An evolutionary dilemma!!!!

a reply to: flyingfish

there will always be people more interested in discrediting evolution under the delusion that if they succeed even a little bit, then the obvious answer becomes creationism. go figure.

a reply to: TzarChasm

Why such panic? This is what I'm interested in.

Clearly, "servant of the lamb" is a christian who takes the Bible absolutely literal. The possibility that ancient people just as fallible as modern people - that we craft stories to make sense of things, and we rely upon the existing knowledge-pool to construct our understanding - is, for me, a very plausible way of thinking.

Servant of the lamb, unbeknownst to his own spiritually inclined mind, is consumed by fear - as if everything that happens in this world is a trick of "satan" - as if satan weren't just a metaphor for "delusion" - and so, represent an incoherent relationship between the organism and its reality.

Creationism is not necessary. Evolution doesn't "replace" God or change anything - it just gives us a very useful way to think about the structures we know in the world. Furthermore, medicine - both physical and mental - is only as good as the framework it operates from. Evolution as a theory - at least with regard to how psychotherapy is conducted - has been an enormous boon to understanding how to heal people.

In short: you don't need to be so opposed and aggressive - indeed, when people do that to themselves they incarnate the actual meaning of "satan" i.e. to be an adversary, to see problems where ever you look - and choosing explanations that have far less empirical support than "holy scripture".

Frankly - this way of thinking is dangerous. If you keep referring to your scripture - the Muslim will do the same, as well as the Jew - and then what? Holy-war to resolve the conflict?

F.uck that. People need to embrace a more abstract way of understanding the world and themselves i.e. a way that transcends story-telling and looks to actual processes in reality for an objectively accessible vantage point.

a reply to: Astrocyte

No, that's not all I've said. The point I'm trying to help you understand is that the organism represents an emergent property of the ecological relations it has with it's environment.

The idea that organisms are simply at their core emergent properties of a complex system and nothing more seems to veer awful close to physicalism, or should I say it implies that our mental states are nothing more than emergent properties that are the result of their physical base properties. The philosophical implications of such a conclusion leads us to a conundrum. If your mental states are nothing more than the result of previous physical causes, then the addition of these emergent mental properties cannot add anything new that was not going to happen anyway. Meaning if your view is correct I cannot help but disagree with you. My disagreement was predetermined by some set of previous physical interactions within the environment and inside my own body. Every thought I express is not my thought but a predetermined necessary fact of the physical elements at hand. It could be no other way. So if this is true how can one believe they can truly think, feel, or come to know truth?

It means that when the environment changes significantly, the organism's thermodynamic structure either a) adapts by countering the effect of the environment, or b) dies off.

Okay, so let's say we agree on this, how does that effect anything in the OP? This is a red herring though I understand it may not be intentional. Nothing about your statement here explains the dilemma I've posed. Maybe you can elaborate on how you think it solves the problem, because to me it seems like a red herring.

Sometimes, the organism becomes simpler in its organization, whereas other times the organism becomes more complex.Thus, evolution from prokaryotes to eukaryotes to sponge onward is a process of dynamic equilibrium with the environment, and, as the process continues, fusions and symbioses occur between cells, leading to a complexification of the total system i.e more elements, and indeed, symbioses like this entail a sort of "emegent property", where large-scale features of the environment (mechanics in movement, for instance) 'act down' upon the organization of the smallest elements.

So what you have said here is that organisms can get more complex, or they can get simpler. I think I can agree with that, but the nature of the development process puts a lot of limitation on how complex or simple a system can get and not totally destroy itself. Biologist call this feature of the dGRN canalization. I listened to about a thirty minute interview with Terrence Deacon discussing his book Incomplete Nature and another 1 hour talk on the semiotic nature of language universals, because I think an understanding of semiotics leads one to ID. I'd love to hear him and John Lennox have a discussion on the semiotic nature of DNA.

He thinks about the canalization of the dGRN in a different way. The canalization would be a result of the thermodynamic constraints on the system in his view. So in other words it can be explained in terms of what the system is not doing, however the question inevitably arises, what mechanisms allow organisms to by pass the canalization of the system? If a constraint on a system won't allow it to output anything different irrespective of changes to input, then how do new morphological features arise? Again this has nothing to do with what was mentioned in the OP, but it is an interesting topic and another thing I think evolutionist have a hard time answering. We cannot just assume these constraints can be bypassed, and produce a system that is still self-regulating. There would need to be a chemical pathway in which these things could occur. If we take his analogy in the talk I listened to of a car engine, it would seem that the more constraints you remove on the system the quicker entropy takes hold. It seems observation shows it is the same with the development process of organisms. The more restraints you remove or modify and the higher they are in the hierarchy of the dGRN the more catastrophic the effect on the resulting system will be, and the less likely it is that this system will be viable and self regulating.

I mentioned Terrence Deacon because you would do well to understand the concept of orthograde and contragrade, which helps explain how evolution could progress through non-stop oscillation between stability and organized chaos. An orthograde state corresponds to an attractor (a stable condition or a "structural coupling" with the environment) whereas a perturbation triggers a contragrade state, which, at this point, experiments with different adaptations to the pertubation to maintain its systems continuity. It's in contragrade states that growth and increased coherency can occur - what the ecologist Robert Ulanowicz calls "ascendance".

I'd never heard of him, but I like the fact that he takes philosophy seriously. I think that is the reason for the consistency in his view of the world. I completely agree that if God does not exist, then mind would ultimately be an illusion of the physical processes around and inside of us. So his position is consistent with naturalism, physicalism, and determinism, which he seems to believe all three. Now I hope you realize that I don't think the problem I've posed OP requires us to throw the idea that organisms change over time nor would it require us to throw out natural selection. I am simply saying that the current theories of how these things came about leave us with some tough questions in the area of genetics and fossils. I am not saying we should get rid of the idea of natural selection or change over time.


From my understanding an othrograde change would be a change that implies an absence of constraint along a potential gradient. Where as a contragrade change would be a change that implies the presence of constraint that must be overcome for the change to occur(i.e. work must be done). What you seem to be getting at is that since the environment of organisms has an orthograde tendency toward disorder(Second Law of Thermodynamics), then these orthograde changes in the environment might act as the work, or help bypass some constraints, for the contradgrade change to occur inside an organism. This makes perfect sense, but Deacon seems to want to take it one step further and conclude that these contragrade changes can cause the spontaneous emergence of a new form via the addition of some new highly-ordered constraint added upon the system. (Continued it next post)

a reply to: Astrocyte

This is a plausible hypothesis but I feel it is at odds with observation. Let us again consider the car engine as thermodynamic system. You may be able to add, modify, or even remove entire constraints on that system and make it work better, but it is also just as reasonable to conclude that you may add, modify, or remove a constraint that is detrimental to the performance of the system. The latter seems to be more probable if the orthograde change in the environment that does the work for the contragrade change inside the organism is not controlled. The hierarchical nature of the dGRN makes certain constraints a necessity for the production of a new self-regulating system. So again I don't see how this helps one bypass the canalization of this system. Seems to be yet another problem for body plan morphogenesis.

Also, and for someone who calls himself "seresnt of the lamb", it would be nice if you could be more mindful in your choice of words about what I mean i.e. "Are you just trying to use words you think most people won't take that time to look up?". This isn't an appropriate way of speaking - at least in real intellectual conversations, this would be regarded as an 'ad hominem' attack. Its also cynical and assumes that I am not making sense.

Well 'ad hominem' would be me saying your argument is wrong, because of some flaw in your character. I never did that. At no point in time did I say you weren't making sense. The last post had no substance for me to respond to. It was just extremely general so since I don't know you personally this seems to be a perfectly reasonable question to ask, however since it offended you I will say I am sorry.

No, what makes sense - and what you should understand, is the diachronic nature of existence. You are obviously committed to a biblical timetable formulated in a period of human history where narrative and story-telling took the place of empirical study.

Please elaborate on what you mean by diachronic nature of existence. The statement is to general. Diachronic simply means concerned with the way in which something, especially language, has developed and evolved through time. So you are just saying I should understand that as things exist they develop and evolve thru time. I never denied that. I just think there are obviously limitations on what can happen when we study population genetics and the developmental biology. The reason empirical study took off was because theist in the 16th and 17th century wanted to read the book nature, which they thought gave you knowledge of God and was even a form of worship to them.

To know the mighty works of God; to comprehend His wisdom and majesty and power; to appreciate, in degree, the wonderful working of His laws, surely all this must be a pleasing and acceptable mode of worship to the Most High, to whom ignorance can not be more grateful than knowledge. --Copernicus

Those who study the stars have God for a teacher. -- Tycho Brahe

I do not feel obliged to believe that the same God who has endowed us with sense, reason, and intellect has intended us to forgo their use. --Galileo Galilei

When I reflect on so many profoundly marvelous things that persons have grasped, sought, and done, I recognize even more clearly that human intelligence is a work of God, and one of the most excellent. --Galileo Galilei

Our piety is deeper, the greater is our awareness of creation and its grandeur. --Johannes Kepler

We astronomers are priests of the highest God in regard to the book of nature. --Johannes Kepler

Thus I see plainly that the certainty and truth of all knowledge [scientiae] depends uniquely on my awareness of the true God, to such an extent that I was incapable of perfect knowledge [perfecte scire] about anything else until I became aware of him. -- Rene Decartes

There are two kinds of people one can call reasonable: those who serve God with all their heart because they know him, and those who seek him with all their heart because they do not know him. --Blaise Pascal

"The vastness, beauty, orderliness of heavenly bodies; the excellent structure of animals and plants; and other phenomena of nature justly induce an intelligent, unprejudiced observer to conclude a supreme, powerful, just, and good author." --Robert Boyle

Many if not all of these were Christians, so yes where this thought process originated was story-telling and narrative, but that doesn't mean that it leads one to think empirical study should not be used. As we can tell it lead to the opposite.

Do you pay attention to your emotions when you write? This is another mean-spirited thing to say. I understand you - I'm not an idiot. You don't need to call the other person stupid if it you - in fact, who is having the problem understanding the nature of the criticism I'm making.

It's not mean spirited to point out when you think someone isn't grasping a concept. You haven't made a criticism on the dilemma I've posed, everything I've responded to so far is off topic. Its all a red herring, but I felt it was interesting so I let us go down that rabbit hole.

Buddy - I've already answered this. When you scale back billions of years ago into the precambrian you have nothing but different versions of life. You are assuming that life only happened once. I am assuming that the life we see today is the life that survived.

Now, you seem to think that invertebrates HAD to be the ancestor for modern vertebrates. THAT IS NOT NECESSARY. You are completely overlooking how unnecessary that assumption is - but clearly this is where your focus lies. As I've already written - and to which you felt the need to ignore and then mock - invertebrates may be the evolutionary heir to a DIFFERENT EUKARYOTIC ANCESTOR. This is your issue - I've explained it, have told you that this is not that big a problem, but you apparently see it as the death of the evolutionary theory.

Okay and this is exactly what shows me you haven't completely grasped what the problem is. Let's say invertebrates did come from a different eukaryotic ancestor, then we have no evolutionary history for vertebrates in the fossil record. Are you saying we should just assume these vertebrates spontaneously arose from eukaryotic cells 500 million years ago with no evolutionary history to be found in the fossil record?!?? Where is the gradual evolution that takes a long time to occur? Where is the evidence of from this gradual process?? If we take your route we haven't solved the dilemma, the only other option is to say they came from invertebrates, but this puts us in a rock in a hard place as well due to the differences in mitochondria DNA. (To be continued next post)

a reply to: Astrocyte

My resolution: there were different sorts of bacteria with different genetic organizations of their nucleic acids. To say this is impossible is apparently gainsaid by the reality that vertebrates and invertebrates process oxygen in different ways. This merely means that the mitochondria - or ancient bacteria - had different ways of adapting to the presence of oxygen.

It would do you well to understand semiotics and the semiotic dimension carried within DNA. I have said numerous times that I am not just talking about a difference in the organization of their nucleic acids which is what you said here, which tells me you haven't fully grasped what I am talking about. I am saying that vertebrates and invertebrates interpret the same arrangement of nucleic acids differently. Deacon, in his video on semiotics makes a good point, sign vehicles always correlate with some index or reference point in the real world. Codons are certain arrangements of chemicals that act as sign vehicles for the ribosome. In Mycoplasma, the codon UGA references an index that means to build a tryptophan amino acid, while in Human cells the codon UGA references an index that symbolizes the stop of the translation process.

Source in OP:

AGA and AGG were thought to have become mitochondrial stop codons early in vertebrate evolution (Osawa, Ohama, Jukes & Watanabe 1989). However, at least in humans it has now been shown that AGA and AGG sequences are not recognized as termination codons. A -1 mitoribosome frameshift occurs at the AGA and AGG codons predicted to terminate the CO1 and ND6 ORFs, and consequently both ORFs terminate in the standard UAG codon (Temperley et al. 2010).

Several arthropods translate the codon AGG as lysine instead of serine (as in the invertebrate mitochondrial genetic code) or arginine (as in the standard genetic code) (Abascal et al., 2006).

GUG may possibly function as an initiator in Drosophila (Clary and Wolstenholme, 1985; Gadaleta et al., 1988). AUU is not used as an initiator in Mytilus (Hoffmann et al., 1992).

These are differences in the way these codons are interpreted by the ribosomes of certain organisms, it has nothing to do with a different arrangement of nucleic acids. All of those on the NCBI source are different sign vehicles that point to different indices depending on the context of the organism you are in. They are different languages in that sense.

a reply to: TzarChasm

That would require pointing out specific inaccuracies and logical breaks in the evolutionary model, discrediting the evidence and predictions that are made. But, unfortunately for creationists they are not the ones likely to come up with these things because they do not follow the scientific method.
They first start with the conclusion and then set about shoehorning the data to fit the conclusion. The exact opposite of real science.
If there are changes required in evolution it will be real scientists will real peer reviewed data that will discover them, not by reciting dumb lies some creationist came up with.

a reply to: Astyanax

Alright agree to disagree.

a reply to: ServantOfTheLamb

Do you not have a moral duty to try to tell the truth, and you're not even trying.
The things you don't know are hardly the basis of an argument.

Imaginary transitional invertabrets

Much more likely to exist than imagniary deities.

I still don't get why people who are usually against science try to use it to discredit views they don't like?

originally posted by: ServantOfTheLamb
a reply to: Astrocyte

This is a plausible hypothesis but I feel it is at odds with observation. Let us again consider the car engine as thermodynamic system. You may be able to add, modify, or even remove entire constraints on that system and make it work better, but it is also just as reasonable to conclude that you may add, modify. or remove a constraint that is detrimental to the performance of the system. The latter seems to be more probable if the orthograde change in the environment that does the work for the contragrade change inside the organism is not controlled. The hierarchical nature of the dGRN makes certain constraints a necessity for the production of a new self-regulating system. So again I don't see how this helps one bypass the canalization of this system. Seems to be yet another problem for body plan morphogenesis.

Also, and for someone who calls himself "seresnt of the lamb", it would be nice if you could be more mindful in your choice of words about what I mean i.e. "Are you just trying to use words you think most people won't take that time to look up?". This isn't an appropriate way of speaking - at least in real intellectual conversations, this would be regarded as an 'ad hominem' attack. Its also cynical and assumes that I am not making sense.

Well 'ad hominem' would be me saying your argument is wrong, because of some flaw in your character. I never did that.At no point in time did I say you weren't making sense. The last post had no substance for me to respond to. It was just extremely general so since I don't know you personally this seems to be a perfectly reasonable question to ask, however since it offended you I will say I am sorry.

No, what makes sense - and what you should understand, is the diachronic nature of existence. You are obviously committed to a biblical timetable formulated in a period of human history where narrative and story-telling took the place of empirical study.

Please elaborate on what you mean by diachronic nature of existence. The statement is to general. Diachronic simply means concerned with the way in which something, especially language, has developed and evolved through time. So you are just saying I should understand that as things exist they develop and evolve thru time. I never denied that. I just think there are obviously limitations on what can happen when we study population genetics and the developmental biology. The reason empirical study took off was because theist in the 16th and 17th century wanted to read the book nature, which they thought gave you knowledge of God and was even a form of worship to them.

To know the mighty works of God; to comprehend His wisdom and majesty and power; to appreciate, in degree, the wonderful working of His laws, surely all this must be a pleasing and acceptable mode of worship to the Most High, to whom ignorance can not be more grateful than knowledge. --Copernicus

Those who study the stars have God for a teacher. -- Tycho Brahe

I do not feel obliged to believe that the same God who has endowed us with sense, reason, and intellect has intended us to forgo their use. --Galileo Galilei

When I reflect on so many profoundly marvelous things that persons have grasped, sought, and done, I recognize even more clearly that human intelligence is a work of God, and one of the most excellent. --Galileo Galilei

Our piety is deeper, the greater is our awareness of creation and its grandeur. --Johannes Kepler

We astronomers are priests of the highest God in regard to the book of nature. --Johannes Kepler

Thus I see plainly that the certainty and truth of all knowledge [scientiae] depends uniquely on my awareness of the true God, to such an extent that I was incapable of perfect knowledge [perfecte scire] about anything else until I became aware of him. -- Rene Decartes

There are two kinds of people one can call reasonable: those who serve God with all their heart because they know him, and those who seek him with all their heart because they do not know him. --Blaise Pascal

"The vastness, beauty, orderliness of heavenly bodies; the excellent structure of animals and plants; and other phenomena of nature justly induce an intelligent, unprejudiced observer to conclude a supreme, powerful, just, and good author." --Robert Boyle

Many if not all of these were Christians, so yes where this thought process originated was story-telling and narrative, but that doesn't mean that it leads one to think empirical study should not be used. As we can tell it lead to the opposite.

Do you pay attention to your emotions when you write? This is another mean-spirited thing to say. I understand you - I'm not an idiot. You don't need to call the other person stupid if it you - in fact, who is having the problem understanding the nature of the criticism I'm making.

Its not mean spirited to point out when you think someone isn't grasping a concept. You haven't made a criticism on the dilemma I've posed, everything I've responded to so far is off topic. Its all a red herring, but I felt it was interesting so I let us go down that rabbit hole.

Buddy - I've already answered this. When you scale back billions of years ago into the precambrian you have nothing but different versions of life. You are assuming that life only happened once. I am assuming that the life we see today is the life that survived.

Now, you seem to think that invertebrates HAD to be the ancestor for modern vertebrates. THAT IS NOT NECESSARY. You are completely overlooking how unnecessary that assumption is - but clearly this is where your focus lies. As I've already written - and to which you felt the need to ignore and then mock - invertebrates may be the evolutionary heir to a DIFFERENT EUKARYOTIC ANCESTOR. This is your issue - I've explained it, have told you that this is not that big a problem, but you apparently see it as the death of the evolutionary theory.

Okay and this is exactly what shows me you haven't completely grasped what the problem is. Let's say invertebrates did come from a different eukaryotic ancestor, then we have no evolutionary history for vertebrates in the fossil record. Are you saying we should just assume these vertebrates spontaneously arose from eukaryotic cells 500 million years ago with no evolutionary history to be found in the fossil record?!?? Where is the gradual evolution that takes a long time to occur? Where is the evidence of from this gradual process?? If we take your route we haven't solved the dilemma, the only other option is to say they came from invertebrates, but this puts us in a rock in a hard place as well due to the differences in mitochondria DNA. (To be continued next post)

yes, it is a difficult subject to explore. particularly when you insist on educating yourself on a conspiracy forum instead of taking a professional class where people are paid to have this information on hand. its most curious that you would rather interrogate random people on the internet than seek out such experts. there is a reason most of ats is ignoring your thread, they know you are looking for a reason to say "gotcha!" ...keep looking...

a reply to: Phantom423

Idiot, if everyone had the same sequence of nucleotides, everyone would look the same and be the same. The four base pairs make up the codons. And of course they are read differently because they code for different functional parts of an organism.

This is the second time you have tried to make it appear as I said everything needs to have the same sequence of nucleotides, when I have never said or implied anything of the sort. You are being dishonest. I don't think you understand that we are comparing the interpretation of the same codon in two different organisms. Many organisms use the Standard Code which is why for a long time we thought there was a tree of life. Now we know that is wrong. Organisms that don't interpret the same codon in the same way cannot be related.

The alphabet is the database that's used to form words. In English it's "yes", Spanish "Si", French "Oui".

This illustrates redundancy and it is not what I am talking about. DNA is a "database" used to form a particular protein based on the information in mRNA. Different coding languages wouldn't relate to saying the same thing in a different language that would mean they read different codons but came out with the same message. That is the completely opposite of what I am saying. A better analogy would be the use of two programming languages. If I am writing a java program in C# syntax my program isn't even going to compile much less create a working program.

Get over it. Your sources are wrong. Not only are they wrong, but if they were right, the genetic code would be chaotic and there would be no genetic relationship among species on this planet. Common ancestry. It's so obvious that even one of your primate ancestors could figure it out.

Oh yea my peer reviewed sources are wrong because some guy on a blog says so....I'll stick with my sources over you anyday...

a reply to: flyingfish

No.. the truth is we observe gain in function in mutations leading to novel phenotype everywhere we look, from primates to plants. If you actually study this stuff you would know this.

Oh yea, lets ignore the work of people in the field because it doesn't fit my preconceived notions of how you think the world should work. I gave you the resources to show that everything you thought showed a gain in function mutation was not actually a gain in function mutation from the molecular perspective. If you wish to just assert I am ignorant an move on that is your right, but it isn't the intellectually honest route.

a reply to: flyingfish

I have no obligation to hold a conversation with someone who has there hands over there ears going "NO NO NO NO NO NO NO"!!!!!

a reply to: CB328

www.abovetopsecret.com...

Read the part about the reason empirical study took off. Theist have never felt you should reject Science its a stigma pushed on them by atheist.

originally posted by: ServantOfTheLamb
a reply to: flyingfish

No.. the truth is we observe gain in function in mutations leading to novel phenotype everywhere we look, from primates to plants. If you actually study this stuff you would know this.

Oh yea, lets ignore the work of people in the field because it doesn't fit my preconceived notions of how you think the world should work. I gave you the resources to show that everything you thought showed a gain in function mutation was not actually a gain in function mutation from the molecular perspective. If you wish to just assert I am ignorant an move on that is your right, but it isn't the intellectually honest route.

If you're not intentionally lying then you have some mental block preventing you from understanding basic biology. Why don't face the fact that you're no good at this.
Novel phenotypes are gains in function.

a reply to: flyingfish

If you're not intentionally lying then you have some mental block preventing you from understanding basic biology. Why don't face the fact that you're no good at this. Novel phenotypes are gains in function.

No they aren't. If you would cough of the ten bucks for the source I sent you, you would see that it addresses this very claim. All one has to do is read that source and they can tell that you are simply in denial.

a reply to: TzarChasm

Glad to see your response was totally relevant to the topic at hand.

originally posted by: ServantOfTheLamb
a reply to: flyingfish

If you're not intentionally lying then you have some mental block preventing you from understanding basic biology. Why don't face the fact that you're no good at this. Novel phenotypes are gains in function.

No they aren't. If you would cough of the ten bucks for the source I sent you, you would see that it addresses this very claim. All one has to do is read that source and they can tell that you are simply in denial.

The fact that you don't or can't understand studies is not my problem. There are plenty of experiments that show mutations create new alleles.

Here are a few, free of charge!

Bacteria/Microbes
Here they identified 66 mutations to that one focal gene which had an adaptive, or beneficial, effect on the fitness of individual

Abstract
The central role of beneficial mutations for adaptive processes in natural populations is well established. Thus, there has been a long-standing interest to study the nature of beneficial mutations. Their low frequency, however, has made this class of mutations almost inaccessible for systematic studies. In the absence of experimental data, the distribution of the fitness effects of beneficial mutations was assumed to resemble that of deleterious mutations.

link

Here they used these results to develop a mathematical model of the probability of a beneficial mutation reaching fixation.

Abstract
Beneficial mutations are intuitively relevant to understanding adaptation 1, 2 and 3, yet not all beneficial mutations are of consequence to the long-term evolutionary outcome of adaptation. Many beneficial mutations—mostly those of small effect—are lost due either to (1) genetic drift 4 and 5 or to (2) competition among clones carrying different beneficial mutations, a phenomenon called the “Hill-Robertson effect” for sexual populations [6] and “clonal interference” for asexual populations [7]. Competition among clones becomes more prevalent with increasing genetic linkage and increasing population size, and it is thus generally characteristic of microbial populations 8 and 9. Together, these two phenomena suggest that only those beneficial mutations of large fitness effect should achieve fixation, despite the fact that most beneficial mutations produced are predicted to have very small fitness effects 10 and 11. Here, we confirm this prediction—both empirically and theoretically—by showing that fitness effects of fixed beneficial mutations follow a distribution whose mode is positive.

Link

Here is a paper that identified 665 mutations in Pseudomonas fluorescens bacteria, and evaluated their fitness relative to the wild-type bacterium by comparative growth assays on a variety of different media.

These results suggest that the initial step in adaptive evolution—the production of novel beneficial mutants from which selection sorts—is very general, being characterized by an approximately exponential distribution with many mutations of small effect and few of large effect. We also document substantial variation in the pleiotropic costs of antibiotic resistance, a result that may have implications for strategies aimed at eliminating resistant pathogens in animal and human populations.

Link

Nematode worms

Here is a paper that discusses modern techniques for identifying phenotype-altering mutations in model organisms, including nematodes, plants and fruit flies. The specific mutation they focus on is a mutation that alters the developmental fate of stem cells in the nematode, Caenorhabditis elegans (this is a neutral phenotype). If you look through the references for this paper, you will find dozens of studies that talk about methods for screening populations of laboratory organisms for the presence of new phenotypes, and for identifying how each new phenotype is associated with a readily-identifiable mutation.
Link

Chickens
Here is a paper that deals with mutations to pigmentation genes in chickens. The Dominant white allele does not occur in wild jungle fowl (i.e., wild chickens), but does occur in some populations of domestic chickens. Two mutations to the Dominant white locus include Dun and Smoky, both of which mutations have been positively identified. Furthermore, both of these mutants arose spontaneously in known populations, and the exact bird in which the mutation occurred is known.

Sequence analysis showed that the Dominant white allele was exclusively associated with a 9-bp insertion in exon 10, leading to an insertion of three amino acids in the PMEL17 transmembrane region. Similarly, a deletion of five amino acids in the transmembrane region occurs in the protein encoded by Dun. The Smoky allele shared the 9-bp insertion in exon 10 with Dominant white, as expected from its origin, but also had a deletion of 12 nucleotides in exon 6, eliminating four amino acids from the mature protein. These mutations are, together with the recessive silver mutation in the mouse, the only PMEL17 mutations with phenotypic effects that have been described so far in any species.

Link

Humans

Abstract Lipoprotein lipase (LPL) hydrolyzes triglycerides in the circulation and promotes the hepatic uptake of remnant lipoproteins. Since the gene was cloned in 1989, more than 100 LPL gene mutations have been identified, the majority of which cause loss of enzymatic function. In contrast to this, the naturally occurring LPLS447X variant is associated with increased lipolytic function and an anti-atherogenic lipid profile and can therefore be regarded as a gain-of-function mutation.

Link

Abstract Hereditary persistence of fetal hemoglobin (HPFH) is a benign condition in which the normal shutoff of fetal hemoglobin (Hb F) production fails to occur. In the G gamma beta+ type of HPFH, erythrocytes of adult heterozygotes contain approximately equal to 20% Hb F, which is almost exclusively of the G gamma-globin variety, without increased levels of gamma-globin chains from the nearby A gamma-globin gene. Unlike some forms of HPFH, no major deletions in the globin gene cluster have been found by genomic blotting in the G gamma beta+ variety. We report here a family with this condition, from which cosmid clones of the beta-globin gene cluster from the G gamma beta+ HPFH allele have been obtained. Sequencing around the fetal genes has identified a point mutation 202 base pairs 5' to the G gamma-globin gene that is present in genomic DNA of 3/3 unrelated individuals with G gamma beta+ HPFH but in none of more than 100 non-HPFH individuals.

Link

a reply to: ServantOfTheLamb

This is the second time you have tried to make it appear as I said everything needs to have the same sequence of nucleotides, when I have never said or implied anything of the sort. You are being dishonest. I don't think you understand that we are comparing the interpretation of the same codon in two different organisms. Many organisms use the Standard Code which is why for a long time we thought there was a tree of life. Now we know that is wrong. Organisms that don't interpret the same codon in the same way cannot be related.

Yes, they can be related. The obvious reason that they are related is simply the observation that the different organisms contain the same codon i.e. the same SEQUENCE OF NUCLEOTIDES WHICH MAKE UP THE CODON. Divergence of prokaryotes and eukaryotes is not dependent on a single codon translation. A higher level of complexity determined this divergence.
And the mitochondrial analysis you presented is pure fiction.

This paper describes how gene transfer and EVOLUTION address your codon problem:

Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes

Chuan Kua,1, Shijulal Nelson-Sathia,1, Mayo Roettgera, Sriram Garga, Einat Hazkani-Covob, and William F. Martina,2

www.pnas.org...

The origin of eukaryotes was one of life’s major evolutionary transitions (1, 2). Despite much progress in recent years, the issue is far from being resolved to everyone’s satisfaction. There is broad agreement that the last eukaryotic common ancestor (LECA) possessed numerous features that are lacking in prokaryotes, including a mitochondrion, a nucleus, an extensive endomembrane traffic system, meiosis, sex, spliceosomal introns, a eukaryotic flagellum, a cytoskeleton, and the like (2, 3).

The order of events that gave rise to those attributes is still debated (3–5), as are issues concerning (i) the number and nature of prokaryotic partners that were involved in eukaryotic symbioses, (ii) the role of gene transfers from the ancestral mitochondrion, and (iii) the possible role of lateral gene transfer (LGT) from donors that were distinct from the mitochondrial (or plastid) endosymbiont, or its host. Three recent developments have shed new light on the problem of eukaryote origins.

The first is the insight that the host for the origin of eukaryotes is now best understood as a gardenvariety archaeon, one that branches within the diversity of known archaeal lineages (4, 6–9). An origin of the host from within the TACK superphylum (4, 7, 9) is the position most widely discussed at present, but the TACK superphylum was itself only recently recognized through the discovery of new archaeal lineages (7). It is possible that, as new archaeal lineages become discovered, the phylogenetic arrangement of eukaryotes and archaea might undergo further adjustments still (10).

A second development is the recognition that the origin of the roughly 2,000 gene families that underpinned the origin of eukaryotic-specific traits in the eukaryote ancestor required the biochemical power of internalized bioenergetic membranes that mitochondria provided (3). Mitochondria, not oxygen, made the energetic difference that separates eukaryotes from prokaryotes. That is because anaerobic mitochondria generate about five ATP per glucose and fermentations in eukaryotes generate two to four ATP per glucose (11), such that the meager 5- to 10-fold increase in ATP yield per glucose conferred by oxygen respiration is dwarfed by the 104 to 105 increase in ATP yield per gene manifest in cells with mitochondria (3). The key to the orders of magnitude increase in energy available for evolutionary invention that mitochondria conferred is the eukaryotic configuration of internal, compartmentalized bioenergetic membranes relative to genes (3, 5). After all, had oxygen been the key to eukaryote complexity, Escherichia coli would have become eukaryotic for the same reason. Furthermore, eukaryotic aerobes and anaerobes interleave across eukaryote phylogeny (11), and bioenergetics point to a mitochondrion ancestor with a facultatively anaerobic lifestyle (12). Only those cells became complex that experienced the increased energy per gene afforded by mitochondria, and the long puzzling lack of true intermediates in the prokaryote– eukaryote transition has a bioenergetic cause (3).

A third, and more involved, development is the recognition of genomic chimerism in eukaryotes (13), an issue that has been brewing for some time (13–22). Genome analyses showed that genes of bacterial origin outnumber genes of archaeal origin in yeast (21) and other eukaryotic genomes (23, 24) by a factor of about 3:1 and that roughly 15–20% of the nuclear genes in photosynthetic eukaryotes are acquisitions attributable to the endosymbiotic origin of plastids from cyanobacteria (25–27). However, many of the gene acquisitions in photosynthetic eukaryotes do not trace, in gene trees, directly to a cyanobacterial, and thus obviously plastid, origin.

Conclusion

Inherited chimerism is an alternative to the problematic practice of conjuring up additional, gene-donating symbionts at organelle origins to explain gene trees. It merely requires a selective force to associate the symbiont (either plastid or mitochondrion) to its host so that the endosymbiosis (one cell living within another) can be established and gene transfer from the symbiont can commence. It places no constraints on the collections of genes that the plastid and the mitochondrial symbionts possessed, other than that it needs to be a genome-sized collection, not tens of thousands of genes, and it allows freely for LGT among prokaryotes before the endosymbionts become organelles and afterward. LGT among prokaryotes has received much attention in the past decades. Inherited chimerism incorporates LGT among prokaryotes into endosymbiotic theory

Your sources pulled a conclusion out of a hat and just like magic, it looked good, therefore, it worked - who would ever challenge such an innovative conclusion?!! No objective analysis, no lab work, no corroborating references - just a few pages of unreliable gibberish with no evidence. The usual scenario which suits their agenda.

a reply to: ServantOfTheLamb

Oh yea my peer reviewed sources are wrong because some guy on a blog says so....I'll stick with my sources over you anyday...

BTW, would you please provide a list of those peer-reviewed sources. Thank you.