pg g–1 = 0.01 ppb) essential for the quantification of Ir in 1 g sediment core samples.”

[Q] Why should the global Iridium anomaly occur above ballistic deposits? Re: “The global Ir anomaly is a result of stratospheric fallout and should occur above ballistic deposits, as it does at ODP Site 1049 at Blake Nose in the western North Atlantic (Norris et al., 1999), where the ejecta also occur immediately above the marine mass extinction.”

[Q] What are some examples of postdepositional processes?

[Q] Why are the pervasive white clay clasts interpreted as rip-ups resulting from a tsunami that eroded the outer continental shelf and upper slope? Re: “The pervasive white clay clasts are interpreted as rip-ups resulting from a tsunami that eroded the outer continental shelf and upper slope (Olsson et al., 1997, 2002; Norris et al., 2000).”

[Q] Why are echinoid fecal pellets used?

[R] That a subsequent tsunami (not the ones associated with the impact) could be detected or discerned clearly seems doubtful, just based on intuition.

[R] The fact that echinoid fecal pellet concentration increase rapidly after the increase in Iridium concentration seems odd to me.

[T] Define export production, authigenic, aquiclude,

[>] Comparisons of these sections show that in clay-rich sections, the Ir anomaly correlates with the extinctions, but in sandier sections, the Ir is found 6 cm (Bass River) to 20 cm (Tighe Park) lower. The Ir anomaly at Tighe Park 1 is a sharp peak at a redox boundary that occurs 20 cm below the appearance of Danian dinocysts; this is similar to Bass River, where the anomaly occurs 6 cm below the appearance of Danian foraminifera and dinocysts. This differs from the other three sites, where broader Ir peaks are associated with the appearance of Danian dinocysts (Buck Pit 1) or the up-section increase in fecal pellets (Search Farm 1, Meirs Farm 1) that correlates with the appearance of Danian foraminifera and dinocysts.

[T] Create a mermaid diagram of the different sites studied and the forces that can move (mobilize) Iridium or affect its concentration.

[T] Download papers which have cited this paper on Google Scholar.

[R] End at 11:00 PM EST, 2025-12-19. Re-read pg. 869.

1 Preface

[R] Start around 7:15PM EST, 2026-01-11.

[A] BOOK for Gaussian Processes For Machine Learning (2006) by Carl Edward Rasmussen and Christopher K. I. Williams as Rasmussen_GPFML_2006.

[>] The actual science of logic is conversant at present only with things either certain, impossible, or entirely doubtful, none of which (fortunately) we have to reason on. Therefore the true logic for this world is the calculus of Probabilities, which takes account of the magnitude of the probability which is, or ought to be, in a reasonable man’s mind. — James Clerk Maxwell [1850].

[>] “…building systems that can adapt to their environment and learn from their experience…” (Series Forward)

[A] GP for Gaussian Process.

[R] Some high-level descriptions of the scope of the book include: “…the mathematical foundations and practical application of Gaussian processes in regression and classification tasks” and “…how Gaussian processes can be interpreted as a Bayesian version of the well-known support vector machine methods.” (Series Forward).

[R] The goal of the book: “…provide a systematic and unified treatment of this area [”the application of Gaussian process models to machine learning task”].”

[>] “Gaussian processes provide a principled, practical, probabilistic approach to learning in kernel machines.”

[>] “Roughly speaking a stochastic process is a generalization of a probability Gaussian process distribution (which describes a finite-dimensional random variable) to functions.”

[T] Define stochastic process, probability distribution, Gaussian, kernel, support vector machine, random variable, function, basis function, supervised learning, unsupervised learning, …

[>] “By focussing on processes which are Gaussian, it turns out that the computations required for inference and learning become relatively easy.”

[>] “While his own work was focused on sophisticated Markov chain methods for inference in large finite networks, he did point out that some of his networks became Gaussian processes in the limit of infinite size”

[A] NN for Neural Network.

[R] You appreciate the historica remarks concerning NNs and GPs made by the authors.

[E] What did NNs become so popular?

…they allowed the use of adaptive basis functions, as opposed to the well known linear models.

[R] There are likely some very interesting retrospective analyses that can be done with respect to claims and statements made in this Preface concerning aspects of the future of the machine learning (written before the revolution in deep learning).

[T] The preface ought to be read again after the rest of the book is read.

[Q] What is a “more expressive” covariance function?

[E] How do the goals of statistics and machine learning differ?

…in statistics a prime focus is often indata and models understanding the data and relationships in terms of models giving approximate summaries such as linear relations or independencies. In contrast, the goals in machine learning are primarily to make predictions as accurately as possible andalgorithms and predictions to understand the behaviour of learning algorithms.

[E] How do Gaussian processes bridge the gap between machine learning and statistics?

Gaussian processes are mathematically equivalent to many well known models, including Bayesian linear models, spline models, large neural networks (under suitable conditions), and are closely related to others, such as support vector machines. Under the Gaussian process viewpoint, the models may be easier to handle and interpret than their conventional counterparts, such as e.g. neural networks.

[T] Parse through the mathematical abbreviations and ensure you understand the different terms presented there.

1 Introduction

[R] Start (around) 5:30 PM EST, 2025-12-07.

[A] BOOK for Anomaly-CFPTSAEOGE-ED2-2024.

[R-Q] A thought you had before even opening this book was “How self-selecting is the intellectual space surrounding genetic modification?” and then “A left-leaning individual might be inclined to first look up the author, to form a judgement of them before or, possibly, rather than contending with the contents of the work itself” and then “By how much do the personalities (e.g. OCEAN) of those working with genome engineering (and related technologies) in laboratories differ distributionally from those ‘working with’ genome engineering (and related technologies) in ethics and philosophy?”.

[R] The Ultimatum and Public Goods game and the Prisoner’s Dilemna are the only elements of game theory in the table of contents; I imagine there is more in game theory that can be discussed in context of individual and collective decisions concerning assisted reproduction technology and genetic modification.

[Q] Which aspects or examples (perhaps 10) in game theory are most relevant to genetic enhancement of humans (besides the Public Goods and Ultimatum game and the Prisoner’s Dilemna)?

[T] Look these terms up using Perplexity and Claude. Engage with them until you can define the terms and explain their significance.

[Q] How many people actually take to heart the desire for their children to be happy and healthy? How can one evaluate how much a parent cares (intentions and outcomes) for their children? How much leeway do other people (individuals, governments, etc…) have in controlling the behavior of parents with their children? I imagine there are lifestyle decisions (e.g. smoking tobacco) that are made prior to one having children but consequential for the welfare of the child (genetically). What are some examples of these lifestyle choices? How are you personally failing your future children today?

[Q] What does human flourishing actually look like? As in, how have scholars defined or described different scenarios of human floushing? Regarding this last question, how much consensus or convergence is there concerning visions of human flourishing?

[E] What are some examples of interventions for societal good?

Altering ecosystems, modifying crops, imposing vaccines, imposing antibiotics, and imposing compulsatory education.

[Q] Which biological traits are, in expectation, most and least difficult to modify and why?

[Q] What are some examples of monogenic and polygenic diseases?

[P] As an exercise, you should plot fertility data (by demographic factors in the US, by country, etc…; in eggs produced via IVF procedures).

[Q] How are embryos in IVF genetically sequenced? How much damage if any is incurred on the embryo in performing the genetic sequencing?

[I] Once you upload and clean your notes, have Claude and Perplexity go through the questions and generate answers using a template.

[T] Download studies with a (.) next to them (in the notes section of the preface).

[Q] How would one go about improving polygenic scores or devising some other method that is more deterministic?

[Q] What existing theories are there surrounding SNPs? What are the fundamental natural drivers of mutation? Regarding the last question, might something as simple as temperature be involved?

[Q] Besides genetics “being young” (as a field) and the small number of eggs women produce in IVF cycles, are there other limiting factors in embryo selection? Regarding adoption, obviously policy and regulation might be a barrier (whether this is generally beneficial or harmful seemingly remains undetermined).

[Q] How have machine and deep learning improved embryo selection and assisted reproduction technologies? Regarding the last question, what are some major studies or repositories in this space and what are some emerging and or yet-to-be-test methods?

[R-Q] There are some major questions huamns must contend with concerning in vitro gametogenesis: How should governments regulate this? What traits would people prefer their children to have? How might relationships and marriage change? How much value is there in the bionormative mode of human reproduction and development?

[T] Consider donating to a sperm bank and or freezing your sperm (possibly over time, for experimentation purposes). At a minimum, download any datasets on selection preferences for sperm banks.

[Q] What datasets exist involving sperm banks and the traits of donors that are preferred or selected for by receivers?

[Q] What are some fundamental questions humanity must contend with in genetics, assisted reproductive technology, and related fields (or related methods)?

[Q] What work remains to be done to realize in vitro gametogeneis? How DIY or inexpensive might in vitro gametogenesis be one day? A limiting factor for some scenarios seems to be womb availability or capabilities with ectogenesis.

[T] With each new headline, the pressure to finish GET grows. Work on this!

[R] Tentatively, you believe that, at a minimum, in your lifetime, you will experience some highly unnerving developments in human genetic modification prior to the (possible) curtailing or realization of human flourishing via AI. Oftentimes, feelings of “inevitability” coincide with your thoughts of future involving immense transformation of human civilization engendered by AI or genetic engineering (especially, genetic engineering humans).

[T] Define sperm, egg, ovulation, PGT, GWAS, polygenic disease, monogenic disease, in vitro gametogenesis, embryo, SNP, pluripotent stem cell, somatic cell, gamete, and IVF.

[I] An investment strategy for some futures in this space might be collecting biological material from the individuals in possession of highly sought out traits.

[R] You want “human flourishing” but something feels so “off” (as though you are stepping into the depths of completely novel but dark abyss, on the edge of drowning but also of discovery) with the genetic enhancement of humans. The words or phrases “erasure”, “human dignity”, “extinction”, “unnatural”, “left out”, “tragedy”, and “unfair”, are some that come to mind. Some futures seem to include the mass erasure of “flawed” genetic lines (and also of familial heritage or the “family” in general). Although, today, the “unfairness” latent in certain trait distributions (e.g. height for men, IQ, etc…) is mostly tolerated by humanity without much pause.

[R] End (around) 7:00 PM EST, 2025-12-07.

1 Introduction

[A] BOOK for Cockell_AULITU_ED2_2020.

[T] Look up other MOOCs in astrobiology to include on the awesome-astrobiology GitHub page (pg. Acknowledgements)

[R] Routinely, undercurrents of urgency and a general sense of anxiety puncture your halcyon. Reading calms you and clears away some of this jitteriness. Reading for several hours per day seems as though it would be on par with physical exercise w.r.t. it’s positive efficaciousness. Walks w/ “Today I Learned” (TIL) phone calls or real-space conversations might also be positively transformative. In quizzing others you would also further solidify your recent learnings.

[R] Start 11:25 PM EST, 2025-11-01.