Archive for Evolution

Monday (paleo)Organism – Indohyus

Due to the current fossil whale craze, I’ve decided to dedicate this week’s Monday Organism to another famous fossil related to whales. Well, I say “related to whales”, and this much is true for any ancient organism, but the truth is, Indohyus is really, if anything, only a sister taxon to ancient cetaceans – it’s unlikely that whales descended from Indohyus directly.

Indohyus was a fox-sized artiodactyl (even-toed ungulate) that lived around 48 million years ago, exactly when you’d expect to find land mammals, and it was found exactly in the right location: in Pakistani sediments (since Ambulocetus natans was found there, too) – but the show’s not over yet.

Indohyus almost certainly lived on water. Isotope measurements confirmed that Indohyus spent a considerable amount of time underwater, and the structure of his dense bones further reaffrims it. In addition, Indohyus has a particular ear anatomy that, prior to Indohyus’ discovery, was thought to be unique to whales and their fossil ancestors – a structure called “an auditory bulla” (since I know jack diddly about animal anatomy, I’ll leave it unelaborated). The important thing to know here is that this auditory bones in the Indohyus fossil confirm at least a partially marine habitat – and rather hits the nail on the head as far as Indohyus’ marine history is concerned.

Indohyus is a curious find, and is definitely a good clue of how whale ancestors might have evolved, but it’s unlikely that Indohyus is, in fact, the ancestor of whales. For starters, Indohyus is herbivorous, and as such, puts another important node between it and whale ancestors, who are, including modern whales, all carnivorous.

That in mind, it’s important to note that even though fossils provide wonderful evidence for the evolution of taxa, every fossil we use to depict as “ancestral” is almost certainly not, strictly speaking, ancestral per se. Evolution predicts that you’d find fossils of ancestors and their nearest relatives, and that their nearest relatives would have similar traits to ancestors and descendants. Since it’s much more likely to find ancestral relatives (sister taxa) – it’s more parsimonious to assume that this is what we find in most fossils.

For me – Indohyus being herbivorous is a clear sign that this isn’t an ancient whale, or possibly not even a sister taxa to an ancient whale – although it’s definitely a “cousin” or “second-degree cousin” taxon for ancient whales, as clearly shown by its aquatic and whale-like attributes.

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Monday Organism – Amphioxus, Representative of Our Ancient Past


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: To Everything, Fern, Fern, Fern


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.


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.

Some thoughts about plant evolution


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).

Evolution: a Theory in Doubt

The Evolution-Creation debate has turned into somewhat of a frenzied obsession to a lot of people, so much that TV shows, blogs, radio talks, books and law suits have been entirely dedicated to the topic. Becoming another tortured soul engrossed in the evolution of the debate a few years back, I was aware at the onset that the debate isn’t about science at all.
What I wish to do in this post is to actually show a small amount of gratitude towards the creationist movement for being so adament in their doubts of evolution, because without their often duplicitousย  critique of the theory of evolution, I probably wouldn’t have doubted the theory that much, myself.

See, in other well-established theories, where the public’s resistance to them is minimal, there really isn’t a point to go around trying to poke holes in said theories for the passionate layman. Sure, afficionados of any field will probably delve deep into their subject of affection, but the truth is: the enormous resistance to the theory of evolution, both by pseudoscientists and zealots lacking any credentials, has caused a great spark of learning amongst skeptics.

When I first started learning about biology and evolution, probably my number one incentive for learning about certain aspects of biology were various creationist claims about the impossibility or improbability of evolution. I remember reading through the index for creationist claims on talkorigins simply because it was delightful to learn so many new things about biology and other scientific fields through the mirror of pseudoscientific attacks on them.

It’s also a good primer for learning more about good old-fashioned biology, and I remember that very quickly I found myself sticking my nose in biology textbooks, and that was years before I ever entered a college classroom.

So thank you, creationism: for lighting the fire of philosophy in all knowledge-thirsty naturalists. You certainly did that for me.

I only wish you didn’t try to shove it into public education.

I do admit, however, that putting a polemic pressure on the public understanding of evolution probably did a lot to teach more and more people about the theory. I’m sure that most people wouldn’t even know what evolution is if it wasn’t such a big deal to bible-thumping ignorants.

Evidence for TB’s antiquity found in Haifa

Well, I’m not REALLY going to deprive anyone from the pleasure of reading Greg Laden (the guy is simply begging for a horrible pun), but since his recent post enables me to combine two rather distant categories, “Local” AND “Science”, I couldn’t help myself.

Greg writes about a recent archaeological finding in Haifa, up north from here, in a neolithic site dated about 9,000 years old (I can’t help but wondering what young-earthers make of findings like this). The important sciency stuff is all about “paleopathology” (yup), that is, the findings (of infant bones) seem to exhibit TB-like symptoms, which in effect suggests that TB is not only a much more ancient affliction than previously thought, but also that it might have evolved in humans first and not in cows, as was previously thought to be the case.

Yep, evolution, a theory in crisis!

Why Some Creationists Believe in Flood Geology

This is a post I wanted to write for some time, but somehow it slipped off my mind in the general confusion of everyday life.ย  About a month ago, I ran into a YEC blog called “Sirius Knotts” via my valued co-blogger, For Knowledge!
His recent post is also what prompted me to write this post. When I first read Sirius’ post, I was intrigued by the possibility of a biblical paradigm for geology. Sure, I was aware of the need for any “biblical geology” to firmly account for the coherence and consistency of modern geology, with its old earth and the multiple lines of evidence pointing to this old earth.

But still, intrigued I was, nonetheless. Especially since even though flood geologists are relatively (as far as I know) rare as compared to mainstream geologists, they’re still trained geologists, and probably know their way around a pickaxe (horrible metaphor, I know).

I was quite perplexed, of course, when I approached Sirius in this post which he wrote about the fossil record and how it shows evidence of a young earth. (To be fair, he did say he didn’t mean to really show evidence for a young earth in his post, but just to show that the evidence does not show an old one)

See, since I don’t know much about flood geology, or geology in general, I thought of asking a straightforward question: considering the fact that the fossil record, according to Sirius, exhibited evidence for a young earth (or a “not old one”), the most obviously pertinent question would be: “how do you date geological samples on planet earth and does such dating confirm independently that the earth is a few thousand years’ old?”

Allow me to reproduce just the first correspondence between Sirius and myself:


“Sirius, I have a question: Is there anything in flood geology that provides accurate, consistent dating of fossil fauna all dating apx. during a bible-inspired flood date thatโ€™s been corroborated by other date sources?”

(yada yada yada, verbose me)…


“[Sirius comments: I’m not sure how to answer your question, so I’m emailing the guys at for their advice. I’ll get back to you, provided, of course, that they get back to me.]”

O-kay. At this point I was getting confused and a bit suspicious: this guy waxes poetic about the earth being young and gives numerous data to ostensibly establish this argument, and yet doesn’t know how to support his version of the date of the planet? (“I’m not sure how to answer your question” is definitely not how I could describe why I believe the earth is billions of years old!)

But okay, a little humility. I’m no geologist and even though I’ve dabbled a bit in geochronology for fun reading, I’m continents away from being an expert in the field (all the primers in biology included a chapter or two about dating methods).

So, after some back-and-forth Q&A’s, I reached this particular gem:

“My reasons for embracing the Young earth Creation position stem from the fact that I believe their is reasonable evidence to believe that a personal, transcendent God exists, that Jesus Christ rose bodily from the dead and that I can believe the Bible in regards to what it says about the human condition, history and prophecy”

Boy, oh boy. That said, I just had to ask why bother throwing scientific data to disprove evolutionary biology or more pertinently, mainstream geology,ย  if all it takes to believe in a young earth is absolute biblical literalism.ย  It stinks of dishonesty and preying upon the gullible to give the air of scientific credibility to a belief that rests solely upon religious texts. Sure, scientific data can be shoehorned into biblical literalism, but if biblical literalism is completely a priori to any discussion of the age of the earth or the meaning of geological data, then invoking scientific evidence to “prove” a young earth is not only dishonest, it’s also pointless. If flood geologists merely assume the bible to be true and accordingly use data they collect to point out to biblical literalism, then saying that the “evidence points to a worldwide flood” is not only dishonest, it’s also sacrilegious: demanding or even endorsing physical data to espouse belief in the bible is abandoning, so it seems, the blind faith that it demands.

Sirius provided me with two links, one was to a blog written down by a flood geologist and another was a creationist web-page. After tediously going over the web-sites, I was again and again in awe at the fact that whenever addressing the age of the earth, time and again the real, physical evidence for the young earth isย  nothing but the bible, and the mere assumption of the validity of biblical text. The data are all there, they just happen to rest completely on presupposing the bible to be true and thus, by definition, can only lead to verifying the bible. I must say that this pointless dissonance was so bizarre that I physically felt dizzy while reading it.

The thing I found striking the most is that part of “creationontheweb” that spoke of absolute dating by radioisotopes being a subjective presupposition and that the only difference between mainstream geologists and flood geologist is their subjective presuppositions. Apparently, biblical geology professes that it’s okay to presume your conclusion, and assuming the bible is literally true is somehow better than not. No mention of what assumptions absolute radiometric dating uses. There are quite a few, and scientists have masochistically tried to refute them for centuries and have mind-bogglingly corroborated data in endless research. Considering the last sentence, I find it pressing to ask: “how sure do you need to get before you buy into this thing?”.

I wonder if “non-expert creationists” as opposed to “non-expert evolutionists” like me become frightened or disturbed when they try to do the opposite to what I did, that is, look for evidence for an old earth. I can’t help but feeling that being afraid to learn something new is the worst affliction a mind can have.

Oh, and P.S – even the flood geologist that Sirius linked to admitted that there’s no analytical approach that consistently points to nothing but young dates for rocks. Flood geologists either use the same dating methods as mainstream geologists or, most often, they simply assume the bible is true and don’t bother dating rocks at all, since the “biblical geological column” is based on analyzing the bible, not the earth.

Ultra-consvered pseudo-junk DNA?

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

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.

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