Re: Insights I've gained from my Bio class so far

Daniel Harper <daniel_harper@xxxxxxxxxxxxx> wrote:

>On Sun, 29 Jan 2006 15:10:02 -0800, Stanley Friesen wrote:
>> Indeed the tinyness of our branch gets even more profound when you add
>> in the fact that microscopic (unicellular) life forms are under-sampled
>> relative to macroscopic one (due to difficulty in collecting). There
>> are gene assays that suggest a vast diversity of prokaryotes in the soil
>> and elsewhere that have never shown up in any lab culture or otherwise
>> been seen by humans. The proportion of prokaryotes that are actually
>> known is likely to be well under half.
>
>Is there a source where I can get some more information on this?
>
Well, *my* source was the book _Assembling the Tree of Life_, 2004.
edited by Joel Cracraft and Michael Donoghue. Oxford University Press.
Much of it is scattered throughout chapter 4 (several of one-liners
about ciPCR studies). Of course the book also has a good bibliography,
so you could go deeper if you have the time.

For instance on page 55: "However ciPCR suggests that both groups are
much broader, particularly the Crenarcheota. ciPCR also indicates the
possible existence of two additional major divisions of Archaea (fig.
4.3), the Korarcheota, known only from ciPCR studies (Barns et al.,
1996), and the extremely small (0.4 microm.) Nanoarcheota (Huber et al.
2002b)."

And on the next page: "Although all the cultured members of Crenarcheota
are hyperthermophilic and often anaerobic, ciPCR indicates the existence
of mesophilic aerobic taxa throughout the group. Unlike the
crenarchaeal thermophiles, many of the mesophiles appear to be
widespread." [The last with references to Hershberger et al. 1996,
DeLong 1992, and Fuhrman et al. 1992].

These are followed by several additional remarks under several of the
sub-groups of Crenarcheota. There is a similar mention of ciPCR in the
introduction to the section on eukaryotes.

><snip a bit>
>
>>>Furthermore, much of the awareness-changing "heavy lifting" of the class
>>>has happened not so much in the class environment itself, but in the lab.
>>>Sure, these have been very simple labs intended only to show some of the
>>>tools and methods of science, but I suspect that the vast majority of
>>>anti-evolutionists have never spent any amount of time in a serious
>>>biology lab (except perhaps to dissect a frog or two) and have never
>>>examined life through a scientific-quality microscope.
>>
>> I am not sure I would call dissecting a frog a real lab experiment - it
>> is more of an interactive visual aid :-)
>
>And, ironically, it was that sort of thing that had made me decide years
>ago that I "didn't like" Biology -- because instead of dealing with hard
>science like physics or chemistry did, all biologists were up to was
>dissecting things and generally making a mess. (I was young, and I
>apologize.) In 10th grade we dissected frogs, and I _hated_ it, largely
>due to the awful smells and sensations of dealing with preserved flesh,
>and also because memorizing all that anatomy (largely learned off of
>bad-quality Xeroxes of book originals) seemed rather pointless.

Well, it *is* largely pointless unless one actually wants to do research
on the organisms in question, then it becomes critical.
>
>I wonder how many other potential scientists are turned off by such
>things. If my high school biology class had emphasized evolutionary
>processes, survival strategies, et cetera in a more rigorous way, I might
>have found myself much more interested ten years ago.
>
Yeah, I know what you mean. I found high school biology, except for the
Advanced Biology class with Mr. Roth, quite tedious and boring. Luckily
I had a father who *was* a scientist, and knew various professors, so I
knew better. In those years I learned rather more about science by
reading. Take heart, college biology is much more interesting (and
ultimately more difficult).

[More science teachers like Mr. Roth might be nice: how many teachers
keep cool things like rattlesnakes in the classroom?]
>>
>> Ah yes, the measuring lessons. I remember those. Quite enlightening,
>> as you say.
>
>Funnily enough, several of the groups in the lab section quickly sussed me
>out as a science major, since I seemed to already know what to expect in
>that lab. Little did they know that I just worked at a copy shop... :->
>
LOL. At least in science you don't actually have to make them all
identical, you just need to determine the error bars :->
>
>> [Seriously, I would find your job totally frustrating].
>
>Retail in general requires a certain type of personality. Namely, one that
>is willing to put up with extreme amounts of stress due to upper
>management and angry customers for little pay. (No, I'm not bitter at all.)
>
Oh, I have done my share of retail. I hated it with a passion, for the
most part. Only the time working retail was tolerable (though still
unpleasant) was at Bucky's (a burger place no less), and that was
because the owner was such a fun guy.

>> You can see some amazing things under a microscope - especially if you
>> have one of the ones with advanced optics, such as I got to use when I
>> worked for Dr. Bovee years ago. Somewhere I believe I still have the
>> drawings I made of an undescribed species of amoeba I found *once* (and
>> never again, despite several attempts).
>
>Amoeba frieseni? I can buy it.
>
Oh, I doubt I would have the chutzpah to name it after myself. I might
have used _boveei_ though. Technically it would have been in the genus
_Vexillifera_, if I remember correctly. [Genus _Amoeba_ is restricted
to a few largish species with large tubular pseudopodia].

>Seriously, that sounds very cool.
>
Yeah, and if I had been able to collect it more than once I probably
would have described it formally, sigh.
>>
>> Yep. I have even seen wild paramecia, that is ones I found in random
>> water samples from campus rather than a prepared culture. Some of the
>> other ciliates are quite amazing - like the one with the long "neck"
>> (really just a long, motile cellular extension).
>
>We did spend a few minutes examining random "pond water", but I'm afraid I
>didn't have enough time to really get into anything interesting.

You often get more results if you let it grow in the bottle for a while.
The disadvantage of this is that it changes the environment somewhat, so
some of the more narrowly fresh-water species may disappear.

> For some
>reason, my fellow lab mates were more interested in finishing the lab and
>getting the grade than in letting me play with my expensive new toy for a
>few hours. (I'm sure the lab instructor would have been displeased with
>that as well.)
>
Well, that was where working for Dr. Bovee was so cool. When I had no
immediate task at hand he let me play with his microscopes, including
one that would make your lab scope look cheap. Seriously, a job as an
RA (not TA) for a laid-back, cool professor is a major plus for
everyone. [OK, so I *did* have to wash glassware and prepare stinking
growth media made of pre-digested protein, but it was worth it]. Check
the campus job listings. Also, see if you can find time to just *chat*
with interesting professors that in itself can be very educational. It
is amazing how friendly they can be to somebody who shows a *genuine*
interest in their work.
>>
>>> And I actually got to see a Euglena's flagellum in
>>>motion, although they were a bit too faint to see clearly.
>>
>> That is largely due to the motion, which is rather rapid.
>>
>
>We used a bit of methyl cellulose to slow the organisms down, which seemed
>to freeze many in their tracks, and even the Euglena didn't move around a
>whole lot, if at all. We had a prepared slide that we viewed (I used a
>slightly darker setting on the light source) and I got a better view of
>the flagellum. Guess that's why it's a prepared slide.

Yeah, flagella are tricky. I had the advantage of the special optics on
Dr. Bovee's *expensive* microscope. It had a number of fancy contrast
enhancing modes that you do not see on cheaper scopes. [Mid-70s, and it
cost several thousand dollars].
>
>(BTW, does methyl cellulose slow down these organisms by chemical or
>physical means? Is it a poison? I asked the lab instructor, but she seemed
>unsure.)

I am not totally sure myself, but I *think* it is purely mechanical. It
is a rather viscous, fairly inert substance. Think of it as a weird
sort of starchy water (cellulose and starch are closely related
chemicals). I rather suspect the advantage of methyl-cellulose over
starch is mainly optical - it is more transparent.
>
>> If you like microscopy, it is worth pulling water samples out of any
>> pond or puddle you see and letting "ferment".
>
>If I continue in this vein, I may consider buying a 'scope for myself,
>although prices seem to be way higher than I'm in the market to spend for
>the foreseeable future. Any tips for getting the university to let me
>spend some free time (oh, such copious free time) seeing what I can find
>for myself? Or is that just a pipe dream until I get to graduate work?

It is really largely a matter of finding ways of spending "quality time"
with actual professors. There are often even some "courses" called
undergraduate research courses which are really doing this for class
credit, though they are all junior-senior course, AFAIK. I actually did
a small paper for Dr. Bovee on amoeba taxonomy under that rubric, though
I had worked for him for some time prior to doing so, so we knew each
other.
>
>> Just among the
>> unicellular eukaryotes there is an amazing variety to be seen. Ciliates
>> with little rigid bodies shaped like a barrel. Cryptomonds. Amoebas of
>> all shapes and sized (I suspect the ones you used in lab were the common
>> giant amoeba, _Amoeba proteus_ - most species are much smaller).
>
>Yeah, _proteus_ was the one we were examining. I even thought I saw one or
>two with the naked eye at one point, although I could have just been
>seeing air bubbles.

No, you were correct. _A. proteus_ is *just* visible with the naked eye
(I used to pluck individual ones out of the culture bottle). Of the
ordinary amoebae, only _Pelomyxa palustris_ (which I never managed to
see) and _Chaos carolinensis_ (which I purchased cultured) are larger.

Of course these are all tiny compared to the syncytial slime molds, such
as _Physarum_ (which I grew in a petri dish - which it tried to
outgrow). But syncytial slime molds have thousands of nuclei in their
multi-cm wide bodies, so one might argue they are actually multicellular
despite a lack of cell membranes. They also reproduce by spores
produced by fruiting bodies that look like mold (hence the name).
>
>What is it about learning science that just makes you feel _good_? Must be
>all that ignorance leaving your body. :->

Well, I call it the excitement of discovery. The Eureka moments.

Of course there are many *other* fascinating parts of biology, from
walking through a forest and actually *seeing* its structure, to
studying how animals grow [I still remember the embryology lab where we
put windows in fertilized chicken eggs and watched them grow over the
span of the course - of course we had to *draw* and *identify* what we
saw to get credit].

--
The peace of God be with you.

Stanley Friesen

.

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