Created: September 9, 2015
April-June 2017 - ReWrite
     

The Creation Narrative of Science and the Bible
 

Dr. David C. Bossard

Dr. David C. Bossard
Biographical Information

The Purpose of this website

This website concerns the Creation Narrative of modern science and of the Bible. A creation narrative describes how the universe and the earth came to be in their present state. Our purpose is to explain how the two narratives—of Science and of the Bible—compare, a comparison that has been possible only within recent decades. They agree quite well, if one lays aside old misconceptions in the true spirit of a search for truth wherever it can be found.

A full Creation Narrative begins with the creation of the universe, and ends with the Creation of Man. What this website attempts to show is that there is an astounding agreement between the Bible's Creation Narrative (CNB) and the Creation Narrative of Science (CNS). Both narratives, if properly understood, are full narratives in this sense. Each narrative, of course, emphasizes the aspects appropriate to itself: thus CNB emphasizes the activities of the Creator God, and CNS emphasizes the discoveries of science. Each aspect has its proper place.

The full Creation Narrative of Science is quite new, developed only within the past 50 years—and of course continually advances to provide fuller detail. Until the 20th century few scientists thought that a factual scientific narrative was even possible: cosmology was viewed as something beyond the reach of objective science. But scientists today know that a full, scientific narrative is possible, and many (not all) of its parts are now in hand.

The Bible's Creation Narrative has existed for over 3,000 years—but one's understanding of the basic facts of science affects how one understands the Biblical Narrative. Even if you disagree with a particular contemporary scientific view, your understanding of the Bible depends on how you view science. And since science has evolved over time, then naturally and inevitably the interpretation and understanding of the Biblical account has also evolved over time. Even yours has: you no longer think (I trust) that the sun goes around the earth, although that is the superficial appearance of observations, and many very sincere Bible scholars and scientists thought that the Bible took that view.

Science would be impossible if the Divine Creator had not embedded into creation an extensive and detailed narrative line written in a language
01 that can, with effort, be understood by the persistent investigator. This is a basic theme of the 19thpsalm.org website. The Psalmist explains this in the immortal line, "The heavens declare the Glory of God, and the firmament sheweth His handiwork." That glorious statement is followed by an assertion that the Creator has embedded a "line gone out through all the earth" into the natural world, a silent voice that makes this proclamation. This line  can be understood with persistent and determined effort: that is the essence of science and it is not given to us without effort!02  

Within the past century science has interpreted that line with the result that the world today is blessed with a fairly comprehensive description of that Creation Narrative of Science, from the very beginning of the universe through the creation of the elements, of earth, and of life on earth. This narrative has vast gaps which time may fill, but the main outline is now known with some confidence.

The approach used here is to construct a consistent narrative using a number of short presentations. The intent is that these presentations give the essential development in a fairly accessible way, and then point to further resources with various excursions on the general theme.

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Other websites that I have developed or helped develop (and which you, of course, are welcome to visit), are:

- The HMS Challenger Library and the Golden Age of Geology Library
        These libraries are part of my 19thcenturyscience.org website;

- The 19thpsalm.org website which gives a more comprehensive discussion of the various stages of the Genesis creation narrative; and

- The website of the Interdisciplinary Biblical Research Institute,  IBRI.org.
        See that site for a statement of IBRI's purpose and  membership.

These sites record, for the most part, the thoughts and views of many people with expertise in science and theology (although my own views appear on occasion), but this website gives my own views, for which I alone am responsible.



Scattered throughout are some theme boxes, explained here:

silent speech
Silent Speech

sharp points
Sharp Points
connections
Connections


Synopsis: Creation Narratives of Science and of the Bible

The creation texts of the Bible have been established unchanged for almost 3,500 years. This text has led to many diverse narratives, as  Bible scholars and theologians attempted to interpret the text.
My own interpretation (CNB) is based on a valid interpretation of the Bible's text.

Over history scientists and philosophers have also given many narratives based on their best understanding of the science of their day. The latest generally accepted creation narrative of science (CNS), the Standard Cosmological Model was developed within the past century.

This website argues that the two narratives
agree on the essential points.  This agreement has been possible only within the past 50 years or so.

Here are Synopses of the Creation Narratives in pdf and word formats:
     Creation Narrative of Science (CNS): CNS Synopsis(pdf)  .doc
     Creation Narrative of the Bible (CNB):
CNB Synopsis(pdf)  .doc

This website gives some of the details that provide additional support to these synopses.



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[*fn]^n01 Written language before writing. Shortly before 3,000 BC archaeology records the earliest evidence of written language, written in Egyptian, Sumerian and Akkadian (these two alphabetic languages from the region of Ur/Babylon in southern Iraq). The idea of alphabetic language is to represent sounds with "sounds like" images. Archaeology can trace the development of the writing as the images become more abstract—for example, the form of the letter "A": "[It] may have been a pictograph of an ox head ... styled as a triangular head with two horns extended." (See Wiki on "A")

Before writing, how did early humans make records? It is evident that they did, because a literal interpretation of Genesis Day Four, to "measure times and seasons, days and years" requires a retention of observations conducted over long periods of time (discussed later in connection with Day Four). The astronomer Walter Maunder argued that the constellations were a form of "written record" which predated writing. See Walter Maunder, Astronomy of the Bible (1904). The Lascaux Cave paintings appear to include an accurate sky chart from about 17,000 BC, which must have been reproduced from records written down in some way.

Ugarit (Ras Shamra) is a port city on the Mediterranean in Northern Syria, with a fortified wall dating to 6,000 BC, guarding the trade route between the Mediterranean and the Euphrates/Tigris trade routes. It is near to Ebla, the source of the Ebla Tablets, an ancient library from the early bronze age, c. 2500 BC, which contained many hundreds of literary texts and trade records. At the time, Ebla appears to have been a major educational center for prospective scribes.

[NOTE: GET John Healey, The Early Alphabet, and "Egypt, Ancient: Hieroglyphics and Origins of Alphabet" in Encyclopedia of African History 3-volume set]

Wikimedia
Ugaritic tablet from Ebla Wikimedia

[*fn]^n02 One thing that I have learned over time, is that God doesn't usually hand things over to us on a platter. We have to work to get it.  Fortunately, one characteristic of good scientists is dogged persistence, and God rewards that with insight. One of the remarkable and unexpected features of this "line" that God has woven into the natural world, is that it gives a remarkable record of the past—going all the way to the very beginning in the Big Bang. Who would have thought that scientists can discover what took place within fractions of a second after the very beginning of the universe, or could learn what goes on in the interior of stars (which was revealed in that landmark 1957 paper by my one of my favorite scientists, Fred Hoyle, called B2FH after the authors Berbidge (man and wife), Fowler and Hoyle) (see citation below).



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The Science of Cosmology and Beginnings

  It is astonishing that science can determine what happened in the earliest seconds and minutes of creation. This discovery has only been made in the past few decades. Prior to this, many scientists questioned the very notion that it would be possible to study these early moments with rigorous scientific precision, or even that the universe had a definite beginning. Cosmology—the physics of the universe and its beginnings—was relegated to the realm of religion or superstition, declared to be beyond the methods of rigorous science. Today, the science of cosmology is universally recognized as among the exact sciences and capable of fully rigorous mathematical treatment.


    In contrast with the former view, there is now a general understanding and agreement as to the fact of the Big Bang, and how the early universe grew from the Big Bang over the first few minutes. The precise age of the universe is 13.799 billion years old with an error of 21 million years, about 0.1%, based on measurements of the cosmic background radiation. This background radiation is a remarkable example of the Silent Speech of Psalm 19 preserved by God since the very beginning of time to reveal his glory and handiwork.



I. Before the Beginning

One astounding conclusion of CNS is that there was a definite beginning to the entire universe. The observable universe—all of space that scientists can view and measure—is 13.799 billion years old with an error of 21 million years, about 0.1%. This beginning is broadly called the Big Bang. At this beginning, the entire universe began as an intense point of light that has expanded and cooled since that time to the present.

The early seconds and minutes of the universe have two physical explanations at present: Einstein's General Relativity concerns science in the large; and Quantum mechanics concerns science in the small. Richard Feynman (one of my favorite role models in science) developed  Quantum electrodynamics which explains how quantum particles interact.   Both of these theories have an outstanding record of confirmation, but there is no theory at present that combines these two extremes of science in the large and science in the small. The widely accepted overall Standard Model description of the early universe uses insights from both of these theories.

What (if anything) existed before this beginning? Experimental science is unable to say what came before the beginning, because it is limited to the observable universe. In fact, our understanding of quantum theory appears to break down for times less than the Planck Time, 5.39 × 10−44s: an extremely short (but not zero!) time after the Big Bang. At present, experimental science can replicate the temperature of the universe at less than 10−12s after the Big Bang, so many of the events in the early universe can be confirmed by actual experiment.
03a

How do you describe the sitz before the beginning???


A Multiverse? Some scientists speculate that our own universe is just part of a vast (if nothing can be "vast"!) multiverse in which countless universes spawned since eternity past.

There are basically two reasons to postulate a multiverse:

(1) Philosophy appears to demand that any effect must have a cause.  Since many scientists reject the existence of God, the multiverse provides a natural "explanation" for what cause resulted in the observable universe. Another way to state this philosophical view is that anything with a finite existence implies something else with an infinite existence—a view that can be satisfied by having a God as prime mover, or by having eternal physical constructs and processes—a multiverse—that spawned the finite thing;03
and,

(2) Our universe appears to be exquisitely fine-tuned to support the existence of intelligent life04. The multiverse "explains" this fact without a Creator (and of course without fine-tuning!), provided each universe involves an accidental, random selection of laws and constants. Our own universe accidentally has the particular selections in which all of the requirements for life just happen to exist: if it didn't then we would not be around to observe it! When one looks at the figures, this means that there must be vastly many more universes than there are atoms in our own universe—a truly staggering number. If I am struggling to describe the truly staggering number of universes, it's only because the concept itself is staggering—but necessary if one does not accept the concept of a Prime Mover.

I suspect that scientists generally believe that there is some grand unified theory to explain it all, that would not require all of these futile universes. But we just don't know what it is.

What does the Big Bang universe expand into? Creation Narrative descriptions.

By necessity, a creation narrative must say something about the situation before the beginning. Perhaps nothing exists outside of our universe, and after the Big Bang the universe expands into nothing? But frankly that sounds like nonsense: what is "nothing"? From the viewpoint of science, the closest that one can come is to say that before the Big Bang there was no matter, no radiation, no space or time.

There appear to be two early (roughly contemporaneous) religious descriptions of this indescribable state: The Genesis creation narrative, and the Hindu Rig Veda Hymn Nasadiya Sukta.
03b

• Genesis 1:2 states:

2 And the earth was without form, and void; and darkness was upon the face of the deep. And the Spirit of God moved upon the face of the waters.

St. Augustine of Hippo, about 400AD, understood "without form and void" as "formless and empty", meaning the earth did not yet exist. In his view, it had been created "formless" and later made concrete. Eventually, about 900 years later, St. Thomas Aquinas developed this into a theological view in Question 66 of his masterpiece Summa Theologica, Whether formlessness of created matter preceded in time its formation?

St. Augustine extended this concept of formless creation not just to the earth, but to all aspects of creation. I do not agree with this understanding. For me, "without form and void" simply means the earth did not yet exist, without extending the concept to mean "virtual" creation precedes all steps of creation. I do not agree that the intent to create is equivalent to actual creation.
05

• The Nasadiya Sukta states that before the beginning:

Then even nothingness was not, nor existence,
There was no air then, nor the heavens beyond it.
What covered it? Where was it? In whose keeping?
Was there then cosmic water, in depths unfathomed?

Then there was neither death nor immortality
nor was there then the torch of night and day.
The One breathed windlessly and self-sustaining.
There was that One then, and there was no other.

At first there was only darkness wrapped in darkness.
All this was only unillumined waterI.01.
That One which came to be, enclosed in nothing,
arose at last, born of the power of heat.*

...

But, after all, who knows, and who can say
Whence it all came, and how creation happened?
the gods themselves are later than creation,
so who knows truly whence it has arisen?

Translated by A.L. Basham (1914-1986)
Wikimedia

* For a physicist, heat and light are just forms of radiant energy, so I view this "birth" as a reference to the beginning of the universe with the light of Day One.


The words used in these descriptions are figurative, by necessity (after all, there is nothing in the universe to match it!). The Nasadiya Sukta says this very nicely: "even nothingness was not, nor existence" and "darkness wrapped in darkness", "enclosed in nothing" (meaning there were no limits or bounds, no structure). The "Spirit of God" is "The One breathed windlessly and self-sustaining."
06

The Genesis account says the same thing in a minimum of words. Personally, I appreciate the expanded description that this gives.

• One other Bible passage is also set before the beginning. Proverbs 8  is a poem about Wisdom that participated with God in the creation, before the earth existed:

The Lord possessed me in the beginning of his way, before his works of old.
I was set up from everlasting, from the beginning, or ever the earth was.
When there were no depths, I was brought forth; when there were no fountains abounding with water.
Before the mountains were settled, before the hills was I brought forth:
While as yet he had not made the earth, nor the fields, nor the highest part of the dust of the world.
When he prepared the heavens, I was there: when he set a compass upon the face of the depth:
When he established the clouds above: when he strengthened the fountains of the deep:
When he gave to the sea his decree, that the waters should not pass his commandment: when he appointed the foundations of the earth:
Then I was by him, as one brought up with him: and I was daily his delight, rejoicing always before him;
Rejoicing in the habitable part of his earth; and my delights were with the sons of men.
Proverbs 8:22-30


Even the darkness before the beginning was different. Physics would say that the darkness of "nothingness" is absolute zero. This temperature is unattainable anywhere in the universe, because there is always the cosmic background radiation, about 2.7°K, left over from the Big Bang, or more precisely, left over from the onset of darkness when neutral atoms formed about 379,000 years after the Big Bang. See below.

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[*fn]^n03 Before the demonstration that the universe is finite and had a definite beginning, many scientists assumed that our universe was infinite in space and time. So the multiverse concept applies that assumption one step earlier: the multiverse—infinite in space and time—spawned our finite universe and perhaps an infinity of other universes, each perhaps with a different selection of physical laws and constants. Of course, scientists are not entirely happy with this. It would be preferable to have a grand unified theory that would explain how such universes begin, how they chose laws and constants, etc. But, alas, such a (generally accepted) grand theory does not (yet) exist.

[*fn]^n03a See Introduction to Astronomy(pdf).


[*fn]^n03b The Rig Veda was an Early Sanskrit document composed 1400-900 BC (roughly contemporary with the Genesis composition). Hymn 129 "Nasadiya Sukta" concerns Creation. Translation by Ralph T. H. Griffith. Translated by A. L. Basham. It was a long oral tradition until finally put into writing (it is thought) around 900 BC.  The name means "not the nonexistent" and its composition is  possibly contemporary with Genesis (but I'm not ready to go to the stake over this!). Or, more probably, both the Genesis account and the Rig Veda accounts reflect an older oral tradition passed down from the distant past. Genesis and other Old Testament books sometimes cite sources for the information, which no longer are extant.


[*fn]^n04 A number of recent books have been written about this. See Geraint F. Lewis & Luke A. Barnes,
A Fortunate Universe: Life in a Finely Tuned Cosmos(2017). This book is a comprehensive discussion of the topic, and also lists many other recent books.

On the physical events that occurred in connection with the Big Bang, see, for example, Steven Weinberg, The First Three Minutes: A Modern View Of The Origin Of The Universe (1988) and Jonathan Allday, Quarks Leptons and the Big Bang (1998).




[*fn]^n05 St. Augustine of Hippo (13 November 354—28 August 430), The Literal Interpretation of Genesis,ca. 415 AD. His view was that Genesis 1:1 "In the beginning God created the heavens and the earth" is the instantaneous creation of everything, including the earth and all the events of the Creation Days. He couldn't understand why God would create over time, since He is timeless.

My own view is that God created using natural processes when they would achieve the needed result, and created by fiat (instantaneously?) when natural processes were unable to achieve the desired result. The task of the scientist is to find out what can be done naturally, to explore the limits of natural development, but without making the assumption that everything we see must be a natural development (as a scientist who rejects a creator God must necessarily assume). Much of the activity described in the creation Days can be done naturally, and thus, was done naturally and the task therefore took as long as natural processes would require (for example, the development of the shields ("firmament") on Day Two, and the creation of dry land on Day Three).

In my view this Genesis 1:1 and Genesis 2:4 are the "bookends" of the creation narrative, which take place in the intervening verses. St. Augustine says, in Book I, §8, "Are we to understand that by the expression, heaven and earth all that God made is to be included and brought to mind first in a general way, and that then the manner of creation is to be worked out in detail, as for each object the words God said occur? For whatever God made, he made through His Word." My short answer is "yes". However he went on to give this verse a deeper meaning (which I do not agree with).

Augustine concluded that (because God is timeless) the creation of everything was instantaneous (omnia simul), but that they were created in potential, with the realization occurring in time. At one place [V.5.13] he said that God "Created potentially, for time would bring them into view in the ages to come." Henry Woods, Augustine and Evolution (1924) p. 14, remarks on omnia simul: "He conceived creation as proceeding from the Creator, a unit including all things whatsoever that are to exist to the end of time, and corresponding to the single creative mandate. ... [H]e places the analogue of all things, as yet without individual existence, existing in elementary matter as forms in potency, forms decreed to exist, therefore no figments of the mind... distinguishing objectively the things that are to be, from mere possibilities never to be actuated."; p. 16 "St. Augustine takes unformed matter in the scriptural sense for matter without definite external form." As noted earlier, St. Thomas Aquinas formalized his view in Question 66 of Summa Theologica. see http://www.newadvent.org/summa/1066.htm - article1. The answer of Aquinas states that "holy men differ in opinion." He then cites the views of various Church Fathers. This view also provides an understanding of "without form and void" in verse 2. Clearly he did not consider adherence to a particular view as essential to the Faith.

[*fn]^n06 The Bible uses the same root word for "spirit", "wind" and "breathing" (in both the Old and New Testaments). An illustration of this is found in John 3:8, "The wind bloweth where it listeth, and thou hearest the sound thereof, but canst not tell whence it cometh, and whither it goeth: so is every one that is born of the Spirit." In this verse the same Greek word pneuma is translated "wind" and "Spirit".

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Where did these Creation Narrative descriptions originate? Of course nobody knows, but my guess is that both of these narratives came from a common oral or written tradition (see
01). The Bible frequently notes that other sources—now lost—were consulted in its composition.


The Origin of Record-keeping? Writing?
Where did the "unknowable things" of the Genesis Narrative originate?
  It is a mystery to me how and when the principle ideas expressed in the Creation Narrative began. The Genesis account asserts several things that (until within the last century) could not be known by man apart from God's revelation because they concern things that are totally beyond the human wisdom of the day:

1. That the Universe had a beginning and came into being from nothing.
2. That the Universe began with the creation of light.
3. That advanced life (multicellular life) could not exist without an effective shield that separates inner from outer space.
4. That the early earth was completely covered with water: there was no dry land.
5. That dry land emerged from the global ocean, but the ocean still is in one place.
6. That animal life began in water, and later moved to dry land.
I challenge anyone to explain how any of these facts that are now known to be true could have been rationally discovered by  early humans. I would love to see a secular explanation apart from direct revelation from God. In addition there are some known and abundantly clear facts that the Bible notes but no rational scientist can explain how it happened or might conceivably happen:

7. That the first life began as a vastly complex, organized, self-replicating entity in the universe, with no plausible precursor. Anything but random for even the simplest forms of life!
8. That animal life has qualities that cannot be explained by any rational extrapolation from prior life—the nephesh chayah on Day 5.
9. That there is a vast gap between the human creation and any other living creature.
The Genesis creation account emphasizes all of these points, which lifts that narrative far above any other scientific "explanation" or pagan "evolved" myth.

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FOOTNOTES I FOLLOW

[*fn] I.01 The "water" is  not physical water, but conveys the concept of formless fluidity.

I.02[*fn] I.02 Note for I.02

I.03
[*fn] I.03 Note for I.03

I.04[*fn] I.04 Note for I.04

I.05 [*fn] I.05 Note for I.05


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II. Creation of Light in the Big Bang
Creation Day One

3 And God said, Let there be light: and there was light. 4 And God saw the light, that it was good: and God divided the light from the darkness. 5 And God called the light Day, and the darkness he called Night. And the evening and the morning were the first day.
St. Augustine puzzled over these verses for many years.07 Fortunately he recorded his puzzlement in his book,  The Literal Interpretation of Genesis, and so we have a full record of it. I believe no other theologian has given comparable details of his struggles to understand the Bible. He had a truly scientific mind, and he recorded many of his questions "in the raw" so to speak without prettying them up. He asked such questions as, Why is the creation of light so important that it is the very first thing mentioned? Should we understand "light" to be taken literally or figuratively—as for example, perhaps it is "heavenly" light, or perhaps the term is used figuratively for the creation of celestial beings, the "angels of light" so to speak? How is it possible that light was created apart from darkness: doesn't light imply the existence of darkness, so how is it possible that darkness was created later, as verse 4 implies? Was this darkness a different sort of thing from the darkness of verse 2? And how could it take an entire day to merely create light: surely God could just speak the words, and it would be done immediately? Finally, if the light is literal light, how could it have been created in Day One, when the sun itself was not created until Day Four?

I think it is fair to say that—reading between the lines—St. Augustine was not himself completely satisfied with his analysis of Day One.

These are really interesting questions, and many theologians other than St. Augustine have suggested answers. But still these answers seem to require making special assumptions or adding something to the text rather than taking the words with their natural meaning. For example, the Scofield Reference Bible notes on Day One are typical of a line of exegesis that is still strong today. The Scofield Bible was very influential during the first half of the 20th century. He stated,
13"The 'light' here of course came from the sun." To reinforce this conclusion, he had to conclude that the sun was obscured by a heavy cloud cover until Day Four. This led to a whole speculative view that involved a prior ruined earth and other features developed in his notes, but that are not contained in the passage. In fact, the light of Day One did not come from the Sun, answering St. Augustine's puzzlement (note 07).

This situation all changed with the discovery—only since the mid-20th century—of experimental evidence for the Big Bang and the subsequent evolution of the universe since that event. The true facts revealed by  the 
Standard Cosmological Model</big><big> give a natural explanation that does not require all of this added speculation.
 

First and most important, this discovery showed that Day One is not just the creation (or some say, the renewal) of the earth, but it records the creation of the universe itself. From nothing, as far as science can determine.

Why is the creation of light mentioned as the very first act of creation? Because at the Big Bang instant, the entire universe began as a point of light, and has expanded into nothingness at (nearly) the speed of light from that time to the present. Space and time were created at that instant.

Should we understand "light" to be taken literally or figuratively? The light of the Big Bang is physical light, so the light of verse 3 could be interpreted as literal light. It is so concrete an event that its time can be precisely determined (see above remarks). Whether it is also the creation of "spiritual" light is something that the theologians can discuss, but at least the Big Bang was physical, literal light, albeit at such high temperature that no light or heat on earth or in today's universe can compare with it.

So Day One marks the beginning of the universe, of space, and of time. As we remarked above, the setting for Genesis 1:2 is before the beginning.

How is it possible that light was created apart from darkness? There is no contradiction here, since the light is quite physical. Within a small fraction of a second after the Big Bang, the universe expanded and cooled to the point where some of the elementary particles could hang together: electrons, and the quarks that  combine to form protons and neutrons.

About a second after the Big Bang the nuclei of hydrogen and helium began to form. These are the primordial elements from which all of the elements formed much later. [For a very readable description of this see the book First Three Minutes] This continued for about 20 minutes, and then the universe cooled to the point that further fusion ceased for the time being. There was no darkness in this new universe; it was all light created in the original Big Bang.

So, Doesn't light imply the existence of darkness? Answer, No.

How is it possible that darkness was created later?Darkness entered into the universe when the temperature dropped to the point that neutral atoms could form (i.e. Hydrogen and Helium nuclei could hold onto orbiting electrons to produce neutral atoms). This occurred about 379,000 years after the Big Bang, when the background temperature of the universe dropped to about 3,000°K. When this happened, photons of background radiation would not be sucked up by nuclei, and could travel (on average) undisturbed to the edges of the universe.The background sky then darkened and darkness entered the universe. [Something analogous explains why days are bright and nights are dark and show the stars].

Was this darkness a different sort of thing from the darkness of verse 2?  Very interesting question. And I think the scientific answer is (as far as we can determine), Yes. Because the temperature of "nothing" is 0°K (absolute zero) which is a temperature that cannot be reached in the entire universe because of the residual echoes of the Big Bang (about 2.7°K).

... Now I suppose someone could maintain that these verses do not describe the Big Bang. But identifying the Big Bang with these verses provides very nice and scientifically accurate answers to St. Augustine's questions. And if that identity is denied, then they are left with the same puzzles that St. Augustine faced.

Was the sun itself not created until Day Four?  This question has nothing to do with the interpretation of Day One, so it is not necessary to answer it here.



The True Interpretation of Day One
Probably no verses better illustrate the confusion caused by misunderstanding of what is actually being said. It's good, though, that the theologians were puzzled, because in fact they had no basis for understanding the actual events of the day or their true meaning, and so it led to many attempts at rationalization. The basic puzzles (and the true answer from modern science) are:

• Is Day One actually the start of creation, or is it a re-creation?
Answer: Day One is the actual start. It is the Big Bang, the beginning of space and time. At the Big Bang there was no matter: the whole universe consisted of radiant energy—light.
• How could there be light before the sun was (apparently) put in place in Day Four?
Answer: The Sun itself was formed from the light of the Big Bang. There had to be light before there could be the matter needed to form a Sun or the solar system, as nonsensical as that may have sounded to both scientists and theologians before the mid-20th century.
• How could there be light before matter?
Answer: All matter was formed from the light of the Big Bang. But the creation of matter other than the primordial elements Hydrogen and Helium, had to be preceded by the creation of darkness which converted the universe from radiation-domination to gravitation-domination—from a plasma universe to a material universe.
• Is the "light" to be spiritualized or taken figuratively? (Augustine)
Answer: It makes complete sense to take it literally, as meaning radiant energy. Whether there may also be a figurative or spiritual aspect is something the theologians have to figure out! In my own view the Creation account of Genesis 1 only concerns the physical universe—our own space and time—and does not treat the beginnings of the spirit world which is a separate creation.
• Is the light a clearing of earth's atmosphere?
Answer: No. The earth does not exist on Day One. The meaning of "empty and void" in verse 2 means that the physical earth did not yet exist.

With the discoveries of modern physics, the correct interpretation of Day One is evident!

Further Thoughts: From the viewpoint of both theology and of science, these verses of Day One are the most profound and most unexpected statements of the entire creation account, perhaps in the entire Bible. Who would have thought that the proper way to begin a creation account is with the creation of light? And yet, with the insight of modern science, this is exactly the correct way to begin the creation account.08 In truth, the universe did begin with the creation of light—pure radiant energy at intense heat: so hot that no elements, not even protons and neutrons, or the quarks that form them, could exist. This beginning is  the Big Bang.

Who would have thought that light is the most important thing to begin the creation account? Isn't the most important thing something material? Or objects: the Earth and Sky (as the Egyptian myths have it)? Or perhaps that elusive thing life? Or even the Sun and Moon—names that do not appear in the entire Genesis account—and stars? Some people imagine that "light" in this verse is a stand-in for the Sun, and that this verse refers to the light from the Sun (that's Scofield's view09). All of this misses the point—forgivably, because the full truth of the matter was not even known until the mid-1900s. Even Albert Einstein didn't know.




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FOOTNOTES II FOLLOW

II.01 [*fn] II.01 Note for II.01

II.02[*fn]II.02 Note for II.02

II.03 [*fn]II.03 Note for II.03

II.04 [*fn]II.04 Note for II.04

II.05 [*fn]II.05 Note for II.05



[*fn]^n07 St. Augustine, Op. cit., Ch. 19, §38 asks whether this light is "spiritual light … or material light, celestial or supercelestial, even existing before the heavens?[emphasis added]" How close he was to the truth of the matter! This is followed (§39) by the famous statement that warns theologians against making assertions regarding matters of science of which they are ignorant: "Christians should not talk nonsense to unbelievers."

Many theologians thought that the light of Day One should be understood in a figurative or spiritual sense. Augustine tended to move in this direction. See John F. McCarthy, A Neo-patristic Return to the First Four Days of Creation, Part III - The Days of Creation According to St. Augustine (1993) "He puzzled over the creation of light on the first day, if the sun, the moon, and the stars came into place only on the fourth day….Not having found a satisfactory solution to this question, he considered the possibility that the light created on the first day was a spiritual light…."

One theologian even argued that the Creation could not begin with light in Day One, because the creation of matter must come before light. This led to the conclusion that the creation took place in Genesis 1:1. But in fact, the truth is the exact opposite of this: modern science asserts that matter comes from light (radiant energy) and so light must come before matter.

[Give other Refs for interpretations of "light" in Day One]

[*fn]^n08  To my knowledge, Pope Pius XII was the first recent theologian to suggest this deep meaning of Day One. See his paper, "To the Members of the Pontifical Academy of Sciences" 22 November 1951 (Latin: translate with Google Translate).


[*fn]^n09 "The 'light' of course came from the sun, but the vapour diffused the light. Later the sun appeared in an unclouded sky." The Scofield Reference Bible, 1917 Ed., Note 4 on Genesis 1:3.


[*fn]^n13Scofield, (2nd Edition, 1917) note on 1:3 "The 'light' of course came from the sun, but the vapour diffused the light. Later the sun appeared in an unclouded sky."



===

III. Creation of Darkness
Creation Day One
References:
CNS: I. Creation of the physical world.
CNB: II. Day One: The Creation of Light and Darkness. (Genesis 1:3-5).

Genesis 1:4 And God Saw the light, that it was good: and God divided the light from the darkness.

St. Augustine was puzzled about the separate creation of darkness. He thought that light and darkness naturally came together: darkness being the absence of light. His (understandable) error was that he did not realize that light is an actual physical object.
10

About 379,000 years after the Big Bang, when the background temperature of the universe dropped to about 3,000°K,the universe had cooled down enough so that neutral atoms and molecules could form by capturing and holding electrons. Before this time, atoms could only form briefly before the electrons would be stripped away by the energetic ambient heat. Before stable atoms could form, the sky was always bright because photons were constantly being absorbed and scattered from everywhere at once. When stable atoms could form, light photons could travel long distances without being scattered, and hence the sky could appear dark, for the first time since the creation. There was darkness, separate from the light—of course nobody but God was around at this time to witness it.

This creation of darkness was not just an incidental action. It changed the universe from one dominated by strong electrical forces to one dominated by the much weaker force of gravity. The electrical forces were neatly captured into neutral atoms of hydrogen and helium. Over time the gravity caused matter to come together to form stars and galaxies which formed the other elements by nuclear fusion (see  IV. below).



===

[*fn]^n10
Augustine had several perplexities. Ad. Lit. 1.10.19 "Why was the creation of light so delayed until a day had passed and evening came?" (that is evening and morning) … "And the separation of light and darkness was done, surely, in the very act of the creation of light. There could not have been any light unless it was separated from darkness." 1.10.20: "As for the fact that God called the light Day and the darkness Night, how much time could this have taken? … No one certainly would be so foolish as to think that, because God is great beyond all beings, even a very few syllables uttered by His mouth could have extended over the course of a whole day." For these reasons Augustine leaned towards spiritualizing the light, connecting the light with Angels, etc. All is explained once the true meaning of Day One is understood!

Note that the darkness created here is quite another thing from the primordial darkness of Genesis 1:2. It is a new kind of darkness, created as a result of the cooling of the universe to the point where hydrogen and helium nuclei could hold onto electrons to produce neutral atoms.

===

So now we have a universe -- pretty useless at this point. The CNS says what happens next.  There are many excellent books that discuss the next steps in the CNS.


IV.
Formation of Stars and Forging of the Elements.
11


By 20 minutes after the Big Bang, essentially all of the matter in the universe was forged by nuclear fusion, into hydrogen and Helium (with small amounts of beryllium and boron). After 20 minutes the universe was too cool to support further fusion. See Steven Weinberg,First Three Minutes for details.

When neutral atoms formed with the creation of darkness, the matter began to clump and heat up as gravity pulled it together. After about a billion years, the clumps heated up to millions of degrees and ignited into nuclear fusion. The hydrogen and helium fuzed to form heavier elements, beginning with the elements carbon, nitrogen and oxygen that are essential for life. The processes of element formation in the stars were first fully described in 1956 in a famous paper called
B2FH14 after its authors' names. This paper described how each element is formed in star-burning (forming elements up to iron, nickel and copper) as well as in the cataclysmic supernova deaths of stars which caused a tremendous flux of radiation that forged all of the heavier elements through uranium, and filled the surrounding space with its debris.

Over time, this debris of supernovas again coalesced under the force of gravity and formed second and higher generation stars, including the sun and the solar system, which formed about 4.65 billion years ago.12

This description in
B2FH of how the elements form in star interiors and in supernovas is a remarkable feat, because, of course, it is impossible to directly disect a star to see how it is constructed. But the conclusions of this paper have been confirmed repeatedly in high-energy experiments over the 60+ years since the first publicationIV.03, and there would be few genuine scientists that question its main conclusions (although there is a constant effort to test the validity of the claimed results).


Wikipedia











===

[*fn]^n14 B2FH = Geoffrey Burbidge, Margaret Burbidge, William Fowler and Fred Hoyle, Synthesis of the Elements in Stars,
Reviews of Modern Physics 29 (1957) p547-650
. See the Wikipedia article. See also a brief preceding article by the
Burbidges, Cosmical Alchemy (1956).

[*fn]IV.03 For a Forty year update see: G. Wallerstein, Synthesis of the elements in stars: forty years of progress (1997).  This is a prime exemple of what evolutionary theory should do, and which biological evolution lacks. The B2FH paper, op. cit., explains how the evolution occurs with testable assertions.

[*fn]^n12 It was absolutely necessary for the Earth to have been formed from the debris of a supernova because that is how elements up to Uranium were formed and ejected from their mother-stars. The earth could not have remained warm enough for life if it were not for the warming produced by uranium decay deep in the earth's interior. This fact of Earth's long-extended warmth was a source of great puzzlement by physicists in the days before the discovery of radioactivity. Lord Kelvin (William Thomson, 1st Baron Kelvin (26 June 1824—17 December 1907) estimated the age of the earth in 1862 to be 20-400 Ma based on the loss of heat from an initial molten state—unaware, of course, of uranium's radioactive heating. See James Dana, Manual of Geology (1896), p. 1026. [EDITOR QUESTION: To what extent does the earth's surface temperature depend on heating from the Sun, as compared with uranium heating in the earth's interior?]

[*fn]^n11 See Introduction to Astronomy(pdf).

===

V.
Preparation of a Haven For Life
Creation Day Two


The solar system had to have many specific physical features in order to be a host for living species. Here are the first requirements.

(1) The solar system is near the co-rotation radiusV.01 of the Milky Way galaxy. At this distance from the center of the Milky Way, the Solar System is protected from collisions with nearby stars. This placement avoids passing the solar system through the dense arms of the solar system for the billions of years needed to prepare the earth to host higher forms of life.

(2) The earth's orbit must remain in the habitable zone of the sun.
The habitable zone is defined as the distance from the sun that will have liquid water temperatures—the ambient surface temperature must be between freezing (0°C) and boiling (100°C), roughly between Venus and Mars, with Earth situated about midway within this zone.

In particular, the earth must remain within this zone throughout the entire time required to fit the earth to support advanced life. This time must be on the order of billions of years (for reasons that will be explained below), which is such a long time that there is no mathematical way to ensure or demonstrate such a high level of stability (See the following sharp point).

The Needed Stability of Earth's Orbit

The creation of life required that the Earth remain habitable for billions of years. Why this long time? One reason is that the production of fixed nitrogen using the nitrogenase molecule is a very slow process (see comments below), and a large supply of fixed nitrogen is required for all advanced life. Only sun-like hydrogen burning stars have lives on the order of billions of years.V.04


The remarkable stability of the earth's orbit over billions of years cannot be explained by any mathematical demonstration. Newton himself, the first to describe the planetary orbits in exact mathematical form, wrote about his puzzlement in the Principia, his seminal work on gravity.

The problem that he saw is that the planets form a many-body systemorbiting the sun, and the orbits of such a system, are chaotic; that is, very minor perturbations in the orbits can result in long-term instability. This phenomenon is sometimes called the Butterfly Effect. Newton concluded that God had to tweak the earth's orbit from time to time to keep it in a stable orbit.V.02


About 100 years after Newton, a French mathematician Laplace wrote a book, Celestial Mechanics, in which he claimed to prove that the earth's orbit was stable. There is a famous exchange with Napoleon in which he asserted that he "had no need for that hypothesis", meaning Newton's remark about God's tweaking. However Laplace was wrong, and there is no known way to prove the stability for Earth's orbit for billions of years, which in fact was needed to provide a place for advanced life (as will be seen below). At present, the limits of provable stability are on the order of 100 million years, too short by a factor of 10.

To put it another way, the long-term stability of Earth's orbit for billions of years depends critically on the precise value of the gravitational constant—far more than can be computed by today's science (six significant figures).



(3) Within the habitable zone shields
are needed to protect life on the surface of the earth. The habitable zone places the earth too close to the sun. As a result the earth is subject to sterilzing hard alpha (charged) and gamma (uncharged) rays and coronal mass ejections from the sun as well as from outer space. The only solution is to place shields around the earth to protect it from this bombardment.

These shields are the specific subject of CNB, Day Two:

6 And God said, Let there be a firmament in the midst of the waters, and let it divide the waters from the waters. 7 And God made the firmament, and divided the waters which were under the firmament from the waters which were above the firmament: and it was so. 8 And God called the firmament Heaven. And the evening and the morning were the second day.


The "firmament" in Day Two is a shield or fence between inner space and outer space. It is a protection of the Earth from the rest of the universe, so that the project of life can proceed. Proverbs 8:27 describes it as "he drew a circle" (ESV) or "he set a compass" (KJV) on the face of the deep – literally "encircling" or "encompassing"; i.e. placing a fence: the same Hebrew word chuwg can be a noun or verb.

No life could exist without an effective protection from outer space: a shield is an absolute necessity.  In Hebrew, this shield is called the raqia, a word derived from an ancient meaning of "expanse" or "covering"—i.e. a shield. The word does not include the concept of solidity. That is an ancient addition that was inserted when the Hebrew was translated into the Greek Septuagint by the most advanced scientists of the ancient world. The best science of the day recognized the need for a separation of inner and outer space. They figured this must mean a something solid. So the translation of the Hebrew raqia into the Greek stereoma, and the Latin firmamentum seemed to these early scholars as simply expressing the obvious fact that the raqia had to be a concrete, solid entity to shield the earth.

However the Hebrews made no such presumption of solidity—as is evident in the fact that later in the same creation account, Genesis 1:20 says that fowl fly above the earth in the open firmament, using the same word raqia.V.03

A shield is absolutely necessary to protect inner space, but this shield is not solid; in fact multiple shields exist, each essential to the existence of advanced life on earth: Examples: a magnetic shield to deflect high-energy charged rays and solar mass ejections of plasma (see the box below)

In the case of any "habitable zone" surrounding a star, these shields against high energy particles (charged and neutral) are needed because this zone is necessarily too close to the star: all life exposed to these rays would be killed without the shield. This need for a shield is why animal life began in water, before the shields were fully built: the water itself provides an effective shield a Life on land and in the air had to wait until the ozone shield was in place some 100 million years later (around 400 Million years ago).

Note that the ozone shield is neither solid nor visible, so early man, however "scientific" could not know about it.


Shields between inner and outer space (Day Two)

A number of shields are needed to protect inner-space life from outer space. The most important are:

• The Magnetosphere surrounding the earth which deflects charged rays (hard alpha (+) and beta (-) rays) from outer space, and also the periodic (charged) coronal mass ejections of  plasma from the sun's surface which may flood over the earth during solar storms that occur  in the direction of earth.


Magnetosphere shield surrounding Earth
wikipedia


• The ozone shield also protects the earth from hard (uncharged) gamma rays that come from the nuclear fusion within the sun and from outer space. This shield was effective around 400 million years ago, which marked the first movement of life from the oceans to land and the air.

• The massive outer planets also deflect many large space objects that might otherwise cause catastrophic collisions with the earth. A recent example is the 1994 Shoemaker-Levy comet which Jupiter swept up.




===

[*fn]V.01 Co-rotation Radius.
See Rich Deem, The Incredible Design of the Earth and Our Solar System for a number of remarkable features about the Sun and Earth, including placement of the solar system near the co-rotation radius of the Milky Way galaxy. "The Sun and our Solar System have been located in a stable orbit within our galaxy for the last 4.5 billion years. This orbit lies far from the center of our galaxy and between the spiral arms. The stability of our position is possible because the sun is one of the rare stars that lies within the 'galactic co-rotation radius.' Typically, the stars in our galaxy orbit the center of the galaxy at a rate that differs from the rate of the trailing spiral arms. Thus, most stars located between spiral arms do not remain there for long, but would eventually be swept inside a spiral arm....We are removed from the more densely occupied areas, where stellar interactions can lead to disruption of planetary orbits...The 4+ billion year longevity of life on earth (the time needed to prepare the planet for human occupation) would not have been possible at most other locations in our galaxy." See also Preben Grosbol, et al, Spiral Structure in the Milky Way: Confronting Observations and Theory(2010) on the co-rotation radius "just outside the Sun".


[*fn]V.02 Many-body problem. 
The difficulty is the so-called "Many-body problem". Systems of more than two objects (such as the sun and multiple orbiting planets) are inherently unstable, because minor influences can cause unpredictable long-term effects, popularly called the Butterfly Effect. Even the round-off error in the known physical parameters (gravitational force, etc.) can result in unknown behavior in the long run. The present known accuracy of the gravitational constant is known to about six significant figures, which can ensure stability only for about 100 million years. Wikipedia notes "The gravitational constant is a physical constant that is difficult to measure with high accuracy. This is because the gravitational force is extremely weak compared with other fundamental forces."

Isaac Newton noted this stability problem and concluded that God had to "tweak" the orbits from time to time. (See ???GET QUOTE). A century later the mathematician LaPlace claimed to prove the stability of the earth's orbit, in his famous (and erroneous) remark "I have no need for that hypothesis," referring to the necessity for God's stabilizing the earth's orbit. However LaPlace was in error, as is acknowledged by later mathematicians. Modern computations cannot predict stability of the earth's orbit beyond about 100 million years, much less than the required billions of years.


[*fn]V.03 The so-called Hebrew Cosmology is a modern invention which purports to describe a cosmological construct something like the Egyptian depictions which survive on ancient monuments. There is no such ancient monument to support such a supposed "Hebrew cosmology." Indeed it is unlikely that such a cosmology would have been formulated. The ancient Hebrews were peculiarly uninterested in such myths.

[*fn]V.04 The following chart from
B2FH shows that only Hydrogen-burning stars have lives on the order of billions of years.


Timescale for star burning (From B2FH)



V.05 [*fn]V.05 Note for V.05

V.06 [*fn]V.06 Note for V.06

V.07 [*fn]V.07 Note for V.07

V.08 [*fn]V.08 Note for V.08

V.09 [*fn]V.09 Note for V.09

V.10 [*fn]V.10 Note for V.10

===

fractal.gif



VI. The Creation of Life ItselfVI.01


The creation of microbial and plant life occurs next. The CNB implies but does not specifically mention the creation of life itself, and CNS typically ignores the philosophical implications of the overwhelming difficulties. Lawrence J. Henderson remarked on the attitude of science in the early 1900s, a remark that is still relevant today.

"As for the existence of life, in spite of our utter ignorance, it must be admitted that a half century has greatly diminished the number of substantial biologists who really look forward to its scientific explanation.... The chemist puts his mind at rest regarding the existence of life, just as the physicist calms his regarding the existence of matter, simply by turning his back on the problem. Thereby he suffers nothing in his practical task as a man of science. ... Biochemists are more than ever unable to perceive how such a process is possible, and without taking any final stand prefer to let the riddle rest."
Lawrence J. Henderson, The Fitness of the Environment:
an inquiry into the Biological Significance of the
Properties of Matter (1913) p309-10.

"The advance of science has assuredly not made the origin of life easier to imagine, or even to think about. On the contrary I am fully persuaded that it has made the task far more difficult."
Lawrence J. Henderson,The Order of Nature (1917), p.115

The first mention of living matter in CNB is plants that grow on the dry land on Day Three (see below). However the natural world—the silent voice of Psalm 19—speaks volumes on this subjectVI.07. So this is one place where the proclamation of "God's glory and handiwork" in nature forms an indispensible part of the creation narrative. The story that nature tells about the beginnings of life is extensive, deep and detailed—and growing: it will continue to give abundant fruit for many years to come. The account of life's beginnings is an amazing tale of tenacity and fitness. And it leads to the inevitable conclusion by a rational person, hinted at in these quotations, that a rational intelligence is an indispensible part of the unfolding narrative. This is the reason why scientists "prefer to let the riddle rest," as these quotes imply. This is an indictment against the way that science is practiced, because it implies an attitude that is exactly the opposite of rational inquiry that science should presuppose.


How Special is Life?
At times in the decades after 1859, the publication of Origin of Species many scientists thought that science would soon find a scientific explanation for the origin of life. Ernst Haeckel made the remark in 1876VI.02  that the "general explanation of life is now no more difficult to us than the explanation of the physical properties of inorganic bodies." That optimism did not last long.  Within a few decades, as scientists probed the nature of this protoplasm (German urschleim) the vast complexity of life began to unfold. No longer was it possible to argue for the simplicity of this "slime."

Today, there are three areas where probes have only increased the mystery of how it all began. These are:

(1) Discoveries of the exceedingly special nature of a universe that supports life. This concerns the possible range of parameters and laws;

(2) The incredibly complex digital nature of the central dogma, combined with the vast number of complex molecules and processes that must be present for any self-reproducing life to exist; and

(3) The vast array of unique genes and processes that define the major body types of life.

To my knowledge there is no demonstration of how such seminal changes could have evolved by natural evolutionary change.

The logical conclusion is that the whole project of forming a universe capable of life, of designing the complexities of the central dogma; of creating the many specialized and complex molecules needed to support metabolism and reproduction;  and the engineering of the various major classes of living species, point to a Intelligent creator. Those who deny this are in peril of committing to  the vast and foolish fantasy that St. Paul warned against in Romans 1:22, "Professing themselves to be wise, they became fools."


There is so much fascinating and incredible detail to the beginnings of life that it would be easy to lose sight of the overarching story. To avoid this, we will mention just some of the major points, and leave further details to appendices, so the overall flow can be got at without getting bogged down. 

Perhaps sensing the complexity of the question, Darwin  was quite careful to avoid speculation on the origin of life, contenting himself only to assert that once life existed, it evolved its many species by natural means according to Darwinian principles.VI.03


Darwin's acolytes, such as Ernst Haeckel, tried to argue at first that life was, at root, simple. But the more the question was studied, the more complex life appeared to be, leading by the early 1900s to Henderson's comment above: it is so complex that scientists do not "really look forward to its scientific explanation."

As time passed from that remark in the early 1900s to the present time, things have just become more and more complex, with a seismic event in mid-century as the details of its digital basis in DNA came to light. Today, many scientists acknowledge that the phenomenon of life is exceedingly improbable, quite possibly unique on earth in the entire universe. Even the most polemical atheists acknowledge this—their only sense of self-correctness maintained by claiming that the "probability of God" is even smaller ("so's yours!").

So here are the facts, gleaned from the multiple lines of evidence that the natural world offers.

When did life first appear on earth? The answer is startling: evidence of life appears almost as soon as conditions allow it to occur. Basically this means as soon as the earth had cooled from a molten state, and a (hot) global ocean had formed. Ancient rocks on Akilia Island just off GreenlandVI.04, dated to 3.8 billion years ago show traces of organic carbon [a carbon isotope mix that is characteristic of life]. The "biological carbon" is the result of carbon fixing by the RuBisCO molecule that is part of the sugar-making process of photosynthesis VI.05. RuBisCO is the only known natural catalyst for converting CO2 to make biologically useful carbon. It preferrentially fixes carbon-12 which results in a slightly higher ratio of 12C to 13C, the two stable forms of Carbon.

Recently (2017) some actual carbon fossils have been discovered in this same vicinityVI.06.


Bacterial Life. The first life was bacterial. The creation of this life required the invention of many special molecules, procedures and even molecular machines, all defined and controlled by the Central Dogma, which is essentially the same for all forms of life.

The first bacterial life had the daunting task of scrabbling an existence from an inhospitable and inorganic earth. Its primary task was to prepare the earth for more advanced forms of life by preparing food in the form of organic wastes, including particularly fixed nitrogenVI.08 and carbon. This task literally took billions of years to distribute organic food worldwide and thus prepare the earth for ...

Eukaryotic Life. Eukaryotes are characterized by the existence of a nucleus in each cell. But that is only the most obvious feature. Eukaryotes are so much more complex than bacterial life (itself vastly complex) that it might be viewed as a further creation of life. Eukaryotes have many specialized organelles which amount to factories which produce many special components of advanced life. All visible plants and animals, both single-celled and multicellular, are eukaryotes.

Eukaryotes cannot make all of their own food—they require this food to be already prepared in advance. In particular eukaryotes cannot make the fixed nitrogen needed in abundance by every living cell. This is why eukaryotes appear billions of years after their bacterial predecessors.

Most (all?) eukaryotes respire oxygen, which must be available in the earth's atmosphere. The presence of atmospheric oxygen on a planet is thus a marker of advanced life. To my knowledge only the earth shows such a presence among all the planets discovered in the universe. [check this]




===

VI.01 [*fn]VI.01 Notes for VI.01

[*fn]VI.02 Ernst Heinrich Philipp August Haeckel (February 16, 1834 – August 9, 1919), The History of Creation (1876): Vol. I, On the Protoplasm Theory, p.99ff. "protoplasm [= German urschleim, the original slime] is the most essential (and sometimes the only) constituent part of the genuine cell." [p406] "the general explanation of life is now no more difficult to us than the explanation of the physical properties of inorganic bodies." Further investigation showed much greater complexity than appeared at first. See George Goodale, "Protoplasm and its History", Science XIV no. 385 (November 22, 1889) (note the date) who remarked: "instead of regarding the protoplasmic basis as comparatively simple, it is now known to be exceedingly complex [my emphasis] ... [R]esults compel us to recognize in protoplasm a substance of bewildering complexity of composition and constitution... Instead of believing, as formerly, that all the granules within the cell arise de novo from the protoplasm in which they are embedded, we are now forced to regard all of them as springing from pre-existent bodies of the same character."  The true nature of this vast complexity, and details of the genetic code and processes were not known until almost a century later, when, in the 1960s, an outline of the Central Dogma first revealed its vast complexity. Since that time, the perception of complexity has increased manyfold.

[*fn]VI.03 Charles Darwin, letter (1863)
"It is mere rubbish thinking at present of the origin of life; one might as well think of the origin of matter." Quoted in John Theodore Merz (1840 - 21 March 1922), A History of European Thought in the Nineteenth Century, II, p406, n1.]

 [*fn]VI.04Mojzsis, et al. in 1996 reported their find of ancient rock from the Akilia Island off S. Greenland, which showed evidence of organic carbon. See Mojzsis, et. al., "Evidence for life on Earth before 3,800 million years ago", Nature 384:55-59 (07 November 1996): "The carbon in the carbonaceous inclusions is isotopically light, indicative of biological activity; no known abiotic process can explain the data." This claim has been fortified in a later re-visit to the region in 2006, reported in Science News, "Scientists Strengthen Case for Life on Earth More Than 3.8 Billion years Ago", 06 July 2006, which states: "Scientists look for evidence of life in ancient rocks like those from Akilia Island by searching for chemical suggestions and isotopic evidence. ... The light carbon, 12C, is more than 3 percent more abundant than scientists would expect to find if life were not present, and 3 percent is very significant, Harrison said. ... While critics noted there are ways to make light carbon in the absence of life, Harrison considers those possibilities to be 'extremely unlikely,' especially in light of another discovery of rocks in Western Greenland, not far away, of the same age, and a similar ratio of 12C to 13C."


[*fn]VI.05
RuBisCO molecule

[*fn]VI.06
Science Magazine, March 1, 2017, 3.77-billion-year-old fossils stake new claim to oldest evidence of life—alleged actual fossils (not just organic carbon) from Greenland's Isua Greenstone Belt. Until this finding is verified, I will accept the dating of the earliest actual fossils as reported in J. William Schopf, Cradle of Life (1999). He dated cyanobacteria-like fossils in the Apex chert of Western Australia to 3,465 ± 5 Million years ago. This accuracy is possible because the fossils are sandwiched between lava flows that contained zircon crystals capable of precise dating. See figure 3.9 (p.89) in Schopf's book.



[*fn]VI.07 See my website Psalm19.org for an extensive discussion of the silent speech embedded in nature.

[*fn]VI.08 Some forms of fixed nitrogen are "inorganic" but that is an accident of nomenclature. It is generally thought that saltpeter and other "inorganic" nitrogen salts were byproducts of biologic nitrogen-fixing. See See David W. Wolfe, Tales from the Underground (2001) and G. J. Leigh, The World's Greatest Fix (2004).

VI.09 [*fn]VI.09 Note for VI.09

VI.10 [*fn]VI.10 Note for VI.10


===

VII.
Creation of Dry Land
Creation Day Three

 
9 And God said, Let the waters under the heaven be gathered together unto one place,  and let the dry land appear: and it was so. 10 And God called the dry land Earth;  and the gathering together of the waters called he Seas:  and God saw that it was good.

As a scientist, these words stand out from the Genesis account with a clarity (perhaps perplexing clarity!VII.01a) and profundity that is second only to the creation of light in Day One. The mental image is exactly right: out of water, dry land  arose.VII.01 And again, as with Day One, the accuracy of these words was only understood by geological scientists within the past century, when the concept of tectonic plate movement was accepted as true based on overwhelming evidence, after many years of sometimes disparaging opposition to the lone scientist who first suggested it.VII.02  It even appears to be true that the present continents began in "one place"VII.03(called Pangaea) although that may be reading too much into a short statement.

The setting at the start of Day Three is this—both CNS and CNB agree. The primordial earth was covered in a global ocean, with no permanent land to break the ocean surface. A smooth crust had recently (in geological terms) formed on the hot, molten earth. There was a gaseous atmosphere, mostly nitrogen (as today), with a lot of water vapor, some carbon dioxide, but almost no oxygenVII.04.  As the earth slowly cooled over millions of years, the water vapor precipitated out of the atmosphere and formed a global ocean that covered the smooth crust to a depth of over 1000 feet.

I say "smooth": the nearby orbiting moon constantly wrenched the Earth's thin crust with strong tidal forces, daily distorting its shape. Ocean tides were sometimes hundreds of feet high -- tidal forces a hundred times more powerful than is experienced today.VII.05  Violent volcanic activity accompanied the wrenching of the crust. Volcanic cones frequently broke the ocean surface, but the exposed cones quickly washed back into the sea because of the monstrous tides, mocking the "dry land" that had briefly been exposed.

Nonetheless, over time regions of focused volcanic activity resulted in a slight distortion of the smooth crust, and led to extensive tidal shallows, formed from the washed debris of the volcanoes. Here is where the first life began, as described above.

Still, there was no permanent dry land. Over time, massive, slowly moving currents developed in the mantle -- the viscous rock below the crust.VII.06These currents dragged the crust, which broke into a number of large plates. The plates collided or separated under the tug of the mantle currents. Lines of volcanic activity today  trace out these plate boundaries.VII.09 At the collision points, one plate thrusts under the other, and melts as it plunges into the molten upper mantle. The lighter molten material crystallizesVII.10, forming granites. This process forms permanent dry land because the granites that form the base of the continents float over the denser magma that forms the ocean floors and upper portion of the mantle.

The process of continent formation has always been very slow, and it continues today. When the "greening of the land" commenced, dry land had been forming for over 3 billion years.VII.11






===

FOOTNOTES VII. FOLLOW

[*fn]VII.01a The mental picture seemed all too clear to the theologians, and it seemed to contradict what was thought to be known about how nature works.
St. Augustine (about 315 AD) remarked,
"Now, where were the waters gathered if they had originally covered the whole earth? When some were pulled back to lay bare the land, to what region were they brought? If there was some bare portion of the earth where they could be gathered, dry land already was in evidence, and the waters were not occupying the whole. But if they had covered the whole, what place was there in which they might be gathered so that dry land might appear?" St. Augustine Ad Lit. I.12.26 (415 AD); H.D.M. Spence-Jones,  The Pulpit Commentary (1890) (a popular protestant commentary) on Gen. 1:9 "The retirement of the waters from its surface, is to reverse the ordinary processes of nature"; C.F. Keil and F. Delitzsch, Biblical commentary on the Old Testament (1869) on Gen. 1:9: "But of this we have no physical explanations... By the divine act of naming the two constituents of the globe [that is, the land and the waters], and the divine approval which follows, this work is stamped with permanency." The sense of the commentators is perplexment upon perplexment. And believe me, the theologians felt it! The correct solution, that is, the rising of the land above the ocean surface was apparently too preposterous to be contemplated, and yet that is exactly the correct solution, which scientists generally accepted only in the 1950s.

[*fn]VII.01 Obviously "dry land" does not mean "arid", but that it is not underwater and is designed to stay that way.

[*fn]VII.02 Alfred Lothar Wegener (November 1, 1880—November 1930) first proposed continental drift in 1912. See the remarks from paleos.org.

[*fn]VII.03 The modern continents began as a super-continent called Pangaea. See the Wikipedia articles on plate tectonics and Continental drift.

[*fn]VII.04 An oxygen environment is a strong indication of life's presence, which is, of course, absent on the newly-formed early earth. The universe is strongly reducing [= has excess hydrogen] and so any extra-terrestrial planets can be expected to have reducing (oxygen-free) atmospheres—unless, of course, life is present. From the viewpoint of chemistry, oxygen likes to combine with hydrogen to form water, and with many other elements, to form oxides—particularly at the high temperatures of the early earth. So, free oxygen is "unnatural" and would not remain long in the earth's atmosphere, except that it is constantly renewed by plant life. The Mars Rover searched without success for methane as a marker of life (although a marker if life is present, methane could be formed by non-biological processes, as on Titan, a moon of Saturn). See "NASA Curiosity Rover Detects No Methane on Mars", Science News, 22 September 2013.

[*fn]VII.05 The assertion that life began as "extremophiles" who lived deep in the ocean is, in my view, implausible. For one thing, the genetic makeup of these extremophiles is more advanced than that of "ordinary" surface life, which indicates to me that it is a later development, derived from surface life. I am confident that in time, genetic (cladistic?) studies will confirm this. On the other hand, the first life (see the previous chapter) lived in very warm waters—perhaps near the temperature at which milk is pasteurized.

[*fn]VII.06 There is no consensus among scientists as to when, how and why these currents formed. There are a number of plausible ways that this might happen, but the precise details are not yet agreed upon. Certainly heat convection—the movement caused by cooling—was involved, and the tug of the moon following the tidal distortions, would nudge the currents to take an easterly or westerly orientation.

VII.07  [*fn]VII.07 Note for VII.07

VII.08  [*fn]VII.08 Note for VII.08

[*fn]VII.09 The volcanic lines that mark these crust boundaries were well-known in the 19th century, but the interpretation was not known. See Sir Charles Lyell, Principles of Geology (8th Ed. 1850), Chapter 33 and Plates VI: Map of Volcanic Band in SouthEast Asia, a plate produced in 1832. The mountain ranges worldwide also trace out the upthrust effects of the boundary collisions.

 [*fn]VII.10 This process is called fractionation or fractional crystallization, also magma differentiation or Igneous differentiation. In essence a mixture of molten minerals (the magma) crystalizes with like materials forming crystals (the granites) that have a density lower than the original molten mixture.


 [*fn]VII.11 Tectonic maps over geologic time are available at number locations. See Christopher R. Scotese, The Paleomap Project, in particular the Pangea Animation (200 Mya to present). Other animations: see   Earth Through Time (290 Ma to Present), Paleogeographic Maps, and  Mollewide Plate Tectonic Maps. See also the Paleogeographic Atlas Project of the University of Chicago, and the palaeos.com maps. The fact that scientists can form these maps of the distant past is a remarkable example of how God has invested his Creation with a silent speech that proclaims his glory and handiwork. These maps result from a close analysis of fossil formations worldwide and correlation of index fossils which identify and date particular geologic periods. One such marker is the minute conodonts which were the "teeth" of early chordates that lived between the Cambrian and Triassic periods (520-200 million years ago) and are extensively studied in petroleum exploration.

===

VIII.
Plant Food for Life on Land: The Greening of the Land
Creation Day Three


11 And God said, Let the earth bring forth grass, the herb yielding seed, and the fruit tree yielding fruit after his kind, whose seed is in itself, upon the earth: and it was so.

This is the first mention of life in the Genesis account and celebrates the creation of land plants. After forming dry land, the next step is to fill it with food. This is appropriately called the "greening of the land". Three words in this verse imply greening. One might (loosely) translate the Hebrew to read "Let the earth green (dasha) green (deshe) greens (eseb)." 

The "greening" is essential for the advanced plants and animals, because the more complex life becomes the more it depends on pre-packaged nourishment. It simply can't take the time or energy to prepare its own food in addition to all of its other tasks. Plants (but not animals) can fix carbon using sunlight, but neither plants nor animals can fix nitrogen. Every advanced species needs millions of fixed carbon and nitrogen atoms. As we saw earlier, fixing is a very slow process.  So the task of this part of Day Three is to fill the dry land with food.

The Earth's fossil record beautifully complements this brief account in Genesis with an extensive description of how this greening of the land was doneVIII.01, a story whose full details are by no means yet known; it will continue to reveal fascinating insights for many years to come.

The particular plants mentioned in these verses come at the end of a long process. They are the flowering seed plants that are the staples of agricultural life: grasses, grains and fruits. Without them, civilization could not exist.

Before the greening of the land could occur, two things had to happen:

•     The dry land had to have organic nutrients in place before plants could grow (particularly fixed carbon and nitrogen). This meant that the movement into the continental interior progressed slowly as the biomass accumulated; and

•     Harsh cosmic rays had to be filtered so that plants could survive. This was accomplished by the Ozone shield which began to form after the atmospheric oxygen content stabilized at about 25%. It took over a billion years from this point for the shield to reach adequate levels.VIII.02

The fossil record shows this advance of plant growth onto land.VIII.03  It reveals a long progression of plant growth on land, from pithy plants that lived along shorelines, in marshes and swamps to the movement inland to higher elevations, first forests of pine-like species and finally the broadleafed plants and trees (the flowering plants).

•     Devonian Age (410-360 Ma = Million years ago)—low plants, mostly fern-like at the start to tall jungle-like pith-centered trees (lycopods).
•     Carboniferous Age (360-295 Ma)—Continued growth of jungle-like pith-centered trees in marshes and low areas; early pine-like gymnosperms in higher elevations. Major coal formations come from this age.

•     Permian, Triassic, Jurassic (295-135 Ma)—woody trunked gymnosperms (conifers) generally take over from pithy trunks. Ancestors of many present-day conifer families. Source of oil and gas.
•     Cretaceous Age (136-65 Ma)—Angiosperms (the flowering seed plants) take over from gymnosperms. Explosion of angiosperms about 115 Ma. Source of oil and gas.
•     Cenozoic Age (65 Ma to Present)—Diversification of angiosperms; Grasses (Family Poaceae—monocots) "the most important of all plant families to human economies" (Wikipedia). The "greening" of Day Three.

The early geologists often noted that a major task of the earlier ages was to prepare the great deposits of ores and fuels without which the industrial revolution could never have occurred.VIII.04  The recent fracking revolution retrieves gas and oil from the Cambrian age and onward.VIII.05

The geological fossil record preserves a marvelous and detailed record of how this greening of the land began.  The record begins with a cameo showing land plants in 3-dimensional microscopic detail. This is the Rhynie ChertVIII.06which has marvelously preserved fossils of small land plants from the early Devonian age (about 410 Ma), in 3-dimensional "forests", placed in their natural growth positions and showing soft-body parts in exquisite microscopic detail, preserving all stages of growth.

Rhynie Chert
Rhynie Chert (ca. 410 Ma)
Early Land Plants
University of Münster
Palaeobotanical  Research Group

The preservation in the Rhynie Chert is so detailed and complete that it is as if the plants had been photographed in three-dimensional form, in an instant of time, including "live" action shots such as the ejection of sperm cells from sporangia. The preservation includes all growth stages of these vascular plants, and so are ideal for a deep scientific understanding of these, the first plants to migrate to land.

Seed after his kind. The final creative act mentioned in Day Three is the creation of seeds that reproduce "after his kind". This opens up a new dimension in the creation narrative, and new possibilities for misinterpretation of what the Genesis account actually says.

The phrase is a celebration rather than a command. The emphasis is on "kind" as a celebration of the fact that living species can reproduce new living species like themselves. The emphasis is not on the restriction of the amount of variation.VIII.07  It is a celebration of the ability of a radish to pass on its own blueprint (DNA) so that its "seed" will produce similar offspring. The seed of a radish is the start of another radish, not a cabbage (though the seeds in fact look very much alike!).VIII.08   The phrase is not a command that puts the Bible in a position that rules out evolution. It is a celebration of a marvelous provision in God's creation of all "kinds" of plants and animals—that they pass on their blueprints. In fact, sexual reproduction exists precisely so that offspring can vary from the parents—they are not exact clones. The wonder is not just that God created life and created living plants to populate the land and provide food for future plants and animals, but that he created them able to make spore and seeds—that look nothing like the parents—but which reproduce multiple living copies of the parents, to "fill the land".

Early geologists misread the fossil evidence to conclude that the creation of animals preceded plants.VIII.09  That is not strictly true: vast mats of algae, kelp and other water plants existed far longer than animals. The earliest plants show their presence in microscopic pollen, spores and seeds, the science of Palynology —literally, the "study of dust". Spores and pollen appear from the early Ordovician (ca. 500 Ma). The following figure shows spores from the Ordovician/Silurian boundary (430 Ma),

early plantlife and spores
Early Spores (Ordovician - 435 Ma)VIII.11  Cambrian Green Algae (Chengjiang formatiom)VIII.12

probably released by floating beds of algae and blown over land. These are very small—about the size of an average bacterium (20 µm). Through Palynology, the geological record shows another interesting fact: that sexual reproduction among plants was in place was already in place long before the greening of the land. This is demonstrated by the characteristic "trilete" shape of the spores in the figure. The trilete marks show the join point of four cells produced by plant sexual reproduction. 



FOOTNOTES VIII

[*fn]VIII.01 See  Body Plans: Beginnings of the Eukaryotic Phyla, which lists the major plant and animal phyla and classes, and indicates the earliest appearances in the fossil record.

[*fn]VIII.02 Bacteria were the first colonizers of land, and came long before the first land plants. These early pioneers were able to survive  under harsh cosmic rays because of their high reproduction rates, and because the damaged bacteria could both shield survivors and provide nutrients for them (particularly fixed nitrogen). The first plant colonizers lived in swamps and marshes and the water provided some shielding. Plants gradually advanced into the interiors away from wet areas over many millions of years.

[*fn]VIII.03  See the Wikipedia article,  Timeline of Plant Evolution.

[*fn]VIII.04 See, for example, William Buckland, Geology and Mineralogy Considered with Reference to Natural Theology, (1837) Chapter XIX "Proofs of Design in the Dispositions of Strata  of the Carboniferous Order", "... an ulterior prospective view to the future uses of Man, formed Part of the design, with which they were, ages ago, disposed in a manner so admirably adapted to the benefit of the Human Race."

[*fn]VIII.05 Examples of gas formations and the corresponding geological ages are: Conesauga Shale (Alabama)—Cambrian (~520 Ma); Utica Shale (Pennsylvania, Ohio, New York and Quebec): Mid-Ordovician (~460 Ma); Marcellus and Antrim Shale (PA, OH, NY, MI, WV, KY, TN): Devonian (400-360 Ma); Barnett and Fayetteville Shale (TX, MS): Mississippian (Upper Carbonaceous) (~325-360 Ma).

At one time, some scientists thought that petroleum might be generated inorganically, refered to as Abiogenic petroleum. After study, scientists generally rejected this hypothesis. Wikipedia states:

The two principal abiogenic petroleum hypotheses, the deep gas hypothesis of Thomas Gold and the deep abiotic petroleum hypothesis, have been scientifically reviewed without confirmation. Scientific opinion on the origin of oil and gas is that all natural oil and gas deposits on Earth are fossil fuels and are, therefore, biogenic. Abiogenesis of small quantities of oil and gas remains a minor area of ongoing research.

The scientific concensus, however, is that essentially all petroleum and natural gas deposits derive from organic sources, confirming the label "fossil fuels."

[*fn]VIII.06 Discovered by William Mackie while mapping the western margin of the Rhynie basin near Aberdeen, Scotland, in 1910–1913. See the University of Münster website The Rhynie Chert and its Flora.


[*fn]VIII.07 The limits of variation is an important question, but that is not the point of creation "after his kind". Early geologists were very interested in this because of the broad, but definitely limited, range of variation that they observed in the fossil record. Major changes appear suddenly, but then this is followed by a long record of variation within the major changes. See {EDIT: ADD THIS OR LINK TO?] Appendix 4, "Magnates Walk First". In current terminology, variation within limits is called microevolution, and is distinguished from macroevolution which assumes random changes that pass over these limits. In my view secular evolutionists have generally avoided deep investigation into the limits of variation, and tend to mix microevolution and macroevolution to "prove" the "fact" of evolution.

[*fn]VIII.08 "according to his kind"—Hebrew le-min. Some scholars claim that this phrase refers to the fixity of species (however defined). Against this, R. Laird Harris, et. al. eds., The Theological Wordbook of the Old Testament (1980), states on "min Kind" (p.503), "Some have argued that when God created min, he thereby fixed the 'species.' This is a gratuitous assumption because a link between the word min with the biologist's descriptive term species cannot be substantiated, and because there are as many definitions of species as there are bioilogists." [I agree]. He goes on, however to assert that "God created the basic forms of life called min which can be classified according to modern biologists and zoologists as sometimes family or order." In my view this is an unsupported assertion. It implies that this statement in the creation account argues against evolutionary change to produce new species. As I understand it, "after his kind" is not about fixity of species (or any particular classification), but about the phenomenal fact that living species are able to pass their genetic signature to their offspring and thus continue the race (of plant or animal). This is a miracle of creative fiat, and is the point of these verses, which say little or nothing about fixity of species as such. All offspring are slight variations of their parents: indeed that is the point of sexual mating, which combines the slightly different dna of the parents to form an offspring that is not an exact image of either parent. That ability to change helps to preserve the species. The issue of how much change is possible is a separate (and very interesting) matter, but which is not covered by the reproduction "after his kind". Michael J. Behe, The Edge of Evolution: The Search for the Limits of Darwinism (2007) explores the issue of the limits of evolutionary change. I recall the remark of Thomas Henry Huxley (4 May 1825—29 June 1895) Darwiniana (1893), Ch. II "The Origin of Species" (written in 1860): "Of all the perennial miracles [Nature] offers, ... perhaps the most worthy of admiration is the development of a plant or of an animal from its embryo."

[*fn]VIII.09 The easily visible geological record gives this impression: sea animals appear in the Cambrian (530 Ma) whereas the strata showing land plants are much higher in the geological column (beginning in the late Permian, around 300 Ma). Microscopic examination (Palynology) corrects this misconception.

VIII.10 [*fn]VIII.10 A product of plant meiosis. See Wikipedia articles on Meiosis, Spore tetrads and trilete spores.

[*fn]VIII.11 From Alain Le Hérissé, Late Ordovician-earliest Silurian Palynomorphs from Northern Chad ... (2013). This article contains many other beautiful photographs and Electron micrographs of "miscellaneous organic debris" from the Ordovician/Silurian boundary. For somewhat later examples, see Adnan M. Hassan Kermandji, Late Silurian-Middle-Devonian Miospores (2012).


[*fn]VIII.12 Xian-guang Hou, et al. The Cambrian Fossils of ChengJiang, China: The Flowering of Early Animal Life (2008) shows several illustrations of Cambrian algae.


fractal.gif

IX. The First Science: Astronomy
Timepieces in the Heavens
Creation Day Four



14 And God said, Let there be lights in the firmament of the heaven to divide the day from the night; and let them be for signs, and for seasons, and for days, and years:

The first three days in the Genesis account prepared a physical habitat for life, and filled the land with food. Every step in this process was essential preparation for the animals that will be created in Days Five and Six.

Day Four is different. It is the first day that gives reasons for what has been created. On earlier days, God said what He did was good, but no reason for its being good is mentioned. Things were just done, that's all, without a rationale for doing them.

Day Four concerns the astounding and breath-taking display of the clear night sky. Its glorious majesty is dimmed in most populated areas today by light pollution and so its reminder of the immediacy and looming presence of God's glory is under-appreciated.

The lights divide day from night and give light on the earth. They also are "for signs" and tick off the passage of time: the seasons, days and years.

connections

Names

There are few specific names used in Genesis 1. In Day Four, the Sun and Moon are not named, but rather just the general "greater" and "lesser" lights.  It seems clear that this is no accident, but why?

In the Genesis account the act of naming things has special significance and implies authority of the name-giver. So God named Day and Night, the Heavens and the Firmament; later in the account Adam named Eve and the animals.

But in the case of the Sun and Moon, the normal names are not used. My guess is that the then-contemporary names for the Sun, the Moon, the stars, and the various "signs" were either themselves the names of gods, or closely tied to pagan deities
IX.01, and the Genesis account pointedly did not want to grant implied naming authority to these so-called "gods".IX.02

In the Bible as a whole—but not in the Creation account—names that come from the names of pagan gods are often used, such as the names of the months in the Hebrew calendar. Indeed even today, the names of the weekdays and some months derive directly from the names of pagan gods. But in the creation account, the writer avoided any such wording.


connections

Was the Sun Created in Day Four?

The statement "God made..." in these verses does not say anything about when they were made; in particular it doesn't imply that they were not already in existence—as of course we know they must have been in order for the earth, plants, and other things mentioned in the previous days.

The Hebrew language does not have verb tenses: present, past, future, etc. as most modern languages have. Hebrew verbs designate continuing action or completed action, and leave the context to indicate the time of the action. Thus we can assume—because its the only thing that makes sense in the context—that "God made" means "God had made", meaning that the heavenly bodies were already made prior to the tasks of Day Four. And the ancient Hebrew audience would have taken that for granted, without requiring any remark to that effect. The context makes that clear: the Sun, etc. did not show up for the first time on Day Four.
IX.03



connections

Signs in the Heavens: Writing in the Sky?
When were the Constellations named?


Let there be lights in the firmament of the heaven ... and let them be for signs, and for seasons, and for days, and years:

What is meant by the heavenly "signs"? Walter Maunder's book The Astronomy of the Bible is a comprehensive discussion of the Biblical references to the constellations and argues that the constellation "signs" record events in pre-history, before the invention of writing (see Chapter II "Genesis and the Constellations").

The constellations of the Zodiac follow the Sun's path in the night sky. Over the course of a year the Sun travels through the 12 signs of the Zodiac (See Astrological Age), remaining in the "house" of each Zodiac sign for about a month. The "head" of the Zodiac is the sign that pertains to the Spring Equinox (nominally March 21). Over thousands of years this "head" slowly changes, taking about 26,000 years to pass in turn through all of the Zodiacal signs. This is called the precession of the equinoxes. We are presently in the Age of Pisces and will transition to the Age of Aquarius in the next century or so.

Slide
The Constellations, Ecliptic and Zodiac Signs

When were these zodiac signs first recognized and named? Of course the time was long before the invention of writing, so there is no written record. Here we enter into a fascinating and rich subject that we don't fully know, because "sky writing" began long before recorded history, long before writing was invented. But much, much has been learned within the past century, and even as recently as the last decadeIX.04.

The paintings in Lascaux Cave clearly show the constellations including Orion's Belt, Taurus (the Hyades in the bull's head) and the Pleiades (See Figure 2). These paintings form a sky chart that can be dated to the Fall equinox about 17,700 BC based on comparision with the actual night sky projected using modern sky mapping software.
IX.05




The Lascaux cave was discovered by accident, in 1940 in Southern France during World War II. This shows just one section from the Hall of Bulls. The preservation of these paintings for the tens of thousand years and their first discovery in modern times is absolutely amazing and a definite mark of God's providence. The first of these were found in the late 1800s, and showed evidence of such advanced artistic skill that many of the scientists of the day thought that they were fakes. That phase is fortunately over and they are known to be genuine. But herein lies what I claim is a providential act, and this applies to all of the cave art discovered since that time. The art paintings are very fragile and decompose when exposed to air, human breath, sweat, humidity and the bugs that come along with the discovery. As a result, unless extraordinary efforts are made to protect the paintings, they flake off, fade away and basically vanish over time, measured in just decades, even though the paintings were preserved for many thousands of years prior to their discovery. 

Thus if these paintings had been discovered, say, 500 years ago instead of in modern times, they would be reduced to memories or folklore long before they could survive to modern times. They would be filed with the tales of Atlantis and other fantasy accounts. Who would believe the remarkable tales that they tell of long-ago human skill and achievement? This is an unavoidable bias—and weakness—of a skeptical scientific approach: yet who would countenance any other  approach?




FOOTNOTES IX. FOLLOW

IX.01 The Hebrew name for Sun is shemesh from an unused root meaning "brilliant". A Canaanite city west of Jerusalem (then "Jebus") at the time of Joshua's invasion of Palestine was named "Beth Shemesh", "the house of the Sun" and named for the sun-goddess Shemesh. Was the Sun named after the goddess or was the goddess named after the Sun? The name for the Moon is yareach or yerach, "wandering" or "paleness", from an unused root of unknown meaning. Some say it is the name of the moon god Yarikh and that "Jericho" is derived from this. The word for "star" (the only object mentioned by name) is kowkab "blazing", again from an unused root.   The word for Month is chodesh meaning "renewed". Did the names derive from these meanings, or from the names of gods?  The plain fact is the origins are unknown and of unknown significance.

On the other hand, outside of the creation account, the Bible generally used the contemporary Hebrew names for the months, which come from Abraham's homeland, Ur, a Sumerian city-state: Egypt and Sumer were the first civilizations in the region, possibly in the world. The names all appear to be names for gods—just as today the names for the weekdays and months derive from names of gods (Janus =  January, etc.) or Roman Caesars (who were officially declared to be gods after they died). So naming is complex, problematic and mixed with possible pagan associations—perhaps good reason for the Genesis creation account to steer clear of using specific names.

IX.02  Certainly it is unlikely that God would have named the Sun and Moon after pagan gods, and so perhaps it would be unseemly to say "God called the greater light Sun" etc. Many ancient cities were named after their patron gods which they apparently worshipped with fervor. So much so that the Assyrian empire collapsed suddenly when a total solar eclipse on May 18, 603 BC caused panic among the Assyrian defenders who apparently thought their Sun god had been destroyed. This is recorded in Xenophon's book Anabasis—the Greek Classic of Alexander's conquest of the Near East. See Maunder's description in Chapter 11 and the Appendix of E. Walter Maunder, The Astronomy of the Bible (Annotated) (1922). As a result of Xenophon's mention of this eclipse, many events in the Old Testament history that involve Assyria can be determined quite accurately because the timing of total solar eclipses can be computed quite accurately. See, for example, NASA's List of total solar eclipses which extends back to 2,000 BC.  It seems ironic that many Biblical critical "scholars" of the early 1800s viewed the Biblical accounts of Assyria as mythological fiction until the capital of Ninevah was discovered by archaeologists in the mid-1800s after having been lost to history for some 2,500 years.

IX.03  Some commentators go to a great length to "explain" this late appearance of the Sun and Moon in Day Four—such as that there was a cloud cover that obscured the Sun. This is un-necessary to make sense out of the narrative—and shows a lack of understanding of the use of language and the common sense of the ancient audience of the Genesis account. Now indeed there may have been cloud cover that obscured the Sun (that is an interesting question that science may be able to settle!), but such a consideration is not needed to make sense out of Day Four.

IX.04  I have in mind the Antikythera Mechanism, discovered in 1901. For many years this complex clock-like device (an analog computer—see its listing in the Timeline of (analog) Computing Hardware) puzzled the museum experts as to its meaning and significance. Clearly it was an elaborate mechanism of a complexity that was totally unknown to exist before the astronomical clockworks of 1500 AD or so. This mechanism was dated, based on the visible writing and circumstances of its discovery to around 150 BC. But still its use was a total mystery until it was examined with delicate x-ray tomography in 2006, when it was discovered that its main mechanism is for the purpose of predicting lunar and solar eclipses using mathematical formulations that had been developed by the Babylonians and were well-known to them as early as 800 BC. The amazing discovery not only confirmed those ancient formulations but also showed the amazing skill of these ancient scientists at designing the clockworks using a multitude of delicate toothed gears—including elliptical orbits for the Moon and the Sun (as viewed from Earth). See Jo Marchant, In Search of Lost Time, Nature (30 November 2006). She later expanded this into the fascinating book Decoding the Heavens (2009). "More than 100 years after Captain Kontos and his crew raised the Antikythera mechanism from its resting place at the bottom of the sea, the mysterious device had finally been decoded. Whoever turned the handle on the side of the wooden case became master of the cosmos, winding forwards or backwards to see everything about the sky at a chosen moment. Pointers on the front showed the changing positions of the Sun, Moon and planets in the zodiac, the date as well as the phase of the Moon, while spiral dials on the back showed the month and year according to a combined lunar-solar calendar, and the timing of eclipses. Inscribed text around the front dial revealed which star constellations were rising and setting at each moment, while the writing on the back gave details of the characteristics and location of the predicted eclipses. The mechanism's owner could zoom in on any nearby day—today, tomorrow, last Tuesday—or he could travel far across distant centuries." [Decoding the Heavens, p. 260.]

IX.05 See Lascaux.19thpsalm.org for further details. Around 17,000 BC the Sun would be in the house of Taurus during the Fall equinox (September 21).  The Lascaux painting corresponds to the time that Taurus falls below the horizon on its daily transit around the Fall Equinox.

IX.06 IX.06

IX.07 IX.07 Note for IX.07

IX.08 IX.08 Note for IX.08

IX.09 IX.09 Note for IX.09

IX.10 IX.10 Note for IX.10


X. Creation of Marine Animal Life
Creation Day Five

20 And God said, Let the waters bring forth abundantly the moving creature that hath life, and fowl that may fly above the earth in the open firmament of heaven. 21 And God created great whales, and every living creature that moveth, which the waters brought forth abundantly, after their kind, and every winged fowl after his kind: and God saw that it was good. 22 And God blessed them, saying, Be fruitful, and multiply, and fill the waters in the seas, and let fowl multiply in the earth. 23 And the evening and the morning were the fifth day.

Day Five is a major pivot in the creation narrative. In Day One through Day Four, the focus is on preparing the earth for animal life, which is then described in Days Five and Six. The signal for this pivot is  the word barà = to create (by God), the first creation day to use this special word for creation by God. On the earlier days God spoke and made—even on Day One, when he created the universe itselfX.05—but here he created using barà, a word only used of God's own actions. This word will only be used on one more occasion, in Day Six when Adam is created in God's image.

This is a curious fact. As a scientist, I look with awe at the creation of the universe with the light of Day One, I marvel at the creation of life itself—the first microscopic life with all of its vast digital complexity: the invention of the digital coding of life in the genes; the use of many motor molecules to copy the gene coding into working proteins; of complex processes to fix carbon (RuBisCo) and nitrogen (Nitrogenase)—one of the most difficult "fixing" tasks in all of the natural world.

In Day Three the first visible life appears—green plants—to prepare the land with food for the future plants and animals. Life itself, even the most "primitive" involves the invention of the many elaborate processes involved in photosynthesis that apparently appeared on earth together with the first living species—making the energy batteries (ATP and ADP) to store energy, inventing the sugar-making Krebs cycle to store energy in the form of sugars as food, creating specialized cells to fix nitrogen using the nitrogenase molecule—a very fussy process that is easily poisoned by the waste oxygen produced by photosynthesis.

But the creation of animals that have life—nephesh chayah, having life or breath—is celebrated with the word barà. It celebrates the sort of life that has soul—not the soul in the sense of Man's immortal soul, but animal soul: something that is capable of movement, feelings and emotions, a certain amount of free will (it seems), and the ability to make (limited?) decisionsX.01, in contrast to plants and bacteria, which, although alive, do not have any of thisX.02. This is a considerable step beyond just life itself, as miraculous as that is. Evidently it is such a step that it qualified for the special word barà.

The Day begins with another word that is repeated: the waters "bring forth abundantly"— sharatz, a verb, "moving creatures"—sheretz, a collective noun: literally, swarms of (small) swarming creatures. This thought is repeated in verse 21: "… creature that moveth"—ramas, to glide swiftly or swarm, in analogy to sharatz—"which the waters brought forth abundantly." It is interesting that the "great whales" and the (small) swarming creatures are mentioned as being created in the same sentence, the same breath so to speak: the point is not the size of the creature but its animal nature and vast complexity, regardless of size.

This suggests to me that the creation of animal life—the animal soul—involves a depth and complexity of creative activity that is not fully appreciated in science today—much like the incredible miracle of the creation of life itself was not appreciated by science a century ago (and by some, even today!). I expect that time—probably not in my lifetime—will unfold some of the special marvel of this creation, with new evidence of the Creator's divine handiwork.

The "fowl"—Hebrew òwph—include birds and flying insects. Flying insects such as locusts are also called "fowl"X.03. It makes sense to refer to such insects as creatures that the "waters brought forth abundantly" because the insect egg and larval stages are in water. In the fossil record, flying insects accompany the movement of plants to land. Birds do not come until much later (in Day Six). So at this point, I would understand the "fowl" to be flying insects. This is another case where the geological record beautifully supplements the Genesis account with vast amounts of additional information about the development of early animal life in water.

One thing that is evident in this account: animal life is first mentioned as living in a water environment, and this is exactly what one finds in the geological record.

The Cambrian Explosion. The geological record goes on with many great surprises. Perhaps the greatest surprise is the sudden appearance of animal life during the Cambrian period, with many of the Phyla (basic body plans) appearing within a short period of 10-20 million years.X.04 This is barely a blink of time from the perspective of geological timescales, hence the name "the Cambrian explosion". 

connections

Preparation for future life on Dry Land:
Eggs and the Amniotic Sac

The "fowl" that "waters brought forth abundantly" represent animals that require a watery environment for fertilization and nourishment the early growth stages. This includes most sea creatures and the reptiles which may live on land for part of their lives, but must begin (at least) in water or at an early stage of development. Reptiles typically live near shorelines.

Eggs are an advance because the egg includes a protected "watery" environment and some initial food. Many reptiles lay eggs (or hatch them internally). This is an advance because they may, in principle, live their entire lives on dry land. The eggs have a shell to prevent drying out. Among fishes, some breed in water (spawning fish) and some mate and develop the young internally, bearing them live. The coelacanth, one of the most ancient "fossil fish", gives us an example of live birth, at least the modern ones.

All mammals have an amniotic sac, which holds, feeds and protects the embryo during development. This completes the move away from dependence on a watery environment during embryo development—by providing each embryo with its own custom-made "watery environment."

The newly born of mammals often require help from adults until they reach the adult stage.





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FOOTNOTES TEMPLATE X FOLLOW


[*fn]X.01  The Scofield remarks (Genesis 1:24, note 2) that "In itself, nephesh, or soul, implies self-conscious life, as distinguished from plants." It's not clear to me what he means by "self-conscious". A distinguishing feature of humans is self-awareness: the ability to make rational assessments and decisions about one's own actions. For example, the long record of Neanderthal tools shows little apparent ability to "think about" the purpose of the tools with the aim at improving them—for hundreds of thousands of years there was little evidence of advancement in the skills of tool-making.

[*fn]X.02  Except in the embryonic or larval stage when they do have the ability to move. But this motility is only visible under a microscope.

[*fn]X.03 The word in Leviticus 11:20 refers to "fowls" that "creep on all four", and names locusts.

[*fn]X.04 See Body Plans: Beginnings of the Eukaryotic Phyla, which lists the major animal and plant phyla.  See also (in construction): Development of the Animal Classes and Development of the Plant Classes (in construction).

[*fn]X.05 Some Bible Commentators interpret the lack of the word barà to mean that Day One is not the original creation of the heavens and the earth. I disagree with this view, preferring to take the use of the word in the positive sense to point to an especially remarkable act of creation.

X.06 [*fn]X.06 Note for X.06

X.07 [*fn]X.07 Note for X.07

X.08 [*fn]X.08 Note for X.08

X.09 [*fn]X.09 Note for X.09

X.10 [*fn]X.10 Note for X.10

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XI. Creation Day Six
Animal Life on Land



And God said,  Let the earth bring forth the living creatureXI.01  after his kind, cattle and creeping things, and beast of the earth after his kind: and it was so. And God made [asah] the beast of the earth after his kind, and cattle after their kind, and every thing that creepeth upon the earth after his kind: and God saw that it was good.
Genesis 1:24-25

Day Six celebrates the creation of land animals, and finally of Man, the crowning event of the entire creation narrative. The words "God said" and "made" indicate that the creation of the land animals is a new phase of the work of creating animals begun on Day Five, rather than a new departure. The movement of animals to land (and birds in the air) had to wait until the Ozone layer was fully in place, which happened around 400 million years ago (Ma), at about the same time that plants began to "green" the land on Day Three. 

As with the plants in Day Three, and the sea creatures of Day Five, the animals mentioned are the most advanced land animalsXI.02 —from the highest, most developed body plan, the Craniata (or VertebrataXI.03). These are the animals that have a (greater or lesser) ability to think, emote, and other characteristics that are, I believe, implied by the statement that they are "living souls" (translated here "living creatures")XI.04.

Only general terms for the animals are mentioned and the terms used appear to refer to familiar categories of modern animals:

• The Behemah (the word is a transliteration of the Hebrew) appear to refer to grazing animals such as cattle and sheep—in the book of Job, the behemoth is probably the hippopotamus (a grazing animal).

• The Creeping Things (remesh) may refer to burrowing and ground animals, and

• The Beasts of the Earth (chayyath) may refer to wild animals -- carnivores?

The classes of vertebrate land animals are: amphibians (Class Amphibia)XI.05, reptiles (Class Reptilia)XI.06, mammals (Class Mammalia)XI.07, and birds (Class Aves)XI.08, and this is the order (lower strata to upper strata) in which the land animals first appear in the geological record. Of course, each of these classes involves a broad range of shapes and sizes.

Once again, the geological record fills in the narrative with an extensive description of how the creation of land animals proceededXI.09. The kinds of animals changed over the geological ages in parallel with the changes in the climate and available food. The process was gradual and deliberate.

The earliest land animals, the amphibians, lived near water—on shorelines, near streams and rivers, in lowland swamps and marshes. That is, of course, where the food was, because the plants of Day Three followed the same progression.

The major Classes of the phylum Craniata are:

Class Amphibia—Lungs and gills. Larval stage in water. four limbs. These were the first vertebrates to move to land. They inhabit shorelines of lakes, rivers, oceans. All have one stage of life in which they live in water. They first appeared in the mid-Devonian (about 380 Ma). They are often identified by tracks.

 Amphibius footprints
Carboniferous (325 Ma) Amphibian Tracks in MudXI.10
note the tail mark

Class Reptilia—(lungs; amniotic egg, internal fertilization. Lizards, dinosaurs). Mesosaur (280 Ma) is probably the earliest amniote. Recently a fossil dinosaur embryo was discovered, demonstrating that some of these dinosaurs gave live birthXI.11.  

 Mesosaur Embryo
Mesosaur Embryo
Lower Permian (280 Ma) - Uruguay
length of embryo about 1 cm.

Reptiles are able to live on dry land away from water for their entire life cycle. Some remarkable footprints of dinosaurs were found by the geologist Edward Hitchcock along the Connecticut River.XI.12

 

Jurassic (160 Ma) Dinosaur Tracks
Connecticut River


Class Aves—Wings; feathers, warm-blooded. Birds and mammals are warm-blooded. All other vertebrates are cold-blooded. The Archaeopteryx is the earliest fossil showing feathers. It may be a dinosaur or a bird (some dinosaurs appear to have feather-like plumage. Birds have a remarkable innovation: light-weight bones. XI.13

 
Jurassic-Dana-Archaeopteryx

Archaeopteryx
Late Jurassic (ca.  150 Ma)

Class Mammalia (mammary glands). Mammals are characterized by being warm-blooded, and possessing hair, three middle ear bones for balance and hearing, and mammary glands. Red blood cells (lacking a nucleus) and a 4-chambered heart are also characteristics. Many of the mammals most familiar to us first appear in the fossil record 50-25 Ma. The earliest to appear are the Marsupials (most of the development of the fetus occurs outside of the womb) followed by the Placentals (most of the development occurs in the womb).

[SHOW PIX OF MAMMALS??]

Mammals have dominated animal life since the K-T extinction event (66 Ma) which wiped out the dinosaurs and many other species, but left some small mammals.
 


 
FOOTNOTES TEMPLATE XI FOLLOW

[*fn]XI.01 
  Living Creature = nephesh chaya or "living souls" using the same terms as in Day Five. This terminology may be intended to single out the most advanced animals, excluding lesser animals—the general range of invertebrate land animals (worms, slugs, scorpions, etc.). Note that the word asah = made is used rather than barà. It is a continuation of the special creative activity established in Day Five.

[*fn]XI.02 
  As representatives of the land animals, not necessarily the first land animals (according to what are called animals in modern classication), a comment that applies equally to the types of plants in Day Three.
  
[*fn]XI.03
Body plans with a brain connected to a central spinal cord: the brain is enclosed in a skull that forms the head. The spine is also enclosed in a reticulated, bony or cartilaginous spinal column.

[*fn]XI.04 
  The word nephesh ( ) is most often translated "soul" in the King James, and is commonly used in reference to animals.


[*fn]XI.05
The amphibians have gills and lungs, external fertilization and a larval stage, both occurring in water. The earliest fossils are from the Mid-Devonian strata (ca. 380 Ma). Fossils are rare because they are largely soft-bodied. Salamanders are amphibians. Cold-blooded.

[*fn]XI.06
The reptiles have lungs, internal fertilization and an amniotic egg (that is the egg includes liquid nourishment). The amniotic egg allows them to live and reproduce on dry land away from water. Lizards and dinosaurs are reptiles. Fossil lizards appear in the mid-Carboniferous strata, about 340 Ma. Cold-blooded.

[*fn]XI.07
Mammals are named for their mammary glands. Some lay eggs but most have internal amniotic sacs and give live birth. They are warm-blooded, and have a 4-chambered heart with red blood cells. They have hair and inner ear bones for balancing and hearing. The oldest fossils appear in the Jurassic strata, around 160 Ma.

[*fn]XI.08
Birds have wings and feathers. Most (but not all) can fly. They have light-weight bones, and are warm-blooded. The earliest birds appear in the Jurassic strata (ca. 150 Ma).

[*fn]XI.09 
  See  Body Plans: Beginnings of the Eukaryotic Phyla, an illustrated list of the major plant and animal phyla and classes, with the earliest appearances in the fossil record.

There were two annhilation events that strongly impacted animal life on land. The first, called the Permian–Triassic (P–Tr) extinction event or the Great Dying, occurred at the end of the Permian age, 252.28 Ma.  In this event up to 96% of the marine species and 70% of land vertebrates went extinct [Wikipedia], as well as a mass extinction of insects. The second annhilation event is the Cretaceous–Paleogene extinction event (also called K-T extinction) at the end of the Cretaceous age, 66 Ma, perhaps best known as the time that the dinosaurs and all large mammals suddenly disappeared from the fossil record. An asteroid impact in the vicinity of the Yucatan Penninsula (Mexico) is generally accepted as the cause of this annhilation. About 75% of all species were wiped out. See the lectures of Glen Penfield that describe his discovery of this impact area: Part 1  Part 2.

[*fn]XI.10
See James Dana, Manual of Geology (1896) p. 684 for images of amphibian tracks from the late Carboniferous strata (~300 Ma).
  Ibid, p. 684.

[*fn]XI.11  Charles Choi, "Earliest Pregnant Reptile Pushes Back Fossil Record of Live Birth", LiveScience, (2012)

[*fn]XI.12  Edward Hitchcock, Description of the Footmarks of Birds on new Red Sandstone in Massachusetts (1835).

[*fn]XI.13 The Archaeopteryx is dated about 150 Ma (upper Jurassic) and is generally considered the earliest bird fossil. Image from James Dana, Manual of Geology (1896), p. 788. Solnhofen Quarry, Germany discovered in 1861.

XI.14 [*fn]XI.14 Note for XI.14


XI.15 [*fn]XI.15 Note for XI.15

XI.16 [*fn]XI.16 Note for XI.16

XI.17 [*fn]XI.17 Note for XI.17

XI.18 [*fn]XI.18 Note for XI.18

XI.19 [*fn]XI.19 Note for XI.19

 
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XII. Creation of Man
Creation Day Six



1:26 And God said, Let us make man in our image, after our likeness: and let them have dominion over the fish of the sea, and over the fowl of the air, and over the cattle, and over all the earth, and over every creeping thing that creepeth upon the earth. 27 So God created man in his own image, in the image of God created he him; male and female created he them.

2:7 And the Lord God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul.

2:22 And the rib, which the Lord God had taken from man, made he a woman, and brought her unto the man.


There are several notable things about the creation of humans. First, this is the third place that bará is used, and it is a threefold repetition, a common narrative device to emphasize the point that God performed this act and that the creation was in His image. This is a way to stress the unique importance of this particular act of creation: God gifted his human creation with part of Himself—His image. It is reasonable to conclude that this image is not material—not part of the DNA or of the regulatory apparatus that makes up the human species' unique signature. From a natural point of view, this is a separate aspect of the creation of man that is not made from some material thing.

Second, the creation of man is a two-step process (asah...barà in Genesis 1, and yatsar ...naphach in Genesis 2) that is unique for humans alone, from which one can reasonably conclude that forming the human body—the physical aspect—is specifically distinguished from forming the whole human with the additional investment of God's image (= the breath of life).

Third, the body begins with pre-existing matter: dust, in 2:7, and Adam's rib in 2:22. What was the "dust?" I take it that the "dust" was not just inorganic matter, but included organic matter from which God formed humans.  Perhaps this may provide some insight into how God created all plants and animals, using pre-existing matter—"dust"—to form novel kinds of plants and animals. That is certainly what the geological record would imply, including the record of hominids. The Bible doesn't assert or deny this, of course, but one might use the description of the creation of man to imply that He formed new species by a combination of harvesting previously existing genetic material (or its blueprints) with genetic innovations and natural evolutionary processes to adapt species to various environments . For this reason, the use of a similar gene package in widely separated species does not—for a creationist—necessarily imply a common ancestor, which is a common assumption of secular scientists.

The geological record gives a lot of additional information, and a lot of claims and counterclaims regarding how humans descended from other similar hominids. This is a complex subject, and is an area in which one must carefully avoid firm conclusions (while accepting the factual data) that take for granted that humans evolved from other animals by purely natural processes.

Humans are classified in the genus Homo. Since about 125 Ka there were only two members of this genus: Homo sapiens (also called AMH = anatomically modern human), and Homo neanderthalensis. A lot of information about the culture and intellectual capacity of these two lines can be learned from various artifacts that are associated with these lines.  The outstanding fact of interest to us is that somewhere around 50-40 Ka , Homo Sapiens shows a dramatic change in cultural attainment (Homo sapiens sapiens?), reflected in excellent and subtle artwork such as the Chauvet cave paintings, 32 Ka (first discovered December, 1994), and in the Lascaux Cave paintings, 17.3 Ka (constellations and a sky chart, discovered in 1943). This indicates that the creation of Adam was probably around this time.

At times Neanderthals may have lived near to humans. For example, two archaeological sites in Southern France, Lascaux Cave (AMH) and le Moustier (Neanderthal) are in the same river valley and separated by about 20 miles.

Map of le Moustier and Lascaux

le Moustier and Lascaux
from a map of Southern France Archaeological Sites.XII.01

Since the record of Neanderthals ends around 25 Ka, this leads to the question of whether humans and Neanderthals may have intermixed. The next section discusses this question.
  



FOOTNOTES XII FOLLOW

 
[*fn]XII.01 The full map is here from Don Hitchcock, Don's Maps: Southern France Archaeological Sites.

XII.02 [*fn]XII.02 Note for XII.02

XII.03 [*fn]XII.03 Note for XII.03

XII.04 [*fn]XII.04 Note for XII.04

XII.05 [*fn]XII.05 Note for XII.05

XII.06 [*fn]XII.06 Note for XII.06

XII.07 [*fn]XII.07 Note for XII.07

XII.08 [*fn]XII.08 Note for XII.08

XII.09 [*fn]XII.09 Note for XII.09


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POST-SCRIPT
XIII. "Giants in the Land"
Remarks on Humans and Neanderthals



There were giants (nephilim)XIII.01 in the earth in those days; and also after that,
when the sons of God came in unto the daughters of menXIII.02, and they bare children to them, the same became mighty men which were of old, men of renown.
Genesis 6:4



One reason to extend the Creation Narrative to include Genesis 6 and the Flood is that this is the final step in defining the human race: all humans, according to this account, are descendents of Noah through his sons Shem, Ham, and Japheth. It may reasonably be assumed that these men and their wives and families are all pure descendents of Adam through SethXIII.03, without any other blood lines entering into the genetic mix. The subject of this chapter seems to involve the introduction of a different blood line.XIII.04

What was that other line? Could the nephilim be Neanderthals? The issue is relevant because of the possibility that the geological record suggests that Neanderthals may have coexisted with Adam's descendents for a period of time until—according to the current evidence of paleoanthropology—Neanderthals disappear from the geological record about 25 KaXIII.05.

It is clear from the first verses of Genesis 6, that some sort of outside race, the "giants" or nephilim in vs. 4, intermarried with the Adamic line.XIII.06  Who were these nephilim? Nobody knows for sure, and speculations abound. I will contribute to this speculation and suggest that the nephilim are Neanderthals. This implies two things, which future archeoanthopology may confirm or refute: that Neanderthals and humans (AMH) mingled in some sense, and that "marriage" between these two races was both possible and resulted in fertile offspringXIII.07.

There are substantial differences between the Neanderthal and Human physical features. Perhaps the most evident is that the Neanderthals were stronger than humans -- the placement of the skeletal muscles was somewhat different and resulted in this greater strength.XIII.08  It would not be surprising that mixed marriages (if fertile) would result in "mighty men".

In addition, it seems pretty clear (see above map of le Moustier (Neanderthal) and Lascaux (Human) above) that neanderthals and humans may have mingled or at least co-habited the same regions and possibly overlapped in time. Lascaux Cave (definitely a human habitation and possibly dating from as early as 32 KaXIII.09), is about 10 miles from le Moustier, both sites overlooking the Vézère River in Southern France.

Adding to this, it has long been known that the words translated "sons of God" and "daughters of men" may have other meanings—in fact, almost the opposite! The "sons of God" are sons of elohim, a word that is sometimes used of judges, princes or (a race of?) mighty menXIII.10, and might (I suggest) refer to Neanderthals. The "daughters of men" is literally "daughters of adam" and may mean "daughters of Adam". This verse may thus describe the forcible abduction of human women by Neanderthal raiders, with offspring resulting.

Recent research has some remarkable and unexpected contributions to this question. In 1997, some actual mitochondrial DNA (mtDNA) was obtained from a 39 Ka Neanderthal shoulder bone, and subsequent analysis has concluded that Neanderthals are NOT ancestors to modern humansXIII.11. This was a conclusion hard-fought over the next decade, because many scientists assumed the opposite, namely, that humans must have either come from or intermixed with Neanderthals. The reason for the conclusion is that mtDNA is passed on by the mother, not the father, and the analysis of the Neanderthal DNA showed that it was about halfway between human and chimpanzee mtDNA, far too "distant" to be related to humans.

Genesis 6:4 (with the above understanding of "sons of God" and "daughters of men") states that human daughters mated with Neanderthal sons, resulting in "mighty men". Only the  daughters pass on mitochondria through the egg, so the mating would only pass on the human (female) mitochondrial dna.

But if such a hybrid race did appear, it is then quite clear why God may have judged that a universal flood was needed to rid the human race of the Neanderthal contamination. By restricting the survivors of the flood to humans who had not had Neanderthal ancestors, the Adamic race would be preserved. This would also give a rational reason for the restriction in marriage to descendents of the Adamic line.XIII.13

In conclusion, I suggest that Genesis 6 records the unfortunate cross-mating of these two homo species, but that the line from Adam leading to Noah had remained uncontaminated by Neanderthal DNA. Only the un-mixed line from Adam survived the flood, and so no modern humans have Neanderthal ancestry.

The only mention of the nephilim after the flood is probably an exaggeration in the fear-filled report of the spies sent to explore Canaan during the Exodus.

 



[*fn]XIII.01
The nephilim. The word appears in only one other place in the Bible (Numbers 13:33)—probably an exaggeration brought back to Joshua by fearful spies. In my view the nephilim were destroyed in the Flood.

[*fn]XIII.02  I suggest the translation should be: "when the sons of the mighty men [elohim ?= Neanderthals] came in unto the daughters of Adam (adam = man)" See Allan A. MacRae, Old Testament History (2016) p. 261ff—The Flood. He gives various optional interpretations. But regarding the option "Descendants of Seth marrying descendants of Cain" he remarks "We don't, I think, have anywhere in the Scriptures, as far as I know, a statement that all of Cain's sons are ungodly; I imagine that most of them were. Nor a statement that all of Seth's descendants were godly, though we know that some of them were; and we don't know of anywhere in the Scripture a command that these two lines should remain permanently separate from one another." (p. 263) In conclusion (p.264) Dr. MacRae states that "I don't see any evidence that it is true; that is all, that these are the descendants of Cain and the descendants of Seth. I don't know why they should be called sons of God and daughters of man. It is purely a conjecture; it may be a correct one, but I know of no reason to think that it is. It may mean something entirely different that we are not familiar with." ... such as, I suggest, the human race (in the image of God) mating with Neanderthals (not gifted with the image of God).

[*fn]XIII.03  The Biblical records of Jewish history are adamant regarding marriage, that it must be marriage "in the family"—within the Jewish race (or in the case of Genesis 6, restricted to descendents of Adam). Thus, I assert, the Adamic line through Noah (and his marriage partner) would be "pure" in the sense that all ancestors of Noah would have been sons of Adam, and probably also sons of Seth, although it is possible that some ancestors (through marriage) may have been descendents of Cain.

[*fn]XIII.04   Scofield notes on this verse, "The uniform Hebrew and Christian interpretation has been that verse 2 marks the breaking down of the separation between the godly line of Seth and the godless line of Cain." But were the descendents of Cain necessarily "godless"? See Allan A. MacRae, op. cit. Note XIII.02.

[*fn]XIII.05  One must realize, of course, that all dates from geological artifacts apply to those specific objects. The dates of various cultures—Neanderthal or Human—will usually extend both earlier and later than the dates of the specific objects, but that is all we have to go on. Thus ranges of dates of various humanoid cultures are always tentative. When we assert that Neanderthals vanished from the scene about 25 Ka, what that means is that the most recent artifacts associated with the Neanderthal cultures are from that date. The Neanderthals could have been around for some (necessarily indeterminate) time after that.

What identifies human culture is artifacts that show careful  planning, such as dressed (shaped) spear tips. Before humans, such tips appear to have been discovered by accident—by striking a rock to get chips that may or may not be suitable as spear tips. Dressed stones show evidence of deliberate design and planning, human traits. The Chauvet cave art (about 32,000 BC) shows very advanced and realistic figures, which indicated careful thought and planning in the execution, indicating human activity. The Lascaux cave art similarly shows advanced thinking, and is taken as the work of fully developed humans.

[*fn]XIII.06  It is not clear (based on present research) that such a mating would produce offspring.

[*fn]XIII.07 Unlike, for example, the mating of a horse and donkey to yield a sterile mule.

[*fn]XIII.08  Origins of Humankind (PBS) "Neanderthal bones are thick and heavy and show signs of powerful muscle attachments. Neanderthals most likely would have been extraordinarily strong by modern standards, and their skeletons show that they endured brutally hard lives." Schrenk & Müller, The Neanderthals (2008), p.57 "On the whole, Neanderthal bones were far more strongly built than those of modern humans ... Their shoulder area shows evidence of totally differen muscle starting surfaces than in people today." p. 58: "the multitude of differences ... make it plain that we are dealing with two different species, Homo sapiens and Homo neanderthalensis." See a comparison of Human and Neanderthal skeletal features from Don's Maps (Don Hitchcock).

[*fn]XIII. 09 This is the time that the first true humans are known from the geological record—two skulls at le Moustier date to about 40Ka, Chauvet cave is dated about 32Ka and Lascaux cave paintings date from about 19.3 Ka. The Lascaux paintings were painted over earlier paintings, "The oldest were probably painted around 30,000 BC, making them about 32000 years old."

[*fn]XIII.10 See, for example the use of "elohim" for "judge" in I Sam. 2:25, also Ps. 82:6, "I have said, ye are elohim."

[*fn]XIII.11  Richard E. Green, et al.,  Complete Neanderthal Mitochondrial Genome Sequence, Cell, June 21, 2008. See also Neanderthals Didn't Mate with Modern Humans, Study Says, National Geographic News, August 12, 2008. See also the Smithsonian web page on Neanderthal Mitochondrial DNA: "The Neanderthal mtDNA sequences were substantially different from modern human mtDNA." However mtDNA samples of Cro Magnon [the now-disused term for AMH—dcb] specimens dated 25-23,000 BP "were within the range of variation for modern human mtDNA sequences."

[*fn]XIII.12 whether the pure Adamic line is the "sons of God" or the "sons of Man" in v. 2 is of no consequence to this argument, but note that "man" is 'adam (אָדָם), so that "daughters of men" could be read as "daughters of Adam". Note also that the "sons of God" are sons of Elohim, which is a word that can also refer to "mighty men" or "men of renown", possibly referring to Neanderthals rather than to God. See, for example the use of "elohim" for "judge" in I Sam. 2:25, also Ps. 82:6, "I have said, ye are elohim."

[*fn]XIII.13   Some authors have questioned the implied "incest" among the immediate descendents of Adam and Eve. In my view this is a non-issue, because the original parents would have (it is presumed) genetic material that was not compromised by the damages of time. The practical prohibition against incest is because of the risk of amplifying the effects of such damage. That would not apply to the earliest generations after Adam.

XIII.14 [*fn]XIII.14 Note for XIII.14
   
XIII.15 [*fn]XIII.15 Note for XIII.15

XIII.16 [*fn]XIII.16 Note for XIII.16

XIII.17 [*fn]XIII.17 Note for XIII.17

XIII.18 [*fn]XIII.18 Note for XIII.18

XIII.19 [*fn]XIII.19 Note for XIII.19


 

 
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Miscellaneous Topics



These appendices add some remarks and further details about the creation narrative, particularly the creation of life itself.


connections

Evolution:
What is Natural Evolution?


With a suddenness which to many seemed catastrophic Darwin's hypothesis of natural selection changed the whole aspect of the problem.
Lawrence J. Henderson (1913)M.01


Evolution is the modification of an existing set of plans by natural processes. Secular evolution is  evolution from an empty set of plans (as a mathematician would say it)—or, if you prefer, from a set of plans that consists only of natural laws: no designs, blueprints or established protocol.M.02 Another equivalent expression for secular evolution is evolution by purely natural means.

Many modern day "evolutionists" are secular evolutionists, and atheists are necessarily secular evolutionists. Darwin was an evolutionist but not a secular evolutionist: he did not claim that life itself arose by purely natural means, calling such speculation "mere rubbish"M.03

The thrust of these Appendices is to point out that all evidence from the natural world points to the fact that science and nature and even the outlines of the development of life itself are exceedingly complex and intricately designed—which implies a Creator.M.04 This still leaves a lot of room for evolution: how much of the variation in the basic plans is the result of natural variation and adaptation; that is, represents evolution from the basic plans?M.05  That question, to me, is a fascinating area of research, and is the proper place for scientific nvestigation. No subject is off-limits—even the possibility of secular evolution is worthy of legitimate investigation. The sad fact, though, is that atheists cannot approach that investigation, or follow the empirical facts, with the same unbiased mind that entertaining the possibility of a Creator can. An open inquiry is ruled out.

Needless to say, I believe that the facts point irresistibly to a "set of plans", leaving only the fascinating question of how extensive those plans are—i.e. to what level the Creator altered the natural (undirected) course of events.M.06 As a Christian, I believe that "by Him all things consist"M.07 means that Christ has absolute control, but whether this is because of His "engineering skills" in making a perfect design that requires no meddling, or the opposite, I cannot say, and leave that as an exciting query for scientific investigation.





connections

Science and Falsifiability
This concerns the question: Is Evolution Falsifiable?


"In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality." Karl Popper (1934)M.11

"The criterion of the scientific status of a theory is its falsifiability, or refutability, or testability." Karl Popper (1963)M.12

This note is necessary because many atheists claim the mantle of science for themselves. By some accountingM.13, about half of all scientists are either atheists or agnostics (that is, they refuse to take a position), and a much higher percentage disbelieve in a personal GodM.14.

A scientific assertion is (potentially) falsifiable, or else it is a belief and not science. However, an atheist must demand that the "fact"M.15 of natural evolution is non-falsifiable, whatever concessions Karl Popper may have madeM.16. To an atheist, there is no alternative to natural evolution, since by definition no higher power is available.M.17

Furthermore, an atheist must extend the fact of natural evolution to include the creation of life itself by natural means, something that Darwin did not claim for his theory of natural selectionM.18. Because atheists have claimed to own science they have forced science itself into a non-falsifiable position—which is a contradiction. The atheist's need for natural evolution is non-falsifiableM.19, therefore it is not science.

A theist—one who believes in a God or gods, not necessarily a personal God—has no such constraint. Science, evolution, the beginnings of life all involve falsifiable concepts. The theist's belief in God is non-falsifiable (otherwise they would not be theists), but he does not have to extend that non-falsifiability to science, as does the atheist.


WORKING HERE 21 Jun

connections

Size Limits of Very Small Microorganisms:
This concerns the Minimum Size of the "simplest" life of any sort


A 1998 symposium held by the National Academy of SciencesM.20 asked the question: how small can a living cell be—any sort of life anywhere in the universe, not just life on earth? The approach used was to estimate the smallest possible number of genes needed to carry on the minimum cell activities, and then go on from that estimate to determine the smallest physical cell size that could package it.

The answer is: not simple at all; in fact the simplest conceivable life form is itself very complex—not just "life as we know it" but to any sort of "alien" life.

This is relevant to the very first living species on Earth, because it addresses the question of how "simple" can that life be? The issue that precipitated the symposium was the NASA claim to have found "Martian fossils". Presumably these "fossils" would represent life forms that could exist under conditions similar to the first living species on Earth.

Size of Existing Species on Earth. The following figure shows the genome and (number of DNA base pairsM.21) and physical size of the various living species.

Viruses are not capable of independent living (they depend on a host cell to provide metabolism) so the smallest size would be that of the smallest bacterium, which (at the time of the symposium) was Mycoplasma genitalium, a small bacterium of the urinary tract, with a DNA of about 580,000 base pairs encoding 520 genesM.22.  However genitalium is not capable of independent existence (as the first living species must) because it relies on food supplied by its environment. But the symposium concluded that this was close to the minimum possible size.


genome size

Still the question arises: how small could the DNA of a living species possibly be, and still be able to metabolize and reproduce? Perhaps all species today are much larger than the minimum size possible. The following table compares species according to physical size. Note the size of the Mars "fossils".

The consensus of the symposium was that "Free-living organisms require a minimum of 250 to 450 proteins along with the genes and ribosomes necessary for their synthesis. A sphere capable of holding this minimal molecular complement would be 250 to 300 nm in diameter." This is far larger than the alleged Martian fossils.

A statement of the minimum genome size varied among the participants. One participant suggested 320,000 bp coding for 256 proteins (p.43), but without asserting that this size could be free-living. A "cell that synthesizes all of its cellular material from CO2 requires... closer to 750 genes." For comparison the symposium estimated that the smallest actual modern autotrophM.23  has about 1500 genesM.24.  Using 1000 bp as the size of an average gene, the minimum genome size for an autotrophy must be at least 750,000 bp. Such a bacterium must include DNA coding to manufacture the nucleotides and amino acids, because these building-blocks of life do not occur naturally in significant amounts. Even this size assumes the availability of fixed nitrogen.

The conclusion has great implications about the basic complexity of the first living species. In short, it is so complex, that the likelihood of its arrival by undirected natural processes is vanishingly small.

The Essential Chemicals of Life.  Could some other radically different forms of life exist somewhere in the vast universe? Several prominent authors have asked this question.  The answer, in short, is "No!" All conceivable life must be based on liquid water, carbon chains, amino acids -- all of which are built up of the essential elements H, C, O, and N. Thus the conclusions of the symposium appear to apply to any living matter, anywhere in the universe.

Protein Inventory for E. Coli and M. genitalium

 
Functional Class of Genes
# of Genes 

E. coli
M. genitalium 
Regulation 178 7
Structure
237 17
Phages and other inserted elements
87 0
Transportation and binding 427 34
Energy Metabolism
243 31
DNA Replication, etc. 115 32
Transcription 55 12
Translation 191 101
Intermediary metabolism 658 37
Other cell processes 188 21
Other enzymes and identifiable genes 277 27
Unknown 1632 152
Total 4288 471







connections
The Magnates Walk FirstM.30
First appearances of new kinds of life


The more I examine the universe and the details of its architecture, the more evidence I find that the universe in some sense must have known we were coming.
Freeman Dyson (1979)M.31

We know, further, so far at least as we have yet succeeded in deciphering the record,—that the several dynasties were introduced, not in their lower, but in their higher forms; that, in short, in the imposing programme of creation it was arranged, as a general rule, that in each of the great divisions of the procession the magnates should walk first.
Hugh Miller (1850)M.32


Hugh Miller, one of the prominent early geologists, states that in the course of creation, the earliest members of a race are not the simplest but tend to be the most complex, the "magnates", with simplification and specialization, rather than its opposite, occurring with the passage of time. This is a theme that recurs many times throughout the creation narrative. Louis Agassiz, another prominent geologist of the mid-19th Century calls such evidence of pre-planning "prophetic types". Sir Charles Lyell made a similar remark (see below)M.33.  Another term for this is Reductive evolution, the concept that the ancestors of a given species are more complex than the descendents.

This phenomenon was widely regarded by some early geologists as plausible evidence for a divine Creator because of the lack of fossil precursors, and as a counterpoint to the apparent general rule of progressive development (which is also clear in the fossil record). Perhaps the classic example of this is the trilobite, an arthropod that appears in the early Cambrian strata suddenly and full-formed.
When Darwin's Origin of Species appeared in 1859, there was a wholesale movement towards the adoption of evolution by purely natural means. This meant, in effect, that the sudden appearance of novel classes was overlooked, "removed into a more distant and dimmer region" as Lydia Miller noted about 10 years later, in 1869.M.34  The facts still remained but were de-emphasized and in the end, ignored.

Given the complex ancestor, one may construct a plausible chain of evolutionary events to explain reductive evolution: the elimination  of superfluous features (such as the eyes of blind cave fish) or the elimination of redundant and overlapping genes. Such change towards simplification  may be understood to be plausible and reasonable; but this reasoning does not explain a complex ancestor that appears to have no precedent. The usual "explanation" is the incompleteness of the fossil record, or the lack of hard parts which can be fossilized.

The recent ability to conduct detailed genetic studies has led to the conclusion that even "the first eukaryote" appears to have been an example of this phenomenon—see below, The Eukaryotic Big Bang.

The following are direct quotes from early geologists regarding this feature of the fossil record.

Early Geologists on "The Magnates Walk First"


William Buckland, Geology and Mineralogy Considered with Reference to Natural Theology (2nd Edition, 1837)

p.294 [regarding fossil fish] "A kind of retrograde development, from complex to simple forms, may be said to have taken place. As some of the more early Fishes united in a single species, points of organization which, at a later period, are found distinct in separate families, these changes would seem to indicate in the class of Fishes a process of Division, and of Subtraction from more perfect, rather than of Addition to less perfect forms. ... In no kingdom of nature, therefore, does it seem less possible to explain the successive changes of organization, disclosed by geology, without the direct interposition of repeated acts of Creation."

p. 312 "The history of Chambered Shells tends further to throw light upon a point of importance in physiology, and shows that it is not always by a regular gradation from lower to higher degrees of organization, that the progress of life has advanced, during the early epochs of which geology takes cognizance. We find that many of the more simple forms have maintained their primeval simplicity, through all the varied changes the surface of the earth has undergone; whilst, in other cases, organizations of a higher order preceded many of the lower forms of animal life; some of the latter appearing, for the first time, after the total annihilation of many species and genera of a more complex character [emphasis added]".

Charles Lyell, Principles of Geology (1850) Eighth Edition, Ch. 35: "Transmutation of Species"

p. 546 "Lamarck enters upon the following line of argument: The more we advance in the knowledge of the different organized bodies which cover the surface of the globe, the more our embarrassment increases, to determine what ought to be regarded as a species, and still more how to limit and distinguish genera. ... The greater the abundance of natural objects assembled together, the more do we discover proofs that every thing passes by insensible shades into something else. …  [p. 549] I must here interrupt the author's argument, by observing, that no positive fact is cited to exemplify the substitution of some entirely new sense, faculty, or organ, in the room of some other suppressed as useless. All the instances adduced go only to prove that the dimensions and strength of members and the perfection of certain attributes may, in a long succession of generations, be lessened and enfeebled by disuse; or, on the contrary, be matured and augmented by active exertion. It was necessary to point out to the reader this important chasm in the chain of evidence, because he might otherwise imagine that I had merely omitted the illustrations for the sake of brevity; but the plain truth is, that there were no examples to be found; and when Lamarck talks "of the efforts of internal sentiment," "the influence of subtle fluids," and "acts of organization," as causes whereby animals and plants may acquire new organs, he substitutes names for things; and, with a disregard to the strict rules of induction, resorts to fictions, as ideal as the "plastic virtue," and other phantoms of the geologists of the middle ages. It is evident that, if some well-authenticated facts could have been adduced to establish one complete step in the process of transformation, such as the appearance, in individuals descending from a common stock, of a sense or organ entirely new, and a complete disappearance of some other enjoyed by their progenitors, time alone might then be supposed sufficient to bring about any amount of metamorphosis. The gratuitous assumption, therefore, of a point so vital to the theory of transmutation, was unpardonable on the part of its advocate."

p. 560 "We must suppose that when the Author of Nature creates an animal or plant, all the possible circumstances in which its descendants are destined to live are foreseen, and that an organization is conferred upon it which will enable the species to perpetuate itself and survive under all the varying circumstances to which it must be inevitably exposed."

Adam Sedgwick, Discourse on the Studies of the University, 5th Ed, (1850)

p. lxiv    (in a critique of Vestiges by Robert Chambers) "All our most ancient fossil fishes belong to a high organic type; and the very oldest species that are well determined fall naturally into an order of fishes which Owen and Müller place, not at the bottom, but at the top of the whole class." ... "Fishes of the very highest organic type existed during the period of some of our old Palaeozoic strata; and no Fishes of an inferior organic grade have been found below them."

Edward Hitchcock, Religion of Geology and its Connected Sciences (1851)

p. 255 "But a special appeal has been made on this subject to geology. The history of organic remains, it is thought, corresponds to what we might expect, if the hypothesis of development is true. In the oldest rocks we find chiefly the more simple invertebrate animals, and the vertibrated tribes appear at first in the form of fish, then of reptiles, then of birds, then of mammals, and last of all of man. What better confirmation could we wish than this gradually expanding series? ... But the tables are turned when we descend to particulars. ... for the onchus (a genus of fish) has been found in the ... lower silurian rocks [modern Ordovician—dcb] of Bala. (¶) It is also a most important fact, that this fish of the oldest rock was not, as the development scheme would require, of a low organization, but quite high on the scale of fishes. The same is true of all the earliest species of this class ... the very oldest species that are well determined fall naturally into an order of fishes which Owen and Müller place, not at the bottom, but at the top of the whole class."

Hugh Miller, The Old Red Sandstone (7th Edition, 1858—First published 1841)

p. 325 "We know, further, so far at least as we have yet succeeded in deciphering the record,—that the several dynasties were introduced, not in their lower, but in their higher forms; that, in short, in the imposing programme of creation it was arranged, as a general rule, that in each of the great divisions of the procession the magnates should walk first."

p. 40 "The argument is a very simple one. Of all the vertebrata, fishes rank lowest, and in geological history appear first. We find their remains in the Upper and Lower Silurians, in the Lower, Middle, and Upper Old Red Sandstone, in the Mountain Limestone, and in the Coal Measures; and in the latter formation the first reptiles appear. Fishes seem to have been the master existences of two great systems, mayhap of three, ere the age of reptiles began. Now fishes differ very much among themselves: some rank nearly as low as worms, some nearly as high as reptiles; and if fish could have risen into reptiles, and reptiles into mammalia, we would necessarily expect to find lower orders of fish passing into higher, and taking precedence of the higher in their appearance in point of time, just as in the Winter's Tale we see the infant preceding the adult. If such be not the case —if fish made their first appearance, not in their least perfect, but in their most perfect state —not in their nearest approximation to the worm, but in their nearest approximation to the reptile —there is no room for progression, and the argument falls. Now it is a geological fact, that it is fish of the higher orders that appear first on the stage, and that they are found to occupy exactly the same level during the vast period represented by five succeeding formations. There is no progression. If fish rose into reptiles, it must have been by sudden transformation — it must have been as if a man who had stood still for half a lifetime should bestir himself all at once, and take seven leagues at a stride. There is no getting rid of miracle in the case — there is no alternative between creation and metamorphosis. The infidel substitutes progression for Deity; Geology robs him of his god."

Hugh Miller, Footprints of the Creator (3rd Ed. 1858—First published 1850)

p. 307 "There is geologic evidence, as has been shown, that in the course of creation the higher orders succeeded the lower. We have no good reason to believe that the mollusc and crustacean preceded the fish, seeing that discovery, in its slow course, has already traced the vertebrata in the ichthyic form, down to deposits which only a few years ago were regarded as representatives of the first beginnings of organized existence on our planet, and that it has at the same time failed to add a lower system to that in which their remains occur. But the fish seems most certainly to have preceded the reptile and the bird; the reptile and the bird to have preceded the mammiferous quadruped; and the mammiferous quadruped to have preceded man."

p. 308 "All the facts of geological science are hostile to the Lamarckian conclusion, that the lower brains were developed into the higher. As if with the express intention of preventing so gross a mis-reading of the record, we find, in at least two classes of animals, - fishes and reptiles, - the higher races placed at the beginning: the slope of the inclined plane is laid, if one may so speak, in the reverse way, and, instead of rising towards the level of the succeeding class, inclines downwards, with at least the effect, if not the design, of making the break where they meet exceedingly well marked and conspicuous."

Louis Agassiz, Contributions to the Natural History of the United States of America (1860)

Vol I, p.117 "Recent investigations in Palaeontology have led to the discovery of relations between animals of past ages and those now living, which were not even suspected by the founders of that science. It has, for instance, been noticed, that certain types which are frequently prominent among the representatives of past ages, combine in their structure, peculiarities which at later periods are only observed separately in different, distinct types. Sauriod Fishes before Reptiles, Pterodactyles before Birds, Ichthyosauri before Dolphins, etc.

There are entire families, among the representatives of older periods, of nearly every class of animals, which, in the state of their perfect development exemplify such prophetic relations, and afford, within the limits of the animal kingdom, at least, the most unexpected evidence, that the plan of the whole creation had been maturely considered long before it was executed. Such types, I have for some time past, been in the habit of calling prophetic types. The Sauroid Fishes of the past geological ages, are an example of this kind. These Fishes, which have preceded the appearance of Reptiles, present a combination of ichthyic and reptilian characters, not to be found in the true members of this class, which form its bulk at present. The Pterodactyles which have preceded the class of Birds, and the Ichthyosauri which have preceded the appearance of the Crustacea, are other examples of such prophetic types. [emphasis added]"

Edward & Charles Hitchcock, Elementary Geology (1860)

p. 363 "Sixth Law.—Complexity and perfection of organization as well as intelligence increase as we ascend in the rocks. This is true as a general fact; but in particular tribes we find the reverse, viz., retrogradation from a lower to higher, condition. 'All our most ancient fossil fishes,' says Professor Sedgwick,  'belong to a high organic type; and the very oldest species that are well determined, fall naturally into an order of fishes which Owen and Miller place, not at the bottom, but at the top of the whole class.' ... 'The Cephalopods, the most perfect of the molluscs, which lived in the early period of the world,' says D'Orbigny, 'show a progress of degradation in their generic forms. The molluscs as to their classes have certainly retrograded from the compound to the simple, or from the more to the less simple.'"

p. 367 "Thirteenth Law.--Many of the fossil animals had a combination of characters which among living animals are found only in several different types or classes. Agassiz very appropriately calls such types Prophetic Types. For they form the pattern of animals that were to appear afterward."

Alexander Winchell, Sketches of Creation, (1870)

p. 314 "Nature has always issued her bulletins. It is a most interesting fact in the history of the animal creation that Nature advertised her plans in the very earliest creative acts. In our study of the relics of the primeval ages we do not find the grand and fundamental purposes of Infinite Wisdom unfolding themselves by degrees as type after type of organic life made its advent upon our planet. ...Nature had her plans, and these were mature in the very beginning."

p. 315 "[U]pon the very threshold of Paleozoic Time representatives of Radiates, Molluscs, and Articulates burst into multifarious being almost simultaneously. So nearly simultaneous was the appearance of each of these types, that all hypothesis of their genealogical succession is rationally precluded."

p. 317 "There is no successional relation between the four sub-kingdoms of animals, nor even between the several classes of the invertebrate sub-kingdoms; but among the orders of the several classes and the classes of the Vertebrates we find generally a progress from lower to higher in the order of introduction. But there is another principle, complementary to this, which needs to be united to it in order to present us with a true view of Nature's method. There has generally been a downward as well as an upward unfolding of each type from the central forms in which it was first embodied. Trilobites, the first representatives of the Crustacean type, belong indeed to the lowest group, but do not lie at the bottom of the group. The earliest reptiles were not the lowest of the Amphibians, but Labyrinthodonts, the highest Amphibians; Vertebrates began, not with the lowest fishes, but with a grade of fishes above the mean level of the type... We shall arrive, therefore, at the truest expression of the plan of Nature in reference to the succession of organic beings by saying that each type was first introduced at a nodal point, from which the stream of development proceeded in both directions...."

James Dana, Manual of Geology, (1896)

p. 1031 "No successional lines among Insects appear to have passed between the higher tribes of Neuropters, Orthopters, Coleopters, Lepidopters, Hymenopters; but each was derived from some early [unwitnessed - dcb] comprehensive forms."

p.487 "The Lower Cambrian species have not the simplicity of structure that would naturally be looked for in the earliest Paleozoic life. They are perfect of their kind and highly specialized  structures. No steps from simple kinds leading up to them have been discovered; no line from Protozoans up to Corals, Echinoderms, or Worms, or from either of these groups up to Brachiopods, Mollusks, Trilobites, or other Crustaceans. This appearance of abruptness in the introduction of Cambrian life is one of the striking facts made known by geology."

p.716-8 "Principles of Biological Change and Progress for Animals: Outline [somewhat edited]:
1. From the simple, regular, or primitive in structure to the specialized.
   a.  From a structure with two or more functions to organs, each with its specialized function.
   b.  From a single-function organ has several uses, to special forms for each kind of use.
   c. From simpler forms of specialization to more complex, better adapted forms.
   d. From any specialized form to others adapted to newly acquired uses  
   e. From a head with large sense-organs and mouth-organs to one with smaller and well-compacted organs.
   f,  From large aquatic structures to smaller terrestrial structures.
2. Approximate parallelism between geological succession of structures and embryological succession in development.
3. Degeneration:
    a.  Of an organ to a more primitive form;
    b. Diminished size or disappearance of an organ; production of low-grade structures that have needed form and activity  

4. From diffuse to concentrated structures.
   a.  From elongated to abbreviated;
   b. From multiple, indefinite number of segments, to limited numbers and arrangement;
   c.  From posterior locomotive organ to anterior locomotive organ;
   d. From stronger posterior limbs (merosthenic) to stronger anterior limbs (prosthenic)."




connections

The Central Dogma of Molecular BiologyM.40
The Common genetic processing used by every living cell

The Central Dogma of molecular biology is the machinery that exists in every living cell. Its function is to transcribe digital genetic content contained in DNA to form proteins, which build all of the specialized molecules that carry out a cell's metabolism. The most remarkable fact is that the basic operations of the Central Dogma are virtually the same for every species, from the simplest microbe to humansM.41.

The first surprise is that all of life, every living species, uses digital coding to specify everything that defines and is characteristic of that physical species. It involves many complex innovations that, as far as is known, must all work together before anything can be called "living". The following table is a partial list of the necessary innovations.

It is estimated that every living cell, however simple, requires the DNA to include at least 150 genes requiring 250,000 base pairs to set up and implement the central dogma, in addition to whatever genes are needed to do the regular cell functions.M.42  In my view, given the size of this DNA molecule and the list of specialized molecules just to carry out the Central Dogma, it is utterly incredible to assert that this all came about by undirected natural processes.

COMPONENTS OF THE CENTRAL DOGMA

Innovation

Function


Adenosine tri-phosphate (ATP)


The universal "battery" storage to power most cell metabolism in every known living species. In particular it powers the Central Dogma. Not known to occur naturally.


ATP Synthase and ATPase
See Box on Photosynthesis


ATP Synthase is a proton motor molecule which adds a 3rd phosphate to ADP to form ATP. ATpase performs the opposite function, releasing energy. These processes are "widely used in all known forms of life." "Essentially the same structure and activity of ATP synthase enzymes are present in all kingdoms of life."M.43

DNA

The repository of a cell's genetic coding, the genes. A spiral ladder structure in which the rungs are nucleotides.


Nucleotides: A (adenine), C (cytosine), G (guanine), and T (thymine)M.44
The "rungs" (= base pairs (bp)) in DNA consisting of pairs A-T and G-C. Codons are three nucleotide pairs that specify for a particular amino acid (or "start" and "stop" markers) in gene transcription.

Genes (250 to thousands, depending on species complexity)

Specify for proteins or RNA regulatory  molecules. Average gene size about 1000 bp.


DNA Polymerase

Duplicates the DNA molecule. Essential for cell reproduction. This is the most basic (but only one of many) step in the remarkable ability of all living species to "reproduce after its kind".


RNA transcription factor
RNA Polymerase (RNAP)


Factors bind to DNA and Polymerases transcribe  genes to form messenger RNA (mRNA) for a particular gene. Found in all living species. Factors control gene expression by the RNAP.


Amino Acids: 21 varieties

All proteins are chains of left-handed amino acids. A few of the simpler ones have been observed in outer space, probably formed by random assembly.


Ribosomes
"The smartest living nanomachine"

A complex (2-part) molecular motor that removes amino acids from tRNA to build protein chains from mRNA. Ribosome biogenesis involves the coordinated function of over 200 proteins and ribosomal RNA (rRNA) in its synthesis. This is true for all species, however simple or complex. The ribosomes include a built-in error correction mechanism to reduce errors.M.45

Transfer RNA (tRNA)


Each codon triplet requires its own t-shaped tRNA molecule that associates a codon triplet at one end to a particular amino acid attached to the opposite end. The complete set of tRNAs defines the "codon table", which is essentially the same for all species of life. Every species manufactures its own tRNA taking about 150-250 genes to specify the codon table (506 tRNA genes in humans and 36 in Mycoplasma genitalium).


Chaperone Proteins

Form a mature protein by folding and/or modifying the amino acid chain. Many proteins require a specially-designed chaperone. This is the subject area of the Levinthal Paradox (below).


Cellular Proof-reading

Error-checking of all molecular reproduction. This is the subject of the Eigen Paradox (below)M.46.

Notes to table

Is this molecule known to exist in inorganic form (e.g. found in outer space (Y or N)? Is there a known way to build this molecule using natural processes (a plausible natural scheme done outside of a laboratory) (Y or N)?

* A few of the simpler amino acids have been observed in outer space.






connections

Photosynthesis and Carbon Fixing
How it works.

Life cannot exist without an energy input from outside itself. That could be organic food (products of earlier life), energy from sunlight, thermal vents, etc. Obviously organic food is not an option for the very early species, which appear in the geologic record at almost earliest possible moment after the earth had cooled to a "livable" temperature, at around 3.8 Ga (Billion Years Ago)—a very hot temperature, perhaps about that of pasteurization (150°F)M.50.

The organic carbon found as early as 3.8 Ga, and the fossils of what appear to be cyanobacteria (or their ancestors) around 3.45 Ga indicate that photosynthesis, harvesting of energy from sunlight, appeared with the first life, or very soon thereafter.M.51 

Photosynthesis is an incredibly elaborate process, and the basic parts of it are essentially the same for all photosynthetic life. The cyanobacteria conduct photosynthesis in folded membranes called thylakoids ("light reaction" in the following figure). Plants conduct photosynthesis in Chloroplasts as show in the Figure.M.52  

A number of complex molecules, some actually nano-sized motors, are involved in photosynthesis. There are two stages: the light reaction which harvests energy from light, and the dark reaction (Calvin Cycle in the following diagram), which uses the products of the light process to fix carbon and make sugars. The dark reaction does not harvest light but exchanges products with the light reaction.

Photosynthesis


The following (deceptively simple) chemical equation describes the action of photosynthesis:

6H2O+6CO2+light energy -> C6H12O6+6O2
Water + Carbon dioxide + light energy -> sugar + (waste) oxygen.

The Light Reaction.

The light process centers around chlorophyll: molecules that harvest light with the help of a central magnesium atom. There are two forms of chlorophyll which work cooperatively but have, remarkably, opposite characteristics—one is a strong oxidizer, and the other is a strong reducer—each the best known design for its particular task to be found in all of nature.

Photosystem II, involving P680 Chlorophyll: absorbs yellow (680 nm) light. This is the strongest known biological oxidizer. It oxidizes water to produce protons (H+ = P) and  oxygen (O2) as a waste product in the Oxygen-evolving complex. It is "II" because it was discovered after Photosystem I. The protons are used in the manufacture of ATP, the universal "energy battery" used, in particular, in the dark process. A summary of its action is:

H2O + light energy ->  2 H+ + O2
water + light energy -> protons + oxygen.

Photosystem I, involving chlorophyll P700: absorbs orange (700 nm) light. This is the strongest known biological reducer. It uses light energy to prepare a precursor molecule NADPH for sugar production in the dark process.

The protons of Photosystem II supply protons (H+) to Photosystem I to make NADPH, and also propel a marvelous and complex rotary proton nanomotor, ATP synthase, which prepares ATPM.53   (see figure).


Photosynthesis


Photosynthesis

ATP Synthase

The Dark Reaction.


The dark reaction  fixes carbon and then uses it to form glucose, C6H12O6, used by the cell to form starch, amino acids and other sugars. The following remark emphasizes the importance of carbon fixing.

"Carbon is essential to life. All of our molecular machines are built around a central scaffolding of organic carbon. Unfortunately, carbon in the earth and atmosphere is locked in highly oxidized forms, such as carbonate minerals and carbon dioxide gas. In order to be useful, this oxidized carbon must be "fixed" into more organic forms, rich in carbon-carbon bonds and decorated with hydrogen atoms.M.54

This is done by a complex motor molecule, RuBisCO. It is the most common protein on earth—about half of all the protein. The RuBisCo molecule is large (consisting of two subunits),  very slow (it can fix about 3 CO2 molecules per second) and very inefficient, because it spends about 20% of its time "fixing" oxygen instead of carbon: "a wasteful process"M.55 called photorespirationM.56.  One author called the molecule "dim-witted."  Nonetheless, despite many billions spent seeking an improved RuBisCO, no practical substitute has been found. The RuBisCO active site uses a Magnesium atomM.57  to perform its function. The overall reaction can be summarized as:

CO2 + H2O + ATP → CH2O + O2
carbon dioxide + water + ATP -> sugar (fragment) + oxygen + ADP + P+++

where ATP is the energy "battery" with three phosphates, one of which is released generating energy, ADP and a phosphate ion. This is repeated three times in the Calvin cycle.

RuBisCO discriminates against the isotope 13C in preference to 12C. This arises due to slight differences in kinematics and binding energy in the CO2 molecule. Thus organic carbon is slightly deficient in 13C compared with inorganic carbon.



connections

Nitrogen Fixing

Before life can get started, there has to be abundant H, C, O, and N available, because these are the most basic of life's building blocks. Photosynthesis uses the complex molecule RuBisCO to split CO2 into C and O2, with the C used to make the sugar glucose (C6H12O6). But how do living cells get N?  Every living cell requires millions of N.M.60

The earth's atmosphere is mostly nitrogen gas, N2, but the atoms are so tightly bound together that it is practically inert, and unusable by living cells. Ammonia (NH3) will do, but inorganic sources (such as a byproduct of lightning discharge) are not reliably available in sufficient amounts to supply living cells, or at least to allow them to reproduce in abundance.

The solution to this quandary is a fussy, very complex molecular factory, the nitrogenase molecule. This molecule is virtually the same throughout the hundred or so bacterial species that can fix nitrogen, and it is the only known molecule that can perform the task.M.61

The overall equation for nitrogen fixation is:

N2 + 8 H+ + 8 e  + 16 ATP → 2 NH3 + H2 + 16 ADP + 16 P
nitrogen + 8 protons + 8 electrons + 16 ATP -> 2 ammonia + hydrogen + leftovers

where ATP is the energy "battery" and leftovers are recycled in the light reactions of photosynthesis.

At its core is a Molybdenum (occasionally Vanadium) atom, a rare element, but sufficiently abundant for the purpose. At tremendous expenditure of energy (relative to the normal biological processes), and at a very slow pace (1.25 s to convert a single N2 molecule to two atoms of ammoniaM.62), the nitrogenaseM.63 molecule can break nitrogen gas into N atoms and form ammonia, which then makes N available for use.

By "fussy" I mean that oxygen, the normal waste product of photosynthesis, poisons nitrogenase, and elaborate precautions must be made to keep it away the nitrogenase. Most bacteria and all eukaryotes are unable to fix nitrogen for this reason. The only possible solution to this is that before advanced life could exist on earth, it was necessary to fill the earth with organic matter that would feed these advanced species.

Is it not clear now, why it took the very first living species well over 2 billion years to prepare the Earth for "greening" (Day 3)M.64  and for advanced animal life (Days 5 and 6)?

In contrast to the carbon-fixing RuBisCO, which is the most abundant protein (40-50% of all the protein on earth), Nitrogenase is extremely rareM.65: It has been said that all of the nitrogenase in the world would fit into a single bucket.M.66

Only a few species—about 100—of bacteria and archaea are known to fix nitrogen, and then only, as I said, with extraordinary cautionary preparations. One of these is cyanobacteria (the phylum of blue-green bacteriaM.67), which appear to be among the very first living species, able to conduct photosynthesis and also to fix nitrogen.

In the case of cyanobacteria, special cells called heterocysts are produced to fix nitrogen. These cells have thick walls to isolate the cell contents, and then produce nitrogen, receiving sustenance from neighboring cyanobacteria. Because oxygen poisons nitrogenase, these special cells cannot perform some of the normal tasks of the regular cyanobacteria cell; in particular, they are dependent on adjacent cells for a supply of food and energy (ATP), which is needed in abundance to feed the nitrogenase.

In a typical low-nitrogen medium, about one in 15 cells in a (modern) cyanobacteria chain is a heterocyst (see figure). Frequently the immediate neighbor to a heterocyst is another specialized cell called an akinete, which can survive under harsh conditions—freezing, starvation and dehydration—for long periods of time. Since the early earth was constantly changing with no permanent dry land or shorelines, the ability to survive and resume growth in another locality or time was important. In addition the ability to go into a kind of suspended existence also allowed the cyanobacteria to drift with the ocean currents and distribute life and nutrients worldwide.


Akinetes & Heterocysts
Cyanobacterial chain

WORKING

connections

The Big Bang Creation of EukaryotesM.70

"An organic being is a microcosm, a little universe  formed of a host of self propagating organisms inconceivably minute, and as numerous as the stars in heaven."
Charles Darwin (1887)M.71

"The origin of eukaryotes is a huge enigma and a major challenge for evolutionary biology."
E. V. Koonin (2010)M.72

The most visible difference between prokaryotes and eukaryotes is the existence of a nucleus which holds the cell's DNA (see figure). This is only one of many important differences, some of which are mentioned below.

ProkEukDNA 

The sudden appearance of eukaryotes at about 1.8 Ga (Billion years ago), with no clear predecessors and with major structural and genetic changes, has been described as a "Biological Big Bang". Not only do the eukaryotes appear on the scene suddenly and without warning or obvious predecessors, but even within the major types of eukaryotes there is no clear line of antecedence—no clear "archeotype". Indeed the first eukaryote appears to be an example of "the magnates walk first"M.73—the (unknown) ancestor is more complex than any of the descendents. This is a recurring theme in the development of species.M.74

The first eukaryotic cells were single-celled (the protists), as bacteria are. Multicellular structures formed by cyanobacteria are actually individual single-celled microbes that live attached, and may have some cell specialization such as the nitrogen-fixing heterocysts and akinetes. But the structural and transport features of the proper cell have the potential for far more, and thus led in time to multi-celled species, and eventually to the visible, multi-cellular plants and animals.

There are six major groups of eukaryotes (see Wikipedia), and the inferred "common ancestor" must have been more complex than any existing (very complex) group. Many traits  of eukaryotes are unique to them and have no analog in bacteria.M.75

Features include:

• Eukaryotes are a radical advance in organizational complexity over all prokaryotes.

• All eukaryotes display a large package of genes that are unknown—let alone separately existing—in any prokaryotes.

• The genes that do appear to be shared with prokaryotes seem to be indiscriminately selected from both archaea and bacteriaM.76. There is no plausible scenario in which this might occur by natural evolution—even given lateral gene transfer, which is well-established, demonstrated in the laboratory, and can occur between unrelated species.

The following table lists some of the Eukaryote innovations. The mitochondria are the "powerhouse of the cell"—main producers of ATP, and use oxygen to do this: this is the reason why all eukaryotes require oxygen (even plants—derived from photosynthesis).

Eukaryote Innovations

Prokaryote
Eukaryote

DNA
Single loop in cell body
non-looped chromosomes in nucleus

Mitochondria
None
Membrane-bound organelle:
Consumes O2 to generate ATP energy "batteries"

Cell division
binary fission, a remarkable and complex process.
mitosis and cytokinesis (non-sexual cell division with mitotic spindle for division of cell & nucleus)
Sexual reproduction
None Meiosis to form sperm and egg cellsM.77
Structure
balloon-like: Shaped by pressure.M.78  See the range of shapes displayed in the Merck Manual. Cytoskeleton: shape & internal structure. See a chart of the many ciliate shapes.
Membrane-bound organelles
Absent
Organelles with controlled micro-environments for specialized tasks: the nucleus, nucleolus, mitochondria, golgi apparatus, endoplastic reticulum, etc.

Internal Transport
Diffusion
Kinesin (see Figure below) and other transport motor molecules to carry food and waste along microtubules within the cell (e.g. between organelles).

Programmed death
Absent
Ubiquitin found in all eukaryotes. Directs protein recycling (programmed cell death).

Kinesin
Kinesin

The invention of the eukaryotic cell came at a critical time in the history of the Earth, at a time when most of the reduced minerals in the oceans and Earth crust had oxidized and the atmosphere's oxygen content had reached a level that could poison cyanobacteria.

The invention of the original eukaryote could be another example of starting with a "magnate" (see above).  With the advent of detailed gene studies, one might have hoped that the problem of complexity of the first "proto-eukaryotes" might be solved, but such is not the case. Consider the following statement regarding the identity of the very earliest eukaryotes, summarizing a decade of intensive genetic research on the origin of the six major groups of eukaryotes:

"There are therefore no grounds to consider any group of eukaryotes primitive... Rather it is becoming increasingly clear that most or perhaps all of them evolved from more complex ancestral forms by reductive evolution. Reductive evolution refers to the evolutionary modality typical of parasites: they tend to lose genes, organelles and functions when the respective functionalities are taken over by the host. So the archezoan (crown group) phylogeny seems to have been disproved, and deep phylogeny and the theories of the origin of eukaryotes effectively had to start from scratch."M.80




WORKING


connections

The Four Paradoxes of Natural Evolution
    Inexplicable features of natural evolution.

There are four paradoxes involved in the program of creating life. All of these paradoxes concern logical problems with producing complex life through purely natural means. In my own view, the paradoxes are unanswerable, and they amount to sharp points as regards the origin of life.

The Combinatoric Paradox. This was the subject of a conference at Philadelphia's venerable Wistar Institute in 1966.M.81  The paradox is that it is impossible to assume that random change could produce from scratch even a few of the critical genes of a living cell. Thus, if natural evolution did occur then the only plausible conclusion is that it occurred as a result of some unknown natural laws—but then those natural laws should be the focus of evolutionary research, not some facile claim that the power of random selection produced life or species. What are those laws? Where is the laboratory evidence for them?

The combinatoric paradox has been expressed in many ways, always leading to an absurd conclusion. Many analogies have been made—how many thousands or millions of Britannica encyclopedias of information are represented in even a single moderate-sized genome, how long it would take monkeys typing at a keyboardM.82 to generate one, etc. One famous scientist made the following remark:

"I was constantly plagued by the thought that the number of ways in which even a single enzyme could be wrongly constructed was greater than the number of all the atoms in the universe. So try as I would, I couldn't convince myself that even the whole universe would be sufficient to find life by random processes -- by what are called the blind forces of nature."

Such remarks are so obvious that nobody makes them any longer. There simply is no direct response.

I should note that random—that is, undirected—evolution becomes increasingly less plausible as one moves up the chain of species complexity. Bacteria, at the bottom of the chain, reproduce in great abundance—it was once said that if the descendents of a single e-coli survived, in a single day the descendents would bury the entire earth to a depth of several feet.M.83 This fecundity gives undirected evolution the maximum opportunity to effect changes. At the opposite extreme, the mammals reproduce very slowly, so opportunities for random change are drastically reduced. If there is a combinatoric paradox for bacteria, it is a doubly implausible paradox at the higher end of the chain of life.

Sometimes it is argued that we can get around the combinatoric problem by building up large genes by combining small segments, which is assumed to avoid the combinatorial problem. This particular suggestion sounds to me (as a mathematician who specialized in probability) like the classical fallacy stated as "there is no combination or betting system that will turn the odds into your favour."M.84 The odds of getting a very low probability result cannot be helped by any “system”. The fact is that although some genes do appear to be repeated copies of small segments,  that is not true of most genes.

In the end, the only reasonable response to the combinatorial paradox is that there must be unknown natural laws. Well, if that is the case, then the evolutionists should get on with it and find them. Thus far, to the best of my knowledge, the search has come up pretty empty.

The Eigen Paradox. The second hurdle is what is called the Eigen Paradox, after its formulator Manfred Eigen in a 1971 paper.M.85 In essence this paradox states that a gene with over 100 base pairs must be accompanied by error-correction code (also encoded in genes) that is more complex than the original gene.M.86


Without error-correction, the effect of mutations will overwhelm the stability of the gene.M.87 This paradox has been called by Wikipedia "one of the most intractable puzzles in the study of the origins of life." I think that this says it as well as anything I could say, so I will leave it at that.

Every budding computer expert soon learns to his chagrin that debugging computer software always takes more work than writing the original code. That's just a microcosm of the Eigen Paradox. The implication is that it is impractical to try to “bootstrap” the building of large functional genes by random, undirected processes.
 
The Levinthal Paradox. The third hurdle is the Levinthal paradoxM.88 after its formulator Cyrus Levinthal in 1969. The Levinthal paradox has to do with the fact that proteins, after they are formed by the ribosome, fold into a unique 3-dimensional shape, which is essential to carry out the function for which that protein exists. This folding occurs when the ribosome has completed the protein chain.

 Protein folding
Protein Folding
From Wikipedia

The problem is that there are a huge number of ways that a given protein chain might fold. In fact, for a chain of 100 amino acids, there are as many as 3198 = 3x1094 ways to fold. Considering that there are only about 1080 atoms in the entire universe, picking out a particular folded configuration is like finding a particular atom in 100 trillion universes. Unless you are much more optimistic than I, I assume that you agree that this is hopeless.

In actuality, the folding of proteins is partly spontaneous (for not fully understood reasons) and partly aided by chaperones, which are other molecules whose specific task is to help proteins to fold into the correct configuration. In Eukaryotes, the folding frequently occurs in the endoplasmic reticulum. It's anyone's guess how they "know" which folding is correct. Again, I suppose we have to invoke unknown "laws."M.89  

The Regulatory Paradox. The expression of genes coded in the DNA are guided by a complex regulatory schemeM.90 to make the proteins which carry out all of the life functions. This complex working procedure appeared seemingly out of nowhere, much as the universe itself seems to have appeared from nothing. Some scientists assert that the regulation that specifies how and when to transcribe the genes encoded in the DNA, has even greater complexity and information content than is found in the DNA itself.

One function of the regulatory machinery is to modify the mRNA after transcription, but before expression into proteins. "Many of these post-translational modifications are critical to the protein's function."M.90a

A fertilized egg forms its DNA by combining the DNA of the sperm with the DNA from the egg (each is haploid—that it has a single-strand DNA; the fertilized egg is diploid—a double-strand DNA). That is all the sperm contributes. The rest of the egg also contributes ribosomes and the initial regulatory machinery to begin building the embryo. Without this start-up machinery, the fertilized cell would not be able to begin its growth.




connections

The Anthropic Principle
    Inexplicable features of natural evolution.



The new anthropic vision of the physicist and the Darwinian contingent paradigm which dominates modern biology are diametrically opposed worldviews. Yet where physics led in the seventeenth century, biology eventually followed, and it is doubtful whether modern biology can for long resist the new teleological current now flowing within cosmology and the physical sciences.
Michael J. DentonM.91


In recent years, a number of discoveries have made the point that we live in a very special sort of world that appears to be particularly suited for human habitation. Two quotations illustrate this point:

First from Fred HoyleM.92:

 "A common sense interpretation of the facts suggests that a super intellect has monkeyed with physics, as well as with chemistry and biology, and that there are no blind forces worth speaking about in nature. The numbers one calculates from the facts seem to me so overwhelming as to put this conclusion almost beyond question."

Second, from Freeman DysonM.93:

The more I examine the universe and the details of its architecture, the more evidence I find that the universe in some sense must have known we were coming.

These are just the tip of the proverbial iceberg. Hoyle's remark came about because of strong evidence that the most basic parameters of physics appear to be finely tuned. Dyson's remark points to the fact that  we live in a teleological universe, that is, that the natural world displays purpose and direction, an arrow of development. The historical record does not show the characteristics of random, undirected, pointless (or whatever adjective you like) change overall, despite what some of the supposed experts claim.M.94  Of course, everyone agrees that there are accidents, chance events and random activity in the small, but that does not characterize the large picture.

These observations are wrapped up in a major theme that has developed over the past half-century, known as the Anthropic Principle: briefly, that the world appears to be designed specifically for human habitation.M.95  This is, of course, no surprise for those who accept the truth of God's revelation in the Bible, but it is surprising that the conclusion comes from Book of Nature, not just from the Book of Revelation.

The term comes from Brandon Carter's paper presented at a symposium celebrating Nicolaus Copernicus' 500th birthday.M.96  It is the subject of a major work, The Anthropic Cosmological Principle, by John D. Barrow and Frank J. Tipler,  and many papers and articles since.

The theme, though, if not the terminology, has been around much longer—since, at least, remarks by Alfred Russel Wallace in a 1903 lecture series.M.98 He remarked that

[When] the growing power and perfection of the telescope and of improved astronomical instruments ... showed us the utter insignificance even of our sun and solar system among the countless hosts of stars and the myriads of clusters and nebulæ, we seemed ... to be forced to recognize the fact that this vast, stupendous universe could have no special relation to ourselves any more than to any other of the million suns and systems, many of which were probably far grander and more important than ours...

But during the last quarter of the past century the rapidly increasing body of facts and observations leading to a more detailed and accurate knowledge of stars and stellar systems have thrown a new and somewhat unexpected light on this very interesting problem of our relation to the universe of which we form a part; and although these discoveries have, of course, no bearing upon the special theological dogmas of the Christian, or of any other religion, they do tend to show that our position in the material universe is special and probably unique, and that it is such as to lend support to the view, held by many great thinkers and writers to-day, that the supreme end and purpose of this vast universe was the production and development of the living soul in the perishable body of man.

This, coming as it does from one of the collaborators of Charles Darwin himself in developing evolutionary theory, is a remarkable statement, and it has only been reinforced by science since that time.

The Anthropic principle has been developed in many directions. In physics and chemistry, the theme goes under the rubric "fine tuning"—the discovery that many parameters have precise values that allow the world and life as we know it to occur, and without these precise values, we, as humans, would never have been around to observe it! This fact in just one area—the creation of carbon and oxygen in the stars—is what led Fred Hoyle to the above quoted remark. Hugh Ross lists many of these fine tuning "coincidences".M.99

In biology, Michael Denton, makes similar remarks:

I believe the evidence strongly suggests that the cosmos is uniquely fit for only one type of biology—that which exists on earth—and that the phenomenon of life cannot be instantiated in any other exotic chemistry or class of material forms. Even more radically, I believe that there is a considerable amount of evidence for believing that the cosmos is uniquely fit for only one type of advanced intelligent life—beings of design and biology very similar to our own species, Homo sapiens.M.99a

His book concludes:

All the evidence available in the biological sciences supports the core proposition of traditional natural theology—that the cosmos is a specially designed whole with life and mankind as its fundamental goal and purpose, a whole in which all facets of reality, from the size of galaxies to the thermal capacity of water, have their meaning and explanation in this central fact.
... Four centuries after the scientific revolution apparently destroyed irretrievably man's special place in the universe, banished Aristotle, and rendered teleological speculation obsolete, the relentless stream of discovery has turned dramatically in favor of teleology and design, and the doctrine of the microcosm is reborn. As I hope the evidence presented in this book has shown, science, which has been for centuries the great ally of atheism and skepticism, has become at last, in these final days of the second millennium, what Newton and many of  its early advocates had so fervently wished—the "defender of the anthropocentric faith."M.99b

This is a large subject, but the bottom line is that this universe is not accidental, and the record of life leading up  to the creation of humans is not the result of random, undirected happenstance.






 
FOOTNOTES M FOLLOW

[*fn]M.01 Lawrence J. Henderson The Fitness of the Environment: An Inquiry into the Biological Significance of the Properties of Matter (1913) Lowell Lectures at Harvard College, p. 4. The "problem" was the hypothesis of purpose in nature. "Until the middle of the nineteenth century the countless adaptations of organisms to the environment and the manifest fitness of nature for the activities of living things seemed to many biologists only explicable as the result of some directing force." ibid., p. 3

[*fn]M.02 The modern trend in science is to go a step further, and assert that the  natural laws themselves are randomly determined with no plan or design. This is a reaction to the exquisite precision of the physical constants that are needed for life to exist, which goes under the label Anthropic Principle. Clearly physical constants cannot "evolve", and so the answer is to postulate the concept of "multiverses" in which there are approximately an infinity of universes (!), each based on a random selection of physical laws and constants, of which the vast majority self-destruct, and the vast majority of the others would have no observers, because they lacked the essential parameters needed for advanced life to exist.


[*fn]M.03 "It is mere rubbish thinking at present of the origin of life; one might as well think of the origin of matter." Charles Darwin (ltr, 1863) quoted in Merz, History of European Thought, II, p406, n1. It is not known, even at this time, whether Darwin was an atheist—I would think, probably not. But it is hard to say because in most corners of England, at least, true atheism ran against the cultural and even academic mores of the day, and would be expressed, if at all, in muted tones. Lawrence J. Henderson in The Order of Nature (1917), he wrote (p.117), "In spite of Darwin' great labors, we remain largely in ignorance... [W]e still have but the vaguest ideas concerning the development of living things as products of nature. And regarding their origin we have no ideas at all."

[*fn]M.04 In particular, the natural world gives strong indications of purposeful development and design. See the Freeman Dyson quote (Ch. 1, note 14), and Michael J. Denton, Nature's Destiny: How the Laws of Biology Reveal Purpose in the Universe (1998), and his earlier book, Evolution: A Theory in Crisis (1985). A sequel to this last book is Evolution: Still a Theory in Crisis (2016).

[*fn]M.05 In this spirit, Darwin's book Origin of Species (1859) asserts that all species naturally evolved from the first living species, but does not assert, or even provide a plausible mechanism for, how that first life came about. His closest acolytes, such as Thomas Huxley and Ernst Haeckel, boldly advanced such notions, but were soon embarrassed when the true complexity of life began to be understood more fully in the late 1800s. Today, that perception of complexity is multiplied a million-fold.

[*fn]M.06 The following Notes give examples of the vast complexity and sudden appearance of life itself, the quantum leap in complexity of the first eukaryotes, the Cambrian Explosion of the basic animal body plans, and the "Magnates walk first" principle expressed by the early geologist Hugh Miller.

[*fn]M.07 Colossians 1:17—or "hold together". Christian doctrine states that Jesus Christ was the Creator in his pre-incarnate state. The word translated "consist" or "hold together"—συνέστηκεν—has a large range of possible meaning, which does not at all constrain scientific investigation or even pre-judge whether any given aspect may have evolved (possibly by random chance or by an as-yet unknown natural law). It even allows (implausibly, I would say) for a stand-offish Creator who just set the ball rolling, so to speak. See Gerhard Kittel, Ed., The Theological Dictionary of the New Testament (1971) on συνίστημι, which gives five senses of meaning: "the use is most varied".


M.08 [*fn]M.08 Note for M.08

M.09 [*fn]M.09 Note for M.09

M.10 [*fn]M.10 Note for M.10

=====

[*fn]M.11 Karl Popper (28 Jul 1902—17 Sep 1994), The Logic of Scientific Discovery, (1934), p. 314. See Wikipedia on Falsifiability and Bruce Wightman, (Muhlenberg University),  Popper’s Ghost: The Dark Side of Falsification in Science (2012).

[*fn]M.12 Karl Popper, Conjectures and Refutations, (1963), p. 36.

[*fn]M.13 In the Pew Research Center Religion & Public Life Project (2009) survey of religious belief among scientists who belong to the American Association for the Advancement of Science (AAAS), overall 48% don't believe in a god or "higher power". One would expect that a higher percentage don't believe in a personal God, which is a stronger criterion—see the next note.

[*fn]M.14 "Scientists Speak Up on Mix of God and Science," New York Times, August 23, 2005, "They note that when Dr. Larson put part of the same survey to "leading scientists" - in this case, members of the National Academy of Sciences, perhaps the nation's most eminent scientific organization - fewer than 10 percent professed belief in a personal God or human immortality."

[*fn]M.15 Carl Sagan, the host of the PBS series Cosmos, is famously quoted as saying "Evolution is a fact not a theory." R. C. Lewontin, Richard Dawkins and others have made the same assertion. See Wikipedia, Evolution as Fact and Theory.

[*fn]M.16  It is famously known that Karl Popper once stated that Evolution was non-falsifiable, but later retracted the statement (presumably under peer-pressure). For the record, and for myself as an evangelical Christian, I agree that evolution is falsifiable, but it is not falsifiable to an atheist. Thus the pressure to call natural evolution a "fact" not a "theory", see previous note. The irony is that atheists claim that theists cannot be good scientists, but the truth is exactly the opposite: atheists cannot be good scientists because their belief requires that evolution by undirected natural means be non-falsifiable. A non-falsifiable belief (specifically atheism) is non-scientific. This does not judge its  truth value, but only argues that it is not scientific, and has no right to claim exclusive ownership of science. So, to the extent that the possibility of God is denied in the name of science, to that extent evolution is non-falsifiable, any evidence that would suggest the contrary is consciously suppressed or derided, and natural evolution is presented as unassailable "fact". In a possibly apocryphal story, Chinese paleontologist Jun-Yuan Chen (Professor, Nanjing University) criticized Darwinian predictions about the fossil record [Jun-Yuan Chen, The sudden appearance of diverse animal body plans during the Cambrian explosion, Int. J. Dev. Biol. (2009)] and was met with dead silence from a group of scientists in the U.S. He quipped, “In China we can criticize Darwin, but not the government; in America you can criticize the government, but not Darwin.”

[*fn]M.17 One possible deus ex machina is powerful unknown laws which are able to bootstrap a chaotic natural world into its present highly organized form. But such laws are just gods by other names. They are quite different from the familiar laws of chemistry and physics, and diligent search has revealed nothing of the sort. Of course computer simulations of "evolution" can perform all sorts of organizational miracles—such as the Weasel program promoted by Richard Dawkins: this effort is based on goal-directed change that has no known analog in the real  world, and has been thoroughly refuted by John Lennox in God's Undertaker (2012) and other authors. One common palliative is a sort of Anthropic principle: "there must be such laws because ... here we are—we exist!" On this, see remark of John Lennox, Appendix 9, note 1.

[*fn]M.18 Darwinian evolution concerns survival of the fittest descendents of a species. Indeed "evolution" of life itself is an oxymoron: one must begin with something viable to modify it by evolution, and viability itself presumes life.

[*fn]M.19 an atheist must have natural evolution, and since atheism dominates natural science, evolution is non-falsifiable in the sense that there can be no evidence (such as the ridiculously low probability—see Appendix 9, note 2—that life itself could come about by undirected random happenstance) of a Creator that would convince an atheist. So, to the extent that the possibility of God is denied in the name of science, to that extent evolution is non-falsifiable; any evidence that would suggest the contrary is consciously suppressed or derided, and natural evolution is presented as unassailable "fact".


[*fn]M.20 The report of this  symposium was published by the National Academy of Sciences in 2000, titled Size Limits of Very Small Microorganisms.

[*fn]M.21 The base pair (bp) count i s a rough measure of the number of genes required for the species, the average gene requiring about 1000 bp.

[*fn]M.22 See The Minimal Genome Project for a list of the smallest bacteria. In 2002, a smaller bacterium was discovered, but it too is incapable of independent existence. Note from the figure that the genome size only weakly correlates with the complexity of the species: for example, the human DNA is only of middling size when compared with other mammals, and many plants have dna that is orders of magnitude larger than the human DNA. See Claire M. Fraser et. al. The Minimal Gene Complement of Mycoplasma genitalium,  Science Vol. 270, 20 October 1995.

[*fn]M.23 An autotroph is a plant that gets its nourishment from inorganic sources. However, no plant is a strict autotroph in this sense, because no eukaryote is able to fix nitrogen. The only reliable source of fixed nitrogen (until the 20th century discovery of the Haber process) is organic waste, derived from the bodies or waste products of earlier life.

[*fn]M.24 Ibid, pp 77-78. Among modern bacteria on earth, the smallest known autotroph requires over 1 million bp.

M.25 [*fn]M.25 Table from Size Limits, op. cit., Peter B. Moore, "A Biophysical Chemist's Thoughts on Cell Size." For current sizes of these genomes see Wikipedia or The Minimum Genome Project (op. cit.)

M.26 [*fn]M.26 The question of regulation involves much more than a count of the regulatory genes. In sexual reproduction the egg carries with it an ongoing regulatory environment derived from the mother. This is why, for example, the mitochondrial DNA comes from the mother: it is passed on from the contents of the egg, and not from the sexually-formed DNA. At the moment the egg is fertilized, this regulatory environment has already determined the initial expression of the embryonic DNA. This is the miracle implied in the phrase "according to his kind".

M.27 [*fn]M.27 Lord Alfred Russel Wallace (8 January 1823 – 7 November 1913), one of Charles Darwin's the early and enthusiastic collaborators wrote the seminal book, Man's Place in the Universe (1903) on this subject. He followed this in 1911 by The World of Life: a manifestation of creative power, directive mind and ultimate purpose. In 1913 Lawrence J. Henderson (June 3, 1878, Lynn, Massachusetts – February 10, 1942 wrote The Fitness of the Environment: An inquiry into the Biological Significance of the Properties of Matter. A recent follow-on to Henderson's book is A. E. Needham, The Uniqueness of Biological Materials (1965), which has extensive discussions of the most essential elements and molecules required for life. A more recent update to Henderson's book is Michael J. Denton, Nature’s Destiny, op. cit.

M.28 [*fn]M.28 Note for M.28

M.29 [*fn]M.29 Note for M.29



[*fn]M.30 For a modern-day assertion of this, see Koonin EV, Appendix 8, footnote 1. He calls the phenomenon "reductive evolution".

[*fn]M.31 Freeman Dyson, Disturbing the Universe, Basic Books (1979) p. 250. Quoted in The Anthropic Cosmological Principle (1986) by John D. Barrow and Frank J. Tipler, p. 318.

[*fn]M.32 Hugh Miller, Foot-prints of the Creator, (3rd. Edition, 1858) p. 325.

[*fn]M.33 See also Michael J. Denton, Nature’s Destiny: How the Laws of Biology Reveal Purpose in the Universe, Free Press, 1998.

[*fn]M.34 Lydia Miller, Sketchbook of Popular Geology, 4th Edition (1869), p. xxxi.

M.35 [*fn]M.35 Note for M.35

M.36 [*fn]M.36 Note for M.36

M.37 [*fn]M.37 Note for M.37

M.38 [*fn]M.38 Note for M.38

M.39 [*fn]M.39 Note for M.39



[*fn]M.40 The word "dogma" was originally used as an ironic epithet by Francis Crick in 1956. See his article, Central Dogma of Molecular Biology (1970 - PDF). As used conventionally, there is a narrow and a broad meaning to "central dogma." The narrow meaning is just the claim that DNA->RNA->proteins (but not the reverse). Here we use the broad meaning—the full panoply of machinery that produces proteins from DNA.

 [*fn]M.41 This fact is unexpected because many aspects of the central dogma appear to be contingent, that is, they appear to be somewhat arbitrary features that could easily have been quite different: such things as the exclusive use of  left-handed amino acids, the specific associations of cordons to particular amino acids, etc. This universal use of the same contingencies in all species leads to the (reasonable) conclusion that the scheme was "invented" only once—it is exceedingly improbable that the same scheme could have arisen by happenstance more than once.


[*fn]M.42 See Size Limits above.The DNA for even the smallest microorganism requires over a half-million C and a million N atoms, and this doesn't take into account any of the molecules required to build and carry out the cell's purpose. Almost all C and N used in a living cell have to have been fixed by specific (and slow!) molecular machines either by the cell itself or found in its food and produced by another living cell at some time in  the past. Very few bacterial species can generate their own N, and these species are unable to carry on the full range of cell functions, because of the extreme sensitivity to the presence of Oxygen.

[*fn]M.43 The quotes are from Wikipedia articles on ATPase and  ATP Synthase.

[*fn]M.44 In 2011 NASA suggested that meteorites may have A and G formed in outer space.

[*fn]M.45 See The Smartest Living Nanomachine, (pdf), Los Alamos Science and Technology Magazine, August 2008.

[*fn]M.46 Wikipedia, Error Threshold calls this "one of the most intractable puzzles in the study of the origins of life." The paradox is this: "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."

M.47 [*fn]M.47 Note for M.47

M.48 [*fn]M.48 Note for M.48

M.49 [*fn]M.49 Note for M.49



[*fn]M.50 Some scientists believe that the first life was extremophiles such as live near thermal vents in the oceans. This would move the possible time of the first life even earlier, around the boiling point of water. Personally I think that extremophiles are a later development. See, for example, Cell Biology, " Archaea are microbes that are more closely related to Eukaryotic cells than they are to the Bacteria". The Archaean ribosomes appear to be closer to Eukaryotes (much later) than to bacteria—see Margulis & Chapman, Kingdoms and Domains (2009), Figure B-3, "Ribosome morphology".

[*fn]M.51 Haselkorn, Koonin, et al, The cyanobacterial genome core and the origin of photosynthesis (PNAS, 2006). They assert that the earliest cyanobacteria already had both the light and Calvin processes in place. These are two very complex and subtly linked processes and involve many specialized molecules working together. Processes and complex molecular motors accompanying photosynthesis: energy storage (ATPase), and carbon fixing (RuBisCO) to make sugars. Nitrogen fixing (Nitrogenase) also accompanied photosynthesis —by necessity—but it is a separate process. According to these authors, "These are such complex biological processes, that the complexity and early appearance on earth seems to indicate planning and design."

[*fn]M.52 In Eukaryotes, photosynthesis takes place in the chloroplast. In bacteria, the thylakoids, like the DNA itself, is located in the undifferentiated general cell contents.

[*fn]M.53 See an ATP Synthase animation by Donald Nicholson (Leeds  University) and a more detailed molecular view by John Walker (Cambridge). See the description from Davidson College. See also the article on ATP Synthase from  lifesorigins.com, which calls it "the smallest rotary motor in the world. ... ATP synthase was one of the first enzymes because it is absolutely necessary for many of the organisms that are thought to have existed on the primitive earth. All of the bacteria that oxidize non-organic chemicals to obtain energy use ATP synthase to make ATP." The molecule is constructed from six subunits. The first recognized nanomotor, the bacterial flagellum, was offered to an incredulous scientific world in the 1980s. At first the discovery of this motor was met with great skepticism; it was thought that the flagellum did not rotate but simply whipped back and forth. The proof came when a scientist found a way to glue the flagellum to a glass slide, and when this happened, the bacterium spun around the flagellum. Since then literally thousands of nanomotors have been identified.

[*fn]M.54 Buick, R. "Earliest Evidence for Life on Earth" Bulletin of the American Astronomical Society, Vol. 34, p.12 (2002).

[*fn]M.55 Wasteful, because the cell must expend time and energy to reverse this error.

[*fn]M.56  To fix carbon, food, energy: fix Rubisco (Biofuels Digest, 2010).

[*fn]M.57 Occasionally Vanadium is known to substitute for the Magnesium atom.

M.58 [*fn]M.58 Note for M.58

M.59 [*fn]M.59 Note for M.59



[*fn]M.60 The smallest known living cell (see the Minimum Genome Project) is Mycoplasma genitalium, a small bacterium of the urinary tract, with a DNA of about 580,000 base pairs. Every base pair requires either 7 (A-T) or 8 (C-G) nitrogen atoms, and the RNA and proteins of the cell require many times this. Genitalium is dependent on its surroundings to provide organic food: to this extent it is not an autotroph (that is, able to make its food from inorganic sources): its genome is too small.

[*fn]M.61 Similarly, there is only one practical commercial way to fix nitrogen, called the Haber process. This process was first used commercially in 1913. Before that time the only practical source of fixed nitrogen involved the nitrogenase molecule. The Haber process is completely impractical as a biological substitute for nitrogenase: it operates at very high pressure and temperature.

[*fn]M.62 John Postgate, Nitrogen Fixation, 3rd Ed. (1998), p. 20. See also the very readable David W. Wolfe, Tales from the Underground, (2001), Chapter 4 "Out of Thin Air" (about nitrogen fixing). p. 78: "Nitrogenase is composed of two giant proteins that physically separate and come back together eight times, over the course of 1.2 seconds, to convert one molecule of N2 to one molecule of ammonium. Most chemical reactions occur in nanoseconds. A duration of 1.2 seconds, thousands of times longer than most biochemical processes, is almost unheard of and reflects the difficulty of nitrogen fixation."

[*fn]M.63 There are a number of molecules called nitrogenases. They all are built and operate in a similar way, and all are centered around a Mo or Va atom.

[*fn]M.64 Plants are often called "autotrophs", but in fact no plants can exist without a supply of nitrogen, which must come from organic wastes—at least prior to the time that the Haber process was invented in 1909. The Haber process requires high temperature and pressure. Natural fixing with nitrogenase (also the only natural way to fix nitrogen) is at normal temperature and pressure.

[*fn]M.65 The yearly worldwide production of fixed nitrogen accounts for no more than 10-20% of the annual requirement (Wolfe, op. cit. p84)—hence the need for a large reserve of organic food to supply the deficit. This was especially true prior to the invention of inorganic nitrogen fertilizer.

[*fn]M.66 David Wolfe, Tales From the Underground (2009), p.78, "The entire world's supply of nitrogenase could fit into a single large beaker or bucket! Lose this and life on Earth as we know it would come to a screeching halt." See also G.J. Leigh, The World's Greatest Fix (2004).

[*fn]M.67 Often misnamed "blue-green algae". Algae are eukaryotes (as are all plants). Cyanobacteria are bacteria, not eukaryotes.

M.68 [*fn]M.68 Note for M.68

M.69 [*fn]M.69 Note for M.69


[*fn]M.70 Koonin EV: The Biological Big Bang model for the major transitions in evolution. Biol Direct 2007, 2:21, "Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. ... In each of these pivotal nexuses in life's history, the principal 'types' seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate 'grades' or intermediate forms between different types are detectable."

[*fn]M.71   Charles Darwin, Animals and Plants, p.ii, p399 (1887).


[*fn]M.72 Koonin EV, "The origin and early evolution of eukaryotes in the light of phylogenomics", Genome Biology 2010, 11:209. He continues, "There is a sharp divide in the organizational complexity of the cell between eukaryotes, which have complex intracellular compartmentalization, and even the most sophisticated prokaryotes (archaea and bacteria), which do not... [R]econstructions show that the characteristic eukaryotic complexity arose almost ‘ready made’, without any intermediate grades seen between the prokaryotic and eukaryotic levels of organization. ... it is becoming increasingly clear that most or perhaps all of them evolved from more complex ancestral forms by reductive evolution."


[*fn]M.73  "Even the most widely accepted notion that eukaryotes originated from prokaryotes is problematic because traits unique to eukaryotes, such as the nucleus, endomembrane system, cytoskeleton, and mitosis, are found in all taxa with no intermediate stages left as signposts of their evolution."


[*fn]M.74  This is sometimes called Reductive Evolution.

[*fn]M.75 Gross and Bhattacharya, Uniting sex and eukaryote origins in an emerging oxygenic world, Biology Direct 2010, 5:53.

[*fn]M.76 Bacteria and Archaea are the two domains of bacteria, with archaea also called "extremophiles" because they live under extreme conditions (such as near hot deep ocean vents). The name "archaea" implies greater antiquity, but this is probably not the case because in fact archaea are intermediate between bacteria and eukaryotes in genetic complexity. In my view the archaea are a later development of bacteria. See Margulis & Chapman, Kingdoms and Domains (2009). The ribosomes (which make proteins) of archaea are more complex than the bacterial ribosomes, and seem to be closer to the eukaryote ribosomes.

[*fn]M.77 Two cell divisions resulting in four cells. Tetrad spores reflect this: "Envelope-enclosed spore tetrads are taken as the earliest evidence of plant life on land" dated to 470 Ma during the Ordovician.

[*fn]M.78 Osmotic or turgor pressure.

[*fn]M.80 Koonin EV: The origin and early evolution of eukaryotes in the light of phylogenomics Genome Biology 2010, 11:209.


[*fn] M.81 Moorhead & Kaplan, Eds., Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, Wistar Institute Symposium Monogram No. 5, 1967. Prominent scientists at the conference included the mathematician Stanislaw Ulam, and biologists Ernst Mayr and George Wald. Be warned! It is difficult to find a balanced exposition of the "conclusions" of this symposium on the internet. It seems that the subject polarizes those who are even aware of the mathematical challenge. The point of the conference is stated by a participant, Dr. Murray Eden in his paper "Inadequacies of Neo-Darwinian Evolution  as a Scientific Theory" as: "It is our contention that if 'random' is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical and biological." (p. 109). For recent comments on the significance of this symposium, see Lennox, God's Undertaker,  "What say the mathematicians?" p112ff. "Ulam argued on the basis of mathematical calculations that it was highly improbable that the eye could have evolved by numerous small mutational changes since the available time was simply not available. Sir Peter Medawar replied: '... It is, indeed a fact that the eye has evolved; and that ... shows that ... [Ulam's] formulation is, I think, a mistaken one.' ... This astonishing interchange is very revealing. It is surely a 'curious inversion' of the normal scientific process to assume the truth of what you want to prove and on that basis discredit evidence that is brought against it."

[*fn]M.82 Robert C. Newman, Some Calculations Demonstrating Scientific Problems of Evolution, quotes Carl Sagan as comparing the information content of a simple living cell to 100 million pages of Encyclopedia Britannica. Newman then notes that just to have a monkey randomly peck at a keyboard to type "ENCYCLOPEDIA BRITANNICA" at the rate of 3 letters per second would take about 30 billion billion monkey-years (compared with a 13.6 Billion year age of our universe. See also Hugh Ross, Probability for Life on Earth (2004) which computes a probability for "attaining the necessary characteristics for a life support" at 1 in 10282. Since there are about 1080 atoms in the universe, if each atom represented a whole universe, and each atom of each of these universes represented a whole universe, this is comparable to selecting one particular atom in this universe of universes of universes. See also Fazale Rana, Too Good to be True: Evolution and the Origin of Bioinformation (2013). Other probability calculations are even much smaller.


[*fn]M.83 An e-coli splits about 2-3 times per hour if adequate food is available. Of course the lack of food to support such a profligate reproduction rate will prevent this.

[*fn]M.84 See Roulette Betting Systems.

[*fn]M.85 Eigen, M. (1971) Self-organization of matter and evolution of biological macromolecules. Naturwissenschaften 58 (10): 465–523.

[*fn]M.86 Effective error correction of a protein requires (in effect) another protein of even greater length. Wikipedia states it as follows: "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."

[*fn]M.87 Error Correction: Origin of Life website states it this way: “Primitive organisms would not have had the ability to manufacture complicated error-correction enzymes. However without the ability to correct errors at all, early organisms would have been very limited to in the amount of information they could carry without suffering from an error catastrophe.”

[*fn]M.88  Cyrus Levinthal, "How to Fold Graciously" (1969), Proceedings: Mossbauer Spectroscopy in Biological Systems.

[*fn]M.89 On the Levinthau Paradox, Wikipedia states: “Computational approaches to protein structure prediction have sought to identify and simulate the mechanism of protein folding, however these have been largely unsuccessful.” See also Martin Karplus, The Levinthal paradox: yesterday and today (1997), "Despite the considerable effort, both theoretical and experimental, that has been devoted to this problem, we are still not able to give a detailed description of the mechanism by which any protein folds."
 
[*fn]M.90 See, for example, John Lennox,
 
[*fn]
M.90a From Wikipedia article on proteomics.

[*fn]M.91 Michael J. Denton, Nature's Destiny (1998), p. 17.

[*fn]M.92 Fred Hoyle, Steady-State Cosmology Revisited, Cardiff Press, 1980.


[*fn]M.93 Freeman Dyson, Disturbing the Universe (1979) p. 250

[*fn]M.94 See Phillip E. Johnson, Defeating Darwinism by Opening Minds (1997), p. 15 quotes the 1995 official Position Statement of the American National Association of Biology Teachers: "The diversity of life on earth is the outcome of evolution: an unsupervised, impersonal, unpredictable and natural process of temporal descent with genetic modification...." ...Which, I would add, gives all the appearance of careful design!

[*fn]M.95 Some try to trivialize this: "Of course it is tuned for humans, because otherwise we wouldn't be here to observe it." But that trivializes what is in truth a remarkable body of facts.

[*fn]M.96 Brandon Carter, M.S. Longair, "Large Number Coincidences and the Anthropic Principle in Cosmology", Proceedings of the IAU, 63:291-298, 1974.

[*fn]M.98 Alfred Russel Wallace, Man's Place in the Universe, lectures at Lowell Institute, Boston (1903).

[*fn]M.99 Hugh Ross, Fine-Tuning for Life in the Universe (2009). Also see Hugh Ross, Creator and the Cosmos (2001) and Luke A. Barnes & Geraint F. Lewis, A Fortunate Universe: Life in a Finely Tuned Cosmos (2017).

[*fn]M.99a Denton, Nature’s Destiny, op cit. p. xiii.

[*fn]M.99b Ibid., p. 389.


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ADDENDUM
Table of Questions


#
Subject
Ref.
Synopsis
1
Day One: Creation of physical light
1:3-5
Why does the Genesis Creation Narrative begin with the creation of light? What sort of light is it? The first act of creation: creation of light in the Big Bang. Universe—space and time—created from nothing; expands into nothing. Second act of creation: creation of darkness. Light of Day One  preceeds the creation of the Sun and Solar System.
2
Day Three, Part 1—Creation of Dry Land
1:9
How could dry land appear out of the global ocean? Dry land appeared out of a global ocean. Oceans form one global water-mass. Dry land also began as one mass. Role of plate tectonics.
3
Before Day One
1:2
Why does the Genesis Creation Narrative begin with verse 2—before Day One? What is the setting of Genesis 1:2? Before Creation began. Earth did not yet exist—"shapeless and empty". Contemporary use of words indicate this—Rig Veda. Universe expands into "the deep"—empty nothingness.
4
Day Two
1:6-7
(Creation of the earth implied before Day Two)
What is the "firmament" in Day Two? Why is its description the second event in the Genesis Creation Narrative? A Raqia shields "inner space" from "outer space". Mis-translated in earliest Greek LXX by "firmament". Error persists to today.

Summation

Summary thus far: Creation of the Physical and Chemical worlds.

The Geological Record of Life

Introduction to Life: The Geological Record from Science.
5
When did Life Begin?
(Implied before Day Three)
Overwhelming complexity and unity of all life. When did life first appear on earth? First evidence on earth as soon as liquid oceans cooled to below pasteurization temperatures (~4.85 Billion years ago). No plausible scientific (falsifiable) explanation of how life began (within the timeframe of the entire universe). Remarks on complexity of the "minimum" possible form of life and the 1998 NAS Symposium on this question.
6
What is “Advanced life” and when could earth support it?

The early earth could not support advanced life. First living bacteria prepared for advanced life over a span of 2 billion years. How did the earth prepare for it? The critical pathways: photosynthesis; carbon fixing; nitrogen fixing. Formation of oxygen atmosphere to provide oxygen respiration required by all advanced life. Distribution of fixed carbon and nitrogen worldwide. What is advanced life? The eukaryotic cell, visible plants and animals. Cambrian explosion. These answers come from science, not from the Bible. But science, in turn, gets its answers from the “silent voice” which God wove into the natural world. “It is unreasonable that we can answer these questions.”
7
Day Three, Part 2—The Greening of the Land
1:11
When did Plants appear on dry land? The Fossil record of migration to land in the Silurian/Devonian era. The Rhynie chert. Ozone shield; concurrent appearance of flying insects.
8
What does "creation after its kind" mean?
1:11b
Sexual reproduction and implications. Preparation of food on land for animals. Spores (tetrad spores imply sexual reproduction), Seeds and Fruits.
9
Day Four: How do stars mark off the seasons, days and years?
1:14-19
Unexplainable stability of the solar system. Early development of Astronomy as the first deliberative science. Earliest (current) evidence for advanced Astronomical observation at Lascaux cave in 18th Millennium BC.
10
How do animals differ from plants?
1:20-23
First reference to special creation by God—barà. Significance. The animal "soul"—nephesh. Cambrian Explosion of animal phyla (body types)
11
Why did advanced life begin In the Oceans?

Note about reproduction in water environment. Eggs and amniotic sac as a sort of “water environment”. Eggs. Dry land sterilized before ozone shield completed.

12
What are the longest extant animal species?

Meaning of "kind" in this context. extant shellfish lines.  Bony Fishes—The Coelacanth "living fossil"
13
Day Six, Part 1—When did land animals first appear?
1:24-25
When did animals appear on dry land?
14
Day Six, Part 2—When did true humans first appear?
1:26-27
2:7
2:21-22

Creation of Adam. When did true humans first appear? Note: Only other use of barà in the creation narrative. Applies to both man and woman. Mandate to reproduce and “fill the earth” What is the scientific evidence for the earliest appearance of humans. Dressed stones, bows and arrows, Cave art. Chauvet Cave ~30k BC Lascaux Cave ~18k BC. Later evidence: boats, advanced tools.
15
When did the alphabet and writing first appear?

Coincident with bronze age (smelting) ~3000 BC. Mid-East. (All written languages appear to derive from early cuneiform. (Chinese, Egyptian, etc.) Evidence for accurate astronomical record-keeping as early as the 18th millennium BC.





Other questions to tease your mind:
• When did the first smelting occur? (See Gen. )
• Earliest clock mechanisms?
• Are Humans and Neanderthals related?
• When was the Flood? Coincident with the annihilation of neanderthals?
===That's enough for now===



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REFERENCES
Many references appear in the above text and footnotes

Luke A. Barnes & Geraint F. Lewis, A Fortunate Universe: Life in a Finely Tuned Cosmos (2017).

B2FH = Geoffrey Burbidge, Margaret Burbidge, William Fowler and Fred Hoyle, Synthesis of the Elements in Stars, Reviews of Modern Physics 29 (1957) p547-650. See the Wikipedia article. See also a brief preceding article by the Burbidges, Cosmical Alchemy (1956).

Richard Dawkins, The Greatest Show on Earth: The Evidence for Evolution, Free Press, 2009.

E. Walter Maunder, Astronomy and the Bible (annotated) 4th Ed. (1922). Annotated by Robert C. Newman and David C. Bossard (2017).

Space Studies Board, National Research Council, Size Limits of Very Small Microorganisms, Proceedings of a Workshop of the National Academy of Sciences (1999) (available as a PDF download).




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