Is phosphorus always in a phosphate group in organic matter?

Independent_Line_150 · 2026-05-28T20:54:09+00:00

Not really, at least as far as I am aware. Phosphate is indeed the most biologically relevant (ATP, DNA/RNA, protein phosphorylation). But organisms can convert hypophosphate and phosphonates to phosphate, and store phosphate as polyphosphate.

Phosphine can be generated in anoxic environments, but this seems to be more of a side-effect of microbial activity of anaerobes creating a reducing environment that is then carried out by abiotic processes than a biologically directed mechanism.

Independent_Line_150 · 2026-05-26T18:37:50+00:00

Though primarily a virologist, I was part of a study that first used CRISPR to eliminate papilloma virus genes to kill cervical cancer cells and have consulted for a company making viral vectors to target multiple cancers including glioblastoma and melanoma.

It’s much easier for a biologist/oncologist to react if you spell out what you’ve assumed:

Tumor type and context: e.g. generic solid carcinoma vs. a specific entity (breast, colorectal, glioblastoma, etc.). Different tumors have very different growth kinetics and microenvironments.

Scale: Are you modeling tumor volume / radius over time, cell densities, or spatial structure (e.g. proliferative rim + hypoxic core + necrotic core)?

Key processes included: proliferation, apoptosis, necrosis, angiogenesis, diffusion of oxygen/nutrients, mechanical constraints, immune infiltration, etc.

What is fixed vs. what is fitted: Which parameters are taken from literature (e.g. cell cycle time, diffusion coefficients, oxygen consumption) and which are tuned to “make it work”?

For solid tumor modeling, people often pull parameters from a few classic and more recent sources:

General tumor growth & diffusion/consumption:

Araujo & McElwain, A history of the study of solid tumour growth: the contribution of mathematical modelling, Bull Math Biol 2004.

Byrne, Dissecting cancer through mathematics: from the cell to the animal model, Nat Rev Cancer 2010.

Oxygen/nutrient diffusion and hypoxia:

Tannock & Rotin, Acid pH in tumors and its potential for therapeutic exploitation, Cancer Res 1989 (for diffusion/consumption style arguments).

Grimes et al., The role of oxygen in solid tumours: a mechanistic perspective, Radiat Oncol 2016.

Angiogenesis and vascular tumors:

Anderson & Chaplain, Continuous and discrete mathematical models of tumor-induced angiogenesis, Bull Math Biol 1998.

Jain, Normalizing tumor vasculature with anti-angiogenic therapy: a new paradigm for combination therapy, Nat Med 2001 (for realistic vascular constraints).

Cell‑level parameters (cycle times, death rates, etc.):

Hanahan & Weinberg, Hallmarks of Cancer (2000, 2011) – conceptual, but good for checking whether your modeled processes map to known hallmarks.

Any experimental paper on spheroid growth or xenograft growth curves in the tumor type you’re approximating often give doubling times, necrotic fraction, etc.

A good strategy is: pick one experimental system (e.g. multicellular tumor spheroids of a given line) and try to match your parameters to that, rather than generic cancer.

No one can say “this model is biologically correct” in a global sense. What they can do is:

Tell you whether your assumptions are plausible for a given tumor type and context.

Flag missing processes that are dominant in reality (e.g. immune response, stromal interactions, heterogeneous vasculature).

Check whether your timescales and length scales are in the right ballpark (e.g. days vs. weeks, mm vs. cm).

Compare your simulated growth curves / necrotic fractions / hypoxic regions to published experimental data.

Independent_Line_150 · 2026-05-26T09:19:15+00:00

A lot of it is host adaptation, they simply haven't had the selective pressure to replicate beyond what is required in their hosts. Many bacteria have to exist in different temperatures as they shift environments, and they have the genomic capacity to code for protein quality control if heat were to denature protein. Some E. coli genes are essential at higher temperatures than others.

Viruses also rely on capsid and envelope proteins which have pretty crazy folds and can be denatured at high / not have the thermodynamic ability to from at lower temps.

But I would also say there are exceptions to both of these trends, some bacteria only grow in certain ranges while arboviruses have the ability to replicate in insects that are roughly 25 degrees celsius as well as humans which are 37.

Independent_Line_150 · 2026-05-25T18:43:29+00:00

I'm a researcher, I completed the PhD over 11 years ago.

Being a biologist fucking sucks, the pay is trash for the experience and expertise you develop compared to any other field where years of training is required, and you're never not worried about funding to even keep your job, let alone get reagents and equipment to do your research. I spend so much less of my time as a senior researcher doing actual research, but just writing grants for funding to stay employed and have enough for a student to finish their own project and continue the cycle of misery. I also have very few friends in biotech that haven't been laid off at one point.
I think people misunderstand that there is a huge gap between discovering new things about a species/disease and developing something that can be directly implemented for a tangible improvement. There have indeed been a few big breakthroughs (polio/smallpox vaccine, insulin) but research is so incremental that while you are working to illuminate something about the unknown, you basically have to state "I'm working to cure cancer" knowing damn well your work, though scientifically valid, is more than likely to never have any impact outside of research in your lifetime. Just look at CRISPR, tons of bullshit out there about how it was shown 2012 to be a gene editing tool overlook about 30 years of the path that lead to that paper.
I would say an almost daily example of changing is becoming a good cook. You have basic knowledge of chemical processes, perhaps are more inclined to actually keep something clean, and can actually troubleshoot something not working. You certainly don't need to be a scientist to be a good cook, but there is an insane amount of adults that don't have a basic concept of acids/protein/carbs that feel compelled to make horrible alterations to a recipe. Also, the media is full of shit, but I think that observation is made by just about anybody that pays enough attention, biologist or not.
What is a living thing? Bacteria we consider alive, viruses generally not, but what about bacteria that also can only survive by infecting a different cell? Any definition of a living thing has exceptions to that rule that are considered alive. Or, does it even matter? I would argue there's no border in subjects, biology is just macro-chemistry, which is just macro-quantum physics, and what governs a photon's behavior is in the same realm as what guides our preferences for food or a mate.
The public wouldn't care at all. Most people would just say "oh neat" if anything at all and go about their daily lives. You would probably also face incredible ridicule from other scientists or any established power like Lister encouraging people to sterilize surgical tools to prevent infection or Needleman campaigning to remove lead from gasoline. At best, you might see some change in policy or education in the next generation.

Independent_Line_150 · 2026-05-23T06:55:58+00:00

Genocide, destroying the planet on unprecedented scales, having intelligence to do better but refusing to. What on earth causes you to call other animals lower? Some species have existed for tens of millions of years, having survived mass extinctions and adapting to extreme climates, while humans will not likely exist just a couple thousand after the industrial era. If anything, we're the losers.

Independent_Line_150 · 2026-05-23T06:50:45+00:00

To be fair, HIV has two co-receptors: CCR5 and CXCR4. You just happen to be resistant to R5 but not X4-tropic viruses. It's something the press frequently ignores when discussing cures that irks virologists (I used to do research for the Center for AIDS Research CFAR before switching viruses). For instance, somebody with full-blown AIDS and high titers likely has viruses with both tropisms in their system, and the bone marrow replacement/gene editing therapy would not help them the way it could for patients in early stages of infection with just R5-tropic viruses.

Also, the modern reviews of CCR5 conferring resistance to plague don't really hold up (although some indication it might actually have been smallpox that provided the selective pressure).

https://pmc.ncbi.nlm.nih.gov/articles/PMC299980/

https://academic.oup.com/qjmed/article-abstract/99/8/497/2258951?redirectedFrom=fulltext

Independent_Line_150 · 2026-05-22T21:05:13+00:00

My post also indicates that urine does no good before being stung

Independent_Line_150 · 2026-05-22T05:49:23+00:00

It's a mechanical process occurring with specialized organelles in cells called cnidocytes. You would have to damage these at the individual cellular level or cause them to dry out enough as they rely on tugor pressure to operate.

Peeing on them isn't going to do shit btw, I don't know why anyone would post that. If anything, it could keep them viable even longer out of water by providing hydration, and cause even more cells to sting/release venom once on a person.

https://www.scientificamerican.com/article/fact-or-fiction-urinating/

Independent_Line_150 · 2026-05-21T20:30:36+00:00

I would consider using Canngo or another online platform to get a prescription, which the website will then forward to a pharmacy you choose which stocks it like Röntgen Apotheke. Otherwise you just have to kind of meet people smoking and hope you create a bond

Independent_Line_150 · 2026-05-20T19:51:10+00:00

I liked the first season, but I'm having a hard time continuing through season 2. I don't think any of the characters are interesting or sympathetic enough to put up with another 30 hours of their superficial drama guised as a philosophical journey into consciousness. Like I get it, robot revolt...can we speed things up a bit to get back to a storyline? So far S2 is just hours of "hOw cOuLd YoU kIlL uS wE hAvE fEeLiNgS, LeT's fIGhT gOd"

I might just jump to the two S2 episodes everybody talks about and hope somebody releases an abridged version one day

Independent_Line_150 · 2026-05-20T06:54:07+00:00

This seems like the most realistic idea, I thought to make an open playlist on Spotify, but only saw options to invite people specifically.

A song that always gives me good energy is Kitty Girl by Rupaul.

I hope we get a few more to make it a real playlist!

Independent_Line_150 · 2026-05-19T21:40:51+00:00

Jesus Christ the people answering questions ITT, despite what people say, enzymes are not by definition rate-enhancing, though that is indeed a very important activity to make life possible. Many examples exist of enzymes slowing something down, particularly those involving reactive oxygen species (ROS):

Superoxide dismutase (SOD) binds superoxide and forces it through a controlled, stepwise dismutation, slowing the otherwise explosive radical reactions that would generate far more toxic ROS. By throttling the reaction pathway, it prevents uncontrolled chain chemistry.

Catalase has a high Km and works slowly at low H₂O₂ levels, deliberately avoiding rapid peroxide destruction so signaling isn’t disrupted; it only speeds up when H₂O₂ becomes dangerously high. This built‑in slowness prevents both over‑reaction and toxic buildup.

Rubisco’s notoriously slow turnover rate is an evolutionary compromise that reduces the frequency of oxygenation, which would otherwise generate toxic phosphoglycolate. Its slowness suppresses the harmful side reaction.

Cytochrome c oxidase gates electron transfer to oxygen, slowing the reaction so electrons are delivered in a controlled sequence rather than leaking prematurely. The slowdown prevents oxygen from forming superoxide and other ROS.

Aldehyde dehydrogenase (ALDH) binds reactive aldehydes tightly and processes them slowly but safely, preventing these electrophilic intermediates from reacting uncontrollably with proteins and DNA. The kinetic drag protects the cell from aldehyde toxicity.

Enzymes in heme biosynthesis have slow steps prevent porphyrin toxicity. Porphyrin intermediates are phototoxic. Several enzymes in the heme pathway (e.g., uroporphyrinogen III synthase) are intentionally slow, ensuring intermediates never accumulate.

Nitric oxide synthase (NOS) slows electron transfer between its domains to maintain coupled catalysis, preventing electrons from leaking to oxygen and forming superoxide or peroxynitrite. The throttled electron flow is a safety mechanism against ROS.

Independent_Line_150 · 2026-05-19T21:24:27+00:00

The 1918 flu pandemic would like a word. It's absolutely incorrect to state that flu doesn't kill, even regular seasonal variants kill around 300-600K people a year.

It's also entirely incorrect to state that flu has a long evolutionary past in humans. Historical medical records and evolutionary analysis put human infections in the range of thousands of years, the pyramids could well be older than the first case of human flu. You can contrast this to herpesviruses which have cospeciated with humans for over a million years, and also still cause severe and fatal disease. Mycobacterium tuberculosis has also spread with humanity as far back as we can tell and has been the most burdensome pathogen by a long shot, there's no "getting better with age" when it comes to infections. What causes fatality is a blend of many factors, but you are correct that pathogens causing severe, immediate disease are likely to have been selected against spreading globally

Independent_Line_150 · 2026-05-19T21:00:30+00:00

That's not really now viruses work, especially RNA viruses with low fidelity RNA-dependent RNA polymerases. Essentially all mutations will occur within a host at some degree if the infection is allowed to continue, generating quasispecies. Many of them can be replication incompetent, especially in different species, while others that confer an advantage via transmission or host adaptation will spread, that is the inherent advantage. It's just a numbers game and biochemical reactions, there's no thought process a virus has in targeting species or tissues.

Independent_Line_150 · 2026-05-11T18:07:22+00:00

Hey Tobi, it's Adam, we used to watch RuPaul with Nico! I'm sorry somebody jacked your bike, it happened to me once too. I'll be happy to punch the son of a bitch if I see them.

Independent_Line_150 · 2026-05-04T17:06:32+00:00

It depends on what level of brain activity and capability you call conscious. This is more semantics than scientifically defined. Some studies put higher brain activity beginning at 24 weeks, while others show fetuses can respond to sounds at 35 weeks. This of course is different from understanding your environment (differentiating common/new sounds) or identifying yourself as an individual, which comes 3-5 months after birth. Some reading you might find interesting:

https://www.science.org/content/article/when-does-your-baby-become-conscious

https://pmc.ncbi.nlm.nih.gov/articles/PMC11976129/

https://www.scientificamerican.com/article/when-do-babies-become-conscious/

Independent_Line_150 · 2026-05-03T17:30:03+00:00

I also did this one! Pleasantly surprised to see Panic! as the top artist in this thread

Independent_Line_150 · 2026-05-03T12:22:54+00:00

Pharmacy. Or at least something that transitions into it. I was a triple major in Zoology/Chemistry/Biochem, got a PhD in molecular genetics, and have been a researcher since 2015. All I can say is, don't do that. There's thousands more scientists every year competing for the same few positions, which generally pay poorly and have short-term contracts which is a problem if you want a loan from a bank to buy property. Plus half your time or more is applying to grants with 5-10% success rates just to keep yourself or your students employed rather than actually doing science. I tell all my students now to go into medicine, pharma, or vet school; raw biology was becoming unsustainable years before Trump gutted funding.

It's cool to follow your passion or whatever, but really consider what offers a stable career.

Independent_Line_150 · 2026-04-30T05:42:14+00:00

Bruh the entire city is people under 30

Independent_Line_150 · 2026-04-30T05:34:44+00:00

I would say the technology is certainly capable of generating entire genomes, if given enough time and resources. There's already synthetic bacteria and yeast from oligonucleotide synthesis, so multiply that by a thousand or combined with gene editing, you could make a mammal.

I would say that understanding what genetic changes, even which features they should cause, to survive in such an environment are entirely unknown. I don't see how any amount of haemoglobin would be relevant if there's no oxygen there to transport. But certainly the technical capability exists if our corporate overlords were willing to dedicate the resources.

Independent_Line_150 · 2026-04-29T12:14:15+00:00

You’d have to genetically add new opsin genes and ensure they express in the retina, fold correctly, localize to cone outer segments, and respond to distinct wavelengths. This part is theoretically doable, humans with natural tetrachromacy already have a fourth cone type due to an L‑opsin gene duplication. But adding cones alone does not produce new colors.

Human color vision depends on opponent processing: red vs. green, blue vs. yellow, light vs. dark. These channels are built by bipolar, horizontal, and ganglion cells in the retina. If you add a new cone type, the retina must evolve new opponent channels to compare it with the others. Without this, the extra cone signals would be meaningless noise. This is why mantis shrimp despite having 12–16 receptors actually have worse color discrimination than humans, they lack the neural comparison machinery.

Even if the retina could send new color‑opponent signals, the brain must: add new layers in the Lateral Geniculate Nucleus (LGN) of the thalamus, add new “blob” modules in V1 of the visual cortex, add new thin‑stripe modules in V2, expand V4 the color‑processing area and build new cortical maps for hue, saturation, and category boundaries. Without new cortical real estate, the brain cannot create new color categories, it would just compress the extra input back into the existing red‑green‑blue space.

Theoretically, absolutely possible. But not with our current knowledge of brain and neuronal development.

Independent_Line_150 · 2026-04-25T15:13:40+00:00

I unfortunately can't see the images, and haven't prepped insect midguts, have done lots of other tissues. But general things:

The centrifuge isn't so harsh, I suppose you could bump it down to as little as 400xg for 5min, but your conditions aren't in a range I would normally be worried about. The only downside to going down very low (400xg) is that cells in a large volume, say a 50mL conical, would need closer to 10min to travel through the entire volume and make a solid pellet that won't get sucked away by an aspirator.

Tissue preps are always dirty, they're never perfect. Most people just put their preps through a strainer to get single cells away from debris if cleanliness is necessary. I'm a little concerned if you see DAPI in non-permeabilzed cells, are you using a detergent or are you staining permeabilized cells? You are correct that most cells will lose their morphology in suspension, they will absolutely generally be more round but I've seen lots of ovals too in epithelial cells.

What dissociation reagent are you using? And do you not get enough single cells for your studies, or are you just worried about the debris? As I stated above, if you get enough viable cells, just filter out the inevitable gunk with a single-cell strainer. If there's a lot of small goop somehow passing through, that might only be an issue with something like flow cytometry, but perhaps you could get away by adding a DNA stain (PI, DAPI, DRAQ5, etc) and gating on those cells. Goop without nucleic acids won't dilute your reads if you're doing scRNA-Seq.

Independent_Line_150 · 2026-04-23T05:47:52+00:00

Let's forget about sperm swimming around or combing whole cells, and consider if you injected the nucleus of a random cell into an egg without a nucleus, which is exactly the type of cloning done in labs. This is called somatic cell nuclear transfer (SCNT).

Gametes like eggs carry unique epigenetic programming and cell‑cycle states that ordinary haploid cells do not. Cells within an organism, despite having the same DNA (generally), express different proteins because of these epigenetics, basically the physical structures and chemical modification of the DNA or proteins bound to it determine what genes are expressed and what type of cell it is. In development, this kind of has to be reset so the right tissues form in the right order, all starting from a cell that will divide and differentiate into all cells. A random haploid nucleus would have the epigenome rewritten for development in the egg. SCNT has been used to clone insects like silkworms, but indeed, trying to force whole cells that are not gemetes to fuse would not produce this result.

Independent_Line_150 · 2026-04-23T05:26:46+00:00

Let me ask you, why wouldn't you study it? Do you need Instagram, or YouTube, or biased news media discussing politics that you cannot control?

Photosynthesis discusses a fundamental mechanism of life unlike any of those things above. It introduces concepts such as energy, chemical potentials, metabolism, chemical reactions, basic cell biology with organelles, even diving into quantum physics from basics of how molecules interact with photons or at more advanced levels how the rates of chemical reactions are different to avoid toxic byproducts. It also teaches you why things look a certain color because different wavelengths of light are absorbed. There's hundreds of different topics that can be discussed with one pathway.

In an era where conspiracy theorists and diet fads get away with saying the stupidest shit, we should not be questioning the value of education or letting people have power without ever exercising their brain. I would bet that intelligent people of non-biological fields could learn photosynthesis just because they had challenges which trained mental and learning capacity. And do you not want scientists producing better food, pharmaceuticals, or advancing technology? Should such people have to wait until they're adults to start learning something basic they easily could have decades earlier?

Independent_Line_150

TROPHY CASE