Paralith

I agree with SkepticLance that you need to define the way you are using the world empiricism - it does not seem to match the technical definition of the word. Scientists are themselves only human, so there are of course some of us that will give in to using political/media-esque spin on our work. But science in general does not depend on this, and most certainly not the life sciences. Discoveries in this area may be more subject to media spin due to their complexity and the ease with which they can be misunderstood. But again, I do not think this is the fault of the science involved - that the theory is not advanced enough, as you put it, that it is like gambling. The theories in life science is no different from those in physics and chemistry in that they are built upon methodical testing and re-testing against gathered data. You call physics and chemistry the only rational influence on life sciences, but that is because they form the first and more basic levels of biology. Higher and higher levels involve increasingly complex phenomenon, as you yourself say, which in turn makes that much more difficult to reduce the phenomenon we see into simple and easy to understand "rules" such as the speed of light is 2.99 x 10^8 m/s. I feel I speak for most life scientists when I say we are doing the best we can with such a complex system, and that I challenge you to find a better way to do it.

But knowledge of what? Isn't science about building our knowledge of the nature of our world, of the true nature of our world? If you don't like the word "truth," how about the "reality" instead - knowledge of the reality of our world. What other kind of knowledge would we be pursuing? I don't understand the distinction you're making.

I don't think I really agree with you about the greed/intelligence thing. The guiding force of any society is power. Money is one avenue to power, by buying your way there, essentially. I don't know that much about Chinese history, but just going off of what you said, think about it - who set up this system of the smart people working in government? The leaders at the time must have set up the examination system, and perhaps even over time a cultural belief in the importance of serving the government (/king/emperor/county, etc) - and those leaders drafted all the smart people to come work for them. Sounds like another good way to gain power - control all the intellectuals in the country for their own uses. But I think this is getting off topic, we should probably steer back.

You're definitely right about the quality of data. It's an issue whose existence the popular media seems blind to. But the OP referred to the incorporation of conflicting data into "empirical correlations" - and if we're simply talking about data itself, then it seems rather obvious to me that yes, some data points will appear to conflict with the trend that the other data points follow. This will depend largely on the nature of your object of study, and not necessarily on the quality of the science involved - though obviously, better methods of measurement/observation/etc can at least make the gathering of data more accurate. Not all smokers develop lung cancer due to the complexities of cancer - the very nature of the subject leads to the existence of conflicting data points. To say that this conflict is a fault of science is not something I would agree with. Am I misunderstanding the OP?

I'm not so sure I agree. A correlation is - well, a correlation. It's not a theory, it's not an explanation, it's a correlation. It says, these two (or more) things generally change at the same time. That's all a correlation says. Now if the popular media decides to take that correlation and say it means something more than that, they're wrong. A correlation is more of an avenue towards more in depth research, something from which you create a hypothesis, which you then test more thoroughly to see if there is actually a causal relationship between the two things. That's why correlations aren't held to high standards, because a correlation is only an observation, and by itself without further research can mean nothing.

to agentchange: I think you may be focusing a little too much on the appetites of modern humans in industrialized nations. We eat WAY more food than we need to survive, and plus we have all the technology (and the resources to produce that technology) to reap all that we can. A hunter-gatherer family could probably live off one fat deer for a solid week, maybe more. And they would, because hunting deer isn't that easy if you don't have camo gear and lures and rifles with laser sites and enough spare time to sit in a tree all weekend for that one good shot, even with all the technology. Hunter-gatherer cultures also can't sustain the same amount of people as an industrialized group can. Agriculture itself is what allowed humans to develop large, stable, year round populations that might have been able to strip the local area of most natural resources. To foodchain: Being a migratory generalist does not necessarily lead you to being highly destructive. Look at mice. Mice are all over the world, in varying species perhaps, but all in all extremely similar to each other. Mice are generalists, they are able to eat many different types of food - but they're not particularly destructive. I think SkepticLance has struck on the key, that being human technology. It's our technology that has made us so destructive - our technology, like agriculture, that allowed us to grow to huge numbers, to require such huge amounts of resources, our technology that has spoiled us, in a manner of speaking, so that many of us desire and think we need much more than we actually do - our technology that allows us to act out these desires.

I definitely agree with someguy in that modern human society really only requires a few people to be truly gifted, in a manner of speaking, to be the ones to make the real advancements, as those advancements will then be disseminated culturally to the rest of the species. But let's apply this to the question of race. Races arose largely due to a certain degree of geographical separation, which each subgroup adapting to its specific environment without too much dilution from other groups. So wouldn't the people in each geographical area need their few smart people in order to make the necessary cultural advancements? The nature of these advancements will of course vary according to the cultures and the environments, thus the nature of "intelligence" and "knowledge" will not be the same for all races. But this certainly doesn't mean that only one geographical area, only one race needed their smart people, while the others all had it so easy that all the smart genes dropped out. As far as intelligence being heritable, look at what lucaspa said: Intelligence is BOTH heritable and determined by the environment. While genes may give you a tendency towards low or high intelligence, that tendency may not make much of a difference if the environmental conditions are those that highly favor the cultivation of intelligence, the proper development of your brain. Perhaps the brain needs to be challenged enough, or perhaps a child needs to be encouraged to learn and then they will learn more, or other things along those lines. Obviously we're not 100% sure what all these factors are and/or how they work, but they definitely make a difference. Heck, we can even wade waist deep into wild conjecture and say that perhaps every human has within them the capacity for high intelligence, so that in the chance event that those few smart people of the species don't reproduce genetically intelligent children, environmentally smart children can step in and take their place, thus ensuring that species never goes without their intelligent caretakers.

I'm assuming you're talking about transformation of bacteria colonies and inducing them to take up a DNA fragment. The point of this is to maintain and amplify the DNA, so obviously the protocol won't include any conditions that will destroy the DNA. Usually the DNA used is also a fragment that was synthesized in vitro, with PCR or the like, so the DNA won't be methylated - but I would assume that after transformation, when the bacteria replicate, that the DNA within the bacteria would then become methylated, since it is being synthesized in vivo. I'm not entirely sure about that, though.

I think your suppositions have a high probability of being correct, Phi for All. I personally know someone who's job it was to cruise forums, assess opinions of certain movies or tv shows or video games, and to attempt to change them in one way or another. Yes, he was paid to do it. However, he was probably better at it, because he told me the rules were that he had to have at least 100 neutral posts in the forum, thus establishing himself as a real member, before he began to make his influential posts. Apparently this person has just jumped right in.

As a small addition to lucaspa's excellent post, predators don't have to be fought tooth and nail in order to drive them away, either. They also wish to avoid injury, and they won't put more energy into a certain prey item than they are going to get out of it by eating it. Getting away with a chimp isn't worth the time and energy it might take to fight it into submission. Studies on this phenomena have been done with snakes hunting lizards - if the lizard struggles long enough, the snake will probably let it go. It's become too much trouble to subdue the animal, and the calories gained from eating it won't balance out, so they just let it go to prevent further loss of energy or risk of injury. So it's not as though the australopithecines would need to inflict serious damage to any predators they encountered - as long as they made themselves just too much trouble to catch, the predator would most likely happily find some other prey. They wouldn't necessarily need spears to do this.

Simple extrapolations from modern, extant species back to their ancestors isn't usually a good move, at least not without evidence to back it up. Just because chimps today use tools doesn't necessarily mean that their ancestors, especially as far back as the human-chimp split, also used simple tools. They might have, but we can't make that assumption. Also, bonobos and chimps are equally related to humans, so by your thinking of a progression, they both should have about the same amount of tool use relative to humans, and they don't. I just don't think a linear progression should be applied to something like a cultural development, at least not without proper evidence to back it up.

How big was the troup of baboons? Was there anything worth protecting where they were? Just because you are capable of making a stand and putting up a fight doesn't mean you always have to risk it. Maybe their numbers were too small, maybe it was easier to just get up and leave that particular patch of rock. You can't take one instance found on film and apply it to all situations. Besides, there are mutliple advantages of being in a big group besides directly fighting off predators. One of the main advantages is vigilance. More members means more eyes looking out to see predators - so that as soon as one comes in to view, the alarm will sound and everyone can escape well before the predator can sneak closer for an attack. And that definitely increases survival rate, making group living quite favorable. Yet another advantage that still involves running away is confusion. It's hard for a single predator, like a leopard, to pick out and follow one target if several dozen baboons are running around like maniacs every which way. By the time the smoke clears, everyone is gone.

I can't speak much to the mechanism, but I have a few bits of knowledge that might answer the phylogenetic aspect. What few people know is that all reptiles (which includes birds, despite their having evolved to a very different form) have color vision. Mammals and reptiles are also sister groups. So you might think that color vision evolved in the common ancestor between reptiles and mammals. However, a great many mammals do not have color vision. Primates are one of the notable exceptions. (One theory has to do with primates being primarily frugivores - it's hard to tell when a fruit is ripe if you can't tell what color it is.) So if anything, primates probably evolved color vision independently from reptiles. Birds and mammals share quite a few independently derived characteristics, such as being warm blooded. It would be interesting to think about what aspects of the two groups' evolution caused this.

(thanks, the link worked ) I'd have to agree with SkepticLance. Like people in the article said, there are many reasons why bones and tools and buildings would accumulate in one place that would not include permanent year round settlement. It could have been a place they visited yearly, during a season when fishing was particularly good, or maybe even a place they went to bury their dead. I'd like to see the argon dating information. A researcher in the article said none of the artifacts were dated except typologically, so what exactly did Ziegert date with potassium argon?

The point is we could be living in a constructed reality that is programmed to show us instruments and computers acting in a certain way. I'm sure we've all had dreams where, say, dogs could talk, and everybody knew dogs could talk, and dogs had always talked and would always talk. And if you were trapped in that reality and didn't know it, all would seem right with the world. I feel like this is kind of a pointless thing to discuss, though. We could be trapped forever and everything could be an illusion that will never break and never let us free!!! Well, yes. But from my point of view this life isn't so bad, and at least it's fairly consistent, and we can use logic and science to function within it. If we're actually trapped in an alternate reality, there's nothing we can do about it. *shrugs*

hmm - the link to the article doesn't seem to work. Any way to stop the link from getting truncated like that?

I took a philosophy class a long time ago, and I know for a fact one of the big players addressed this idea - basically, we could be brains in a box being fed everything we think we're experiencing, and we wouldn't know it. I just don't remember who exactly it was. /^^ I tend to think of it in the same way I think about the existence of some god who could be conjuring all the scientific evidence in the world just to fool us into thinking we're figuring it all out. If it's true - well, there's nothing we can do about it. Better to continue to function in reality as we know it then to try and prove something that is completely impossible to prove - or disprove, if you break the rules of the thread and follow science/logic.

huh - I never knew that about melatonin. I thought it just helped you feel sleepy. I had this little theory that I remembered my dreams better because my brain was more active - around the time I started with the dreams, I began studying and working in a way that I hadn't for months before hand. Either that, or because I just wasn't sleeping very well on our old bed, haha. But we have a nicer one now and nothing has changed.

I also know that #2 is true as well - in fact, you usually have anywhere from 3-5 dreams a night, you just only remember them a few nights a week. Something weird has been happening to me lately, though. A few months ago, I started remembering my dreams every morning. And I still do. Every morning I wake up and I remember at least several dreams that I've had during the night. I've tried researching why this might be the case, but I haven't gotten anywhere. *shrugs* food for thought, I guess. <unrelated note> congrats insane_alien! =)

The reason why reproductive isolation causes speciation is that it blocks the exchange of genes between species. Now even though a chihuahua may not be physically capable of mating with a great dane, genes can still be passed from one to another through intermediary matings. This is similar to the idea of a ring species - both sides of the debate can be reasonably argued. (http://en.wikipedia.org/wiki/Ring_species) Dogs probably aren't the best example to argue species concepts with though, because their breeding is so carefully controlled by humans. If all the breeds were let loose in the wild to do their thing, we can't be entirely sure what would happen to the extreme breeds. Most dogs will mate with whatever female dog they can manage with, and aren't choosy about breed, so after time the chihuahua and great dane breeds could possibly have a great comingling of genes.

I feel like this thread happened twice. First, SkepticLance tells us what Lomborg says about habitat loss. Then some of us (myself included) respond with anger at the idea that habitat loss isn't a major cause of extinction. Then SkepticLance tells us that if we're so darn sure, go and find clear cut examples. So, we go looking for examples, because we know they must be out there somewhere. Lucaspa did a better job than I did, but all in all most cases brought up do have some other contributing factors involved. We come to the conclusion that habitat loss is the weakening blow that allows other contributing factors to really hurt, but which do we blame for the extinction in the first place? Finally, SkepticLance agrees that habitat loss is bad thing (but a general, major contributing cause? he never quite concedes it), and then says that it's all about prioritizing conservation efforts. But what makes habitat precious? And what are non-precious habitats? Isn't a habitat precious because of the treasure of species diversity it holds within it, that cannot be found in other habitats? Or just because photos of the place make for good wall art? And once the poachers are stopped and alien species aren't coming in, how does the endangered species in question make a comeback if it's living in an area too small to support a strong, stable population? Habitat loss is important, and it needs to be addressed. If conservation efforts are the ultimate subject of this thread, I think that much can be said with certainty.

I realize now that I should have read your previous thread about chrial life and your blog entry earlier. I didn't know that this thread was an extension of that previous one - I thought you were trying to find ways to control and adjust existing ecosystems. Now I see that you're trying to find a way to design a new ecosystem, just pick and choose which organisms you want, change their chirality, set it up, and let it run. I think this is a very challenging goal. Ecosystems are very complex and to design one from scratch, and be sure that it can sustain itself autonomously and still have the high rate of food production that you're looking for - that's a tall order. There's still so much we don't know. As already mentioned by someone else in your other thread on chirality, there's all sorts of micororganisms that are beneficial and perhaps even necessary that we may not know much about yet. And in selecting the organisms that we change the chirality of, we could miss vital ones and not know it. You also seem overly optimisitic in our ability to achieve mirror chirality in the first place. Do you have any outside opinions or research that would support your idea? The minimum unit that would have to be mirrored (for humans and other sexually reproducing animals, at least) would be the very beginnings of an embryo - at the single diploid cell stage. At that stage you have the entire genome, and you have the necessary machinery (proteins) available to express that genome correctly. This is still a lot of stuff to change. The entirety of the genome, enough of the proteins to make it work. That's a LOT, a lot of things to recreate accurately and correctly. And again, we would also need to consider exterior microbes that later become necessary. And make sure we have them all. And as you said, then we need the right form of food. And I have a feeling most people won't be happy eating a boring paste of the correct chirality. To keep human life at the same quality it is now, a LOT of things would have to be changed, accurately, and correctly. How will the templates be read? How will the new molecules be made? How will they be constructed? I'll admit I don't know a lot about nanotechnology, but do you? I haven't see you reference anything to support your idea that this is going to be possible. That would be my first step, if I were you.

You have to think about it in the right context. Thanks to our cultural and technological advances, many humans today don't have to put a lot of effort into simply surviving. A person in a modern-day first world country could get by his whole life working in a fast food joint flipping burgers and going home and playing video games. And if he manages to get married and have kids along the way, then he's been reproductively successful. In evolutionary terms, that's fine. Nothing wrong with that. But you and I look at that and say, what an empty, boring, wasteful life. We say, it's better to challenge yourself, it's better to have some "stress," as you say, to motivate us to do better things with ourselves. But I think this is more of a human-created value, and not one that is necessarily better when it comes to reproductive success. I think the idea of sort of creating a stable, productive ecosystem for the production of our food is one that the agricultural industry is probably actively studying - they may not be thinking in the same terms as you, but I think the end goal is the same. Though a monoculture of corn isn't really an ecosystem. Yes, if you remove all the corn's parasites, are their diseases, and anything that could possibly compete with them for resources, and only allow organisms to stay that form a beneficial mutualistic symbiosis with corn - then that corn will produce much more.

A eukaryotic protein-coding gene will have certain characteristics that will allow you to pick it out from a given stretch of DNA. In front (upstream) of the gene are usually promoter sequences, sequences that interact with proteins that aid in or repress gene expression. The gene begins with a start codon, a specific 3 nucleotide code that marks the beginning of a protein. After being transcribed into mRNA and taken to a ribosome, the start codon tells the ribosome where to start reading and adding amino acids. Within a gene, there may be introns, sequences that, once transcribed into mRNA, are removed before moving on to translation. These introns are usually flanked by predictable sequences, so that the proteins that splice them out can recognize them. Finally, the gene ends with one of three possible stop codons, which in mRNA tells the ribosome to stop adding amino acids and to release the mRNA and the newly formed protein. By looking for these patterns, we can get an estimate of how many protein coding genes there are in the human genome. I hope that helps.

From what I understand about the hormesis article you linked to, this phenomenon does not always hold and is still very uncertain. It seems to me that hormesis would better be defined as a characteristic of certain, specific situations, rather than a rule. Certain toxins or stressors have different effects when given in low doses than when given in high doses. That makes sense, especially in terms of the rationale given - that the small dose may prime the body to prepare defenses or other recovery mechanisms ahead of time. This is not unlike how a vaccine works - a small dose of the virus is given so that your body will learn to recognize it, and if encountered again in dangerous amounts, your body will already have mechanisms in place to fight it. Let's think about the nature of stress for a minute. If an organism is stressed, that basically means something is wrong. The organism has a parasite that is taking away needed energy; there is less food in the area than the organism needs; there is a predator nearby that could injure or kill the organism. Since something is wrong, then something must be done about it. The immune system will kick in to kill the parasite - the organism will migrate to a new area with more food - the organism will constantly stay alert and on guard, listening for the predator. All of these are energy requiring responses. Stress, no matter what kind or what amount, will elicit a response, and that response will require energy. This is nothing special, and I don't think it has much to do with hormesis. This is why stress is in general so bad - all the organism's energy is being spent on other things, leaving less energy for growth, health, and reproduction. Elderly people are a special case. Today's humans are living much longer than they ever have in human evolutionary history. Their bodies are naturally declining - they have lived through and past reproductive age, and are entering a time that, metaphorically speaking, evolution is blind to. Our bodies are not adapted to maintainthemselves into such old age. At this point, it's a game of "use it or loose it." Muscles will atrophy, bones will weaken - unless they keep active, sort of fooling their bodies into thinking that maintaining these structures is necessary, because they are being used. Memory and cognitive ability will fade, unless the brain is actively used, unless you keep learning - again, making maintenance necessary because it is being used. Just because this is true does not mean that stress in general is good. Because it isn't. I think you also need to throw out point 2. Elimination of "weak" animals - ones not suited to surviving in this ideal ecosystem of yours - will happen naturally. Stress will happen naturally. The organisms will adapt, leave, or die. And if they adapt well enough to survive and reproduce, I don't think even you can call them "weak." I think point 1 is the only one that has any merit, though again, population control will also often happen naturally, and there are many other ways to do it than with diseases or parasites. Predator-prey relationships, space and resource limitations, etc.