All cellular functions are  irreducibly complex
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04-09-2015, 12:10 AM
RE: All cellular functions are  irreducibly complex
For any lurkers, guests or newcomers, irreducible complexity has already been refuted on Godexist's previous thread on the same subject and he ignored all the points raised

http://www.thethinkingatheist.com/forum/...lex-system
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04-09-2015, 12:13 AM
RE: All cellular functions are  irreducibly complex
(20-08-2015 02:52 AM)Mathilda Wrote:  So to summarise Godexist's technique.

You have two scientists. Scientist A believes in RNA-first replication, scientist B believes in metabolism-first. Each has evidence to support their theory.

Godexists comes along and says that it can't be either and selectively quotes each scientist's argument against the other theory. He completely ignores each scientist's argument for their own theory and does not admit to any possibility that there is something that has not yet been considered.

Godexists then says that his own particular God did it without actually putting forward any evidence to support his own assertion or explaining how this is possible or giving us any reason to suspect that this could be the case.


0/10 Must try harder.
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04-09-2015, 12:15 AM
RE: All cellular functions are  irreducibly complex
(17-08-2015 06:47 AM)Mathilda Wrote:  
(17-08-2015 06:35 AM)unfogged Wrote:  What exactly is the mechanism that stops small changes from accumulating into large changes over time?

This. This. This.

Godexists won't be able to answer this. The most he'll be able to say is "nobody knows" but at the same time won't be able to provide any evidence that small changes do not accumulate to large changes over time.

Yet there is plenty of evidence to show that small changes do accumulate to large changes over time. Fossil records, genetic algorithms, neurophysiology and analysis of DNA are several that immediately spring to mind.

Even on this very thread I remember seeing a link to how the eye evolved. This is clear evidence that Godexists is deliberately and dishonestly ignoring evidence.
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04-09-2015, 12:15 AM
RE: All cellular functions are  irreducibly complex
(16-08-2015 06:53 AM)Mathilda Wrote:  
(16-08-2015 06:32 AM)Godexists Wrote:  A irreducible complex system can indeed change over time. Thats called micro evolution. We know for example that ATP synthase has many variants, that change by microevolutionary mechanisms. So one, micro evolution, adds to the other. The fundamental structure is irreducible, but small changes for adaptation are normal, and based on the inbuilt mechanism that permits such changes. They make part of the overall design .

Evolutionary scientists recognise that evolution happens in small steps but that these steps build up over time to move a system very far away from its original form.

The term 'micro-evolution' is only used by creationists. They do this to pretend that evolutionary scientists are telling people that evolution works by making very large steps. Again, another dishonest tactic.
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04-09-2015, 12:16 AM
RE: All cellular functions are  irreducibly complex
(02-09-2015 01:46 PM)Godexists Wrote:  All cellular functions are  irreducibly complex

http://reasonandscience.heavenforum.org/...ly-complex

Prokaryotes are thought to differ from eukaryotes in that they lack membrane-bounded organelles. However, it has been demonstrated that there are bacterias which have membrane bound organelles named acidocalcisomes, and that V-H+PPase proton pumps are present in their surrounding membranes. Acidocalcisomes have been found in organisms as diverse as bacteria and humans. Volutin granules which are equivalent of acidocalcisomes also occur in Archaea and are, therefore, present in the three superkingdoms of life (Archaea, Bacteria and Eukarya). These volutin granule organelles occur in organisms spanning an enormous range of phylogenetic complexity from Bacteria and Archaea to unicellular eukaryotes to algae to plants to insects to humans. According to neo-darwinian thinking, the universal distribution of the V-H+PPase  domain  suggests the domain and the enzyme were already present in the Last Universal Common Ancestor (LUCA).

http://reasonandscience.heavenforum.org/...estor#3992

If the proton pumps of Volutin granules were present in LUCA, they had to emerge prior to self replication, which induces serious constraints to propose evolution as driving factor. But if evolution was not the mechanism, what else was ? There is not much left, namely chance, random chemical reactions, or physical necessity.

But lets for a instance accept the "fact of evolution", and suppose as the driving force to make  V-H+PPase proton pumps.  In some period prior to the verge of non-life to life, natural selection or an other evolutionary mechanism would have had to start polymerisation of the right amino acid sequence to produce V-H+PPase proton pumps by addition of one amino acid monomer to the other. First, the whole extraordinarly  production line of staggering complexity starting with DNA would have to be in place, that is  :

The cell sends activator proteins to the site of the gene that needs to be switched on, which then jump-starts the RNA polymerase machine by removing a plug which blocks the DNA's entrance to the machine.  The DNA strands do shift position so that the DNA lines up with the entrance to the RNA polymerase. Once these two movements have occurred and the DNA strands are in position, the RNA polymerase machine gets to work melting them out, so that the information they contain can be processed to produce mRNA 2 The process follows then after INITIATION OF TRANSCRIPTION through RNA polymerase enzyme complexes, the mRNA is  capped through Post-transcriptional modifications by several different enzymes ,  ELONGATION provides the main transcription process from DNA to mRNA, furthermore  SPLICING and CLEAVAGE ,  polyadenylation where a long string of repeated adenosine nucleotides is added,  AND TERMINATION through over a dozen different enzymes,    EXPORT FROM THE NUCLEUS TO THE CYTOSOL ( must be actively transported through the Nuclear Pore Complex channel in a controlled process that is selective and energy dependent  )  INITIATION OF PROTEIN SYNTHESIS (TRANSLATION) in the Ribosome in a enormously complex process,  COMPLETION OF PROTEIN SYNTHESIS AND PROTEIN FOLDING through chaperone enzymes. From there the proteins are transported by specialized proteins to the end destination. Most of these processes require ATP, the energy fuel inside the cell.  

http://reasonandscience.heavenforum.org/...t=function

The genetic code to make the right ~600 amino acid sequence would have to be made by mutation and natural selection. But mutation of what, if there was no functional protein yet ? . The problem in this stage is,  when there is no selective advantage until you get the final function, the final function doesn't evolve. In other words, a chain of around 800 amino acids is required to make a funcional V-H+PPase proton pump, but there is no function, until polymerisation of all 600 monomers is completed and the right sequence achieved.

The problem for those who accept the truth of evolution is,  they cannot accept the idea that any biological structure with a beneficial function, however complex, is very far removed from the next closest functional system or subsystem within the potential of "sequence space" that might be beneficial if it were ever found by random mutations of any kind. In our case the situation is even more drastic, since DENOVO genetic sequence and subsequently amino acid chain for a new formation of a new amino acids strand is required.  A further constraint is the fact that 100% of  amino acids used and needed for life are left handed, while DNA and RNA requires D-sugars.  Until today, science has not sorted out how nature is able to select the right chiral handedness. The problem is that the pre-biotic soup is believed to be a warm soup consisting of racemic mixtures of amino acid enantiomers (and sugars). How did this homogenous phase separate into chirally pure components? How did an asymmetry (assumed to be small to start with) arise in the population of both enantiomers? How did the preference of one chiral form over the other, propagate so that all living systems are made of 100 percent optically pure components?

What is sequence space ?
Imagine 20 amino acids mixed up  in a pool, randomly mixed , one adjacent to the other. The  pool with all the random amino acids  is the sequence space. This space can be two dimentional, tridimensional, or multidimensional. In evolutionary biology, sequence space is a way of representing all possible sequences (for a protein, gene or genome).  Most sequences in sequence space have no function, leaving relatively small regions that are populated by naturally occurring genes. Each protein sequence is adjacent to all other sequences that can be reached through a single mutation. Evolution can be visualised as the process of sampling nearby sequences in sequence space and moving to any with improved fitness over the current one.

Functional sequences in sequence space
Despite the diversity of protein superfamilies, sequence space is extremely sparsely populated by functional proteins. That is, amongst all the possible amino acid sequences, only a few permit the make of functional proteins. Most random protein sequences have no fold or function. To exemplify:  In order to write METHINKS IT IS LIKE A WEASEL , there are 10^40 possible random combinations possible to get the right sequence. But only one is correct.

Enzyme superfamilies, therefore, exist as tiny clusters of active proteins in a vast empty space of non-functional sequence.The density of functional proteins in sequence space, and the proximity of different functions to one another is a key determinant in understanding evolvability.
Protein sequence space has been compared to the Library of Babel a theoretical library containing all possible books that are 410 pages long. In the Library of Babel, finding any book that made sense was impossible due to the sheer number and lack of order. 


How would a bacterium evolve a function like a single protein enzyme? - like a V-H+PPase proton pump? The requirement is about 600  specified residues at minimum.  A useful V-H+PPase cannot be made with significantly lower minimum size and specificity requirements.   These minimum requirements create a kind of threshold beyond which the V-H+PPase function simply cannot be built up gradually where very small one or two residues changes at a time result in a useful change in the degree of the proton pump function. Therefore, such functions cannot have evolved in a gradual, step by step manner.  There simply is no template or gradual  pathway from just any starting point to the minimum threshold requirement.  Only after this threshold has been reached can evolution take over and make further refinements - but not until. Now, there are in fact examples of computer evolution that attempt to address this problem;

All Functions are "Irreducibly Complex" 

The fact is that all cellular functions are irreducibly complex in that all of them require a minimum number of parts in a particular order or orientation.  I go beyond what Behe proposes and make the suggestion that even single-protein enzymes are irreducibly complex.  A minimum number of parts in the form of amino acid residues are required for them to have their particular functions.  The proton pump function cannot be realized in even the smallest degree with a string of only 5 or 10 or even 500 residues of any arrangement.  Also, not only is a minimum number of parts required for the proton pump function to be realized, but the parts themselves, once they are available in the proper number, must be assembled in the proper order and three-dimensional orientation.  Brought together randomly, the residues, if left to themselves, do not know how to self-assemble themselves to form a much of anything as far as a functional system that even comes close to the level of complexity of a even a relatively simple function like a proton pump.  And yet, their specified assembly and ultimate order is vital to function.
Of course, such relatively simply systems, though truly irreducibly complex, have evolved.  This is because the sequence space at such relatively low levels of functional complexity is fairly dense.  It is fairly easy to come across new beneficial sequences  if the density of potentially beneficial sequences in sequence space is relatively high.  This density does in fact get higher and higher at lower and lower levels of functional complexity - in an exponential manner.  

It is much like moving between 3-letter words in the English language system.  Since the ratio of meaningful vs. meaningless 3-letter words in the English language is somewhere around 1:18, one can randomly find a new meaningful and even beneficial 3-letter word via single random letter changes/mutations in relatively short order.  This is not true for those ideas/functions/meanings that require more and more letters.  For example, the ratio of meaningful vs. meaningless 7-letter words and combinations of smaller words equaling 7-letters is far far lower at about 1 in 250,000.  It is therefore just a bit harder to evolve between 7-letter words, one mutation at a time, than it was to evolve between 3-letter words owing to the exponential decline in the ratio of meaningful vs. meaningless sequences.  

The same thing is true for the evolution of codes, information systems, and systems of function in living things as it is for non-living things (i.e., computer systems etc).  The parts of these codes and systems of function, if brought together randomly, simply do not have enough meaningful information to do much of anything. So, how are they brought together in living things to form such high level functional order?


HEY FUCKSTICK!

PERSONAL INCREDULITY IS NOT EVIDENCE OF ANYTHING!

Other than you need to get yourself a damn education, you fucking ignorant scrub.

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04-09-2015, 12:17 AM
RE: All cellular functions are  irreducibly complex
(12-08-2015 02:06 PM)Mathilda Wrote:  
(12-08-2015 02:01 PM)Unbeliever Wrote:  So let the thread die, if all it's become is pointless repetition.

Do you honestly believe that theists like Godexists and Blowme actually want these threads to die? No, they want to keep posting the same rubbish again and again until everyone gives up and they're left to proclaim that they have won.
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04-09-2015, 12:20 AM
RE: All cellular functions are  irreducibly complex
If the mods are not prepared to ban Godexists then they should just merge all this threads about irreducible complexity into one mega thread.
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04-09-2015, 12:21 AM
RE: All cellular functions are  irreducibly complex
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04-09-2015, 03:04 AM
RE: All cellular functions are  irreducibly complex
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"Theology made no provision for evolution. The biblical authors had missed the most important revelation of all! Could it be that they were not really privy to the thoughts of God?" - E. O. Wilson
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04-09-2015, 03:06 AM
RE: All cellular functions are  irreducibly complex
[Image: evolution-of-man.jpg?w=632&h=452]

"Theology made no provision for evolution. The biblical authors had missed the most important revelation of all! Could it be that they were not really privy to the thoughts of God?" - E. O. Wilson
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