I need Matt:

I can't follow any of this. Does this paper have any validity in explaining the vast store of information in biologic organisms?-http://procrustes.blogtownhall.com/2010/06/08/voom!_evolution_in_fourier_space_final_part_4.thtml

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I can't follow any of this. Does this paper have any validity in explaining the vast store of information in biologic organisms?
> 
> http://procrustes.blogtownhall.com/2010/06/08/voom!_evolution_in_fourier_space_final_pa... apologize for my unexpected hiatus--Been consumed with getting (and training) a new puppy as well as doing all the crap to the house we'd been deferring for 5yrs. Kitchen's almost done, just got the tree to trim and... probably the roof, but hey, I didn't start a fancy new job without the great chance I'd have to y'know, not see any of the $$. -I'll peek at this site as soon as my mind returns to math... right now I've been reading "The Lucifer Principle," a book I'll discuss here soon; it's an attempt to explain why evil exists, and has some great attacks on "Individual Selection." (Doesn't explain altruism--or suicide/apoptosis.)

--
\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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I can't follow any of this. Does this paper have any validity in explaining the vast store of information in biologic organisms?
> 
> http://procrustes.blogtownhall.com/2010/06/08/voom!_evolution_in_fourier_space_final_pa... just spent about 30min trying... -I'm of the opinion that this guy either doesn't know what he's talking about or he has NO skill whatsoever in explaining himself. He jumps--erratically--across topics that have no real relationship to each other. His explanation of FFT is pretty good actually, but he fails to make a point with this at all... -He states that some of the results of FFT's such as Parseval's theorem can be used to "prove" something or other in theology; The first blog post you showed me made me wary, but now I'm pretty convinced this guy's a nut. Mathematical theorems might serve as an inspiration to theology, but they cannot prove anything about theology. -Further down he states that "life cannot happen by random chance" but he provides no argument for this. Apparently I have to just accept that assertion.-The last section attempts to bring in some more information-theoretic ideas, but they are impenetrable. At least, I can say that Dembski's work is readable. This guy is incoherent. -The best I can get out of that section: He generally states that by building functions out of the different things you see in biology, stringing them together, and performing an FFT operation on them, you get the "voice of God." -I wish I could give you more, but his writing is as bad as what you get from a Postmodern writer. I think he's working from the same DI playbook as Dembski, though I can safely say that if someone could write a function to describe life--in other words, if it was as easy as he says it is--it would have been done. The fact that he babbles instead of doing such a thing... Meh.-So no--it's not just you. Incomprehensible.

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> So no--it's not just you. Incomprehensible.-Thank you. My math is minimal to start with. I couldn't follow him at all, and it seemed very fanciful.

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I need Matt again.I can follow to some degree this line of thinking and the hierarchy, as one sees in software algorithms and can be seen in the hierarchy in DNA/RNA controls. But does this meet math requirements, the 1+2+3+4=10, means what?-http://www.uncommondescent.com/evolution/functional-hierarchy/#more-13790

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I need Matt again.I can follow to some degree this line of thinking and the hierarchy, as one sees in software algorithms and can be seen in the hierarchy in DNA/RNA controls. But does this meet math requirements, the 1+2+3+4=10, means what?
> 
> http://www.uncommondescent.com/evolution/functional-hierarchy/#more-13790-Heh. The Pythagoreans. I find it intriguing that he's attempting to resurrect esoterica from a group of mathematicians that denied the reality of irrational numbers. -From a math perspective, the study he shows is childishly easy. Ultimately it's nothing more than a mathematical replica of the "Irreducible complexity" argument. For all other "functions" to exist, it requires another function. But he too ignores origins and is scouting the forest while missing the trees. -Origins aside, mutations in an organism are often completely random; when you study the genetic differences in say, hemoglobin among primates, you see exactly the kind of slow, methodical--and random--processes one would expect in a traditional evolutionary perspective. New-world primates have drastically different hemoglobin sequences than old-world primates. We all split from the same ultimate common ancestor, so why does the change appear to be linearly slow? Again, I bring this up because he seems to exclude randomness entirely when discussing life. (and we all know I tend to hate absolutes.) -I've often said here that trying to untangle life by looking at the way it is now is impossible.

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> I've often said here that trying to untangle life by looking at the way it is now is impossible.-Thank you. I knew the right angle triangle theorum, but th rest seemed like wild garbage.

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> > I've often said here that trying to untangle life by looking at the way it is now is impossible.
> 
> Thank you. I knew the right angle triangle theorum, but th rest seemed like wild garbage.-> > 
> > I've often said here that trying to untangle life by looking at the way it is now is impossible.
> 
> Thank you. I knew the right angle triangle theorum, but th rest seemed like wild garbage.-Pythagoreans had some very interesting thoughts--and they influence modern Pagan movements--for whatever that's worth to you. It's very new-age. -I never thought I'd say this, but this guy wastes your precious time. You should stick to Behe/Dembski. Not to quash the guy's freedom of speech, but the moment I see "Tetractys" I see someone who grabbed an ancient symbol and is... letting his imagination run with him. -The theorem he references is a pinnacle theorem in "Mystical Geometry." Being of Jewish descent you might find it at least an interesting cultural peculiarity; it was ultimately one of several figures coopted into Qabbalist practice during the Jewish golden age in... well during the Moorish occupation of Spain. (1300's maybe? Shaky there.) -But... I won't want to bore you if you don't think it has any real merit.

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I am thrilled that we have a qualified mathematician with us. Matt look at this argument on protein folding and the conclusion that the specificity at the tertiary level requires a process other than Darwinian chance. Is this mathematically reasonable?-http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.1

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I am thrilled that we have a qualified mathematician with us. Matt look at this argument on protein folding and the conclusion that the specificity at the tertiary level requires a process other than Darwinian chance. Is this mathematically reasonable?
> 
> http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.1-David...-You really need to reply to my own replies... I don't always look at the right-hand bar when I log in (and when you posted this, I was about ready to go to DC!) And again--Computer scientist, if I may be so bold... but as close to a mathematician as we currently have. -Critique:-Starts with the assertion of a search problem. They set up the search function initially as f(x) = possible gene mappings. However I get concerned when he sets the framework as using existing protein structures. The reason why is this: If you start with current structures, you can set up an arbitrary argument (slippery slope) to prove that current structures cannot come about by what the author terms as "evolutionary processes." I don't have a problem with the conclusion beyond the fact that they use a slippery slope. We shall see!-The first injection of math discusses the number of ways (n^L) 20 amino acids can combine. This is my conjecture, but his argument will be that picking 1 sequence (for a successful protein) out of 20^L sequences is simply something that could not have happened by chance. -I will have to pause at this point: the argument here is dense. It will take me a couple days to chew on this.

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David, the question bothered me overnight, so I got up extra early to tackle it. -> I am thrilled that we have a qualified mathematician with us. Matt look at this argument on protein folding and the conclusion that the specificity at the tertiary level requires a process other than Darwinian chance. Is this mathematically reasonable?
> 
> http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.1-At base, I checked all the calculations he provided, and yes--they are sound. However he has one critical flaw here (from a mathematical perspective.) He claims that the evolutionary "search algorithm" wouldn't be capable of the success needed. That's fine, except that he provides no actual mathematical function beyond that which I described last night: he declares an f(x), but provides no machinery for it to work. Nor does he provide an alternate g(x) search function for comparison. He throws out plenty of math, and some good discussion of biochem, but no actual comparison ever ensues; it's not a mathematical argument, only an argument that uses some math.-Why it is important that he defines functions explicitly is this:-compute a sequence f(x) = x^2, and g(x) = x*log(x). Plot the results. (Don't worry I'll show you. (These also provide examples of what an analysis of algorithms SHOULD look like!) -f(x) = http://webspace.ship.edu/cawell/Sorting/bubanal.htm
g(x) = http://www.iti.fh-flensburg.de/lang/algorithmen/sortieren/quick/quicken.htm-http://www.... For a view of a very formal (and complete) algorithmic analysis. -If he doesn't provide input sets with functions, with computed output sets... then there's no comparison, and more importantly, no time-complexity analysis. -His analysis implicitly asserts that evolution is an exhaustive search function, that his function is a linear search that must search through all elements. He asserts f(x) = x. The time complexity of this would have a theoretical upper bound of x, but in practice linear searches rarely have to search through the whole set. And--some searches will have issues depending on the algorithm--the quicksort I showed you above, has an average time case and a worst time case. And I haven't even started talking about how his data sets are modeled... data structures themselves can have an immense impact on search time. -So, I leave you with this: it's a convincing argument until you ask yourself what exact search functions is he comparing? His argument is akin to showing you bubble sort as the "Darwinian" search algorithm, and suggests that something better is out there... without telling you what it is.

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> So, I leave you with this: it's a convincing argument until you ask yourself what exact search functions is he comparing? His argument is akin to showing you bubble sort as the "Darwinian" search algorithm, and suggests that something better is out there... without telling you what it is.-I really appreciate the time you spent analyzing this. When I read stuff like this, it sounds great, but I have no math background for it. The examples you showed me are sites that make my eyes roll back. I can't follow any of it. Never had calculus, never needing it for med school. I know I need it now to be analytical. As you know I think evolution is driven from with the genome, so when I see an article like that I'm drawn to it, but stuck with the author's conclusions. Thisis where I need peer review! ) Thank you.

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David,
> > 
> > So, I leave you with this: it's a convincing argument until you ask yourself what exact search functions is he comparing? His argument is akin to showing you bubble sort as the "Darwinian" search algorithm, and suggests that something better is out there... without telling you what it is.
> 
> I really appreciate the time you spent analyzing this. When I read stuff like this, it sounds great, but I have no math background for it. The examples you showed me are sites that make my eyes roll back. I can't follow any of it. Never had calculus, never needing it for med school. I know I need it now to be analytical. As you know I think evolution is driven from with the genome, so when I see an article like that I'm drawn to it, but stuck with the author's conclusions. Thisis where I need peer review! :-) ) Thank you.-To guide you when you see similar papers in the future: Ask yourself if they formally define 2 functions. If they only declare one, check assumptions: It wouldn't be unlikely that they'd simply assume a random walk--but it should still be explicitly stated. If they define no functions at all, take it as a definite sign that something is afoot. But in ANY paper defining something as a search function, and it is making an assertion that there isn't enough time, it is essential that they explicitly define the search algorithm, and define a time-complexity function for it--and most importantly--they define it against another function. -Modern biology doesn't look at evolution as a random walk--maybe abiogenesis, but life is clearly some kind of "guided" search function--and before you jump on me there, by "guided" I mean that it looks at its current state and alters it using what it has; clearly a narrowly defined set. The good question is how the set became narrowed.

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> To guide you when you see similar papers in the future: Ask yourself if they formally define 2 functions. If they only declare one, check assumptions: It wouldn't be unlikely that they'd simply assume a random walk--but it should still be explicitly stated. If they define no functions at all, take it as a definite sign that something is afoot. But in ANY paper defining something as a search function, and it is making an assertion that there isn't enough time, it is essential that they explicitly define the search algorithm, and define a time-complexity function for it--and most importantly--they define it against another function. 
> 
> Modern biology doesn't look at evolution as a random walk--maybe abiogenesis, but life is clearly some kind of "guided" search function--and before you jump on me there, by "guided" I mean that it looks at its current state and alters it using what it has; clearly a narrowly defined set. The good question is how the set became narrowed.-Matt, I don't know what to ask you about the above. What is a search function? I know the example of random walk, with the drunk trying to make the lamp post from the bar door, but I have no idea how it works. Thanks for trying, but I've never had any math like this, and it's a little too late for college courses.

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