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Tags evolution , genetics , neo-darwinism

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Old 17th April 2008, 05:23 AM   #81
wogoga
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Originally Posted by wogoga View Post
So whereas the genetic information of a human only constitutes a small fraction of the storage capacity of a DVD disc of 4.7 Gigabyte, in order to store all the synaptic connections of a three-year-old child, around a million DVD discs are needed.

Originally Posted by Reality Check View Post
Congratulations Wolfgang - you have just proved that learning is impossible since all of the synapse connections in the brain are hard-coded in DNA!

What I have shown is this: If all the synaptic connections of a three-year-old child were hard-coded (ignoring details such as location in the brain, length of axons, synaptic plasticity, etc.), in the order of 10^16 byte = 10,000,000 Gigabyte would be needed. Yet the whole active DNA of a human is less than 10^8 byte = 0.1 Gigabyte. And this information is assumed to be responsible also for many thousand enzyme species, differentiation into more than two hundred cell types, the highly complex anatomy of the human body at all levels, human learning capacity, instinctive behaviour and even talents.

Or take the brain of a newborn instead of a three-year-old. The complexity of this brain is the main precondition for learning after birth.


Originally Posted by Reality Check View Post
As any biologist can tell you, neural development starts from a mostly random network of synaptic connections. Connections are then reinforced by learning.

An extract from your link (emphasis mine):
"Some landmarks of embryonic neural development include the birth and differentiation of neurons from stem cell precursors, the migration of immature neurons from their birthplaces in the embryo to their final positions, outgrowth of axons from neurons and guidance of the motile growth cone through the embryo towards postsynaptic partners, the generation of synapses between these axons and their postsynaptic partners, and finally the lifelong changes in synapses which are thought to underlie learning and memory.

Typically, these neurodevelopmental processes can be broadly divided into two classes: activity-independent mechanisms and activity-dependent mechanisms. Activity-independent mechanisms are generally believed to occur as hardwired processes determined by genetic programs played out within individual neurons. These include differentiation, migration and axon guidance to their initial target areas. These processes are thought of as being independent of neural activity and sensory experience. Once axons reach their target areas, activity-dependent mechanisms come into play. Neural activity and sensory experience will mediate formation of new synapses, as well as synaptic plasticity, which will be responsible for refinement of the nascent neural circuits."
Wikipedia on Axon guidance:
"Axon guidance (also called axon pathfinding) is a subfield of neural development concerning the process by which neurons send out axons to reach the correct targets. Axons often follow very precise paths in the nervous system, and how they manage to find their way so accurately remains a major puzzle."
One thing is sure: the information cannot come from the DNA, simply because the DNA does not contain enough information. If you try to understand the following quote from Psychons and their Evolution, you can resolve this major puzzle yourself.
The maturation of a protein from the corresponding amino acid chain can happen in the following way:
In important (evolutionarily older) sequences of the chain, amino acids become active, that is they get animated by psychons. Because of environment continuity these psychons are the ones which have built up the same protein (or the same sequence of different proteins) innumerable times. These psychons build up protein parts which can be animated as a whole by other psychons which then build up the complete protein.
So it also becomes comprehensible that RNA sequences (introns) are able to cut out themselves or that order is maintained during DNA recombination.
Cheers, Wolfgang

Use as few hypotheses as possible, but not fewer!
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Old 17th April 2008, 05:28 AM   #82
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Originally Posted by wogoga View Post
One thing is sure: the information cannot come from the DNA, simply because the DNA does not contain enough information. If you try to understand the following quote from Psychons and their Evolution, you can resolve this major puzzle yourself.
What puzzle?
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Old 17th April 2008, 07:54 AM   #83
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Originally Posted by wollery View Post
I think you guys are missing the point.

Wogoga isn't saying that evolution didn't happen. His argument is that evolution by natural selection of mutations didn't happen because the probability is too low, so it must have been directed by an external agency.
I obviously missed it. Since it's cherry-picking, it seems to me that evolution happened by (insert favourite paranormal agent here) is the same as saying evolution didn't happen.
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Old 17th April 2008, 08:12 AM   #84
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Originally Posted by wogoga View Post
Or take the brain of a newborn instead of a three-year-old. The complexity of this brain is the main precondition for learning after birth.
More made up suff, wonderful.
Quote:






An extract from your link (emphasis mine):
"Some landmarks of embryonic neural development include the birth and differentiation of neurons from stem cell precursors, the migration of immature neurons from their birthplaces in the embryo to their final positions, outgrowth of axons from neurons and guidance of the motile growth cone through the embryo towards postsynaptic partners, the generation of synapses between these axons and their postsynaptic partners, and finally the lifelong changes in synapses which are thought to underlie learning and memory.

Typically, these neurodevelopmental processes can be broadly divided into two classes: activity-independent mechanisms and activity-dependent mechanisms. Activity-independent mechanisms are generally believed to occur as hardwired processes determined by genetic programs played out within individual neurons. These include differentiation, migration and axon guidance to their initial target areas. These processes are thought of as being independent of neural activity and sensory experience. Once axons reach their target areas, activity-dependent mechanisms come into play. Neural activity and sensory experience will mediate formation of new synapses, as well as synaptic plasticity, which will be responsible for refinement of the nascent neural circuits."
Oh boy, more loaded language, target, find a neurology source for that?
Quote:

Wikipedia on Axon guidance:
"Axon guidance (also called axon pathfinding) is a subfield of neural development concerning the process by which neurons send out axons to reach the correct targets. Axons often follow very precise paths in the nervous system, and how they manage to find their way so accurately remains a major puzzle."
Funny how some questions have answers: PubMed 'axon guidance', what mystery?
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Quote:
One thing is sure: the information cannot come from the DNA, simply because the DNA does not contain enough information.
Duh, and so if a cell release chemicals that cause groth of axons around it, then what is that?

Duh.
Quote:
If you try to understand the following quote from Psychons and their Evolution, you can resolve this major puzzle yourself.
The maturation of a protein from the corresponding amino acid chain can happen in the following way:
In important (evolutionarily older) sequences of the chain, amino acids become active, that is they get animated by psychons. Because of environment continuity these psychons are the ones which have built up the same protein (or the same sequence of different proteins) innumerable times. These psychons build up protein parts which can be animated as a whole by other psychons which then build up the complete protein.
So it also becomes comprehensible that RNA sequences (introns) are able to cut out themselves or that order is maintained during DNA recombination.
Cheers, Wolfgang

Use as few hypotheses as possible, but not fewer!
Yeah I found psychons all over PubMed too!
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Old 17th April 2008, 09:51 AM   #85
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Originally Posted by wogoga View Post
What I have shown is this: If all the synaptic connections of a three-year-old child were hard-coded ...
Which they aren't

Quote:
And this information is assumed to be responsible also for many thousand enzyme species, differentiation into more than two hundred cell types, the highly complex anatomy of the human body at all levels, human learning capacity, instinctive behaviour and even talents.
Substitute "known" for "assumed", and that's about right.

Quote:
"Axon guidance (also called axon pathfinding) is a subfield of neural development concerning the process by which neurons send out axons to reach the correct targets. Axons often follow very precise paths in the nervous system, and how they manage to find their way so accurately remains a major puzzle."
Typical crank reasoning. "If I can't explain it, then I can explain it, psychons do it by magic". Usually it's not psychons, but God or space aliens or the Secret Consipracy of Evil Jews.

Quote:
One thing is sure: the information cannot come from the DNA, simply because the DNA does not contain enough information.
If that was "sure", then wouldn't you have a scrap of a shred of evidence for it?

All you need to do is find a protein the synthesis of which is not directed by DNA.

Of course, this would not confirm the "psychons" hypothesis and more than it would confirm the goddidit hypothesis, the "space aliens are telporting proteins into my body" hypothesis, the "magic gene fairy" hypothesis, or the hypothesis that it's synthesized by some non-magical biological process that we haven't found out about yet.

But it would be a start. So, please name one human protein that doesn't have a corresponding gene.

Quote:
So it also becomes comprehensible that RNA sequences (introns) are able to cut out themselves or that order is maintained during DNA recombination.
Actually, that's comprehensible in terms of biochemistry, without dragging in imaginary invisible entities. If you want to know how self-splicing introns self-splice (and most introns, BTW, are not self-splicing) then you could start with that article on [swiki]splicing[/swiki] that I keep referring you to, or you could go directly to this link.

Last edited by Dr Adequate; 17th April 2008 at 09:52 AM.
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Old 17th April 2008, 09:53 AM   #86
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Originally Posted by wogoga View Post
What I have shown is this: If all the synaptic connections of a three-year-old child were hard-coded (ignoring details such as location in the brain, length of axons, synaptic plasticity, etc.), in the order of 10^16 byte = 10,000,000 Gigabyte would be needed. Yet the whole active DNA of a human is less than 10^8 byte = 0.1 Gigabyte. And this information is assumed to be responsible also for many thousand enzyme species, differentiation into more than two hundred cell types, the highly complex anatomy of the human body at all levels, human learning capacity, instinctive behaviour and even talents.
I agree hard-coding all the connections of the adult would be quite tricky. Also, if our brains were hard-coded, we probably wouldn't have things like variation in memory from person to person, personalities determined by experience, accumulation of knowledge.

Of course no one would argue the connections are completely hard-coded.

As you said there is activity dependent and activity independent development, but its really more fair to characterize it in four stages. Neurogenesis, Migration, Axonal projection, Activity dependent tuning. Postnatally there is also another phase of activity dependent tuning and neural die off. Without explaining all the details, basically the brain gets the neurons roughly connected then uses test patterns and later real sensory stimuli to decide which of the connections to keep.
If you are curious about how this happens I would look up Netrins, or Bone Morphogenic protein or Sonic Hedge Hog(the axonal guidance cue that was named after the sega character), its not really that mysterious.

So I guess your point is well....pointless.

This means you've dropped your silliness about evolution,too. Ya wogoga?

Last edited by zosima; 17th April 2008 at 09:53 AM.
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Old 17th April 2008, 09:54 AM   #87
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Quote:
What I have shown is this: If all the synaptic connections of a three-year-old child were hard-coded (ignoring details such as location in the brain, length of axons, synaptic plasticity, etc.), in the order of 10^16 byte = 10,000,000 Gigabyte would be needed. Yet the whole active DNA of a human is less than 10^8 byte = 0.1 Gigabyte.
If all the items in the set of natural numbers were hard-coded data in the order of infinite Gb would needed. Yet the whole of the Peano Axioms can be written on the back of a cigarette packet.

Mathematics is clearly a fradulent enterprise.
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Old 17th April 2008, 11:11 AM   #88
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Originally Posted by wogoga View Post
What I have shown is this: If all the synaptic connections of a three-year-old child were hard-coded (ignoring details such as location in the brain, length of axons, synaptic plasticity, etc.), in the order of 10^16 byte = 10,000,000 Gigabyte would be needed. Yet the whole active DNA of a human is less than 10^8 byte = 0.1 Gigabyte. And this information is assumed to be responsible also for many thousand enzyme species, differentiation into more than two hundred cell types, the highly complex anatomy of the human body at all levels, human learning capacity, instinctive behavior and even talents.
(clip...)
Equations, formulae, computations, calculations, etc., are only models of reality. For any mathematical model to be useful, it must be capable of predicting real-world outcomes with better accuracy than mere guesswork.

If your mathematics is correct, you should be able to predict something about the future of human evolution with some amount of certainty -- and you should be able to demonstrate your predictions using your math.

So...show us how evolution actually works with a mathematical model -- use that model to predict future outcomes with reasonable certainty, and we will applaud you. Otherwise, all of your "math" is really just a talisman -- one that we've all read one hundred times before.
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Old 17th April 2008, 11:41 AM   #89
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Originally Posted by kjkent1 View Post
Equations, formulae, computations, calculations, etc., are only models of reality. For any mathematical model to be useful, it must be capable of predicting real-world outcomes with better accuracy than mere guesswork.

If your mathematics is correct, you should be able to predict something about the future of human evolution with some amount of certainty -- and you should be able to demonstrate your predictions using your math.

So...show us how evolution actually works with a mathematical model -- use that model to predict future outcomes with reasonable certainty, and we will applaud you. Otherwise, all of your "math" is really just a talisman -- one that we've all read one hundred times before.
Wogoga's math sucks. Wogoga's problem is that he has a hard time producing a mathematical model that is actually correct.

Also, why does he use bytes to describe the information in the genome? I'm not an expert in genetics, but I was under the impression that the preferred unit was bp, kbp,mbp,gbp. Basically orders of magnitude of base pairs. Where does he even go from 10^15 synapses to 10^16 bytes? Somehow he's decided you need 10*2^3 bits to code the connection of a synapse? Why that number. Also I'm not even sure he's using byte correctly.

For example 10^16 bytes =~ 9,000,000 GB = 8.8 PB(peta bytes)
A gigabyte is actually 2^30 bytes not 10^9 bytes That said all the rest of the assumptions are bunk, so there is no reason that this one is any worse than the rest, only demonstrative of them.
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Old 17th April 2008, 12:08 PM   #90
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Originally Posted by wogoga View Post
"Activity-independent mechanisms are generally believed to occur as hardwired processes determined by genetic programs played out within individual neurons. These include differentiation, migration and axon guidance to their initial target areas. These processes are thought of as being independent of neural activity and sensory experience. Once axons reach their target areas, activity-dependent mechanisms come into play. Neural activity and sensory experience will mediate formation of new synapses, as well as synaptic plasticity, which will be responsible for refinement of the nascent neural circuits."
You are under the mistaken impression that the brain of a newborn is complex -- it is not. It is more like solid block of stone before the sculpter has started working on it. Or an empty flash drive.

Originally Posted by wogoga View Post
Wikipedia on Axon guidance:
"Axon guidance (also called axon pathfinding) is a subfield of neural development concerning the process by which neurons send out axons to reach the correct targets. Axons often follow very precise paths in the nervous system, and how they manage to find their way so accurately remains a major puzzle."
The "puzzle" part here refers to a lack of data, not a lack of understanding of the data.

Originally Posted by wogoga View Post
One thing is sure: the information cannot come from the DNA, simply because the DNA does not contain enough information.
Yes, it does. Try defining "information," then looking at how much of this "information" needs to come from DNA, and maybe you will learn something.
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Old 18th April 2008, 07:19 AM   #91
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Originally Posted by Dr Adequate View Post
Typical crank reasoning. "If I can't explain it, then I can explain it, psychons do it by magic".
Typical dogmatic reasoning: "Despite contradictions and lacking explanations, our beliefs are nevertheless correct."

Substantial scientific progress is only possible if we take seriously the problems of our current theories and explanations, and if we are able to play with other hypotheses. As a result of biological evolution, uncommon hypotheses seem to be in contradiction with reality. However we should not forget that what seems to us as reality, is also a construction of our souls and brains.

A typical sign of dogmatism is ignoring logical inconsistencies. For instance: On the one hand, the fact that computer-implemented algorithms cannot be improved by randomly changing bits or bytes, is declared irrelevant because "genes are not computer programs". On the other hand, the highly complex architecture of the human brain at birth is explained by the assumption that the necessary information is somehow generated by an algorithm. Do you have any idea, how enzymes could implement such an algorithm?

And by the way, panpsychism (or better: pandualism) is a fully legitimate hypothesis with a long tradition. I know that it is a long and difficult process to substantially change one's own world view, e.g. from pure materialism to the recognition of psychons. For me, this step was not so difficult, because already in former lives I had considered panpsychism as a reasonable scientific hypothesis. See also my posts #29, #51 and #270 from "Reincarnation as a trivial scientific fact".

Some further arguments suggesting information in the form of psychons from the psychon theory:
Not even the assumption that proteins are fully coded by the DNA is true. The genetic code includes twenty amino acids. Apart from these amino acids many proteins contain other amino acids and other components, which are not coded. The genetic code is not universally valid as it was initially assumed. Several exceptions have been found.

Genes of plants and animals regularly contain non-coding sequences. These introns must be cut out from the RNA copies of the genes. The information indicating which regions represent no code and must be removed is not coded. Some introns even cut out themselves. In several cases, RNA nucleotides are changed, deleted or inserted (RNA editing) before translation starts. In order to produce correct proteins, ribosomes sometimes skip nucleotides instead of translating them. Even from the translated sequences sometimes parts are cut out before protein folding starts. All this is not coded!

After transcription, many amino acid sequences efficiently take on a stable form. Biotechnologically produced, random sequences do not fold to a protein. The common explanation is that proteins have been selected during evolution to fold properly. Yet, if only a very small proportion of possible sequences take on a stable form, only this small proportion can undergo selection of protein function, and the probability that random mutations destroy stability is very high. Furthermore, it is improbable that a protein, selected for a stable form, also acts as a catalyst for complex functions. On the other hand, there are related proteins of similar form and function, whose amino acid sequences have drifted apart substantially. There are even cases where the completely different amino acid sequences, corresponding to different reading frames of a given RNA sequence (frameshift), result in correct proteins or parts of proteins.
Cheers, Wolfgang
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Old 18th April 2008, 08:12 AM   #92
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Originally Posted by wogoga View Post
A typical sign of dogmatism is ignoring logical inconsistencies. For instance: On the one hand, the fact that computer-implemented algorithms cannot be improved by randomly changing bits or bytes, is declared irrelevant because "genes are not computer programs".
Goodness me. They can't?

You haven't heard of "genetic algorithms"? I spent something like five years of my life doing exactly that --- randomly changing bits and bytes in computer-implemented algorithms and looking to see which of the random changes resulted in performance iimprovements. I've personally published something like thirty papers based on findings generated by this technique.

More importantly, they're not papers about "genetic algorithms" per se. You can't get papers published about "genetic algorithms," any more, since the technique is so standard no program committee will consider it novel. GA are yet another optimization technique (like hill-climbing, but better at avoiding the problem of local maxima); any reearcher in any field of modelling, from aeronautics to zoology, is generally familiar with GA as a generic problem-solving technique if they're at all competent.

Should I return my Ph.D. on the grounds that what I did -- and what the committee saw me do, and accepted, and what thousands of researchers world-wide do routinely on a daily basis -- is impossible?

Quote:
And by the way, panpsychism (or better: pandualism) is a fully legitimate hypothesis with a long tradition.
So is the four humour theory of disease; that dates back to Galen. Something else the two hypotheses have in common is that they're both completely and entirely wrong. Geocentrism? The flat Earth? Sympathetic magic? People have been wrong for a very long time.

Quote:
I know that it is a long and difficult process to substantially change one's own world view,
Not at all. I'm a professional researcher. Show me some evidence that my worldview is wrong, and I'll change it. But you've got no evidence.

Last edited by drkitten; 18th April 2008 at 08:17 AM.
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Old 18th April 2008, 08:22 AM   #93
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Originally Posted by wogoga View Post
Typical dogmatic reasoning: "Despite contradictions and lacking explanations, our beliefs are nevertheless correct."
And the fact that you don't address specific point and just continue to repeat your self is what?

Care to comment about how natural selection works and counter the multiple explanations given?

No because you are dogmatic.
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Substantial scientific progress is only possible if we take seriously the problems of our current theories and explanations, and if we are able to play with other hypotheses.
Considering you haven't a shred of evidence your hypothesis will remain speculation solely.
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As a result of biological evolution, uncommon hypotheses seem to be in contradiction with reality. However we should not forget that what seems to us as reality, is also a construction of our souls and brains.
that is fantasy, not reality.
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A typical sign of dogmatism is ignoring logical inconsistencies. For instance: On the one hand, the fact that computer-implemented algorithms cannot be improved by randomly changing bits or bytes, is declared irrelevant because "genes are not computer programs".
well they aren't nor is the nucleus and mitochondria like a CPU, nor is the gene like RAM and on and on.

Building upon bad analogies does not make science, it makes bad generalization.
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On the other hand, the highly complex architecture of the human brain at birth is explained by the assumption that the necessary information is somehow generated by an algorithm.
You haven't demonstrated the first part yet, still ignoring the evidence?

Figures.
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Do you have any idea, how enzymes could implement such an algorithm?
I linked to twent papers on PubMed on one small part of it.

But please act ignorant.
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And by the way, panpsychism (or better: pandualism) is a fully legitimate hypothesis with a long tradition. I know that it is a long and difficult process to substantially change one's own world view, e.g. from pure materialism to the recognition of psychons. For me, this step was not so difficult, because already in former lives I had considered panpsychism as a reasonable scientific hypothesis. See also my posts #29, #51 and #270 from "Reincarnation as a trivial scientific fact".
Yeah and I was a giant clam and a tree, might as well say that a fairy told you.
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Old 18th April 2008, 08:30 AM   #94
drkitten
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Originally Posted by zosima View Post
Also, why does he use bytes to describe the information in the genome? I'm not an expert in genetics, but I was under the impression that the preferred unit was bp,
The units for information are bits and bytes. The problem with base pairs as a unit is that we don't really know how much information a base pair contains (we have an upper bound of 2 bits/pair, but that's not that helpful....)

In order to make a synapse, you need to know which of the 10^11 (~= 2^40) or so neurons is the synapse target, yes? If you assume (dangerous word there) that the target distrubution is uniiform, then it requires forty bits per neuron to specify the target.

Of course, the information doesn't all need to come from the DNA (the environment is informative, too) and we have no reason to assume that the target distribution is uniform (which is a worst-case scenario).
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Old 18th April 2008, 08:54 AM   #95
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Originally Posted by wogoga View Post
A typical sign of dogmatism is ignoring logical inconsistencies. For instance: On the one hand, the fact that computer-implemented algorithms cannot be improved by randomly changing bits or bytes, is declared irrelevant because "genes are not computer programs". On the other hand, the highly complex architecture of the human brain at birth is explained by the assumption that the necessary information is somehow generated by an algorithm. Do you have any idea, how enzymes could implement such an algorithm?
What Dr Kitten said, genetic algorithms. I had a friend whose PhD was almost entirely based on implementation of a genetic algorithm. The entire point was that the algorithm adapted, keeping changes which improved its fitness, and rejecting changes which diminished its fitness.
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Old 18th April 2008, 12:04 PM   #96
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Originally Posted by drkitten View Post
The units for information are bits and bytes. The problem with base pairs as a unit is that we don't really know how much information a base pair contains (we have an upper bound of 2 bits/pair, but that's not that helpful....)
So then there really isn't a way to go from bp to bits/bytes.

I don't think bits and bytes are units of information in the same sense that a meter is a unit of length. Its just a measure of the number of binary digits we can use to write down a number, so essentially just a range of numbers.

Originally Posted by drkitten View Post
In order to make a synapse, you need to know which of the 10^11 (~= 2^40) or so neurons is the synapse target, yes? If you assume (dangerous word there) that the target distrubution is uniiform, then it requires forty bits per neuron to specify the target.
Ya, I was trying to draw attention to the weakness of this assumption. The idea that neural connections would somehow be specified by neuron name is tenuous at best. There are no molecules during development that could serve as a way to 'address' or 'target' neurons specifically. The best that might be able to happen is if you had a number of opposing chemical releasers around the brain that would set up a coordinate system you could use to do some sort of rough positional targeting.


Originally Posted by drkitten View Post
Of course, the information doesn't all need to come from the DNA (the environment is informative, too) and we have no reason to assume that the target distribution is uniform (which is a worst-case scenario).
I would agree, the majority of the information from the genome only gives a rough outline.

I'm really not sure what you mean by uniform target distribution. How are you imagining that synaptic connections are set up?
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Old 18th April 2008, 01:03 PM   #97
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Originally Posted by zosima View Post
So then there really isn't a way to go from bp to bits/bytes.
Oh, there is, but we don't know it yet.

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I don't think bits and bytes are units of information in the same sense that a meter is a unit of length. Its just a measure of the number of binary digits we can use to write down a number, so essentially just a range of numbers.
No, that's exactly what bits and bytes are. The underlying mathematics (and theory) is given in Claude Shannon's classic 1948 paper "A Mathematical Theory of Communications" and the sixty-odd years of work in "information theory" since then; it's a quite well-developed branch of mathematics, physics, and computer science. A "bit," technically speaking, is the amount of information contained in the tossing of a (fair) coin, and that can be generalized as a function over any probability distribution. The rolling of a fair die, for example, has between two and three bits of information; a loaded die will contain slightly less information because the die itself is more predictable. Rolling an 8-sided die (they look like octahedra) gives exactly three bits of information, while rolling
a 16-sided die gives you four. This isn't really an appropriate place for me to give you a thirty-page tutorial on information theory, but if you can't get satisfaction from Google, feel free to ask and I (or Complexity, for that matter) will be happy to answer.

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Ya, I was trying to draw attention to the weakness of this assumption. The idea that neural connections would somehow be specified by neuron name is tenuous at best.
On the other hand, there is definitely something that guides the dvelopment of neural pathways, whether it be a chemical gradient, and there must be something that tells a neuron to grow here and not there. Since a neuron could in theory grow anywhere, but doesn't, there must be some process that tells it wher to go -- and since the set of possible paths is much much larger than the set of paths that we actually see, there must be something adjusting path-space. That "something," by definition, contains information in some form.

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I'm really not sure what you mean by uniform target distribution. How are you imagining that synaptic connections are set up?
There are approximately 10^11 neurons in the human brain, and in theory, any particular synapse can be connected to any of those. If for some reason a particular neuron in the visual cortex never connects to any of the neurons in the hippocampus, then that "reason" must have a a biological specification detailing which neurons it will not connect to. The mechanism is irrelevant -- all that is relevant is that the specification exists and can dictate where the synapses can and cannot go.

Numerically, the worst possible case is where any neuron "could" in theory connect to any other one, with equal probability. In this case, determining which neuron will be connected to contains exactly as much information as in the rolling of a 10^11-sided die, which is about 40 bits or 8 bytes. If the probabilities are not equal, then it's the rolling of a loaded 10^11-sided die, which has less information (depending upon how loaded the die is).
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Old 18th April 2008, 02:34 PM   #98
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Originally Posted by drkitten View Post
Oh, there is, but we don't know it yet.
There might be an average amount of information, but there is no way to assume its not a variable mapping. We know it is a variable mapping, because some amino acids can be coded in more than one way. And that doesn't even take things like protein structure into account.

Originally Posted by drkitten View Post
No, that's exactly what bits and bytes are. The underlying mathematics (and theory) is given in Claude Shannon's classic 1948 paper "A Mathematical Theory of Communications" and the sixty-odd years of work in "information theory" since then; it's a quite well-developed branch of mathematics, physics, and computer science. A "bit," technically speaking, is the amount of information contained in the tossing of a (fair) coin, and that can be generalized as a function over any probability distribution. The rolling of a fair die, for example, has between two and three bits of information; a loaded die will contain slightly less information because the die itself is more predictable. Rolling an 8-sided die (they look like octahedra) gives exactly three bits of information, while rolling
a 16-sided die gives you four. This isn't really an appropriate place for me to give you a thirty-page tutorial on information theory, but if you can't get satisfaction from Google, feel free to ask and I (or Complexity, for that matter) will be happy to answer.
I understand how information theory works. I also understand the mathematics behind it, and I know that bit ends up being a bit because of the application of the base 2 logarithm in Shannon's theory. Logarithm's in other bases tell you just as much. Thats why I would say its a measurement but its not unit. In the sense that it has a no correspondence to some calibrated physical property. It simply distinguishes the number of states that a system or an information channel can take. In the same way that you can have physical quantities with units that cancel and become unit-less quantities. In the same way that probabilities, counts, and ratios don't have units. The log of a probability, or distribution, or number of states, also doesn't have units.

Or I could just take the much more conservative tack and say, it's not SI, it doesn't have an SI correspondence, and it certainly isn't derived from a combination of SI units. I mean its not like there is some ideally balanced coin stored in France somewhere that allows us to be sure just how much information is in a bit. I guess we flip that coin whenever we have to calibrate computer chips. LoL...just to make sure their bits are fair....

Originally Posted by drkitten View Post
On the other hand, there is definitely something that guides the dvelopment of neural pathways, whether it be a chemical gradient, and there must be something that tells a neuron to grow here and not there. Since a neuron could in theory grow anywhere, but doesn't, there must be some process that tells it wher to go -- and since the set of possible paths is much much larger than the set of paths that we actually see, there must be something adjusting path-space. That "something," by definition, contains information in some form.
Yes that something is well understood. Axons follow chemical gradients, amongst other things. But they're generally just attractive or repulsive and there aren't even close to enough types to attract every single axon to every single axon. They're essentially very rough instructions, they're in no way exact. Of course the information has to come from somewhere, but in all likelihood, its coming from the environment in a pretty high entropy sort of way. It's easier to think of the specific connections in the human brain as underspecified by both the genome and the information we have about the womb. In other words that information is going to vary a lot between individuals. Thats why the brain uses a competitive algorithm with pruning and die-off. It maintains an equivalence of result but not of architecture specifics.


Originally Posted by drkitten View Post
There are approximately 10^11 neurons in the human brain, and in theory, any particular synapse can be connected to any of those. If for some reason a particular neuron in the visual cortex never connects to any of the neurons in the hippocampus, then that "reason" must have a a biological specification detailing which neurons it will not connect to. The mechanism is irrelevant -- all that is relevant is that the specification exists and can dictate where the synapses can and cannot go.

Numerically, the worst possible case is where any neuron "could" in theory connect to any other one, with equal probability. In this case, determining which neuron will be connected to contains exactly as much information as in the rolling of a 10^11-sided die, which is about 40 bits or 8 bytes. If the probabilities are not equal, then it's the rolling of a loaded 10^11-sided die, which has less information (depending upon how loaded the die is).
Sure you can think of it that way, but as I've explained above its pretty unilluminating. Basically neurons in one tissue just project position to position to another tissue, with quite a bit of variance.

To put it in a more human understandable form the genome has instructions like:
Project: Retina->Thalamus
Project reverse layering: Thalamus->V1

So 40 bits is such a loose bound, insofar as it tells us about information thats conserved between individuals ,that its essentially useless.
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Old 18th April 2008, 03:37 PM   #99
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Originally Posted by wogoga View Post
A typical sign of dogmatism is ignoring logical inconsistencies.
A typical sign of an internet troll is to always avoid the argument of one's opponents, by:

1. Ignoring them.
2. Ridiculing them.

Followed by restating one's position again as if it were self evidently correct.

Anyone can poke a hole in a dam. Very few can build a dam. Your argument is just another attempt to poke a hole in evolutionary theory. The theory remains standing, despite occasional holes, because those who know how to build a dam, work on the holes until they are filled.

So, poke away -- it will avail you not. Only when you actually build your own "dam" theory and that theory holds "water," will anyone take your theory seriously.

...that is, anyone who matters.
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Old 18th April 2008, 05:15 PM   #100
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Originally Posted by kjkent1 View Post
A typical sign of an internet troll is to always avoid the argument of one's opponents, by:

1. Ignoring them.
2. Ridiculing them.

Followed by restating one's position again as if it were self evidently correct.

Anyone can poke a hole in a dam. Very few can build a dam. Your argument is just another attempt to poke a hole in evolutionary theory. The theory remains standing, despite occasional holes, because those who know how to build a dam, work on the holes until they are filled.

So, poke away -- it will avail you not. Only when you actually build your own "dam" theory and that theory holds "water," will anyone take your theory seriously.

...that is, anyone who matters.
Well to Wogoga's credit, he has written a lot on a theory of reincarnation via "psychons" . In the language of your analogy it is a little pile of dirt which makes mud better than it holds water.
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Old 18th April 2008, 08:03 PM   #101
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Originally Posted by wogoga View Post
Typical dogmatic reasoning: "Despite contradictions and lacking explanations, our beliefs are nevertheless correct."
I expressed no beliefs about how axon guidance works. Nor ddid I claim that the beliefs that I don't have were correct. Nor did the views that I didn't express have contradictions in them.

My point, let me restate it, is that lacking a complete explanation for something does not allow you to conclude that psychons are doing it, still less to take the absence of a complete explanation as evidence for psychons.

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A typical sign of dogmatism is ignoring logical inconsistencies. For instance: On the one hand, the fact that computer-implemented algorithms cannot be improved by randomly changing bits or bytes ...
This is not true.

Another sign of dogmatism is ignoring facts.

Look up, e.g. Tierra.

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On the other hand, the highly complex architecture of the human brain at birth is explained by the assumption that the necessary information is somehow generated by an algorithm. Do you have any idea, how enzymes could implement such an algorithm?
Just as I challenged you to find an enzyme without a gene, now I'd like you to find a metabolic process without an enzyme of functional RNA.

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And by the way, panpsychism (or better: pandualism) is a fully legitimate hypothesis with a long tradition. I know that it is a long and difficult process to substantially change one's own world view, e.g. from pure materialism to the recognition of psychons. For me, this step was not so difficult, because already in former lives I had considered panpsychism as a reasonable scientific hypothesis.


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Not even the assumption that proteins are fully coded by the DNA is true. The genetic code includes twenty amino acids. Apart from these amino acids many proteins contain other amino acids and other components ...
I am not sure which of many facts well-known to biologists you're trying to refer to, but the mechanisms underlying these facts are well-known and do not involve psychons doing magic.

Now, let's make it simple. Find me a polypeptide without a gene. It's a simple question. Don't waffle, don't try to teach your grandmother to suck eggs, fiind a polypeptide without a gene.

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The genetic code is not universally valid as it was initially assumed. Several exceptions have been found.
I know that; I have no idea why you mention it.

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Genes of plants and animals regularly contain non-coding sequences. These introns must be cut out from the RNA copies of the genes. The information indicating which regions represent no code and must be removed is not coded.
Wrong.

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Some introns even cut out themselves. In several cases, RNA nucleotides are changed, deleted or inserted (RNA editing) before translation starts. In order to produce correct proteins, ribosomes sometimes skip nucleotides instead of translating them. Even from the translated sequences sometimes parts are cut out before protein folding starts. All this is not coded!
Wrong.

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After transcription, many amino acid sequences efficiently take on a stable form. Biotechnologically produced, random sequences do not fold to a protein.
Every polypeptide is a polypeptide. Do you mean that most of them don't have a stable tertiary structure?

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The common explanation is that proteins have been selected during evolution to fold properly. Yet, if only a very small proportion of possible sequences take on a stable form, only this small proportion can undergo selection of protein function, and the probability that random mutations destroy stability is very high. Furthermore, it is improbable that a protein, selected for a stable form, also acts as a catalyst for complex functions.
It would be even more unlikely if an unstable structure could act as a catalyst.

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On the other hand, there are related proteins of similar form and function, whose amino acid sequences have drifted apart substantially.
Yes, biology is robust, isn't it?

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There are even cases where the completely different amino acid sequences, corresponding to different reading frames of a given RNA sequence (frameshift), result in correct proteins or parts of proteins.
I know that, too. This is just standard creationist fare. "It's complicated, so it can't have evolved".

But the fact (which you denied above) that computer programs and electronic circuits and so forth produced by variation and selection show similar complexity despite a similar apparent lack of robustness shows that your incredulity is misplaced.
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Old 18th April 2008, 09:01 PM   #102
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Originally Posted by wogoga View Post
For instance: On the one hand, the fact that computer-implemented algorithms cannot be improved by randomly changing bits or bytes, is declared irrelevant because "genes are not computer programs".
It might be relevant if it were, true, but your claim is false.

First randomized algorithms are incredibly important in computer science. There is an entire complexity class, the foundation of quantum computing, called bounded probabilistic polynomial(BPP). Second, computer programs, have been evolved using random evolutionary algorithms for all sorts of tasks. Theorems have been proved this way, novel FPGA designs have been created, neural networks and other cognitive systems have been generated and honed this way. Don't assume that its not done in research just because you aren't aware of it being done in Windows, or Word, or IE.

Originally Posted by Wogoga
On the other hand, the highly complex architecture of the human brain at birth is explained by the assumption that the necessary information is somehow generated by an algorithm. Do you have any idea, how enzymes could implement such an algorithm?
Yes....I've been talking to doctor kitten about this very topic in this very thread. The algorithm is as follows:

Neural connections are very roughly specified by axonal guidance cues(I've got mention my favorite again, Sonic Hedge Hog(Shh)). Randomly some connections are good and others bad, some useful, some not. Activity at sensory systems then serve to hone the rest of the brain's connections. This normally involves eliminating connections that are too weak or too strong. Sometimes neurons that are under-stimulated often commit suicide(called apoptosis).

That is the rough outline of the algorithm, if you want the details then you should go to grad school in neuroscience in a lab that studies developmental neurobiology, cause only very specialized people know the majority of the details.


Also Wogoga, you've already conceded that complex adaptations can be generated by random mutations as long as the mutations independently aren't harmful. So your only chance of making a useful, potentially believable, quality argument, is to show that there is some complex multi-step adaptation where a necessary intermediate step was harmful.
You have yet to even suggest something hypothetical, much less something plausible. In absence of this you'll be denying the overall conclusion to evolution even though every objection you've made has been carefully and methodically addressed by several people.

As an analogy to how you're behaving. Imagine we're in a rowboat on a lake. You claim there is a hole in the boat and that we're going to die. I examine the boat and find no hole and show you this. I show you that there is no water in the bottom of the boat. I show you that the edge of the boat is just as high above the water at one time then five minutes later. I also note that even if the boat were sinking we're wearing life preservers and that the shore is only thirty or forty feet away. So we're certainly not going to die even if the boat does sink. You insist that boat is still sinking, you say it must not be a hole, it must be the termites eating boat frame and even if we don't drown we'll probably catch some disease from the water that will kill us anyway. Do you see how this works? The process repeats, you continually insist on the same conclusion but the reasons you claim for believing change each round. Do you see how presupposing the conclusion is illogical, how its silly, how it doesn't make sense?
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Old 18th April 2008, 11:32 PM   #103
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There might be an average amount of information, but there is no way to assume its not a variable mapping. We know it is a variable mapping, because some amino acids can be coded in more than one way. And that doesn't even take things like protein structure into account.
You're talking about the difference between interpretation and representation.

A bit stream of 8 characters represents at most 8 bits of information. A DNA sequence of 4 base pairs contains at most 8 bits of information. Mapping one to the other is very trivial.

When it comes to how one may interpret that information that is dependent on the language - and since one may have an infinite number of languages there's an infinite number of interpretations with perhaps an infinite amount of information that could be represented.

The "language" of chemistry is clearly highly complex and so is the interpretation of the meaning of DNA.

But this complexity is not to be found within the encoding of the DNA itself - this is a classic error of reasoning of the type wogoga is making when he says there is not enough information with in the DNA.
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Old 19th April 2008, 08:27 AM   #104
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Originally Posted by zosima View Post
I understand how information theory works. I also understand the mathematics behind it, and I know that bit ends up being a bit because of the application of the base 2 logarithm in Shannon's theory.
So far, so good.

Quote:
Logarithm's in other bases tell you just as much. Thats why I would say its a measurement but its not unit.
Er,.... huh?

If you take the log in other bases, you get other units. The most common alternative formulation is by using natural logs (base e), in which case the units that you get are called "nats." Nats used to be more commonly used in Europe than in the US (BTL was a US company, after all), but I almost never see them used any more.

But,.... so what? Meters are units of lengths, and centimeters are also units of length, and there's a well-established correspondence between the two --- but that doesn't invalidate either one of them.


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In the sense that it has a no correspondence to some calibrated physical property.
Well, if you're measuring a non-physical entity, I'd be surprised if your measurement would correspond to any specific physical property -- how many inches correspond to a farad? Length and capacitance are incommeasurable.

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The log of a probability, or distribution, or number of states, also doesn't have units.
Certainly it does. Depending upon the base of the log, you get bits, or nats, or something less usual --- and the units are critical, because you can't subtract bits from nats without conversion, any more than you can subtract six feet from two meters and get a meaningful -4.


Quote:
Or I could just take the much more conservative tack and say, it's not SI, it doesn't have an SI correspondence, and it certainly isn't derived from a combination of SI units.
So? There's not an SI standard "dollar" either, but prices are most certainly measurements, and a "dollar" is certainly a unit of price. There are, in fact, many units of price that do not correspond to any physical object (when was the last time you saw a single Turkish lira, or a US mill?) At my university, courseloads are measured (and paid for) in "credits," and of course there's no SI standard credit, either.

And the "dollar" isn't a physical unit, so it doesn't correspond to any physical process. It is, nevertheless, an economic unit, just as a "credit" is an educational one. (And my "credits" may or may not correspond with those at your "university," because our unit bases are different. If you're using a trimester system and I'm not, for example....)
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Old 19th April 2008, 12:26 PM   #105
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@Dr Kitten

Its kinda funny because I think we both understand what each other are saying. So I'm just gonna lay it out one more time. If you disagree, thats fine but I don't think more discussion can add that much more to what I say.

There is a difference between a measure and a unit. Many measures are unitless. What you are saying is that taking a logarithm of a unitless quantity will somehow add a unit. But if that were the case then whenever you take a logarithm it would have to add a unit. That is not the case. Thus it is a measure without units.

If I look at your examples,
The dollar, is pretty interesting, because even though its not SI, countries maintain huge apparatuses to precisely calibrate it. It allows us to relate abstract numerical quantities to a physical amount of value, and doing so is no simple feat. Note: Log_2(n dollars) != n dollar-bits

The farad too is very demonstrative. It, of course, is not equal to length, but it actually is commensurable, that is part of what makes it a little different than something purely abstract. F=C^2/(N*m) The farad helps us take some numerical quantity into a specific amount of physical capacitance. The idea of what does and does not constitute a unit actually makes a lot of sense if you look at it in terms of the unit cancellation equations that often show up in physics and chemistry.

I said this before, but I'll say it again, the usage of bits and bytes in computer science is different than the sense in which you would normally use a unit, in the sense that you use it to take an abstract quantity and establish a correlation to something in the physical world. You might say its the difference between Unit and unit. A precise technical term and a colloquial use that bears some relation to the technical term. A colloquial use that is also a more convenient way of talking about something that you don't want to have to explain every time you type it. So in the sense that we can use it as a shorthand to talk about a logarithm of a count or a probability; a way to relate two purely abstract quantities, then yes its a unit. But its not in the sense that Unit is used more technically in empirical sciences to take an abstract relation into a physical relation.

I think we can agree on that, yes? If you don't agree thats fine, but I don't think any more discussion on the topic is going to add anything that isn't available in our previous posts. So rebut me one more time, if you must, and as long as you are nice and as reasonable as you were in your previous posts, I intent to leave the issue as it stands.
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Old 20th April 2008, 12:13 PM   #106
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Originally Posted by wogoga View Post
On the one hand, the fact that computer-implemented algorithms cannot be improved by randomly changing bits or bytes, is declared irrelevant because "genes are not computer programs".

Originally Posted by drkitten View Post
You haven't heard of "genetic algorithms"? I spent something like five years of my life doing exactly that --- randomly changing bits and bytes in computer-implemented algorithms and looking to see which of the random changes resulted in performance iimprovements.

The by far most important principle of life is neither mutation nor selection but the finalistic principle of reproduction. Organisms must at first be able to create viable copies of themselves (see also).

(In the case of humans, reproduction implies the formation of far more than 10^20 apriori rather improbable chemical uphill bonds. There are uncountable possible errors in cell replications. The assumption that the only errors worth a mention are correctly bonded DNA changes and that a substantial proportion of these changes has even positive effects is totally unjustified within reductionist materialism.)

In the case of genetic algorithms we have in principle on the one hand data sequences and on the other hand algorithms creating new data sequences using already existing data sequences. Whether we call such data sequences genotypes, phenotypes, individuals or something else is irrelevant. Relevant to this discussion however is that such data sequences are passive entities manipulated and copied by a computer program, which cannot improve itself by randomly changing its own bits or bytes (see also).

So genetic algorithms do not resemble very much real life. They are much closer to handwritten chain letters which also "are capable of evolution" if humans do the real work of creating new individuals. Also computer simulations such as Tierra are rather based on the chain-letter principle than on the principle of biological evolution.

Cheers, Wolfgang
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Old 20th April 2008, 12:54 PM   #107
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Originally Posted by wogoga View Post
Relevant to this discussion however is that such data sequences are passive entities manipulated and copied by a computer program, which cannot improve itself by randomly changing its own bits or bytes
This far into the discussion, and you are already forgetting that Natural Selection is not a theory that relies on purely random changes.

Natural Selection is an algorithm that non-randomly selects from available variety.

Arguing that complex features cannot come about by randomly changing bits, is not a valid argument. Evolutionary biologists will already agree with you. That is why the selection process is Non-Random: Dependant on environmental and other fitness landscape factors.

Originally Posted by wogoga View Post
Also computer simulations such as Tierra are rather based on the chain-letter principle than on the principle of biological evolution.
It makes no difference what principals you think it is based on. The fact that it works, is an admission that Evolution is plausible. Tierra represents an idea of how it is possible for complexity of life to emerge from an evolutionary process. Arguing that such a thing is "impossible", is no longer viable.
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Old 20th April 2008, 02:20 PM   #108
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Originally Posted by wogoga View Post
In the case of genetic algorithms we have in principle on the one hand data sequences and on the other hand algorithms creating new data sequences using already existing data sequences. Whether we call such data sequences genotypes, phenotypes, individuals or something else is irrelevant. Relevant to this discussion however is that such data sequences are passive entities manipulated and copied by a computer program, which cannot improve itself by randomly changing its own bits or bytes (see also).
In exactly the same way, the laws of chemistry cannot change themselves by "manipulating their own bits and bytes".

The analogy is fairly precise.

---

Here's a question for you. Why did you think that this was a good analogy when you wrote that "computer-implemented algorithms cannot be improved by randomly changing bits or bytes", and now think that this is a bad analogy when it turned out that you were talking rubbish and know that computer-implemented algorithms can be improved by randomly changing bits or bytes?

If the claim that this couldn't happen was an argument on your side, then surely the fact that it can is an argument on ours.
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Old 20th April 2008, 04:56 PM   #109
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Originally Posted by wogoga View Post

In the case of genetic algorithms we have in principle on the one hand data sequences and on the other hand algorithms creating new data sequences using already existing data sequences. Whether we call such data sequences genotypes, phenotypes, individuals or something else is irrelevant. Relevant to this discussion however is that such data sequences are passive entities manipulated and copied by a computer program, which cannot improve itself by randomly changing its own bits or bytes (see also).
You're obviously not a LISP or Prolog programmer.

The distinction you wish to create between data and algorithms is a false one. Any data stream can be executed; any algorithm can be encoded as data. In some languages there is an algorithmic transcription process; in others, the data is directly executable as an algorithm

So,... no.

And as Dr. A. pointed out, the computer analogy is yours. Why were self-modifying computer programs a good model of evolution twenty posts ago and now a bad one?
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Old 21st April 2008, 07:20 AM   #110
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Originally Posted by Dr Adequate View Post
Substitute "known" for "assumed", and that's about right.

So your credo is:
It is known that the active genetic information of less than 0.1 Gigabyte is essentially enough to determine many thousand enzyme species, differentiation into more than two hundred cell types, the highly complex anatomy of the human body at all levels, the complex brain architecture at birth, human learning capacity, instinctive behaviour and even talents.
I'm sure that at the latest in a future life you will wonder how educated persons of the beginning third millennium were able to belief in such a thing. Have you ever thought how much information is needed in order to build e.g. a computer?


Originally Posted by Dr Adequate View Post
All you need to do is find a protein the synthesis of which is not directed by DNA.

I'm not sure whether psychons being able of doing that still subsist. But even if they still exist, it may be rather difficult to detect them, because of their inefficient replication they may nowhere reach a high enough concentration in order to be detectable with our current biotechnological means. (The same was valid before the 1980s with e.g. viruses such as HIV). And to demonstrate definitively that such proteins cannot somehow be the result of uncommon splicing and composition, of frame shifts or changes analogous to error correction, could be quite difficult.

However, it is a quite obvious consequence from the hypothesis of a continuous evolution that before the invention of the highly complex translation, proteins were somehow able to create copies of themselves without DNA and RNA. A quote from the psychon theory:
During evolution, psychon animated molecules have been joining together in always bigger units. Animated molecules such as amino acids and nucleotides began sometime to form chains. By specialization psychons emerged which dominated such chains. Proteins are conceivable which replicate by adding corresponding amino acids to one chain end, until an identical protein can split off. Reproduction by base pairing of two complementary strands is even more efficient. The invention of translation, a complex symbiosis of various ribosomal psychons, was certainly one of the most essential steps during the evolution of life.
Cheers, Wolfgang
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Old 21st April 2008, 07:32 AM   #111
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Originally Posted by wogoga View Post
So your credo is:
It is known that the active genetic information of less than 0.1 Gigabyte is essentially enough to determine many thousand enzyme species, differentiation into more than two hundred cell types, the highly complex anatomy of the human body at all levels, the complex brain architecture at birth, human learning capacity, instinctive behaviour and even talents.
That is unfortunately a complete misrepresentation of the process of embryological development. The idea that DNA contains "all" the information necessary to build a living creature is at best outdated and at worst active deception.

Creatures are built as a result of an interaction between the DNA and the chemical and physical environment in which that is expressed. As a simple example of this --- sex development in mammals seems to be almost purely genetically determined. For reptiles, however, it is a complex combination of genes and environment (mostly temperature) Alligators are good examples. An egg incubated above about 90 degrees will always be male. Below 86 degrees, it will always be female. Between 86 and 90 degrees, it is genetically determined. What's "really" going on is that the expression of DNA is a complex chemical process and the speed and outcome of almost any chemical process is temperature dependent (try seeing how much salt you can dissolve in hot vs. cold water for a simple example).

But from an information-theoretic perspective, this means that sex (in alligators) is not a function of genetics, but of genetics PLUS the environment. The environment contains information that is crucial to the proper development of the organism.

Mammals don't have this issue, of course, because mammals are incubated at roughly uniform temperature. But in this case, again, the proper temperature (and environment otherwise) is crucial to the proper development of the organism; the mother's womb as well as the DNA provides "information."

You are trying to use "psychons" to fill in the information-theoretic holes. Why not use something that actually exists, like a mother?
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Old 21st April 2008, 08:47 AM   #112
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Originally Posted by Jimbo07 View Post
hmmm...

Attachment 10620

From Here
Oh come on, we know that is a guy in a suit...oh wait, wrong thread...nevermind
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Old 21st April 2008, 08:50 AM   #113
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Originally Posted by wogoga View Post

It is difficult to discuss with persons who, if necessary, deny the obvious in order to defend their dogmatic beliefs...

Cheers, Wolfgang
Pot meet Kettle.
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Old 21st April 2008, 01:02 PM   #114
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Quote:
I'm sure that at the latest in a future life you will wonder how educated persons of the beginning third millennium were able to belief in such a thing. Have you ever thought how much information is needed in order to build e.g. a computer?
Hmm, I'm guessing that I'll definitely need to know the position of every single atom in the computer. That's got to be the smallest representation possible!
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Old 21st April 2008, 02:43 PM   #115
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Originally Posted by wogoga View Post
So your credo is:
It is known that the active genetic information of less than 0.1 Gigabyte is essentially enough to determine many thousand enzyme species, differentiation into more than two hundred cell types, the highly complex anatomy of the human body at all levels, the complex brain architecture at birth, human learning capacity, instinctive behaviour and even talents.
I'm sure that at the latest in a future life you will wonder how educated persons of the beginning third millennium were able to belief in such a thing.
Well, that was amusing.

Quote:
Have you ever thought how much information is needed in order to build e.g. a computer?
Yes. And I know that it is much smaller than the amount of information you can fit on a computer.

Quote:
I'm not sure whether psychons being able of doing that still subsist.
Well, that was honest. So, are you going to drop the assertion that DNA can't code for all the proteins from your website?

Quote:
But even if they still exist, it may be rather difficult to detect them ...
I'm not asking you to detect the psychons, just a polypeptide without a gene. For starters.

Quote:
However, it is a quite obvious consequence from the hypothesis of a continuous evolution that before the invention of the highly complex translation, proteins were somehow able to create copies of themselves without DNA and RNA. A quote from the psychon theory:
It is not at all obvious. For example, many people think that the RNA came before the proteins.

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Old 22nd April 2008, 03:25 PM   #116
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Originally Posted by wogoga View Post
Genes of plants and animals regularly contain non-coding sequences. These introns must be cut out from the RNA copies of the genes. The information indicating which regions represent no code and must be removed is not coded. Some introns even cut out themselves. In several cases, RNA nucleotides are changed, deleted or inserted (RNA editing) before translation starts. In order to produce correct proteins, ribosomes sometimes skip nucleotides instead of translating them. Even from the translated sequences sometimes parts are cut out before protein folding starts. All this is not coded!
Originally Posted by Dr Adequate View Post
Wrong.

Some quotes from SkepticWiki:
"A gene may have no introns; it may have dozens. In eukaryotic organisms (i.e. organisms whose cells have nuclei, such as plants and animals) the typical gene consists mostly of introns. An average protein-coding gene will be about 8000 nucleotides long, whereas a average piece of mature mRNA after splicing will only be 1200 nucleotides long (figures from Campbell and Reece, Biology)."

"Group 2 introns are also self-splicing, with no assistance whatsoever: purely as a result of the sequence of bases in the RNA, they curl themselves up and snip themselves out of the RNA, with the excised intron ending up in what is known as a lariat structure --- a loop of RNA with a tail."

"Nuclear introns are far from being self-splicing: rather, they are spliced with the aid of a rather complicated bit of cellular machinery called a spliceosome".
According to the psychon thesis, group 2 introns are fully self-splicing because corresponding psychons have survived. Folding of a chain into an enzymatic active form always depends on corresponding psychons, which are limited in number. So one can predict that such introns cannot always cut themselves out if genes with such introns are expressed at a too high rate.

This can be verified by experiment: Take an intron which is not very widespread, transfer it into a crucial and widely expressed gene of a fast growing organism. At some point in time, it will become impossible to further increase the genetically modified organism in number, because introns will no longer be able to cut themselves out, thus impeding the correct expression of the crucial gene. This is similar to the principle of psychon-deficit diseases.

You assume that some RNA-sequences cannot be used as information-carrier because physical and chemical laws will induce these sequences to cut out themselves (and to correctly bond the two open ends of two remaining information sequences). This seems very unrealistic to me.

In the case of introns which depend on spliceosomes you probably assume: The information which parts must be removed from the mRNA and which of the remaining parts have to be put together in which way (alternative splicing) is somehow coded in the DNA of the spliceosome or of other enzymes. That this is a rather implausible explanation can be better seen if we deal with the case where by "programmed frame shifting" a ribosome corrects a fatal mutation consisting of an insertion of one base pair.

The hypothesis that such a fatal mutation coincides with other mutations being able to correct the error can be excluded. However, if we accept the simple and logically consistent psychon thesis, then such strange error-correction behaviours can easily be explained, because memory is a fundamental principle of psychons (and of life in general).

The psychons involved in the corresponding protein biosynthesis had so often in the past created correct proteins and had become so accustomed to create correct proteins, that they simply were able to ignore the newly introduced fatal mutation. Think about the monks of the past who copied the same texts again and again by writing them. They certainly were able to recognize and correct some errors in such texts, even if they didn't understand the texts.

Cheers, Wolfgang
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Old 22nd April 2008, 06:56 PM   #117
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Originally Posted by wogoga View Post
According to the psychon thesis, group 2 introns are fully self-splicing because corresponding psychons have survived.
And this conclusion is utterly untrue, since we know the biochemistry of group 2 introns, and they do it all according to the laws of chemistry with no magic psychons required.

Now, if this stuff about psychons was a real scientific hypothesis which really implied the necessity of psychons for self-splicing of group 2 introns, then this fact would disprove the psychon hypothesis.

But it isn't and it doesn't so it won't.

Quote:
This can be verified by experiment: Take an intron which is not very widespread, transfer it into a crucial and widely expressed gene of a fast growing organism. At some point in time, it will become impossible to further increase the genetically modified organism in number, because introns will no longer be able to cut themselves out, thus impeding the correct expression of the crucial gene.
I don't quite follow this, but when you say this can be experimentally verified, do you actually mean that there are some experiments which have been done which verify it, or do you mean that you know of no facts that prevent you from daydreaming about an experiment that proves you right?

Quote:
You assume that some RNA-sequences cannot be used as information-carrier because physical and chemical laws will induce these sequences to cut out themselves (and to correctly bond the two open ends of two remaining information sequences). This seems very unrealistic to me.
I do not understand what you think I am assuming or why, which suggests that I am not.

Quote:
In the case of introns which depend on spliceosomes you probably assume: The information which parts must be removed from the mRNA and which of the remaining parts have to be put together in which way (alternative splicing) is somehow coded in the DNA of the spliceosome or of other enzymes.
Yes, appart from the word "assume", which is a funny term to apply to a belief supported by all the data. But if you will do as I asked and show me a process that is not dependent on enzymes or functional RNA, then I shall rethink my position. Knock yourself out.

Quote:
That this is a rather implausible explanation can be better seen if we deal with the case where by "programmed frame shifting" a ribosome corrects a fatal mutation consisting of an insertion of one base pair.

The hypothesis that such a fatal mutation coincides with other mutations being able to correct the error can be excluded. However, if we accept the simple and logically consistent psychon thesis, then such strange error-correction behaviours can easily be explained, because memory is a fundamental principle of psychons (and of life in general).

The psychons involved in the corresponding protein biosynthesis had so often in the past created correct proteins and had become so accustomed to create correct proteins, that they simply were able to ignore the newly introduced fatal mutation. Think about the monks of the past who copied the same texts again and again by writing them. They certainly were able to recognize and correct some errors in such texts, even if they didn't understand the texts.

Cheers, Wolfgang
Summary: you don't understand programmed frameshifting, so psychons do it by magic.

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Old 23rd April 2008, 09:38 AM   #118
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I've been trying to tell people, its not magic or psychons, its the spaghetti monster. He weaves the nucleotides in our genome in such a way to make us tastier for when he sweeps us up in the night and eats us to create demographic decline. I don't know why you people can't see the obviousness and simplicity of the spaghetti monster. It must be that you scientists are too frightened by the truth and are worried about losing your funding....how terribly unethical. Shame of you, you evidence believing, parsimonious, sell-outs!

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Old 23rd April 2008, 03:00 PM   #119
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Just out of curiosity (and forgive me if I missed the relevant post), has wogoga ever given us a testable hypothesis regarding psychons? If not, I suggest focusing on that: Until he does develop such a testable hypothesis he:
1. is not really engaging in science
2. has no right to criticize another idea that does help us develop testable hypothesis
3. should probably read a good, basic book on how science is done, if anyone has any recommendations
4. will probably rant and rave in incredibly ill-informed ways until he takes points #1 to 3 into consideration.

That is all.
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Old 23rd April 2008, 08:16 PM   #120
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Originally Posted by wogoga View Post
One thing is sure: the information cannot come from the DNA, simply because the DNA does not contain enough information.
I think you misunderstand the role of DNA in embryology. DNA is NOT like a blue-print. There is NO one-to-one mapping of genes to parts of the body or brain.

DNA is more like a recipe. Several genes act with each other, and the emergent system is one we call a complete life form.

In a cake recipe, for example, there is no one-to-one mapping of a letter in the text to a specific piece in the cake. The whole recipe works, together, to make the whole cake.

So, of course it would seem like there is "not enough information" in DNA to do everything it does. It's not a matter of "how much" information, but how it is used.

And, as others have mentioned, physics plays a role in providing "information" into the system, as well.
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