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Genetic Limits


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#1 NewPath

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Posted 13 May 2012 - 01:22 AM

Despite many types of genetic mutation that are possible and are observed there is an observed phenomenon of Limits to Advantageous Genes (LAG) in every species. I will refer to this as LAG from now on. All species have their own maximum number of advantageous genes. You cannot increase the number of advantageous genes through natural means and improve a species. All observed mutational increases to the number of genes involve "DNA junk", inactive genes, or loss of function (damaging genes).

This point shows that evolution as an explanation for the appearance of complex life forms with many active genes is an interesting hypothesis, yet with no evidence because genetic observations only support LAG until now.
Observations are evidence for a theory, and due to the observation of LAG, the evidence favours the appearance of advanced complex life-forms, rather than evolving and mutation causing the observed complexity in DNA.
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#2 gilbo12345

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Posted 13 May 2012 - 07:22 AM

Despite many types of genetic mutation that are possible and are observed there is an observed phenomenon of Limits to Advantageous Genes (LAG) in every species. I will refer to this as LAG from now on. All species have their own maximum number of advantageous genes. You cannot increase the number of advantageous genes through natural means and improve a species. All observed mutational increases to the number of genes involve "DNA junk", inactive genes, or loss of function (damaging genes).

This point shows that evolution as an explanation for the appearance of complex life forms with many active genes is an interesting hypothesis, yet with no evidence because genetic observations only support LAG until now.
Observations are evidence for a theory, and due to the observation of LAG, the evidence favours the appearance of advanced complex life-forms, rather than evolving and mutation causing the observed complexity in DNA.


Exactly what I have been trying to point out with real world examples of domesticated animals and how when we push for one trait it leads to a detriment somewhere else.

Bigger pigs = leg problems + decreased maternal cabability
Longer pigs (more ribs) = back problems
Increased maternal capability = decreased size and muscle mass


This would lead to selection against extreme variants of a trait, meaning evolution via variation is impossible since the extreme changes are whittled away despite those being the changes required for evolution.

#3 AFJ

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Posted 13 May 2012 - 11:45 AM

Exactly what I have been trying to point out with real world examples of domesticated animals and how when we push for one trait it leads to a detriment somewhere else.

Bigger pigs = leg problems + decreased maternal cabability
Longer pigs (more ribs) = back problems
Increased maternal capability = decreased size and muscle mass
This would lead to selection against extreme variants of a trait, meaning evolution via variation is impossible since the extreme changes are whittled away despite those being the changes required for evolution.

That's good gilbo. Kind of in a hurry, or I would try to find it, but I had a couple or three abstracts on the touted citrate digesting E.coli. After thousands of generations, along with the naturally selected (in forced environments) ability to digest citrate, the bacteria had elongated cell walls. which is a decrease in fitness from wild type E.coli. Also they had revertants in a lactate environment, which only makes sense. It's like yeah, selection is a scientific observation, but it's not a directional driver, it's more like a gyroscope. It keeps the species alive in differing environments. But that doesn't mean it's going to keep progressing in certain direction until some kind of new perfect objective is acheived--like a wing, or a heart, or a lymphatic system.

I got them now (editing) gilbo. Plus some other abstracts on the trade-offs you speak of.

Evolution of Penicillin-Binding Protein 2 Concentration and Cell Shape during a Long-Term Experiment with Escherichia coli
http://www.ncbi.nlm....?tool=pmcentrez
Peptidoglycan is the major component of the bacterial cell wall and is involved in osmotic protection and in determining cell shape. Cell shape potentially influences many processes, including nutrient uptake as well as cell survival and growth. Peptidoglycan is a dynamic structure that changes during the growth cycle. Penicillin-binding proteins (PBPs) catalyze the final stages of peptidoglycan synthesis. Although PBPs are biochemically and physiologically well characterized, their broader effects, especially their effects on organismal fitness, are not well understood. In a long-term experiment, 12 populations of Escherichia coli having a common ancestor were allowed to evolve for more than 40,000 generations in a defined environment. We previously identified mutations in the pbpA operon in one-half of these populations; this operon encodes PBP2 and RodA proteins that are involved in cell wall elongation. In this study, we characterized the effects of two of these mutations on competitive fitness and other phenotypes. By constructing and performing competition experiments with strains that are isogenic except for the pbpA alleles, we showed that both mutations that evolved were beneficial in the environment used for the long-term experiment and that these mutations caused parallel phenotypic changes. In particular, they reduced the cellular concentration of PBP2, thereby generating spherical cells with an increased volume. In contrast to their fitness-enhancing effect in the environment where they evolved, both mutations decreased cellular resistance to osmotic stress. Moreover, one mutation reduced fitness during prolonged stationary phase. Therefore, alteration of the PBP2 concentration contributed to physiological trade-offs and ecological specialization during experimental evolution.


Evolutionary genomics of Ecological Specialization
http://life.bio.suny...pers/pnas04.pdf

'...Adaptation to mixed sugars is characterized by simililar mutations, but lac duplications and mglmutations usually arise in different backgrounds, producing ecological specialists for each sugar. This suggests that an antagonistic pleiotropic tradeoff ...retards the evolution of generalists....' http://en.wikipedia....ropy_hypothesis


Trade-offs of ecological specialization: an intraspecific comparison of pumpkinseed sunfish phenotypes
http://findarticles....77/ai_18066346/
Specialization is the ability to perform a few activities well, often at the expense of performing other activities poorly....First, comparative studies of functional trade-offs between species are inappropriate because trade-offs at this level can arise after ecological specialization. Instead, the appropriate level of comparison is within a single species, where trade-offs can be studied among coexisting phenotypes. Second, the salient differences among the coexisting phenotypes must be genetically heritable. Third, evidence of functional trade-offs and genetic differentiation at the intraspecific level is sparse. Their analysis gives the impression that there is little solid evidence to support many commonly held ideas on the evolution of specialization....


Gilbo would you have any info on what those "commonly held ideas on the evolution of specialization" would be? Not trying to put you on the spot. I can imagine what some of them would be, but I'd like to hear any thoughts from you on this subject.

#4 gilbo12345

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Posted 13 May 2012 - 03:20 PM

That's good gilbo. Kind of in a hurry, or I would try to find it, but I had a couple or three abstracts on the touted citrate digesting E.coli. After thousands of generations, along with the naturally selected (in forced environments) ability to digest citrate, the bacteria had elongated cell walls. which is a decrease in fitness from wild type E.coli. Also they had revertants in a lactate environment, which only makes sense. It's like yeah, selection is a scientific observation, but it's not a directional driver, it's more like a gyroscope. It keeps the species alive in differing environments. But that doesn't mean it's going to keep progressing in certain direction until some kind of new perfect objective is acheived--like a wing, or a heart, or a lymphatic system.

I got them now (editing) gilbo. Plus some other abstracts on the trade-offs you speak of.






Gilbo would you have any info on what those "commonly held ideas on the evolution of specialization" would be? Not trying to put you on the spot. I can imagine what some of them would be, but I'd like to hear any thoughts from you on this subject.


Good finds :)

Try as I might I can always make claims from my own observations however I have very little in the way of references to articles that define the limits to change.



I hope I'm answering your question properly.

The ideas of specialization that I know or heard of is mostly the same claims we hear on here.

- we observe change in nature
- life has existed for millions of years
-over time life will change
- millions of years of change MUST lead to evolution


Now this assumes the last point, (hence the capitals), since as you aptly put it selection doesn't necessarily mean it will select in a singular fashion driving towards a certain goal, (despite it being totally random ;) ). I think I kinda touched on this in the following premises stated in a previous forgotten thread

1- Selection is based on environmental pressures
2- Environmental pressures change over time and are rarely constant for long

Therefore selection will also change over time, thus leading to a selection inconsistent with the evolutionist worldview. In order to have constant selection for something you would need constant environmental pressure. This can be achieved via domestication, (and is why I think it has a much stronger driving force than nature ever will), yet as I said with the pig example even then we see limitation to traits.
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#5 NewPath

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Posted 13 May 2012 - 11:07 PM

Exactly what I have been trying to point out with real world examples of domesticated animals and how when we push for one trait it leads to a detriment somewhere else.

Bigger pigs = leg problems + decreased maternal cabability
Longer pigs (more ribs) = back problems
Increased maternal capability = decreased size and muscle mass


This would lead to selection against extreme variants of a trait, meaning evolution via variation is impossible since the extreme changes are whittled away despite those being the changes required for evolution.


Thank you for your support Gilbo. Your point may be correct , but even so is not really the point I was trying to make. I believe there can be large variations through slow changes of time within the existing gene pool of a species. Even if you take just the two sets of 32000 genes from one male and one female, the number of combinations is "close to infinite". Correct me if I'm wrong, each gene has AA AB BB BA, which is 4 possible variants per gene. If you take a gene sequence of 100 genes, this would result in a trillion x trillion x trillion x trillion x trillion possible genetic combinations just among those 100 genes. (4x4x4x4x.....). This variation could very well result in functional gene combinations that we have not seen before via natural selection over time. It would just require enough time for the whole genome to settle into the best combination of allele frequencies. The "balance" required can only be obtained by multiple generations of breeding within a slowly and steadily changing environment. Nature shows that allele frequncies do differ between populations of the same species, and so I feel this is an observed reality, but being a bible literalist I feel there has not been enough time (only 6000 years) to observe extreme changes to allele frequencies. A

theoretical example, if nature releases masses of methane, a strong greenhouse gas, we would have a "greenhouse effect". The atmospheric equilibrium would be broken whereby the amount of gasses released into the atmosphere is less than the amount generated by natural processes. You would then have an atmospheric build-up of pressure on the earth's surface. This would solve your pig's problem, pig's already have a well-suited allele frequency, the fact that you cannot change it now succesfully is because of the static conditions, change the conditions and the pig can handle more ribs because the ATM has increased allowing for less gravitational effect (eg as experienced by athletes at the coast who get better times due to higher air pressures). Please don't pull apart the example, its just the point I'm trying to make, changed conditions lead to changed allele frequencies.

The theory of evolution however REQUIRES continuous significant increases in the number of genes, a point evolutionists seem to dismiss in their concentration on natural selection arguments like I have expressed. It is these beneficial increases to the number of genes that I regard as unobserved, the number of beneficial genes always having a ceiling which is the standardised size of that species genome length. Insert genes, and the extra genes do not help.

#6 NewPath

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Posted 14 May 2012 - 04:19 AM

I meant the amount of gasses released into space is less than...

#7 Stripe

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Posted 14 May 2012 - 08:56 AM

Has anyone read this guy on Maximum Genetic Distance?

Pretty interesting. :)
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#8 gilbo12345

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Posted 15 May 2012 - 01:03 AM

Has anyone read this guy on Maximum Genetic Distance?

Pretty interesting. :)


Here is a quote from that paper.



"Biology will not become a true science on
a par with mathematics or physics until it can evolve from a
positive science, describing how things are, into a normative
one, telling nature how things should be. An intuition-based
theory is true on its own logical coherence (like a
mathematical proof) and does not in principle need
validation from empirical data
. In contrast, no amount of
experimental data could prove a provisional theory that is
based on observations. And a single exception is sufficient
to doom such a theory regardless how many supporting
data it may have.
A truly scientific theory must not allow any
exceptions within its domain of application, because once it
does, it automatically renders itself non-testable or makes
testing meaningless, and would no longer have any
predictive value or qualify as scientific.


The Neo-Darwinian theory is the dominant mainstream
theory for evolution and widely taught to biologists and the
public at large. However, it is not possible to use this theory
to explain the major facts of molecular evolution. Its ad hoc
substitute for the domain of molecular evolution, the
molecular clock hypothesis, is essentially unknown outside
the circle of evolution specialists. This hypothesis must
negate the idea of selection, the cornerstone of Neo-
Darwinism. The co-existence of two vastly different and
non-connected theories to account for two different but
inseparable aspects of evolution, phenotype versus
genotype, is plain evidence that neither is a complete theory
of evolution. Indeed, all existing theories of evolution have
numerous factual contradictions and take exceptions for
granted.
Therefore, there should exist a better theory that
can explain all major facts of evolution via a single universal
theme."
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#9 JayShel

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Posted 15 May 2012 - 03:56 AM

Wow I can't believe Nature let that pass the ole "peer review"...thats pretty condemning to what they stand for. I would think they would just censor it and be done with it.

Edit: My mistake, it is by nature precedings, not nature.

#10 gilbo12345

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Posted 15 May 2012 - 05:16 AM

Wow I can't believe Nature let that pass the ole "peer review"...thats pretty condemning to what they stand for. I would think they would just censor it and be done with it.

Edit: My mistake, it is by nature precedings, not nature.


I was surprised too, and this is merely the introduction part.

Its a shame that papers with valid different points of view are rarely accepted.




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