Posts Tagged ‘Science’

I Am as Religious as Albert Einstein

February 21, 2009


In Einstein’s religion’s terms, I have no qualms declaring words like this as prophetic, inspiring – in their appeal, similar to that which the religious hold divine.

And it does not require, and would be wasted upon,  a deity.

Yet Another “Mother Whale Fossil Found With Fossil Fetus” Post

February 4, 2009


Not what you might call a typical “Yet another X” line, I know. I wanted to write a post about the matter this morning, and in the interim, I found out that pretty much half of scienceblogs wrote eloquent, descriptive and fascinating posts about this.

So, just to mention this to anyone who’s not an avid scienceblogs reader – a new fossil found in Pakistan of a protocetid (ancient whale). Finding a well-preserved fossil of a transitional form is amazing already, but, and this is the kicker:

The fossil was of a female pregnant whale, and contained a fossilised fetus in it.


Good Shit – Defecation-Induced Orgasm – Case Study Overview

February 4, 2009



Sign Language Is Better, People!

January 6, 2009

Once again, science confirms that sign language is better for everyone. :-). In a recent study published in the Journal for Applied Behavioral Analysis, several infants were trained to use sign language (either instead of crying or regardless) with astounding results.



Monday Organism: To Everything, Fern, Fern, Fern

December 8, 2008


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,  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 up  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 🙂

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 are  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. 🙂

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. 🙂

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

November 30, 2008

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 had  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.


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 :  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.

Some thoughts about plant evolution

November 20, 2008


Well, I’ve been brewing a post about ISL ethics for a few days now, but besides my chronic procrastination due to school and work, I had another reason to postpone this post, which is that just today I got the first paper from Cocoon about ISL ethics and I think this one really calls for some homework!

Anyhow, as a brief hors d’oeuvre, I would like write a brief post on some nagging thoughts and doubts I had about plant evolution due to this week’s biology class.

First, some background: this semester is “botany-semester”, meaning that all labs and all classes that are specifically about biology (and not, say, math 101, physics 101 etc.) are mainly focused on plants, algae, etc.
Second, before I write a about the nitty-gritty of my argument, let me just say that every single one of my professors, lab chiefs and even the guy who instructs our lab team have either your garden variety yarmulke, or in the case of the PhD student who instructs our lab team, a yarmulke and those curly braids that the hassidic Jews have. I’m really not too privy to the that whole “Hassidic spectrum”, but since he doesn’t wear those penguin suits the Jerusalem Hassidim wear, I can’t say he’s as fundamentalist as those kooks in Jerusalem are.

But anyway,

What I wanted to say is that every single one of my professors, lab chiefs and lab instructors is, well, REALLY JEWISH, really religious and god-fearing, and completely, unabashedly, evolutionist. These guys speak of evolution as if the fact that it’s true is so ho-hum that it doesn’t even worth a second thought. Shiesh. It’s only the major kooks in Israel who have any qualms with it, I guess.

And now, to the batmobile!

The theory of plant evolution goes roughly like this: a great number of yonks ago, prokaryotes endosymbiontly evolved into eukaryotes (something I find totally reasonable), and the variety of prokaryotes that evolved photosynthesis (namely, Cyanobacteria or Cyanophytae, or blue algae), coupled with endosymbiosis, turned into the first eukaryotic algae. So far so good, but the problems I have with plant evolution start here.

A good analysis of algae evolution can be done by looking at the various evolutionary pathways observed in various algae phyla. It’s probably no coincidence that all green algae and all plants have the same preservative polysaccharide (namely starch, unlike our glycogen), all have the same (and rather unsually so for the 7 or so algae phyla) characteristic photopigment (chlorophyll a), all have similar sexual reproduction and all are surrounded by cell walls composing of cellulose (also an “anomaly” among algae phyla)

This is a good and credible explanation for the origin of land plants (plantae or metaphyta). However, things start to get really shaky when you look at the other algae phyla, who have indiscrepant levels of development, which make it rather futile to try to pinpoint who evolved when. For example, the multicellular alga “Chara” has a superficial “stalk” and a complex sexual reproduction system, but it does, however, use isogamy as a means for zygogenesis (the production of zygotes from gametes). Isogamy is rightly considered to be archaic, as it is less efficient, less specialized and is more characteristic of primitive organisms than of evolved ones.

So how come Chara has an unevolved sexual reproduction while Volvox, which is a microscopic colonial alga that has no sexual organs, uses oogeny for zygogenesis, which is strikingly reminiscent of human zygogenesis (the male gamete is small and motile, the female gamete is large and static). The professor merely said that certain things evolve at different paces, and this is a good explanation and a very reasonable one, but I find it hard to accept it while at the same time claiming that this or that phylum evolved before or after based on comparative anatomy.

In cases like this, I prefer to say “I don’t know, but…” rather than to firmly put my finger on a phylogeny (which I can comfortably do regarding green algae and plantae).

I bet creationists won’t object to carbon dating THIS time.

October 28, 2008





Richard Levy also said something quite inspiring, and I quote:


Pull the other one?

To that I say: damn straight!

Ultra-consvered pseudo-junk DNA?

October 10, 2008

Here‘s why I’m dreaming of one day becoming a developmental biologist and/or geneticist. Stanford researchers identified a group of DNA regions which are extremely conserved (80-100 million years of mammalian evolution and going strong) in macaque monkeys, mice, dogs and humans. They could call this DNA “junk” because it’s redundant, at least on the short scale.

Junk DNA on its own is a fascinating phenomenon. It’s curious that some regions are in fact called “junk” and by the same token, extent the metaphor in the respect that even junk can be useful, and if not to its original owner, then to someone else. You can call ERV’s junk, but I bet the original viruses didn’t think so, and you can call a hypothetical stretch of DNA with an apparently invisible or completely redundant function that serves nothing but aiding commensal organisms junk, and, again, I bet they wouldn’t think so.

It’s also important to define junk DNA on the basis that the removal of junk DNA affects no physiological function in the organism, even more undoubtedly when there are copies of DNA that are partially removed, leaving other copies intact.

Since having an excess is in fact having too much (I can get a copy or two of a seemingly meaningless strand of DNA, but hundreds and thousands? Improbable and effectively ridiculous) – these DNA regions are appropriately called junk.

But, see, here’s the thing: because junk DNA is classically known to be neutral and its removal or modification are observed to be undamaging, I think this particular research shows rather clearly that it is NOT, in fact, junk DNA.

In case some creationist twerp decides to quote-mine this, I do not mean that this research shows evidence of a divine plan in our nucleic acids. The evidence obviously shows that this DNA is important, but nobody can figure out why, and more interestingly, to whom.

The researchers suggested that it could be a special “immunity” bank, to be deployed should a particular disease or bacterial infection comes about.

I find this suggestion curious and I think I can stretch it even further: it is possible that mammalian evolution allowed for certain mechanisms to stay relatively dormant to allow greater response to a selection pressure that comes regularly to a species, or even to the entire mammalian class.
It is unlikely, however, that such special genetic equipment stays precisely the same for 100 million years. Even if a series of great extinctions bottlenecked the entire mammalian population in the near past, that is, the past 65 million years, it is laughably improbable that complete regions remain ultra-conserved for ANY reason, even, perhaps, “anti-extinction genes”.

There has to be a more likely, simpler (and probably harder to detect) explanation to the conservation of pseudo-junk regions. If the reason for the conservation is elusive enough to escape detection after being pulled out of the genome without harming the organism, it is possible that the only reason that this DNA is conserved is because it serves its own purpose as a “hijacker DNA strand”. This is a phenomenon called “drive” by geneticists, and there’s already a huge repository of documented cases for drive, even in whole chromosomes. Perhaps the only thing unique about these stretches of DNA is that they somehow inhibit their own mutative nature. Should ANY region be able to do just that, you could say that it’s got the most positive selection pressure thinkable.

I’m only surprised this doesn’t happen more often. Then again, it is possible that other regions of DNA would benefit just as much by producing qualities that inhibit the inhibition of these selfish DNA regions to mutate.

Second case of parthenogenesis in sharks

October 10, 2008

A second documented case of shark asexual reproduction has been confirmed. The pup had not male DNA and, I’d bet, is probably a last resort to the mateless female that begat it.

Here’s the full story, bioheads.