Archive for Biology

Monday Organism – Amphioxus, Representative of Our Ancient Past

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Aย  Amphioxus/Branchiostoma is a primitive chordate that would probably look to most non-biologists like a tiny fish or even a tadpole. Thing is, amphioxuses aren’t fish, they’re not even vertebrates!

In fact, amphioxus belongs to a sister subphylum, “cephalochordata” (any pharyngulites who might be reading this will reconize “cephalo” from “cephalopod”. This is because “cephalo” means “head” and apparently, octopussies walk on their heads ๐Ÿ™‚ ).

Both vertebrates and cephalochordates belong to the phylum Chordata – which began it’s history pretty much with most of modern-day phyla, somewhere in the cambrian explosion.

The amphioxus shows some amazing qualities that make it an interesting animal to know about, and also an interesting model species for comparative anatomy and evolutionary research.

The reason for this being that the amphioxus presents a lot of qualities that make him a living transitional fossil, or simply, a transitional species.

First of all, this critter gives all the indication for being a primitive invertebrate with distinct differences from the more modern taxa.

Second, it shows characteristics that are peculiar to the amphioxus, but are also highly indicative of “later”, evolved traits.

Third, it shows characteristics that although primitive, are still extant in variations today.

Let’s start with the primitive stuff. The amphioxus has no vascular system, that is, he doesn’t breathe! The amphioxus absorbs his oxygen via diffusion, which is an extremely poor method of gaining oxygen, and at any case, results in much less oxygen absorption. The reason for this is that amphioxus has a very small body with a very relatively large surface area. This means that by diffusing the oxygen, the amphioxus gets just what he needs.

Also, the amphioxus has no real brain or “brain concentration” – he does have a neural system – which belongs more to my second category.

The amphioxus also has no eyes, and he spends most of his time buried in the sand, filtering food (he doesn’t have teeth, of course, while not having a backbone as well).

Things start to get interesting when you look at traits in amphioxus that are uncannily “vertebrate-like”. For starters, the amphioxus has a precursor for the liver that doesn’t function like one. It has similar hepatic characteristics, yet a stubbornly “non-hepatic” function in the amphioxus. This is the “hepatic diverticulum”, and I’ll leave it at that for anyone nerdy enough to get deeper into it.

Also, amphioxuses have dorsal segmental muscles, much like the muscles we have between our vertebrae in our back.

The most amazing feautures about the amphioxus are the features which shed light on chordate evolution. For starters, amphioxuses have glands very much like vertebrates do, which is funny, since if you guys were paying any attention, you’d remind me that I just said that he has no vascular system. Since glands are used to secrete hormones, which are signal molecules transmitted through the blood, it’s kinda hard having signal molecules sent through blood when there isn’t any!

The amphioxus glands are fascinating because of their location and their mode of operation. For example.ย  There is a structure called Hatschek’s pit exactly where the hypothalamus should be. It has a “hypophysis” or pituitary gland-like structure called “Rathke’s pouch” in a similar location and similar structure, that produces “exohormones”! This primitive gland secretes external signal molecules, and, according to one zoology professor I had, these molecules are similar in function and chemical activity to the hormones modern vertebrates secrete from their evolved pituitary glands!

So, really, what we have here is not just another squiggly tadpole, but a precursor to modern vertebrates, with genes, anatomy and physiology to tell us the story of how we evolved.

Monday Organism: Strange Mammals!

This week’s Monday Organism is not going to be about evolution, and also, not going to be about one organism. Since I rather keep these posts non-technical (not an easy thing to do), I’m going to write a little exposee on two truly amazing mammals:ย  the Aye-Aye and the Flying Squirrel.

A.The Aye-Aye – Daubentonia madagascariensis

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The Aye-Aye is one of those rare occurences that can only happen in a place like Madagascar. That might not be 100% accurate, but the fact Madagascar is ecologically detached (for land animals, anyway) from mainland Africa has probably done some evolutionary magic to create the wondrous biota living there.

The Aye-Aye has a somewhat (for Primatology laymen anyway) esoteric taxonomy, it is a Strepsirrhine. Strepsirrhines are what can only be reasonably called “wet-nosed monkeys”, although the Aye-Aye, at least, has some attributes that make it quite unlike the normal “monkey image” in our head.

The Aye-Aye looks like a mix of a rodent, a squirrel, a monkey, and a demon. I say “demon” because the Aye-Aye is a nocturnal primate (and the largest known, at that) – which means he has quite large eyes that glow ominously at night (the presence of the Aye-Aye is considered ominous in Malagasy villages).

The most distinguishing feature in the Aye-Aye, however, is in fact his middle finger. The Aye-Aye’s have an elongated middle finger with an alarmingly developed “fingernail”, although this finger is distinct mainly due to its unusual, “evil-witch” bone-structure. This finger is used to forage food by probing tree-holes for grubs, seeds, etc. This is basically the same thing a woodpecker does, only with fingers!

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B. The Flying Squirrel – Pteromyini

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The Flying Squirrel is a not just an amazing animal, it’s also a visual (and intellectually painful) reply to the notorious creationist question: “what good is half a wing?”. Well, apparently, it’s a world of goodness, at least for the flying squirrel. The Flying Squirrel is a moniker for a family of species who all have the same distinct “gliding organ”: the Patagium: Flying Squirrels have an extension of skin on their back not unlike that of bats, which can be steered to control their gliding in the air (making them actually “gliders” and not really “flyers”, hence “half a wing”).ย  They also use their tales as stabilizing and to monitor their speed (it can be used for “braking” when the squirrel needs to “land”).

Monday Organism: To Everything, Fern, Fern, Fern

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Back in the old forum days, I used to write on specific organisms frequently. Now that I’m doing Botany, I think this little spot would be missing a lot if I didn’t give some spotlight to the greater picture, especially in regard to groups of organisms most of us take for granted, such as plants.

This last week brought us undergrads face-to-face , for the first time,ย  with real hardcore terrestrial plants, and the first such plants were a group of organisms called Ferns.

Even though I’m alt-tabbing the wiki article for fact verification (and digging up fun facts as well), I can, sans wiki, sum upย  what are the interesting differences between Ferns and all the other plant taxa we’ve learnt of so far.

Ferns are similar to mosses in some respects, and like mosses and all evolutionary descendants of mosses, they’re embryonic plants, with distinct sporophytic stages that develops from a protected embryo that is grown and shielded within the parent fern.

Ferns actually have independent sporophytic stages, which is a bit odd. Flowering plants don’t have that, and neither do mosses (which can be very roughly considered the evolutionary “befores and afters” of Ferns). In mosses, the sporophyte is, if not completely “parasitic” on top of the gametophyte, is still an attached (above-ground) outgrowth of it.

In flowering plants, the gametophyte is situated atop the sporophyte, which is the reverse for mosses. I won’t get any deeper into that, since I haven’t studied about them yet ๐Ÿ™‚

Ferns are distinguished in the plant kingdom as the first truly Vascular Plants. It’s not that more primitive plants don’t have some means of relaying organic material and water around the body of the plant, but in Ferns, we witness the first instance of complex, all-body vascular organs, namely, the Xylem and the Phloem. The X and P are just fancy words for “tube for shifting organic compounds” and “tube for shifting water”, respectively. As the first hardcore terrestrial plants, vascular organs are a must-have adaptation. Growing taller is a logistic nightmare, but with the enormous selection pressure on short plants that compete on the same sunlight, it’s a must. It’s a good evolutionary explanation for why those Ferns went through all the trouble, and this is actually a distinguishing feature in Ferns: they’re specialists. Their penchant for being taller is just the tip of the iceberg (they’re also adapted to hostile habitats, habitats which constrain the flowering plants but not Ferns).

The most revealing innovation in Ferns is the organ that most of us seem to readily associate with plants: Leaves.

To begin with, I was simply delighted to finally understand what this organ actually is. Up until next week, leaves to me, as they are to most laymen, were simply “green bits on them flowers and whatnot”. There’s more to that, or merely, a more accurate description. Leaves are firstly defined as the photosynthetic organs. In short, what the mouth does for heterotrophs like us, the leaves do for autotrophs like plants. In short, it’s the plant’s way of getting chow. Up until now, photosynthesis wasn’t confined to specialized organs, and hence, leaves areย  truly a hallmark of evolutionary innovation.

As an aside, it’s interesting to note that evolutionary innovations are often a precursor to two things:
A.Enormous comparative fitness (evolutionarily-speaking, as opposed to simpler organisms)
B.An evolutionary dead-end. Jacks-of-all-trades have more “promotion possibilities” than “Masters-of-one-trade”. This is why bacteria outlived many metazoa (and will probably outlast us!)

Since I’m an evolution afficionado, I want to have the finishing part of this post to focus on some interesting evolutionary tale, but I think I can combine that with some cool info on Ferns in general. What I mean by that is that you can actually see for yourself the evolutionary “nodes” in Fern evolution by observing the various stages of leaf evolution.
Like Is said, leaves are the photosynthetic organs of plants, but leaves haven’t sprouted de novo out of ancient moss-like thalluses (even though even weeds have leaflike apparatuses).

The first instance of leaves comes in the shape of protophylls (ancient leaves). Protophylls are nothing but dandruff like scales without any actual vascular tubes for carrying the photosynthetic products to the body of the plant. Since the protophylls are usually small and aggregate, this is not a big problem, and obviously this is an ample condition for evolutionary advance: now that we have the specialization in order, all we have to do is grow some tubes. ๐Ÿ™‚

Psilotum - a protophyllic fern

Psilotum - a protophyllic fern

The second and third stages of leaf evolution are very similar: Microphylls and Macrophylls. The noted difference between the two is that microphylls have only one artery-like tube and macrophylls have a branching like web of vascular tubes. It’s quite easy to imagine how one evolved to the other, but not so easy to come up with how protophylls evolved into either, or should I say, to one and then the other. ๐Ÿ™‚

Lycopodium - a microphyllic fern

Lycopodium - a microphyllic fern

So, yet again, we come across an oft-taken-for-granted plant group and find that it tells us fascinating evolutionary stories. Mainly, that those cheeky bastards are opportunistic little buggers that probably gave us the precursors for modern plants, meaning that Shakespeare and other like-minded cupid-heads should give them some credit. The true journey to dry land starts with Ferns, and so the true evolution for the plants we hold as familiar starts with them.




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Monday Organism (Yes, I’m Aware It’s Sunday) – Cyanobacteria

On most Sundays, I won’t be around to post, except in the evening, half-brain dead from ISL class. Anyhow, I’m a day off to recuperate from last week, so I have time to post my very first “Monday Organism”, and a day early, at that!

Since this is the first weekly organism, I think it’s appropriate to explain why there is, in fact, a weekly organism. Since this blog is about biology, it’d be mighty improper unless it hadย  periodical items about animals, don’t you think? I mean, come on, it’s no use running a blog about biology without fluffy animals in it (or angry wobbly ones or, well, extremely tiny ones).

Also, the Monday Organism is sometimes going to be about higher taxa as well (usually very high taxa, mainly to illustrate an interesting point about evolutionary biology)

The first Monday Organism is actually not an Organism, but a Phylum: Cyanobacteria.

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Cyanobacteria literally means “blue bacteria”, but they’re actually called “blue algae” in Hebrew. The wiki on Cyanobacteria states that the taxonomy of Cyanobacteria is under revision, which is no surprise. In class, this group was even (I think most appropriately) called “Cyanophyta”, meaning “blue algae”.

Cyanobacteria are a fascinating group, and their existence is sound evidence for various evolutionary theories, the most important one is probably the evolution of the chloroplast organelle, the organelle in plant cells in which photosynthesis occurs.

The truly amazing thing about Cyanobacteria is the fact that they’re actually prokaryotes (having no distinct cell nuclei), and yet, they have photosynthetic pigments in their cells which are used to produce organic material by absorbing light energy from the sun. This means, in effect, that Cyanobacteria are the evolutionary precursor for the eukaryotic plants.

While it is obvious that all algae are commonly related, the truly interesting characteristics of Cyanobacteria are the ones that point out to the evolution of plant organelles. When I first learnt about Endosymbiont theory, I was plainly told that “endosymbiont bacteria eventually became permanent organelles”. Now these endosymbiont bacteria have a name: Cyanobacteria. In fact, the evidence shows that the Cyanobacteria themselves evolved into the chloroplast, and it is quite possible that every plant cell is, in a way, a symbiotic colony of eukaryotes and prokaryotic photosynthetic bacteria!

Obviously, the radiation of photosynthetic taxa is prolific enough to rule out such a simplistic story, but the evidence shows similar genetic and biochemical traits in modern day chloroplasts and in the makeup of Cyanobacteria. Since this isn’t an encyclopedic article and I rather focus only on one interesting concept at the time, I’ll give just one example for “evidence” of the common descent of CB and chloroplasts :ย  the genetic makeup of chloroplast DNA (yes, they have their own DNA and they replicate on their own!) is similar to Cyanobacteria DNA. This alone is solid evidence for common descent for the two.

There’s lots of special cases of endosymbiosis that show not-so-common descent, but rather “common descents”, but I’ll leave that to the avid reader.

The main point of this post is not so much to tell about CB anatomy (warning: other posts might deal with interesting anatomy and physiology!), rather it is to illustrate classic tools in evolutionary research: genetic, anatomical, biochemical and physiological comparison as instruments for detecting common descent. It’s a crucial way of thinking in all of biology, and it highlights the sometimes elusive practical value in evolutionary theory: knowing the genetic relationship between different taxa can be critical in any biological endeavor. If one seeks to find antibiotic weaponry against infection and disease, knowing the culprit’s phylogeny can be of tremendous use, and phylogeny is best derived from the comparative tools I’ve briefly illustrated here.