Friday, January 29, 2010

Hypothesis: An idea you can test

Recently Nova ran a special biographical film on Charles Darwin, called Darwin's Darkest Hour. One of my favorite parts was how it showed him and his children exploring and learning together. Basically he made a game out of learning and he taught his children how to do scientific experiments.

Last night Alejandro wanted to put his leftover pear slice into the refrigerator. At first I was reluctant, because I know about oxidation and pears. I told him that the pear would get yucky. He was sure I was wrong. So I decided to emulate Charles Darwin. We came up with a hypothesis. Alejandro actually knows what it means from one of his favorite shows, Dinosaur Train. Buddy, the T-Rex, really likes the word "hypothesis." According to his adopted sister, "it means an idea you can test." So we came up with a hypothesis, Alejandro decided that it would turn into a yummy apple slice.

The next morning, we opened the fridge to find a slightly browned pear slice. He decided that it was an apple slice. I cut up an apple slice so that way he could taste if they were the same. When he actually tasted it, he turns to me and says. "Daddy, the apple slice turned back into a pear." So much for science.

It's about time

I found in my e-mail inbox an update from Adventist Today. The faculty senate at La Sierra University have voted to affirm the concept of academic freedom and the biology faculty. It is a strong statement of support for education and science. Much better than the vaguely worded press releases and articles in the Pacific Union Recorder. I suspect that the denizens of educate truth are not happy. Or maybe they are since they now have clear evidence that supports their position. But here is the problem. If they were actually successful, La Sierra's accreditation would be in jeopardy. If La Sierra loses that, it would close its doors shortly afterward.

Thursday, January 28, 2010

E-reader field getting crowded

A couple of new companies have announced that they will be manufacturing e-readers. Acer announced that they will be releasing a reader in the summer and Apple rolled out their new tablet computer that will also double as a reader with the unfortunate name of iPad. Click here for a funny take on the name and here for an upcoming trademark dispute. This is added to the Sony Reader, Kindle, and Barnes and Noble's "The Nook."

Personally, I own a Sony Reader. Mine is several years old, so it doesn't have all the nice wireless options that the newer model's have. However it has excellent battery life. Usually I can go about three weeks between charges. The Reader has a really clean design. I have always thought the Amazon Kindle looks clunky. I currently have about 150 books in memory. When I purchased the book, they made 100 classic books available for free (with a little work, I could have gotten these books from Project Gutenberg.) It is fun to think that I am carrying in one little device a bookshelf full of books.

I am finding more and more publishers are making electronic versions of their books available. I was able to find many books on my list that weren't there before. I think it is finally getting to the point where electronic readers are as compelling as paper books. For those of you, who haven't seen the e-ink displays that are typically used by these readers, you owe yourself a trip to try one out.

Tuesday, January 26, 2010

Book Review: Genesis - The Scientific Quest for Life's Origins

Some science books are good because of the quality and quantity of the information. But in order for science book to be a compelling read for the lay person, it needs more to be a great book. Robert Hazen is not only a scientist; he is a story teller and he told a great story in his book Genesis: The Scientific Quest for Life's Origins. When he talks about his colleagues, it is with enough detail that you can visualize them as you read. The science is described in a logical building fashion, but the book also includes biographical elements of the researchers that draws in the reader. It includes conflict, rejection, and successes.

The current state of origins research has many good theories about how the raw building blocks of life can be created chemically, including cell membranes. Once RNA is created they know fairly well how these simple organisms evolved to what we see today. However there is a large gap between the building blocks and a microbe with RNA that is not well understood. There are several ideas, but so far they haven't been supported by experimental evidence.

One of the most compelling stories in the book relates how a grad student that worked in his lab came up with an idea on how RNA could be created. This particular student had been working on a PhD for almost five years. He was easily distracted by new concepts, so he hadn't made any progress. His visa was running out and he had no degree and no job lined up. Just a few short weeks before his scheduled defense, he came up with an intriguing proposal. After some late nights, he had fleshed the idea out, defended his dissertation, gotten his idea rejected for publication, and had a job lined up so that he could run the required experiments to prove or disprove his idea. The book was written a couple of years ago, so it might be worth doing a literature search to find out if there was any success or not.

It isn't often that science authors will use a cliff hanger as a literary device. Dr. Hazen was telling a story about his first foray into origins research. He described the hypothesis, the experimental setup, and then just before he got to the review of the results, he ended the chapter. I had to wait for several chapters before I learned the chemical make up of his brown goop.

Because the book discusses an interesting and not well known field of science and because of the compelling writing, I would rate this book as one of my five favorite science books. Of course I may have more than five books in my list of five favorite science book, but I would prefer not to quibble with such details.

Monday, January 25, 2010

Sponges of Knowledge

I've long had an interest in artificial intelligence and machine learning. Before you can implement a program that is capable of learning, you have to have a model of learning. These are typically based on simplified versions of how the process of learning is observed in real life. Even knowing some of the theories and models, it never prepares you for some of the surprises that happen on a frequent basis as a father of a 3 year old boy. Almost every day provides some surprise.

Last week I ran some errands with Alejandro in the back seat. As he was getting ready to go to bed, he replayed our conversation almost word for word to Angie. Yet another reminder that I need to be careful what I say in front of him. Fortunately I was careful, but it was fun hearing him say to Angie "and that would be tragic."

Just yesterday, we were originally going to go to the bookstore. I was almost finished with the book that I was reading, so I wanted to purchase the next book on my list. Since I found that many of the books that I wanted were now available on the Sony Reader, I no longer needed to go. Unfortunately, Alejandro already had his evening planned. We were going to go to the bookstore and daddy was going to buy him a book on trains. I wasn't planning on buying him anything, but he some how had figured out, that when it comes to books, I have a hard time saying no to him. So I started to explain that we weren't going to Powell's after all, but we were going to Best Buy instead. At the mention of Best Buy, books were forgotten and he launched into a lengthy discussion of how he was going to play "Lego Rock Band" at Best Buy. We ended up playing "Beattle's Rock Band" and when we got home he even tried to sing "We are living in a yellow submarine" to Angie (after hearing it only three times.)

On Saturday we were discussing friends of his. I mentioned one friend in particular. He hasn't been to her house in about six months. However the moment I mentioned her name, he started going on and on about her jeep. She owns one of those electric ride on toys, in this case a Barbie Jeep. After going through several colors he finally settled on pink, which is the correct color.

We are getting to a stage were not only is he remembering individual facts, but he is able to make connections between facts. That is what is most fun about it, because I can tell he truely understands the concept by the connections he makes and it is more than a simple repeat of information.

Friday, January 22, 2010


When I was growing up, I hated testimonies. Church services tended to be long and I would be staring at the clock watching as the minutes and hours inched passed 12 o clock, 1 o clock, and sometimes as late as 2 pm. All the adults seemed to be excited about some theological concept (righteousness by faith) that they as a church community had recently discovered. It mostly went over my head since I had not grown up during the more oppressive time periods of Adventism when the church as a whole was very legalistic (meaning that God only saved you if you were good enough.)

As I have grown older, I have learned to enjoy testimonies. I enjoy hearing testimonies in church and I have enjoyed reading them on the internet. I guess the appeal is usually the person is brutally honest about some aspect of themselves. In the Christian context it seems like that brutal honesty always concerns the past (the life of sin.) But it gives a glimpse into that person that isn't normally seen in the normal "How's it going", "so nice to see you", and "Welcome to church" conversations.

What I have found, is that it isn't only the Christians that enjoy testimonies. It seems popular among a certain subset of atheists. Usually it seems like those atheists who once were conservative Christians. Here is one example that I found this week. In fact there is a site that has archived a large number of these testimonies. Basically people are sharing their stories of how they transitioned from a Christian to an atheist, their de-conversion story.

Sometimes I wonder if I am on the same path. Many times I wished that testimonies in church would contain more of the present day struggles. Life is never as simple as "I was once a sinner, but Jesus saved me." I suspect that many of the people that I go to church with are also on that de-conversion path. What would a church look like, if somebody could stand up and honestly express their struggles? I think that sharing our current doubts and struggles would make the church a stronger community.

There is another testimony blog that I have started following. The author has struggled with some of the same issues that I have, but somehow he was able to not only stay a Christian, but still work as a Pastor up in Washington. I highly recommend his "memoir" blog and also his opinion blog. I don't know what the future will hold, but I am at peace with myself and I am enjoying the journey.

Thursday, January 14, 2010

Book Review: Evolution - What the Fossils Say and Why It Matters

This book ended up having a slightly different focus than I expected. Dr. Prothero is a well respected expert paleontologist, specializing in fossils of large mammals. In his book, Evolution: What the Fossils Say and Why It Matters, Prothero goes beyond the well known fossils to showcase the fossil evidence for Evolution. When most people think of fossils they think of dinosaurs. However there are many, many other fossils, in fact over 100,000 different species and more being discovered every day.

Early in the book, he has an interesting section on cladistics. I remember in school we learned about different types of creatures and how to organize them into logical groups(for example reptiles, fish, amphibians, birds, and mammals.) All of this is now obsolete. In fact it was obsolete when I was learning it in school. For example, we now know that crocodiles are more closely related to birds than they are to other reptiles like lizards and snakes. (Just in the last week, an interesting study has come out that shows that alligators and crocodiles breathe like birds.) The desire is to include the species and all descendant species in a single group (mono-phyletic). So fish no longer makes sense as a group since all land vertebrates are descended from them. Same for amphibians. The coolest part about the whole thing is that not all the dinosaurs disappeared. That sparrow outside your window is part of the dinosauria group.

In general Dr Prothero has organized the book to cover fossils that are more distant from us in time and genetics first. His discussions of invertebrate fossils precede those of early vertebrates and he ends his discussion with a look at hominid fossils. This book was written before this year, so his knowledge of "Ardi" is out of date, but he does have an interesting section on "Tiktaalik".

At times it was difficult reading, since there is so much detail. However when covering a field as broad as this, I am not sure how he could have done it differently. My main annoyance was the constant harping on creationist authors. Yes, they are frequently quoting out of date sources. Yes, they are usually speaking without having even looked at the fossils. I get it. I don't think it needed to be mentioned every single section of every single chapter. I am guessing he is tired of creationists distorting his field of research. I sense a concern with the deterioration of science education in America. However it did interrupt the flow of the book.

One key item that sticks out is how much attention to detail is required to separate out differences and identify which group a fossil belongs to. Usually only the conclusions make it to the popular press. However there are detailed observations that support those conclusions. This leaves the impression that scientists are just guessing. For this reason, I would recommend reading this book.

Monday, January 11, 2010

Speaking of Viruses and Carl Zimmer

Just after I posted my last note. I noticed this from Carl Zimmer's blog. He is discussing research into how some of the key genes in placental development are actually co-opted from a virus.

By the way if you are interested in science, Carl's blog is probably one of the best to follow. By training he is a journalist, but he is very careful to get the science correct. But since he is a writer, he is able to present these complicated topics very clearly.

DNA and form

I remember when I was a YEC (young earth creationist), whenever presented with the similarity of DNA between species, the common counter-argument to a common ancestor was that similar organisms would have a similar DNA structure because they were similar in shape. God was basically reusing a good design. So humans and chimps would have similar DNA because they had a similar body shape (because God created them that way) and not because they shared a recent common ancestor. At a high level it makes sense, but I have a hard time answering several questions.

Why would a cow have more genetic similarity to a whale than a horse? Or what about the Hippo? The hippo has more genetic similarity to a whale than it does to pigs or cows. Clearly, the similarity in DNA does not dictate a similarity in form. I am trying to find an article that is easier to read, but here is the original scientific paper. Through fossil evidence scientists had figured out that whales had descended from hooves animals, specifically ungulates. Cows are ungulates, but horses are not. A good resource to learn more is Carl Zimmer's book, At the Water's Edge: Fish with Fingers, Whales with Legs, and How Life Came Ashore but Then Went Back To The Sea.

Why do we have a disabled gene in our DNA that is used by birds and reptiles to make egg yolks? Not only do we have that gene, but when we look at the DNA for a chicken, that same gene is in a fairly similar region. Again the paper is hard to read if you aren't used to reading scientific papers.

Why do we share fragments of viral dna with other apes? Certain types of viruses use their host's DNA to replicate. Occasionally the DNA strands get mixed up and the virus's dna is incorporated as our own. There was a recent article that was discussed by two bloggers, Ed Yoong and ERV. Basically new research is out estimating that 8% of our DNA are viral leftovers. Now the freaky part is that there are numerous sequences that we share with apes and not only do we have the same viral leftovers, but they are in the exact same positions in our DNA. I first learned about this on Talk Origins.

Now I see all of these as strong evidence for common descent. If at any point evolution would be proven wrong it would have to be with the discovery of genetics. But it seems to me that the case for evolution is only stronger.

Wednesday, January 6, 2010

So what happened

I was thinking about this the other day. What happened to my faith? Then I realized that from the time I was 12, I went to fairly liberal churches or at least churches that were accepting of liberal view points. During that time my beliefs had changed significantly. It wasn't until the last year or two that I realized that not only had the church at large not changed with me, but they don't really want people like me to be a part of the Seventh Day Adventist church.

So first off, I guess I should explain where I am at today when I am in a good mood. First off, I believe that the Bible is not "The Word of God." It is a history of God's interaction with certain people. But it is written from the person's perspective (this is how I get past all the genocide.) Secondly the evidence that all life descended from a common ancestor through the process of evolution is overwhelming and inescapable. Thirdly my conception of God is probably best described as panentheism. When I am in a bad mood, I am a straight up atheist. But even in my atheist moments, I believe that religion currently has the best answer to the problems in this world. Also, I love the Seventh Day Adventist church and consider it my family. I love our emphasis on health, I love the concept of sabbath, I love our humanitarian work and work on religious liberty for all, and I love our holistic thinking (body and soul are one.)

More and more, I started to realize that my family no longer wanted me. It started with Clifford Goldstein, the editor of the Adult Sabbath School Lesson. In the Adventist Review a few years back he wrote an article, which said
If you honestly reject a literal six-day creation in favor of theistic macroevolution, fine; now turn that honesty into integrity and go somewhere where you won't have to cloak your views under the anfractuosities of language.

This year there have been countless articles in the official Adventist publications about how evolution is not compatible with Adventism. It was partly due to this year being the 150 year anniversary of the Origin of the Species and partly due to the effort to expel biology professors from La Sierra.

Recently I saw a disturbing video of a Q&A Session (found the link here at the Educate Truth site.) A fairly large group of Vice Presidents of the church were answering questions on several topics at a GYC conference. I wasn't able to watch all of it, but I found the sections on evolution and homosexuality to be full of narrow mindedness, arrogance, and ignorance. They definitely made it clear that people who are not Young Earth Creationists are not wanted. People who believe that we shouldn't oppose gay marriage because of religious liberty concerns are not wanted (even the ones who believe it is a sin.)

A new blog for a new phase

Much has changed in my thinking, which makes my previous blog somewhat obsolete. When I first started blogging, I was interested in posting notes about religious topics because of my role as a Sabbath School teacher in my local Seventh Day Adventist church. Because of areas of significant disagreement with the church, I doubt I will be allowed to return to that role. This blog will discuss my thoughts about interesting events, books, and ideas. I am interested in science, religion, philosophy, and technology and I may include auto biographical material as well.

For reference on my past thoughts, visit my other blog. The views presented were my views at one point in time but may not reflect my current thinking. Additionally, the words you read on this blog will reflect my views at the point in time they were written. I reserve the right to change my mind at any point in the future.