CharonY

It is like saying that folks should be allowed to be drunk driving. Y'all got airbags after all. It makes no sense.

Or that maintaining a pool of infected increases the chance of new variants (I mean that has only been the driver of at least three waves...). Or increase the risk of folks for which vaccines won't work, or that filling up hospitals and thereby restricting health care is bad for everyone etc, etc. I keep being astonished that 2 years into a crisis of this magnitude folks are able to learn nothing.

A couple of things: many archaea are difficult to cultivate and therefore presence and diversity of archaea were underestimated for a long time. Cultivation-independent has remedied that somewhat (but only ramped up fairly recently), but without an accessible pure culture it is not easy to study their physiology and pathobiology. There is some evidence that in certain anaerobic dental infections and abcesses archaea are present, but without a good model system it would be hard to figure out whether they caused it, or were just opportunistic. There is at least study where folks tried to infect mouse models with methanogens, resulting in higher mortality compared to controls, but there is not a huge body of evidence out yet. Moreover many of these studies are fairly new (a couple of years, really) and more studies and a better understanding of the role of archaea in our microbiome is needed.

While many certainly have a confirmation bias, the sad thing is that in that climate there are many that appear to be genuinely unclear about what is fact or fiction.

I mean, anti-vaccination has a history basically as long as vaccinations and many of the original arguments still echo today. E.g. safety of vaccines, which in the 19th century were certainly much more valid than today. The internet definitely has allowed the spread of stupid things much more easily for sure, though and I think it is drowning out the information. See if you tell folks something like only 1 in 1 million will have issues, that is a good message. But if you start being more precise like the studies have shown something like 1 in 100k with milder issues, or that some subgroup may have a higher frequency of non-serious complications etc to contextualize the data, you start confusing folks. Thus, science being precise is seen by many folks as science being uncertain. It is something that the medical officers are also facing. Either make simple declarative statements, but then it is an issue if you need to revise them due to new situations. Or you make more complicated, but more precise statements, which leaves many folks confused and hence less trusting.

This is perhaps one of the weirder experiences I had related to the pandemic. We had several discussions with students and members of the public who had concerns about vaccines. We were somewhat prepared to have some crazies and there were indeed questions that were borne out of conspiracy theories (e.g. 5g, vaccines are lethal made with aborted fetuses etc.). Yet, surprisingly we found that engaging with them and explaining it why that was silly did help to assuage their fears. I.e. it seems that some folks are not on the level of a true "believer" but they are utterly confused by the existing information and they apparently have no ability to distinguish between the nonsense in social media and actual facts (and it seems to go though all age categories). It does seem to me that there is a fundamental erosion of trust in public messaging and that individual connections might be believed more. The issue there of course is that everyone can go to youtube, call themselves Dr. so-and-so and create inane narratives that then spread like wildfire. Many of the ideas are so far out that you would assume that one has to be a conspiracy nut to believe them. The positive way to think about it is that even if folks believe crazy things, they might be amenable to education. The negative way to think about it is that apparently not only crazies are susceptible to this internet nonsense.

I think the strength of the scientific endeavor is that it is amenable to mentioned examination. That tricky bit however being that at least in more complicated areas a certain level of expertise is required for cross-examination is needed and this is where a certain level of trust is necessary.

Sorry, I think my comment might have been a bit cryptic. I just meant to say that viral evolution or the development of mobile genetic elements in general are what has been discussed under the catchy umbrella of "Selfish genes" i.e. genetic elements that propagate without conferring selective benefits to their host (or being detrimental to them). Which is a bit of a different line than thinking of virus as reduced organisms (I think that line of thought was mostly fueled by the discovery of "giant" viruses).

One line of thought assumes that they developed from mobile genetic elements (think transposons, plasmids, integrons and so on), which incidentally fits the original thread (Selfish gne) quite well.

Viruses do not have an active metabolism- they use the host to make their proteins but provide the genetic material (RNA or DNA) to do so

You mean this question? I.e. what molecules would likely be the first? As mentioned (I think) this is an open question. I mostly only remember that there is still an ongoing dispute regarding whether there really was a an RNA world predating a DNA world. There is even more uncertainty regarding molecules that may have dominated before that. As you have noted, it is unlikely that RNA itself is a prebiotic molecule. There is a good report here, but it is a oldish and I am not really up to date on the latest findings. https://doi.org/10.1016/S0092-8674(00)81263-5 I think some work have been focused on thermodynamic models for early molecules and alternative pathways for formation of early carbon bodies.

In my original reading of your it seemed to me that were arguing that the viral RNA was also a ribozyme or somehow a catalyst, but maybe I misread. I am not disputing that RNA can have catalytic functions.

That is not the common definition of a catalyst, though. The closest is a ribozyme, which are a kind of RNA that have catalytic functions. But those that "only" code for a protein for example have not catalytic functions themselves. Proteins certainly came later as there is evidence that even small peptides can have catalytic functions. But as mentioned ribozymes could also have play a role. In addition, there are some who think that we are looking at the thermodynamics wrong and that at the beginning of life certain reactions may have been energetically favourable even without more complex molecules, but I don't know how strong the evidence for that currently is.

Ah I see. Fundamentally redoxreactions are at the core of it. I could have said oxidative phosphorylation, right? And anaerobic fermentation is basically just a means to recycle reducing equivalents. However, they do not need to go through membranes as such. That being said, it is assumed that fermentation might have created excess of acids (as the and proton pumps may have been an early development to deal with it. These are then potentially the precursor of electron transport chains. However, this is based on student-level reading, I don't know how much these assumptions have changed in the last two or so decades. Ancestral metabolism is not my specialty.

As with other forms of categorization it is obviously a bit arbitrary and at least theoretically based on genetic distance and/or fossil similarity. But obviously that is not trivial and fossils do not show linear progression. This article has a nice discussion https://doi.org/10.1098/rstb.2015.0237.

IIRC they didn't puzzle over it for long. Rather they were worried that found their could interfere with Curiosity's sampling and analyses.

Photosynthesis proteins as well as ATP-synthases arose a fair bit later. A common assumption is that substrate level phosphorylation was at the beginning. There are other hypotheses around which are based on how other reactions were potentially thermodynamic favourable, but i haven't looked at those for a while.

I think you are just fine. Binary symbols often have these ambiguity and often these things are not universal. Sometimes they have an indicator for the active state, so if pressing a button results in these icon being highlighted or appear it can provide more clarity. I think the the answer is yes. Ultimately many of these decisions are made to make things less cluttered and slick. At the same time it means that it conveys less information. The basic idea is probably that after trying it out once you get the idea. There are whole discussions about resolving ambiguity in UIs. Often the answer seems to be setting design standards, but if folks cannot agree on them, it will remain ambiguous. I also think that smartphones are designed to make us less smart, but I guess that is another discussion :).

I think exactly that make is difficult, though. If we try to quantify, we would start with e.g. creating categories. But what an experimenter create might be based on their own experiences. So let's say you have language that has, say 5 categories for drinking vessels, but only 1 for eating bowls and conversely one that has only 1 for drinking, but 5 for eating, and then you have one that has one or two for each. if you used drinking vessels to build your model the first and last would group together and if you used the eating vessels it would be the latter. If you used both they might separate differently, but adding yet another concept would change the model entirely again. Then some cultures or languages might have sophisticated categorization in areas that do not even exist in others and so on. I.e. whatever you select to look at will influence what your outcome will be. Finding a truly neutral ground where comparisons of divergent languages can be done with this is approach is seems incredibly difficult to me. That being said, I suspect the matter is sufficiently complex that I would require some serious reading (such as the Kemmerer, which I am not familiar with) to contribute anything meaningfully.

I suspect it is quite complicated. There attempts to map rough distance between language using a wide range of metrics and at least from what I understand there really is no good agreement on any overall methodology. In the above example I suspect that depending on what aspect is shown the differences are likely to be all over the place. Language is often context-driven and so are categories created in a given language. Even within speakers of a language there is inherent vagueness. While this paper from Hancock and Volante focusses on linguistic uncertainties, I think categorizations are not as static and/or discrete as they might appear. In the example in OP, depending on what item groupings you provide, they might invoke different contexts for the viewer which may be more cultural than linguistic. Also I am not sure whether the proposed measure handles certain ambiguities well. For example in the above example I am not sure why Germans would use fewer words than the Dutch, considering that equivalent words exist in both languages, though there are many local variations (e.g. Pott) or variations using contractions (Kaffee- or Teetasse/ becher) or more formal usages that are less common (Trinkgefaess). I.e. the measures would vary potentially wildly even within a language region.

Lorenz and Immelmann (Einfuehrung in die Verhaltensforschung) were folks who originally made me want to study ethology. Unfortunately the funding situation turned me off from it (I did learn how to catch finches with bare hands without injuring them so there is at least that). Sometimes I wished I had stuck with the original plan (greener grass and all that).

No worries, it wasn't meant as criticism (and I assumed that is what you meant), but just trying to adjust language a bit as I learned that in public discussions folks get hung up on such concepts and that it can lead to severe misunderstanding of health messaging. But I also found that explaining these things does seem to help to mitigate spread of false or misleading information to some degree. In the spirit of OP one could probably add that with Omicron the even vague hope of herd immunity is even more shattered (if that was even possible). While some folks start claims regarding endemicity, it is important to point out that we are not even there yet. We are still very much in the outbreak phase and it is rather unclear when transmissions will drop to a level where we actually enter the endemic phase. Moreover, given the reservoir of infected people, the risk of new variants remain extremely high and given the spread (Omicron arrived almost everywhere in less than a month) creating an even more uncertain timeline. This is a serious issue for health messaging, as folks demand some level of certainty about how things are going forward, but the current lack of clear answers drives folks to the crazy parts of the internet.

The relationship is a bit complicated, depending on the type of virus. IIRC some older studies on viruses similar to the coronavirus (mouse hepatitis virus is a common surrogate, for example) found that at either very low or high humidity some viruses exhibited better survival at various air temperatures than at moderate humidity. I remember one particular graph from a paper showing a non-monotonic relationship and I believe it it was published around 2010, but I cannot recall the author right now. But specifically for SARS-CoV-2 there was a review suggesting that warm and wet areas might actually reduce spread but the effects were not very strong: https://doi.org/10.1371/journal.pone.0238339

! Moderator Note That is on my, apologies, I thought I had posted a mod-note, but apparently did not. The reason why it is moved to speculations is because it appears that in OP some original assumptions were made that do not seem to relate to existing literature (or if so, no references were given). As such it seems to be original speculation, which can be further developed in the speculations thread as outlined in the guidelines. Speculations do not need to contradict established mainstream, but (as the name implies) allows for speculations in areas where the science is not established. However, if the hypothesis is grounded in mainstream science, it would be great if either references can be given or at least the context is outlined with respect to mainstream science. Some questions could be related to whether how categorization in the brain works and whether it is uniquely related to language? How does it relate to category learning in animals, for example?

You seem to interpret rather than read and forget what actually has been said. You said EHEC required a single cell, I said lit says 10-100. No one was talking about children at this point. I said the real value is likely higher as plate counting often underestimates cell counts (which applies mostly to dried or processed food). Then you came with an unreferenced wiki (which actually states to having quality issues) indicating id1 of around 8 for children. This introduced children for the first time. While it is unclear how they calculated this, as for EHEC you cannot make actually dose response curves and especially not in children, it does not provide evidence of single cell infection beside your gut feeling. I think I should stop taking it off-topic further, especially in the face of strong resilience to information. For those interested, one of my references above actually estimated the minimal infective dose in children as low as 2. But I also mentioned why the methodology (self-reporting) is problematic.