All cellular functions are irreducibly complex

All cellular functions are irreducibly complex
http://reasonandscience.heavenforum.org/t2179-all-cellular-functions-are-irreducibly-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/t2176-lucathe-last-universal-common-ancestor#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/t2067-there-is-no-selective-advantage-until-you-get-the-final-function?highlight=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?

No they aren’t!

All cellular functions are irreducibly complex http://reasonandscience.heavenforum.org/t2179-all-cellular-functions-are-irreducibly-complex [etc.]
Evolution, maybe?

Read a book

God, not again.
Cap’t Jack

And I thought Origins was only broadcast on Cornerstone TV, silly me. It seems the brainless creationists have invaded this forum.

One of the worst mistakes of the anti-evolutionists is the claim that evolution is random, it is not, evolution is always responding to the environment in whatever way best suits survival, evolution is anything but random.

The inability to understand cellular function does not make them Irreducibly complex, it just means that you do not understand them.

Prior to the origin of the first living cell, all proteins had to be synthesized de novo, that is, from zero. In order to do that however, all the machinery to make proteins had to be in place. To propose that ribozymes would have done the job, without template, without coded information is far fetched. Beside this, the machinery itself that makes proteins,is made of proteins. Thats a catch22 situation. The cell furthermore would have a) know how to select the right left handed amino acids in a mixed pool of amino acids, b) select amongst inumerous amino acids, just the amongst the 20 required for life, and then select each one correctly, and bond one to the other in the right sequence. A protein chain cannot evolve from zero without the machinery in place, and the right information. Period. As the proton pump for example. First, it emerged prior to replication, which cancels evolution as a possible mechanism. Secondly, there is no function until the protein chain is fully formed with at least 600 amino acid residues linked each one correctly to another, all L amino acids selected, and the protein folded correctly. Trial and error will simply NEVER provide you that result. Thats impossible. This is true for one protein. Not to speak for the thousands in the whole immensly complex cell. Take lottery balls with 20 different colors, amongst the colors black. nuber them all from one to 600. But on 600 balls, you write left, and on another 600, you write right. Total 24000 balls. Now play lottery , and see how many trials will get you a chain of aligned numbers, from 1 to 600, only with balls written left on them and black. Or put it another way. let us consider a simple protein containing 600 amino acids. There are 20 different kinds of L-amino acids in proteins, and each can be used repeatedly in chains of 600. Therefore, they could be arranged in 20^600 different ways… Would you bet a dime on such odds ?

Therefore, they could be arranged in 20^600 different ways....... Would you bet a dime on such odds ?
When you have millions of years, and billions of opportunities for it to happen, the odds of it happening are close to certainty. And the whole chain didn't need to form at once, there could have been short sections forming all the time, till they started linking together. FYI, I don't gamble, and how much you are willing to bet, has nothing to do with how true the statement is.
Prior to the origin of the first living cell, all proteins had to be synthesized de novo, that is, from zero. In order to do that however, all the machinery to make proteins had to be in place. To propose that ribozymes would have done the job, without template, without coded information is far fetched. Beside this, the machinery itself that makes proteins,is made of proteins. Thats a catch22 situation. The cell furthermore would have a) know how to select the right left handed amino acids in a mixed pool of amino acids, b) select amongst inumerous amino acids, just the amongst the 20 required for life, and then select each one correctly, and bond one to the other in the right sequence. A protein chain cannot evolve from zero without the machinery in place, and the right information. Period. As the proton pump for example. First, it emerged prior to replication, which cancels evolution as a possible mechanism. Secondly, there is no function until the protein chain is fully formed with at least 600 amino acid residues linked each one correctly to another, all L amino acids selected, and the protein folded correctly. Trial and error will simply NEVER provide you that result. Thats impossible. This is true for one protein. Not to speak for the thousands in the whole immensly complex cell. Take lottery balls with 20 different colors, amongst the colors black. nuber them all from one to 600. But on 600 balls, you write left, and on another 600, you write right. Total 24000 balls. Now play lottery , and see how many trials will get you a chain of aligned numbers, from 1 to 600, only with balls written left on them and black. Or put it another way. let us consider a simple protein containing 600 amino acids. There are 20 different kinds of L-amino acids in proteins, and each can be used repeatedly in chains of 600. Therefore, they could be arranged in 20^600 different ways....... Would you bet a dime on such odds ?
You are making a number of incorrect or misguided assumptions. First you are assuming that the current biochemistry of life is the only way in which molecules can reproduce. That is as flawed as assuming that sexual reproduction is the only way in which life can reproduce. Much if not all of the biochemistry of earth is lost to history. Just because you can't find current examples we don't have the knowledge or the imagination to yet to come up with another way in which this can occur does not prove that other effective methods of molecular reproduction don't exist that cold have preceded current day systems and evolved into what we have today. Its incredibly naive and self serving to assume that DNA is the only molecule capable of storing information and reproducing and that DNA can only reproduce itself using complex mechanisms like the current suite of enzymes that control the process today. Once again as with all creationists your approach is to claim that if we don;t have an answer the answer must be god. When exactly did we all vote to make god the default explanation for things we don't have complete answers for. I vote no on that idea.
Therefore, they could be arranged in 20^600 different ways....... Would you bet a dime on such odds ?
When you have millions of years, and billions of opportunities for it to happen, the odds of it happening are close to certainty. And the whole chain didn't need to form at once, there could have been short sections forming all the time, till they started linking together. FYI, I don't gamble, and how much you are willing to bet, has nothing to do with how true the statement is. You're also missing that there is a different kind of math needed here] Simply taking the whole that we have now and assuming it came together randomly is to ignore how it got to be how it is. Most of those non-useful options were never tried because their predecessors weren't successful, they didn't survive. Instead of millions of dice being rolled, imagine a wheel with spokes with new wheels at the end of each spoke. If all of those wheels were created you'd get your 20^600, but actually, only a few survive because only a few fit their environment. Those are the ones we see.
FYI, I don't gamble
Every time you choose to step outside your door and walk (or drive) into the busy world you are taking a calculated gamble. :coolsmirk: But, more to the point. (I couldn't find it or I'd link to it but) years ago Time/Life I believe it was came up with a little book that listed the 100 most basic organic molecules in sequence. A simple set of statistics, properties and molecular formula diagrammed. I remember looking through it and the amazingly beautiful simple accumulating complexity of the thing, based on very few elemental atoms - in basic arrangements - a world of potentials was opened up. It was one of those cosmic-giggles writ large - BS Albert, god certainly does play dice with the Universe! Dice using the most basic building blocks - some click and can do fantastic things, most grind or fizzle to nothing. Sounds like cosmic gambling to me. :cheese:

Oh my Glob! You blew my mind, man! Jesus! Jesus, where for art thou, Jesus!
Oh mightyJesus
Who came from nothing
Blessed be thy name
For though you poofed from nothing
And are most complex
It’s cool cuz that’s what the Bible says
And from that nothing
You magicked up some dirt
And from that dirt
You did create us
And everything else on Earth
And though it’s all cray complicado
That’s no big biggie
Because that’s what your priests did say
And we do so believe them
Because they’re super wisemen
Cuz that’s what they said you said
And all that they say
Is God’s own wisdom
Because they do say it’s so
And they do say
All’s made by your space magic
And that’s good enough proof for us
EDIT
Stuff. And lots of it.
Word to your mother.

Oh my Glob! You blew my mind, man! Jesus! Jesus, where for art thou, Jesus! Oh mightyJesus Who came from nothing Blessed be thy name For though you poofed from nothing And are most complex It's cool cuz that's what the Bible says And from that nothing You magicked up some dirt And from that dirt You did create us And everything else on Earth And though it's all cray complicado That's no big biggie Because that's what your priests did say And we do so believe them Because they're super wisemen Cuz that's what they said you said And all that they say Is God's own wisdom Because they do say it's so And they do say All's made by your space magic And that's good enough proof for us EDIT Stuff. And lots of it. Word to your mother.
A poet! I never knew.

DM! Glad once again to see you back man, and with a profoundly philosophical statement concerning “irreducible complexity” which totally discounts evolution, therefore Dog (my dyslexic brain acting up again). I wonder how our doubting Thomas buddy feels about the newly discovered Hominin species found in the Rising Star cave, Homo Naledi? Well, it was discovered two years ago but National Geo is popularizing the find. And what a find it is! Three million year old remains of at least 15 Hominins who’s group members placed them in the cave, clearly showing that they had at least some rudimentary belief system. And these guys were contemporary with Homo Erectus! Imagine them sitting around a fire discussing such topics as how the eye couldn’t possibly have evolved, therefore God! I’d like to have been a primative fly on the wall for that discussion! Whatdaya think?!
Cap’t Jack

Og: “Dude, where do you think our eyes came from?”
Thag: “What? I don’t know. Who cares?”
Og: “Do you think the Great Spirit really gave them to us so we could hunt and wouldn’t get lost, like the shaman says? Or do you think it was something else? Like selection pressure or heredity?”
Thag: “One, shut up. Two, I don’t know what the nut ‘selec’-whatever is. And three, shut up. You’re gonna get us killed. There are cat monsters all over here.”
Og: “But it’s. . .Ahhhh! My torso! It’s eating my torso!”
Thag: “Told you so.”

All cellular functions are irreducibly complex http://reasonandscience.heavenforum.org/t2179-all-cellular-functions-are-irreducibly-complex Prokaryotes are thought to differ ...

… of anything. So, how are they brought together in living things to form such high level functional order?


Seems copyright infringement to me. Copy/paste of a nearly complete article.
At least it is a very cheap way of discussing: copy/paste an article from elsewhere.

FYI, I don't gamble
Every time you choose to step outside your door and walk (or drive) into the busy world you are taking a calculated gamble. :coolsmirk: Sounds like cosmic gambling to me. :cheese:
Taking a risk, perhaps, gambling, no. When the cosmos throws the dice, it is assuming that some combination will come up, and every time it throws the dice, a combination does come up. Gambling would be to try to predict which combination is going to come up, and then there would be the possibility of being wrong and loosing, but the cosmos does not care which combination comes up, it will just keep throwing the dice till the combination that comes up, works.
One of the worst mistakes of the anti-evolutionists is the claim that evolution is random, it is not, evolution is always responding to the environment in whatever way best suits survival, evolution is anything but random.
I agree with your post, but differ on a detail. The process of natural selection is random, but evolution is proof of having escaped this natural testing process. Random DNA mutations are subject to natural selection for a chance to procreate. How many "failed species" (tries) does it take to produce a single viable one? However, even here we find inconsistencies. The Silvery Salamander should have gone extinct long ago. Yet it survives through a remarkably ingenious method, clearly not intended by any Watchmaker, but pure chance (a lucky unlucky roll of the dice).
In 2005, a population of Silvery Salamanders (Ambystoma platineum) was discovered on the site of Skyline High School. This rare species is unusual in that all silvery salamanders are female. The species is a hybrid of Blue-spotted and Jefferson salamanders, and egg development is stimulated by the presence of sperm from these related species, but genes from the sperm do not actually enter the egg.
IOW, all silvery salamanders are clones of the mother. https://localwiki.org/ann-arbor/Silvery_Salamander Also, in regard to "evolution", it starts with very small changes, which are either detrimental. (most of them) or advantageous to surviving in its local environent. Why does a grey colored mouse on a grey rocky environment escape the eye of the eagle, while the sand colored mouse is easily spotted and picked off. However, the reverse is true and in a sandy environment the grey mouse is the one in danger. Oddly, these different colored mice are of the exact same species and may have both colors in a single litter. But each minor abberation (haircolor) has found a survival niche, by Natural selection, so it's evolution has 'forked" (branched) into grey and sand colored cousins. If anyone is still clinging to the "Blind Watchmaker" proposition, ask which watch has no reducible components, yet is the most accurate clock to date.. You may want to check out the new "Optical clocks", and the "Quantum clocks, now being tested. "Intelligent assembly not required". BTW. Here is excellent lecture bt Ken Miller on the Kitzmiller-Dover Trial : https://www.youtube.com/watch?v=AK0CYZvaJLw&feature=related