Tuesday, September 25, 2012

The Lord of Pleiotropy

My wife and I were talking about missionary work and I said the phrase "He is the Lord of Pleiotropy!" and wanted to share it.

Pleiotropy is a genetics word, or my definition comes from there, meaning a gene that has multiple effects. For instance a gene could effect both the facial structure and mental capacity of an individual.

Anyway, in the context I was referring to with my wife I was making the argument that the purpose of missionary work wasn't just about helping investigators understand baptismal covenants and the Gospel of Jesus Christ. It is also important for the development of the missionaries themselves. We live in a difficult world and having the Gospel from your youth doesn't guarantee lifelong devotion to the covenants essential to endure to the end.

I think the title of "Lord of Pleiotropy" is more universal than just missionary work, our Heavenly Father seems to be able to manage a complex interaction of promises and purposes essential for His work. Another example is the scriptures. It seems every time I read them they were inspired for just that moment in my life.

Sunday, September 23, 2012

Big Cats and Genetics

My family went to the zoo on Friday and saw the elusive snow leopard. Such a beautiful creature. My wife goes regularly and said the most she usually sees is a tail or spine. We got to see much more when I went, probably due to the late time of our visit. The leopardess looked pretty hungry or desperate to have her sick cubs:

Courtesy of my wife.

This morning I was reading the science page of The New York Times and came across an article about a different big cat, the cheetah. Dr. Stephen O'Brien, now of St. Petersburg State University in Russia and formally of the NIH National Cancer Institute, and some of his colleagues have figured out the genetic variant that changes the type of spotting pattern in different cheetahs:

The one on the right is called a king cheetah. This same gene, Taqpep, is also involved in tabby patterns of domestic cats. Overall pretty cool, and these types of discoveries are helpful in our understanding some questions in evolutionary genetics.

This gene is one of large effect. "Large effect" means that the genetic variant has a direct consequence on the appearance (phenotype). When people think of genetics this is usually the type of variation they are familiar with. Eye color (found in HERC2), hair color (red comes from MC1R), and others, but it turns out that most phenotypes are not derived from genetic variation of large effect, especially for ones of primary interest to us, such as diseases like obesity or autism. They call these latter type of traits complex phenotypes because they usually involve many genes of small effects.

Height is a good example of a complex trait because we know genetics contributes significantly to variation in height (nutrition is important as well). However, height is a composite of many different aspects of our bodies: the length of our necks, the length of our torso, the length of our femur, and so on. In other words height represents an amalgamation of genetics acting on multiple traits all with a much smaller effect. Only when taken together do we see the larger change.

I have been thinking a lot about the genetics of complex diseases/traits and how we may best understand them. I mention it here to introduce the topic, which I will hopefully talk more about soon.

Saturday, September 22, 2012

Spanish fresco restoration again

I wrote about the story of the lady in Spain who painted over the fresco of Christ. She over estimated her talent, well now she is requesting compensation for it which she will give to charity.

I'm really not sure what to think. She claims that since there has been increased tourist traffic to the Church to see her "restoration", she should be given a portion to do with as she wishes. My guess is that it is more of a mockery than anything. They are not going to admire artistry, but a person going beyond themselves and making light of a monkey depiction of the Savior. Not a fan if that is the case. Hopefully I am wrong.

Makes me want to double check where I think my own skills are. And if I should be as confident as I thought.

Thursday, September 20, 2012


A grateful heart, then, comes through expressing gratitude to our Heavenly Father for His blessings and to those around us for all that they bring into our lives. This requires conscious effort—at least until we have truly learned and cultivated an attitude of gratitude. --Pres. Thomas S. Monson (source)

Monday, September 17, 2012

Forgetfulness and Self-introspection

I am unsure why last week was so hard to blog. I just completely forgot with everything going on. I'm not sure it was particularly busy, though a lot did happen. I think mostly I fell out of the habit of looking for things.

I taught Elders Quorum yesterday and really enjoyed the discussion. One of my favorite quotes from Pres. George Albert Smith was:
A man once said to me—or remarked in a place where I happened to be—“Why, these people here seem to think I am full of the devil, but I am not.” And I said to him, “My brother, did you ever know anybody that was full of the devil and knew it?” That is one of the tricks of the devil: To get possession of you and keep you from knowing it. And that is one of our difficulties. (source)
I like how it strikes at a fundamental issue we all face. Nobody wants to look at themselves and think, I am wrong or bad. We think we are generally good and give ourselves the benefit of the doubt. Its that old adage about how we judge ourselves by different standards than we judge others. My new favorite example of this is Judge Frollo from The Hunchback of Notre-Dame. He considers himself the ultimate example of piety, but we learn through his actions that he is the true monster of the story.

As a class we came up with some solutions to protect ourselves or at least fight against this tendency: self-introspection, humility as the main issue here is pride, and listening to friends we trust. I think these are all good ideas and I know I could do better at all of them.

Monday, September 10, 2012

Lorenso Snow for Next Year

So I was ordering some church materials and came across this link, to the Manual for Priesthood and Relief Society for next year. Pretty exciting!!

One cool quote with 10 minutes of perusal:
There is no necessity for Latter-day Saints to worry over the things of this world. They will all pass away. Our hearts should be set on things above; to strive after that perfection which was in Christ Jesus, who was perfectly obedient in all things unto the Father, and so obtained His great exaltation and became a pattern unto His brethren. Why should we fret and worry over these temporal things when our destiny is so grand and glorious? If we will cleave unto the Lord, keep His commandments, pattern after His perfections and reach out unto the eternal realities of His heavenly kingdom, all will be well with us and we shall triumph and obtain the victory in the end. (pg. 102)
Something I have been needing to remember lately.

Friday, September 7, 2012

Research Making a Difference

So my wife pointed out a cool article on a NY Times article describing the results of a research study looking at duration of CPR and outcomes. The main conclusion was that in some cases longer durations turned into better outcomes:

The findings challenge conventional medical thinking, which holds that prolonged resuscitation for hospitalized patients is usually futile because when patients do survive, they often suffer permanent neurological damage. To the contrary, the researchers found that patients who survived prolonged CPR and left the hospital fared as well as those who were quickly resuscitated. (emphasis added)
I do not do anything close to this kind of research, but things like this give me hope that as we move forward more and more people will benefit from the inspiration and revelation that comes through research. In this case a measurable and direct effect on the lives of ER patients. So very cool. For me it also gives impetus to do the research well so that others, albeit indirectly, can benefit in some small way.

Research needs to be thorough and measured. For example at the end of the article one of the main authors says:

You don’t want to be on the low end of this curve. Hospitals that are outliers should reassess what they’re doing and think about extending the duration of their CPR....There isn’t going to be a magic number. If you’re in there 10 to 15 minutes, you need to push higher, but as you get up higher and higher, you get to the point of very little return. - Dr. Stephen J. Green
His interpretation calls for change and reevaluation of previous assumptions, not the call for new ones. Conscientious change.

Update: I realized the connection to what I posted the previous day and have added a link.

Wednesday, September 5, 2012

Hugh B. Brown on Academic Research

We should all be interested in academic research. We must go out on the research front and continue to explore the vast unknown. We should be in the forefront of learning in all fields, for revelation does not come only through the prophet of God nor only directly from heaven in visions or dreams. Revelation may come in the laboratory, out of the test tube, out of the thinking mind and the inquiring soul, out of search and research and prayer and inspiration. We must be unafraid to contend for what we are thinking and to combat error with truth in this divided and imperiled world, and we must do it with the unfaltering faith that God is still in his heaven even though all is not well with the world. - Hugh B. Brown "A Final Testimony," from Edwin B. Firmage, ed., The Memoirs of Hugh B. Brown: An Abundant Life, Signature Books, Salt Lake City, UT, 1988. (I took it, along with the reference info, from here)
Today was a busy day so I figured I could share one of my favorite quotes. Maybe I will be able to discuss it later.

Monday, September 3, 2012

Trials and Blessings of Having a Neurostimulator

At the outset I want to state that having a neurostimulator is an absolute miracle in my life. During fast and testimony meeting yesterday many were discussing the miracles in their lives and I didn’t get up to add my piece. My thoughts were tied too much with what I have been thinking for other blog posts and I didn’t think the pulpit the right medium for those thoughts.

There has been one challenge with it though; my muscles are so sore from “working out”. I am able to mask the neuropathic pain and almost any other sensation so well that I don’t know when I have over done it. So Saturday watching my kids alone for most of the day and doing some chores around the house significantly worked out muscles I haven’t used in awhile. Hopefully over time this will become less of a challenge as the muscles become stronger, and in the end it may be a further blessing, but right now I am just very sore.

Sunday, September 2, 2012

Signs and Design

So the stars aligned this week as I was reading today’s Sunday School lesson (Hel. 6-12) and finishing up the biography of Asa Gray (who is my newest hero). The major theme of the lesson is the pride cycle, but as I pointed out earlier there is a significant reference to signs. Signs are interesting as it isn’t always the non-believers that are asking for them. Sometimes believers need them and refuse to believe any challenge or information that may conflict with those previously perceived signs.

The main story that spurred this thought comes from chapter 8: Nephi is calling his community to repentance, as they harbor a secret society, which gains power through murder and subterfuge. The judges who were members of said secret society didn’t like what he was saying so they incited some of the people against him

Finally, he states:
24 And now, seeing ye know these things and cannot deny them except ye shall lie, therefore in this ye have sinned, for ye have rejected all these things, notwithstanding so many evidences which ye have received; yea, even ye have received all things, both things in heaven, and all things which are in the earth, as a witness that they are true. 25 But behold, ye have rejected the truth, and rebelled against your holy God ...
He then further condemns them for harboring murderers and states: “27 Yea, behold it is now even at your doors…” and makes a prophesy about the murder of the chief judge. The people then select five people to confirm his statements They say they don’t believe Nephi, but will if what he says about the Chief Judge proves true. What he had said is true, converting the five and causing them to keel over. The corrupt judges though are unconvinced, saying that Nephi must be in league with whoever committed the murder. Nephi proves his innocence by telling the people how to get the true murderer to reveal himself. This vindicates him both as a prophet and as a non-murderer.

I realized on reading this story that signs figure heavily in our understanding of faith. In this case, signs convert the five who were sent, others believed Nephi’s words alone, and the judges refused to accept even with the evidence of the sign in hand. I think there is a fourth kind of individual out there, those that believe first, but enjoy/need/desire some confirmation of this faith through tangible signs and miracles. These groups are then comparable to atheists (judges, as they refuse to believe), agnostics (five men converted only by concrete evidence), and two groups of people of faith (those believing the words only and those needing signs after the fact).

In the biography of Asa Gray there is a chapter summarizing his attempts to argue for the reconciliation of evolution (at that time Darwinism) and religion. He first made an argument that God could use “beneficial lines of variation” which did not go over well among the agnostics including the main inner circle of Darwin and his supporters*. Gray abandons this line in later years calling it an incomplete metaphor for what he was really trying to say. I didn’t get his full argument clearly from the biography, but apparently Gray published a book called Darwiniana, which I am now interested in reading. In essence, Gray was attempting to save the design argument: nature can only be so beautiful, complex, and inexplicable because of a Designer. This was a consistent conversion tool as well as a buttress against non-believers. It could be used to tell the “five who ran” that if you want a test for the existence of God, look at nature and all that is around you.

For agnostics and atheists, evolutionary theory negated this argument, as biodiversity was not as mysterious. Gray’s philosophy was that “science is neutral” with respect to God (and faith), and a design argument could still be made with evolution. Ie God using natural selection to design species where we would see how advantageous the traits they possess are for their survival. This was still rejected by agnostics, as it is a weak argument**

As I said at the beginning, what I think is more telling is the response of the faith community. Some liked Gray’s attempts, but many did not like evolution primarily because it caused a challenge to the design argument. They felt frustrated with evolution because now non-believers could respond to the design argument with “yes, look all around you we can explain that with science.” The believers were not challenged in their faith, but wanted the sign as evidence and were/are reluctant to give up the argument as lost. Now the sign they saw before is more important than understanding more about the natural world, which we can get through methods like science.

So how do we reconcile evolution or science in general with scriptures (among my favorite) such as Moses 6:63:
63 And behold, all things have their likeness, and all things are created and made to bear record of me, both things which are temporal, and things which are spiritual; things which are in the heavens above, and things which are on the earth, and things which are in the earth, and things which are under the earth, both above and beneath: all things bear record of me.
I think the key is to understand that nature testifies or gives witness of God and it is not given for logical argumentation. It requires a desire to believe. If one has the perspective of belief, you can see the hand of God in all that is around us. We can even learn more about the nature of God, His way of interacting with us, and how we can be more like Him. If one decides not to believe then it is hard to distinguish what exactly is the hand of God. Here is the main problem: there is no control as God created everything or viewed from an atheist perspective nothing***. I mean by this that no one aspect of nature can be contrasted with another to test if it was designed or not. It is all the same in this respect.

Just because something now falls into the preview of a scientific theory, meaning we have a reasonable idea of how it happened, does not take away the miracle of it. It still testifies of God when viewed through the lenses of faith. Some don’t like to accept this, requiring a miracle to be inexplicable. This philosophy makes me feel sad for all the miracles they miss everyday.

*As an aside, Darwin’s agnosticism was rooted in his difficulty with theodicy: how could an all-powerful, all-knowing being be benevolent AND let bad things happen. Something many today still struggle with.

**While I agree it is a weak argument I don’t think parsimony (elimination of extraneous complexity) is always reality and it is my belief that to see God in nature first requires faith, something that does not go well with argument, as it is by definition illogical. “...faith is not to have a perfect knowledge of things; therefore if ye have faith ye hope for things which are not seen, which are true.”.

*** I’m not a huge fan of strict dichotomies as they usually prove false, but in this case I am relying on scriptures: Colossians 1:16-17, among many others.