DNA: Mutations, Versatility and Probability

[Job 33:6]

facepalm

 

[Job 33:6]

No they don't and you thinking the Grand Canyon was formed by a river is beyond absurd. Especially when you have no evidence to support you speculation.

The fact that there are meandering rivers going through it is telling.

What else would form meanders but a meandering river?

 

[Job 33:6]

High velocity flood waters wouldn't meander like that. Only regular meandering rivers.

 

[omega2xx]

The fact that there are meandering rivers going through it is telling.

What else would form meanders but a meandering river?

The only thing your photo prove is that there a a river meandering through the Grand Canyon. There is no evidence it caused the canyon. There are rivers much bigger than that one , but no canyons attributed to them.

 

[stevevw]

May I see research you are referring to, where biologists discuss predominantly deleterious mutations? And further i would ask if they simultaneously are proposing that speciation would no longer occur due to this degredation?

There are a few research papers that mention this.

This paper is saying that most if not all genome wide mutations are deleterious and questions if there is even any beneficial mutations. It mentions that most researchers agree that mutations that affect phenotypes are deleterious. It also supports the paper below which states that genomes are finely tuned and need to remain stable to maintain their delicate finely tuned structures. Introducing mutations can destabilize these structures.
Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations?
It is argued that, although most if not all mutations detected in mutation accumulation experiments are deleterious, the question of the rate of favourable mutations (and their effects) is still a matter for debate.
Most researchers agree that mutations with phenotypic effects are usually deleterious. Indeed, when considering a population that has evolved for a long time in a constant environment, one can postulate that the population is composed of genotypes finely tuned with respect to a myriad of biotic and abiotic conditions and that a random mutation will probably disrupt such fine tuning (Fisher, 1999, pp. 38–42).
http://www.nature.com/hdy/jour.....7270a.html

Here it seems that 80% of insertion muations in competition experiment tests of over 10,000 generations on 226 mutant clones of bacteria were negative and none had a significant positive effect.

Distribution of fitness effects caused by random insertion mutations in Escherichia coli
At least 80% of the mutations had a significant negative effect on fitness, whereas none of the mutations had a significant positive effect.
http://www.springerlink.com/co.....q5l0q3832/

This seems to be saying that what appears as a neutral mutation is actually a slightly harmful mutation being tolerated. But it will get to a threshold point where the accumulation of these mutations will have a cost to fitness.

Robustness–epistasis link shapes the fitness landscape of a randomly drifting protein
Thus, under a low selection pressure, a large fraction of mutations was initially tolerated (high robustness), but as mutations accumulated, their fitness toll increased, resulting in the observed negative epistasis. These findings, supported by FoldX stability computations of the mutational effects6, prompt a new model in which the mutational robustness (or neutrality) observed in proteins, and other biological systems, is due primarily to a stability margin, or threshold, that buffers the deleterious physico-chemical effects of mutations on fitness. Threshold robustness is inherently epistatic—once the stability threshold is exhausted, the deleterious effects of mutations become fully pronounced, thereby making proteins far less robust than generally assumed.
USQ Systems Logout

It appears there is even a limit to how many mutations a complex organism can tolerate per genome and generation. The finely tuned complex genetic networks cannot handle too many mutations as they will undermine those complex structures intoducing a spanner into the works. It seems livingthings already have complex genetic material that needs to be maintained the same rather than run the risk of introducing mutations. This seems at odds with what Neo-Darwinism says that creatures need mutations to change those complex structures so they can add variations.

Beyond A 'Speed Limit' On Mutations, Species Risk Extinction
If enough mutations push an essential protein towards an unstable, non-functional structure, the organism will die. Shakhnovich's group found that for most organisms, including viruses and bacteria, an organism's rate of genome mutation must stay below 6 mutations per genome per generation to prevent the accumulation of too many potentially lethal changes in genetic material.

"As organisms become more complex, they have more to lose and can't be as radically experimental with their genomes as some viruses and bacteria."
https://www.sciencedaily.com/releases/2007/10/071001172753.htm

This paper relates to how the DNA is highly complex and therefore needs to maintain its integrity. It is not as simple as a mutation/s coming along and making alterations to add variations for evolution becuase it seems that the DNA is polyfunctional meaning there is more than one layer of complex coded information that are connected together. As mentioned in the paper the sequences will be constrained in terms of sequence improvement via random mutations because of the multiple connections which rely on each other.

The mutation cannot positively affect all levels of functioning and the chances are that even if a mutation has a slighly rare benefit or neutral affect on one level it will have a adverse affect on another. So in this sense most mutations will have some sort of harmful affect on the DNA and the probability of beneficial mutations is reduced the more complex those layered functions are.

Our analysis confirms mathematically what would seem intuitively obvious — multiple overlapping codes within the genome must radically change our expectations regarding the rate of beneficial mutations. As the number of overlapping codes increases, the rate of potential beneficial mutation decreases exponentially, quickly approaching zero. Therefore, the new evidence for ubiquitous overlapping codes in higher genomes strongly indicates that beneficial mutations should be extremely rare. This evidence combined with increasing evidence that biological systems are highly optimized, and evidence that only relatively high-impact beneficial mutations can be effectively amplified by natural selection, lead us to conclude that mutations which are both selectable and unambiguously beneficial must be vanishingly rare. This conclusion raises serious questions. How might such vanishingly rare beneficial mutations ever be sufficient for genome building? How might genetic degeneration ever be averted, given the continuous accumulation of low impact deleterious mutations?
http://www.cs.cmu.edu/~gmontane/pdfs/montanez-binps-2013.pdf

And it seems that mutations should not be viewed in isolation. When mutations accumulate they work against each other including beneficial ones to end up becoming harmful and having an overall cost to fitness.
Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population
Epistatic interactions between mutations play a prominent role in evolutionary theories. Many studies have found that epistasis is widespread, but they have rarely considered beneficial mutations. We analyzed the effects of epistasis on fitness for the first five mutations to fix in an experimental population of Escherichia coli. Epistasis depended on the effects of the combined mutations—the larger the expected benefit, the more negative the epistatic effect. Epistasis thus tended to produce diminishing returns with genotype fitness, although interactions involving one particular mutation had the opposite effect. These data support models in which negative epistasis contributes to declining rates of adaptation over time.
http://science.sciencemag.org/content/332/6034/1193

 

[stevevw]

double post

 

[stevevw]

I know of no experts who say that most mutations in humans are deleterious. There are experts who are worried that humans are degenerating, but that's because we have relaxed the selective pressures on us as a species, because of medicine, agriculture, sanitation and the like. "Genetic entropy" is a term I've only seen used by creationists.

The answer for this would be mostly with what I wrote for KomatiiteBIF reply above. I did not say or at least mean for humans alone. These findings seem to come from tests performed on bacteria.

Who says this?

I have read this a few times in various papers/articles. It seems to make sense that a process that has a mechanism that goes about repairing any changes to its already good functional system would regard a mutational change of any sort less optimal even if it seemed neutral. The fact that it has to use more energy to reproduce that less optimal change to me says it is a small cost even if it does not affect the organism at the time.

Rate, molecular spectrum, and consequences of human mutation
Despite the current status as the dominant organism on earth, the human species is confronted with substantial mutational challenges imposed by at least three baseline genetic features: (i) a relatively high per-generation germline mutation rate at the nucleotide level; (ii) a further inflation in the mutational rate of production of defective alleles associated with aspects of gene structure; and (iii) a large cumulative burden of somatic mutations imposed by a relatively late onset at maturity.
Rate, molecular spectrum, and consequences of human mutation

"Moreover, there is strong theoretical reasons for believing there is no truly neutral nucleotide positions. By its very existence, a nucleotide position takes up space, affects spacing between other sites, and affects such things as regional nucleotide composition, DNA folding, and nucleosome building. If a nucleotide carries absolutely no (useful) information, it is, by definition, slightly deleterious, as it slows cell replication and wastes energy.,, Therefore, there is no way to change any given site without some biological effect, no matter how subtle."
- John Sanford - Genetic Entropy and The Mystery of The Genome - pg. 21 - Inventor of the 'Gene Gun'

The Human Gene Mutation Database (HGMD®) constitutes a comprehensive collection of published germline mutations in nuclear genes that underlie, or are closely associated with human inherited disease. At the time of writing (March 2017), the database contained in excess of 203,000 different gene lesions identified in over 8000 genes manually curated from over 2600 journals. With new mutation entries currently accumulating at a rate exceeding 17,000 per annum, HGMD represents de facto the central unified gene/disease-oriented repository of heritable mutations causing human genetic disease used worldwide by researchers, clinicians, diagnostic laboratories and genetic counsellors, and is an essential tool for the annotation of next-generation sequencing data.
The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies

 

[Job 33:6]

The only thing your photo prove is that there a a river meandering through the Grand Canyon. There is no evidence it caused the canyon. There are rivers much bigger than that one , but no canyons attributed to them.

Canyon - definition - "a deep gorge, typically one with a river flowing through it."

It is commonly known that rivers create and widen meanders as they flow. This is observable in the world today. When we look at the photo i posted, we see wide meanders indicating the presence of a river that would create them. When we look deeper in the canyon, low and behold, a river flows, ie the source of the meanders and the deep gorge/canyon, a river.

Do you recognize the reality that a river carved out those meanders? The feature is one known to be caused by a regular river. High velocity flood waters (powerful enough to annihilate rock, like those commonly spoken of by YECs) are too strong for the formation of meanders.

1.The widest and longest river, the amazon, is widening its own meanders and making new ones, right now. This is observable.

2.Rivers also erode away soils and rock beneath them. This is why at the end of rivers, we have river basins.

Do you accept this reality?

 

[Job 33:6]

The only difference between the rivers that carved out the Grand Canyon, and rivers that have carved out other gorges in the world, is that the rivers of the grand canyon have carved deeper than gorges of say, the amazon.
Once we understand that rivers meander and erode material beneath them, then we can discuss orogenesis, the source of deeper cutting than other rivers.

But first it starts with understanding rivers and what they do. They erode, they meander.

And there are no tricks with the above post. The reason it sounds simple is because it is simple. This is geomorphology 101, literally.

 

[omega2xx]

Canyon - definition - "a deep gorge, typically one with a river flowing through it."

It is commonly known that rivers create and widen meanders as they flow. This is observable in the world today. When we look at the photo i posted, we see wide meanders indicating the presence of a river that would create them. When we look deeper in the canyon, low and behold, a river flows, ie the source of the meanders and the deep gorge/canyon, a river.

Do you recognize the reality that a river carved out those meanders? The feature is one known to be caused by a regular river. High velocity flood waters (powerful enough to annihilate rock, like those commonly spoken of by YECs) are too strong for the formation of meanders.

1.The widest and longest river, the amazon, is widening its own meanders and making new ones, right now. This is observable.

2.Rivers also erode away soils and rock beneath them. This is why at the end of rivers, we have river basins.

Do you accept this reality?

Let me offer you a little real reality. The grand canyon is unique. There are other rivers wider, longer and more powerful that I am sure you would claim have been in existence as long as the one winding through the Grand canyon. Yet they have not come close to forming a canyon like the Grand canyon.

Is the Amazon as old as the Colorado? Why no canyon there? Can you accurately determine the age of river water?

What I have found over the years in discussing the creation/evolution debate is that the evolutionist don't seem to evaluate what is being said. They are willing to accept almost anything presented in the name of evolution, not because of any real evidence, but because that is what they want to believe and they have been taught over the years that evolution is based on science. Yet you can't provide the evidence for one doctrine of the TOE.

 

[omega2xx]

There are a few research papers that mention this.

This paper is saying that most if not all genome wide mutations are deleterious and questions if there is even any beneficial mutations. It mentions that most researchers agree that mutations that affect phenotypes are deleterious. It also supports the paper below which states that genomes are finely tuned and need to remain stable to maintain their delicate finely tuned structures. Introducing mutations can destabilize these structures.
Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations?
It is argued that, although most if not all mutations detected in mutation accumulation experiments are deleterious, the question of the rate of favourable mutations (and their effects) is still a matter for debate.
Most researchers agree that mutations with phenotypic effects are usually deleterious. Indeed, when considering a population that has evolved for a long time in a constant environment, one can postulate that the population is composed of genotypes finely tuned with respect to a myriad of biotic and abiotic conditions and that a random mutation will probably disrupt such fine tuning (Fisher, 1999, pp. 38–42).
http://www.nature.com/hdy/jour.....7270a.html

Here it seems that 80% of insertion muations in competition experiment tests of over 10,000 generations on 226 mutant clones of bacteria were negative and none had a significant positive effect.

Distribution of fitness effects caused by random insertion mutations in Escherichia coli
At least 80% of the mutations had a significant negative effect on fitness, whereas none of the mutations had a significant positive effect.
http://www.springerlink.com/co.....q5l0q3832/

This seems to be saying that what appears as a neutral mutation is actually a slightly harmful mutation being tolerated. But it will get to a threshold point where the accumulation of these mutations will have a cost to fitness.

Robustness–epistasis link shapes the fitness landscape of a randomly drifting protein
Thus, under a low selection pressure, a large fraction of mutations was initially tolerated (high robustness), but as mutations accumulated, their fitness toll increased, resulting in the observed negative epistasis. These findings, supported by FoldX stability computations of the mutational effects6, prompt a new model in which the mutational robustness (or neutrality) observed in proteins, and other biological systems, is due primarily to a stability margin, or threshold, that buffers the deleterious physico-chemical effects of mutations on fitness. Threshold robustness is inherently epistatic—once the stability threshold is exhausted, the deleterious effects of mutations become fully pronounced, thereby making proteins far less robust than generally assumed.
USQ Systems Logout

It appears there is even a limit to how many mutations a complex organism can tolerate per genome and generation. The finely tuned complex genetic networks cannot handle too many mutations as they will undermine those complex structures intoducing a spanner into the works. It seems livingthings already have complex genetic material that needs to be maintained the same rather than run the risk of introducing mutations. This seems at odds with what Neo-Darwinism says that creatures need mutations to change those complex structures so they can add variations.

Beyond A 'Speed Limit' On Mutations, Species Risk Extinction
If enough mutations push an essential protein towards an unstable, non-functional structure, the organism will die. Shakhnovich's group found that for most organisms, including viruses and bacteria, an organism's rate of genome mutation must stay below 6 mutations per genome per generation to prevent the accumulation of too many potentially lethal changes in genetic material.

"As organisms become more complex, they have more to lose and can't be as radically experimental with their genomes as some viruses and bacteria."
https://www.sciencedaily.com/releases/2007/10/071001172753.htm

This paper relates to how the DNA is highly complex and therefore needs to maintain its integrity. It is not as simple as a mutation/s coming along and making alterations to add variations for evolution becuase it seems that the DNA is polyfunctional meaning there is more than one layer of complex coded information that are connected together. As mentioned in the paper the sequences will be constrained in terms of sequence improvement via random mutations because of the multiple connections which rely on each other.

The mutation cannot positively affect all levels of functioning and the chances are that even if a mutation has a slighly rare benefit or neutral affect on one level it will have a adverse affect on another. So in this sense most mutations will have some sort of harmful affect on the DNA and the probability of beneficial mutations is reduced the more complex those layered functions are.

Our analysis confirms mathematically what would seem intuitively obvious — multiple overlapping codes within the genome must radically change our expectations regarding the rate of beneficial mutations. As the number of overlapping codes increases, the rate of potential beneficial mutation decreases exponentially, quickly approaching zero. Therefore, the new evidence for ubiquitous overlapping codes in higher genomes strongly indicates that beneficial mutations should be extremely rare. This evidence combined with increasing evidence that biological systems are highly optimized, and evidence that only relatively high-impact beneficial mutations can be effectively amplified by natural selection, lead us to conclude that mutations which are both selectable and unambiguously beneficial must be vanishingly rare. This conclusion raises serious questions. How might such vanishingly rare beneficial mutations ever be sufficient for genome building? How might genetic degeneration ever be averted, given the continuous accumulation of low impact deleterious mutations?
http://www.cs.cmu.edu/~gmontane/pdfs/montanez-binps-2013.pdf

And it seems that mutations should not be viewed in isolation. When mutations accumulate they work against each other including beneficial ones to end up becoming harmful and having an overall cost to fitness.
Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population
Epistatic interactions between mutations play a prominent role in evolutionary theories. Many studies have found that epistasis is widespread, but they have rarely considered beneficial mutations. We analyzed the effects of epistasis on fitness for the first five mutations to fix in an experimental population of Escherichia coli. Epistasis depended on the effects of the combined mutations—the larger the expected benefit, the more negative the epistatic effect. Epistasis thus tended to produce diminishing returns with genotype fitness, although interactions involving one particular mutation had the opposite effect. These data support models in which negative epistasis contributes to declining rates of adaptation over time.
http://science.sciencemag.org/content/332/6034/1193

There are no examples of a mutation changing the species. The person or animal who becomes an albino because of a mutation remains the exact same species as its parents and its offspring will also be the exact same species as its parents. All mutation only affect the characteristics of the species.

Mutations have no final evolutionary effect---Pierre Paul Grasse(A French zoologists),

 

[Job 33:6]

Let me offer you a little real reality. The grand canyon is unique. There are other rivers wider, longer and more powerful that I am sure you would claim have been in existence as long as the one winding through the Grand canyon. Yet they have not come close to forming a canyon like the Grand canyon.

Is the Amazon as old as the Colorado? Why no canyon there? Can you accurately determine the age of river water?

What I have found over the years in discussing the creation/evolution debate is that the evolutionist don't seem to evaluate what is being said. They are willing to accept almost anything presented in the name of evolution, not because of any real evidence, but because that is what they want to believe and they have been taught over the years that evolution is based on science. Yet you can't provide the evidence for one doctrine of the TOE.

You aren't even acknowledging my post. How can we have a conversation if you wont respond to my words?

Did you even read it? Do you acknowledge that rivers both meander, and erode away material beneath them? Or do you deny this?

 

[Job 33:6]

Let me offer you a little real reality.

ya know what, dont even bother responding, im just going to ignore you. You have seem to be unable to hold a normal conversation and enjoy being rude for no apparent reason. Why? I don't know, but it isn't worth my time either way.

 

[omega2xx]

The only difference between the rivers that carved out the Grand Canyon, and rivers that have carved out other gorges in the world, is that the rivers of the grand canyon have carved deeper than gorges of say, the amazon.
Once we understand that rivers meander and erode material beneath them, then we can discuss orogenesis, the source of deeper cutting than other rivers.

But first it starts with understanding rivers and what they do. They erode, they meander.

And there are no tricks with the above post. The reason it sounds simple is because it is simple. This is geomorphology 101, literally.

Neither simple or complex is evidence. Why is the Colorado the only river that has created a canyon? We have bigger and stronger rivers with no canyons and we have canyons with no rivers.

You have made a necessary assumption to try and reinforce your belief. You say you are a Christian, so why not accept that our omnipotent God created the universe the was we see it today?

We Presbyterians have a question in our catechism, What is the chief end of man? Answer - The chief end of man is to glorify God and enjoy Him forever.

What would give God the most glory, God did it or a river did it?

 

[omega2xx]

ya know what, dont even bother responding, im just going to ignore you. You have seem to be unable to hold a normal conversation and enjoy being rude for no apparent reason. Why? I don't know, but it isn't worth my time either way.

IOW you can't produce any evidence for what you say.

If you will post anything I have said to you that is rude, I will apologize. It seems that you think disagreeing with you is being rude. If it is you are also being rude to me.

Have a very + day.

 

[omega2xx]

You aren't even acknowledging my post. How can we have a conversation if you wont respond to my words?

I respond to all post sent to me. If I have not respond, I did not see it. If you will give the information I need to find the one(s) in question, I will respond.

Did you even read it? Do you acknowledge that rivers both meander, and erode away material beneath them? Or do you deny this?

That rivers meander and erode is self evident. That they erode to the extent you claim and formed the Grand Canyon is not evident, and there is no evidence that is true.

 

[sfs]

The answer for this would be mostly with what I wrote for KomatiiteBIF reply above. I did not say or at least mean for humans alone. These findings seem to come from tests performed on bacteria.

Bacteria and humans have very different selective constraints on their genomes.

Rate, molecular spectrum, and consequences of human mutation
Despite the current status as the dominant organism on earth, the human species is confronted with substantial mutational challenges imposed by at least three baseline genetic features: (i) a relatively high per-generation germline mutation rate at the nucleotide level; (ii) a further inflation in the mutational rate of production of defective alleles associated with aspects of gene structure; and (iii) a large cumulative burden of somatic mutations imposed by a relatively late onset at maturity.
Rate, molecular spectrum, and consequences of human mutation

Not clear why you quoted this, since it doesn't address the question.

"Moreover, there is strong theoretical reasons for believing there is no truly neutral nucleotide positions. By its very existence, a nucleotide position takes up space, affects spacing between other sites, and affects such things as regional nucleotide composition, DNA folding, and nucleosome building. If a nucleotide carries absolutely no (useful) information, it is, by definition, slightly deleterious, as it slows cell replication and wastes energy.,, Therefore, there is no way to change any given site without some biological effect, no matter how subtle."
- John Sanford - Genetic Entropy and The Mystery of The Genome - pg. 21 - Inventor of the 'Gene Gun'

Sanford has never demonstrated any competence in population or evolutionary genetics. I meant scientists in the field, not creationists. (And no, inventing a gene gun does not imply competence in population genetics.)

The Human Gene Mutation Database (HGMD®) constitutes a comprehensive collection of published germline mutations in nuclear genes that underlie, or are closely associated with human inherited disease. At the time of writing (March 2017), the database contained in excess of 203,000 different gene lesions identified in over 8000 genes manually curated from over 2600 journals. With new mutation entries currently accumulating at a rate exceeding 17,000 per annum, HGMD represents de facto the central unified gene/disease-oriented repository of heritable mutations causing human genetic disease used worldwide by researchers, clinicians, diagnostic laboratories and genetic counsellors, and is an essential tool for the annotation of next-generation sequencing data.
The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies

Yeah, I know. I spent years working in human genetics. Again, it does not address the actual claim you made.

 

[Job 33:6]

That rivers meander and erode is self evident. That they erode to the extent you claim and formed the Grand Canyon is not evident, and there is no evidence that is true.

How else could the meanders be so deep without having been carved by the river? A meander is what it is, it is a feature of a meandering river. Yet you seem to be proposing that a meandering river, is not what made the meanders which the river flows through.

 

[omega2xx]

How else could the meanders be so deep without having been carved by the river? A meander is what it is, it is a feature of a meandering river. Yet you seem to be proposing that a meandering river, is not what made the meanders which the river flows through.

God created the Grand Canyon, then put a river in it.

 

[Job 33:6]

God created the Grand Canyon, then put a river in it.

So God made these meanders, then just put a river into them. Even though rivers naturally meander and erode/create meanders...this one in particular, God made without the river, then put the river into it...