Jump to content


Photo

Genetic Entropy & The Mystery Of The Genome


  • This topic is locked This topic is locked
5 replies to this topic

#1 Bruce V.

Bruce V.

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,153 posts
  • Age: 54
  • Christian
  • Creationist
  • Northern Califiornia

Posted 09 April 2008 - 07:18 PM

My review of Genetic Entropy & the Mystery of the Genome. I thought you may be interested in the contents.

I wrote it out so I could better understand it and I may have misunderstood the contents, so feel free to correct me.

There is an assumption that mutations in the human body are building upward: That small incremental steps that will eventually lead into a large morphological change. This is what Dr. Sanford was trying to say about deleterious mutations:

1. More negative than positive mutations: The ratio is between 10,000 to 1,000,000 harmful mutations for every one that is beneficial. Most view the ratio closer to 1,000,000.

2. That the mutations in the human genome is too high: Sanford states that the average mutation is around 300 mutations/individual. Most or only mildly negative.

3. Neo-Darwin Evolutionist (NDET) assumes that natural selection will take out all of the bad mutations and leave only the good. This is not true. Sanford uses a gamma (not a standard distribution) curve which show ~ 99% of the mutations are harmful. Curve generated by population NDET geneticist Kimura. This ensures that natural selection see many more deleterious mutations for every good mutation. Thus, the genome will suffer from “genetic entropy”. (Many of these “beneficial” mutations actually end up giving the organism a net decrease in fitness (as in the case of homeostasis in cold-climate creatures to warm climates or drug-resistant bacteria) making them deleterious in reality)

4. NDET assumes that one negative mutation can be filtered out selectively. In reality, however, it is an entire gene that is selected for or against. What happens is the genes see many more bad mutations (minimum 10,000/1) and evolution will either select or reject the whole gene not the individual mutation. He calls this the “Muller’s Ratchet” (named after another population geneticist). Even if a gene with a beneficial mutation is selected for, it will carry many, many more deleterious mutations. This inevitably causes genetic entropy, not a complexity increase.

5. Most mutations are only slightly negative like a spelling error and the genome more or less ignores them for a while. The problem is that over time these spelling errors build up and create noise which reduces fitness with successive generations.

6. The best do not always survive. Sometimes the plant seed, for example, with the greatest fitness lands on rocky soil, or in a deep valley with little sunlight, while the less fit lands on a hill that receives sunlight. Sometimes it isn’t the survival of the fittest it is the survival of the luckiest. Again, Sanford sites NDET population geneticist, Kimura which states that heritability due to phenotypic superiority (i.e. fitness) is as low as 0.4%! Hence, even that 1/10,000 (very optimistic) chance of a beneficial mutation has only 1/250 chance of surviving because random environmental factors.

7. Most mutations are recessive and it usually takes two similar mutations, one from each s@x to become “fixed”. Sanford sites NDET geneticist J.B.S. Haldane it would take 300 generations to make a genetic trait fixed in a population.

8. I.D. sees DNA like a computer code and it is the instruction manual for building proteins. NDET assumes the code is linear. Sanford states DNA sequences are “poly-constrained” That is, DNA sequences can have meanings on several different levels. For example, imagine a coded message that has a valid meaning when read forward, another valid meaning when read backwards, another every 5 letters, and yet another when placed on top of another few messages (making it 3D). DNA also has sub-routines and reuses the same genes for multiple tasks. Thus any mutation affects the whole code not just one element. So one good mutation can have many unintended side effects.

9. Irreducible complexity: Sanford sees life as a total system where individual parts rely on many other parts: One is not any good without the other. You take out one part if effects the other parts. That life is integrated.

#2 MRC_Hans

MRC_Hans

    Member

  • Banned
  • PipPipPip
  • 576 posts
  • Age: 59
  • no affiliation
  • Agnostic
  • Denmark

Posted 10 April 2008 - 12:54 AM

My review of Genetic Entropy & the Mystery of the Genome. I thought you may be interested in the contents.

I wrote it out so I could better understand it and I may have misunderstood the contents, so feel free to correct me.


I have no immidiate plans to read the book, but I have some comments to your extract.

There is an assumption that mutations in the human body are building upward: That small incremental steps that will eventually lead into a large morphological change. This is what Dr. Sanford was trying to say about deleterious mutations:


That is not a correct assumtion. There is no 'upwards'. A life-form will evolve in the direction of the selection pressure. This direction is not necessarily 'upwards', i.e. towards more complexity.


1. More negative than positive mutations: The ratio is between 10,000 to 1,000,000 harmful mutations for every one that is beneficial. Most view the ratio closer to 1,000,000.


It is impossible to establish an exact ratio, because you cannot exactly define a 'beneficial' mutation, since this depends on context. For instance, a mutation that makes a fish blind is not beneficial, except if the fish happens to live in a cave where there is never any light.

2. That the mutations in the human genome is too high: Sanford states that the average mutation is around 300 mutations/individual. Most or only mildly negative.


I don't know where this figure comes from, but there IS indeed a constant slight shuffle of DNA data. Since most DNA is inactive, this is usually without any effect at all.

3. Neo-Darwin Evolutionist (NDET) assumes that natural selection will take out all of the bad mutations and leave only the good. This is not true.


Incorrect. Now, I don't know exactly what a Neo-Darwin Evolutionist is, but current evolution theory does not claim that all 'bad' mutations are weeded out. Those individuals whose negative mutations make them less fit are weeded out.

Sanford uses a gamma (not a standard distribution) curve which show ~ 99% of the mutations are harmful. Curve generated by population NDET geneticist Kimura. This ensures that natural selection see many more deleterious mutations for every good mutation. Thus, the genome will suffer from “genetic entropy”. (Many of these “beneficial” mutations actually end up giving the organism a net decrease in fitness (as in the case of homeostasis in cold-climate creatures to warm climates or drug-resistant bacteria) making them deleterious in reality)


The basic mistake here is the notion that we can deem a mutation beneficial, harmless, or harmful, regardless of context. As already mentioned above, we can't; the same mutation can be all of these, depending on the external situation.

4. NDET assumes that one negative mutation can be filtered out selectively. In reality, however, it is an entire gene that is selected for or against.


Again, I don't know that NDET is, but the assumtion that any mutations are filtered individually is, of course, naive (and I don't think it is seriously held by anyone). Natural selection works on the level of the whole individual, at least (sometimes even on population level).


What happens is the genes see many more bad mutations (minimum 10,000/1) and evolution will either select or reject the whole gene not the individual mutation. He calls this the “Muller’s Ratchet” (named after another population geneticist). Even if a gene with a beneficial mutation is selected for, it will carry many, many more deleterious mutations. This inevitably causes genetic entropy, not a complexity increase.


I don't really see where this idea is leading. Are they claiming that life-forms cannot keep existing? I'm sorry, but observations show the opposite.

5. Most mutations are only slightly negative like a spelling error and the genome more or less ignores them for a while. The problem is that over time these spelling errors build up and create noise which reduces fitness with successive generations.


Well, it seems life-forms can cope with that: They're still here.

6. The best do not always survive. Sometimes the plant seed, for example, with the greatest fitness lands on rocky soil, or in a deep valley with little sunlight, while the less fit lands on a hill that receives sunlight. Sometimes it isn’t the survival of the fittest it is the survival of the luckiest. Again, Sanford sites NDET population geneticist, Kimura which states that heritability due to phenotypic superiority (i.e. fitness) is as low as 0.4%! Hence, even that 1/10,000 (very optimistic) chance of a beneficial mutation has only 1/250 chance of surviving because random environmental factors.


Well, yes. You need to be both fittest and lucky. You cannot state a generic percentage, however, because the survivability of offspring varies greatly among species. If you're a cod egg, you have a chance of 1:10,000,000 of making it to the reproductive age, if you're a human infant OTOH, your chance is close to 1 (depending somewhat on where you happen to be born).


7. Most mutations are recessive and it usually takes two similar mutations, one from each s@x to become “fixed”. Sanford sites NDET geneticist J.B.S. Haldane it would take 300 generations to make a genetic trait fixed in a population.


Well, this is in glaring opposition to what we observe in the real world. While this is, of course, the result of a very intensive selection, experience shows that in domesticated animals, traits can be bred clean (and thus fixed) in as few as five generations.


8. I.D. sees DNA like a computer code and it is the instruction manual for building proteins. NDET assumes the code is linear. Sanford states DNA sequences are “poly-constrained” That is, DNA sequences can have meanings on several different levels. For example, imagine a coded message that has a valid meaning when read forward, another valid meaning when read backwards, another every 5 letters, and yet another when placed on top of another few messages (making it 3D). DNA also has sub-routines and reuses the same genes for multiple tasks. Thus any mutation affects the whole code not just one element. So one good mutation can have many unintended side effects.


And, what may appear as a negative effect can have positive effects, too.

9. Irreducible complexity: Sanford sees life as a total system where individual parts rely on many other parts: One is not any good without the other. You take out one part if effects the other parts. That life is integrated.


Irreducible complexity is always sought by evolution opponents, and for good reason, since this is one of the things that could falsify evolution. So far, none has been found, however.

Hans

#3 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 10 April 2008 - 03:58 AM

I have no immidiate plans to read the book, but I have some comments to your extract.
That is not a correct assumtion. There is no 'upwards'. A life-form will evolve in the direction of the selection pressure. This direction is not necessarily 'upwards', i.e. towards more complexity.


It´s not what this article is saying First 'rule' of evolution suggests that life is destined to become more complex

It is impossible to establish an exact ratio, because you cannot exactly define a 'beneficial' mutation, since this depends on context. For instance, a mutation that makes a fish blind is not beneficial, except if the fish happens to live in a cave where there is never any light.


Be blind in a cave without light is not beneficial, it´s less harmful.A fish with eyes has the same chance of surviving in a cave without light as a fish without eyes.
And you are right, beneficial mutation is so rare, that it´s difficult to establish an exact ration.But be beneficial is not enough for evolution, it needs mutations which can build up new traits.


I don't know where this figure comes from, but there IS indeed a constant slight shuffle of DNA data. Since most DNA is inactive, this is usually without any effect at all.


It´s not correct.You must update your knowledge about DNA.

* A 2002 study from the University of Michigan showed that segments of junk DNA called LINE-1 elements, once thought to be "leftovers from the distant evolutionary past" now "deserve more respect" because they are capable of repairing broken strands of DNA.

* A 2003 study from Tel Aviv University found crucial uses for "junk" sequences in human DNA.

* A 2004 study from the Cell Press suggests that "more than one third of the mouse and human genomes, previously thought to be non-functional, may play some role in the regulation of gene expression and promotion of genetic diversity."

* An article from BioEd Online details DNA which appears crucial although no function has yet been discovered.

* A 2005 study from the National Institutes of Health found that social behavior in rodents (and, possibly humans ) was affected by portions of the genetic code once thought to be "junk."

* A 2005 study from University of California-San Diego suggested that junk DNA is "critically important to an organism’s evolutionary survival."

* Findings from Purdue University in 2005 stated that "many DNA sequences previously believed to have no function actually may play specialized roles in cell behavior."

* A 2006 study by the McKusick-Nathans Institute of Genetic Medicine (Johns Hopkins) stated that "Junk DNA may not be so junky after all."

* Researchers at the University of Illinois Society for Experimental Biology found an antifreeze-protein gene in a species of fish which "evolved" from junk DNA.

* A mathematical analysis of the genetic code by IBM identified patterns that suggested junk DNA had an important role after all.

* In 2006, University of Iowa researchers documented segments of RNA (previously considered "junk") that regulated protein production, and could generate microRNAs.

* A 2007 study from Stanford University School of Medicine found that "Large swaths of garbled human DNA once dismissed as junk appear to contain some valuable sections

Incorrect. Now, I don't know exactly what a Neo-Darwin Evolutionist is, but current evolution theory does not claim that all 'bad' mutations are weeded out. Those individuals whose negative mutations make them less fit are weeded out.


What he is saying is that if any individual has on average 200 mutations, even if one is beneficial, some of the others will be deleterious, so it´s impossible to acumulate only beneficial mutations.

The basic mistake here is the notion that we can deem a mutation beneficial, harmless, or harmful, regardless of context. As already mentioned above, we can't; the same mutation can be all of these, depending on the external situation.


He´s not talking about phenotype.He´s not evaluating the mutation by the trait it generated, he´s talking about mutations that cause diseases or has deleterious effects in the organism.


Irreducible complexity is always sought by evolution opponents, and for good reason, since this is one of the things that could falsify evolution. So far, none has been found, however.


It´s not true. We have many examples of irreducible complexity.I can give one:

"Bacterial flagellar system of motility"

#4 MRC_Hans

MRC_Hans

    Member

  • Banned
  • PipPipPip
  • 576 posts
  • Age: 59
  • no affiliation
  • Agnostic
  • Denmark

Posted 10 April 2008 - 06:13 AM

It´s not what this article is saying First 'rule' of evolution suggests that life is destined to become more complex


Incorrect. There is no destiny involved in evolution. It is true that there seems to be some reward for complexity, otherwise there would only be one-celled organisms, but that does not equal a destiny.

Be blind in a cave without light is not beneficial, it´s less harmful.A fish with eyes has the same chance of surviving in a cave without light as a fish without eyes.


Incorrect. Eyes consume energy and are vulnerable. Therefore they are a disadvantage in an environment where sight is useless.

And you are right, beneficial mutation is so rare, that it´s difficult to establish an exact ration.But be beneficial is not enough for evolution, it needs mutations which can build up new traits.


What is the difference between beneficial and building new traits (apart from the fact that a new trait could be non-beneficial).

It´s not correct.You must update your knowledge about DNA.

    * A 2002 

    * A 2003

    * A 2004

    * A 2005

    * A 2005

    * A 2006

    * In 2006,

    * A 2007


:) DNA research moves so fast right now, that even 2006 studies may be outdated. However, it is correct that the term 'junk DNA' has been severely revised. I was not necessarily referring to junk DNA, however. While the rest may not be junk, it is still a fact that the majority of most life forms' DNA plays no direct role in determing phenotype, and mutations in that DNA has therefore no immidiate impact.


It´s not true. We have many examples of irreducible complexity.I can give one:

"Bacterial flagellar system of motility"


And why is that irreducibly complex?

Hans

#5 Bruce V.

Bruce V.

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,153 posts
  • Age: 54
  • Christian
  • Creationist
  • Northern Califiornia

Posted 10 April 2008 - 12:20 PM

7. Most mutations are recessive and it usually takes two similar mutations, one from each s@x to become “fixed”. Sanford sites NDET geneticist J.B.S. Haldane it would take 300 generations to make a genetic trait fixed in a population.


Well, this is in glaring opposition to what we observe in the real world. While this is, of course, the result of a very intensive selection, experience shows that in domesticated animals, traits can be bred clean (and thus fixed) in as few as five generations.

Hans

View Post


Hi Hans,

I think Sanford was talking about a new trait becoming fixed. Not one that is already in the genetic code not selective breading in what is already in our code.

But I am interested in you experience and how it relates.

#6 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 10 April 2008 - 03:33 PM

Incorrect. There is no destiny involved in evolution. It is true that there seems to be some reward for complexity, otherwise there would only be one-celled organisms, but that does not equal a destiny.


is That your belief or you have some study about it ?

Incorrect. Eyes consume energy and are vulnerable. Therefore they are a disadvantage in an environment where sight is useless.


Please, show me numbers.
1 - What´s the quantity of calories that the fish with eyes will consume more than the eyeless fish ?
2 - What´s the increase in fitness that that gain will represent ?

What is the difference between beneficial and building new traits (apart from the fact that a new trait could be non-beneficial).


For example , if a mutation gives an eye to a eyeless fish then that is building a new trait, but that will not be beneficial in a place without light.

And why is that irreducibly complex?


Because it cannot be built step by step.




0 user(s) are reading this topic

0 members, 0 guests, 0 anonymous users