PhDP

This is completely unfair, you present an idea; It is a fact that you have no proofs, no evidences, no references, and then you basically say we're blind because we have doubts ? Evolution, and science as a whole, is based on more than just your impression, it's not sufficient to get an idea that looks good, that looks credible, you need facts, predictions, data...

CharonY, I'm not against the idea of an extended synthesis, but I'm against the view that evo-devo is so big that it should be considered the starting point of THE extended synthesis, IMO we already had a couple of important revisions. Personally, one of my biggest concern is to rehabilitate natural selection in molecular evolutionary biology, which implies a much better integration of genetics in population genetics, and a less naive of view of natural selection (we really have to get rid of that notion that natural selection is everywhere and explains everything from the color of the eyes to all tiny details at the molecular level). And, to me at least, this basic understanding of how the different mechanisms interact to drive evolution; that's the core of theory of evolution.

Sorry, but that's just mythology, or, if you prefer, an ad hoc fallacy. You don't provide any proof or any predictions, you've just created a semi-plausible story, some elements might be true, some are certainly not, but in the end, nothing is achieved. This kind of thing annoys me much more than creationism.

You would think that the Iraq war would show Americans that, even when it comes to the war against 'Evil', you CAN be too aggressive. Attacking foreign countries, unilaterally and with no good reasons; that's just stupid. It's such a great gift to terrorists. The cost/benefit analysis on the War on Terror is just horrible, how many lives, how many $$$, and in the end, for what ? Probably no results at all, and the problem is probably even bigger now. At the very least we can say this war has damaged the reputation of the U.S, reduced its influence in the world, embolden Iran, and Mr. Murdoch; we're far from the '$20 a barrel for oil' you promised us. Yet, and this is the surprising part; McCain is still considered stronger when it comes to security issues, so I guess very little will change, at least for now. Still, I think (hope) that in the end this war will serve as an example against proponents of aggressive foreign policies vs. the proponents of more diplomatic approaches. I don't see this as an example against interventionism at large, after all, the most interventionists (that is; democrats) were generally opposed to this war. BTW, I actually think that what will happen in Iraq in the near future is largely irrelevant to this question. After all, the U.S. have not invaded Iraq because of some humanitarian concern, they did this to fight terrorism.

Of course it's consistent, the theory of evolution (which is not, BTW, called 'Darwinism') doesn't say that every change is caused by the modification of the genetic structure of a population. Because the phenotype often depends on both the genotype and the environment (a very basic principle of genetics, which is especially well integrated into quantitative genetics), then of course you can see change in the phenotype without any evolution going on.

Shouldn't this tread be in the 'Evolution' section ? Anyway... I think we already had a couple of new syntheses within the field of evolutionary biology; in the 60s-70s, we had the molecular revolution (a true revolution, IMO), right now we're beginning the era of population genomics. Evolutionary quantitative genetics, thanks to people like Russell Lande, finally gets the attention it deserves... and yes, evolutionary developmental biology (evo devo) is an important new field. In fact, it's a field I'm very interested in, especially the relationship between theoretical population genetics and evo devo. But I don't think it's the biggest thing since the modern synthesis, and I'm not even sure it will be the most important subfield in the coming years.

It's a great board game, in fact it's nearly perfect, except perhaps that the rule for *advanced start* should ALWAYS be used, otherwise the game can be unfair, and it's better with 3-4 players, IMHO. It can be tried online at http://www.brettspielwelt.de/, but if you want to try it there you should probably do so with people you know.

Yet, I think the board game industry is growing, most of my favorite board games are actually pretty recent; Imperial (2006); Looks like a wargame, but it's actually a game about $$$. You invest in nations (France, Germany, Italy, UK, Russia, Austria), the player with the highest investment has the control. You need to tax, to invest, to wage war, and of course, you need to be sure that the armies you built in England to attack France won't be used against you (say, if the player controlling France invest in England, take control, and send the troops to your precious Germany). No dice, no cards, it's a perfect information game like chess. Tigris & Euphrat (1997); A tile-placement game. The rules are a little weird, but when you get used to it you understand why it's nearly always considered among the top 10 board games. Lots of tension, dept and strategy. Hive (2001); A simple, fast, and very original tactical board game (can be tried here).

Knol just opened, let's see if it'll do well. ...but for now, there is no support for mathematical equations.

In what is it different from before ?

Mitt Romney is, IMO, a very credible candidate for the VP spot. He's obviously smart & competent, actually, I now think he was a better candidate than McCain (from the republican side, at least). Apparently, this guy, Bobby Jindal, is a serious candidate. He's pro life with no exceptions (his words), he supports creationism/ID in the classroom, and he supposedly encountered a demon and practiced an exorcism (Jindall, B. 1994. "Physical Dimensions of Spiritual Warfare", New Oxford Review). wow.

First thank you very much for all the info you give me, I appreciate it. I must admit I never seriously considered functional languages such as Haskell, but you convinced me to take a serious look at it (but later, for now C/C++ is on the top of my list). Honestly, I'm not even sure I will use C within Python, I mostly want to learn C/C++ because of the speed and the wonderful libraries available for mathematics. Using hotspotting is certainly something I consider, but I don't know much about it, also, the structure of the programs I have to write is generally simple, so it would probably be easier to write the entire program in C/C++. Something is certain; most of the simulations I have to write involve a few lines where the program spend 95%+ of its time, for example; for i in range(0, y): f,t=a0,0 while ((f>0)&(f<N)): a = 0 p = ((1+s)*f)/((1+s)*f+N-f) [color="Red"] for k in range(0, N): if r() < p: a += 1[/color] f=a t+=1 if f==N: fix+=1 F=hstack((F,t)) elif f==0: ext+=1 E=hstack((E,t)) ...it's a small Python program to estimate the % and time of fixation/extinction of an allele with drift + selection, using the Wright-Fisher model. Very often, both N and i are much greater than 1000 (and the while loop can easily be repeated more than 1000 times/simulations). I would be curious to see how fast this code would be if everything remained in Python BUT the few lines in red. I heard about it, but I never tried it. Flexible... at least from the perspective of someone 'raised' with Maple & MatLab.

It depends on how you see it, Python IS slow compared to C, but it's as fast as one of the most popular "language"; MatLab. Also, with Numpy/Scipy, Python is very similar to MatLab, which is a very important advantage. Also, with Cython (or Pyrex), which is basically a way to use C within Python, you can get about as fast as C. I don't want to start one of those "my language is stronger than yours" debate, but for scientists like me, Haskell is not very attractive. The language is very different from everything I've seen, it's not as flexible as Python (which support functional programming btw) and, most importantly, it's not very popular, so I would not be able to send the source code to my colleagues, and I will certainly not find wonderful libraries like this one.

True, but the 1st law of sociodynamics says; if the number of people killed by 'X' << number of people killed by 'Y', but 'X' involves big explosions; it will be considered by a majority to be significantly more dangerous. Let's face it, cancer has caused much more harm than terrorism (but to be fair, pretty much anything has been more dangerous than terrorism), and air pollution is certainly more dangerous than nuclear plants.

...but scientific computing is mostly about two things; clarity & speed. If you're looking for clarity, you will likely end up with MatLab/Octave, Python, or some similar very high level language. If you're looking for speed, you're going to use either C/C++ or Fortran. For most of its history, JAVA was much slower than C/C++/Fortran, and considering that it's not much clearer, it's easy to understand why it was never really popular with the scientific community. Now that it's getting faster, it might get more popular, but personally I prefer to stick with Python and use Pyrex/CPython when I need more speed.

I read Linus' post, but I don't know enough about computer science to say if what he says is true, and anyway, it doesn't seem relevant to me. I'm only interested in scientific computing (simulations, solving math problems). and I'm especially concerned with relatively simple programs with for/while loops. I want to use Python as my primary language, but I would also like to know how to handle a faster language. I know C and C++ are different, but they share a very similar syntax and for what I want to do they are basically the same. C/C++ seems to be the way to go (although Fortran is a serious alternative), it's widely used, fast, and it can be used with my beloved Python (go Cython!). AFAIK, both JAVA and C# are not widely used for scientific computing.

I'm looking for a good introduction to C/C++, either a book, an ebook, a website, anything. I already know JAVA and Python, so I'm not completely new to programming.

There is also http://academictree.org/ (with many evolutionary biologists).

...it's not just about physics, most people have only heard of Darwin, and sometime Gould and Dawkins. Some people also think "great science popularizer = great scientist", even if the great science popularizer in question made no original contribution in the field. I'm also not sure of how far you can get in science with plain English. I cannot imagine how someone with a good understanding of the mathematical structure of physics could support the crazy interpretations of quantum physics, or the notion that thermodynamics prove evolution is wrong. It's possible, but it seems much easier to believe that quantum physics proves that telepathy is possible when you think the uncertainty principle means the mind can change the behavior of matter at distance. Those weird interpretations exist because of how much information we lose when we try to translate equations into plain English, after all, concepts such as entropy and energy are clearly defined in physics, but not so easy to define with simple words. I'm convinced that most basic concepts in science can be explained with only a little algebra, a little probability theory, and with basic knowledge of differential equations. But of course, it requires a little effort...

- Darwin discovered one mechanism; natural selection (and even then). Others have discovered other mechanisms, so, yes, obviously, we have to surpass Darwin, and we did a long time ago. Personally, I think the scientific theory of evolution was born with Morgan, Yule, Fisher, Wright, Haldane, ... - Chaos theory is a framework to study the qualitative behavior of dynamical systems (i.e.: systems of differential equations). We have little to no use for that in evolutionary biology, mostly because we have much better; probability theory. - Mathematics is obviously very present in genetics & evolutionary biology. - Life certainly does NOT always find a way, our genomes are full of mistakes. But ultimately, nobody ever said that mutations were random in the strictest sense. It's just that we have no way of knowing where exactly a mutation will hit, and there is no way, simply no way chaos theory could lead to a deterministic model of evolutionary biology, for at least two reasons. First, chaos theory is, in great part, about qualitative behavior, while the information we need in evolutionary biology is, most of the time, quantitative in nature. Also, theses system are too complex to be analyzed with chaos theory, and most importantly, we don't need to know this information. Knowing the mutation rate in a particular region is good enough. I highly suggest that you get Strogatz's 'Nonlinear Dynamics and Chaos' and a good book about population genetics. You will see that randomness (again, not in the strictest sense) is prevalent in today's evolutionary biology, and much more than it was before. And you know what, it's also increasingly predictive.

95%+ of the time, texts are hard to read because; - The formatting (i.e.: not written with TeX). It should be illegal to write mathematical equations in plain text . Long paragraphs and bad punctuations are also to blame. - The author is making a deliberate effort to make things complicated, either because he's "cool" and doesn't care if you understand his alternative spelling, or he likes to express simple ideas in a complicated matter (e.g.: poetry, the Devil's language). - But most of the time, it's simply because the author can't express his idea clearly, either because he can't express any idea clearly, or because he's not familiar enough with the language. Honestly I really don't care about spelling & grammar, I think we should keep our language as simple as possible, which means we should be more tolerant of small deviations, as long as we can understand. A language is just a tool to express ideas, we should only enforce rules if they really help us achieve that goal.

Just as I think we should wait a little and teach physics with calculus, I think we should teach Mendelian Genetics/Evolution along with basic probability theory/statistics. In high school biology I learned a bunch of names, organs, bones... In short, they thought biology was about reading a dictionary. Which is basically the exact opposite of what science is, and it's what my signature is about; science is not just a series of unrelated facts, it's an attempt to unify our knowledge of nature. I would argue that a simple concept such as diffusion is much more relevant to our understanding of life than the names of a few of our ancestors, or the name of the xth bone of the leg. I also think that, when evolution is based on the solid foundations of Mendelian genetics, yes, you'll get a little more math, but in my opinion this is a necessity to truly understand the mechanisms of evolution. Hopefully, we would get a little less of the kind of storytelling which is in my opinion highly deleterious to evolutionary theory.

Evolution & survival are not about the greater good, they are about individual fitness (well, there is a case for some form of group selection but I doubt it would apply here). This theory is about morality, not religion (AFAIK). After all, there is no proof that a lack of religious belief lead to less cooperation.

Lucasca, Futuyma actually says that, on average, beneficial mutation have a coefficient of 's' around 0.1 ? I would be surprised by this. Can you give me the exact reference ? It's an elementary textbook I doubt he covers the complex question of the distribution of fitness effects. And BTW, it doesn't really mean anything is 's' is around 0.1 unless it remains positive for a long time, this is why molecular evolutionary biology is so useful to answer these kind of questions, it allows us to study long-term patterns. [it's s>1/(2N) BTW, and it's a little too optimistic] Actually, you said; As long as s (the selection coefficient) is at all positive, the equations are clear that the allele (mutation) will become fixed. It's a question of probability of fixation, you say it will become fixed (probability approx. 1). And then for some reason you used an equation which has nothing to do with this, it's just an equation to calculate the expected change in frequency with selection, you'll never find this kind of use in a serious paper. I never said drift was more important, I said it was more important when the product 'Ns' was small. You said pop size didn't matter, and you even said that, as long as s>0, the "equations" (i.e.: the inappropriate equations) showed that fixation would occur. The math, and the science, says otherwise, it's basic population genetics. I disagree with the incorrect use of mathematics and the thing you said about the time of fixation, I also think you tend to simplify evolution too much. For your argument against Behe; I couldn't care less. I'm not interested in creationists, unless they publish in serious journal (hint: they won't). I'm much more concerned about the bad use of evolutionary theory by evolutionists.