Slashdot Mirror


User: Samantha+Wright

Samantha+Wright's activity in the archive.

Stories
0
Comments
4,268
First seen
Last seen
Profile
(view on slashdot.org)

Comments · 4,268

  1. Re:Super8 on Microsoft Is Working On a Cloud Operating System For the US Government · · Score: 1

    Perhaps they'll call the NSA backdoor Shadowfax?

  2. Re:evils of sugar on Study Ties High Blood Sugar To Dementia · · Score: 1

    Admittedly that may not have been clear in my post. My point was that you shouldn't fear the molecule, that's all. You'll always be deriving energy from glycolysis, and it'll always be a more efficient energy source.

  3. Re:evils of sugar on Study Ties High Blood Sugar To Dementia · · Score: 1

    Ah, snap. Sorry. I was using the number of measurements. (I promise I know my basic stats, even if not how to read. It's my day job.)

  4. Re:evils of sugar on Study Ties High Blood Sugar To Dementia · · Score: 4, Informative

    Sugar is the most basic kind of energy source. It's extremely important to your body, but as with everything, there are limits on what intake is healthy. (As Stephen Fry once said, 'Well of course too much is bad for you, that's what "too much" means you blithering twat. If you had too much water it would be bad for you, wouldn't it?')

    Don't worry about the dementia thing too much. While it's a very strong correlation, it only increases the risk of developing dementia to 120% of normal for nondiabetics and 140% of normal for diabetics, which is still only about 1-2% of the people in their study.

    As for the other consequences, it may help to understand them a bit better:

    Tooth decay is caused by sugar left on your teeth. You can consume a ton of sugar and never have any tooth issues if you brush aggressively. Cavities are caused by bacteria in your mouth breaking down food left on your teeth, which causes them to release acidic byproducts. Starches like potatoes, corn, and bread are actually much more of a problem, however, and are the primary cause of cavities.

    Gaining weight happens because the human body isn't prepared, evolutionarily, to regulate its own food intake very well. We have a high inclination toward absorbing and storing extra energy because that gives us the best chance of surviving a famine. Because sugar is the most basic kind of food, the body uses it as a clue to say "it's time to absorb nutrients!", hence sugary foods make you gain weight even faster. This is part of the normal purpose of the hormone insulin.

    Diabetes isn't only caused by high sugar intake; it can be inherited too. Technically it's an inability to recognize sugar and absorb it, which (amongst other things) causes gradual starvation if not managed properly. Sugar causes it only if you consume a great deal for a long period of time, which makes your body start to ignore insulin. Diabetes can also be caused by pancreatic damage (type 1) or temporarily by pregnancy.

    Acne is a weird issue; it's also caused by bacteria, in this case sitting on the skin. The immediate cause is a spike in testosterone, which can be induced by a number of sources, because it roughens up the surface of the skin. Sugar is one of those sources, but simply having overactive hormones as a teenager is probably a more dominant issue.

    And as Slew said, sugar isn't acidic, it's just the breakdown of it that gets to be that way. This doesn't really have much of an effect on your body unless you're already suffering from acidosis (acidic blood), and you'd die very quickly if it stopped entirely, so don't worry about it.

  5. Re:What do we have here? on Bacteria Behaviour Can Shed Light On How Financial Markets Work · · Score: 2

    Wait, wait, work through this with me. Are you saying you're the only fountain of abuse on Slashdot? It was just you the whole time? This changes everything.

  6. Re:This is a surprise? on Bacteria Behaviour Can Shed Light On How Financial Markets Work · · Score: 5, Insightful

    Economists have a history of borrowing scientific theories to explain their field, often overindulging in analogy to the point where the metaphor becomes useless. Consider the following paragraph from the article:

    But when bacteria were exposed to acid, something unexpected happened: Those that invested almost nothing into managing stress, and instead favored growth at all costs, succeeded. Gudelj doesn’t yet know the actual mechanism behind this, but she suspects that it’s down to the particulars of the life cycle of the bacteria and its stressor. When taking this analogy to businesses, it appears there are certain types of difficulties for which being nimble and focusing on growth is a better strategy than facing difficulty by trying to manage it.

    The author is unable to suggest what these types might be; he simply assumes that the theory is valid and that bacteria must have something to tell us. This kind of growth works for bacteria because they are able to subdivide indefinitely and aren't a monolithic organism. To stretch an already-abused metaphor, the closest example to this kind of growth is creating many similar products or entering a large number of markets to try and find something that works, both of which can be hazardous because of the paradox of choice and loss of investor confidence. Moreover, if a core market collapses, at best all that will be left is the parts of the company that entered the market that succeeded; for bacteria, it's considered "good enough" for a couple of cells to survive, but this is not generally considered acceptable for business. Bacterial survival simply isn't analogous to business success.

  7. Re:From the summary: on Nvidia CEO: We Are Working On Next Generation Surface · · Score: 1

    Not only were there Microsoft watches previously, but there are currently Android watches, Apple watches (slightly discontinued), and a Microsoft table platform that used to be called Surface. They definitely have plans to take over walls, but so far that's still limited to projector-powered prototypes at Microsoft Research as far as I know.

  8. Re:Outlook? on Nvidia CEO: We Are Working On Next Generation Surface · · Score: 1

    Well, there are these.

  9. Re:Outlook? on Nvidia CEO: We Are Working On Next Generation Surface · · Score: 1

    Perhaps the saddest thing is that when Microsoft killed the Courier, the only substantial reason we heard was that its email interface wasn't Outlooky enough.

  10. Re:From the summary: on Nvidia CEO: We Are Working On Next Generation Surface · · Score: 1

    And while they're at it, a battery! And a keyboard! And a start bar! And... these examples were supposed to be obvious and childish in order to make light of a rather alarming shortcoming, but I can't come up with anything that doesn't sound like a genuine putdown. Help?

  11. Re:better feel for stability in the 70s/80s on Back To 'The Future of Programming' · · Score: 1

    No, no, don't think like that. All CS graduates need is to love and appreciate the nature of the fine bureaucracy at Central Services. If you don't know what a BeanFactory is, you're not a programmer!

    If it's any consolation, the experience of getting a feel for system stability can be acquired by writing a really complex program in a terrible environment, such as PHP or classic Visual Basic. Perhaps a pithy book on the topic of the art of programming might help bring some of that back.

  12. Re:How's that working out? on Back To 'The Future of Programming' · · Score: 1

    I'm not sure how that proves traditional programming paradigms are better than some of the alternatives we have available.

  13. Re:Yeah but on Back To 'The Future of Programming' · · Score: 1

    And all such traditions have been vastly improved by subsequent paradigm shifts towards more willingness to experiment with radical ideas.

  14. Re:Epic facepalm on Back To 'The Future of Programming' · · Score: 1

    Massively out of context. The quote is about how people have been taught to assume procedural programming is the only way of programming. The point is that creative people are being limited by these mistaken assumptions.

  15. Re:Sorta on 4-Billion-Year-Old Fossil Protein Resurrected · · Score: 1

    ColdWetDog pretty much nailed it: endosymbiosis is believed to have happened in the Proterozoic era, only 2.5 billion years ago, based on DNA evidence. This is also the same period that the archaeological record suggests. Mitochondria and other plastids are actually just bacteria that hitched a ride; the mitochondrion is from a purple sulphur bacteria, the chloroplast is from cyanobacteria, and so on.

    Personally, I don't believe that a lack of wildly different chemistry is proof there was a LUCA, although its existence would be strong evidence of disproof. The reason we believe in a single LUCA is quoted really well in the appropriate Wikipedia article: the number of genes in common between Archaea and Bacteria is much too high for them to have been shared later.

  16. Re:"resembled those that existed when life began" on 4-Billion-Year-Old Fossil Protein Resurrected · · Score: 1

    In other words, it's yet another research paper where they claim to have dealt with an problem without actually having done so. For example, high precision results which are compared and fitted to an extremely poorly understood past.

    The results are not fitted; the observation that the enzyme performs better under an acidic environment was spontaneous and unguided.

    While I agree that this is an attempt to deal with my final concern below (about the biases that evolution puts into place) this is also a great way to introduce researcher biases into the final results. Recall that "time steps" are degree of change of the protein and have at best a vague positive correlation with the passage of time. So what "time steps" are important and how to group that high precision data? These are subjective choices that can influence the outcome.

    The time steps are actually the most recent common ancestors of various clades, and are not arbitrary at all. There is nothing subjective involved in this part of the process, and no dates for these are claimed explicitly in the paper; only the roots of trees. The only claim to a specific date being made is that the last universal common ancestor lived about four billion years ago, which is an extrapolation based on a wide range of evolutionary and fossil-record evidence, not just the molecular clock.

    For example, maybe they're actually reconstructing a much later period where universal selection pressure shifted all organisms a certain way. And there's the possibility that there were considerably more protein changes per unit time in the past (which had a more radioactive environment than today, both in background decay radiation on Earth and likely a higher cosmic ray background as well).

    Fluctuations in the Earth's magnetic field are so frequent and minor that they're already averaged out across the molecular clock, which greatly diminishes the potential for changes in cosmic ray impact. Geologically, it is evident that the magnetic field is at least 3.54 billion years old, which limits the potential range in which anything so dramatic could happen. It is perhaps possible that isotopic decay has had a significant impact on the global rate of evolution, and that DNA repair mechanisms took time to evolve, but an underestimate is more likely due to saturation of mutations. I'm not a complete expert on the molecular clock, and it's possible that the 4 Gya figure is a little controversial, but since we have evidence for 3.8 billion-year-old archaean fossils, which would have to be after the LUCA split by most theories, it's not an unreasonable figure.

    The procedures you describe wouldn't have gotten around the inherent biases of evolution. In language where the technique started, there isn't an inherent survival value to how you pronounce "father". Tribes who pronounced words in a certain way weren't more likely to die off. I don't think such evolutionary biases would show up in this method because organisms exhibiting those weaker protein patterns would have billions of years to go extinct and hence wouldn't be around to be measured today. And no matter how detailed a reconstruction you do, you aren't going to reconstruct extinct branches from existing organisms.

    There definitely are evolutionary pressures in tribal pronunciation choice, although they're not very common: on one extreme, you have the shibboleth, where intertribal pressure forces conservation of pronunciation, and on the other, a language can only tolerate so many homophones.

    Extinct branches are of no interest to this reconstruction. They're trying to find the ancestor of the current surviving crop, not rediscover what all life was like at the time. A more serious concern is that some convergent mutation occurred in all descendants where

  17. Re:"resembled those that existed when life began" on 4-Billion-Year-Old Fossil Protein Resurrected · · Score: 1

    Yeah, all journals have retractions, and they've been getting worse for a while as people become more pressured by lazy employers with shallow performance metrics. I think there's some sampling bias that makes it less likely such stories will hit the mainstream press (perhaps a case of science journalists not messing up?) but they do happen; mounting pressure to get high-profile publications is met with mounting editorial rigour.

  18. Re:Does anyone, and i mean ANYONE, question the ag on 4-Billion-Year-Old Fossil Protein Resurrected · · Score: 1

    Don't be so hard on the RIAE; they were simply exercising their legal freedom to shoot themselves in the foot by destroying their whole industry. (Although if you're semi-vaguely-actually curious, the Venter Institute put a watermark in the Mycoplasma laboratorium genome a couple of years ago, which everyone thought was in terribly bad taste. Such sequences usually mutate randomly into illegibility in a few decades because nothing depends on them staying put.)

  19. Re:Sorta on 4-Billion-Year-Old Fossil Protein Resurrected · · Score: 5, Interesting

    The LUCA dates range from 3.5 to 4 gya, so it's even broader than that. Different estimates come from different sources and with different precision, though, so it's not quite right to give a single symmetrical error measurement. I'd personally vote for saying 3.8 +0.2/-0.3 gya. In the case of this article, however, they chose 4 exactly because of their molecular clock predictions.

    The article doesn't clarify between the Archean and Hadean periods, however, and it's probably bad to equate the LUCA with the beginning of life because we have pretty strong evidence that the LUCA was already a very well-developed organism, with a complete central dogma, hundreds of enzymes, and a preference for potassium ions over sodium ones. Wikipedia cites several science journalism pieces that argue for a Palaeoarchaean LUCA.

    As for what the LUCA actually looked like, I would say somewhere between Archaea and Bacteria, but defying both categories. Archaeans have a number of later innovations that definitely disqualify them from being good representatives, since they can do sophisticated chromatin modelling (folding DNA to make gene transcription more efficient) and have a unique membrane composition (which I personally like to imagine may be evidence of multiple abiogenesis events, but that's a bit of an uninformed theory.) Bacteria, on the other hand, are known to have a tendency towards simplifying their genomes. If anything the bias seems to be toward Bacteria as the root; no one has recently proposed that Archaeans pre-date Bacteria.

  20. Re:"resembled those that existed when life began" on 4-Billion-Year-Old Fossil Protein Resurrected · · Score: 4, Informative

    To be fair, the IB Times article doesn't do a very good job of explaining the lengths the researchers went to in order to avoid that. Here's a summary:

    • - The researchers were acutely aware of the exact problem you described, and spent several paragraphs on it in their background section.
    • - Their way of getting around it was to ensure consistency at various time-steps, which revealed a gradual change in the shape of the protein overall that wouldn't have been evident if they'd just used a multiple sequence alignment and gone with the maximum parsimony route.
    • - The models they ended up generating are extremely high-precision and based on a ton of data.
    • - The final results perform optimally in an environment similar to ones from 4 gya according to archaeological evidence. They didn't try to force that, which means they must've gotten it very close to right.

    In the future, here's how to read scientific news stories (at least molecular biology ones):

    • - If the article was published in Nature or Science, it's a really big deal. Any shortcomings you can see are probably failures on the part of the journalist. I think PNAS is in this category, too, but as a bioinformatician I don't know quite enough to comment.
    • - If the article was published in Cell, it's also almost certainly really serious, although you should note that the authors have no scruples because they're publishing in an Elsevier journal.
    • - If the journal name sounds like it's just a description of the field with no organization attached ("Journal of Microbiology") then it's probably from a fake journal. (But not necessarily. Tread with caution. In particular, one-word journal titles don't fall in this category.) Any exciting claims made by the journalist are probably exaggerations.
    • - If the article came from PLOS ONE (and only that journal; there are lots of good PLOS journals) it was terrible or boring science and couldn't cut it anywhere else. Anything exciting in PLOS ONE is probably a typo.
    • - Any other journal (e.g. Oxford Bioinformatics) is fairly reputable but not infallible. It's unlikely that the journalist understands more than half the article.
    • - If the source is a university press release, it's complete crap. Unless you're a potential donor, in which case you should eat it up.
  21. Re:Al? on AI Is Funny - a Generative Joke Model · · Score: 1

    Actually, the questions were pitifully easy to get right. It was multiple choice, and none of the other options were remotely plausible. I know this because of reasons.

  22. Is this a joke about campaign contributions? Because it's not really a joke...

  23. Re:"resembled those that existed when life began" on 4-Billion-Year-Old Fossil Protein Resurrected · · Score: 3, Informative

    ...sorry, I've read the article a little more closely and I made a couple of factual errors in my other reply to you and the one before it. There were small structural changes, and the primary purpose of this paper was to investigate ways of detecting them. Convergent evolution (every copy changes at once after a split) does occur in protein structure and sequences, primarily due to large-scale environmental changes.

    The paper's primary contribution is that they stepped back gradually, rather than doing a bulk sequence alignment (what they called a "vertical" approach rather than a "horizontal" one) and found that to maintain function, certain shifts had to occur. (The details of which are rather boring.) Rather encouragingly, they found that, by the time they'd stepped back all the way to the beginning, the changes the protein experienced meant that it would perform optimally in a chemical environment much like the one archaeology has shown us was ubiquitous in the Precambrian era. Not only does this support the idea that their results are very close to being correct, it also tells us that the LUCA probably had a fair amount of time to evolve its thioredoxin to that environment.

  24. Re:Does anyone, and i mean ANYONE, question the ag on 4-Billion-Year-Old Fossil Protein Resurrected · · Score: 2

    Which is quite honestly a reasonable thing to say, as that's what the molecular clock dictates. It probably means that thioredoxin was a little more variable at first than it is today.

  25. Re:"resembled those that existed when life began" on 4-Billion-Year-Old Fossil Protein Resurrected · · Score: 2

    Yeah, I'm actually a fan. I wanted to be an historical linguist when I was a teenager, but I was worried about job security and ended up in evolution as a result. There are lots of different sophisticated evolutionary systems out there that all obey the same basic structure (governments, cultures, religions, public-domain code snippets, Linux distros...) and the little nuances that distinguish them from each other can be downright mesmerising. (But to be honest I find the whole Germanic language family boring. Xenophilia, probably.)

    Related factoid: the first phylogenetic constructions of biological sequences were based on principles borrowed directly from stemmatics.