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CharonY

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Posts posted by CharonY

  1. 43 minutes ago, mar_mar said:

    And I still don't understand is evolution a change or development? So simple question, why don't you answer.

    Evolution is a change in the gene pool of a given population over time, as has been stated before. Not sure what you mean with development, as I do not see it well (or at all) defined in your posts. Individual development is a different discipline.

     

    2 hours ago, Luc Turpin said:

    While searching for my infamous study on bacteria reschuffling their DNA deck, I stumbled on these:

    Evolution is not as random as previously thought - ScienceDaily.url 88 B · 0 downloads

    The title is interesting, the article even more. There seems to be a non-randomized process at play in evolution

    These Species Can Recode Their Own Genetics.url 86 B · 1 download

    Squid and octopus can edit and direct their own brain genes - New Scientist.url 232 B · 0 downloads

    "Unlike other animals, cephalopods – the family that includes octopuses, squid and cuttlefish – do not obey the commands of their DNA to the letter.'

    Squid and octopus can edit and direct their own brain genes - New Scientist.url 232 B · 0 downloads

    I have not read any of them, but the text and title alone are pretty horrible for the most part. None obeys the command of their DNA to the letter, during conception we shuffle or DNA as part of the process, we modify our DNA throughout our lives epigenetically, our immune cells do recombination to create antibody diversity. The first link goes to a rather horrible interpretation of a PNAS paper, where they looked at the pangenome of a bacterium and basically found that that it is more shaped by selection than drift (based on a machine learning models). While interesting, there was no supposition that evolution is super random in the first place. What is unknown for any given population is what the contribution of each to the current shape is.

  2. 2 hours ago, Phi for All said:

    But it should give The People back some skin in the game, which We haven't had for a few decades. The Republicans gave up representing The People and started focusing on corporate interests under Reagan, and the Democrats did the same under Clinton. The difference in donations was too much to pass up. Now We have major issues that 70% of us all agree on, but the corporations don't so we get no action on what could be some of the best, easiest solutions available to us. 

    Overpopulation is quite closely related to capitalism from what I've read, so perhaps it's finally time for the US to embrace public and state funding with no private leeching allowed. That would be the old European way, but perhaps I'm over glamorizing a system I didn't live in.

    I think you might be glamorizing it a bit more. There is something to say regarding better representation. But, in recent times, wedge issues are also immensely successful in disruption these processes. Take the rise of the far-right, for example. They do echo the US situation, while having a very distinct political system. The mixed economic model is probably as a whole better in many areas, especially for folks not swimming money. But there are also distinct issues there. I think in some areas there are clear advantages, but I don't think that they are necessarily to the political system, but based on what folks mange to agree on.

    Sure bi-partisan system encourages taking sides, but populations are not necessarily passive receivers. The immigrant-averse stance permeating much of the European population is quite at odds with many parties and which has fueled the success of the far-right. They also happen to be more aligned with the GOP, potentially due to the right-wing networks which have sprung up with suspected funding from Russia.

    Ultimately it is an interplay between system and sentiments in the population. And they often cross-feed each other. If folks did not had the simmering resentments, Trump and the GOP would not be able to profit from them. But once they did, they managed to shift the Overton window to more acceptance of previously considered extreme sentiments. That in terms gave an opening for even more radical changes and so on.

  3. 3 hours ago, exchemist said:

    If you buy these industrial concoctions you are asking for it. Why use 5 ingredients when 25 will do, eh? Worse than a Yotam Ottolenghi recipe.😄

    I mean, looking at the ingredients it does not seem too bad. The second one might have different design principles as they used a lot of coloring, potentially suggesting that the ingredients were not of great quality (though this is probably true for all sauce packages). The use of caramel for color is generally not harmful, but should not be found in decent quality soy sauce. It darkens during the fermentation process naturally, so adding colour just makes it appear to have aged longer, without providing the flavour.

    It is also possible that the production process bleaches out the colour and they restain it, but chances are that this will impact taste, too. But for bloating onion is a good first assumption.

  4. 57 minutes ago, Phi for All said:

    Offhand, I'd allow ranked-choice voting, just so we can break with the two parties that only represent corporations, and get some actual citizen representation going.

    Well, looking at Europe I don't think that representative parties are a clear solution. 

  5. 21 minutes ago, Pooh said:

    First, thanks to everyone who replies. It takes time to read and your reply, at least, shows that you are interested in this topic. I'm grateful of that.

    What you are saying is exactly the problem of logic. A once logical conclusion can be debunked by a single observation, and, therefore, logic is not a reliable tool. (Let's say fact first and personal feeling later. ). If you don't agree this statement, explain the logic behind it. Why is logic still reliable, when it gives misleading conclusion again and again? We can only use logic as a common point for communication. 

    Why are people using hammers when screwdrivers are so much better at putting screws into walls? 

    The reason is that different tools are used for different purposes. Logic is helpful to investigate conclusions in relation to a given premise. If the established premise is valid for a given question, the conclusion might also be. Even if the premise is incorrect, it allows for speculative investigations. Logic is a structural element in thinking about a given issue and allows for the creation of nonsensical connections. 

     

  6. Not sure without seeing the whole protocol, but from what I see there no urgent red flags. TCEP being a few year old is not ideal, if it was opened years ago and not stored under nitrogen, or at least well-sealed. That being said, I have used fairly old powder without too much trouble (but used it in excess). As you are using Ni-NTA I presume that there are no metal chelators involved. I would probably run the sample through mass spec to see what I got. I am not a big fan of dialysis, as I tended to lose too much. But then that was decades ago, so perhaps the dialysis systems have improved.

  7. 25 minutes ago, Luc Turpin said:

    When using the word survival, I was talking about collective not individual survival.

    Does not matter, selection happens on the individual not on the collective level. Also, the same issue applies. It is about reproduction not only survival. A group entirely composed of mails may survive as many hardships as they want, their gene pool will end with them.

     

    26 minutes ago, Luc Turpin said:

    As in something else than inheritable traits under positive selection; another selection mechanism.

    Well, that is a semantic issue, something can be either under positive, negative or neutral selection. It does not refer to the mechanism itself under which they are positive, negative or neutral. 

    28 minutes ago, Luc Turpin said:

    As an explanatory note, I am not questioning the core of evolution theory, but pondering the possible need to reshape its outer shell. Pretentious is my contention that a growing body of evidence on the prevalence of intelligence in nature may be chipping away at the edges.

    I think the issue is that you might be have a view on evolution that is not the one used in science. There is no real necessity to see intelligence as a fundamental different trait than, say the ability to use oxygen to create energy, for example.

  8. 7 minutes ago, StringJunky said:

    Yes. Affluence is no indicator of  environmental concern. Affluent areas will naturally have more 'string pullers' who can get others to do it for them. Rubbish is as likely to fly out of a high-end Mercedes as a shed on wheels.

    Even worse, generally speaking affluent folks consume more and produce more garbage. As you noted, they are just better able to pay folks to clean it up and frequently things get dumped into poor areas/countries. 

  9. 3 hours ago, Luc Turpin said:

    'Survival does not equal passing on genes", but do you not need to be alive (have survived) to pass on your gene pool?

    Yes at the time of reproduction, but if you manage to stay alive at the cost of not reproducing you are not contributing. Conversely, if you reproduce and then die, you still contribute.

    This is like in the example of salmons. If they don't go through the trouble of migration to their spawn sites, they would live a fair bit longer. But they would not contribute to the gene pool. In other words, if there was a mutation that prevents them from conducting that migration, it would improve their survival, but eliminate them from the gene pool and would therefore vanish as trait (negatively selected).

     

    3 hours ago, Luc Turpin said:

    Additional questions, again, if I may: Can you tell me what role if any has intelligence played in human evolution? And if there is a role for intelligence, are we talking then of inheritable traits under positive selection? or not? or something more? or something else?

    Intelligence has shaped our environment, so the contribution to human evolution is indirect. We change selective pressures and that can affect our gene pool. The one part that could be somewhat considered direct is sexual selection. What is considered to be attractive in a mate can be culturally shaped and this could lead to proliferation of specific traits.

    Evolution and intelligence is harder to assess as we really do not know how it is inherited and estimates of inheritability have been diverging quite a bit. Mostly because it is seemingly a very malleable on top of the inheritable bits. I don't understand what you mean with your last questions.

    2 minutes ago, mar_mar said:

    Since it is the evidence of origin of life. Origin of nature as well

    It's not about magic. It's about origin of life. And i thought it is an open question in science. 

    Evolution is not about the origin of life. 

  10. 1 hour ago, Luc Turpin said:

    What would then be the term to be used for improving one’s chance for survival, as in some form of intelligence improving one’s odds of surviving and passing on his-her genes to the next generation

    You are mixing different things here. Survival does not equal passing on genes. They can increase chances, but very contextually. Conversely, there are multiple species where reproduction is coupled to death. Secondly, improving chance of survival does not necessarily involve intelligence. 

    Effectively one would need go back to the basic definition of evolution, where we ultimately end up with terms like inheritable traits that are under positive selection, for example. 

     

  11. 33 minutes ago, AIkonoklazt said:

    The second issue is that organisms shaping their environment has to do with guided evolution of the environment, and not those organisms. Let's not confuse what the term "guided evolution" refers to. Do you see the correspondence between the bolded parts of the previous statements? You're mixing everything together.

    I would argue that this not the case either. Mechanistically shaping the environment one or another might change selective forces acting on an population. But so does virtually any interaction as selective forces are only static in models. And if we call any action changing the selective landscape guiding, then, as others already pointed out, we would expand the term guidance likely to a non-meaningful way. 

    I would probably rather state that guidance requires a sort of intention and goal, which are absent in this cases. I.e. the intent and goals of these actions are related to proximate survival but not with the intention focused on evolution (the only exception I could come up with would be breeding programs with specific goals).

  12. 34 minutes ago, Phi for All said:

    Exactly, and I think it's extremely sloppy to broaden the definition of "intelligence" just because cell communication has a similar pattern to sentient communication. IOW, I disagree with your author since I don't think there's a question there to be answered. Animal intelligence is completely different to the cellular processes described here. To equate the two is a big mistake and gives us no meaningful benefits. It's anthropomorphizing at the cellular level.

    It is like saying that mitochondria are the power plants of eukaryotic cells. Hence evidence for industrial revolution in cells.

  13. 21 minutes ago, Robin Wilding said:

    The Eastern view, not trivial, did no science because they did not believe in an authoritative creator or in certainty or in the separate existence of anything.

    I'll contest that. There have been different approaches to creating knowledge and the issue here is that Western science has trouble recognizing other school of thoughts. In fact, quite a few of the early Western science approaches loaned concepts from elsewhere but only over time did it become so successful. One important bit is that it actually did away with the spiritual aspects and became increasingly materialistic. 

    In addition, there are many non-Western religious systems believing in some form of creator, so it really seems like cherry-picking the arguments a bit.

  14. 2 hours ago, mar_mar said:

    What evolutionary changes happened to humans since starting walking straight? Do humans still evolve? What is the evidence?

    It is fairly simple actually. Having no evolution means that the gene pool does not change from generation to generation. This is a situation we call the Hardy-Weinberg equilibrium https://en.wikipedia.org/wiki/Hardy–Weinberg_principle

    In order for that to happen it requires certain conditions to be satisfied, such as infinite population size, entirely random mating, no mutations etc.

    These are obviously not true for human, or in fact almost all populations. In other words, evolution is the normal situation and having no evolution is in fact an extraordinary claim. How would you, for example ensure that the next generation has the same genetic composition as the previous? Simple answer is, you cannot. What you might be thinking about are likely large-scale changes in visually obvious traits, but that is not what happens in the short time humans have been around. Rather, the level of phenotypic change you should be thinking about are things like, the shift in lactose tolerance, pigmentation. A fun study found that shift in folks growing up in the UK were an allele associated with higher nicotine dependency was weeded out because folks died young (due to high smoking habits). In populations where smoking was rare and also in modern times (again, fewer smokers) these alleles are becoming more frequent again (as selective pressure have lessened).

    In short both theoretical as well as empirical evidence clearly demonstrate ongoing evolution and one might need to revise ones preconception of what evolution is to fully realize that.

     

  15. 2 hours ago, J.C.MacSwell said:

    I was only assuming a single common ancestor based on the claim in the link, I was going to later ask how that was known.

    Is it determined that that specific haplotype can only have come from a single mutation event and not been duplicated by some other identical mutation rather than only from being passed on?

    Just very quickly and generally (not really specific to the trait in question). We can start at the locus (site) of the mutation that provides the trait of interest and then look at the surrounding regions, which presumably are not under the same selective pressures. If the mutation arose in different persons independently, we would expect to see some variations in those surrounding areas (think of it as different persons providing different backgrounds for the mutation).

    Blue eyes arose likely not due to a mutation in a  gene associated with eye color (OCA2)  but in an upstream regulatory element. The interesting bit is that the surrounding area is also conserved in all (tested) folks with blue eyes suggesting that they all share a common ancestor providing this mutation. However, as this analysis relies on testing of folks who are still alive, it obviously cannot tell us if there had been other mutations with the same phenotype or even independent cases of the same mutations.

    I.e. we can say all currently living folks with blue eyes (who have been tested) have the same common ancestor, we we cannot say that there were no other cases of blue eyes in the past.

  16. On 12/30/2023 at 8:56 PM, J.C.MacSwell said:

    Single common ancestor...so from the simplest blue/brown model that ancestor could not have had blue eyed kids...but at earliest could have blue eyed grandkids given an incestuous relationship of those kids...assuming they had at least two with the recessive blue gene.

    It does not have to be. It is possible that other variants existed, but they vanished with this specific haplotype being the sole survivor.

  17. 3 hours ago, Luc Turpin said:

    You would be surprised by how intelligent cells can be and they have no brains. Just the cilia and its role of scrutinizing the outside (of cell) world is astonishing.

    Your definition for intelligence seems to include simple biochemical processes, as such it does not seem to be a useful definition. I.e. you could as well use the term life or survival instead of intelligence. And none of those are directly linked to evolution. You could survival all you want, but if you do not procreate, it matters little for evolutionary purposes. The premise you seem to make is similarly broad. Everything contributing to survival is consider guidance. This is not only overly broad but also seems to suggest that there is a target that is being guided towards to, without specifying it.

    Together, these definitions are immensely unhelpful to discuss evolution, as it mostly ignores the actual connection to evolution, focuses on individuals rather than populations and largely ignores environmental selective pressures as well as stochastic mechanisms of evolution in favour of sliding the term "guided" in.

    5 hours ago, mar_mar said:

    Homo sapiens, who has evolutionary changes in one's development.

    Not sure what you mean, but I want to emphasize that evolution happens on the population level (i.e. the composition of the gene pool of a given population).

    5 hours ago, mar_mar said:

    What time?

    Generations.

  18. 3 hours ago, mar_mar said:

    Evolution is the change in the heritable characteristics of biological populations over successive generations

    heritable /ˈhɛrɪtəbl/ adjective      (of a characteristic) transmissible from parent to offspring.

    So. Who is the "parent" of intelligence?

     

     

    Not really, evolution is the change in the total genetic composition (i.e. gene pool) over time. Even if no traits are changed, the gene pool can. However, selection happens on heritable traits, which is what you are thinking about. But this is only one aspect of evolution and not the only one. And what parents transmit to the next generation are not identical traits, it is the genetic material. This is an important distinction as depending on the mix the next generation(s) receive, the traits might be quite different from those of the parents.

  19. 1 hour ago, Phi for All said:

    but we also get college-aged people who are simply used to writing like that, so how do we tell the difference moving forward?

    Well, the way it is going, college-aged people will sound like chat GPT, because all the writing comes from there (or will be soon). Probably a bit off-topic, but we will likely see fewer folks writing more complex texts with their own voice. Mostly, because they never learn to do so.

  20. 25 minutes ago, zapatos said:

    As I said, that only works if both sides agree. Israel can spend all they want on the Palestinians, but if the Palestinians want Israel to die and keep lobbing missile, it won't work. The part you seem to bypass whenever you suggest alternatives to violence is that BOTH SIDES have to agree to alternatives to violence.

    I think a fundamental challenge is building trust between the groups. And from what I see, these happen mostly on the ground with local association and between activists. But Oct. 7 put a heavy strain on these initiatives. And the political entities in this conflict are very  apt in leveraging the distrust. 

  21. 1 hour ago, mattrix said:

    Clearly I don't understand evolutionary genetics. Can anyone suggest a good book?

    I think the seminal undergrad text book on evolution is still Futuyma. 

    The 1-2% with chimpanzees is a different type of count, and was really base on looking at genes (i.e. excluding large non-coding areas) and even then it was based on a subset of genes. In addition, I believe they were based on substitutions. For example, let's say humans have a stretch of DNA being GCTTA and chimpanzees at the same locus it would be GGTTA then there would be one substitution (C->G). But there are also regions with deletions and insertions. E.g. GCTTA becomes GCAAGCGCTTA, the question is how you quantify the additional AAGCGC (or the missing part, depending on perspective). The original 1-2% differences simply ignored them. I believe lining up the genomes and matching the bases would still yield something like 80% match, but not entirely, memory gets a bit hazy.

     

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