S E M P E RP H A G E

publications
research interests
bacteriophage ecology
Stephen T. Abedon
microdude+@osu.edu
photo welcome wave
school links
weather
© Phage et al.

S E M P E RP H A G E

(more below)









                                                         
                 Stephen T. Abedon, Ph.D.                
                                                         
          "Man of 1000 Faces and Hair Styles!"           
                                                         
             Assistant Professor Microbiology            
                The Ohio State University                
                                                         
         /            /              /           /       
         \            \              \           \       
    [:<]==[  -->  [:)]=[-  -->  [:)]==[  +  [:)]==[      
         /            /              /           /       
         \            \              \           \       
                                                         
    address: 1'   MicroDude+@OSU.edu                     
             2'   Abedon.1@OSU.edu                       
             3'   SAbedon@pop.service.ohio-state.edu     
             4'   297 Bromfield                          
                  1680 University Dr.                    
                  Mansfield, OH 44906                    
             5'   (419) 755-4343 (phone)                 
             6'   (419) 755-4327 (fax)                   
                                                         
    office hrs:                                          
    appointment:                                         
    drop in:      same as immediately above              

(more below)











Evolution of Man

Teaching About Evolution and the Nature of Science

Microbiology and Immunology at OSU

Safe Sun?

Sounds Like Science

Additional Links



evolvefish.com
Scientific thinking is simply a semi-efficient means by which one avoids wasting one's own time and that of others. Non-scientific thinking takes longer at discovering truths, with lack of rigor and infinite time scales proceeding hand in hand. If you insist on viewing the world without rigor, that's fine, just don't waste my time with your irrational actions or rantings.

- Nodeba Bob -
So what is the hurry to apply our notions so quickly? Often we make discoveries simply because our knowledge base is so tiny that we are bound to learn new things. This means that our ignorance is so great that we have virtually no capacity for prescription, that is, little capacity to recommend ways to correct problems that we encounter.

- David Suzuki -

(the answer, by the way, is that it's a Prisoner's Dilemma out there and if we don't defect to gain the glory, money, or reproductive edge, then somebody else will)


dyehappy.com

waldonet.com
What features of your daily life do you expect to be improved by a further increase in population?

- Garrett Hardin -
The LCV scores range from 0 to 100, where high scores represent pro-environmentalist positions. . . Attitudes toward environmental legislation are clearly apparent in party voting patterns; the average Republican score in the House is 24, compared with 72 for Democrats. In the Senate, party differences are even greater: Republicans there average 12 and Democrats 86.

- The League of Conservation Voters -


Alistar B. Fraser

dharmatrading.com
So, so you think you can tell, Heaven from Hell, blue skies from pain. Can you tell a green field, from a cold steel rail? A smile from a veil? Do you think you can tell? And did they get you to trade, your heroes for ghosts? Hot ashes for trees? Hot air for a cool breeze? Cold comfort for change? And did you exchange, a walk on part in the war, for a lead role in a cage?

- Roger Waters -
. . . almost anything an experimenter does to increase the internal validity of a test situation (e.g., controls for experience, order, appropriateness of model, etc.) compromises the external validity of the test (e.g., the extent to which the results can be generalized to other situations).

- Stephens, Nishimura, and Toyer (1995, J. Theor. Biol. 176:457-469) paraphrasing A. C. Kamil -

killer homepage webring
prevrandomindexnext

(more below)












R
e
s
e
a
r
c
h

I
n
t
e
r
e
s
t
s


Ecology is the study of plants and animals at home, that is to say, in their natural environment (from the Greek word oikos, a house). Evolutionary ecology is the branch of this subject that considers how organisms have evolved to become adapted to their environment, including in this term their interactions with members of their own and other species (the biotic environment) as well as the physical environment; it examines the selective pressures imposed by the environment and the evolutionary response to these pressures. Ý Darwin (1859) proposed natural selection as a unifying principle to explain two things: the transmutation of species and the adaptation of organisms to their environment. Evolutionary ecology takes the second of these as its field of study. Its aim is to explain, in the light of current knowledge, "how the innumerable species inhabiting this world have been modified, so as to acquire that perfection of structure and coadaptation that most justly excites our admiration.'

- Michael Bulmer -
bacteriophage lysis . . . evolution of virulence . . .
evolution of cooperation . . . bacteriophage therapy . . .

My research has a broad but ultimately coherent focus, combining interests in ecology, microbiology, experimentation, and theory. Bacteriophage T4 is a virus that infects the common, enteric bacterium, Escherichia coli, and is my primary research organism. I am particularly interested in bacteriophage lysis, the virus-induced host destruction required for virus-progeny dissemination. T4 lysis is complex. It involves (i) a default mechanism (called lysis from within), (ii) an induced mechanism of lysis avoidance (called lysis inhibition), (iii) an extracellularly induced lytic mechanism (called lysis from without), (iv) a mechanism of induced-lysis avoidance (called resistance to lysis from without), and (v) a mechanism of lysis of lysis-inhibited cells (called lysis-inhibition collapse). I employ mutants defective in lysis from within, lysis inhibition, lysis from without, resistance to lysis from without, or lysis-inhibition collapse. The deviations from wild-type physiology associated with these mutants influence T4 virulence. I am simultaneously developing a theory of lytic bacteriophage virulence while collaboratively elucidating the molecular mechanisms of T4 lysis. My goals are to employ bacteriophage virulence mutants to test existing hypotheses and develop new ones on the evolution of virulence in pathogenic microorganisms. I am also interested in related hypotheses on the evolution of intraspecific cooperation. My long-term goal is to apply this knowledge to the development of bacteriophage therapy, an alternative to the chemotherapeutic treatment of bacterial infection. My major accomplishments include (i) the theoretical elucidation of the ecological function of lysis inhibition, (ii) the discovery of the mechanism and ecological relevance of lysis-inhibition collapse, (iii) the elucidation of one mechanism (resistance to lysis from without) underlying the resistance-to-premature-lysis-inhibition-collapse phenotype that is defective in T4 imm, sp, and 5ts1 mutants, and (iv) the popularization of the idea that bacteriophage latent-period length may evolve as a function of host-cell density.

R
e
s
e
a
r
c
h

I
n
t
e
r
e
s
t
s





P
u
b
s

P
u
b
s

P
u
b
s

P
u
b
s

P
u
b
s

P
u
b
s

1. Abedon, S.T. (1999). Resistance to lysis-inhibition collapse. Genetical Research 74:1-11. ---

P
u
b
s

P
u
b
s

P
u
b
s

P
u
b
s

P
u
b
s

P
u
b
s

2. Paddison, P., Abedon, S.T., Dressman, H., Gailbreath, K., Mosser, E., Neitzel, J., Guttman, B., Kutter, E. (1998). Lysis inhibition and fine-structure genetics in bacteriophage T4. Genetics 148:1539-1550. ---
3. Abedon, S. T. (1994). Lysis and the interaction between free phages and infected cells. The Molecular Biology of Bacteriophage T4. Jim D. Karam (ed). Washington, DC ASM Press. pp. 397-405. abstract
4. Abedon, S. T. (1993). The isolation of T-even phages (feces -?-> P.C./PC --> gamma --> T2; Sewage -?-> T4/T6). T4 News (February 7). abstract
5. Abedon, S. T. (1992). Lysis of lysis-inhibited bacteriophage T4 infected cells. Journal of Bacteriology 174:8073-8080. abstract
6. Abedon, S. T. (1992). Bottle lysate T4 stock preparation: What if your cultures won't clear? T4 News 6(1). ---
7. Abedon, S. T. (1990). Selection for lysis-inhibition in bacteriophage. Journal of Theoretical Biology 146:501-511. abstract
8. Abedon, S. T. (1989). Selection for bacteriophage latent period length by bacterial density: A theoretical examination. Microbial Ecology 18:79-88. abstract

(more below)










[1998, press for enlargement]

Is such a virus living? The question is unanswerable without a definition of 'life'. And any definition of life must be arbitrary.

- George W. Beadle -

With millions of species, each one with an almost unimaginably complex history and genetic makeup, we would have a source of intellectual and aesthetic enjoyment for generations to come.

- E. O. Wilson -

[1997, press for enlargement]

[1990, press for enlargement]

. . . we live in the Age of Bacteria (as it was in the beginning, is now and ever shall be, until the world ends) . . .

- Stephen Jay Gould -

Ecologists who are not thoroughly familiar with the organisms involved risk wasting a great deal of time.

- Nelson G. Hairston, Sr. -

[1995, press for enlargement]

[1995, press for enlargement]

Is it responsible for scientists to hold out the hope that endless population growth can be matched by endless doublings of world food production? At some point, probably sooner rather than later, we are going to run into the limits set by the law of conservation of stuff. The people of the world would be better served if we scientists gave our primary attention to the achievement of zero or negative population growth, first in the United States and then worldwide, so that further increases in agricultural production could be devoted to substantially improving diets worldwide.

- Albert A. Bartlett -

A more valid ecology of U.S. science might start from the fact that the world's most productive scientific community exists within the world's most robust total economy. The notion that such a science- and technology-based economy can be maintained in the long run with a smaller investment in research is the assumption that should be 'critically examined.' Those who argue that the complex process of scientific inquiry can be bypassed in favor of immediate 'problem resolution' or 'measurable results' might well consider the fate of the goose that laid the golden eggs.

- Roger Geiger -

[press for enlargement]

[1987, press for enlargement]

...scientific observations and discoveries don't necessarily require giant government grants and huge teams of researchers with specialized degrees. Small science still works, and it often works during off hours, weekends, and holidays when professionals are generally at home or on vacation.

- Forrest M. Mims III -

Amazon, you had so much and now so much is gone. . . What a lucky man to see the earth before it touched his hand. . . A greedy man never knows what he's done. . . A natural beauty should be preserved like a monument to nature.

- Neil Young -

[early 80s, press for enlargement]

[1998, press for enlargement]

There is nothing more rewarding than watching someone change their behavior toward the environment.

- Sylvia Mitraud -

When Bertrand Russell was sent to prison for opposing England's entrance into the first World War, the warden asked him what his religion was. Russell replied "agnostic." After asking Russell how to spell it, the warden sighed and said, "Well, there are many religions, but I suppose they all worship the same God." "This remark," Russell adds in his autobiography, "kept me cheerful for about a week.

- Martin Gardner -

[1998, press for enlargement]

[Erlan Ramanculov et moi, 1998]

The biological sciences are moving away from the era of analytical reductionism... from taking biological systems apart to see what the pieces are and how they work, to putting the pieces back together to understand how the totality works together.

- National Science Foundation Task Force report -

T
e
a
c
h
i
n
g


P
h
i
l
o
s
o
p
h
y


Read, Learn, Ask!
A Statement of Teaching Philosophy

A student will get out of their studies about as much as they are willing to put in. I see my job as creating environments that model, select for, or otherwise encourage student behaviors that maximize learning. In particular, learning is a challenging task but that does not mean that it cannot also be an enjoyable one. My primary pedagogical goals are to motivate students to read, to encourage them to learn from their reading and then to get them to ask questions. To read, to learn, to ask. How to accomplish these goals? My approach in a typical lecture period-teaching small-class introductory courses-consists of various permutations of the following:
During the previous lecture I will have disseminated "lecture notes" (which limit the material covered on exams, extend material the instructor deems especially relevant, and allow an emphasis on concepts over memorization) plus I will have assigned text reading. I will additionally have supplied past-exam questions for review. At the beginning of lectures, I quiz on mastery of text material. Test banks bundled with texts often supply questions well suited to this task. These reading comprehension quizzes are followed by short discussions of questions. Next is the core of the lecture where I discourse, encourage the asking of questions, encourage discussion of text reading, and encourage discussion of "lecture notes." At the end of periods (not necessarily on the same day as reading quizzes) I again quiz, this time on lecture-note-presented material and using instructor-written questions. These quizzes are then followed by brief post-quiz discussions. Quizzes are graded in such a way that they may help but cannot hurt a student's grade.
This approach combines efforts to encourage out-of-classroom learning with an in-classroom problem-solving-based learning environment, one tailored to memory-intensive disciplines such as biology. The motivated students are rewarded for their efforts, the less-motivated student is encouraged to study prior to the night before the exam, and the least-motivated students receive unrelenting evidence of the inadequacy of their efforts. Read, learn, ask.

Restating the thesis: What is more important to a student's learning and then earning good grades: teachers expending more and more effort taking on more and more of the responsibility for a student's learning, or students expending more and improved effort studying? I argue that the latter is by far the more crucial to a student's academic and professional success. In a world in which students do not study or do not know how to study, there is much to be gained by expending one's limited instructional resources on encouraging students both to study and to study well. Regardless of milieu, I keep myself available to students to discuss material and to answer questions. Future instructional goals consist of a further refinement of the principles and practices outlined above. Finally, I encourage highly motivated individuals to participate in undergraduate research.

T
e
a
c
h
i
n
g


P
h
i
l
o
s
o
p
h
y


...I have to be molecular. Who is not?

- André Lwoff -

Is an experiment an experiment without audio input? When NPR gets redundant, then what?
The Allman Brothers Band , The Beatles , Beethoven , WCPN's Blues with Fitz [SIC?] , Ray Charles , Charlie Byrd , Concrete Blonde , Counting Crows , Dire Straits , Donovan , Elvis , Stan Getz , Haydn , Jethro Tull , Led Zeppelin , Mazzy Star , Midnight Oil , Tom Rush , Frank Sinatra , Neil Young.
About three a.m., the end of a 15 hour day, gobs of data, so tired I've begun to hallucinate: Gregorian Chants!

The Face of the Phage


Five things you should do to reduce the rate at which you contribute to the environmental rape and impoverishment of planet Earth:
  1. plant trees
  2. do not support the development of undeveloped land
  3. have one or fewer children
  4. reduce the environmental impact of your travels
  5. live sustainably and with low impact: think before you buy/destroy/discard/kill
Defectors, please at least acknowledge your selfishness, and stop pretending that personal pleasure or reward is synonymous with virtue. It's not.

- Nodeba Bob -
...belief in the sort of miracles that constitute suspension of the ordinary laws of nature is destructive of the ability to approach ordinary life rationally. Not only that, but it is destructive of belief in a rational God, which to my mind seems a kind of blasphemy.

- Albert Rogers -

Unfortunately, despite our cultural prowess, we as a species are still locked into a pattern of enhancing our own short-term fitness (e.g., our immediate comfort and personal reproductive output) at the expense of the fitness of our descendants, our species, and our planet--with every hedonistic evolutionary impulse further converting our metaphorical Garden of Eden, a.k.a., planet Earth, into one big, polluted, weedy, desertificated mess.

- Nodeba Bob -

Click for Flagstaff, Arizona Forecast Click for Mansfield, Ohio Forecast Click for Burlington, Vermont Forecast
Bacteria and other microbes have been central to the rapid development of our understanding of both biochemistry and molecular biology, and I predict that they will prove to be of similar importance in helping us better understand the fundamental principles of ecology as well.

- Val H. Smith -

10 really poor excuses for having a child/more children

  1. We really like babies/want the experience of having a baby (that is, babies don't stay babies forever)
  2. We come from big families
  3. We are too ignorant/lazy/horny to use birth control
  4. We want to get it all over with as soon/fast as possible
  5. We are trying for a boy/girl this time
  6. We already own all of the stuff
  7. We never really think about it
  8. We don't want our child to be an only child/lonely
  9. Our parents want grandchildren/more grandchildren
  10. Everybody else is doing it

10 really good excuses for having a child/more children

  1. We want to increase the political power of our race/ethnic group/religion/family
  2. We want to maximize our family's exploitation of the world's resources
  3. We want to constrain the reproductive choices of others
  4. We are into habitat destruction
  5. We don't "believe" in evolution/ecology/environmentalism (Malthus, what?)
  6. We honestly believe that the world still doesn't have enough people (6 billion and still increasing as of October 12, 1999)
  7. If we don't, somebody else will
  8. Might makes right
  9. Hey, it's a free country
  10. We really don't care
- Nodeba Bob -
If we could shrink the world's population to a village of 100 people, maintaining all the existing ratios, the village would look like this: 57 Asians, 21 Europeans, 14 from the western hemisphere (North, Central and South America) and 8 Africans. Seventy of the 100 would be nonwhite. Seventy would be non-Christian. Six people would control 50% of the world's wealth and all of them would be citizens of the U.S. Seventy people would be unable to read, more than half would suffer from malnutrition and 80 would live in substandard housing. Only 1 of the 100 would have attended college. Some believe we do not inherit our land from ancestors but borrow it from our children. What we leave them will be determined by an increasing population and the calendar. Our failure to solve the population problem will no longer be a fault; it will be a judgment.

- Val H. Smith -
The process of life is to question how you live it. Nobody takes the time to do things right.

- Yvon Chouinard -
Acquisition without commitment is the primary enabler of over-consumptive materialism, which in turn is the root of our affluence-driven, throw-away-society, over-exploitation of Earth's non-renewable resources.

- Nodeba Bob -
We do not know exactly how language might have emerged in one local population of H. sapiens, although linguists have speculated widely. But we do know that a creature armed with symbolic skills is a formidable competitor-and not necessarily an entirely rational one, as the rest of the living world, including H. neanderthalensis, has discovered to its cost.

- Ian Tattersall and Jay H. Matternes -
People rarely act without knowing why. We almost always have something to say about what we do--even if, as is usually the case, the explanation is inadequate and influenced more by ideology than by the truth.

- Ian Tattersall and Jay H. Matternes -
It is only since the 19th century that families have routinely seen more than two children survive to the next generation-otherwise there would have been a population explosion centuries ago. Large families are a recent, and temporary, anomaly. Small families reduce stress on the environment, benefit economies-and gain directly themselves... Ultimately, we have to construct a world in which we take no more from the environment than it can replace and put out no more pollution than it can adsorb.

- Malcom Potts -
Many of our major advances in science were based on an element of chance, such as the discovery of penicillin. From a statistical perspective, then, the greater the number of scientists working on diverse projects, the greater the chance of the important, unexpected discovery.

- Donald S. Dwyer -
How could one understand the intricate processes of life with experiments that examined only one phenomenon at a time?

- Manju M. Hingorani -
It isn't self-evident that mankind is really progressing, at a level deeper than machines, any more than it is that any of us is wiser than our parents.

- Pico Iyer -
It does not matter. No one knows.

- Thomas A. Edison -
(Edison, as he was dying, gave this answer when asked if he had ever thought about a life hereafter)
Peace, social justice and defense of the environment are a triad to pit against the imperial triad of war, economic exploitation and environmental exploitation.

- Jonathan Schell -
Engineers look at problems and try to find answers; biologists look at answers and try to find out what the problem was.

- Julian F. V. Vincent -
Haze won't distill.

- Randy E. Keith -

Contact Steve Abedon (microdude+@osu.edu) with suggestions, criticisms,
comments, or anything else that might help make this a better site.