Tough Questions in Science 8

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Origins 8: Why do we need proteins and what are they?

Welcome to the amazing and wonderful world of proteins. DNA uses a large part of its genes to give building instructions for proteins.  What are they, and why do we need them? 

First let’s talk about how the body uses them. Proteins are built into the cell wall.  Without proteins, there would be no way to get nutrients, oxygen, and energy into the cell and no way to get waste and carbon dioxide out.  Proteins also control electric charge motion in and out of the cell.  Hormones are made of proteins that control many other reactions in the body like emotions and sensory stimulation.  Enzymes are also proteins that help us digest food and speed up (catalyse) chemical reactions in the cell.  Proteins control various parts of DNA, activating some parts and blocking others.  Cells use proteins to read and translate DNA, and all proteins in the body are constructed by other complex proteins.  Cells use proteins to keep DNA and amino acids from changing into undesirable forms.  In fact, proteins are the working molecule in the cell.

What are proteins?  All proteins are made of building blocks called “amino acids”.  There are twenty amino acids used in proteins. Think of the amino acids like an alphabet. Instead of spelling words and sentences amino acids “spell” proteins.

Here is a picture of the general structure of all amino acids.

Black spheres represent carbon, reds oxygen, blues nitrogen, and whites are hydrogen atoms.  The unconnected bond is where any organic structure can be bonded to make a particular amino acid.

Here is the structure of glycine on the left. Alanine is on the right.

The simplest amino acid, glycine, has another hydrogen on the stick, but there are an infinite number of possible amino acids, and only twenty are used by the body (and all other life forms).

But there is more.  The amino acids can be combined together in many ways, but all proteins are structured with only one allowed bonding pattern.  The only allowed bonding site is the OH bond on the end of the amino acid. It must bond with one of the hydrogen atoms bonded to the nitrogen atom at the other end to produce a protein and a water molecule.  This allowed bond is called a “peptide” bond.

Proteins used in life can have as few as 24 amino acid building blocks. Adrenaline is an example.  But this is rare.  The average protein is made of 300 amino acids, and some, like titin, have almost 27,000 amino acids.  Titin is an elastic protein that builds muscle.

So, if the smallest word in the protein language is made of 24 letters (amino acids), the longest would take almost thirty-eight pages of type.  In English, if a spelling mistake occurs we can usually make sense of the words, but if too many mistakes are made, the sentence is gibberish.  This is the same for proteins.  A few errors can be tolerated without losing much function, but too many and the protein is useless.  Even small errors can degrade function.  There are some places in the protein chain where any substitution makes the protein useless. 

The body needs to produce two million red blood cells a second, and a single red blood cell has 170 million hemoglobin molecules. Hemoglobin is a protein. Wow! Each hemoglobin molecule has 574 amino acids in four protein chains.  Thus, the body has to build twenty thousand trillion (20,000,000,000,000,000) peptide bonds per second for a functioning blood supply.

Our bodies use about one hundred thousand (100,000) different proteins to function properly.  And interestingly, proteins are constructed by other proteins (ribosomes) in the body. Ribosomes contain both RNA and proteins. They build protein from scratch using a blueprint from DNA. (We’ll talk about ribosomes, RNA, and DNA in more detail in a later blog.

Many parts of DNA are coded for constructing proteins, but we need proteins to build the proteins. We also need proteins to interpret the DNA.  About fifty proteins are involved in building proteins.  Who built the proteins that interpret the DNA so that they can build proteins? It’s an interesting kind of chicken and egg problem.

We can build proteins in the laboratory.  Here is a quote from MIT News (May 28, 2020): “Their tabletop automated flow synthesis machine can string together hundreds of amino acids, the building blocks of proteins, within hours.” We are not even close to keeping up with the ribosomes who string together three to five amino acids each every second (over 14,000 an hour) to build the proteins we need in every cell. 

The protein is just a molecule, like sugar or baking soda. Yet this molecule, using only a string of amino acids, can decode the DNA (actually, it is first translated into RNA) and then build complete proteins in seconds.  To me, that is amazing!

Tough Questions in Science 7

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Origins 7: The Wonders of Life

Up to now we have been looking at the possible theories of the origin of the universe, the big picture, the macroscopic gaze.  But the most wondrous thing of all is life.  Are we alone in the universe? Are those “aerial phenomena” seen by US Navy pilots evidence of extraterrestrial life?  Is there evidence for rudimentary life on Mars, Europa, or other spots in the solar system?  Are the hundreds of thousands of North Americans who claimed to be kidnapped by aliens, true?

 We will have to wait for answers on these questions till there is more evidence, but so far, the evidence is inconclusive.

I want us to stop, and ponder, and wonder about the miracle of life.  Whether it happened by accident, by evolution, or by creation, it is too wondrous to behold.

Did you know that the body produces about 2 million red blood cells every second?  Did you know that the body holds close to 37.2 trillion cells, the building blocks of life? Did you know that each cell is operated almost completely by molecules called proteins?  Did you know that proteins are made of building blocks called “amino acids”?  Did you know that there are 20 different amino acids in living things?  Did you know that amino acids have handedness, like our left and right hands, and no matter how you rotate your right hand, you cannot make it into a left hand?  Did you know that all the amino acids used by living things are always left-handed?

Did you know that our cells have a molecule called DNA (deoxyribonucleic acid) and that this molecule has the plan for building every protein used by the body?  Did you know that every cell in the body (except red blood cells) has a copy of DNA?  Did you know that if each bit of DNA in our cells were unwound it would be about six feet (2 meters) long?  That means that if we stretched out all our DNA in all our cells, it could reach the sun and back over 80 times, and the distance to the sun is about 150 million km away?

Here are pictures of what DNA might look like if we could see things this small. (Youtube image).

Diagram of DNA

There is a simple plant called “pond scum” that covers shallow calm waters.  It is composed of millions of single celled algae.  These cells can produce a copy of themselves every twenty minutes only using water, air and sunlight? The only waste product it produces is pure oxygen.  Here is pond scum under the microscope from Youtube images.

One type of pond scum
Typical pond scum is made of many types of algae

This is how it looks to us when we look at a pond (Youtube image).

How pond scum looks to us

I hope I have given you some things to think about and wonder about—life is amazing, wonderful, fantastic, and interesting.

Tough Questions in Science 6

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Tough Questions in Science Part 6: Logic

To answer questions, to think, to make decisions, a scientist uses logic. There are three common types of logic.  For some reason, some scientists rarely talk about logic, unless they are criticizing another’s point of view.  The three common types of logic are deduction, induction, and abduction. Let’s examine each in turn.

Deductive logic is the one we hear most commonly. “He made a deduction from the evidence.” Sir Arthur Conan Doyle’s popular fictional character, Sherlock Holmes, often said “Simple deduction, Watson, simple deduction.”  Deduction is when we start from certain premises and come to a conclusion or action. Christopher Columbus believed the world was round, and if China was in the Far East, we could also get there by sailing west. These are best shown in syllogisms.

For example: “All birds have wings. Turkeys are birds, therefore, turkeys have wings.”

The first sentence is called the primary premise. “Turkeys are birds,” is called the minor premise. “Turkeys have wings,” is the logical conclusion.

But notice: “All birds have wings. Buildings have wings.Therefore, buildings are birds.” This is an illogical conclusion.

This form of logic is used extensively in mathematics and science. However, it has its weaknesses. Sometimes the premises are wrong, or more likely are only probably correct. Sometimes the logic is fallacious — a philosophy prof once told me that almost every philosopher made a mistake in logic at some point in their writings.

The second form of logic is called inductive reasoning or logic. It involves recognizing patterns in the behavior of living and nonliving things. You may have noticed that objects fall downwards and never upwards. This pattern may lead you to think that there may be a law of physics here. Just do not visit the international space station where things do not seem to fall at all. Actually, everything in the station always falls at the same rate, but so does the station, so things look like they do not fall at all. Patterns are usually only approximately the same. Sometimes other things change that make the conclusion invalid.  This is why long testing periods with data-collecting experiments are needed before potentially damaging inventions or treatments are allowed for human use.

You may have noticed that effects are preceded by the cause. When you hear a bang, you immediately think “I wonder what caused that?” But just because something precedes an effect it does not make it the cause. After all, sunshine always precedes rain, but it does not cause rain. Day always precedes night, but it doesn’t cause night. Because you won the ball game that time you did not shave, it does not mean you should never shave during the playoffs.  

This form of logic is used extensively by scientists trying to predict things like the weather, or simple formulas for the behavior of objects. It is why we do experiments and try to isolate possible causes by using controls. We observe the pattern, then work out the mathematical formulae that correspond to the pattern.

The third form of logic is called abduction, and in this case, we do not mean kidnapping anyone. Abduction is the logic of looking into the past for causes. It is used for “once only” events or events that do not happen anymore. Usually, it is used when experiments trying to obtain the same results are difficult or impossible.

Crime fighters use abduction to figure out who did the crime. They examine the evidence, looking for whether the person had access, motive, and means. They first check for alibis to eliminate those who could not be there during the crime. They check the weapons or get-away car or the like to establish means. Since there must be a reason to do the crime—they look for a motive. When the investigation is complete, they decide who was or were the most probable perpetrator(s). Investigators can never be sure unless there is photographic evidence of the act, and even that has been known to be misleading at times. Witnesses tend to be easily confused, and forgetful. The conclusion is usually only probably true.

This form of logic is often used by many scientists looking into the past such as archeologists, anthropologists, geologists, and physicists who are examining origins.  

We cannot do an experiment to test the origins of the universe, but we can test the theory to see if it obeys the laws of physics and is internally consistent. Since there are no photographs, or movies proving what happens, all theories of the origin of the universe are only intelligent guesses. As intelligent observers of the product (the universe), we can only judge what is most likely. Probability arguments are all we have.  

Scientists can never prove anything by abductive reasoning. The best we can say is “this outcome is very probable.” To say, “Science says” is very dangerous. Disagreement among scientists is common and necessary to advance understanding of the way things work.

Theories about the past, especially origins, are at best probably true — but beyond testing for self-consistency, there is no way to check. 

Tough Questions in Science part 5

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The Big Bang and Energy

If I throw a rock straight up into the air, it will slow down and then stop in midair for an instant before falling  back to Earth.  If I get Superman to throw it, he can throw it fast enough to put it into an elliptical orbit which will always come back to him (if we ignore air resistance).  Or Superman could give it a super throw and put the stone in orbit around the Sun.

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What about the Big Bang?  Where does its initial energy come from?  If it has too little energy the expansion of the universe should eventually stop and start to collapse on itself.  If there is exactly the right amount of energy, the energy of motion of the galaxies will exactly balance their collective gravity — the universe’s expansion will slow down and after an infinite amount of time just stop.   If there is too much energy the Universe’s expansion will slow down but never stop.

If the energy is too little, the universe might expand, collapse, expand, collapse, forever.  We call this the oscillating model, or the bouncing model.  When it collapses back to a point, we call that the “Big Crunch”.  Of course, we know that this model does not fit the data.  

If the energy exactly balances gravity we would have the equivalent of an object in orbit, the universe’s expansion would gradually slow down and move towards stopping, a kind of steady state.  Unfortunately, the data does not support this model either.  It would be nice though, since this model would need zero initial energy.

If the energy was greater, then the universe’s expansion would slow down, but it would keep expanding forever.  However, this model does not fit the data, either.

In fact, the Universe’s expansion is accelerating.  Hold on now, if it is accelerating, isn’t there some force pushing it, like Newton’s second law (F=ma)?  Well, there are no forces acting except gravity, and it is attractive and trying to pull everything back together.  And then there was that early on great expansion called “inflation”.  What caused that?  And if it is accelerating where is the extra energy coming from?

Nobody knows, but we have called whatever it is by the name “Dark Energy”.

A group of stars in space

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Hubble telescope (almost every spot of light in this photo is a galaxy) Photo credit: NASA

Now the expansion does not seem to be happening inside galaxies, only between galaxies.  It is like the vacuum of space is a fabric that is stretching with galaxies painted on it.  The distance between galaxies is measured in millions of light years, about a hundred times the size of our galaxy, so matter seems to occupy about 4% of space, the rest is vacuum. Now we know that the vacuum of space is made of energy.  This energy, sometimes called the “zero-point energy”, is estimated to be 1 nanojoules (10-9) per cubic meter. This has been measured through a few different experiments.  The exact number does not matter, the point is that the more vacuum (space) we have the more energy we have.  Where is this energy coming from? 

To summarize, it seems that our universe is making energy in contradiction to physics as we know it.  Where did the energy that started the Big Bang come from?  Where does the energy that is being created by the universe come from?

Tough Questions in Science part 4

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The Missing Mass Problem

Kepler’s Three Laws

Johannes Kepler, in 1609, noticed that the ratio of the period squared of a planet divided by its distance from the sun cubed was a constant for all the planets.  In 1687, Isaac Newton was able to show that his data was correct for all planets.  The constant was related to the mass of the sun.  However, when we apply those calculations to galaxies and clusters of stars using the virial theorem (which is based on Newton’s work) we get masses much greater than the observable mass of the system.  It would mean that all the galaxies, globular clusters, open clusters, etc. would be breaking apart.  The universe would be unstable and fall apart.

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Galaxies above and a globular cluster below (pictures are courtesy of NASA)

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In the twentieth century, we “knew” that the universe had lasted billions of years. These structures would be stable if there was a large amount of invisible mass. It was dubbed the “missing mass” problem. 

Two classes of objects were looked for:  W.I.M.Ps and M.A.C.H.Os.  WI.M.P.s are “weakly interacting massive particles” and their primary candidates were neutrinos.  In the 1970’s we thought neutrinos were without mass, but later experiments did find a very small mass.  So, we looked for neutrinos using huge vats of dry-cleaning fluid well beneath the Earth’s surface.  But the numbers of neutrinos found were way too small to account for the missing mass.  Now M.A.C.H.Os are massive clusters of halo objects—like black holes, neutron stars, and brown dwarfs (stars that are just too small to ignite nuclear processes).  The name was a bit of science humor to contrast with W.I.M.Ps.  Again, the data did not give nearly enough mass to fit the need.  The halo of a galaxy is an imaginary sphere that just contains all the stars in a galaxy.  

So, since neither W.I.M.P.s nor M.A.C.H.O.s did the job, we invented the name dark matter”.  The amount of dark matter necessary to do the task is five or six times the amount of visible matter out there.  This a tremendous amount of matter to not be explained.  

If dark matter is real, then it should speed up the velocity of stars far from the galactic center, like our sun.  And indeed, our sun seems to be exceeding the escape velocity of our galaxy, as are other stars around us.  So, if the dark matter is extensive in the region of our sun, shouldn’t the planets in our Solar system also be sped up?  But they obey Kepler’s third law in direct violation of a region with tons of dark matter around it.  Our planets act like the sun is the only really massive object close by. 

So, we have a contradiction.  Although our belief in dark matter works well for the galaxy and globular clusters, it does not work well for our Solar system.  Without dark matter the universe would fly apart.  We need something to hold it all together.

Colossians 1:16-17 

For in him all things were created: things in heaven and on earth, visible and invisible, whether thrones or powers or rulers or authorities; all things have been created through him and for him. He is before all things, and in him all things hold together.” 

Tough Questions in Science part 3

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The fine tuning of the universe, the Goldilocks syndrome.

During the Big Bang we find that not only are time and space created, but the laws of Physics and the constants that Physicists use in their formulas are also created.  

For example, the universal constant of gravitation G is estimated to be 6.67257×10-11 Nm2/kg2.  It is this constant that tells us how hard gravity pulls on us.  If this constant were larger, we would weigh more.  It also tells how hard the sun pulls on the molecules and ions that are in its make up.  If gravity was too large the sun would quicky become a black hole, if too small, it would not be able to get hot enough in its center to sustain nuclear reactions.  These reactions are what causes the sun to shine.  It is estimated that changing the value of G in the 35th decimal place will cause stars to become unstable or never form.  We do not even know G to 35 decimal places, but we do know that changing G by very much is very bad.  

The element Carbon is essential to all life.  This wonderful element is able to bond with itself and other elements to make very complex molecules.  One molecule in the cells of all living things is the ribosome. This molecule contains over 20,000 atoms and is a critical part of the machine that changes DNA into actual molecules the body needs.  The charge on the electron is known to 16 decimals.  But the smallest change in the value of the electron charge will stop carbon from being able to do this.  Also, carbon is allegedly formed in dying stars.  The nuclear reactions that build carbon as discovered by Fred Hoyle, depend on the fact that the structure of the carbon nucleus is extremely delicate, any deviation by more than a infinitesimal amount will make it impossible for stars to build carbon.  Also, the quarks, which are the building blocks of neutrons and protons, must have very specific masses or life is impossible.  

Oxford physicist. Roger Penrose, a Nobel prize winner, estimates the precision of the constants that make up the universe must all be finely tuned.  If they deviate by more than a tiny bit, life does not happen, or chemistry does not even happen, nor do stars happen.  Now he calculated the probability of these constants being chosen at random, and also various energy concerns, caused by the Big Bang, to be one part in ten billion to the one hundred and twenty third power.  That is 1 part in 1010123 a number that is so huge it is a one followed by more than a trillion trillion trillion trillion trillion trillion trillion trillion trillion trillion  trillion books each of 200 pages filled with nothing but zeroes.  

Andromeda Galaxie

None of this suggests a random beginning to the universe, but rather its constants were chosen by a brilliant intellect. As an alternative, some scientists have proposed that our wonderful universe is one of an infinite number of universes with different constant selection.  Since only one of these can support life, it is only natural that we would exist in that one.  These scientists call this “the multiverse”.  However, is it scientific if we can never do experiments to prove the multiverse exists, or visit there, or even see them?

We live in an amazing universe, a Goldilocks universe, that is just perfect for us because it was designed for us.  

Tough Questions in Science part 2

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In the beginning God created the heavens and the earth. Now the earth was formless and empty, darkness was over the surface of the deep, and the Spirit of God was hovering over the waters. And God said, “Let there be light,” and there was light. …”

 Most physicists say “In the beginning was the Big Bang, and there was light”.  It is suggested by the standard model (the one most scientists accept), that we do not know what happens exactly at the first instant of time, but working our universe backwards it seems there was a point in space-time where the whole universe explodes.  Time and space begin here.  There is no time before so we cannot ask what caused it because a cause must precede the effect and since there was no time before, there is no preceding the big bang. Now space starts out as a point and is infinitely dense with infinite energy at an infinite temperature. Then the universe quickly expands and as it expands, it cools. At a time shortly after the beginning, (a billionth of a billionth of a billionth of a billionth of a second,) the universe suddenly expands tremendously (called the inflationary period) to at least 1026 (that is a 1 followed by 26 zeroes or 100 million billion billion times) as large as it was.  Some scientists have suggested the cause of  this is something called dark energy (which we presently do not understand).  As the universe cools it forms electrons and protons and neutrons and Hydrogen.  Somehow this explosion has embedded within it the information necessary to produce structure to the universe: stars, planets, galaxies, clusters of galaxies, etc.

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To summarize, the standard model suggests that 13.7 billion years ago the universe exploded at a point, (which we do not understand), became inflated shortly after by dark energy (which we do not understand) and produced the galaxies, stars, planets, and eventually Earth.  

In this case the universe is a very complex system of galaxies, stars, planets, and Earth. If we looked at a building, would you assume it began as an explosion of a pile of concrete, rocks, bricks, wire, pipes, and fixtures? 

 Why did the point explode—with its high density wouldn’t it rather form a black hole?

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Hmmm.  Another possibility is that a being of high intelligence living outside of space and time designed the whole thing.  But that would sound like religion and so is “unscientific”.  Science demands that all conclusions be testable by experimentation.  But discussions of origins are not experimentally testable as we have only one universe.  However, science can test to see whether the conclusions are self-consistent and logically proceed from the presumptions.  Religion however depends on “faith”, not on experiment.  

Does science also depend on faith?  When I asked 40 science teachers “What is science?”, a quarter answered “It is a faith system.”

However science and mathematics often name things that they cannot evaluate or explain. For example, we name the square root of -1 as “i” for an imaginary number.  Such naming can be powerful as it allows us to proceed.  Could naming “dark matter”,  “dark energy”, or “charge” be worthwhile? More about these ideas in a later blog

Tough questions in Science Part 1

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“For his invisible attributes, namely, his eternal power and divine nature, have been clearly perceived, ever since the creation of the world, in the things that have been made. So they are without excuse.”

Romans 1:20

“The history of the Universe has been summed up thusly: “Hydrogen is a light, odorless gas, which, given enough time, turns into people.” 

http://Smithsonanmag.com

I am a scientist.  I have the PhD. I have done research.  I have published papers.  I have taught for many years.  But I am deeply concerned with much of science and “science in the media” that removes design from the equation as if it is a necessary beginning.  Science should be about finding the truth, and that means being open to the possibility that the universe (and us) might have been designed with a purpose.

I invite you to join me on this journey, to ask the hard questions of me, of science, of God, of each other and to even debate each other.

We will be examining at the largest scale such things as exoplanets, black holes, neutron stars, supernova remnants, galaxies, the origins of the universe and the big bang, life in the universe, dark matter, dark energy, etc.

We will be examining matter at the smallest places, and what those pieces are made of: molecules, atoms, protons, neutrons, electrons, neutrinos, pions and muons, and omega particles, and how they are discovered.

We will be examining the building blocks of life, the cell, mitochondria, ribosomes, DNA, RNA, and processes in the cell and the questions surrounding life itself.

And we will be looking at the big questions of mankind:  what is consciousness?  beauty? selflessness? humility? Love? Justice? Death? God? Afterlife? and other topics you would like to talk about

I hope you will join us.

Our Father Isaac (Laughter) Gen 26-28

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This section is very short compared to the space given to the other patriarchs.  Of interest is that Isaac has the same courage problem with Abimilech (is it the same one?).  The courting of Rebekah is rather interesting.  I think Rebekah was almost too much woman for lowly Isaac.

Also note the favoritism in the family and how it distorts and defines the family.  Esau and Edom both mean red, I think.  I had never seen a red haired Jew until recently, but there appears to be more of them than you might think.  Of course, Jacob lives up to his name (Usurper).

I am confused about Esau losing his birthright as he seems to have a lot of staff (400 men) and herds when he meets Jacob later.

Our Father Abraham Gen:20-25

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In chapter 20, Abraham pulls the same stunt he did with pharaoh, asking his wife to lie.  To me this is so cowardly, and stupid.  But this great man is only human, too.  And after bargaining to save Sodom, he is incapable of seeing God’s protection in his own life.   This standing in the gap between man and God is a tribute to Abraham’s courage.   Cowardice and great courage in the same group of chapters.

 

 So Isaac is born, and Hagar and Ishmael are protected, and Abimelech made peace with.

 

The climax of Abraham’s life occurs here in chapter 22 when God asks Abraham to sacrifice Isaac, the child of promise.  (The Muslims believe it was Ishmael that was to be sacrificed.)  To read this properly you need to put yourself in Abraham’s shoes and struggle with the awful task God has asked you t do.  Then reread the passage pretending you are Isaac.  Hebrews tells us that Abraham believed God would raise Isaac form the dead.  Now that takes great faith.  The name of God (Jehovah Jireh) “The God who provides” comes from Abraham’s prophecy that God Himself would provide the sacrifice.  In the immediate sense, the prophecy was satisfied by a ram, although Abraham misinterpreted his own prophecy thinking it would be Isaac.   Of course God really does give Himself as the sacrifice on the cross.

Seeking a bride for Isaac is an interesting study in faith and prayer.  The nobility of Rebekah is outstanding.

 

Abraham goes on to have six more sons by Keturah, his second wife.  So the song is wrong as Abraham has at least eight sons not seven.  However, he only had seven sons by his wives.  Notice that Abraham also had concubines (and sons by them). How does this work with pluralistic marriage (polygamy).  Are all of these true sons, or are the sons of concubines, bastards?  Was Hagar a wife or concubine?   If she was a concubine, why was Ishmael blessed by God?