Simple Examples of Irreducible Complexity - Evolution Impossible

a reply to: cooperton

There are no articles that show that the process of peptide polymerization can "self-assemble".

One of many articles:

Self-assembly of bioactive peptides, peptide conjugates, and peptide mimetic materials
Charlotte J. C. Edwards-Gayle and Ian W. Hamley ORCID logo*
Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK. E-mail: [email protected]

Received 4th May 2017 , Accepted 22nd June 2017
First published on 26th June 2017

pubs.rsc.org...

Molecular self-assembly is a multi-disciplinary field of research, with potential chemical and biological applications. One of the main driving forces of self-assembly is molecular amphiphilicity, which can drive formation of complex and stable nanostructures. Self-assembling peptide and peptide conjugates have attracted great attention due to their biocompatibility, biodegradability and biofunctionality. Understanding assembly enables the better design of peptide amphiphiles which may form useful and functional nanostructures. This review covers self-assembly of amphiphilic peptides and peptide mimetic materials, as well as their potential applications.

Peptide self-assembly

Self-assembly is defined as the ability of a molecule, without guidance of external factors, to associate through non-covalent interactions to form highly ordered 3-dimensional structures.1 This occurs through a bottom-up approach. Most self-assembling molecules have both hydrophobic and hydrophilic components, and are termed amphiphilic.1 Lipids are perhaps the simplest molecule displaying amphiphilicity, with a hydrophilic head group, and a hydrophobic tail group. Peptides and proteins are more complex in their amphiphilicity. This is largely due to folding, giving rise to ‘faces’, different folded surfaces which are exposed to different environments. For example, a β-sheet peptide may contain alternating hydrophilic and hydrophobic residues, resulting in the side chains being exposed on opposite sides of the sheet.2 Self-assembly is commonly found in nature. A natural example of a self-assembled structure is the phospholipid bilayer, which is the basis of cell membranes, vesicles and organelle membranes in cells and bacteria.3 Another example is microtubules, which are cytoskeletal components of eukaryotic and some prokaryotic cells. Microtubules are a main component of the mitotic spindle in cell division which contracts to pull apart chromosomes in eukaryotes, and in prokaryotes make up the internal structure of cilia and flagella in bacteria enabling movement.4,5 Other examples include protein folding in enzymes, DNA double helix formation and the formation of the virus protein capsid around a nucleic acid core.6 In aqueous environments, self-assembly is driven by non-covalent forces to form ordered structures ranging from the manometer to micron size.7 These non-covalent interactions include van der Waals forces, hydrophobic interactions, electrostatic interactions, hydrogen bonding and π–π stacking (aromatic) interactions.1,8 These interactions are weak, for example the backbone hydrogen bonding in peptides having an estimated energy of 4.2 kcal mol−1 in a gaseous environment, which decreases in solution.9 However, these interactions are enough to stabilise these robust structures. In turn, this means self-assembly can be influenced by temperature, pH and concentration. Some of the most common structures (Fig. 1) include micelles, vesicles and fibrillar structures (nanotubes, fibres).10

So your wish that complex functional proteins can just self-assemble from scratch peptide monomers is totally unfounded in the literature.

You still don't get it. SELF ASSEMBLY IS A PROCESS. Where did I say that they self assemble in a vacuum outside the process?

You're making it up again.

You're done - again. I was hoping that at the very least you would take an interest in the dynamics - but as per usual, you had your answer before reading the documentation. You continually ignore what the research says to conform to your false and irrational ideas about nature.

As for the physics of protein folding, when you can discuss the thermodynamics and the actual experiments, let me know.

a reply to: cooperton


Self-assembly of bioactive peptides, peptide conjugates, and peptide mimetic materials
Charlotte J. C. Edwards-Gaylea and Ian W. Hamley*a
Author affiliations

pubs.rsc.org...#!divAbstract

Abstract

Molecular self-assembly is a multi-disciplinary field of research, with potential chemical and biological applications. One of the main driving forces of self-assembly is molecular amphiphilicity, which can drive formation of complex and stable nanostructures. Self-assembling peptide and peptide conjugates have attracted great attention due to their biocompatibility, biodegradability and biofunctionality. Understanding assembly enables the better design of peptide amphiphiles which may form useful and functional nanostructures. This review covers self-assembly of amphiphilic peptides and peptide mimetic materials, as well as their potential applications.

edit on 26-7-2019 by Phantom423 because: (no reason given)

con't

Self-assembly is commonly found in nature. A natural example of a self-assembled structure is the phospholipid bilayer, which is the basis of cell membranes, vesicles and organelle membranes in cells and bacteria.3



Another example is microtubules, which are cytoskeletal components of eukaryotic and some prokaryotic cells.
Microtubules are a main component of the mitotic spindle in cell division which contracts to pull apart chromosomes in eukaryotes, and in prokaryotes make up the internal structure of cilia and flagella in bacteria enabling movement.4,5 Other examples include protein folding in enzymes, DNA double helix formation and the formation of the virus protein capsid around a nucleic acid core.6

a reply to: Phantom423

These are all in reference to protein folding, not polymerization. Polymerization is the adding of peptide monomers to make polypeptide chains, giving rise to the "primary protein". This does not self-assemble, it needs genetic code sequences, transcription and translation to assemble properly. "secondary" and "tertiary" proteins, which are folded polypeptide chains, can self-assemble according to chemical attraction laws, but they often self-assemble incorrectly without the aid of chaperone proteins.



Regardless, the irreducible complexity remains because in order for the many components of the muscle unit to be made, it requires the DNA sequence for all polypeptide chains involved, as well as the necessary co-factors that properly fold the chain into the correct tertiary protein. In order to by-pass irreducible complexity, the entire protein would have to be shown to be able to self-assembly from peptide monomers to avoid the necessity of DNA coding, transcription and translation. But these tertiary proteins cannot self assemble from scratch peptide monomers, meaning the dilemma of irreducible complexity remains.

a reply to: cooperton

You didn't read the papers. You also did not do a literature search. Do a search specifically for AMINO ACID self assembly and then PEPTIDE polymerization.

originally posted by: Phantom423
a reply to: cooperton

You didn't read the papers.

I went no further than the abstract because none of them were about self-assembly of peptide polymerization. It would blow away conventional science if it were found that transcription and translation were not necessary for polypeptide formation.

This part of biology does not self-assemble, it needs the genetic code, transcription and translation, meaning it is still irreducibly complex.

originally posted by: cooperton

originally posted by: Phantom423
a reply to: cooperton

You didn't read the papers.

I went no further than the abstract because none of them were about self-assembly of peptide polymerization. It would blow away conventional science if it were found that transcription and translation were not necessary for polypeptide formation.

This part of biology does not self-assemble, it needs the genetic code, transcription and translation, meaning it is still irreducibly complex.

Where did you ever get the idea that transcription/translation were not part of the process? You're poking holes where there are none.

a reply to: cooperton

Self-assembly of bioactive peptides, peptide conjugates, and peptide mimetic materials

BIOACTIVE PEPTIDES. What is that?

originally posted by: Phantom423
a reply to: cooperton

Self-assembly of bioactive peptides, peptide conjugates, and peptide mimetic materials

BIOACTIVE PEPTIDES. What is that?

Bioactive peptides are generally 3–20 amino acid residues in length and both animal and plant proteins are known to contain potential bioactive sequences. They remain inactive while the sequences are kept within the parent protein. They are active once released by enzymatic hydrolysis by peptidases.

a reply to: cooperton

This paper describes peptide self assembly in detail

www.paper.edu.cn...

Emerging biological materials through molecular
self-assembly
Shuguang Zhang*
Center for Biomedical Engineering 56-341, Massachusetts Institute of Technology, 77 Massachusetts Avenue,
Cambridge, MA 02139-4307, USA
Accepted 5 September 2002

3. Molecular self-assembly in nature Biomimicry and designing nature-inspired materials through molecular self-assembly is an emerging field in the coming years of the 21st century.

Nature is a grand master at designing chemically complementary and structurally compatible constituents for molecular self assembly through eons of molecular selection and evolution. Chemical evolution from the first groups of primitive molecules through countless iterations of molecular self-assembly and disassembly has ultimately produced more and more complex molecular systems.

In the last decade, considerable advances have been made in the use of peptides, phospholipid and DNA as building blocks to produce potential biological materials for a wide range of applications (Schnur, 1993; Ghadiri et al., 1994; Bong et al., 2001; Zhang et al., 1993, 1995; Holmes et al., 2000; Aggeli et al., 1997, 2001; Alivisatos et al., 1996; Mirkin et al., 1996; Winfree et al., 1998). The constituents of biological origins, such as phospholipid molecules, amino acids and nucleotides have not been generally considered to be useful materials for traditional materials science and engineering. The advent of biotechnology and genetic engineering coupled with the recent advancement in chemistry of nucleic acids and peptide syntheses has resulted in a conceptual change. Molecular self-assembly is emerging as a new route to produce novel materials and to complement other materials, i.e. ceramics, metals and alloys, synthetic polymers and other composite materials. Several recent discoveries and rapid developments in biotechnology, however, have rekindled the field of biological materials engineering (Urry and Pattanaik, 1997; Huc and Lehn, 1997; Petka et al., 1998).

There are ample examples of molecular self-assembly in nature. One of the well-known examples is the silk assembly. The monomeric silk fibroin protein is approximately 1 mm but a single silkworm can spin fibroins into silk materials over 2 km in length, two billion times longer! (Feltwell, 1990; Winkler et al., 1999). Such a marvelous engineering skill can only make us envy. Human ingenuity and current advanced technology is far behind the seemingly easy task by the silkworm. Likewise, spiders are grand master materials engineers who can produce many types of spider silks through self-assembly of the building blocks in a variety of ways, thus, producing spider silk fiber with tremendous strength and flexibility. These building blocks are often at the nanometer scale. However, the resulting materials could be measured at meters and kilometer scales. Likewise, the size of individual phospholipid molecules is
approximately 2.5 nm in length, but they can self-assemble into millimeter-size lipid tubules
with defined helical twist, many million times larger. A number of applications have been
developed (Schnur, 1993; Spector et al., 1996). The power of molecular self-assembly can
never be underestimated. Molecular self-assembly can also build sophisticated structures and
materials. For example, collagen and keratin can self-assemble into ligaments and hair,
respectively. In cells, many individual chaperone proteins assembly into a well-defined ring
structure to sort out, fold and refold proteins (Sigler et al., 1998). The same is true for other
protein systems, such as seashell biomineralization (Morse, 1999; Weiner and Addadi, 1991).
Likewise, mammals build their teeth through self-assembly of a protein scaffold that is made of
many individual proteins first and recruit calcium ions to the sites for biomineralization.

4. Self-assembling peptide systems A new class of peptide-based biological materials was serendipitously discovered in yeast (Zhang et al., 1993) from the self-assembly of ionic self-complementary peptides (Zhang et al., 1993). A number of peptide molecular self-assembly systems have been designed and developed (Table 1). This systematic analysis provided insight into the chemical and structural principles of peptide self-assembly. These peptides are short, simple to design, extremely versatile and easy to synthesize. Three types of self-assembling peptides have been

a reply to: cooperton

That's the last link I 'm going to post about self assembly. If you don't understand it by now, then it's hopeless. It's a natural process from beginning to end. NO THIRD PARTY IS REQUIRED.

originally posted by: Phantom423
There are ample examples of molecular self-assembly in nature. One of the well-known examples is the silk assembly. The monomeric silk fibroin protein is approximately 1 mm but a single silkworm can spin fibroins into silk materials over 2 km in length, two billion times longer!

Fibroin is a primary protein, meaning it is a polypeptide sequence. I was asking for peptide polymerization self-assembly, not the polymerization of tertiary proteins. Again, tertiary proteins assemble spontaneously via chemical law (with help from post-translational factors), but you still need the DNA data, transcription and translation to create the primary protein. These polypeptides (fibroin) do not simply self-assemble from peptide monomers.

Do you understand this distinction?

The dilemma of irreducible complexity remains.

originally posted by: cooperton

originally posted by: Phantom423
There are ample examples of molecular self-assembly in nature. One of the well-known examples is the silk assembly. The monomeric silk fibroin protein is approximately 1 mm but a single silkworm can spin fibroins into silk materials over 2 km in length, two billion times longer!

Fibroin is a primary protein, meaning it is a polypeptide sequence. I was asking for peptide polymerization self-assembly, not the polymerization of tertiary proteins. Again, tertiary proteins assemble spontaneously via chemical law (with help from post-translational factors), but you still need the DNA data, transcription and translation to create the primary protein. These polypeptides (fibroin) do not simply self-assemble from peptide monomers.

Do you understand this distinction?





The dilemma of irreducible complexity remains.

Absolutely not true. Look up in-chain conjugation, amino acid coordinated self-assembly and amino acid polymerization. You don't understand the chemistry of the process, hence, you don't understand self assembly.

I'm not doing your work for you either - YOU look it up.

a reply to: Phantom423

Do you understand this distinction ?

You never answered the question.
He is getting very specific here, whereas your answer might be correct for part of the process, but not this very specific process he is covering.
Making you nervous or something ?

originally posted by: Blue_Jay33
a reply to: Phantom423

Do you understand this distinction ?

You never answered the question.
He is getting very specific here, whereas your answer might be correct for part of the process, but not this very specific process he is covering.
Making you nervous or something ?

Please don't ask stupid questions. At least Coop is engaging in a conversation which is scientifically oriented, even if we disagree. Make a contribution or be quiet.

originally posted by: Phantom423

Absolutely not true. Look up in-chain conjugation, amino acid coordinated self-assembly and amino acid polymerization. You don't understand the chemistry of the process, hence, you don't understand self assembly.

I'm not doing your work for you either - YOU look it up.

Are there any examples where polypeptide chains self-assemble from scratch monomer peptides? Because I could find none. Such a finding could totally revolutionize biology so I am almost certain it has never been observed in a lab.

a reply to: Phantom423

And you still never answered it but deflected once again......

originally posted by: cooperton

originally posted by: Phantom423

Absolutely not true. Look up in-chain conjugation, amino acid coordinated self-assembly and amino acid polymerization. You don't understand the chemistry of the process, hence, you don't understand self assembly.

I'm not doing your work for you either - YOU look it up.

Are there any examples where polypeptide chains self-assemble from scratch monomer peptides? Because I could find none. Such a finding could totally revolutionize biology so I am almost certain it has never been observed in a lab.

www.abovetopsecret.com...

www.abovetopsecret.com...

It's all in the links I posted. I suggest you read them.

originally posted by: cooperton

originally posted by: Phantom423

Absolutely not true. Look up in-chain conjugation, amino acid coordinated self-assembly and amino acid polymerization. You don't understand the chemistry of the process, hence, you don't understand self assembly.

I'm not doing your work for you either - YOU look it up.

Are there any examples where polypeptide chains self-assemble from scratch monomer peptides? Because I could find none. Such a finding could totally revolutionize biology so I am almost certain it has never been observed in a lab.

13.3 Classification of Self-Assembly

Self-assembly is a native process. It can be classified into two types: static and dynamic [10]. Most research studies done in self-assembly have been focused on static type while the study of dynamic self-assembly is still in its infancy. Static self-assembly involves systems that are at global or local equilibrium and do not dissipate energy [10]. In static self-assembly, formation of the ordered structure may require energy, but once it is formed, it is stable. A few examples of static self-assembly phenomenon tailored by nature are lipid molecules forming oil droplets in water, four hemoglobin polypeptides forming a functional hemoglobin protein, and the combination of RNA and ribosomal proteins to form a functional ribosome. The other common examples of static self-assembled structures have been illustrated in Figure 13.1. Dynamic self-assembly occurs when the formation of an ordered state of equilibrium requires dissipation of energy. In other words, the interactions responsible for the formation of structures or patterns between components occur only if the system dissipates energy [10]. The examples of dynamic self-assembled structures have been illustrated in Figure 13.2.

www.sciencedirect.com...

originally posted by: Phantom423

www.abovetopsecret.com...

www.abovetopsecret.com...

It's all in the links I posted. I suggest you read them.

There is nothing in there about peptide monomers self-assembling into polypeptides. If I missed it, please quote it.