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NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 17 2015,10:44   

Quote (cryptoguru @ Feb. 17 2015,10:39)
...
Let me rephrase my original question again, because it seemed to keep getting lost in piles of straw men.
Show me a mechanism that can generate the equivalent information of an ORFan gene (i.e. significant amount of new genetic material, not just a couple of point mutations in regulatory genes that switch other code off/on) using only random mutations and an environmentally driven competition model (i.e. doesn't cheat by rewarding micro-feature improvements that wouldn't be selectable in a natural environment.)
...

I've bolded and italicized the  2 entirely unwarranted and unjustified assumptions that prejudice the result, oddly enough, in your favor.
Duplication and modification of the duplicate suffices.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 17 2015,10:45   

Quote
Cretaceous birds are often "modern" in some aspects while not in others

Incorrect, birds have been found in modern form ... and this parrot!
http://www.berkeley.edu/news....il.html
Where are the transitional forms? We just have Archaeopteryx, which could be argued is a Mendelian variant on a modern day Hoatzin ... or equally argued a distinct avian variety that is extinct.

Quote
Descent of birds from theropods is not an "assumption", but a comclusion, based on cladistic analysis of data from comparative anatomy

Cladistic analysis is extremely subjective, you can make it say what you want. That's synonymous with an assumption. Lot's of evolutionists don't accept the dinos->bird story anyway ... so we creationists are not the only ones banging this drum.

But let's leave the bird chat to later ... I don't want to go off-topic yet.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 17 2015,10:48   

Quote
Let me rephrase my original question again, because it seemed to keep getting lost in piles of straw men.
Show me a mechanism that can generate the equivalent information of an ORFan gene (i.e. significant amount of new genetic material, not just a couple of point mutations in regulatory genes that switch other code off/on) using only random mutations and an environmentally driven competition model (i.e. doesn't cheat by rewarding micro-feature improvements that wouldn't be selectable in a natural environment.)
Avida cheats on 2 accounts, it rewards micro-feature improvements by testing if a logic function (target) has been achieved on mutation and not simply on the performance of the resultant organism ... and it only requires a small amount of new information to generate new features (e.g. 9 commands can perform EQU). ORFan genes represent thousands of unique sequences of base-pairs that must be demonstrated can arrive through simple mutation and natural selection.

For those who may be tempted to argue that you don't need to prove anything algorithmically, I've previously shown that the physical evidence is open to interpretation .... but even if it wasn't, you should be able to demonstrate that the general theory of evolution applied to biology can work in principle. (random mutation plus competition can create significantly quantifiable, more complex and apparently designed solutions to problems). We can't use known targets for this, or it is simply a stochastic search and not evolution. Mutation should also allow degeneration of functionality, in the genome, all the organism's functionality can be affected by mutation; even it's most basic operations are defined and built by the code itself. Therefore mutations should be able to break replication and all other basic survival processes of the organism, not only shuffle some existing functionality.


Although the public is mostly aware of mutations that have bad effects, the majority of mutations have no effect whatsoever, but some are indeed beneficial.  "Disadvantageous" and "beneficial" can also depend on context.  One form of mutation that happens quite commonly (in geological terms in some types of organisms is whole-genome duplication: this is how many plants have become garden-plant ornamentals and crop plants for food.  Duplication of smaller numbers of genes can be helpful by providing back-ups for key genes that might fail, or workable genetic material that can get modified later (the immune system and the vision system have benefitted from multiple versions of genes that have been slightly modified by minor mutations.  Myostatin-blocker mutations offer some obvious benefits for their possessors, along with some potential disadvantages, depending on which blocker mutation we are considering, so there it is a matter of whether the advantages outweigh the disadvantages in any given situation or not.  Lenski's E.coli becoming able to live on a new food resource was a significant novelty arrived at by mutation.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 17 2015,10:55   

Quote (cryptoguru @ Feb. 17 2015,10:45)
Quote
Cretaceous birds are often "modern" in some aspects while not in others

Incorrect, birds have been found in modern form ... and this parrot!
http://www.berkeley.edu/news.......il.html
Where are the transitional forms? We just have Archaeopteryx, which could be argued is a Mendelian variant on a modern day Hoatzin ... or equally argued a distinct avian variety that is extinct.

Quote
Descent of birds from theropods is not an "assumption", but a comclusion, based on cladistic analysis of data from comparative anatomy

Cladistic analysis is extremely subjective, you can make it say what you want. That's synonymous with an assumption. Lot's of evolutionists don't accept the dinos->bird story anyway ... so we creationists are not the only ones banging this drum.

But let's leave the bird chat to later ... I don't want to go off-topic yet.

That agrees with what I said.  That fossil is a Neornithine from the very end of the Cretaceous (65-70 m.y. ago, Maastrichtian: http://www.nature.com/nature....a0.html ), after Neornithines began to replace enantiornithines, which began about 80 million years ago.  Most Cretaceous birds, through most of the Cretaceous, were markedly more primitive and not like modern birds in their details.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 17 2015,11:02   

Crypto, Archaeopteryx is a bird? Are you sure?

Table of archaeopteryx features

1 = present; * = present in some; ? = possibly present; x = absent
    Dinosaurs           Archae            Birds
1        *                  1                1
2        x                  1                1
3        *                  1                1
4        *                  1                1
5        x                  x                1
6        x                  x                1
7        *                  x                1
8        *                  1                x
9        1                  1                x
10       1                  1                x
11       1                  1                x
12       1                  1                x
13       1                  1                x
14       1                  1                x
15       1                  1                x
16       6                  6            11-23
17       1                  1                x
18       1                  1                *
19       1                  1                x
20       1                  1                x
21       1                  1                x
22       1                  1                x
23       1                  1                x

From Talk origins and references are here: http://www.talkorigins.org/faqs....fo.html

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Feb. 17 2015,11:14   

Speaking of going off-topic, Cryptoguru missed an important step:

Admitting that his original "challenge" has been met.

After that, he can set up another challenge. But until that time, it would be off-topic to treat Cryptoguru's digression as anything other than exactly that.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 17 2015,11:15   

Wesley R. Elsberry: sorry, you are correct ... it was 17 .. which is still trivial from a cumulative search point of view.
In fact it's always a trivial problem if you set targets at that level.

I do understand how it works

Avida selects by using complete logic gates plus IO as symbols, this could be compared to bacterial "evolution", which is accomplished by swapping entire operons (multiple genes) on one plasmid symbol. I agree that swapping out an entire chromosome is large enough to select on. But, a nucleotide is waaay too small a symbol to select for universally in multi-cellular organisms, except of course for a few edge cases where a point mutation happens to have the effect of switching on/off a whole gene ... but this cannot explain the arrival of new information.

A single improvement needs to have an increase in fitness of greater than 10% (probably more like 50%) to be selected over environmental noise.

Also, you would need less than 1 average symbol mutation per organism  per generation to keep any advantages you have accrued. There are thousands more "neutral" or bad mutations compared to advantages, so there's no way to hold any good ground you may have covered in your previous mutations.

Also, only bacteria have hundreds or thousands of offspring. These evolutionary algorithms only work in large populations with small mutation rates. Mammals particularly don't have hundreds of children.

So as I was saying, you may be able to demonstrate a simple shuffling on the order of bacterial operons, with large populations and very short generation lengths. But anything more complex cannot be modelled by Avida or anything else, and to a mathematician like me ... seems utterly dumb!

Maybe others are fooled when you use really long time scales ... but the complexity ramps up exponentially from these simple toy problems you're solving with programs like Avida. You don't have anywhere near enough time .. and even if you did, you wouldn't be able to keep hold of any benefits anyway. This is what we observe.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 17 2015,11:36   

Quote (cryptoguru @ Feb. 17 2015,10:45)
               
Quote
Cretaceous birds are often "modern" in some aspects while not in others

Incorrect, birds have been found in modern form ... and this parrot!
http://www.berkeley.edu/news.......il.html
Where are the transitional forms? We just have Archaeopteryx, which could be argued is a Mendelian variant on a modern day Hoatzin ... or equally argued a distinct avian variety that is extinct.

               
Quote
Descent of birds from theropods is not an "assumption", but a comclusion, based on cladistic analysis of data from comparative anatomy

Cladistic analysis is extremely subjective, you can make it say what you want. That's synonymous with an assumption. Lot's of evolutionists don't accept the dinos->bird story anyway ... so we creationists are not the only ones banging this drum.

But let's leave the bird chat to later ... I don't want to go off-topic yet.


Sorry, a little more on birds, since you brought it up and unloaded a pile of manure.

You are just tossing words in the air.  Cladistic analyses are closer to objective than subjective.

From Jaime Headden at https://qilong.wordpress.com/2013.......ding-me                
Quote
Cladistic analysis is a robust, ever improving process of using mathematical algorithms to find “best-fit” arrangements of fixed morphological sequences to unfixed species arrangements, and under various assumptions (all spelled out and clear) how robust this data is and how “well” these species are arranged in comparison to variation in the resultant trees.


One could throw an analysis by ignoring a bunch of data (the Birds Are Not Dinosaurs people have done this repeatedly by removing characters that link birds to dinosaurs), but it is obvious when that happens, and any competent re-analysis shows when this happened.  It's blazingly obvious.  See http://dml.cmnh.org/2001Feb....05.html

With regard to where the transitional forms are, bear in mind that the nature of a transitional form (particularly structural intermediates and stem forms, rather than a guaranteed blood-line ancestor; a great-uncle rather than a grandfather if you will) between A & B is that you can't tell whether it belongs to the A or B lineage.  In this regard, Archaeopteryx, Anchiornis, Xiaotingia, Eosinopteryx, Aurornis, Jinfengopteryx, and scansoriopterygians are excellent examples of of creatures that are extremely hard to identify as basal troodontids, basal dromaeosaurs, basal "birds", or other small side-branches near the bottom of the same bush.  They show quite well what the ancestor to birds must have looked like, because it is highly unlikely that all their many shared characteristics were all separately but identically evolved from an entirely different common ancestor. (One or two features can be evolved convergently, but that is unlikely for all of them, including nonfunctional features and features with very different functions.)

Hoatzins differ from Archaeopteryx in having fused carpals and metacarpals, fusion of the astragalus and the calcaneum, fusion of that into a fused tarsometatarsus, lighter (more hollow) bones, a stronger supracoracoideus muscle that goes over a bony process lacking in Archaeopteryx, lots of heterocoelous cervical vertebrae, many more vertebrae fused into the sacrum, a retroverted hallux (apparently lacking in Archaeopteryx on the basis of the most recent restudy), a short pygostyle-type tail, a strut-like coracoid, a sternum that is both bony and fused, reduced manual unguals, flattened manual phalanx II-1, no pubic symphysis or foot, a highly retroverted pubis, trochanteric crest, hypotarsus, no teeth, no third-finger claws, no long ascending astragalar process, no interdental plates, no obturator process of the ischium, no long chevrons in the tail, and no abdominal ribs.  Other than that, dang near identical (snark, if that wasn't clear).  If all that is available to "Mendelian variations" (a few different alleles), then you ascribe much greater evolutionary powers to minor mutational differences than I do.

Edited to add: I see OgreMkV got there first with much the same information, while I was busy typing things like "no pubic symphysis".

Note the irony in your dissing cladistics by asserting (wrongly) that "Cladistic analysis is extremely subjective, you can make it say what you want", while in the exact same post you made the completely subjective but objectively totally wrong statement, "Archaeopteryx, which could be argued is a Mendelian variant on a modern day Hoatzin".  Sorry, based on that performance, I'll take science over you any day.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 17 2015,17:58   

N.Wells: last thing on the bird topic for now ...

Quote
while in the exact same post you made the completely subjective but objectively totally wrong statement


That is my point, if I wanted to I could use cladistics to assert that Archaeopteryx is directly related to Hoatzin. I can do what I like with cladistics ... it'll only be an "accepted answer" if it supports the pre-existing evolutionary assumption of common descent.

Cladistics is just terminology that means "hey this looks like this and does the same sort of thing, therefore one of them morphed into the other over time" ... but tries to make it sound like proper science. Actually Phylogenetic Systematics sounds even more sciency doesn't it, you should probably use that next time to convince the ignorant creationist that you're doing some really heavily objective analytical stuff.
Ancestry is assumed, therefore it is circular reasoning whether you use a Consistency Index or a Retention Index.
It's just fancy language designed to make it sound like you're doing something way more advanced than pointing at animals and saying "cow goes moo" ... "sheep goes baaa".

Let's get back to the genome discussion, which is much less slippery. In my last post I put forth a coherent argument for why I think evolution of multi-cellular organisms is impossible ... explain how I am wrong without either just saying "you are wrong" or "you don't understand evolution" ... or doing what McOgre does and linking to articles without explaining how they apply to the argument. e.g. "here's 5 articles I'm linking to, if you read them all you will see I'm completely correct and you are completely wrong"

You keep assuming Common Descent in your argument, which is circular reasoning ... I don't accept CD for the origin of different kinds of living things. I believe in variation within a kind, which is what we observe. We see dogs become hugely variant different types of dogs (in that case artificially bred by humans), not by evolution but by standard Mendelian genetics. We don't see them becoming something other than a dog ... the genome restricts the limit of variation. You may want to call them new species of dog because they look different, but they are still dogs and my toddler could identify that.

Your assumption of evolution has led you down the path that you have to be able to explain the morphology of one kind of animal to the next ... we don't see that in the fossil record, or happening now. Sure you can pick an animal out that looks similar to another and claim it's an ancestor, but you have absolutely no evidence for this assertion except for the fact you believe the rock layers denote different ages of history and you believe that all living organisms on earth came from one blob of soup.
So my point stands, claiming one thing evolved from another because they look similar is begging the question ... you have to assume Common Descent, and even with that assumption you can't prove that fossil you're holding ever had any offspring.

  
Cubist



Posts: 559
Joined: Oct. 2007

(Permalink) Posted: Feb. 17 2015,18:05   

Quote (cryptoguru @ Feb. 17 2015,09:39)
I'm back through popular demand ... can't be bothered to read through all the replies since I last visited.

Okey-dokey. I'll just cut-and-paste from one of those earlier replies that you "can't be bothered to read", in the hope that this time you'll actually define your terms and clarify WTF you mean and all that good stuff.

Or if you choose to continue with the bafflegab, that's good, too.

Re-posting the paragraph about how come it's gotta be both "new" and "novel" which you ignored: Why must the "genetic material" of "new information" be both "new" and "novel"? I ask because "new" and "novel" strike me as basically synonymous, hence, using both words is gratuitous redundancy. But perhaps you weren't being redundant; perhaps you actually are using distinct referents for "new" and "novel", such that the two words are not, in fact, gratuitously redundant. Please explain how "genetic material" which is "new" differs from "genetic material" which is "novel".  Is it possible for "genetic material" to be "new" without also being "novel"? Is it possible for "genetic material" to be "novel" without also being "new"?

Perhaps you'll deign to honor the questions in that paragraph with answers, cryptoguru. Or not. [shrug]

Onward.

     
Quote
     
Quote
Does the mutated nucleotide sequence qualify as "new and novel genetic material"? Does the mutated nucleotide sequence contain any "new and novel genetic material"?

The issue here is one of scale ... changing a single nucleotide and getting new functionality is more adequately describing a side-effect of switching a control gene rather than amazingly arriving at a new functional sequence through mutation and selection.

You may be right that "scale" is, indeed, the "issue". But regardless of whether or not "scale" is any kind of "issue" anywhere, I note that you didn't answer either of the questions in the text you quoted. That's okay, I can ask those questions again.

[clears throat]

Let's say that Sequence X is the arbitrary 150-nucleotide sequence "gcc tac agg gat cgt ggg gac ctt acg aat ggc ctt ttt gac tat tct tcg aat cta agc tca gca tca ttc ccg tct acg gga agt ccc ttc cca ata cat atc ctc ggc acc gca ctt gca ggc tca cgc ttc gcg tca ttt agg tca". Let's also say that Sequence X1 is the 149-nucleotide sequence "gcc tac agg gac gtg ggg acc tta cga atg gcc ttt ttg act att ctt cga atc taa gct cag cat cat tcc cgt cta cgg gaa gtc cct tcc caa tac ata tcc tcg gca ccg cac ttg cag gct cac gct tcg cgt cat tta ggt ca" that results when one removes the "t" from the fourth codon in Sequence X.

One: Does Sequence X1 qualify as "new and novel genetic material"? It's a yes-or-no question, cryptoguru; either yes, Sequence X1 does, in fact, qualify as "new and novel genetic material", or no, Sequence X1 does not, in fact, qualify as "new or novel genetic material". It's all well and good to go on about "probability" and "scale" and yada yada, but I really would like to see a yes or a no, and thus far, I ain't seen a yes or a no.

Two: Does Sequence X1 contain any "new and novel genetic material"? Again, it's a yes-or-no question, to which either yes, it does or no, it doesn't would both be relevant responses. Going on about "scale" and "probability" and yada yada, contrariwise, is not a particularly relevant response, as best I can tell.

 
Quote
So evolution claims that all the differences between a chimp's DNA and ours are caused by random mutation on 2 hereditary lines from a common ancestor. Find a sequence of unique DNA in the human genome (yup you can use the "junk DNA" now too, now we know it's not junk). Now that string you're holding has arrived by random mutation ... selection has preserved it, but mutation created it. That's what I mean by new/novel/unique information.

That's nice. You didn't mention "unique" before. Please explain how "genetic material" which is "unique" differs from "genetic material" which is either "new" or "novel".  Is it possible for "genetic material" to be "unique" without also being either "new" or "novel"? Is it possible for "genetic material" to be "novel" without also being "new" or "novel"?

Does Sequence X1 qualify as "unique"?

     
Quote
You may be able to handwave that the switching of a few control genes could happen randomly…

I'm not handwaving a thing, cryptoguru. I'm attempting to get you to explain the meaning of your statement that "New information is new and novel genetic material…".

     
Quote
So to summarise my answer ... when I'm talking about new information ... I'm talking about a unique DNA sequence in an organism.

Groovy. Is Sequence X1 a "unique" DNA sequence?

  
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Feb. 17 2015,19:28   

Quote (cryptoguru @ Feb. 17 2015,17:58)
N.Wells: last thing on the bird topic for now ...

Quote
while in the exact same post you made the completely subjective but objectively totally wrong statement


That is my point, if I wanted to I could use cladistics to assert that Archaeopteryx is directly related to Hoatzin. I can do what I like with cladistics ... it'll only be an "accepted answer" if it supports the pre-existing evolutionary assumption of common descent.

Cladistics is just terminology that means "hey this looks like this and does the same sort of thing, therefore one of them morphed into the other over time" ... but tries to make it sound like proper science. Actually Phylogenetic Systematics sounds even more sciency doesn't it, you should probably use that next time to convince the ignorant creationist that you're doing some really heavily objective analytical stuff.
Ancestry is assumed, therefore it is circular reasoning whether you use a Consistency Index or a Retention Index.
It's just fancy language designed to make it sound like you're doing something way more advanced than pointing at animals and saying "cow goes moo" ... "sheep goes baaa".

Let's get back to the genome discussion, which is much less slippery. In my last post I put forth a coherent argument for why I think evolution of multi-cellular organisms is impossible ... explain how I am wrong without either just saying "you are wrong" or "you don't understand evolution" ... or doing what McOgre does and linking to articles without explaining how they apply to the argument. e.g. "here's 5 articles I'm linking to, if you read them all you will see I'm completely correct and you are completely wrong"

You keep assuming Common Descent in your argument, which is circular reasoning ... I don't accept CD for the origin of different kinds of living things. I believe in variation within a kind, which is what we observe. We see dogs become hugely variant different types of dogs (in that case artificially bred by humans), not by evolution but by standard Mendelian genetics. We don't see them becoming something other than a dog ... the genome restricts the limit of variation. You may want to call them new species of dog because they look different, but they are still dogs and my toddler could identify that.

Your assumption of evolution has led you down the path that you have to be able to explain the morphology of one kind of animal to the next ... we don't see that in the fossil record, or happening now. Sure you can pick an animal out that looks similar to another and claim it's an ancestor, but you have absolutely no evidence for this assertion except for the fact you believe the rock layers denote different ages of history and you believe that all living organisms on earth came from one blob of soup.
So my point stands, claiming one thing evolved from another because they look similar is begging the question ... you have to assume Common Descent, and even with that assumption you can't prove that fossil you're holding ever had any offspring.

Creepto, common descent is a conclusion based on observation of the evidence, not an assumption.

How fucking stupid are you having been told that countless times not to get it?

Please, Creepto fuck head, provide evidence that common descent is an assumption.

Right, I didn't think so.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 17 2015,19:28   

Quote (cryptoguru @ Feb. 17 2015,17:58)
N.Wells: last thing on the bird topic for now ...

     
Quote
while in the exact same post you made the completely subjective but objectively totally wrong statement


That is my point, if I wanted to I could use cladistics to assert that Archaeopteryx is directly related to Hoatzin. I can do what I like with cladistics ... it'll only be an "accepted answer" if it supports the pre-existing evolutionary assumption of common descent.

Cladistics is just terminology that means "hey this looks like this and does the same sort of thing, therefore one of them morphed into the other over time" ... but tries to make it sound like proper science. Actually Phylogenetic Systematics sounds even more sciency doesn't it, you should probably use that next time to convince the ignorant creationist that you're doing some really heavily objective analytical stuff.
Ancestry is assumed, therefore it is circular reasoning whether you use a Consistency Index or a Retention Index.
It's just fancy language designed to make it sound like you're doing something way more advanced than pointing at animals and saying "cow goes moo" ... "sheep goes baaa".

Let's get back to the genome discussion, which is much less slippery. In my last post I put forth a coherent argument for why I think evolution of multi-cellular organisms is impossible ... explain how I am wrong without either just saying "you are wrong" or "you don't understand evolution" ... or doing what McOgre does and linking to articles without explaining how they apply to the argument. e.g. "here's 5 articles I'm linking to, if you read them all you will see I'm completely correct and you are completely wrong"

You keep assuming Common Descent in your argument, which is circular reasoning ... I don't accept CD for the origin of different kinds of living things. I believe in variation within a kind, which is what we observe. We see dogs become hugely variant different types of dogs (in that case artificially bred by humans), not by evolution but by standard Mendelian genetics. We don't see them becoming something other than a dog ... the genome restricts the limit of variation. You may want to call them new species of dog because they look different, but they are still dogs and my toddler could identify that.

Your assumption of evolution has led you down the path that you have to be able to explain the morphology of one kind of animal to the next ... we don't see that in the fossil record, or happening now. Sure you can pick an animal out that looks similar to another and claim it's an ancestor, but you have absolutely no evidence for this assertion except for the fact you believe the rock layers denote different ages of history and you believe that all living organisms on earth came from one blob of soup.
So my point stands, claiming one thing evolved from another because they look similar is begging the question ... you have to assume Common Descent, and even with that assumption you can't prove that fossil you're holding ever had any offspring.


"That is my point, if I wanted to I could use cladistics to assert that Archaeopteryx is directly related to Hoatzin."  Then you made your point unbelievably badly and you do not understand cladistics.  You made a noncladistic assertion that was wrong, without any evidence.  Cladistics does not work the way you say: it is a statistical analysis of similarity akin to cluster analysis and in its fundamental form without shortcuts no assumptions of ancestry are needed to perform the analysis.  Cladistics would (entirely legitimately, if pointlessly) pair hoatzins and the Archaeopteryx as sister groups if and only if you had no other birds (even an enantiornithine) and no other maniraptorans in the analysis (for example in an analysis of a beetle, a newt, an elephant, Archaeopteryx, and the hoatzin).  Otherwise, you would need to lie and make up or delete data in order to create a desired outcome, but that would be obvious the moment anyone checked your data or redid your analysis.

If you pay attention to my words, I never claim "direct ancestry" when dealing with fossils, precisely because that cannot be known.  I claim degrees of similarity from which I infer degrees of relatedness, and I use words like "structural intermediate" and "stem members" and "basal forms", and I will say that one animal is the closest candidate that we currently know of to the ancestry of a group.  If you are going to argue over something, get your facts right and don't argue about strawmen.

In the same vein, you are apparently under a delusion that change through recombination does not constitute evolutionary change (even below the level of speciation).  Again, you might try arguing with argue with real issues, rather than your misunderstandings of them.

Your claim that the Archaeopteryx is a "Mendelian variant" of the hoatzin is a more extreme assertion of ancestry than anything I care to make.  However, if you could show that you could get from the one to the other by genetic recombination you would in fact have lost your war: you would have just demonstrated an easy transition across a very large morphological/anatomical distance (did you not understand the lists that OgreMvK and I provided?) and you would have demonstrated that evolution is much easier than I think it is, let alone than you think it is.


Edited to add: I want to add to something Doc Bill said.  You keep saying that biologists assume evolution, and people keep replying that it's a conclusion, not an assumption.  Just as in day-to-day physics people do not go about re-proving Newtonian mechanics and the electron theory of electricity, biologists find the evidence in favor of evolution to be so overwhelming that they spend very little time directly testing the overall idea and instead spend most of their time trying to expand on the theory of evolution and to test its predictions and implications and find some new wrinkles.  In that sense one could say that there is a sort of an assumption of evolution.  However, evolutionary theory has passed so many tests that biologists see it as proven.  Also, if it were false, standard ongoing research would be generating endless quantities of enigmas and contradictions each year, and that is just not happening.  The fact that there are people who must reject the evidence because of their religious beliefs and because they clearly don't understand it does not enter into the calculation.  Geographers do not put off making maps while awaiting yet another test of the spherical earth theory just because there are still a few vocal flat-earthers out there.  Until you show that your criticisms are founded in knowledge rather than ignorance and blindness (or, somewhat more likely, until fundamentalist republicans get their act together to the extent of defunding the sciences they don't like), your objections are not going to be relevant.

  
The whole truth



Posts: 1554
Joined: Jan. 2012

(Permalink) Posted: Feb. 17 2015,19:42   

Quote (cryptoguru @ Feb. 17 2015,15:58)
N.Wells: last thing on the bird topic for now ...

Quote
while in the exact same post you made the completely subjective but objectively totally wrong statement


That is my point, if I wanted to I could use cladistics to assert that Archaeopteryx is directly related to Hoatzin. I can do what I like with cladistics ... it'll only be an "accepted answer" if it supports the pre-existing evolutionary assumption of common descent.

Cladistics is just terminology that means "hey this looks like this and does the same sort of thing, therefore one of them morphed into the other over time" ... but tries to make it sound like proper science. Actually Phylogenetic Systematics sounds even more sciency doesn't it, you should probably use that next time to convince the ignorant creationist that you're doing some really heavily objective analytical stuff.
Ancestry is assumed, therefore it is circular reasoning whether you use a Consistency Index or a Retention Index.
It's just fancy language designed to make it sound like you're doing something way more advanced than pointing at animals and saying "cow goes moo" ... "sheep goes baaa".

Let's get back to the genome discussion, which is much less slippery. In my last post I put forth a coherent argument for why I think evolution of multi-cellular organisms is impossible ... explain how I am wrong without either just saying "you are wrong" or "you don't understand evolution" ... or doing what McOgre does and linking to articles without explaining how they apply to the argument. e.g. "here's 5 articles I'm linking to, if you read them all you will see I'm completely correct and you are completely wrong"

You keep assuming Common Descent in your argument, which is circular reasoning ... I don't accept CD for the origin of different kinds of living things. I believe in variation within a kind, which is what we observe. We see dogs become hugely variant different types of dogs (in that case artificially bred by humans), not by evolution but by standard Mendelian genetics. We don't see them becoming something other than a dog ... the genome restricts the limit of variation. You may want to call them new species of dog because they look different, but they are still dogs and my toddler could identify that.

Your assumption of evolution has led you down the path that you have to be able to explain the morphology of one kind of animal to the next ... we don't see that in the fossil record, or happening now. Sure you can pick an animal out that looks similar to another and claim it's an ancestor, but you have absolutely no evidence for this assertion except for the fact you believe the rock layers denote different ages of history and you believe that all living organisms on earth came from one blob of soup.
So my point stands, claiming one thing evolved from another because they look similar is begging the question ... you have to assume Common Descent, and even with that assumption you can't prove that fossil you're holding ever had any offspring.

Wow, there are so many things wrong with what you preach.

With this in mind:

"You keep assuming Common Descent in your argument, which is circular reasoning ... I don't accept CD for the origin of different kinds of living things. I believe in variation within a kind, which is what we observe. We see dogs become hugely variant different types of dogs (in that case artificially bred by humans), not by evolution but by standard Mendelian genetics. We don't see them becoming something other than a dog ... the genome restricts the limit of variation. You may want to call them new species of dog because they look different, but they are still dogs and my toddler could identify that."

Tell me about the insects that were taken on the so-called ark during the alleged year long, world wide flud 4,000 years ago. There were just two insects (one pair of one 'kind'), right? A male and a female, right? Which species were they? How did that pair of insects become all of the insect species that have existed since the flud?

In regard to some non-insect critters, what about the microscopic arachnids that live in/on peoples' skin (including yours) and the skin of other mammals? There was just one pair of one species (one pair of one 'kind') of them on the ark, right? Which person's or animal's skin did that pair live in/on during the flud and how did noah know that he was taking just one pair of one species on the ark? If he had taken more than one pair he would have been defying a command from 'God', right? And did that pair of microscopic arachnids become, without evolving, all of the species of arachnids that have existed since the flud? If that pair wasn't the source of all post-flud arachnids, which other pair of one arachnid species was?

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Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 17 2015,20:07   

Quote
Which person's or animal's skin did that pair live in/on during the flud and how did noah know that he was taking just one pair of one species on the ark? If he had taken more than one pair he would have been defying a command from 'God', right?

And which of Noah's family carried syphilis, which one had gonorrhea, who had AIDS, who had chlamydia, who carried smallpox, who had measles, who had chickenpox, who carried rubella, who had tapeworms, who had guinea worm, who had HPV, who had genital herpes, who had trichomoniasis, who had all the pubic lice and head lice, etc., etc., etc. and how did they manage to care for the animals while suffering from all those diseases and parasites, let alone walk off the ark and repopulate the planet?

  
fnxtr



Posts: 3504
Joined: June 2006

(Permalink) Posted: Feb. 17 2015,22:19   

Holy crap.

Did he really just use the Crockoduck Argument?

Game, set, and match.

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"[A] book said there were 5 trillion witnesses. Who am I supposed to believe, 5 trillion witnesses or you? That shit's, like, ironclad. " -- stevestory

"Wow, you must be retarded. I said that CO2 does not trap heat. If it did then it would not cool down at night."  Joe G

  
The whole truth



Posts: 1554
Joined: Jan. 2012

(Permalink) Posted: Feb. 17 2015,22:40   

cryptoguru, I don't recall anyone here claiming that different dog breeds are different species.

If someone were to claim that, why would it bother you? The only reason would seem to be that you don't accept the fact (or even the idea) that there are different species of biological entities, whether they be different species of dogs (canids) or anything else, and it appears that you lump all biological entities into 'kinds'.

How many 'kinds' are there right now, and what 'kinds' are they? How many 'kinds' were originally created on Earth by your chosen, so-called 'God', and what 'kinds' were they? How many 'kinds' were there on Earth the day before the flud started, and what 'kinds' were they? How many 'kinds' were  taken on the ark, and what 'kinds' were they? How many 'kinds' got off the ark after the flud, and what 'kinds' were they? How many 'kinds' were there on Earth 1000 years, 2000 years, and 3000 years after the flud, and what 'kinds' were they? And on what basis do (or could) you know any of that?

And one more question for now: If you had a great, great, great, great, great, great, great, great, great aunt, would it be accurate to label her as one of your ancestors?

Edited by The whole truth on Feb. 17 2015,20:46

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Feb. 18 2015,05:23   

Quote (cryptoguru @ Feb. 17 2015,11:15)
Wesley R. Elsberry: sorry, you are correct ... it was 17 .. which is still trivial from a cumulative search point of view.
In fact it's always a trivial problem if you set targets at that level.


26^17 ~= 10^24, which looks like a pretty non-trivial problem space. Even Cryptoguru's fake number of 9 instructions for EQU leads to 26^9 ~= 10^12, which would be an excessively large for a lottery. Powerball uses a base space of a bit more than 10^8.

Nor is "cumulative search" appropriate as a dismissal for what is happening in Avida. I've already noted multiple times that Avida is awarding merit on behavior, not on any examination of Avidian genome content.

   
Quote (cryptoguru @ Feb. 17 2015,11:15)

I do understand how it works


Then why is it that pretty much everything Cryptoguru has said about Avida other than that it is a computer program is wrong?

   
Quote (cryptoguru @ Feb. 17 2015,11:15)

Avida selects by using complete logic gates plus IO as symbols,


Wrong. Avidian instructions in the 2003 paper do not correspond to digital circuit logic gates. The functions being awarded merit in the 2003 paper correspond to typical logic functions (AND, OR, NOT, etc.). Cryptoguru is making this into a persistently repeated error.

   
Quote (cryptoguru @ Feb. 17 2015,11:15)

this could be compared to bacterial "evolution", which is accomplished by swapping entire operons (multiple genes) on one plasmid symbol.


What a confused statement. Between the utter ignorance of anything to do with Avida and the confusions about the biology, saying the above declaration is worthless insults rubbish. "Plasmid symbol" is apparently jargon from the "Bioshock" game. Nor is Avida limited to broad-brush analysis as Cryptoguru claims, which he should now by now because I told him before:

   
Quote

This is not in the original challenge, and is thus irrelevant to answering the original challenge. The Avida instruction set includes "mov-head", "jump-head", and "set-flow", which can and do change expression dramatically. Avida itself has been used to perform in silico experimentation on overlapping genes:
               
   
Quote

One consequence of overlapping genes is to reduce the tolerance for mutation. Virtual experiments conducted within the past several years using a software system called Avida have indicated that overlapping reduces the probability of accumulating so-called neutral mutations in a gene (mutations that have no effect). Neutral mutations are unlikely with overlapping genes, because the mutation must have no effect on two genes with different reading frames.



You can't do experimentation about overlapping genes if your model doesn't permit changes within its gene model. QED.

But wait, there's more... some time back, Cryptoguru made a different claim about level of Avidian genome:

   
Quote

Section D:
comparison of AVIDA to biological evolution
1) an analogy must be drawn between AVIDA commands and the genome
2) it possibly makes most sense (I concede) to assume that AVIDA commands are analogous to codons (and not proteins), so that any mutation will always create a set of valid codons.
3) the level AVIDA is selecting at is therefore analogous to a folded functional protein.


That this is entirely incompatible with the new claim that Avida only acts on multi-genic blocks is evident.

   
Quote (cryptoguru @ Feb. 17 2015,11:15)

I agree that swapping out an entire chromosome is large enough to select on. But, a nucleotide is waaay too small a symbol to select for universally in multi-cellular organisms, except of course for a few edge cases where a point mutation happens to have the effect of switching on/off a whole gene ... but this cannot explain the arrival of new information.


The premise was false, thus whatever conclusion was drawn has no validity.

   
Quote (cryptoguru @ Feb. 17 2015,11:15)

A single improvement needs to have an increase in fitness of greater than 10% (probably more like 50%) to be selected over environmental noise.


Um, BS. Effectiveness of selection over drift is a function of a variety of factors conveniently omitted from the above. Nor do I see any authority stating any such thing, nor do I recall any such large change in fitness being mentioned as necessary in my classes or further reading.

   
Quote (cryptoguru @ Feb. 17 2015,11:15)

Also, you would need less than 1 average symbol mutation per organism  per generation to keep any advantages you have accrued. There are thousands more "neutral" or bad mutations compared to advantages, so there's no way to hold any good ground you may have covered in your previous mutations.


Cryptoguru also is confused about the potential of where mutations happen and the actual extent to which they happen. Yes, there are lots more ways things can go wrong than ways they can go right. But selection can both eliminate the bad and preserve the good (assuming those turn up in separate organisms). So, what about Cryptoguru's claim of 1 average base mutation per organism?

From here:

   
Quote

In particular, examination of sequence conservation between humans and primates implies that ~ 38% of coding sites are maintained by selection, and that the net mutation rate is high: U ~ 4.2 per generation. (46)


That's an average of 4.2 SNP mutations per human individual. The notion that 1 is a limit is false. If it were true, the human race would be in a world of hurt from mutational load already. One has to look at the likelihood that a mutation will effect the gene that has accrued an advantage, not just the general mutational load. I discuss the general form of that calculation with respect to the "weasel" program here.

The quoted article covers a variety of limiting factors for selection. Unlike Cryptoguru, it sets things out in a reasonable way and takes notice of actual evidence.

   
Quote (cryptoguru @ Feb. 17 2015,11:15)

Also, only bacteria have hundreds or thousands of offspring. These evolutionary algorithms only work in large populations with small mutation rates. Mammals particularly don't have hundreds of children.


Bacteria don't have hundreds or thousands of offspring, at least not at one time.

Since we were talking about Avida in particular, we once again come up with the simple observation that Cryptoguru is completely clueless on the topic. The Avida environment of the 2003 paper had a limit of 3,600 Avidians. While that is a sizable number, it isn't a large effective population relative to the sorts of biological populations whose members do have hundreds or more offspring at a whack. Nor is the Avida mutation rate "small" by comparison to biological exemplars.

Finally, Cryptoguru knows bugger-all about mammalian biology. It took seconds to find this discussing naked mole rats, a mammal:

   
Quote

Many breeding females in captivity have reared offspring for more than 15 years, and our most fecund female reared >900 pups over her 11-year reign (10).


   
Quote (cryptoguru @ Feb. 17 2015,11:15)

So as I was saying, you may be able to demonstrate a simple shuffling on the order of bacterial operons, with large populations and very short generation lengths. But anything more complex cannot be modelled by Avida or anything else, and to a mathematician like me ... seems utterly dumb!


What seems to me to be utterly dumb is to continue to spout fabricated nonsense about topics one doesn't have a clue about, but Cryptoguru seems eminently comfortable doing just that. Avida is not doing shuffling on the order of bacterial operons. The notion that Avida cannot model anything more complex than what we have been discussing is wrong, too. I've mentioned that before, so one wonders exactly how slow Cryptoguru is on the uptake:

 
Quote

Avida has been used to generate and evaluate UML models and for the generation of firmware for wireless sensors to be deployed in wireless sensor networks, and those are a couple of applications that I knew about before I left MSU back in 2009. MSU got the BEACON grant shortly thereafter, and things have been hot in the lab since then.


   
Quote (cryptoguru @ Feb. 17 2015,11:15)

Maybe others are fooled when you use really long time scales ... but the complexity ramps up exponentially from these simple toy problems you're solving with programs like Avida. You don't have anywhere near enough time .. and even if you did, you wouldn't be able to keep hold of any benefits anyway. This is what we observe.


Wrong again. Cryptoguru hasn't been right often enough to be able to substantiate a claim to have observed anything. I've noted Cryptoguru's complete lack of addressing the math of retaining genetic benefits. Nor would I characterize what Avida has been applied to as being all toy problems. (And that's a list from just one of my former colleagues.)

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 18 2015,05:58   

Quote
And which of Noah's family carried syphilis, which one had gonorrhea, who had AIDS, who had chlamydia, who carried smallpox, who had measles, who had chickenpox, who carried rubella, who had tapeworms, who had guinea worm, who had HPV, who had genital herpes, who had trichomoniasis, who had all the pubic lice and head lice, etc., etc., etc. and how did they manage to care for the animals while suffering from all those diseases and parasites, let alone walk off the ark and repopulate the planet?

Hehe that's the stupidest logic I've heard so far on this thread .. maybe next to the guy who talks about the "flud".

The HIV virus that causes AIDS in humans came from a different species, where it wasn't harmful. I don't believe that viruses that are harmful to an organism originated in that organism, observation backs that up. This is similar to bacteria ... which are very useful (good) in certain applications (e.g. digestion, plant decomposition etc), but can be very bad if the wrong bacteria is carried by the wrong organism, or if the balance of a specific bacteria is violated. So no, I don't think all these negative-effect viruses, parasites were carried by Noah & family etc (some may have been) ... but much more likely, they were carried by animals that had a symbiotic relationship with them. (as is the case now)

Quote
Which person's or animal's skin did that pair live in/on during the flud and how did noah know that he was taking just one pair of one species on the ark?

Man ... this is so off-topic it hurts, so very quick answer. Noah was never commanded to take one of every species on the ark, he was told what kinds of animals to take. He wasn't instructed to take fish or microscopic organisms or sea-dwelling mammals or molluscs etc. etc.


Quote
If you pay attention to my words, I never claim "direct ancestry" when dealing with fossils, precisely because that cannot be known.  I claim degrees of similarity from which I infer degrees of relatedness, and I use words like "structural intermediate" and "stem members" and "basal forms", and I will say that one animal is the closest candidate that we currently know of to the ancestry of a group.  If you are going to argue over something, get your facts right and don't argue about strawmen.

OK, so you don't know then ... it isn't hard fact that birds came from dinos? You simply know that there are "degrees of similarity" upon which you are inferring descent.

Quote
You keep saying that biologists assume evolution, and people keep replying that it's a conclusion, not an assumption.  Just as in day-to-day physics people do not go about re-proving Newtonian mechanics and the electron theory of electricity, biologists find the evidence in favor of evolution to be so overwhelming that they spend very little time directly testing the overall idea and instead spend most of their time trying to expand on the theory of evolution and to test its predictions and implications and find some new wrinkles.  In that sense one could say that there is a sort of an assumption of evolution.

A conclusion based on a faulty premise is the wrong conclusion, and holding to it as fact in the face of challenges to the faulty premise is an assumption. Common Descent was assumed to be true by Darwin, this has been accepted as an atheistic axiom. i.e. if you don't believe there's a God, then there was no creation. Therefore, everything must have happened spontaneously and the unlikely spontaneous arrival of life must have started off as a simple cell that natural processes worked on to create the diversity of life that we now see. This is an assumption ... based on the belief in no creator. When you start with that assumption you look at similarities as proof of your assumption, but THAT is circular reasoning. There is no hard evidence to show ancestry from one kind of animal to another, except that you believe it did and you interpret any data in that light. Even when the data disagrees (ORFan genes, no junk DNA, no clear transitional forms in fossils, no observed DNA mutation to produce a fundamentally different organism) you will simply state that perceived contradictions don't actually contradict Common Descent and you will adapt your argument to accommodate the new data somehow without challenging the core assumption.

I am simply pointing out that none of the science you've mentioned proves anything; it only supports your view when you hold to the assumption of Common Descent and a purely natural explanation of all variation must be adhered to. This does not make what you are believing science ... just because you say it is objective, does not make it so.

Quote
Also, if it were false, standard ongoing research would be generating endless quantities of enigmas and contradictions each year, and that is just not happening.

Well yes it does, but unsurprisingly they don't get published as contradictions ... these are the things that creationists comment on that annoy evolutionists. Evolutionists will defend their view of the world irrespective of the data, you seem to have a romantic view of scientists as objective, impartial and purely truth-seeking ... when in fact scientists are human with the need to be recognised, the desire for fame and wealth, the fear of being ridiculed and mocked, the need to fit in and be accepted. Funding is not available to people who have evidence that contradicts the primary axiom that all life can be explained through random mutation and natural selection. Academics who already have influential position and change their mind and reject evolution on the basis of their research are shunned, mocked, sacked from their positions and denied the ability to publish or share their results in the scientific community. This level of censorship and ethnic cleansing has driven most professional scientists who are creationists to keep their mouths shut and toe the party line in fear of not having a job. Some areas of academia will humour anti-evolutionists (e.g. mathematics, engineering), but it is not tolerated in any area of science that has an influence in origins.

Quote
One: Does Sequence X1 qualify as "new and novel genetic material"? It's a yes-or-no question, cryptoguru; either yes, Sequence X1 does, in fact, qualify as "new and novel genetic material", or no, Sequence X1 does not, in fact, qualify as "new or novel genetic material". It's all well and good to go on about "probability" and "scale" and yada yada, but I really would like to see a yes or a no, and thus far, I ain't seen a yes or a no.

Two: Does Sequence X1 contain any "new and novel genetic material"? Again, it's a yes-or-no question, to which either yes, it does or no, it doesn't would both be relevant responses. Going on about "scale" and "probability" and yada yada, contrariwise, is not a particularly relevant response, as best I can tell.

This is the fallacy of many questions (e.g. Do you still beat your wife?) ... it is the rhetorical trick of asking a question that cannot be answered without admitting a presupposition that may be false.
I defined what I meant by "new and novel" ... I am qualifying new material as that which is quantifiably non-trivial. A small change can occur by chance, so can a few small changes. A lot of change in a short period of time that is quantifiably useful for new purpose and not pre-existant is what we observe in ORFan genes. Scale is important and is affected exponentially. So when you use a single symbol mutation to try and demonstrate how an entire program could arise, you have missed the mark by a catastrophic proportion.
Let me expose your argument with a similar analogy:-
I present to you a piece of sheet metal ... I show you that if I drop it on the floor it bends a corner of it. I show you that the angle that the corner is bent at matches a bend on an Aston Martin Vantage, you agree. I claim that if I drop that piece of metal enough times, I will eventually get an Aston Martin Vantage body. Now you would agree that is stupid reasoning .. that is what you are doing here. You want me to agree that X1 is different to X, yes it is ... but you're wanting to claim that just applying a single mutation multiple times will produce the complexity ... well it maybe would if you had a big enough population size and low enough mutation rate and an intelligent scoring mechanism so that the problem becomes a stochastic search algorithm with an in-built target. This is not the problem we are trying to solve, it is a different problem to what you claim is happening in Biology
You are conflating the idea of any change ...  with specific, substantial and complex change that solves a complex problem.

It seems that the assumption of purely natural processes being able to create new information is making it difficult for you guys to be able to argue rationally.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 18 2015,07:36   

Sorry, my mistake on AIDS.  However, if you are looking for bad logic on this thread, I'd go with your false claims about AVIDA that Wesley has documented, or your claim that there's no great difference between having and lacking fused carpals and metacarpals, fusion of the astragalus and the calcaneum, fusion of that into a fused tarsometatarsus, lighter (more hollow) bones, a stronger supracoracoideus muscle that goes over a bony process, heterocoelous cervical vertebrae, large numbers of vertebrae fused into the sacrum, a retroverted hallux, a short pygostyle-type tail, a strut-like coracoid, a sternum that is both bony and fused, reduced manual unguals, flattened manual phalanx II-1, no pubic symphysis or foot, a highly retroverted pubis, trochanteric crest, hypotarsus, no teeth, no third-finger claws, no long ascending astragalar process, no interdental plates, no obturator process of the ischium, no long chevrons in the tail, and no abdominal ribs.

 
Quote
Noah was never commanded to take one of every species on the ark, he was told what kinds of animals to take. He wasn't instructed to take fish or microscopic organisms or sea-dwelling mammals or molluscs etc. etc.
That does point to some flaws in the story.  Setting aside the problem that the water would have been well beyond boiling due to either the potential energy released in its fall from the heavens or due to release of heat on turning from vapour to liquid (http://www.holysmoke.org/cretins/fludmath.htm ; http://infidels.org/library....od.html ), you could maybe get saltwater fish to survive in a salty flood or freshwater fish to survive in a fresh flood, but not both.  Worse, in the creation-science interpretation, the Noachian flood laid down all or most of the world's Phanerozoic strata, which requires a flood that is muddy enough to lay down an average of 8000 m of sedimentary strata over the continents (but much less in the ocean basins, and how did that happen?).  Let's suppose a flood that is 10000 m deep over the continents: that suggests a flood that is on the order of 8 buckets of mud to every 10 buckets of water over the continents: good luck getting any fish or aquatic mammals to survive in that!  2000 to 20000 NTU over merely 24 hours is lethal for 50% of individuals in a variety of riverine fish species, which generally have very high tolerances for mud.  How this translates to ppm depends on the nature of the sediment, but it's on the order of 7000 to 70000 ppm, which is .7 to 7% suspended sediment.  
https://www.niwa.co.nz/freshwa....ish-dss
https://www.niwa.co.nz/our-sci........eak
http://www.transportation.alberta.ca/Content....its.pdf
Worse, all the Phanerozoic evaporites would have had to be dissolved in the flood waters, which would have rendered it hypersaline, which none of the fish could have survived.

Quote
ethnic cleansing
.   Really?

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 18 2015,08:06   

Having been schooled, Crypto now takes that most common of creationist tactics... change the subject by seizing on some minor point that someone else brought up.

I suspect that we will hear about AVIDA again in a few weeks once he thinks we've forgotten about the comments.

This never works. But they always try.

Crypto: Define "kind".

Keeping in mind that if your definition is at any taxonomic level above genus, then you have to explain evolution at rates 10 times higher than any biologists thinks is even possible, much less safe.

Of course, if you choose kind to be at a taxonomic level of genus or lower, then you have to explain how Noah got a bajillion organisms on his boat and cared for them for a year.

And you might want to talk to Ken Ham. He needs some help. Apparently, he just discovered that you can go OUT of the same door you came IN. His mind is just astounding.

--------------
Ignored by those who can't provide evidence for their claims.

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NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 18 2015,09:24   

I'd be very interested to hear his definition of 'information'.
Clearly, pretty much unarguably, natural processes can produce vast amounts of information.
Stellar spectra are information.  They are produced by natural phenomena.
Tides are information.  They are produced by natural phenomena.
Fingerprints are information.  They are produced by natural phenomena.

I would be very interested in hearing about any sort of information at all that isn't produced by 'natural phenomena'.  Humans are as natural as protozoa, and by most measures, less complex than stars.
To assume, or rather assert that humans aren't natural phenomena and so must be explained by recourse to other non-natural phenomena is a huge case of question begging.
We have precisely zero reason for assuming humans are not natural phenomena.
We are, in fact, still waiting for clarification on what the heck a 'non-natural phenomenon' is.

But please, 'information' first.  What is information?  How is it determined that it is never produced by natural phenomena, particularly given the examples of stellar spectra, absorption spectra, the orientation of slightly magnetized iron needles in a magnetic field, and a host of other purely natural phenomena.
The only recourse is to use double-talk for 'information' or to abandon the notion of 'natural phenomena', which goes not further than does taking all phenomena as natural, except it violates Ockham's razor in a big way.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 18 2015,10:05   

Quote (NoName @ Feb. 18 2015,09:24)
I'd be very interested to hear his definition of 'information'.

Dollars to donuts it'll involve "meaning", "new functions", and/or "complexity".

--------------
Ignored by those who can't provide evidence for their claims.

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Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Feb. 18 2015,10:24   

Creepto wrote:
Quote
I am simply pointing out that none of the science you've mentioned proves anything;


Another fine graduate of Kurt Wise U.

I about blew my coffee when Creepto wrote that he was a "mathematician."

Right!  And I once pulled lobsters from Jane Mansfield's arse!

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 18 2015,10:53   

Quote
I'd be very interested to hear his definition of 'information'.
Clearly, pretty much unarguably, natural processes can produce vast amounts of information.
Stellar spectra are information.  They are produced by natural phenomena.
Tides are information.  They are produced by natural phenomena.
Fingerprints are information.  They are produced by natural phenomena.


Natural laws can produce ordered output, e.g. fractals, orbits, crystals etc.
This is not information ... information is "What is conveyed or represented by a particular arrangement or sequence of things" i.e. has meaning
http://www.oxforddictionaries.com/definit....rmation

Waves can produce patterns on the beach, this is not information ... it is a pattern enforced by a natural system.

DNA holds information about how to build an organism ... it is an instruction set that is meaningful to the processing logic of a biological cell. This is not like a fractal or a wave, this is a deterministic sequence of instructions that is understood by the cell and is used to perform specific tasks.
The data sent to a radio controlled car is information, which has intended purpose in the control of the car ... the wind blowing the car off course is not information, even if it makes a pattern, the car is not deriving meaning from the interaction.

this is stuff a 3 year old would understand ... if you put a sandwich in a DVD player it won't play a movie. In fact, you can't put a CD in a DVD player and expect to watch a movie ... the information isn't there.

Information can't be created randomly. That's utter nonsense.


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Wrong. Avidian instructions in the 2003 paper do not correspond to digital circuit logic gates. The functions being awarded merit in the 2003 paper correspond to typical logic functions (AND, OR, NOT, etc.). Cryptoguru is making this into a persistently repeated error.

You obviously don't know what a logic gate is ... AND, OR & NOT are all logic gates. I did not mean in a digital circuit, we are both talking about the same thing ... wow talk about completely misrepresenting what I'm saying.
Avida tests the instruction set to see if it is performing a logical operation (AND, OR, NOT) and rewards the organism if it is. This IS CHEATING!!! I can only assume you don't really understand programming or even basic logic if you don't get this point ... rewarding the organism for performing an anatomical operation is biasing the organism to win based on the fact it has achieved a known target. Explain how this is not so.

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which he should now by now because I told him before

Yeah you keep saying you "told me before" and that should be proof of your argument. I've made a clear description of the issue at stake here and you keep side-stepping it and then simply claiming you've already told me that I got it wrong.

AVIDA REWARDS THE ORGANISM BASED ON KNOWN LOGICAL TARGETS (AND, OR, NOT ...) THIS IS NOT NATURAL SELECTION

This is not new information magically appearing, this is testing a random sequence of commands that we know can result in logical operations against the known logical operations ... blatantly cheating!

Quote


Quote

Section D:
comparison of AVIDA to biological evolution
1) an analogy must be drawn between AVIDA commands and the genome
2) it possibly makes most sense (I concede) to assume that AVIDA commands are analogous to codons (and not proteins), so that any mutation will always create a set of valid codons.
3) the level AVIDA is selecting at is therefore analogous to a folded functional protein.


That this is entirely incompatible with the new claim that Avida only acts on multi-genic blocks is evident.


It's the same issue written a different way. Avida is rewarding fitness at a level high enough to identify functionality (like a protein or a multi-genic block) but low enough to not be concerned with the overall fitness (like an organism or a whole genome). Again, the scale of the Avida complexity is orders of magnitude lower than a real genome

[/QUOTE]26^17 ~= 10^24, which looks like a pretty non-trivial problem space[QUOTE]
That's a completely arbitrary statement ... 10^24 is non-trivial if you're randomly searching ... but that's not what Avida is doing, it rewards combinations that we know get us closer to the final solution. This is more like a decision tree bisection method, where we have a good confidence level for making the right decision at each branch based on the bias that the reward system has enforced. The problem space is now possibly of order log(N), maybe even linear. Can you not see that? Can you not see that it is pushing the solution to a convergence by falsely rewarding the correct organisms based on a criterion that REAL natural selection could not work on?

  
socle



Posts: 322
Joined: July 2009

(Permalink) Posted: Feb. 18 2015,10:54   

Quote (cryptoguru @ Feb. 17 2015,11:15)
So as I was saying, you may be able to demonstrate a simple shuffling on the order of bacterial operons, with large populations and very short generation lengths. But anything more complex cannot be modelled by Avida or anything else, and to a mathematician like me ... seems utterly dumb!

Just out of curiosity, what's your field, if you don't mind me asking?

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 18 2015,11:22   

Quote (cryptoguru @ Feb. 18 2015,11:53)
     
Quote
I'd be very interested to hear his definition of 'information'.
Clearly, pretty much unarguably, natural processes can produce vast amounts of information.
Stellar spectra are information.  They are produced by natural phenomena.
Tides are information.  They are produced by natural phenomena.
Fingerprints are information.  They are produced by natural phenomena.


Natural laws can produce ordered output, e.g. fractals, orbits, crystals etc.
This is not information ... information is "What is conveyed or represented by a particular arrangement or sequence of things" i.e. has meaning
http://www.oxforddictionaries.com/definit....rmation

Waves can produce patterns on the beach, this is not information ... it is a pattern enforced by a natural system.

And you're saying that these patterns are meaningless???
That's absurd.  The patterns enforced by the natural system of physics and chemistry provides meaningful information about the stellar composition and processes of stars.  This isn't 'just some random pattern', it is incredibly meaningful, and the meaning is tightly coupled to very specific and very precise natural laws.

     
Quote
DNA holds information about how to build an organism ... it is an instruction set that is meaningful to the processing logic of a biological cell. This is not like a fractal or a wave, this is a deterministic sequence of instructions that is understood by the cell and is used to perform specific tasks.
The data sent to a radio controlled car is information, which has intended purpose in the control of the car ... the wind blowing the car off course is not information, even if it makes a pattern, the car is not deriving meaning from the interaction.

this is stuff a 3 year old would understand ... if you put a sandwich in a DVD player it won't play a movie. In fact, you can't put a CD in a DVD player and expect to watch a movie ... the information isn't there.

The information contained in a sandwich is not the same as the information contained in a DVD or a CD.  But that it is useless for one purpose does not mean it is meaningless, or that it is without purpose.
You're cheating, badly and transparently, by applying entirely artificial constraints on to what meaning you find, and  where, solely due to your preselected purposes.
That's not how it's done.

     
Quote
Information can't be created randomly. That's utter nonsense.

Blatant assertion, without support.  Information is precisely distinct from randomness, viz. Shannon.
Constrained randomness produces information literally all the time.
[your argument with Wesley snipped]
New information does not appear by magic.  
Yet your claim amounts to the assertion that it does.
We have two alternatives -- natural law and magic.
If you reject the one, and look, you did so right at the top of your post, then you're stuck with magic.
It is YOUR position that information appears by magic.
It is OUR position that information appears naturally, by the operations of nature, which, btw, include randomness.

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 18 2015,11:33   

To append to my previous post -- it is only because the operations of natural law provide information, in your sense not just Shannon's, that science is possible.

One wonders why you are pleased to use the products and insights of science in all parts of your life, in all aspects applying to the world, except when it comes to biology.  And generally, not biology as such, but human biology.

You are the very picture of prejudiced thinking, of seeking support for conclusions you've already adopted, without evidence or reason.

So once again, science, what we do, or magic, what you and your ilk do.
I'll take science and a world filled with information.

As a coda, I think we need to ask you just what you mean by 'random'.  It's a slipperier term than you might suppose, but it's clear you're leveraging every bit of slipperiness you can in service of your prejudiced agenda.
So, what do you mean by 'random'?

  
Freddie



Posts: 371
Joined: Oct. 2009

(Permalink) Posted: Feb. 18 2015,11:42   

Quote
this is stuff a 3 year old would understand ... if you put a sandwich in a DVD player it won't play a movie. In fact, you can't put a CD in a DVD player and expect to watch a movie ... the information isn't there.

Ahem ... Video CD Format.  Still supported on many DVD/BD players today, actually!

--------------
Joe: Most criticisims of ID stem from ignorance and jealousy.
Joe: As for the authors of the books in the Bible, well the OT was authored by Moses and the NT was authored by various people.
Byers: The eskimo would not need hairy hair growth as hair, I say, is for keeping people dry. Not warm.

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 18 2015,11:52   

Quote (Freddie @ Feb. 18 2015,12:42)
Quote
this is stuff a 3 year old would understand ... if you put a sandwich in a DVD player it won't play a movie. In fact, you can't put a CD in a DVD player and expect to watch a movie ... the information isn't there.

Ahem ... Video CD Format.  Still supported on many DVD/BD players today, actually!

And you can put a CD in and listen to music.
That the information he wants/needs/expects is not there is no warrant for assuming that therefore there is no information there.  My DVD players happily recognize CDs, SACDs, DVD-As, etc., and do the right thing based on the information read from the disk.

The level of dishonesty it takes to put forth the sorts of arguments he does is far beyond what a 3 year old would be able to muster up.  Or recognize.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 18 2015,12:03   

So, I guess the question is

If a DVD contains data, but you don't have a device to read it, then does it contain information?

What if the DVD contains data, but it's in Swahili, then does it contain information (you can't read it)?

If the DVD contains data, but you must use a decryption program, with the proper passcode, does it contain information?

If the answer to any of those is "yes", then the you must accept that information is not equal to meaning. None of those DVDs will have any meaning for you, but they all contain information.

As usual, we have someone who rejects evolution because they don't understand how information works and how it's different than meaning.

Let's try again.

Let's say you have a gene. A person is born with a mutant allele for that gene. It results in a 1% decrease in efficiency of that protein. Has information in the gene changed? Has the information content OF THE POPULATION changed?

What if that mutant allele, decades later has another effect that increases the chance of survival of the organism? Has the information increased, decreased, or stayed the same? Why?

I know you won't answer these questions. No ID/creationist has yet.

--------------
Ignored by those who can't provide evidence for their claims.

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