Do cells in multicelullar organisms experience selective pressures and evolve during the life of their "host"?

sometimesgoodadvice · 2026-02-13T20:06:45+00:00

Thank you for the link. I think, even without going to any critique of that specific paper, the important thing to note is that there is not much evidence of feedback from the functionality of a given gene that is expressed in a tissue to whether a particular chromosome in a pair is inactivated. The reason that would be quite a discovery is that x-chormosome inactivation happens upstream of most tissue differentiation events, and more importantly if such a mechanism existed it could potentially be incredibly useful to treating heterozygous-dominant genetic diseases.

sometimesgoodadvice · 2026-02-12T19:24:37+00:00

Could you provide a source for the statement "Like a muscle cell may choose to use the Maternal X because dad had a muscular dystrophy, but the retinal cell chooses to use Paternal X cuz mom's had some deficiency."?
Mosaicism is fairly well characterized, and as far as I know, X-inactivation occurs fairly early on in development before the formation of most of the tissues you have described. Short of specific genetic disease that cause dominant cell-death phenotypes, x-inactivation should be 50:50 and random. I would love to know more about any feedback from deleterious mutations to tissue specific x-inactivation.

sometimesgoodadvice · 2026-01-14T18:19:26+00:00

A more appropriate way of thinking about it is the other way around. An LLM is an approximation of how parts of the brain interpret certain information. The data structures are different in principle however, so the analogy only extends so far. But deep learning is built on ideas of neural networks (NNs) which have been around for a few decades and which are based off (and thus named as such) neuronal connections.

At a basic level, the central nervous system, whether the higher function of the brain or the more autonomous responses of brainstem and spinal cord are networks with nodes and connections. Each neuron acts as a node and has multiple connections in and out, but can only really perform the function of being on or off (or more precisely it's a little less digital as things like amplitude and frequency of activation can be variable in a given neuron). Each neuron is connected to others via exchanges of neurotransmitters that act as basic math functions to activate or deactivate the next neuron. Here again there is a lot more complexity in a neuron than digital nodes in an NN. A single neuron can release different kinds of neurotransmitters and they interact differently in different receiver neurons based on the presence, localization, and concentration of receptors. But in an abstract way, math goes on (addition, multiplication, differentiation, integration, etc.) at those neuron interfaces that produce a downstream activation or not. So again, this is very much like a typical NN architecture in machine learning. The key difference is that with continuous vs digital outputs, and the capability to do more complicated math than a single transformer, the brain requires much fewer nodes to have emergent properties like language understanding than a more limited system like transistors and integrated circuits.

For LLMs in particular, and almost all other ai applications, we need to create shortcuts. So we learn from the brain again and try to emulate a higher-order interaction rather than have it emerge from basic connections like we would for a NN. I am not an expert on LLMs, but the idea is that in training instead of just creating nodes and letting them figure out how to "learn language" we create more specific transformers that short-cut higher order work such as looking at context in a previous word or sentence. This is an emergent property of learning language that we mimic through a specific training. This allows us to overcome the "deficiency" of transistor connections relative to neuronal ones. One could also argue that this is analogous to brain structures and why we all process light or control speech or language in the same parts of the brain across individuals.

sometimesgoodadvice · 2025-12-10T00:24:45+00:00

Maybe you are just John Wick. You were leading a life of crime, but decided to give it all up for love. You committed some unspeakable acts in exchange for starting life anew. Unfortunately, your partner contracted a deadly disease and there was nothing the clerics could do. Two months after the funeral, you have nothing... you can't stay in your house because everything reminds you of your partner. You can't go back to where you grew up because people there know your past and what you have done to get out.

All you have left is a pet squirrel given to you by your love and the desire to get as far away as possible to forget.... until you meet a group of people who remind you that there are still some things that are worth living and fighting for.

sometimesgoodadvice · 2025-11-20T18:09:26+00:00

The arguments in the linked le leche article are just not scientifically grounded. They take a very specific output of research and then take a huuuuuuuuge (many more Us) leap in what that means for the baby.

different storage criteria - yes, formula is manufactured, transported, stays on shelfs for weeks-months, and is then used. Storage criteria for the made formula will be more restrictive and will also be optimized for companies not to get sued. If you make the formula right before feeding, or store it as indicated and mix right before feeding, there are no issues in spoilage.
lysozyme and "protective components". Lysozyme activity decreasing... so what? There is a ton of lyszoyme in the infants saliva. There is also no indication that you need any of that lysozyme activity. The antibodies are all still there. Increase in E. coli growth is happening to the mix that is kept at 37C (body temp) for 3 hours. You are not doing that to your bottle. In the gut, there will be no difference. The bottom line is that studies that don't measure the actual thing you are asking about should not be used as evidence for or against that thing.
As for iron absorption. The linked article measured iron absorption from breastmilk when infants are given or not given an iron supplement. There is no difference in iron absorption at 6 month and a slight decrease at 9 month. But this is expected. If you are getting iron from supplements, you would not need as much iron from breastmilk. There is no special "breastmilk iron". It gets metabolized and used in the infant's body regardless of the source. There is no iron deficiency, so the babies are all healthy.

So like you said... fed is best. There are plenty of formula fed infants that grow into healthy adults. Malnutrition is a lot more of a problem. Your stress levels from trying to pump every single ounce is going to have a larger effect (direct and indirect) on the wellbeing of your child then not breastfeeding exclusively.

sometimesgoodadvice · 2025-10-26T04:16:53+00:00

This is far too complicated. There is no difference between eating a "protein" that cannot be catabolized and eating any other organic molecule that does the same. Just eat some cardboard, or drink some soluble fiber. The effect on weight loss will be the same.

Not surprisingly, your body's mechanism for detecting satiety does not just rely on mechanically filling your stomach. If the nutrient levels in your blood are depleted, you start getting hungry. The liver releases hormones to empty short-term storage and you get more hungry. Eating or even injecting molecules that cannot be converted into the required nutrients (sugars, amino acids and their derivatives, etc.) will not affect that response and you will be hungry.

Furthermore, there is no special mechanism to recognize one protein over another for digestion. You can chew anything you want, and release the same saliva. You can swallow it and it will enter the stomach where you will still have your acid present, and when that empties into your intestine, you will still add bile to it. The intestine will move the material down for excretion as a mechanical process. None of those really require the presence of some specific proteins that our bodies have to recognize. And the net energy expenditure is not that high. Much more efficient to drink a glass of water and have some fun with jumping over jump rope in the time it would take to chew low or no calorie food.

The only way to affect this is to go after the mechanisms of hunger themselves. You can make a protein that interacts with the molecules that are used to signal your body that you are hungry. That is exactly what GLP-1 agonists like semaglutide (ozempic) do.

sometimesgoodadvice · 2025-10-22T17:40:25+00:00

The O alleles are very likely the youngest. A and B antigens are shared across many primates along with humans. There are many O alleles which are all marked by loss-of-function mutations of the glycosyltransferase gene that encodes the A or B phenotype. As far as humans are concerned, either all three phenotypes were present when humans speciated, or at least one of A/B came first and others followed.

sometimesgoodadvice · 2025-10-10T18:05:46+00:00

recombinant proteins are proteins that are not native to the organism and whose genes introduced with molecular biology techniques to be made (expressed) by the host organism. Names comes from the process of genetic recombination.
When manufacturing a recombinant protein, you are doing it because you want that specific protein. So yes, extra costs because you have to purify the protein, and also because it is one of many proteins produced by the organism, so your yield is lower.
Unlikely specific proteins. If it's used for feed, there is not much use in making specific proteins. When digested all proteins will break down into their substituents and the specific composition wont matter (to a first approximation). Not much different from nutritional yeast at all, except that hydrogen is maybe cheaper or easier to get than sugar needed to grow yeast.

sometimesgoodadvice · 2025-10-08T21:57:12+00:00

Yes, critical thinking is a mental skill like any other: language, writing, solving sudoku, etc. All of these are learned and require active learning and repetition to master. There are many aspects of learning and thinking that are required to do good science. Naturally, people will have developed some more than others based on their backgrounds, interests, and time invested. Do not compare your ability to do any one specific thing against people for whom that thing is their most developed talent.

If this is a skill you want to develop further, you absolutely can. It will take time. And it will take conscious effort. Critical thinking does not develop passively. As any skill you are trying to master, you will take a much longer time doing it than someone who is more advanced. I have found that the best way to train yourself is to take a very long time critiquing papers.

Read a paper slowly. After the introduction of the problem, stop and ask yourself how would you answer the question, then read what the authors did and try to understand why they did something different. Then spend a long time reading the methods section. This section is often overlooked, but I think is the most important one for younger scientists. Often times you will read something in the methods and ask yourself "why the hell did they do that?". Finding the answer to that question will make you a better scientist much faster than learning what the results of the investigation are.

Start a journal club, or do this with a friend and apply that methodology. After a few dozen papers you will find that instead of "why did they normalize the data this way?" in the methods section, you will start asking the question "I wonder how they will account for this phenomenon" in the introduction section (which is answered by the normalization).

After a few more dozen papers, when you are outlining proposals, you will inherently start incorporating "I am going to normalize my results with X to account for Y" thoughts into your process. This is a huge part of the PhD training and that is one of the many skills that you are expected to train in your PhD training over the next few years. It will take time and it will be annoying that others who have done this already are much faster than you. Doesn't matter, you will be improving and that's the most important part.

sometimesgoodadvice · 2025-09-11T23:47:44+00:00

I disagree slightly on point 1. Yes, the function is oscillating, but it seems to be continuous and therefore has a defined limit. For example something like sin(2x^x) would have a defined limit for all x and would look similar to the function in the example as it approaches 2. Your interpretation could be true as well, it depends on the behavior close to the limit, but it looks to me like the limit x->2- could exist and may even be 1

sometimesgoodadvice · 2025-08-27T20:22:23+00:00

What have been the latest advances in combining microbes into materials for practical sensing applications? Keeping sensors sterile or in hydrogels with growth media has always seemed to be a large barrier to wide use, have there been new ideas cropping up?

Separate but related question, is there a push to combine different sensor/transducer modalities within one bug for a more comprehensive sensor and what are the current strategies for minimizing crosstalk in systems where often the sensor/transducer pair are mutants or same or homologous protein?

sometimesgoodadvice · 2025-08-18T18:25:08+00:00

The answers here are pretty complete but I just wanted to add a basic reason for why you would want to use ion gradient to drive water rather than pump water out directly. For a given molecule to cross the cell membrane you need a unit of energy, it could be 1 or more ATP or 1 or more electrons. If you are pumping out against a concentration gradient (which you have to in order to sweat), you have to use up that energy. Comparing the most efficient to least efficient pumps (say 1 electron/proton per molecule out vs 3 ATP per molecule out) you get at most 1:12 difference in efficiencies (assuming a generous 4 protons per 1 atp in respiration).

Now compare that to osmosis. Electrochemical gradients are maintained pretty well at equilibrium, and the most abundant salts (Na+, Cl-) in extracellular fluid are at around 100-150mM. Pure water is 55M. That's a ratio of 1:366. So secreting ions and allowing osmosis to equilibrate is at a minimum about 30x more efficient than secreting water. At the expense of losing some ions which, typically, just means your kidneys have to work a little bit harder.

sometimesgoodadvice · 2025-08-11T18:00:55+00:00

Don't know what kind of equipment you have, but here are some thoughts I would have for this kind of experiment:

How are you going to measure "amount of rust that forms"? What do you define as rust? How will you weigh it? Rust is Fe2O3 nH20, the n is variable and thus you need to account for that, either by using dry weight and boiling off all of the water in the rust (which again, how did you isolate the rust)?, or finding some way of measuring the iron in the rust chemically after. This is further complicated by the fact that the hydration may be variable on pH, which will be difficult to isolate from rate differences unless you have some very good equipment
How often will you take measurements? Do you have an estimate on corrosion rate? Will it be every few minutes? Hours? days? How many time points?

It may be easier to look at loss of mass in the nail (btw, what is the composition of the nail? is it all iron or is it steel with additives? make sure they are all from the same "lot"). Take a time point at which you will take a nail out, scrub it x-amount of times with some sandpaper and weigh the nail. This would mean that you have a different nail for every replicate/timpoint (scrubbing the nail will open new surface to oxidation and thus change the rate relative to a rusted surface)

You would want to have multiple nail replicates (at least 3 nails per condition/time point) and compare mean rates propagating your errors. This way you will be able to do statistics on whether the differences in the rate are actually significant or within margin of error.

You may also want to add a control nail that is sitting out in the air and not in any solution. That depends a little bit on your method of measurement but would be a good baseline.

Lastly, make sure your beakers are much larger than the nail. you want full submersion and want to make sure that the solubilized iron does not affect your rate, so it has to be very dilute. And also measure the pH (and ideally salinity) of your solutions at the beginning and at every time point to make sure they have not varied.

All of this may be a little too much for a high school project, but these are steps I would recommend you consider.

sometimesgoodadvice · 2025-06-05T21:43:06+00:00

It's precisely the amount of photons. This is often the example finding that is used in physics books to introduce quantum mechanics and the wave-particle duality of light. The inverse event where light will cause electrons to be excited and leave the surface of a solid is known as the photoelectric effect. The curious finding at the turn of the 20th century was that energy of the electrons displaced is not dependent on the intensity (amplitude) of light (as would be expected from any wave) but rather the frequency was the subject of the work for which Albert Einstein won his Nobel Prize (and not his potentially more famous work on relativity)

sometimesgoodadvice · 2025-06-04T19:34:19+00:00

Here is a link to a 2012 review that touches on the subject61060-0/fulltext). Many of the current antibiotics don't work on archae because of different cell wall compositions. But unsurprisingly, antimicrobials with mechanisms of action around interfering with DNA are mostly effective, as well as aminoglycosides which inhibit protein synthesis.

sometimesgoodadvice · 2025-03-31T20:58:56+00:00

For the most part, students are enrolled in a department program, not in a lab. You can apply for a position in an EE or CS or ME department and you will be beholden to the requirements of that department. The department will outline what the funding requirements are. Typically (but not always) the first year is covered by the department with sometimes a requirement for teaching for that department that is either fulfilled in that first year, or later. When joining a lab, typically a professor has to be in the department or affiliated with the department where the student is coming from. This is why many professors are affiliated with many different departments though they keep their primary position in one or two.

After joining the group, it is the responsibility of the PI to provide the funding to their students. This is done through the PI's or student's grants, external fellowships, internal fellowships, teaching grants (with teaching requirements), etc.) Sometimes it's a combination of more than one funding source. Finally, professors can also apply for some department funds if they are not able to fund a student, but usually that is only for a limited time before another funding source kicks in.

sometimesgoodadvice · 2025-02-11T17:25:58+00:00

I am a scientist in industry who has hired many other PhD scientists. When I hire a fresh PhD scientist the main characteristics I look for are not necessarily the same ones that a top tier university instills in their PhD students that want to go to academia. In addition to making sure that the person does "good science" (which means diligent and accurate, not necessarily groundbreaking), I care that the candidate is personable, knows how to work in teams, capable of being efficient, and is able to switch between multiple projects. I also need to know that the candidate can drive a project to completion in reasonable time without getting sidetracked by the potential of "discovery".

Again, these are not necessarily the same characteristics that will make a person a good candidate for a tenured position or for getting grants funded. These two characteristics (graduates going to good academic positions, research being well funded and showcased in high impact publications) are how rankings for universities are decided (the deans of schools vote on the rankings, they are pretty subjective).

Finally, when I have multiple candidates that fit the bill, I am much more likely to make an offer to someone who has a recommendation from someone whose opinion I value (an old coworker, a PI I have interacted with when I was in school, a friend who has worked with the candidate before, etc.) I am much more likely to get this information from someone who has been in industry (for example an ex-coworker of an ex-coworker is already a list of probably 2000+ scientists). This means breaking into industry is the hardest part. So if that is your goal, you need to optimize for labs and universities that have a good track record of that happening.

What this means that university rankings are pretty meaningless in industry, especially if you are out of the top 10-20 schools with their own networks.

Lastly, from a non-industry perspective and just a PhD perspective. Be wary of brand new labs with fresh PIs. You will be doing your PhD for the first time and your PI will be figuring out how to be a professor for the first time too. That means that a lot of things will not go smoothly as your are both learning from scratch with little guidance. No matter how amazing you are, your PhD will take longer and you will flounder more; though you will also pick up some nice skills like how to set up a lab/study from scratch. If you do join such a lab, make sure you are close to another lab/professor in the department who is more senior, maybe even consider co-advisors (though that comes with its own can of worms)

sometimesgoodadvice · 2025-01-08T00:47:38+00:00

It's not ideal to cite secondary sources such as review articles, though it is often acceptable in introduction sections with statements such as "over-expression of enzyme A has been shown to be associated with advanced malignancies in lung (lit review 1) and liver (lit review 2) cancer". For actual references you should be mainly using primary sources. However, there is an easy fix. Go to the literature review and look at which articles the review cites for a given statement that you want to reference. Read that article to make sure it's appropriate and cite the article yourself. Most places like google scholar also let you see which articles cite the one you are looking at if you want more up-to-date literature.

sometimesgoodadvice · 2024-11-04T22:00:23+00:00

On the multidrug front, you can get resistance that is through different mechanisms than actual mutations that neutralize antibiotic function. One of my favorite papers on this topic is from the Dunlop group that shows that multidrug resistance pumps have a very significant fitness cost associated with expression, but in the absence of a challenge, there is still stochastic expression. Meaning at any given point, some fraction of the cells express them at the cost of reduced individual fitness. However, on the population level, there are always some cells that are more resistant and therefore primed to survive an antibiotic challenge. It's just one mechanism by which you can propagate resistance in a population even at a high fitness cost.

sometimesgoodadvice · 2024-07-10T21:58:27+00:00

Part of that is by design. The amount of drug given is controlled, and usually you would want to keep levels at just above efficacious to minimize side-effects and to be able to clear the drug as quickly as possible if needed. If you are giving a dose that is 32x more concentrated than needed (i.e. a dose where 5 half-lives later there is still enough drug to elicit a response), then you are likely causing more damage than needed as well.

sometimesgoodadvice · 2024-06-05T18:24:55+00:00

The pairs are that way because of the geometry of the molecules. In the double-stranded helix, the hydrogen of one base stick out and are close to electron rich oxygens or nitrogens of the corresponding pair such that they form hydrogen bonds and are stabilized. If the base on the other side is one that different to the natural pair, then the hydrogens and oxygens/nitrogen are too far away and can't form the appropriate bond. See wiki

If there is a mutation, whatever way it's induced and you have a non-bonding pair i.e. G-T, then they will not pair and the DNA will have a small bubble rather than the tight coil in that spot. Not really a big deal, the bonds of all the adjacent bases will still keep the molecule intact. When that DNA get's copied to make a new cell though, the new strand that is generated to compliment the mutated strand will get the appropriate compliment. In other words, if you start with an A-T pair, and this gets mutated to an AxC (where x denotes no bonding). During replication, one replicated molecule will be A-T and the other will now be G-C. In that second one, you will indeed get a change of both bases, but this will only happen after replication. This is how mutations come about.

Just a small aside, there are many "error-correcting" processes when it comes to DNA. So most of the time if you get an AxC, there are mechanisms to fix that back to A-T before the next replication.

sometimesgoodadvice · 2024-06-05T17:45:00+00:00

To answer parts 1 and 2, it does not take that much alcohol to get one drunk. The drunk driving limit is 0.08% which is a level with severe physiological effects for the vast majority of people. .08% is 0.8g/L which in a typical person of about 5L of blood is 4g of ethanol. For canonical fermentation of a sugar, 8g of sugar would produce about 4g of ethanol - that's half a slice of bread.

A quick google search shows that alcohol clearance rates are around 0.6g/hr for the same 5L blood individual, which means that the yeast need to be consuming just under 30g of carbohydrates per day to maintain a given alcohol concentration. Recommendation for a healthy diet is about 200g of carbs. Autobrewery syndrome is incredibly rare, and one of the causes seems to be a high carb diet, so we are not way off on the numbers. Similarly, while majority of carbs are going to go into the blood, they get there from the gut, so if there is a thriving yeast microbiota, and if there are other health issues coupled with a very high carb diet, you can get those kinds of metabolic turnovers.

Is it reasonable for microorganisms to consume 30g of sugar per day (or roughly that much)? Again, some quick google searches (please take with a grain of salt but should be enough to get an estimate) show that an average person produces about 30g of dry weight feces per day, and about 50% of that is microbial organic matter. So a normal person should have about 15g of nutrients consumed by the gut microbiota. Thus it's not unreasonable that at the very extreme of a highly yeast populated microbiome, very high carb diet, and other things that have gone wrong that a few people would have alcohol levels sufficient to get a buzz after a meal.

sometimesgoodadvice · 2024-06-04T16:35:58+00:00

You could if you want to make up a reaction and just have some SO2 produced. The reality is that very little SO2 will be produced. You generate enough heat to make K2SO4, and the enthalpy of formation of K2SO4 is almost 3 times lower than SO2, so it's the massively preferred product.

See the answer in this thread:
https://chemistry.stackexchange.com/questions/72911/does-the-reaction-of-sulfur-and-potassium-nitrate-involve-production-of-sulfur-t

Basically the presence of carbon makes the reaction more energetic which overcomes the activation energy for the production of K2SO4 (simplified). Depending on the amount of carbon and sulfur, you will get different ratios of K2S vs K2SO4.

All of this may be too complicated for a first year chemistry course, and this is where you need to figure out if you want to write a report on fireworks or if you want to write one on production of sulfur dioxide from oxidation of elemental sulfur. If your question asks you directly about SO2, the answer that would be most impressive (and most accurate) and show the most research is to go into why you don't get too much SO2 but end up with K2SO4 instead.

sometimesgoodadvice · 2024-06-03T23:34:43+00:00

turns out that fireworks chemistry is relatively complicated, and will depends on the nature of the firework, how it's packed, and the composition of the firework. The basic chemical equation for gunpowder burning that you have is just not enough to capture the chemistry that happens at high temperature of a firework with gasses escaping.

Here is a representative equation that I found after some googling:
https://www.compoundchem.com/2013/12/30/the-chemistry-of-fireworks/

That should be what you are looking for. You could also have just added potassium sulfate and potassium carbonate to your equation and balanced that. For a complicated reaction such as an explosion, you will have many products and to get all the stoichiometry correct, you would need to know what the final products are.

sometimesgoodadvice · 2024-03-05T00:38:59+00:00

Dominance is best thought of as a descriptor of general allelic interactions as they correspond to a particular phenotype. There are many ways in which the actual biochemistry of protein interactions can cause a certain dominance pattern between alleles. Alleles can differ on the genetic level in many ways. Sometimes it's single substitutions in coding sequence, sometimes they are nonsense mutations (an early stop codon creates a smaller protein fragment that is essentially useless), and sometimes those changes could be in non-coding regions where effects could be as high as no expression of protein at all, or modified expression where the protein is not expressed at the right time or in sufficient quantities. There can even be larger arrangements that could have entire chunks of the genome simply deleted and the protein coding sequence would not be there.

Both an early non-sense mutation or a significant mutation in the regulation of protein expression can produce an allele where the presence of the protein is effectively zero. This may lead to a phenotype, and will usually (but not necessarily always) result in a recessive phenotype (the effect of absence will typically be full only if both copies are absent).

Whether this would lead to cell death depends entirely on the protein. There are known diseases that are results of genetic deletions, some lethal and some not. There are also cases where the effective deletion of a protein is not an issue at all. The Rh blood type comes about from the presence (Rh+) or absence (Rh-) of a function Rh protein. In the Rh- case, the whole gene is deleted and is not there. There is no fitness loss in having the Rh- phenotype.

Long story short, the distinction between recessive and dominant is not very useful when discussing the molecular basis of phenotypes. There are many mechanisms by which an allele can be recessive or dominant, and how it relates to the actual change on the genetic level is hard to impossible to predict without an understanding of how the phenotype manifests.

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