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Ben_Dover's avatar

How do amino acids form themselves into proteins?

Asked by Ben_Dover (4208points) September 21st, 2010

I understand we have yet to be able to duplicate how proteins form in nature. We can replicate all the conditions in which it happens..and prod the aminos along, but the proteins don’t seem to form in laboratory conditions.

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89 Answers

poisonedantidote's avatar

Here is a link that explains a few things. one of the things it states is:

“To form protein, the amino acids are linked by dehydration synthesis to form peptide bonds. The chain of amino acids is also known as a polypeptide. Some proteins contain only one polypeptide chain while others, such as hemoglobin, contain several polypeptide chains all twisted together. The sequence of amino acids in each polypeptide or protein is unique to that protein, so each protein has its own, unique 3-D shape or native conformation. If even one amino acid in the sequence is changed, that can potentially change the protein’s ability to function. For example, sickle cell anemia is caused by a change in only one nucleotide in the DNA sequence that causes just one amino acid in one of the hemoglobin polypeptide molecules to be different. Because of this, the whole red blood cell ends up being deformed and unable to carry oxygen properly.”

Also, here is a video by carl sagan, where they conduct and experiment where amino acids and proteins are created by mixing gases.

I hope it helps.

cockswain's avatar

Well now you’re asking the right questions. This is pure chemistry. Here’s a link to translation in cells:http://www.youtube.com/watch?v=NJxobgkPEAo

If it isn’t clear, tell me what you don’t get and I’ll explain.

Ben_Dover's avatar

@cockswain @poisonedantidote
Yes, actually I understan how amino acids form themselves into proteins.

The real question here is why have we not been able to get proteins to form from amino acids under laboratory conditions?

Not whether or not we can synthesize proteins, just why have we not been able to get amino acids to form into proteins on their own?

Why can we not duplicate the forming of proteins from amino acids when all the conditions necessary for such formation are present?

I’m talking about the amino acids forming into proteins on their own. Without help from the lab tech.

cockswain's avatar

You mean without the presence of enzymes?

iamthemob's avatar

@cockswain

I don’t know if this is what @Ben_Dover means, but I would ask how it’s been proposed it happened as it is theorized it happened prior to protein existing. How under natural circumstances is it explained that the amino acids formed the protein chains when, given all conditions necessary, it cannot be replicated in the lab?

shilolo's avatar

Simple, it’s an RNA world. Most likely, RNA molecules formed that could act as both genetic material and enzymes, and were able to catalyze enzymatic reactions including peptide bond formation. In this model, RNA predated proteins and DNA, and these RNA replicons eventually acquired the ability to synthesize proteins.

Ben_Dover's avatar

@iamthemob Thank you. this is what I was trying to get at.

@shilolo Interesting hypothesis. However, we have never been able to get these RNA molecules to assist the amino acids in forming proteins when attempting to replicate primeval conditions wherein life arose somewhat spontaneously.

This experiment was tried unsucessfully by Stanley Miller in 1953. Stanley was a grad student at the University of Chicago.

Response moderated (Off-Topic)
RealEyesRealizeRealLies's avatar

@Ben_Dover “it appears to us that you’re baiting people on purpose”

Who is “us” and WTF are you talking about?

@shilolo “Simple, it’s an RNA world.”

Close, but no cigar. You can’t say “Simple”, and then give an explanation of “Most likely”.

@poisonedantidote “The sequence of amino acids in each polypeptide or protein is unique to that protein”

It’s almost lost unless you know what to look for… “The sequence…”

_________________

It is simple, and most perplexing at the same time.

RNA does exactly what the DNA programs it to do. The DNA alphabet (code) is translated (transcription) into the RNA alphabet (code). The RNA executes the translated code upon enzymes to form specific proteins. Simple right?

No, not so simple. Although we are aware of the process, the mechanism, we have not deciphered why or how RNA splits a specific chain of DNA to retrieve that code. It is a closed loop communication protocol, and we have no idea whatsoever why it is so, and why it is so specific to individual proteins needed at any given time.

As well, there is no accepted or promoted explanation except for the theory of Abiogenisis to account for how these mechanisms could have arisen from a prebiotic world in the first place. Yet Abiogenisis is pseudo-science at best, for nothing of the sort has ever been demonstrated in the lab without the use of a synthetic ribosome. IMHO, a synthetic ribosome is not suitable for founding a hypothesis upon.

When dealing with code, one thing is known. All codes have sentient authors. No exceptions. It cannot begin by chance alone. The math isn’t even close.

shilolo's avatar

@Ben_Dover What do you mean by “we”? Indeed, you are mistaken. The core of the ribosome, the cellular structure responsible for protein synthesis is RNA. The carrier molecules of amino acids are RNAs (tRNAs). Catalysis is mediated by RNA. The entire process can occur with RNA alone.

RealEyesRealizeRealLies's avatar

That’s a theory at best. It’s never been demonstrated in reality. And only one of the four enzymes needed has ever been produced in a lab, and that was only with a synthetic ribosome.

Not good enough.

RealEyesRealizeRealLies's avatar

Something had to encode the RNA.

shilolo's avatar

@RealEyesRealizeRealLies Wow, you’re so definitive in your statements, which by the way, are false. Code does not “need” a sentient author. It is trivial to generate random combinations of bases. Eventually, over eons, some randomly connected bases developed useful functions that allowed them to replicate. It isn’t that hard to accept.
Which “enzymes”?

iamthemob's avatar

@shilolo

That seemed pretty definitive in and of itself. Why should I accept that if you can’t prove it will, must, or even can happen? If it’s a scientific hypothesis, then I would accept it when it has been proven through experimental research yielding consistent and repeatable results.

RealEyesRealizeRealLies's avatar

Please provide a precedent to support a hypothesis that code may be generated without the need for sentient authorship.

@shilolo “Eventually, over eons, some randomly connected bases developed ”

Poppycock! There is no math or science to support such a statement.

Google and every credit card company bases their entire business model upon the notion that code cannot by any measure be created by chance.

And it’s more than code. It’s so much more. How did the transmitter, receiver, alphabet A, alphabet B, mapping protocol, error correction, redundancy, noise reduction, syntax, semantics, and intent all arise by chance simultaneously?

The Infinite Monkey Theorum has been soundly defeated by Kittle and Kroemer a while ago. And that’s even with giving the monkeys the alphabet and typewriters as a given to start with. It can’t happen. And if it did, it would be an absolute supernatural miracle.

RealEyesRealizeRealLies's avatar

see you in the morning… good night

shilolo's avatar

RNA does not need to be encoded by anything. The old paradigm of DNA > RNA > protein has been overturned, repeatedly. RNA can make DNA, and RNA can self-assemble as well.

@iamthemob What are you talking about? There is ample data for RNA mediated peptide bond formation as well as multiple other enzymatic activities for RNA. We have identified ribozymes, riboswitches, siRNAs, miRNAs, RNA splicing and many more activities.

@RealEyesRealizeRealLies Wow. Poppycock? That’s your answer? Prove that DNA (or any other native genetic code) was “coded” by an author. Who is (was) it? Even in its nascent form, abiogenesis provides a better explanation than creationism. That we cannot replicate events from billions of years ago, when we don’t know the exact conditions present at the time nor do we have the benefit of billions of years of observation, doesn’t negate the much higher likelihood that chemical reactions led, eventually, to more complex chemicals (RNA, proteins, DNA).

iamthemob's avatar

@shilolo

Is RNA mediated peptide bond formation demonstrable and experimentally repeatable proof of the certainty that it self-assembled and began replicating in conditions known to exist at the time RNA is supposed to have self-assembled on Earth?

If not, why is it better than the previous DNA model? Or any of these theories on the page you linked to?

I’m not saying that I believe something else and therefore think you’re wrong. I am saying, however, that you’re making an assertion, when really it doesn’t seem that there’s a “simple” answer at all, only a lot of theories based on a lot of assumptions. It’s the assertion that’s poppycock…not the suggestion. This is the point where you can ask someone else to prove their solution. Codes we are familiar with that communicate instructions for the performance of certain tasks have been, invariably, the product of design. To say that one could arise randomly in conditions we have no idea about is to make a fantastic assertion. It is the responsibility of the person making such an assertion to prove it more likely, and not say that it’s more likely because they like it better.

shilolo's avatar

@iamthemob That the computer code we see today was written by a human doesn’t mean therefore that the genetic code must have been written by someone else. I really have no time for the the whole “intelligent design” meme running through this thread. (I eagerly await the experiments testing the hypothesis of a “code writer” for our evolutionary forebearers.)

That said, I have a feeling that we will never be able to prove, definitively, what were the exact conditions when Earth was formed, and what precise “spark” or “event” led to the first replicons. We probably will, eventually, be able to mimic formation of replicating units, but the precise order of events will never be known. That Earth was formed so long ago, and life as we know it didn’t develop until much later suggests that there was a long delay during which time many “experiments”, chemical or otherwise were occurring. Eventually, a successful replicating unit formed and the rest is history.

RealEyesRealizeRealLies's avatar

If by chance, the code assembled itself, then the Atheist is left in an uncomfortable paradox. For that would ultimately mean that the blind, deaf, and dumb cosmos has somehow spoken and listened. Where there be code, there must be a speaker and a listener. I for one reject any hypothesis which promotes the unsupportable notion that begs a universe to speak.

The late Leslie Orgel (renowned Abiogenesis proponent) said: the self-organization of the reductive citric acid cycle without the help of “informational” catalysts would be a near miracle.

But let’s go ahead and take a leap of faith and start with “a membraine enclosed ribozyme capable of plymerising itself and its counterpart copy…”

Martin Line makes a great case in A Hypothetical Pathway from the RNA to the DNA World, but in the end still warns us that:

“The pathway proposed is not intended to represent reality”

and requires “a formidalbe conceptual leap” and hopes that

“If support for some of these steps can be shown, final resort to an intelligent creator for the origin of life (Gibson, 1993) may yet be premature”

This is Abiogenesis proponents own words about their own research. Even they know it’s a joke.
______________

Getting the building blocks is one thing. Any physical medium can be used as an alphabet. But equating an alphabet with an author is unwarranted. Self assembly does not account for programming. Only sentient authors can program.

And sorry, I do not believe in Creationism or Intelligent Design. I believe in Intelligent Evolution.

It is a proven fact that code can be programed to act upon stimuli fed by sensory equipment. A.I., Robotics, Computer Science, all confirm this in spades. But in every case, the program must be written with that functionality from the very beginning. This is advanced programming, above and beyond a simple miracle hoping for molecules to arrange themselves into something meaningful by accident.

To falsify intelligent authorship of code, all one need do is demonstrate a non intelligent mechanism that can author. One can claim all they want that non intelligent authorship is possible. But I have no reason to accept a claim lacking evidence and flies against all mathematical probability.

I also accept the predictability of sentient authorship of code. And I accept the repeatability of sentient authorship for code, notwithstanding the 30,000 years of precedent with billions of empirical examples every single day.

No other mechanism has ever been demonstrated.

iamthemob's avatar

“And Science said, ‘And then there was life!’ And Science saw that it could not explain life, and claimed it could not be explained. So thereafter, whatever dogma science declared was truth, became truth. It was a bright cold day in April, and the clocks were striking thirteen.”

Sorry to be glib – but it’s amazing how this is the very same style of argument that evolutionists criticize creationists for. The intelligent design model doesn’t preclude an evolutionary model except if you discount the random mutation or random assembly, etc., moments of it. These are, of course, the most fantastic and completely unsupported concepts behind the theory. When we accept aspects of a theory as accepted science when they are based on an estimate drawn from fossil records estimated to be one tenth of one percent, and there is debate about whether a fossil represents a new species or a new form of an old species, we are accepting word as faith.

Why do we just not say “We don’t know. This is how I believe we should approach the problem, and I’m following that line. What do you think?”

The arrogance associated with dismissing counter theories in this context is actually staggering.

shilolo's avatar

Where’s the beef?

By that I mean, where are the experiments testing these “hypotheses”? Oh, they can’t be done? Oh…....

cockswain's avatar

@iamthemob I haven’t read all of the above, but I like your last statement. I have zero problem at all when discussing creation vs evolution saying the current limits of human understanding do not tell us exactly how all life began. The problem I have is when proof shows humans are descended from chimpanzees that this is ignored. I have a good friend who is a creationist. However he has no problem accepting the fact we evolved from bacteria, and likely something before it, like viruses, which have a protein coating, so probably more like amino acids. He relates the Adam and Eve story to saying something was created somewhere that spawned life. I have no problem allowing the argument that maybe God created amino acids, because I have no better theory. The bothersome point is denying our primate lineage.

iamthemob's avatar

@cockswain

See, then we need to get back to the other thread – because I have problems with that.

I think that it’s much, much more reasonable an assumption, but I still think it’s more assumption than theory. (but we derail…)

@shilolo

I hope you’re applying that statement to all included and discussed hypotheses…including the RNA world. If so, spot on. If not, that’s some willful, willful blindness….

cockswain's avatar

@iamthemob Yes, I posted better details there, but sort of brief. A good video is there now.

Yes, it is an assumption, but not one I have the big problem with because it isn’t denying the far more proven data. As long as creationists accept the extremely supported science, I have less issue with the misinformation they are spreading.

iamthemob's avatar

@cockswain

I saw! And I will watch the video before responding.

cockswain's avatar

I just read the rest of this thread. Truth is this is at the limits of human knowledge and we currently don’t know how the pre-biotic world spawned life. At least no data I’ve seen has supported a really solid and growing theory.

@RealEyesRealizeRealLies I don’t agree with your logic that because all codes have an author, the genetic code must have an author. That’s really just a guess, even though it isn’t irrational to guess that.

@shilolo and @iamthemob I think I agree with both of you. We just don’t know enough about that to say how it occurred.

Again, this is the territory in which I have no problem with creationist or theist beliefs. It is the territory in which I don’t consider myself a pure atheist. We just don’t know enough about it yet. The only beef I have is with denying all the science that gets us to that world first. That is where the open and closed minded creationists diverge.

iamthemob's avatar

@cockswain

For me @RealEyesRealizeRealLies’ point is valid, though, because it shows that in all cases before it has been one way, and these theories are making a claim that this, somehow, is different, and not supporting the claim with anything but the theory itself. This is the “fantastic argument” accusation that “rational” thinkers throw at people who are willing to take into account “supernatural” causes. So it’s a situation where what’s good for the goose is good for the gander.

cockswain's avatar

@iamthemob Well, that’s why I’m saying his belief isn’t irrational. There isn’t strong compelling evidence against what he’s saying, so we can’t say he’s being unreasonable. I’m perfectly content to state “i don’t know” about anything we don’t have info about.

iamthemob's avatar

@cockswain

I’m not talking about his belief. I’m saying that his argument is an accepted standard that we’ve observed. If you argue against that, you have to show real, hard, tangible proof of the exact way it happens. Otherwise, you can’t say that it’s based in fact at all, because the facts universally suggest the contrary.

It’s basically who has the burden of proof in this case for their assertion. If you have the burden and don’t have the proof – you’re not necessarily wrong, but don’t come at me like you’re right. Then you’re an evangelical.

cockswain's avatar

I thought I understood, but maybe not. What facts supports @RealEyesRealizeRealLies ‘s theory that the genetic code has an author? Similarly, what facts suggest there isn’t an author at some level? I guess we’re mis communicating since I don’t get what you mean when you’re saying ” because the facts universally suggest the contrary”.

Maybe I’ve misunderstood @RealEyesRealizeRealLies stance?

I mean, I completely agree with this: “It’s basically who has the burden of proof in this case for their assertion. If you have the burden and don’t have the proof – you’re not necessarily wrong, but don’t come at me like you’re right.”

If anyone thinks they have a theory, it is meaningless without hypotheses to support it. I was taking the position that @RealEyesRealizeRealLies is saying there is an author (but he doesn’t have proof), and @shilolo is saying he knows there isn’t because @RealEyesRealizeRealLies is saying he hasn’t proven there is. But neither know the actual answer, but neither of them (nor you) could be proven wrong yet.

Are we on the same page?

iamthemob's avatar

@RealEyesRealizeRealLies has stated that all code that we know of was designed (not random). (this is as I understand it). Because all code has been designed, it is reasonable to assume that all code is designed unless proven otherwise. If you are asserting something otherwise, then you are asserting a less reasonable position. Therefore you must have solid proof if you are arguing that your theory is better.

I’m not considering @RealEyesRealizeRealLies’ argument as truth or fact. I’m saying that it demonstrates how we understand code. As DNA is a code (and not in a metaphorical sense – it very much is one), then positions that state it was randomly created need to be supported by clear evidence.

So again, it’s not that one side is right or the other wrong, or necessarily better. But if the theory of random assembly is to be considered better it better prove it. If it can’t, it’s reasonable to consider it worse (I would just say could be anything personally).

cockswain's avatar

Oh I see what you’re saying. Here’s where we differ: I think the assumption the code is designed is equally valid to the position is not. We can’t say because all human made codes we’ve ever observed are designed, and since DNA is a code, therefore it is valid to assume the DNA code was designed. This could be a matter of opinion, but i would consider the above argument to be an weak inductive argument from analogy, premise is “all codes are designed” isn’t strong in this case. The debate we have now is is “all codes are designed” a strong or weak premise as it pertains to DNA.

So I don’t think @shilolo can say @RealEyesRealizeRealLies is either right or wrong.

iamthemob's avatar

@cockswain

Now—same page. I can accept that

shilolo's avatar

@iamthemob Sorry, the burden I proof falls on those that argue for a creator. There isn’t a shred of evidence save pure conjecture for thus idea, and in any event it is false logic. Does the existence of an airplane mean that all flying objects were designed? Does the existence of the Notre Dame cathedral mean that the beautiful caves with cathedral like spires were designed too?

The fact is that there is a growing body of actual data showing that abiogenesis is possible, as I listed before. There is no DATA (and there never will be) for a creator. Please provide said data, and not conjecture, and I will reevaluate. For now, since there exists significantly more, albeit incomplete, data for biogenesis, that is what I accept as closest to the truth.

shilolo's avatar

Excuse the typos. Stupid iPhone autocorrect feature rears it’s head (damn code writers).

iamthemob's avatar

@shilolo

Please see above at cockswain’s last statement. If you are saying that the idea of code we have is different from code as DNA, I’ve seen arguments about that and can accept that. However, then all parties are asserting theories with no demonstrable evidence. If none can provide proof showing their theory is more true than all others, then there is no reason to believe one over the other.

I’m more than willing to believe the RNA world as a hypothesis. I’m amazed to see how close minded others seem to be, and how rhetorical rather than factual this all is.

cockswain's avatar

@shilolo I agree there is no proof of a creator, but lots of people just believe that one exists. While I personally agree with you, I don’t think there is an argument that will persuade one to abandon their faith without science to support it. Again, my beef is with those who have neither studied nor understand the science, yet deny its validity. That’s irrational.

Ben_Dover's avatar

There is no DATA (and there never will be) for a creator.

Talk about close-minded. However, I am surprised this has become a debate about God’s existence. I was merely curious to know why we cannot seem to get a handle and how and why the 1st amino acids took it upon themselves to form proteins. After all, aren’t proteins extremely important to human life (and possibly chimpanzee life, too)?

So then the bottom line is that science hasn’t a clue to this enigma, nor does it seem likely we will ever know…and so scientists are merely proposing hypotheses from their own guesswork.

So in this case it seems that it is science that has failed to analyze a naturally occuring phenomenon, one on which the very existence of humans depends quite heavily. Hmmm.

cockswain's avatar

@Ben_Dover You need to watch the video I put on the other thread. Science has not failed because it hasn’t been able to unlock mysteries yet. Nor does its failure to accomplish something prove it’s entirety is invalid, nor substantiate a creator. But my problem isn’t with a creator going back billions of years, it is denying human evolution going back millions of years.

shilolo's avatar

@Ben_Dover That simply isn’t true. That you aren’t familiar with the experiments doesn’t mean they don’t exist. There are lots of experiments demonstrating peptide assembly with amino acids and RNA. I agree wholeheartedly with cockswain that a lack of scientific education is the real and underlying problem.

shilolo's avatar

FWIW, abiogenesis and evolution are distinct processes, though evolutionary principles would likely apply to early “life” as well, if we accept self-replicating entities as subject to evolutionary pressures.

iamthemob's avatar

@shilolo

- isn’t it required that we accept self-replicating entities as subject to evolutionary pressures in order to both explain how self-replicating entities eventually developed into organism that reproduce sexually?

- isn’t it true that evolution makes more sense if we assume abiogenesis as the starting point for life on earth?

- aren’t the experiments referenced, if they apply to theories regarding life formation, described as taking place in “plausible” prebiotic conditions?

RealEyesRealizeRealLies's avatar

Find an anonymous code from any source, we infer sentient authorship because that’s exactly what the scientific method demands us to do.

We certainly don’t infer that the code and communication mechanisms randomly assembled by chance because there is no support for such a thing and no experiment has ever succeeded in making such a thing happen. Shall we find an anonymous note on the ground, or carving in a tree, and conclude that they must have authored themselves simply on the merit of not knowing who the author is? Methinks not.

cockswain's avatar

@RealEyesRealizeRealLies But even though that’s a rational guess, it doesn’t mean there is data to support it. Just argument from analogy.

shilolo's avatar

@RealEyesRealizeRealLies Do you have evidence (stress, EVIDENCE) for a creator that doesn’t rely on inference? Methinks not.

@Ben_Dover I now realize what the problem is with this thread, as well as this recent question. People have this mistaken belief that science “knows” everything, or should. Even though we live in the “modern era”, we still are only in the nascent period of understanding basic molecular biology. Scientists have only recently discovered ribozymes (1980s), RNA interference (2000s), and the structure and function of the ribosome (1990s) (to name but a few discoveries). That science doesn’t have definitive proof of a linear series of events that occurred billions of years ago (and likely required eons to develop) doesn’t mean that that data won’t be forthcoming. Indeed, the formation of the peptide bond can be achieved entirely using rRNA and tRNA. Here and here are but two recent reviews on RNA based polymerization and ongoing research into this process. Here is another review on the subject.

This thread has devolved into a discussion of the conditions of the prebiotic era, which are unknown. That said, it is naive to assume a linear path. It is highly likely that amino acids, nucleotides, nucleosides and membranes were available to coalesce into simple “virus-like” particles that eventually evolved into bacteria, and subsequently everything else. Scientists are still debating and testing, but it is reasonable to predict that the coming millenium will see a fundamental advance in knowledge on the prebiotic world.

Ben_Dover's avatar

I doubt that many educated people believe that science comes even close to knowing everything, nor that it should.
We do, however, expect scientists to back down when they are shown to be completely ignorant of the subject upon which they are discussing.

It was most enjoyable to pose a question which has stumped the experts here and in the real world.

RealEyesRealizeRealLies's avatar

Science is not a game of proof. Science sets out to disprove. And when it cannot, it makes inferences.

Science cannot disprove that all codes have authors, and that is the foundation for any experiment involving such.

1 – Ask a question…
What is the source of code?

2 – Do background research…
Code is defined by Purlwitz, Burks, and Waterman as probability space A mapped to probability space B. It is the formal definition adhered to by Information Theory, Computer Science, Genetics, Biology and all other disciplines. Hubert Yockey modeled the transcription process of DNA/RNA directly from the protocols set fourth by Claude Shannon as defined in his seminal work A Mathematical Theory of Communication and also adheres to Purlwitz, Burks, and Waterman’s definition of code.

From Yockey’s book, Information Theory, Evolution, and the Origin of Life

Yockey’s model of transcription here

Shannon’s communication model here

They are identical models. You will note that Message is paramount in the very first step.

therefor the Atheist is forced to admit that the blind, deaf, and dumb cosmos can somehow author a message, yet offers no demonstrable mechanism to accomplish such a task

3 – Construct a Hypothesis…
All codes are the product of, or ultimately traceable to sentient authorship.

4 – Test Hypothesis by Doing an Experiment
This thread will suffice.

5 – Analyze Your Data and Draw a Conclusion
Upon inspection, I conclude that all codes apparent on this thread are the result of sentient authorship.

6 – Communicate Your Results
This thread exists because of code, and would not exist otherwise. The code of this thread is attributable to sentient authorship, and would not exist otherwise. Therefor, sentient authorship is thus far the only known mechanism which can account for the creation of code.

Therefor, anonymous code is inferred to be the product of sentient authorship as well.

This conclusions stand until science disproves it, thereby toppling the inference of sentient authorship.

RealEyesRealizeRealLies's avatar

We confidently infer the existence of an invisible immaterial force called gravity, because the ball drops the same way every time. Science is free to keep bouncing the ball for all of eternity, but until it bounces differently, and unpredictably, then science shall continue to infer the existence of gravity.

Information deserves the same respect.

cockswain's avatar

@RealEyesRealizeRealLies Reinforcing your assertion that codes are man-made so therefore DNA, as a subset of codes, must be also man-made still doesn’t provide any evidence there is an author. It doesn’t disprove an author either. It just makes a comparison and suggests it might be worthwhile to investigate a way to detect and define the presence of an author.

Are you saying you are convinced beyond doubt that there is an author to the genetic code?

shilolo's avatar

Gravity is measured. A creator can neither be measured nor demonstrated. Your “code hypothesis” is simply a bunch of mumbo-jumbo. None of it is testable. You misuse the word “message” to mean that someone or something is “sending us a message” or “communicating with us”, when in fact the information contained within genetic code is merely a means to an end—propagation of a species (virus, bacteria, eukaryote). Meanwhile, scientists can demonstrate how chemicals can combine to form complex structures, some of which, over time, evolve to propagate themselves and generate a “message”. In any event, it is not the job of science to disprove the existence of an entity (a creator) that is itself imaginary and unproven. Just because the mind imagines or dreams up something (ghosts, demons, devils, creators) doesn’t mean that science has to actively pursue research to disprove their existence.

cockswain's avatar

@Ben_Dover You’re saying because science hasn’t defined the pre-biotic era, it can’t, and scientists are generally ignorant of their field?

What do you do for a living? What is your educational background? How old are you? You keep saying nonsense. I’m guessing you have a very limited scientific background unless you state otherwise.

RealEyesRealizeRealLies's avatar

Gravity is not measured. The effects of gravity are measured. Information is not measured either, but the code that represents it can be.

@shilolo ”...mumbo-jumbo. None of it is testable…”

I just ran an experiment. The attribution of sentient authorship of code on this thread is quite testable indeed.

@shilolo —”...scientists can demonstrate how chemicals can combine to form complex structures…”

Agreed. But complexity and code are polar opposites. They should not be conflated as related whatsoever.

@shilolo ”...some of which, over time, evolve to propagate themselves and generate a “message”....”

Pure unsupportable conjecture, to put it politely.

And if you really believe that, then you believe the cosmos can speak. Oddly, that supports ancient myth and folklore of whispering streams, talking trees, and burning bushes that instruct Moses to shout “Let my people go!”

I cannot allow science to go there, even at the expense of an Atheist becoming a parody of the religious fanatic they would otherwise mock.

shilolo's avatar

There is no voice to the cosmos, and development of replicating organisms from the primordial soup does not require a “voice” of any kind. I don’t know where you get that ludicrous idea. Your “experiment” is also a farse. I concede that people wrote the code that allowed me to make this post. That in and of itself does not mean that a guiding hand created the first replicating structures or their (eventual) genetic code. Your logic is, as they say, made of fail.

iamthemob's avatar

@cockswain

I think it’s unfair to assume all of that from @Ben_Dover‘s comment. He’s simply stating that so much of this is based on assumptions that can’t be proven. They may be. Design may be proven. At this point, we believe that we can figure it out. But claiming these things have been proven, or that they are the most likely methods of explaining what’s happening, is intellectually dishonest. Claiming they’re reasonable, and based on measured phenomena, is appropriate and a position that is unassailable.

cockswain's avatar

He’s not addressing any of the details despite my repeated questions directed at what his specific objections are, both in this and the other thread. If he’d address the details, I’d be fine. Instead he throws out a flippant, untrue statement here and there and ignores my questions. I’m led to believe he knows very little abut this subject and doesn’t want to actually spend hours and hours learning it. He just wants to spout simplistically derived criticisms and platitudes about science.

But you’re entitled to your opinion of how he’s conducted himself.

RealEyesRealizeRealLies's avatar

All speaking requires a code. All codes say something. If the cosmos is the source of the code, then the cosmos has spoken.

You may repeat my experiment from this thread on any instance of code in existence. Failing to apply the results of known authored code to anonymously authored code is suggesting that a book with its cover ripped away must have somehow written itself.

cockswain's avatar

So are you just saying that DNA is an expression of the cosmos (or something)?

shilolo's avatar

@RealEyesRealizeRealLies Your comment about “saying something” is purely philosophical and not relevant to whether a genetic code is 1. saying something and 2. designed. I can type ahdgkla;dhjsglkadsjhgkladsjgkasdhjgklasdhjglkzsdjglkdsjkg (which is interpreted by computer code but has no meaning and is a bunch of gibberish). In any event, your reverse “logic” is deeply flawed. Does the presence of a man-made (and designed) wind tunnel prove that wind is designed? Does the presence of a wave pool prove that waves are designed? Man-made lake -> natural lake? Airplane -> bird? Scuba gear -> dolphin? I could go on and on, but clearly the answer to all of these is a big, fat, NO. Just because in the very recent past (especially in the scale we are discussing) have codes been written by humans doesn’t mean that billions of years ago the first replicons were somehow “written” also.

In any event, all of this is moot. Even when scientists recreate a chemical synthesis that leads to a replicating unit, that will not prove that that particular event occurred. It will simply provide a plausible explanation/framework for the genesis of life.

iamthemob's avatar

@shilolo

That last paragraph is totally reasonable. Unfortunately, the same with religion, if you don’t openly admit the flaws, and you say it all often enough, people accept it as true because other people said so.

Whether the general public supports the theory or not should be immaterial. The general public should be informed of all possibilities, told the most favored by scientists, but while showing the vast amount that still needs to be learned. Then maybe we all could start thinking outside the box.

shilolo's avatar

@iamthemob Except the problem is that at least with my model, there will be verifiable, reproducible, testable experiments that can be used to buttress the theory. It is unreasonable and disingenuous to hold up two theories as “equal” when one has supporting data (albeit incomplete data) while the other has none.

iamthemob's avatar

@shilolo

Nevermind. I’m out.

RealEyesRealizeRealLies's avatar

Yes, the genetic code says “fat” with fat genes and “blue eyes” with blue eye genes. Genes are words that mean something very specific to RNA transcription. Forensics will confirm that for you after your next crime spree.

And yes again, I did address if the genetic code was designed. The fact that it’s a code is the smoking gun to confidently infer that it is. If you disagree, then please present another demonstrable mechanism that accounts for code other than sentient authorship. Otherwise please accept the evidence at hand with my above experiment.

You are free to find a black swan at any time. But I have no inclination to believe in one until one actually appears. It could be out there. But stating that it is without evidence is unwarranted, especially when we do have a viable, testable, repeatable, predictable mechanism that does explain the existence of code.

shilolo's avatar

Are you trying to educate me about molecular biology? I think not. The genetic code does not say “fat” or “blue eyes”. Genes are transcribed to RNA, which is translated to protein. The physiologic effects of the protein depend on a number of factors unrelated to the genetic code itself. Code is simply your way of trying to tie this together. The genetic code could easily be called a pattern. As it stands, you cannot confidently infer anything from the presence of a pattern. You may continue to attempt your “inference-to-design” rationalizations (taken from Dembski and Behe), but those arguments have long been discarded.

In any event, it is not up to me to present contrary evidence. It is up to YOU and everyone who believes in “intelligent design” to provide direct evidence for a designer. As I suggested, that humans designed airplanes to look a bit like birds does not mean birds were designed. Likewise, our ability to recreate waves of water doesn’t mean that a creator designed waves. Your argument is conjecture, pure and simple. At the very least, science establishes a hypothesis and then tests it. Where is your test?

RealEyesRealizeRealLies's avatar

@shilolo “Are you trying to educate me about molecular biology? I think not.”

When the student is ready, the teacher will appear. No, I don’t believe there will be any education coming from me to you whatsoever. But the least I can do is share what I’ve learned from science. It is up to you to accept or reject it. I find that Atheists are just as likely to let their own dogmatic perceptions prevent them from considering the evidence at hand for what it is. Especially since you played the Demski/Behe card earlier, before editing your comments. Why did you remove their names from your statement ”...YOU and everyone who believes in “intelligent design” to provide direct evidence…”?

Though you present their argument very well, it’s clear that you don’t understand mine if you think I’m promoting ID/Creationism.

At the risk of repeating myself, let me clarify again, I do not accept Intelligent Design. I do not accept Creationism.

I do not accept the arguments put forth by Demski/Behe specifically because I do agree with Dawkins rejection of Paley’s Watch argument based upon the principle of what he (Dawkins) calls “Apparent Design”. I fully agree with Dawkins on this notion. But that is only half the notion, and it doesn’t mean that Dawkins covered all the bases. In honor of Dawkins coining the term “Apparent Design”, I have coined the term “Apparent Information”. ID/Creationists never mention such a thing.

I adhere to principles of Intelligent Evolution. I do this from knowledge learned from Pulitzer Prize Winner Barbara McClintock, James Schapiro, Hubert Yockey, Claude Shannon, Norbert Weiner, Perry Marshall and others, including the two Abiogenesis proponents quoted earlier.

If ID/Creationists are tagging what I’ve learned as their own, then it is by default of desperately clinging to their subjective dogma. But I don’t really know what “they” are up to because I don’t keep up with their latest proclamations.

Conflating my argument with theirs has the affect of souring the milk (so to speak) against any intelligent discussion on the matter. They are far too eager to sling the mud of traditional God concepts and foist Jesus Christ upon the science at hand. They don’t even understand their own religions, much less principles and implications of interdisciplinary studies of Information Theory, Linguistics, Genetics and Biology.

I will separate myself as far as possible from ID/Creationism. It is unprofessional, speculative, and quite subjectively directed to a pre-established agenda. Unfortunate if anyone would conflate my argument as standard or evolved ID/Creationism. Doing so only demonstrates their own dogmatic inclinations against the pursuit of truth in science.

If anyone would like to know more about what I call Intelligent Evolution and Apparent Information, I’d be happy to discuss it further. Basically, it involves noting the intelligence of the cell, refuting random mutation, and understanding what information actually is, and what it isn’t.
_______________________________________

@shilolo “The genetic code does not say “fat” or “blue eyes”. Genes are transcribed to RNA, which is translated to protein.”

Nucleotide = Character
Codon = Letter
Gene = Word
Operon = Sentence
Regulon = Paragraph
Chromosome = Chapter

Look @shilolo, I hate to say this, because it sounds like I’m preaching and I’m sure you believe you understand how all this works. But let me present a different scenario for your consideration, or at least your entertainment.

Where to begin with your simple statement…?

Nothing is “translated to protein”. Proteins are built, not translated. Proteins have no receiver mechanism to accomplish anything remotely close to translation. Proteins have no alphabet to map a translation with either. Proteins are built, that’s all.

As well, you can’t say “The genetic code does not say “fat” or “blue eyes” and then claim “Genes are transcribed to RNA”. That’s a contradiction. What do you think is being transcribed? Words from the quaternary DNA code (alphabet A) are being mapped (translated) into words of the ternary RNA code (alphabet B). Some of those words say “fat”, some of them say “diabetes”. The RNA pulls instructions from the DNA, and then proceeds to build a protein.

It’s no different than you pulling instructions from a manual to build a cheap desk from Office Depot. The transcription/translation took place from the Instruction Author, to Your Mind. But after the desk was built, it would be crazy to say that the desk translated your mind, but your mind didn’t translate anything from the instructions.

@shilolo “The physiologic effects of the protein depend on a number of factors unrelated to the genetic code itself.”

Wha? The protein would never have been assembled in the first place if the RNA had not unzipped and READ the double helix. What are you talking about?

@shilolo “Code is simply your way of trying to tie this together.”

In case you haven’t heard, modern Biology and Genetics are with me on this one. There is a worldwide race to discover more about the genome, specifically because some pretty smart folk understand that “code” is what “ties this together”.

@shilolo “The genetic code could easily be called a pattern.”

And I could call an Oxen a Fruitcake, but it wouldn’t make it so. Let’s see what Yockey has to say about it.

“The linear structure of DNA and mRNA is often referred to as a “template”. A template is two-dimensional, it is not subject to mutations, nor can it reproduce itself. This is a poor metapher as anyone who has used a jigsaw will be aware. One must be careful not to make a play on words.”
Hubert Yockey, Information Theory, Evolution, and the Origin of Life Chapter 2 paragraph 2.

@shilolo “As it stands, you cannot confidently infer anything from the presence of a pattern.”

You really should consider spending more time studying science and Information Theory. Science infers a relationship between the patterns of Growing Seasons and patterns of Tree Rings all the time. We infer relationships between patterns of Erosion with patterns of Flooding. Patterns of Solar Flares are inferred as related to Coronal Mass.

Patterns and Code are complete opposites.

Codes are reducible, always, down to a factor of 1 bit.

Patterns are irreducible complexity.

Codes may reproduce themselves, sometimes just by being looked at.

Patterns never reproduce themselves.

Codes may be copied exactly, always.

Patterns cannot be copied exactly, ever.

Codes may be mapped to other codes and retain the essence of meaning.

Patterns can’t be mapped, unless observed and codified by a sentient being.

Codes are the product of sentient authorship.

Patterns may be created from code, or chaos. Those from chaos need no sentient author, thus a snowflake, or a solar system need no author to exist. But if science ever uncovers a code to the Universe (or to Paley’s Watch for that matter), then the scientific method (described above) demands that we infer the existence of sentient authorship.

To falsify this statement, all one need do is demonstrate a chaotic natural mechanism which can produce code, and the required protocols to run it. Until then, let’s not foist our Personal Jesus upon science, just to make it fit the bill.

Response moderated (Flame-Bait)
RealEyesRealizeRealLies's avatar

Are you denying what Yockey states in his book?

shilolo's avatar

Yockey is, fundamentally, FOS, especially with respect to his calculations regarding probabilities.

RealEyesRealizeRealLies's avatar

I highly recommend that everyone (including scientists) consider reading Yockeys book. It’s a lovely tale of how DNA was discovered to be a code, and specifically not a template, or blueprint. Fascinating to hear the story of how the Russian Linquist Gamov escaped his country in the middle of the night to come to America. Humpty Dumpty is used to explain the importance of word play… it’s a fun book, and explains why Yockeys protocol is used to this day as the standard for mapping the transcription process and how it arose from Claude Shannon’s Information Theory.

Available for free on Google Books here

I’ve pulled some of my favorite quotes about code, information, and the transcription process here. Please enjoy!

RealEyesRealizeRealLies's avatar

More Yockey quotes… ya gotta read this book folks!

13.1
“One of the more important contributions in this book, and in two previous papers, is to point out that no code exists to send information from protein sequences to sequences in mRNA or DNA. Therefore, it is impossible that the origin of life was “proteins first”... Scientists cannot get around it by clever chemistry. This restriction prevails in spite of the concentration of protein in a “prebiotic soup”....”

“Most of the publications on the origin of life are based on chemical reactions that under “plausible prebiotic conditions” (as though mankind is capable of deciding what is plausible) are presumed to provide an Urschleim from which proteins are alleged to have originated in the early ocean…. NASA is totally committed to the Oparin dialectical materialist speculations on the origin of life. Most of the origin of life projects supported by NASA and other funding agencies are “proteins first” are are due to go the way of perpetual machines. They may produce interesting chemistry but they have nothing to do with the origin of life.”

“Belief in a primeval soup on the ground that no other paradigm is available is an example of the logical fallacy of the false alternative. In science, it is a virtue to acknowledge ignorance.”

“Although majority logic redundance plays an unimportant role in telecommunications it is controlling in the genetic communication system. This shows without a doubt that evolution and genetics cannot be understood except by information theory.”

shilolo's avatar

You quote a physicist writing about biology, which, in many cases, he didn’t understand? He makes the mistaken assumption that events occur in isolation, as if de novo protein synthesis had to occur before RNA or DNA synthesis. Indeed, with the appropriate chemicals around, proteins could have been made contemporaneously with RNA-like or DNA-like molecules. As an example, a simple 32 amino acid protein is able to self replicate and RNA can use RNA to self-replicate (here too). Furthermore, we now know that prions are infectious agents that self-replicate and consist entirely of protein (i.e. no nucleic acid). Thus, multiple self-replicating units (either protein or RNA) could have developed simultaneously, and either in competition or cooperation, settled on a pathway to “life”.

I find it funny that you quote Yockey as if he was some sort of genius. His are opinions that are both outdated, and in many cases, wrong. Yockey assumes, wrongly in my opinion, that the 4 bit code of DNA that exists today must have been the code in the distant past. On that basis, he concludes that it would be impossible for life to have simply “happened”. He does not really entertain the idea that a 3 bit or 2 bit code could have existed, which over time led to self-replication, and eventually led to our current 4 bit code. He goes on to calculate the probability of the random formation of a single specific protein, which is quite large. The probability he calculates is very low, but it is based on faulty logic. The early events could have favored formation of any self-replicating protein, not one very large one. Indeed, scientists have already discovered a 32 amino acid self-replicator (as I showed above), and the probability of formation of such a protein is actually relatively large. Furthermore, processes do not occur necessarily in series. It isn’t like nature “tried” one peptide, then another, and another, and so on. Billions of syntheses could (and likely were) occurring simultaneously, thus greatly increasing the chances of a viable self-replicating protein.

I understand that you like information theory, but I wouldn’t trust a physicist to do the job of a biologist (and vise versa).

RealEyesRealizeRealLies's avatar

“no code exists to send information from protein sequences to sequences in mRNA or DNA. Therefore, it is impossible that the origin of life was “proteins first”... Scientists cannot get around it by clever chemistry. ”
Yockey

“The self-organization of the reductive citric acid cycle without the help of “informational” catalysts would be a near miracle”.
Leslie Orgel (Abiogenesis proponent) emphasis mine
________

And Martin Line warns that even with “a membraine enclosed ribozyme capable of plymerising itself and its counterpart copy…”

“The pathway proposed is not intended to represent reality”

and requires “a formidable conceptual leap” and

“If support for some of these steps can be shown, final resort to an intelligent creator for the origin of life (Gibson, 1993) may yet be premature”
Martin Line, A Hypothetical Pathway from the RNA to the DNA World

shilolo's avatar

Did you notice my very first comment on the RNA world? I guess not. As I also said above, it is far too simplistic to assume that chemical events between pre-amino acids and pre-nucleotides were occurring in a vacuum or that the amino acids we observe today are the same as those that existed long ago. You clearly reveal your ID intent. I’m done.

RealEyesRealizeRealLies's avatar

How does quoting Atheists Yockey, Orgel, and Line reveal my “ID intent”? I’m simply sharing what they say.

I’m sorry you don’t understand the differences between ID/Creationism and the Intelligent Evolution that I’m actually promoting. I’ve offered to explain it further, but it’s safer to just label me however makes you comfortable. Label me with what I’ve rejected twice… nice.

Well, as far as assumptions are concerned, why is it safe to “assume” that what we don’t know, but not allowable to “assume” or “infer” scientific theory upon that which we do know? That being, codes have sentient authors.

cockswain's avatar

You don’t know that codes in nature have sentient authors. You just think they might.

RealEyesRealizeRealLies's avatar

Does anyone here have a demonstrable mechanism other than sentient authorship which can account for the existence of code? If so, then please present it, and get your Nobel Prize acceptance speech ready. If not, then please give credit where credit is due, to the uniqeness of sentient authors, and to the scientific method.

Science moves forward by acknowledging what we DO know. And we know that sentient authorship is a viable mechanism for authoring code. If another mechanism is demonstrated at a later time, then science will do well to accept it, and move forward accordingly. But until that day, we must accept what IS known, lest we hold science back, forcing it to bend under our will. That wouldn’t be science at all.

cockswain's avatar

Codes written and defined by humans doesn’t necessarily mean codes in nature are written by some self-aware being. I don’t even know why you’re so hung up on something no one on the planet actually knows anyways. I’ve said before, it’s a reasonable thing to guess, but you’re acting like you know it to be true.

RealEyesRealizeRealLies's avatar

That’s because IT IS TRUE.

Sentient Authors are the only known source of code creation. Science moves forward upon truth statements. Science is held back with “maybe what if could be if we only tried harder” statements.

It’s the same logic that we use to attribute sentient authorship as the source for anonymous notes found on the street, “I love you” carvings on trees, and ancient manuscripts sans authors but must be deciphered. We don’t automatically “assume” that these codes wrote themselves just because we don’t know who the author is.

A code is a code when it conforms to Purlwitz, Burks, and Watermans formal definition and runs through the Shannon protocols with flying colors. DNA/RNA transcription does that. Nothing else from your beloved “nature” does.

The implications of this are profound by all measure. It forces us to re-examine our current notions of what “nature” is and how we as humans relate to it. Isn’t that what good science is supposed to do?

And I’ll let you in on a little secret. I’ve never discussed this aspect on this forum, but it is most important to understand if you’ll give it the proper consideration it deserves. This issue is way beyond the simplistic code that we humans use. We’re not talking about primitive binary or spoken language. DNA is a quaternary code, and RNA is a tertiary code. This is so advanced that we can barely begin to decipher it.

To put a perspective on this, there is a monumental difference between the logic capacity of binary and ternary. It’s almost incalculable to determine logic to the quintic or sixth power.
a 16-bit microcomputer with on-board memory has access to no more than 216 bits of directly accessible memory (about 65k bits), while that same microcomputer with memory based on ternary logic would have direct access to 316 or 43 Mbits of memory.

That’s 65KBit vs 43MBit simply jumping from binary to ternary.

…729 commutative functions in ternary logic as opposed to 8 in binary logic…

It’s a huge difference.

…Binary logic is like driving through Manhattan and only to be able to drive straight and make right turns. Ternary logic is being able to drive straight and turn left and right. Not only can you get somewhere potentially faster, in a one-way grid, you now can reach places you couldn’t reach before.

Sorry folks, but this is way beyond the possibility of accidental code authoring. This is supremely advanced programming.

Now as the Russian scientist Gariaev (father of Wave Genetics) has discovered DNA to also be transmitting sound and light waves, it is possible that DNA has approached the level of quintic logic or even a magnitude to the sixth power.

…these images are read by the light and sound radiations of the chromosomes, transmitted to the neighboring cells informing them about the condition of the cell sending the information.

And Gariaev has even demonstrated a phantom effect, suggesting that science is finally beginning to uncover an immaterial realm with even more extensive layered “holographic” programming capacity.

A quartz cuvette with a DNA sample is moved from one location to another. And a trace, a phantom, is left in the air in the original location of the sample. This phenomenon was registered using the laser spectroscopy method by P. Gariaev in 1984 in Russia and by the group of R. Pecora in 1990 in the U.S.A. Gariaev also investigated the stability of the phantom and he found the following. After blowing the phantom away by the gaseous nitrogen, it comes back in 5–8 minutes. And the phantom disappears completely after 1 month. We remark that sound waves radiated by the DNA molecules were registered in these experiments.

You honestly expect me to believe that this level of extremely superior programming just popped into existence by accident? Without a supremely superior mind behind it all? We can’t even find a “natural” code that transmits and receives “1+1=2” anywhere in the our known universe. Who’s praying for a miracle here?

shilolo's avatar

Well, now I’m convinced (of something).

Jabe73's avatar

@Ben_Dover I can’t believe you didn’t get 1 GQ vote so there you go.

@RealEyesRealizeRealLies This is not my subject of expertise here but are you saying there is a difference between intelligent design and intelligent evolution? So you are not technically a theistic evolutionist it seems.

Personally I never heard of the term “intelligent evolution”. Can you give a brief description in layman’s terms here on what this is? I’m not a scientist or mathematician.

I was aware of living cells showing some forms of intelligence from some basics I’ve read about them. Some are now even saying that even atoms and their sub-atomic energy particles have a form of their own intelligence as well. Jumped off topic a bit here but it was a social question and I was curious.

RealEyesRealizeRealLies's avatar

”...are you saying there is a difference between intelligent design and intelligent evolution?”

Yes, absolutely.

“So you are not technically a theistic evolutionist it seems.”

No, not at all.

“I never heard of the term “intelligent evolution”.”

Neither have I. I.E. is my own terminology. I coined the term about five years ago and have been promoting it ever since. It takes a while for a meme to catch on.

Imagine my surprise when I recently heard the term used in a podcast by Terrence McKenna from the mid-1980’s. I hadn’t heard the term before I crafted it. Although I found that Terrence was brushing over some of the same issues that I present, his use of the term was in a passing sentence, and not meant necessarily to embody a world view. His research on the subject is vast, but he had not delved into it as deeply as I have for the past decade.

So as much as I’d like to take credit for coining the term Intelligent Evolution, in all truth, I cannot. I’m confident that Terrence would be very pleased with what I’ve put together.

“Can you give a brief description in layman’s terms here on what this is?”

Thank you for asking.

First, Intelligent Evolution is different from I.D./Creationism by the fact I.E. does not require a traditional God concept to be the designer. I don’t even promote a Designer. I promote an Author. There is a difference. Designers can create without a code. Designers take readily available materials and bend, mold, sculpt a likeness out of their minds eye. It is only later when that object is codified with careful description. And even then, no mechanism is functional until a code is authored describing its intended function.

An Author however, begins with code, never a drawing made, nor a hunk of clay molded until the plans have been written. The plans may exist totally within the mind, and not be of physical substance whatsoever until it is desired to form it into physical material. That is the process of Information… In-form-ation, the process of manifesting thought in-to-form.

Where I.D./Creationists typically insist upon a biblical perspective of the Christian God, my thesis of Intelligent Evolution makes no claims whatsoever about the nature of the required Author. It could be Aliens. It could be Time Travelers. It could be that the cosmos is actually a sentient entity in its own right and actually did speak by authoring a code of life. It could be God, or a version of God. I don’t know and I don’t claim to know. I have my theories, but those are based on a different subject matter altogether and not a part of an I.E. dissertation. With I.E., I only claim that there must in fact be some form of Sentient Author to account for the existence of the genetic code of life.

I do not believe in the supernatural or miracles. I’m quite confident that if this Author exists, then it is perfectly natural for IT to exist. Its existence may seem supernatural, but that is only because of our inability to comprehend, at this stage of human awareness.

Intelligent Evolution is a logical bridge between Hard Marxist Dialectic Materialism and all Ancient Wisdoms based upon principles of The Word. It is no more related to Christianity than it is to the Sphota Theory of Language presented by Bhartrihari, and in fact, Bhartrihari explains it better than any Biblical Scholar could ever hope to.
_____________

As to the workings of Intelligent Evolution, the theory is based upon Classic Darwinian Theory, Computer Science, and the legacy of Barbara McClintock supported by James Shapiro. Terrence McKenna has presented other support and I am currently researching his claims.

First, Darwin NEVER mentioned the term “Random Mutation” in Origin of Species. He proposed Natural Selection as the method which Evolution worked, but he did not know the mechanism which NatSel operated upon. Within the first ten pages, he notes an as of yet undiscovered mysterious unknown force that NatSel must operate upon. But he makes no claims as to what that force was (is). In the race to find that force, scientist coined the term Random Mutation and set Biology off on a wild goose chase for the next hundred years.

Random Mutation means, “we don’t have a clue, but we’ll get lots of grant money if we make you think that we do”. They may just as well have called it “Singularity”. It means nothing, and is as far away from actual science as unicorns are.

Along comes Barbara McClintock. Being a woman was hard enough to get recognized, but when her research challenged the establishment based upon random mutation, she was demonized and forced underground with her findings for two decades. She was the first to note the intelligence of the cell.

_“A goal for the future would be to determine the extent of knowledge the cell has of itself, and how it utilizes this knowledge in a “thoughtful” manner when challenged.”
Barbara McClintock, Gifts of Speech

Thankfully, McClintock was awarded with the Nobel Prize for her work. James Shapiro and others like him have been confirming her research and the implications of her findings.

“Molecular genetics has amply confirmed McClintock’s discovery that living organisms actively reorganize their genomes (5). It has also supported her view that the genome can “sense danger” and respond accordingly (56).”
James Shapiro, A 21st Century View of Evolution

Finally, Computer Science teaches us that codes can and do re-author themselves based upon input from stimuli. A.I. research, robotics, computer science, all confirm this. But in every case, that code is embodied with this functionality from the very beginning by a Sentient Author.

Gariaev, the father of Wave Genetics, is also promoting the extremely advanced quaternary/tertiary language of DNA as intelligent, perhaps to the quintic power or greater.

“The basic principle of these languages is similar to the language of holographic images [5] based on principles of laser radiations of the genetic structures [6] which operate together as a quasi-intelligent system”.
_____________________________

Now, as to the intelligence of sub-atomic particles, well yes, it seems as such. But I am not willing to go there until an actual code has been uncovered. This is what I would call “Apparent Information”, in honor of Dawkins term “Apparent Design”.

To take this discussion further, we would have to isolate what a code actually is, what it does, and how Informaton and Information Theory relate to this subject. But hopefully you’ll get the jest of what I’m talking about with Intelligent Evolution, and why it is far away from any philosophical notion of Intelligent Design or Creationism. I.D./Creationism doesn’t require a code, and typically rejects all forms of Evolution. I.E. supports Evolution in the most Classic Darwinian sense, and actually hopes to relieve science of the dogma of Random Mutation in favor of a more realistic approach of Controlled Mutation.

I have found, over the years, that where there be two firmly held positions such as Marxist Dialectic Materialism vs Religious Fundamentalist, that neither side of the argument is capable of getting past their dogmatic perspectives long enough to consider the actual Truth, which is Truthfully, most often found sitting somewhere in the middle.

shilolo's avatar

Just so people don’t get a disorganized and disoriented view of science, what @RealEyesRealizeRealLies stated above is both absurd, and more troubling, entirely taken out of context. Barbara McClintock received the Nobel Prize for her work on mobile genetic elements. There is nothing in her work that acribes an “author” or sentient being. Likewise, the quote from James Shapiro is completely misinterpreted and out of context. Yes, genomes rearrange all the time, but it is not guided by some unseen hand. The “sensing danger” part relates to the accumulation of mutations/DNA damage, not some 6th sense on the part of DNA.

In summary, the above “thesis” is nothing but random ramblings and disconnected thoughts. No one takes this seriously.

RealEyesRealizeRealLies's avatar

I certainly never once claimed that McClintock or Shapiro suggest an author, a sixth sense, or an unseen hand. They only refute random mutation. And you can say what it’s not all you want. I’m interested in what it is.

I’m unsure of what is meant by “accumulation of mutations/DNA damage” when speaking of McClintock/Shapiro. Have you read them @shilolo? It’s very clear that is not what either one of them are talking about.

They are specifically speaking of controlled mutations and reject any suggestion of “DNA damage” being responsible for authoring code.

“Over the years I have found that it is difficult if not impossible to bring to consciousness of another person the nature of his tacit assumptions when, by some special experiences, I have been made aware of them. This became painfully evident to me in my attempts during the 1950s to convince geneticists that the action of genes had to be and was controlled. It is now equally painful to recognize the fixity of assumptions that many persons hold on the nature of controlling elements in maize and the manners of their operation. One must await the right time for conceptual change.”
Barbara McClintock

“The conventional view is that genetic change comes from stochastic, accidental sources: radiation, chemical, or oxidative damage, chemical instabilities in the DNA, or from inevitable errors in the replication process. However, the fact is that DNA proofreading and repair systems are remarkably effective at removing these non-biological sources of mutation.”

“Evolutionary genomic change occurs largely by a process of Natural Genetic Engineering.”

”…the degree to which these genome reorganization activities are not random is poorly appreciated. Non-randomness is evident at three levels: mechanism, timing, and sites of action.”

“These examples make it clear that natural genetic engineering occurs episodically and non-randomly in response to stress events that range from DNA damage to the inability to find a suitable mating partner.”
James Shapiro

shilolo's avatar

Do you study science? Do you even understand what they are talking about? When McClintock talks about “controlling gene expression”, she is talking about the fact that DNA is not static, that it is indeed changing, and that there are genetic elements that facilitate those changes. Again, you misunderstand her quotes and take them out of context. She is not saying changes are “controlled” by an author or sentient being, but rather that there are formal mechanisms (genetic and otherwise) that mediate some examples of genetic mutation.

You also quote James Shapiro as if one person’s ideas are “fact”. The reality is that DNA randomly mutates all the time in the lab (and in nature). Bacteria exposed to certain antibiotics spontaneously mutate to resist said antibiotic (i.e. a strong selective pressure helps facilitate the growth of mutants that can survive). HIV mutates randomly at a very rapid pace to develop resistance to antiviral medications. Humans over their lifetimes develop mutations that lead to cancer (despite the proofreading mechanisms inherent to most cells). Whole genome comparison of closely related species demonstrates single nucleotide changes responsible for whole-sale phenotypic changes. Humans have single nucleotide polymorphisms that accumulate over time that differentiate us from each other. Those SNPs are not “guided” or “controlled”. They occur randomly, and over time, SNPs that facilitate a survival benefit persist, while those that don’t die out. The list goes on and on.

Please stop spamming this link with your wild and irrational ramblings.

RealEyesRealizeRealLies's avatar

I am not a scientist. I do study science. I research science. I work with many scientists.

I don’t recall ever stating that McClintock said, “changes are “controlled” by an author or sentient being”.

I don’t recall ever stating that myself. I’m not really sure where you get that from. You’re either misreading me, misunderstanding me, or your dogmatic perception is not allowing you to really digest what I actually am saying.

@shilolo “Bacteria exposed to certain antibiotics spontaneously mutate to resist said antibiotic…”

If a Theist used the word “spontaneously” to describe something, you’d probably disregard it as belief in the miraculous. But when a scientist uses that word, we’re supposed to accept it as some kind of legitimate answer. Spontaneous, is a non-answer.

Random is a non-answer too. It is belief in the miraculous. “It just happens!”

I prefer to believe there are actual reasons behind the mutations. As both McClintock and Shapiro suggest, there are accidental mutations, and there are controlled mutations. But there are no random mutations. Sometimes accidental mutations do take place, but a species cannot survive on a house of accidental mutations. And our genetic mechanisms do their best to prevent accidental mutations. The beneficial mutations are those which are controlled, as in “intentional”. And as McClintock/Shapiro both suggest, they are based upon “knowledge” that the cell has of itself, and the “response” it intelligently engages in a “thoughtful” manner.

shilolo's avatar

There are NO intentional MUTATIONS (i.e. point mutations). DNA can rearrange, or transpose, and some of that is under the influence of stress, but many of the transpositions insert into important regions of the cell which disable vital functions. McClintock has never “suggested” that cells have “intelligence” or a “thought process”. You can attempt to anthropomorphize random or stochastic events, but there is no evidence to suggest those things occur. How do you explain the mutations that occur in the HIV genome? Cancerous mutations are “thoughtfully” acquired by malignant cells? Species “think ahead” and “create mutations” so that their ancestors can become new species? Your ideas are absurd and not supported by a shred of evidence. No mas! Bye bye.

RealEyesRealizeRealLies's avatar

“A goal for the future would be to determine the extent of knowledge the cell has of itself, and how it utilizes this knowledge in a “thoughtful” manner when challenged.”
Barbara McClintock, Gifts of Speech

Jabe73's avatar

@RealEyesRealizeRealLies From reading more of your posts it seems your views are more similar to mine than anyone else’s on here. For one I do not believe in a literal creative “god” myself. In fact I do not have a clue what/who this author is myself. Some eternal form of an intelligent author/force that just always was?

I agree with you about the two major philosophies we are given to go with here. Either way path seems to lead to miracles here. On one camp you have the miracle of intelligent life forming randomly from nothing than on the other side you have the super miracle of an omnipotent magical “god” who decided one day to start creating things from nothing. I often wondered what this type of god was doing all them years before his creation. I take somewhat of a middle road type of approach myself here. I also do not believe in the “supernatural” myself, just perhaps an undiscovered branch of physics we cannot at this current time observe and comprehend.

Barbara McClintock was not the only person/scientist/inventor demonized for unorthodox scientific views. In all fairness in the name of science itself we can only get to the truth of anything by studying what we can observe and measure at our current point in time so even though I have some unorthodox views myself I still cannot criticise the majority of scientists here. I appreciated your detailed answers here. I appreciate Shilolo’s responses as well.

PS I know you wanted to talk about intelligent evolution to begin with.

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