Archive for: July, 2006

>Circus of the Spineless #11 at Words & Pictures

Jul 31 2006 Published by under Carnivals

>The latest Circus of the Spineless is up at Words & Pictures, exploring mountain mollusks, ancient spiders, sex and cannibalism, exploding jellies and other wonders of the invertebrate world.

Read the 11th edition here.

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>DNA's Underlying Code; Erudition #12

Jul 30 2006 Published by under Genetics, Links, Physiology, [Politics]

>From "Scientists Say They've Found a Code Beyond Genetics in DNA," by Nicholas Wade of The New York Times:

The genetic code specifies all the proteins that a cell makes. The second code, superimposed on the first, sets the placement of the nucleosomes, miniature protein spools around which the DNA is looped. The spools both protect and control access to the DNA itself.

The discovery, if confirmed, could open new insights into the higher order control of the genes, like the critical but still mysterious process by which each type of human cell is allowed to activate the genes it needs but cannot access the genes used by other types of cell.

I blogged about another discovery made a few months back involving nucleosomes/histones (DNA segments) and their function in determining growth in children and adults:

Imagine this: fundamentally, our DNA is spun around little protein spools called histones. These histones provide a structure for DNA and assist in gene regulation, or the process of turning genes on and off. Genes, obviously, cause development.

There are two histone sites where the methyl-marking (methylation) occurs; the K4 site and the K27 site. At the K27 site, the DNA is bound very tightly to the histone complex, not allowing any strands to become available for transcription (expression of DNA into protein). These sites are marked in adults.

At the K4 site, the strands are loosely bound, more accessible. K4 sites are marked in young, undifferentiated cells, like embryonic stem cells.

What this says, in a nutshell, is that they have found the areas where gene expression is a go (marked K4 region, in young cells) and where it is shut down (K27, in adults).

Certain genes do not have to be "turned on" when we are fully grown - especially genes that direct limb or organ growth - and the marked K27 site prevents that area of DNA to be accessed.

However, the K4 site would need to marked in the blastocyst and the DNA made available in order to start the differentiation process, so the cells could be directed into whatever is needed: liver cells, muscle tissue, bone, neurons, etc.

We're getting closer by the month, it seems.

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Why Spiders Aren't Insects IV: Molecular Homology

Photo by: Gerald Yuvailos


This is the fourth part in an ongoing series discussing the distinction and evolution of spiders and other arthropods.
Part I, part II and part III have led up to this point:

In the last post of this series, we established that spiders descended from marine arthropods called the eurypterids, distinct and separate from insects, appearing in the fossil record in the late Silurian/early Devonian, about 425 million years ago.

The cladogram we used to analyze the spider's history was based on the organism's morphological characteristics, that is, visible structures like chelicerae and book lungs that can be tied to other organisms that possess the same structures. Limulus (the extant horseshoe crab) has both of these structures and predates the spiders, placing them further back in the chelicerates' evolutionary history.

Homologous bones from human (I), dog (II), pig (III), cow (IV), tapir (V) and horse (VI):
r — Radius, u — Ulna, a — Scaphoid, b — Lunare, c — Triquetrum, d — Trapezium,
e — Trapezoid, f — Capitatum, g — Hamatum, p — Pisiforme

Paleontologists call this comparison of physical characteristics homology (coined by Richard Owen an anatomist and, ironically an opponent of Darwin). The mouth parts of a spider are homologous to the mouth parts of Limulus because of the cherlicae's exact form and function. This is a different designation than analogy; analogous structures may function in the same way, but they are different in form because of their different lineage. For this reason, scientists call analogy an artificial classification system.

A good example of analogous structures are wings from bat and bird. They perform the same function in varying degrees, but they have evolved very different forms. A bat's wing is basically a modified mammal hand, while the bird wing is a modified tetrapod arm.

Homology is essential in building an organism's phylogeny (evolutionary history). More recently, geneticists have employed this classification technique to analyze and find similarities among the less visible traits in life, RNA (ribonucleic acid) and the building blocks of proteins, amino acids.

Think of these cellular chemicals this way: If DNA is the blueprint of life, RNA is the builder and its materials are amino acids. When these amino acids are placed in the correct sequence by RNA, they become proteins, the framework of our body. And, since the genetic code for protein constructions is nearly universal*, geneticists can compare entire swaths of RNA from one organism to those of another and find homology at the molecular level.

Here's an example (sequences are greatly abbreviated for the sake of our sanity):

Organism 1: ACGC-CCCCC
Organism 2: ACGC-CCCUC
Organism 3: ACGU-CUCUC

Basically, from noting the differences in each RNA sequence, and determining the homologous sequences (such as the ACGU sequence above), a cladogram can be constructed that shows common ancestry without the murky distinctions that sometimes cloud the comparison of bones to bones, or mouth parts to mouth parts.

The problem with this molecular system of analysis is that it often provides vastly different cladograms than the ones crafted through morphological analysis. This is not necessarily the case between the spiders and and Limulus, the molecular evidence supports the fossil record's interpretation of ancestry, but it calls into question the descent of insects from chelicerates like spiders.

In short, the molecular evidence agrees with the morphological evidence: spiders are more closely related to horseshoe crabs than insects. But where and when did the insects arise?

Next time we'll tackle the more recent movements to elucidate the phylogeny of arthropods, including a discussion on the significance Hox genes and evolutionary-developmental biology (evo-devo).

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>Only One Month Left...

Jul 25 2006 Published by under Editing, Evolution, Publishing, Writing

>...and I still have loads to do.

School starts back up in a little over a month, and I am a bit behind in my article writing. For those that don't know, The Voltage Gate is going to print starting this school year as a hard copy supplement to this blog.

Anyway, I told myself at the end of last semester that this summer I would crack down and have six or so non-timely articles ready for publication by the end of August.

Publishing gets to be a bear when you fill multiple roles. At the beginning of last semester I was news editor, music editor, managing editor, layout design and, of course, staff writer. By the end of the semester I had passed several of those roles to our most competant staff members. Hopefully this semester I can keep it to layout, columnist and editor.

I have a great handful of ideas for the column, discussing everything from evolution in plain terms to the science of homosexuality to the general misinterpretation of science. The list goes on almost indefinitely.

The Bottom Line's new website is finally coming together, and even in its early stages it is leaps and bounds beyond our last set up (although in defense of our old website, it was entirely created and run by one student; College Publisher does not have such limitations).

So, all in all, expect a lot of cross traffic here at TVG, from The Bottom Line website to its blog to the new blogs of our columnists. I have high hopes for the coming year.

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>Right Compares Al Gore with Hitler; Erudition #11

Jul 21 2006 Published by under Climatology, Environment, [Politics]

>
But, I would like to point you in the direction of a post from Jen at Studying Biology and Environmental Science who quotes an article about the general denial of human-induced climate change, even going so far as to compare Al Gore with Hitler.

It's worth a read for both sides of the fence; conservatives can see what nonsense their representatives are spewing on television and in print, and liberals can continue to build up their ammo stores for 2008, platforming about environmentalism as if it we just another political issue. Enjoy.

As a side note: There are very few blogs that I read on a daily basis; Jen's in one of them. Go check it out.

My brother is coming up this weekend, so I won't be blogging until Sunday evening.

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>"Crossing the Moral Boundary": The Science Behind Bush's Stem Cell Veto

Jul 19 2006 Published by under Genetics, Links, Physiology, [Politics]

>This situation is unfortunate. Bush is foolish on so many levels, but mainly in the fact that other countries will get the jump on us if NIH is not properly funded to begin research. Bone marrow transplants (aka adult stem cells) are incredibly painful and extremely limited in variety of function. Adult stem cells are what is called "unipotent," which means they can only differentiate into one type of cell at a time.

Embryonic stem cells are "pluripotent," which means they can differentiate into all types of cells, from muscle to neuron, to germ cells - eggs and sperm. They are the mutable macro-building blocks of an organism, but undirected by its genes.

So, adult stem cells are undifferentiated cells residing in differentiated tissue, and therefore limited; while embryonic stem cells are undifferentiated cells in undifferentiated "tissue," and potentially limitless in capability to replicate, well, anything for anyone.

If you take nothing else with you from this post, consider this: embryonic stem cells are taken from a literal ball of cells (the blastocyst, below) in such an early stage in life that it remains unattached to the uterus. No nervous activity, no "parts," only cells.


This is another scientific issue dragged into the political arena, like evolution and climate change, discussed and debated by people who don't even understand (or want to understand) the real science behind the curtain.

All is not lost, however. State institutions like Johns Hopkins in Baltimore was recently given the go ahead by Ehrlich, and $15 million was given to Hopkins for research. And Maryland is not the only state that is bypassing the federal government. We'll get there eventually; then maybe we can save some lives and make some technical headway.

Hopefully I can tie this post in with a discussion of Hox genes when we tackle part IV of "Why Spiders Aren't Insects."

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Why Spiders Aren't Insects III: The Evolutionary Advantages of Mass Extinction

So far we have established that spiders are distinct from insects for two reasons: physiology (mouth parts, body plan, respiratory structures) and more importantly, evolutionary history (or phylogeny, as scientists call it).

But where did spider's come from? How did they crawl out of the water as euryterids and speciate (become a distinct organism that cannot interbreed)?

The answer, like many in invertebrate paleontology, is cloudy. Organisms without hard, thick shells rarely become fossilized. In fact, for any organism's parts to become fossilized, even vertebrates, is a profound rarity, as Bill Bryson illustrates in A Short History of Nearly Everything:

Only about one bone in a billion, it is thought, ever becomes fossilized. If that is so, it means that the complete fossil legacy of all the Americans alive today - that's 270 million people with 206 bones each - will only be about fifty bones, one quarter of a complete skeleton.

Needless to say, invertebrate paleontologists are having a heck of a time piecing things together from such a paltry fossil record. But that doesn't mean there's no evidence.

According to morphological and geological evidence, and therefore directly observable comparison, spiders and their brethren descended from the eurypterids, many of which were sea-going creatures. The eurypterids arose in the Ordovician, a period that began with the decimation of perhaps 60% of all marine life, and consequently ended with another more devastating cataclysm, which which some paleontologists rank as the second most destructive extinction event in the history of the world (by extinction of family). This has become known, quite appropriately, as the end-Ordovician event.

Mass extinctions make room for the evolution of unique characteristics as dictated by an organism's environment, and the environment changed drastically for the eurypterids at the end of the Ordovician. Glaciers began to creep down from the upper latitude, as the greenhouse gas carbon dioxide was depleted from the atmosphere, reducing the Earth's ability to trap the sun's heat energy. As the glaciers encroached, sea levels dropped and global temperatures cooled. This rapid progression decimated habitats, and destroyed a species' equilibrium with its environment.

But the end-Ordovician event was comprised of two parts: glaciation and then a period melting, an interglacial. Temperatures warmed once more, glaciers melted, flooding the land, and raising sea levels once more. The world had completely lost almost 50 percent of the families of life, but the ancestors of the spiders had survived. The Silurian period had begun, and new ecological niches were available for exploitation, a habitat opportunity that eventually would produce the spider.

That's about how it stands from a morphological perspective. But more recently scientists have been delving into molecular evidence and crafting very different explanations of not only the rise of the spider, but the vast diversification of arthropods in general.

Next time we'll address the new cladograms produce by this molecular evidence, and what ramifications it might have in interpreting the diaspora of the most abundant creatures on the planet.

*Interestingly enough, we are in the middle of an interglacial right now, the Holocene. Much like the success of the spider, our current interglacial, which began about 16,000 years ago, may have contributed to the ultimate "success" of Homo sapiens.

Resources:

Pechenik, J. A. (2000). Biology of the Invertebrates. : McGraw Hill Companies.

Gradstein, Felix, James Ogg, and Alan Smith, eds., 2004. A Geologic Time Scale 2004 (Cambridge University Press)

Baez, J. (2005). Temperature. Retrieved July 18, 2006, from http://www.math.ucr.edu/home/baez/temperature/

Webby, Barry D. and Mary L. Droser, eds., 2004. The Great Ordovician Biodiversification Event

University of Bristol. (2004). Fossil chelicerates and evolution. Retrieved July 18, 2006, from http://palaeo.gly.bris.ac.uk/Palaeofiles/Fossilgroups/Chelicerata/fossils.html

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>Tom Brokaw Tackles Global Warming

Jul 16 2006 Published by under Climatology, Environment, Journalism, [Politics]

>Tonight at 9 p.m. on the Discovery Channel, Tom Brokaw presents "Global Warming: What You Need to Know," which is less about his journey (a la Al Gore) and more about the evidence for human-induced climate change.

Update: The link above has a listing of the other show times this week.

The program was excellent, as I expected. Brokaw talked to the big climatologists - Oppenheimer, Hansen - plus ecologists and biologists who explained the potential for a mass extinction crisis.

If you have a spare two hours this week and any of those times fit into your schedule, please sit down with your loved ones with an open mind. This issue could unify us as a country once more.

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Why Spiders Aren't Insects II: A Primer on Cladistics

So how is it that spiders are more closely related to horseshoe crabs - marine arthropods that haven't changed much in the past 250 million years - than to a more obvious choice, the insects?

The answer to that question is more complex than you might think.

Up until the middle of the 20th century, before evolutionary theory was completely accepted by mainstream biology and supported by genetic analysis, taxonomists (scientists who place organisms in groups) classified organisms according to their modern anatomy. If organisms shared common physical structures (like chelicerae or mandibles) they would be placed in groups (like subphylums and classes) that put like with like. The Linnaean system of classification is still used today, but a more recent mode of classification has been able to answer how evolution plays a part in giving rise to new anatomy, and how organisms are related through common ancestry.

Common ancestry is what evolution is all about when it comes down to it, and this relatively new way of studying common ancestry is called cladistics (links to a great BBC explanation).

Open up this evolutionary tree into a new window/tab and follow along with me. This tree, a cladogram, represents the evolutionary history of all the chelicerates; spiders ("other arachnids"), horseshoe crabs ("Xiphosurida"), eurypterids, and scorpions. The cladogram labels time periods at the top from approximately 550 millions years ago (the Cambrian era) to about 250 millions years ago (the Permian era). We're mainly interested in that bracket on the bottom encompassing the "true chelicerates."

Notice on the cladogram that you can trace each group back to one point where it splits between one group and another. Take the "other arachnids" branch for example. You can trace its branch back to the split with the scorpions, and at that split there is a common ancestor from which both other arachnids - including spiders - and scorpions descended.

So basically, cladograms are family trees that evolutionary biologists can use to determine the ancestry and hierarchy of modern organisms.*

Ernst Haeckel's artistic representation of two species of eurypterids.

Keep tracing that line back from the common ancestor of spiders and scorpions. The next stop is the eurypterids (image above) the extinct relatives of the spider. Go even further back and there's a split between the common ancestor of eurypterids (and subsequently spiders and scorpions) and another extinct group of chelicerates, the Chasmataspida.

Finally, follow that last split back, all the way back to the Ordovician period, over 400 million years ago, to where the horseshoe crabs arose. That is where the true connection between the horseshoe crab and the spiders lies, in their common ancestry, not merely in their modern anatomical similarities.

Nowhere on this cladogram do you see insects giving rise to the spiders. In fact, modern insects would arise in later periods, millions of years after the first spiders crawled on land, although the details of the appearance of insects is still debated.

But how did spiders become distinct from their marine ancestors? The transition from water to land (and sometimes from land back to water) for all organisms is one the most interesting aspects of evolutionary biology, and though it remains somewhat of a mystery for spiders, we'll delve into the facts tomorrow.

*Cladograms are closer to what Darwin suggested for phyletic analysis in Origin of Species than the Linnaean system.

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Why Spiders Aren't Insects I

Jul 15 2006 Published by under Animals, Basic Concepts, Evolution, Invertebrates, Physiology

This is the first in a series of discussions on the evolutionary significance of the spider and its relatives.

Perhaps nothing will spark a lengthy dissertation from an entomologist more quickly than calling a spider an "insect." And lengthy can be well, hours.

Truly, spiders do seem rather buggish; they're creepy, have loads of legs and the thick outer structure (an exoskeleton) that other bugs possess. In short, if it looks like it, feels like it, tastes like it (?!), well, it must be...

That rule doesn't apply here. When you look more closely at a spider, one thing becomes immediately clear: it only has two segments, the most important of which is called the prosoma. The prosoma in spiders is the smaller segment and bears both the spider's head and all of the spider's walking legs, while the larger part, the abdomen, bears another part spiders are famous for, silk-secreting spinnerets (we'll discuss silk production in a later post).

The major distinction between spiders and insects is in the mouth. While insects have evolved leaf and flesh shredding mandibles from small appendages on the head evolved from a common ancestor of both spiders and insects, spiders have more primitive feeding parts called chelicerae tipped with well-known and well-feared fangs with which spiders subdue and tear prey into digestible pieces. Chelicerae can be used like knives or scissors depending on the species of spider.

For this reason more than any other, spiders are placed as a class under the subphylum Chelicerata (Greek: claw) and insects are placed into the subphylum Mandibulata*, (Greek: jaw).

Chelicerata incorporates not only the arachnids (spiders, scorpions and mites), but also the extant horseshoe crabs, the extinct eurypterids (perhaps the largest arthropods ever to live, reaching lengths of over six feet) and the relatively obscure pycnogonids or "sea spiders."

So in essence, spiders are more closely related to horseshoe crabs than insects. Not only do they have a prosoma and chelicerae, but they also respire in much the same way, from a oxygen exchanging structure that closely resembles a book.

Tomorrow we'll discuss the ancestry of spiders; once upon a time, they may have left the sea millions of years ago just to scare the curls out of you in your basement.

*With the inclusion of extinct arthropods into this subphylum, taxonomists dispute whether or not more than one subphylum is required to accurately classify these organisms.

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