This is the paper to read: Palazzo & Gregory's The Case for Junk DNA. It clearly and logically lays out the complete argument from evidence and theory for the thesis that most of the genome is junk. It's not revolutionary or radical, though: the whole story is based on very fundamental population genetics and molecular biology, and many decades of accumulated observations. And once you know a little bit of those disciplines -- you don't need to be a genius with a great depth of understanding -- the conclusion is both obvious and in some ways, rather trivial.
Here's that conclusion:
For decades, there has been considerable interest in determining what role, if any, the majority of the DNA in eukaryotic genomes plays in organismal development and physiology. The ENCODE data are only the most recent contribution to a long-standing research program that has sought to address this issue. However, evidence casting doubt that most of the human genome possesses a functional role has existed for some time. This is not to say that none of the nonprotein-coding majority of the genome is functional—examples of functional noncoding sequences have been known for more than half a century, and even the earliest proponents of “junk DNA” and “selfish DNA” predicted that further examples would be found. Nevertheless, they also pointed out that evolutionary considerations, information regarding genome size diversity, and knowledge about the origins and features of genomic components do not support the notion that all of the DNA must have a function by virtue of its mere existence. Nothing in the recent research or commentary on the subject has challenged these observations.
The whole ENCODE debacle, in which hundreds of millions of dollars was sunk into an effort to identify the function of every bit of the genome, was a PR disaster. Larry Moran asks how Nature magazine dealt with the errors; the answer seems to be with denial. Authors of the ENCODE report are claiming they were "misunderstood & misreported" and that they aren't "backing away from anything".
I'm not too dismayed that science journalists didn't understand how the claims of ENCODE conflicted with evolutionary biology, since I don't expect journalists to have the same focus on the science (this is not a knock on science journalism; I have a lot of respect for the good practitioners of the art, but just that they have different priorities than the working scientists who have to deal with the background details). But what really shocks me is that big-name genomics researchers, people who get awarded lots of money to study the structure of the genome, don't understand the fundamentals laid out for them in the Palazzo & Gregory paper. It's not that I expect every scientist to know the entirety of a gigantic field -- heck, I get confused and lost every time I read a bioinformatics paper -- but these are scientists paid in big money and prestige to study genome function who don't have a grasp on the evolutionary constraints on genome function, which seems to be a rather critical omission. And these scientists without a clue get elected to the Fellowship of the Royal Society.
How does that happen? I had this fantasy that science was a meritocracy and that great scientists advanced by having deep knowledge and doing great work, but it seems another way to succeed is leap into a new field and bamboozle everyone with technology.
I am so disillusioned.
You write: " whole ENCODE debacle, in which hundreds of millions of dollars was sunk into an effort to identify the function of every bit of the genome, was a PR disaster. " It is not clear to this reader whether you think that the the money spent on ENCODE to gain knowledge was a waste (although the use of "sunk" implies that). Palazzo & Gregory use the ENCODE data to support their thesis. Interpretation bias is one thing, but the data itself appears to have considerable value. One question that also needs to be addressed: is there a variable, controlling mechanism that allows genome sizes to vary so much, or does this happen randomly?
THE SAME HOLD TRUE in the field of physics and that which pertains to the shape and structure of the atom and molecule. I believe 99.9 percent of physicists can not detail a single molecule beyond 4 to form a 3 Dimensional model. They may try to draw or detail a single representation but then try to put them together. they can't. Because the information taught is a lie. I have detailed every pure element up to magnesium in a 3 dimensional mass. no one has this model representation as far as I can find. I can construct it or tear it apart and and still maintain purity.
The reason why they don't highlight the so-called junk DNA, is that it contradicts our current understanding of evolution (Neo-synthesis) type, which we are led to believe is the only theory we have. It isn't, and the newer discoveries in natural science, particularly biological fields that aren't evolutionary biology as they adhere to Darwinian theory for their interpretations, are getting it. Wake Up everyone. It's all in the JUNK. for more info see http:diggingupthefuture.com
Sorry if my comment is seen as off topic and is not comprehensible due bad English translation and different world view:
Junk DNA never will be deciphered while the scientific world view keeps separating cosmological evolution from biological evolution. The first 300 genes of the first DNA of the first eukaryotic cell not only has registered data from abiogenesis events, but, also all data from 13;7 billion years of cosmological evolution. That's what is suggesting the models of Matrix/DNA Theory, after the suggestion that DNA is merely the biological shape of a system that arose together with the Big Bang, encoded into light waves. DNA is the biological shape of a universal matrix, which formula is showed by the theory, and the matrix is the essence of atoms, galactic systems, as DNA is the essence of all biological organisms. Then, the data inserted into DNA contains the data that came from its ancestor, the matrix, and this data is the junk DNA. For composing an astronomical system from a nebulae of dust the matrix applied a certain mechanism, which is applied again for composing a human skeleton from a nebula of cells called "morula, blastula", but, since that skeletons does not need certain galactic results, this mechanism from the matrix is not functional at DNA, despite that the mechanisms is still there, waiting for a chance if a new species needs it for survival.
There is no way for deciphering the junk DNA and founding the connections that performs functions while the scientific knowledge ignores cosmological evolution and Astronomy , as Physics and Math are suggesting wrong atomic and astronomic theoretical models. The Matrix/DNA Theory's logistic offers the foundations for correcting these mistakes.
Also, you seriously cite the Whirled Nut Daily? What next, the Weekly World News?
BTW, you forgot the //.
The first 300 genes of the first DNA of the first eukaryotic cell
How would anybody know what those were? And what does "the first" even mean?
Excuse my ignorance of genetics and my high school level understanding of biology, but I share Albert Hall's confusion with regards to ” whole ENCODE debacle, in which hundreds of millions of dollars was sunk into an effort to identify the function of every bit of the genome, was a PR disaster. ”
Isn't learning that a majority of the genetic code is junk as important as learning that it has a direct function? It doesn't seem (to me, at least) like a waste to learn which parts of a genome "do things" and which don't, because I suspect that the "junk" actually serves a purpose.
My un-educated suspicion is that the so-called "junk" DNA is the primary and nececessary source of mutations. Without a large component of the genome available for random re-arrangements, evolution would grind to a halt. Learning the size of that "genomic scratch pad" seems a pretty important thing to know. At some point, does the ratio of "junk" to useful code create too many or too few mutations? Is there a "sweet spot"? Is that ratio itself selected through natural selection? Has it varied over time? Does it vary with the complexity of the organism?
Like I said, my understanding of biology is pretty limited and perhaps this is a stupid suggestion. If those questions have already been answered, I would love to be pointed in the right direction to read about those answers.
The paper linked to in the OP is in open access! Everyone here should read it. :-)
Isn’t learning that a majority of the genetic code is junk as important as learning that it has a direct function?
Sure, but it was already known that most of it can't have a function.
It doesn’t seem (to me, at least) like a waste to learn which parts of a genome “do things” and which don’t
Unfortunately, ENCODE didn't do that; it only let us learn to which parts any protein ever binds, and – as the paper explains – it's not at all surprising that pretty much all of the genome occasionally binds a protein.
My un-educated suspicion is that the so-called “junk” DNA is the primary and nececessary source of mutations. Without a large component of the genome available for random re-arrangements, evolution would grind to a halt.
Most mutations are not rearrangements, they are point mutations – substitutions, deletions or insertions of a single base pair, caused by the fact that DNA polymerase isn't perfect.
Learning the size of that “genomic scratch pad” seems a pretty important thing to know.
Behold the onion test, prominently cited in the paper.
To David Marjanovic
Thanks for reading, replying with useful comments.
You suggested the site: "http:diggingupthefuture.com"
It means that you did not understand the Matrix/DNA Theory. There are big differences between these two theories, and the people from this site does not know/does not like Matrix/DNA Theory. While the "Darwin Delusion" try to debunk evolutionary theory, Matrix/DNA keeps the foundations of Darwinian 3 mechanisms (VSI) but ads more 4 mechanisms ( coming from cosmological evolution) for explaining the whole history of biological evolution.Matrix/DNA is not ID.
You: "Also, you seriously cite the Whirled Nut Daily? What next, the Weekly World News?"
I don't understand what are you suggesting here, maybe due our differences about world view/culture, or merely, my fault to understand English. When I say "scientific world view", I am based on the very fact that Matrix/DNA Theory is suggesting that the modern academic official scientific method has been driven by a specific way/mindset, in the same way that the scientific community aligned with ID approaches natural phenomena by a specific method. Both are different from Matrix/DNA method, so, we have at least three different world views.
You said: "How would anybody know what those were? And what does “the first” even mean?"
My answer: "If we does not know the informations "encoded" in the DNA of LUCA ( the Last Universal Common Ancestor), evolutionary theory are at the position that are astronomers today, who does not know what caused the Big Bang. ID has its theory: the source of those informations was God;the Darwinian modern synthesis has its theory: it was by chance. Matrix/DNA has its theory: the universal past history of 13,7 billion years.
It is comprehensible that you think a reference to the first "living being" as meaningless. Matrix/DNA does not think same way, because Matrix/DNA does not says "living being", but says "biological system", for differentiating from other natural systems, like atom system, astronomical system, etc. For us there is no external causes interfering on the long chain of causes and effects coming since the Big Bang, as would be events by pure randomness/transcriptions errors, etc.
Our idea is based on the discovery of a fundamental pattern existing inside all natural systems. This pattern is suggested as a diagram/software formula, called "the Matrix/DNA". This formula changes the current Academic Biology method, approach and mindset about natural biology. I am not seeing that I believe that Matrix/DNA is right and the academic mindset is wrong, since that both are theories to be tested and proved or debunked.
The mention to the "first DNA" is about the complete DNA that emerged with the first emerged complete biological system, more appropriately, the first real and complete cell system. One can not understand this mention without knowing what's a real complete natural system, which is the Matrix/DNA formula. Cheers...
You write: ” whole ENCODE debacle, in which hundreds of millions of dollars was sunk into an effort to identify the function of every bit of the genome, was a PR disaster. ”
How could one identifying the function of something, if it is not working, not expressing its function, just now?! Do you think that the genetic informations for "wings", or insect's antenna, are not in the human DNA? Ok,maybe we don't have scientific data for proving they are there, but, it is not proof that they are not there. Maybe they are there, at the middle of the so called "junk DNA", not being expressed, not functional just now, but... could be expressed if a new species needs it. The Matrix/DNA's models and results are suggesting they are there, despite not being expressed. But the suggestions from Matrix/DNA Theory seems "weird" to modern Biology view point. As it is weird the suggestion that the informations for making a new stellar system from inter-stellar dust must be there, encrypted at human's DNA, not being expressed because this is not the appropriate environment/moment for expression.
The unique way for grasping possible useful informations at the "junk DNA" regions, is the whole understanding of Universal Evolution, not merely biological evolution... if Matrix/DNA Theory's results are more true than the current scientific mindset.
I will suggest an example for explaining why current biological method is not understanding "junk DNA". The long repetitive chains of AAAAAAAAA, are not DNA's errors. They have registered information from cosmological evolution, which is biological ancestor like reptiles and/or bacterias are human ancestors. It happens that any evolutionary top species at cosmological evolution stands at the top by billion years, instead the million/thousands years that biological shapes stands at the top. It happens that DNA is a synthesis of history and shapes. History is necessary for DNA registering the whole universal evolution of the unique natural system that is coming evolving since the Big Bang. This system had, at cosmological evolution, its "genetic blueprint", called "universal matrix", which has evolved into DNA at biological evolution. So, atoms systems and astronomical system also have their "DNA", counterpart, which is suggested by Matrix/DNA Theory as a formula in shape of diagram/software.
The evolution of this universal system is performed by cycles of degradation of the last shape, mutation and transformation of its "matrix/DNA", growing of a new shape/species. At the transformation stage, the matrix is fragmented, rearranged into slices, then, the several slices converges into a unique system by symbioses. If the matrix does not registry every slice and its evolutionary history, the modern DNA would transmit "irreducible complexity", with no links among its data.
Then, for registering the periods of transformation of cosmological evolution ( based on billion years), Matrix/DNA needs to insert repetitive letters about the time that refers to evolution of each respective slice, a time that the others slices were evolutionary stopped/ waiting.
Try to write cosmological evolution into a biological DNA, which is merely a micro-cycle of the universal matrix evolution, without inserting repetitive pauses relating to the astronomical time... it is impossible.
By the way, I understand that you will not understand my post because you learned to separate cosmological evolution from biological evolution and does not know the evolutionary links between them. In another hand, maybe my models of those evolutionary links are not the right ones, or maybe they are far away from being completed. So, my intention here is alerting you that the "junk DNA" is not for our understanding facing the poor universal evolution data we have today.
You suggested the site: “http:diggingupthefuture.com”
Quite the contrary! Maria O'Hare suggested it (her own site) in comment 4, and I commented "too long; didn't read" and ridiculed it for citing extremely unreliable sources.
My answer: “If we does not know the informations “encoded” in the DNA of LUCA ( the Last Universal Common Ancestor), evolutionary theory are at the position that are astronomers today, who does not know what caused the Big Bang. ID has its theory: the source of those informations was God;the Darwinian modern synthesis has its theory: it was by chance.
1) No, no, we have a pretty good idea which genes LUCA had. It just doesn't make sense to talk about "the first 300" of them. In a circular genome, where do you start counting? Or do you mean the oldest 300? Not much progress has been made in figuring out which ones those might be.
2) No, the theory of evolution doesn't postulate chance alone. Mutation and drift are random, but selection is not – it is determined by the environment!
It is comprehensible that you think a reference to the first “living being” as meaningless.
Whether it's meaningless depends on whether you've first defined what "living" means, because life is a matter of degree. However, LUCA was not the first living being under any definition. Many genes found in organisms today come from duplications that can only have happened long before LUCA.
How could one identifying the function of something, if it is not working, not expressing its function, just now?!
The ENCODE project defined "this piece of DNA has a function" as "anything ever binds to it". This way, it was able to identify the "function" of lots of junk that has no real function at all.
Do you think that the genetic informations for “wings”, or insect’s antenna, are not in the human DNA? Ok,maybe we don’t have scientific data for proving they are there, but, it is not proof that they are not there.
Nope – it is well understood which genes work in which ways to make insect wings or bat wing membranes or feathers or insect antennae, and those things – those exact forms of the genes with those exact promoters, enhancers, silencers etc. – are not present in the human genome. The entire sequence of the human genome is known, and those things are simply not there.
I will suggest an example for explaining why current biological method is not understanding “junk DNA”. The long repetitive chains of AAAAAAAAA
No such things occur in junk DNA.
They have registered information from cosmological evolution, which is biological ancestor like reptiles and/or bacterias are human ancestors.
Evolution means descent with heritable modification. Organisms can evolve, so can languages and other cultural features to some extent, and so can computer simulations of the above. That's pretty much it. Maybe universes can evolve, but understand that I'm talking here about the multiverse as a sort of population where universes reproduce by making black holes, not about the contents of any particular universe. Interstellar dust does not reproduce, so it does not inherit or descend from anything; logically, it cannot evolve as that term is used in biology.
any evolutionary top species
There is no top in evolution. There is no "up", no "higher" or "lower", no "forward", no "progress". Mutation and drift are random, and selection goes wherever the environment makes it go – in any direction.
So, atoms systems and astronomical system also have their “DNA”, counterpart, which is suggested by Matrix/DNA Theory as a formula in shape of diagram/software.
But what would that be?
DNA is a real, tangible thing. Proteins (such as the transcription machinery) bind to it by electrostatic attraction. What do you postulate as your cosmological analogue?
Then, for registering the periods of transformation of cosmological evolution ( based on billion years), Matrix/DNA needs to insert repetitive letters about the time that refers to evolution of each respective slice, a time that the others slices were evolutionary stopped/ waiting.
And then a random mutation comes and destroys the repetition. Oopsie.
The only way a DNA sequence can remain unchanged over billions of years is if natural selection removes those individuals that have mutations in that sequence. For this to be possible, the sequence must do something. If it's just junk, mutations in it are invisible to natural selection, so nothing stops them from happening and accumulating.
(This is also why creationist frontloading is impossible. But I digress.)
To Davis ( thanks, this is a good test for Matrix/DNA Theory)
You: "we have a pretty good idea which genes LUCA had".
Theoretically, since that LUCA and its DNA has no observable fossil. And our difference here is that yours "LUCA" should be microscopic and existed at Earth surface, while my LUCA should be astronomical ( the system that Earth belongs to), so never existed here. Yours theory think about life emerging at one specific point at the planet from which arose the diversification that populated the planet; my theory suggest that this point is the whole galaxy which collapse by entropy populated planets causing diversification. Who is right? No known scientific data for judging it today.
You: "In a circular genome, where do you start counting? Or do you mean the oldest 300?"
The genome is about informations of a system. Primordial systems were built by penetrations of light waves coming from or before the Big Bang. Light waves propagates and collapses in space like yours own body propagates and collapses in size/space/time due a life's cycle. It is because the sequence of vibrations/frequencies seen at electromagnetic spectrum are the same intensity of energy of any other system under a process of life's cycle. So, primordial light waves had the force, the dynamic, for imprinting life into inertial matter. The method used by nature for creating systems is applying this dynamics of lifecycle through light waves over an initial species of body. The different frequencies leads the bodies changing their shapes. After that each shape connects to its neighbour shape by symbiosis, the final result is a new functional system.
But, the evolution from astronomical systems into biological systems was performed by spreading the bits-information on the air, so, at a planets surfaces first are composed slices, lines, till the symbiosis between the slices becomes a whole new system, when the "lines" becomes circular. So, the primordial biological molecules or organisms here had RNA//DNA in shape of lines, opened circles. The question if the primordial DNA was the oldest or the newest does not matters: it is dependable of what point you begins to narrate evolution. I use starting from now, so, the oldest DNA is just the nowaday DNA.
You: "2) No, the theory of evolution doesn’t postulate chance alone. Mutation and drift are random,but selection is not – it is determined by the environment!"
Since that the primordial environment ( be it the Big Bang or prebiotic Earth was produced by chance and randomness) - by yours theory, not mine - the whole subsequent process is ruled by chance. I understand that selection - if it is produced by the environment - it must be an ordered ruler/process, but, accordingly to yours theory, the producer of selection is an environment produced by selection from a prior environment, which was produced by chance.
My method has lead me to suspect that this Universe is merely the stage where is occurring a natural genetic process of reproduction of the unknown thing that produced it...
(Sorry... I will come back commenting yours other issues...cheers)
the whole galaxy which collapse by entropy populated planets causing diversification
I don't understand what that's supposed to mean.
Light waves propagates and collapses in space like yours own body propagates and collapses in size/space/time due a life’s cycle.
It is because the sequence of vibrations/frequencies seen at electromagnetic spectrum are the same intensity of energy of any other system under a process of life’s cycle.
Sorry, this is word salad. It doesn't mean anything. You've taken a bunch of technical terms and arranged them at random. There is no such thing as a "sequence of vibrations/frequencies seen at electromagnetic spectrum", for example!
Please explain what you mean. Learn what the words you use mean before you use them.
But, the evolution from astronomical systems into biological systems was performed by spreading the bits-information on the air, so, at a planets surfaces first are composed slices, lines, till the symbiosis between the slices becomes a whole new system, when the “lines” becomes circular.
Since that the primordial environment ( be it the Big Bang or prebiotic Earth was produced by chance and randomness
Well, and the laws of physics...
To David: "This ( my general theory about the world) is word salad...
My friend,...that's funny...Yours and all world views, including creationism, "are word salads". You had picked up the words "protein", "molecules", RNA, etc., - which all them are merely a bunch of atoms - and made a salad called "abiogenesis". Like Christians picked up words as "origins", "death", "soul" and made another salad, called "christianism". I picked up another bunch of words, like "waves of light", "natural systems", "life's cycles", and got a salad, with another different taste. The Universe is relativistic, it has several faces, each one for fitting the taste of the customer observer. We have maybe 10% of pieces for trying to see the final picture, as those jigsaws. Each one makes its preferred arrangements of these few pieces, getting a poor tasting salad, which are not - of course - the best preferred salad by the Universal Nature.
I think that the evolution of human mind is dependable of the debate among these different interpretations of the same natural phenomena. I am very interested to learn every different world view, included yours, that is the cause every day I try to read the new peer-reviewed and published scientific papers. As I like to go to Amazon jungle asking to natives what they have learned lately. If you stop a debate because you see others' world views as word salad - they really are - you never will see the faults of yours investigative method, so, these faults are growing and you are going far away off the beam - the real natural universal world. Krauss is already there, with his "Something from Nothing", which is an evident absurd, but he lost the control of his mind, like any fundamentalist deist. Or Richard Dawkins saying that genes ( merely a bunch of atoms) has the tendency ( a purpose) for its own reproduction, doing the antropormofation over genes. Or Steven Hawkins seeing ghost monsters called black holes in the sky and advocating impossible natural events as "extreme singularity". But... the majority of people indoctrinated by this virtual culture that dominates the scholar curriculum accepts this word salad as a good taste. Same way was happened at the Middle Age with the scholar curriculum elaborated by a virtual culture coming from the Church.
Who is invading and tasting, observing the invisible and untouchable ( to ours natural human sensors and natural brain) by yours investigative method is electro-mechanic tentacles, the sensors linked to an electro-mechanic brain, and through "computational simulations"is that brain that are thinking the world for you. They are discriminating data, selecting the eletro-mechanic face of any natural phenomena and ignoring the others faces of the same phenomena, like ignoring the actions among the hierarchy of systems. But you can not perceive this trap that you are falling into, alone, if you don't go to the middle of the brute and salvage nature for taking a shower from the real world. For instance, the astronomical and atomic systems' building blocks are visible electromagnetic into solid and gaseous states of matter, so, the electro-mechanical brain can grasp this aspect of atoms and galaxies, but... yours atomic and astronomical models can't show in these models where and how were the forces and elements that evolves into life's properties. The natural brain at the middle of the jung that knows the same real data that you know produces different atomic and galactic theoretical models which includes those forces and elements at less evolved states. Then, my atoms and galaxies has a cover of biological organization of matter, which never will have for humans brains that were replaced by the electro-mechanical brain. Who is right? Of course, both are wrong, non-complete, because these brains and theirs sensors can not understand the final thru (if there is one), I know that my models are far away from the final truth models, but, I don't know if my salad or yours salad is the most similar to the preferred salad of the universal nature.
The question is not which human produced salad is the thru, but, it is which is the salad that fits the taste of Universal Nature. And we don't have enough data for any scientific statement here. It is better for me that I continuing to testing my salad making comparisons to yours salad, and I am grateful that you are making efforts for elaborating a different salad. I can perceive and correcting some mistakes.
We are inside the same boat, navigating a dark unknown world. We say that "we must go to North", I say that "we must go to South". The deist says "we must go up to the sky", while the materialist says "I think that we must go down.." The best solution is sharing the boat into four boats, each one goes to its preferred direction. But the secret of the our success is dependable if we keep the communication, the cellular phone working. - "What are you seeing there? What have you finding?"
Don't do that, go alone straight to North, and if the North is the wrong way, you are lost forever. I know: you will not make it, because you think I am totally wrong. That's why all prior civilizations, emperors, have been destroyed by the real natural world.
Me: "It is comprehensible that you think a reference to the first “living being” as meaningless."
You: "Whether it’s meaningless depends on whether you’ve first defined what “living” means, because life is a matter of degree. However, LUCA was not the first living being under anydefinition. Many genes found in organisms today come from duplications that can only have happened long before LUCA"
Me: "It is very difficult for understanding a new world view that we never knew/imagined before.First we need trying to know the other's definitions of words. And it is very difficult to communicate an unknown world view by the language of the receiver. We agree that "life" is a matter of degree. We agree that LUCA was not the first living being. We agree that had genes duplication before LUCA. So, what's our problem? I never thought about this problem of "talking same thing" but thinking that the other is talking a different thing. And, really, we talking different things. Different interpretations, different meanings, different theories, about the same real facts.
We had established the age of 18 for a person driving a car, 21 for buying cigarettes and alcohol..separating in a time scale the adult and teenager shapes of a human body. This method works for social arrangements, it works also for separating biological systems shape from non-biological systems shapes, because the evolution of a unique universal system has obeyed the process of life's cycle that the human body obeys. Our problem is our difference of beliefs about "who or what has ruled those differences among degrees", because the ruler is a hidden variable: neither me, neither you, can show it. You says it is natural selection produced by environment, I say it is natural selection produced by the natural process of life's cycle, which produces different environments. My classification of degrees is based on the different known shapes of a unique and same natural systems that has evolved since the Big Bang. So, theses shapes of a unique system are: 1) eletromanetic level as particles and atoms systems; 2) electro-magnetic plus the gaseous and solid states of matter composing astronomical systems; 3) electro-magnetic plus the gaseous, solid and liquid states of matter composing biological systems. There is the quantum level, and now the consciousness level, but, these levels are still full of metaphysics, let's us forget them here.
If my method of classification will be proved the best one, the differences of degrees among natural systems obeys same rules as our human body obeys under the process of life's cycles. I mean: our body changes shapes, from the initial morula/blastulae shape till the cadaver shape. Makes it any sense to say "the first adult of a human body" when referring to its lifelong vital cycle? Of course, not, so, it not makes sense saying "the first living being"... There is no a fixed point in time/space for separating the adult shape from the teenage shape. But, for easing our tentative to fix these different shapes into a graphic scale, we can take "the male first sexual ejaculation as the fixed point starting its shape as adult". So, I have took the first biological system's self-reproduction as the first real and complete "biological system', aka "living being". Because only here, at the first complete cell's system, I can identificate all universal systemic functions and working I can't see them at prokaryotes, virus, archaeans. It is merely a resource for better locating events in a time scale. Like the adult's properties were existing at less evolved state at the teenager shape, the biological systems properties were existing at less evolved state at the Earth/and its astronomical systems shape. By the way, I think that debate about our different concepts must be avoided, now is time for debating ours different interpretations focusing on real natural phenomena.To me, it seems that was a first real and complete biological system (aka living being), the eukaryotic cell, because it was the first system at earth that had all seven natural systemic functions. The others ancestors systems at earth were missing functions, were not complete working systems.But, then, you need know my "theoretical" model of a universal natural system.
Me:"How could one identifying the function of something, if it is not working, not expressing its function, just now?!"
You: "The ENCODE project defined “this piece of DNA has a function” as “anything ever binds to it”. This way, it was able to identify the “function” of lots of junk that has no real function at all"
I agree that the ENCODE project is not able to define that "this piece of DNA has a function", but i also think that you is not able to say that "this piece of DNA has no function". We have no enough scientific data for defining it now. I will explain:
Do you think that the bone skeleton of our body has any function in relation to our brain operations? The answer here must be the answer for the role between junk DNA and functional genes.You are free for choice.
Genes functions mutates, evolves, as everything natural does. Junk DNA is the skeleton of functions developed into functions of working genes. They are about the states of these functions billions years ago. I don't know if taking out the skeleton of my body, my brain still will works... but I know that I don't wish making such experiment.
There are systemic universal level of functions for doing the skeleton of the Universe ( galaxies as its cells), they are registered into the DNA, they have evolved a little bit for making skeletons of vertebrates, and they could be called for working again if the brain will need a new sensor. ( these are merely thoughts from Matrix/DNA world view). By the way, I think it is better spending money on new researches - the weird it can seems to us - than spending money making wars or luxury mansions.
Nature has discarded the tails of apes. We can grasp Nature's reason when remembering that we does not need climbing trees and tails are very bad for sitting and driving a car. But Nature has not discarded the junk DNA. Must be there a good reason: they are still useful, performing a function.
To David: “This ( my general theory about the world) is word salad…
Perhaps, perhaps not. I can't tell – because your presentation of it is word salad. That's what "This" referred to.
But Nature has not discarded the junk DNA. Must be there a good reason:
No, that's not how it works. There is no mechanism that could recognize junk DNA and cut it out; the only way to lose junk DNA is to wait for random deletion mutations, which may or may not happen more quickly than new junk DNA is generated by other random mutations.
Please, please, please learn some basic molecular biology before you continue. Walk into a university library (they're public where I come from) and grab a textbook, or perhaps start at Wikipedia.
Oh, something else that's important: if junk DNA is useful, why do different species have such crazily different amounts of it? Every hypothesis about junk DNA must pass the onion test.
And if you had read the open-access paper PZ linked to in the very first line of his post, you'd already know that.
"The Onion Test is about the local/type Nature skills for doing Nanotechnology" - from Matrix/DNA Theory.
First of all you need to familiarize with the reasoning that I have applied for 7 years at virgin Nature of Amazon jungle observing every natural phenomena, which lead me to elaborate this world view. Taking an onion ( or similar wild fruit) in my hands I ask: "This shape is similar to planet Earth: here we have a central nucleus, external layers like the geological layers.Is it merely coincidence? Or it means that the same laws, mechanisms, processes that Nature used for shaping planets were used for shaping onions? If so, where were these forces and elements at the state of the world before onions' origins? Let's me putting the model of that state over the table and search for them..." Ok, I finally found them, but since that my atomic, astronomic, and Matrix/DNA models, are merely theoreticals, these forces and elements, as every results, results must go to tests, accumulating evidences or finding a real proved scientific fact that debunks the whole idea.
You know that Nature applies nanotechnology long before humans origins, and my models are suggesting "since the first atomic nebulae at the Big Bang, forming stellars systems". Nature resumes all data from an adult human body 150 pounds and 2 meters into a microscopic genome, or a new baby with 6 ponds and 30 cm. And I need to create a word for natural reverse process, let's say "giantology".
If humans have advanced technology, they can put the whole data stored at Britain Library inside the head of a pin;if not, they will need a pin the size of the Empire State Building. With Nature is something, it is dependable of environmental materials, turbulences, and the easing for the free flow of bits-information.
It is easier to insert a entire galaxy inside a head's pin than a human body: the most quantity of galactic atoms are merely repetitions carrying the same information, when we need only one of each information.
How Nature inserts whole galaxies inside microscopical biological systems? As DNA has its building blocks ( nucleotides), galaxies have them also, you don't need to resume the entire galaxy, only its building block. And the galactic building block, despite being a complete system, is merely any astronomical body. The building block is a perfect closed system, composed by seven different kinds of astronomical bodies, but here we need apply the Heisenberg uncertainty principle, due the astronomical body is under the process of life's cycle ( it is obvious: Earth has not created from nothing the process of life's cycles that we see at her creation - the biological systems. Earth merely reproduced itself, its properties, as a astronomical system, genetically, nannotecnologicaly). You can not see an entire human body at space and time at the same moment: if you fix its shape just now in a point of space, as teenage or adult, you can not see its entire shapes developed at its entire existence. Primordial astronomical bodies were same thing, they was changing shapes, from initial "seeds" to planets to pulsars to stars, etc. LIke the cell's systems had two different method for formation ( the first was symbiosis, the second, it learned to self-replicate), so it happened with galaxies, making the differences between old and new galaxies). Heisenberg did not know that particles are under the process of life's cycle also, ( coming from primordial light waves), so, there is no "uncertainty" here, it is merely a relativistic issue. But, astronomers does not consider it also. I do, so, the difference of our atomic and astronomic models.
Inserting an astronomical building block ( which shape and functional configuration is exactly the shape and functional configuration of a lateral-pair of nucleotides, as suggested with formulas and pictures at my website) into microscopic dimensions is easy for Nature: it is enough applying degeneration by entropy over a star, the radiation emits its bits-information in shape of photons, which invades terrestrial atoms, driven them to reproduce the astronomical system.
For understanding what's the large regions of non expressed informations at the DNA into proteins, we need understand what is the meaning, the natural function of that bunch of atoms organized as proteins. But, then, it is necessary to look the theoretical model of natural perfect closed system, the Matrix/DNA. Proteins are a bunch of atoms invaded by photons coming from the stars, which driven those atoms to new connections, and reproduces biologically the external spherical systemic circuit. The entire circuit is broken into small texts, slices, that's the cause of thousands of different proteins. Proteins reproduces the invisible events and shapes between two systemic parts, like the invisible events/shapes between the human shape as baby and as adult. Proteins are related to waves of time, which becomes particles, the systemic shapes/parts, which are related to the dimension of pace.Now, let's go back to "junk DNA" and the onion test.
Why the onion's genome is larger than humans genome? Oh...my God: if you don't know, technology evolves also. So, it does natural nanotechnology. Billions years ago Nature was doing giants Empire State Buildings as genomes, today she learned about Earth's materials and conditions and is able to resume that genome inside a microscopic chromosome. I love Nature, I am kissing her every time in the jungle: Nature is a hard working genius!
But...why Nature did not discards the big amounts of repetitive bits-information that you call "junk DNA"? It is obvious: they still have a function. They performs to DNA the function that bones skeletons performs at human bodies. If you resumes the mass of my human skeleton I will have problems for keeping the optimum size of my stomach, brain, etc. People had called me "the macaque man" because I advocate Darwin's Theory and came from the jungle. But... now it seems that you want to make me the "worm man"... with a microscopic bone skeleton, moving like snakes?. Why are you so bad with me and the junk DNA?! Do you know? I have the wish to build a statue of the "junk DNA" for adoration. It had avoid humans to have the shape of worms. And, also: like several diseases, pains, comes from human's skeleton, I suspect that several millenar diseases comes from DNA's skeleton. It is better watching it: that's the cause I approve any tentative for searching better understanding of junk DNA, like this ENCODE Project. Cheers... and don't forget that I don't believe on my results and world view, I know they have a lot of mistakes and is not complete, what is written above are merely hypothesis...that makes lots of sense to me.
Do you know a possible future application for the "junk DNA"? You know that human species maybe will need leave out this planet and trying to adapt to other different conditions of other planets. Maybe it is a planet where the environment still is at primordial times. At the junk DNA have registered the informations about shapes and events that the DNA ancestor, the universal matrix ( the DNA of atoms and galaxies), had used for transforming the primordial nebulae of atoms into stellar systems, or those into galactic systems. It used gravitational different environment, different materials, etc. Keeping those skills there, we maybe will call them again, it can save our species in the future.
You: "Please, please, learn some basic molecular biology before you continue."
This not molecular biology, this is about theories elaborated about hidden variables working in Nature, like the forces and elements causing those mutations. How could you prove that they are produced by randomness, if you does not know the entire Nature? Remembering Godel's theorem ( it is good for me and for you also); Nobody can knows the final thru of a system, standing inside it" Had you going outside the Universe, perhaps?
Me: "It is because the sequence of vibrations/frequencies seen at electromagnetic spectrum are the same intensity of energy of any other system under a process of life’s cycle."
You: "Sorry, this is word salad. It doesn’t mean anything. You’ve taken a bunch of technical terms and arranged them at random. There is no such thing as a “sequence of vibrations/frequencies seen at electromagnetic spectrum”, for example! Please explain what you mean. Learn what the words you use mean before you use them."
Me: "I can't bring here the pictures of my website called "The Electromagnetic Spectrum - Light Wave as the template for all natural systems and life's cycles" and "The Matrix/DNA Universal Formula for Natural Systems as Diagram's Software of Closed perfect System", which are necessary for explaining what these words means. But I will try:
White positive light waves emitted by any natural source begins as gamma-ray ( 10(12)), goes to X-ray (10(10), to microwave (10(2)) or radio(10(3) - it is dependable of the observer - till broken into photons. Dark, Negative light waves begins with alignment of photons and makes the reverse way. This is what I call a "sequence", I don't know any "natural" situation where this sequence could be changed ( throwing a stone towards water and observing the formation, speed, propagations of those waves are enough for understanding that sequence, if one is able to distinguish the differences of time/space dimensions). Now I will try to explain (synthesizing a very complex issue) what I mean translating it into English - sorry I can't check every word in an English dictionary. It should be easier you asking about a specific word that you think does not fit the text). You need to understand that there is no way for talking about any natural phenomena from the systemic perspective without calling into the narrative every system that composes the universal hierarchy of systems. For example, explaining the origins, formations and functions of mitochondria, which is a piece of cell system, is necessary talking about the forces and elements that caused its origins, which are synthesized into stars, the corresponding piece of astronomical system. So, you go and came back from cells to plants to galaxies to light waves at light speed in a unique phrase. That's why it seems a word salad. You can't explain an Arabian suicide bomber without talking about the systems that has influences on him, like the Islam religion.
Think about white light waves emitted by the source called Big Bang. And suppose that the space is full of a substance, called dark matter. That light waves expands into space, penetrating this inertial substance. At the region of dark matter that is occupied only by gamma-ray, there is the corresponding vibrational state, which must be different from the region occupied by any other frequency of the same wave. The regions are separated into portions of dark matter+its slice of light wave, creating different vibrational/shapes portions. When different but neighbors portions meets, they are automatically connected into the same prior sequence, making packets, and when all different portions are joined together, the final end links to the initial end, creating a spherical circle. It happens that the set becomes a complete closed perfect natural systems, because all necessary functions for a working system are there. And it happens that all parts - with different shapes/vibrational states - performs the dynamics of a process that we see at biological systems, changing, transforming the shapes of an organism, during its lifetime. We, human beings, call this process as "life's cycle". Matrix/DNA Theory calls it also as "the breathing/pulsar of the Universe).
Ok, the above is a very abstract and almost metaphysical hypothesis. Extraordinary claims requires extraordinary evidences. We need to conform this entire board of light/dark matter elaborated by biological and systemic methods/thoughts into the cosmological model elaborated by Physics/Math methods/thoughts, called Standard Model. We need see how the initial quantum vortexes creating particles as quarks, leptons could existing with this picture of light/dark dynamics. It is simple: the quantum vortexes are the sources of those white positive pulsars of light waves, at microscopic scales.
Is that "word salad"? Yes, it is, for one observer that does not know the entire Matrix/DNA world view. because all formulas and models of that theory are pointing straight to a final solution: it is in the light.
If you see the picture called , and see "the universal formula for natural systems", you will understand what I am talking about.
This is not an issue for believing, tasting, humans flavors. It is a war, a combat, where the guns at the camp are only the real proved, known scientific facts. And the dialogue between the diplomats are only the evidences, real evidences.
My first evidence is the real object that every diplomats will bring to the table: the human hands. Can you see how that sequence of white light wave is the template for the different shapes of ours fingers? Being the palm hand the source? No? Look to the universal formula used by Nature when creating any new or additional architecture/accessory claimed by any creature for survival. I know you will not "believe". Sorry, beliefs are not my business, real facts are. Then, explain to me, based on yours word view, based on yours cosmological models, yours abiogenesis and evolutionary theory, every evolutionary step of that primordial forces and elements that evolved, from the Big Bang to yours hands. Like Matrix/DNA does it. And, now you can ask to Matrix/DNA Theory all other natural phenomena ( like human stomach or cell's ribosomes or event horizon surrounding black holes), the entire history of their origins and development, from the Big Bang till their shapes just now. But pay attention to the description, or you will think that it is a big word salad.
Oh $deity , what a bizarro loon showdown in the comments.
DNA/Matrix theory? Light waves in fingers ?
You can't make this up... at least without 'shroomery
“The Onion Test is about the local/type Nature skills for doing Nanotechnology”
Colorless green ideas sleep furiously.
Dark, Negative light waves
Me: "Nature has discarded the ape's tail and had a good reason for doing it; Nature "has not" discarded the junk DNA, so, the natural logics leads us to consider that nature had a good reason for it and this reason can be one hypothesis: the junk DNA must have a function, yet.
You: " No, that’s not how it works. There is no mechanism that could recognize junk DNA and cut it out; the only way to lose junk DNA is to wait for random deletion mutations, which may or may not happen more quickly than new junk DNA is generated by other random mutations"
Me: "I think that it is obvious that there are lots of mechanisms for doing it. But, our difference is that yours evolutionary theory focuses biological evolution alone, while my evolutionary theory considers biological evolution under the rules, the laws, of cosmological evolution. At this larger picture, I think that we can see more mechanisms at work. One of them is the law of conservation of energy. Nature controls the balance of initial potential energy by cutting off not useful wastes. Other mechanism is the selection of species that goes to the trunk ( which have no final end) of the evolutionary tree and the discards of species that becomes branches with a final end.It must happens within DNA also, keeping genes or discarding not useful informations.
By the way, me and you have merely, theories. Our goal is to advocate our personal theory and criticize the other's theory. But, above our ego, we need be "humanists", as representing and thinking as the whole Humanity. Then for the good of Humanity, is not honest to impose my theory, and so, searching the best and more thru theory.
Yours theory above is rational, maybe mine is wrong. But...why do you appeals for "waiting for random deletions mutations"", when you are focusing junk DNA, and seems that you forget this argument in relation to apes'tail? The apes are fighting for "life" at the same way that genes does. There is the factor of "independent selectors". So, why the natives of Amazon jungle, under a different selector in relation to caucasian selector, does not have some reminiscence of that tail?
My answer: there is a hierarchy of "natural selectors agents". Obeying the same rules of the hierarchy of natural systems.At a more immediate level, acts the selector as the immediate environment. At a more further level, also acts the larger environment, where the geographic terrestrial locations belongs to. So, look also to the sky. Towards the astronomic system that created this biosphere, these environments, and which are encrypted into our DNA. You will not know deeply biological evolution without doing it. I do it, maybe making wrong interpretations, and in relation to the non-coding regions of the DNA, I will bet that it relates to informations/functions coming from the superior system, which informations sometimes does not have a visible and necessary function, but they have the deeply function of internal structure for DNA, like the bone skeleton have the function of internal structure that supports my brains' operations and life.
Finally, you need understand the responsibility of this scholar academic theory that you advocates. The young scientists mentally educated by this theory, will not have stimulus for watching and researching the junk DNA, waiting that nature applies the random deletion mutations. That's why some people becomes furious about spending money on such research as the ENCODE Project. What should happen with human health if our Middle Age medicine had decided to forget the bone skeleton because the future was suggesting that humans would have a new shape without bones, as pure soul? What if some millenar and mortal diseases are coming from the inner structure of DNA's skeleton? And I will advise you: my theoretical models are suggesting lots of different approaches for fighting those diseases. One motive for diseases is the asymmetry between the environment built by our astronomical creator and the artificial environment that we are creating for living. Included our psychological hard-wires are against the configuration hard wired by the astronomical system, than, the chock and the disease. LIke the penetration of HLDL into the cholesterol circuit making the bad cholesterol that is killing and torturing human beings. It is a matter of responsibility to put our theories under others world views. Even that it could prejudices our career as teacher, our amount of money, etc. Our future generations deserve it. Cheers...
Me:" “The Onion Test is about the local/type Nature skills for doing Nanotechnology”
You: " Colorless green ideas sleep furiously."
Me: " Since my young times as naturalist philosopher I have the knowledge that any colorless ideas could prejudice my investigation, that's the cause I choose the comparative anatomy method, never going to a next step when building a new theory without finding a real proven scientific fact as parameter for my prior premises. If Hawking had this discipline, he never would develop a new equation without linking that prior equations on real facts, and never would see ghosts black holes in the sky, because we does not have known fact as parameter for such thing. There are no black holes, merely there are central nuclear vortex created by a nebulae of stellar dust under rotation.There is no extreme singularity after the initial singularity at the Big Bang: if there were return to singularity would not have galaxies and the Universe today.
There was no "origins"of universes and no origins of life. If you want to keep the natural reasoning, cut this word from yours dictionary. It is a bad word, creating mysticism, like deism and atheism, because "origins" means an event outside the long chain of causes and effects coming since the primordial times of this universe, an event produced by super-natural sources, like magical gods and magical randomness. Everything is product of slow transformations and evolution, so, no "origins of anything". There is no "genetic code". The word "code" leads a mind to believe on the existence of mystical forces acting at Nature, sometimes suggesting a marvellous Nature where it that does not exists - like here, at this chaotic biosphere. DNA is merely a pile of diversified copies of a unique system - the astronomical system that produced the DNA. The building block, the fundamental unit of information of DNA is a lateral pair of nucleotides, which has the same configuration of the building block of all astronomical ( and atomic) systems. It makes sense that the total diversification of living species composes a set that is a "code"? What code? Code for what? Same absurd is telling about a code composed by genes.
These wrong concepts are coming from colorless mechanicist materialists ideas sleep furiously and colorless magical thinking ideas sleep furiously. But maybe, me, who is saying that they are wrong concepts, is under another colorless kind of ideas sleep furiously, I don't know. Maybe you are right when suggesting that humans have invented for first time the mechanism for nanotechnology, creating it from nothing. My world view suggests that it should be impossible.
Dark, negative light waves is a suggestion that is coming from my theoretical models, but I am not alone in it. There are respected Physicists suspecting they exists also, I have registered those works at my website, with pictures of electromagnetic spectrum suggesting how it should work, if really it exists. But... its existence is a rational imperative. First, think why nature has produced cycling movements, like the oceans tides. I don't know the exactly English words here, but you know that when the waters waves goes ahead, they goes back. Why yours light waves does not goes back?! How do you know they does not exists?
You: "Dark, Negative light waves, don’t exist."
I am suspecting that yours mind can not accept this theoretical suggestions, and you never thought about it, due the belief that the Universe is under expansion, towards the infinite or disappearing into nothing. This world view from yours was built by Physics and Math disciplines, under the rules of the reductionist method - I think.
My world view was built based on the biological organization level of matter and going back, to the Physics' organization level of matter, so, a reverse way. Instead the reductionist method, I applied the systemic method. Yours worldview was built at urban environment with labs and advanced technology My world view was built at salvage, wild, environment, poor technology like the Galileos' telescope and Pasteurs' microscope, by collecting data obtained by the reductionist method plus the data collected from the jungle. Then, our different results and worldviews. Both methods must have mistakes and it is good for us, making comparisons, we can correct ours mistakes.
I know that you considers my method and salvage conditions as merely a thing of children and macaques, but, I ask you a little time for reading the curious results we got doing that. Starting with Biology for trying to build models of the Universe, I found that human embryogenesis is the best parameter for a model of Universe's origins and evolution ( the long chain of causes and effects without supernatural interferences suggests that the Universe creates things by the same process that it was created). At least, this exercise does not breaks the real natural known laws, recognized also by yours method. So, my Universe is under expansion? We are seeing the movements of galaxies, the cosmic wave background, the informations coming with distant sources of light, etc., but these are not enough evidences for a credible model. The best rational answer is at human embryogenesis: is the womb under expansion? Yes.
What is the process leading to this expansion? At human embryogenic level is the transformation of a primordial substance, called amnion plus placenta, into an embryo's cells, tissues, etc. And it is due the absorption of nutrients coming from the placenta. So, maybe the universal expansion is due the transformation of the spatial substance (dark matter?, ether?) into the universal systems' apparatus. And absorption of unknown nutrients of something beyond the universe, which seems to be the source of the big bang and those light waves.
What's the source of this expansion? For the universe is the big bang of something unknown yet, for human embryogenesis is the big bang of an spermatozoon membrane at the center of the ovule.
Let's go back to the question about natural light waves. My method is suggesting that the universal big bang triggered emissions of light waves through out the dark matter of the universe, like the ovule's big bang triggered emissions of genome throughout the amnion of the ovule. It is due my models suggesting that the primordial natural light waves has the code for building natural systems using inertial mass, as dark matter, as the primordial genome has the code for building embryos using the amnion.
Finally, there is a structure under expansion due existing a structure under contraction, and not due the "nothing" creating new things, as believe Lawrence Krauss. Like the embryo is under expansion due the amnion under contraction.
But... genes are building cells from amnion, and populating those new cells. because genes can replicate themselves as genes. Primordial light waves are building natural systems, like atoms and galaxies, and populating those systems, replicating themselves through natural re-transmitters, like stars and protons. These replicated light waves are broken into photons, the primordial shape of biological genes, units that can store informations. In relation to amnion, as in relation to dark matter, which are bots under contraction, white positive light waves are dark negative light waves. Is it wrong?
By the way, you are leading me to directions that I don't like, usually I don't invest my little time thinking about it. These dimensions needs lots of metaphysics, and we need practical results from our models just now. Why don't you keep the topic at the junk DNA and evolutionary biology level?
At every level, from the biological micro-scale to the planetary cosmic scale, the same principals apply. Once you understand the principals (scaling laws of physic for example and fractal-like equations) you begin to get an insight into how all life unfolded. Even though some physicists are beginning to get it - AKA West and others, I believe that because they still hold unto the Darwinian paradigm (which is really not correct in its assumptions judging by my own particular research) they are hindered. Let's just go back to the beginning and leave all the Darwininan stuff aside and re-investigate (scientifically) evolution and the junk DNA starts to make sense. It is the entire story of evolution if you look at it from a particular clear perspective. The tiny percent of coded DNS (non-Junk) that codes for proteins is only a tiny slither of the whole story.
Sorry, DNS should be DNA - it's late here in Ireland
I think that it is obvious that there are lots of mechanisms for doing it.
Please name one. Keep in mind that DNA replication and repair is well understood.
I'm sorry I don't have time to read the rest of your comments. Just so much – evolution, as biologists use the term, means descent with heritable modification; how can there be such a thing as "cosmological evolution" under this definition?
It is the entire story of evolution if you look at it from a particular clear perspective. The tiny percent of coded DNS (non-Junk) that codes for proteins is only a tiny slither of the whole story.
Well, yeah. Junk DNA tells the story of gene duplications, slippage of DNA polymerases, mitochondria, and retroviruses. So many retroviruses! More than half of the human genome consists of retrovirus corpses in all stages of decay.
Me: " I think that it is obvious that there are lots of mechanisms for doing it ( for cutting out or keeping junk DNA)".
You: " Please name one. Keep in mind that DNA replication and repair is well understood - by our current official academic world view)"
Me: "No, it is not. You have very well described events that you can observe and how it occurs, but you does not understand the natural final meaning of the event. Because the event is not product of the immediate environment alone, there are others forces acting and driven the event, coming from natural systems larger/smaller than those that you see. Replication is the biological shape of the mechanism of self-recycling that exists at ancestors systems as galaxies and atoms and also ruled by electro-magnetism, thermodynamics, quantum mechanics. It is clear when you have the universal natural formula for all those systems. DNA's repair of translations errors does not exist because there is no "translations". How did you get into the theoretical trap that a bunch of atoms can do "translations", as humans? It does not make sense if one says that "his/her baby is a translation of his/her own body". Proteins are products of self-reproduction of species composed by nucleotides, the entire cellular process is the same used by sexual reproduction. You are not seeing it because yours current academic world view did nor learned how to link alpha and omega by a unique evolutionary logistic.
It is like a journalist describing the event when a suicide-bomber blows inside a hotel. Invisible systems like a religion organization acting over the mind of that guy are not perceived/mentioned by the journalist. To me, understanding in full the event is more important than merely its immediate description.
Is it merely coincidence that all living species that reached super-specialization went towards their extinction? Or are there mechanisms that recognize them as "junk species"? And acts with forces invisible to you because you are not seeing the source they are coming from? Like the laws of energy conservation coming from the aspects of thermodynamics that rules the astronomical system where these events are occurring? Making the effort for linking cosmological evolution with biological evolution, as I did in Matrix/DNA Theory, my results are suggesting that the natural process of evolution ( and not our theories about this natural process) have at least seven variables and not merely the three discovered by Darwin (VSI - Variation, Selection, Inheritance) and those more discovered by Modern Synthesis, as horizontal genes transfers.
But, you have searched and knows the mechanisms that applies over populations, the set of all populations, junk-species, at the visible size. And does not believe that the same mechanisms are being applied over populations of genes, junk nucleotides?! Show to me where and how the long chain of causes and effects was broken and mutated during the period between nucleotides and biological species, due supernatural forces coming outside that chain...
Why evolution did not selected the galactic or stellar system for continuing evolution towards an intelligent living astronomical system, and went back, collapsing those systems for using them as environment, driven the evolutionary flow internally, towards biological shapes? Like if evolution decides that humans bodies are no long suited for continuing evolution and applies evolution upon the cellular bacterias existing inside our bodies?
For "understanding" the events, as replication you need know the systems that were ancestors to biological systems and identificate the primordial forces and elements doing "replication", at non biological level... I mean: identification and observing how replication was occurring at atoms and astronomical systems. How was this process/mechanism at the first instant following the Big Bang.
Universal evolution is curve, not linear. This is what we see when rolling the initial system emerged at the Big Bang in a Cartesian graphics having time and space as coordinates. The curvature is produced by reversing the time (from future towards the past) of the system keeping the normal flow of time of the environment. That's why, for instance, instead evolution continued from dinosaurs went back to those smallers and less complex cynodonts for getting mammals. That's why instead continuing evolution at macroscopic level of galaxies, nature went back re-organizing the smallest and less complex atoms into organic matter and biological systems. But, when you see evolution as curve, you see also more mechanisms acting over observable events.
You: "Well, yeah. Junk DNA tells the story of gene duplications, slippage of DNA polymerases, mitochondria, and retroviruses. So many retroviruses! More than half of the human genome consists of retrovirus corpses in all stages of decay."
Me: "But... my friend! The story of gene duplications, slippage of DNA polymerases, mitochondria and retroviruses, etc... this whole history, was created and driven by the stupid matter of this lost planet?! I think one needs a lot of faith on this "magical" stupid matter, because like any other religion, their believers does not shows the stupid matter doing it. It is like saying that the whole history of 9 months of embryogenesis that produced my body was created and driven by the stupid amnion contained inside the lost ovule.
No, my friend, this history you are talking about is itself replication of a cosmological history that Nature is repeating since the Big Bang ( and maybe, almost certainly, before the Big Bang). As said Tyson at the latest episode of Cosmos, (universal) life repeats itself narrating its histories. That is what you discover that the "common essence" of all biological system - called RNA/DNA - is merely a terrestrial biological level of matter organization coming from the common essence of all natural systems, included atoms and galaxies.Which are yours ancestors. There was no "abiogenesis" here. There was astronomical embryogenesis with natural nanotechnology and mutations. The retroviruses into decay is merely half history. The whole history is about galaxies into decay... registered at our genome.
There is no future for this academic oficial word view while it keeps separating the universal history into two blocks without any evolutionary link between them. There is no bridge between those two blocks, only an monstrous dark abysmal, which needs magical think for producing the elements that could fit the gap, as magical randomness... or magical God. I am sad because it means that Nature will deal with this world view as junk-theory and will apply its mechanisms for discarding it. Worse, it will apply the mechanisms for destroying its productions, as this civilization, as Nature have destroyed dinosaurs and every prior human civilizations, built by wrong interpretations, absence of larger meanings, understandings... Still is time for you avoiding it, paying attention to others' theories, like Matrix/DNA.
About Maria O'Hare post:
It is wonderful knowing that there are more people saying "I am not a creationist/intelligent design proponent or an ex of Richard Dawkins. No, I’m a researcher; a tenacious and curious human who just wants to find the truth and understand our complex world.". And it is wonderful discovering that there are websites/books like this link, lots of stuff to read.
But, I don't like the tittle "Darwinian Delusion", because I have not discovered how Darwin's theory could be a total error. It is not complete, far away off the natural evolution process as I am seeing it, but the basic foundations ( transformations, variation, selection, inheritance, etc) are not wrong, I think.
Even supposing that Darwin could be wrong, he still is my hero. Trial and error, is the way our knowledge advances, and we need those that make errors as those that make it right. Darwin sacrificed his life and better age in London for facing the hell in search of thru, that's enough for me, be it with bias or no bias. The Pope does not leave the accommodations of the Vatican for facing the hell at the jungle, where he could change his mind and elaborating the Darwinian theory of the Stupid Designer.
Maria says that "At every level, from the biological micro-scale to the planetary cosmic scale, the same principals apply." Listening it my first question is: "how cosmological scales applies the principals of sexual reproduction, metabolism, life's cycle, and every property of biological micro-scale?" I am excited for reading the website/book searching these answers. At Matrix/DNA Theory I am suggesting new models of galaxies and atoms containing all those principals, but since that nobody else has used my methods, I am sure Maria will suggest different principals. Very good opportunity for correcting my mistakes and learning new things. I have applied comparative anatomy between living and non living natural systems, maybe she has applying the practical method of archeology developed at terrestrial level as the template for a theoretical archeology applied over galaxies and the whole Universe? Why not? Trial and error, applauses for her.
it is necessary to understand that the natural process of evolution is under evolution, itself. All natural laws are under evolution, like the human tribal laws evolved into modern countries constitutions. So, primordial brute forces, as strong and weak forces, attraction and repulsion, tendency to expansion versus tendency to contraction, has evolved into modern human psychological components. So, it is no good saying that the same principals applies, without the ability for doing calculations at light speed when making comparison between cosmological and biological scales, with thoughts going ahead and back in a vertiginous way.
Maria talks about "scaling laws of physic for example and fractal-like equations". Yes...if the same principles applies for cosmological and biological scales, must be thru that Nature is composed by fractals, as the universe being the biggest fractal and a particle its image. Our problem is to define what is a natural fractal. There is the fractal defined by physics and calculated by Math. Its is a extatic, deadly, definitive, fractal. It suggests that we are previously determined, so, we have no free-will for choosing our fate. The Universe lose its beauty saw from this world view. At Matrix/DNA Theory our models are suggesting that the natural fractal is a living thing, different than that theorized when you use only Physics and Math, and includes Biology, Neurology, everything. It is a working system. It is a quantum primordial vortex as it is the human brain. It is under evolution, from the simple to most complex. How could it be? How the most complex system is the same simplest system? The answer is: the difference of expression of informations, as required by the environment and the historical point in time/space that locates the fractal.
What means that cosmological scale is the fractal for micro-scale and vice-versa? it is the same saying that a human parent is the fractal for his/her baby, and vice versa. because this Universe is merely the body of ancestors (galaxies) where is occurring an internal natural process of genetic reproduction of the unknown thing that caused the Big Bang. That's the biggest dimension of this universal living fractal.
At the Matrix/DNA Theory we had calculated the face of this universal fractal as a software/diagram, and called it "Universal Matrix/DNA". Of course, like Darwinian theory, it is not complete. Trial and error, welcome the errors, Darwin. Marie O'hare ( you are in the same boat with Darwin, doing the same that Darwin did), and not the conservative accommodated Popes and the academic researches comfortable under air conditioner writing books like "Something from Nothing".