Symbiology

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2006-03-13T06:06:00.000-05:00

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Technically Speaking: Alpha-Proteobacteria

2006-02-21T05:59:00.000-05:00

The evolution of Eukaryotes is thought to have resulted from several major symbiotic events. This technical document describes the alpha-proteobacteria as an important initial source of genetic diversity among eukarya, as described in the background of this article. Ancestral relatives of these germs are thought to have provided the original mitochondrion.

The alpha-proteobacteria are a highly intriguing group, being identified in Rickettsia and subcuticular bacteria, a poorly understood endosymbiont in marine invertebrates. Furthermore, alpha-proteobacteria are thought to be the cause of juvenile oyster disease (JOD).

So, the alpha-proteobacteria are thought to 1) have been the precursor to eukaryotic mitochondria, 2) are curious, poorly understood endosymbionts of at least one highly successful phylum of marine invertebrates, and 3) are causative agents of disease in both marine organisms and man. But, there's more. One diverse group of alpha-Proteobacteria are those belonging to the genus Wolbachia. This intracellular symbiont is known to occur among a wide array of arthropods, often affecting the reproductive fitness of their hosts. More on Wolbachia can be found here. There is much current research involving genome mapping of Wolbachia from a variety of hosts archived in massive databases.

Are these microbes providing us a modern picture of earliest evolutionary events from which life diversified? Are there any examples of alpha-proteobacteria that are not pathogenic/parasitic, but rather represent a symbiont in a commensal or mutually beneficial arrangement?

What Is Phoresy?

2006-02-19T13:13:00.000-05:00

Phoresy is a type of symbiosis in which one organism "uses" another for transportation. This example, is a rather disgusting one, in which a parasitic fly (the Torsalo Fly) utilizes other parasites (in this case a mosquito) to adhere its eggs to. Upon contacting its warm blooded meal, the mosquito, concerned only about its own well being, provides the attached parasites eggs to begin development.

This would appear as a highly co-evolved parasitism in that the vector is actually another parasite. The bot fly itself is a parasite during the larval stage of its life cycle. During the adult stage, however, it relies on another organism to fulfill its work in distributing its offspring.

More detail on this rather ugly human parasite is here, to which we credit the image above.

Google:Symbiosis

2006-02-16T09:42:00.000-05:00

On occasion, I run a Google search for "symbiosis" just to see what the latest biology on the web describes for the term. At the number one spot today came The Symbiosis Institute of Business Management, the link to which is not currently working. I just find it noteworthy that a Business Management school (its a .edu extension) would find the top slot for symbiosis! Can biology catch a break?

The apparent importance of symbiosis in business decisions notwithstanding, the #2 search return came back with this, an informative, if not very sexy, website for a biology curriculum: Kimball's Biology Pages. A brief perusal of the page shows Dr. Kimball's thorough understanding of symbiosis and its importance in modern applied science. He describes the three major types of symbiosis starting with mutualism and ending with parasitism. The page concludes with a brief speculation on how symbioses evolve. "It seems plausible that what begins as a parasitic relationship might over the course of time evolve into a mutualistic one as the two organisms evolve to minimize the damage to the host."

This process, he indicates, is supported by Kwang Jeons work with amoebae. This appears to be the current working model of the evolution of symbiosis and deserves much future discussion on this blog. The other important take away from this position is that it implies a "complex homeostasis" in symbioses, an area I devote a bit of attention to below.

The Jeon ameoba example suggests an energetic imbalance that is corrected by co-evolution. As a parasitic relationship, is the driving force, as Dr. Kimball asserts "the two organisms evolve to minimize the damage to the host"? This area is worth a closer look.

Image courtesy of the Center for Biological Sequence Analysis. No copyrights are known.

Its Backwards

2006-02-13T15:55:00.000-05:00

A clearcut example of making a posteriori hypotheses to fit a foregone conclusion.

Here I was under the assumption that the scientific method first requires hypotheses, and then observations, and then tests, results-conclusions, and then more reproducible tests of those conclusions. Is it fair to frame the hypotheses to fit a set of known conclusions?

The site linked to here has a series of hypotheses that are set after the fact, in an attempt to show the predictive nature of ID. While not specifically related to symbiosis, I found this approach intriguing in that it seems to reverse the scientific method. And yet, the ID proponents can't understand why their ideas do not fit within the mainstream scientific community.

The Applied Science of Symbiosis

2006-02-13T13:03:00.000-05:00

Happy Day After Darwin Day!

An interesting article from MSNBC published today regarding the conversion of biomass to fuel using gut bacteria from insects and cellulolytic fungi. This area holds alot of promise in reducing the costs of synthetic fermentation in my opinion.

Check it out.

The significant phrase "directed evolution" caught my attention....

Through a genetic modification known as directed evolution, Iogen has souped up fungus microbes so they spew copious amounts of digestive enzymes to break down straw into sugars. From there, a simple fermentation — which brewers have been doing for centuries — turns sugar into alcohol.

...as did the closing paragraphs.

At the California Institute of Technology, Jared Leadbetter is mining the guts of termites for possible tools to turn wood chips into ethanol. Leadbetter said there are some 200 microbes that live in termite bellies that help the household pest convert wood to energy.

Those microbes or their genetic material can be used to produce ethanol-making enzymes. So scientists at the Energy Department’s Joint Genome Institute in Walnut Creek, Calif., are now sequencing the microbe genes in hopes of finding a key to ethanol production.

“We have this idea that microbes are pests,” said Leadbetter, who has been studying termite guts for 15 years. “But most microbes are beneficial.”

Photo of worker termites courtesy of M. Potter, Univ. of Kentucky.

The Role of Symbiosis in Physiology and Evolution

2006-02-09T17:56:00.000-05:00

This link provides an overview of the types of symbioses and some of the players involved in their research. From the conference abstract...

A variety of new and exciting models of symbiotic associations have been developed to investigate symbiotic relationships among organisms, their role in physiology, and especially the evolution of the organisms involved. The association host/symbiotes creates a new biological unit, the symbiocosm, itself subject to natural selection.

Different types of association exist as demonstrated by six different models. The symbiotes can be outside (ectosymbiosis) or inside the host, in the intestine or in some invaginations of the integument (endosymbioses), or inside the cells (endocytobioses). In integrated symbioses the symbiote (a bacterium) is perfectly controlled by the host (location and number), and looklikes a new cell organelle, only transmitted to the progeny by the mother. In other cases the symbiote is not perfectly controlled and invades most cells (Wolbachia), but not the entire the host population.

In the Squid-Vibrio model (extracellular symbiosis), the bacterium is transmitted horizontally, or cyclically, and can be grown in vitro. The colonization of the luminous organ modifies processes of recognition and specificity. Another endosymbiosis is that seen among termites. The gut lumen harbours protozoa and/or bacteria. They help the digestion. Transmission is horizontal. A coevolution host/symbiotes is highly probable.

Among endocytobioses another model is a protozoan, the amoeba, living symbiotically with a bacterium. The formation of the symbiosis has been observed in the laboratory. The bacterium, which was originally a parasite, has coevolved with the host cell thereby becoming obligate and thus integrated. The role of symbiote in co-evolution is also spectacular with the Wolbachia model, a bacterium associated with many insects and other invertebrates.

The aphid model presents an integrated and obligate symbiosis. The changes of the symbiotic bacterium during symbiosis are spectacular, most notably the reduction of the genome, which has been recently sequenced.

A last model is a weevil (Coleoptera), where symbiosis is perfectly integrated, but surprinsingly not always obligate. Comparison of symbiotic and aposymbiotic strains that lack symbiotes allows an understanding of the exact role of symbiosis. The symbiocosm is there controlled by interactions of four different genomes: nuclear, mitochondrial and symbiotic (principal endocytobiotes and Wolbachia).

Symbioses appear as important factors in evolution. Consequently, symbiology must be recognized as an important field of Zoology, Botany and Genetics.

Fitting In

2006-01-20T02:25:00.000-05:00

Mimicry is one clear example of natural selection . Animals of all types fit in by camouflage. These maskings serve to trick predators and thus would appear to provide enhanced fitness. In the oceans, bioluminescence is often used as a means of fitting in with animals as they ascend at night to feed in the shallows. The moonlight from above is matched by the luminescent bacteria housed in tissues of a variety of pelagic invertebrates.

My personal favorite: the bobtailed squid, Euprymna scolopes. This creature uses symbiotic, bioluminescent bacteria housed in specialized organs, to shine downward upon predators looking up for an easy meal. These squid would appear defenseless: small, tender, and slow. The bacteria in these organs produce light that serves to hide the mollusk's silhouette against the moonlight, effectively camouflaging the host.

The molecular interactions between host and symbiont are of particular interest to scientists. The mechanisms of transmission from generation to generation of squid is also an area of intense research in addition to the host's developmental changes incurred from the association. Finally, the genome mapping of the symbiont is an active field.

Young Earth

2006-01-19T19:18:00.000-05:00

What was young earth like? What forces operated, what materials existed, and what combination of these provided the initiation of replication?

The thought struck me recently upon viewing a documentary about the moon and its influence on earth. The documentary described the young earth as a violently volcanic sphere in a desparate tug of war with the young moon. At the time, of course, the moon was closer to earth than it is now- the early stages of spiral extraction from earth's gravitational grip.

The moon had an influence of its own. Its tug on the earth, being as close as it was, was considerably greater than today and thus the tidal forces were much more extreme. Come to find out, there is a great deal of interest in the moon among those arguing for and against Intelligent Design.

Add these components together and we may hypothesize a young earth that was extremely energetic. There was little or no atmosphere to diffuse the intense solar radiation of a relatively young sun. There was the compression of matter still settling inward from earths original creation and its concurrent release of heat. There was the moons tug.

Extreme radiation from above. Extreme heat from beneath. And extremely high levels of dissolved minerals.

Is this where life first made entrance? What clues exist today that support the notion that life emerged in this hostile place? Why would the evolution of a mutualism be postulated as an important characteristic of young earth?

I have always been intrigued with extremophiles. Life's origin was at one time thought to have come about in a calm cesspool of delicate embrace. I find this concept absurd. Young earth was anything but delicate by our most contemporary assessments. We are finding more about this as we continue our pursuit of the mysteries of deep space. The youngest of material spheres seem to have this extreme component in common.

Biological Oceanography of Young Earth

Can we hypothesize that the young earth plausibly consisted of hydrologic characteristics that resembled hydrothermal vents, mid-ocean ridges, commonly around the sphere? And can we not also assume that a minimal atmosphere probably allowed a much higher intensity solar radiation to young earth's surface? Add now to these assumptions the following: that a more closely positioned moon had a greater gravitational effect on the ancient oceans?

Now imagine the collision of land and sea. Did that interface have the most opportunity to spawn the first replicating molecule? Would these fantastic energetic inputs not have a tremendous increase in the kinetics of the entire young earth system? Would this not also have a combined effect of adding the minerals of shallow seas, volcanic rifts and associated matter (H2S-based reductive environment), and UV radiation for good measure? Add to all of this a tidal force that acted to slosh around this chemical cocktail of briny nutrient. Such an assemblage would have made the spontaneity of a nucleoside more likely, would it not?

Nitrogen was plentiful, as it is today. Hydrogen, hah! More than enough to go around. But where was the oxygen?? This was an anaerobic young earth, O2 was lacking. We can't have DNA without it. What we would more plausibly have would have been akin to RNA genesis. Whatever the replicating molecule was at the time, it could have easily formed given the kinetics of this open system. And if this hypothesis of the young earth environment is anything close to being true, I would not be surprised to find the beginning of life itself. Perhaps, something even more primitive than stromatolites?

What? No ecology??

2006-01-09T20:19:00.000-05:00

http://www.arn.org/docs/positivecasefordesign.pdf

Being an amateur eco-physiologist, I found it intriguing that the case for ID involves neither ecology nor physiology.

Both of these are absolutely in the center of the case for adaptive radiation and systematic evolution. The understanding of symbioses have much to offer in the study of evolutionary biology.

Photo courtesy of: Wilhelm A. Bögershausen

Gut Flora

2006-01-09T19:01:00.000-05:00

http://www.msnbc.msn.com/id/10754238/site/newsweek/

Do we have symbiotic bacteria in humans? Definitely!!

In this current article, we see the benefit that microorganisms offer in terms of digestion. These bacteria play an important role in the digestion of foodstuffs, and as the article points out, may benefit us indirectly by warding off bacteria that are harmful.

This finding is not new, however. There are examples all over the natural world of bacteria aiding in digestion and it appears as though this is a common theme. The gut of higher organisms offers a well-regulated climate controlled environment, while the bugs offer a few enzymes that their hosts lack.

It would appear that the results are mutualistic.

ID vs. Darwin

2005-12-29T13:22:00.000-05:00

http://www.actionbioscience.org/evolution/nhmag.html

Symbiology In Architecture?

2005-12-29T02:09:00.000-05:00

http://www.contemplativemind.org/splinter.html

I found it interesting that the term symbiology would be used in modern architecture, but upon reflection it does make perfect sense. Architectural design, after all, involves humans living together, often with pets and so forth. But from building design to community design, the "study of organisms living together" must be central to planning I would think.

Credit Zook

2005-12-29T02:05:00.000-05:00

http://www.bu.edu/bridge/archive/2003/02-14/symbiol.htm

Upon reading this article, it occurred to me that Symbiology should be dedicated to Dr. Douglas Zook, for his emphasis on the need for its study. It was first mentioned much earlier, in truth, in Read CP 1970. Parasitism and Symbiology, Ronald Press Co., New York.

Of course, it is also necessary to credit Dr. Lynn Margulis as well, for her contributions to the field. And numerous others such as those who discovered and continue to explore hydrothermal vent communities, at great risk, and so on and so on.... http://www.botos.com/marine/vents01.html

I must also thank my professors throughout college who have given me insight and knowledge and a resolve for the truths of the natural world. This web log wouldn't have been possible without these.

Symbiosis and Complex Homeostasis

2005-12-28T09:07:00.000-05:00

http://www.winwenger.com/homstas.htm

In this article, Dr. Win Wenger describes the importance of balance in nature in complex homeostasis. He contends that once you understand basic systems behavior, you come to understand so much else about the natural world around you. Here he describes systems as being complexly homeostatic: that is, they are systems maintaining multiple equilibria at multiple levels. This is a concept seen in symbioses.

He emphasizes the importance of complex homeostasis for critical consideration in the field of medicine, describes direct applications for it, and details how important systems education is early on in its understanding. This is also a call of the wild for scientists working in a variety of areas to consider how complexly homeostatic their own problem is. I contend that Symbiology is worthy of this consideration under the merits I've previously described, in addition to justifications yet to come. This is merely a budding field after all.

If one assumes that symbioses always involve a sharing of at least one resource (food or space in time), then the host and its guest must make coordinated accomodations of balance in order to maintain a close association with each other. Otherwise, one has competed only to be competed against later, as seen in the Prisoners Dilemma. Under this simple homeostatic model, an equilibrium is reached as we've seen. "Tit-for-tat" is operating in symbioses, from parasites to mutualisms.

In real life, symbioses are complexly homeostatic. For simplicities sake, I will assume them to be simple homeostatic, unless specifying otherwise in the case of examples. Here I am dealing with symbiology and thus, organisms living closely together and assuming to share at least one resource, making the math models easier to understand.

Other Dr. Win Wenger works are here...
http://www.winwenger.com/winwin.htm Win-Win/ Incentive Equilibrium Analysis
http://www.winwenger.com/string.htm In String Theory
http://www.winwenger.com/ideagen.htm Idea Generator

Prisoner's Dilemma, The Game

2005-12-24T10:25:00.000-05:00

Prisoner's Dilemma, The Game

http://serendip.brynmawr.edu/playground/pd.html

This "game" is a fun exercise in homeostatic mechanisms. When the option of compete/cooperate is given, select variants of each and assume each variant to represent an individual "symbiont" strategy for survival and Serendip as the "host". You are both attempting to compete for a limiting supply of resources (coins). The host and symbiont (you) are bound to cooperative balance, but neither option is necessarily preferable, in theory. In fact, when you try to trick Seredip, you always end up getting spited.

This is a model feedback loop. Zero is never reached, but as either opponent attempts to capitalize, they find they are returned the favor. There is a feedback to your moves, in that your opponent is "conditioned" to adjust accordingly. The thermostat model is an everyday example here: http://physioweb.med.uvm.edu/homeostasis/simple.htm

Understanding symbiology requires a general understanding of feedback loops.