First Advent Sunday

"The Christmas message is that there is hope for a ruined humanity—hope of pardon, hope of peace with God, hope of glory—because at the Father's will Jesus Christ became poor and was born in a stable so that thirty years later He might hang on a cross." ~ J. I. Packer, Knowing God

Today is the first Sunday of the Advent season. The season begins four Sundays before Christmas and ends on Christmas Eve. Advent tradition has its roots deep in Christian history that can be traced as far back as the 6th century AD with certainty (possibly as far back as the 4th with some question). It is marked with anticipation and preparation for the celebration of the birth of the Messiah. It is anticipation and preparation for the celebration of the coming of "hope of pardon, hope of peace with God, hope of glory" that came with Christ. It is also a celebration and anticipation of the second advent (second coming) of Christ still to be realized in the future.

Isaiah 9:6-7

For to us a child is born,

to us a son is given;

and the government shall be upon his shoulder,

and his name shall be called

Wonderful Counselor, Mighty God,

Everlasting Father, Prince of Peace.

Of the increase of his government and of peace

there will be no end,

on the throne of David and over his kingdom,

to establish it and to uphold it

with justice and with righteousness

from this time forth and forevermore.

The zeal of the LORD of hosts will do this.

We are entering a time where we celebrate the coming of the Messiah who did establish and does uphold His kingdom "with justice and righteousness" and we look forward to His second coming where all He inaugurated will be consummated. Perhaps today could be the day? We can hope and pray.

By His Grace,
Taylor

99% Chimp... but also 35% Daffodil?

"In the context of a 35% similarity to a daffodil, the 99.44% of the DNA of human to chimp doesn’t seem so remarkable. After all, humans are obviously a heck of a lot more similar to chimpanzees than to daffodils. More than that, to say that humans are over one-third daffodil is more ludicrous than profound. There are hardly any comparisons you can make to a daffodil in which humans are 33% similar." ~ Dr. Jonathan Marks, What it Means to be 95% Chimpanzee: Apes, People, and their Genes

You have probably heard it before, "Humans are 99% chimp!" The percentage number of genetic similarity reported ranges from 90-99% (the actual number is probably closer to 90% when one takes into account indels--insertions and deletions in the DNA sequences--but that is not really important for our purposes here). This statement is based on work done by Mary-Claire King and A. C. Wilson in 1975. Their work showed several human and chimpanzee proteins display a 99% agreement in amino acid sequence. This indicated that humans and chimpanzees are closer genetic relatives than anyone at that time had thought. Soon popular evolutionary news caught wind of this and the field has never been the same since. It seems like compelling evidence for an Darwinian paradigm. Is it?

Not really, actually. As Dr. Marks states above, we could also say that humans are 35% daffodil based on this method of comparison, which is absurd. Comparisons based on the percent similarity of genetic sequences is basically meaningless. It being meaningless has led others, like Science correspondent Jon Cohen, to write, "Now it’s totally clear that it’s [the 99% genetic similarity] more a hindrance for understanding than a help." Most of the scientific community that supports naturalistic evolution has largely abandoned this comparison since it has no value. Yet, this icon of evolution is still floating around in popular media and text books.

Why does this comparison have little value? Well, let me try to explain it using an example. Assume that you and I each have a box of colored pencils. Each of our boxes contains 100 pencils. When we compare the boxes we find that 99 of our colors are the same and we each have one color the other does not have. If we each start to draw are we going to come up with pictures that are 99% similar? No, of course not. Why? Because the pictures depend not so much on the colored pencils we use but on the way we express ourselves in our drawings, how the colored pencils are used functionally. We may be using the same supplies but we would use them in vastly different ways. Well, genes are like that. Genetic similarity in organisms counts for nothing, it is how the genes are expressed that really matters. Having similar genes means nothing because functionally they operate very differently in different organisms.

Recent work on the FOXP2 gene creates a great example of this. (This is going to get a little technical but I think it is very helpful in illustrating my point above with an important, real-life example.) This gene has gotten a lot of attention lately because of its importance to language capability. This gene codes for a DNA-binding protein, which are proteins used in differential gene regulation--the controlling of activity in genes much like a volume control. They can turn genes "on" or "off" or regulate their activeness anywhere in between. The FOXP2 gene plays this role in humans and other organisms, like chimpanzees.

In humans this gene is critical for language capability. A study done by the Max Plank Institute (published in Nature in 2001) showed that any modification of this gene in humans cripples language capability. It not only disables the ability of the humans to make the sounds necessary for language but it also disables their ability to comprehend language completely. In this study they also looked at the amino acids that make up the protein that this gene produces--the FOXP2 protein--in chimps, mice, and humans. Out of the 715 amino acids that make up the protein in chimps, mice, and humans, the mouse and human protein differed by only three amino acids and the chimp human protein differed by only two amino acids (that is about a 0.3% difference).

In a recent paper also published in Nature, a team of scientists from several universities reported on an analysis they did of how this difference in the FOXP2 gene for humans and chimps affected biological development. In order to study the effect they culture two sets of neurons that had the FOXP2 gene removed from them. (They did this so they could have the same starting point for each gene they were studying.) In one set they introduced the human FOXP2 gene and in another set they introduced the chimp FOXP2 gene. They then observed how the neurons were affected by the different genes. What they found was profound. In the set of neurons with the human gene there were 60 other genes that were up-regulated (more active) by this protein compared to the chimp neurons and there were 50 other genes that were down-regulated (less active) by this protein compared to the chimp neurons. So, the introduction of one human gene that is 99.7% similar to the chimp version of the gene had a profound affect on 110 other genes in development! A two-out-of-715 amino acid difference had significant biological consequences.

This study illustrates how a 90-99% genetic similarity between humans and chimps really means nothing. Even if one were to grant that the similarity is 99% (as I briefly mentioned above, the number is closer to 90%), that 1% genetic difference has profound implications when it comes to gene expression in each species. Gene similarity is meaningless. Gene expression is what is important.

By His Grace,
Taylor

The Bumpy Ride

"...She had mapped out a perfect life, without failures or disappointments. But that is more of a flawed life-plan than the bumpy ride God inevitably maps out for us. People who have never suffered in life have less empathy for others, little knowledge of their own shortcomings and limitations, no endurance in the face of hardship, and unrealistic expectations for life. As the New Testament book of Hebrews tells us, anyone God loves experiences hardship (Hebrews 12:1-8)." Tim Keller, Counterfeit Gods

God is good. Any Christian would agree with that statement. We can even say that God is perfectly good, and He is all the time. We take great comfort in those words, as we should, but there is a side of God’s goodness that we often misunderstand. We often think that God loving us means He will not allow us to experience "the bumpy ride." Many of us have found, however, that is simply not the case.

When C. S. Lewis lost his wife, Joy, he started journaling about his struggles with God. Eventually one of his friends read his journal and convinced Lewis to publish it because he knew how much it would help many others. Lewis did publish it (initially under a pseudonym) with the title A Grief Observed. In it he wrote about God’s goodness:

The terrible thing is that a perfectly good God is in this matter hardly less formidable than a Cosmic Sadist. The more we believe that God hurts only to heal, the less we can believe that there is any use in begging for tenderness. A cruel man might be bribed-might grow tired of his vile sport-might have a temporary fit of mercy, as alcoholics have fits of sobriety. But suppose that what you are up against is a surgeon whose intentions are wholly good. The kinder and more conscientious he is, the more inexorably he will go on cutting. If he yielded to your entreaties, if he stopped before the operation was complete, all the pain up to that point would have been useless. But is it credible that such extremities of torture should be necessary for us? Well, take your choice. The tortures occur. If they are unnecessary, then there is no God or a bad one. If there is a good God, then these tortures are necessary. For not even moderately good Being could possibly inflict or permit them if they weren’t. Either way, we’re in for it.

I think we often miss this when we consider what a "good God" would be like. In today’s culture, we want to believe that a truly "good God" would not discipline us, allow us to take a path that will hurt us, or use the evil in the world to accomplish His good plans for making us more like Jesus. We try to fit God into a box where His goodness is subject to our desires and comfort. Is that good though? Is a parent who does not discipline their child doing that child a favor? It is painful to have a broken bone set, but if the medic acquiesced to the pleas to stop before the bone was set, would that be good? In each case the child or the injured individual may be thankful at the time, but in the long run, they would be hurt a great deal more. Thankfully we have a wise and a good God who knows better than to stop before He is finished. It is also kind of frightening to believe in such a God because we then have to come to grips with the reality that He may do something for our good that is extremely unpleasant. We have to realize that He uses suffering to produce Christ-like character and hope in us (Ro. 5:3-5). That means there will be times when we may wish that He would be subject to bribes like some kind of "Cosmic Sadist," but if He were, He would not be good. During these times we have to remember what Charles Spurgeon once said, "When you can’t trace God’s hand, trust His heart."

By His Grace,
Taylor

True Joy II

Remember, O my soul,
  It is thy duty and privilege to rejoice in God:
  He requires it of thee for all His favours of grace.
Rejoice then in the Giver and His goodness,
Be happy in Him, O my heart, and in nothing
   but God,
  for whatever a man trusts in,
  from that he expects happiness.

He who is the ground of thy faith
  should be the substance of thy joy.
Whence then comes heaviness and dejection,
  when joy is sown in Thee,
   promise by the Father,
   bestowed by the Son,
   inwrought by the Holy Spirit,
   thine by grace,
   thy birthright in believing?

Art thou seeking to rejoice in thyself
  from an evil motive of pride and self-reputation?
Thou hast nothing of thine own but sin,
  nothing to move God to be gracious
  or to continue His grace towards thee.
If thou forget this thou wilt lose thy joy.
Art thou grieving under a sense of indwelling sin?
Let godly sorrow work repentance,
  as the true spirit which the Lord blesses,
  and which creates fullest joy;
Sorrow for self opens rejoicing in God,
Self-loathing draws down divine delights.
Hast thou sought joys in some creature comfort?
Look not below God for happiness;
  fall not asleep on Delilah’s lap.
Let God be all in all to thee,
  and joy in the fountain that is always full.
~ "A Colloquy on Rejoicing", The Valley of Vision


I have quoted from The Valley of Vision before so some of you may already know this but this work is a collection of Puritan prayers, poems, and devotionals. I love reading from it because each prayer is short yet so rich with good theology and the glory of God. I like this one because it reminds me of a lot of the Psalms that David wrote calling his soul to rejoice in God and bless His name (Psalms 31, 32, 103, and 104 to name a few).

I also like it because it reminds me of what our purpose on earth really is. The first question of the Westminster Shorter Catechism asks, "What is the chief end of man?" and answers "The chief end of man is to glorify God [Isaiah 43:7; 48:11; I Corinthians 10:31] and enjoy Him forever [Psalm 16:5-11; 144:15; Isaiah 12:2]." One of my favorite things about this answer is how it wisely combines enjoying and glorifying God. Do you see it? The "chief end" (singular) has two components--glorifying God and enjoying Him forever. Glorifying God and enjoying Him are not two different ends but two aspects of one end. We cannot have one without the other. True, endless joy is only found in Him and only in enjoying Him can we truly glorify Him.

Jonathan Edwards (a Puritan preacher and American philosopher) wrote on this subject often. One of my favorite things he wrote is in The End for Which God Created the World:

God in seeking His glory seeks the good of His creatures because the emanation of His glory... implies the... happiness of His creatures. And in communicating His fullness for them, He does it for Himself, because their good, which He seeks, is so much in union and communion with Himself. God is their good. Their excellency and happiness is nothing but the emanation and expression of God's glory. God, in seeking their glory and happiness, seeks Himself, and in seeking Himself... He seeks their glory and happiness.

Another quote on this subject, that I have previously written about here, which I love comes from Augustine's Confessions:

Forbid it, O Lord, put it far from the heart of Thy servant, who confesses to Thee--far be it from me to think I am happy because of any and all the joy I have. For there is a joy not granted to the wicked but only to those who worship Thee thankfully--and this joy Thou Thyself art. The happy life is this--to rejoice to Thee, in Thee, and for Thee. This it is and there is no other.

May we always remember that any other joy we might experience is not true joy, but fleeting, and that we can only have true joy in God. Even all those things that God has blessed us with were given to us so that we could have joy in Him through happiness in His gifts. If we ever start to look to the gifts for joy, instead of Him, they will cease to satisfy, but if, while enjoying the gift, we look past it to the Giver, we will find true joy in Him.

By His Grace,
Taylor