Computing Sidebar: TeX stuff

I recently upgraded my setup to Mac OS 10.11, which broke a few things, one of which was my TeX installation.  TeXshop is an open source distribution avaialble for Mac OS X that is installed with TeX Live when you download MacTex from the home page of the TeX Users Group (www.tug.org).  TeX is frequently used (including by me) for publications and dissertations (yay!)

Reinstalling MacTeX is relatively painless and well described by the instructions on the MacTeX download page (http://www.tug.org/mactex/mactex-download.html), so I will not repeat them here.  However, I did find that upon attempting to run the Tex Live Utility, I was unable to use the utility to update packages, and repeatedly encoutering the error “Listing Failed” under the update section

My problem was that the utility was unable to access the server for the repository that it was attempting to use for the software updates.  After searching blogs on some slightly different bugs and problems (e.g. http://mirror.ctan.org/systems/texlive/tlnet), I finally resolved the issue by switching to a new repository.  The steps: 

1. Select the menu “Configure" —> “Manage repositories”
2. Choose another repository by double-clicking or whatever you do for your computer to follow a link selection

This should ask you about using the new repository as your home repository as well (I accepted; probably not necessary), and give a confirmation dialog.  I was also prompted to accept an update of the infrastructure of the utility, which I also accepted.  

I recommend restarting the TeX Live Utility after the repository change, and particularly after the update to the infrastructure.

The infrastructure can also be updated by selecting “Reinstall TeX Live Manager” from the “Actions” menu.

Finally, after the repository change and upgrading the utility, I am able to use the utility to update my TeX packages by selecting “Update All Packages” from the “Actions” menu (updating selected packages is also possible).

This fix was performed for Tex Live Utility v1.23 on Mac OSX 10.11.2  (El Capitan).

 

Voila! Happy TeXing!

My Favorite Psalm

"The heavens declare the glory of God; and the firmament sheath his handiwork.

Day unto day uttereth speech, and night unto night sheweth knowledge. 

There is no speech nor language, where their voice is not heard.

Their line is gone out through all the earth, and their words to the end of the world.  In them hath he set a tabernacle for the sun, 

Which is as a bridegroom coming out of his chamber, and rejoiceth as a strong man to run a race.

His going forth is from the end of the heaven, and his circuit unto the ends of it: and there is nothing hid from the heat thereof.

The law of the Lord is perfect, converting the soul:  the testimony of the Lord is sure, making wise the simple.  

The statutes of the Lord are right, rejoicing the heart:  the commandment of the Lord is pure, enlightening the eyes. 

The fear of the Lord is clean, enduring for ever:  the judgements of the Lord are true and righteous altogether. 

More to be desired are they than gold, yea, than much fine gold:  sweeter also than honey and the honeycomb. 

Moreover by them is thy servant warned:  and in keeping of them there is great reward. 

Who can understand his errors? cleanse thou me from secret faults.  

Keep back thy servant also from presumptuous sins; let them not have dominion over me:  then shall I be upright, and I shall be innocent from the great transgression. 

Let the words of my mouth, and the meditation of my heart, be acceptable in thy sight, O Lord, my strength, and my redeemer."

Psalm 19

Picture credit:  NASA Astronomy Picture of the Day, July 14, 2014 (http://apod.nasa.gov/apod/ap140714.html)

Life takes GUTs....

The intricacy and unity of the universe is one of the coolest and most amazing things to think about. It's funny how many things "matter but don't" (but do). The strong force keeps the very nuclei of atoms from ripping themselves apart, but acts over distances so short that it's undetectable on macroscopic scales. Gravity holds the galaxies in clusters, but is weak enough in everyday life to be bested, at least temporarily, by a little girl jumping or tossing her doll.
Life is the same. We eat, we sleep, we fight, we play. At the end of it all, the only thing that really matters is what we do with the priceless gift of salvation offered by God's Son, Jesus. But the little things on this side still matter. They can draw people to Jesus or help them find reasons to back away. They can show growth of character or the onset of compromise. The "equations" you live by can unify or unravel in an inconsistent mess...

Quantum Mechanics and the Gospel

In physics, as in mathematics, one often deals with *asymptotes*, defined by Google as "a line that continually approaches a given curve but does not meet it at any finite distance". This concept shows up pretty much everywhere. When you're talking about asymptotes, the bottom line is that basically, you follow this smooth line forever and ever, but it never quite gets you where you're trying to go, never quite reaches that point that it's trying to hit. You approach a value, getting closer and closer, but by less and less, and ultimately, you fail.

For weeks, maybe months, this is the picture that I've gotten in my head when I think of the concept of works righteousness versus grace. You can do all you can do to earn your salvation, but in the end, the Bible says that "all our righteousness is as filthy rags" (Isaiah 64:6) . You just won't get there. You just can't do it. There's a huge, unbridgeable gulf between what we can do and what God requires, and unlike in math, you never even get close enough to "assume" you're there and move on.

So what can you do? Nothing, if you just keep following that line. But, chips ahoy! There's hope! It's like ... A quantum leap!

Now we're looking at a little change of metaphors. In quantum mechanics, particles don't go smoothly from one state to another, because contrary to the assumptions of calculus, the energy states aren't continuous - there are only a few, particular, separate states in which it can exist, and it can only change states when the right amount (and nothing less) of energy has been absorbed or released by the system to permit it. Adding less than required and trying to give it a chance to "build up" won't work. (If you like science and aren't familiar with this, check out the photoelectric effect. Its discovery is actually the reason that A. Einstein won the Nobel Prize.) The set of possible energies is discrete. However, though there's a vast and gaping discontinuity between one state and the next, if there is something that can provide what's needed to make the change, it can be made.
And this is the hope that Jesus provides for us. We couldn't do it, but he met the standard and paid the price, fully. Nothing more was needed. The thing is done.

Hollapraize :)

Repost!

So, I really will update and finish this soon. There's been kind of a lot going on. In the meantime, I merged this with an older version of the blog, so if some of the dates are a little surprising, well, that's what happened. Look forward to posting more soon!

Free Particles

(Author’s Note:  In order to post entries in a timely manner, it has become clear that it will be necessary to break some entries into several  posts, even if some of the posts are quite short.  This is one of those entries…)

One of the interesting concepts of physics is that of a free particle. 

Often when the word “free” is used in the general vernacular, it invokes a sense of unlimited choice.  Be who you want to be, do what you want to do – no rules, no limitations.  The possibilities are endless.  There is no right or wrong.  This is not quite correct.

“Free” is a much richer concept than “having an endless supply of options”.

To be continued…

Preface: A Christian and a physicist

Psalm 19:1-3 states:  “The heavens declare the glory of God, and the firmament sheweth His handiwork.  Day unto day uttereth speech, and night unto night sheweth knowledge.  There is no speech nor language, where their voice is not heard.”

This is one of my favorite verses in the Bible.  The very creation that we observe each moment gloriously displays the majesty and beauty of our God.  As both a Christian and a physicist, I am fascinated whenever I notice a parallel between a natural law and biblical truth.

I would like to establish my position from the outset.   I am a Christian.  My worldview is that God created the heavens and the earth from nothing.  I believe that the Bible is literally true.  I believe that Jesus is the Son of God who came to Earth and died on the cross for my sin, rose again on the third day, and now sits at the right hand of God the Father, preparing a place for me.  I believe that I have been born again and filled with the Holy Spirit, that God is my Father, and that I will live for ever and rule and reign with Jesus the Anointed one in the ages to come.

I also believe that God has called me to be a physicist.  I believe that well- conducted observations and experiments on natural systems can lead to the discovery of useful and decipherable patterns, which in turn can be used to describe the universe in which we live and make reliable predictions regarding the evolution of those systems.  I believe that through repeated experimentation, accurate, reliable results can obtained and used to enhance our understanding of the world around us.  I believe that, properly understood, some of these results can reveal and illuminate the character of God.

I believe that the Bible is the final authority on any subject.  This means that where there is uncertainty or speculation, the Bible is the final, ultimate Word of God on the subject.  Future illumination may come.  When it does, to be sure it will uphold what has already been revealed in the recorded word of God.  I believe that the aid of the Holy Spirit is essential in the correct interpretation of the Bible, as is the careful application of hermeneutics and exegesis.  Christians call this “rightly dividing the word of God”, as in 2 Timothy 2:15. 

I believe that there are some subjects on which the Bible is largely silent, and others in which few details are provided.  In many of these cases, I believe that speculation can be sustained, as long as:
1.  The speculation doesn’t contradict known biblical truth.
2.  The truth of the Gospel is upheld.
3.  There is strong evidence in favor of the hypothesis.
4.  The understanding that the hypothesis or speculation is subject to change with additional revelation or new evidence is upheld.

I believe that true, objective science ultimately points to the conclusion that there is a Creator, that the Creator is the God of the Bible, and that His interactions with man have been real and historical. 

I do not want anything that I say or write in this blog to become a point of contention for members of the Church, or a stumbling block for those who are genuinely looking for a relationship with God and His people.  There have been instances in history where some aspect or theory of the contemporary science was connected with a particular interpretation of scripture, and the Church unfortunately fell into the trap of dogmatizing the associated interpretation.  Later, when the theory was superseded or discredited through new evidence, many saw it as a threat to or a proof against the scripture as well.  This led to all kinds of strife, antagonism, and animosity both within the church and between the church and the world that they were supposed to evangelize.  This is not my aim.  I simply want to share my excitement over what I believe are fascinating and telling parallels between the laws of physics as we know them and the laws of God as they have been revealed to us. 

I hope that you enjoy sharing my journey.