61 replies to this topic

[Viper Of Hades]

what you tryina say?

[CodeCat]

I'm saying that anything can be understood given time. Problems might become more and more complex as time goes on, but we also gather more and more previous knowledge and experience.

[Viper Of Hades]

but the more knowledge we gain the more knowledge we know

[Soul]

I know this is out of nowhere, but my sisters cat had a kitten with an extra toe on it's two front paws(It had a claw on those extra toes too) and it could actually use them, my friend called it a freak cat .

Edited by Soul, 31 May 2007 - 04:00 PM.

[anonymous]

You know what i find hysterical? The fact that not one person has mentioned the brain or mind in relation to evolution. Last time I checked without thought nothing happens! If an animal needs to jump to escape a predator it must first have the thought to do so! What does this say about the theory of evolution..... at its core where does evolution truly begin??? Is it ALL purely chance that drives evolution even though the mind chooses a path or direction? Disconnect the brain and your basically dead. To go a little further with evolution, we don`t even know why we have such big brains because apparently we do not use most of it according to science. If you believe that load of horse shit I have a flying lap top to sell you. The brain is hardwired to act upon commands. What commands, whos commands, how was thought manifested? These are just a few questions science or purley BIOLOGICAL entities must ask before making RANDOM assumptions. Blind faith in religion and nothing are one and the same in the minds eye. They are Theory not truth.

Now mind you this is all wild speculation on my part.........

[CodeCat]

If you put it that way, there is no truth. There's certainly no truth in science, I can tell you that much. Pretty damn accurate models of the world, and theories that fit for by far most of the situations, yes. But no truth. Truth can be found only within oneself, from what one perceives of the world.

But now to that brain thing. Single-cell organisms have no brain. Their means of passing information into the cell is by directly releasing chemicals into the cell. Production and release of these is in turn is triggered through responses of various parts of the cell. One important one is the ribosomes. They produce proteins based on the cell's genetic makeup. These proteins can be used to control all kinds of processes within the cell, and some can also be used externally to signal nearby cells or perhaps as a primitive defence mechanism (antibodies).

So the signalling system is already there at the cellular level. Now, imagine that due to mutation, one particular cell type had developed the (otherwise pretty useless) defect that it would release all of its proteins in a sudden burst whenever it was stimulated in a way. This burst could then stimulate other cells, causing a chain reaction of chemicals to be released. The mutation spread across different types of cells within the organism, causing several different types of chemical to be released depending on what chemicals that cell was currently producing. Some would trigger release in other nearby cells, others would inhibit it. That's how nerve cells would have been born. The advantage is obvious because now, an organism with this system could send signals to respond far faster than was previously possible. For example a small macro-organism could release lots of chemicals in one go in response to a threat, or the sudden burst could cause it to shoot away or cause something else to happen. But more importantly, this made more complex organisms possible because the different parts could be connected in a way not previously possible.

Now, think a bit further along. Organisms have evolved further, and nerve systems are a fact. However, the response between nerves is still limited because they're basically 'lines' between parts of the body. But since the system of nerves has also increased in complexity, there start to form small parts of the body where nerve cells meet. At this point, a small switching system would have emerged, since a certain configuration would have been more advantageous (quicker response, more 'intelligent' response). As this switching system evolved further (it would do so because it would make the organism ever better at quickly responding to its environment) there would have eventually been a point where the nerve system proved to be better at instantaneously controlling the body as a whole than the previous, semi-autonomous system. This could only have happened if the nerve system was efficient enough to ensure survival. And this in turn could only occur with a sufficient amount of central switching capacity. So this is where the brain is born.

[peterete]

wowwww really interesting topic, good job man

[anonymous]

OK, so when did it become aware of itself and how was the disconnect made between an organism (in your synopsis) of a pure reactive nature to one of concious thought? Unless what you are saying, which mind you I think you are, is, there is no such thing as true thought. Our make up is simply chemicals reacting to stimulous randomly (Once it stops reacting randomly it trancends its original form, no). I may be wrong in my interpertation of your view on what we are and what our true process is. But if our process originates at a chemical level I can only assume that thought does not reside in a chemical state or is actual awareness, conciousness or what ever you want to call it the mutation or catalyst of evolution? The concept is no more outrageous than the belief that chemicals or the primordial ooze contains the essence of awareness.

By the way CodeCat great response.

Edited by anonymous, 01 June 2007 - 01:15 AM.

[Hostile]

That's why evolution is a theory. Because it can't account for drastic changes in the developement of species. Things just don't grow extra limbs because of something called "common ancestry"

I think you're getting words mixed up here. A hypothesis is a 'try' at a theory, something that is still under construction basically. However, a theory is something that's supported by evidence, and accurately describes the world around us up to a degree. A theory is the highest level of truth that science has, basically. Science has no absolute truth.

Olli hit the nail right on the head here. A theory will never explain everything, and all theories have small discrepancies that are unaccounted for. But that doesn't make the entire theory invalid. It just means the theory is incomplete. With my experience with linguistics, I've noticed that quite often, languages evolve through regular changes in sound patterns. But sometimes, there's just one that doesn't fit.

A classic example (if you want to know more) is the exceptions to the sound shift known as Grimm's law. These were later accounted for in an extension to the theory, named Verner's law. So while the original theory fit most of the time, the inaccuracy was later also accounted for, and the resulting theory was accurate near 100% of the time.

So Hostile, what you're basically criticising is that science isn't fast enough for you. You're saying they should work faster and harder to account for the discrepancies in existing established theory. Good luck with that. I don't see you doing much to help them, though. Except tell them to hurry up, that is.

You know, if you said that to a mod leader, you'd get scolded from all sides.

I agree with everything you said, except one. The flaws of the theory are actually extremely huge. Like precambrian to cambrian mass arrival of organisms and such. Or the growth of limbs.

I can find great pieces about how limbs changed. But none that show how organsims first grew limbs or how organsims grew additional limbs that contrasted common ancestry.
http://www.sciam.com...A3083414B7F0000

Great one on mutated limbs but still no creation of limbs or genetically growing more limbs and passing on the traits.
http://www.news.wisc.edu/7783

Ok this is a money shot. Page 4 starts the good stuf. The good doctor explains how nubs start that will eventually grow into limbs. Though he states alot of the theores don't hold water.
http://www.ijdb.ehu....03078/ft573.pdf

Now I'm gonna give alot of assumptions on this one that I know there aren't asnwers for. I'm gonna assume it's possible to grow additional limbs through a genetic mutation and that this mutation can be passed on to offspring. Even though I've NEVER seen any evidence of it. But for the sake of the argument, let's assume this.

So I am told to believe, that one single organism has a wild mutation and is so successful that it passes it's genes on and over time surpasses the billions of other organisms of the same genetic material as the mutants parents? The odds are too small to be measured.

Let alone the fact this must have happened more times that what could be possible through the above small chance. It's a paradox that needs to be pointed out. A single organism mutating and passing that on to grow additional limbs, lungs, sonar, wings, and so on is mathamatically impossible.

Plus how does an organsim accidently grow some nubs and have the advantage to survive and pass them on unless these mutations happened ALOT. Here's a mutated organism with some nubs, oops he got eaten. End of limbs.

But if mutations happend frequently enough for all these mutated evolutions, than why haven't any fundamental evolutions or mutations happend within the last 250 million years? Four legged animals remain four legged animals.
http://www.ucmp.berk...n/silurian.html
http://www.ucmp.berk...an/permian.html The biggest mass extinction so far up to that point. All these mass extinctions, yet all these mutations causing evolution. Where are all these mass mutaions within the last 50 million years?

It's like evolution and mutations slowed down to a crawl. Unless it's not evolution (in it's current form) that changes these organisms. Maybe thier is a deeper factor.

But that's not what happened. Limbs happened on a MASSIVE scale during the cambrian times (400+ million years ago).
http://www.ucmp.berk...brian/camb.html

Yet
http://www.ucmp.berk.../paleozoic.html
http://www.ucmp.berk...ordovician.html

there two mass extictions.

When you take into account two mass extinctions during that period and the massive mathmatic improbabilities of mutations occurring and passing on thier genes, you can now understand why theory of evolution has seriously big holes in it.

It actually only holds water on a small % of what happened. Not enough for me to claim it as fact. And that's why I don't think it should be taught as cold hard facts when in honesty it's easily disprovable.

IMO teaching it should include alot of IMOs, it is our belief, and mention the massive oddities that cannot be explained. But that's not that way it's taught, only cold hard fact without mentioning the massive flaws in it.

In addition to micro-evolution (as I'll refer to it's relevancy) I can only surmise the existance of something deeper, some large macro force that made these massive changes happen. Maybe it was condusive to the environment of the planet.

Maybe alot of a certain chemical was in a certain place early in the earth history to actually produce mass mutations. But it would have had to produce the same mass mutations. But that's not really plausible either because you can't duplicate that today under any lab conditions.

You can't add a chemical compound to water and make a new species. So how did these mass changes occur? Not by random mutations. Solar flares? Unlikely. God? I'm not even going there.

So how did it happen?

[CodeCat]

OK, so when did it become aware of itself and how was the disconnect made between an organism (in your synopsis) of a pure reactive nature to one of concious thought? Unless what you are saying, which mind you I think you are, is, there is no such thing as true thought. Our make up is simply chemicals reacting to stimulous randomly (Once it stops reacting randomly it trancends its original form, no). I may be wrong in my interpertation of your view on what we are and what our true process is. But if our process originates at a chemical level I can only assume that thought does not reside in a chemical state or is actual awareness, conciousness or what ever you want to call it the mutation or catalyst of evolution? The concept is no more outrageous than the belief that chemicals or the primordial ooze contains the essence of awareness.

By the way CodeCat great response.

You're assuming there's a disconnect. I'd say there was a gradual increase of the state that we call 'awareness'. As the brain developed, more and more cells could be dedicated to processing the surroundings of an organism independent of the actions of the organism itself. Essentially it slowly gained an ability to 'think' about things around it rather than simply responding to it. This would have made things such as 'choice' possible since the switch was no longer a one-on-one switch. And with this, it could have also developed the capacity to store certain nerve patterns, making them part of the processing cycle and thus influencing future reactions. This gave the organism the ability to learn and improve on the fly, rather than rely only on the bonds that were formed at birth (i.e. instinct). The disadvantage was that anything learned would not be passed to the next generation, however the ability to learn certainly gave it an increased chance of survival over its peers.

So I don't think thought is something that should be seen as a separate thing. Thought is more or less the firing of nerve cells in the brain without (usually) a corresponding action elsewhere in the body. Essentially it's just 'internal processing' within the brain. Like I said, to make that possible, the brain must first be complex enough to be able to afford dedicating cells to that purpose. But there's no point where thought begins, neither for consciousness, awareness, etc. There are merely varying levels of these depending on the capacity of the brain to utilise internal processing. Awareness is therefore a result of our brain, not independent of it.

Of course you have to realise that the human brain is immensely (lol) complex. There are many factors influencing the nerve patterns, because you have to remember at the base level the exchange of signals is still conveyed through the release of chemicals between nerve cells. Chemicals from outside can therefore influence it, but also signals coming from nearby cells can. It's in such a way that everything in our brain is interconnected, and just about anything can directly or indirectly influence any other. Thought is therefore by nature very chaotic, and this gives lots of trouble in actually explaining what thought really IS. But it's not something that defines itself in opposition to something else, because there's no line.

[Calamity_Jones]

I think a good way to think about it is in terms of a computer, something we are all very familiar with. The brain is, of course, by far the most powerful processor, most expansive data storage device and easily the best graphics card that has ever existed. (Though some games are starting to look more real than reality O_o )

A computer is a big magic box with a screen, keyboard, mouse and speakers attached. Somebody who knows nothing about computers would understand the computer in terms of it's physical external hardware. Input and Output, stuff goes in from the keyboard and mouse, and comes out on the screen and speakers. A person can be summed up in similar terms, input and output, we have senses and we can manipulate the environment. That's the skin deep view, you don't need to know the workings, just that stuff goes in and other stuff comes out.

At the next level in our computer, we have the physical bits and bobs in the tower unit, the motherboard, hard drive, graphics card, power supply, RAM, cooling fans etc. We don't need to know how they work, just that they do work and they each carry out a function that compliments each other and allows the whole to operate... Our computer that eats input and spits out output needs these bits and bobs to do that, remove some of them and your computer won't work at all, remove some others and it doesn't work quite as well. Again, this is just like our bodies, we have organs inside of us, distinct components that all do a specific little job and all work in harmony with each other to accomplish the overall task of handling the input and producing the output.

Going deeper in, our hard drive contains platters, a reading head and magnets. Our mother board contains chips, heat sinks, card slots, wire connections etc. Same story as before, lungs contain blood vessels, alveoli, tubes etc. Again, all we need to know is that these parts define what that particular organs purpose is. The lungs are 'designed' to process air. Hard disk drives are designed to store information. We don't need to know how the oxygen is transferred to the blood stream or how the head reads and writes information to the disk platter. They just do their jobs.

Going in further, our Hard disk platter is a disk with a layer of magnetic material on one surface, manufactured to incredible tolerances. Our Mother board is a PCB, a plastic board with chips mounted on it, the chips are wafers of silicon planted inside a polymer body. Our brain is a mass of interconnected cells that can rearrange themselves and form an unimaginably complex network. We now know that to store information, our computer sends it to the Hard Drive and the hard drive records that information on a platter using magnetism. We know to a degree how our computer stores data. We know that our motherboard delivers the orders to other organs, asking for input and delivering orders to produce the output and it must be fed a supply of electricity to do this. We know that our brain is the central processor that deals with all of the input and output coming and going through our bodies, to do this it must be fed a concoction of chemicals, carried in blood that is oxygenated via passing through the lungs that operate by sucking air through tubes (which is in turn controlled by the brain and so the system works together in a harmonious network.)

Going in further still, the computer moves information around as a flow of electrons in an electrically conductive material. The structure of the metal is a lattice of ions surrounded by a "sea" of electrons, and shoving 10 electrons into one end will spit 10 out of the other end, thus allowing a flow of electrons, a flow of electricity and information. Our computer chip contains a silicon wafer, and the silicon wafer is in fact just a miniaturised circuit board containing millions of switches and components.

Now, we know how it's built, but how does it work? A computer uses at the most basic level binary language, on or off, one or zero. On top of that there's more complicated programming languages, and these are compiled into data that the computer is hard wired to understand and operate upon. Thus giving rise to phenomena like the operating system, and then on top of the operating system we have more complicated programs.

Now we know how our bodies are built, how do they work? We are programmed to assimilate information, that is how we learn, when we're born we're designed to learn stuff so that we can pick up language and learn to become part of our society. There are countless more complex things too, we're designed to get angry when somebody does something bad to us, we're programmed to take our hand off of the boiling hot pan we just grabbed and burnt ourselves with, we're programmed to fall in love and reproduce.

When you look at a computer and don't understand it, you see it as a magic box, just something that you plug in and switch on. You type on your keyboard and the letters appear on your screen. Magic! You don't know how it works, it just does its job.

When you look at a person, you see another being that can learn, make decisions, feel emotions, invent and imagine. Another person that has a personality and a mind like you. It's magic, you don't know how it works, but it just does!

My point is this, we, just like our computers, are nothing more or less than a machine. One is biological, one is not. A computer can take input, think about it and deliver output, just like a person can. The only difference is that we are much MUCH more complicated and advanced. When you look at our bodies, just like our computer, we are made up of countless separate little components, countless little things that are all wonderfully complicated in their own way and all work together to give the magical end result.

A bacteria is a very simple machine, a toaster is a very simple machine, they do very simple things. A human body in an immensely complex machine and it does immensely complex things. We can feel, understand, imagine, invent, talk, build societies, build civilisations and cultures. A computer can carry out millions of calculations every second, it can create complex interactive moving images on a screen, it can let you talk to people thousands of miles away instantly.

Finally, look at the history of computers, what was the first computer like? It was the size of a house and it could barely calculate two numbers multiplied together! Something a modern computer can do millions of times every second. Did our computer technology suddenly jump from huge room full of vacuum valves to a TFT monitor and dual core processor? No, over many years things got smaller, faster, cheaper and better. We went from valves to transistors. We made chips. Processors went from a few megahertz to many gigahertz. Computers went from there being 3 or 4 in the whole word to almost every person in the developed world owning one. Computer technology evolved, and it still is, it's getting better and better at an absolutely staggering pace. The first computer was not your modern desktop, but over time we have arrived at the point of the magic box that does all these wonderful things and most people don't know how.

Look at this, then this and compare it to this. You don't start with the modern shiny HDD platter than can hold mountains of information, that's at the end of the line. You get there in the end through many gradual small improvements, a punched card over manually moving levers, electronic transistors over a mechanical valve, a 300gb hard drive over a 160Gb hard drive. Things evolve because they are beneficial. We don't use floppy disks any more because they stored a tiny amount of information and took up lots of space compared to their capacity. We have evolved something that is an improvement, the CD, and later the DVD and now the Blue Ray and so on.

It's all so simple as long as you don't get blinded by that magic box. We're just machines, very complicated machines that can do many wonderful things and we got to this point through lots and lots of tiny little improvements over a very long time, and if it isn't an improvement, then the change doesn't persist.

Edited by Calamity_Jones, 01 June 2007 - 08:22 PM.

[Boomerang Python]

Oh nooooooooooo! Cry babies go hooome!

[olli]

i REALLY cant be arsed to read all of that but im sure it explain a lot

[anonymous]

You know i had this whole post done took me a long as time to write it. And would`nt you know it the page expired.
Long story short not going to even try and re-post it but i can tell you this codecat it would have blown your freakin mind......................

[Calamity_Jones]

That's why you copy it into a text document before posting just in case...

[Boomerang Python]

Cal has experience in these things...

[olli]

its happened to me numerous times- and its so frustrating

[MSpencer]

Well I still have to use a webproxy to even look at the Revora Forums, so I'm going to post now and clear up the gross misconceptions flying around here...

Allow me to preface my remarks by saying:
Movie Mutation = 100-legged giraffes
Real Mutation = Genetic changes in a population resulting in a change in phenotype.
Most of you guys use mutation in movie-terms, and believe that that's how evolution works. It's not. Discrete changes in organisms are only revealed after numerous generations, and unfortunately, we're all looking at the intermediates and finished products, thus contributing to confusion.

No I realise that, I just meant that evolution will never end and organisms will never perfect themselves, as a perfect prey becomes imperfect once the predator becomes more perfect. I know evolution isn't intentional.

evolution occurs because of mutations. which are causes by radiation and chemicals. if we wipe the cause of mutations completely off the planet. theoretically, scientificall, hypothetically...etc etc evolution would stop. but of course im sure some other weird and wonderful thing would happen, something that nature decides to throw at us.

Mutations are a consequence of having a gene pool, or even of simply having genes. DNA is not 100% perfect, mistakes happen, mutations form. Exposure to mutagens accounts for very, very small percentages of mutations in a population. The only way to stop genetic shifts in a population is to destroy the population, something which will have a genetic effect on everything that interacted with that population.

That's why evolution is a theory. Because it can't account for drastic changes in the developement of species. Things just don't grow extra limbs because of something called "common ancestry"

Even if that duck had baby ducks, they'd still have 2 legs. Excess legs are caused by imbalances of certain hormones during the embryo formation. Not genetically.

And, tacked on to common ancestry, evolutionary history.
I think you've come a long way since six months ago.

How did dolphins evolve echo detection? Some mutant dolphin sent out a sound wave and recieved it and passed it on to ALL the other dolphins through breeding it's genes? Impossible if you understand biology.

But you were doing so good...
Dolphins do not predate echolocation. In fact, echolocation is a sense which, I'm sure, could be practically traced back to the Cretaceous. Abilities and behavioral patterns develop through species over millions of generations, echolocation is one of these things.

The excess legs are due to e genetic mutation, possibly caused by hormonal imbalance (not gonna debate the reason of mutation here).

I disagree. Hormones are simply activators and facilitators. You will not find native hormones acting as mutagens in any organism on the Earth. Hormones simply direct the transcription of genes from the genome, and can also act as signal ligands to perform certain cellular actions (Or, alternatively, they stimulate the production of mRNA carrying the information for the synthesis of enzymes, which help to synthesize signal ligands).

Never the less, that characteristic would be part of the ducks genetic makeup. If the genes that cause the extra legs were dominant, the offspring would have that characteristic too.

Developmental change = no genetic change = no passing on to offspring.
That is, unless it is a genetic change. An over-presence of hormones will never cause mutation, and since there is no evolutionary history of four legs for ducks, it is highly unlikely that a normal genetic mutation will occur naturally.

Close but you're not quite there yet. Let's use your dolphins as the example here. You're right, one dolphin with a mutation wouldn't be able to pass it's mutation on to ALL other dolphins. It's mutation (if part of a dominant gene) would be pass onto it's numerous offspring, who would then pass it onto thier numerous offspring. This would eventually result in many mutant dolphins having a distinct advantage over the rest. The mutated dolphins would be able to compete much better against the other dolphins which would see a speeded increase in the population, whereas the non-mutated dolphins would lose out in competition and be slowly breeded out and weined out of the general population.

This would be true if dolphins independently developed echolocation, but they didn't. More correctly, this change as described above happened over the course of millions of generations through likely dozens of species and several clades.

Will continue the jihad when I get a chance tomorrow.

[Hostile]

Don't patronize me. I still have yet to find an answer to how limbs formed. And then additional limbs. We know mutations did not do it. So how did additional limbs form to even come to "common ancestry?"

How do organisms evolve if mutations really only explain so little? How do these complex changes occur?

Most importantly...

How did orgaisms form distinct biological functions? Such as appendages, lungs, organs, hair, warm blooded/cold blooded.

These functions simply appeared, they didn't evolve. How did they appear? Don't tell me over the course of millions of years. Tell me what method it used.

Mutations? Even if you isolate a population, and a species diversifies, it may be a seperate species but it's still the same genus.

What system does "evolution" use in the course of things to change itself if mutations are scientifically proven to not be the way? If you can answer that on a level I can understand, than you win.

[MSpencer]

How do organisms evolve if mutations really only explain so little? How do these complex changes occur?

There are mutations, and there are mutations. Mutations in the sense being described by these articles are essentially freaks of nature, things which are so statistically improbable that they so very rarely happen (And only on developmental terms). Genetic "mutations" (A misnomer when considered in the modern sense) are essentially the result of selection pressures on the gene pools of populations. When you have a prolonged pressure on a population's gene pool (Ideally represented as a normal distribution for a model population of over 1,000 organisms), you essentially force it in one direction by changing the proportions of genes in the population. We're talking bell curves for every gene, every locus, including every organism in the population. This is naturally a theoretical thing, as such a thing could never be practically accomplished without spending trillions of dollars running the genes of certain organisms, but ideally, this model holds true. Essentially, the actions upon these bell curves are the accumulated and generalized force of natural selection upon the population as a whole, while the bell curves are models of the genes being affected by these pressures.
Understanding of this very basic model is absolutely crucial to what will follow.

Forget what you know about mutations. Forget what you think you know of population biology. Forget what you know of organisms, individual organisms; instead, it is time to think in terms of populations.
Accumulated genetic changes result in speciation. This is simply a fact. Since this, unfortunately, is such a gradual process, we can't measure "Oh, this is a different species" after one generation by comparing mother and offspring and attempting to mate them, but a safe bet to determine if two different species are in play, you could always compare one organism 1000 years prior to the current organism, attempting to breed them (Naturally, impossible), or you can attempt to breed a current organism with an organism from another, isolated population to determine the organism's true identity. However, most cases of speciation are rather clean cut, we see organisms fossilized from 500 million years ago, we compare them with older specimens or similar specimens, and if they look significantly different, they were probably different species. There are about ten ways to determine the identity of an organism in species terms, and they all depend on what branch of biology you're in. Biochemists look at biochemical makeup, geneticists look at genetic identity, developmental and general biologists (As well as underexposed students) are trained to look at the mating potential of two generations, and paleontologists look at skeletal structure and overall physical characteristics. None of these are necessarily correct, they all have their flaws, and that's why identifying species is constantly debated and is something constantly in the news.

Now, let's go back to the pseudo-mathematical model for population stresses. With enough accumulation, these organisms of a population will be so sufficiently different from their previous "configuration" that they will exhibit different phenotypes and significantly different genotypes. That, in a nutshell, is evolution; that eventually, genetic changes experienced by a population through natural selection will, after a period of time, produce two or more distinct species. Naturally, these species, if restricted to about 1000 organisms, would probably die out, but when you're talking about massive populations of 10,000+ organisms which span geographic areas with a climate and environment receptive to the new population, it is very possible they will become a common species.
The most important part of this is to remember that there is no point at which an organism ceases being a member of its previous species. Instead, this change is gradual, very gradual, it takes time, and comparing two organisms side by side from the same time and same population, you will not be able to notice any clear cut differences. This is because the word "mutation" is contorted in its current usage. There are no mutations. The mutations are mutations on a population level, they are mutations in the entire genome, and in this context, mutation means shift. Mutations described by these articles do not exist in an evolutionary sense. Absolutely, completely, undeniably, these are not mutations in the evolutionary sense.

That puts that issue to rest.

Now, on to the point about limbs.

How did orgaisms form distinct biological functions? Such as appendages, lungs, organs, hair, warm blooded/cold blooded.

These functions simply appeared, they didn't evolve. How did they appear? Don't tell me over the course of millions of years. Tell me what method it used.

You seem to cling on to this argument for dear life, perhaps because it is the only bit of ammunition you have left, but either way, you put far too much faith into it.

Organisms do not form distinct biological functions. Stop thinking of species as different things, instead, think of species grouped together in things more than genus. We have the unfortunate disadvantage of being unable to imagine things outside our current frame of view, essentially meaning that we have very little sense of rates of change over time. It is important to note that a salamander did not pop out of the ocean one day produced by the union of two members of its ancestral species. Organs and physical features are gradually developed by genetic shifts. Would you like me to explain how the liver developed? I couldn't do it in terms you'd accept, because you're looking for something to have happened overnight, but it unfortunately did not. These things did take hundreds of precursor steps to reach where they are today in certain organisms. The most suitable example is the reaction to direct stimulus (I.E. touching). There are certain organs which regulate that sort of sense, and you can track it back through hundreds of different clades. Each of them independently developed this sense through different means, but eventually, several modern examples pervaded, one of them coming from a group of fish in the Devonian era, a group which we share a pretty close linking to.
Unfortunately, I do not have knowledge of every single organism ever. Hearts, however, developed as an early method to circulate nutrients, and ended up favored by aerobic respiration (Which is favored very highly by chemistry) thus resulting in their increased propagation and sophistication. These functions certainly did not just appear, they came from precursor organs which served a similar function in precursor species. On the simple multicellular level, proto-organs would likely be visible, or similar functions would be performed by certain slightly differentiated cells. Unfortunately, we're well beyond simple multicellular organisms, in fact, one of those species is one of our ancestors, but you can certainly see the same, or similar, functions being performed in these types of organisms (With what little we know of them). It is important to note that bacteria did not suddenly morph into complex multicellular organisms, even modern eukaryotic cells are rather new things. The need for the processes to occur have always been there. There has always been a need for a filtration system, and the mammalian liver is a new thing. Previously, this role would be fulfilled by simple differentiated cells, now, it's a structure consisting of differentiated cells. Arguably, several hundred million years ago, these livers would be quite a bit different, perhaps a bit more or less complex, but the principle remains the same. Perhaps a bit less than a billion years ago it was still on the dozens of cells level, and the proto-organ was quite a bit less complex, but it still certainly served the same purpose, filtering toxins.
Organ development is similar to the evolution of complex organisms, they're both intertwined. As organisms complexified and began to get larger with even more demands on their organs, the organs kept up. It's a lovely case of co-evolution, and eventually, and naturally, after a few hundred million years ago, a single cell serving as a filtration system would form a liver. The same is true of all the other organs, the purpose was always there, it was just a gradual movement from differentiated organelle, to differentiated cell, to differentiated tissue, to differentiated structure. Welcome to the confusing and continuous world of evolutionary biology.

And if you find this explanation to be insufficient, then I don't know what to do except to be patronizing. Things don't happen overnight in the field of biology, I've offered essentially the "right answer" (Really just the current model), but if you find this insufficient, I recommend you re-examine your view of the evolution of organisms.