quinta-feira, 21 de julho de 2016

The complexity of the initial Enzymatic and Metabolic network of the first living cells ( progenote/LUCA ) demonstrates the requirent of a intelligent , powerful Creator

Following shows the minimal metabolic network that was required in the first supposed last universal common ancestor. Consider that this extremely complex network could not emerge through evolution, since evolution depends that this very own metabolic network was fully operational, beside dna replication, on which evolution depends. 

So the only two mechanisms that remain to explain its origin is chance/luck/self organisation, or physical necessity. We know of intelligence being able to construct electric circuits all the time.

We do not know of lucky accidents with the same capacity. We can infer therefore confidently, that the metabolic network to create the first living cell was designed. 

The Enzymatic and Metabolic Capabilities of Early Life 


We reconstruct a representative metabolic network that may reflect the core metabolism of early life forms. Our results show that ten enzyme functions, four hydrolases, three transferases, one oxidoreductase, one lyase, and one ligase, are determined by metaconsensus to be present at least as late as the last universal common ancestor. Subnetworks within central metabolic processes related to sugar and starch metabolism, amino acid biosynthesis, phospholipid metabolism, and CoA biosynthesis, have high frequencies of these enzyme functions. 

quinta-feira, 28 de abril de 2016

Cytochrome bc complexes, origin, biosynthesis etc.

The Cytochrome b6-f Complex Connects Photosystem II to Photosystem I

The electrons extracted from water by photosystem II are transferred to plastoquinol, a strong electron donor similar to ubiquinol in mitochondria. This quinol, which can diffuse rapidly in the lipid bilayer of the thylakoid membrane, transfers its electrons to the cytochrome b6-f complex, whose structure is homologous to the cytochrome c reductase in mitochondria. The cytochrome b6-f complex pumps H+ into the thylakoid space using the same Q cycle that is utilized in mitochondria, thereby adding to the proton gradient across the thylakoid membrane. The cytochrome b6-f complex forms the connecting link between photosystems II and I in the chloroplast electron-transport chain. It passes its electrons one at a time to the mobile electron carrier plastocyanin (a small copper-containing protein that takes the place of the cytochrome c in mitochondria), which will transfer them to photosystem I (Figure 14–50).

Photosystem I then harnesses a second photon of light to further energize the electrons that it receives.

The structure and function of the cytochrome b6 f complex

Molecular mechanisms of photosynthesis, Robert Blankenship, page 120

The cytochrome b6 f complex is an essential player in noncyclic and cyclic electron flow. The cytochrome b6 f complex is similar in most ways to the cytochrome bc1 complex. However, there are some important differences. The structure of the cytochrome b6 f complex is shown in Fig. 7.7.

Table 7.2 gives the identity and masses of the proteins of the cytochrome b6 f complex.

 In addition to the proteins, the complex contains chlorophyll and carotenoid molecules of unknown function. Cytochrome f is a c-type cytochrome that serves a similar functional role to cytochrome c1 in the cytochrome bc1 complex. However, the two cytochromes have very different structural features. It is an elongated protein, with largely 𝛽-sheet secondary structure. The 𝛽-sheet structure is very unusual compared with other c-type cytochromes, which are largely 𝛼-helical. Cytochrome f has a single transmembrane helical segment near the Cterminal end of the protein, which anchors the globular domain to the luminal side of the thylakoid membrane. In some species, this segment is easily cleaved from the globular portion that contains the covalently attached heme group. Cytochrome f is also unusual in that the N-terminal amino group is one of the ligands to the Fe in the heme. It donates electrons toplastocyanin (or, in some organisms, the soluble cytochrome c6). The Rieske Fe–S protein in the cytochrome b6 f complex consists of two domains: an N-terminal transmembrane helical region that anchors the protein to the membrane and a soluble domain located on the luminal side of the thylakoid membrane that contains the Fe–S redox cofactor . The soluble domain is largely 𝛽-sheet in secondary structure and is further divided into two subdomains. One of the subdomains contains the Fe–S cofactor and is structurally almost identical to the corresponding part of the Rieske protein from the cytochrome bc1 complex, while the other subdomain is very different. This is thought to reflect the different reaction partners (cytochrome c1 vs. cytochrome f) of the Rieske protein in the two types of complexes. Another important difference between the cytochrome b6 f and the cytochrome bc1 complex is the cytochrome b portion of the complex. In the cytochrome bc1 complex, cytochrome b is an integral membrane protein with eight trans membrane helices, as discussed above. However, cytochrome b6 is much smaller, with only four trans membrane helices predicted. Another subunit of the cytochrome b6 f complex, called subunit IV, exhibits sequence similarity to the C-terminal half of the cytochrome b in the bc1 complex. Subunit IV contains three predicted transmembrane helices; the eighth transmembrane helix of the cytochrome bc1 complex is missing. A surprising difference between the cytochrome b6 f and bc1 complexes is the presence of an additional heme group, called heme cn in the cytochrome b6 f complex. This heme has a single thioether linkage to the protein instead of two linkages found in almost every other c-type cytochrome. This was first discovered in the cytochrome b6 f complex isolated from the green alga Chlamydomonas reinhardtii , but is also found in the complex from cyanobacteria. In addition to the subunits described above, the cytochrome b6 f complex contains some other protein subunits not found in the cytochrome bc1 complex (Table 7.2). The cytochrome b6 f complex surprisingly contains one molecule each of chlorophyll and 𝛽 carotene, although it is not known if these pigments serve an important functional role. The cytochrome b6 f complex is also dimeric in vivo, like the cytochrome bc1 complex, although it can easily become monomeric and inactive once isolated .

quinta-feira, 23 de julho de 2015

Vault, made by a 3d Polyribosome nano-printer 


Polyribosomes Are Molecular 3D Nanoprinters That Orchestrate the Assembly of Vault Particles

In a time in which efficient 3D manufacturing is predicted to have a revolutionary effect on mankind, nature unveils that it has already been using this technique for millions of years. Vaults are very large ribonucleoprotein particles found widely in eukaryotes. Our discovery of the unique assembly mechanism of the vault particle reveals an unforeseen function of the polyribosome as a very sophisticated cellular 3D nanoprinter. 4

Three-dimensional printers fabricate a gamut of products such as medical devices, toys, and even specialty chocolates. Now a new study suggests that eukaryotic cells evolved a 3-D nanoprinter millions of years ago, in the form of polyribosomes. These clusters of ribosomes strung along a single messenger RNA appear to be responsible for the intricate 3-D assembly of a mysterious large, barrel-shaped protein complex called the vault particle 5

“I had never in my life seen anything like these rolls,” Mrazek says. “Normally, when you get misassembled proteins you see ugly tangles, but these were so symmetric.” Mrazek concluded that the rolls must reflect structural intermediates during the vault assembly process. Ribosomes moving along an mRNA normally synthesize individual protein strands, which then come off the ribosome and fold into their 3-D shapes. On the basis of the proposed helical geometry of the polyribosome, Mrazek hypothesized that as an individual MVP molecule gets translated by a ribosome in the cluster, it could form a dimer with the MVP synthesized by the ribosome next to it. As they’re formed, adjacent dimers could then arrange side by side to form the vault particle. The vaults take shape bit by bit as the dimers are completed and come off the polyribosome, much like a 3-D printer might build up the layers of a plastic object. The sixth mutation in the MVP somehow disrupts the pinching off of the vault particle after the 39th dimer assembles, resulting in the long, rolled-up vaults.

Ribosomes are molecular machines that function in polyribosome complexes to translate genetic information, guide the synthesis of polypeptides, and modulate the folding of nascent proteins. Here, we report a surprising function for polyribosomes as a result of a systematic examination of the assembly of a large ribonucleoprotein complex, the vault particle. Structural and functional evidence points to a model of vault assembly whereby the polyribosome acts like a 3D nanoprinter to direct the ordered translation and assembly of the multi-subunit vault homopolymer, a process which we refer to as polyribosome templating. Structure-based mutagenesis and cell-free in vitro expression studies further demonstrated the critical importance of the polyribosome in vault assembly. Polyribosome templating prevents chaos by ensuring efficiency and order in the production of large homopolymeric protein structures in the crowded cellular environment and might explain the origin of many polyribosome-associated molecular assemblies inside the cell.

Polyribosomes May Act As 3-D Nanoprinters To Fabricate Vault Particles

Vaults are large barrel-shaped ribonucleoprotein particles that are highly conserved in a wide variety of eukaryotes (1). Although several functions have been proposed for vaults since their discovery in 1986 (2–10), including roles in multidrug resistance, cell signaling, and innate immunity, their cellular function remains unclear. Most vault particles are present in the cytoplasm, but a few of them localize to the nucleus 1

The proposal that vaults could act as a cellular transporter implies that these particles must present a highly regulated opening mechanism in order to efficiently incorporate and deliver the specific vault cargo. Even so, both the precise regulation of the opening mechanism and the structural characteristics that can allow such surprising dynamics still have to be clearly defined 2

A 2014 paper found “a surprising function for polyribosomes as a result of a systematic examination of the assembly of a large ribonucleoprotein complex, the vault particle”. Beyond merely orienting ribosomes in crowded conditions to avoid aggregation of freshly produced peptides, polyribosomes act “like a 3D nanoprinter” spinning out the many copies needed for this homopolymer, which they called ‘polyribosome templating’. That is, the interactions are not being minimised for fear of dangerous aggregation, but controlled to orchestrate favourable interactions to produce vaults. 3

So how are Vaults and their " made of " best explained ? Design, or natural mechanisms ? 

1) http://www.sciencemag.org/content/323/5912/384.full
2) http://digital.csic.es/bitstream/10261/88208/1/New%20features.pdf
3) http://biochemistri.es/vault-particles
4) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245718/
5) http://cen.acs.org/articles/92/web/2014/11/Polyribosomes-Act-3-D-Nanoprinters.html
6) http://bioinformatics.org/firstglance/fgij//fg.htm?mol=2ZUO

segunda-feira, 6 de julho de 2015

Transfer RNA, and its biogenesis, best explained through design

Transfer RNA is an ancient molecule, central to every task a cell performs and thus essential to all life. The enzyme is one of only two ribozymes which can be found in all kingdoms of life (Bacteria, Archaea, and Eukarya) The three major RNAs involved in the flow of genetic information are messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). All these RNAs participate in the protein-synthesizing pathway in cells. tRNA has two distinct characteristics. It carries an anticodon corresponding to the mRNA codon and it binds to the corresponding amino acid in a reaction catalyzed by a specific aminoacyl-tRNA synthetase.  tRNA's are therefore essential components in the sequential information flow process from DNA to mRNA to proteins. No tRNA, no proteins, no advanced life.  tRNA's are transcribed and processed in a extremely complex manner by several holoenzymes and proteins. tRNA is a key bridging molecule between ribonucleotide information (RNA world) and peptide information (protein world). Therefore, tracing the  origin of tRNA molecules is likely to cast light on the processes that led to the establishment of the central processes of life. 

tRNA's are very specific molecules, and the " made of " follows several steps, requiring a significant number of proteins and enzymes, which are often made of several subunits and aided by essential co-factors and metals. 

The challenge for evolution to the fact, that biological systems incorporate several essential parts, that cannot be eliminated without losing the core function of the  system in question, and that these parts have no function of their own and could therefore not be product of natural mechanisms, of gradual evolutionary steps,  is in my view more severe than most philosophers of science  and scientists like Behe exemplify. In systems of enormous biological complexity like the cell,  thousands of parts are essential , many more parts, than the well known examples like the flagellum. Irreducibility is found from the highest level of biological organisation and systems, to  a single DNA deoxyribonucleotide, which loses  function if reduced to its single components, the bases, phosphate or sugar. Just take off one, and the molecule loses its function. Same goes for the cell. Take off one building block, like the spindle apparatus, and mitosis and cell division is not possible, and life could not reproduce itself.

The make of proteins is similar to the make of cars in a car factory. If the grinder machine to make the motor pistons  has a mal function,  the pistons cannot be finished,  the car's motor block cannot be  assembled with all parts, and the motor would not function without that essential part. Amongst thousands of parts, just a tiny one will compromise the function of the whole system. In biological nano-factories, the solutions to overcome problems like damage must all be pre-programmed, and the repair "working horses" to resolve the problem must be ready in place and "know" what to do how, and when. If a roboter in a factory assembly line fails, employees are ready to detect the error and make the repair . In the cell, the mal function of any  part even as tiny and irrelevant as it might seem, can be fatal, and if the repair mechanisms are not functioning correctly and fully in place right from the start, the repair can't be done, and life ceases.  These repair enzymes which cleave, join, add, replace etc. must be programmed in order to function properly right from the start. Aberrantly processed pre-tRNAs for example are eliminated through a nuclear surveillance pathway by degradation of their 3′ ends, whereas mature tRNAs lacking modifications are degraded from their 5′ends in the cytosol.  

B.Alberts writes:  Eucaryotic tRNAs are transcribed from DNA by RNA Polymerase III. Afterwards, tRNA's are covalently modified before they are allowed to exit from the nucleus. Both bacterial and eucaryotic tRNAs are typically synthesized as larger precursor tRNAs, which are then trimmed to produce the mature tRNA. In addition, some tRNA precursors (from both bacteria and eucaryotes) contain introns that must be spliced out.  tRNA splicing uses a cut-and-paste mechanism that is catalyzed by proteins.  Trimming and splicing both require the precursor tRNA to be correctly folded in its cloverleaf configuration. Because misfolded tRNA precursors will not be processed properly, the trimming and splicing reactions are thought to act as quality- control steps in the generation of tRNA's. All tRNA's are modified chemically—nearly 1 in 10 nucleotides in each mature tRNA molecule is an altered version of a standard G, U, C, or A ribonucleotide. Over 50 different types of tRNA modifications are known. Some of the modified nucleotides—most notably inosine, produced by the deamination of adenosine—affect the conformation and basepairing of the anticodon and thereby facilitate the recognition of the appropriate mRNA codon by the tRNA molecule.  This means, if the basepairing of the codons of mRNA with the anticodons of tRNA does not fit and match correctly,it will affect the accuracy with which the correct amino acid is attached to the tRNA , or it is eventually not even capable of identifiyng the right tRNA. In other words, its like the key that must fit in the door lock. It it does not fit, the door will not open. If the match of the codons do not fit precisely into the anticodon's of the mRNA, the precise assignment of the amino acid is compromised, or not possible, and proteic amino acid chains cannot be sinthesized successfully. So that is another keystep.

The processing into mature tRNA  happens through  the removal, addition and chemical modification of nucleotides. Processing for some tRNA involves

1) removal of the leader sequence at the 5 prime end 
2) replacement of two nucleotides at the 3 prime end by the sequence CCA (with which all mature tRNA molecules terminate) 
3) chemical modification of certain bases and  
4) excision of  introns. The mature tRNA is often diagrammed as a flattened cloverleaf which clearly shows the base pairing between self-complementary stretches in the molecule.

Each of these steps is a essential requirement for the synthesis of tRNA, if one doesn't do its job properly, tRNA cannot be made. The biosynthesis of tRNA is a irreducible complex process. 

To give a example in tRNA maturation in Homo sapiens, following Enzymatic  complexes are involved in the process:


CCA tRNA nucleotidyltransferase 1 , 
Zinc phosphodiesterase ELAC protein 2

and  Enzymatic  complexes:

Ribonuclease P
tRNA ligase complex 
tRNA-splicing endonuclease

CCA tRNA nucleotidyltransferase 1 uses a Magnesium co-factor, Zinc phosphodiesterase ELAC protein 2 uses zinc as co-factor,  Human nuclear RNase P consists of 10 Protein subunits and one RNA subunit, the tRNA ligase complex uses 6 protein components, and tRNA-splicing endonuclease uses 4 protein subunits. In total 20 proteins subunits, one RNA subunit, and 2 different co-factors.

Each of these protein complexes exercises very precise coordinated tasks, which all have to be pre-programmed in the genome. Lets have a look at the special capabilities:

Ribonuclease P has the function  to cleave off an extra, or precursor, sequence of RNA on tRNA molecules. For ( supposedly )  billions of years and still to this day, the function of RNase P -- found in nearly all organisms, from bacteria to humans -- has been to cleave transfer tRNA. If the tRNA is not cleaved, it is not useful to the cell. 

Once RNase P recognizes tRNA, it docks and, assisted by metal ions, cuts one chemical bond.

This happens in  a stepwise, orderly process, where the enzyme " knows " exactly where to cleave with a precise target. How could such a function have arisen ? trial and error ? coding the genetic instructions until the right sequence permitted to cleave off the right nucleotides ? why at all would some unknown mechanism do this  trial and error ? Or had chemicals a end goal ? or the goal of " survival of the fittest " ( despite the fact that they are not alive ) ? if the enzyme cleaved too much or too less, tRNA could not be used properly, so its function had to be programmed correctly in the genome right from the start, otherwise, well, no life.... Not only the cleavage at the right place has to be explained, but also the arise of this sophisticated mechanism, which follows precise , complex steps in a machinelike manner.

In the paper The enigma of ribonuclease P evolution, the authors,  Enno  Roland K. Hartmann write :

The simplest interpretation is that RNase P has an ‘RNA-alone’ origin and progenitors of Bacteria and Archaea diverged very early in evolution and then pursued completely different strategies in the recruitment of protein subunits during the transition from the ‘RNA-alone’ to the ‘RNA-protein’ state of the enzyme.’

The authors write about recruitment and strategies. Its interesting that they atribute  mental and conscient activities to chemical processes and reactions. But as such, they have no end goal, so how does it make sense to write in these terms ? Furthermore, recruitment of what ? of extant subunits ? were they readily available to choose from in the surrounding ?  how could RNase know which ones to select  and  how to incorporate them correctly in its system ? Is that not one more nice example of pseudo science ?

As Luskin of the discovery institute writes : When certain biologists discuss the early stages of life there is a tendency to think too vaguely. They see a biological wonder before them and they tell a story about how it might have come to be. They may even draw a picture to explain what they mean. Indeed, the story seems plausible enough, until you zoom in to look at the details. I don't mean to demean the intelligence of these biologists. It's just that it appears they haven't considered things as completely as they should. Like a cartoon drawing, the basic idea is portrayed, but there is nothing but blank space where the profound detail of biological processes should be.

Would these five conditions not have to be met in order to recruit and insert the subunits into the system ?

C1: Availability. Among the parts available for recruitment to form the system, there would need to be ones capable of performing the highly specialized tasks of individual parts, even though all of these items serve some other function or no function.

C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.

C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.

C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a system are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.

C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if sub systems or parts are put together in the right order, they also need to interface correctly.

( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)

In the paper tRNA-nucleotidyltransferases: Highly unusual RNA polymerases with vital functions, the authors Stefan Vörtler, and Mario Mörl write:

tRNA-nucleotidyltransferases are fascinating and unusual RNA polymerases responsible for the synthesis of the nucleotide triplet CCA at the 3′-terminus of tRNAs. As this CCA end represents an essential functional element for aminoacylation and translation, these polymerases (CCA-adding enzymes) are of vital importance in all organisms. Elucidation of the role of the CCA enzyme in the cellular network of tRNA quality control and the identities of the RNases accompanying the CCA enzyme constitute new questions that warrant active investigation.

CCA-adding enzymes obviously can count until three: after the addition of three nucleotides, the polymerization reaction is efficiently stopped.  Additionally, and most interestingly, the CCA-adding enzymes recognize if nucleotides are previously added to a tRNA primer and incorporate then only the missing ones, completing thereby the CCA triplet. A tRNA that carries already the first C residue of the CCA terminus is elongated only by one C and one A, while on a tRNA ending with CC, only the terminal A residue is added. This feature shows that CCA-adding enzymes are not only responsible for the de novo synthesis of CCA ends but have an important maintenance and repair function for tRNA ends. This stringent sequence and length control of the tRNA CCA end reflects the recognition requirements for aminoacylation and translation.

( This is amazing. How did it " learn "  that feat ? trial and error ?  ) 

Furthermore, positioning in the ribosome during translation and even peptide release from the ribosome depend on an intact CCA end, which is critical for water coordination and efficient hydrolysis of the ester bound translation product. 

These facts indicate that an accurate CCA end participates, beyond simple recognition and binding, as an integral part in several reaction mechanisms and is therefore of vital importance for the cell.
Surprisingly, these polymerases with such unusual features evolved twice in evolution, leading to classes 1 and 2 CCA-adding enzymes

Convergence is evidence against evolution, and the author supposes evolution prior the existence of a replicating cell.......

While class 1 is exclusively found in archaea, class 2 tRNA-nucleotidyltransferases are present in eukaryotes and bacteria, where they fulfill identical functions. Structural organization of classes 1 and 2 CCA-adding enzymes. While both enzyme versions have a hook-like shape of similar size, the allocation of secondary structure elements in neck, body and tail domains are quite different. In class 1 enzymes, these regions contain alpha-helical as well as beta-sheet elements. Class 2, on the other hand, has exclusively alpha-helical structures in these domains. The catalytic cores, located in head and neck domains of both enzyme versions, are indicated by the grey arrows. The rainbow color bar represents the consecutive protein regions from N- (blue) to C-terminus (red).

One of the most fascinating aspects of both classes of tRNA-nucleotidyltransferases is the fact that CCA-addition does not require an external nucleic acid as a template – somehow these enzymes “know” when to incorporate which nucleotide.

Indeed. Or maybe the intelligent designer programmed them in order for them to know ?? what makes more sense, inanimated matter to know something, or a intelligent creator programming these enzymes to exercise special tasks and functions upon pre-programming ? 

Crystal structures of both classes 1 and 2 enzymes revealed a set of highly conserved amino acid residues located in the single nucleotide binding pocket that interact with the incoming nucleotide by forming Watson/Crick-like hydrogen bonds.

So these enzymes do not only " know " when to incorporate which nucleotide, but also " know " how to bind each nucleotide to the next through hydrogen bonds..... amazing.
Structural organization of classes 1 and 2 CCA-adding enzymes. While both enzyme versions have a hook-like shape of similar size, the allocation of secondary structure elements in neck, body and tail domains are quite different. In class 1 enzymes, these regions contain alpha-helical as well as beta-sheet elements. Class 2, on the other hand, has exclusively alpha-helical structures in these domains. The catalytic cores, located in head and neck domains of both enzyme versions, are indicated by the grey arrows. The rainbow color bar represents the consecutive protein regions from N- (blue) to C-terminus (red).

One of the most fascinating aspects of both classes of tRNA-nucleotidyltransferases is the fact that CCA-addition does not require an external nucleic acid as a template – somehow these enzymes “know” when to incorporate which nucleotide.

Indeed. Isn't that a magnificient example and evidence of design ?

Crystal structures of both classes 1 and 2 enzymes revealed a set of highly conserved amino acid residues located in the single nucleotide binding pocket that interact with the incoming nucleotide by forming Watson/Crick-like hydrogen bonds

So these enzymes do not only " know " when to incorporate which nucleotide, but also " know " how to bind each nucleotide to the next through hydrogen bonds..... amazing.

So the question  arises : Did natural processes have foresight of the end product, tRNA, to make these highly specific nano robot - like molecular machines which  remove, add and  modify  the nucleotides of tRNA? If not, how could they have arisen, since without end goal, there would be no function for them ? neither could they have been co-opted because of their high specificity and uniqueness, required only in these molecular machines? They are specifically made for the production and make of tRNA's. Isnt the make of tRNA not another prime example of intelligent design ? 

My contemption is once more that naturalistic explanations are  inadequate to explain this sophisticated mechanism in question. While a designer, which had the intention to make life, could have well invented the process, and set it up.

Pierre Grasse on evolution


Pierre Grasse was the most distinguished of French zoologists, the editor of the 28 volumes of Traite de Zoologie, author of numerous original investigations, and ex-president of the Academie des Sciences. His knowledge of the living world is encyclopedic.

Grasse believed in something that he called "evolution." So did Dobzhansky, but when Dobzhansky
used that term he meant neo-Darwinism, evolution propelled by random mutation and guided by
natural selection.

Grasse used the same term to refer to something very different, a poorly
understood process of transformation in which one general category (like reptiles) gave rise to
another (like mammals), guided by mysterious "internal factors" that seemed to compel many
individual lines of descent to converge at a new form of life. Grasse denied emphatically that
mutation and selection have the power to create new complex organs or body plans, explaining
that the intra-species variation that results from DNA copying errors is mere fluctuation, which
never leads to any important innovation.

The genic differences noted between separate populations of the same species that are so often
presented as evidence of ongoing evolution are, above all, a case of the adjustment of a
population to its habitat and of the effects of genetic drift. The fruitfly (drosophila
melanogaster), the favorite pet insect of the geneticists, whose geographical, biotropical, urban,
and rural genotypes are now known inside out, seems not to have changed since the remotest

Grasse insisted that the defining quality of life is the intelligence encoded in its biochemical
systems, an intelligence that cannot be understood solely in terms of its material embodiment
The minerals that form a great cathedral do not differ essentially from the same materials in the
rocks and quarries of the world; the difference is human intelligence, which adapted them for a
given purpose. Similarly,

Any living being possesses an enormous amount of "intelligence," very much more than is
necessary to build the most magnificent of cathedrals. Today, this "intelligence" is called
information, but it is still the same thing. It is not programmed as in a computer, but rather it is
condensed on a molecular scale in the chromosomal DNA or in that of every other organelle in
each cell. This "intelligence" is the sine qua non of life. Where does it come from? . . . This is a
problem that concerns both biologists and philosophers, and, at present, science seems incapable
of solving it.... If to determine the origin of information in a computer is not a false problem,
why should the search for the information contained in cellular nuclei be one?

Grasse argued that, due to their uncompromising commitment to materialism, the Darwinists
who dominate evolutionary biology have failed to define properly the problem they were trying
to solve. The real problem of evolution is to account for the origin of new genetic information,
and it is not solved by providing illustrations of the acknowledged capacity of an existing
genotype to vary within limits. Darwinists had imposed upon evolutionary theory the dogmatic
proposition that variation and innovative evolution are the same process, and then had employed
a systematic bias in the interpretation of evidence to support the dogma. Here are some
representative judgments from Grasse's introductory chapter:

Through use and abuse of hidden postulates, of bold, often ill-founded extrapolations, a
pseudoscience has been created.... Biochemists and biologists who adhere blindly to the
Darwinist theory search for results that will be in agreement with their theories.... Assuming that
the Darwinian hypothesis is correct, they interpret fossil data according to it; it is only logical
that [the data] should confirm it; the premises imply the conclusions.... The deceit is sometimes
unconscious, but not always, since some people, owing to their sectarianism, purposely overlook
reality and refuse to acknowledge the inadequacies and the falsity of their beliefs.

Grasse was an evolutionist, but his dissent from Darwinism could hardly have been more radical
if he had been a creationist. It is not merely that he built a detailed empirical case against the
neo-Darwinian picture of evolution. At the philosophical level, he challenged the crucial doctrine
of uniformitarianism which holds that processes detectable by our present-day science were also
responsible for the great transformations that occurred in the remote past. According to Grasse,
evolving species acquire a new store of genetic information through "a phenomenon whose
equivalent cannot be seen in the creatures living at the present time (either because it is not there
or because we are unable to see it)."

Grasse even turned the charges of mysticism against his opponents, commenting sarcastically
that nothing could be more mystical than the Darwinian view that "nature acts blindly,
unintelligently, but by an infinitely benevolent good fortune builds mechanisms so intricate that
we have not even finished with analysis of their structure and have not the slightest insight of the physical principles and functioning of some of them."

What was different about Grasse was that he was willing to give unprejudiced consideration to the possibility that science does not know, and may never know, how new quantities of genetic infommation have come into the world.

domingo, 5 de julho de 2015

The proposal of intelligent design in nature is a littlebit older than most might expect:

. . . Is it possible for any man to behold these things, and yet imagine that certain solid and individual bodies move by their natural force and gravitation, and that a world so beautifully adorned was made by their fortuitous concourse? He who believes this may as well believe that if a great quantity of the one-and-twenty letters, composed either of gold or any other matter, were thrown upon the ground, they would fall into such order as legibly to form the Annals of Ennius. I doubt whether fortune could make a single verse of them. How, therefore, can these people assert that the world was made by the fortuitous concourse of atoms, which have no color, no quality—which the Greeks call [poiotes], no sense? [Cicero, THE NATURE OF THE GODS BK II Ch XXXVII, C1 BC, as trans Yonge (Harper & Bros., 1877), pp. 289 - 90.]


quinta-feira, 2 de julho de 2015

There is no selective advantage until you get the final function

Lenksi et al published a article in Nature 8 to which Luskin of the Discovery institute replied upon which Richard B. Hoppe at  the Panda's thumb in his article desperately dissing Avida  replied again. 7  The debate is interesting as it touches some core questions of the evolution x intelligent design controversy.

Hoppe writes following as reply to Luskin:

Co-option and modification of existing structures is a ubiquitous phenomenon in evolution at levels ranging from molecular mechanisms to high-level structures like wings.

this is a confortable way to avoid the relevant  questions, and Hoppe keeps avoiding them despite Luskin  pointed  out that its not only about modification and co-option of existing parts, but  how  de-novo genes evolved to start the make of new features. How did new structures and new kind of cells begin to evolve ?

Biological structures are well organized , structured, and build up like human made factories and machines. The process takes place fully automated inside the cell. The process of protein production ,starting from the genes, is extremely complex, and several steps are required.  Bruce Alberts writes in "The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists," 9 :

But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we  had ever considered. We now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines. 

Ordered Movements Drive Protein Machines 
Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like the machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts. Within each protein assembly, intermolecular collisions are not only restricted to a small set of possibilities, but reaction C depends on reaction B, which in turn depends on reaction A—just as it would in a machine of our common experience.

Underlying this highly organized activity are ordered conformational changes in one or more proteins driven by nucleoside triphosphate hydrolysis (or by other sources of energy, such as an ion gradient).the nearly ubiquitous use of energy-driven conformational changes to promote the local assembly of protein complexes, thereby creating a high degree of order in the cell, has become universally recognized.

We have also come to realize that protein assemblies can be enormously complex. Consider for example the spliceosome. Composed of 5 small nuclear RNAs (snRNAs) and more than 50 proteins, this machine is thought to catalyze an ordered sequence of more than 10 RNA rearrangements as it removes an intron from an  RNA transcript. As cogently described in this issue of Cell by Staley and Guthrie (1998), these steps involve at least eight RNA-dependent ATPase proteins and one  GTPase, each of which is presumed to drive an ordered  conformational change in the spliceosome and/or in its bound RNA molecule. As the example of the spliceosome should make clear, the cartoons thus far used to
depict protein machines  vastly underestimate the sophistication of many of these remarkable devices.

Many different types of chemical reactions are required to produce a properly folded protein from the information contained in a gene 1)

The journey from gene to protein is complex and tightly controlled within each cell. It consists of two major steps: transcription and translation. Together, transcription and translation are known as gene expression. 4

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 3 )  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.

Each of these steps requires extremely complex proteins and enzymes, the working horses of the cell, which work like robots in a assembly line in  highly regulated precise steps, and  these machines are by themself encoded in the genome. Not only is the information to make them stored in the genome. But these machines require further , different proteins and enzymes in order to be prepared and assembled. And the information for these processes taking place is also recorded in the genome. And a few genes contain the information to produce  molecules that help the cell assemble proteins, that is, the build up of the whole machinery must also be pre-programmed, and happen in a sequencial special, ordered manner. Many different processes need to happen at the same time, driven by ATP, which means, the ATPase powerhouse and proton gradient and membranes must be extant since the beginning. In the same way, that we build a machine, each part must be mounted at the right place, at the right time, in the right sequence and order, and the parts must fit together in a functional and precise way. And the right materials are needed. In a car engine, the pistons must be made by the right temperature resistant metals, and so it is also inside the cells. Most enzymes have reaction centers , where special substrates and reacton factors are required to exercise their specific reactions, and many enzymes require the presence of other compounds - cofactors - before their catalytic activity can be exerted. 5 How could natural mechnisms " figure out " what special materials, like metal-ion-activators, are required to produce given reaction ? Trial and error ? Furthermore, following is required:

C1: Availability. Among the parts available for recruitment to form a biological system consisting of multiple parts, there would need to be ones capable of performing the highly specialized tasks of the specific system, even though all of the items serve some other function or no function in another system where they were recruited from.
C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.
C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.
C4: Coordination.The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if the subunits  are put together in the right order, they also need to interface correctly. The parts must be coordinated in just the right way: even if all of the parts of a ribosome are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.
C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if the subunits  are put together in the right order, they also need to interface correctly.

So these further questions arise :

For what reason would natural processes produce the machines like for example Ribonuclease P, which processes pre-tRNA, which contains additional tRNA sequences at both the 5’ and 3’-ends and need to be removed ? For what reason would natural processes produce tRNA which are required inside the Ribosome , the central molecule in the translation process ? ( lets mention that  the very own factories that are made through them, make these enzymes and proteins..... Catch 22..... )
P Ribonuclease P would have no function by its own. tRNA has no function by its own. The Ribosome has no function by its own. These individual parts exercise only their function, if interlocked and working in a interdependent way together. Supposing everything would start through natural processes, how could these machines arise separately, in a stepwise fashion, if they do not have any use by their own ? Its not that we can argue that we simply don't know yet. What we do know, permits us rationally to infer, that naturalistic explanations are entirely inadequate to explain the phenomena in question.  A initial blueprint is required, where the whole process is pre-programmed, which is the case in the genome, where all the information to build a cell is stored, and the whole process has to start all at once. That seems to be best explained through a intelligent designer.  

Mark Perakh then goes on in another article, published in The Panda's thumb, and writes :

Dembski’s new definition of IC means in fact “the death” of IC because it adds an impossible condition for a system to be recognized as IC. This condition does in fact require proving a universal negative: to be IC, the system, according to Dembski’s new definition, must be such that its function cannot be performed by any other simpler system. With this requirement no system can ever be asserted to be IC because it is impossible to assert that there is no other, simpler system anywhere in any form that can perform the job, even at a lower level of fitness. If we can’t point to such a simpler system, it does not mean it cannot exist; the possibility that such a system exists but we simply don’t know about it can never be excluded.

Well, thats a evident strawman argument. We know that DNA cannot exercise its function, unless 3 essential parts, namely the bases, the phosphate backbone, and the deoxyribose sugar are in place. Take any one of the 3 parts away, bye bye functionality. Take away 3 of the 4 bases, bye bye with the genome's language. Take away the energy of the cell, ATP, and almost all action would cease. The list could go on and on. So, i think the exposed facts here give further reason to infer design as the most adequate, capable, potent, precise and correct explanation for what we observe in the natural world, and specially inside the cell.

As uncommondescent 10 puts it:

ID is not proposing “God” to paper over a gap in current scientific explanation. Instead ID theorists start from empirically observed, reliable, known facts and generally accepted principles of scientific reasoning:
(a) Intelligent designers exist and act in the world.
(b) When they do so, as a rule, they leave reliable signs of such intelligent action behind.
(c) Indeed, for many of the signs in question such as CSI and IC, intelligent agents are the only observed cause of such effects, and chance + necessity (the alternative) is not a plausible source, because the islands of function are far too sparse in the space of possible relevant configurations.
(d) On the general principle of science, that “like causes like,” we are therefore entitled to infer from sign to the signified: intelligent action.
(e) This conclusion is, of course, subject to falsification if it can be shown that undirected chance + mechanical forces do give rise to CSI or IC. Thus, ID is falsifiable in principle but well supported in fact.

In sum, ID is indeed a legitimate scientific endeavor: the science that studies signs of intelligence.

1) Bruce Alberts, Molecular biology of the cell, 5th ed. pg.399
2) http://m.phys.org/news/2008-11-molecular-machines-gene-revealed.html
3) http://www.nobelprize.org/educational/medicine/dna/a/transport/ncp_complex.html
4) http://ghr.nlm.nih.gov/handbook/howgeneswork/makingprotein
5) http://www.worthington-biochem.com/introbiochem/chemNature.html
6) http://www.ideacenter.org/contentmgr/showdetails.php/id/1319#critique
7) http://www.pandasthumb.org/archives/2005/09/desperately_dis.html
8 )http://myxo.css.msu.edu/papers/nature2003/Nature03_Complex.pdf
9) http://ac.els-cdn.com/S0092867400809228/1-s2.0-S0092867400809228-main.pdf?_tid=0c9b2ab6-211a-11e5-aa39-00000aab0f26&acdnat=1435883326_afc8928f7e91c03d19c01581858d99b8
10) http://www.uncommondescent.com/faq/#gaps_god