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#101 Guest_Tommy_*

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Posted 12 January 2010 - 09:40 PM

List them for us . Many scientists around the world wanna know  :)

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All biologists already know as do you, me and anyone else who has read this thread. You have even responded to my reference to RNA catalysis with a link of your own; I have also mentioned prions. I have addressed your assertion that a self-replicating molecular process is unobserved and continually stressed that a detailed abiogenesis scenario is yet to be established.

Since I piped up in post 17 I have seriously answered all questions put to me (despite accusations of "bias", "bastardization of chemistry", "fantasyland" and "chicken or egg") and have not found any substantive objections to the natural emergence of autocatalysis or chemical evolution. Does your designer reach beyond physical first causes? As the only person engaging with me recently has been Deadlock (whose last posts have been sarcasm and smilies) I shall retire from this thread.

#102 Bruce V.

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Posted 12 January 2010 - 10:25 PM

OK, I had thought cell wall might be a bit obvious.  I am partial toward those abiogenesis hypotheses that have the self-replicating molecules getting into protective sheaths as soon as possible.

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Hi Tommy,

I have been away from a computer and couldn't address this topic until now.

You see a big picture of how it could work. I am asking you to go one step further and ask how your big picture works in reality. Is your theory possible beyond the concept? For example, how do molecules get into protective sheaths? Large chemicals are inherently unstable. Are you saying life had to start in reducing atmosphere? What are the ramifications of that? Tommy you have to take your concept to the next step and put some meat on the theory? When you go through the steps I think you will find that chemicals can not evolve.

A cell is gloriously complex.  Complexity does not necessarily entail a designer.  Selective pressures are a bias for which arrangements work, whether streamlined or convoluted.

Is there a determined bound to what a sequence of modifications can accomplish?
Is the absurd number “more than the number of atoms in the Universe”?

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Does complexity mean a designer. That requires a very long explanation. The short answer is that complexity in and of it self does not. But complexity that provides form and function based on information does.

Believe it or not that have estimates of how many atoms are in the universe. You can also multiply estimate the time involved in nanoseconds. The product of those 2 is much smaller than is required to make a short RNA strain. In other words, given all the atoms interacting with every other atom every nanosecond would not create a probability great enough to create a small RNA chain. I can prove this but it takes work and I want some feedback if I put in the effort. Also, if a reaction is so unbelievably unlikely, it would be indistinguishable from a miracle.

Non-genetic self-replicating chemicals can certainly adapt – protein folds (prions), the keystone of this thread, being an example.   That experiment I linked was a response to Deadlock’s assertion in post 73 that self-replicating molecules don’t exist; it is not a candidate for the original self-replicator.

Any long, specific sequence might seem an improbable outcome just as would any life story.  Life might have emerged by many specific paths into many specific forms just as our lives could have taken many turns.

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The pathways have to have some scientific basis. You have to move beyond concept and work out the details of your theory. Life is a miracle and I know this because I have looked into the scientific literature. Life is simply not possible without a designer. Be a critical thinker and be open to finding a creator. If you rule him out as a first assumption than you will never have a real basis for your faith, whether as a believe or not.

#103 Bruce V.

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Posted 12 January 2010 - 10:51 PM

From the link: "The authors use the term “cross-replication” to describe this because they found that it works best with two distinct RNA chains, each of which catalyzes formation of the other one from supplied precursors.  But since either of these RNAs could potentially kick the process off (by forming the other), much of the commentary on this widely publicized study refers to it as an example of self-replication."

One primeval self-replication process might have been a molecule forming "a negative" of itself which in turn produces a replica of the grandparent.  The determining aspect of an autocatlytic process is that the product can catalyze the initial reaction and that the process generates all necessary catalysts without outside help.

The experiment demonstrates a process that amounts to the autocatalysis of RNA molecules.  If one molecule encountered the other's components outside of the lab it could prompt them to bind.  Observation of a replication process through one binding renders replication through several bindings conceivable.

Exciting times!

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Hi Tommy,

The reactions is based on RNA templates prebuilt in the lab. The reaction stops when the templates are consumed.

The templates are not realist in any OOL scenarios. This is quick and dirty. Please think critically and move beyond the concept into application

1. The reaction was designed by a computer program working out various scenarios. This is designer molecule from the get go.

2. How do you synthesize RNA templates: Each bond has to be chirally correct and be bonded by a peptide bond.

3. The chemical has to be sequenced properly.

4. There are competing reactions that have to accounted for.

5. Some reactions require designer catalyst for them to proceed.

6. Some reactions require an energy boost to overcome activation energy's (ATP)

7. Some reactions are endothermic and others exothermic. What does the energy balance look like. You have to watch exothermic reactions so they don't cascade, undo or start undesired reactions.

8. Ribose has to made separately because it will react immediately with amino acids and has a very short 1/2 life.

In other words, Joyce's RNA templates are not representative of any OOL scenario. They require and enormous amount of human interaction and intelligence to create. The experiment IMHO shows that life needs a designer.

#104 Bruce V.

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Posted 12 January 2010 - 10:54 PM

Hey deadlock, which came first? The chicken or the egg?

All of these "self replicating" experiments uses a catalyst....proteins.  So which came first the catalyzing agent of the self replicating molecules?

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The RNA and RNA templates work as catalyst. So enzymes are not needed.

RNA as a catalyst is very limited but it works in this case.

#105 Bruce V.

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Posted 12 January 2010 - 11:00 PM

There’s nothing prohibiting external catalysts and reactions building the catalyzing product and components prior to the onset of autocatalysis.

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Yes and no. The reactions require designer catalyst. Even clay catalyst are designer catalyst. Alumina Oxide and zeolites are used as catalyst and catalyst supports.

It takes a kind of zeolites ( Y or Z) to be used as an effective catalyst. You have to purify the zeolites you want to get satisfactory results. Again, these are designer catalyst and heterogeneous zeolites supported catalyst are limited in the reactions they catalyze.

#106 Bruce V.

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Posted 12 January 2010 - 11:07 PM

Back to the thread.

Ribosomes are what is used to fold proteins. Look at some of machinery in the ribosomes.

Posted Image

Ribosomes are factories inside cells where messages coming from genes are decoded and new proteins pieced together on an assembly line. For the first time, scientists have a detailed picture of the ribosome trapped together with elongation factor G (EF-G), one of the enzymes that nudges the assembly line to move forward.


This is very cool.

#107 Bruce V.

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Posted 12 January 2010 - 11:34 PM

Do you have a cite to the literature from which you took your ATP claim?  Thanks

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I will do a quick and dirty post. I will engage you more but I don't want rapid fire questions without feedback from you.

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video

It’s not just figurative speech to call ATP synthase a rotary motor. It actually generates torque (the subject of the paper in Nature sited below). The authors compared it to a Wankel engine – the kind that powers a Mazda car, and used the word “motor” 30 times in the paper. They said the first studies of this molecular machine revealed it “resembling a three-chambered molecular Wankel engine, therefore strongly suggested that rotation, rather than alternation, was nature’s choice, and that the synthesis of ATP might be mechanically driven by rotation....” Synthesis of ATP (thus the name) is its job. ATP (adenosine triphosphate) is the energy currency for all of life. The ATP molecule is a nucleotide with extra phosphate groups attached. It requires energy to attach the phosphate groups; energy is liberated when they are removed. Most molecular processes in the cell (and in all of life) use that liberated energy that comes from ATP. Plants use it for photosynthesis; animals use it for respiration. Quadrillions of these rotary engines in a human body manufacture ATP constantly, day and night, to keep those processes operational. If they suddenly stopped, you would be dead before you hit the floor.
ATP synthase has several parts; a rotor, a stator, and a camshaft. It’s actually two motors in one. The top half (called F1) is a three-chambered assembly factory that pushes the phosphates onto the nucleotide. Three pairs of lobes in this stepping motor turns loading ADP and phosphate, assembling them, and releasing ATP molecules. They are powered underneath by a waterwheel-like rotating motor that runs on proton motive force Taking advantage of the ever-present Brownian motion and electrostatic interactions, the protons turn the wheel. This simultaneously turns a coupled camshaft-like mechanism that protrudes into the top half, which transfers the torque to the ATP-assembling lobes. The engine can work in either direction, constructing ATP molecules or breaking them down, depending on the concentration gradient.
Scientists have been intrigued by the mismatch of gear ratios between the top and bottom halves of the engine. In some animals, for instance, there are 11 units in the rotating half, but 3 in the top half. This implies some transfer of elastic energy in the camshaft. Whatever is happening, it works: scientists say this machine approaches 100% efficiency. For a taste of the discussion from the paper for those who know physics, they are discussing the match between the energy needed for ATP hydrolysis and the mechanical work done by the motor. source

We know that getting 3 positive mutations is sequences in beyond what random mutation and natural selection can do base on empirical data (malaria). How many mutations would be required to make this- many. What is the evolutionary pathway required? It is well beyond what evolution can do.

This is fairly new finding. Look at the machinery required to make ATP.

nature link

Scientist marvel at the design of the process.

ATP synthase (FOF1) is a molecular machine that combines the electrical, mechanical and chemical aspects of enzyme function.  These are neatly separated, readily attributed to its different subunits, and reasonably well understood thanks to a wealth of structural and kinetic data.  However, understanding the enzyme fully at a molecular level will require considerable efforts, both experimental and theoretical.  There are five outstanding issues.... Only when we have solved these problems will we come close to a full understanding of this remarkable piece of cellular machinery.


The match implies 100% efficiency for the conversion of the Gibbs free energy of ATP hydrolysis into mechanical work performed on the elastically strained filament.  This is not surprising given the approximate thermodynamic equilibrium of the enzyme (long)-filament construct.  It is more informative to say that there is no slip between ATP hydrolysis in F1 and rotation in FO under the given conditions.2  Rotary slip in FOF1 in chloroplasts and bacteria has been detected, but only under single-site occupancy, that is, at nucleotide concentrations significantly below 100 nM.  The momentary torque can be larger (for example, during a particular power stroke) or smaller (during a kinetic dwell) than its equilibrium average.  This may account for the still puzzling independence of the torque from the ATP concentration in the nanomolar to millimolar range (see ref. 2 for a review).  It is worth mentioning that the other technique for determining the torque from the rate of rotation underestimates its magnitude because it neglects viscous flow coupling between the filament and the enzyme-supporting surface.



#108 deadlock

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Posted 13 January 2010 - 05:55 PM

All biologists already know as do you, me and anyone else who has read this thread.  You have even responded to my reference to RNA catalysis with a link of your own; I have also mentioned prions.  I have addressed your assertion that a self-replicating molecular process is unobserved and continually stressed that a detailed abiogenesis scenario is yet to be established.

Since I piped up in post 17 I have seriously answered all questions put to me (despite accusations of "bias", "bastardization of chemistry", "fantasyland" and "chicken or egg") and have not found any substantive objections to the natural emergence of autocatalysis or chemical evolution.  Does your designer reach beyond physical first causes?  As the only person engaging with me recently has been Deadlock (whose last posts have been sarcasm and smilies) I shall retire from this thread.

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Dont be so arrogant. Your link and posts about self-replicating molecule are a flawed and dishonest attempt of proving abiogenesis is possible, and you know that.

#109 AFJ

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Posted 13 January 2010 - 08:58 PM

All biologists already know as do you, me and anyone else who has read this thread.  You have even responded to my reference to RNA catalysis with a link of your own; I have also mentioned prions.  I have addressed your assertion that a self-replicating molecular process is unobserved and continually stressed that a detailed abiogenesis scenario is yet to be established.

Since I piped up in post 17 I have seriously answered all questions put to me (despite accusations of "bias", "bastardization of chemistry", "fantasyland" and "chicken or egg") and have not found any substantive objections to the natural emergence of autocatalysis or chemical evolution.  Does your designer reach beyond physical first causes?  As the only person engaging with me recently has been Deadlock (whose last posts have been sarcasm and smilies) I shall retire from this thread.

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I am just coming in here. Don't mean to judge you, but I see by the terminology "your designer," you would not account anything to the divine--since in your mind he is a myth.

I am wondering then how enzymes were produced? They are proteins. For instance DNA gyrase and the helicase work together to split the DNA. They had to be assembled by the necessary gene expression, in transcription and translation (which all have there own enzymes).

But how could the DNA, by chance, sequence the proper codons to make just two (and you know there are more) of the enzymes which would unwind it and split it?

Quite a monumental stroke of coincidence, I would say!

#110 Adam Nagy

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Posted 13 January 2010 - 09:01 PM

Quite a monumental stroke of coincidence, I would say!

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AFJ, you intellectual rebel. Given enough time anything can happen. Just trust those evolutionists. Defining science to reject reality is for your own good. :(

#111 Bruce V.

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Posted 13 January 2010 - 09:57 PM

Somebody asked me about given enough time anything is possible but I couldn't find the question.

Anyway this is about protein folding, probability and time.

Video - I tried to embed this but failed.

2nd video.

#112 AFJ

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Posted 16 January 2010 - 06:51 AM

Somebody asked me about given enough time anything is possible but I couldn't find the question.

Anyway this is about protein folding, probability and time.

Video - I tried to embed this but failed.

2nd video.

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So the video said the chances of unguided evolution producing one 150 amino acid chain (there are alot of proteins around this length), it is 10^130! There are only 10^65 atoms in the universe.

Funny no one answered this video, nor did they answer my question . How did natural selection and mutation produce DNA gyrase and the helicase, both of which are required for DNA to split? If DNA can't split, then it can not replicate, and life stops.

I understand there was theoretically an RNA world. If that is the case, then somewhere there was a jump to the DNA double helix and along with it the codons for DNA gyrase and helicase at the same time. This is not even to mention the elegant "surgery" these two enzymes do "without guidance."

Please understand that the "oldest fossils" found are cyanobacteria, which are living fossils and have DNA. This is evidence that DNA has been around since the beginning in either model. In the accepted geologic timescale model, cyanobacteria (blue green algae) are responsible for the O2 (oxygen crisis) in our atmosphere.

#113 Ron

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Posted 16 January 2010 - 07:07 AM

AFJ, you intellectual rebel. Given enough time anything can happen. Just trust those evolutionists. Defining science to reject reality is for your own good. ;)

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:)

#114 jason777

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Posted 16 January 2010 - 07:38 AM

Somebody asked me about given enough time anything is possible but I couldn't find the question.

Anyway this is about protein folding, probability and time.

Video - I tried to embed this but failed.

2nd video.

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Thanks Bruce,

That video "Darwins' Dilemma" is where I saw the paper reference for the thread.Anyway here is the youtube version.

M4FvdOxIDfU&hl=en_US&fs=1

#115 jason777

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Posted 16 January 2010 - 07:45 AM

Please understand that the "oldest fossils" found are cyanobacteria, which are living fossils and have DNA. This is evidence that DNA has been around since the beginning in either model. In the accepted geologic timescale model, cyanobacteria (blue green algae) are responsible for the O2 (oxygen crisis) in our atmosphere.


Precambrian cynobacteria are twice the size of modern cynano,which is evidence that there was twice as much oxygen in the atmosphere from the beginning as well.



Enjoy.

#116 Ron

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Posted 16 January 2010 - 07:52 AM

I disregard pseudoscience, creation science (and its offspring) and the softer end of the social sciences (like sociology).  Do I get three points?

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Creation science is no more pseudo-science than evolutheistic science Tommy (or its offspring evolutheistic cosmology) and the softer end of the social sciences (like strict Darwinism). So no, you don’t get any points for opinionated positing sans empiricism it requires for foundational evidence.


I mentioned an external energy source in post 63 so the entropy issue doesn’t seem to apply; the keq thing I wasn’t aware of but I see no reason why self-replication need be a chemical equilibrium process.

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The external energy source would have to come from somewhere Tommy, it didn’t create itself. Plus, you were “only feigning” remember?

I have no inclination to trade punches for points like in an amateur boxing bout. 

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Actually, Tommy, professional boxer’s trade punches for points as well. That’s how they’re scored (i.e. bad analogy).

I only reply because I am asked questions or you scoff with “pigs might fly” clichés.

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Also, if you believe the evolutionary propagandistic religiosity, given enough time, pigs are capable of “evolving” wings and flying (Just add Miiiiiiiiiiiiiillions of years and anything can happen).

#117 AFJ

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Posted 16 January 2010 - 08:15 AM

AFJ, you intellectual rebel. Given enough time anything can happen. Just trust those evolutionists. Defining science to reject reality is for your own good. ;)

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:)

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:) Yeah, thanks! If you can't go through, do the end around.

I've noticed evolutionists ignore any form of irreducible complexity, so I like showing it to them in all it's fashions. Like how does DNA code "one step at a time" for the two enzymes that cause it to replicate, when it can't replicate without them?

This has nothing to do with time. It shows that common sense is also required for good science. :o

#118 AFJ

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Posted 17 January 2010 - 04:29 PM

So the video said the chances of unguided evolution producing one 150 amino acid chain (there are alot of proteins around this length), it is 10^130!  There are only 10^65 atoms in the universe.

Funny no one answered this video, nor did they answer my question .  How did natural selection and mutation produce DNA gyrase and the helicase, both of which are required for DNA to split?  If DNA can't split, then it can not replicate, and life stops.

I understand there was theoretically an RNA world.  If that is the case, then somewhere there was a jump to the DNA double helix and along with it the codons for DNA gyrase and helicase at the same time.  This is not even to mention the elegant "surgery" these two enzymes do "without guidance."

Please understand that the "oldest fossils" found are cyanobacteria, which  are living fossils and have DNA.  This is evidence that DNA has been around since the beginning in either model. In the accepted geologic timescale model, cyanobacteria (blue green algae) are responsible for the O2 (oxygen crisis) in our atmosphere.

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Would anyone like to answer this question. If irreducible complexity is not true and evolution is--then there should be an answer for this riddle.

How did natural selection and mutation produce DNA gyrase and the helicase, both of which are required for DNA to split? If DNA can't split, then it can not replicate, and life stops? According to Dawkins and Darwin this should happen one step at a time--but you need the entirety of both enzymes for any kind of DNA replication.

#119 Ron

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Posted 18 January 2010 - 02:55 PM

How did natural selection and mutation produce DNA gyrase and the helicase, both of which are required for DNA to split?  If DNA can't split, then it can not replicate, and life stops?  According to Dawkins and Darwin this should happen one step at a time--but you need the entirety of both enzymes for any kind of DNA replication.

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:(

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Posted 19 January 2010 - 03:03 AM

Please understand that the "oldest fossils" found are cyanobacteria, which are living fossils and have DNA. This is evidence that DNA has been around since the beginning in either model. In the accepted geologic timescale model, cyanobacteria (blue green algae) are responsible for the O2 (oxygen crisis) in our atmosphere.


Precambrian cynobacteria are twice the size of modern cynano,which is evidence that there was twice as much oxygen in the atmosphere from the beginning as well.
Enjoy.

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Hey Jason can you please clarify what you mean here???




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