Biochemical Soul Musings on Nature, Science, Evolution, Biology, and Education

18Apr/09Off

Nature Walk #4.2 – Birds

Spring is Here!

This Nature Walk edition continues from #4.1 - Arthopods.

I've broken this post up into four parts due to the large number of images:

The images are highly compressed for bandwidth's sake, but you can click on the images for larger versions (and a few are much deserving of an extra click).

As always feel free to give me any species identifications where I have failed to do so or done so incorrectly.

Birds

Other than all the other scurrying, fluttering, swimming, and pulsing critters of the world, birds are my favorite.

I've managed to snap quite a few good bird images over the past few days (though more eluded me, such as the dastardly killdeer that continually thwarted my focusing attempts). Here are some of them.

First, the Eastern Bluebird (Sialia sialis). This bird was hanging out over by the Environmental Protection Agency (near the NIEHS). It was quite a distant shot, but turned out pretty well, considering. I am rarely able to get close enough to bluebirds around here. They're just so skittish.

Eastern Bluebird (Sialia sialis)

Eastern Bluebird (Sialia sialis)

Eastern Bluebird (Sialia sialis)

Eastern Bluebird (Sialia sialis)

This next is my favorite bluebird image ever. Today I just happened to walk by this birdhouse nestled in in the woods at the treeline (the NIEHS campus is covered with them), and I saw this single eye staring out at me.  Priceless!

Eastern Bluebird (Sialia sialis)

"Please don't eat me, please don't eat me, please don't eat me!"

And the cutest thing I've seen this spring: a Mallard (Anas platyrhynchos) mother with eleven ducklings.

Mallard (Anas platyrhynchos)

Mallard (Anas platyrhynchos)

Mallard (Anas platyrhynchos)

Swimming among the algal mats - Mallard (Anas platyrhynchos)

Mallard (Anas platyrhynchos)

Check out the front baby's face! - Mallard (Anas platyrhynchos)

And to top it off, I even have some video:

As I've mentioned before, one of the great things about the National Institute of Environmental Health Sciences (and the EPA) is the large lake in the middle of campus. We are a stopping ground for all sorts of migratory water fowl, with several species appearing and dissappearing throughout the year. (see the ruddy ducks from a previous Nature Walk)

One bird that I've seen alot of this year is the Double-crested Cormorant (Phalacrocorax auritus).

Double-crested Cormorant (Phalacrocorax auritus

Double-crested Cormorant (Phalacrocorax auritus)

Double-crested Cormorant (Phalacrocorax auritus

So regal!

Double-crested Cormorant (Phalacrocorax auritus)

"Do I look fatter to you?"

Of course, our campus is infamous for the gazillion Canada Geese (Branta canadensis) that stalk the grounds.  Right now the females are mostly nested, with the males hovering nearby - both ready to start a hissy fit (literally) if you get near the nests.

Canada Geese (Branta canadensis)

Canada Goose (Branta canadensis)

Canada Geese (Branta canadensis)

"Back off!"

Canada Geese (Branta canadensis)

"And you think we don't have teeth"

To truly appreciate their menacing display (more hiss than bite) you must see the video:

Don't worry - this goose was not overly stressed by me.  They nest about 3 feet from the walking trail. This female makes this display probably about a hundred times per day as each jogger strolls by.  It's quite hilarious actually. One has to admire their ability to keep up the front (I know of quite a few people who find them dangerous and terrifying - trust me, they are neither once you've figured out their game. It's the same as a defensive opossum: open your mouth and hiss alot - that's it).

As I was walking along, a Great Blue Heron (Ardea herodias) plopped down right next to me.

Great Blue Heron (Ardea herodias)

Great Blue Heron (Ardea herodias) coming in for a landing

Great Blue Heron (Ardea herodias)

Great Blue Heron (Ardea herodias)

Back at the homestead, I captured another priceless avian expression: an American Goldfinch (Carduelis tristis) suddenly noticing that I had snuck up behind the feeder.

American Goldfinch (Carduelis tristis)

American Goldfinch (Carduelis tristis)

Nearby, a White-breasted Nuthatch (Sitta carolinensis) skittered up the huge poplar tree in my front yard:

White-breasted Nuthatch (Sitta carolinensis)

White-breasted Nuthatch (Sitta carolinensis)

A Northern Mockingbird (Mimus polyglottos) perched as well.

Northern Mockingbird (Mimus polyglottos)

Northern Mockingbird (Mimus polyglottos)

Finally, I managed to capture a far away American Kestrel (Falco sparverius) scoping the farmland below for tasty treats. I grew up calling these "Sparrow Hawks," which is apparently a common misnomer - they are actually falcons (not hawks).

American Kestrel (Falco sparverius)

American Kestrel (Falco sparverius)

American Kestrel (Falco sparverius)

American Kestrel (Falco sparverius)

Who says the dinosaurs went extinct?

See the rest of this Nature Walk:


28Feb/09Off

Nature Walk #2 – Birds and a Burger

For my next Nature Walk, on my Friday lunch break I decided to take a quick stroll around the lake at the NIEHS campus, camera in hand. Over the past couple of month several coworkers have spotted two river otters in the lake (which is strange indeed). I even managed to spot one while staring out the cafeteria window.

Unfortunately, I did not see the otters, though I will most certainly be attempting to capture them on digital film next week... I did see the following... (FYI: I am not an experienced birder - if I misidentify, feel free to let me know. Also: these are highly compressed images to limit bandwidth - click for higher res).

Beautiful lake between the NIEHS and EPA campuses

Beautiful lake between the NIEHS and EPA campuses

First up, a flock of ruddy ducks (Oxyura jamaicensis):

Ruddy Ducks

Sleepy...

Ruddy Duck

so my tail's stiff...what of it?

Ruddy Duck

Get back to work...

And of course, our ubiquitous Canada Goose (Branta canadensis). We literally have hundreds of these birds all over campus year round, covering every surface with green refuse. I look forward to nesting season when they develop severe huffy attitudes that involve a lot of loud hissing (but they're really all talk).

A while back they hired a company to capture most of them and relocate them...yeah...that didn't work (too many geese leads to many problems, environmental and otherwise).

Bring it on Cobra Kai

Bring it on Cobra Kai

Walk on by...

Walk on by...

And the less exotic, but still wonderful American Robin (Turdus migratorius) far away and HIGH up in a tree (I was surprised this photo even turned out at all.

Fluffed

Fluffed in the wind

After my walk around the lake, I went for a burger at Wendy's (I know - horrible - but they're so tasty). All of the following were taken from my car in the parking lot and at my parked eating spot.

Every year about this time, a huge flock of Ring-Billed Gulls (Larus delawarensis) shows up in this fast-food district. You coastal folks may bore of them, but we are pretty far inland, and I grew up in landlocked Arkansas, so I still find gulls utterly fascinating.

Loves me some burgers

Give me fries!!

Call me Narcissus...

Call me Narcissus...

Beautiful eyes.

Beautiful Eyes (mature vs. immature)

One sad bird had a severely gimpy foot. But it seemed to be surviving...thanks to fast-food throw aways. I must say that it looked to be in some pain walking.

Victim of a fisherman

Victim of a fisherman (tangled line and rig)

And finally, I retreated to my favorite natural spot to eat, parked near a tiny copse of pines. Despite the fact that I always pay attention to nature, I somehow had never managed to see the following bird. I could tell it looked like a nuthatch - I'm very familiar with the White-Breasted Nuthatch (Sitta carolinensis) as we had hundreds on my property in Arkansas - but I had no clue what it was and had to look it up when I got home.

It's a Brown-Headed Nuthatch (Sitta pusilla). He was pretty cute - he would look in the hole and poke around, then jerk his head around to make sure no one was watching, then do it again and again.

Paranoid much?

The Paranoid Nuthatch

The Brown-Headed Nuthatch in action...

Shortly thereafter it was back to the lab...

Previous Nature Walks:

19Feb/09Off

I and the Bird #94 – The Birder’s Report

For the first time ever, I have been included in the blog carnival for the birds: I and the Bird #94!  And wow are there alot of people who are into birding! Each edition is jam packed with stories of birds, pictures of birds, and recipes of birds (not really).

So set aside some time over the coming days to peruse through the avian wonders. My own post on the Great Blue Heron and the Catfish is included in this 94th edition (with pretty cool videos).

7Feb/09Off

Dino Visions of the Future? Not a Chance!

Easy as pie...

Easy as pie...

Once, again the past decades of developmental biology research has been forgotten amidst the layman's limited understanding of the potential wonders of genetic technology.

It started off innocently enough: Time.com began a series of articles on "Visions of the 21st Century."

With daily headlines on the rampant success of molecular, genetic, organismal, and evolutionary biology, it seems natural and predictable that in the wake of movies like Jurassic Park and the now perennial reports of various animal cloning successes that imaginative folks would ask "Will we clone a dinosaur?"

As one might expect, the Time article made it to the front page of Digg - where I found it.

It started off as any good article on the subject should - with sobriety:

"The short answer is no. The slightly longer answer is definitely not. The Jurassic Park idea - amber, insects and bits of frog dna - would not work in a million years, and it was by far the most ingenious suggestion yet made for how to find dinosaur genes. Cloning a mammoth - flash frozen for several thousand years - might just prove feasible one day. But dinosaurs, 65 million years old? No way."

Sad, but true.

Unfortunately, with one illogical slight of literary hand, the next sentence erased the reality upon which the article had set itself up to expound.

"It is only when you ask the question the third time that you begin to see a glimpse of an affirmative answer."

Huh?

"Start with three premises. First, dinosaurs did not die out; indeed there are roughly twice as many species of their descendants still here on Earth as there are mammals, but we call them birds. Second, dna is turning out to be a great deal more "conserved" than anybody ever imagined. So-called Hox genes that lay down the body plan in an embryo are so similar in people and fruit flies that they can be used interchangeably, yet the last common ancestor of people and fruit flies lived about 600 million years ago.

Third, and most exciting, geneticists are finding many "pseudogenes" in human and animal dna - copies of old, discarded genes. It's a bit like finding the manual for a typewriter bound into the back of the manual for your latest word-processing software. There may be a lot of interesting obsolete instructions hidden in our genes.

Put these three premises together and the implication is clear: the dino genes are still out there."

Ahh, now I see where they're going with this...

The next part in the article makes decent scientific sense. Essentially, they lay out a path whereby over the coming decades, scientists may use the decoded DNA of birds, along with alot of computationally intensive lineage analyses to essentially reconstruct a dinosaur genome. There are many potential problems with this, but from the perspective of thinking futuristically, it's not completely implausible (unless you consider regulatory regions - see below). We very well may be able to resurrect a close enough approximation of a dinosaur genome from DNA sequences existing in modern avians, using chunks from other types of organisms as well.

Alright, so let's say we've done it - we've sent our text file containg the complete dino genome sequence to a high-tech DNA synthesis company and we now have a tube full of the actual DNA. What now?

To quote Reg of the People's Front of Judea (or was it the Popular Front?),

"Where's the fetus going to gestate? You going to keep it in a box?"

Simple, right? Apparently...

"The rest is as easy as Dolly the sheep: call up a company that can synthesize the genome, stick it into an enucleated ostrich ovum, implant the same in an ostrich and sit back to watch the fun."

Really? Oh, well yes - if we ignore everything we've learned about early embryogenesis. You see, we now know that early development of an embryo is controlled by MUCH more than just the genome and gene products of the embryo itself. A mother creates an egg - a single-celled oocyte - which eventually becomes isolated from the mother's tissues by an eggshell (unlike placental creatures). The embryo goes through most of it's tissue and organ development inside that egg.

That means that everything the embryo needs - from nutrition to the intricate balance of hormones, growth factors, asymmetry cues, etc. - must be deposited by the mother during oocyte creation inside the egg in the exact position and concentration necessary.

So the crux of the question of feasibility is this: has the internal oocyte generation machinery inside an ostrich changed much over the last 65+ million years? I can't imagine anything but a resounding "yes" coming from any developmental biologist.

In fact I would be more than utterly shocked if a dino DNA genome/enucleated ostrich oocyte could even make it through the first cell division, much less complete gastrulation and neurulation. The author does hint at potential developmental issues in a couple of sentences:

"Of course, there will be teething troubles - literally. Or somebody might have forgotten to cut out the song bird's voice genes, so the first struth chirps like a sparrow. Or maybe the brain development did not quite hang together and the creature is born incapable of normal movement."

My bet is that the defects would be far far worse than a brain not quite holding together. It doesn't take much to perturb early development by mucking with just a gene or two. But combining this issue with the almost certain incompatibility between a 65+ million year old dino genome and a modern avian oocyte, my guess is that cloning a dinosaur is almost completely impossible.

It would be like taking a caveman and telling him to build a spaceshuttle without telling him which parts to use or how to build it - times 65 million!

This doesn't even address another large issue with the article. It claims that scientists are discovering that DNA is far "more 'conserved' than anybody ever imagined." True.  But this is largely beacuse we have learned that most organisms more or less have the same "genetic toolkit." That is, we have the same basic genes, but what has changed is how they are expressed. Assembling the correct regulatory regions surrounding genes (or lying thousands of base pairs away in the case of many enhancers) based on extant birds seems incredibly unlikely.

But hey - I could be wrong. Maybe - just maybe - we will become advanced enough to alter the maternal contributions in the oocyte prior to or during dino DNA implantation AND somehow gain knowledge of what should be put in the egg in the first place AND assemble a genome with correct expression regulating regions.

What do you think?

Images:
ostrich: http://pro.corbis.com/images/
dinosaur http://gamewallpapers.com