Posts by bohm

40

GENETICS- CREATIONISTS need not be INTIMIDATED.

by hooberus in

genetics- creationists need not be intimidated.. .

internet evolutionists almost universally and repetitiously proclaim that modern neo-darwinian evolutionary theory is supported by overwhelming evidence and that there is no evidence for biblical creation (or even mere intelligent design) for that matter.

they will dogmatically claim that evolution receives universal support from all the real scientists and all the facts from genetics, biology, geology, paleontology, and every other ology that one can think of.

bohm

Hooberus: And lets have a small talk about scholarship.You can read the following in the last article you cited:

For example, under Shannon information, which the NCSE would claim is “the sense used by information theorists,” the following two strings contain identical amounts of information:

String A:
SHANNONINFORMATIONISAPOORMEASUREOFBIOLOGICALCOMPLEXITY

String B:
JLNUKFPDARKSWUVEYTYKARRBVCLTLODOUUMUEVCRLQTSFFWKJDXSOB

Both String A and String B are composed of exactly 54 characters, and each string has exactly the same amount of Shannon information—about 254 bits. 9 10 Yet clearly String A conveys much more functional information than String B, which was generated using a random character generator.

Further down he write:

"In contrast, proponents of intelligent design would define “new” genetic information as a new stretch of DNA which actually performs some different, useful, and new function. For example, consider the following string:

DUPLICATINGTHISSTRINGDOESNOTGENERATENEWCSI

This 42-character string has ~197 bits of Shannon information. Now consider the following string longer:

DUPLICATINGTHISSTRINGDOESNOTGENERATENEWCSIDUPLICATINGTHISSTRINGDOESNOTGENERATENEWCSI

This procedure just added 42 “new” characters, but no new function has been produced."

This sound really interesting, and i tried to read about the author, Casey Luskin:

"Casey Luskin is an attorney with graduate degrees in both science and law. He earned his B.S. and M.S. in Earth Sciences from the University of California, San Diego. ... Casey has published in both law and science journals, including Journal of Church and State; Montana Law Review; Geochemistry, Geophysics, and Geosystems; Hamline Law Review; and Progress in Complexity, Information, and Design. He has published in print and online popular media such as Research News and Opportunities in Science and Theology; Human Events; U.S. News & World Report, BeliefNet; Salvo Magazine; Touchstone Magazine; the Tampa Tribune; the San Diego Union Tribune; the Washington D.C. Examiner, and the Philadelphia Inquire"

Now something seemed quite odd about his vocabulary, he mix up terms that are not the same but i thought that a man you quoted, who apparently had a degree and has puplished in this field, would know the terms he described surely even a creationist would not make such a stupid-ass mistate to write about shannon entropy without knowing what it is. Boy was i surpriced! The thing about shannon entropy is that you want to define it based on a propability distribution. It is clear from the last quote he calculate it based on the uniform propability distribution and thus arrive at 197 bits for the string:

"DUPLICATINGTHISSTRINGDOESNOTGENERATENEWCSI"

However this is completely bogus. If you want to use calculate the information in a signal, you want to use the propability distribution the signal is generated from, ie. you can measure from the signal. Doing that you arrive at something more interesting. First off, in the first example the actual amount of information is the signal is:

"DUPLICATINGTHISSTRINGDOESNOTGENERATENEWCSI" : 157 bits.

and for the other Strings:

A : 211 bits

B : 232 bits

As we expect, Shannon entropy allow us to understand which signal is generated from a random number generator, and which is not. This is how it is usually used. And if you want to argue that i should use the uniform distribution, keep in mind that he is talking about detecting design. if we assume no design, ie. completely random numbers, we would expect shannon information to give that answer - i challenge anyone to find a good argument for that use, or any example in genetics where it is used like that. Shannon information is allways used this way i described above when you want to use it as a meaningfull measure in text, image or sound data, except when you are Dr. Casey, apparently.

Why on earth can a creationist so-called expert in entropy not properly explain what it is, or use it to calculate the entropy of very simple text strings, but still puplish papers about the subject and be seen as an authority?

40

GENETICS- CREATIONISTS need not be INTIMIDATED.

by hooberus in

genetics- creationists need not be intimidated.. .

internet evolutionists almost universally and repetitiously proclaim that modern neo-darwinian evolutionary theory is supported by overwhelming evidence and that there is no evidence for biblical creation (or even mere intelligent design) for that matter.

they will dogmatically claim that evolution receives universal support from all the real scientists and all the facts from genetics, biology, geology, paleontology, and every other ology that one can think of.

bohm

Hooberus: "Actually his program allows for the selection of positive mutations".

Well im not really sure what you mean, but lets just agree that the statistics and weighting he use on positive vs. negative mutations are stacked so highly AGAINST positive mutations per default that he will allways detect a population crash, though a good mutation may be selected here and there.

Then you wrote: " Interesting, since this is actually similar to the operation of the pro-evolution computer simulation that you recommended on this forum (http://www.jehovahs-witness.net/jw/friends/183269/2/Mitochondrial-Eve-for-dummies )". My post is not about validating evolution in one swoop. What i talked about is if the mechanisms of evolution can produce information, ie. find non-trivial solutions to hard problems. That is what those programs do, and that is what i argued for (actually it is not an argument, it is a simple observation that has been done over and over again in computer science and engineering).

This discussion show two things: With some assumptions on how nature works, bad mutations will drown the good and we get a population crash. This is what Dr. sanford show with his computer program. Also we have seen that under another set of assumptions, the principles of evolution can produce novel solutions to hard problems, that is what is seen in GA's and various artificial-life simulations. Can we agree on this?

Now the big question is what set of assumptions best describe nature? In that case the only thing you can do is to validate your assumptions against nature, so far Dr. Sanford has not done that, and therefore it is not evidence for anything.

FURTHERMORE you will notice Dr. Sanford make some assumptions that seem quite unphysical, for example tying the positive effect of a mutation to the inverse of the genome length (a-what?), or that he predict humans has only been here for 6000 years (are you really sure you believe in that to?), with the added effect that life forms with the same genome length as humans but a much shorter life span should have gone extinct a long time ago. Unfortunately Dr. Sanford never really address these problem.

17

GOD------------the ANTI-Concept!

by Terry in

telling you what something is not is the opposite of identification.. .

god is:.

1.someone the human mind cannot grasp.. 2.not human.

bohm

BTS: Very few atheists will actually go to a long length arguing God cannot exist or something like that, i certainly wont. But I think Terrys observation is spot on about how God is described and thats cool with me (and i suspect Terry as well) when seen in isolation, the probem arise because people who believe God exist usually use that very loosely defined concept to argue some very concrete and silly things.

23

Scientology Down to 25,000 Members?

by cameo-d in

http://www.nytimes.com/2010/03/07/us/07scientology.html.

quotes:.

it was all built on lies, mr. collbran said.

bohm

Nephilim: Have you seen the south park episode with mormons? Its priceless! DUMB DUMB DUMB DUMB DUMB

It will be interesting to see what happends to scientology in the near future, ie. how such a religion dies.

18

2012 and The Fall of the Watchtower

by Clint Bussey in

jw
friends

i know you may call me another russel or something, but i am just showing what i've found.

i am very amazed by what seems to be an uprising inside and outside of the jehovah's witness religion against the governing body and watchtower corporation.. it seems that all the scriptures about babylon and the apostasy apply to them today.

but check these two things out.

bohm

Clint: Do yourself a giant big favor. Take out a piece of paper and write: "I Clint Bussey, using the exact same methology that has led people to predict things for more than 2000 years that has not happened, now predict (like many others) that 2012 is going to be *the* year.
If it, like all the other predictions for the past 2000 years turn out to be false, i will not be so dumb i find a vague argument to add 3-5-10 years and make a new prediction, because this should really tell me the METHOLOGY of adding random numbers together to get new numbers is just as reliable to predict the future as making a blind guess, and i wow not to waste more of my precious life to persue such a stupid idea.". Then save that paper for 2013.

I got bad news, 2012 is going to come and go with nothing special happening. No shame about that, you will hardly be the first. Whats going to be a defining moment in your quest for truth is if you are then going to say: "oh, 2014 sound really important to, let me see if i can find 2 years somewhere in my calculation.."

25

"The Faux Pas of Modern Atheist Unity"

by leavingwt in

jw
friends

i enjoyed reading some of these criticisms.

the faux pas of modern atheist unity.

1. the plea for atheist unity.

bohm

'Brights' - damn that sound retarded. How on earth are you supposed to use it?

"Catholic: Hello, i saw you were reading 'the davinci code', are you a catholic?"

"Asshat Atheist: No, i am BRIGHT!"

FAIL

11

JW-girls on Dutch XFactor

by Lady Viola in

jw
friends

very funny video from 2 jw girls on the dutch xfactor.

it will start at about 2.33.. one of the jury (left) says 'they have such smug faces, they look like jehovah's witnesses'.

when they tell him they are jw's, he's laughing his head off.... http://www.rtl.nl/components/shows/x...ctor_s3_a3.xml .

bohm

I started a thread about the danish X-factor which actually has a JW girl in it, and she sing quite well!

http://www.jehovahs-witness.net/jw/friends/189470/1/A-JW-in-X-Factor

(videos of a couple of performances)

23

A JW in X-Factor!

by bohm in

jw
friends

i saw today that one of the contstants in the danish x-factor is a jw, and she is quite good!

a tabloid had a newspaper where she described her faith, she sounded quite nice and said she had never been teased by her faith.

the whole article can be found here (foreign language warning!).

bohm

I think there is a weekly installment on the way! Here she is singing number 69 from the new songbook, "fighter":

http://www.youtube.com/watch?v=w-DorZhwObQ

She aint half bad!

40

GENETICS- CREATIONISTS need not be INTIMIDATED.

by hooberus in

genetics- creationists need not be intimidated.. .

internet evolutionists almost universally and repetitiously proclaim that modern neo-darwinian evolutionary theory is supported by overwhelming evidence and that there is no evidence for biblical creation (or even mere intelligent design) for that matter.

they will dogmatically claim that evolution receives universal support from all the real scientists and all the facts from genetics, biology, geology, paleontology, and every other ology that one can think of.

bohm

BTS: Thank you for your long answer - it allmost deserve a topic of its own!

First i got to admit i am in over my head on the biological side here. I dont really know a lot about biology, it is not my field and i have not even read an introductuary textbook. The way evolution has been an interest of me is from an information-theoretic perspective: The genomen clearly contain 'information' (though it is hard to quantify exactly how much), and the process of life can be seen as a chanel of communication from now and n generations forward, and what happends in between - selection, mutation, horizontal gene transfer, etc, lets call them all 'process E' - is what creationist and evolutionist is talking about: Is it possible that these processes may increase the amount of 'information', or does it just work as a noise filter that decrease it?

So having stated my ignorance i think you will understand why i have properly misunderstood you. The way i read your original post was that all DNA in the genomen was there for a reason, ie. it was like a house of card: If we removed anything, the whole thing would tumble down and you wouldnt get a human. I think the misunderstandment come from how i understand the term 'junk-dna'.

When you and i can taste sweet things its because a part of our DNA code for a specific protein that allow us to do so. In cats the situation is different. That gene has a point mutation so that it does no longer 'work', ie. now it does not produce any proteins and the cat cannot taste sugar.

Thats what i mean by 'junk'. A region that serve no function in th sence you can pretty much flip all the 'bits' in the dna string and you would still get a cat. The damaged gene /may/ still have a weak function (structually), and there may be some constraints on how many bits you can flip, but those restrictions is much, much weaker than on the other parts of the genomen (a way to say that is the entropy is higher), but pretty much all random flips of this part of the genomen should have no effect on the cat.

The reason that i expect such 'junk' is properly a bit strange for a biologist. As i have written many times over 'evolution' (or genetic algorithms) is a well-known optimization strategy in engineering, and i believe what works and what does not work when you work with genetic algorithms can tell us something about what to expect from our DNA. If you take down a textbook on how you build a genetic algorithm it will properly give you the following guidelines:

"Your representation (genomen) must be very redundant and as large (wastefull) as possible". So thats what i expect from our genomen: That there are many duplicated, nonfunctional or partially nonfunctional structures, and that the functional structures are often coded in a very wastefull manner; that is, junk dna.

Actually i think a program such as dr. Sanfords can say something about this situation. In a bacteria a much larger DNA (full of 'true' junk) would be bad, because building the dna is a very expensive thing compared to the other stuff the bacteria does. Because of this the 'junk' factor in with a higher relative value in the bacterias 'fitness function', and because there is a huge population of bacteria they are under a more fine-grained selection function and hence in bacterie it is possible for evolution to weed out 'junk'.

In humans it is different. Our fitness function is much, much more advanced because we consist of 40 billions cells and interact with a much more complicated enviroment. Furthermore there are allmost none of us compared to bacteria. Therefore i would expect evolution would have a much harder time to weed out 'junk' in our genomen, and thus i would expect humans (on average) to contain more junk propertionally compared to a bacteria strain, given the same initial conditions.

40

GENETICS- CREATIONISTS need not be INTIMIDATED.

by hooberus in

genetics- creationists need not be intimidated.. .

internet evolutionists almost universally and repetitiously proclaim that modern neo-darwinian evolutionary theory is supported by overwhelming evidence and that there is no evidence for biblical creation (or even mere intelligent design) for that matter.

they will dogmatically claim that evolution receives universal support from all the real scientists and all the facts from genetics, biology, geology, paleontology, and every other ology that one can think of.

bohm

The problem with Sandford

Hello! I have read a couple of papers on Sanfords model of evolution (Mendels Accountant) where he test his hypothesis that darwins first axiom is wrong.

From my reading of his papers this is what his program does:

First it assign a fitness (initially 1) to each individual in the population and a genomen. The fitness indicate how likely the individual is to replicate, and how many offsprings it get.

Here is the thing: We have already left the land where the simulation is biologically realistic.

The world does not work like that. Ask yourself what the fitness of a 'dog' is. Is the fitness of a 'dog' larger than a cat? An E-Coli? What does it mean the fitness increase or decrease by a small amount? how does that look?

In reality fitness is a function of the world. Mutations that are bad in one context are good in others -longer legs may be good in Africa, but bad in Greenland. Im not saying this invalidate the ability of the model to say something about the world, not at all! Almost all models of the world rely on strong assumptions, im just saying that we are throwing out a *lot* of complexity, and at some point we need to check if we threw out something essential.

ANYWAY. The fitness of the animal are in his simulation affected by a variety of factors, the most important is mutation. Mutations are small changes to the genomen. Each change is assigned a 'change in fitness', just a small random number, which is drawn from a distribution and alters the total fitness of the individual. Here is the crucial thing and where many feel his model is wrong:

He assume per default there is a much higher likelihood of a 'bad' (negative) change than a 'good' (positive),

in particular the ratio is 0.0001, but whats even worse, he assume that given if it is a good or bad mutation,

the fitness effect is found through a Wiebull function that is furthermore SCALED by a paremeter d_sf = -1 (bad mutations) and d_sf = 0.01 (good). Otherwise the two Wiebull functions use the same parameters.

Okay in laymans terms: He first state there are 10000 more bad than good mutations. Then he state that the change in fitness of a bad mutation is on average 100 times stronger than good.

This has the following effect: There will be a gazillion 'bad' mutations that individually affect the overall fitness very little, but will always draw downwards, and often the bad mutations will kill the individual directly (fitness 0). Very rarely there will be good mutations, but they will have so little effect to the total

fitness that they are very easily drowned in 'noise' and hence cannot be selected for.

It is clear to anyone that with a finite population size (typical size in his simulations is 1000) the effect will be a population crash. How quickly depends on the input, but an order of 300 generations for a human population of 1000. Sanford has on various conferences used this to support the claim that humans has been here in less than 300 generations, and claim that the reason they lived for 500 years right around the flood was because their 'fitness' was higher.

Why this is bullshit:

One can make many theoretical objections to Sanfords model, or indeed just show him examples that the very ting he says his program show is impossible, that positive mutations are selected for, actually happends in nature. Here are a couple of links:

http://www.nature.com/nature/journal/v413/n6855/full/413514a0.html

http://www.nature.com/nature/journal/v419/n6909/full/nature01140.html

http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030170

http://www.nature.com/nature/journal/v437/n7055/full/nature04072.html

http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040072

http://scienceblogs.com/evolgen/2006/03/detecting_natural_selection_pa.php

And this is where Sanfords is so badly wrong. Science is about describing the nature, and when you want to evaluate an add-hoc model like Sanfords you got to evaluate it based on how well it describe nature. ALL models, no matter how good they look, have to undergo that test. I write computer simulations of statistical models that describe systems much, much simpler than what Sanford try to describe, and i have NEVER read an article that did not contain validation against ACTUAL DATA FROM THE REAL WORLD.

So how does Sanfords model describe a population of E-coli? of the mice on the ark? Fruitflies? Sanford are very silent of those systems, and the reason is clear: E-coli would go extinct several times a year with his model of evolution, so clearly his model is not biologically realistic.

Thats what i mean by validation. The stuff you linked to was only validation that his program does what he sayes it does (not that it matters, but after the source was made puplic it was found it was riddled with bugs, but lets not go there), not that his model actually describe the essentials of evolution. I can easily make a program that validate evolution, heck, lets write it right now:

1) Initialize a population of 1000 individuals, each with a fitness of 1.

2) (mutation) Add a number uniformly distributed from (-1, 1) to each individuals fitness.

3) (replication) Delete the 500 individuals with lowest fitness. Copy them to get to 1000 again. Go to 2).

but that does not prove jack shit because i have not validated it against reality.