Faith

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Apr 13, 2017
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Don't dodge. There is a HUGE difference between metaphysical and methodological naturalism and from what I read, that difference seems hugely relevant to the thread topic.

I, for example, subscribe to methodological naturalism - eventhough I don't subscribe to it dogmatically.

If tomorrow science discovers the supernatural and develops the tools necessary to gauge it, great.

Until that time, methodological naturalism seems perfectly reasonable for scientific investigation.
"If minds are wholly dependent on brains, and brains on biochemistry, and biochemistry (in the long run) on the meaningless flux of the atoms, I cannot understand how the thought of those minds should have any more significance than the sound of the wind in the trees."

— C. S. Lewis, The Weight of Glory and Other Addresses, page 139


Is science or empirical observation the only way for us to know reality?
 






Lisa

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First of all, that's a blatant shift of the burden of proof. YOU are claiming that these stories are accurate. Upto you to support them.

Secondly, I don't think I ever claimed that these are fairy tales. I just don't believe these stories to be accurate. And the reason for that is failure of people like you to meet the burden of proof. What I will say though, is that because you fail to meet your burden of proof, these stories are indistinguishable from fairy tales.

Asking to prove that a character in a story is a fictional character, moreover, is a dishonest request in and off itself, because it's a logical impossibility to do so.

You can't demonstrate the non-existance of something like that. You can only demonstrate the opposite.
At best, you can point out that there is no contemporary independent corroborating evidence to support the existance of said character. But that doesn't mean the character didn't exist. It just means that there is currently no valid reason to think otherwise.


So, all in all, your request here is a prime example of fallacious reasoning from top to bottom.
Meet your own burden proof.
The scientists you believe in can’t prove what they are saying is true..they just try to build ‘science’ around their theories...which I don’t think works.

I do have evidence..that is the world around us. Even our bodies are amazing. One I guess could think that this world just oozed into existence bit how can you really think that when the world fits us perfectly? Can the world just miraculously form from nothing to fit us perfectly or would that take a creator? What are the odds..and considering the other planets around us..isn’t it a miracle in itself?

You are proving that Christians aren’t the only ones with faith. To not believe in God takes a lot more faith..it’s less provable...I at least have the world around us, what do you have again? A theory that doesn’t actually work?
 






LittleLady

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"there are lots of other religions which I don't believe in, therefore my religion is true"


You don't believe in millions of other gods, we atheists just don't believe in one more than you.
First off, I never said that. You comprehended that the wrong way. I'm telling you that there's multiple religions so we can be confused and be led away from God. By the way, since you keep on telling the others about how you basically disagree with everything they have to say, you might as well come to the conclusion that you're just not going to find God and go about your day. I feel sorry for you, but not everyone is chosen. Personally, I still hope God chooses you at some point, but if not, it is what it is.

I guess there's no point in me saying anything further since you're just going to disagree.
 






TagliatelliMonster

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Messages
145
The scientists you believe in can’t prove what they are saying is true..they just try to build ‘science’ around their theories...which I don’t think works.

I do have evidence..that is the world around us. Even our bodies are amazing. One I guess could think that this world just oozed into existence bit how can you really think that when the world fits us perfectly? Can the world just miraculously form from nothing to fit us perfectly or would that take a creator? What are the odds..and considering the other planets around us..isn’t it a miracle in itself?

You are proving that Christians aren’t the only ones with faith. To not believe in God takes a lot more faith..it’s less provable...I at least have the world around us, what do you have again? A theory that doesn’t actually work?
Science also deals with the history of the universe. The theory of biological evolution and the Big Bang theory are both about processes that unfolded over billions of years, and how our universe constructed itself without a conscious builder. This was the second wave of science. You're referring to the first wave - how the universe conducts its business day to day like a giant clockwork, also without the aid of gods. Electrons move through a wire in a circuit without needing angels to push them. The sun rises and sets without needing gods to drag it through the sky.

Real science is anything generated by the scientific method, the validity of which has been demonstrated repeatedly. The method generates ideas that anticipate nature, allowing us to do great things that have improved the human condition dramatically. That's how one knows that the underlying assumptions forming the foundations of science are valid.

It's also the way that we know that ideas like creationism are incorrect. They can't be used for anything - just like astrology, another faith-based system of beliefs.
 






fotw

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Lisa

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Messages
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Science also deals with the history of the universe. The theory of biological evolution and the Big Bang theory are both about processes that unfolded over billions of years, and how our universe constructed itself without a conscious builder. This was the second wave of science. You're referring to the first wave - how the universe conducts its business day to day like a giant clockwork, also without the aid of gods. Electrons move through a wire in a circuit without needing angels to push them. The sun rises and sets without needing gods to drag it through the sky.

Real science is anything generated by the scientific method, the validity of which has been demonstrated repeatedly. The method generates ideas that anticipate nature, allowing us to do great things that have improved the human condition dramatically. That's how one knows that the underlying assumptions forming the foundations of science are valid.

It's also the way that we know that ideas like creationism are incorrect. They can't be used for anything - just like astrology, another faith-based system of beliefs.
Scientists can’t recreate what happened to make our world so they can’t be right can they? Or even on the right track. All they have are guesses and nothing all that substantial. With the Bible..we know exactly what happened.
 






Red Sky at Morning

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Science also deals with the history of the universe. The theory of biological evolution and the Big Bang theory are both about processes that unfolded over billions of years, and how our universe constructed itself without a conscious builder. This was the second wave of science. You're referring to the first wave - how the universe conducts its business day to day like a giant clockwork, also without the aid of gods. Electrons move through a wire in a circuit without needing angels to push them. The sun rises and sets without needing gods to drag it through the sky.

Real science is anything generated by the scientific method, the validity of which has been demonstrated repeatedly. The method generates ideas that anticipate nature, allowing us to do great things that have improved the human condition dramatically. That's how one knows that the underlying assumptions forming the foundations of science are valid.

It's also the way that we know that ideas like creationism are incorrect. They can't be used for anything - just like astrology, another faith-based system of beliefs.
I congratulate you on articulations the popular positioning statements for creation and evolution. And yet... an increasing number of scientists have come out as being “sceptical of Darwinian theory”.


Perhaps with a nod to the Reformation, Dr James Tour wrote an open letter of apostasy from the faith of evolution.



An Open Letter to My Colleagues
James Tour

CHEMISTRY / CRITICAL NOTES / VOL. 3, NO. 2

James Tour is a synthetic organic chemist at Rice University.

LIFE SHOULD NOT EXIST. This much we know from chemistry. In contrast to the ubiquity of life on earth, the lifelessness of other planets makes far better chemical sense. Synthetic chemists know what it takes to build just one molecular compound. The compound must be designed, the stereochemistry controlled. Yield optimization, purification, and characterization are needed. An elaborate supply is required to control synthesis from start to finish. None of this is easy. Few researchers from other disciplines understand how molecules are synthesized.

Synthetic constraints must be taken into account when considering the prebiotic preparation of the four classes of compounds needed for life: the amino acids, the nucleotides, the saccharides, and the lipids.1 The next level beyond synthesis involves the components needed for the construction of nanosystems, which are then assembled into a microsystem. Composed of many nanosystems, the cell is nature’s fundamental microsystem. If the first cells were relatively simple, they still required at least 256 protein-coding genes. This requirement is as close to an absolute as we find in synthetic chemistry. A bacterium which encodes 1,354 proteins contains one of the smallest genomes currently known.2

Consider the following Gedankenexperiment. Let us assume that all the molecules we think may be needed to construct a cell are available in the requisite chemical and stereochemical purities. Let us assume that these molecules can be separated and delivered to a well-equipped laboratory. Let us also assume that the millions of articles comprising the chemical and biochemical literature are readily accessible.

How might we build a cell?

It is not enough to have the chemicals on hand. The relationship between the nucleotides and everything else must be specified and, for this, coding information is essential. DNA and RNA are the primary informational carriers of the cell. No matter the medium life might have adopted at the very beginning, its information had to come from somewhere. A string of nucleotides does not inherently encode anything. Let us assume that DNA and RNA are available in whatever sequence we desire.

A cell, as defined in synthetic biological terms, is a system that can maintain ion gradients, capture and process energy, store information, and mutate.3 Can we build a cell from the raw materials?4 We are synthetic chemists, after all. If we cannot do it, nobody can. Lipids of an appropriate length can spontaneously form lipid bilayers.

Molecular biology textbooks say as much. A lipid bilayer bubble can contain water, and was a likely precursor to the modern cell membrane.5Lipid assembly into a lipid bilayer membrane can easily be provoked by agitation, or sonication in a lab.

Et voilà. The required lipid bilayer then forms. Right?

Not so fast. A few concerns should give us pause:6

  • Researchers have identified thousands of different lipid structures in modern cell membranes. These include glycerolipids, sphingolipids, sterols, prenols, saccharolipids, and polyketides.7 For this reason, selecting the bilayer composition for our synthetic membrane target is far from straightforward. When making synthetic vesicles—synthetic lipid bilayer membranes—mixtures of lipids can, it should be noted, destabilize the system.
  • Lipid bilayers surround subcellular organelles, such as nuclei and mitochondria, which are themselves nanosystems and microsystems. Each of these has their own lipid composition.
  • Lipids have a non-symmetric distribution. The outer and inner faces of the lipid bilayer are chemically inequivalent and cannot be interchanged.
The lipids are just the beginning. Protein–lipid complexes are the required passive transport sites and active pumps for the passage of ions and molecules through bilayer membranes, often with high specificity. Some allow passage for substrates into the compartment, and others their exit. The complexity increases further because all lipid bilayers have vast numbers of polysaccharide (sugar) appendages, known as glycans, and the sugars are no joke. These are important for nanosystem and microsystem regulation. The inherent complexity of these saccharides is daunting. Six repeat units of the saccharide D-pyranose can form more than one trillion different hexasaccharides through branching (constitutional) and glycosidic (stereochemical) diversity.8 Imagine the breadth of the library!

Polysaccharides are the most abundant organic molecules on the planet. Their importance is reflected in the fact that they are produced by and are essential to all natural systems. Every cell membrane is coated with a complex array of polysaccharides, and all cell-to-cell interactions take place through saccharide participation on the lipid bilayer membrane surface. Eliminating any class of saccharides from an organism results in its death, and every cellular dysfunction involves saccharides.

In a report entitled “Transforming Glycoscience,” the US National Research Council recently noted that,

very little is known about glycan diversification during evolution. Over three billion years of evolution has failed to generate any kind of living cell that is not covered with a dense and complex array of glycans.9
What is more, Vlatka Zoldoš, Tomislav Horvat, and Gordan Lauc observed: “A peculiarity of glycan moieties of glycoproteins is that they are not synthesized using a direct genetic template. Instead, they result from the activity of several hundreds of enzymes organized in complex pathways.”10

Saccharides are information-rich molecules. Glycosyl transferases encode information into glycans and saccharide binding proteins decode the information stored in the glycan structures. This process is repeated according to polysaccharide branching and coupling patterns.11 Saccharides encode and transfer information long after their initial enzymatic construction.12 Polysaccharides carry more potential information than any other macromolecule, including DNA and RNA. For this reason, lipid-associated polysaccharides are proving enigmatic.13

Cellular and organelle bilayers, which were once thought of as simple vesicles, are anything but. They are highly functional gatekeepers. By virtue of their glycans, lipid bilayers become enormous banks of stored, readable, and re-writable information. The sonication of a few random lipids, polysaccharides, and proteins in a lab will not yield cellular lipid bilayer membranes.

Mes frères, mes semblables, with these complexities in mind, how can we build the microsystem of a simple cell? Would we be able to build even the lipid bilayers? These diminutive cellular microsystems—which are, in turn, composed of thousands of nanosystems—are beyond our comprehension. Yet we are led to believe that 3.8 billion years ago the requisite compounds could be found in some cave, or undersea vent, and somehow or other they assembled themselves into the first cell.

Could time really have worked such magic?

Many of the molecular structures needed for life are not thermodynamically favored by their syntheses. Formed by the formose reaction, the saccharides undergo further condensation under the very reaction conditions in which they form. The result is polymeric material, not to mention its stereo-randomness at every stereogenic center, therefore doubly useless.14 Time is the enemy. The reaction must be stopped soon after the desired product is formed. If we run out of synthetic intermediates in the laboratory, we have to go back to the beginning. Nature does not keep a laboratory notebook. How does she bring up more material from the rear?

If one understands the second law of thermodynamics, according to some physicists,15 “You [can] start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant.”16 The interactions of light with small molecules is well understood. The experiment has been performed. The outcome is known. Regardless of the wavelength of the light, no plant ever forms.

We synthetic chemists should state the obvious. The appearance of life on earth is a mystery. We are nowhere near solving this problem. The proposals offered thus far to explain life’s origin make no scientific sense.

Beyond our planet, all the others that have been probed are lifeless, a result in accord with our chemical expectations. The laws of physics and chemistry’s Periodic Table are universal, suggesting that life based upon amino acids, nucleotides, saccharides and lipids is an anomaly. Life should not exist anywhere in our universe. Life should not even exist on the surface of the earth.17



  1. See James Tour, “Animadversions of a Synthetic Chemist,” Inference: International Review of Science 2, no. 2 (2016); James Tour, “Two Experiments in Abiogenesis,” Inference: International Review of Science 2, no. 3 (2016). ↩
  2. See Wikipedia, “Minimal Genome.” ↩
  3. David Dearner, “A Giant Step Towards Artificial Life?” Trends in Biotechnology 23, no. 7 (2008): 336–38, doi:10.1016/j.tibtech.2005.05.008. ↩
  4. A small towards this goal was achieved when a synthetic genome was inserted into a host cell from which the original genome had been removed. The bilayer membrane of the host cell and all of its cytoplasmic constituents had already been created by natural biological processes. See Daniel Gibson et al., “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome,” Science 329, no. 5,987 (2010): 52–56, doi:10.1126/science.1190719. ↩
  5. Bruce Alberts et al., Molecular Biology of the Cell, 4th ed. (New York: Garland Science, 2002). ↩
  6. See F. Xabier Contreras et al., “Molecular Recognition of a Single Sphingolipid Species by a Protein’s Transmembrane Domain,” Nature 481 (2012): 525–29, doi:10.1038/nature10742; Yoshiyuki Norimatsu et al., “Protein–Phospholipid Interplay Revealed with Crystals of a Calcium Pump,” Nature 545 (2017): 193–98, doi:10.1038/nature22357. ↩
  7. See Lipidomics Gateway, “LIPID MAPS Structure Database.” ↩
  8. Roger Laine, “Invited Commentary: A Calculation of All Possible Oligosaccharide Isomers Both Branched and Linear Yields 1.05 × 1012 Structures for a Reducing Hexasaccharide: The Isomer Barrier to Development of Single-Method Saccharide Sequencing or Synthesis Systems,” Glycobiology 4, no. 6 (1994): 759–67, doi:10.1093/glycob/4.6.759. ↩
  9. National Research Council, Transforming Glycoscience: A Roadmap for the Future (Washington, DC: The National Academies Press, 2012), 72, doi:10.17226/13446. ↩
  10. Vlatka Zoldoš, Tomislav Horvat and Gordan Lauc, “Glycomics Meets Genomics, Epigenomics and Other High Throughput Omics for System Biology Studies,” Current Opinion in Chemical Biology 17, no. 1 (2012): 33–40, doi:10.1016/j.cbpa.2012.12.007. ↩
  11. Adapted from Maureen Taylor and Kurt Drickamer, Introduction to Glycobiology (Oxford: Oxford University Press, 2006). ↩
  12. Gordan Lauc, Aleksandar Vojta and Vlatka Zoldoš, “Epigenetic Regulation of Glycosylation Is the Quantum Mechanics of Biology,” Biochimica et Biophysica Acta – General Subjects 1,840, no. 1 (2014): 65–70, doi:10.1016/j.bbagen.2013.08.017. ↩
  13. Claus-Wilhelm von der Lieth, Thomas Luetteke, and Martin Frank, eds., Bioinformatics for Glycobiology and Glycomics: An Introduction (Chichester: Wiley-Blackwell, 2009). ↩
  14. James Tour, “Animadversions of a Synthetic Chemist,” Inference: International Review of Science 2, no. 2 (2016). ↩
  15. See Jeremy England, “Statistical Physics of Self-Replication,” Journal of Chemical Physics 139 (2013), doi:10.1063/1.4818538; Paul Rosenberg, “God is on the Ropes: The Brilliant New Science That Has Creationists and the Christian Right Terrified,” Salon, January 3, 2015. ↩
  16. Natalie Wolchover, “A New Physics Theory of Life,” Quanta, January 22, 2014. ↩
  17. The author wishes to thank Anthony Futerman of the Weizmann Institute and Russell Carlson of the University of Georgia for information on lipids and saccharides, respectively. ↩
Published on August 2, 2017 in Volume 3, Issue 2.
 






TagliatelliMonster

Established
Joined
Dec 29, 2019
Messages
145
I congratulate you on articulations the popular positioning statements for creation and evolution. And yet... an increasing number of scientists have come out as being “sceptical of Darwinian theory”.


Perhaps with a nod to the Reformation, Dr James Tour wrote an open letter of apostasy from the faith of evolution.



An Open Letter to My Colleagues
James Tour

CHEMISTRY / CRITICAL NOTES / VOL. 3, NO. 2

James Tour is a synthetic organic chemist at Rice University.

LIFE SHOULD NOT EXIST. This much we know from chemistry. In contrast to the ubiquity of life on earth, the lifelessness of other planets makes far better chemical sense. Synthetic chemists know what it takes to build just one molecular compound. The compound must be designed, the stereochemistry controlled. Yield optimization, purification, and characterization are needed. An elaborate supply is required to control synthesis from start to finish. None of this is easy. Few researchers from other disciplines understand how molecules are synthesized.

Synthetic constraints must be taken into account when considering the prebiotic preparation of the four classes of compounds needed for life: the amino acids, the nucleotides, the saccharides, and the lipids.1 The next level beyond synthesis involves the components needed for the construction of nanosystems, which are then assembled into a microsystem. Composed of many nanosystems, the cell is nature’s fundamental microsystem. If the first cells were relatively simple, they still required at least 256 protein-coding genes. This requirement is as close to an absolute as we find in synthetic chemistry. A bacterium which encodes 1,354 proteins contains one of the smallest genomes currently known.2

Consider the following Gedankenexperiment. Let us assume that all the molecules we think may be needed to construct a cell are available in the requisite chemical and stereochemical purities. Let us assume that these molecules can be separated and delivered to a well-equipped laboratory. Let us also assume that the millions of articles comprising the chemical and biochemical literature are readily accessible.

How might we build a cell?

It is not enough to have the chemicals on hand. The relationship between the nucleotides and everything else must be specified and, for this, coding information is essential. DNA and RNA are the primary informational carriers of the cell. No matter the medium life might have adopted at the very beginning, its information had to come from somewhere. A string of nucleotides does not inherently encode anything. Let us assume that DNA and RNA are available in whatever sequence we desire.

A cell, as defined in synthetic biological terms, is a system that can maintain ion gradients, capture and process energy, store information, and mutate.3 Can we build a cell from the raw materials?4 We are synthetic chemists, after all. If we cannot do it, nobody can. Lipids of an appropriate length can spontaneously form lipid bilayers.

Molecular biology textbooks say as much. A lipid bilayer bubble can contain water, and was a likely precursor to the modern cell membrane.5Lipid assembly into a lipid bilayer membrane can easily be provoked by agitation, or sonication in a lab.

Et voilà. The required lipid bilayer then forms. Right?

Not so fast. A few concerns should give us pause:6

  • Researchers have identified thousands of different lipid structures in modern cell membranes. These include glycerolipids, sphingolipids, sterols, prenols, saccharolipids, and polyketides.7 For this reason, selecting the bilayer composition for our synthetic membrane target is far from straightforward. When making synthetic vesicles—synthetic lipid bilayer membranes—mixtures of lipids can, it should be noted, destabilize the system.
  • Lipid bilayers surround subcellular organelles, such as nuclei and mitochondria, which are themselves nanosystems and microsystems. Each of these has their own lipid composition.
  • Lipids have a non-symmetric distribution. The outer and inner faces of the lipid bilayer are chemically inequivalent and cannot be interchanged.
The lipids are just the beginning. Protein–lipid complexes are the required passive transport sites and active pumps for the passage of ions and molecules through bilayer membranes, often with high specificity. Some allow passage for substrates into the compartment, and others their exit. The complexity increases further because all lipid bilayers have vast numbers of polysaccharide (sugar) appendages, known as glycans, and the sugars are no joke. These are important for nanosystem and microsystem regulation. The inherent complexity of these saccharides is daunting. Six repeat units of the saccharide D-pyranose can form more than one trillion different hexasaccharides through branching (constitutional) and glycosidic (stereochemical) diversity.8 Imagine the breadth of the library!

Polysaccharides are the most abundant organic molecules on the planet. Their importance is reflected in the fact that they are produced by and are essential to all natural systems. Every cell membrane is coated with a complex array of polysaccharides, and all cell-to-cell interactions take place through saccharide participation on the lipid bilayer membrane surface. Eliminating any class of saccharides from an organism results in its death, and every cellular dysfunction involves saccharides.

In a report entitled “Transforming Glycoscience,” the US National Research Council recently noted that,


What is more, Vlatka Zoldoš, Tomislav Horvat, and Gordan Lauc observed: “A peculiarity of glycan moieties of glycoproteins is that they are not synthesized using a direct genetic template. Instead, they result from the activity of several hundreds of enzymes organized in complex pathways.”10

Saccharides are information-rich molecules. Glycosyl transferases encode information into glycans and saccharide binding proteins decode the information stored in the glycan structures. This process is repeated according to polysaccharide branching and coupling patterns.11 Saccharides encode and transfer information long after their initial enzymatic construction.12 Polysaccharides carry more potential information than any other macromolecule, including DNA and RNA. For this reason, lipid-associated polysaccharides are proving enigmatic.13

Cellular and organelle bilayers, which were once thought of as simple vesicles, are anything but. They are highly functional gatekeepers. By virtue of their glycans, lipid bilayers become enormous banks of stored, readable, and re-writable information. The sonication of a few random lipids, polysaccharides, and proteins in a lab will not yield cellular lipid bilayer membranes.

Mes frères, mes semblables, with these complexities in mind, how can we build the microsystem of a simple cell? Would we be able to build even the lipid bilayers? These diminutive cellular microsystems—which are, in turn, composed of thousands of nanosystems—are beyond our comprehension. Yet we are led to believe that 3.8 billion years ago the requisite compounds could be found in some cave, or undersea vent, and somehow or other they assembled themselves into the first cell.

Could time really have worked such magic?

Many of the molecular structures needed for life are not thermodynamically favored by their syntheses. Formed by the formose reaction, the saccharides undergo further condensation under the very reaction conditions in which they form. The result is polymeric material, not to mention its stereo-randomness at every stereogenic center, therefore doubly useless.14 Time is the enemy. The reaction must be stopped soon after the desired product is formed. If we run out of synthetic intermediates in the laboratory, we have to go back to the beginning. Nature does not keep a laboratory notebook. How does she bring up more material from the rear?

If one understands the second law of thermodynamics, according to some physicists,15 “You [can] start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant.”16 The interactions of light with small molecules is well understood. The experiment has been performed. The outcome is known. Regardless of the wavelength of the light, no plant ever forms.

We synthetic chemists should state the obvious. The appearance of life on earth is a mystery. We are nowhere near solving this problem. The proposals offered thus far to explain life’s origin make no scientific sense.

Beyond our planet, all the others that have been probed are lifeless, a result in accord with our chemical expectations. The laws of physics and chemistry’s Periodic Table are universal, suggesting that life based upon amino acids, nucleotides, saccharides and lipids is an anomaly. Life should not exist anywhere in our universe. Life should not even exist on the surface of the earth.17



  1. See James Tour, “Animadversions of a Synthetic Chemist,” Inference: International Review of Science 2, no. 2 (2016); James Tour, “Two Experiments in Abiogenesis,” Inference: International Review of Science 2, no. 3 (2016). ↩
  2. See Wikipedia, “Minimal Genome.” ↩
  3. David Dearner, “A Giant Step Towards Artificial Life?” Trends in Biotechnology 23, no. 7 (2008): 336–38, doi:10.1016/j.tibtech.2005.05.008. ↩
  4. A small towards this goal was achieved when a synthetic genome was inserted into a host cell from which the original genome had been removed. The bilayer membrane of the host cell and all of its cytoplasmic constituents had already been created by natural biological processes. See Daniel Gibson et al., “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome,” Science 329, no. 5,987 (2010): 52–56, doi:10.1126/science.1190719. ↩
  5. Bruce Alberts et al., Molecular Biology of the Cell, 4th ed. (New York: Garland Science, 2002). ↩
  6. See F. Xabier Contreras et al., “Molecular Recognition of a Single Sphingolipid Species by a Protein’s Transmembrane Domain,” Nature 481 (2012): 525–29, doi:10.1038/nature10742; Yoshiyuki Norimatsu et al., “Protein–Phospholipid Interplay Revealed with Crystals of a Calcium Pump,” Nature 545 (2017): 193–98, doi:10.1038/nature22357. ↩
  7. See Lipidomics Gateway, “LIPID MAPS Structure Database.” ↩
  8. Roger Laine, “Invited Commentary: A Calculation of All Possible Oligosaccharide Isomers Both Branched and Linear Yields 1.05 × 1012 Structures for a Reducing Hexasaccharide: The Isomer Barrier to Development of Single-Method Saccharide Sequencing or Synthesis Systems,” Glycobiology 4, no. 6 (1994): 759–67, doi:10.1093/glycob/4.6.759. ↩
  9. National Research Council, Transforming Glycoscience: A Roadmap for the Future (Washington, DC: The National Academies Press, 2012), 72, doi:10.17226/13446. ↩
  10. Vlatka Zoldoš, Tomislav Horvat and Gordan Lauc, “Glycomics Meets Genomics, Epigenomics and Other High Throughput Omics for System Biology Studies,” Current Opinion in Chemical Biology 17, no. 1 (2012): 33–40, doi:10.1016/j.cbpa.2012.12.007. ↩
  11. Adapted from Maureen Taylor and Kurt Drickamer, Introduction to Glycobiology (Oxford: Oxford University Press, 2006). ↩
  12. Gordan Lauc, Aleksandar Vojta and Vlatka Zoldoš, “Epigenetic Regulation of Glycosylation Is the Quantum Mechanics of Biology,” Biochimica et Biophysica Acta – General Subjects 1,840, no. 1 (2014): 65–70, doi:10.1016/j.bbagen.2013.08.017. ↩
  13. Claus-Wilhelm von der Lieth, Thomas Luetteke, and Martin Frank, eds., Bioinformatics for Glycobiology and Glycomics: An Introduction (Chichester: Wiley-Blackwell, 2009). ↩
  14. James Tour, “Animadversions of a Synthetic Chemist,” Inference: International Review of Science 2, no. 2 (2016). ↩
  15. See Jeremy England, “Statistical Physics of Self-Replication,” Journal of Chemical Physics 139 (2013), doi:10.1063/1.4818538; Paul Rosenberg, “God is on the Ropes: The Brilliant New Science That Has Creationists and the Christian Right Terrified,” Salon, January 3, 2015. ↩
  16. Natalie Wolchover, “A New Physics Theory of Life,” Quanta, January 22, 2014. ↩
  17. The author wishes to thank Anthony Futerman of the Weizmann Institute and Russell Carlson of the University of Georgia for information on lipids and saccharides, respectively. ↩
Published on August 2, 2017 in Volume 3, Issue 2.
And why should we care about the personal opinion of a nanotechnologist and chemist against the overwhelming scientific consensus and evidence?

And where's the connection between his claims about abiogenesis and evolution?
 






Red Sky at Morning

Superstar
Joined
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Messages
9,966
And where's the connection between his claims about abiogenesis and evolution?
If a car won’t start, it won’t take you anywhere. I believe (and many others do too) that Abiogenesis is functionally impossible. Given that premise, the “science“ that is built on that sandy foundation must therefore be questionable.
 






TagliatelliMonster

Established
Joined
Dec 29, 2019
Messages
145
If a car won’t start, it won’t take you anywhere. I believe (and many others do too) that Abiogenesis is functionally impossible. Given that premise, the “science“ that is built on that sandy foundation must therefore be questionable.
Not debating any points yet. I am just offering a bit of help. One site that I like for this discussion is that of Nobel Prize winning Jack Szostak:

Szostak Lab: Home


It not only describes some of the processes of abiogenesis as they are understood today, it also has links to the latest peer reviewed work by Szostak lab:

https://molbio.mgh.harvard.edu/szostakweb/publications.html



There are a number of reasons.

First, RNA is more flexible and can catalyze a number of biologically important reactions as well as providing genetic material.

Second, at the heart of the DNA->protein synthesis is the ribosome, which is made from RNA (rRNA). RNA is also the link that transfers from the DNA to the ribosome (mRNA). And, RNA is what identifies which amino acid corresponds with which codon (tRNA).

In other words, RNA is at the heart of the reactions that read and decode DNA. It can also do a substantial amount of the basic metabolism itself.

There are *viruses* that have no DNA: when they infect a cell, they translate the RNA to DNA that the cell then reads. But viruses are a strange, special case, being parasitic by nature and probably NOT the original form of life.


If we set up the conditions that mimic those on the primitive Earth and do not otherwise intervene, we have shown intelligence isn't required for the resulting reactions. We know those basic chemicals are common in the universe, so no intelligence is required for them to be on the early Earth.
 






TagliatelliMonster

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This reference concerns the mechanism of the chemical evolution of inorganic phosphates to organic phosphates.

From: Scientists Just Found a Vital Missing Link in The Origins of Life on Earth




Scientists Just Found a Vital Missing Link in The Origins of Life on Earth
Meet diamidophosphate.


MIKE MCRAE
7 NOV 2017
Carbon might be the backbone of organic chemistry, but life on Earth wouldn't be what it is today if it weren't for another critical member of the periodic table – phosphorus.


Transforming run of the mill hydrocarbons into the kinds of molecules that include this important element is a giant evolutionary leap, chemically speaking. But now scientists think they know how such a vital step was accomplished.

Researchers from The Scripps Research Institute in California have identified a molecule capable of performing phosphorylation in water, making it a solid candidate for what has until now been a missing link in the chain from lifeless soup to evolving cells.

In the classic chicken and egg conundrum of biology's origins, debate continues to rage over which process kicked off others in order to get to life. Was RNA was followed by protein structures? Did metabolism spark the whole shebang? And what about the lipids?

No matter what school of abiogenesis you hail from, the production of these various classes of organic molecules requires a process called phosphorylation – getting a group of three oxygens and a phosphorus to attach to other molecules.

Nobody has provided strong evidence in support of any particular agent that might have been responsible for making this happen to prebiotic compounds. Until now.

"We suggest a phosphorylation chemistry that could have given rise, all in the same place, to oligonucleotides, oligopeptides, and the cell-like structures to enclose them," says researcher Ramanarayanan Krishnamurthy.

Enter diamidophosphate (DAP).

Combined with imidazole acting as a catalyst, DAP could have bridged the critical gap from early compounds such as uridine and cytidine. That might not seem overly exciting, but phosphorylating nucleosides like these is a crucial step on the road to building the chains of RNA that could serve as the first primitive genes.
 






Red Sky at Morning

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@TagliatelliMonster

I wonder if you are missing the big picture here? Many scientists are strenuously attempting to demonstrate the ability to get useful organic compounds in sufficient concentrations to provide a kind of makeshift lab for the miracle of life to spring forth.

The presumption seems to be that if once the difficulty of getting the ingredients together in the kitchen, the pie will happen sooner or later!

I simply disagree.

 






TagliatelliMonster

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@TagliatelliMonster

I wonder if you are missing the big picture here? Many scientists are strenuously attempting to demonstrate the ability to get useful organic compounds in sufficient concentrations to provide a kind of makeshift lab for the miracle of life to spring forth.

The presumption seems to be that if once the difficulty of getting the ingredients together in the kitchen, the pie will happen sooner or later!

I simply disagree.

Even if we can't make it happen in a lab in tens of years versus the billions of years that the universe had doesn't mean that it didn't actually happen, and it certainly doesn't mean that "god did it" is more reasonable an answer than "we don't know but we're still trying to figure it out."

Here's the thing, though: the pie happened. We can look around and see that the pie happened. So looking for the mechanism is an interesting task. And you can dispute the way that they're doing this, and that's fine. You're free to propose your own experiment to work out the mechanism.

The theory of evolution has been around for over 150 years. It's a foundational principle for our understanding of biological sciences. Even though we don't fully understand how the first biological organisms came into existence yet, I know of no serious scientist who doesn't fully expect to have an explanation at some point. Obviously it happened (we're here), but we don't understand the mechanisms yet. Reverse engineering the process just takes time.
100 years ago we had no idea that other galaxies even existed, and the only thing required to prove it was sufficiently high powered telescopes to look at the sky. We simply don't have the knowledge and tools (yet) to prove how life sprang forth, but there's nothing magical about the materials that make up living organisms. It's always a challenge educating the scientifically illiterate.
 






Red Sky at Morning

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The pie was either created by a chef or it came about due to an earthquake in a pantry resulting in the ingredients falling into the right pans, with the aftershocks causing an electrical fault that got the thing cooked.

3F733268-9CED-46BA-8E54-0F255468A006.jpeg

I submit that if you hate the very idea of a chef, even the least plausible alternative that could be “conceivable” is therefore preferable.
 






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