Archive for the ‘genetics’ Category

My regrets for not being able to post the thoughts of my heart these last few months. Life’s events have managed to overtake us and we are now beginning to get back to a normal level of chaos.

I did make one major gesture to try to get myself re-oriented. I proposed a presentation for the Kirtland Symposium scheduled for October 17 and 18. The proposal was accepted so I will be on the agenda for the meeting.

The topic? Something new and different. The topic of my 90-minute session is Faith, Evolution, and Intelligent Design. This is a subject that has been working in the back of my mind for a number of years and I felt that it was the right time to speak to the questions and concerns as I worked through my crisis of faith. I plan to provide the perspective of an engineer as I analyze several key aspects of evolution and the ‘un-scientific’ intelligent design. What are the elements of the evolution of life that are problematic to me as I ponder the elements of matter, energy, and information necessary to install and proliferate living organisms? How much faith does it really require to adhere to the doctrine of a designer or to the doctrine of a natural evolution of life?

Hope you can join me in Kirtland for this event.

I had the opportunity recently to hear Leigh Anne Touhy speak at a function recently. Her effort to rescue a young black man from the streets of Memphis was immortalized in the Michael Lewis book “The Blind Side” and a movie by the same name.

Leigh Anne saw a person walking down the street in shorts and no coat on a cold day in November. She turned the vehicle around and asked the young man if they could do anything to help him. He only wanted to be dropped off at the closest express bus stop. Later, Leigh Anne, not willing to be satisfied, went to the school where this young man, Michael Oher, had recently transferred. She was told repeatedly to drop her interest in the young boy as he was a lost cause.

You probably know the story – this lost cause, adopted by the Touhy family, played football at the University of Mississippi and was drafted by the Baltimore Ravens.

In her presentation, Leigh Anne also told the story of the father and son walking down the beach after a storm. The boy was busy throwing starfish that had been washed ashore back into the water. When his father asked the boy why he thought he could make a difference, the boy replied, tossing the starfish back into the water, “I made a difference to that starfish.”

starfish on beach

She also talked of her faith in God, relaying that we are not to be the judge of those in need. God will judge those who receive our help, and God will judge us for our help or non-help of others.

As she talked of this topic, I was reminded of the scripture in the sermon by King Benjamin regarding retaining a remission of one’s sins found in Mosiah, chapter 4:

16  And also, ye yourselves will succor those that stand in need of your succor; ye will administer of your substance unto him that standeth in need; and ye will not suffer that the beggar putteth up his petition to you in vain, and turn him out to perish.

In this day, can we rightly assume that ‘the government’ will step in to help those who are in need of succor? With the great safety net provided to all who reside in our country’s borders, are there any truly needy?

17  Perhaps thou shalt say: The man has brought upon himself his misery; therefore I will stay my hand, and will not give unto him of my food, nor impart unto him of my substance that he may not suffer, for his punishments are just—

Did the person in need not try hard enough in school? Did they choose to be lazy? Were they not given the appropriate role models to understand how to be successful?

18  But I say unto you, O man, whosoever doeth this the same hath great cause to repent; and except he repenteth of that which he hath done he perisheth forever, and hath no interest in the kingdom of God.

No place in the kingdom of God if one does not help the needy? How much background information do we need before we should be willing to help?

19  For behold, are we not all beggars?  Do we not all depend upon the same Being, even God, for all the substance which we have, for both food and raiment, and for gold, and for silver, and for all the riches which we have of every kind?

What is really ours? We are born, we live, we pass away. We are not able to take any of our substance, our gold and silver and riches, with us when we move on.

20  And behold, even at this time, ye have been calling on his name, and begging for a remission of your sins.  And has he suffered that ye have begged in vain?  Nay; he has poured out his Spirit upon you, and has caused that your hearts should be filled with joy, and has caused that your mouths should be stopped that ye could not find utterance, so exceedingly great was your joy.

Does receiving a remission of our sins not bring joy into our lives? Does it ‘rewire’ our view of others? Being born again does fill our hearts with joy. It does change our view of our place in the world.

21  And now, if God, who has created you, on whom you are dependent for your lives and for all that ye have and are, doth grant unto you whatsoever ye ask that is right, in faith, believing that ye shall receive, O then, how ye ought to impart of the substance that ye have one to another.

Does becoming a son or daughter of God place us in a position of responsibility to help those around us who are in need?

22  And if ye judge the man who putteth up his petition to you for your substance that he perish not, and condemn him, how much more just will be your condemnation for withholding your substance, which doth not belong to you but to God, to whom also your life belongeth; and yet ye put up no petition, nor repent of the thing which thou hast done.

Does the beggar need to be in danger of perishing before we are obligated to help? How do we know when this is the case?

23  I say unto you, wo be unto that man, for his substance shall perish with him; and now, I say these things unto those who are rich as pertaining to the things of this world.

Who, reading this, could not be considered ‘rich’ today when those considered poor have access to food stamps and free cell phones?

24  And again, I say unto the poor, ye who have not and yet have sufficient, that ye remain from day to day; I mean all you who deny the beggar, because ye have not; I would that ye say in your hearts that: I give not because I have not, but if I had I would give.

25  And now, if ye say this in your hearts ye remain guiltless, otherwise ye are condemned; and your condemnation is just for ye covet that which ye have not received.

If one is poor relative to the things of the world and hates his neighbor who has more, they are equally condemned?

26  And now, for the sake of these things which I have spoken unto you—that is, for the sake of retaining a remission of your sins from day to day, that ye may walk guiltless before God—I would that ye should impart of your substance to the poor, every man according to that which he hath, such as feeding the hungry, clothing the naked, visiting the sick and administering to their relief, both spiritually and temporally, according to their wants.

27  And see that all these things are done in wisdom and order; for it is not requisite that a man should run faster than he has strength.  And again, it is expedient that he should be diligent, that thereby he might win the prize; therefore, all things must be done in order.

We are told in these verses that we are all beggars, that we are to share of our substance with those that are less fortunate without judgment. We cannot know what is in the heart of those people we see who are in need. As I pondered these things, my mind went back to those occasions when I was too busy to stop for a moment and provide financial help to those who are less fortunate. I asked myself if I would have taken the same steps as Leigh Anne Touhy and turned around to help a black youth on the streets of Memphis. I doubt I would have had the courage.

Rock Waterman, in his June post, http://puremormonism.blogspot.com/2013/06/of-alms-and-offerings.html, hit the nail on the head. It is easy for many of us to make the assumption that we are covered because of our donations to the church. We give our tithing, fast offerings and other items by check each month and are absolved of any need to help? I believe that is not the case. We are, as instructed, in the passage above, to help those people in need that we encounter on a daily basis. We are to give of our substance to those people who are less fortunate. We are to do it without judgment

Leigh Anne told a story of her son at a gas station. The electronics at the pump were not working so all customers had to go inside to prepay. As her son, Collin, waited to pay, the man ahead of him gave the clerk a $5 bill. Questioning, in his mind, why someone would only ask for five dollars worth of gas, Collin reached forward and added a $20 bill to the man’s request.

Outside, the man came to Collin with tears in his eyes. He didn’t have enough money to pay for gas to get to work that week. Both the man and Collin went away from the event with joy in their hearts.

We are told in the scriptures that it is our obligation to help those in need. We cannot know the true circumstances of another person, only God does. I recall, years ago, going to catch a flight at O’Hare airport in Chicago. I came across a nicely dressed man who asked me for some change to make a telephone call (this is before the era of cell phones). I gave him several coins and went on my way. The next week, I saw the same man who made the same request. I challenged him on being there a week earlier and refused to give him any assistance.

I look back now on that experience. The man was not enhungered, he did not appear to be destitute, he was wearing nice clothes.  I judged him as being deceitful and did not give him of my substance. Is there an obligation on the part of the ‘poor’ to be honest? Was it judgmental of me to not give the man more money?

There is a lot of deceit in the world today. We see scams and viruses, derivatives and pyramid schemes. We see reports of the activity of greed swirling about us. There is a natural reaction to question the motives and real circumstances of anyone who approaches us. I can only hope to rely on the Spirit to guide me in these circumstances.

If we are to ‘retain a remission of our sins’ as promised by King Benjamin, we are required to give of our substance without questioning the motive of the poor. We are to feed the hungry, provide clothing to the naked and provide spiritual nourishment to those in need.  A giver and a receiver.

In the end, all my questions are moot. There is little room for self analysis. If we are to be about God’s work, we should be looking for ways, after the poor are clothed and fed, to seek to uplift them spiritually. To expand our vision beyond our little spot on earth is very challenging. There is much hunger and nakedness in the world at large, how are we to make a difference in this vast ocean of pain, misery, hunger, disease, malnutrition, and filth?

The physician we have chosen to use locally spends much of his time in places where people are in great need. He uses the income from his practice to participate in Doctors without Borders. He collects computers and has volunteers who help him prepare them for use in areas where he visits. He has adopted a school in Haiti that takes much of his time and energy. There are others that give of their time and talents to help those unfortunate enough to be born in the ‘wrong’ place.

Is doing good healthy? In a recent study conducted by scientists at UCLA and the University of North Carolina found that there were positive immune system affects from living a ‘purposeful’ life, while a hedonistic life style had an adverse affect at the genetic level. Here is a quote from BioscienceTechnology.com:

People who have high levels of what is known as eudaimonic well-being— the kind of happiness that comes from having a deep sense of purpose and meaning in life (think Mother Teresa)— showed very favorable gene-expression profiles in their immune cells. They had low levels of inflammatory gene expression and strong expression of antiviral and antibody genes.

However, people who had relatively high levels of hedonic well-being— the type of happiness that comes from consummatory self-gratification (think most celebrities)— actually showed just the opposite. They had an adverse expression profile involving high inflammation and low antiviral and antibody gene expression.

Favorable gene expression equates to a positive health environment. So, charity is good for the immune system, as well as the soul.

What think ye?

Yesterday, I had the privilege of attending the graduation ceremony for the UC Berkeley school of Molecular and Cell Biology. The invited speaker was Dr. Bruce Ames, a noted scientist, who for decades has produced ground breaking work in genetics and how various substances impact our health at the molecular level. Dr. Ames provided a concise review of his most recent research into nutrition. According to his research, there are 40 micro-nutrients that are essential for our health and continued existence. Remove any of these 40 substances from our diet and we will weaken and die. His research points to the damage at the cellular level that occurs when any of these nutrients are missing.

He also noted that the body, when confronted with a deficiency of one of these critical nutrients, would direct its application to areas that benefit short-term performance while other body functions are deprived. This restriction leads to cellular damage that presages diseases like cancer. He cited statistics suggesting that a significant percentage of the population is deficient in some of these necessary nutrients. More information is available on Dr. Ames’ website: www.bruceames.org.

As I pondered the words of this esteemed scientist, I was struck by the thought that this idea could just as easily be applied to our spiritual health. Are there micro-nutrients that are necessary for our spiritual health? Do we, by ignoring the consumption of the proper spiritual foods, weaken our faith and set the stage for damage induced spiritual death?

Dr. Ames assailed the ‘modern’ foods made to look attractive in our day such as carbonated sugar water that contains no meaningful value and represents ‘empty calories.’ Are there activities or rituals in which we engage that represent no meaningful spiritual value yet consume a significant component of our faith diet? What represents the empty calories in our spiritual diet as a ‘soda pop saint?’

As I look around me, I see many members who are busily engaged in various activities such as home teaching, genealogy, and fulfilling their callings. While these activities can be perceived as worthwhile, do they represent the equivalent of ‘empty calories’ in a spiritual sense? Yes, it is important that we strengthen one another and perform activities that support the greater good of the congregation, but what do these activities to do our own spiritual metabolism? Are we feeding our spiritual selves the necessary nutritional elements through these activities? In many cases, I think not.

What are the essential nutrients for a healthy spirit?

First, we must seek to understand what the gospel is and apply it in our lives. I believe these nutrients are found in places like 3 Nephi, chapter 27 and D&C 33:11-12. It is not enough to simply recite that faith, repentance, baptism by water, and the sanctification through the baptism of fire and the Holy Ghost is sufficient. One must dig deeply into the meaning and substance of these spiritual concepts. We must ingest these concepts and make them available to every segment of our spirituality.

Second, we must strive to comprehend the mysteries of God. We read the following from Alma, chapter 12:

[9] And now Alma began to expound these things unto him, saying: It is given unto many to know the mysteries of God; nevertheless they are laid under a strict command that they shall not impart only according to the portion of his word which he doth grant unto the children of men, according to the heed and diligence which they give unto him.

[10] And therefore, he that will harden his heart, the same receiveth the lesser portion of the word; and he that will not harden his heart, to him is given the greater portion of the word, until it is given unto him to know the mysteries of God until he know them in full.

[11] And they that will harden their hearts, to them is given the lesser portion of the word until they know nothing concerning his mysteries; and then they are taken captive by the devil, and led by his will down to destruction. Now this is what is meant by the chains of hell.

 What else is spiritual death than the ‘chains of hell?’ One should continually strive for the essential nutrients found in the mysteries of God if they are to avoid the spiritual destruction cited in this scripture.

A great example of a mystery is, in my opinion, found in Alma 40: 3:

Now, I unfold unto you a mystery; nevertheless, there are many mysteries which are kept, that no one knoweth them save God himself. But I show unto you one thing which I have inquired diligently of God that I might know — that is concerning the resurrection.

 

The mystery that Alma then began to expound upon, the resurrection, isn’t normally considered a mystery of God. It was to Alma. How many spiritual concepts that we take for granted are truly mysteries inside? The mysteries of God are obtained through the application of diligent study and prayer. This same Alma speaks of his efforts in Alma 5:46:

Behold, I say unto you they are made known unto me by the Holy Spirit of God. Behold, I have fasted and prayed many days that I might know these things of myself. And now I do know of myself that they are true; for the Lord God hath made them manifest unto me by his Holy Spirit; and this is the spirit of revelation which is in me.

Our spiritual health depends on our continual acquisition of the essential spiritual nutrients. We must continually strive to feed our spirits, not with the empty calories of the works of man but of the bounty of the wisdom of God bestowed through the Holy Ghost

We ‘modern day Mormons’ seem to be starving our spiritual side by filling them with empty calories. The rich feast of the knowledge and wisdom of God awaits them who diligently seek these principles and strive to ingest the mysteries.

What think ye?

I am going to diverge from my usual discussion items relating to doctrines in this post. I want to spend some time rehearsing some of my thoughts on genetics and the human soul. I have a son who is finishing his PhD in Molecular Biology at Berkeley. I have been ‘forced’ to educate myself on the topic so as to be conversant with him on his research and studies.

First, please understand that I am by training a computer engineer so this relieves me of any claim of expertise in my presentation on the topic. Here is some base information on the topic. The human genome is made up of 3.2 billion base pairs. These base pairs are made up of four different sugar and phosphate-based molecules which have been identified as adenine (A), thymine (T), cytosine (C) and guanine (G). As you may know, DNA is represented by a twisted ladder with pairs of these ‘chemicals’ loosely mated together by nitrogen based compounds where adenine and thymine (A-T pair) and cytosine and guanine (C-G pair) form the steps. So, you have the 3.2 billion rung ladder that represents the set of instructions that are used to guide the operation of our bodies. These base pairs are grouped together by function into genes of which there are about 30,000 in humans. These genes are grouped into chromosomes. All living things use this same template of base pairs and genes. The number of base pairs range from about 1.8 million in the influenza bacteria to 100 million in plants to 2.6 billion in mice and up to our 3.2 billion pairs.

Every cell in our body (with the exception of sperm and eggs) contains the complete DNA string described above. Every cell also only ‘activates’ a small portion of its genetic information in the production of proteins which are necessary for the purpose of that particular cell. In the normal operation of a cell, the nucleus or center of the cell manufactures a particular protein that is then transported to the edge of the cell where it is used for some purpose. So, a liver cell has the same base information as a skin cell but they operate completely differently with selected gene being activated in each circumstance.

Hopefully that is enough background for what I would like to discuss. For those interested in this topic, I would highly recommend the book Genome by Matt Ridley.

One aspect of this topic that amazes me is how incredibly complex the process is to get us to a functioning human being. What begins as a single cell, the union of sperm and egg, results in a uber-complex body with each subsystem working off the same ‘template.’ As this original single cell begins to divide, it is only a few days before these cells are called upon to begin to specialize. The mass of cells, which were originally identical, now are called upon to form every organ, bone and muscle found in our bodies. How does one cell know what it is to do? Right now there are only theories on how a cell at one end of the mass of cells is guided to start forming the head and its components while another at the other end works of the feet and toes. How do these cells ‘communicate?’ At this time, I have only found theories that suggest the original mass of cells differentiate based on the presence of electrical or chemical markers that vary by the position in the cell mass. I find these theories woefully inadequate in explaining how my fingers and finger nails formed at the end of my arms rather than on the top of my head ;-].

The other amazing aspect of ‘life’ is commonly referred to as ‘instinct.’ Those innate abilities that we are born with that seem to be hard-wired into our brains. One example is that kittens separated from their mother before their eyes are opened will attempt to cover their fecal matter. Is there some ‘universal’ cat etiquette that is carried into the next generation?

One of my favorite examples of instinct is the cuckoo bird. There are species of cuckoo bird that do not build nests but simply lay their eggs in the nests of other birds. The cuckoo egg is ‘programmed’ to hatch before the eggs of the host nest and the young cuckoo chick pushes the other eggs out of the nest. Having removed the competition, the young cuckoo bird now is nurtured by the host. The thrush, in this picture from Wikipedia, continues to feed what is an obvious (to us) intruder. I think that the positive aspect here is that there are no bounds to the love of a parent. Looking at the size of the nest, you can get some perspective on how ‘out of context’ this situation is.


So… how does the young cuckoo bird know to push the other eggs out of the nest? It had no clues from its parents or the environment to trigger this behavior. How is this invasive species able to continue this behavior over generations?

These are only a couple examples of instinctive behavior among living beings. How does a human baby begin life with the innate ability to suckle from the breast of their mother? How does a sea turtle deposited as an egg in the sand of the beach inherently know to move toward the ocean when it emerges from the egg? How does a spider know how to create a web even though they are separated from any examples?

These are all questions related to how species-related information is transferred to offspring. Through the miracle that is the development of a living organism; basic skills are, somehow, implanted in the brain. In many cases, these implanted skills, or instincts, are necessary for survival.

So, this brings me to the crux of the matter. How can a sequence of sugars and phosphates linked by nitrogen-based chemicals govern the incredibly complex process in the development of a living entity? How can this sequence of chemicals develop into a cognitive being with certain skills imbedded in their brain?

As I peruse the available scientific literature, I find references to this information contained in what is currently called ‘junk DNA;’ segments of our genetic material that has no apparent purpose. There are other theories regarding how this information is carried in the DNA structure but none seem to satisfy the programmer in me. We share with other mammals between 70 and 90% of our genetic material. The unique material is what differentiates us physically from the mice and birds and whales in the world. I find it implausible that the same code used to build the physical body could also contain the programming.

In my mind, the argument is the same as saying a computer parts list when assembled correctly will automatically contain the operating system. As an engineer, I know that I can easily assemble a computer if I have all the physical elements needed. I also know that the computer will not be viable until an operating system is installed. The operating system is the set of instructions needed to make use of the physical components.

Our brain and the associated body are not viable without the equivalent operating system software. In my opinion, the ‘instincts’ we are born with partially represent the fundamental equivalent to this operating system. This is where I need to inject the spiritual aspect of this discussion. I hold that we, as souls or living beings, are a combination of spirit and body.  I believe the spirit which is embedded in the physical body at some point when the cells begin to differentiate carries with it the basic information needed to act in the ‘role’ defined.

It is easy for me to believe that all living things are a combination of physical and spiritual entities. The spirit of the yet to be born bird, or spider, or for that matter, any other living thing brings with it the necessary instincts and basic operating system to function in the context of its existence. We begin with this basic instinct to build our knowledge. I believe that this basic toolkit with which we are born gives us not only the basic tools but also the intrinsic uniqueness that every living thing enjoys.

As I contemplate the incredible complexity of my own body and as I have watched the process wherein new life is brought about, I find it much easier to believe in a creative God than in evolution’s process of trial and error .

From Genesis, chapter one, we read:

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.

The miracle of life is a testimony to me of the existence of this unseen world. There are clues all around us, if we but pay attention.

What think ye?

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