Friday, May 6, 2016

Research Week: Projects at Core Academy

I'm wrapping up my research week today with a short post on research projects ongoing at Core Academy.

First up, our trillium project.  Three years ago, when Roger Sanders and I launched Core Academy, we spent a lot of time exploring the woods in the southern Appalachians, and one day in May, we stumbled across a funny-looking trillium flower: It was all petals.  I was mildly intrigued by this, and I had not heard of such things before.  After reading up on the subject, it turns out that trilliums have lots of weird growth forms known, but none of them have been carefully characterized with modern technology.  In other words, we don't know exactly what causes trilliums to have weird flower forms.  The next year, we went back to check on it again, and we found it growing in the very same spot.  At that point, we recruited a student intern to work on the project (or she recruited us - it's kind of hard to tell sometimes), and she's been going at it full steam since then.  We tried cloning the plants last year (unsuccessfully), and this year we're going for DNA sequencing.  This year's fourth annual survey of the growth site revealed something even more interesting: there are other weird growth forms in the same location, including that four-leafed trillium in the picture above.

Why is any of this interesting?  The southern Appalachians are the most diverse location on the planet for trillium species (and lots of other species too).  Why do we have so many different forms of trillium here?  Do these weird growth forms have anything to do with the difference between a large-flowered trillium and a nodding trillium?  That's what we want to find out.

I'm also working on a big mammal baraminology project.  You might recall that baraminology has to do with identifying "created kinds."  The statistical methods I use have been criticized by some for a variety of reasons.  Back in 2009, I tried to do a study to see if there was some consistency to the results of these studies, but my analysis was inconclusive.  There was definitely a bias in favor of baraminology, but it was not significant.  Since then I did a much larger survey but I didn't do the full baraminology analysis, so once again, I don't think those results were entirely decisive either.  Over the next year, I hope to finish a huge survey of mammal created kinds that I hope will help me settle this question: Is baraminology finding anything real or is it just a bunch of statistical mumbo jumbo.

Roger Sanders is busy doing a similar project with flowering plants.  Roger's an expert in flowering plant systematics, and I'm really excited to see how his project turns out.

In addition to these main projects, we're also collaborating and contributing to other projects.  Roger is working with Steve Austin on coal and floating forest research.  Joe Francis and I are throwing around some ideas on human disease, and just this morning, I was plotting a fossil project with Paul Garner.

All of that is great stuff, but the best thing is coming on Monday.

Feedback? Email me at toddcharleswood [at] gmail [dot] com. If you enjoyed this article, please consider a contribution to Core Academy of Science. Thank you.

Thursday, May 5, 2016

Research Week: Mysteries of the Channel Islands

Off the coast of California, the Channel Islands are home to many unique and fascinating creatures.  Dwarf mammoth fossils have been found there, and I previously wrote about the local scrub jays, which is worth reading again:
Next, a recent article in Evolution from Langin et al. details the fascinating discovery of what we might call "speciation in progress" on Santa Cruz island.  Santa Cruz is home to a unique species of jay called the island scrub jay.  They're substantially bigger than mainland scrub jays in nearby California.  The typical explanation for unique island species (ever since Darwin) is that they diverged from their mainland cousins when they were cut off on the island from the mainland.  The isolation of the island is thought to be important to making new species.  If the island and mainland populations were able to mingle, then they presumably would not diverge into different species.  Except, with this research, we find that that doesn't always hold.  On Santa Cruz island (just west of Oxnard, CA), Langin et al. found significant differences in the bill shape of scrub jays inhabiting oak forests and those inhabiting pine forests.  Even though the pine and oak forests are adjacent habitats, Langin et al. still found reduced gene flow between the populations, meaning that oak-inhabiting scrub jays tend to mate with other oak-inhabitors and pine-inhabitors tend to mate with other pine-inhabitors.  This isn't the first evidence of divergence on a single island (For example, see the palms of Lord Howe Island), but it is surprising that something as mobile as a bird would show this pattern of divergence.
This week, I was alerted to a new article in Current Biology that reports on research on another Channel Island species, the island fox (Urocyon littoralis).  The foxes are cat-sized little guys that are active during the day (they're diurnal).  Chances are if you visit the visitor center on Santa Cruz, you'll see one of the foxes lurking around.

The research article by Robinson et al. reports on genome sequencing of seven different island foxes, including two from the distant island of San Nicolas.  Remarkably, where the scrub jays seem to be differentiating into two breeding populations, the foxes exhibit very little genetic difference.  Robinson et al. call it "genomic flatlining."  In particular, the foxes from San Nicolas are nearly identical, with hotspots of variation found in regions associated with the sense of smell (olfactory receptors).

This is fascinating because normally that kind of genetic similarity is associated with an unhealthy population.  As genetic variation goes down, the chances of producing genetically abnormal offspring goes up.  This is called inbreeding depression.  The foxes are considered to be an outbreeding population, and it's surprising to find so little genetic variability without the signs of a declining population.  Somehow these foxes are able to thrive even though the genetics suggest that they shouldn't.

I find this especially interesting since inbreeding depression is a very common counterargument to the Flood.  Supposedly, land creature populations could not survive if they were reduced to a single breeding pair, but here on the Channel Islands, the foxes seem to be contradicting that common wisdom.  Creation is full of surprises.

So the Channel Islands harbor a scrub jay population that seems to be in the process of splitting into different breeding populations (species?) and a fox that is so genetically similar, it probably shouldn't be surviving at all.  According to basic theory in population genetics, neither of those things should be happening. What other secrets do the Channel Islands hold?

Tomorrow, I'm going wrap up Research Week and talk about the future of research at Core Academy.  And don't forget the big announcement coming on Monday!

Robinson et al. 2016. Genomic Flatlining in the Endangered Island Fox. Current Biology DOI 10.1016/j.cub.2016.02.062

Feedback? Email me at toddcharleswood [at] gmail [dot] com. If you enjoyed this article, please consider a contribution to Core Academy of Science. Thank you.

Wednesday, May 4, 2016

Research Week: Directed Mutations

A long time ago (seven years to be precise), I wrote about an article by Jean Lightner on skin color variation, in which she proposed that "directed mutations" could account for nonrandom patterns of nucleotide differences that we observe in the present.  It was an interesting idea, and I like interesting ideas.  In my post, I was very favorable towards the concept.

Truth is: I was always a bit uneasy about the idea.  Just a bit.  I think there's a fine line in creationism between using creationist beliefs to think creatively about the world around us and being ad hoc and explaining away interesting trends.  I'm not always sure where that line is, and that's awkward.  I've always respected Lightner's proposal because it could be true, but deep down I wondered if it crossed the line into ad hoc speculation.

Then, things change.  An article last month in Genome Research described something kind of similar to what Lightner suggested.  Pinto et al. looked at an enzyme called APOBEC3G, that is part of a family of genes in human and ape genomes that deaminate cytosines.  "Deaminating cytosine" is a sort of "directed mutation," because that chemical reaction changes the sequence of DNA at a single nucleotide position.  When Lightner proposed this idea of directed mutation, she had in mind the notion of altering single nucleotides in DNA.

APOBEC enzymes are thought to defend human cells against viruses by mutating them so they don't work any more.  Pinto et al. wondered if there might be evidence of APOBEC enzymes acting on human and ape genomes as well.  Think of it as a sort of "collateral damage" in the war against viruses.  In their survey, they found eight thousand unique clusters of mutations that look like APOBEC mutations in the human genome, as well as the genomes of Neandertal and Denisovans.  They found almost a half million that were unique to the entire genus Homo.  The fact that these mutations are unique to these different forms of human indicates that this enzyme has indeed altered human genome sequences since creation.  And that's just one version of an enzyme family that has multiple variants in the human genome.

Now, we have to put this into perspective.  APOBEC doesn't account for all variations in the human genome, or even most of the variations.  It doesn't explain why the human genome is nearly identical to other ape genomes.  All we get from this research is one example of how an enzyme really could alter a human genome sequence at one nucleotide position.  That's pretty exciting stuff, though, and it greatly alleviates my unease about "directed mutations."  They really can happen.

Now the question is: How many other enzymes like APOBEC3G could also alter human genome sequences?

Tomorrow, research week continues as we "take the wings of the morning and dwell in the uttermost parts of the sea."  Well, maybe not the "uttermost," but at least we'll head out to an island and talk about tiny populations.

Pinto et al. 2016. Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity. Genome Research doi:10.1101/gr.199240.115.

Feedback? Email me at toddcharleswood [at] gmail [dot] com. If you enjoyed this article, please consider a contribution to Core Academy of Science. Thank you.

Tuesday, May 3, 2016

Research Week: The Kuiper Belt

It's Research Week here, and I'm highlighting some interesting and fun new research results that have been published lately.  When I started thinking about blogging about Pluto again, NASA and the New Horizons team released a new map of Pluto, and I got excited about making a little animation.  Then I started looking up information about Pluto and other Kuiper Belt objects, and my little animation started growing. The next thing you know, this video happened.

This video is especially iffy because I'm a biochemist reacting to some very unfamiliar science that I read about on the internet.  Now I did read pages from NASA and other scientists, so it's not like I'm just summarizing Wikipedia or some crackpot.  But I suspect I'll be getting some emails from astronomers and/or fellow creationists anyway.  My apologies for being a complete amateur, but I am an enthusiastic amateur!

Still, it was a lot of fun taking a break from my normal life and learning a little bit about the solar system beyond Neptune.  What an amazing place we live in!  "If I ascend into heaven, You are there!" (Ps. 139:8).

Tomorrow, we'll descend into some depths, all the way to the submicroscopic level of the human genome, and God will be there too!

Feedback? Email me at toddcharleswood [at] gmail [dot] com. If you enjoyed this article, please consider a contribution to Core Academy of Science. Thank you.

Monday, May 2, 2016

Research Week: The Wonder of it All

Most of you know that I love research.  I love learning new things, and I get a huge charge out of discovering new things.  Being a scientist is a perfect job for me, because I get to discover new things pretty regularly.

This week, I'm kicking off a special week of blog posts celebrating the wonder of discovery.  Every morning I'll be posting a new article looking at some interesting new development in the world of science.  Some of them will have obvious creationist applications, and others will not.  These posts are all leading up to a big announcement next Monday morning, and I hope you'll stick around for that.

I think research is so wonderful because it is the Lord's work that I study.  In a sense, all research is "creation research," because the physical world that we study is the creation.  The world around us isn't just a passive, inert place for us to live.  God's creation is infused with His glory.  The universe declares His power and wisdom.  Every rock, every leaf, even the tiniest bugs you can't see take part in praising the wonder of their Creator.

Studying God's works lets us join that song of praise.  As I get older, this sense of wonder gets bigger and bigger.  Every time I find something new I didn't know before, I'm overwhelmed with gratitude to my Creator and Savior for letting me see these things.  What a privilege it is to praise the Lord!

Tomorrow, we ascend into heaven, and He will be there!

Feedback? Email me at toddcharleswood [at] gmail [dot] com. If you enjoyed this article, please consider a contribution to Core Academy of Science. Thank you.