Nathan Flinn

I guess 2^9, as per Conway's Game of Life. Actually they are a bit higher

Have I really? Where do I claim that there is only one factor contributing to the mutation rate? I focus on one factor (the variability of fitness landscape) in order to support the point that there is a possibility of teleology in evolution. An even more straightforward factor would be simply the distance from a local maximum. Considering the latter you still end up with a strong positive correlation. But what does this have to do with the question we are dealing with? If someone asks you where is the bloody remote control, do you start listing "other factors"? This statement makes no sense. The position in fitness landscape affects the mechanisms of replication. There are also other factors that have an effect on the mechanism of replication. There are other factors that have an effect on the location of the bloody remote control. Right. This is mainly my point. But where do I claim that other, non-selective, factors have no effect on mutation rates? [...] Here you reach the the point of the total collapse of your "arguments" and their transition towards the pile of... I never assumed any teleology. I claimed that teleology may be possible in evolution. Prove that I have oversimplified things! What data are you referring to? I can also say that you are "ignoring the data". What data? Look, there are both upper and lower limits for writing preachy, empty and somewhat boring, not to mention illogical, statements, with the lower being the restriction of variability and higher being the rise of nonsense.

Imagine you are playing a game where the opponent hides an object somewhere in a room and your partner is directing you to it by calling your moves "hot" or "cold" (close and far from the target respectively) . If you are very far from the target (very "cold") you will increase the average distance of your exploratory movements (because your risk of missing the target is very low). On the other hand, when you get to a "hot" area, you should move less (lower exploration) because the target is close and you don't want to miss it. Fitness landscape can be represented in 3D as follows: let x and y axis be any two features on which selection operates, and let z (up) be the fitness. The peaks in this landscape are where evolving populations "want" to be. Mutations cause populations to move in certain directions in this landscape (like your exploratory movements in the room of the above analogy). The mutation rate determines by how much they move.The problem is that this landscape is not static. The peaks of fitness move and the evolving populations must keep finding them. (To make it more complicated the peaks tend to move more when populations get close to them.) Therefore in unpredictable environments the movement amplitudes should be higher. And then again, if a peak you are approaching is a relatively low local fitness maximum, it would be better to increase the mutation rate so much that the peak would be missed altogether (otherwise the population gets stuck to this peak because consistently moving downhill is prohibited). No, that's what I meant. I use the term in a regular way (the mainstream meaning). It does not suggest any agency is at work (and few rational people will understand it so). But this is how language evolves For example, why do mathematicians call "network theory" "graph theory"? It is so annoying but you just have to live with it. You mean purely functional explanation? The mechanistic explanation I have provided directly: a very messed up DNA-RNA reverse transcription process. But this mess has a function: increased exploration in an extremely unpredictable environment. Because the mechanism is simply the inefficiency itself. But if this inefficiency is a function of environmental variability then we can talk about teleology. This is similar to predicting the risk in finance: nobody knows what the market is going to be tomorrow but we can change the dynamics of investments as a function of unpredictability itself. In less jumpy markets we can focus the investments more than in crazy markets of the time of this writing. Think Wall Street for a moment. ... continued from the beginning Indeed he may. It would be irrational to dismiss natural selection from the theory of evolution (in fact it is the major force in evolution). But there are other, non-Darwinian, forces in operation. I concentrated on one of them (regulation of exploration) to bring out the point that evolution could have a teleological component. Again, you can have replication before sufficiently low mutation rate and before selection. Such replicators would (and likely did and perhaps still do) evolve by "genetic drift" rather than by variation and selection. This being said, of course you are right that replication mechanisms of most known organisms evolved by mutation and selection. It was the DNA repair mechanism that probably presented the critical event in the origin of Darwinian, selection driven, evolution. You are complicating -- unnecessarily so. Yes, in more unpredictable environments the mutation rates should be higher. The non-coding regions in Eukaryotes mutate for various reasons (lack of selection, the regulation of gene expression [proximity to enhancers and such] , proximity to centromers, etc) but as you suggest* this measure is irrelevant for the topic. What matters are the coding regions (as mutation rate can vary even within the genome!). I am also not claiming that retroviruses evolved high mutation rates denovo. I am aware of historical constrains. BTW: Prokaryotes may inhibit extremely invariant niches. * Mutation rate/genetic density is the measure we are discussing.

1. Mutation may or may not be chance driven (depending on the replicator). But it sure is a stochastic process. 2. Replication in a broad sense can exist in the regime of error catastrophe and do just fine. But replication as we know it exists despite not because of mutation. 3. Natural selection does not require extinction. (Mare differential reproduction rate will suffice.) [sarcastic mode] Right. [/sarcastic mode] Consider the DNA repair machinery. It is itself a selected feature of an organism. The efficiency of the DNA repair machinery could vary as a function of the amplitude of environmental fluctuations (at least in microorganisms). The exploration should increase with uncertainty of the future environmental conditions. So in relatively constant environments populations will keep a low mutation rate (efficient DNA repair machinery) and will move toward a local fitness maximum. But in less predictable conditions, where the peaks of maximal fitness shift, the mutation rate will increase (to follow the shifts). In other words, mutation rate can be viewed as a rate of exploration. The regulation of the mutation rate is itself a selected feature. Example: think of the HIV's inefficient RNA-DNA mutation prevention mechanism. Due to the unpredictability and the adaptive nature of the immune system the local fitness peaks are running all across the field. So the mutation rate must be high. See, the evolution of (at least) this virus is teleological. This is a very simple algorithm: adapt the mutation rate to the predictability of the environment. The bottom line: evolution, at least when it comes to mutation rate, is teleological. You are talking about probability when you are talking about stochastic processes. There is nothing to exclude God from the laws of thermodynamics.

You can narrow down "what we really mean by God" to the point when it really becomes incompatible with natural selection. But by doing this you would explain nothing. The only theory incompatible with natural selection would be the one that logically excludes it. It doesn't seem to me that popular teleological views are incompatible with natural selection. There may be purpose in everything, even in the laws of probability. Likewise it is not obvious that what people really mean by God is not compatible with natural selection. Even deeply religious folks will often refer to the Genesis as a metaphoric script. There is no reason for a believer and a practitioner of a religion to take any script literary. In fact biblical scholars or pretty much any Rabbi will tell you that taking the script literary is equivalent to completely destroying it. I suspect that the attack on the theory of evolution in general is more of an ideological, political and cultural issue than a theological one. Religions are almost by definition conservative and many people feel that their "family life" is threatened by the age of science and reason. So they use their religion to defend.

Sorry for not delivering exactly what you are asking for but I am curious why are you interested in such a publication? Any given reviewed or non-reviewed article on any given topic will do the trick. Natural selection (you can drop the caps) is indeed logically fully compatible with the "designed view". There is just no evidence for the "designed view". But there is tones of evidence that evolutionary process is either blind (bad local solutions replace good global solutions) or that the designer is an idiot or that the designer is hidden in the laws of probabilities (in which case we would have to reconsider the meaning of "design").

Sensation is a low level representation of the world (activity of particular photo-receptors in the retina, for example) and can be objectively measured (by electrophysiology, for example). Subjective experience is by definition not directly observable. It is only reported. Logically it is impossible to know if what you and I call "red" is in fact the same experience. This is an age old question. There are some quasi-objective measurements of experience for colors: yellow is reported to be light in "weight" as compared to red. There seems to be a scale of "weights" for colors that is quite universal. But this poses another question, namely: is the experience of weight subjective in the same sense as that of color is? Anyways, it is a good question.

The fields you listed all provide evidence for the theory of evolution and use the understanding of evolution to explain certain observations. Understanding of how anything in the universe works is itself a contribution to what makes humans interesting (to humans). Understanding very fundamental phenomena creates a greater connectivity in the network of knowledge and enables generalizations of the understood principles to phenomena found in other fields of study (even if those fields don't exist yet). I just want to mention two 'cases': 1) A method called fMRI has revolutionized not only many basic sciences but also more applied fields such as diagnostics. The method originates from curiosity of minds unconcerned with its potential applications. (These minds were concerned with questions like how atomic nuclei resonate in magnetic field. Understanding of these phenomena had absolutely no obvious contribution to anything practical at the time. We should be glad that such matters were of no concern to the pioneers.) 2) Evolutionary algorithms (little programs based on the principles of biological evolution) are used routinely in machine learning, image processing, artificial intelligence, optimization,... Fields such as developmental biology (including "evo-devo") would be baseless without basic understanding of evolutionary principles. This being said, the so called Darwinian evolution is only one manifestation of a more general evolutionary principle (development of brain circuits can be explained by non-Darwinian [or not-so-Darwinian] evolution). Finally, even if winning debates with fundamentalists (wishful thinking) were the only application of understanding of the theory of evolution, it would be worth it.

Very cool. Any references to that? Thanks. PS: Good luck with your research. This is a great "new" field. Hmm... Not necessarily so. Mammals save energy by keeping the derivative of metabolic rate over various ranges of environmental temperatures at zero. The cost is still significant but it really depends on what part of the life cycle and the species you are focusing on. Many lizards spend energy moving from place to place to bath in the sun and then eat in environments that do not favor their heat balance. This movement costs! (Not just in kinetic energy -- which is minor -- but predominantly in unfavorable temperature gradients.) This is an example of a problem that is complex mechanistically speaking but simple in economics: if an energy investment into maintaining a constant blood temperature is less then the energy obtained by consequently expended range of ground an animal can explore to obtain energy (food), then the investment was energetically good. Mammals are very efficient in producing* and using the least efficient form of energy (heat). So they are efficient in harvesting energy. * This, of course, is a paradox. Producing heat is, by definition, inefficient ------ A proud mammal who never breaks the laws of thermodynamics.

Nice finding. Any refs?

Right. Simple rules can produce complex games. Most eusocial organisms (bees, multicellular bacteria, your cells, Portuguese man of war -- a bilateral colony of radially symmetrical polyps, human markets, etc) read local information. That is, they play by local rules to establish structures "imperceptible" to them. Such "perception" is not needed by neither the group nor individual member. If a fish in a school of fish benefits by following the local rules (and it does) then that's all that matters. Until cancer sets in...

Every mutalism (equal exchange of costs and benefits between species) evolves out of some kind of parasitism (but not always the other way around). If the parasite is too hard on a host the fitness of the latter decreases and consequently the parasite's follows. Eventually the parasite has to contribute something to the host that will compensate for the lost fitness. And the moment the fitness of the host reaches the level of other, parasite-free, members its species, boom: mutalism. Energy is only one way in which the bacteria can contribute. There are many metabolic processes that your cells do not carry out. For example, vitamin K, without which your blood would not clot, is produced by some of the intestinal bacteria. The energy is a currency in this case. Also, bacteria positively affect the efficiency of intestinal absorption. Again, they don't need to contribute energy if they can increase your efficiency of energy usage.

Just what kind of junk are you reading anyway? Before making straw man attacks on one of the fastest growing and most multidisciplinary fields in science, I suggest you do a wiser search of literature. There is a difference between "studies" and well designed experiments and observations in neuroscience. Oh, BTW, the booze thing might be true

Interesting question. Since all mDNA is maternal one could suppose that there are unlikely to be many paternal alleles (nuclear) that would survive over generations if such conflicts could arise (although at very low frequencies practically any allele can survive because selection does not operate on that level). Although with populations separated for a long time anything is possible. But if this were the reason one could expect incompatibility to hit the nucleus first anyways... leading towards spaciation. Off topic: the conflict between the parasitic nucleus and host mitochondria was most likely resolved by transfer of genes from the latter to the former.

You insist on using terms that some of us here explained are inaccurate. A snake is "cold blooded" yet its blood can be warmer than yours when she is bathing in the sun. In fact many "cool blooded" animals can regulate their body temperature to a quite narrow range by modifying their behavior. But this is not your biggest problem. You seem to push the idea that very low metabolism can allow an animal to grow bigger. This is not completely wrong but it is rather rare. You mention crocodiles. As I have pointed out already, salt-water crocodiles can to a large extend regulate their temperature from within, so they are endotherms, or "warm blooded" (well, almost). So even this, carefully picked example by you, has some issues. Overall it seems that most if not all dinosaurs were endotherms (the jury is still out there). The amount of food they had to eat to maintain that status explains why the "nuclear winter" following the catastrophic meteor hit was so detrimental to them. I think the explanatory power of this view is stronger than what you are pushing. BTW: There is good evidence that many dinosaurs sat on their eggs (not unlike modern birds). Why would that work if they were "cold blooded"? It is not clear why birds made it. Could be that their small size and living in the trees (safe from mammalian predictors) was a niche taken from other dinosaurs (many of whom were small but did not occupy the trees). There are many "hypothesis generating" speculations out there. Some interesting some less so.

Those were not dinosaurs. They came from the other branch of amniotes (Synapsida), which includes modern mammals (and not much more). Also, I agree with Moontanman that the function of those structures was probably to get rid of heat (or display).

First of, dinosaurs survived (as birds). So that clears this subject. Now, we don'd know if the great dinosaurs (those that did not make it) were "cold blooded" (ectotherms) or weather they could regulate their body temperature from within (endotherms). The latter is more likely. You are right that energy is spent on maintaining constant body temperature but energy is also saved because all the enzymes work more efficiently at their optimal temperature. Moreover, endotherms have a greater felxibility of behavior and migration. It turns out that bigger animals are more likely to go endotherm (has to do with surface-volume ratio and some other reasons we can discuss elsewhere). Two examples of large almost endotherms: tuna fish, salt water crocodile. Both had been classically thought of as ectotherms. Turns out they can regulate their body temperature from within. (Ever tried a sushimi directly from the boat? Well, you should )

The main problem that I have with the book specifically and with Dawkins in general is that he is not only offering a different perspective. It seems to me that he is making a claim that genes are the only selfish units of selection (and "memes" in cultural evolution). This is wrong on many levels: 1) Genes do not code for their own position in the genome. The expression of a gene is, among other factors, a function of its position on the DNA. So a large portion of info is stored in various positions in the genome and not in the genes alone (think of genes as "words" and genomes as "stories"). Ergo: the genome itself is also a selfish unit of selection. 2) Epigenetics. Another level of selection works on the protein patterns surrounding DNA (histones, methilation, etc). These epigenetic patterns can be passed down with the DNA. Importantly, epigenetic patterns can be modified with experience (behavior of mother rats will affect epigenetics of pups and some features of the behavior will be passed to the third generation; this is not genetic inheritances nor cultural transmittance). In short: chromosomes are also selfish units of selection. 3) Cytoplasm contains information about embryonic development. It can be passed down with egg cells. Ergo: selfish cytoplasm. 4) Dawkins hates group selection and runs into troubles when explaining mutalism and eusocial behaviors (ants and other social insects). In short (this is a subject of a new topic) genes have to interact in complex networks in order to be selected. But in a sense one could simply say that these networks are themselves selected (selfish network structures). 5) ...

The problem is that there is more to feeding behavior than just consumption. You mention fiber to keep the digestion busy (although there are other reasons for fiber, that's a good point). The optimal diet pill will have to have very carefully designed schedules. Normally your circadian rhythm takes care of that (that's why jet-lags feel so bad for digestion -- they are). But I am not sure that you can entrain the circadian clock with pills. It actually takes pleasure of eating. (Also a part of the reason for the "French miracle" -- outdated.) And this is just one aspect of why "real" food can hardly be substituted with anything but food. But in principle it is possible as is a substitute for sex (why waste time?).