p-value testing will never be the same again

[lee_merrill]

This has been done - the two examples i know of are use of a scaffolding protein to build a large complex, followed by its loss, and the duplication and diversification of a single gene that forms a polymeric complex.

Can you provide details on these? Thanks...

Blessings,
Lee

[lee_merrill]

… you need to tell me why scaffolding does not require generating a structure more complex than (say) a flagellum!

I don't need to do any such thing.

Well, you certainly do, if you're going to propose scaffolding as the method of evolution of the flagellum.

Blessings,
Lee

[lee_merrill]

The purpose of the evolution of the scaffolding of the flagellum. There was no need to evolve a more complex structure with a different purpose. The same is true for the eye. It evolved from the very simple to the complex eye through different pathways of evolution, but once the complex eye evolved to serve its purpose it evolved no further.

But evolution of the eye as you describe it does not involve scaffolding.

Misrepresentation of the reference. Please explain. The article you cite does not support your assertions. In fact it refutes them completely.

I'm speaking of the generation of the first protein, which presumably had to come about randomly.

Blessings,
Lee

[shunyadragon]

But evolution of the eye as you describe it does not involve scaffolding.


I'm speaking of the generation of the first protein, which presumably had to come about randomly.

No, it would not come about randomly. It would come about naturally based on the laws of nature. The contemporary research has demonstrated polymerization of amino acids to form proteins, and it is caused by the laws of nature. Randomness would not be the cause, because it is only the observed variation in the outcome of cause and effect events.

The following is a good summary of the hypothesis concerning the polymerization of amino acids to proteins in abiogensis including the chemistry and geologic environments.It is very extensive and includes many references on the research.

Source: https://www.sciencedirect.com/science/article/pii/S1674987117301305

Life is generally characterized by the following three functions: (1) compartmentalization: the ability to keep its components together and distinguish itself from the environment, (2) replication: the ability to process and transmit heritable information to progeny, and (3) metabolism: the ability to capture energy and material resources, staying away from thermodynamic equilibrium (Fig. 2; Nakashima et al., 2001, Ruiz-Mirazo et al., 2004, Ruiz-Mirazo et al., 2014). All these functions are operated by biopolymers such as DNA, RNA, protein, and phospholipids (Fig. 2). Phospholipids are made of two fatty acids esterified to a glycerol phosphate molecule. DNA and RNA are made of nucleosides (composed of (deoxy)ribose and nucleobases) bound by phosphodiester linkages, while proteins are made of amino acids linked together by peptide bonds (Fig. 2). It is typically assumed that these vital components were synthesized abiotically, accumulated somewhere, condensed into polymers, interacted mutually, and eventually evolved into a self-sustaining system through natural phenomena on the primitive Earth. A considerable number of laboratory simulations have been made to explore the most plausible conditions for these processes, especially for the synthesis, accumulation, and polymerization steps of organic monomers.

The aim of this review is to provide a framework for thinking about geochemical situations necessary for life to originate from mixtures of simple inorganic compounds (e.g., CO2, N2, H2O, H3PO4) on the Hadean Earth. To date, a number of varied environments have been proposed as being favorable for prebiotic chemistry (Deamer et al., 2006, Ricardo and Szostak, 2009, Benner et al., 2012, Mulkidjanian et al., 2012a, Mulkidjanian et al., 2012b). However, these discussions have focused on a limited stage of chemical evolution, or emergence of a specific chemical function of proto-biological systems. To cover all stages, we first summarize reported experimental and theoretical findings for prebiotic chemistry, including availability of biologically essential elements (N and P), abiotic formation of life's building blocks (amino acids, ribose, nucleobases, fatty acids, and nucleotides), their polymerizations to bio-macromolecules (peptides and oligonucleotides), and emergence of biological functions of replication and compartmentalization. These summaries are used to make a list of reaction conditions necessary to complete the chemical evolution from the beginning to the end. A relevant geochemical setting for each condition is then discussed while considering the Hadean surface environments proposed in the literature (e.g., Maruyama et al., 2013). It should be noted that the origin and early evolution of metabolism have been discussed over the last twenty years (Wachtershauser, 1988, Russell et al., 1994, Braakman and Smith, 2013). However, laboratory simulations on this topic have still focused on syntheses of simple metabolic intermediates (e.g., pyruvate) and amino acids (e.g., Cody et al., 2000, Guzman and Martin, 2009, Huber et al., 2012). Many uncertainties remain about how proto-metabolic systems emerged and evolved into modern counterparts. Inclusion of this process as a part of the whole scenario must be done later, at a time when sufficient experimental support is available in the literature. It is also noteworthy that it is possible life started with different inventories of organic/inorganic compounds that are not used in modern biochemistry (e.g., Cairns-Smith, 1982). Owing to a lack of experimental support, our survey does not refer to the works done on this topic. Evaluations of the availability, reactivity, and function of the “standard” building blocks of life as we know it should provide an important insight to elucidate the components as well as the geological settings for the origin of life.

Prior to proceeding to the prebiotic chemistry that led to the origin of life, we briefly survey three standard hypotheses; (1) prebiotic soup theory, (2) hydrothermal origin of life, and (3) extraterrestrial origin of life. Because many laboratory simulations have been done following these three, this review accordingly focuses on chemical reactions under conditions relevant to these hypotheses.

© Copyright Original Source

More references to follow . . .

[shunyadragon]

Research in real science focuses on the natural mechanisms of polymerization, and not the bogus Intelligent Design approach of juggling all or nothing 'randomness' in the misuse of probability.

Source: https://link.springer.com/article/10.1007/BF01731368

The role of metal ions in chemical evolution: Polymerization of alanine and glycine in a cation-exchanged clay environment

The effect of the exchangeable cation on the condensation of glycine and alanine was investigated using a series of homoionic bentonites. A cycling procedure of drying, warming and wetting was employed. Peptide bond formation was observed, and the effectiveness of metal ions to catalyze the condensation was Cu2+ > Ni2+ ≈ Zn2+ > Na+. Glycine showed 6% of the monomer incorporated into oligomers with the largest detected being the pentamer. Alanine showed less peptide bond formation (a maximum of 2%) and only the dimer was observed.

Introduction
Various models have been proposed for the composition of the primitive atmosphere on Earth, and, when such atmospheres are subjected to energy inputs (e~., electrical discharge, heat, UV irradiation), organic molecules of varying degrees of complexity are formed (Miller and Orgel, 1974). Support for the theory of chemical evolution has also been found by the identification of complex organic compounds in extraterrestrial materials such as meteorites (Kvenvolden et al., 1971; Lawless et al., 1971; Lawless et al., 1974). But, in addition to the biological synthesis of organic molecules in primitive environments, a number of other steps in the origin of life process must have occurred. Among these are: 1) a selection for the biological subset of monomers from the random population of organic compounds available, 2) a mechanism for the concentration of this subset so that subsequent interactions and chemical reactions could occur, and 3) a mechanism for the formation of polymers such as polypeptides and polynucleotides which is a necessary preamble to the formation of proteins and nucleic acids. To elucidate the latter, several investigators have attempted to carry out prebiotic synthesis of polypeptides. A large number of polymeric substances has been made using metaphosphate esters as the condensing agent (Schramm et ai., 1962; Schramm, 1965). These polymers were obtained by heating the metaphosphate esters of the monomer to above 100°C. Others have made polyamino acids from free amino acids by heating them on pieces of lava at 170°C. B

© Copyright Original Source

[shunyadragon]

Well, you certainly do, if you're going to propose scaffolding as the method of evolution of the flagellum.

The scientific references and research demonstrate the natural evolution of the flagellum in significant detail.

[shunyadragon]

But evolution of the eye as you describe it does not involve scaffolding.


I'm speaking of the generation of the first protein, which presumably had to come about randomly.

Blessings,
Lee

Did not say it does, but it involves evolution in stages from the simple to the complex, with specific purpose in the steps, and confirmed by the genetics of eye evolution as is the case with the flagellum.

[Roy]

Well, you certainly do, if you're going to propose scaffolding as the method of evolution of the flagellum.

I'm not going to propose that.

How about you stop asking others to support claims they haven't made, and instead support the claims you have made?

You can start by supporting (or retracting) your claim that the paper Shunyadragon referenced is about generating the first proteins.

[TheLurch]

Can you provide details on these? Thanks...

Blessings,
Lee

Sure.

Scaffolding: Let's say that a bunch of proteins involved in the same biological process work most efficiently when in proximity. So, if a protein develops affinity for two of them, it would be evolutionarily favored. Adding affinities for more proteins would increase the favorability. While the proteins are in proximity, they can also evolve affinities for each other. Once that happens, the original scaffolding protein can be lost with no effect. But, lose any of the remaining proteins, and the complex falls apart.

Duplication/diversification: This is what seems to have happened with a protein degrading complex. In archaea, it's a complex of 12 (i think) identical proteins, all produced from the same gene. But duplicate the gene, and it can start to evolve more specialized functions. Duplicate these genes some more, and you grow the number of proteins in the complex, all while maintaining interactions among them. As a result of a similar process, the eukaryotic version of the complex is (again, going from memory, could be wrong) is still 12 proteins, but they now come from 6 different genes. Loss of any of these genes causes the complex to fall apart.

[shunyadragon]

Well, their conclusion is in some dispute, even in evolutionary circles.

You are selectively quote mining and misinterpretation of the article based on your agenda. The article did not dispute the steps nor the process of the natural evolution of the flagellum, but as is normal in science critiques the research and conclusions cited.

Source: https://www.cell.com/current-biology/fulltext/S0960-9822(07)01338-3

So we evolutionists need not take on the impossible challenge of pinning down every detail of flagellar evolution. We need only show that such a development, involving processes and constituents not unlike those we already know and can agree upon, is feasible.

© Copyright Original Source

Now I wonder why Liu and Ochman above didn't make this point. And a homologous structure does not demonstrate how one might change into the other, through selectable steps.

It is common that researchers over state their conclusions, and it is normal in science for peer review to bring things back to reality. Over time this process confirms the reliability of science as science.

You re still faced with the problem that the scientists that support Intelligent Design HAVE NOT proposed a falsifiable hypothesis to support Intelligent Design. As with your unfortunate selectively citing the partial paper referring to "highly optimal" sets of amino acids based on a religious agenda. The paper indeed offered a viable hypothesis for the natural process for the evolution of an 'optimal' set of 20 amino acids.

Still waiting . . .

[TheLurch]

Just noticed that the paper he's ostensibly discussing already shows how an irreducible protein complex can evolve that's identical to my explanation 2:
"“the flagellar rod-hook-filament complex has clearly evolved by multiple rounds of gene duplication and subsequent diversification, starting from just two proteins (a proto-flagellin and a proto-rod/hook protein)”."
(that's from this: https://www.cell.com/current-biology...22(07)01338-3)

So, is it a failure of reading comprehension, or simply extremely selective processing of information?

[lee_merrill]

Sure.

Scaffolding: Let's say that a bunch of proteins involved in the same biological process work most efficiently when in proximity. So, if a protein develops affinity for two of them, it would be evolutionarily favored. Adding affinities for more proteins would increase the favorability. While the proteins are in proximity, they can also evolve affinities for each other. Once that happens, the original scaffolding protein can be lost with no effect. But, lose any of the remaining proteins, and the complex falls apart.

This doesn't sound IC to me though, losing a protein means the process works less efficiently, right?

Blessings,
Lee

[lee_merrill]

Just noticed that the paper he's ostensibly discussing already shows how an irreducible protein complex can evolve that's identical to my explanation 2:
"“the flagellar rod-hook-filament complex has clearly evolved by multiple rounds of gene duplication and subsequent diversification, starting from just two proteins (a proto-flagellin and a proto-rod/hook protein)”."
(that's from this: https://www.cell.com/current-biology...22(07)01338-3)

Yes, but even granted their scenario, they have not explained the generation of these two proto-proteins.

Blessings,
Lee

[shunyadragon]

Yes, but even granted their scenario, they have not explained the generation of these two proto-proteins.

Blessings,
Lee

Classic 'arguing from ignorance.' The Creation fundamentalist modus operandi. It is well past time for them to come up with a falsifiable hypothesis instead of playing 'shell games.'

[The Barbarian]

No, if the focus is on an event before it happens, then the probability can vary from 100%. For example, if you pick one snowflake pattern, and then look for that to occur, then the probability is 10²⁵⁰⁰ (according to their calculations).

The same argument could be made for poker hands. I don't think God is designing poker hands.