Tuesday, September 29, 2015

Reflections on Intelligent Design--
Good, Bad or Indifferent Science?

Free RNA strand, from Univ. of Chicago at Illinois
"If evolution really works, how come mothers only have two hands?” 
― Milton Berle
 "Intelligent Design is a remarkably uncreative theory that abandons the search for understanding at the very point where it is most needed. If Intelligent Design is really a science, then the burden is on its scientists to discover the mechanisms used by the Intelligent Designer."  Michael Shermer, Why Darwin Matters: The Case Against Intelligent Design
 “That the universe was formed by a fortuitous concourse of atoms, I will no more believe than that the accidental jumbling of the alphabet would fall into a most ingenious treatise of philosophy." Jonathan Swift
It is really quite amazing by what margins competent but conservative scientists and engineers can miss the mark, when they start with the preconceived idea that what they are investigating is impossible. When this happens, the most well-informed men become blinded by their prejudices and are unable to see what lies directly ahead of them." Arthur C. Clarke, 1963


I try to learn from blog comments that disagree with my preconceptions.  One such (on my post  The Theology of Water--Is Design Intelligent?) said that Stephen Meyers' book, The Signature in the Cell,  showed that the Intelligent Design hypothesis was good science, a position with which I did not agree.*   Although as a Catholic I believe in an intelligent Creator,  I do not consider an article of faith like that could be dealt with by scientific methods.   After reading The Signature in the Cell I've modified this stance--somewhat.


In the past, Fr. Stanley Jaki's and Pierre Duhem's descriptions of science have been my guideposts:
"...[a] laboratory [is] a place where one works ...to make observations or measurement which are accurate so that accurate predictions can be made on their basis.   Science, in that sense, is synonymous with measurements, which are accurate because they can be expressed in numbers."  Fr. Stanley Jaki, The Limits of a Limitless Science
"Therefore, if the aim of physical theories is to explain experimental laws, theoretical physics is not an autonomous science; it is subordinate to metaphysics..." Pierre Duhem, The Aim and Structure of Physical Theory.
Pierre Duhem's limitation on physics is based on the following:
  • physics cannot by itself  explain why physics works;
  • a scientist must assume that some rational order exists if his/her work is to be meaningful.   
Fr. Jaki's requirement for quantitative predictions  based on replicated experiments would place much of biology and geology, among other disciplines, into a non-science basket.   Therefore I and others have found this latter limitation to be not altogether satisfactory.

Fortunately, there is another perspective on science, that of "historical science", which Meyers describes in some detail in his book.   Historical science infers from present data what past events might be.    The data may be quantitative, as in cosmology and some parts of molecular biology, or qualitative, as in geology and paleontology.   Historical science uses  "Inference to the Best Explanation"(IBE) ,  or more concisely "abduction", a method which has been criticized by some philosophers of science**.   Nevertheless, it is the only approach possible in those sciences for which replicated laboratory experiments are not feasible.

An everyday example (given by Meyers) of  "Inference to the Best Explanation" (IBE) follows:   You look out your window and see the driveway is wet;  the following three explanations occur to you--it has rained; the sprinkler has been on and set so as to wet the driveway; your car has been washed.   You notice that neither your street nor the grass is wet; thus the rain and sprinkler explanation is eliminated;  accordingly  the remaining one, your car has been washed, must be correct.   Confirmatory evidence for this last would be a pail of water by your car.


"The Signature in the Cell" is particularly concerned with the application of two  principles for understanding the beginning of life, the formation of cells and their critical constituents--proteins, DNA and RNA:
  • "specified information" ("specified complexity") is manifested in biology and molecular biology;
  • such specified information can be brought about only by an intelligence, a designer;  it can not occur by chance or by the working of physico-chemical laws (e.g. chemical affinities).
The second of these principles was expressed in the quotation by Jonathan Swift above.

As an example of "specified information",   consider the phrase "cat in the hat".    This conveys information (for Dr. Seuss fans--a book title and an image).   If one was to draw characters out of a large bag containing the appropriate proportion of spaces, t's, c's,  etc., the probability of getting them in the order "cat in the hat" would infinitesimally small...for all practical purposes, zero***.   Accordingly, if you saw that phrase on a table next to a large bag of characters, you'd assume that a Dr. Seuss fan had arranged them.

Another way of putting the second principle is that specified information is conserved.   Although this seems reasonable at first glance, there is no proof of such that I can find.   If an inverse relation between Shannon information and entropy is made (the greater the information content, the lower the entropy), there is no application of the Second Law that would apply to conservation of information:   The Second Law says that in an isolated system entropy increases (by irreversible processes) or stays constant (for a system at equilibrium) and for open systems sets no general conditions.     So we'll have to accept the second principle as possible, but not proven--a hypothesis.


Meyers discusses how proteins, DNA and RNA are biomolecules encoding specified information.    He argues convincingly that this encoding can not proceed from chance or by natural law.   The probabilities of the sequences occurring by chance are too small, and this view agrees with that of a number of other scientists, not all of whom support intelligent design.

According to Meyers, specified information does not proceed from chemical or physical principals--chemical affinities and attraction, for example, yielding protein folding shapes or sequence order of bases in DNA or RNA.    Were such operative, they might yield order (as, for example, gravity and coriolis forces yield whirlpool shapes in water going down a drain).   However,  such order could not provide for the variety of base sequences needed to encode for the synthesis of many different proteins, nor for the different conformations involved in folding of proteins that yields enzymatic activity.

An important criterion for a theory to be "scientific" is that it can make testable predictions, predictions that can be falsified.   Meyers makes 12 such predictions. The problem with many of the predictions is that they propose  results that may be found with sufficient research, but if they aren't, it won't signify falsification of the prediction.  For example.
"Investigation of the logic of regulatory and information-processing systems in cells will reveal the use of design strategies and logic that mirrors...those used in systems designed by engineers.  Cell biologists will find regulatory systems that function in accord with a logic that can be expressed as algorithms." Stephen Meyer, The Signature in the Cell, Appendix A.
If such results are obtained, it will strengthen the Intelligent Design hypothesis, but it will not necessarily confirm it.

Several predictions propose that positive results from origins of life computer simulations or laboratory work to show spontaneous self-organization require information input.   For example
“Informational accounting will reveal that any improvements in replicase function in ribozymes are the result of active information supplied by ribozyme engineers.” ibid.
I'm not sure how one would show the above, but the fact that it couldn't be shown does not amount to an adequate test of the prediction.  And again, finding such results would strengthen ID, but not confirm it.

The only prediction amongst those listed that might  be falsified--and even here, if the contrary isn't shown, it won't necessarily show the prediction to be true--is the following:
“ No undirected process will demonstrate the capacity to generate 500 bits of new information starting from a nonbiological source." ibid.


The first criticism is given in the quote by Michael Shermer.    Although proponents of Intelligent Design argue that information is put into cell components, they suggest no mechanism as to how this might occur.   Another opponent of the neo-Darwinian thesis, the philosopher Thomas Nagel, has proposed in his book, Mind and Cosmos, that teleology should be considered as a general operating principle in nature.   Although this requirement--purpose as a part of nature--just names, rather than explains the issue, it is a starting point.  And it puts it in such a way that Intelligent Design might proceed from fundamental principles.   Paul Davies puts it very well: 
“...the hypothesis of an intelligent designer applied to the laws of nature is far superior than the designer ...who violates the laws of nature from time to time by working miracles in evolutionary history. Design-by-laws is incomparably more intelligent than design-by-miracles.[emphasis added]Paul Davies,  The Cosmic Jackpot: Why our universe is just right for life." p.200)
The second criticism is that the fundamental assumption of conservation of specified information or specified complexity is assumed.  Although this seems at first like a reasonable assumption, it is necessary that it be justified  from first principles, outside of the realm of biology,  if Intelligent Design is to be considered science.

To sum up,  I do believe in an intelligent Creator--indeed, an omniscient one who orders all for ultimate good--but that belief is an article of faith, not of science. I am glad that I read "Signature in the Cell", because I found a new perspective on what constitutes science, "Historical Science".   But there is still much that proponents of Intelligent Design must do in order that it qualifies as a testable scientific theory.


*I should note that some 15 years ago when I first read Michael Behe's book, Darwin's Black Box, I thought that Intelligent Design revealed a whole new realm of science, manifesting biology as the handiwork of the Creator.

**See, for example, works by Bas van Fraassen or Nancy Cartwright.

***The phrase has 14 characters:  3 spaces, 3 t's,  2 a's,  2 h's, 1 c, 1 e, 1 i, 1 n.  By combinatorial algebra, there  are14!/[ 3!3!2!2!] =  605,404,800 possible combinations of these 14 characters.   If one uses rules such as 1) no initial space; 2) no final space; 3) no two like characters next to each other, 4) t followed by space, h, a, e or i...etc.  the number of possible combinations can be reduced, but it will still be very large.  Thus the probability of getting "cat in the hat" by randomly drawing letters from a large bag filled with the appropriate proportion of characters will be very small.

****Although I have published nmr papers dealing with biochemistry and molecular biology, I am not expert in these topics.    Accordingly what Meyers says in these areas I'll assume to be true.

Sunday, September 20, 2015

Repentance, Atonement, and Forgiveness:
Catholic Thoughts on Yom Kippur, the Day of Atonement

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
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 whatsoever).     I would 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.

Wednesday, September 16, 2015

"What is Truth?" Said the Scientist to the Theologian.

Quid est Veritas. by Nikolai Ge
"Pilate therefore said to Him, 'Are You a king then?'
Jesus answered, 'You say rightly that I am a king. For this cause I was born, and for this cause I have come into the world, that I should bear witness to the truth. Everyone who is of the truth hears My voice.'
Pilate said to Him, 'What is truth?'  And when he had said this, he went out again to the Jews, and said to them, 'I find no fault in Him at all.' " 
John 18:37-38 (KJV)
"... it is still a metaphysical faith on which our faith in science rests--that even we knowers of today, we godless anti-metaphysicians still take our fire too, from the flame lit by the thousand-year old faith, the Christian faith which was also Plato's faith, that God is Truth; that Truth is 'Divine' [emphasis added]" Friedrich  Nietzsche, "On the Genealogy of Morality"
Last night I dreamt that I was judge, prosecutor, defense attorney and defendant in a trial about my conversion to the Catholic faith.   Here, as best as I can recall (having fudged the details) is an account of that trial.   (I'm not learned in the law, and it was a dream, so ...legal beagles, please excuse the deviations from procedure.)*


The defendant has foresworn his devotion to reason and truth:  he has adopted a faith that has no rational or empirical basis.   He has wasted years of training (much of it at public or charitable expense).   As an apostate to the devotion of science, he has attempted to reconcile the ideals of his new-found faith with the corruption of fallible humans in the Catholic Church hierarchy, and with the continued criminality and licentiousness of its institutions.

Not satisfied with debasing himself, he has attempted to corrupt others by posting articles in his blog purporting that Science gives only a limited view of reality (1, 2, 3, 4, 5, 6, 7, 8, 9 , 10).    Further, he has perverted Science by trying to reconcile the teachings of the Catholic Church with modern scientific theories, particularly those of quantum mechanics (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 1617).

Finally, the defendant has invaded the sphere of public policy, claiming that morality trumps public interest.  His Catholic ideology. with its peculiar notion that human life is endowed by a supposed Creator, requires him to oppose policies for reproductive choice and ending suffering of the aged, policies supported by science and social justice (1, 2, 3, 4).

For these offenses and others too unspeakable to mention, we demand that the defendant be banned from blogging and sentenced to hard time in a room where he will encounter his secret fear**.


DEFENSE ATTORNEY, THEOLOGY: Cross-examination of Prosecutor***:
Question (defense attorney)::  How does science judge a theory or proposition to be true?
Response (prosecutor) By seeing what predictions a theory makes, and then making measurements to see if those predictions are met within some sort of error limits.

Question (defense attorney):  OK, then what predictions would a theory about quality of music make concerning the relative merits of Bach and Berlioz, and what would the measurements be?
Response (prosecutor): That's an easy one--you'd poll a sample of people and ask them to rate their liking for Bach and Berlioz on the standard Likert scale.
Comment (defense attorney):  Gee, there seems to be some missing elements in your answer.    What's the theory;  how do you define who would be in the sample--music critics, teen-agers, or ???;  and what would be...
Interjection (judge):  You're getting off-track, Theologian.   Get to the point!
Reply (defense attorney):  My apologies,  M'Lord****.   I was trying to show that science is not competent except in a very limited sphere and therefore cannot criticize the defendant for saying that science gives a limited view of reality.  It is not competent to make judgments in aesthetics, ethics, or any other matter which can't be subjected to replicated quantitative assay.

Question (defense attorney):  You've said that the defendant has foresworn his devotion to reason and truth.   Do you say that only science has reason and truth?
Response (prosecutor):  Well, I'd say that's the opinion of many scientists.  (Laughter in the court).    OK, that's a joke, but maybe not so much.   Science has given results that have made men's lives better and shown them what the universe is like.   What has religion done for men?
Question (defense attorney):   You didn't answer my question, so I'll repeat it.
Does science have a monopoly on reason and truth.
Response (prosecutor):  I plead the Fifth Amendment--refuse to testify on the grounds I'll incriminate myself.
Comment (defense attorney):  I'll answer for you.   There are a host of theologians and philosophers who have used reason to discover truth, from the ancient Greek philosophers--Aristotle and Plato--through the Catholic saints--Augustine and Thomas Aquinas--on up to present time.
Interjection (judge):  Mr. Kurland, that last comment was entirely out of order (although I agree with it).   Be careful or I'll eject you from the court.
Reply (defense attorney):  M,Lord, Judge Kurland, just to keep the record straight, my title is Dr. Kurland.

Question (defense attorney): You've said that the defendant has attempted to reconcile the ideals of his new-found faith with the corruption of fallible humans in the Catholic Church hierarchy.   Could you be more explicit about that corruption?
Response (prosecutor):  Well, you'd have to go back to the Renaissance, the Borgias and all those, and the Inquisition, and also those pederastic priests.
Comment (defense attorney):  I'll invoke what Queen Kristina of Sweden said after her conversion to the faith: "The Catholic faith must be true since the Church has survived so many bad people."    And your comment about the Inquisition and "pederastic priests" has been rebutted by others*****.

Question (defense attorney):  You said the defendant has attempted to reconcile the teachings of the Catholic Church with contemporary science, including quantum mechanics.    Can you point out any errors in the science he has discussed?
Response (prosecutor):  No I can't, but I bet there are some.

Question (defense attorney):  You said that the defendant has published articles against public policy on abortion and euthanasia.   How does science show that public policies promoting abortion and euthanasia would be correct?
Response  (prosecutor):  I can't in a limited space answer that question.
Comment (defense attorney):  In other words, you can't answer the question and the charge is not justified.


At this point the dream ended, as the Judge was pronouncing the verdict "I 
find the defendant .... "   (Dear reader, you fill in the blank.).   And we never did get around to finding out what was truth, but maybe that will come later.


*Some of the Science Prosecutor's comments are drawn from an article by Lawrence Kraus, All Scientists Should Be Militant Atheists  and from comments on a post by Matt Briggs on this article.   I was originally going to do a trial, patterned after that in Prof. Peter Kreeft's audio book "Faith and Reason", in which Socrates would question me and Richard Dawkins, but I'm not sharp enough to emulate Socrates and I'm leery of putting words into Dawkins' mouth that might make him appear more informed and intelligent than he actually is.

**Shades of 1984!   My secret fear is being forced to eat gourmet food cooked by chefs who are "Chopped" judges.   What's yours?

***I told you this dream did not proceed according to standard legal procedures.

****The judge is also me, but the dream is in an English court so he is wearing a wig and addressed as "M'Lord.    (I'd been watching reruns of "Rumpole of the Bailey" that evening.)

*****See Myths about Priestly Pedophilia, Google Search Myths about Inquisition

Sunday, September 13, 2015

More Good Advice from St. Augustine:
Love the Creator in the Creature

St. Augustine and the Fire of Wisdom
As I said in a previous post, it has been my habit to read every night before going to bed, and before the Night Prayer, a daily reading from the works of St. Augustine, Augustine Day by Day, compiled by John Rotelle, O.S.A.

The reading for September 12th, "Love the Creator in the Creature", is for those who every once in a while feel the pull of agnostic beliefs that they may have formerly held.

"Now, may our God be our hope.  He Who made all things is better than all things.  He Who made all beautiful things is more beautiful than all of them.   He Who made all mighty things is more mighty than all of them.   He who made all great things is greater than all of them.
Learn to love the Creator in His Creature, and the maker in what He has made."
  Commentary on Psalm 38,9
Thoughts anticipating those of St. Anselm and St. Thomas Aquinas?

Shalom and Happy New Year!
bob k.

Wednesday, September 2, 2015

There's Hope Yet!

Sometimes you hear / see something that makes you feel there's hope for the world yet...
Please go to the linked video .

Singer Rachel Platten and a youthful cancer patient join in her "This is My Fight Song"

Pray for the little boy.