Scientific Publishing

Two things I've read recently have caused me to re-think my earlier ideas on scientific publishing (mySDscience, subscription required). I won't rehash all of my previous musings on the subject here, but in short, I suggested that authors be able to publish whatever they'd like into an online repository, as long as they had the approval (and potential co-authorship) of a faculty member. No more journals, no more peer-review, just what scientists think should be published.

After reading much about the arsenic-based bacteria touted recently by NASA (Google News search link), and having just enjoyed thoroughly The Atlantic profile of Dr. John Ioannidis, and his corresponding PLoS Medicine and JAMA articles from 2005, I am convinced that the current model of scientific publishing is broken. What then should or even could we do to fix it?

I believe most scientific research is publicly funded. Therefore, why shouldn't the public have the opportunity to access the research they are funding? I would be completely willing to participate in a publishing system that required me to daily upload my experimental procedures, code, data, and results, and also would accept regular summaries similar to today's publications in scientific journals. These archives would be read-only (unable to be tampered with after the fact), and would accept comments only from those also publishing in a similar way in the same system (no anonymity and no trolls without a vested interest in their own results). I can think of a few questions about such a system:

1. Wouldn't you worry about being scooped?
   Not really, if someone read of an idea published on my research feed, there would be a record of their accessing it and it would be easy to demonstrate that I had arrived at that idea or result first.
2. Wouldn't this be overly burdensome on the scientists?
   No more than the current best practices of daily recording results, backing up data, etc. In fact, this would serve as a great insurance against the loss of data.
3. Wouldn't this expose non-scientists to the inner workings of science and not a 'united front' as some scientists have recently called for in relation to climate change, evolution, and even arsenic-based bacteria?
   Reading the articles linked above would go a long way to dispelling this notion of how science should be done.

To conclude, if I had some reasonable assurance from hiring committees at major universities and research institutions that my work would be considered in the same way as those with publishing records in traditional journals—that the quality of work would be judged, not the journals where the work was published—I would easily, and happily adopt such a system of publishing my day to day research findings.

Image courtesy of Vmenkov on Wikimedia Commons

Living Water

I've really enjoyed God as living water as revealed in the book of Isaiah. According to John 4:14b, this actually covers the entire Bible. Below are some of the outline points from two messages that really explain the depth and riches of this matter.

Points from the Crystallization-study of Isaiah:

Message Two - The Revelation of the Lord Jehovah, the Eternal God

The Lord Jehovah has become the divine water. In the book of Isaiah God considers that He is our salvation as living water. To be our salvation, the Triune God was processed to become the life-giving Spirit as the living water, the water of life.

In totality, what Christ is and has accomplished is just the divine water, which is the consummated Spirit as the consummation of the Triune God for us to drink and enjoy.

Message Eight - Drawing Water with Rejoicing from the Springs of Salvation

God's intention in His economy is to be the fountain, the source, of living waters to dispense Himself into HIs chosen people for their satisfaction and enjoyment.

We need to know the difference between the words fountain and springs. The fountain is the source, the springs are the issue of the source, and the river is the flow.

The Triune God, while unfathomably profound, is also very simple. The Father is the hidden source, the Son is the spring, and the Spirit is the flow. What God wants from us, in order to fulfill His eternal purpose, is simply that we drink Him as this water. One of the best ways to do this is by calling on the name of the Lord.

Philosophy and the Sandwich

The thesis is taking most of my time, but I remembered an interesting interaction I had several years ago and thought to commit it to the cloud.

I was invited to a UCSD Philosophy Club discussion regarding theodicy, or the supposed problem of an apparent contradiction between an omnipotent, benevolent God and the existence of evil. While not getting into this pointless debate too much, I'd like to make two observations.

First, every time I hear this matter come up, I am dumbfounded at the consistent lack of defining the terms before the discussion. What is "good"? What is "evil"? It is always assumed that everyone present knows what these terms mean, but how can you debate good and evil, let alone God, without defining the terms?

Second, at this particular discussion, I created a peculiar metaphor for our discussion that goes as follows. It was like we were sitting around a table with a cover on it, and the proposition being debated was the existence of a sandwich underneath the cover. The Christians at the debate, believing in the sandwich because many of them had tasted it at one time or another, argued strongly for its existence. The atheists, never before having tasted the sandwich, argued that it could not possibly exist. However, no one simply lifted up the cover, picked up the sandwich, and took a bite. That's what I would have done, and that is what I would encourage any aspiring philosophers to do. Eat the sandwich; then you'll know once and for all whether or not it exists.

Finally, to the aspiring philosophers, should any actually find this post: don't summarize philosophy, do philosophy. I could not believe how much of that pointless debate was the summarizing and quoting of previous philosophers' works, and how little was actual synthesized ideas from the participants.

Grandpa in Pictures

See part 1 for the story of Grandpa.



Grandpa and me





Grandpa, Jen, and me

Being Preserved

all verse links are to the Recovery Version for comparison

In a copy of the NIV with footnotes written by Charles Ryrie:
Gal. 3:16

The promises were spoken to Abraham and to his seed. The Scripture does not say "and to seeds," meaning many people, but "and to your seed," meaning one person, who is Christ. (NIV)

The note on this verse says:

seed. Since Paul's argument here is based on the singular form of the word in the OT (Gen. 22:17-18), he must have believed in the accuracy of the very words of Scripture.

Ryrie goes on to use this and another example from Matthew to explain the inerrancy of every word in the Bible—even singular, plural, or tenses of words are important.

However, when we come to 1 Thessalonians 5:23 or Hebrews 4:12,

spirit, soul and body should not be understood as defining the parts of man, but as representing the whole man.

Such is the contradiction by those who insist that man is merely two parts—body and soul (which is supposedly the same as the spirit)—and ignore or explain away the many verses in the Bible that speak of the three parts of man. In Greek, spirit is pneuma and soul is psuche, two distinct words. So according to the fact that every word of the Bible is God-breathed and inerrant, soul and spirit should refer to two distinct parts of man. The tendency to confuse the two is even apparent in the translation of the NIV in 1 Thessalonians 5:23 referred to above—the conjunction and is removed from between "spirit" and "soul," although it is unquestionably there in the original Greek text.

More important that simply being correct on this doctrinal point, however, is the idea put forth in the verses from 1 Thessalonians 5 that we must be preserved in all three parts of our being. Verse 23 uses two marvelous words, "(sanctify you) wholly" and "(be preserved) complete," to speak about this preservation. From the footnote, and explained in more depth in Life-study of 1 Thessalonians messages 23 and 24, wholly is quantitative and complete is qualitative. Therefore, we must not only know that we have three parts—spirit, soul, and body—but we must go on to know our three parts and open to the Lord that they be sanctified wholly and preserved completely.

Goldilocks and the Three Dinosaurs

Creative consultation by Jolene

Once upon a time, there was a little girl named Goldilocks. She lived in the woods with her father, who was an inventor. One of his inventions was a time machine. But she wasn't allowed to play in it. However, Goldilocks didn't always obey, and she was very curious.

So one day, when she was playing with her dog, her dog jumped into the time machine, and she climbed in to get him. But he jumped out to go chase his ball. She was about to climb out of the time machine, but she noticed that there was a spot on one of the buttons. Not wanting to leave it dirty, she started to wipe the spot off, but as it came off, the button accidentally depressed and started the time machine. Before she could climb out, the time machine went back 150 million years to the Age of the Dinosaurs.

Goldilocks climbed out of the time machine and heard a noise coming from the trees to her left. As she poked her head through some bushes, she saw a clearing, and right in the middle was a small Allosaurus. He had his leg caught in some logs and was trying to get it out.

Goldilocks walked over to him and said, "Hello." the Baby Allosaurus replied, "Can you help me get my leg out?" Goldilocks said, "Sure," and proceeded to wiggle his leg loose from the logs in which it was trapped. Just as the leg came loose, there was a terrible crashing and two larger Allosaurus came through the trees, roaring loudly. Goldilocks began to be a bit frightened, but the Baby Allosaurus looked at the larger dinosaurs and called, "Hi Daddy, hi Mommy, this person just helped me get my leg out." Goldilocks looked up at the fearsome predators and said, "Nice to meet you, my name is Goldilocks."

The smaller of the two adult dinosaurs replied, "I am the Mommy Allosaurus and this is the Daddy Allosaurus. Thank you for helping our Baby Allosaurus free his leg."

"You're welcome," said Goldilocks.

"We were about to get dinner," said the Baby Allosaurus, "would you like to join us?"

Goldilocks said she would and she followed the three carnivores as they stalked and caught a stegosaurus. After a delicious meal of stegosaurus steaks. Goldilocks said she had to be going and made her way back to the time machine. After getting in and going back to the instant she left, she realized that she had forgotten her camera and hadn't taken any pictures of her new friends.

Grandpa

8/28/1919 to 11/26/2009

While many pages could be written about what Grandpa accomplished in his lifetime of over ninety years, one memory stands out to me.

Jen and I were visiting him and Grandma Dorothy several summers ago, about a year after we had finished the full-time training in Anaheim. On our way to Corning, I asked the Lord how Grandpa was with Him. I didn't know how to bring up the subject with someone so much older than me, and whom I respected to the uttermost. So as he and I were sitting on the sofa while Jen and Grandma Dorothy were off doing something else, I wanted to say something, but didn't know what.

That's when Grandpa turned to me and said something like, "You know, Ben, I feel like the Lord has been taking care of me my whole life."

I was first amazed, and then thankful to the Lord for answering my earlier prayer. Grandpa proceeded to tell me of an experience he had while in the Air Force, flying a large cargo plane. While flying in formation, the pilot to his left began to roll right too early, heading directly for Grandpa's plane. Grandpa gave it power and pulled up as fast as he could in a plane that large, causing the two to miss by less than 50 feet. Once on the ground, the other pilot was devastated thinking of the accident he had almost caused, but Grandpa was stern yet forgiving.

What was even more impressive than this story was how Grandpa's comment reflected the end of the life of another man of God, Jacob. Genesis 48:15-16 says:

And he blessed Joseph and said, The God before whom my fathers Abraham and Isaac walked, The God who has shepherded me all my life to this day, The Angel who has redeemed me from all evil, bless the boys; And may my name be named on them, and the name of my fathers Abraham and Isaac; And may they be a teeming multitude in the midst of the earth.

Praise the Lord who both shepherded Jacob all his life, and who took care of Grandpa his whole life.

Every time we visited Grandpa in the last decade of his life, he always had a new story to tell me, one I had never heard before. And the final time we saw him, this past summer, he got to meet his Great-grandson, who shares his middle name, Jesse, and who is the first boy of his generation to bear the last name Gallarda.

Thank You, Lord, for Grandpa.