Archive for November, 2008

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 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.

Can I do research?

I know I’m only a biology undergrad, but I can’t help thinking that I might not have what it takes to be a researcher. Am I creative enough? Smart enough? Innovative enough? What does it take? Can I get a clue now before I spend 10 years on my life pursuing a career I won’t be any good at?

Yes, We Can (rob you)!


For all you non-Israelis (erm, there’s about 6 people who read this blog and I suppose 5 of them aren’t 🙂 ), let me just point out that Shas is a Hebrew acronym for “Shomrei-Torah Sfaradim”, this means, literally, “Sefardic observers of the Torah”, or in short, the ultra-orthodox Jewish party.
I’m not a political expert, but my experience with Shas is that they are a sectarian party. They work almost entirely for the benefit of their electorate, which is, well, not a big issue unless you’re in Israel, where there’s about a dozen or so types of electorate, and if you unite a certain parasitic electorate (I’ll get to that right away), you basically give a foothold to a bunch of lazy, sanctimonious thieves in the Knesset (the Israeli parliament).
Now, now. I’m not saying that Shas doesn’t do charitable things, like try to help the poor (religious poor, anyway) and promote socialist agendas (maybe as a side-effect to, say, their insistence on using tax-payer money to sustain the multitudes of the huge families that the ultra-orthodox are mandatory to found as per the Torah),

but –

well, Shas seems to really dislike the idea of personal freedom (an fundamentalist political party with an anti-liberal agenda? Say it ain’t so!).

In many respect, they are an anti-freedom party. If Shas was the sole party in Israel, then Israeli law was indistinguishable from Senhadrin law, and that means literally a Jewish theocracy.

So far, what Shas mainly does is try to ban pornography (fuck that!), censor internet material (guess who they want in charge of reviewing the “inappropriate material”?) and ban public transportation on Saturday (something that’s actually quite widespread in Israel already).

What I found mind-numbingly ironic is that Shas’ current campaign slogan is “Yes, we can!”, just like, yep, you said it, Barack Obama’s successful slogan. It’s so cute. They think that if it got the American people to vote for a guy who isn’t an obvious hack, then the Israeli population is going to be duped into voting for the most self-serving, anti-democratic, fundamentalist party in the Jewish political spectrum, (well, maybe there’s worse, this IS Israel, after all)

Anyhow, it’s made extremely ironic due to the fact that the ultra-orthodox refuse to serve in the IDF because they must practice the Torah (oh yeah? I REALLY wanted to start this biology degree here at 18 and not at 23, you bearded sacks of shit!). These assholes pay about 4 times (!) less than I do to social security, as Yeshiva boys, to be precise. (A student, of any kind, who works, immediately has to pay social security as per the type of work he’s in, say, self-employed people like me have to pay 9.82% of our income to social security, they have to pay about a quarter of that).
Every time Shas reveals its intentions to the public, every political move, every bill proposed, every statement given, it’s always anti-democratic, anti-civil-rights, religiously bigoted and ultimately, anti-humanity. This party is actively trying to promote a world that has no freedom, and endless power to a caste of corrupt avaricious acolytes.

Adding a new page: ” Quirky Search Entries That Brought People Here”

No need to elaborate 🙂

Just check the left side bar for the darnest search entries that found their way to this blog!

Overheads Underfoot

Yeah, yeah, I keep jabbering on and on about how this is not a personal blog. Well, a lot of the topics I write about eventually have to go through the person writing them, but I don’t like much writing “personal diary entries”. But I’m going to do this time, anyway.

Anyway, I skipped yesterday’s Latin and today’s Botany because of “fatigue overheads”. I was too tired after Sunday’s 13-hour long day, so I skipped yesterday’s Latin so I could have more time to finish up stuff for today, and then I skipped today’s Botany so I could wrap up things for tomorrow. I’m still going to Botany labs because we have a quiz every week (this week’s on fungi, ah, what fun (yeah, yeah) .

In short, I’m kind of freaked out that this might be a slippery slope. Since I’m 4 weeks into the semester, it’s possible that the combination of training, working, studying and trying to lead an almost non-existent social life (while still being Dad’s son) is wearing me down.

Bah. What can I do if coffee doesn’t work on me?

Another Reason to Hate Judaism

I just remembered that last night, a woman from the Deaf club near campus (I had a small typing gig there after class) intervened during a legal lecture and said that the local Rabbinate refused to acknowledge her as witness for the writing of a will by one of her own family members.

The reason for said refusal: “You’re deaf, you cannot be a witness”.


The Power of Sign Language


This past few weeks have been tumultuous for me. I’m constantly reshaping my view on sign language and interpreting for the Deaf. When I started studying ISL, I was determined to acquire the skills and credentials of an ISL interpreter because of a combination of my love to Mother and my life-long infatuation with the Deaf, mainly as a result of reflecting the love I have for Mom and Dad on the entire Deaf community.

At the onset, Cocoon stated firmly that “wanting to help the Deaf” is a dangerous agenda for an interpreter. The Interpreters’ code states clearly that objectivity must be had in relation to both Hearing and Deaf. In every interpretation event, the Hearing are my clients too, and as a professional sign language interpreter, I must avoid any biases against the hearing just as much (and equivalently so) as I should avoid biases in favor of the Deaf.

So how do I do it?

At first, I thought that it is impossible for me to uphold the Code without turning against my own ideals as well, but I’ve come to reshape this thought in the past week:

The best thing I can do for the Deaf is to be as professional an interpreter as possible.

This is not to say that there aren’t any ethical issues to be had, but as a basic principle, it does absolve me of the self-torturous occupation with my agenda as an interpreter.

This week’s article was all about interpretation ethics. Besides from recapping the code as we’ve discussed it in class, it brings some real-world examples of collision between the Code and a person’s own ideals and moral principles.

I will use one such example to clarify the remaining dilemma I have with the ethical code:

An interpreter was sent to interpret for a deaf patient who was visiting a gynecologist about having her uterus removed. The interpreter notices that clearly, the doctor is not giving this patient all the care (he believes) she deserves, and it is easy to see that the deaf patient hasn’t a clue that she’s being mistreated.

What would I do?

Well, if it was Mom and Dad, I’d probably turn the table and use loud-volume complaints and admonition, as my agenda is clear: I’m here for Mom and Dad, and I wouldn’t give a rat’s ass about the doctor’s interests so long as he takes care of them.

As soon as I do that, I’m no longer a sign language interpreter, end of story. I’m a “signer representing my deaf parents”. Cocoon firmly stated that anyone who’s ever signed to his family (or even his friends!) has never “interpreted”. Knowing how to sign does not perforce mean “being an interpreter”.

The article offers one interesting possibility of upholding the code without hurting the interpreter’s conscience: resigning the instant there’s a clash between ethical and personal principles.

The issue, however, remains for me unsettled. In my case, I would resign and then immediately become very, very subjective and particular about what happened. I would admonish the doctor for his malpractice, I would feverishly explain to and negotiate with the deaf patient, even to the point of arguing with her that going through this or that length of research and so on would be the best thing for her.

I would be making a stand, I would be appointing myself as an advocate and guardian without receiving this appointment from my deaf client.

My instinct would probably be to self-appoint myself as a guardian for the deaf without their consent, merely because it’s a life-long habit. I’ve yet to find a deaf person who didn’t happily accept that, by the way. I’m sure that a lot of deaf people would refuse to be belittled (although I don’t actually belittle, not consciously, anyhow), and I will immediately cease playing “Signman” at their expense if they ask me to, but still, this is what I would do by default, unless requested otherwise. I highly respect and revere the Deaf, and I only feel obliged to appoint myself as their “savior” because I’m horribly empathetic to them, not because I think they’re weak or incompetent.

So, in conclusion, I would still be breaking the code, or be improper by exploiting the information I received (the doctor being an ass) to promote my personal (and the deaf patient’s) agenda.

As of right now, I have no idea what I would do that aligns itself both with the Code and with my moral principles. And that, frankly, keeps me awake at night.

In class, Cocoon suggested that it is proper (and okay with the Code) to not so much as intervene in anyone’s favor in the interpretation-scene, but to simply supply the patient with some healthy advice that doesn’t assume any actual responsibility or, heavens forbid, requires contamination of spoken content with agenda-ridden signs.

She suggested, for example, to cordially ask the patient if she’s sure of what she’s going to do and humbly recommend her to consider her actions (such as signing the form that authorizes her surgery) well before anything potentially harmful happens.

This is a prudent and somewhat cunning alternative to breaking the code or letting a deaf person rot in the course of upholding it, but I still think it’s problematic. In a way, I AM breaking the code, or at least jabbing it hard enough to leave a crack. Personally? I’d do just what Cocoon suggested because I haven’t thought of a better idea. Perhaps I’d be a bit more adamant with my “cordial suggestions”, but I admit that I wouldn’t replace Mom and Dad with the deaf patient, I have to remain professional, for everyone’s sake.

Getting more intimate with sign language and the deaf is like a dream coming true for me, but I’m appalled as I wrestle with the horrible acknowledgment of the fact that sign language interpreters and the Deaf can never be friends and “work together” at the same time. The power to mediate between the hearing and the Deaf creates a chasm between Hearing and Deaf. The all-encompassing notion that one side is impaired and depended on the other makes the politics of this situation too cumbersome. I believe that although not impossible, being a professional sign language interpreter to a Deaf friend is highly unlikely.

I find this notion to be the most tragic conclusion from this course imaginable.

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).

Why We Sign


The basis for the post’s title is the title of the 9th episode for the epic WWII drama by Stephen Spielberg: “Band of Brothers”. As it so happens, the episode answers the question one particular soldier asked himself throughout the war: why did he fight and why did his friends have to die for it. He got a heart-shattering answer when he and his company discovered and liberated a concentration camp. It was probably also one of the most shocking and intense parts of the mini-series.

ISL school is fascinating enough when we deal with the origin and structure of this fascinating language, and with the tenets of translating and interpreting. Not surprisingly, it’s turning out to be more complicated than I thought. For starters, being a signer, apparently, does not make you a sign-language interpreter. Also, being an interpreter does not make you a translator. What’s going on?

To begin with, everyone in the program knows how to sign. It’s about 70% CODAs, so us CODAs obviously know Sign. There’s teachers and social workers and the occasional Interested Individual (probably my best friend in the program to date). On the whole, the sign-language part comes in-built in every one of the students.

So why do we need a program? Why 2 years?

Even though the rationale for interpreting has been clear to me all these years, I’ve never put it under the microscope. To me, signing was never designed to “act as professional proxy”. To me, signing always meant: “Do as your parents tell you”. I developed a relationship with Mom and Dad and I signed so I could help them.

Apparently, sign language interpreting does not focus, at least professionally, on helping the deaf.

Obviously, signing helps the deaf tremendously. They’re practically helpless, sometimes, without it (at least the old deaf population, which is far from being techno-savvy and isn’t going anywhere for the coming decades. Also, I’ve personally interpreted for techno-savvy deaf students. They’re not independent and aren’t going to be anytime soon).

But, and this is important, Cocoon (this is how I’m going to call the program administrator, a CODA whose husband is deaf) heavily admonished me for saying that I’m in this business to help the deaf. Cocoon says that such an attitude towards interpreting is not professional. A professional translator has to be 100% objective, with no bias towards the deaf nor the hearing. How do I reconcile that? In short, I don’t.

One of most pivotal issues in the program is Translation Ethics. An issue I’ve never dealt with and, says Cocoon, is of enormous import and is probably one of the main reasons for the establishment of a professional ISL-interpreters’ program.

It seems that I’ve violated the ISL ethical code when I stayed after class and helped my student with her homework, it appears that I’ve violated the code when I got involved, personally, with my clients and became their friend, helped them better understand the material, answered their questions before tests, etc. At one time, (and this, I admit, was wrong on every level), I even signed an answer to a question in a test when my deaf student looked at me with puppy eyes and begged me to help her with the test.

Well, I don’t know if I’ll have the minerals to say “no” to a deaf student in distress, but apparently, this is part of my professional responsibility. I might even lose my license if I do that when I go pro.

And here comes to the main point of the post, which is not why “We” (the interpreters) sign, but why “I” sign. I sign to help the deaf. It’s the reason I got into the program and without that reason, I have no place there. I come to impart my childhood habit of helping my deaf parents upon non-parenting deaf individuals. I come to reflect the love I had for my parents, deaf or not, upon all deaf individuals. It’s practically barbaric, in a way, but without it, I simply don’t know how to be so fatally enamoured with the deaf community as much as I am.

So this is a secret I probably should keep hidden from Cocoon, and it’s also reason enough for me to risk my license. I come to the deaf community in order to help them.

This does not mean that I’m going to be biased for the deaf as far as the contents of the signs is concerned. I am going to sign to them EXACTLY what the hearing person said, and I’m going to voice exactly what the client signs. I am, however, going to get personal with my deaf clients, and give them advice as far as I can. Not during the interpreting session, but as a friend. The certificate is only a bridgehead into the deaf community.

I will follow the ethics and rules to the letter, but I will not remove myself from the Deaf community itself. I will come to sign for them as a professional, hopefully model translator: Impartial to either Deaf and Hearing – but after the session is complete, I will address them as a friend of the Deaf, their hearing child as I’ve always been, and the de facto parent I always felt I was to the Deaf community.

I sign because I want to help.

I sign because I need to help.


We are truly most shaken by exposure to and immersion in the knowledge and opinions of those who are most unlike us. The greatest things to be learnt are by those not doing the things we do better, but by those who do things utterly differently from us.

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