Should genesis be taken literally?

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An Open Letter to My Colleagues
James Tour

CHEMISTRY / CRITICAL NOTES

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.1The 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.5 Lipid 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 Science2, 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 Science2, 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.
https://inference-review.com/article/an-open-letter-to-my-colleagues
 





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Yes some parts of Gensis are true. Are they true as they are described (or apparently described) in the bible? Who knows.

However if you look towards of antediluvian mythologies from various cultures around the globes it becomes pretty apparent that there was a creation before modern human and there was an advanced civilization on this planet before the younger dryas cataclysmic event.

Look at the Assyrian mythology and the Incan mythology, the Enuma Elish and Zep Tepi from the Egyptians.
 





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Yes some parts of Gensis are true. Are they true as they are described (or apparently described) in the bible? Who knows.

However if you look towards of antediluvian mythologies from various cultures around the globes it becomes pretty apparent that there was a creation before modern human and there was an advanced civilization on this planet before the younger dryas cataclysmic event.

Look at the Assyrian mythology and the Incan mythology, the Enuma Elish and Zep Tepi from the Egyptians.
There definitely seems to have been advanced civilisation (s) before a cataclysm took society back to square one.

Who they were and what they were up to is an interesting question. There is overlap and contradiction, as though two or more competing narratives of history have been doing battle for millennia.
 





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Even the Jews say the book came with the oral tradition ie the wisdom explaining the intent. That it wasn't literal but metaphorical terminology.

Genesis was written in a way that was peculiar for its intended audience....ie their mythos.

But I suppose you really do believe God was walking about in the garden looking for Adam and Eve. Or that God created day and night even before stars
Or that god regretted creating humans, flooded the earth and then..........




*Drumroll*









regretted it.

Even Maimonides wrote a book called "Guide for the PERPLEXED" in the middle ages because even then Jews lost belief in a literal interpretation of the Torah.
 





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Yes and no. All children of God have the Holy Spirit dwelling in them. The holy spirit discerns for us what is meant to be literal and what is symbolic, or parables etc. The holy spirit gives us the tools, and broadens our understanding of God’s word. ^_^
 





Dalit

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Do you take genesis literally ? I noticed most people are selective about what to take literally from it. And it's kind of understandable, there are some tough pills to swallow in it if we take everything literally. If we take all of it as allegory it kind of become confusing and raises even more questions. Usually Bible is quite clear about itself. There is dreams, visions ,interpretations, parables, prophecies. And there is history scrupulous with dates and chronology... However genesis is mysterious and and doesn't hint too much or even leaves some details out of story on purpose . So how you approach it and how you decide ? Some usually arguable topics i can think off the top of my head...I don't need specific answers about those, sure insights are welcome but i posted them just to help visualize and remember :)
Seven days
Eden
Trees and apples
Snake and his seed
Angels having sex with humans
Giants
Two or more of every kind on earth in boat
Tower of babel
Sodom and Gomorrah
Fact: 7 of every clean animal, 2 of every unclean, and this before the established Torah. So how did Noah know what was clean and unclean? YHVH must've told him. :)
"You shall take with you of every clean animal by sevens, a male and his female; and of the animals that are not clean two, a male and his female;" (Genesis 7:2)

Ah, I see you have the "more", but after reading this for years thinking I knew this and that Genesis had nothing new for me...oh, the arrogance of youth...this is why I love the Bible because there's always more you have to learn. It's so layered and detailed.
 





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maxresdefault (1).jpg

Definition
  1. soul, self, life, creature, person, appetite, mind, living being, desire, emotion, passion
    1. that which breathes, the breathing substance or being, soul, the inner being of man
    2. living being
    3. living being (with life in the blood)
    4. the man himself, self, person or individual
    5. seat of the appetites
    6. seat of emotions and passions
    7. activity of mind
    8. activity of the will
    9. activity of the character
 





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Do you take genesis literally ?
YES. The secret things belong to The Lord our God; but those things that are revealed belong unto us and our children forever...…………… (Deut. 29:29). All Scripture is given by inspiration of God, and is profitable for Doctrine, for reproof, for correction, for instruction for righteousness, that the man of God may be perfect, thoroughly furnished unto all good works (2 Tim. 3:16-17)
Christ confirms the OT Scriptures: Creation Matt. 19:4; The Flood Luke 17:24; The destruction of Sodom Luke 17:29; Lot's wife Luke 17:32; Jonah Matt. 12:40; Naaman Luke 4:27. The Psalms of David and prophetical books were inspired Mark 12:36. If you do not believe Christ, Then you are left with the question you asked...I believe and am grounded in His Word. Those that do not believe Christ do not have Him at all!
 





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There is at least a few centuries separating the writing of Chapter 1 and Chapter 2. It was not written by Moses wandering in the desert. Come on now.
It is all the word of God...So what is your point. If you do not believe Scripture is true...Then you do not have Christ, because He confirms that Moses wrote The Book! (John 5:46)
 





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I do not know this man, but I do know Christ...rather, Christ knows me. I only take Scripture as the Lord has drawn me to Himself. To show you how the Lord works with His elect, I had a friend I grew up with, I had not seen or heard from him for 40 years. A couple of weeks ago the Lord put it in my heart to pray for him. A week later, his daughter looked me up on Facebook and told me that Her father was very sick (he is not saved). I'am witnessing to him about the Lord. God is alive and working in His servants. Amen.
 





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It is all the word of God...So what is your point. If you do not believe Scripture is true...Then you do not have Christ, because He confirms that Moses wrote The Book! (John 5:46)
It’s true but not literal.

I do not know this man, but I do know Christ...rather, Christ knows me. I only take Scripture as the Lord has drawn me to Himself. To show you how the Lord works with His elect, I had a friend I grew up with, I had not seen or heard from him for 40 years. A couple of weeks ago the Lord put it in my heart to pray for him. A week later, his daughter looked me up on Facebook and told me that Her father was very sick (he is not saved). I'am witnessing to him about the Lord. God is alive and working in His servants. Amen.
Ok.
 





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"No one, I think, can doubt that the statement that God walked in the afternoon in paradise and that Adam lay hidden under a tree is related figuratively in Scripture so that some mystical meaning may be indicated by it. The departure of Cain from the presence of the Lord will obviously cause a careful reader to inquire what is the presence of God, and how anyone can go out from it. "
-Origen
 





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"No one, I think, can doubt that the statement that God walked in the afternoon in paradise and that Adam lay hidden under a tree is related figuratively in Scripture so that some mystical meaning may be indicated by it. The departure of Cain from the presence of the Lord will obviously cause a careful reader to inquire what is the presence of God, and how anyone can go out from it. "

-Origen
Christ confirms all the OT Scriptures as actual and not mystical or allegoric in the NT. (including creation!) The Lord is coming by the whole of the Scriptures....Not by allegations! Scripture is not by private interpretation, You must be born again. I posted a study on the full Gospel of Jesus Christ and the Gospel of the Kingdom of heaven which was preached by Christ and the Apostles...yet no one understood it. Just because you don't understand it does not make the Scriptures untrue.
 





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Christ confirms all the OT Scriptures as actual and not mystical or allegoric in the NT. (including creation!) The Lord is coming by the whole of the Scriptures....Not by allegations! Scripture is not by private interpretation, You must be born again. I posted a study on the full Gospel of Jesus Christ and the Gospel of the Kingdom of heaven which was preached by Christ and the Apostles...yet no one understood it. Just because you don't understand it does not make the Scriptures untrue.
You will never convince me to accept YEC ( an 150 year old idea from the whack job 7th Day Adventist’s) as it would require me to abandon all reason and logic and accept magical thinking which I will not. Literalism is a dangerous heresy and I will spend the rest of my life countering the damage done by fundamentalists.
Funny you interjected on this-- I was reading about it just last night.

Just curious... have you read any exegesis on it, yourself?
Yes, I try and research all the information not just what supports my views.