Degeneration > evolution

[Vegan Charity]

Important assumption:
- Mutations are responsible for evolution.

You are partially correct.

Mutations are in fact important, but do not forget other very important factors:
Geology
Population
Predator Adaptations
Climate


A mere climate change will encourage Natural Selection, no mutations are necessary for that to occur. Your assumption is "unfair" (premature) for that reason.

Hypothesis: degeneration > evolution

There is no direction to evolution, I heard here, so you can say that devolution/degeneration is another word for evolution. Or in the mathematical way: degeneration = evolution.

Alright, I accept your hypothesis.

1. The enzyme-encoding genome as a lossless system

I’m not suggesting that a random process can’t favour an increase in information. No! common information theory says that random datasamples contain more information than any other set of samples. But this works fine only within lossy systems. In a lossless context, like a text document, you’re damaging the information on the higher level of words!
The genome contains a lossless (for enzymes encoding) part and a lossy part (not encoding for enzymes, and with no known meaning). It’s like a text document with a picture embedded. The part we are interested in is the enzyme encoding part: the lossless system. So we have to be aware of the level of words/enzymes.

First, you need to define the word "Information". Creationists can get by with this claim only by leaving the term "information" undefined, impossibly vague, or constantly shifting. By any reasonable definition, increases in information have been observed to evolve. We have observed the evolution of:

* increased genetic variety in a population
* increased genetic material
* novel genetic material
* novel genetically-regulated abilities

If these don't qualify as information, then nothing about information is relevant to evolution in the first place

Second, you need to properly define the process of encoding.
What you have described can be expressed metaphorically as "Photocopy of a photocopy of a photocopy", that is called Analog copying. However, genome encoding does not work like Analog encoding. Its better expressed as "Binary encoding". The DNA material does NOT evolve, it stays the same no matter how many copies you make of it. It gets rearranged, but it does not evolve. However, there is an occasional fluke, occasionally a mutation will occur. Different Cytochromes have their own predictable rate of mutation. In lineage of species, some cytochromes will mutate quickly (in only a few 1000 generations), other cytochromes mutate very slowly (possibly 10s of millions of generations). No, the mutations do not occur entirely randomly, that is a misinterpretation of Evolution, its probably the single reason why most anti-Evolutions reject Evolution. Most mutations are neutral (neither beneficial nor harmful), some mutations are harmful, some mutations are beneficial. And as I noted above, mutations are not necessary to encourage evolution.

Third, if lossyness of genome information is harmful to the animal, Natural Selection not tend to favor that creature. If this problem were evident in a population, it would probably spell the end of the population, or perhaps mutations which occur would be favored. That is still evolution.

Fourth, mutation can and does add genetic material. Since anything mutations can do, mutations can undo. Some mutations add information to a genome; some subtract it.

Fifth, A mechanism which is likely to be particularly common for adding information is gene duplication, where a long stretch of DNA is copied, followed by point mutations which change one or both of the copies. Genetic sequencing has revealed several instances where this is likely the origin of some proteins. For example:

* Two enzymes in the histidine biosynthesis pathway that are barrel-shaped, structural and sequence evidence suggests, were formed via gene duplication and fusion of two half-barrel ancestors
* RNASE1, a gene for a pancreatic enzyme, was duplicated, and in langur monkeys one of the copies mutated into RNASE1B, which works better in the more acidic small intestine of the langur.
* Yeast was put in a medium with very little sugar. After 450 generations, hexose transport genes had duplicated several times, and some of the duplicated versions had mutated further.

A PubMed search (at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi) on "gene duplication" gives more than 3000 results.


Sixth, According to Shannon-Weaver information theory, random noise maximizes information. And this is not just playing word games. The random variation which mutations add to populations is the variation which selection acts upon. Mutation alone will not cause adaptive evolution (I've already made this point several times by now), but by eliminating nonadaptive variation, natural selection communicates information about the environment to the organism, so that the organism becomes better adapted to it. Natural selection is the process by which information about the environment is transferred to an organism's genome and thus to the organism

2. Influences of mutations on the enzyme level is different

There are three possibilities that a DNA chain will code for another sequence of enzymes (due to mutations). First, mutations can let a chain code for a new enzyme, or a range of new enzymes. Second, mutations can change the code that way that a new enzyme replaces an old one. Third, mutations can damage the information for an existing enzyme so that it’s not possible to form it, or a mutated one, anymore. I would like to call the first two options evolution and the third one degeneration. In the first case there is some genetic information added on the enzyme level, in the last case the genetic information on the enzyme level decreases.

I dont know what your argument is.

3. A decrease in information on enzyme level results in a decrease in information on gene level.

When a DNA chain isn’t encoding for an enzyme anymore, the information it contains is useless with respect to nature. It’s decomposing fast because the mutations don’t have any influence on the to be decoded enzymes.

Enzymes are not ever forever lossy systems, see above.

4. There are more degenerating than evolutioning mutations

In the analogy of a text document, if you’re substituting a letter with another (or any other transmutation you may think of) it’s more likely to damage a word than to create a new one. I suppose that the same is true in genetics in regard to nucleotides and encoding chains.

You have a false analogy.

In the English Language, there are 26 letters. Each letter can be strung together, throwing letters together compeletely isnt likely to create an intelligible word.

However, in DNA, there are only 4 letters. G, C, A, T. When speaking about DNA, the letter G can only be paired with C (and vice versa), the letter A can only be paired with T (and vice versa). A rearrangement in letter sequences means there are no such things as misspellings (or damage to the enzyme).

Keep in mind, analogies are to establish clarifications, they do not establish arguments.

I think I should make a point that Mutations are not rare. There is roughly 0.1 to 1 mutation per genome replication in viruses and 1/300 mutations per genome per replication in microbes. Mutation rates for higher organisms vary quite a bit between organisms, but excluding the parts of the genome in which most mutations are neutral (the junk DNA), the mutation rates are also roughly 1/300 per effective genome per cell replication. Since sexual reproduction involves many cell replications, humans have about 1.6 mutations per generation. This is likely an underestimate, because mutations with very small effect are easy to miss in the studies. Including neutral mutations, each human zygote has about 64 new mutations. Another estimate concludes 175 mutations per generation, including at least 3 deleterious mutations.

5. Nature doesn’t prefer evolution above devolution

The keyword in nature is adaption. It makes no sence that a mutation is due to ‘evolution’ or ‘devolution’ for nature. It sees a white ermine, not that its colourloss is due to ‘evolution’ or ‘devolution’. So, whatever has happened with genetic information (additions or damages), it doesn’t interest nature at all. Natural selection doesn't make any difference!

Natural selection is truly real, for it talks about some organisms actually surviving and reproducing in life's struggles and others failing to do so. Some of our would-be ancestors lived and had babies and others did not. There was a differential reproduction.

Your claim Natural Selection doesnt make a difference is at best, very very false.

6. Degeneration > evolution

So, I want to claim that degeneration occurs on a higher speed then evolution.

As new harmful mutations enter the population, selection removes existing harmful traits. The genetic load of a stable population is an equilibrium between the two.

Bacteria mutate much faster than plants and animals do, yet their populations are not becoming less viable.

Consequences
- Beings on the end (in regard to time) of an evolution line has a smaller gene pool
- If this is not the case then evolution from ancient unicellular live to current live isn’t possible!
- If this is not the case then evolution from Noah’s arc’s animals to current live isn’t possible!

To continue with...
- What’s the share in the story of "DNA not encoding for enzymes"?
- Are there other biological mechanisms than mutations in the game?

I'm afraid you have some misunderstandings about evolution.

 

[Saviourmachine]

A mere climate change will encourage Natural Selection, no mutations are necessary for that to occur. Your assumption is "unfair" (premature) for that reason.

Okay, you're right, natural selection plays a big role in evolution, but I wouldn't criticize her part. So, that natural selection occurs is another asumption.

1. "Information" is not defined

You need to define the word "Information"

We have observed the evolution of:
* increased genetic variety in a population
* increased genetic material
* novel genetic material
* novel genetically-regulated abilities

If these don't qualify as information, then nothing about information is relevant to evolution in the first place

I would define "Information" as the number of enzymes that can be decoded from a DNA chain.

2. The process of encoding isn't defined
I agree with you, enzymes and the like are binary encoded. I'm now at mutations looking in a lossless system. I should have declared that term: it's the opposite of a lossy system, where encoding and decoding doesn't preserve all information exactly. So I like to call it "binary encoding" too.

3. Losing of genome information is harmful to the animal
Yes, indeed, you're right, there is something harmful, but it's not for the animal, it's for species on the long term. The loss of information (look at my definition) did make the animal adapt better then his fellows without loss. Only a fast, fast "adding genome mutation" can prevent this specie from her loss.

If losing of information is only harmful for a specie (not for the individual) natural selection tend not to favour anything.

4. Mutation can and does add genetic material.
It does add information, yes I know.

5. Other mechanisms then point mutations
Yeah, so when I'm reading mutations as point (letter like) mutations then I'm not able to see leaks in my reasoning. If you're speaking about mutations as crossing over and gene duplication I've to think it over!

6. Natural selection always adds information to the organism?

Natural selection is the process by which information about the environment is transferred to an organism's genome and thus to the organism.

I agree with you, but because I stated that adaption by losing information occurs more often then by adding information, I doubt the final effects.

7. No misspellings

A rearrangement in letter sequences means there are no such things as misspellings (or damage to the enzyme).

So, your statement is that every sequence decode for an enzyme? There are no such misspellings that makes an enzyme disappear?

8. Mutation rates are high
That does matter! It makes the equation look like: degeneration >> evolution!

9. Natural selection does make a difference!

Your claim Natural Selection doesnt make a difference is at best, very very false.

It makes a difference between adapted and not-adapted. But it doesn't make a difference in regard to the increase or decrease of enzymes!

Conclusion
- Point mutations aren't adding information (I'm still convinced of this )
- There are other mechanism that has to be looked at: gene duplicating, crossing overs and the like.

Thanks for your thought-out response! Let's go on like this.

 

[Saviourmachine]

Im curious, what suggests that the lose of genetic information is more likely to give a beneficial mutation than an increase of genetic information?

That's not what I'm suggesting. It doesn't make any difference for nature, how the adaption became! By increase or by decrease.

I'm stating that losing of information happens more often then increasing the amount of information (looking at the character of random mutations). So I'm suggesting that an adaption by lost information is more likely then adaption by added information. It's the other way around!

Besides: if it's occuring both, nature selection should prefer the adding on the long term. I don't know if that's the case.

An example:
The ancestor of the polar bear had black hair (or maybe brown, it doesn't matter). They were living in a white environment.
Option 1: One polar bear lost an enzyme that decoded for this black colour, he became white. In this nature selection favoured him above all the other and all his offspring did extremely well. So, all his black fellows in this white environment became extinct. It was the end of the gene that once encoded for this black colour.
Option 2: One polar bear became an extra enzyme that decoded for a white colour, he became white. This goes on like option 1.
Option 3: Two polar bears became white, one by adding, one by losing an enzyme. They got offspring in the same ratio.

Now, what I'm stating is, that if losing enzymes is 'easier' then adding, option 1 will occur most often and will lead to a decrease of genes in the gene pool.

 

[Saviourmachine]

Do you have anything you can cite to support your thesis?

No, actually not, it's only build on 'coherent' logic .

What maybe bothers some persons here, is that I'm stating on one side that there is an evolution mechanism (there are still some persons who bluntly deny that), but on the other side that it doesn't work that fine (when you accept some term like 'degeneration' or 'information loss' on a higher level then the bits/nucleotides).

Until now, everything I stated was about random point mutations. I have some ideas to extend it to other then point mutations (maybe somebody wants to help ), but I don't think that it's possible to extend this reasoning to non-random mechanisms.

Some data about evolution and degeneration rates would be fine. Or amounts of adaptions by mutations that increased and that decreased the amount of information (see definition) in a specific specie. I'm not interested in every mutation, if it's not an adaption it's worthless!

 

[ForeRunner]

No offense, but your entire hypothesis is utter nonsense. In order to "de-evolve" an organism would have to travel back in time, as far as I am aware no organism can do that. Evolution and natural selection are a one way street.

Not only that, but what may appear to you as a "loss of information" may not, in fact be a loss. Take humans for example. We have the genes that code for a tail, then we have more genes that STOP our body from making said tail. What looks to you like us losing the information for making a tail is, in reality, just us having MORE information in our genome to STOP the production of the tail. That is far, far more common than a part of a geneome simply falling out of existance.

An example:
The ancestor of the polar bear had black hair (or maybe brown, it doesn't matter). They were living in a white environment.
Option 1: One polar bear lost an enzyme that decoded for this black colour, he became white. In this nature selection favoured him above all the other and all his offspring did extremely well. So, all his black fellows in this white environment became extinct. It was the end of the gene that once encoded for this black colour.
Option 2: One polar bear became an extra enzyme that decoded for a white colour, he became white. This goes on like option 1.
Option 3: Two polar bears became white, one by adding, one by losing an enzyme. They got offspring in the same ratio.

That is a terrible example. For starters, polar bears do not have white fur, they have transparent fur. "White" is not the absence of an enzyme for darker color. It is information added to make the hair transparent, whether by by making an enzyme that stripes all pigments from the protein or by having genetic code that stops all production of the pigment in their fur.

To say that because some organism "looks" like it doesn't have a part of a phenotype anymore does not mean it is no longer in its genetype. New genes supress old genes as much, if not more, than they code for new adaptations.

 

[Saviourmachine]

Do you want to declare something about what you meant by de-evolving and time traveling? Am I suggesting that if we change the environment of tomorrow to that of the past, we ultimately get uni-cellular live?

We have the genes that code for a tail, then we have more genes that STOP our body from making said tail.

That's a perfect example of adding information (see my definition), if it is true that it promotes the creation of blocking enzymes. Thanks!

That is a terrible example.

I beg you pardon for this terrible example, I have indeed, no idea about polar bears in reality. Sorry. It had only to clearify my point a little bit.

 

[ObbiQuiet]

SaviourMachine gets a +rep for how maturely he is leading this discussion; it's a huge break from the norm.

 

[SirKenin]

probably because we hear the same 3-5 creationist arguments over and over and over again

lol I can't believe this. I was thinking the same last night after I posted that... Just funny seeing it pop up here after. And you're right, it's true, they do use the same ones as well.

No wonder the same discussions end up in the same fashion over and over again

 

[shenzhou]

I'm stating that losing of information happens more often then increasing the amount of information (looking at the character of random mutations).

The way to test this hypothesis is to compare the genomes of closely related organisms. If your hypothesis is correct we should see evidence of gene loss - correct?

These comparisons have been done with the yeast species Saccharomyces cerevisiae. S. paradoxus, S. mikatae and S. bayanus and little evidence of gene loss was found but 35 unique, presumably new genes were found in cerevisiae 5 new in paradoxus 8 in mikatae and 19 in bayanus. This would suggest that gene gain is more common than gene loss (1)

comparisons of chlamydias species revealed 11 duplicated genes and less evidence of gene loss and gene losses were smaller and less common (2) again suggesting the degeneration hypothesis is incorrect.

It should also be remembered that gene expression is also responsible for most differentiation between species and most of the allelic differences within populations. Nearly all human difference is not down to gene numbers but genetic changes that alter how the genes are regulated.

1) Nature. 2003 May 15; 423(6937): 241-54. Sequencing and comparison of yeast species to identify genes and regulatory elements. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES.

2) J Mol Evol. 2002 Jul; 55(1): 24-36. Measuring genome divergence in bacteria: a case study using chlamydian data. Dalevi DA, Eriksen N, Eriksson K, Andersson SG.

 

[Saviourmachine]

If your hypothesis is correct we should see evidence of gene loss - correct?

Which hypothesis?
1. That at the end it appears to be degeneration < evolution, maybe due to other mechanisms like gen duplication as I admitted in later posts. So, if you're right the effect of random point mutations can still be criticized.

I'm stating that losing of information happens more often then increasing the amount of information.

2. You're right, it attacks this hypothesis. If you're right, this one is wrong.

These comparisons have been done with the yeast species Saccharomyces cerevisiae. S. paradoxus, S. mikatae and S. bayanus and little evidence of gene loss was found but 35 unique, presumably new genes were found in cerevisiae 5 new in paradoxus 8 in mikatae and 19 in bayanus. This would suggest that gene gain is more common than gene loss (1)

comparisons of chlamydias species revealed 11 duplicated genes and little evidence of gene loss (2) again suggesting the degeneration hypothesis is incorrect.

That sounds promissing for you, I admit.

Questions I have to ask in regard to hypothesis 2:
1. Do you know the amount of gene loss?
2. Was the gene loss and gain result of adaption? Were they beneficial?
3. What's the influence of duplicated genes in terms of enzymes or the like?
4. New genes, I assume they were called so, because they encode for enzymes and that specific DNA chain didn't that before?

Question I have to ask in regard to hypothesis 1:
1. Were the genetical changes due to random point mutations?

 

[Talcos Stormweaver]

Important assumption:
- Mutations are responsible for evolution.

Not exactly. Natural selection is responsible for evolution, mutations provide variation. With this mixed population, it allows for a microcosm of biodiversity.

Hypothesis: degeneration > evolution

There is no direction to evolution, I heard here, so you can say that devolution/degeneration is another word for evolution. Or in the mathematical way: degeneration = evolution.

Sorry, but they are evidently incorrect in this case. Evolution is design, evolution is guided. The enviromental (external) factors that affect the creature in question determine everything. If that population has some who have a variation who can survive in that condition or are more favorable, then they will live longer to (possibly) reproduce while those who do not possess this trait usually do not survive (not necessarily death, but enough to make sure that they are less favorable in the conditions). We soon see that this leads to new and very specific conditions which mold and reshape the species.

1. The enzyme-encoding genome as a lossless system

I’m not suggesting that a random process can’t favour an increase in information. No! common information theory says that random datasamples contain more information than any other set of samples. But this works fine only within lossy systems. In a lossless context, like a text document, you’re damaging the information on the higher level of words!
The genome contains a lossless (for enzymes encoding) part and a lossy part (not encoding for enzymes, and with no known meaning). It’s like a text document with a picture embedded. The part we are interested in is the enzyme encoding part: the lossless system. So we have to be aware of the level of words/enzymes.

Can you provide some evidence? Sorry, during my time in this forum I have become rather cynical of new information presented.

3. A decrease in information on enzyme level results in a decrease in information on gene level.

When a DNA chain isn’t encoding for an enzyme anymore, the information it contains is useless with respect to nature. It’s decomposing fast because the mutations don’t have any influence on the to be decoded enzymes.

That alone is irrevelant. A decrease or increase in information is not necessarily good or bad. Which is why mutations are not the leading factor for evolution, natural selection is. If they are unfavorable, they have a less chance of passing on theses unfavorable characteristics. Adding a negative or positive side to a mutation relies solely on the context of the situation given in the enviroment.

4. There are more degenerating than evolutioning mutations

In the analogy of a text document, if you’re substituting a letter with another (or any other transmutation you may think of) it’s more likely to damage a word than to create a new one. I suppose that the same is true in genetics in regard to nucleotides and encoding chains.

However, if it, in the context of the situation, is indeed a mutation that is harmful for the species at the time, then the individuals that possess it will probably not live or reproduce as much.

5. Nature doesn’t prefer evolution above devolution

The keyword in nature is adaption. It makes no sence that a mutation is due to ‘evolution’ or ‘devolution’ for nature. It sees a white ermine, not that its colourloss is due to ‘evolution’ or ‘devolution’. So, whatever has happened with genetic information (additions or damages), it doesn’t interest nature at all. Natural selection doesn't make any difference!

Of course it will interest the natural processes! If the color white makes it invisible to its predators (for example), then it is beneficial in the eyes of Natural Selection. The fact remains that mutations and other variations provide diversity. Thus, given the fact that a population can grow to be very large, there is a large chance that this diversity will produce something useful out of the masses.

Also, you are correct on one part. It (natural selection) does not make any difference because if it does not interest nature, thus natural selection will have no role on it. Thus, your point (in that case), is meaningless. There are many examples in nature, and you have chosen one in which it does not apply. Such an argument is but a fallacy, for you are assuming everything in this world is like the white ermine example you gave.

6. Degeneration > evolution

So, I want to claim that degeneration occurs on a higher speed then evolution.

But, if it there is an example of degeneration, and the degenerated are less favorable (logically, given the context of the situation in the enviroment), then it will have no effect on the population.

Consequences
- Beings on the end (in regard to time) of an evolution line has a smaller gene pool

Firstly, you are making the assumption that the individual mutations control the population. No, instead it is what the population itself possesses that is favorable that can survive. The weak and degererated ones will not reproduce as often, thus making it so it has no effect on the population whatsoever.

- If this is not the case then evolution from ancient unicellular live to current live isn’t possible!
- If this is not the case then evolution from Noah’s arc’s animals to current live isn’t possible!

Strawman, I believe.

 

[shenzhou]

Questions I have to ask in regard to hypothesis 2:
1. Do you know the amount of gene loss?
2. Was the gene loss and gain result of adaption? Were they beneficial?
3. What's the influence of duplicated genes in terms of enzymes or the like?
4. New genes, I assume they were called so, because they encode for enzymes and that specific DNA chain didn't that before?

Question I have to ask in regard to hypothesis 1:
1. Were the genetical changes due to random point mutations?

2:1 I don't think a specific number of losses was mentioned

2:2 difficult to tell, in most cases impossible without many experiments but in yeast most of the unique genes were involved in sugar metabolism and gene regulation suggesting they did have a useful adaptive function. It is also unlikely that a duplication that was not adaptive would continue to exist for a long time in the genome.

2:3 it seems to increase the number of unique protein coding genes and enzymes

2:4 the same DNA sequence didn't seem to exist defore duplication and divergence.

1 the duplications seem to have occured in regions that are prone to duplications (like telomeres) or were next to transposable elements that would also have made duplciation likely. Interestingly parasite contingency genes (genes important in interactions with the host) tend to be located near telomeres making them more likely to evolve faster due to an increased random mutation rate in those regions. There is no reason to think that the subsequent divergence was not due to random substitution.

In some cases evolution does favour the loss of genes. This is particularly true of parasitic and symbiotic organisms. There you tend to see a rapid loss of genes that are not needed anymore indicating that if there isn't selection to keep genes organisms will lose them very rapidly. In this case the selection is for lower energy requirements (less protein prodcution) and maybe faster division also (it's quicker to replicate a small than a large genome).

Interestingly in the case of symbiotic organisms although they lose genes after they enter a relationship with another organism the overall complexity of the system increases. An example would be mitochondria, which are the the remnants of a bacterium that has lost nearly all of it's genes (and transferred some to the nucleus) but this process led to the eukaryotic cell as a whole becoming much more complex and efficient.

 

[lucaspa]

Important assumption:
- Mutations are responsible for evolution.

The assumption is wrong. What mutations provide are the raw material for evolution. Evolution here is the change in populations over time. The designs in that change (natural seleciton) is a two-step process:
1. Variation. Mutations are part of this.
2. Selection among variations.

Hypothesis: degeneration > evolution

There is no direction to evolution, I heard here, so you can say that devolution/degeneration is another word for evolution. Or in the mathematical way: degeneration = evolution.

Sorry, but no. True, there is no direction in evolution as in getting at an ultimate goal. There is no such thing as "devolution". That's a creationist strawman.

1. The enzyme-encoding genome as a lossless system

I’m not suggesting that a random process can’t favour an increase in information. No! common information theory says that random datasamples contain more information than any other set of samples. But this works fine only within lossy systems. In a lossless context, like a text document, you’re damaging the information on the higher level of words!
The genome contains a lossless (for enzymes encoding) part and a lossy part (not encoding for enzymes, and with no known meaning). It’s like a text document with a picture embedded. The part we are interested in is the enzyme encoding part: the lossless system. So we have to be aware of the level of words/enzymes.

2. Influences of mutations on the enzyme level is different

There are three possibilities that a DNA chain will code for another sequence of enzymes (due to mutations). First, mutations can let a chain code for a new enzyme, or a range of new enzymes. Second, mutations can change the code that way that a new enzyme replaces an old one. Third, mutations can damage the information for an existing enzyme so that it’s not possible to form it, or a mutated one, anymore. I would like to call the first two options evolution and the third one degeneration. In the first case there is some genetic information added on the enzyme level, in the last case the genetic information on the enzyme level decreases.

I see where you are going but now we have to distinguish between the individual and the population. Mutations happen to individuals. Evolution happens to populations of individuals.

1. Mutation can destroy the activity of the gene/enzyme.
2. Mutation can alter the activity of the enzyme. The enzyme does the same thing but its activity either
a. Decrease
b. Increase
c. Neutral = stay the same.
3. Mutation can give an entirely new activity of the enzyme.

Now, 1 and 2a are what you call "degeneration". 2b and 3 are what you call "evolution". 2c is genetic drift.

Your problem is that this happens to the individual. Since evolution is what happens to the population, we have to see what happens to the individual with these various mutations under selection.

1. If the enzyme/gene is essential, the individual will either:
a. Not form as an embryo at all = dead.
b. Not be a viable embryo = dead
c. Not be a viable newborn = dead young.
d. Be at a selective disadvantage compared to individuals with 2b and 2c and thus not be able to compete in the Struggle for Existence = dead with no offspring. All of these options result in the mutation being removed from the population. Therefore no "degeneration" because the mutation isn't around.

2. If the enzyme is not essential for survival then

a. The loss would let the individual live but still be at a selective disadvantage compared to 2b and c. In that case it is still removed from the population.
b. Have the same fitness as 2b and c. In that case it will be kept in the population at low frequency (few individuals) by Mendelian genetics.
​

Now, let's look at option 2.
2a. Since it decreases the activity, the individual is at a selective disadvantage to 2b and c, so the individual is eliminated by natural selection. No degeneration.
2b. The individual does better against 2a and 2c and thus the mutation becomes fixed in the population.
2c. The mutation remains in the population at low frequency.

Option 3.

a. The new activity is either neutral or disadvantageous in the environment. The individual/mutation will be eliminated from the population.
b. The new activity is advantageous in the environment. Selection will cause it to be fixed in the population = evolution.
​

3. A decrease in information on enzyme level results in a decrease in information on gene level.

When a DNA chain isn’t encoding for an enzyme anymore, the information it contains is useless with respect to nature. It’s decomposing fast because the mutations don’t have any influence on the to be decoded enzymes.

The information isn't "decomposing" but rather is changing. This has been demonstrated experimentally by finding a suppressed developmental pathway in Drosophila. The pathway is suppressed by heat shock protein 90. But when the fly is under heat stress during development, the HS-90 is used to counter the heat and no longer suppresses the alternate developmental pathway. So that pathway is used and you get flies, but some really weird looking ones due to the mutations in the pathway that were not removed by natural selection when the pathway was suppressed.
2. E Pennisi, Heat shock protein mutes genetic changes. Science282: 1796, Dec. 4, 1998. Describes Nature article on acceleratedevolution. HSP 90 suppresses some developmental pathways, allowing themto accumulate mutations. When HSP 90 is tied up protecting from heat stress,then these pathways become active, giving large morphological changes since thesmall mutations are in HOX genes.
3. SL Rutherford and S Lindquist, HSP90 as a capacitor for morphological evolution. Nature 396: 336-342, Nov.26, 1998. Primary paper for above. Look at pictures of large changes in the flies.

4. There are more degenerating than evolutioning mutations

In the analogy of a text document, if you’re substituting a letter with another (or any other transmutation you may think of) it’s more likely to damage a word than to create a new one. I suppose that the same is true in genetics in regard to nucleotides and encoding chains.

Not really. The genetic code has been selected to minimize mutations. For many amino acids, the third codon (3rd out of 3 bases needed to code for an amino acid) is irrelevant. Any substitutions there gives you the same amino acid. No change in the enzyme. Also, most amino acids are hydrophobic (water hating) so that changing one hydrophobic amino acid for another has no effect on the enzyme. What is not generally realized is that there are thousands of versions of each protein all of which are equally active.

What recent work has discovered is that only about 2.6 per thousand mutations are directly harmful to an individual. That is, directly affect its lifespan independent of selection. The overwhelming majority of mutations (997.4 per thousand) are either beneficial or have no change.

5. Nature doesn’t prefer evolution above devolution

The keyword in nature is adaption. It makes no sence that a mutation is due to ‘evolution’ or ‘devolution’ for nature. It sees a white ermine, not that its colourloss is due to ‘evolution’ or ‘devolution’. So, whatever has happened with genetic information (additions or damages), it doesn’t interest nature at all. Natural selection doesn't make any difference!

Natural selection doesn't make a difference in the type of mutations you get. That is true. However, natural selection makes all the differencein the mutations you keep in the population. Those mutations that do result in less enzyme activity such that the individual can't compete as well against the individuals without that mutation will be eliminated from the population as that individual fails the competition and either doesn't survive or doesn't produce offspring. So, the mutations you are calling "degenerate" are not kept in the population. Tough luck on the individual but good news for the population.

6. Degeneration > evolution

So, I want to claim that degeneration occurs on a higher speed then evolution.

The evidence says otherwise.

Consequences
- Beings on the end (in regard to time) of an evolution line has a smaller gene pool

What is a "gene pool"? It is the number of alleles in the population. And the data says that, most of the time, this is not true. For instance, humans now have more genetic diversity than they did 100,000 years ago. In some cases, where the population is well-adapted to a specialized niche, this would be true because of purifying selection.

If this is not the case then evolution from ancient unicellular live to current live isn’t possible!

Run this one by me again, please? If gene pools at the end of an evolutionary line have larger gene pools than at the begining, then evolution is not possible? Why?

To continue with...
- What’s the share in the story of "DNA not encoding for enzymes"?
- Are there other biological mechanisms than mutations in the game?

1. Are there other mechanisms? YES! SELECTION! Mutations only provide the raw material for selection to work on. Selection is the prime player here.
2. Some non-coding stretches of DNA used to be coding sections that have lost the "start" sequence. These are called pseudogenes. Some of the non-coding areas are portions of the DNA that bind to proteins called "transcription factors" that control when and how long genes are expressed. Much of the non-coding sequence is "introns" and these 1) stabilize the DNA and 2) provide information on how the coding regions are to be spliced. Also, much of the DNA is in the form of base repeats. In the human genome, for instance, fully 10% of our genome is the Alu repeat. The functions of these are just now being found

4. E Pennisi, How the genome readies itself for evolution, Science 281:1131-1134, Aug. 21, 1998. Built into the genome's DNA sequences areregions that can promote rapid and extensive genetic changes. Summary of the meeting Molecular Strategies in Biological Evolution, June27-29, 1998. Many genes contain adjustable repeats (as one mechanism)that can affect dramatic changes by either expressing or repressing a few repeats.

 

[lucaspa]

I'm not talking about harmful mutations, but of mutations that decrease the amount of enzymes, thats all!

Anne, if the enzymes are necessary for the biochemical processes of life, then decreasing the amount of enzymes (number of enzymes) is going to be harmful because some essential chemical reaction is not going to happen. The organism will die.

If you mean descreasing the number (amount) of protein molecules, that too will usually have a harmful effect. For instance, cytochrome c is an enzyme that transfers electrons from oxygen to make the energy molecule ATP. If the amount of cytochrome c is reduced, the organism can't be as active, can't make as many other proteins as it needs, etc. That would be harmful and the individual with that mutation would not survive the Struggle for Existence.

Your whole argument assumes that losing some enzymes will not have a harmful effect on the organism and therefore such a loss will be kept in the population. But that assumption is wrong. There are any number of "knockout" studies in mice by now. In these studies enzymes are artificially removed from the genome and the effects studied. Many times, the embryo either fails to develop at all or dies shortly after birth. Search PubMed and you will find literally thousands of studies by now.

 

[Arikay]

Lucaspa: Question, what is the probability that a deletion mutation will result in a beneficial mutation and what is the probability that an addition mutation will result in a beneficial mutation (if the probability is possible to know)?

 

[Saviourmachine]

Thanks, shenzou, for your arguments, especially of post 29. Talcos Stormweaver, you should read post 29 and 30.

1. The amount of gene loss
So, does anybody know about some statistical studies on this subject?

2. A result of adaption?

It is also unlikely that a duplication that was not adaptive would continue to exist for a long time in the genome.

You're right, actually I'm thinking the same . If I am looking around for stuff, I've also to remember that the gene loss has to beneficial. Many amounts contain also the gene losses that are inhibiting the adaption of the specific individual. This point is actually favouring your side.

3. Influence of duplicated genes on enzymes and the like

it seems to increase the number of unique protein coding genes and enzymes

I guess so, but still, I'm not kidding. Does it increase the number of unique enzymes?

4. Really new genes/enzymes?
I had to check point 4, it's okay. If it were other enzymes before that changes, it was still okay, more a less .

A lossy system?

1 the duplications seem to have occured in regions that are prone to duplications (like telomeres) or were next to transposable elements that would also have made duplciation likely.

Oops, you're kidding! That will mean that whole the story is about lossy systems (lossy as information theory states / like pictures vs text)?

No selection

There you tend to see a rapid loss of genes that are not needed anymore indicating that if there isn't selection to keep genes organisms will lose them very rapidly.

The gene losing adaption has to be an adaption! There has to be a form of selection, yes.

Symbiotic systems

Interestingly in the case of symbiotic organisms although they lose genes after they enter a relationship with another organism the overall complexity of the system increases.

I wouldn't share this (like gen duplication and crossing overs) under random point mutations.

 

[lucaspa]

Okay, you're right, natural selection plays a big role in evolution, but I wouldn't criticize her part. So, that natural selection occurs is another asumption.

That natural selection occurs is not an assumption. Mendelian genetics provided a very precise way to test for the presence of natural selection. In Mendelian genetics, the frequency of an allele (form of a gene) in a population does not change from generation to generation unless acted upon by an outside force. That outside force is natural selection. So what you can do is track a genetic trait or the allele itself across generations and see that the frequency changes. Natural selection happens.

1. "Information" is not defined


I would define "Information" as the number of enzymes that can be decoded from a DNA chain.

Bad definition. Because many proteins are not enzymes but structural genes or controlling genes. For instance, during embryonic chick development you can change the circular wrist bones to elongated bones like the forearm bones simply by letting BMP be expressed for an extra 2 hours. That has a huge information effect on the body of the chick, but isn't a change in the number of enzymes.

2. The process of encoding isn't defined
I agree with you, enzymes and the like are binary encoded.

I don't think so. Since the coding comes from a 4 base coding system, that can't be binary (2 element coding).

3. Losing of genome information is harmful to the animal
Yes, indeed, you're right, there is something harmful, but it's not for the animal, it's for species on the long term.

No, it's for the animal. If the animal can't survive due to the loss of the genome information, then it never passes that loss on to its offspring and the species (population) doesn't change.

The loss of information (look at my definition) did make the animal adapt better then his fellows without loss. Only a fast, fast "adding genome mutation" can prevent this specie from her loss.

Run this by me again. Demonstrate how you mean this. I may have missed it among the pages but I don't see any example where you lose an enzyme and the animal is better adapted.

If losing of information is only harmful for a specie (not for the individual) natural selection tend not to favour anything.

The problem is with the "if". Natural selection works on the individual. And losing the information I've seen you talk about is going to be harmful

4. Mutation can and does add genetic material.
It does add information, yes I know.

No, mutation can add genetic material. Natural selection adds the information.

5. Other mechanisms then point mutations
Yeah, so when I'm reading mutations as point (letter like) mutations then I'm not able to see leaks in my reasoning. If you're speaking about mutations as crossing over and gene duplication I've to think it over!

6. Natural selection always adds information to the organism?

I agree with you, but because I stated that adaption by losing information occurs more often then by adding information, I doubt the final effects.

Adaptations does not occur this way. All the examples of "degeneration" we have been able to find -- loss of teeth in birds, loss of eyes in some vertebrate species, etc. -- all turn out to be the addition of information at the genetic level. You lose features but gain information.

7. No misspellings

So, your statement is that every sequence decode for an enzyme? There are no such misspellings that makes an enzyme disappear?

All sequences code for a protein with some biological activity. What you are saying is that if you have the enzyme trypsin, which is a protease that catalyzes the cleavage of other proteins at the amino acids arginine or lysine, and modify it, then it may no longer cleave the proteins at arginine or lysine. What you want to say is that trypsin stops being a protease at all. However, in doing that, it may become a transferase and catalyze a different reaction.

One enzyme activity disappears, another appears. Or you can change other properties of the enzyme. For instance, here http://www.prinsep.com/resources/pdf/EN-150insert.pdf is a description of modification (mutation) of trypsin where it stays trypsin but works at a different temperature.

Yes, there are misspellings that can either 1) destroy the activity of the enzyme entirely or 2) cause the gene not to be expressed (screws up the start sequence). If there are no backup activities in the organism, then that individual is going to die, not be adaptive.

9. Natural selection does make a difference!

It makes a difference between adapted and not-adapted. But it doesn't make a difference in regard to the increase or decrease of enzymes!

Yes, it does. When decreasing enzymes is non-adaptive, then natural selection operates to eliminate those mutations. When having an increase in enzymes is adaptive, natural selection will work to make sure that mutation is kept and becomes part of the genome of every individual in the species.

Conclusion
- Point mutations aren't adding information (I'm still convinced of this )

Sometimes they do. They can add the information of 1) a new gene if the point mutation is an insertion/deletion, 2) add the information of a new enzyme activity in the same protein (many enzymes have two activities, did you know that?), 3) add the information of how and when the enzyme works.

1a. E Cabiscol and RL Levine, The phosphatase activity of carbonic anhydrase III is reversibly regulated by glutathiolation. Proc. Natl Acad. Sci. USA93: 4170-4174, 1996. Enzyme with two active sites: an anhydrase and a phosphatase.

 

[Saviourmachine]

1. If the enzyme/gene is essential, the individual will either:
a. Not form as an embryo at all = dead.
b. Not be a viable embryo = dead
c. Not be a viable newborn = dead young.
d. Be at a selective disadvantage compared to individuals with 2b and 2c and thus not be able to compete in the Struggle for Existence = dead with no offspring. All of these options result in the mutation being removed from the population. Therefore no "degeneration" because the mutation isn't around.

I suggest that there is fifth possibility:
e. Be at a selective advantage compared to individuals with 2c, because the environment changed and this enzyme that was once essential is now a drawback.

I agree with you about
- Natural selection isn't an asumption, it's proved. Okay!
- The DNA chain isn’t composing, but changing. You call it like that.
- Information: the amount of proteins that can be distinguished in a DNA chain. Okay! (I mean the words versus letters in the analogy of a text document).
- The coding isn’t binary, okay, it’s a 4 base coding system. I don’t know how to call that in English .

Minimizing mutations
That nature minimizes mutations does change the speed of evolution and degeneration.

There are very few harmful mutations
Says nothing about harmless mutations.

Anne, if the enzymes are necessary for the biochemical processes of life, then decreasing the amount of enzymes (number of enzymes) is going to be harmful because some essential chemical reaction is not going to happen. The organism will die.

Maybe there are changes in the environment that put such a presure on the individual that what was once essential, isn’t essential anymore...

Your whole argument assumes that losing some enzymes will not have a harmful effect on the organism and therefore such a loss will be kept in the population. But that assumption is wrong. There are any number of "knockout" studies in mice by now. In these studies enzymes are artificially removed from the genome and the effects studied. Many times, the embryo either fails to develop at all or dies shortly after birth. Search PubMed and you will find literally thousands of studies by now.

I’m even stating that it can be beneficial for an organism.

I don't see any example where you lose an enzyme and the animal is better adapted.

I don’t know why you’re refuting to accept this possibility 1e. This never, never occurs? I didn’t suspect that! It sounds very strange to me that it should never occur, can anybody help me with an example out of the field?

So I’m quoting Arikay on the end:

Question, what is the probability that a deletion mutation will result in a beneficial mutation and what is the probability that an addition mutation will result in a beneficial mutation (if the probability is possible to know)?

 

[lucaspa]

Lucaspa: Question, what is the probability that a deletion mutation will result in a beneficial mutation and what is the probability that an addition mutation will result in a beneficial mutation (if the probability is possible to know)?

As you know, what an insertion or deletion mutation does is shift the reading frame. DNA is "read" for amino acids in groups of 3 bases -- the codon. BUT, there is no punctuation. So, when you insert or delete a base you change the entire reading frame and get a completely brand new protein downstream of the insertion/deletion. How extensive that will be depends on how far into the protein the insertion/deletion happened and when the new "stop" codon will appear. Yes, you do have special codons that say "start" and "stop".

We have used one insertion mutation that created the nylonase enzyme as an example of a "beneficial" mutation. But how many others there are out there compared to the number of proteins is quite simply unknown and therefore there are no probability calculations.

 

[lucaspa]

I suggest that there is fifth possibility:
e. Be at a selective advantage compared to individuals with 2c, because the environment changed and this enzyme that was once essential is now a drawback.

From one generation to another, is there really going to be an environment change? Since the environment is everything external to the organism, why would there be an environment change just at this time?

I agree with you about
- Natural selection isn't an asumption, it's proved. Okay!
- The DNA chain isn’t composing, but changing. You call it like that.
- Information: the amount of proteins that can be distinguished in a DNA chain. Okay! (I mean the words versus letters in the analogy of a text document).
- The coding isn’t binary, okay, it’s a 4 base coding system. I don’t know how to call that in English .

I do not agree with you about information. Having more proteins does not necessarily mean more "information" in the colloquial sense. Again, a lot of the "information" to make an organism comes from how long the protein is expressed in embryonic development or how many of the protein molecules are made to set up a concentration gradient.

Minimizing mutations
That nature minimizes mutations does change the speed of evolution and degeneration.

You haven't demonstrated "degeneration" yet, so you can't say anything about it's "speed". After all, what is the speed of the tooth fairy?

There are very few harmful mutations
Says nothing about harmless mutations.

Yes, it does. Every mutation that is not harmful is harmless. It may even be beneficial but beneficial mutations don't do any harm, right? So they are harmless also!

Looking at the number of alleles -- varations of genes -- in populations shows a huge number of alleles. Since each allele is a mutation, that number shows that most mutations are neutral. But neutral is still harmless. Most mutations are neutral in a given environment. This provides a huge amount of variation present in the population in case there is a shift in the environment. Suddenly the lucky individuals that had a neutral variation now have a beneficial one.


Maybe there are changes in the environment that put such a presure on the individual that what was once essential, isn’t essential anymore...


I’m even stating that it can be beneficial for an organism.


I don’t know why you’re refuting to accept this possibility 1e. This never, never occurs? I didn’t suspect that! It sounds very strange to me that it should never occur, can anybody help me with an example out of the field?

So I’m quoting Arikay on the end:[/QUOTE]