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Cell Requires Hundreds of Kilobases for Mature Micro-RNA

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Here’s todays headscratcher from Phys.Org.

It appears that to contrive a “mature” micro-RNA (mi-RNA), involved in gene regulation, the cell requires hundreds of kilobases of sequence. How odd. “Mature” mi-RNA’s are ~22 bases in length, and hundreds of thousand of nucleotide bases are needed (of primary-mi-RNA) to effect this ~22-nucleotide regulatory element?

Here’s what they say:

MicroRNAs are short noncoding RNAs that play critical roles in regulating gene expression in normal physiology and disease. . . .

Although mature miRNAs are only ~22 nucleotides, their transcripts are up to hundreds of kilobases long. Primary miRNA transcripts, or pri-miRNAs, are quickly processed into mature miRNAs from hairpin structures located in the exons or introns of pri-miRNA transcripts.

One remarkable feature of primary miRNAs is their extreme length, even in cases where they function only to produce a single ~22 nucleotide miRNA,” said Joshua Mendell, corresponding author of the study. “Although it seems wasteful to produce such long RNAs, most of which will be immediately degraded, this organization may have arisen to allow complex mechanisms of regulation of the encoded miRNA.

As usual, they’re “surprised” about their findings (very likely they are ‘surprised’ because they weren’t expecting things to turn out so complex). And, as usual, the pro forma reaching out to “evolution” as the explanatory mechanism, when, in fact, no explanation is given at all: . . . this organization may have arisen to allow complex mechanism of regulation of the encoded mi-RNA.”

It may have; but, it may have not. Is this scientist willing to consider this other possibility, or is it simply an article of faith that “evolution-did-it”? One wonders.

Comments
Carpathian:
The debate is about whether we were designed.
That debate is over and you lost. You don't have an explanation for our existence. You don't have anything but your strawmen. Virgil Cain
Carpathian:
When a student asks the IDist teacher the same ones I’m asking,
Students aren't as ignorant as you are. Students will be able to understand what ID is and why your questions are irrelevant. Virgil Cain
Carpathian:
Obviously you still don’t have evidence for biological ID.
We have positive evidence for biological ID. Your ignorance is not a refutation. The science of ID is in the detection and study of design in nature. And no amount of your ignorant spewage will ever change that fact. Also that is more science than your position has- well any science is more than your position has. Virgil Cain
"Where do you think it comes from?" God, of course. Andrew asauber
"Our ability to design comes from years of evolutionary pressure." I'm not sure I understand what you mean by pressure in this context. Is this pressure detectable/measurable by some kind of calibrated instrument? Andrew asauber
asauber:
I’m asking you what you think. Can you let me know what you think?
Our ability to design comes from years of evolutionary pressure. Where do you think it comes from? Carpathian
"Why are you implying that our ability to design came from some other intelligence?" I'm asking you what you think. Can you let me know what you think? Andrew asauber
asauber:
Debate indeed. From what did the ability for humans to design come from, do you think?
Why are you implying that our ability to design came from some other intelligence? Show me evidence that we were designed. Carpathian
Virgil Cain:
Carpathian: If your side truly believes it’s science you should already have performed the analysis of whether it’s logistically possible. That doesn’t follow. Obviously you are just an ignorant arse.
Of course it follows. Do you believe in biological ID? If so, it should be possible for you come up with a plan. Show how to add an IC structure to an existing population of organisms. Carpathian
"LOL!!! Yes!!!! There is no debate that humans design things. The debate is about whether we were designed." Debate indeed. From what did the ability for humans to design come from, do you think? Andrew asauber
Mapou:
I see that Carpie, the idiot materialist troll, is still swimming in a river of stupidity of his own making. Virgil, please stop feeding the carps.
I see that you don't have any scientific arguments either. When a student asks the IDist teacher the same ones I'm asking, they'll use your response, because they still won't have answer, 10, 20, 50 or a 100 years from now. Carpathian
I see that Carpie, the idiot materialist troll, is still swimming in a river of stupidity of his own making. Virgil, please stop feeding the carps. Mapou
asauber:
So in your world, humans can design without having been designed themselves? Do I have that right?
LOL!!! Yes!!!! There is no debate that humans design things. The debate is about whether we were designed. Carpathian
Virgil Cain:
That doesn’t follow. Obviously you are just an ignorant arse.
Obviously you are still Joe. Obviously you still don't have evidence for biological ID. Show the logistics of biological ID. Logistics...., logistics......., logistics..... It doesn't exist. Carpathian
"The target of the ID is biological, not the designer." So in your world, humans can design without having been designed themselves? Do I have that right? Andrew asauber
Carpathian:
If your side truly believes it’s science you should already have performed the analysis of whether it’s logistically possible.
That doesn't follow. Obviously you are just an ignorant arse. Virgil Cain
Carpathian- You are obviously just an ignorant troll. The science of ID is in the detection and study of design in nature. And no amount of your ignorant spewage will ever change that fact. Also that is more science than your position has- well any science is more than your position has.
Does the ID side have evidence of biological ID being performed?
Yes, genetic engineering including Venter's synthetic DNA, Fox's protocells and GMOs. Virgil Cain
Virgil Cain:
Carpathian: The logistics is a barrier to biological ID. Virgil Cain: That’s your opinion. And your opinion is shit so no one cares.
Neither of our opinions count so just show me the evidence. Point me to an ID book that has worked out the logistics of ID. If your side truly believes it's science you should already have performed the analysis of whether it's logistically possible. Carpathian
asauber:
One of the many pieces of evidence that biological ID exists is that human ID works (humans are biological). What about that do you not get?
What do you not get about what is meant by biological ID? The target of the ID is biological, not the designer . All that IDists have ever shown is that humans can perform non-biological ID like building airplanes or computers. Does the ID side have evidence of biological ID being performed? I'm not talking about gene splicing. I'm talking about rolling out a new IC structure in an existing organism for example. Where is a book that contains the logistics analysis of actually performing ID? It must exist if ID can be done at all. Carpathian
Carpathian:
The logistics is a barrier to biological ID.
That's your opinion. And your opinion is shit so no one cares. Virgil Cain
"No, you have shown that human ID works. You have zero evidence that biological ID exists." Carpathian, One of the many pieces of evidence that biological ID exists is that human ID works (humans are biological). What about that do you not get? Andrew asauber
Virgil Cain:
Carpathian: No IDist here has ever shown any work on the logistics side Virgil Cain: It’s a strawman that only losers on an agenda use.
The logistics is a barrier to biological ID. No scientist would leave such a huge unanswered question about their own theory. Carpathian
Carpathian:
You have zero evidence that biological ID exists.
We have plenty of evidence that biological ID exists. You are just too ignorant to understand it. And you definitely don't have any alternative explanations.
No IDist here has ever shown any work on the logistics side
It's a strawman that only losers on an agenda use. Virgil Cain
Virgil Cain:
Carpathian: You have not shown that biological ID exists. Virgil Cain: Yes, we have and you don’t have any other explanation. So stuff it.
No, you have shown that human ID works. Humans design computers and pyramids. You have zero evidence that biological ID exists. It's what the debate is about. No IDist here has ever shown any work on the logistics side and you have ducked that question too. Carpathian
Carpathian:
You have not shown that biological ID exists.
Yes, we have and you don't have any other explanation. So stuff it. Virgil Cain
Virgil Cain:
To sum up- Using scientific methodology we have shown that Intelligent Design exists.
You have not shown that biological ID exists. That is what the debate is about, biological ID. IDists have to prove that biological ID is possible. No IDist anywhere has proven that biological ID is possible by actually working through the logistics of doing it. I'm not talking about gene splicing, but rather the logistics and system analysis required. If you have an organism that needs an IC structure added, how do you get the change into the organism? How do you find them all? How many do you have to do to ensure sexual reproduction doesn't get rid of your change? Anyone who has thought about it could fill a book just describing the problems you would need to solve to perform biological ID. Carpathian
Carpathian:
If he is not infallible, he’ll make mistakes he has to fix.
How do you know? Mistakes could be made that don't require fixing.
Does biological ID exist?
Yes, if we are to believe our knowledge and ability to scientific inferences. The work is shown by eliminating materialistic explanations, which was easy because there aren't any, and seeing if the design criteria is met. All of that has been done. OTOH you still have nothing but your ignorance. To sum up- Using scientific methodology we have shown that Intelligent Design exists. That means it was obviously possible. And until someone can come up with a way to test materialistic scenarios the design inference is very safe. Virgil Cain
Virgil Cain:
Carpathian: Obviously, if biological ID is impossible, it doesn’t exist. Virgil cain: It exists so obviously it was possible, duh.
That is what the argument is about. Does biological ID exist? If it is impossible to do, by definition, it can't exist. Show that it's possible. Do the work. Don't just make assertions. Simply making assertions won't be accepted by students. Show your work. Carpathian
Virgil Cain:
Carpathian: 1) Unless he’s infallible, he would have to fix any mistakes he or his team have made. Virgil Cain: Your opinion is not an argument.
How is that an opinion? If he is infallible, he won't make mistakes he has to fix. If he is not infallible, he'll make mistakes he has to fix. Carpathian
Carpathian:
Obviously, if biological ID is impossible, it doesn’t exist.
It exists so obviously it was possible, duh.
Show the world of biology that biological ID is possible.
We have shown the world it exists and no one has a viable alternative. IOW we have the science and all you have is whining.
1) Unless he’s infallible, he would have to fix any mistakes he or his team have made.
Your opinion is not an argument.
2) If an organism cannot “evolve” new functionality, he would have to add it.
Why would they need new functionality? Virgil Cain
Virgil Cain:
AGAIN- we use science to show that Intelligent Design exists. Obviously if it exists it is possible.
Obviously, if biological ID is impossible, it doesn't exist. Show the world of biology that biological ID is possible.
Carpathian: How else could he make his modifications to an organism that is already in an ecosystem? Virgil Cain: Why would he have to?
1) Unless he's infallible, he would have to fix any mistakes he or his team have made. 2) If an organism cannot "evolve" new functionality, he would have to add it. 3) If his organisms can produce new functionality on their own, then "Darwinism" works as stated. Carpathian
AGAIN- we use science to show that Intelligent Design exists. Obviously if it exists it is possible. Virgil Cain
Carpathian:
But you’re not showing that ID can account for any of these either.
That is the only thing that can.
Then we wouldn’t be discussing “Darwinism” if ID had proof/evidence of a designer.
We have to for the reasons provided- it exists and the way to the design inference is through it and all like it.
That’s exactly how I would expect an ID instructor to be like.
Explaining what ID is and what it isn't? That is what I would expect. I would also expect the students to be able to grasp the simple facts.
How else could he make his modifications to an organism that is already in an ecosystem?
Why would he have to?
We’re not talking “Darwinism” where a successful mutation propagates through a population.
Talk about oversimplification. What is "successful" is relative and changing.
We’re talking about a necessary modification from outside the organism.
What necessary modification? Virgil Cain
Virgil Cain:
Carpathian: If he did not have the capability to design self-adapting life, then how is it possible to make changes to billions of living organisms all at once? Virgil Cain: Why is that a requirement?
How else could he make his modifications to an organism that is already in an ecosystem? We're not talking "Darwinism" where a successful mutation propagates through a population. We're talking about a necessary modification from outside the organism. Carpathian
Virgil Cain:
We don’t, moron. If the student is too stupid to grasp the fact that ID is about the DESIGN and not the designER then that student is in the wrong class.
That's exactly how I would expect an ID instructor to be like. Carpathian
Virgil Cain:
AND if your position had something then we wouldn’t even be discussing ID, yet here we are watching you hump your strawmen.
Then we wouldn't be discussing "Darwinism" if ID had proof/evidence of a designer. Prove ID is possible . There is no such evidence from Dembski, Behe, or anyone else in the ID camp. Carpathian
Virgil Cain:
The laws that govern the universe; living organisms; ATP synthase; bacterial flagella; cilia; the genetic code- if you could show that materialistic processes can account for any of those then ID would be in deep trouble.
But you're not showing that ID can account for any of these either. Show me that ID has an answer. Don't say something to the effect of; the guy who painted my house must have been called Bob because you can't prove his name is Steve. Prove there was an intelligent designer. You also haven't even attempted to answer how you would roll out a change into a billion organisms spread out over the world. If you attempt to answer it, you'll find out it can't be done. Carpathian
Carpathian:
Not even trying to examine the designer or his mechanisms would convince me you don’t believe in the science of ID yourself.
Umm, the science of ID is in the detection and study of intelligent design. We can't study the designers of Stonehenge. We use the existence of Stonehenge to posit the designers also existed. AND if your position had something then we wouldn't even be discussing ID, yet here we are watching you hump your strawmen. Virgil Cain
Carpathian:
If the intelligent designer created life that could respond to changes in the environment, why bring up the intelligent designer at all?
We don't, moron. If the student is too stupid to grasp the fact that ID is about the DESIGN and not the designER then that student is in the wrong class. That said, only an intelligent designer can explain the intelligent design.
If he did not have the capability to design self-adapting life, then how is it possible to make changes to billions of living organisms all at once?
Why is that a requirement? Virgil Cain
Carpathian:
Detectives don’t stop at; “ Someone must have done it, case closed.”
Detectives aren't scientists. If there aren't any witnesses then all they have is what forensic science tells them. Then sure, they can pound on doors and harass people in the hope something will turn up.
Show me the evidence for an intelligent designer.
The laws that govern the universe; living organisms; ATP synthase; bacterial flagella; cilia; the genetic code- if you could show that materialistic processes can account for any of those then ID would be in deep trouble. Virgil Cain
Virgil Cain:
Why not? There is plenty of evidence for an intelligent designer so obviously there was opportunity.
Cuz you say so? That’s not an argument. Show me the evidence for an intelligent designer. How do you make a change in billions of organisms spread out over the planet? How long would it take in years? How long would it take in generations? Is it done all at once like updating your browser over the internet? If so, how are organisms networked? If they're not networked, how do you get feedback from them in order to plan an update? Carpathian
Virgil Cain:
Carpathian: When a detective investigates a case, he doesn’t just look at circumstantial evidence, but also looks into motive and opportunity. Virgil Cain: Detectives are not the forensic scientists. And they don’t always find out who did it. But the crime still exists.
That doesn't change the fact that they look into motive and opportunity. This is done to exclude some probable suspects from suspicion and also to exclude all the crackpots who call in to confess to famous crimes. The crime still exists but the active work of the detectives can lead to conclusions that might include suicide or accident instead of an assumption of murder, which would not have happened if they had closed their case without looking into motive and opportunity. Detectives don't stop at; " Someone must have done it, case closed." Carpathian
Mapou:
Why do we continue to waste our time with this stupid troll? What is our motive?
Your motive is to get creationism in schools. The problem ID has is that it can't answer the questions an average student would ask. That's why you get frustrated with people like me. I ask questions, and you don't have answers. Here's a few questions students might ask. If the intelligent designer created life that could respond to changes in the environment, why bring up the intelligent designer at all? If he did not have the capability to design self-adapting life, then how is it possible to make changes to billions of living organisms all at once? Carpathian
Carpie:
There is no motive for an intelligent designer. There is no opportunity for an intelligent designer. That rules out an intelligent designer as a suspect.
Why do we continue to waste our time with this stupid troll? What is our motive? Mapou
Carpathian:
When a detective investigates a case, he doesn’t just look at circumstantial evidence, but also looks into motive and opportunity.
Detectives are not the forensic scientists. And they don't always find out who did it. But the crime still exists.
There is no motive for an intelligent designer.
Cuz you say so? That's not an argument.
There is no opportunity for an intelligent designer.
Why not? There is plenty of evidence for an intelligent designer so obviously there was opportunity. OTOH your position still has nothing. Virgil Cain
Virgil Cain:
That is a scientific requirement. Look, obviously you are just an ignorant troll. Why do you even bother posting seeing that you are so ignorant as to not understand anything?
When a detective investigates a case, he doesn't just look at circumstantial evidence, but also looks into motive and opportunity. Why doesn't ID? I can tell you. There is no motive for an intelligent designer. There is no opportunity for an intelligent designer. That rules out an intelligent designer as a suspect. Carpathian
Carpathian:
If you really want to make headway, find the programmer.
That is a scientific requirement. Look, obviously you are just an ignorant troll. Why do you even bother posting seeing that you are so ignorant as to not understand anything? Virgil Cain
Earth to Alicia Cartelli- Your position cannot explain biology. It cannot explain Drosha nor Pasha. So please buy a vowel. Virgil Cain
bornagain77:
As to the fact that the cell is a sophisticated biological computer, programmed far above anything man has ever accomplished in his machines, do you disagree with that fact? If so you are more ignorant of biology than expected in spite of how hard you toot your own horn.
The dispute between evos and IDists is exactly whether the cell has been programmed by an intelligent agent or not. What you have implicitly said is, "We are right since we are obviously right" That's not a very scientific argument. If you really want to make headway, find the programmer. Find how designs are updated across millions of population members distributed across continents. It shouldn't be difficult since you have his/her/their designs. That would convince people. Not even trying to examine the designer or his mechanisms would convince me you don't believe in the science of ID yourself. Carpathian
You guys are funnyyyy! I mean really, the people that actually study quantum dynamics barely understand it. And I'm supposed to believe that the keyboard warriors here have enough of a grip on it to apply it in a conversation about biology? Please. You guys have a lousy understanding of biology and yet love to talk about its complexities, and it shows. I can only imagine how a conversation with both molecular biology and quantum mechanics intertwined would go. When someone wants to talk about BIOLOGY and not the far-flung field of "quantum biology" that apparently exists, I will be here. Alicia Cartelli
SA, “We’re smarter than you, so evolution wins” yes exactly. :) Moreover, this whole “We’re smarter than you, so evolution wins” argument has been around for a very long time. In fact, Paul describes their “We’re smarter than you, so evolution wins” strategy all the way back in Romans 1:22-23
Romans 1:22-23 Professing themselves to be wise, they became fools, And changed the glory of the uncorruptible God into an image made like to corruptible man, and to birds, and fourfooted beasts, and creeping things.
bornagain77
BA77
Of course, wd400 beat you to that whole ‘shtick’ years earlier. i.e. ‘You just don’t understand evolution
That's the best. :-) "We're smarter than you, so evolution wins". Silver Asiatic
BA77 @ 122 -- LOL. Some great arguments there. :-) I love this one:
"You brought up quantum dynamics and molecules carrying out computations. What you have said simply makes no sense to me, and is far removed from any actual biology."
Or, in translation: "It's not the linear sequence that Darwin proclaimed in the 19th century, so it's not real biology". Or a better translation: "The quantum dynamics in protein folds are irreducible to my primative materialistic worldview, so I don't want to talk about it". If she keeps working that shtick she might land a nice stand-up routine in the Catskills. Ba-da-bump. Silver Asiatic
“Mystery at the heart of life” https://uncommondescent.com/intelligent-design/mystery-at-the-heart-of-life/ “The third way…” https://uncommondescent.com/evolution/a-third-way-of-evolution/ bornagain77
BA77 Please, would you mind to letting your 'nice' interlocutor know that there's plenty -over 1600 (combined) references to recent research papers- to talk about biology (the real deal) in the discussion threads (started by News) "Mystery at the heart of life" and "The third way...". Thank you. Dionisio
Of supplemental note to protein folding. Protein folding is now found to belong to the world of quantum physics and not to the world of classical physics as is presupposed in the reductive materialism which undergirds neo-Darwinian thought:
Physicists Discover Quantum Law of Protein Folding – February 22, 2011 Quantum mechanics finally explains why protein folding depends on temperature in such a strange way. Excerpt: First, a little background on protein folding. Proteins are long chains of amino acids that become biologically active only when they fold into specific, highly complex shapes. The puzzle is how proteins do this so quickly when they have so many possible configurations to choose from. To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,, Today, Luo and Lo say these curves can be easily explained if the process of folding is a quantum affair. By conventional thinking, a chain of amino acids can only change from one shape to another by mechanically passing though various shapes in between. But Luo and Lo say that if this process were a quantum one, the shape could change by quantum transition, meaning that the protein could ‘jump’ from one shape to another without necessarily forming the shapes in between.,,, Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins. That's a significant breakthrough. Luo and Lo's equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics. http://www.technologyreview.com/view/423087/physicists-discover-quantum-law-of-protein/
bornagain77
Ahh, we were starting to like your 'shtick'. i.e. "Its junk I tell you because I am so much smarter than you!" :) Of course, wd400 beat you to that whole 'shtick' years earlier. i.e. 'You just don't understand evolution' LOL You guys really need to get a new routine! bornagain77
And there you have it. Goodbye bornagain. Anybody who wants to talk about biology, I'll be checking in every once in awhile. Alicia Cartelli
Alicia Cartelli, you did not answer my question, i.e. are you a true believer in neo-Darwinian evolution or are you among the growing number of heretics? Please clearly state your religious preference. :) I promise the beheading will be merciful :) Since you apparently hate 'cut and paste', (i.e. knowledge), Alicia, not to mention hating any empirical evidence that might hint at design, and I certainly don't want to hurt your love for your delusional atheistic religion, you can just ignore the rest of my post Alicia Cartelli as it will not be addressed to you. (and since you will ignore the relevant points of evidence anyway) ========= For onlookers, Alicia Cartelli displays her self imposed neo-Darwinian ignorance here:
"What you have said simply makes no sense to me, and is far removed from any actual biology."
Actually, despite her apparently self-imposed Darwinian ignorance of biology, 'quantum computation' is turning out to have everything to do with biology. From Protein folding to DNA repair, to who knows what else, quantum computation is strongly implicated to be essential in bio-molecular processes. For prime example, one of the most profound puzzles in molecular biology is the question of how does a protein find its final folded form so quickly. Specifically, it is now known that proteins do not find their final folded form by random search as would be expected in a neo-Darwinian view of things:
The Humpty-Dumpty Effect: A Revolutionary Paper with Far-Reaching Implications - Paul Nelson - October 23, 2012 Excerpt: Anyone who has studied the protein folding problem will have met the famous Levinthal paradox, formulated in 1969 by the molecular biologist Cyrus Levinthal. Put simply, the Levinthal paradox states that when one calculates the number of possible topological (rotational) configurations for the amino acids in even a small (say, 100 residue) unfolded protein, random search could never find the final folded conformation of that same protein during the lifetime of the physical universe. Therefore, concluded Levinthal, given that proteins obviously do fold, they are doing so, not by random search, but by following favored pathways. The challenge of the protein folding problem is to learn what those pathways are. http://www.evolutionnews.org/2012/10/a_revolutionary065521.html Confronting Science’s Logical Limits – John L. Casti – 1996 Excerpt: It has been estimated that a supercomputer applying plausible rules for protein folding would need 10^127 years to find the final folded form for even a very short sequence consisting of just 100 amino acids. (The universe is 13.7 x 10^9 years old). In fact, in 1993 Aviezri S. Fraenkel of the University of Pennsylvania showed that the mathematical formulation of the protein-folding problem is computationally “hard” in the same way that the traveling-salesman problem is hard. http://www.cs.virginia.edu/~robins/Confronting_Sciences_Logical_Limits.pdf
Linking together a few hundred thousand computers has shortened the time to a few weeks
A Few Hundred Thousand Computers vs. (The Folding Of) A Single Protein Molecule – video https://www.youtube.com/watch?v=lHqi3ih0GrI
The reason why finding the final form of a folded protein is so hard for supercomputers is that it is like the ‘traveling salesman’ puzzle, which are ‘Just about the meanest problems you can set a computer (on) ‘.
DNA computer helps traveling salesman - Philip Ball - 2000 Excerpt: Just about the meanest problems you can set a computer belong to the class called 'NP-complete'. The number of possible answers to these conundrums, and so the time required to find the correct solution, increases exponentially as the problem is scaled up in size. A famous example is the 'travelling salesman' puzzle, which involves finding the shortest route connecting all of a certain number of cities.,,, Solving the traveling-salesman problem is a little like finding the most stable folded shape of a protein's chain-like molecular structure -- in which the number of 'cities' can run to hundreds or even thousands. http://www.nature.com/news/2000/000113/full/news000113-10.html
And protein folding is indeed found to be a 'NP-complete' problem
Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results – 2009 Excerpt: Protein Folding: Computational Complexity 4.1 NP-completeness: from 10^300 to 2 Amino Acid Types 4.2 NP-completeness: Protein Folding in Ad-Hoc Models 4.3 NP-completeness: Protein Folding in the HP-Model http://www.cs.brown.edu/~sorin/pdfs/pfoldingsurvey.pdf
Yet it is exactly this type of ‘traveling salesman problem’, i.e. NP complete problem, that quantum computers excel at:
Speed Test of Quantum Versus Conventional Computing: Quantum Computer Wins - May 8, 2013 Excerpt: quantum computing is, "in some cases, really, really fast." McGeoch says the calculations the D-Wave excels at involve a specific combinatorial optimization problem, comparable in difficulty to the more famous "travelling salesperson" problem that's been a foundation of theoretical computing for decades.,,, "This type of computer is not intended for surfing the internet, but it does solve this narrow but important type of problem really, really fast," McGeoch says. "There are degrees of what it can do. If you want it to solve the exact problem it's built to solve, at the problem sizes I tested, it's thousands of times faster than anything I'm aware of. If you want it to solve more general problems of that size, I would say it competes -- it does as well as some of the best things I've looked at. At this point it's merely above average but shows a promising scaling trajectory." per Science Daily Scientists achieve critical steps to building first practical quantum computer - April 30, 2015 Excerpt: If a quantum computer could be built with just 50 quantum bits (qubits), no combination of today's TOP500 supercomputers could successfully outperform it (for certain tasks). http://phys.org/news/2015-04-scientists-critical-quantum.html
That proteins have the inherent ability to perform quantum computation, and thus provide an adequate solution to the protein folding enigma, is established by the fact that proteins are now found to have quantum information embedded within them:
Classical and Quantum Information Channels in Protein Chain - Dj. Koruga, A. Tomi?, Z. Ratkaj, L. Matija - 2006 Abstract: Investigation of the properties of peptide plane in protein chain from both classical and quantum approach is presented. We calculated interatomic force constants for peptide plane and hydrogen bonds between peptide planes in protein chain. On the basis of force constants, displacements of each atom in peptide plane, and time of action we found that the value of the peptide plane action is close to the Planck constant. This indicates that peptide plane from the energy viewpoint possesses synergetic classical/quantum properties. Consideration of peptide planes in protein chain from information viewpoint also shows that protein chain possesses classical and quantum properties. So, it appears that protein chain behaves as a triple dual system: (1) structural - amino acids and peptide planes, (2) energy - classical and quantum state, and (3) information - classical and quantum coding. Based on experimental facts of protein chain, we proposed from the structure-energy-information viewpoint its synergetic code system. http://www.scientific.net/MSF.518.491
And Quantum information is indeed the 'physical resource' by which quantum computation is accomplished:
Quantum Entanglement and Information Quantum entanglement is a physical resource, like energy, associated with the peculiar nonclassical correlations that are possible between separated quantum systems. Entanglement can be measured, transformed, and purified. A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. The general study of the information-processing capabilities of quantum systems is the subject of quantum information theory. http://plato.stanford.edu/entries/qt-entangle/
supplemental note on quantum information in DNA:
Classical and Quantum Information in DNA – Elisabeth Rieper – video (Longitudinal Quantum Information along the entire length of DNA discussed at the 19:30 minute mark; at 24:00 minute mark Dr Rieper remarks that practically the whole DNA molecule can be viewed as quantum information with classical information embedded within it) https://youtu.be/2nqHOnVTxJE?t=1176
bornagain77
I also said I would entertain anything that was "biologically relevant." You brought up quantum dynamics and molecules carrying out computations. What you have said simply makes no sense to me, and is far removed from any actual biology. I fear that "the sequences have...some type of computational purpose, perhaps quantum...molecular information is expressed ...to allow an appropriate computation to take place," is just you trying to work in your typical copy/paste quantum dynamics-post nonsense. You either need to explain yourself better, give an example, or admit that you actually have no idea what you are talking about when it comes to biology (and quantum dynamics while were at it). Cue the "spooky actions at a distance" and the other usual nonsense copy/paste job... Alicia Cartelli
Alicia Cartelli, you said that you would 'shoot it down'. Thus the burden is on you to provide, not your opinion (as if I care what your blowhard opinion is anymore given your dogmatic antics thus far), but the appropriate experimental evidence that, to use your words, 'shoots it down'. As to the fact that the cell is a sophisticated biological computer, programmed far above anything man has ever accomplished in his machines, do you disagree with that fact? If so you are more ignorant of biology than expected in spite of how hard you toot your own horn. bornagain77
Born, can you give an example of the molecular information expressed and/or the computation that's being done? PLease keep the response short, to the point, and in your own words. We've all seen too much of your usual schtick already. Alicia Cartelli
Alicia Cartelli, I say the sequences have, among other things, some type of computational purpose, perhaps quantum, in which essential molecular information is expressed at the appropriate time to allow an appropriate computation to take place at the right time. And yes, there is sufficient reason to suspect that this might be the case. When a computer operating system was compared to regulatory networks, guess which one was more efficiently organized?
(Comparing Computer Operating Systems to Regulatory Networks in E-Coli) What Is The Genome? It's Not Junk! - Dr. Robert Carter - video http://www.metacafe.com/watch/8905583/ Comparing genomes to computer operating systems - Van - May 2010 Excerpt: we present a comparison between the transcriptional regulatory network of a well-studied bacterium (Escherichia coli) and the call graph of a canonical OS (Linux) in terms of topology,,, http://www.ncbi.nlm.nih.gov/pubmed/20439753
An extremely easy way to prove the sequences are non-funcional and wasteful as you hold would be to do knockout experiments of the sequences in question and see what happens. When 'knockouts' been done in the past with supposed junk DNA sequences, the results, as usual, did not conform to neo-Darwinian expectations. I see no reason to suppose that it will be any different this time if the experiments are ever done.
Jonathan Wells on Darwinism, Science, and Junk DNA - November 2011 Excerpt: Mice without “junk” DNA. In 2004, Edward Rubin] and a team of scientists at Lawrence Berkeley Laboratory in California reported that they had engineered mice missing over a million base pairs of non-protein-coding (“junk”) DNA—about 1% of the mouse genome(actually 1mb from a mouse genome is about .03%, not 1%.)—and that they could “see no effect in them.” But molecular biologist Barbara Knowles (who reported the same month that other regions of non-protein-coding mouse DNA were functional) cautioned that the Lawrence Berkeley study didn’t prove that non-protein-coding DNA has no function. “Those mice were alive, that’s what we know about them,” she said. “We don’t know if they have abnormalities that we don’t test for.”And University of California biomolecular engineer David Haussler said that the deleted non-protein-coding DNA could have effects that the study missed. “Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years,” he argued. In 2010, Rubin was part of another team of scientists that engineered mice missing a 58,000-base stretch of so-called “junk” DNA. The team found that the DNA-deficient mice appeared normal until they (along with a control group of normal mice) were fed a high-fat, high-cholesterol diet for 20 weeks. By the end of the study, a substantially higher proportion of the DNA-deficient mice had died from heart disease. Clearly, removing so-called “junk” DNA can have effects that appear only later or under other circumstances. https://uncommondescent.com/intelligent-design/jonathan-wells-on-darwinism-science-and-junk-dna/
. Also Alicia, I noticed that you did not answer my question on the modern synthesis. Are you still a believer? Or are you among the growing number of 'heretics' who reject neo-Darwinian explanations? bornagain77
Like I said, there is simply too much working against your hunt for unknown regulatory mechanisms. Thousands of bases to reconcile, the efficiency of Drosha leaves little time for regulatory processes to even occur(even on a molecular scale), and the unprotected strands that have been excised out are degraded by nucleases. That's my argument. When someone has an idea or two with actual biological relevance, I will do my best to shoot them down. I'm not here to argue about arguing. =) Alicia Cartelli
I have no problem admitting “we simply don’t know,” when necessary.
WHEN NECESSARY ... when the (fine-tuned) universe needs to be explained from nothing, morality from indifference, consciousness from unaware particles, freedom from determinism, rationality from nonrationality, the unity we call "organism" from chaos and the information in life from ... chance. "When necessary" means: when we cannot allow a divine foot in the door. Box
So an appeal to future discoveries is only allowed as long as it justifies the materialist position, and Is absolutely not allowed if it props up something that is anti-ID. No evidence for abiogenesis? Give us time, it's only been 50 years. This study appears to show a waste in energy? Done deal... The designer would not have done it like that. Highly unlikely any future test will show anything different. scottH
AC
I have no problem admitting “we simply don’t know,” when necessary.
It is necessary in this case because you don't know how it works and you don't know the origin of any of it - so you can't know that is has no function. Your resistance to that fact is telling, as I see it. Silver Asiatic
"I have no problem admitting “we simply don’t know,” when necessary." Apparently you have a huge problem with admitting 'you simply don't know' since you insist on making the same mistake, (i.e. I think its junk therefore its junk), over again that Darwinists have been making for decades, going all the way back to their original vestigial organ argument.
“There are, according to Wiedersheim, no less than 180 vestigial structures in the human body, sufficient to make of a man a veritable walking museum of antiquities.” -evidence submitted to the Scopes trial Vestigial Organs: Comparing ID and Darwinian Approaches - July 20, 2012 Excerpt: A favorite criticisms of ID is that it is a science stopper. The opposite is true. The Live Science article shows that the "vestigial organs" argument has not changed for over a century, since Wiedersheim coined the term and listed over a hundred examples (in 1893). Evolutionary theory, in fact, has been worse than a science stopper: its predictions have been flat out wrong. Only a handful of alleged vestigial organs remains from Wiedersheim's original list, and each of those is questionable. http://www.evolutionnews.org/2012/07/vestigial_organ062281.html “The thyroid gland, pituitary gland, thymus, pineal gland, and coccyx, … once considered useless by evolutionists, are now known to have important functions. The list of 180 “vestigial” structures is practically down to zero. Unfortunately, earlier Darwinists assumed that if they were ignorant of an organ’s function, then it had no function.” "Tornado in a Junkyard" - book - by former atheist James Perloff
Moreover, I hold that anyone who claims that they know for certain that most of what goes on in the unfathomed complexity of the cell is mostly useless noise is not looking at the evidence we now have in hand in an objective manner, but is looking at the evidence through the biased philosophical presupposition of reductive materialism.
Venter: Life Is Robotic Software - July 15, 2012 Excerpt: “All living cells that we know of on this planet are ‘DNA software’-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions,” said (Craig) Venter. http://crev.info/2012/07/life-is-robotic-software/ How we could create life - The key to existence will be found not in primordial sludge, but in the nanotechnology of the living cell - Paul Davies - 11 December 2002 Excerpt: Instead, the living cell is best thought of as a supercomputer - an information processing and replicating system of astonishing complexity. DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff - hardware - but as information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won't work because it addresses the problem at the wrong conceptual level. http://www.theguardian.com/education/2002/dec/11/highereducation.uk The Cell as a Collection of Protein Machines "We have always underestimated cells. Undoubtedly we still do today,,, Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each which is composed of a set of large protein machines." Bruce Alberts: Former President, National Academy of Sciences; http://www.imbb.forth.gr/people/aeconomou/documents/Alberts98.pdf
bornagain77
Alicia Cartelli, do you still adhere to the central dogma of the modern synthesis of neo-Darwinism? Or have you allowed your views to appropriately change now that the evidence has come in undermining that simplistic 'bottom up' gene centric view of life? If not why not?
Podcast - Richard Sternberg PhD - On Human Origins: Is Our Genome Full of Junk DNA? Part 5 (emphasis on ENCODE findings and the loss of the term 'gene' as a accurate description in biology and also how that loss directly undermines the modern synthesis of neo-Darwinism) http://www.discovery.org/multimedia/audio/2014/11/on-human-origins-is-our-genome-full-of-junk-dna-pt-5/ Why the 'Gene' Concept Holds Back Evolutionary Thinking - James Shapiro - 11/30/2012 Excerpt: The Century of the Gene. In a 1948 Scientific American article, soon-to-be Nobel Laureate George Beadle wrote: "genes are the basic units of all living things.",,, This notion of the genome as a collection of discrete gene units prevailed when the neo-Darwinian "Modern Synthesis" emerged in the pre-DNA 1940s. Some prominent theorists even proposed that evolution could be defined simply as a change over time in the frequencies of different gene forms in a population.,,, The basic issue is that molecular genetics has made it impossible to provide a consistent, or even useful, definition of the term "gene." In March 2009, I attended a workshop at the Santa Fe Institute entitled "Complexity of the Gene Concept." Although we had a lot of smart people around the table, we failed as a group to agree on a clear meaning for the term. The modern concept of the genome has no basic units. It has literally become "systems all the way down." There are piecemeal coding sequences, expression signals, splicing signals, regulatory signals, epigenetic formatting signals, and many other "DNA elements" (to use the neutral ENCODE terminology) that participate in the multiple functions involved in genome expression, replication, transmission, repair and evolution.,,, Conventional thinkers may claim that molecular data only add details to a well-established evolutionary paradigm. But the diehard defenders of orthodoxy in evolutionary biology are grievously mistaken in their stubbornness. DNA and molecular genetics have brought us to a fundamentally new conceptual understanding of genomes, how they are organized and how they function. http://www.huffingtonpost.com/james-a-shapiro/why-the-gene-concept-hold_b_2207245.html DNA is life's blueprint? No, master controller of the cell - 13 June 2015 by Claire Ainsworth Everything we thought we knew about the genome is turning out to be wrong as The Deeper Genome and The Developing Genome make clear. New metaphors, anyone? Excerpt: Take DNA. It's no simple linear code, but an intricately wound, 3D structure that coils and uncoils as its genes are read and spliced in myriad ways. Forget genes as discrete, protein-coding "beads on a string": only a tiny fraction of the genome codes for proteins, and anyway, no one knows exactly what a gene is any more. A key driver of this new view is ENCODE, the Encyclopedia of DNA Elements, which is an ambitious international project to identify the functional parts of the human genome. In 2012, it revealed not only that the protein-coding elements of DNA can overlap, but that the 98 per cent of the genome that used to be labelled inactive "junk" is nothing of the sort. Some of it regulates gene activity, some churns out an array of different kinds of RNA molecules (RNAs for short), some tiny, some large, many of whose functions are hotly debated. Parrington quotes ENCODE scientist Ewan Birney as saying at the time, "It's a jungle in there. It's full of things doing stuff." And that is one of the most apt genome metaphors I've ever read. Recent insights into what some of this "stuff" is reveal problems with another classic idea: that DNA is the master controller of the cell, with information flowing in one direction from it, via RNA, to proteins. Some of ENCODE's mystery RNAs control gene activity, others make changes that the cell remembers and passes on when it divides, and which can even be passed down generations. The RNAs may be one way the environment alters the behaviour of genes without changing their DNA sequences, a phenomenon known as epigenetics.,,, That genetics is complicated isn't news, but Parrington and Moore underline the limitations and the power of trying to understand its complexity by reducing it to simpler divisions. For example, the molecular and computing technologies spawned by such attempts are now giving researchers the potential to work out how to integrate it all to form a greater whole. Time, surely, to rip up the old metaphors and create some new ones. http://www.newscientist.com/article/mg22630251.000-dna-is-lifes-blueprint-no-master-controller-of-the-cell.html#.VXySfUbcBCB
bornagain77
I have no problem admitting "we simply don't know," when necessary. But in this case there is simply too much working against your hunt for unknown regulatory mechanisms that would involve thousands of bases of a transcript that is rapidly cleaved and then degraded. Sorry. Alicia Cartelli
Dr JDD
I remember questioning, how do they know it is junk? Just because they don’t know of a function NOW with our current understanding and technology doesn’t mean one day we won’t find function – surely that is what science is about! I was OK with not knowing what that was – but I have always wanted to know what that function may be and definitely wanted people to study it.
Interesting point. In order to declare that 99% of it is junk, they would have to know, for certain, its origin and its relationship to everything within the cell. But the fact is, this is unknown. The resistance to stating "we don't know" is telling, since it is a resistance to the truth of things. As the 99% junk number changed, it revealed the error of those who made the claim. But they were willing to risk being exposed like that, rather than simply admit "we don't know, but it could be 99% junk". It remains the same. AC is willing to bet her soul on it, rather than just admit that she doesn't know the origin and doesn't have a full understanding of how it works. Silver Asiatic
Right, so we need to invent some new regulatory mechanism to support your argument. Got it. Degradation of the strands of thousands of extra bases is not linked directly to their cleavage from the pri-miRNA, so unlikley. Free nucleases still need to find these strands to liberate the individual nucleotides. And it definitely would not be of any energetic benefit, so don't try that road. I must admit, though, it would be pretty cool if the pri-miRNA could fold into some sort of ribozyme or something. Who knows. Highly unlikely though. Alicia Cartelli
Thanks for your sober and insightful input Dr JDD. Of related interest to the bogus 99% junk figure is the bogus 98% similarity figure. Here are a few relevant notes in that regards:
The Myth of 98% Genetic Similarity (and Chromosome Fusion) between Humans and Chimps - Jeffrey Tomkins PhD. – video https://www.youtube.com/watch?v=EKO5mtdA0o4 Geneticist Jeff Tomkins vs. Evolutionary Biologist who got laughed off stage - August 12, 2013 Excerpt: Tomkins described the origin of the fallacious comparison as a myth that got started in reassociation kinetic methods of comparison in the mid-1970's prior to the advent of modern sequencing techniques (like Illumina and Solexa). Reassociation kinetics was a technique where fragments of chimp and human DNA were mixed in the same chemical soup, and the DNAs that were reasonably similar would pair up, hence we got a biased sampling! If we take genes that are found in both humans and chimps and disregard the indels, we get the 98% figure. When indels are considered, the similarity drops to 80-85%! When including other sequences, the similarity drops even further, down to 70%. But that 70% figure itself, imho, is too generous. I don’t think Tomkins used ORFans or pseudo genes or many other intergenic sequences, and he explicitly avoided the complication of Synteny.... Tomkins pointed also to reports where lab workers may have contaminated the sequencing labs for Chimps with their own human DNA and thus biasing the figures! Hence re-sequencing has been done, and there is more sequencing pending to clean up these errors. He joked about the coughing and sneezing that may have gone on to cause contamination. https://uncommondescent.com/genetics/icc-2013-geneticist-jeff-tomkins-vs-evolutionary-biologist-who-got-laughed-off-stage/ Human and Chimp DNA--Nearly Identical? by Jeffrey Tomkins, Ph.D. - 2014 Excerpt: Major research published over the past decade comparing human and chimpanzee DNA was recently reviewed and critiqued.1 In every single publication, researchers only reported on the highly similar DNA sequence data and discarded the rest—apparently because it was too dissimilar. In fact, when the DNA similarities from these studies were recalculated using the omitted data, markedly lower levels—between 81 and 86 percent similarity—were found. Even the well-known chimpanzee genome paper published by evolutionists in 2005 provides a genomic similarity of only about 80 percent when the discarded nonsimilar data are included and only 70 percent when the estimated size of the chimpanzee genome is incorporated.2,3,,, Not counting the Y-chromosome, the results of my comparison showed variability between 66 and 76 percent similarity for the different chimp chromosomes, with an overall genome average of only 70 percent similarity to human chromosomes. In reality, many chromosomal regions are vastly different between chimps and humans, and several areas of the genome that are present in chimps are completely absent in humans—and vice versa. While it is true that there are sections of the chimp genome that are very similar to humans, this is not the complete picture. DNA sequence comparisons that include all the relevant data plainly show that the human and chimp genomes are not nearly identical at all. Instead, they are as distinct as one might expect based on the obvious differences in the resulting anatomies and behavioral capacities. Hypothetical evolutionary processes cannot explain the extremely broad differences between chimp and human DNA when the whole genomes are considered. The similar regions between genomes are easily interpreted as the basic reuse of effective code—a concept very familiar to software engineers.,,, http://www.icr.org/article/7892/ Chimp DNA Mutation Study—Selective Yet Surprising - Jeffrey Tomkins - August 16, 2014 Excerpt: It was initially noted by another group of evolutionary scientists that when comparing random chimp genomic sequence only "about two thirds could be unambiguously aligned to DNA sequences in humans”(2). In confirmation of this widely known, but seldom discussed, inconvenient fact among those evolutionists working in the field was a comprehensive study published in 2013 by this author (3). In that research, I compared each individual chimpanzee chromosome to human (piece-by-piece) and it was shown that the chimpanzee genome was only 70% similar on average to human, with only short regions being highly similar. ,,, 30% difference in their genomes—some 900,000,000 DNA letter differences.,,, When the entire genomes are compared between humans and chimps, it becomes clear that they were each engineered uniquely and separately by an Omnipotent Creator. http://www.designed-dna.org/blog/files/baf81fbc404eb8e24c9b6bd7953817c5-110.php
The same lack of integrity is found in the way Darwinists handled the supposed Chromosomal fusion evidence:
More DNA Evidence Against Human Chromosome Fusion - Jul 31, 2015 Excerpt: First, the sequence was only about 800 bases long—not the 10,000 bases or more you would expect if two 5,000-base (or larger) telomeres fused together. Second, the fusion-like sequence was very degenerate and only 70% similar to what one would expect of a pristine fusion sequence of the same size. Even if you assume an evolutionary timeline of up to six million years since the fusion event occurred, the data do not match up with known mutation rates or the variability found in human DNA. A third major problem is the fusion site contains no type of sequence called satellite DNA (satDNA). In chromosome fusion events that occur in nature in living mammals—a very rare event—the DNA signature always involves satDNA producing a DNA signature that occurs as either satDNA-satDNA or satDNA-teloDNA sequence.4,5,6 Thus, the alleged fusion event should contain satDNA—a problem the fusion site discoverers openly acknowledged in their initial 1991 paper. When teloDNA-teloDNA fusions do occur in humans, they involve tissues and cell lines associated with cancerous tumors.7,8,9 A fourth major problem for the alleged fusion signature on chromosome 2 is that it occurs in a region of the genome that is full of genes. Telomeres do not contain genes, yet the fusion site is in the midst of a hotbed of genetic activity. The gene neighborhood surrounding the alleged fusion lacks overall synteny (similar gene order) to the chimp genome and does not support a fusion scenario in any way. This was first noticed in 2002 by secular researchers, although the chimp genome had not been well sequenced at that time.10,11 This author has recently verified that an overall lack of synteny supporting fusion still holds true for over 2.7 million bases surrounding the fusion site based on the most recent version of the chimpanzee genome compared to human (Tomkins, unpublished data). Despite all of these serious difficulties, the greatest problem that evolutionists now have is the fact that the alleged fusion sequence is located in the middle of a functional gene.12 It is not a fossil remnant of a chromosomal accident at all but an important DNA regulatory feature called a promoter (genetic switch) inside a highly expressed gene. More specifically, the purported fusion site is located inside a crucial RNA helicase gene called DDX11L2 that produces long non-coding RNAs. This gene is expressed in at least 255 different tissue and cell types in humans and is highly coregulated with many other important genes in the cell.12 So not only is the gene highly active throughout the human body, it is tightly networked with many other genes, including those that are involved in the development of blood cells. But the evolutionary fusion story gets worse. The fusion-like sequence itself has an important functional purpose based on recent data available at the UCSC Genome Browser (genome.ucsc.edu) genomic database. Specifically, the fusion site sequence binds to at least 11 different transcription factors, including RNA polymerase II, the key enzyme that transcribes genes. Transcription factors are specialized proteins that turn genes off and on. The fact that these proteins specifically bind to the alleged fusion site sequence indicates that it is a promoter located inside the gene (Figure 2). It is common for human genes to have these promoter regions located both in front of the main body of the gene and inside them. http://www.icr.org/article/8830
bornagain77
Alicia - I don't know. Perhaps the sequences themselves offer a regulation event of some description. Perhaps there is a necessity to rapidly liberate a vast number of nucleotides in the vicinity of the finalised miRNA for some sort of event requiring large numbers of free nucleotides (hence rapid degradation in proximity to the miRNA for some purpose). Probably not though, I'm just making that up. However, it is OK to say that "I don't know why this happens" as long as it is followed by "we should try to understand why that happens as there may be a good purpose for it." I think nature even if you are a materialist has earnt that assumption - we see purpose in virtually everything else that functions in the cell to such level of complexity and efficiency yet we aren't willing to give the same grace to this process and say, hey, you know what, maybe there is a good reason the cell does that as generally it does things for a good reason! However it then removes the low-hanging fruit that evo's like to grasp at to mock and chastise any supposed creator or designer as a poor one at best. I remember as an undergraduate studying biochemistry being told 99% of the genome was junk, at 18 years old. I remember saying I didn't believe that and there must be some function we just don't know about it. I remember questioning, how do they know it is junk? Just because they don't know of a function NOW with our current understanding and technology doesn't mean one day we won't find function - surely that is what science is about! I was OK with not knowing what that was - but I have always wanted to know what that function may be and definitely wanted people to study it. And over time more and more that 99% figure has come down and down and in one of my most naive states as a scientist I made an accurate prediction - not through any special intelligence or that I had some insight but rather through what I believe is the best science. Things happen for a reason. However that approach leads to the rational and logical conclusion that there is a reasoner behind the reason. That is what people don't like, probably yourself too. Dr JDD
JDD, if not regulation based on binding sites, what other forms are we talking about? Alicia Cartelli
Alicia @ 96: You are presuming what PaV or others are referring to by equating regulatory function with regulatory binding sites alone. I don't think PaV or anyone here is being that simplistic. Far from it, we are being quite the opposite and expect great complexity. Let us put this into context. Back a number of years ago in the early 00's we "had the technology" to be able to sequence the human genome and annotate it with genes and other genetic elements. These were well defined and we were confident and proud of our acheivement. Yet the technology used was flawed and simplistic - it relied on methods that are now out of date and superceded. For example, it could not cope with areas of large repetition. Things had to be assigned based on other sequenced genomes (like a chimps genome, for example). It was litered with inaccuracies and a serious point - it assumed that one human's genome would look the same as another right down to a "consensus" sequence that was the norm. Roll forward into the age where NGS (next generation sequencing) is becoming more standard in gene analysis and sequencing, a real buzz word in the biotech and pharma industry, and you will find talking with genetics that they are already stating the limitations of NGS, and newer technologies or complementary technologies need to be used to be more precise and accurate. Talk further with proper geneticists and they will tell you that if you sequence a common tumour suppressor gene of one human and compare it to the next - in healthy individuals - they won't be the same. What is "wild-type" even then? It does not really exist and the variation is much greater than most think. Now go a step further and think how we define genes and how confident we have been about that for years. Then realise that there are "genes" that are non-coding and have completely different promoter, initiation, transcription sites etc that are non-canonical. The look at draft copies of the human proteome which used sensitive mass spectrometry to identify proteins in various tissues by their fragments (which are probably outdated already in terms of sensitivity and accuracy as MS seems to move quite fast in that regard) and see that only 50% of the identified peptides could be attributed to the current ProtRefSeq data out there. So yes we have technology that allows us to study things - just like they had technology to sequence the human genome 10-15 years ago. But that does not mean it provides the most accurate picture, the actual full picture, and is not limited in detection of something that is really going on but the techniques and methodologies currently around cannot begin to tease apart. Dr JDD
Alicia Cartelli sums up evolutionism:
Where we talk about things we know nothing about, everything’s made-up, and the points don’t matter.
:cool: Virgil Cain
"This is over-simplification" Welcome to UD. Where we talk about things we know nothing about, everything's made-up, and the points don't matter. Alicia Cartelli
Carpathian, Please produce the evidence that supports your claim. Or keep your unscientific opinions to yourself. Virgil Cain
Virgil Cain:
Does Alicia know how emails get transmitted? How much of what is transmitted is the actual message, Alicia? Would you say that all of the other stuff is junk?
You're not just comparing apples and oranges here, you're not even in the same food group. Computer communications and life cannot be compared at this level. This is over-simplification. Carpathian
Does Alicia know how emails get transmitted? How much of what is transmitted is the actual message, Alicia? Would you say that all of the other stuff is junk? Virgil Cain
"Darwinism" cannot account for any miRNAs. It can't account for the system that breaks down the miRNAs. If that system broke, well "Darwinism" could explain that. Virgil Cain
No, we can study the pri-miRNA sequences now, that's what the point of the original article was. We now have the ability to study potential early regulatory mechanisms of miRNA production. What my issue has been from the start is that the production of miRNAs is tightly regulated pre-transcriptionally, just as genes are, but the transcript itself is 10,000s-100,000s of bases long while the final product merely ends up being a few fragments of this. You're talking about finding regulatory function in thousands of bases of the transcript, when binding sites for regulatory proteins are typically on the order of only 5-20 bases. The speed with which Drosha functions also means that any post-transcriptional regulatory processes would have to be incredibly fast to have an effect on miRNA production. Like I said, I won't hold my breath. Alicia Cartelli
AC: Dr JDD has stated it well: what prevents us from finding function in these areas is the lack of proper technology, right now, at least. The fear is this: as more function is found in the 1000's of nucleotides you feel are "wasted," the response will be: "Oh, but of course it has function. We knew all along that it would have function. How can you have that many nucleotides involved and not think there's function." And off the EVO's go. We can almost even now that this will become the standard answer. Science cannot advance with this disregard for failed predictions. Time will tell. Maybe six years from now, we'll have the right answer. Just don't forget this discussion. That's all I'm asking. (And, of course, this bit of advice cuts both ways!);) PaV
All I'm saying is that if function(s) can be determined for just half of any pri-miRNA sequence, then I will denounce "darwinism" and pray to the god of your choice. It ain't gonna happen =) Alicia Cartelli
AC
If they find a function for let’s say half of the pri-miRNA sequence, of just one specific miRNA, then I will denounce “Darwinism” and begin praying to the god of your choice. =)
It sounds like you're establishing the existence of God on the percentage (50% in this case) of function found in those sequences. Do you think that evolution sufficiently explains the percentage of function already observed, but it could not explain it if it was 50% or more? If so, that would be something to add to Edge of Evolution arguments, although you should be more precise. For example, "Evolution can explain up to 49.99% function but at 50% it's definitely evidence of ID". Silver Asiatic
Yes, Pav, it’s unexpected because huge nucleotide strands are being generated and then immediately degraded. Hence why I called it a massive waste of energy. They have found a potential regulatory mechanism in a subset of pri-miRNAs, but still this doesn’t account for the vast majority of the transcribed bases and the majority of miRNAs. If they find a function for let’s say half of the pri-miRNA sequence, of just one specific miRNA, then I will denounce “Darwinism” and begin praying to the god of your choice. =) Be sure to let me know when that happens. That’s how confident I am that most of the transcribed bases are what I, at least, would call “waste.” Alicia Cartelli
eigenstate, scientists not in the thrall of scientism because wilfully blinkered by atheism, would be absolutely fascinated to discover something that suggested that there is no divine, intelligent designer. It is simply that your sneered at 'God of the Gaps', as someone mentioned, is in fact, the God of everything, so that sneer, God of the Gaps' does nothing but highlight the gross inadequacy of that expression as a slur. It is simply too inane to make sense, never mind, serve to disparage and mock. You are throwing Brer Rabbit into the most luxuriant briar patch imaginable. But then you couldn't see it, never mind, imagine it. What people 'with eyes to see' (and understand QM even in layman's terms) cannot avoid seeing, no matter how hard they try, you can't begin to see. "The eye is the lamp of the body; so then if your eye is clear, your whole body will be full of light. 23 But if your eye is bad, your whole body will be full of darkness. If then the light that is in you is darkness, how great is the darkness!" Axel
Dr JDD: The walls are cracking and crumbling, and the foundation will soon be found to be absent and it will come crashing down.
Great post Dr JDD! Box
This is just the tip of the iceberg. Every time this is brought up the staunch evolutionists decry that these novel RNA’s and novel functions are a mere drop in the ocean, and that the majority of the genome is still junk. That is always the answer I hear. Yet for years, many including myself have stated that a genome vastly full of junk goes against the prediction of design therefore as a design advocate our model predicts functionality to these apparent “junk” regions and that we will soon find function, it is just we are limited by our technology and what we currently know.   This is something we actually agree on with our materialist friends – that a genome vastly full of junk provides more credence towards a materialistic accidental sloppy mechanism than it does a designer. Yet, what we predict is that if we find function for the majority of the genome, this is very good evidence for design and also given the amount of information contained in genomes around us including our own, if this is not vastly junk the complexity itself becomes too large (although it can be argued it already is too large) for accidental evolution to account for, in the time frames considered to be relevant for divergence and OOL.   It is clear that the driving force behind labelling much of the genome as junk is a mixture of arrogance (seeming to believe our technology is at its peak for detecting function at the molecular level) and a need for the materialistic paradigm. As stated above, it relied on most of the huge genome being junk, and if that is not true, materialistic evolution is found to be the emperor without clothes.   So what are the most recent publications on this matter pointing towards?  
SINEUPs: A new class of natural and synthetic antisense long non-coding RNAs that activate translation Abstract Over the past 10 years, it has emerged that pervasive transcription in mammalian genomes has a tremendous impact on several biological functions. Most of transcribed RNAs are lncRNAs and repetitive elements. In this review, we will detail the discovery of a new functional class of natural and synthetic antisense lncRNAs that stimulate translation of sense mRNAs. These molecules have been named SINEUPs since their function requires the activity of an embedded inverted SINEB2 sequence to UP-regulate translation. Natural SINEUPs suggest that embedded Transposable Elements may represent functional domains in long non-coding RNAs. Synthetic SINEUPs may be designed by targeting the antisense sequence to the mRNA of choice representing the first scalable tool to increase protein synthesis of potentially any gene of interest. We will discuss potential applications of SINEUP technology in the field of molecular biology experiments, in protein manufacturing as well as in therapy of haploinsufficiencies.
 
Widespread Inducible Transcription Downstream of Human Genes Summary Pervasive transcription of the human genome generates RNAs whose mode of formation and functions are largely uncharacterized. Here, we combine RNA-seq with detailed mechanistic studies to describe a transcript type derived from protein-coding genes. The resulting RNAs, which we call DoGs for downstream of gene containing transcripts, possess long non-coding regions (often >45 kb) and remain chromatin bound. DoGs are inducible by osmotic stress through an IP3 receptor signaling-dependent pathway, indicating active regulation. DoG levels are increased by decreased termination of the upstream transcript, a previously undescribed mechanism for rapid transcript induction. Relative depletion of polyA signals in DoG regions correlates with increased levels of DoGs after osmotic stress. We detect DoG transcription in several human cell lines and provide evidence for thousands of DoGs genome wide.
[Emphasis JDD]  
Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes. Abstract A number of long noncoding RNAs (lncRNAs) have been reported to regulate transcription via recruitment of chromatin modifiers or bridging distal enhancer elements to gene promoters. However, the generality of these modes of regulation and the mechanisms of chromatin attachment for thousands of unstudied human lncRNAs remain unclear. To address these questions, we performed stringent nuclear fractionation coupled to RNA sequencing. We provide genome-wide identification of human chromatin-associated lncRNAs and demonstrate tethering of RNA to chromatin by RNAPII is a pervasive mechanism of attachment. We also uncovered thousands of chromatin-enriched RNAs (cheRNAs) that share molecular properties with known lncRNAs. Although distinct from eRNAs derived from active prototypical enhancers, the production of cheRNAs is strongly correlated with the expression of neighboring protein-coding genes. This work provides an updated framework for nuclear RNA organization that includes a large chromatin-associated transcript population correlated with active genes and may prove useful in de novo enhancer annotation.
 
Role of chromatin, environmental changes and single cell heterogeneity in non-coding transcription and gene regulation Abstract The number and variety of factors underlying control of gene expression have been frequently underestimated. Non-coding RNAs generated through pervasive transcription have recently been implicated in shaping the transcriptional landscape in different organisms from bacteria to higher eukaryotes, adding a previously unexpected layer of complexity to the process of gene regulation. In this review, we highlight non-coding transcription-dependent regulatory mechanisms linked to chromatin organization and environmental changes, and particular emphasis is given to single-cell approaches, which have been crucial in dissecting cell-to-cell variability. These studies have revealed that non-coding transcription can underlie the extensive heterogeneity in patterns of gene expression within a cell population.
[Emphasis JDD]   These are a handful of peer-reviewed journal articles published in the last 3 months alone. This field is about to explode. The poor technology for sequencing of old and newer sequencing technologies and research (and taking these things seriously rather dismissing them as mere junk) mean that we must rethink the genome as a whole. In fact, protein translation is the overwhelmingly small role of the genome and genes. Only a fraction of the genome produces proteins yet this is entirely what the NS+RM paradigm has focused on! Despite this it appears that a whole host of other sequences and genetic material that is non-coding are highly important in the proper functioning of complex organisms and cellular mechanisms and regulation.   The irony of this all is that many molecular biologists are open to this complexity, and excitedly seeking it out. Those who oppose such novel work and adding importance to such sequences in the genome are the ones who truly understand the implications for materialistic evolution – namely those loudest proponents such as our friend Prof Moran and associates. They commonly play down (as we see on UD all the time) the importance of such findings and negate them to a fraction of the genome with little importance, with ad hominem attacks on those who cite these papers as not understanding this and how this in no way affects evolutionary thinking.   Further, one way they justify this approach (which is quite clever as it guarantees their theory stays intact) is to cite the best way to determine functionality of all these RNA transcripts is to demonstrate homology (to other organisms on the UCD tree). Prof Moran commonly will make that point and this therefore negates the possibility that some of these regulatory elements lack homology but still have important roles and function in the cell they are found, thus dealing a fatal blow to the materialistic view of evolution and common decent from accident.   “If it ain’t homologous, it ain’t important.”   The walls are cracking and crumbling, and the foundation will soon be found to be absent and it will come crashing down. (Yet I predict we will still hear some amongst the rubble crying out “evolution always predicted function for the majority of the genome – this is exactly what we expected!”) Dr JDD
It must suck to be a Moran. Mapou
Larry "Junk DNA Disproves Intelligent Design Creationism" Moran are you reading this? Box
Folks, Money shot clip from JDD's link:
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003569 Much of the human genome is composed of intergenic sequence, the regions between genes. Intergenic sequence was once thought to be transcriptionally silent “junk DNA,” but it has recently become apparent that intergenic regions can be transcribed. However, the scope, nature, and identity of this intergenic transcription remain unknown. Here, by analyzing a large set of RNA-seq data, we found that >85% of the genome is transcribed, allowing us to generate a comprehensive catalog of an important class of intergenic transcripts: long intergenic noncoding RNAs (lincRNAs). We found that the genome encodes far more lincRNAs than previously known. A key question in the field is whether these intergenic transcripts are functional or transcriptional noise. We found that the lincRNAs we identified have many characteristics that are inconsistent with noise, including specific regulation of their expression, the presence of conserved sequence and evidence for regulated processing. Furthermore, these lincRNAs are strongly enriched with intergenic sequences that were previously known to be functional in human traits and diseases. This study provides an essential framework from which the functional elements in intergenic regions can be identified and characterized, facilitating future efforts toward understanding the roles of intergenic transcription in human health and disease.
Translation, Darwinist expectations of abundant junk DNA were real, and are now dead. This is a new world. One in which the obvious candidate is that a lot of DNA is carrying out programmed control of cell processes in ways we are just beginning to get hints of. Where, this is being directly tied to medical issues. FSCO/I is staring us in the face and is pointing to its only known, only credible explanation. Intelligently directed configuration. KF kairosfocus
Dr JDD # 81 - Absolutely. It is a worldview issue, a matter of faith. It is absolutely impossible to prove anything to anyone unless they choose to hear. If it is more convenient to live in a world where there is no purpose, there's nothing one can do. EugeneS
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003569 Plenty more out there when people shake off their biased EVO mindset and actually ask "why is this here?" and "maybe this has a function" rather than "this is sloppy genomes from accidental evolution". Yet we will still here things like lincRNAs actually areonly a very small percentage of the genome as countering rebuttals... Dr JDD
PaV:
The pressure keeps building; soon, I suspect, the ‘dam will burst.’
Yes. And it will happen sooner than most suspect and it will come from the one place that nobody would expect. In fact, it's almost at the door. And it won't be pretty either. But it will be spectacular and will shake the foundations of civilization. Wait for it. Just saying. Mapou
Dr JDD: I always appreciate your comments on this board. As to the link, and "transcriptional noise," evolutionary biology is under tremendous pressure to change. The pressure keeps building; soon, I suspect, the 'dam will burst.' PaV
http://www.nature.com/nrmicro/journal/v12/n9/full/nrmicro3316.html PaV - they will never admit they were wrong nor will they change their view because it is a necessity for their worldview. But keep writing as you are because it is helpful for those reading who are not committed to materialism yet and are seeking answers and truth to be exposed to their hypocrisy. The literature is full of examples where people (evos typically) have pushed a view of uselessness and lack of function to support their worldview, and then new evidence comes to light explaining functionality. Usually by those who are not in the evo field so have little to lose... Dr JDD
What they describe is unexpected and peculiar. No reason, then, to extrapolate this as some byproduct of randomness. I can't explain this any better than that: the implications are there to be seen. I'm glad, though, that you're at least open to the possibility of function being found. Are you open, also, of said found function to make you look at the Darwinian narrative differently? PaV
"there’s no reason to believe that this shouldn’t be happening all the time. But it isn’t. So why don’t we see this happening everywhere within the genome? Why just here?" You're not making sense anymore, Pav. And sure, ill wait and see if they find any function in the thousands of bases that are transcribed and then immediately chopped off and degraded. Won't hold my breath though. Alicia Cartelli
What? wd400
So, evolutionary biologists always knew there was some purpose for so-called "junk-DNA"; but, of course, there IS "junk-DNA," and ID is silly. Quite a trick. PaV
But it isn’t. So why don’t we see this happening everywhere within the genome?
~20% of the human genome is intronic. Some introns have regulatory sequences, but they're mostly junk. And, as I said earlier, there are plenty aberrant transcripts in eukaryotic cells. wd400
AC: My major area of study these days is in physics. What I work at is neither physics nor biology. Molecular biology has become incredibly more complex over the last 10 years. I don't have the time to become expert. And, I don't have the financial wherewithal to buy journals willy-nilly; nor do I work at a university where journals are avaiable online. So you'll have to excuse the fact that I haven't read the article. But, I don't think that's the issue here. My whole point is that the ID perspective, and the Darwinian perspective, are very different. We approach the same set of facts in different ways. You talk about "waste." I say, "No, it's not waste; there must be some kind of function." This contrast in views parallels the "junk-DNA" controversy. Whereas "junk-DNA" was, and still is, thrown in the face of IDers as proof of randomness, nowadays many, if not most, evol. biol. say, "Oh, we never thought it was 'junk'." So, this becomes a good exercise in trying to determine which scientific viewpoint has more explanatory power since we don't know where all of this is heading. You firmly take the position that all this is "waste," and you don't think anything will ever be found to change this story. Well, it may take years to finally determine what we're looking at here with all thee bases, but it offers a chance for "objectivity," a chance of testing the viewpoints. I've invited you to take advantage of this opportunity, but your mind is made up: "End of story." In writing the following, you seem to miss the obvious: My point remains that a massive amount of energy is being wasted during transcription of pri-miRNAs. They can be 100,000s of bases long and yet the vast majority will be immediately chopped up and do not serve regulatory purposes. Maybe a few miRNAs are alternatively spliced, meaning some more of the transcript is functional than I was aware of, but there are still a massive number of bases that are transcribed and then immediately degraded. End of story. Here's what you're missing: If you reach the conclusion that this is a "wasteful" process ("End of story"), then there's no reason to believe that this shouldn't be happening all the time. But it isn't. So why don't we see this happening everywhere within the genome? Why just here? This has all the hallmarks of a critical design where "margins of errors" are built into the design. Intuition suggests that "function" will be found. Time will tell. And we can all reevaluate our views when that time comes. PaV
Alicia Cartelli, contrary to how confident you may be that it must be a huge waste of energy, you simply have no evidence to back up your claim other than your own self exalted opinion of your knowledge in these matters. In fact, you were shown empirical evidence directly contradicting your claim that the cell must be extremely inefficient in its energy usage. i.e. The 'horrendously complex' metabolic networks of the cell are found to be 'optimal'. That you still insist that it must be a huge waste of energy for the cell, in spite of being shown otherwise, thus does not, indeed can not, flow from the empirical evidence in hand but must flow from your faulty theological presupposition of 'God would not have done it that way because I would not have done it that way'. I'm not impressed. In fact, as was amply demonstrated with the junk DNA fiasco, your Darwinian theology is a science stopper! Considering the unfathomed complexity being dealt with in the cell, and considering the fact that unguided material processes have never been observed to create even a single protein of that unfathomed complexity, I suggest you swallow your arrogant pride and allow the possibility that God just may know how to design life a little better than you do. Now if you really want to impress me with your all your superior knowledge of biology, so that I start to respect your chest thumping opinion in these matters, I suggest you go create life in the lab first. Until then I consider you a arrogant blowhard, no better than a drunk bragging that he can defeat the heavyweight champion of the world. bornagain77
Alicia:
Every single base of the thousands of extra bases incorporated into the pri-miRNA requires an energy input that the cell must account for. Now, hundreds of pri-miRNAs can be transcribed at any given moment in a single cell. The extra bases are then degraded and rephosphorylated to restore the pool of NTPs, processes that also all require energy.
And your position cannot account for any of that-> the process nor the energy. And again there could be a valid reason that we don't grasp because of our ignorance due to the adherence to evolutionism. Virgil Cain
Elizabeth:
Every single base of the thousands of extra bases incorporated into the pri-miRNA requires an energy input that the cell must account for. Now, hundreds of pri-miRNAs can be transcribed at any given moment in a single cell. The extra bases are then degraded and rephosphorylated to restore the pool of NTPs, processes that also all require energy. You, like Pav it would seem, have no idea what you’re talking about.
Why do you kou keep repeating the same lame, blah-blah strawman? The design hypothesis predicts that, as soon as we get a better understanding of what is really going on, we will find out the reason for the observed mechanism. The argument against your position is that ID is correct and it was designed for a purpose by a highly advanced and knowledgeable group of designers. So given ID, there is a purpose that obviously escapes you and everyone else. Otherwise, you would not be here arguing about something that you are, after all is said and done, really ignorant about. Soon, you will be proven wrong because we continue to learn and we have powerful computers to do it with. And one more thing. You don't own science. Science is nobody's dog. In fact, true science is the Darwinist's worst enemy. Mapou
Bornagain, I think you have me confused with someone else. But anyways, it is not an unsupportable claim in the slightest. Every single base of the thousands of extra bases incorporated into the pri-miRNA requires an energy input that the cell must account for. Now, hundreds of pri-miRNAs can be transcribed at any given moment in a single cell. The extra bases are then degraded and rephosphorylated to restore the pool of NTPs, processes that also all require energy. You, like Pav it would seem, have no idea what you’re talking about. Alicia Cartelli
BA77 don't you crush Alicia's dreams of sweet purposelessness. Let us be kind. Her good heart makes a little jump on those extremely rare occasions that something in biology doesn't strike us as sublimely designed. Box
Alicia:
My point remains that a massive amount of energy is being wasted during transcription of pri-miRNAs.
And natural selection and drift explain that, how, exactly? Virgil Cain
Also of related interest: Here is, according to a Darwinist, a ‘horrendously complex’ metabolic pathway chart:
ExPASy - Biochemical Pathways - interactive schematic http://biochemical-pathways.com/#/map/1 Map Of Major Metabolic Pathways In A Cell – Picture http://2.bp.blogspot.com/-AKkRRa65sIo/TlltZupczfI/AAAAAAAAE1s/nVSv_5HRpZg/s1600/pathway-1b.png
And remember, Darwinists have yet to demonstrate how a single protein of that 'horrendously complex' metabolic pathway came about (Axe; Gauger). Moreover, as if that were not ‘horrendously’ bad enough for Darwinists, metabolic pathways are found to operate on ‘Quarter Power Scaling’ parameters. i.e. Metabolic Pathways operate as if they were ‘four-dimensional’ not as if they were 3-dimensional as would be expected if the processes had been 'cobbled together' by natural selection:
Kleiber’s law Excerpt: Kleiber’s law,[1] named after Max Kleiber’s biological work in the early 1930s, is the observation that, for the vast majority of animals, an animal’s metabolic rate scales to the 3/4 power of the animal’s mass. http://en.wikipedia.org/wiki/Kleiber%27s_law 4-Dimensional 'Quarter Power Scaling' In Biology – video http://www.metacafe.com/w/5964041/ The predominance of quarter-power (4-D) scaling in biology Excerpt: Many fundamental characteristics of organisms scale with body size as power laws of the form: Y = Yo M^b, where Y is some characteristic such as metabolic rate, stride length or life span, Yo is a normalization constant, M is body mass and b is the allometric scaling exponent. A longstanding puzzle in biology is why the exponent b is usually some simple multiple of 1/4 (4-Dimensional scaling) rather than a multiple of 1/3, as would be expected from Euclidean (3-Dimensional) scaling. http://www.nceas.ucsb.edu/~drewa/pubs/savage_v_2004_f18_257.pdf
Jerry Fodor and Massimo Piatelli-Palmarini put the insurmountable problem that Quarter Power Scaling presents to Darwinism this way:
Post-Darwinist - Denyse O'Leary - Dec. 2010 Excerpt: They quote West et al. (1999), “Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection." They comment, "In the words of these authors, natural selection has exploited variations on this fractal theme to produce the incredible variety of biological form and function', but there were severe geometric and physical constraints on metabolic processes." "The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection. It's inconceivable that so many different organisms, spanning different kingdoms and phyla, may have blindly 'tried' all sorts of power laws and that only those that have by chance 'discovered' the one-quarter power law reproduced and thrived." Quotations from Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79.
The primary reason why ’4-Dimensional’ metabolic pathways are impossible for Darwinism to explain is that Natural Selection operates on the 3-Dimensional phenotypes of an organism. ’4-Dimensional’ metabolic pathways are simply ‘invisible’ to natural selection. The fact that 4-Dimensional things are completely invisible to 3-Dimensional things is best illustrated by ‘flatland’:
Dr Quantum - Flatland - video https://www.youtube.com/watch?v=BWyTxCsIXE4
In keeping with the preceding claim of the 'invisibility' of these 4-Dimensional processes to natural selection, such 100% efficiency and optimality being found metabolic processes is hard (impossible?) to explain on Darwinian terms given that selection rarely even 'sees' the fittest mutations:
Study demonstrates evolutionary ‘fitness’ not the most important determinant of success – February 7, 2014 – with illustration Excerpt: An illustration of the possible mutations available to an RNA molecule. The blue lines represent mutations that will not change its function (phenotype), the grey are mutations to an alternative phenotype with slightly higher fitness and the red are the ‘fittest’ mutations. As there are so few possible mutations resulting in the fittest phenotype in red, the odds of this mutation are a mere 0.15%. The odds for the slightly fitter mutation in grey are 6.7% and so this is far more likely to fix, and thus to be found and survive, even though it is much less fit than the red phenotype.,,, By modelling populations over long timescales, the study showed that the ‘fitness’ of their traits was not the most important determinant of success. Instead, the most genetically available mutations dominated the changes in traits. The researchers found that the ‘fittest’ simply did not have time to be found, or to fix in the population over evolutionary timescales. http://phys.org/news/2014-02-evolutionary-important-success.html
As should be needless to say Liddle, I find your theological claim that 'it's just junk therefore God would not have done it that way' to be, besides being grossly unscientific, to be without empirical merit. bornagain77
Elizabeth Liddle I thought you had been banned for lying, lack of integrity, or something along that line? Anyways you state:
"My point remains that a massive amount of energy is being wasted during transcription of pri-miRNAs. They can be 100,000s of bases long and yet the vast majority will be immediately chopped up and do not serve regulatory purposes."
Aside from your arrogant 'I would not have done it that way therefore God would not have done it that way, therefore it must be junk' theologically laden science, I find your claim that a 'massive amount of energy is being wasted' to be a empirically unsupportable claim. I certainly don't claim to be as smart as you think you are in biology, (and in your Darwinian Theology for that matter), but from my scant understanding of the metabolic processes of the cell, the energy efficiency in the cell is found to be astonishingly optimal. Thus, although the RNAs being rapidly degraded may not suit you particular engineering druthers, for you to say there is absolutely no purpose for the process, especially considering the astonishing integrated complexity already found in the cell, is naive at best and most likely 'not even wrong' in its conclusion. Here are a few notes establishing the amazing energy efficiency of the metabolic processes of the cell:
Metabolism: A Cascade of Design - 2009 Excerpt: A team of biological and chemical engineers wanted to understand just how robust metabolic pathways are. To gain this insight, the researchers compared how far the errors cascade in pathways found in a variety of single-celled organisms with errors in randomly generated metabolic pathways. They learned that when defects occur in the cell’s metabolic pathways, they cascade much shorter distances than when errors occur in random metabolic routes. Thus, it appears that metabolic pathways in nature are highly optimized and unusually robust, demonstrating that metabolic networks in the protoplasm are not haphazardly arranged but highly organized. http://www.reasons.org/metabolism-cascade-design Making the Case for Intelligent Design More Robust - 2010 Excerpt: ,,, In other words, metabolic pathways are optimized to withstand inevitable concentration changes of metabolites. http://www.reasons.org/making-case-intelligent-design-more-robust Optimal Design of Metabolism - Dr. Fazale Rana - July 2012 Excerpt: A new study further highlights the optimality of the cell’s metabolic systems. Using the multi-dimension optimization theory, researchers evaluated the performance of the metabolic systems of several different bacteria. The data generated by monitoring the flux (movement) of compounds through metabolic pathways (like the movement of cars along the roadways) allowed researchers to assess the behavior of cellular metabolism. They determined that metabolism functions optimally for a system that seeks to accomplish multiple objectives. It looks as if the cell’s metabolism is optimized to operate under a single set of conditions. At the same time, it can perform optimally with relatively small adjustments to the metabolic operations when the cell experiences a change in condition. http://www.reasons.org/articles/the-optimal-design-of-metabolism Life Leads the Way to Invention - Feb. 2010 Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale. http://creationsafaris.com/crev201002.htm#20100226a
Also of related interest to the 'optimal' energy efficiency of the cell, it is found that the integrated coding between the DNA, RNA and Proteins of the cell apparently seem to be ingeniously programmed along the very stringent guidelines laid out in Landauer’s principle, (by Charles Bennett from IBM of Quantum Teleportation fame), for ‘reversible computation’ in order to achieve such amazing energy/metabolic efficiency as it does.
Logical Reversibility of Computation* - C. H. Bennett - 1973 Excerpt from last paragraph: The biosynthesis and biodegradation of messenger RNA may be viewed as convenient examples of logically reversible and irreversible computation, respectively. Messenger RNA. a linear polymeric informational macromolecule like DNA, carries the genetic information from one or more genes of a DNA molecule. and serves to direct the synthesis of the proteins encoded by those genes. Messenger RNA is synthesized by the enzyme RNA polymerase in the presence of a double-stranded DNA molecule and a supply of RNA monomers (the four nucleotide pyrophosphates ATP, GTP, CTP, and UTP) [7]. The enzyme attaches to a specific site on the DNA molecule and moves along, sequentially incorporating the RNA monomers into a single-stranded RNA molecule whose nucleotide sequence exactly matches that of the DNA. The pyrophosphate groups are released into the surrounding solution as free pyrophosphate molecules. The enzyme may thus be compared to a simple tape-copying Turing machine that manufactures its output tape rather than merely writing on it. Tape copying is a logically reversible operation. and RNA polymerase is both thermodynamically and logically reversible.,,, http://www.cs.princeton.edu/courses/archive/fall04/cos576/papers/bennett73.html Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. Bennett - September 2003 Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,, http://www.sciencedirect.com/science/article/pii/S135521980300039X Logically and Physically Reversible Natural Computing: A Tutorial - 2013 Excerpt: This year marks the 40th anniversary of Charles Bennett’s seminal paper on reversible computing. Bennett’s contribution is remembered as one of the first to demonstrate how any deterministic computation can be simulated by a logically reversible Turing machine. Perhaps less remembered is that the same paper suggests the use of nucleic acids to realise physical reversibility. In context, Bennett’s foresight predates Leonard Adleman’s famous experiments to solve instances of the Hamiltonian path problem using strands of DNA — a landmark date for the field of natural computing — by more than twenty years. http://link.springer.com/chapter/10.1007%2F978-3-642-38986-3_20
The amazing energy efficiency possible with ‘reversible computation’ has been known about since Charles Bennett laid out the principles for such reversible programming in 1973, but as far as I know, due to the extreme level of complexity involved in achieving such ingenious ‘reversible coding’, has yet to be accomplished in any meaningful way for our computer programs even to this day:
Reversible computing Excerpt: Reversible computing is a model of computing where the computational process to some extent is reversible, i.e., time-invertible.,,, Although achieving this goal presents a significant challenge for the design, manufacturing, and characterization of ultra-precise new physical mechanisms for computing, there is at present no fundamental reason to think that this goal cannot eventually be accomplished, allowing us to someday build computers that generate much less than 1 bit's worth of physical entropy (and dissipate much less than kT ln 2 energy to heat) for each useful logical operation that they carry out internally. http://en.wikipedia.org/wiki/Reversible_computing#The_reversibility_of_physics_and_reversible_computing Can reversible computing really dissipate absolutely zero energy? Of course not. Any non-equilibrium physical system (whether a computer or a rock) dissipates energy at some rate,,, Okay, then can reversible computing really make the energy dissipation of a computation be an arbitrarily small non-zero amount? Only insofar as the computer can be arbitrarily well isolated from unwanted interactions, errors, and energy leakage,,, But, despite all these caveats, it may yet be possible to set up reversible computations that dissipate such amazingly tiny amounts of energy that the dissipation is not a barrier to anything that we might wish to do with them - I call such computations ballistic. We are a long way from achieving ballistic computation, but we do not yet know of any fundamental reasons that forbid it from ever being technically possible. http://www.cise.ufl.edu/research/revcomp/faq.html#zeroenergy of note: I hold the computation in the cell being done for such things as protein folding and DNA repair to indeed be 'ballistic'
bornagain77
Well if you had bothered to read the paper, Pav, you’d realize how much of a stretch “dramatically expanded” is. The major finding of the paper is the sequence information and predicted secondary structures of the pri-miRNAs. The secondary findings are the use of alternative promoters, clustered miRNAs, and alternative splicing of miRNAs. Notice that the first two are pre-transcription, so they do not help your argument. The only thing that helps your argument is a tiny paragraph near the end that corroborates the findings of another paper. They found that a few select miRNAs happen to have splice sites that could potentially alter their function. Notice that some variation of the word “potential” is sprinkled throughout the parts of the paper that talk about regulatory mechanisms as well. Much of what you are trying to use as evidence for your argument is largely speculation on the researcher's part. I'll let it slide though. My point remains that a massive amount of energy is being wasted during transcription of pri-miRNAs. They can be 100,000s of bases long and yet the vast majority will be immediately chopped up and do not serve regulatory purposes. Maybe a few miRNAs are alternatively spliced, meaning some more of the transcript is functional than I was aware of, but there are still a massive number of bases that are transcribed and then immediately degraded. End of story. Don’t confuse pre- and post-transcriptional regulatory mechanisms. We are talking about post-transcriptional regulation. And for the last time, you are using the word “primer” wrong. The original transcript is the 10,000-100,000nt pri-miRNA, it is cleaved to 70nt pre-miRNA, and then processed to ~20nt miRNA. I have never seen “primer” used in the way you are trying to use it. Also, you accuse my knowledge of being out of date, but the only thing out of date here is the wiki article you cite. The abstract you, yourself copy/pasted says “the majority of pri-miRNAs are transcribed as poorly characterized noncoding RNAs that are 10’s to 100’s of kilobases in length.” So when wiki says its ~80nts, you should have realized the mistake. Like I said, wiki does not replace an education in biology. It is obvious you are no expert. Alicia Cartelli
PaV @64, Thanks for that revealing and devastating comment. Elizabeth is such a good little Darwinist soldier that she took it upon herself to start on a new trail that leads to more ridicule being piled on top of Darwinism. The whole edifice of Darwinism is crumbling at an astonishing rate. It's painful to watch the demise of a once mighty religion. Mapou
From the abstract of the Genome Research paper:
Precise regulation of microRNA (miRNA) expression is critical for diverse physiologic and pathophysiologic processes. Nevertheless, elucidation of the mechanisms through which miRNA expression is regulated has been greatly hindered by the incomplete annotation of primary miRNA (pri-miRNA) transcripts. While a subset of miRNAs are hosted in protein-coding genes, the majority of pri-miRNAs are transcribed as poorly characterized noncoding RNAs that are 10's to 100's of kilobases in length and low in abundance due to efficient processing by the endoribonuclease DROSHA, which initiates miRNA biogenesis. Accordingly, these transcripts are poorly represented in existing RNA-seq data sets and exhibit limited and inaccurate annotation in current transcriptome assemblies. To overcome these challenges, we developed an experimental and computational approach that allows genome-wide detection and mapping of pri-miRNA structures. Deep RNA-seq in cells expressing dominant-negative DROSHA resulted in much greater coverage of pri-miRNA transcripts compared with standard RNA-seq. A computational pipeline was developed that produces highly accurate pri-miRNA assemblies, as confirmed by extensive validation. This approach was applied to a panel of human and mouse cell lines, providing pri-miRNA transcript structures for 1291/1871 human and 888/1181 mouse miRNAs, including 594 human and 425 mouse miRNAs that fall outside protein-coding genes. These new assemblies uncovered unanticipated features and new potential regulatory mechanisms, including links between pri-miRNAs and distant protein-coding genes, alternative pri-miRNA splicing, and transcripts carrying subsets of miRNAs encoded by polycistronic clusters. These results dramatically expand our understanding of the organization of miRNA-encoding genes and provide a valuable resource for the study of mammalian miRNA regulation.
I bothered to search for this abstract, AC, because you insist your understanding is replete. Their "understanding" has been "dramatically expand[ed]." Isn't it ironic that what they discovered---which was not mentioned specifically in the release from the OP---fits in almost exactly with what I said should be expected from an ID perspective?
And they are immediately cleaved to a few 70-nucleotide fragments based on the formation of secondary structure by the RNA.
We can all find this in Wikipedia. None of this has changed from before; but, we're talking about all that "waste." Well, it seems like it "interacts" and "regulates". Didn't I suggest this?
Goodluck finding a function in the thousands of extra transcribed bases, do you know of any possibilities?
Isn't a "regulatory mechanism" functional within the transcription process? As to "primer," the "primer" appears to be the original, non-coding transcript. Later, it is chopped down, and, from what Wikipedia seems to be saying, it then becomes "pre-miRNA." I'm not expert in molecular biology; not even close. Nevertheless, I will comment upon it when I think it's appropriate. As to "pre-miRNA": from Wikipedia:
miRNA genes are usually transcribed by RNA polymerase II (Pol II).[47][56] The polymerase often binds to a promoter found near the DNA sequence encoding what will become the hairpin loop of the pre-miRNA. The resulting transcript is capped with a specially modified nucleotide at the 5’ end, polyadenylated with multiple adenosines (a poly(A) tail),[47][51] and spliced. Animal miRNAs are initially transcribed as part of one arm of an ?80 nucleotide RNA stem-loop that in turn forms part of a several hundred nucleotides long miRNA precursor termed a primary miRNA (pri-miRNA)s.[47][51] When a stem-loop precursor is found in the 3' UTR, a transcript may serve as a pri-miRNA and a mRNA.
It doesn't appear that I'm confused at all about what the length of "primer miRNA" was thought to be. The prevalence of Drosha made finding it difficult, that's all. Now they know a way around the problem. PaV
wd400:
And if you want examples of wasted transcription just check out eukaryote protein synthesis. There’s a whole system dedicated to cleaning up the mess that makes.
And another system that neither natural selection nor drift can explain. Virgil Cain
Alicia:
I highly doubt all three of those statements, Virg.
So what? You have nothing to offer.
And so you believe that organisms were once much more efficient and since then have only “devolved?”
If natural selection and drift are the mechanisms then that is the only fate.
Interesting, the only problem is that your belief flies in the face of everything that people who actually understand biology have agreed upon.
LoL! Who cares what people agree upon? In science it only matters what people can demonstrate. And evolutionary biologists cannot demonstrate natural selection and drift actually producing something. Look your position cannot account for gene regulation. It cannot account for transcription factors. Yours is forced to start with all of the stuff that requires an explanation. Yours cannot account for molecular biology. Virgil Cain
Yes, much longer. The original transcripts are ~10,000-100,000 bases long. And they are immediately cleaved to a few 70-nucleotide fragments based on the formation of secondary structure by the RNA. Goodluck finding a function in the thousands of extra transcribed bases, do you know of any possibilities? You’re using the word “primer” wrong as well. It doesn’t mean what you think it does. What I know is not outdated. It is part of the RNA-induced silencing mechanism currently being taken advantage of by researchers and has been studied carefully for many years now. And I was not off by a factor of anything if that was what you were trying to say; wd400 has already straightened you out as far as that goes. Wiki does not replace an education in biology. I suggest you let this be an experiment in whether you should be talking about molecular biology in much detail. Hint, the answer is no. I’m plenty open minded. I’ve seen both sides and I understand the arguments of both sides. Alicia Cartelli
If Darwinists run with this ball, it will turn out to be another junk-DNA type debacle. Just saying. LOL Mapou
FWIW, the ~70nt sequences are the pre-miRNAs, not the pri-miRNAs. And none of these sequences are primers. And if you want examples of wasted transcription just check out eukaryote protein synthesis. There's a whole system dedicated to cleaning up the mess that makes. wd400
AC: You write: The pri-miRNA is transcribed with thousands of extra bases, only a small fraction of which play an important role in the next steps. This is where ID and Darwinism part company. I would not make this simple statement. Here's part of the orginal press release on this topic: Because processing occurs very quickly, standard methods such as RT-PCR or RNA sequencing detect full-length pri-miRNAs with poor sensitivity. Many miRNA genes, therefore, lack annotated features such as a promoter or splice sites, hindering progress in understanding their transcriptional and post-transcriptional regulation. The whole point of the article is that the pri-mi-RNA is much, much longer (which they have demonstrated) than was thought before, and that the techniques used before--the very techniques that you rely on when you criticize my position---were simply not powerful enough to enable experimenters to fully understand how the primer processing was taking place. The authors report the techniques they employed will help future experimenters to properly elucidate this processing. Your answer to me was telling me how these primers are processed. The article is telling us that the information you think you know is now outdated. [Here, for example, is what Wikipedia says about primer length: A single pri-miRNA may contain from one to six miRNA precursors. These hairpin loop structures are composed of about 70 nucleotides each. Only off by a factor of a thousand.] And I'm suggesting that you let this be an experiment in whether the Darwinian point of view, of which you are guilty, is the correct one, or that of ID. Just be open-minded about these things. PaV
I highly doubt all three of those statements, Virg. And so you believe that organisms were once much more efficient and since then have only “devolved?” Interesting, the only problem is that your belief flies in the face of everything that people who actually understand biology have agreed upon. You’re going to advise me that my view is completely wrong, Pav? That’s a good one. The production of miRNA certainly is carefully directed. And this is done by a host of transcription factors, just as the expression of protein coding genes is. The pri-miRNA is transcribed with thousands of extra bases, only a small fraction of which play an important role in the next steps. This small fraction of bases forms a hairpin loop which is immediately cleaved by Drosha, while the excess bases dissociate and are chewed up by the cell’s nucleases. There is no methodical paring, just one cut removes the thousands of extra bases and later in the cytoplasm the small loop of the hairpin is cut to get an inhibitory ssRNA molecule. It doesn’t suggest that miRNA will “turn out to have a crucial role.” It is already well known how important it is in regulation and I have no idea why you think this would make me “abandon my Darwinian viewpoint.” I’m sorry to say this, but your pseudoscientific drivel may pass with the average person, but you would be laughed at by anyone who actually understands biology. Alicia Cartelli
Evolution entails energy efficiency. Except when it doesn't. Mung
AC:
Transcribing thousands of extra bases, the vast majority of which will just be chopped up, seems like an “intelligent search or fault elimination process?” Search for what? What faults? And can this be done in another way, without this huge waste of energy?
While this might be your natural inclination, I would advise you that your view is, almost likely, completely wrong. From my personal viewpoint, consistent with ID thinking, it is much, much more likely that what we're seeing is the production of something (the miRNA) whose effects are so powerful that its production must be carefully directed ('engineered'). Hence, there must be some kind of interplay between the long stretch of primal-RNA and other proteins, regulatory RNA elements, and genetic engineering elements in the DNA, which methodically (step-by-step) pares down the long stretch of RNA bases to the critical length. Analogously, we're very careful how we store explosive compounds. Instead of a simple can or jar, exotic steps may need to be taken to store it properly. Again, from my personal ID perspective, what we see here suggests that these miRNA will turn out to have a very crucial and pivotal role in the overall regulation of protein production and cell homeostasis. If you want to be fair-minded, then think this through ahead of time. Tell yourself that if this doesn't prove to be the case, and that, instead, there has been wasteful excess nucleotide production in the manufacture of miRNA, then this proves Darwinism is on the right track. But, if it turns out that there is some precise mechanism at work, involving many kinds (levels of interplay (interactions), with miRNA turning out to be much more important in regulation than at first thought, then you will abandon your Darwinian viewpoint, and begin to think along the lines of ID. PaV
eignestate:
But this is precisely what does NOT happen with evolutionary theory.
Really? Didn't Darwin tell us that if the fossil record did not extend way into the distant, distant past, that this would invalidate his theory? Yes, he did. But the fossil record does extend that far back. If the paucity of fossil intermediates did not increase, then, Darwin said, this would be a difficulty on his theory. Yes, we have a whole lot of new "fossils," claimed to be "intermediates," but, are they true intermediates. The famous "eohippus" intermediates was proven not be true, and that was one of the 'best' such attempts. Stephen J. Gould, himself, has written about this. Then there was Mendelian geneetics, which turned out not to be of the type that Darwin has foreviewed in his Origins. The laws of genetics pointed in the direction of a kind of stasis. Something "new" had to develop, lest genetics ran the risk of just shifting things around ad infinitum, with little change. Fisher's Fundamental Theory of Evolution, based on two differential equations expressing birth rates and death rates, seemed to help. But this would lead to the idea that though enough variation would slowly build up via evolution, NS would be needed to maintain the "selected" new variants. Associated with this 'maintenance'was Haldane's Dilemna of undue genetic load. Now, when proteins began to be analyzed, and it was found that there was a tremendous amount of variability within them, Haldane's calculations made RM+NS untenable. It lead to the Neutral Theory of Motoo Kimura. He thought some other kind of explanation was required to explain the discovered level of polymorphisms. Darwinism wouldn't do it. Darwinists, trying to defend their view, said that "junk-DNA" was the likely outcome for a process that involves random events. They said the genome was full of junk. When ENCODE shattered this myth, they did to that team what they did to others before: throw scorn at them and deride them. "Junk-DNA"--- or shall we say its absence---disproves Darwinism (Modern Synthesis) once again. These are facts. And they are facts just like those that drove the move from CM to QM. Now, if you want to pretend none of this happened . . . . . well, I guess you're free to believe in unknown, unseen, untestable multiverses. You're free to do this. But DON'T call it "science." \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ ppolish:
I’m an IDiot, but I wonder – can ID be falsified?
There's lots of ways of falsifying it. (1) Find fossils that show a gradual development of features. By "gradual," of course, this means an extremely long list of fossil intermediates with small gradations in form. Claims are made; but, one must be a "true believer" to accept the parse evidence given. (2) The slow build-up of genes, starting with the most primitive forms, and ending with the most recent. What is most commonly found, and commented on elsewhere, is what could be termed "front-loading," an example of which is that the 'gene' for forming digits in the vertebrate hand is already present in the sea anemone (or sea sponge?). (3) Some natural law, or principle---like "least action"---at work in extremely simple biological systems that has the potential of bringing about change in such a way as to efficiently arrive at useful solutions. This is NOT what we see happening. E.g., in "The Edge of Evolution," Michael Behe demonstrates that the malarial parasite must simply "crunch out" the right answer, taking around 10^20 replications for it to do so. There appears to be not 'short-cuts' to this raw 'crunching out' of solutions. This severely hampers and limits what Darwinian evolution can bring about, hence the "Edge." Darwinists, of course, denounce him as a charlatan, who knows nothing, whose numbers are all wrong and deceiving. But, as you know, belittling someone's work doesn't mean you've disproved it. PaV
Elizabeth uses speculation as fact. Darwinists do that all the time. It's a favorite pastime. Mapou
Alicia:
It’s not propaganda, it’s an explanation of how evolution works geared toward laymen like you.
LoL! I understand how evolution is supposed to work. However I also understand the way it is supposed to work is impotent and cannot be modeled. BTW I bet this layman understands evolution and biology at least as well as you do.
ID is goal oriented?
Yes.
Why is the designer’s goal to waste massive amounts of energy transcribing and then destroying long stretches of nucleotides? Does that make sense?
Did you miss this: Yes but the alleged waste we do see could be due to random effects on that once much more efficient design. And it could be that there is a valid purpose that we just don't understand. Virgil Cain
All in a days' work, UB. Another day, another dollar. Imagine what evamolution could do if it ever got some grey cells! Axel
Crazy. Blind chaos can unleash itself from local dynamics to create an IC representational code, complete with open-endedness, efficient copying, and error mitigation, that will last for billions of years. It can put hollow bones, flo-through lungs and wings on the same frame. It can create the eye. And yet, those darn microRNAs... Upright BiPed
My understanding of what is actually going on is correct. A lot of research depends on using RNAi correctly. Transcribing thousands of extra bases, the vast majority of which will just be chopped up, seems like an “intelligent search or fault elimination process?” Search for what? What faults? And can this be done in another way, without this huge waste of energy? “I predict that future research will uncover a few surprises.” You don’t say. I certainly hope it does. Great prediction. It’s not propaganda, it’s an explanation of how evolution works geared toward laymen like you. ID is goal oriented? Why is the designer’s goal to waste massive amounts of energy transcribing and then destroying long stretches of nucleotides? Does that make sense? Alicia Cartelli
Alicia:
The bottom line is that evolution works with what is already present and isn’t goal-oriented.
That's propaganda, not evidence. Intelligent design evolution is goal-oriented
There is no “intelligence” involved in evolution, just making things more suited to the environment or better at survival, little by little.
More propaganda. A process in which whatever is good enough survives and reproduces wouldn't do that.
A design that avoids transcribing thousands of unnecessary bases in a nucleic acid sequence that will then be rapidly degraded and recycled (with each reaction requiring energy), just to generate a 22base sequence would seem a little more intelligent, no?
Yes but the alleged waste we do see could be due to random effects on that once much more efficient design. Virgil Cain
Elizabeth:
A design that avoids transcribing thousands of unnecessary bases in a nucleic acid sequence that will then be rapidly degraded and recycled (with each reaction requiring energy), just to generate a 22base sequence would seem a little more intelligent, no?
Only if your understanding of what is actually going on is correct. You're just speculating. It looks more like the actual process is some kind of intelligent search or a fault elimination process. I predict that further research will uncover a few surprises. It always does. We've seen the bad design argument many times before. Remember junk DNA? As soon as one gets knocked down, another takes its place. It's old. Give it a rest. Mapou
Elizabeth:
The bottom line is that evolution works with what is already present and isn’t goal-oriented. There is no “intelligence” involved in evolution,
Which is why it's a stupid theory. The curse of dimensionality kills it dead before it can get out of the gate. Mapou
We know a good amount about “what is really going on during that process,” actually. Feel free to read-up on RNA interference. The bottom line is that evolution works with what is already present and isn’t goal-oriented. There is no “intelligence” involved in evolution, just making things more suited to the environment or better at survival, little by little. A design that avoids transcribing thousands of unnecessary bases in a nucleic acid sequence that will then be rapidly degraded and recycled (with each reaction requiring energy), just to generate a 22base sequence would seem a little more intelligent, no? Alicia Cartelli
Well don't we have something interesting here! Evolution can produce complex highly efficient proteins essential for life. In distant species it can converge multiple times independently to find the same complex solution to a common problem under different selection pressures. It can form complex organisms with coordinated nervous, secretory, vascular, lymphatic...etc...systems that work together in utter synchronicity. Yet what it really CANNOT do is evolve a regulatory system of a very short genetic component of 22bp in length but is stuck and unable to get around the horribly inefficient process of a huge genetic section needed for this small regulatory sequence. But this fits exactly what the theory of evolution predicts - nothing. If anyone honestly doesn't find this somewhat conflicting then they really lack the ability of discernment. Dr JDD
Alicia:
So ID is the “other possibility?” Sure.
Actually it is the only possibility. Unguided evolution, ie natural selection and drift, are impotent.
There is nothing intelligent about a massive waste of energy.
And yet here you are. Virgil Cain
Daniel King:
You’ve been at this for a long time.
Not as long as evolutionary biologists have been at it and they still have nothing. Unguided evolution is useless as a research heuristic.
What plans have you come up with?
Synthesize the parts one at a time- Venter already did the DNA.
Any ideas about the nature of the missing ingredients?
Software, ie immaterial information. Virgil Cain
That massive "waste of energy" eventually led to a discussion of massive "waste of energy". Oops, you're right - massive waste of energy:) But isn't there some law about the impossibility of wasting energy? Doesn't it just move around or something? ppolish
I just love it with these dirt worshippers. They never address or even acknowledge the weaknesses of their little pseudoscientific cult that others point out. Instead, they continually send their interlocutors on a wild goose chase. Lizzie:
Now my next question is where is the “intelligence?” Why spend so much energy transcribing so many bases, the vast majority of which will just be chopped up? There is nothing intelligent about a massive waste of energy.
You very well know this is a lame strawman argument on your part since you have no clue as to what is really going on during that process. A newborn's brain similarly has a huge numbers of synaptic connections, most of which disappear by the time the infant is a few years old. Lizzie would ask, "why connect them in the first place?" and Lizzie would be showing her cluelessness. Why does Lizzie think she can get away with her stupid tricks here? She's not very bright, that's why. But then again, very few Darwinists/materialists are. Mapou
So ID is the "other possibility?" Sure. Ok, so the "design" is that the thousands of extra bases that are transcribed are part of a regulatory mechanism for the miRNA. Now my next question is where is the "intelligence?" Why spend so much energy transcribing so many bases, the vast majority of which will just be chopped up? There is nothing intelligent about a massive waste of energy. Alicia Cartelli
Daniel, most bio research today is looking at design.
Design by an unidentified intelligence? What does "looking at" mean? Daniel King
Find the software of life. If ID is right then living organisms are more than just matter, energy and what emerges from their interactions. We just need to formulate plans to flesh out the missing ingredients.
You've been at this for a long time. What plans have you come up with? Any ideas about the nature of the missing ingredients?
Intelligent designers invariably use a hierarchical architecture to manage complexity and the timing of events. Computational genetics researchers should search for this hierarchical structure in every genome.
Do you have any suggestions to guide that search? Daniel King
King:
What is your research program for further investigation of Design?
Intelligent designers invariably use a hierarchical architecture to manage complexity and the timing of events. Computational genetics researchers should search for this hierarchical structure in every genome. Once it is found, it will open up a deluge of previously hidden information. One man's opinion. Mapou
Daniel King:
What is your research program for further investigation of Design?
Find the software of life. If ID is right then living organisms are more than just matter, energy and what emerges from their interactions. We just need to formulate plans to flesh out the missing ingredients. Virgil Cain
Daniel, most bio research today is looking at design. Of course, there are a few bonehead studies like the "E.coli Long Term Evolution" part time experiment. That's a waste of $$, but not very much. ppolish
There is plenty of benefit to attributing something to a designer. For one it eliminates entire classes of possible causes and for another is tells us how to conduct any further investigation.
That might save a lot of time and money. What is your research program for further investigation of Design? I'll bet there are people who will fund it. Daniel King
ppolish @21:
ID.,,,putting the logical back into biological.
I like that. Mapou
ID...putting the logical back into biological. ppolish
All stochastic search algorithms (e.g., RM+NS) are killed dead by the combinatorial explosion. They are only good for very small search spaces and toy applications. This is the reason that logical people look for an alternative but logical candidate, one that is nonstochastic. It turns out that the best candidate is intelligent design. The worst is dirt-did-it. If you are in the dirt-did-it camp, you are an idiot or an effing a-hole, or both. Mapou
Throwing around the word "design" is more useful scientifically than throwing around the word "evolution", Alicia. That's why you see it being thrown around more these days. ppolish
Alicia:
The word design is thrown around a lot by scientists, but they never mean ID because there is no benefit to just attributing something to some designer in the sky.
There is plenty of benefit to attributing something to a designer. For one it eliminates entire classes of possible causes and for another is tells us how to conduct any further investigation. BTW Alicia, ID is not anti-evolution which means it isn't enough to say "evolution did it". You have to be more specific. You have to show how unguided evolution can produce regulatory networks. Good luck with that as no one has been able to do so- it cannot be modeled. Virgil Cain
Alicia Cartelli: So no one is offering up some “other possibility?” What are you talking about? I listed quite a few. Mapou: Alicia @18, obviously you have a reading impediment. Well, my post in response came right after the post asking the question, so I understand how it could easily be overlooked. Mung
Alicia aka Elizabeth Liddle:
there is no benefit to just attributing something to some designer in the sky.
There is, of course, plenty of benefit to just attributing it to dirt-did-it. You just got to love dirt worshippers. Mapou
"Designer in the sky" is an atheist phrase lol. Why pay any credence to that? Just one more example of Atheism stunting the science:) The "Appearance of Design" contingent is also stunting science:( ppolish
Science doesn't "stop at surprising," don't worry. The word design is thrown around a lot by scientists, but they never mean ID because there is no benefit to just attributing something to some designer in the sky. What I originally asked for, was the alternative. Instead of evolution giving rise to what seems like a massively inefficient process, maybe you can tell me about the possible intelligence and reasoning behind this "design." Alicia Cartelli
Alicia, seems obvious to me the "other possibility" PaV suggests is ID. Made it pretty clear really. So Science should not stop at "surprising", but try to understand the ID. Can actually move Science ahead that way. Many modern scientists are so afraid to use the "D" word, and it is truly stunting science sigh. ppolish
The “other” possibility is that “evolution” can’t explain this result. You DON’T have to have another model in place to know that there is a conflict between what a theory expects and what is actually found. That’s how science operates.
You'd have to be able to point to where there is a conflict between what the the theory entails and what is actual found. The theory of evolution is not in trouble if scientific consensus the first stone tools used by hominids occurred X mya, and next week we find evidence from archeologists that under thorough analysis indicates that the first stone tools were used 2 million years earlier than X. That would be unexpected (else the consensus would not be a consensus) but that is not a problem with the model, the theory. Evolutionary theory does not predict or entail X or X-2mya for stone tools. Denyse will be happy to ring in her fee for filling post quotas here with amusement that those know-it-all scientists were "surprised" by the finding, but there is not problem with the model from these kinds of "don't fits". If we were to find species and lineages that did not share morphologies, and did not have genetics that formed ancestral lineages in a nested hierarchy, THEN we'd a problem with the model. We don't have those kinds of problems in view, and evolutionary theory is conspicuously free of these potent problems.
Quantum mechanics arose because the experimental evidence they uncovered about atomic spectra did not fit into strictly classical mechanical analysis. But the QM mathematical structure would arise later, as a RESULT of the fact that there was a contradiction between CM and the raw data.
This is a very good example of the principle described above. This is "model-problematic", and its entailed clearly by the math. The model cannot accommodate our observations and makes entailed predictions that do not match our empirical input. But this is precisely what does NOT happen with evolutionary theory. We can go over the entailments, the hard commitments of the model, and our empirical data does fit, and is not problematic. It validates the model in an overwhelmingly robust way. A good example of misconception is the creationist suspicions about the Cambrian Explosion. Many believe, through apologetic patterning from Meyer and other or other reasons, that the Cambrian Explosion is problematic for evolutionary theory. It's not, not even a little. It's certainly an area where scientist do not have robust answers for why speciation and radiation happened at the rates the did versus the rates we infer from other periods, but the Cambrian, on its most narrowly compressed timeline, spans way enough millions of years to accommodate all the changes we see and a great deal more. The OP of this thread is yet another example of confusing "surprise" in the details and outcomes from a general framework with a problem in the framework itself. If you can show where the evolutionary model predicts a different outcome than we find, an outcome that is entailed and experimentally at odds with this, then you have a point. But there is not such entailment, no such prediction from the theory on the size of the transcripts must be from miRNAs. If I missed that feature of the model, you'll have to direct me to it. That doesn't mean scientists aren't regularly surprised and won't continue to be. They will and that that's a good thing. There are umpteem million details to discover about the various aspects of biology that are going to surprised, need revision, and perhaps be revised again (and yet again) as more data fills in the huge gaps on the particulars of all these subjects. But these discoveries are not at odds with what evolutionary theory entails in the model -- common descent, nested hierarchies in speciation, cumulative feedback loops driving population genetics, etc.
The fact is that ID can “explain” what we see happening in terms of an intelligent agent. This doesn’t “prove” that the ID explanation is true; but, at least it has the merit of being able to explain, if not predict, the experimental evidence.
Explaining in this is story-teller terms is trivial. We can explain anything with "Goddidit", literally anything, and that has been a "go-to" alternative for humans since time immemorial. What is challenging, but worthwhile in terms of epistemology and knowledge building is explaining with a model. This makes the explanation accountable and compatible with the rest of scientific knowledge if successful. QM models, like you referenced above, are a good example of this, and a stark contrast to what ID provides as explanation, which is "story-teller explanation". ID's story telling may be correct. But if so, it's not addressable as science. To explain what we have happening around us in terms of an intelligent agent AS part of a scientific model is a formidable task, no doubt. But that's how science operates. As it is, it all works out as it should. ID advocates are fine with story-telling models, from what I've seen and neither need nor particularly value the epistemic gains that would come from a scientific model that was centered around an intelligent designer, if such a model were to succeed when it came into contact with empirical tests. eigenstate
Well, the author of the original paper proposed that the transcription of a massive nucleotide strand in order to ultimately produce just a ~22bp fragment allows for complex regulation of the miRNA. I am asking what the "other possibility" is, that was mentioned by the UD author. Alicia Cartelli
Other than what, Alicia Cartelli? Other than the Modern Synthesis? How about EES or ID? ppolish
Alicia @18, obviously you have a reading impediment. Mapou
So no one is offering up some "other possibility?" Alicia Cartelli
ppolish - it's interesting because self-organization is evidence for ID on one side and evidence for "just the way it is" on the other. But ID is more reasonable since it proposes a source for self-organizing powers. Ultimately, evolution and ID trace back to the same source for organization, function, purpose, the appearance of design, ordering principles and systems ... to whatever it was at the very beginning. The multiverse story could simply claim that self-organization of molecules to organisms to the earth's biosphere were already present at the big bang (and are the lucky result of one of an infinite number of universes). Or it's even easier just to say that the big bang possessed all those qualities just by virtue of being a thing that could go bang. Proposing that purpose and functional order have their origin in an ultimately purposeful source of order and design, is more parsimonious and philosophically coherent. It makes sense of much more than merely the organization of molecules -- namely, it makes sense of human cognition, self-awareness, purpose, moral judgement and religious sense that has always been present in every human culture. The multiverse gives a just-so story about origins, and everything that follows is "just the way our universe happened to be". Silver Asiatic
"That’s how science operates. Exactly, PaV. A scientific theory can never be proven true - there is always a chance it can be falsified by experiment. I'm an IDiot, but I wonder - can ID be falsified? Like a Multiverse, ID can explain the the impossible complexity and fine tuning in Nature. But I'm not sure it can be falsified.. Although the evidence supporting ID is much stronger than the evidence supporting unguided purposeless oops. I mean it's the same evidence for both, but ID explains that evidence in a more scientific way. Evo Design better than Evo Oops. EES moving in that direction though. When the Extended Evolutionary Synthesis (EES) speaks of Evolution Design, I don't think they mean "appearance of design". They've move past that.,, ppolish
eigenstate: The "other" possibility is that "evolution" can't explain this result. You DON'T have to have another model in place to know that there is a conflict between what a theory expects and what is actually found. That's how science operates. Quantum mechanics arose because the experimental evidence they uncovered about atomic spectra did not fit into strictly classical mechanical analysis. But the QM mathematical structure would arise later, as a RESULT of the fact that there was a contradiction between CM and the raw data. The fact is that ID can "explain" what we see happening in terms of an intelligent agent. This doesn't "prove" that the ID explanation is true; but, at least it has the merit of being able to explain, if not predict, the experimental evidence. PaV
The question of design is a binary one. Either design is the case or it's not. "Who is the designer" is irrelevant to the question of design. I accept that "how x came to be" is not indicative one way or the other relative to this question. I also accept (IMHO) that the question while a binary one, can and should only be analyzed as a matter of probability. Even if blind-watchmaker evolutionary processes were the case they can easily be a false positive for non-design as science is limited in scope to what it can observe and measure collectively and beyond. So I conclude, that ID is a viable hypothesis and the design question cannot be limited to science (at least not the current version), but must incorporate all aspects of reality including our experiences which themselves should be weighed in as evidence as I feel since we're the product of this design that we should therefore understand it better than a rock. computerist
eigenstate, A few points and I'm gone. 1. Your or anyone else's understanding of what Yahweh (or any other hypothetical designer) can or cannot do is irrelevant to the theory. 2. Your or anyone else's belief that there was or was not a designer is irrelevant to the theory. 3. The three items in the first list are not predictions. They are the hypotheses of the theory. 4. Hypotheses are assumptions. Predictions are claims that will falsify the hypotheses (hence the theory) if they don't pan out. That is all. I don't wish to discuss this anymore. Sorry. Mapou
@Mapou, I guess i missed this part of your comment on the first pass:
So there you have it, 3 falsifiable predictions based on intelligent design. And guess what? Items 1 and 2 have already been corroborated by direct observation. Item 3 is in the process of being corroborated as we begin to use computers to unravel the secrets of the genome. One cannot be more Popperian than this.
Let's just focus on the first one in efforts to keep things simple. You gave us this generalization for #1:
1. They conduct fact finding or what-if experiments.
That's not a prediction of a model, but if I understand you, this would translate to a prediction like this: 1. The Designer has to conduct fact finding or what-if experiments or simulations to determine what some aspects or outcomes of a candidate design will be. That strikes me as way underspecified, but setting that aside for now, how would we test for falsification of this? That is, what test could we run that would show us this prediction is false, if it were indeed false? eigenstate
@Mapou, Kudos for at least giving this a go, which is more than most everyone else on the pro-ID side is willing to venture.
Well, here goes. Intelligent design supposes the existence of intelligent designers. We know a lot about how intelligent human designers design things and we can use that knowledge to make a few predictions about how living organisms were designed. We know that intelligent designers do the following: 1. They conduct fact finding or what-if experiments. 2. They reuse existing designs as much as possible. 3. They organize complex systems hierarchically.
Ok, I think all these are reasonable as typical or practical tasks for intelligent designers we know of.
1. Multiple waves of species explosions followed by sudden extinctions should exist in the fossil record. Given the complexity of terrestrial ecology, these fact-finding experiments could conceivably last tens or even hundreds of millions of years. There are certain things that cannot be calculated in advance because the combinatorial explosion will not allow it. They must be allowed to run their course.
This does not follow. For some conceivable designer, perhaps. For every supposed Designer that qualifies, you can match it with a Designer that is not so bound, or so limited. Just to name a popular example, Yahweh as our putative Designer would not have any trouble with forward-looking calculations, no matter how complex or chaotic (he is an omni-god, after all doncha know). So right here, you'd have to start "giving shape" to your Designer in your model. That's good and well, but now you have a Designer than cannot probe or simulate far into the future.
2. Organisms should be classifiable in a mostly nested hierarchy.
Doesn't follow, is not entailed. If I'm imagining an extraterrestrial/alien style Designer, something like a (smarter human), this is plausible, but even then in no way is it entailed. More importantly though, nothing precludes a Designer that designs each species "from scratch", or maybe just starts anew with each "baramin". There are no rules or expectations to be had, and thus no predictions that can be deduced from the "imaginary space of Designer candidates" you are drawing from. Why not a Designer who eschewed all three of your "typicals"? Einstein didn't have that problem because his model was mathematical, and was ultimately fully entailment-rich by virtue of the math. It was just a matter of symbolic calculus, you or I could have calculated the same perihelion for Mercury as he did as a prediction of the model. Just offering that for stark contrast with the problem ID proponents have in this area.
3. The genome is organized within a strict control hierarchy.
We have NO Designer in view, even as a conjecture, to deduce this from. If there was a Designer, then I wouldn't be surprised to find that was "trait" of this Designer, simply because that's the pattern we observe in genetics. But this is the Texas Sharpshooter Fallacy redux: you're looking at what is -- 'where the bullet hit' -- and mapping human characteristics to an unspecified, abstract Designer -- 'painting a target around the bullet hole'. Scientific models go the other way, which is what grounds the epistemology. We conceive of a model we suppose might account for the phenomena, but which is not dependent on that phenomena, or beholden to it -- it's general. We can apply it to new and previously unconsidered scenarios and ask "what does the model predict", and then test it. With your anticipations here, none of them proceed from any model. We might just as well say that none of them apply or that a putative Designer maybe adopts (1) but not (2) or (3). And the evidence being what it is won't help you, because there's nothing in the model that compels it to be that way. blockquotes, spelling eigenstate
eigenstate:
What novel predictions does this competitor model entail? How would those predictions be different than the current (hypothesized) model, and how would that be tested? It would be awesome to see something substantive proposed here, something that could be put through the same testing and evaluation regimen as the current (mainstream biological) model. So, let’s see the alternative model, already!
Well, here goes. Intelligent design supposes the existence of intelligent designers. We know a lot about how intelligent human designers design things and we can use that knowledge to make a few predictions about how living organisms were designed. We know that intelligent designers do the following: 1. They conduct fact finding or what-if experiments. 2. They reuse existing designs as much as possible. 3. They organize complex systems hierarchically. For each of the hypotheses listed above, we can make the following predictions: 1. Multiple waves of species explosions followed by sudden extinctions should exist in the fossil record. Given the complexity of terrestrial ecology, these fact-finding experiments could conceivably last tens or even hundreds of millions of years. There are certain things that cannot be calculated in advance because the combinatorial explosion will not allow it. They must be allowed to run their course. 2. Organisms should be classifiable in a mostly nested hierarchy. 3. The genome is organized within a strict control hierarchy. So there you have it, 3 falsifiable predictions based on intelligent design. And guess what? Items 1 and 2 have already been corroborated by direct observation. Item 3 is in the process of being corroborated as we begin to use computers to unravel the secrets of the genome. One cannot be more Popperian than this. Don't run from the evidence. Live with it. Mapou
@ppolish,
The “Guided Evo Model” had fewer surprises than the “Unguided Evo Model”, Eigenstate.
Nah. Literally everything that happens in a guided evolution hypothesis is a surprise, unless you incorporate God or the Designer in as part of your model -- and that's never been done. The awesome thing about scientific models and the sucky thing about "guided" models is that the unguided models actually can make entailed predictions, predictions that proceed directly from the dynamics of the model. <blockquote) Instead of being surprised, the Guided Model says “hmmm…how did Nature do that?”. Good question. Good Science. Better than “oops – surprise!” It's not science at all, because "Nature" is not an actor. With a guided model -- which is just code words for "God did it" or "Designer did it", you are immediately at a dead end as soon as you ask the question. How would you determine an answer for "how did Nature do that?" All one can say is that "This is how the Designer/God wanted to do it". The Designer/God is not available to ask (we can't even get a point where we have a rational basis for believing such an entity exists in first place!), we can't test it, can't freeze some variable and see what the Designer/God would do with X free and other key variables isolated, controlled. It's just a dead end. All we can do is whistle in wonder at the impassable ineffable, completely opaque and utterly mysterious nature of the Designer/God. Which is to say, we abandon good science for religion.
Guided Evo Model….”Scientists were impressed to discover…” Unguided Evo Model…”Scientists were surprised to discover…” Impressed Scientists are better than Suprised Scientists. Smarter.
No. It's fine to have a sense of wonder, but what makes scientists better are working models, and the ideas and conjectures from their imagination that can either be falsified, or mechanized into formal, empirically tested and validate models -- theories. Being impressed by a god is a handicap. There are lots of religious scientists who are good scientists, but as good scientists they set their superstitions aside and become "methdological naturalists" to do their work.
Mr Spock was never surprised by a discovery. He would raise an eyebrow and say “Interesting” or if really cool discovery “Fascinating”. Good scientist right there. 1st Science Officer I believe.
You know that was a kitschy sci-fi TV show from the late 60s and early 70s, right? ;-) Gods and cosmic designers are only as interesting and useful to science as they are applicable in scientific models. That's why both are non-factors in science, they don't fit, they're superfluous, useless, ciphers. The door is wide open for anyone to come forward with a working model that incorporated such an entity. They'd be instantly world famous if they could contribute such a thing. But no one does and no one will, because if God/Cosmic Designer exists, all we can do as puzzle and muse about the black box, the impenetrable anti-model it represents in our universe. eigenstate
Guided Evo Model….”Scientists were impressed to discover…” Unguided Evo Model…”Scientists were surprised to discover…”
You forgot one. Perhaps "Evo", meaning common descent, is not really necessary. The results Creation Model... "Scientists were left in awe of the Creator by the discovery of...." tjguy
There IS an alien craft on Mars. Rover. Probably brought some alien microbes there too. ppolish
Headline: ALIEN CRAFT FOUND ON MARS eigenstate: "That's not a testable model therefore the supposition of alien origins is unscientific." Which occurrence is the least likely? englishmaninistanbul
What Computational Biology simulation/program would be more impressive; 1) Oops - a Weasel or 2) How to design a Weasel #2 of course. Why even waste your time on #1? Oh, I think we al know why:( ppolish
The "Guided Evo Model" had fewer surprises than the "Unguided Evo Model", Eigenstate. Instead of being surprised, the Guided Model says "hmmm...how did Nature do that?". Good question. Good Science. Better than "oops - surprise!" Guided Evo Model...."Scientists were impressed to discover..." Unguided Evo Model..."Scientists were surprised to discover..." Impressed Scientists are better than Suprised Scientists. Smarter. Mr Spock was never surprised by a discovery. He would raise an eyebrow and say "Interesting" or if really cool discovery "Fascinating". Good scientist right there. 1st Science Officer I believe. ppolish
Don't be coy then, throw out another model that should be considered as a competitor for the model being hypothesized in the article. What novel predictions does this competitor model entail? How would those predictions be different than the current (hypothesized) model, and how would that be tested? It would be awesome to see something substantive proposed here, something that could be put through the same testing and evaluation regimen as the current (mainstream biological) model. So, let's see the alternative model, already! eigenstate
AC: What “other possibility” are you talking about exactly? Magic. Emergence. Poofery. Effervescent quality. Wishful thinking. Mung
What "other possibility" are you talking about exactly? Alicia Cartelli

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