How close are you in believing ?

originally posted by: peter vlar
a reply to: TzarChasm


It's overflowing with empiricism.

Although you are being sarcastic, it is filled with empirical evidence. The observations of the prophets, martyrs, and seers throughout history have attested to their visions of the Great Spirit. They were so inspired by such a spark of Truth that they were willing to die for what they knew was beyond the limitations of Babylon.

Do you know anyone willing to die for evolution?

originally posted by: cooperton

originally posted by: peter vlar
a reply to: TzarChasm


It's overflowing with empiricism.

Although you are being sarcastic, it is filled with empirical evidence. The observations of the prophets, martyrs, and seers throughout history have attested to their visions of the Great Spirit. They were so inspired by such a spark of Truth that they were willing to die for what they knew was beyond the limitations of Babylon.

Do you know anyone willing to die for evolution?

People are willing to die for a lot of things.

originally posted by: cooperton

originally posted by: peter vlar
a reply to: TzarChasm


It's overflowing with empiricism.

Although you are being sarcastic, it is filled with empirical evidence. The observations of the prophets, martyrs, and seers throughout history have attested to their visions of the Great Spirit.

As none of the above are falsifiable in a scientific sense, no visions of seers or alleged observations by prophets and martyrs can be considered empirical. And if the threshold for empiricism is that low then the answer to your prior query regarding what empirical evidence I had to support my previous post is my own observations and studies should suffice without actually supporting my position with proper citations.

They were so inspired by such a spark of Truth that they were willing to die for what they knew was beyond the limitations of Babylon.

They were willing to die for what they believed to be true. That isn't the same as gnosis.

Do you know anyone willing to die for evolution?

Since evolution is nothing more than bio-chemical processes, similar in its own way to love, lust and desire and as an inherent aspect of biology(or perhaps because of it's nature it is tied to these more base instincts), the only motive that can actually be attributed to it is for any given organism to survive long enough to pass on its genes. With that said, people die willingly all the time in the name of love or lust. People die even more frequently because of base desires. Some Of these desires are the desire to get high and change the chemical state of their brain temporarily, the desire for material things, status... I could go on and on. But back to your specific query... Would people be willing to "die for evolution"?

As a parent, my sole job in the world is to ensure the success and survival of my children. They are my genetic legacy. I am more than willing to die to ensure their continued survival and would be willing to utilize my extensive military training to see them not just survive but thrive. I think the smaller percentage of people are those who would NOT do the same for their own children. It's our one job, our primary focus in this world. To reproduce and then ensure that progeny survive to perpetuate the cycle and continue the spread of our familial genes. Are you UNWILLING to go to the sale lengths to ensure the survival of your own genetic lineage?

originally posted by: PhotonEffect

originally posted by: Phantom423
a reply to: PhotonEffect

Still waiting for a response. Did you bother to read the papers?????

Whenever you're ready

I have a medical emergency with one of my pups - in surgery - bladder stones - I saw your response - will get to it probably tomorrow -

Maksim

a reply to: Phantom423

Sorry to hear that. Beautiful dog.
All the best

a reply to: PhotonEffect

Thanks - he's getting on very well.

Okay, back to the conversation.

I read through the thread to refresh my memory about your question. Basically, your question is: Where does self assembly fit into evolutionary theory. You questioned how the eye could have self assembled into a functional organism.

First, the reason I posted all those papers is to demonstrate that the process of self assembly of functional structures is a known phenomenon. Here's what I said: "About self assembly - three papers which describe macromolecular self assembly and its implications for evolution. " The implications for evolution are obvious - just extrapolate back to an earlier time when only basic organic molecules were present and utilized the same process. The idea that early photoreceptor cells, or "eyespots" as they're called in early organisms, self assembled is not far fetched. Are there other possibilities? Of course there are, but given the preponderance of self assembly in nature, it's not unreasonable to think that a photoreceptor cell could have self assembled. Remember we're talking a highly complex cell which includes the nucleus, the cellular matrix and the phospholipid bilayer - even though it's still the primitive photoreceptor.

This paper was just published this year. It describes the physics of self assembly of biological macromolecules. Actually, it makes much more sense to my mind to understand the thermodynamics and kinetics of self assembly because that's the underlying mechanism that governs the process.

The Physics of Protein Self-Assembly
Jennifer J. McManus 1, Patrick Charbonneau 2, Emanuela Zaccarelli 3, Neer Asherie 4*
1 Department of Chemistry, Maynooth University, Maynooth, Co. Kildare, Ireland.
2 Department of Chemistry, Duke University, North Carolina, USA
3 CNR ISC and Department of Physics, University of Rome, La Sapienza, Italy
4 Department of Physics and Department of Biology, Yeshiva University, New York, USA.

Highlights

• Proteins self-assemble into a large variety of structures with different sizes and
symmetries
• Several important aspects of protein self-assembly can be understood using coarsegrained
models that include the short-range and anisotropic (or patchy) protein-protein
interactions
• The ability to predict and design self-assembled structures is limited, though promising
approaches exist
• Numerous computational and experimental challenges remain

Abstract

Understanding protein self-assembly is important for many biological and industrial
processes. Proteins can self-assemble into crystals, filaments, gels, and other amorphous
aggregates. The final forms include virus capsids and condensed phases associated with diseases,
such as amyloid fibrils. Although seemingly different, these assemblies all originate from
fundamental protein interactions and are driven by similar thermodynamic and kinetic factors.
Here we review recent advances in understanding protein self-assembly through a soft condensed
matter perspective with an emphasis on three specific systems: globular proteins, viruses and
amyloid fibers. We conclude with a discussion of unanswered questions in the field.

1. Introduction

The self-assembly of proteins into small-scale complexes plays a crucial biological role [1].
Under certain conditions, proteins also self-assemble into different structures across a range of
length scales from nm to μm (Fig. 1). This process is almost as ubiquitous as complexation, and
is equally essential to biology.

Some proteins, such as those that make up viral capsids or the
outer shell of bacterial microcompartments, self-assemble by design [2, 3]. Others do so when
something goes wrong: a conformational change triggers the aggregation of amyloid β-protein
(Aβ) into fibrils [4] and a single-point mutation in haemoglobin (Hb) leads to its polymerization
[5]. This type of assembly can also result from simple changes to solution conditions (pH,
temperature, ionic strength, cosolutes, etc.) [6].

Understanding protein self-assembly is fundamental to many physiological and industrial
processes. For example, the fibrillization of Aβ is a feature of Alzheimer’s disease [7] and the
polymerization of the mutant Hb is the primary pathogenic event of sickle-cell anemia [5]; other
protein condensation diseases, for which the pathology is associated with the self-assembly of a
condensed protein phase, include cataract formation [8] and Parkinson’s disease [9]. In the
industrial production of proteins, self-assembly can be harnessed advantageously for protein
purification through crystallization or liquid-liquid phase separation [10], or can be problematic
if encountered during formulation and storage (often at high protein concentration), when the
assembly process is not controlled [11]. Finally, protein self-assembly is essential to structural
biology. Most structures are determined through x-ray crystallography, which requires the
production of high-quality protein crystals [12].

Here we review recent advances in understanding protein self-assembly. We adopt a soft
condensed matter perspective in which simplified models are used to capture the essential
elements of protein interactions to determine their assembly. While it is true that atomic-level
details are sometimes required for a complete explanation of specific phenomena, the near
ubiquitous nature of protein self-assembly suggests the existence of universal elements
governing it, which many experimental, computational and theoretical findings support. We
focus on three specific systems: globular proteins, viral capsids and amyloid fibrils. These
systems formed the core of a 2015 CECAM workshop we organized that brought together
researchers from diverse fields (including material science, crystallography, macromolecular
chemistry and biophysics) to discuss current challenges in understanding protein self-assembly.

This opinion piece builds upon the presentations and discussions at the workshop as well as our
own work in the field to stimulate further research—and perhaps breakthroughs—in the physics
of protein self-assembly.

arxiv.org...

Illustrations from the paper:

a reply to: PhotonEffect

You asked how self assembly fits in with evolutionary theory.

The theory of evolution is quite simple:

The theory of evolution by natural selection, first formulated in Darwin's book "On the Origin of Species" in 1859, is the process by which organisms change over time as a result of changes in heritable physical or behavioral traits. Changes that allow an organism to better adapt to its environment will help it survive and have more offspring.

Evolution by natural selection is one of the best substantiated theories in the history of science, supported by evidence from a wide variety of scientific disciplines, including paleontology, geology, genetics and developmental biology.
The theory has two main points, said Brian Richmond, curator of human origins at the American Museum of Natural History in New York City. "All life on Earth is connected and related to each other," and this diversity of life is a product of "modifications of populations by natural selection, where some traits were favored in and environment over others," he said.

More simply put, the theory can be described as "descent with modification," said Briana Pobiner, an anthropologist and educator at the Smithsonian Institution National Museum of Natural History in Washington, D.C., who specializes in the study of human origins.

The theory is sometimes described as "survival of the fittest," but that can be misleading, Pobiner said. Here, "fitness" refers not to an organism's strength or athletic ability, but rather the ability to survive and reproduce.

www.livescience.com...

_______________________________________

Self assembly, as well as the other dynamics of life on this planet, fall under the category of evolutionary mechanisms.
The theory itself is very straight forward as mentioned in the article above: descent with modification.

a reply to: Phantom423

Yes, self assembly is ubiquitous and underlies the design, development, function of all biological systems. Naturally there would be implications for evolution. But it's not accounted for in the synthesis. There have been many who have argued that it should be considered a mechanism along side natural selection, but it seems those calls have not been heard.

Now about your paper:
This was a curious paragraph

Purposeful vs. incidental self-assembly: As we mentioned in the introduction, some proteins self- assemble by design while others do so only when things go wrong or the solution conditions are perturbed. In other words, the structure of some proteins is such that self-assembly occurs for a specific purpose (such as to encapsulate other molecules), while for other proteins self-assembly is not central to their function—which they carry out in the unassembled state—and only occurs because of incidental physical considerations. It would be interest to compare the properties of proteins involved in purposeful and incidental processes to see whether any new insights may be gleaned regarding the specific and universal features of protein self-assembly

By design? Purposeful processes? Self assembly with a purpose. Is there no other way to describe this you think?

originally posted by: Phantom423
You asked how self assembly fits in with evolutionary theory.

I did, but natural selection has nothing to do with it. They are two separate things.

originally posted by: PhotonEffect
a reply to: Phantom423

Yes, self assembly is ubiquitous and underlies the design, development, function of all biological systems. Naturally there would be implications for evolution. But it's not accounted for in the synthesis. There have been many who have argued that it should be considered a mechanism along side natural selection, but it seems those calls have not been heard.

Now about your paper:

This was a curious paragraph

Purposeful vs. incidental self-assembly: As we mentioned in the introduction, some proteins self- assemble by design while others do so only when things go wrong or the solution conditions are perturbed. In other words, the structure of some proteins is such that self-assembly occurs for a specific purpose (such as to encapsulate other molecules), while for other proteins self-assembly is not central to their function—which they carry out in the unassembled state—and only occurs because of incidental physical considerations. It would be interest to compare the properties of proteins involved in purposeful and incidental processes to see whether any new insights may be gleaned regarding the specific and universal features of protein self-assembly

By design? Purposeful processes? Self assembly with a purpose. Is there no other way to describe this you think?

originally posted by: Phantom423
You asked how self assembly fits in with evolutionary theory.

I did, but natural selection has nothing to do with it. They are two separate things.

Not sure what your question is - "purpose" doesn't mean that someone did it. It simply means that the primary, secondary, tertiary and quaternary conformations of the protein - or any macromolecule for that matter - always finds its lowest energy state. The lowest energy state is the most stable state.


Why are they separate? As described previously, the most stable protein, or whatever, will be selected as the most viable for the organism. It doesn't matter whether the protein was self assembled, partially self assembled or directed by another process. The outcome is the same.

a reply to: Phantom423

originally posted by: Phantom423
Not sure what your question is - "purpose" doesn't mean that someone did it. It simply means that the primary, secondary, tertiary and quaternary conformations of the protein - or any macromolecule for that matter - always finds its lowest energy state. The lowest energy state is the most stable state.

Puzzling, since I thought my questions have been clearly stated. I'm also confounded by your putting "purpose" in quotes while suggesting I think that "someone" is behind the process? I'm hoping you can understand how frustrating that kind of a strawmannirg can be, since I've never once spoken about, nor ever made claims about, some omnipotent being. In fact, I've actually questioned others on this belief system, even right here in this thread. It's also important to note that the words 'purpose' and 'design' were both used by the researchers who authored the paper YOU cited/copied/pasted here to describe the phenomenon in question – a rather vague usage of the terms I might add, which is why I asked.

What you should've put in quotes was the word "someone", as I've done above. That would've been a more accurate and honest usage of the "quote unquote" function, don't ya think?

originally posted by: Phantom423
Why are they separate? As described previously, the most stable protein, or whatever, will be selected as the most viable for the organism. It doesn't matter whether the protein was self assembled, partially self assembled or directed by another process. The outcome is the same.

I'm once again baffled by your asking of "why are they separate?", since it's obvious to me that these are two very different processes. The most basic reason being one of them is widely accepted as the process that leads to biological evolution, while the other is a physical phenomenon that is not even considered in the theory. One deals with the physics of complex systems, the other is simply a matter of probabilities and population dynamics.

I've been talking about the process of self-assembly and your talking about the macromolecule that was selected after it self-assembled. SA does not happen because of natural selection, it happens regardless of it. It does not require it. If you want to say SA sets the stage for NS then I can be reasonable. However, evolution (via NS) can only occur AFTER the structure is already there. It does not create novel structures or body plans – that's the product of self assembly. If you believe evolution creates novelty thanks to NS then it seems you have been mislead, perhaps by the likes of Dawkins, Coyne or someone else of that ilk, or maybe because you are still clutching to a traditional (safe) but woefully antiquated view of evolution. Just my take though.

Here is an article discussing the very issue I've tried to broach here re: the status of self-assembly (they also cite self organization which is technically different than SA) and where it resides in the grand scheme of evolutionary theory. It actually supports your side of our debate with regards to the hierarchy of NS vs SA. I tend to disagree with the author's point of view on this matter, and take the other side which is also mentioned in this article. No matter, I trust it will do a better job than I have at explaining the issue.

bioscience.oxfordjournals.org...

If you'd rather I copy & paste the portions I found interesting than please let me know. I didn't for the sake of keeping this post from becoming longer than it has...

a reply to: PhotonEffect

Puzzling, since I thought my questions have been clearly stated. I'm also confounded by your putting "purpose" in quotes while suggesting I think that "someone" is behind the process? I'm hoping you can understand how frustrating that kind of a strawmannirg can be, since I've never once spoken about, nor ever made claims about, some omnipotent being. In fact, I've actually questioned others on this belief system, even right here in this thread. It's also important to note that the words 'purpose' and 'design' were both used by the researchers who authored the paper YOU cited/copied/pasted here to describe the phenomenon in question – a rather vague usage of the terms I might add, which is why I asked.

It's not puzzling at all. On this board, the minute the words "purpose" or "design" are used, the implication is always something related to ID. I haven't followed all your posts so I wasn't aware that you had challenged the notion of ID previously. That said, I don't have a clue why the authors decided to use those particular words. I don't think it's worth the time and effort to try to figure out what was going on in their heads at the time. We would have to ask them.

I'm once again baffled by your asking of "why are they separate?", since it's obvious to me that these are two very different processes. The most basic reason being one of them is widely accepted as the process that leads to biological evolution, while the other is a physical phenomenon that is not even considered in the theory. One deals with the physics of complex systems, the other is simply a matter of probabilities and population dynamics.

They're not "separate". They are subcategories of evolutionary biology. I may have misconstrued what you meant by "separate" - but in my mind, I'm thinking how it would fit in to the study of evolutionary biology as the main field of study.

That said, natural selection and self assembly most definitely have a relationship. As I mentioned above, systems generally seek the lowest energy state, or thermodynamic equilibrium regardless how they were formed. This article, which I have posted before, describes the thermodynamics of biological systems:

www.quantamagazine.org...

I will read your article later today.

originally posted by: cooperton

originally posted by: peter vlar
a reply to: TzarChasm


It's overflowing with empiricism.

Although you are being sarcastic, it is filled with empirical evidence. The observations of the prophets, martyrs, and seers throughout history have attested to their visions of the Great Spirit. They were so inspired by such a spark of Truth that they were willing to die for what they knew was beyond the limitations of Babylon.

Do you know anyone willing to die for evolution?

That's quite possibly the most ignorant and ridiculous thing I've read online for a while - good job!

originally posted by: stargatetravels

That's quite possibly the most ignorant and ridiculous thing I've read online for a while - good job!

People in the Vedas claimed to have perceived Krishna (your avatar). Do you not think this is empirical evidence? The sages and seers throughout time have given us their testimony of the light - even today many with near death experiences or out of body experiences have perceived the incredible light of the Most High. If you truly were feeling "Sahasrara" you would be perceiving this same thing, but it seems as though you are just embracing Hinduism as a consumer embraces a new clothing fashion.

a reply to: stargatetravels

Don't mind Coop - he still thinks that prophets, martyrs, seers and the tooth fairy should be included in general science.

Of course, much of that "truth" was heavily influenced by outside forces - like drugs and exposure to toxic elements.

"Delphic Oracle's Lips May Have Been Loosened by Gas Vapors"

Waning Power

The power of the Delphic oracle fluctuated and eventually lost favor as Christianity became the dominant religion of the land, said De Boer. Moreover, ancient legend suggests that the concentration of the vapors became weaker—possibly because the absence of a major earthquake failed to keep Earth's narcotic juices flowing.

Today, the water that helped transport the gases to the Delphic temple is tapped and siphoned above the temple to supply the modern town of Delphi.

The work by De Boer and his colleagues is an example of modern science helping archaeologists understand how ancient peoples lived. Another example among the ancient Greeks is the belief in Poseidon as the god of the sea and earthquakes. According to Harris-Cline, modern science associates the two with tectonic movement deep under the sea.

"Our scientific techniques are just beginning to detect the natural phenomena which the Greeks celebrated and appreciated 2,500 years ago with ritual activities at these special places," she said.

news.nationalgeographic.com...

Khat was also used extensively in the Middle East and adjacent countries. Who knows - the Bible and other works of so-called prophets and seers may be the result of hallucinogenic drugs!

a reply to: PhotonEffect

Regarding your article, I think it's really intended for scientists who actually do this sort of work and are familiar with the references. It's interesting but it touches on many different aspects of self organization as it relates to evolutionary biology. I don't do that sort of work in the lab so it's hard for me to say that everything in the article is valid.

That said, the authors do emphasize the importance of physics in understanding self organization. And this is what I mentioned in a previous post with regard to self assembly. The difference between self assembly and self organization can be considered external and internal - external like the viral coat which they mentioned and internal like protein folding and intracellular organization. However, in essence, I think the same physical dynamics are in play. The paper below describes the dynamics of protein folding. There are many other papers with 3-D and 4-D examples which describe the bonding angles and bonding energies. However, I don't think it's useful to begin discussing x-ray crystallography and van der Waals' forces here.

"Protein folding by restrained energy minimization and molecular dynamics"

Michael Levitt

Native-like folded conformations of bovine pancreatic trypsin inhibitor protein are calculated by searching for conformations with the lowest possible potential energy.

www.sciencedirect.com...

The point is that systems can form dynamically in nature. It's structure/function. The most stable structure will be selected to perform a particular function.

originally posted by: cooperton

originally posted by: stargatetravels

That's quite possibly the most ignorant and ridiculous thing I've read online for a while - good job!

People in the Vedas claimed to have perceived Krishna (your avatar). Do you not think this is empirical evidence? The sages and seers throughout time have given us their testimony of the light - even today many with near death experiences or out of body experiences have perceived the incredible light of the Most High. If you truly were feeling "Sahasrara" you would be perceiving this same thing, but it seems as though you are just embracing Hinduism as a consumer embraces a new clothing fashion.

Dimethyltryptamine dopamine and serotonin are all very powerful chemicals that can result in seemingly spiritual experiences. And they are all naturally produced within our bodies.

a reply to: cooperton


I'm not saying that their experiences were not profound or that there isn't some greater truth or cosmic force, I'm saying that you saying 'nobody has died for evolution' and comparing it to religions, some of which date back many millennia, is ignorant & ridiculous - it truly is.
The two are not comparable, one has only been around as a theory for a couple of centuries.
Also there are many people who have been put to death and lost their lives for not believing, praising or worshipping some deity or another - not quite dying for evolution but certainly dying for not believing the religion of choice.
There truly is a connection and a force and a realm of which we cannot see, I am not disputing that so the rest of your post is irrelevant.

a reply to: TzarChasm

Dimethyltryptamine dopamine and serotonin are all very powerful chemicals that can result in seemingly spiritual experiences. And they are all naturally produced within our bodies.

Just so, and the altered perception of reality these chemicals induce in the mind, provide the impression that the experience of reality is actually a construct of the mind. Or at the very most, just a tiny, one sided portion of it.

The application of the sciences can tell us a great deal more than we can perceive about reality through our senses alone, but what if we can perceive more than we can imagine through the correct application of the quantum computer that is the mind?

What if it turns out that we and everything else exist in a kind of quantum computer in a simulation that we call the universe? Why does the idea of a creator always have to come from a religious type 'my way or the highway' perspective? The way I see it is, we have to admit we don't know, not because we can't simply prove it, but because ultimately it is beyond are ken.

originally posted by: surfer_soul
Why does the idea of a creator always have to come from a religious type 'my way or the highway' perspective?

Jesus's teachings are like a how-to manual on rising above the material world into the spiritual awareness of the kingdom of Heaven. You could think of it as "my way or the highway", but it is the law of the land - either find love at its utmost height or pay the karmic consequences of your aberrant actions.

originally posted by: TzarChasm

Dimethyltryptamine dopamine and serotonin are all very powerful chemicals that can result in seemingly spiritual experiences. And they are all naturally produced within our bodies.

I think these chemicals are the natural neurological substrate for "tuning in" to the higher realms that are within us. Pursuing love, humility, selflessness and truth will reorganize your neural circuitry back to its archetypal form. It is difficult to articulate What happens once this state is discovered.

a reply to: Phantom423

originally posted by: Phantom423
On this board, the minute the words "purpose" or "design" are used, the implication is always something related to ID.

That's a problem. You think the implications would be any different if our discussion was taking place in the science forum?

originally posted by: Phantom423
That said, I don't have a clue why the authors decided to use those particular words. I don't think it's worth the time and effort to try to figure out what was going on in their heads at the time. We would have to ask them.

Didn't you read the paper you posted?

originally posted by: Phantom423
They're not "separate". They are subcategories of evolutionary biology. I may have misconstrued what you meant by "separate" - but in my mind, I'm thinking how it would fit in to the study of evolutionary biology as the main field of study.

They are two different processes though. And I'm not sure what could've been misconstrued when I clearly referred to the MES. I think the issue is many folks consider the MES to be synonymous with the current status of evolutionary thinking. Why is that? It couldn't be farther from reality.

originally posted by: Phantom423
That said, natural selection and self assembly most definitely have a relationship. As I mentioned above, systems generally seek the lowest energy state, or thermodynamic equilibrium regardless how they were formed. This article, which I have posted before, describes the thermodynamics of biological systems:
www.quantamagazine.org...

Perhaps there could be a relationship in certain instances of biological systems and their development. But "most definitely" is a bit hyperbolic, and perhaps overstating it, especially when it comes to science. Nothing in science is "most definite."

Plus, there are scientists who think NS takes a back seat in some cases.

From your article:

Having an overarching principle of life and evolution would give researchers a broader perspective on the emergence of structure and function in living things, many of the researchers said. “Natural selection doesn’t explain certain characteristics,” said Ard Louis, a biophysicist at Oxford University, in an email. These characteristics include a heritable change to gene expression called methylation, increases in complexity in the absence of natural selection, and certain molecular changes Louis has recently studied.

If England’s approach stands up to more testing, it could further liberate biologists from seeking a Darwinian explanation for every adaptation and allow them to think more generally in terms of dissipation-driven organization. They might find, for example, that “the reason that an organism shows characteristic X rather than Y may not be because X is more fit than Y, but because physical constraints make it easier for X to evolve than for Y to evolve,” Louis said.

Emphasis all mine.