New Toxic-Site Cleanup Agent: A Bacterium That Gobbles Up Poison

[goforit]

New York Times
<http://www.nytimes.com/2003/10/19/nyregion/19BUGS.html>

The New Toxic-Site Cleanup Agent: A Bacterium That Gobbles Up Poison
By JONATHAN MILLER

Published: October 19, 2003


FAIRFIELD, N.J. — The Caldwell Trucking Superfund site, a few miles west of the Willowbrook Mall, is a nine-acre repository of poison-laced sewage, hauled here and dumped until the 1970's, when the threat of drinking-water contamination was recognized.

About 50 private wells and two public wells had to be shut down, and even more drinking water was threatened as contamination spread toward the Passaic River. The contamination has now mostly been contained, but the latest cleanup stage has progressed fitfully at best.
<snip>
By all accounts, the use of the half-micron-long bacterium with the official name Dehalococcoides ethenogenes has been a success. Technically, the bacterium — a few thousand could fit on the head of a pin — ingests the toxic chemicals the way that people breathe oxygen.

"It looks like the process is really working," said Tom Porucznik, remedial project manager for the E.P.A. The agency will be looking at more results throughout the fall, and will likely decide sometime in the spring whether to continue with the treatment.

The bacterium was discovered in 1997 by a team of scientists at Cornell University. They found that it had a strange natural affinity for devouring dangerous industrial chemicals like the one found at Caldwell Trucking — trichlorethylene, or TCE, which was often used as a heavy cleaner and is suspected of being a carcinogen. The bacteria have an unusual cell wall, and are tiny even by bacterial standards. "They're really weird organisms," said Dr. Stephen H. Zinder, the chairman of the microbiology department at Cornell University.

Using the "bugs" — as both he and others refer to D. ethenogenes — is a vast improvement over the pump-and-treat method, a tactic used at many polluted sites that essentially pumps water to the surface in the hope of removing contamination.

(con't)..............

A :toast: too those whom still care for our environment!!

[bicentennial_baby]

1. Bioremediation is great!

It's really the wave of the future! Did you know they discovered a bacterium that eats TNT?

[goforit]

2. WOW!!!..........TNT??

This is just so remarkable!!!

If only we could clean up nuclear wastes as well or at least
reducing the half life of radiation.

[bicentennial_baby]

3. Yep, here's a little blurb from MIT

"At Cambridge, Dr John Archer and his research group have already done preliminary work on the biology of Rhodococcus - a bug that is already being used by companies to manufacture other drugs, including the contraceptive pill. "It's a fascinating bacterium that originally evolved to eat the trees that died and lay rotting in prehistoric swamps," Dr Archer says. "Today, it's one of nature's dustbins. It eats a vast array of complex molecules, recycling them in the environment. It can do this because it's equipped with a huge library of different enzymes - the molecular equivalent of a Swiss army knife - that helps it eat fuel, carcinogens (cancer-causing chemicals) like benzene, and even explosives like TNT"

http://web.mit.edu/cmi/media/cmi-011101-rhodococcus.html

[DUreader]

4. Need to feed it MTBE

[treepig]

11. if people wouldn't be so paranoid,

and reflexively block any attemp to clean up nuclear wastes, there'd be no problem. the technology exists to dramatically reduce the half life of radioactive wastes - ok, not by bioremediation, but by lasers:

Giant laser transmutes nuclear waste

A giant laser has cut the lifetime of a speck of radioactive waste from millions of years to just minutes. The feat raises hopes that a solution to nuclear power's biggest drawback - its waste - might one day be possible.

"It is not going to solve the waste problem completely, but it reduces toxicity by a factor of 100. That's an attractive proposition," says Ken Ledingham, at the University of Strathclyde in Glasgow, who led the British and German research team.

The transmutation was performed using the Vulcan laser, which is the size of a small hotel and housed at the Rutherford Appleton Laboratory in Oxfordshire. About a million atoms of iodine-129 were transformed into iodine-128. The half-life of iodine-129 is 15.7 million years, meaning it remains radioactive for an extremely long time. In contrast, the half-life of iodine-128 is just 25 minutes.

Iodine-129 is one of the many radioactive isotopes created when uranium is burnt in a reactor. Currently they all have to be discharged, stored or disposed of by the nuclear industry.


http://portland.indymedia.org/en/2003/08/269992.shtml

[diamond14]

14. Funded by tony blair's BNFL...the ENRON of nuclear business..

"BNFL....a British Company in USA...the "ENRON" of nuclear business"

Collecting billions of dollars in American taxpayers money every year, BNFL (a British corporation) doesn't seem to ever get any real work done on nuclear waste, endangers American citizens health and safety, falsifies data, and after collecting billions, just take the money and walk away, frequently leaving a much more dangerous situation for others to take care of....the ENRON of nuclear business... what follows is just a few examples of BNFL work, and that WE THE PEOPLE of the United States of America, continue to award BNFL billions of dollars annual is beyond my comprehension....
although it may be time for some YOUNG ambitious reporter to connect the dots here to the blair/bush Iraqi war, because there are so many dots there....

http://www.wise-paris.org/index.html?/english/ournewsletter/17_18/contents.html&/english/frame/menu.html&/english/frame/band.html

What a Waste BNFL: Privatization Bye, Bye...?

-snip-
The story is unusual, to say the least. The only other case, one can recall, is the falsification of welding x-rays in certain French nuclear power plants years ago. When the UK Nuclear Installations Inspectorate (NII) published its damning report on "MOX fuel data falsification at BNFL, Sellafield", on 18 February 2000, the story had been around for a few months, but few expected such a harsh and unusual judgment by the safety authorities: "In particular, the deficiencies found in the quality checking process will have to be rectified, the management of the plant improved and operators either replaced or retrained to bring the safety culture in the plant up to standard the Health and Safety Executive (HSE) requires for a nuclear installation". In the meantime the incriminated plant remains shut down.

http://archive.greenpeace.org/pressreleases/nucreprocess/1999dec23.html

-snip-
BNFL PLUTONIUM FUEL SCANDAL EXTENDS TO SWITZERLAND Swiss Safety Authorities Confirm to Greenpeace that Damaged Fuel was Rejected 23 December 1999 AMSTERDAM -- The plutonium nuclear fuel scandal that destroyed British Nuclear Fuel's (BNFL) plutonium business in Japan in recent months also extends to fuel used in a Swiss reactor in 1996, Greenpeace has discovered. Swiss authorities revealed to Greenpeace that the BNFL plutonium fuel used in the Beznau power plant in northern Switzerland, and operated by the NOK utility, was removed in 1997 when it was found to be damaged and leaking radiation after only one year.

http://www.ananuclear.org/bnfl.htm

-snip-
We urge you to join us in asking DOE to debar BNFL from holding any contracts to do work at the nuclear weapons complex. We presented a petition to DOE on March 23, signed by 47 groups, asking Secretary Richardson to debar and/or suspend BNFL from any contracts (transmittal letter enclosed). Our groups, and many others, are concerned about BNFL's corporate behavior, which includes falsification of plutonium fuel rod data and massive contamination of the Irish Sea. Already other nations have suspended contracts with BNFL and the US should as well. DOE is conducting an in-depth probe of BNFL's contracts in light of the worldwide scandals regarding its' falsification of data. DOE also has canceled the plutonium incinerator that BNFL was scheduled to build at the Idaho National Engineering and Environmental Lab, after concerns were raised about downwind pollution and BNFL's abysmal environmental track record. BNFL holds major contracts at the Oak Ridge, TN facility and the Hanford, WA site, both of which have already experienced problems and raised serious concerns about BNFL's credibility.

http://www.usbusiness-review.com/0209/08.html

-snip-

BNFL Inc. is part of a large British company, but in the United States it has a specialized niche in decommissioning and demolishing former nuclear energy sites, radioactive waste management and nuclear facility operations. –Kevin M. McCarthy ..........-snip- Miskimin says the environmental management business contracts with the DOE are a $6 billion a year market, and BNFL is working contracts in Oak Ridge, Tenn., Aiken, S.C., and Idaho Falls, Idaho, along with Rocky Flats, Colo., and Hanford, Wash. “We do both classified and unclassified work,” Miskimin says.

http://www.acfonline.org.au/docs/publications/rpt0021.pdf

-snip- (page 9 of 24 pages pdf file)
In 1998 BNFL (a subsidiary of British Nuclear Fuels) was appointed to supervise the cleanup of the contamination legacy . It was hired for its supposed expertise in "glassifying" nuclear waste, a technique by which the waste is dried, combined with moltern glass and then poured into steel. In 2000, BLFL's contract was terminated - after an announcement that its expected costs would rise to $15.2 billion, up from $6.9 billion in 1998. shrub, busy discussing hydrogen cars at the Department of Energy (DOE),while massive waste, fraud and abuse by BNFL occurs on shrub's watchon DOE regulated nuclear sites....

http://www.energy.gov/


BNFL makes Haliburton scandals look like chicken feed....

[tlcandie]

5. Wow!! Great news... thanks!!!!

:bounce: :bounce:

We need all the help we can get!!

[DemBones DemBones]

6. Bioremediation has great promise. I do hope that this project is

being carefully monitored to guard against the unexpected, such as mutations causing the Dehalococcoides ethenogenes to start feeding on something we don't want them feeding on. When applied science goes awry, it does so in the follow-through.


"To those who may wonder about replacing poisons with bacteria in groundwater, officials and scientists say that thus far they see no ill effects. David W. Major, a scientist for GeoSyntec, a company that produces a widely used strain of the bacteria used at the site, said that once the feeding of D. ethenogenes stops, the organism simply dies, with little impact on the environment. Still, Dr. Zinder of Cornell, who along with James M. Gossett discovered the organism, said that unintended consequences were always a possibility.

"I'd say, you never know for sure, which makes people nervous," he said, "but I think as technologies go, I wouldn't consider these pathogens. There's just no evidence."

[diamond14]

8. bioremediation is extremely dangerous...chemists find

the 'unintended consequences', but the biologists don't care, and the EPA won't regulated any NEW chemicals, so we just sit and wait...there will ALWAYS be (and always have been) lots of long-term consequences...the long-term consequences are simply ignored, and cancers, teratogenic, mutagenic effects take a long time to document and can be easily disputed in courts of law (those cigarettes didn't cause cancer....)....these projects should be banned and these companies force to clean-up using the MORE EXPENSIVE and traditional methods the we KNOW work...

[treepig]

10. why are you so terrified of nature?

there are naturally-occurring bacterial genes that convert naphthalene, a major component of crude oil spills, shown on the left:



into pyruvate and acetaldehyde (two compounds that are abundant in your cells!), shown on the right. what can be bad about this strategy?

more information on the bioremediation of oil spills at:

http://www.cas.muohio.edu/~wilsonkg/groups/grp9/Degradation_of_Crude_Oil/degradation_of_crude_oil.htm

[diamond14]

12. not terrified at all, just providing info because I am a CHEMIST...

people need to know about the serious and toxic 'un-intended' consequences of bioremediation, before they embrace big corporations latest FAD in CHEAP and horrifying environmental clean-ups...(and honest scientists know that these 'researchers' are being paid by corporations to come up with the corporate line, and have HUGE conflicts of interest, and their work needs to be reviewed better, and accepted to respectable journals)...

Remember lots of other failed environmental clean-up scams that ended up costing taxpayers piles of money and lives....Love Canal was one (cleaned-up chemicals, capped, and then houses built on top)...how about MTBE??? the ultimate 'un-intended consequence'....it's taken years now to get that chemical on a 'list' to regulate, because it was originally tauted by special interests as the HUGE cheap solution to air pollution, now massively polluting air, and soils over all the country, because it won't degrade and is toxic....

your arguments are typical corporate shilling, like "Arsenic -it's essential to human life"....and sadly...it took tons of time and money to defeat that shrub* ARSENIC theatre...NOW, we get your arguments...oh my, you found TWO chemicals 'abundant?' in human cells...what about the MILLIONS more chemicals formed???? ignore those, don't mention those, and maybe you'll get away with your CHEAP clean-up, and litigate the dead bodies away...

BTW...your chemistry it totally un-balanced in your equations...you are missing a whole lot of carbons, hydrogens, etc. in your final structures' end-product...what kind of chemistry mis-representation is that????!!! your chemical structures would get an "F" in introductory Organic Chemistry....for example, you show 10 Carbons at the beginning of your equation, 7 Carbons in the middle, and then 9 Carbons at the end...and then you argue that there's no other chemicals here !!! nothing here to see folks, move on...it's the shrub disappearing toxic chemicals act, carbons just magically appear and disappear for no reason at all, in treepigs chemistry drawing...like shrub just announced "no more analysis for Dioxins' in sewage sludge...no analyses, no problem...


the shrub approach: distort real science by suggesting that CHEMISTS are 'afraid of nature'...and slam reality by saying 'what can be bad about this strategy?' when you can't even balance your equations (the first skill you must learn in both chemistry and math is to BALANCE the numbers in each part of the equations), and any CHEMIST can see quickly what is BAD ABOUT YOUR STRATEGY....it seems that you learn the 'rush limbaugh' approach to distortion, with application of same approach to science...distort, distract, demolish science...and of course, you will soon be attacking the messenger in order to destroy the message...sad, real sad...

[treepig]

13. did you even have a look at the link i provided?

if you did, you would have seen that the first "step" shown actually involves the action of 6 gene products, and the second "step" requires 5. links within the link i provided give many more details; perhaps your time would have been better spent consulting that information than writing your nonsensical tirade?

in any event, the following paper provides chemical structures of many of the intermediates between naphthalene (and other polyaromatic compounds) and the endproducts (which are common metabolites in human cells) i previously showed:

Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria.

Habe H, Omori T.

Biosci Biotechnol Biochem. 2003 Feb;67(2):225-43.

http://www.jstage.jst.go.jp/article/bbb/67/2/225/_pdf

where you come up with "millions of chemicals" is anybody's guess. and how listing the horrors of the activities of the chemical industry (love canal, mbte, etc) is supposed to reflect badly on bioremediation efforts to solve these problems is also difficult to fathom.

oh well, at least you were upfront about your motivation - you're a CHEMIST - therefore you want to stick with the tried and true (and mostly ineffective) chemical methods to clean up the environment. and co-incidently provide yourself with employment. if you want to get a balance picture of bioremediation efforts, i suggest you go to the nih's PUBMED search engine, at

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed

and type in "bioremediation" and scan through the affiliations of the authors of the research papers. basically none of these people work for monsanto or dow - instead (compared to many other areas of science) you'll find researchers in "second world" countries such as portugal, israel, poland, ireland, singapore (etc) highly represented. in a few years they'll have developed commercial technologies for cleaning up the environment, and we'll be sitting here in the usa scratching our heads trying to figure out why all the jobs are going overseas. well, i submit that attitudes such as yours are one big reason.

[diamond14]

15. yes, I read the whole thing...didn't change my mind one bit...however

I noticed now your ATTACK THE MESSENGER approach...the rush limbaugh/bush/KKKarl rove approach....which I predicted would be coming in my previous scientific reply....

instead of explaining why you can't balance a 'simple' chemistry equation....

-you carefully imply that I haven't read the paper.

-you tell me how to spend my time, and outright call my remarks about your un-balanced chemical equations 'nonsensical tirade' (so I suppose NOW that you called it 'nonsensical tirade, that your chemical reactions are now balanced????, and of course, even with 6 gene products, you forget to mention that is ONLY the second course in Organic Chemistry...still real simple to show balanced equations, especially since you're claiming to show chemicals in the HUMAN BODY, a complex piece of chemistry)

-claiming that I am trying to make money here...and that TRIED AND TRUE chemistry methods should NOT be used...guess what!!! I am making no money here, and TRIED AND TRUE is exactly that, more expensive than corporate shilling FAD stuff, but still TRIED AND TRUE and I'll take it anytime....to prevent un-intended consequences and dead bodies of children, go with the TRIED AND TRUE METHODS,,,


this message is brought to DU readers by the CHEMIST....making people honest with analytical chemistry...

if shrub had his way, there would be NO chemical analyses...
no analyses, no notice, see, it all goes away, no problem...
it' magic...

CHEMISTS...not afraid of nature...able to turn solids to liquids, liquids to gases, gases to solids, liquids to solids, and solids to gases....cool...not afraid of ANYTHING....

[treepig]

16. yup, you're sure keeping me honest with your analytical chemistry

but, i suspect that your expose is largely wasted as i doubt that anyone except yourself mistook the chemical reaction outlined in my first post as being a stochiometrically balanced equation.

anyhow, since you're making a big deal of it, here's the whole pathway:






to go from catechol to pyruvate and acetylaldehyde, please consult this page:

http://umbbd.ahc.umn.edu:8015/umbbd/servlet/dpage?max_rows=0&reacID=r0307


btw, lots of biodegradation pathways are shown here:

http://umbbd.ahc.umn.edu/index.html

and yes, the endproducts of this biodegradation reaction, despite your skeptiscism really are common metabolic intermediates, check out the central role of pyruvate in your cells:

[diamond14]

20. sorry, still an 'F' for intro Organic Chemistry...there are major

problems here....

first...still there is no balance in your structures...you are still missing carbons and gaining carbons and failing to account for that..

second...each time you open up a ring structure, you are creating chiral carbons, which are in ISOMERS...and each isomer is a separate compound that will react differently than other isomers...you show a cis-isomeric structure for cis-1,2-dihydroxy-1,2-dihydronaphthalene, but fail to account for the trans- configuration (and at least 8 other related isomers)...are these just more bush* magic disappearing chemicals???? throughout your entire presention, there is a complete lack of accounting for isomers, and sadly, the few shown fail to account for all isomeric terms (it's more than -cis and -trans, or as you show, only -cis...with -trans magically gone...)

third, your original article listed a variety of "classes" of chemical compounds in oil, yet now, you only show a reaction for ONE chemical, as if NO OTHERS CHEMICALS REACT with your FAD treatment...every single other chemical reacts too...so you get many many more chemical reactions than you are showing...AND soils are chemicals, and how exactly does the chemicals in YOUR chosen water/wastewater/soil system react with the naphthalene and other toxic chemicals in question here, and react at each separate step where you are forming more chemical structures...nature is not ONE chemical reacting ONCE with ONE reaction at ONE time alone...nature is a very complex series of reactions and you show here a complete lack of understanding...

fourth....the posting of a small bit of reactions that occur in the human body is simply a typical rush/bush-diversion from the issues at hand...as I noted earlier, Arsenic is essential to human life, but that doesn't mean that it's OK to add lots to humans and KILL them...and aren't you acting a little condescending by trying to put up those human-body reactions, to teach ME?. I am a CHEMIST and I already know the reactions of the human body, and have University degrees in CHEMISTRY to prove it....so cut out the distractions. The only reactions important to this discussion are the few you improperly show on the top of your post...so now that tried ATTACKING ME...you move on to suggest that MY QUALIFICATIONS are lacking ....rush/bush tactics again...if you don't know your science just resort to rush/bush destruction techniques...

however, you could learn more from the BIGGER terminology for isomers shown in the human body reactions...the D-Lactaldehyde and (R)-S-Lactoylglutathione show some very imporant isomeric identification systems (the D, R, and S in the prefixes)...these terms should also be added to YOUR chemical structures, along with properly balancing the stochiometry and accounting for all the other chemical structures in the water/soil/wastewater system that you intend to conduct these reaction in.....

and your poor showing here simply bolsters my point: the reactions can have un-intended consequences, and we don't know what those might be until diseases and defects show up many years from now..this bioremediation stuff is a cheap FAD that has been around for many years and is DANGEROUS...each time polluters try to push it on the public (because it's cheap), we have to go around again on the same issues...yes, remediation is expensive...let's keep polluters from sliming out using cheap FADS that don't work...

I still recommend the more expensive TRIED AND TRUE solutions....counting birth defects, cancers and deformities is not a good way to evaluated a FAD solution...it simply passes the costs to those who pay with their lives and livelyhoods and children, and ultimately to the taxpayers......

[DrWeird]

25. You're a chemist?

Or did you get a BA in chemistry back in the fifties and now teach science to bored junior high school students?

Because anybody actively involved in real chemistry isn't going to make presentation in chemdraw with proper stereochemistry and then figure out a way to post in on a discussion board. And no organic chemist ever is going to balance a reaction. Especially a multistep biochemical pathway. Shame on you for pretending treepig did anything less than A work in this thread.

Btw, treepig, you would have gotten an A in my O-chem class.

[kodi]

28. i'm a chemist (phd) too & am worried about mutations in those bacterias

which could wind up digesting things no one ever thought about. while i understand that the mitigating circumstance of the reaction mechanism might be stereospecificity, if the bugs are digesting chlorinated alkyls, then i figure they could also devour fluoronated alkyls too, like teflon type polymers.

no one thought that a useful chemical like benzidene was harmful for generations, but it killed thousands from cancers.

btw thanks for refresher on the woodward-hoffman rules

[DrWeird]

43. Well sure, I can understand

that something like this needs significant testing. But that's hardly what this discussion has evolved into. Btw, I only followed treepig as far as the degradation of napthalene, anything that degrades PAHs to metabolites sure looks interesting to me. I didn't see anything about digesting chlorinated alkyls.

Woodward-Hoffman rules? Wtf?

[diamond14]

48. LOL, waking up to the remark about the 'Woodward-Hoffman'

rules, are you now???...hahahahahahaha...it's a joke...a joke that takes a chemistry education to really appreciate....I laughed out loud (LOL) when I first saw it...it's the funniest remark I've heard in months...


for non-chemist DUers, chemical reactions must follow these rules, and Woodward and Hoffman won a Nobel Prize in Chemistry for determining these rules under which chemical reactions occur...which is why I asked for the correct chemical structures to be drawn here...

[DrWeird]

55. Umm, are you posting both as Kodi and Amen1234?

Because if Kodi has his PhD in chemistry, I'm sure he can tell you that the Woodward-Hoffman rules only apply to concerted pericyclic reactions and have nothing to do with this discussion.

[treepig]

44. there is a dramatic difference between fluorinated and chlorinated

alkyls (or other bio-molecules).

fluorinated compounds are ubiquitously used as enzyme inhibitors - since the carbon-fluoride bond is (apparently) almost impossible for enzymes to cleave (although their are efforts underway to engineer catalytic antibodies for this task). typically, when a new enzyme inhibitor is required, the first strategy is to take the natural metabolic substate for the enzyme, and replace one or more OH or H's with a F.

by contrast, chlorinated (or brominated) compounds are common in nature, and can be both synthesized and degraded enzymatically.

[treepig]

26. you seem to lack a basic understanding of metabolic reactions

that are catalyzed by a series of enzymes.

sure if you, as a chemist, tried to produce the stereospecific reactions in this pathway, you'd end up with 8 (or how ever many) enantiomers at many of the steps shown. but enzymes have the capacity to specifically generate only one of many possible chiral configurations. there are a host of such reactions synthesized by enzymes - testosterone is one such molecule:



when the body makes testosterone, according to your analysis, you'd get hundreds of different chemical products (if each isomer at each stereocenter was made). but the enzymes in metabolic pathways that make these complex molecules don't suffer from the limitations that you, as a chemist, do.

also, the enzymes that make up these pathways are typically located in close physical proximity to each other so that the product of one reaction is immediately transferred to the next enzyme, and so on. therefore, the whole process is highly efficient at converting one starting molecule to a small number of products while avoiding all the side reactions experienced by chemical synthetic schemes.

all in all, you seem to have nicely pointed out just why chemistry-based decontamination methods don't work so well. in reality, metabolism-based bioremediation methods exactly avoid the problems you are harping on.

[diamond14]

31. so NOW, you can draw stereospecific reactions....and before,

Dr. Weird gave you an "A" for NOT BEING ABLE TO DRAW stereospecific reactions...even claiming that it's not done at all, coupled with another claim that ALL organic chemists don't balance their reactions...which surprises me because that has not been my experience...

and 'Testosterone'...one of my favorite molecules...shown drawn and posted on DU in the correct stereospecific configuration....spectacular...

you just blew your great big "A" and confirmed why you got an "F" from me, and ruined Dr.Weird's claim that you couldn't do it....also, trying to debate science by simply insulting other chemists is abysmal....it is the reTHUGlican, rovian/bush/limbaugh approach, which suggests that you have nothing to justify your claims...

and no, I do not have a B.A. in chemistry from 1950...and I have never taught school...lots of chemists do not teach, and having a 1950 vintage degree doesn't make you ignorant of chemical reactions, most senior chemists do draw molecules sterospecifically correct and balance equations, and a B.A. is an acceptable degree too, and real chemists have great respect for teachers at all levels...in my case, I am a working CHEMIST, with a B.S. in Chemistry (1971) from the University of Michigan with 44 hours in Chemistry, a minor in Math (16 hours) and a minor in Physics (16 hours) and an M.S. in Chemistry from the University of Colorado (1990) (an additional 32 graduate credit hours in Chemistry) with my thesis on the formation and chemical reactions of humic structures, the organic materials in soils, sediments and water (includes a nice section on enzymatic breaking of bonds in cellulose, hemicelluloses, and lignins under both anaerobic and aerobic conditions...and exactly which enzymes will break which bonds)...

In addition, your big headline accusing me AGAIN of lacking basic chemistry understanding is not appreciated and does not further your arguments....

now, if you would go back and post your original chemical reactions with your newly found skill for drawing correct stereoisomeric configurations, and balance the equations, so as not to deceive DU readers about science....when you get all done that, we can talk about the science involved in your claims....I'll wait...

[treepig]

32. basically, you confirm my point

that you lack of basic understanding of metabolic reactions (where did i ever say you lack basic chemistry understanding? what i don't appreciate is blatant mis-representation of what i wrote).

chemistry done by a cell is quite different than chemistry done by an organic synthetic chemist. for a specific input (such as naphthalene) into a pathway, you have a specific output. for a different specific input, you have a different specific sequence of enzymatically-catalyzed reactions - in some cases leading to the same output while in other cases a different output may be experienced. at no point do you have "millions" of chemical species formed.

furthermore, perhaps you've heard of oxidative metabolism? cells are great at adding oxygen's to hydrophobic molecules (once again, such as naphthalene) to make them more compatible with the intracellular milleau - i provided links that provide details of each reaction in the naphthalene-degradation sequence shown -i don't suppose most readers of this thread are all that interested in the details, but they're there if you look for them (which you seem incapable of doing).

i doubt that continuing this discussion is at all productive, and i suppose i'll have to just be satisfied to remain baffled as to why you're apparently happy to have chemists try to "remediate" toxins (and do so very poorly) while you're paranoid at allowing bacteria do it quite well - factoid: 90% of the exxon valdez oil spill was cleaned-up via bioremediation methods!

[diamond14]

33. IMO, the reason you are simply flinging insults at me....

is that NOW, that you are caught, having shown that you can draw stereoisomers...NOW, you simply won't draw your original molecules with stereoisomeric configurations, because then we could talk about it and I certainly would show you even more of the errors in your claims....

it amazes me how just in one post, you fling out all of this at me:

-that chemists remediate toxins very poorly
-that I lack basic understanding of metabolic reactions
-that I seem incapable of looking at details of chemical reactions
-that you no longer find this discussion at all productive (especially since you are showing improper structures and balancing of the carbons...9,6 or 8 carbons???, the totally unexplained disappearing and re-appearing carbons)

and I will repeat my very simple request...please draw the chemical reactions in your original structures, as balanced and stereochemically correct equations, and then, I will be please to show you the error of your claims...

somehow, based on your responses and discussion, I have a feeling that you have no degree in chemistry at all...I usually sense when I am speaking with someone educated in my profession...if you have no chemistry degree, then upon completion of your corrections, I will also be pleased to explain your errors in a simplier approach that can be understood by someone lacking chemistry education...

on edit: metabolic reactions are indeed chemical reactions...these "reactions" are reactions between molecules....it's real chemistry...bioorganic chemistry is the chemical approach to enzyme action...and as I noted in my graduate thesis....I take my enzymes seriously...my favorite Nobel Prize winners in Chemistry (1987) are Cram, Lehn and Pederson, all pioneers in this field...

[treepig]

38. ok, i'll type very slowly, perhaps that will help

as i've stated many times, details of the metabolic pathways can be found in the links i provided (i do not know how to draw chemical structures in html).

once again, go to the link:

http://umbbd.ahc.umn.edu/naph/naph_map.html

you will see that the first step of the naphthalene degradation pathway is degradation of naphthalene to cis-1,2-Dihydroxy-1,2-dihydro-naphthalene. i.e.,



to



occurs by the action of the enzyme "naphthalene 1,2-dioxygenase"

furthermore, if you click on the enzyme, you get the information you've been deliberately and wrongly claiming doesn't exist - namely, the "missing" chemical structures. in this case, the reaction requires the input of O2, H+, and NADH (and produces NAD+ in addition to the cis-1,2-Dihydroxy-1,2-dihydro-naphthalene).

Now if you add up the inputs

Naphthalene is composed of: 10 carbon atoms + 8 hydrogen atoms
Plus, the cell supplies: 2 oxygen atoms + H+ + NADH


These inputs exactly balance the outputs:

cis-1,2-Dihydroxy-1,2-dihydro-naphthalene is composed of: 10 carbon atoms + 10 hydrogen atoms + 2 oxygen atoms (with NAD+ returned to the metabolic networks of the cell to be regenerated into NADH).

similar information is easily accessed for each and every step of the naphthalene degradation pathway at the link i provided.

note that this information is provided by:



(god, how did rove/bush/bfee/haliburton infiltrate this multicontinental consortium?)

[diamond14]

40. you left out 'pyruvate and acetaldehyde' , which was your whole

point....your claims were that this bio-FAD created just 'pyruvate and acetaldehyde', harmless chemicals that exist all over in human bodies.....

why not tell DUers what 'chemistry education' you have???

[treepig]

42. umm . . . hello reading comprehension?

i provided details of the first step in post #38

i also provided you with the link to find similarly detailed information for the subsequent 10 steps needed to get to pyruvate and acetylaldehyde.

also, i took chemisty in grade 10, that's all i needed to learn that pyruvate is an integral part of cellular metabolism

ever hear of the "krebs cycle" - perhaps the most well known of all cellular metabolic pathways?

[diamond14]

45. you took chemistry in grade 10...well, that about sums up the

bio-FADS....

btw, I like that you can grab chemistry diagrams off university web sites..but somehow, on this one...you missed part of it...the Krebs cycle is what happens when you BREATHE....and in this diagram, it shows the CO2 (carbon dioxide) coming out...but forgot to paste in the part where the O2 (oxygen) goes into your lungs...

For non-chemist DUers, this is why you don't want someone with a 10th grade chemistry education creating the latest bio-FAD nightmare on environmental clean-up sites....

[DrWeird]

46. His grade ten education...

Is clearly better than what you've got. I've seen plenty of citric acid cycle diagrams and not one of them involves lungs or oxygen. Probably because neither of them is involved in the Kreb's cycle. But if you were a scientist, you probably would have known that.

[treepig]

47. i'm happy to give the complete picture

but it's a bit difficult to see the exact chemical structures, and ensure that each equation is stoichimetrically correct:



(that's why i gave the simplified version, but the whole chart shows the central role of pyruvate even more clearly - it's just above the red circular arrows)

[diamond14]

51. hahahahaha...you just didn't know that the oxygen is THE critical

molecule in the Krebs cycle...because the Krebs cycle describes the BREATHING of human beings...like your other disappearing/reappearing chemicals...no O2 (Oxygen), no breathing, no Krebs cycle, and the human ceases to function (reactions stop)...that you missed the oxygen is why CHEMISTS are so worried about your dangerous bio-FAD projects, dreamed up by people with a 10th grade chemistry education...


for you bio-FADS...it goes like this....we breathe in oxygen, and breathe out carbon dioxide...and that's about all you need to know about the Krebs cycle....please continue to breathe...

[treepig]

52. you continue to make yourself look foolish

would you please point out to me exactly where in the krebs cycle, using the chemically-balanced equations shown in post #42, that molecular oxygen is required?

and how do you explain the fact that the krebs cycle functions nicely in organisms such as yeast that do not benefit from "the BREATHING of human beings" ?

in reality, molecular oxygen actually comes into play in the larger picture of cellular metabolism when energy is extracted from the high-energy, reduced products of the krebs cycle (such as NADH). more specifically, two "H"s from two molecules of NADH are combined with molecular oxygen in Electron Transport Chain reactions (which are distinct from the krebs cycle) to produce water. (that's why some desert animals never need to drink water, it's produced metabolically).


perhaps, to use an analogy that perhaps you can understand, consider if i were to point out that an engine was important to the functioning of an automobile. i suspect that you'd start screaming "HA HA TREEPIG DOESN'T KNOW THAT CARS REQUIRE WHEELS TO BE ABLE TO MOVE" well, i do know that, and also that they need a transmission, a steering wheel, a chassis, and many other parts. well, it turns out a cell is even more complex than an automobile, so i suspect that no matter what information i provide, you could go on for a long time pointing out details that i've not bothered to include (just because they're too volumous to do so). i don't think that that tactic really demonstrates that you're super intelligent or anything, and quite frankly, i feel a bit foolish for having played along for so long. bye bye

[DrWeird]

54. Are you still claiming to be a chemist?

Because you've shown over and over that you know very little chemistry. What exactly are your credentials? You've done little here but laugh at other peoples chemistry when in fact they were correct and you were wrong.

[kodi]

34. what horse shit

i did my ms and dissertation investigating the biochemical fragmentation of azo napthalenes and small aromatic compounds and the biological activity of the cleavage products. you dont know what the hell you are talking about. i wouldn't let you anywhere near a chemistry lab.

http://catalog.lib.ncsu.edu/web2/tramp2.exe/goto/A0110msl.003?screen=Record.html&server=1home&item=3


http://catalog.lib.ncsu.edu/web2/tramp2.exe/goto/A0110msl.003?screen=Record.html&server=1home&item=2

[treepig]

36. care to give a specific example of something i said

that's not true?

and once again, who said i wanted to go anywhere near a chemisty lab? furthermore, why are people in this thread being purposefully obtuse by refusing to realize there is a huge difference between the way chemistry is done in the lab, and the way it is done in a cell?

[DrWeird]

39. Don't worry about it treepig.

When people compare arsenic with pyruvate and acetaldehyde you can't take their science seriously.

[diamond14]

37. totally agree....and I also would not let treepig "anywhere near

a chemistry lab"....

the saddest part is that by putting out all this "horse shit", the treepig is able to move so many DUers into acceptance of this FAD stuff...typical rove/rush/bush* stuff...and then repeat, repeat, repeat until DUers accept it....

Environmental clean-ups should be done with TRIED AND TRUE methodology....this bio-FAD is DANGEROUS, un-intended consequences are likely to occur...people who shouldn't be let 'anywhere near a chemistry lab' should NOT be doing these chemistry projects...

[treepig]

41. umm, what 'bio-FAD'?

bioremediation has being going on for thousands (millions? hundreds of millions?) of years.

please describe exactly what alternative "TRIED AND TRUE" methodology is out there that actually works? and if works so well, why are there so many efforts currently ongoing to develop bioremediation alternative? (e.g., a search of 'bioremediation" in PUBMED returns 10,472 peer-reviewed, scientific research papers). in any event, a specific example of a major environmental problem that was remedied with this tried and true technology would also be helpful. i've already provided one example for bioremedation (exxon valdez), and can give plenty more!

[goforit]

22. Wow Treepig!!!!................Are you a professor?.......I am impressed!!

Now you can teach Chemistry/Biology!!!!

Hats off to you and your argument!!!.....You win!!!!

[elfin]

7. Tried to find out if this company is public

... wondered if it was an investment opportunity. But it is private. Would be interesting to see if any publicly traded companies are in this biz - but don't know quite how to find out.

[Nottingham]

9. Awesome! I'll drink to that

:toast:

[Cronus Protagonist]

17. I wonder what the wonder bug does to humans

The article doesn't seem to mention that. Are they just replacing a chemical problem with a bacteriological one?

[enki23]

19. i wouldn't get my panties in a bunch

at least, not about infections. they're not pathogenic.

EDIT: can't find the sulfate-reducing line again, so i may have misread. looking for more info.

EDIT2: found it. it's a green nonsulfur bacterium. still, the nonpathogenic label stands.

[enki23]

18. um....

guess what they often do when they do pump and treat. one of the most common treatments (after you've started pumping) is to use bioreactors with specific microbial communities to chew up the bad stuff. (others include things like ozonation, uv treatment, carbon adsorption, ion exchange, reverse osmosis, filtration, air stripping, chemical oxidation, etc.) in other words: this is nothing new. it's not an "alternative" to pump and treat. the actual *alternative* is to treat in place, which was already an alternative.

this bug is another tool, not a new method, just a bug which seems good at reductive dehalogenation of some substances. and that's great, it really is. but the way this article was written, you'd think it was something which had never been done before. and that's simply untrue.

[htuttle]

21. Has anyone asked this important question?

"What does it eat when it can't find any pollution?"

Just saying...We should know the answer to this...

[goforit]

23. It dies off when there food source is gone: chemicals. But,

When it dies off does it leave anything behind?

[htuttle]

24. That's another good point

But have they actually CHECKED the universe of possible bacteria food to see if it could survive on something already in nature?

And if so, can anything eat this manufactured bacteria? Would it harm something that ate it?

Even introducing a NATURAL non-native organism to a habitat is dangerous as hell (and almost always destructive). Introducing a non-natural organism without having a complete idea of how it will interact with the native organisms is beyond stupid.

[treepig]

27. bacteria that "eat" toxic chemicals

do so because they have developed a metabolic pathway that enables them to do so.

such pathways generally consist of a modest number of gene products (usually enzymes, but sometimes proteins that simply sequester the toxin) - perhaps there are 5 to 25 components in such a pathway.

initially, these genes are gained in addition to the ~1200 genes that a bacteria requires to survive (for comparison, humans have ~30,000 different genes). therefore, for a while, the bacteria can "eat" whatever it was eating before as well as the toxin. therefore, if the toxin disappears quickly, the bacteria would essentially go back to doing whatever it did before.

if the toxin is plentiful, and is capable of completely supplying the bacteria's nutritional requirements for a few hundred generations (which for a bacteria can be only a few days or weeks), or if the bacteria is cultured in a laboratory under artificial conditions where only the toxin is available as a food source, it will likely dispense with the genes it previously used to digest its original food. in this case, it will indeed die out when the toxin is gone.

more generally, the bacterial world is an extremely competitive place, and it's essentially impossible to "engineer" a bug that will outcompete it's wild counterparts and take over the world. that's because bacteria are so able to share genes with each other, and dispense with genes they don't need, that the whole idea of "species" of bacteria is in dispute (i.e., species are reproductively isolated from each other while bacterial genes are far from isolated). the net effect is that the natural complement of bacteria inhabiting the earth is in constant and tremendous flux, allowing bugs to develop that live in the most unlikely of habitats (such as at below freezing and above boiling temperature, inside nuclear reactors (etc) - check out the following website http://www.astrobiology.com/extreme.html ).

why haven't these strange bugs with strange genes taken over the planet? quite simply, while they are adapted to live where nothing else will live, they pay a price for doing so - for example they grow very slowly. in a normal habitat, they would be rapidly out-competed by "normal" bacteria - same thing with the bacteria used for bioremediation.

[stickdog]

30. There's no reason to believe bioremediation is not perfectly safe,

but there's every reason in the world to believe that we have no real way of even contemplating the universe of potential long term unintended risks, much less measuring them.

Don't mind treepig, but I think he wrote this song back in the early 1950's with Edward Teller:

Standing tough under stars and stripes
We can tell
This dream's in sight
You've got to admit it
At this point in time that it's clear
The future looks bright
On that train all graphite and glitter
Undersea by rail
Ninety minutes from New York to Paris
Well by seventy-six we'll be A.O.K.

What a beautiful world this will be
What a glorious time to be free

Get your ticket to that wheel in space
While there's time
The fix is in
You'll be a witness to that game of chance in the sky
You know we've got to win
Here at home we'll play in the city
Powered by the sun
Perfect weather for a streamlined world
There'll be spandex jackets one for everyone

What a beautiful world this will be
What a glorious time to be free

On that train all graphite and glitter
Undersea by rail
Ninety minutes from New York to Paris
(More leisure for artists everywhere)
A just machine to make big decisions
Programmed by fellows with compassion and vision
We'll be clean when their work is done
We'll be eternally free yes and eternally young

What a beautiful world this will be
What a glorious time to be free

[nolabels]

53. I heard this one guy talk about FUNGI in this vane

on Radio, he told of this giant fungus below and how there are all kinds of things we need to learn about this un-researched, unappreciated but very vital life form that can also has strains that love petroleum products, given the correct conditions. Not only that, but he showed why it also has much of a different kind of intelligence people have not figured out yet. There are mushrooms in your future, you just don't know it yet


http://www.microbeworld.org/htm/aboutmicro/microbes/types/fungi.htm


The only above-ground signs of the humongous fungus are patches of dead trees and the mushrooms that form at the base of infected trees. Courtesy of the USDA Forest Service
Fungi straddle the realms of microbiology and macrobiology.

They range in size from the single-celled organism we know as yeast to the largest known living organism on Earth — a 3.5-mile-wide mushroom.

Dubbed “the humongous fungus,” this honey mushroom (Armillaria ostoyae) covers some 2,200 acres in Oregon’s Malheur National Forest.


The only above-ground signs of the humongous fungus are patches of dead trees and the mushrooms that form at the base of infected trees. Courtesy of the USDA Forest Service.


It started out 2,400 years ago as a single spore invisible to the naked eye, then grew to gargantuan proportions by intertwining threads of cells called hyphae.

Under a microscope, hyphae look like a tangled mass of threads or tiny plant roots. This tangled mass is called the fungal mycelium, and is the part of the famous honey mushroom that spreads for miles underground.

If mushrooms and other fungi can get so huge, why mention them on a site about microorganisms?(snip)

[lostnfound]

29. Will it eat the poison put out by Washington? ;-) n/t

[emad]

35. I think the President should try some first, maybe with his

pretzels...

[goforit]

50. LOL!!!!...........a good laugh!!

He's one toxic soul alright.

[Az]

49. Anime connection

There is a new series that came over from Japan called Arjuna in which an oil chomping bug designed to help clean oil spills triggers an end of world scenario that winds up destroying Japan. Careful of what we use to fight our own messes as it may turn back on us and become a bigger problem.