Tuesday, October 11, 2016

Repost: Catholic Thoughts on Yom Kippur, the Day of Atonement: repentance, atonement and forgiveness

Jews Praying in the Synagogue on Yom Kippur
by Maurycy Gottlieb
“The purpose of Yom Kippur is to bring about reconciliation between people and between individuals and God. According to Jewish tradition, it is also the day when God decides the fate of each human being.” – Ariela Pelaia

“Yom Kippur is the supreme day of forgiveness.” – Jonathan Sacks

“On Yom Kippur, the ritual trial reaches its conclusion. The people finally drop all their defenses and excuses and throw themselves on the mercy of the court, yet the same people never lose the conviction that they will be pardoned. This atonement is by divine grace; it is above and beyond the individual effort or merit.” – Rabbi Irving Greenberg


Beginning this evening at sundown (Tuesday, 11th October, 2016) will be the first day of Yom Kippur, the Jewish Day of Atonement.  I thought it worthwhile to repost the article on this from last year.      

Before my conversion to Catholicism, I observed (as a secular Jew) only one religious holiday, Yom Kippur,    My observance was not orthodox, although I did and do now fast (note: Jewish fasts are more stringent than Catholic--no food or drink whatsoever).     My fast this year will be intermediate between the Jewish and the Catholic--I'll have coffee with milk (and maybe a piece of apple--after all, I am 86 years old!)  When I was younger, I'd go to some place far away from the city, think about the past year and ask God to forgive me for all the sins and wrongs I had committed and ask Him to make me better.


My observance of repentance (Hebrew: t'shuvah)--admitting wrongdoing and asking forgiveness from God--was only a part of the Yom Kippur atonement process.   I have found out since then that Orthodox Jews  hold that there are three ways we can sin: against God, against our fellows, and against ourselves.   

To atone for sins against God and ourselves, Jewish tradition requires that we have to sincerely resolve not to commit such sins in the future.    With respect to sins against myself, I am supposed first, to forgive myself (very hard to do in my case) and second, to set up a program whereby I will not commit that sin in the future.

To atone for sins against others, we have to apologize for hurts we have inflicted on them and ask for their forgiveness, and to make restitution when that is possible.  Interestingly, any Twelve Step Program (some years ago I was involved with several) requires atonement, specifying that we attempt to make amends for what we have done wrong:
Step 8:  “Made a list of all persons we had harmed and became willing to make amends to them all.”
Step 9:  “Made direct amends to such people wherever possible, except when to do so would injure them or others.” 
One article (can't find the reference now) gives the following traditional Jewish practice: if the person you have asked for forgiveness doesn't do so after the first request, you can ask two more times; if the person still doesn't forgive you, you can write it off IF you have made a sincere and effective effort to right the wrong you have done.


So, how do all those Jewish observances square with Catholic teaching and dogma about repentance, the Sacrament of Reconciliation, and the sacrifice of Christ, as the lamb of God, to save us from sin?   As a Catholic, do I err or sin by fasting on Yom Kippur and making special prayers and acts of atonement?

There are several important differences.   First, as a Catholic, I acknowledge and glory in the fundamental dogma of the Church: Jesus Christ replaces the scapegoat that was offered by the high priest at the Holy of Holies in the Temple at Yom Kippur;  He is the sacrificial lamb, who gave Himself up for our eternal life.    He, who was without sin,  took on the sins of world by His Passion.

Second, as a Catholic, I should not offer my repentance directly to God.    My confession of sins and request for forgiveness is made to God through a priest,  in persona Christi, to Jesus Christ, the only begotten Son of God.  Much more can be said about the mental preparation for receiving absolution in the Sacrament of Reconciliation, the resolutions, the contrition, the restitution to those injured (as with Jewish teaching), but this is covered in the Catholic Catechism on this Sacrament.

Suppose a priest isn't available--as the example in my Sacramental Theology class put it, you're on a sinking ship and no priest is available.   What do you do then?    The Church takes all things into consideration and that situation also.  There is "an act of perfect contrition":
"Among the penitent’s acts contrition occupies first place. Contrition is ‘sorrow of the soul and detestation for the sin committed together with the resolution not to sin again.’ When it arises from a love by which God is loved above all else, contrition is called ‘perfect’ (contrition of charity). Such contrition remits venial sins; it also obtains forgiveness of mortal sins if it includes the firm resolution to have recourse to sacramental confession as soon as possible" CCC 1451-52
So there are fundamental differences and there are similarities--similarities in being contrite and resolving to do better, in making atonement and restitution to those we have harmed,  but differences in the mediator through whom we offer repentance,  and in acknowledging a Savior who takes on our sins, including Original Sin.

And with this,  "G'mar Hatima Tova”--may you be sealed in the Book of Life.

Friday, September 30, 2016

The Theology of Science Fiction VI: Karina Fabian's "Discovery"

From karinafabian.com

WARNING:  Possible Spoiler 
"any race advanced enough to cross the stars to visit us must also be
 advanced enough to show us how to overcome all those human ills. They look to the aliens to be saviors of mankind." Vatican Astronomer Guy Consolmagno, as quoted by Catholic News Service, 19th September, 2014.


Karina Fabian asked me to be one of the reviewers of her new Catholic science fiction work, Discovery; I readily agreed.    It's a fine book, one that will probably be a classic in the genre, alongside Walter Miller's great work, "A Canticle for Liebowitz".   I started to read it thinking, "oh no--not another book about religious struggling with their vows,"  and then found I couldn't put it down--finished it in two days. 

This post will not so much be a review of the book (see the reviews at the linked title), but will be a springboard for discussing how the book illustrates very well the quote given above from the Vatican Astronomer Guy Consolmagno.    And necessarily it will be a spoiler.    So if you plan to buy the book, and I strongly urge you to do so, please don't read the rest of this post.   Wait until you finish the book, and then come back here. 


In the magnificent Space Trilogy of C.S. Lewis, only man is vile;  the extra-terrestials are deeply religious and not fallen.   Is it a necessary condition that aliens who can cross interstellar space have achieved an ethical stature beyond ours?   Which picture is correct: the savage Borgs, Klingons and Romulans or the Overlords of Arthur C. Clarke's Childhood's End, who shepherded mankind to a new destiny?

The aliens of Discovery are all dead when found, but there is evidence that they are a people (I was tempted to use "species") who love and have visions of an afterlife.  They have an instrument that heals spiritual wounds--an electronic (or?) combination of peyote, magic mushrooms, LSD and.....???   That such an instrument is needed suggests that these aliens are not always well, but sometimes have to use artifice to achieve peace and well-being.

Why do I believe that a race engaged in interstellar travel must achieve a high ethical level?  
  • First,  cooperation and social order must be achieved, and this requires a moral society.   I don't think humans will achieve interstellar travel until resources are no longer devoted to conflict and defense against that, or until there are no longer large segments of society that have be sheltered from poverty, and that will require a greater level of ethical development than we have at present.   
  • Second,  there must be a yearning to explore the unknown. This desire is, I believe, implicitly connected to glorifying the universe God has made.   
  • Third, given that "warp drive"--travel faster than the speed of light--is a device of science fiction and physically unachievable,  a small group enclosed for many years (and possibly many generations) must be able to live together in harmony, and this requires a high level of ethical development.   Science fiction has dealt with this issue:  in Robert Heinlein's, Universe and Common Sense, and Brian Aldiss's Helliconia Trilogy, moral and social standards decline after contact is lost with the larger group of humanity.


That the aliens of Fabian's Discovery have a religious belief is implicit, although there are no indicators of what this belief might be.   If one googles "ethics requires religious beliefs", a host of sites will come up, each with a different point of view.

There is one classic science fiction story in which this question is crucial, "A Case of Conscience", written by James Blish almost 60 years ago.   In this story a race of intelligent amphibians inhabits a planet, Lithia, devoid of mineral resources.   The Lithians have an innate moral sense, but are devoid of any religious feeling.   I won't recount the plot, but only state the misgivings of the Jesuit missionary (part of a scientific team sent to the planet);  he reasons that the Lithians have been developed by Satan to rebut the Catholic doctrine that morality is given by God.  

Br. Guy Consolmagno, S.J.,  has criticized both the science and the theology of the novel (see the linked article).  However, he does not directly address this issue: is totally moral behavior possible without a religious foundation?   He does make this valid point:  creatures who cannot sin are not totally free;  freedom requires the ability to make a choice between doing right and doing wrong.   That the aliens of Discovery require a spiritual healing device, indicates that they are free in this sense, that is to say, free to make moral choices.


The title of Karina Fabian's novel, "Discovery", refers not only to the alien ship, but also, I believe, to the moral insight achieved by the characters who use the alien spiritual device--a cleansing of sins and a guide to living in the future. 

Saturday, September 24, 2016

God's Gift to Molecular Biology: the Hydrogen Bond

 alpha-helix showing hydrogen bonds
It has been recognized that hydrogen bonds restrain protein molecules to their native configurations, and I believe that as the methods of structural chemistry are further applied to physiological problems it will be found that the significance of the hydrogen bond for physiology is greater than that of any other single structural feature. 
--Linus Pauling, The Nature of the Chemical Bond 

The image at the right is a stick model of an alpha-helix structure, like that of DNA; the spiral configuration is held together by hydrogen bonds (see below), shown as yellow sticks (from Wikimedia Commons).


Much has been said of the Anthropic Coincidences, the special values of physical constants and force laws that enable a universe to support carbon-based life.   Even more remarkable, I believe, are the wonderful physical-chemical processes that sustain the life of living things, from the simplest one-celled organisms to us, all of which are made possible by hydrogen bonding.

In an early post, The Theology of Water, I discussed the marvelous and unusual properties of water, properties that stemmed from the nature of the hydrogen bond,  properties that enables an environment friendly to life as we know it on earth.    In this post I want to explore in more detail the nature of the hydrogen bond and its significance for molecular biology and physiology.   Hydrogen bonding plays a role in biochemical reactions, in anti-body mechanisms, and in all of molecular biology and, most importantly,  in how DNA acts as a blueprint for the synthesis of proteins.  A book would be needed to explore all this in detail, so I'll focus on the essentials--the basics of what a hydrogen bond is and its role in the structure of DNA.


Let's imagine God thinking in his design of nature, now I want chemistry to have not only strong interactions between atoms, but also gentle ones:  so that complicated structures can unfold and rewind easily, and so that big and small molecules can come together and join for reactions and go apart readily--Velcro or a zipper, not glue or nails.   What should I use?  I have it--a hydrogen bond.
(Note:  please don't criticize me for heresy here--I'm using a semi-literary device to make a point.   I know God holds an infinite number of thoughts and   plans simultaneously in His infinite mind.)

Here's the basic idea:  H (hydrogen) bonded to O (oxygen) as in H-O-H (water) shows a slight positive electrical charge;  :O, oxygen with a pair of unbonded (lone) electrons, shows a slight negative charge.   Similarly, :N (nitrogen), with a pair of lone electrons shows a slight negative charge, and N-H, hydrogen bonded to nitrogen, show a slight positive charge.     There is an electrical attraction between these small positive and negative charges;  there is also, as nmr experiments have recently shown, a contribution from chemical bonding (sharing of electrons) to hydrogen bonding, so that it is more than simple electrostatic interaction.

In the figure below are shown the types of hydrogen bonds important in molecules of biological interest.

The single dashes represent single bonds;
The = signs, double bonds;
The - - -, hydrogen bonds;
The " : ", lone pair electrons;
Superscripts, delta plus and delta minus, small net positive and negative charges.

Hydrogen bonds energies are about 1/20 to 1/30 the value of ordinary covalent bonds, so the hydrogen bonds can be broken much more easily than covalent bonds; for example the O-H bond energy is about 430 kJoules/mole, whereas the O-H - - - :O   hydrogen bond energy is 21 kJoules / mole


Watson (or was it Crick?) in a moment of insight noticed that the bases (nitrogen containing molecules bound to sugar pieces in nucleotides such as DNA, RNA) matched each other by hydrogen bonding like pieces in a jig-saw puzzle.   They could thus stabilize a helical structure, by links across the spiral, as shown below.
Diagram: double helix of Chromosome CRUK 065
from Wikimedia Commons
  The base pairs are shown below:

Adenine(A)-Thymine(T) Base Pair
from Wikimedia Commons

Guanine(G)-Cytosine(C) Base Pair
from Wikimedia Commons

Adenine(A)-Uracil(U) Base Pair
from Wikimedia Commons

These bases are attached to sugar-type pieces, which in turn have phosphate groups on them that form the links between base units.   The hydrogen bonds linking base pairs are strong enough to hold together the two DNA strands in the spiral helix, but weak enough that they can be "unzipped" by mild chemical action, an enzyme RNA polymerase, which yields messenger RNA.


Before discussing the mechanism by which DNA enables protein synthesis, a few remarks are in order about the bases as letters in a word,  words which  encode which  amino acids are used as building blocks in the protein.   In this process a linear combination of three bases is used to encode which amino acid is put into a protein.   So we can regard the bases as letters and the combination of three bases as a three letter word; the three letter word is called a "codon".   There are four bases* so there are 4^3 = 64 possible codons.  There are 20 amino acids found in proteins, plus codons for beginning and ending protein synthesis, so that several codons may encode for incorporating the same amino acid, i.e. there is a redundancy.   See here and here for tables showing specific codon / amino acid relations.


I'll give just a brief summary here of gene expression--transcription and translation.   More detailed accounts are given in the linked web sites and videos.

STEP 1: transcription--RNA polymerase unzips the double strand and attaches complementary bases to single strand RNA.   See  here and here**   Note that the RNA polymerase is a large protein, much bigger than the DNA strand.   Also note that one strand of the DNA serves as a "template"--bases complementary to bases in the template strand are linked, e.g. G to C,  C to G,  A to T,  U to A, and as they're linked they detach to yield mRNA (messenger RNA).   See the flash animation for a more detailed description of this process.  PLEASE SEE THE LINKED ANIMATIONS--They will be well worth your while.

STEP 2: translation--mRNA leaves the cell nucleus, goes into the cytoplasm
where it attaches to a ribosome, where protein synthesis occurs.   In the process transfer RNA molecules are sent by the ribosome to attach specific amino acids, coded by the m-RNA, to form a protein.


The description is extremely concise--a lot is left out and I urge the reader to look at the recommended links, animations and explanations and to explore this fascinating subject.   Summarizing gene expression in one paragraph is  much like trying to do that for the Bible, Old and New Testaments.

What amazes me is that molecular biologists and those who deal with gene expression, and all the other wonders of molecular biology don't paraphrase Psalm 19A:  "DNA declares the glory of God, and gene expression shows forth the work of His hands..".     Certainly the hydrogen bond, which is a crucial element in these processes, neither too weak nor too strong, is a marvel in itself.
God's providence in molecular biology is as marvelous as it is in physics.

ADDED 25 September, 2016

One of the hymns at Mass today was "O Beauty Ever Ancient" by Roc O'Connor, S.J.  The hymn is taken from St. Augustine's Confessions.  The third verse struck me as a particularly apt close for this post:
"The created world is glorious, yet I could not see within,
see your loveliness behind all,
find the Giver in the gift."


ADDED 1 October, 2016:  There are a series of posts from Biologos that explain in clear detail the gene expression process.   The link above goes to the first in the series.

*Note: uracil replaces thymine in the RNA and is encoded by the complement of thymine, adenine--see the section on gene expression.   The presumed explanation for this replacement is greater chemical stability of uracil compared to thymine.

**Note: scroll down to get to the animation and click on the arrow to start it.

About Me

My photo

Retired, cranky, old physicist.   Convert to Catholicism in 1995.   Trying to show that there is no contradiction between what science tells us about the world and our Catholic faith.   Intermittent blogs and adult education classes to achieve this end (see http://rationalcatholic.blogspot.com/   and http://home.ptd.net/~rkurland)

Extraordinary Minister of Communion volunteer to federal prison and hospital; lector, EOMC.
Sometime player of bass clarinet, alto clarinet, clarinet, bass, tenor bowed psaltery for parish instrumental group and local folk group.

And, finally, my motivation:
“It is also necessary—may God grant it!—that in providing others with books to read I myself should make progress, and that in trying to answer their questions I myself should find what I am seeking.
Therefore at the command of God our Lord and with his help, I have undertaken not so much to discourse with authority on matters known to me as to know them better by discoursing devoutly of them.”
St. Augustine of Hippo, The Trinity I,8.