CharonY

There are several studies hinting at mechanisms (mostly animal models, I can dig them out, I have them on paper only atm. The one to look at would be Diamond et al. "The SARS-CoV-2 B.1.1.529 Omicron virus causes attenuated infection and disease in mice and hamsters"). There are some other in vitro and animal studies, but in summary it appears that the virus accumulates mostly in the upper respiratory tract and is less effective in infecting the lung, where most of the critical damage is happening. That actually often results in more issues (e.g. cytokine storm). When it comes to the immune system, perhaps somewhat counter-intuitively a stronger response is not automatically better. It depends a lot on the type of the response. In fact, stronger immune responses have been associated with more severe progression of the disease in COVID-19. In addition, the fact that folks test positive, indicate that the virus has established itself and propagated. If it was cleared early on, folks would remain below the detection limit. Omicron has shown to reduce protection to infection especially with the AstraZeneca vaccine (where it basically circumvents it without boosters) and reduces infection protection with other vaccines, too. So that definitely affects broad numbers. The issue is that comparisons are not easy, as the vaccination landscape (e.g. boosters), but also reporting methods have changed over time. At this point we need more data from well-characterized cohorts, which are starting to become available. Previous variants were pretty good at infecting young folks. But we just did not notice because many had no symptoms. There are huge regional differences (e.g. only testing of symptomatic patients, use of rapid testing etc.) so the data is difficult to compare. A reason why more young people are detected and hospitalized in some areas is likely because omicron is basically sweeping through the population. There are a lot of briefs coming out but so far it has not widely spread among those population (which also is the highest vaccinated group). So far the basic assumption is that it is still high risk until sufficient evidence to the contrary has come out. Edit: crossposted.

I mean, the chemistry behind is is somewhat complex as there is quite some interplay between the various chemicals. When it comes to chewyness, for example, the wheat proteins (gluten) play a major role. If allowed to interact with water, the glutenins and gliuadins form a strong network that can become rubbery and chewy. Adding fat, inhibits this interaction, making the resulting product more crumbly. The choice of fat also affects how the cookies expands with thinner cookies being perceived as more crisp. By playing around with the water content of the ingredients (e.g. shortening vs butter, granulated sugar vs brown sugar) and the temperature, texture of the cookies can also be changed. I.e. there are a lot of factors to play around with, even if only few ingredients are used.

Well, and to be fair a significant proportion of the population is just unwilling to make even minor (much less major) sacrifices for the community and not only in the US. Especially among the younger folks I keep hearing the mantra: "I did my bit, stayed home for a while, wore a mask and got vaccines so now I am entitled to live my life". Older folks are still terrified. I have not seen the movie it yet, but I fear at least the concept of the movie seems a bit like Idiocracy and the issue is that it does not seem like a clever treatise of the issues we have, but rather just take things as they are and dial it up like in a sketch show. Unfortunately, reality is catching up in real time, and if reality overshadows satire, what is the point? I think folks that look at the whole thing and can at least feel a bit smug about it, can enjoy it. Those that that see to many depressing parallels and are already annoyed that the current reality of things might not.

I am pretty sure that PLOS Biology also requires one to enter contribution into the system, but in a general way. (e.g. X contributed to manuscrupt, y did data analysis and contributed to manuscript, etc.). While most journals have guidelines regarding contributions for authorship, reality is that each group hashes it out according to internal consideration. For example, most of data could be generated by the first author, but they may not have written much of the manuscript. Often PhD students get to write the first draft, but especially if the supervisor is very experienced, not much might be left in the final manuscript. Sometimes, middle authors are on it, because it benefits the group and so on.

I think we need more context to establish what the author means at this point. For all I know it could be a throwaway comment which basically only tries to establish the rather simple fact that a lot of biological processes arise from interactions rather than a top-down program.

Exactly. And it is not like folks are not constantly trying to pursue new ideas. Especially younger scientists starting their own group are expected to go their own directions. It could be true that radical new ideas will have trouble getting funding, as obviously it is difficult to predict whether a new idea will pan out, but if you can break it into chunks and provide evidence that your direction makes sense, you do increase your chances of funding. In theoretical sciences I am not sure how established scientists could actively prevent you from working on what you want.

The way you describe it does not sound like a contradiction to me. Most of the structural events in the development and maintenance of the brain involves genes, it requires post-genetic interactions and more of an emergent property. I think instruction set is not quite the right analogy, either. The instructions are fairly trivial, "produce RNA". All the whens, ifs and other interactions are not as such controlled by the genes. In a way blueprint is perhaps more fitting after all, but on the most technical level it is not a blueprint of the final product, but mostly a blueprint of the individual elements. Perhaps something like the blueprint of legos, but not necessarily of the desired item to be built. However, if all the bits and pieces interact in a biochemical favourable environment, the desired item kind of self-assembles.

My guess is that what he describes is what folks might think how genes work when they hear about DNA being the blueprint (which, in many ways is of course not accurate) and uses it as a starting point to explain how it actually works. In fact, I think fairly early on the brain has been used as one of the examples how you can have higher complexity from (relatively) simple instruction sets.

! Moderator Note Similar topics merged.

I don't think so, but I think it would be less confusing if I had said "less harmful" instead (more harmless is just weird). And exactly that data is missing, but may be incoming and only I have missed it. The latest data I have seen was mostly big picture view, i.e. how many folks infected and how many ending up in hospital. The affected cohorts were mostly vaccinated and young, so likely skewing the results. I.e. at this point it would be safer to assume that disease severity might be similar to Delta. In fact, considering that vaccine protection is lowered, as a whole it might be a bit worse, actually. There is in-vitro data suggesting at a mechanism while it is milder, but it is still difficult to be sure. Generally, higher transmissibility results in much higher number of net infections in the absence of interventions (as the spread sees exponential growth), so the much higher infection rates puts medical folks on high alert.

Not really my area but most look like daphnia.

In uni textbooks are used for reference. It is rare (in natural sciences at least) to have books in the class. You are supposed to use it to deepen your knowledge before and after lectures. The only books I remember used in class are reference books for botany and zoology, for identification of specimens. They are still tiny and portable.

The second edition Gottschalk would be from 1986. Why would folks carry reference books with them? Don't folks nowadays don't have a space to sit and read? Or do you mean high-school books? Are they actually heavy?

I don't think that follows. Textbooks in many cases are supplemental tools, though sometimes publishers like to push overworked faculty members to use their teaching solutions to save time (but I do not know many who actually uses them). But a good textbook is best used as reference material. And obviously more info is generally a good thing. Of course one could slim them down to the essentials, but especially for beginners that tends to be too compact. Some of the modern ones are geared to a different type of experience, specifically to make the information more relatable using some sort of narrative. While I dislike them personally, many younger students tend to prefer such styles. Also typically you have the option between ebook, hard and softcover (as well as loose leaflets). Personally I prefer hardcover, as if I decide to buy one, I use them for years. If seen only as a supplement to a single course, I think they are not used optimally. Also, often small, specialized textbooks can be quite a bit more expensive than big basic textbooks. Bacterial metabolism from Gottschalk is still my go-to, despite being quite old. However, it goes for the same price with around 300 pages as the more five-fold bigger Campbell Biology.

Comparing ongoing omicron infections with the previous wave it seems that in most areas we got data, we have lower hospitalization:infection ratio with omicron in many areas. However, it does not necessarily mean that omicron is intrinsically more harmless, it could for example reflect higher overall vaccination status. However, as transmission is higher, it could still mean that we might end up with overall more hospitalizations without additional measures to slow down transmission.

Well there is a big push by many universities to adopt open source textbooks. Though it does seem that most do not even read those, so not sure whether it is a big issue unless you make them mandatory (but again, I think the trend goes away from that).

I was always partial to "My favourite Bathtime Gurgles".

In recent times I have also seen massive grade inflation, anything below a B (as final degree for BSc or MSc) can be met with administrative issues, it is often easier to let it slide. I also noticed that labs have become less and less popular. They were my favourite part, as I always felt that I applied knowledge most in labs and accordingly learned more. But since you have to do something to earn a grade students consider them risky and they have fallen out of favour. Initially that was a trend observed in pre-meds, as they are obsessed with grades. But rather sadly I see even biology majors trying to avoid laboratory courses (in order to protect their grades). Don't get me wrong, active learning results in better grades, but requires more work. But students in recent times have made it clear they don't like it (we can clearly see it in evaluations). Unfortunately admin sees students as clients and are more interested to attract and retain them, rather than train them.

I am talking mostly about NA-students here (late high school, early college) and there are a lot of issues going on. But roughly speaking most students are: - hyper-focused on exams and exams only - focus more on grades than understanding - prefer memorization above anything else. Last thing I heard, high schools start to give out exam sheets that show a selection of questions that come up in these exams. They are utterly confused (and angry) that we do not do that in college - they do not work on problems. They google for answer and put the first thing they find in, regardless whether it is applicable or not. I.e. there is barely any learning involved for home assignments - they do not read textbooks. This is more relevant for complex topics to get the context surrounding a problem. But they get frustrated if they cannot learn in simple: question-> answer formats - interactive learning gives better outcomes, but student hate it (as seen from evaluations). In fact they get angry if they learned stuff that they actually did not need for the exam. Seriously.. - folks have almost stopped entirely asking for clarifications, typically the question will be something like "do I need to know this for the exam?" - any instructions that leave any degree of freedom (e.g. "work on this problem" vs "do this exactly like this and then the next step is this") will be met with resistance. Even if you have got one or two who enjoy this, there is often kind of a peer-mood that percolates through class and casts these things in a negative light. Not that at every students is like this, but implementing these types of lectures (or things that I did even 10 years ago) becomes an uphill struggle because you get so bloody many complaints. From what I have heard, in HS it is even worse, as at some point the parents also join in complaining. I think part of it is that folks are better at identifying what brings them short-term benefits and focus on that.

Unfortunately that approach likely would not work nowadays anymore.

So much of what I am going to say here is half-remembered discussions with a friend, who is a historian (with specialization in the middle ages), so I might get some things wrong. In Christian angelogy cherubim, seraphim and seats are those closest to god and do not interact with the human world. I.e. they are not the often depicted messengers of god. They are also not generally human (seats are often depicted as flaming wheels, cherubim have four faces of which only one is human, and so on). Typically "angels" in the Christian mythology refer to messengers of god, which are probably closests to malakim in Judaism. These were human-shaped and originally depicted as wingless. This depiction changed around the 4th century when these messengers started to get wings and were depicted as such since then. So to answer OP, the depiction of angelic beings changed over time and since around the 4th century they were created with wings, but likely not before.

A non-peer reviewed article from Imperial College suggests over 5-fold higher reinfection rate with omicron compared to delta. Clinical data is still limited for omicron but in their analysis they did not see lower severity (based on risk of hospitalization or symptoms). So not great news from that data slice. https://www.imperial.ac.uk/media/imperial-college/medicine/mrc-gida/2021-12-16-COVID19-Report-49.pdf

One thing that we observe in many data sets is that putting ordinance in place (e.g. masking mandates, limits of gatherings etc.) often slows down or reduces transmission events after some delay. Even in areas with poor adherence or very weak mandates it seems to have some effect. I have not looked into the lit (only at the data in a very non-data sciency way) but my suspicion is that simply making these public announcements reduces contact events as at least some folks become more careful. This also seems to be age-stratified to some degree, where especially younger groups tend not to care either way (i.e. infection rates seem to decline or slow down less than for the older age groups following such mandates). Conversely, lifting mandates seems to be seen as an endorsement of gathering and other potential risky behaviour, frequently associated with at least short, sometimes sustained spikes of case numbers.

No, you are misunderstand what I am referring to. With single-point lockdown I meant China in your original assertion: While it would be true that an early lockdown could have worked, it is often not feasible to react in time. For new diseases it takes time to realize that a) it is a new disease (China extended the timeline here because of suppression) and b) identify the agent (that was done rather quick though) and c) develop methods to diagnose them. Once we are at step c) in the modern world the disease likely has already crossed borders. The only ways would be either a better method for new disease detection or to lockdown at even the suspicion of an outbreak. The latter would unlikely to be practical. Perhaps to add a timeline to it, antibody tests have indicated that individual cases might have been in Italy as early as September 2019 (See Apolone et al. https://doi.org/10.1177%2F0300891620974755). SARS-CoV-2 was only identified Jan 2020 and the very first indication of clusters in China which were suppressed where also around September. Based on what we know about the original variant, it is likely that it was circulating earlier than that, before it created these clusters, but basically invisibly. While China had a reporting system, it was designed for SARS, so when folks tested negative, it stayed invisible. And again, I think the identification part is where we need to spend a lot of effort on. Otherwise, even if we close the doors really firmly, it will always be after some cows have already escaped the barn.

The timeline is a bit inaccurate- it was detected later on in Korea and Italy, but retrospective studies (i.e. looking back in time to check for evidence of infections) indicate that it was circulating already before the first cases were detected. In fact, the high fatality rate is likely associated with significant underestimate of ongoing cases (i.e. many positive cases were simply not detected, especially in the early months of the pandemic). You are correct that if other countries had followed a zero-COVID strategy going forward (as e.g. New Zealand), it might have burned out, or at least kept levels low enough that vaccines might have eradicated it. My point was that single-point lockdown at least for this pandemic, would not have worked. It would needed to be a more global effort. And if the a next major outbreak has similar characteristics (i.e. positive cases are not easily spotted before transmission happens) it is unlikely, regardless of country in which it happens, that we are able to detect it in time to lock down before it gets out of the country. In other words, we also need better surveillance measures to make public health measures to be effective.