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Theory of Intelligent Design, the best explanation of Origins » Intelligent Design » Irreducible complexity » The cell is a interdependent irreducible complex system

The cell is a interdependent irreducible complex system

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All cellular functions are  irreducibly complex 3

chemist Wilhelm Huck, professor at Radboud University Nijmegen 5
A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity,"

Paul Davies, the fifth miracle page 53: 
Pluck the DNA from a living cell and it would be stranded, unable to carry out its familiar role. Only within the context of a highly specific molecular milieu will a given molecule play its role in life. To function properly, DNA must be part of a large team, with each molecule executing its assigned task alongside the others in a cooperative manner. Acknowledging the interdependability of the component molecules within a living organism immediately presents us with a stark philosophical puzzle. If everything needs everything else, how did the community of molecules ever arise in the first place? Since most large molecules needed for life are produced only by living organisms, and are not found outside the cell, how did they come to exist originally, without the help of a meddling scientist? Could we seriously expect a Miller-Urey type of soup to make them all at once, given the hit-and-miss nature of its chemistry?

Being part of a large team,cooperative manner,interdependability,everything needs everything else, are just other words for irreducibility and interdependence. 

For a nonliving system, questions about irreducible complexity are even more challenging for a totally natural non-design scenario, because natural selection — which is the main mechanism of Darwinian evolution — cannot exist until a system can reproduce. For an origin of life we can think about the minimal complexity that would be required for reproduction and other basic life-functions. Most scientists think this would require hundreds of biomolecular parts, not just the five parts in a simple mousetrap or in my imaginary LMNOP system. And current science has no plausible theories to explain how the minimal complexity required for life (and the beginning of biological natural selection) could have been produced by natural process before the beginning of biological natural selection.

Determination of the Core of a Minimal Bacterial Gene Set

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).

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 it was 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.

The genetic code to make the right ~600 amino acid sequence would have to be achieved not by  mutation , since that would require a pre-existing amino acid sequence, but adding randomly a new amino acid,  and select the advantageous sequence. Instead as by evolution, which evolves pre-existing proteins, in a origin of life scenario proteins would have all to be produced denovo. 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 600 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 its believed there 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 ? 1
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 then.

All Functions are "Irreducibly Complex" 4

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.  Darwinian evolution can work fine when one small step (e.g., a single point mutation) along an evolutionary pathway gives an advantage. The theory of intelligent design has no problem with this.

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?


Last edited by Admin on Wed Dec 28, 2016 6:37 pm; edited 9 times in total

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Last universal common ancestor 'more sophisticated than we thought,' say biologist

The chemical soup out of which all life eventually evolved could have been more complex than was first thought, according to a new study.
The last universal common ancestor (LUCA) is the name given to a crude organism that is now traceable in all domains of life; plants, animals, fungi, algae, etc.
Very little is actually known about this great-grandfather of evolution, and some scientists still debate whether it was even a cell.

But a new study has suggested that LUCA was a more sophisticated organism than presumed, with a complex structure that makes it identifiable as a cell.
The research, published in the journal Biology Direct, builds on several years of study of a previously overlooked feature of microbial cells.
This particular area has a high concentration of polyphosphate, a type of energy currency in cells

The new research argues that this polyphosphate storage site actually represents the first known universal organelle. 

Organelles were not thought to be common to all three branches of the tree of life - bacteria, archaea and eukaryotes - and common scientific consent said they were never found in bacteria.
However, in a 2003 study the same team from the University of Illinois showed that the polyphosphate storage structure in bacteria was physically, chemically and functionally the same as an organelle called an acidocalcisome, which is found in many single-celled eukaryotes.

Acidocalcisomes 3  are rounded electron-dense acidic organelles, rich in calcium and polyphosphate and between 100 nm and 200 nm in diameter.
Acidocalcisomes were originally discovered in Trypanosomes (the causing agents of sleeping sickness and Chagas disease) but have since been found in Toxoplasma gondii (causes toxoplasmosis), Plasmodium (malaria), Chlamydomonas reinhardtii (a green alga), Dictyostelium discoideum (a slime mould), bacteria and human platelets. Their membranes are 6 nm thick and contain a number of protein pumps and antiporters, including aquaporins, ATPases and Ca2+/H+ and Na+/H+ antiporters. They may be the only cellular organelle that has been conserved between prokaryotic and eukaryotic organisms.  2

This meant that the acidocalcisomes arose before the bacterial and eukaryotic lineages of the tree of life split, making the organelle even more ancient than realised.
The new study tracked the evolutionary history of a protein enzyme known as V-H+PPase, which is common to all three branches.
By comparing the V-H+PPase genes found in hundreds of organisms representing all three domains of life, the team constructed a 'family tree' that showed how different versions of the enzyme in different organisms were related.
For the enzyme to be present in all three, it had to have originated in the LUCA, before the three branches of the tree of life were formed.

'There are many possible scenarios that could explain this, but the most likely would be that you had already the enzyme even before diversification started on Earth,' said professor Gustavo Caetano-Anollés.
'The protein was there to begin with and was then inherited into all emerging lineages.'
His colleague Manfredo Seufferheld, who led the study, explained:  'This is the only organelle to our knowledge now that is common to eukaryotes, that is common to bacteria and that is most likely common to archaea.

'We may have underestimated how complex this common ancestor actually was'

'It is the only one that is universal.'
The findings suggest that LUCA may have been more complex than the simplest organisms alive today, and it has simplified itself during the evolutionary process instead of growing more complex, as we might expect.  
'You can't assume that the whole story of life is just building and assembling things,' said James Whitfield, a professor of entomology at Illinois and a co-author on the study.
'Some have argued that the reason that bacteria are so simple is because they have to live in extreme environments and they have to reproduce extremely quickly.
'So they may actually be reduced versions of what was there originally.
'According to this view, they've become streamlined genetically and structurally from what they originally were like.
'We may have underestimated how complex this common ancestor actually was.'

Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome. 4

Prokaryotes are thought to differ from eukaryotes in that they lack membrane-bounded organelles. However, it has been demonstrated that as in acidocalcisomes, the calcium and polyphosphate-rich intracellular "volutin granules (polyphosphate bodies)" in two bacterial species, Agrobacterium tumefaciens, and Rhodospirillum rubrum, are membrane bound and that the vacuolar proton-translocating pyrophosphatases (V-H+PPases) are present in their surrounding membranes. Volutin granules and acidocalcisomes have been found in organisms as diverse as bacteria and humans.

Here, we show volutin granules also occur in Archaea and are, therefore, present in the three superkingdoms of life (Archaea, Bacteria and Eukarya).

Molecular analyses of V-H+PPase pumps, which acidify the acidocalcisome lumen and are diagnostic proteins of the organelle, also reveal the presence of this enzyme in all three superkingdoms suggesting it is ancient and universal.

Using Protein family (Pfam) database, we found a domain in the protein, PF03030. The domain is shared by 31 species in Eukarya, 231 in Bacteria, and 17 in Archaea. The universal distribution of the V-H+PPase PF03030 domain, which is associated with the V-H+PPase function, suggests the domain and the enzyme were already present in the Last Universal Common Ancestor (LUCA).

The importance of the V-H+PPase function and the evolutionary dynamics of these domains support the early origin of the acidocalcisome organelle. In particular, the universality of volutin granules and presence of a functional V-H+PPase domain in the three superkingdoms of life reveals that the acidocalcisomes may have appeared earlier than the divergence of the superkingdoms. This result is remarkable and highlights the possibility that a high degree of cellular compartmentalization could already have been present in the LUCA.

This membrane-enclosed organelle is characterized by its acidic nature, high electron density, and high content of polyphosphates (polyP) including pyrophosphate (PPi), calcium, magnesium, and other elements. In addition, the organelle contains a variety of cation pumps including Ca2+/H+ and H+ pumps. In particular, the vacuolar proton translocating pyrophosphatase (V-H+PPase) proteins have been localized in the acidocalcisomes of bacteria, parasitic protozoans, algae, plants, and recently in cockroaches

Volutin-polyP bodies 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.The volutin granules shown in a number of microorganisms appear to be identical to acidocalcisomes of Agrobacterium and Rhodospirillum and eukaryotes.

The fact that V-H+PPase sequences group many familiar clades monophyletically, and are also ubiquitous among superkingdoms although with poor phylogenetic signal, suggests these proteins are truly ancient.

Crystal structure of a membrane-embedded H+-translocating pyrophosphatase 5

H+-translocating pyrophosphatases (H+-PPases) are active proton transporters that establish a proton gradient across the endomembrane by means of pyrophosphate (PPi) hydrolysis1, 2. H+-PPases are found primarily as homodimers in the vacuolar membrane of plants and the plasma membrane of several protozoa and prokaryotes2, 3. The three-dimensional structure and detailed mechanisms underlying the enzymatic and proton translocation reactions of H+-PPases are unclear. Each VrH+-PPase subunit consists of an integral membrane domain formed by 16 transmembrane helices. IDP is bound in the cytosolic region of each subunit and trapped by numerous charged residues and five Mg2+ ions. A previously undescribed proton translocation pathway is formed by six core transmembrane helices. Proton pumping can be initialized by PPi hydrolysis, and H+ is then transported into the vacuolar lumen through a pathway consisting of Arg 242, Asp 294, Lys 742 and Glu 301. We propose a working model of the mechanism for the coupling between proton pumping and PPi hydrolysis by H+-PPases.

a Ribbon diagram of the overall structure of VrH+-PPase, containing 16 TMs (labelled 1–16). A missing region (residues 42–66) is shown with dotted lines.
b The six inner and ten outer TMs drawn as cylinders and coloured in yellow and green, respectively. This orientation is rotated by 60° from that in a.
c VrH+-PPase dimer shown as a ribbon diagram with height and width dimensions of 75 Å and 85 Å, respectively. The detergent molecules of n-decyl β-D-maltoside are shown as sticks.
d Electrostatic surface potential of the VrH+-PPase dimer (red, blue and white indicate negative, positive and neutral potentials, respectively). In a–c, IDP is shown as sticks and coloured in CPK.

a Six core TMs (yellow ribbon) with IDP-binding residues (sticks).
b The electrostatic surface potential of the IDP binding pocket (red, blue and white indicate negative, positive and neutral potentials, respectively).
c The IDP-binding residues. Mg2+ ions, K+ ions and water molecules are shown as green, purple and red spheres, respectively. Interactions are presented as dashed lines. d The binding site of VrH+-PPase (in white) superimposed on EcPPase (PDB 2AUU; in pink). The Mg2+ ions of the VrH+-PPase (in green, with numbers) and EcPPase (in grey) are shown as spheres. The F− in EcPPase is shown as a blue sphere, and the Watnu in VrH+-PPase is shown as a labelled red sphere. IDP in VrH+-PPase and PPi in EcPPase are coloured in CPK.

a Resting state (R state).
b Initiated state (I state). 
c Transient state (T state). The VrH+-PPase dimer is shown and coloured in green and blue. M6 and M16 are shown as cylinders. The residues involved in proton transport are shown

a The proton transport pathway is formed by six core TMs (M5, M6, M11, M12, M15 and M16). The solvent-accessible surface area is coloured in cyan. The arrow indicates the direction of proton translocation. Right: zoomed-in view of the proton transport pathway. The residues involved in proton transport are shown and labelled. The solvent-accessible surface has been removed. Bottom: the hydrophobic gate around Glu 301. Residues forming a hydrophobic gate are displayed and labelled.
b The electron density map (2Fobs − Fcalc) (in blue) around the proton transport pathway drawn at a contour level of 2σ. The IDP is shown as sticks and coloured in CPK. Water molecules Watnu, Wat1 and Wat2 are presented as labelled red spheres. Water-mediated hydrogen bonds are drawn as black dashed lines.

Vacuolar-type proton translocating pyrophosphatase 1, putative 6

» 97.5% identical to GB:AAF80381.1: vacuolar-type proton translocating pyrophosphatase 1 {Trypanosoma cruzi} (PMID:10998372)
» Located in the plasma membrane and acidocalcisomes of amastigotes, epimastigotes, and trypomastigotes (PMID:9705361;IDA) curator_FSF date_20150319
» The gene encodes a vacuolar proton translocating pyrophosphatase predominantly localized in acidocalcisomes. The protein is also localized in the plasma membrane, Golgi complex and contractile vacuole.

Amino Acids 814 7

Conserved and functional residues in mPPases 8

The amino acid sequences of Na+- and H+ -PPases are highly conserved. The importance of α-helices has been studied showing that TM6 particularly contains many essential residues for the structure and function of mPPases (212). However, it is not trivial to distinguish between direct and indirect functional roles of residues or helices as exemplified by the finding that several residues in TM3, which does not form part of the central ion transport funnel, are required for H+ transport in H+-PPases (213). The significance of conserved and non-conserved amino acid residues has been extensively studied by site-directed mutagenesis (Table 1) (Fig. 7) (214, 215) and random mutagenesis (216). The amino acid residues that have an effect on mPPase function are listed in Table 1.

Figure 7. Amino acid residues (shown as pink stars) important for mPPase function and/or conformational stability according to the literature. The mPPases are from V. radiata (Vr-PPase), Flavobacterium johnsoniae (Fj-PPase), C. hydrogenoformans (Ch-PPase), Bacteroides vulgatus (Bv-PPase) and T. maritima (Tm-PPase). Both conserved and non-conserved residues were shown to be important for mPPase function.

Multiple alignments of PF03030 domain sequences distributed in the three superkingdoms (Archaea, Bacteria, and Eukarya). Shown above is the strongly conserved 57-residue region of the V-H+-PPase

8 )

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3 Fighter Planes and Eukaryotic Cells on Sat Oct 17, 2015 1:06 pm


Fighter Planes and Eukaryotic Cells

The F-22 fighter plane is a highly-sophisticated state of the art military aircraft. It is comprised of thousands of complex parts that all work together to enable the plane to perform a multitude of functions. Individually, these parts cannot operate or fly. But collectively they can fly and execute many different functions.

Now let’s take a hypothetical situation. Let’s imagine the entire earth is covered in huge piles of mechanical parts, thousands and thousands of miles of nothing but pieces of metal, plastic, rubber, etc. Now let’s imagine there are thousands of tornados and hurricanes all over the earth blowing all these parts around and into each other 24-7. Now with all this in mind, do you think it is possible that over the course of thousands or millions or even billions of years, that one of these storms would blow together an F-22 fighter plane in perfect operational condition?
Seems ridiculous right? Given an infinite amount of time, something like this just could not happen…

Now let’s look at the typical human eukaryotic cell. It too, just like the F22, is incredibly sophisticated and complex, but at a much smaller microscopic scale. This cell is also comprised of thousands of working parts (called organelles) that all work together to enable the cell to provide a multitude of functions. Individually, these parts are useless, but collectively they’re necessary. Remove anyone of these important parts and the cell will lose functionality and parish.

So if it is ridiculous to think that a perfectly operational F-22 fighter plane could come into existence via chance, then it is likewise just as illogical to think that such a sophisticated organism could assemble by chance as well. It gets even more absurd to think that this living cell would also form by chance and have the capability to reproduce.
Life cannot come from non-life even if given infinite time and chance. If life could spontaneously generate from non-life than it still should be doing that to this day. However, we’ve never observed it… Hence the Law of Biogenesis: The principle stating that life arises from pre-existing life, not from non-living material.[1] Life is clearly a product of God’s Creation.

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