Going on vacation until June... may not be able to post much there. Although it's not like you'd notice the difference anyway...
Lurk ToLWeb and Paleos to get a bit of a protist fix if necessary. Or read a paper by Tom Cavalier-Smith, or two, or three. That shall keep you busy! mwahaha...
Field of Science
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From Valley Forge to the Lab: Parallels between Washington's Maneuvers and Drug Development3 weeks ago in The Curious Wavefunction
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Political pollsters are pretending they know what's happening. They don't.3 weeks ago in Genomics, Medicine, and Pseudoscience
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Course Corrections5 months ago in Angry by Choice
Another delinquent Sunday Protist -- Euglenids
Kinda busy this week; going on two week vacation on Friday, so naturally stuff just piles up. Thus I'm gonna parasitise off the ToLWeb Euglenida page and send you guys there.
They have cool pictures:
And possibly nearly everything you'd ever wanted to know about Euglenids and their evolution.
Back to chaos...
They have cool pictures:
And possibly nearly everything you'd ever wanted to know about Euglenids and their evolution.
Back to chaos...
Sunday Protist resumed: Acetabularia
I've been thoroughly neglecting Archaeplastida... probably because I see its representatives everyday anyway. Archaeplastida is the superkingdom containing Glaucophytes, red algae, green algae and land plants*. Archaeplastids are characterised by primary plastid endosymbiosis, so most of them are photosynthetic. Hopefully I'll get around to discussing some exceptions later...
Since I like large complicated cells, today's menu features Acetabularia:
(UBC Botanical Garden)
Each of those umbrella-like things is a single uninucleate cell up to 6cm tall. At the base of the stalk is the rhizoid containing the nucleus. This little detail turned out to be extremely useful for establishing the cell organelle responsible for heredity back in the 30's by Hämmerling. A couple species of Acetabularia produce morphologically distinct caps, so Hämmerling cut off the caps and exchanged the stalks between the two species. The morphology of the regenerating cap was determined by the species of the nucleus-containing rhizoid, not the stalk: thereby strongly supporting the central role of the nucleus in heredity and the cell's 'information'.
I'd love to study cell morphogenesis in that thing! There seems to be a bit of work done on it here and there, but it is far from model organism status. Doesn't seem to have its genome sequenced yet, although I may be wrong on that. Being a unicellular organism relatively close to land plants, it could reveal some insights about plant cell development and evolution. The size would be wonderful for studying cytoskeletal dynamics. Acetabularia was at one point used as a model for circadian rhythm studies - it maintains its rhythm in the absence of the nucleus, implying a cytosolic component to biological clock regulations (briefly mentioned here).
However, for all I know, it may be hard to culture, do genetics with, etc.
(personally, I still prefer ciliates... ^_^ )
*Archaeplastida is also alternatively called Plantae, but I resent that naming. After being taught for so long that plants are the terrestrial multicellular green stuff, and being proud of recognising that 'seaweeds' aren't plants after all... they suddenly decide to name the whole freaking group Plants. Sorry, no. I find it rather unsettling when some protistologists refer to red algae or prasoniphytes as 'plants'. The conventional plants are refered to as 'land plants' (which I'm fine with to avoid confusion; although botanists give me funny looks when I do that...) Furthermore, the name Archaeplastida makes sense, since this group is defined by having plastids from primary endosymbiosis. Everything else got their plastids from them via secondary and tertiary endosymbiosis.
Sorry, but your Chlamydomonas is not a freaking plant, kthx.
Since I like large complicated cells, today's menu features Acetabularia:
(UBC Botanical Garden)
Each of those umbrella-like things is a single uninucleate cell up to 6cm tall. At the base of the stalk is the rhizoid containing the nucleus. This little detail turned out to be extremely useful for establishing the cell organelle responsible for heredity back in the 30's by Hämmerling. A couple species of Acetabularia produce morphologically distinct caps, so Hämmerling cut off the caps and exchanged the stalks between the two species. The morphology of the regenerating cap was determined by the species of the nucleus-containing rhizoid, not the stalk: thereby strongly supporting the central role of the nucleus in heredity and the cell's 'information'.
I'd love to study cell morphogenesis in that thing! There seems to be a bit of work done on it here and there, but it is far from model organism status. Doesn't seem to have its genome sequenced yet, although I may be wrong on that. Being a unicellular organism relatively close to land plants, it could reveal some insights about plant cell development and evolution. The size would be wonderful for studying cytoskeletal dynamics. Acetabularia was at one point used as a model for circadian rhythm studies - it maintains its rhythm in the absence of the nucleus, implying a cytosolic component to biological clock regulations (briefly mentioned here).
However, for all I know, it may be hard to culture, do genetics with, etc.
(personally, I still prefer ciliates... ^_^ )
*Archaeplastida is also alternatively called Plantae, but I resent that naming. After being taught for so long that plants are the terrestrial multicellular green stuff, and being proud of recognising that 'seaweeds' aren't plants after all... they suddenly decide to name the whole freaking group Plants. Sorry, no. I find it rather unsettling when some protistologists refer to red algae or prasoniphytes as 'plants'. The conventional plants are refered to as 'land plants' (which I'm fine with to avoid confusion; although botanists give me funny looks when I do that...) Furthermore, the name Archaeplastida makes sense, since this group is defined by having plastids from primary endosymbiosis. Everything else got their plastids from them via secondary and tertiary endosymbiosis.
Sorry, but your Chlamydomonas is not a freaking plant, kthx.
Pipet FAIL
When you set up PCRs, often you first make a master mix and then aliquot it into smaller portions to which you add template DNA (the stuff you need copied). Often you do one extra reaction more than you need, since you tend to run out due to pipeting error. But you don't need that much extra normally...
For the last few months, I kept on running low when aliquoting - often not having enough for the last tube. I would make 10 reactions when I really needed 8, so about 36μL extra, for 18μL aliquots. And STILL I would not have enough for all reactions. I calculated my recipe numerous times in numerous ways, and it should have worked. I tried the most careful pipeting technique I could manage, although it would be a rather exquisite accomplishment for pipeting error to be THAT bad!
I suspected the pipets, but my labmates were all like "Oh don't blame the pipets now!"
So I got sick of this. I grabbed water, and went to the analytical balance. I check the p20 - everything more or less fine. Then I grab my p200...
Yes, it only pipets ~75% of the set volume. FOR THE PAST FIVE MONTHS.
So yes, when all fails... check your pipets. Their calibration could be way off by now... (after changing all the water and buffers and stock solutions, that is.)
Now, my burning question:
How the hell did my PCRs work for the past five months despite all my concentrations being absolutely RANDOM!?
So much for molecular biology being an exact science, hahaaa!
Actually, molecular biology is voodoo. Seriously. You can make things exactly right and they don't work. You can leave your DNA out on the bench for a couple nights and completely screw everything up while pipeting... and it magically produces the bands you want. I think it depends more on the star alignments or something...
For the last few months, I kept on running low when aliquoting - often not having enough for the last tube. I would make 10 reactions when I really needed 8, so about 36μL extra, for 18μL aliquots. And STILL I would not have enough for all reactions. I calculated my recipe numerous times in numerous ways, and it should have worked. I tried the most careful pipeting technique I could manage, although it would be a rather exquisite accomplishment for pipeting error to be THAT bad!
I suspected the pipets, but my labmates were all like "Oh don't blame the pipets now!"
So I got sick of this. I grabbed water, and went to the analytical balance. I check the p20 - everything more or less fine. Then I grab my p200...
Yes, it only pipets ~75% of the set volume. FOR THE PAST FIVE MONTHS.
So yes, when all fails... check your pipets. Their calibration could be way off by now... (after changing all the water and buffers and stock solutions, that is.)
Now, my burning question:
How the hell did my PCRs work for the past five months despite all my concentrations being absolutely RANDOM!?
So much for molecular biology being an exact science, hahaaa!
Actually, molecular biology is voodoo. Seriously. You can make things exactly right and they don't work. You can leave your DNA out on the bench for a couple nights and completely screw everything up while pipeting... and it magically produces the bands you want. I think it depends more on the star alignments or something...
Homage to RefWorks...
I wish Blogger had RefWorks citing capabilities... I've gotten spoiled by clicking the 'cite' button to cite stuff. Here I actually have to write out the full citations. By hand. The horror.
Luckily, I can preformat stuff there and just copy it over here. Blogging has just got a ton easier.
Sadder than my newfound dependency on citation managers is that I actually think they're like the coolest thing ever. There was actually a rush of euphoria when I discovered cursing the process of typing bibliographies is a thing of the past! I even investigated all the various citation styles and...yes, found my favourite one.
I have a favourite citation style: of the Current Opinion series. I even have a rationale for liking it. Look how neat and easy to follow it is:
I randomly blogged about citation styles.
I think I've just reached the epitome of geekdom. To beat that, you must argue for YOUR favourite citation style.
However, in this post is a preview of paper I will be working on translating into English for you guys, from the TC-S dialect of academese... it's on the evolution of eukaryotes from prokaryotes. Fascinating stuff!
Now I'm actually gonna do it...
Luckily, I can preformat stuff there and just copy it over here. Blogging has just got a ton easier.
Sadder than my newfound dependency on citation managers is that I actually think they're like the coolest thing ever. There was actually a rush of euphoria when I discovered cursing the process of typing bibliographies is a thing of the past! I even investigated all the various citation styles and...yes, found my favourite one.
I have a favourite citation style: of the Current Opinion series. I even have a rationale for liking it. Look how neat and easy to follow it is:
Cavalier-Smith T: Predation and eukaryote cell origins: A coevolutionary perspective. The International Journal of Biochemistry & Cell Biology 2009, 41: 307-322.The bold formatting option exists to be used, either for the author or the title. The author is usually first anyway, so it makes more sense to bold the title. The numbered in-text citations [1] make it easy to follow review papers without the clutter of full in-text references. (although the full format comes in handy at time too...) The only issue I have is the year appearing at the end. I prefer the pub year to appear right after the author, since in biology it's fairly important to know when stuff was said/done. I hate that about the wretched MLA: they don't even use year in their in-text refs!
I randomly blogged about citation styles.
I think I've just reached the epitome of geekdom. To beat that, you must argue for YOUR favourite citation style.
However, in this post is a preview of paper I will be working on translating into English for you guys, from the TC-S dialect of academese... it's on the evolution of eukaryotes from prokaryotes. Fascinating stuff!
Now I'm actually gonna do it...
Science as a journey through alien worlds
Running a gel, thus perfect time to blog. Perhaps if I write stuff in the lab, it may actually turn out to be marginally intellectual.
Hopefully my gel won't turn out to be something like this again:
I hate genotyping - the work itself requires the intelligence of a brain-dead foetal monkey, yet manages to find a stunning variety of ways to fail. And when it does work, it usually shows everything was wildtype anyway. Or maybe your mutant-specific primers failed. You should probably remember to run a positive control next time. If you have one, that is. And when it does work, you can brag about find a homozygous line amongs the seeds you ordered from the stock centre. Nature-worthy achievements right there.
Actually, most lab work is about as mundane and intellectually uninvolving. The planning and literature reading, data analysis and troubleshooting(!) can be quite exciting and tend to involve plenty of thinking, but you only do that in-between the endless repetitive pipetting and mixing chemicals and following protocols. I think research probably involves one of the biggest intellectual (and emotional, heh) rollercoasters of all professions, which is why only the very insane can handle it.
[did I run the DNA off the gel yet... no, phew.]
I do enjoy microscopy, however, which is considered by some to be repetitive and mindless as well. I cannot disagree more. It's an artistic break from the gels and protocols - you have a lot of factors to play around with to obtain the best image you can. Microscopy is also very dangerous, a wonderful way to obtain false positives! It's extremely easy to tweak the image to see what isn't there, even unintentionally. A substantial component of the art is to obtain sexy images without sacrificing the scientific validity thereof.
As children, many of us have dreamt of fantasy alien worlds, to be much disappointed upon finding out we would most likely never encounter any; not within our lifetimes anyway. However, it is wonderful to know that alien worlds are not confined to what lies beyond the Earth's atmosphere! (or present time...) They are all around us, ready to provide enchantment and fantasy to anyone who invests enough to explore.
To a mathematician, beauty may lie in quantifying forms or dynamic phenomena, or working with abstract worlds far beyond the imaginative capacity of the human mind. To a fiction writer, fantasy worlds thrive in his mind not much different from the form taken by reality itself. To an astronomer, the alien worlds are almost within reach - just barely visible, yet not ours to manipulate. For me, foreign worlds exist under the lens of a microscope, where if you magnify anything far enough, you can spend a lifetime wandering amidst the surreal landscapes unseen by naked eye. The life of or within a cell is fascinating enough conceptually, but that mysterious aspect of it being beyond our 'scale' makes it not much different from a childhood fairytale or a sci-fi novel - except that it's real!
On a more abstract level, science itself is a foreign world for exploration (along with math, the arts, etc.). Upon liberation from what Carl Sagan calls "the anaesthetic of familiarity", the mundane everyday world around us becomes full of tantilising mystery. Science is a way of unraveling some of this mystery (I'll argue, the optimal way of dealing with natural mystery), an ardurous journey through the unknown worlds. It's rather fractal-like in nature - the more you explore, the more questions arise; the deeper something is examined, the more detail beckons attention.
I think a good analogy for the scientific journey could be hiking or climbing - the act of walking along a trail is quite repetitive: all you do is place one foot before the other. After some time the scenery begins to repeat itself, and one wonders how anyone could enjoy outdoor activities at all. But many do, and probably few ever notice the monotony of walking, or climbing, or paddling a kayak... for there's always something fresh to look at, something wonderful to appreciate and enjoy. It's fairly easy to knock off the 'anaesthetic of familiarity' for an outdoor enthusiast - the escape from the chaos of the human 'world' is sufficient to make the journey worthy of the physical investments. The threat of an occasional failure, the pain of stepping on a too-unstable rock... is usually not enough to deter one from actually enjoying the exploration itself.
Science is quite similar - there is the monotony and rigorous exactness required by the scientific method, the endless protocols, the multitudes of failed and inconclusive experiments. There is the threat of losing one's job upon failure of publication - the world of 'publish or perish'. It seems one must be insane to voluntarily engage in such activity, much less enjoy it. But just like the monotony of walking is instantly forgotten upon the sight of a rare bird or an overpowering landscape, the monotony of science is instantly lifted upon the sight of a contradicted null hypothesis, or the sight of a rare species, or the ability to actually see a cellular process in action in real time... (perhaps for a chemist, the synthesis of a brand new chemical never before produced on earth could induce a similar rush or euphoria?)
But just as one does not go on a hike expecting to see a rare bird (lest the foiled expectations lead to a wrecked mood), one cannot go into science expecting to make great discoveries. The very process itself must be tolerable, and hopefully captivating enough, to keep going. Sometimes you get excited about the potential outcomes of an experiment, only to discover your results are utterly inconclusive and the story is far more complex than previously imagined. I think what makes science quite suitable for an insane type of mind is the ability to actually not mind such disappointments, and savour them as a testament to nature's superiority and infinite complexity.
After all, we may rest assured that we will never run out of work to do, just as an outdoorsman would never run out of places to explore. Now isn't that a comforting form of eternity?
[genotype results: all wildtype. Time for more PCR!]
Hopefully my gel won't turn out to be something like this again:
I hate genotyping - the work itself requires the intelligence of a brain-dead foetal monkey, yet manages to find a stunning variety of ways to fail. And when it does work, it usually shows everything was wildtype anyway. Or maybe your mutant-specific primers failed. You should probably remember to run a positive control next time. If you have one, that is. And when it does work, you can brag about find a homozygous line amongs the seeds you ordered from the stock centre. Nature-worthy achievements right there.
Actually, most lab work is about as mundane and intellectually uninvolving. The planning and literature reading, data analysis and troubleshooting(!) can be quite exciting and tend to involve plenty of thinking, but you only do that in-between the endless repetitive pipetting and mixing chemicals and following protocols. I think research probably involves one of the biggest intellectual (and emotional, heh) rollercoasters of all professions, which is why only the very insane can handle it.
[did I run the DNA off the gel yet... no, phew.]
I do enjoy microscopy, however, which is considered by some to be repetitive and mindless as well. I cannot disagree more. It's an artistic break from the gels and protocols - you have a lot of factors to play around with to obtain the best image you can. Microscopy is also very dangerous, a wonderful way to obtain false positives! It's extremely easy to tweak the image to see what isn't there, even unintentionally. A substantial component of the art is to obtain sexy images without sacrificing the scientific validity thereof.
As children, many of us have dreamt of fantasy alien worlds, to be much disappointed upon finding out we would most likely never encounter any; not within our lifetimes anyway. However, it is wonderful to know that alien worlds are not confined to what lies beyond the Earth's atmosphere! (or present time...) They are all around us, ready to provide enchantment and fantasy to anyone who invests enough to explore.
To a mathematician, beauty may lie in quantifying forms or dynamic phenomena, or working with abstract worlds far beyond the imaginative capacity of the human mind. To a fiction writer, fantasy worlds thrive in his mind not much different from the form taken by reality itself. To an astronomer, the alien worlds are almost within reach - just barely visible, yet not ours to manipulate. For me, foreign worlds exist under the lens of a microscope, where if you magnify anything far enough, you can spend a lifetime wandering amidst the surreal landscapes unseen by naked eye. The life of or within a cell is fascinating enough conceptually, but that mysterious aspect of it being beyond our 'scale' makes it not much different from a childhood fairytale or a sci-fi novel - except that it's real!
On a more abstract level, science itself is a foreign world for exploration (along with math, the arts, etc.). Upon liberation from what Carl Sagan calls "the anaesthetic of familiarity", the mundane everyday world around us becomes full of tantilising mystery. Science is a way of unraveling some of this mystery (I'll argue, the optimal way of dealing with natural mystery), an ardurous journey through the unknown worlds. It's rather fractal-like in nature - the more you explore, the more questions arise; the deeper something is examined, the more detail beckons attention.
I think a good analogy for the scientific journey could be hiking or climbing - the act of walking along a trail is quite repetitive: all you do is place one foot before the other. After some time the scenery begins to repeat itself, and one wonders how anyone could enjoy outdoor activities at all. But many do, and probably few ever notice the monotony of walking, or climbing, or paddling a kayak... for there's always something fresh to look at, something wonderful to appreciate and enjoy. It's fairly easy to knock off the 'anaesthetic of familiarity' for an outdoor enthusiast - the escape from the chaos of the human 'world' is sufficient to make the journey worthy of the physical investments. The threat of an occasional failure, the pain of stepping on a too-unstable rock... is usually not enough to deter one from actually enjoying the exploration itself.
Science is quite similar - there is the monotony and rigorous exactness required by the scientific method, the endless protocols, the multitudes of failed and inconclusive experiments. There is the threat of losing one's job upon failure of publication - the world of 'publish or perish'. It seems one must be insane to voluntarily engage in such activity, much less enjoy it. But just like the monotony of walking is instantly forgotten upon the sight of a rare bird or an overpowering landscape, the monotony of science is instantly lifted upon the sight of a contradicted null hypothesis, or the sight of a rare species, or the ability to actually see a cellular process in action in real time... (perhaps for a chemist, the synthesis of a brand new chemical never before produced on earth could induce a similar rush or euphoria?)
But just as one does not go on a hike expecting to see a rare bird (lest the foiled expectations lead to a wrecked mood), one cannot go into science expecting to make great discoveries. The very process itself must be tolerable, and hopefully captivating enough, to keep going. Sometimes you get excited about the potential outcomes of an experiment, only to discover your results are utterly inconclusive and the story is far more complex than previously imagined. I think what makes science quite suitable for an insane type of mind is the ability to actually not mind such disappointments, and savour them as a testament to nature's superiority and infinite complexity.
After all, we may rest assured that we will never run out of work to do, just as an outdoorsman would never run out of places to explore. Now isn't that a comforting form of eternity?
[genotype results: all wildtype. Time for more PCR!]
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