Now's as good a time as any to update this journal, so I shall.
It's funny to refer to what I go to as "school" since I don't take classes anymore. Research has been going quite well. As I mentioned in a previous post, I inadvertently made two discoveries that have invigorated my dissertation. Just starting typing up the intro for a paper on the first one this week(end). It's been a bit of a lesson in ethics though, since we're using publicly available genomes for a large portion of my projects. It's a difficult gray area in which I'm satisfied with my decision to go forward, but I'm a bit concerned about possibly ticking someone off at some point. Either way, happy with how it's developing.
Much of the Fall/Winter involved the writing of grants/scholarship apps/fellowship apps. I have been rejected by 4 out of the 8 so far, so here's to hoping that I receive something! Worse case scenario, I'll be able to finish my dissertation with no problems. It'll just turn out to be different than I originally envisioned.
Teaching has been great. Fall I taught the discussion for functional anatomy which was the first class I actually 'lectured' for. In all of my other classes I do lecture a bit, but they've been labs so the approach is quite different. It was four 1-hour lectures back-to-back so that was difficult to adjust to initially. It's draining! And grading the short answers for 120 exams was a bit of a pain too. Winter quarter I was back doing the lab for the second functional anatomy class. I was the elder TA this time, so I had a lot of sway on the new TAs, which was sort of nice. I didn't abuse it, of course, but rather I enjoyed not having to justify changing course content to someone above me. Right now I'm back teaching lab for ecology and evolution which I love (so low-key!).
Despite not having received any of the grants/fellowships/scholarships so far, I feel blessed to have received a coveted summer lecture position. I and another grad student (Anne) will actually be teaching the class by ourselves. I've been told that this experience is really important when looking for faculty positions. I'm glad I took the time to apply! 1 out of 9 (so far) ain't bad! Lol.
I recently finished listening to Rolling Stone's 500 greatest albums on Spotify, and I am currently working on their best of the 2000's list. As I expected, there wasn't a ton of music that really grabbed me (unfortunately) but I have gotten a few leads to pursue further.
I'm still reading books on the afterlife, but I've moved away from the more scientifically grounded works to more anecdotal material. At some point, you don't need to be convinced of the validity of the data and you instead want to read all the juicy details (while simultaneously remaining skeptical). I suppose it's like learning about the development, population genetics, fossil record of tigers and then at some point say, "Okay, that's nice...I want to see some tigers!!!"
The truth is that the dense, scientific stuff is incredibly important to me, but it gets exhausting at some point. On a related note, I've gotten back into video games a bit because the things I read can be intellectually and emotionally exhausting. I would take a break from my academic research and read on another aspect of research, and frankly I never felt rested (duh)! Video games, I've realized, bring me mindless breaks in my routine. I bought my first PS3 game in over a year (2 years?) the other day, Metal Gear Rising. Basically, it's fun/badass game about the successor to whom I received my xanga name from (Gray Fox). Not nearly as compelling of a story as the original (Metal Gear Solid) but it's good enough to deserve some replay time. It's possible, after I play some demos at some point, that I'll get back into Call of Duty too. But we'll see. Battlefield 3 sort of turned me off from that genre last year.
I'm happy that my relationship with God has developed some new, more stable aspects. For the past month, I've been spending my first 20 minutes or so just hanging out with Him, usually in my living room. My mom bought me a devotional book (Jesus Calling) that I've been reading daily during the time. I've never done something like a devotional before, so it's a nice deviation from what I'm used to, even if I don't agree with all of the statements within the book. Additionally, I've started to spend a part of that time either reading Jesus' teachings, or focusing on the meaning of some of his words, sayings, etc. I think a lot of Christianity is based on non-Christian (i.e. non-Christ-derived) teachings, and thus I want to make sure I know them all as accurately as possible. For example, Jesus said he didn't abolish the Law, so I reviewed a chapter in a book of mine (Answering Jewish Objections to Jesus: New Testament Objections) that dealt with the subject. More recently, I spent time researching the term Gehenna, which is traditionally rendered "Hell" by contemporary Christians. Just today I downloaded a Strong's Concordance app on my iPhone to further look at the meanings of these terms. Certainly the most serious scriptural study I've ever done.
Finally, I had my second strong year of following football since a decade earlier. Needless to say, watching the 49ers this year was enormously fun, even if we didn't win the super bowl. Lior and I frequently were in contact about the Niners and his Packers, and even arranged to watch the Packers/Niners playoff game together (with Michelle). Plus, Michelle joined me at BJ's frequently to watch games. I had a lot of fun and am looking forward to next season!
Timeline: Friends, Family, Travelling & Other events
One of the nice things about Facebook's timeline is that it's easy to track when photos were uploaded and when I've been tagged at certain locations. It's quite convenient because I almost never take photos, so I can conveniently steal them from others. I will be referring to FB frequently.
On October 2nd, Michelle and I went to our first ever MLB game: Giants @ Dodgers. I had been to a pre-season game with the Diamondback and Brewers in Tucson, but never a regular season game. It was, well...I don't like baseball, so it was rather uninteresting as usual. Haha. Giants won though, so Michelle was happy. She even followed up and saw them in their first playoff game in SF with her brother Allan, which obviously culminated in their World Series win. I remember watching the last game in the gym with her. She was super excited!
On October 30th, I heard about the new Star Wars movies. Initially I was shocked...perhaps concerned...but now I'm totally looking forward to it. 5 Star Wars' over 5 years! Disney is seriously trying to make me happy right now.
November 1st, of course, I got engaged to Michelle (we're celebrating our 6 year on Wednesday).
I was going to do a detailed post of our engagement trip, but I opted not to (since I don't want to sort through photos Miki took). Anyway, the point is that I hated, despised, loathed the idea of spending a bajillion dollars on a ring. I totally respect other people's views on rings, but to me it's an absolute waste of money (it's just a dumb, albeit pretty, rock!). I did end up getting her a ring, but I compensated for my cognitive dissonance by reallocating some of the money towards a trip to Orlando for the two of us.
We got there November 8th after a very early flight. We literally almost missed it, like, by 30 seconds (seriously) thanks to a few factors, despite waking up at 4 am or whatever God-awful time it was. Got to our resort that night and it was surprisingly nice. Decided to go walk around their Downtown Disney, which is huge!! This is where I learned that I have a sweet tooth for Ghirardelli Peppermint Bark (amazing).
On the 9th, we visited Disney World's Animal Kingdom. That was a great park. The general zoo stuff was nice, but the safari was quite a treat. The dinosaur land was silly but cute. They had a cooler dino version of Indiana Jones. The Himalayan land was awesome. The escape from Everest ride has to be one of my new favorites. The Nemo show was very meh, but the Lion King show was very likable.
Miki had to meet Mickey, which was near the Lion King show. He saw the ring and he was gesturing in different ways that were hard to understand (since he doesn't speak). What seems most likely is that he was indicating "don't tell Minnie because then she'll want a ring!" Which, if true, implies that they aren't married...anyway, I look awkward because I got the impression he wanted to be closer to Michelle than me. Once again, he was hard to read though, so I'm not sure. Lol.
On the 10th we went to Universal Studies Islands of Adventure with, of course, one goal in mind: The Wizarding World of Harry Potter. Before I get into it, the rest of the park was nice, with the spiderman ride being rather cool, but seriously by FAR the best part was Harry Potter. We spent possibly half our time there. It was Disney-status: totally immersive. So many cool references throughout. Probably the only thing that could improve it is a solid show. Or, alternately, they should make a park entirely devoted to it...it's really that cool! The rides were fun. The ride in Hogwarts had the coolest line I've ever waited in, but the ride itself truthfully made me a bit motion sick (despite it being awesome otherwise). It was all just very disorienting. The Tri-Wizard tournament roller coaster, however, was completely amazing. Best roller coaster I've ridden, especially if you're at the front. I got a butterbeer (I'm convinced it's cream soda with whipped cream on top) and we ate at the three broomsticks (best theme park food I've ever had). Awesome place!
Michelle harassed this poor guy until he got the photo right (like, the 5th time! Lol)
This was in the line for the tri-wizard champion roller coaster.
The next day was more low-key as we needed to kill time until our flight. Disneyworld is a MASSIVE resort, so we found a cool boardwalk place and had lunch there. At some point, we played "putt-putt" golf (aka miniature golf). This was basically an idea that I got from the Book of Mormon in which the main character sings that he wants to do his missionary trip in Orlando. I sang this song frequently while we were there, and one of the lyrics goes like this: "Orlando (Orlando) I love you, Orlando! Sea World and Disney and Putt-Putt Golfing!" Well, sure enough, I found out that Disney had TWO putt-putt golfing places, so we decided on the Fantasia golf course. Coolest mini-golf course I've ever played. And overall great trip! Way more memorable than a hypothetically more expensive ring.
Around Thanksgiving time, Paul had a birthday party at Rio Brazilian Steakhouse in Clovis. It was expensive, but it was a ton of food (much of which was good).
Nick, Paul and I were making bets about how prego Val was going to look when she got there. I think I was betting watermelon size.
For Thanksgiving, it was myself, my mom, grandma and their friend Kristie (maybe Jenn?).
...oh, and Toby! (we set up X-mas decorations early, in case you were wondering)
On December 6th, my sister and I drove out to Phoenix to join our dad to see Bruce Springsteen in concert. I'm not a huge Bruce fan, but he has a reputation of having amazing concerts so I thought it would be important to see him. He did not disappoint! Loved hearing "Hungry Heart", and new to me was "My City of Ruins", which is now a favorite of mine.
The next day I caught a hockey game (Ontario Reign) with Michelle, her friend Jason, plus Amanda and Andy a couple of grad student friends of mine. Amanda, besides my dad, is the only other person that really likes hockey that I know of, so it was cool to watch with them.
December 9th, Michelle and I went to the Disneyland Candlelight Procession of which actor Lou Diamond Phillips presided over. This was something I entered into a drawing of sorts for, and I was pleasantly surprised! Quite an enjoyable night of the telling of Jesus' birth (surprised they did this at Disneyland) and hundreds of choir members singing Christmas songs.
It was pretty, too!
Apparently the same night we went out with Corrie to get some dinner at a Thai restaurant. Corrie is a food blogger, so she's always open to going to restaurants, and Michelle and I have been constantly on the lookout for good local restaurants, and this place happened to be particularly delicious.
Then on the 10th, we joined Tyler and Jen (who had crashed at our place a couple of nights earlier) at Disneyland.
Here we are on California Screamin'. The photo theme we chose was "eating stuff". Tyler was eating a banana. I think I was imagining a pizza slice dangling.
Here we are on Space Mountain. This photo theme was "cross eyes". I had Tyler's face on this one. It disturbs me greatly.
We had a ton of fun with these two, plus we all met up with Elaine at Buca di Beppo. Great time.
On December 17th, Michelle and I went to the San Diego Zoo to see their "Jungle Bells". Basically it was lights and assorted X-mas things around the zoo. Frankly, I thought it was rather underwhelming, but of greater importance was the presence of these two cuties:
Clouded leopard cubs = amazing. We came back later and got to watch one of them play. I'd upload the video but apparently I can't download it from FB.
Then came Christmas which was generally enjoyable.
Sweatshirts from my dad. I was trying to go for the insane look.
Valerie threw a Christmas part at her place. Got to spend time with people that I don't see much. One unexpected show-up was Jason K.! I hadn't seen him since high school, funnily enough at a party. It was a graduation party and him and Aneel (sp?) told me they were bailing because another party had booze. I told the host later and she was pissed (understandably)! I relayed this story to him all of these years later, resulting in a quite amusing reaction. It was really cool reconnecting with him, especially because the aforementioned memory was the only one I had of him.
Michelle and I on our way to the party. We were APPARENTLY the only ones who dressed up, even though traditionally everyone did! Lol, oh well.
For New Year's Eve, my mom and I joined Michelle's family at the Chaffee zoo for the lights.
Our moms pushing Michelle's grandparents.
On January 8th, Michelle and I belatedly celebrated her birthday at Disneyland's Blue Bayou restaurant (the one you can see from Pirates of the Caribbean). It's incredibly pricey, but she loved the salmon she had. Cool atmosphere, as expected.
I think on Michelle's actual birthday (a couple of days earlier) we went to the San Diego Zoo with my dad and sister. While there, we saw one of the coolest mammals in the world, which I had never seen prior to that day. This is the only zoo they're found in outside of SE Asia, so it was a real treat.
Ladies & Gentleman, a pangolin (it was sniffing my ear at one point!).
Isn't that tongue awesome?? It comes out maybe 1.5 feet or longer.
On February 2nd, Michelle and I went to Huntington Library for the first time. The gardens were certainly beautiful in places. I loved the desert area, as well as the Chinese and Japanese sections. I'm not really big on art so unfortunately much of the material was lost on me, but I did find it rather fascinating to look at some renaissance painting on Mary and baby Jesus. It was rather interesting to think of it in a historical context (btw, did you know they both had blonde hair? Trust me, I saw it in a painting).
Here's Michelle in the Chinese pavilion.
February 8th I saw the Beatles Rain Tribute at William Saroyan Theater with my mom (X-mas present to her). Michelle parents were a bit further down the row. It was great, like last time Michelle and I saw them. My mom was kind of blown away, so that means it was a great present!
On February 11th, I met Val's baby Zach for the first time. Poor Val was exhausted and sleeping the whole time while Vanessa, RJ and I ate dinner and talked.
I'm not a big fan of babies, but this was the first one I've ever 'known' (i.e. family or friends' child). I'm literally examining him out of scientific curiosity in this picture.
For a Valentine's day present, I bought Michelle a ticket to see the Hives at the House of Blues in Downtown Disney February 18th. My dad and Flipp joined us. Minus some obnxious individuals next to us, it was a great concert like last time. Despite them not being Michelle's style of music (which I knew) she enjoyed their on-stage antics.
On February 27th, Michelle was preparing for a science presentation competition at her school. I told her to practice on an imaginary audience. She took it a bit literally...
On March 16th, I went to the Yardhouse in Oldtown Pasadena to join Lior and his friends for his birthday.
March 21st, we joined Corrie on one of our typical food outings, this time also at a Thai restaurant.
These were the three wisest fortune cookies I have ever seen.
We roasted marshmallows and had root beer floats back at Corrie's place.
Spring break was pleasant. Took Toby on several walks over at Woodward Park which he certainly enjoyed, and my mom joined me for two of them.
This was March 28th.
Earlier that week, celebrated Val's birthday at Sakura Chaya. I had gotten sick the last two (three?) times I went there, so this was a test of will power for me! Poor Val was crying for much of it because it was the first major chunk of time she had been away from him. She's now back at work and does this on a daily basis, but it was initially quite difficult for her.
Several of her SoCal friends came out to join us. Later that night we went to Tower District for this wine bar they had heard of. It was actually more like a club, and funnily enough RJ and I got in (before we agreed it was too loud and obnoxious and waited outside for the girls to join us), but the girls didn't! They made them wait in a line. It was the opposite of the cliche where girls get let it whereas guys wait outside. They were sufficiently annoyed so we went to a bar instead. I had a good time with all of them.
Michelle and I also went on a hike in Sequoia National Park during Spring Break. At the end there was a beautiful view of a granite monolith with a waterfall.
Lastly, I'll mention a trip I went on with my friend Lior. He recently finished his Pharmacy school rotations (he'll be truly done in June) and wanted to celebrate with a road trip. I asked, "Okay, where?" "Uh, I don't know...the grand canyon!" Conveniently, my dad has a new house in Phoenix, so we arranged for it to happen. We started our trip on April 11th and headed to the Grand Canyon. On our way there, we passed by a cop. After we passed, I explained to Lior how there are different laws in Arizona that might catch you off guard. One example involved heading to Tucson with my dad and Flip and getting pulled over for driving in the left lane even though we weren't passing. Funnily enough, almost IMMEDIATELY after telling this to Lior, I got pulled over! Similar thing: this law had to do with how close I was to the truck in front of me. I'm actually take the distance between myself and other cars very seriously, so clearly Arizona's law was more strict.
Good thing he didn't find the drugs and dead bodies in my car.
We caught the Grand Canyon at sunset, just so we could. We held hands while watching it set, of course.
We saw maybe 8-10 elk there, plus three deer.
That night we stayed in Flagstaff, and then drove back up to the Grand Canyon the next day to do a hike.
Here's the Bright Angel trailhead. We went down to the 3 mile marker and back since we read that it was basically suicide to do the whole canyon in one day. Regardless, I figured it would be a good intro to hiking the canyon.
I think this was near the 3 mile marker, but perhaps it wasn't. You'll notice that I'm wearing a Giants hat and Lior is wearing a Dodgers hat. You'll also notice that I said earlier in this post that I don't like baseball, and neither does Lior. Regardless, we wondered if people would comment on the hats despite the intense rivalry between the teams. Sure enough, three people said something. Two guys independently said, "A Giants fan and a Dodgers fan are friends??" To which I replied, "We are a symbol of peace in a hopeless world." Another guy told his son, "Now look son: a Dodgers fan and a Giants fan. They must be really good friends."
It was naturally a beautiful hike. Funnily enough, we planned our day around this hike and the advice that it takes twice as long to go up as it does to go down. Well, it took us 1 hour and 10 mins to go down, so naturally we expected to take 2 hours and 20 mins to go up. Apparently I'm a "speed demon" (Lior's words) because I basically made us go up in...1 hour and 10 mins. I explained to him that when I hike and mountain bike, I don't like going uphill so I do everything I can do get it over with quickly. Regardless, our ridiculous climbing speed was rather exhausting at times.
After the hike we headed down to Sedona per my dad's suggestion. It was more beautiful than I had remembered. Here's the view from a restaurant we ate at in their 'downtown':
Not the best picture quality, but trust me, it was gorgeous.
Later that night we headed to Phoenix. We went downtown and looked for some ice cream before heading to my dad's place. I forgot to tell Lior that we had to check for scorpions before we could go to sleep. The traps had even recently caught one. Poor little guy was still alive.
The next day we headed down to Tucson to hike in Saguaro National Park. Northern Arizona is drastically different from Central and South Arizona, so Lior was understandably surprised when he saw the 'real' desert down there.
Here's the Loma Verde trailhead
One of Lior's first saguaro cacti. We hiked on these trails for several miles before we headed to my grandparent's house just to stop by and say 'hi'. It was great seeing them, especially because I only see them once a year or every two years. In fact, this was the first time I saw them without my family. That night we headed to Tempe next to ASU and got some dinner there since Michelle and I had previously thought it was a really cool looking district. The next day we headed back to California, and thus ended our trip. I had a truly great time with him. Most alone time I think I've ever spent with a friend, and we certainly had a lot to talk about.
Thus concludes my lengthy post. I don't even want to proof read it...no wonder I don't do these very much!
Talking with people about evolution and Intelligent Design (ID) has gotten me thinking: if Intelligent Design really did explain some or all aspects of life, how would we know? How could we test it? What predictions would it make?
Critics of ID understandably point out that it lacks the characteristics of a scientific hypothesis, and therefore it's inherently unscientific. But I wonder if that's entirely true.
What IDists tend to do is support a God-of-the-gaps model for perceiving natural phenomena. This means that if you can't explain it, then God must have done it. The problem with this is that an equally viable hypothesis is that we just don't understand the phenomenon in question. Pick any feature of nature and at some point it was likely attributed to some mystical force (God, demons, witchcraft, etc.). We now look back on our ignorance and realize that we simply didn't have the means to explore the question in detail. So as with the God-of-the-gaps, the more we learn, the more these gaps close.
But will all of the gaps ultimately close? And if they don't, does that provide evidence for Intelligent Design? Or, like I suggested, does it just provide evidence for human ignorance and limitations of our search for knowledge?
I recently read an article on rational wiki (which should change its name to obnoxiously, condescending materialist wiki) that said that proponents of a model in which consciousness exists independently of the body are appealing to something analogous to the God-of-the-gaps model. The author caricatured these theorists as arguing that there are some aspects of consciousness that are difficult to explain, and therefore the brain doesn't produce consciousness. I thought about it for a bit, and I concluded that the wiki article was wrong. The proponents of a brain-independent consciousness are able to make predictions and falsify hypotheses by empirically testing these questions. There may be a better model out there, but I'm convinced that this model is superior to the brain-produces consciousness model.
So since there is empirical evidence that strongly contradicts the wiki author's assertions, it makes me wonder if the anti-IDists are suffering from the same blindness. Is there a working model for ID? Is it actually scientific? Can we distinguish it from competing hypotheses? I'm not aware of such a model, but it's got me thinking.
For the record, I think 6-day creationism is a testable hypothesis but it has been falsified on many counts. ID is more tricky because it simply implies that a Designer designed any number of aspects of the universe/life/physical laws/etc. Creationism is much more specific about its predictions and thus that is why it's an appropriate hypothesis.
edit* 3/26 6:15 p.m.
One thing all of this talk is inspiring me to do is read up on Creationist and IDist literature. I've been out of it for years, so I'm curious what the current thoughts are. I think I'm winding down on a subject that has interested me for some time now (near-death experiences), and can possibly shift to this subject soon. But...we will see.
So I applied for an NSF Doctoral Dissertation Improvement Grant last Fall (when I was in Orlando, actually). I just found out today that I didn't receive it. I'm sure I'd be happy if I did get it, but at the same time, I'm not very bummed (which is a good thing!). Part of it stems from my thinking that I myself wasn't even convinced that my project proposal was good enough. It wasn't that I don't think it has plenty of potential, but it was more that I don't have enough data to be convincing to others or myself. I think it has a good theoretical basis, and I really want the data, but in a competitive system they want to good reasons to give you government money, not just good thoughts.
Anyway, it was good experience to write it and it was good experience to read critiques of my work. Perhaps some of my ideas aren't the best after all, and I made some mistakes. Heck, apparently I didn't even define an acronym that was CRUCIAL for my paper and two reviewers were well aware of it! Lol. I must have read it so much, and I'm so familiar with my work, that I didn't even notice it during my editing of the grant.
But here's the cool thing: a week after I submitted the grant, I had two projects related to my research that more-or-less landed in my lap after I made a couple of fortuitous discoveries. Maybe it was God's precognitive compensation for my not getting the grant? And frankly, I like these projects a lot, and my advisor has been backing them extensively. It has actually been more exciting in my opinion than my original project proposal, so if that's my "compensation", I'll take it!
My dad has a friend who is a strong Catholic and an avid anti-evolutionist. I assume it's a hobby of his. He wrote an opinion in my hometown's newspaper that my dad forwarded to me. I decided to reply to his friend and thought it might be nice to have in here too. To protect his identity, however, I've decided to omit the article itself. I quoted the relevant parts of it in bold.
My dad forwarded me your e-mail and I and read over your article in the Bee. A few thoughts on what you said:
"The truth is that for the last 150 years, slightly below the public's perception, Darwin's theory has been mired in controversy, challenged by scientists of every stripe"
A scientific theory is nothing but dogma if it is not challenged by scientists. Every theory in existence has been mired in controversy to some extent (in physics, geology, neuroscience, psychology, etc.). This is a fact that non-scientists might find shocking, but the reality is that we are always striving for the truth and that means our ideas need to be whittled away until all that is left standing are the best possible answers to the questions that we've asked.
As a personal example, just recently a paper that was heralded by the popular media as showing our true mammalian ancestor was published in Science. My advisor, and I, strongly disagree with their conclusions for many reasons, and my advisor is working on submitting a damning reply. But just because there is controversy doesn't mean we are not coming closer to finding out the truth, and it especially does not mean that there isn't a best available answer.
"Animals and plants appear in the fossil record fully formed and remain unchanged through millions of years. No knowledgeable individual denies this."
As for the fully-formed bit: yes, you are correct. But any knowledgeable individual would also know that evolutionary biologists recognize that the fossil record is pathetically incomplete. There's a whole field of research called taphonomy that deals with the preservation bias in the fossil record. Are you aware that many species of mammals are known only from their teeth? We certainly think they had bodies. Are you aware that many species are known only from one specimen? We certainly think there was more than one individual of each species walking the earth. So wouldn't it stand to reason that there must be plenty of transitional species to be found if evolution is true? And sure enough, it seems that every year we find a fascinating new transitional species for some group. Think about how we used to only have birds in the fossil record with no transitional species (besides Archaeopteryx). It sure seemed like those birds came fully-formed. Well, at least until we discovered dozens of theropod dinosaurs with feathers that displayed many transitional characters from other dinosaurs to birds.
For the part about remaining unchanged through millions of years: can you cite a specific example regarding this? I'm not saying you're wrong, I'm just rather skeptical. Mainly because all species that I'm aware of do show at least some characteristics changing over time in the fossil record. Whether it's average body size or a new structure, nothing, that I'm aware of, is completely static. Regardless, stasis in the fossil record, even in a relative sense, it's perfectly reasonable from an evolutionary standpoint. We would expect species to not change if there was no adaptive advantage to it. Let's say you're adapted to a mild climate and you feed on grasses, and that habitat/diet is available for 10 million years. What would be the impetus for evolution? Then suddenly there's a major climatic shift: it's now an arid landscape with no grasses. Better change your habits, or you're dead! There's a reason that evolutionary biologists often focus on major climatic shifts in terms of factors that affect diversity. They don't think that the Cambrian explosion happened 'just because'. They don't think placental mammals exploded in diversity 65.5 million years ago 'just because'. We think they change (i.e. evolution) because there WAS change (in climate or biotic interactions). Stasis may be the rule except when big events happen, and stasis does not mean "no evolution".
"Over millions of generations of laboratory testing, fruit flies, as one example, when subjected to genetic changes have not changed into anything but mutated, crippled fruit flies"
Do you think that they're trying to make fruit flies into different species when they do these experiments? Do you think they expect them to? Because they don't. There are many reasons behind studies of the population genetics of fruit flies, and they do not involve scientists scratching their heads as to why the flies haven't evolved into a "whale" or a "tiger".
"So also much the same thing happened with the famous "Galapagos finches" whose average beak size became bigger when the conditions there made it harder to find food due to bad weather. Then when food became more plentiful, the beak size of those finches that survived returned to normal. Thus the finches changed a little, adapted, while remaining fundamentally unchanged. In this way, nature moves back and forth, in cycles, rather than in a permanent upward climb or downward slide.
Such changes as occurred with these finches are sometimes referred to as "evolution in action." But these infinitesimal changes are not "evolution" in the way that Darwin meant the word."
That seems like an odd thing to say considering the Galapagos finches helped inspired Darwin in his theory. Of course these sorts of changes mattered to Darwin. Just like artificial selection in the breeding of domestic pigeons. He saw the big picture of how small changes over big periods of time could lead to bigger changes in the overall phenotype of an organism.
"For he meant to explain how nature by itself could make something new, how one animal or plant over long periods of time could transform itself into something quite different, like a trout changing into a tiger, or a bacterium into a whale."
This is a gross misrepresentation of how evolutionary biologists, and Darwin, understand evolution. No sane biologist thinks that a trout could become a tiger or a bacterium a whale. Though I am wondering if perhaps you meant something other than what a plain reading of this statement insinuates.
"The 19th century German monk, Gregor Mendel, discoverer of what are now called genes, was opposed to Darwin's progressive idea of "continuous variation" in nature. That is, Darwin wrongly thought that inheritance involved mixing traits, rather like mixing different paints. In contrast, Mendel found that inheriting traits involved something like mixing marbles, discrete characteristics like eye and hair color."
Darwin was simply a product of the general thought of his time, i.e., that traits blend. In fact, he found it to be a difficult barrier to his theory, as did others. If new traits arise, how can they be fixed into a population if they would simply be 'blended' out? Mendel thought that his idea of inheritance actually solved Darwin's difficulties and he sent Darwin a copy of his paper, but apparently Darwin never read it. Mendel's work was eventually incorporated into Darwin's theory in the 1930's, which is now called the Modern Evolutionary Synthesis: http://en.wikipedia.org/wiki/Modern_evolutionary_synthesis
So you seem to have misunderstood what Mendelian genetics meant for evolution by natural selection (and other means). It bolstered it, not weakened it.
Also, it's worth noting that Mendelian inheritance, the idea of discrete traits, is not actually true all of the time. Genetics is far more complex (polygenic traits, pleiotropy and epigenetics are all well-known examples of non-Mendelian inheritance), and there are many traits that are rather continuous. Skin color is an obvious one. Actually, one of the traits you mentioned, eye color, may be under the control of 16 genes and thus would not be an example of Mendelian inheritance.
"DNA studies have confirmed the traditional relationships and "genetic distances" between different plants and animals which have always existed as observed by humans over thousands of years."
Quite the contrary (I'm speaking as an expert on this one, as this is the field of my advisor and myself). While in some cases genetic distances (and the more complex models we use today for determining evolutionary relationships with genes) mirror phenotypic (visual) similarities between organisms, in many, MANY cases it's shown us some quite different things.
So you may be aware that humans are genetically similar to chimpanzees, gorillas and orangutans. Not so difficult to believe right? We're all sort of human-ish in appearance. But would you believe that things that look as different from each other as
would be shown to be related to each other genetically? As in, statistically-robust, without a shadow-of-a-doubt related? What's even more interesting about it is that these are all groups that are historically (and most are contemporaneously) endemic to Africa, so it has a significant biogeographic component . My advisor had a big hand in discovering and establishing this group, which they aptly named Afrotheria.
Or here's another one: what group do lizards, snakes, turtles and crocodiles belong to? They're reptiles, right? Scaly skin, they lay eggs, they're "cold-blooded". Well, genetically speaking (and now thanks to the fossil record and some features of their morphology) we don't think that anymore. Crocs are closest to birds. Crocs+birds are closest to turtles (this was a very recent discovery). And snakes? They're actually a type of lizard. All thanks to genetics!
These, and MANY more examples that I could pull from, show that genetic data in many cases do not confirm what humans have thought for thousands of years. Not by a long shot!
"Resistance to pesticides and antibiotics does not mean that the insects and bacteria who survive these threats have "evolved." Quite the contrary. Those organisms "resist" the antibiotic or pesticide poisoning merely because of some feature of their cellular structure that does not bind with the poison."
If a trait arises in an individual (e.g. pesticide resistance) and that spread throughout the population, then we call it evolution. If it spreads because those without the trait die, and those with the trait live and pass on that trait, then it's evolution by means of natural selection. The insects and bacteria in your examples have indeed evolved.
"Subsequently the tactic was to attack individuals who doubted Darwin by calling them "creationists" -- meaning "crackpots."
When the truths about issues are distorted or told partially, which you have done in your Opinion article in the Bee (whether knowingly or in ignorance), it spreads lies to others who then parrot it to the next person. I have seen many fellow Christians state that all sorts of false things about evolutionary theory who are repeating what their pastor said or they read in the book by a Creationist or IDist. It's sad because I simply tell them that they were told a lie. It's not an opinion, it's something grounded in facts. It makes me think of atheists who read 10 verses in the Bible and then ridicule it based on such a limited understanding. If you're going to tackle this issue, spend more time learning about it, talk with evolutionary biologists personally, get grounded in the facts, stay away from the sound bites, etc.
I never realized how strongly I wanted kids until I read this blog about a film critic showing Star Wars two his 3- and 6-year old boys for the first time. Not only did I find the reactions of the children absolutely hilarious/touching, it's also convinced me that probably the best way to show my own (presumed) future children the saga is in an order that I have come to realize is genius: IV, V, I, II, III, VI. Though, now I'm going to have to test it out for myself.
If you have any sort of vague affection for Star Wars and/or kids, I strongly suggest you read these.