Wrong. His research which is published in peer reviewed scientific journals has methodology to review and then decide if what he has said is correct, indeed one can look here if one desires to look a little further into the article.

The fact that Dr Hovanec has taken that research and used that to form the basis for a commercial product does not mean that if the product fails the research is bad. One could perform research into the cause of the common cold and provide scientific research to show the cause. Then one could take that research and create a cure. If the cure does not work it does not mean that the validity of the underlying research is suddenly called into question.



Gone off on one? If you consider the above to be that you must be very delicate indeed! you seem to be upset that you brought up the fact that Hovanec isn't some altruistic researcher doing his work for the love of aquarists everywhere and that I and others have pointed out that the peer review process makes it immaterial. You seem obsessed with joining his earlier work on discovery with his current commercial work on creating a workable product as if somehow they are inseperable.

This post has been edited by andywg: Jun 8 2008, 12:56 PM

So, we should also be questionable of most 18th, 19th, 20th, and 21st Century scientific advancement? (Well, we should, but not for your reasons, just because of the demands of science) Especially for the last hundred years, very little of your definition of "pure research" happens. Nothing gets funded if there's not a percentage.

This post has been edited by Corleone: Jun 8 2008, 04:28 PM

Don't be silly Corleone ... you evidently don't understand the meaning of 'pure research'. The last bit has become increasingly important in the last couple of decades but it wasn't throughout most of the 20thC ... and even big commercial institutions like IBM still have active pure research projects ... and of course the discovery of DNA was a product of pure research.



Lol, I guess you think all those research scientists at Universities etc don't get paid, they do it for fun do they? What's even more laughable though is that you provide a link and don't even bother to read it yourself. Its more than obvious that Hovanec works for Aquaria Inc (as his CV states Prior to joining Aquaria in 1990, Dr. Hovanec was manager at Aquatic Systems Inc., the major aquaculture producer of hybrid striped bass in the World. ) not for the UCSB as you would like to believe ... so sorry but this is part of his commercial research not some mythical earlier work. The obsession I assure you is all yours.

As for the peer review process making it immaterial ... think again ... do some research.

Even the Journal is one that is aimed at Highlighting research findings applicable to the development of new processes or products, sounds pretty commercial orientated to me.

Like I previously stated. All this ... including the failings of the peer review process ... is completely irrelevant.

Now perhaps you could actually point out where I stated or even implied that Hovanec, his research or his product is in anyway bogus.

This post has been edited by pastabake: Jun 11 2008, 08:21 AM

Now this gets fun for me.



Did I say that? No, I don't think I did.



You appear to have misunderstood me. I was referring to his earlier research works which deal with trying to actually identify the bacteria which are present in our aquaria. If you read his studies you will see there is no mention of how to create a culture that can be sold, but to establish what bacteria are doing the work.

Interesting you seem to be deciding for yourself what I want to believe (see below).



Humour me. You say the peer process is so flawed, provide some examples for me of how it can be flawed and a paper that is 10 years old can go so long without being found out as flawed.



Perhaps you can point out where I implied you said that? I asked if you doubted the work and pointed out that what you have said is an atack on the man, and it is. If you cannot see how it is an attack on the person then I am surprised.

Further, you are making pure assumptions on what Dr Hovanec believes or does not believe, now you are making claims about what I believe or want to believe. Why this obsession with getting inside people's minds?

And, as I stated, if his research is just as valid, why do you have this huge chip on your shoulder about "pure" vs commercial research? The fact you brought up his position would appear to imply that you hoped people to bear that in mind and possibly change their views on Dr Hovanec and/or his work. So I ask again, Why bring it up if it has no effect?

Oh here we go with "various papers". Man if I had a nickel for every time I've heard that as some kind of "evidence" I'd be a rich man. I recently read a paper stating how nitrifying bacteria can come from tap water. The theory was that the bacteria mutate to resist levels of anti-bacterial chemicals such as the chlorine and -mine that we put in city release. It was interesting as it could be possible with some kinds of bacteria, but he either didn't think to consider, or conveniently left out the fact that these autotrophs divide every 24 hours and haven't a prayer to mutate enough times fast enough to ever become a survivable mutation to make it through your faucet. So, see not every "research paper" is applicable in the real world even though it may look really, really smart!

I work in waste water so you just found yourself a debate partner! I work with aerobic bacteria in our aeration tanks and we would never buy nitrospira bacteria for nitrite oxidization in situation. I am a hobbyist too. I have a 120 gallon bow front amazon natural life aquarium and I have a 75 gallon reef. Both cycled in that "how'd you do that??" speed of about 3-4 days.

This whole "waste water" thing I don't know who decided to make that any kind of plausible detail because nitrobacter will work in wastewater, in the aquaruim, or a bucket with an air stone! I've done all three!

Your flippant comment about altruism tells the lie on that comment.

No it is you that appears to have misunderstand the scientific process and the motivations behind this particular piece of research. Lol, are you really that naive ... the commercial bit comes on the patent application, not on the paper. The Patent was in 1998 ... not long after the research ... coincidence? I seriously doubt it. ref:- European Patent EP1032648.

No you humour me and actually do some research before blowing hot air over things you evidently know next to nothing about. What do you think happens when a paper is considered flawed? I'll tell you, absolutely nothing unless it involves gross misconduct. It will still be cited, because flaws will only limit its usefulness not make it completely redundant, for that you would need further research and subsequent papers.

Putting someone and their research into context is nothing like an attack.

No I'm not, and its very rich coming from someone who got their knickers all twisted from making an invalid assumption over something I innocently pointed out. Namely that Dr Hovanec is the person behind Biospira and while many seem to quote Dr Hovanec many also believe his product to be of questionable value.

Well for the same reason that one would point out that the advice from a LFS should be tempered with the knowledge that their primary goal is to get your money. Everything has a CONTEXT and it is only in understanding this that one can make sensible and valid judgements.

I don't have a chip on my shoulder ... commercial research simply isn't as intellectually or scientifically valid as non-commercial, not to mention the potential conflicts of interest - yeah we don't have to into the numerous accounts of falsified pharmaceutical data and other similar cases of selective use and/or manipulation of data to suit purpose. If you knew anything though, you would know that the majority of commercial research is never published and when it is it generally isn't for reasons of furthering the cause of science - that this particular piece of research was published has possibly as much to do with the fact that Aquaria Inc had to outsource to a University to get it done as anything else.

As for the validity of this research ... the paper you linked to ... 10 years ago I can see how it got published. DNA techniques were cutting edge and sexy ... today it wouldn't even get to review. Take a look at it ... the samples were narrow and the results ... now I accept that DNA results often come in the 96% range but lets have a think about this ... his sample also stated a figure of 87% ... so what we have is that for his limited sample range he found no nitrobacter ... ok, not very conclusive across the board evidence but we can forgive that ... what comes next though is that what he found was bacteria that was similar to ... and lets use an analogy - you're at the zoo looking at the monkeys, I'm looking in your general direction and my partner asks what are you looking at. I respond by saying I'm looking at something that is 96% monkey like - I wont even go into how far out the 87% gets you.

So in conclusion this paper that you hold so highly actually states very little of use ... especially when you take into consideration that there are likely to be 100's if not 1000's of species of bacteria in the aquarium. At the very best it says that Nitrobacter wasn't discovered in the [limited both in terms of numbers and diversity of water chemistry] samples and so probably isn't universally responsible ... and So 11 out of 96 a minority and yet these were the ones chosen to be sequenced ... taking into consideration when this research was done and the sheer numbers of still unidentified and most likely un-culturable bacteria present within an aquarium and in particular its filter I'd say that this research is not only well past its sell by date but was also pretty useless right from the offset. Unless of course your motives were other than pure research and your main goal was to sequence and patent the use of a bacteria for an inoculation product. [European Patent EP1032648].

This highlights the deficiencies of commercial research ... this paper has no doubt been cited a number of times and will have framed further research ... there are real consequences.

The irony here is that previously I honestly believed that Hovanec was ok and his product probably worked ... your irrelevant bleatings have now opened my eyes up to the possibilty that they both maybe bogus. Way to go Robin.

Lol, this has changed in a year. Last time you kept saying how you had a Ph.D friend who would give you evidence to prove how Hovanec is so wrong, yet you never provided anything to back it up, nor even the name of your Ph.D friend. Care to provide any actual evidence this time?

Tell you what, how about you post on one of the many scientific threads down the board to give us your expert evaluation.

Woah there. How about we do the argument the old fashioned greek way: you introduce a statement, you provide the evidence to support it. Sound good? You are saying there are serious flaws in the peer review process but telling me to go find them despite you claiming I have no knowledge of them. I don't think that is the right way to do it. Until you actually provide some evidence of these major flaws that will allow an incorrect paper to get through without any major criticism I am afraid I will not accept your point. Do so and I will gladly withdraw.

Is that fair?



Here would seem to be an opinion difference on the motive and it would appear that I have misunderstood you in at least some way, so I shall drop this point and allow yours to stand.



I apologise. As stated above I would appear to have misunderstood you.



Are you really sure on this? I bet there is a whole load of reseearch from the commercial sector which is pretty important. For example, fuel economy in cars is not driven by governments, but by the car firms in competition with each other. Hell, there is a huge debate on public vs private funding in that it is claimed that private research is hugely more productive per £ spent than public. And then, rather than being influenced by a corporate vision, it is influenced by a government's or a civil servant's vision of what research should take place.

I think that to somehow claim that public funded research is always greater than private funded research is to take an extremely simplified view of the argument.



But you said review doesn't matter.



This and his subsequent two; I as well as many others. I hold it highly as it is one of the first papers to actually look at an aquarium specific situation. If you have other science that may contradict it I am more than willing to read it and see. There is little doubt that the huge variety of bacteria in our aquaria, pinning down exactly which bacteria does what will be very hard.



Then perhaps some "pure" researchers should come along and correct it.

More seriously, if he really is wrong then surely someone else would come along and prove it so (such as those who include Nitrobacter in their products).

And you are right, it has been cited a number of times. If there were any major flaws then one would expect someone to provide some evidence to show him wrong. I have looked through a couple of the citing papers available from the same journal (not the best way of judging it, I know) and they don't seem to detrimental to the findings, however I am always willing to read a contrary opinion from scietists on this. It would be great to be able to see what the peer review and the responses to the publication provided, though I am unsure of how we coudl get this without obtaining some form of subscription. It may well be that the points you make have already been raised.



But that is great!

Surely science is about looking at the facts and making your mind up, and not just believing what others tell you? If this thread has caused you to do so and form your own opinion then I am happy.

I think we are all in the same boat here in that part of the reason we dwell on the 3 Hovanec articles is just what Andy said... they are just about the only articles out there really taking a look at "an aquarium-specific situation."

I mean, I hope I'm wrong about that and there are a bunch of other ones out there I've yet to see, but so far everything else I've seen referenced has been "smaller bits of info around the edges" and often really directed at other things, like commercial fish ponds, wastewater and oceanography etc. There's always stuff to learn around the edges but in my case, whether its right or wrong, I can't help but get excited to get to read something very scientific but very aquarium-specific. There's just not much hope we'll get much of this.

One of the things I find most fun is when someone finds and shares other bits from other scientific articles or the web or whereever. The recent bit that BTT shared about how some bacteria can switch between aerobic and anaerobic states was something I'd never heard before, for example. It led to me having a discussion with one of our biochem professors here on campus and I learned that indeed this very type of switch was something that Pasteur looked at with yeast and in fact it is put to use in winemaking - just something I'd never thought about.

When communicating with bits of text stretched out over time there's enormous room for misunderstandings and miscommunications. I'm just glad when people keep finding stuff, sharing it and keep attempting to work with each other.

~~waterdrop~~

The arguments surrounding the PR process are hardly difficult to find and TBO I don't think that its up to me to bring people up to speed on common knowledge.

To understand the flaws in the PR process you have to understand how it works.

The 'peers' are only those that want to do it. Request for reviews are sent out ... the potential reviewers should check to see if (1) They actually know anything about the subject and (2) If there are any conflicts of interest. (3) Then they decide whether they have the time. A serious review will take a day, the annual cost of the review process is about £1.2bilion ... a professor at a top institution maybe being paid ~£80k his time doesn't come cheap for his employers.

Lets examine each point in more detail.

(1) Often there aren't the experts, and where there are their expertise might not cover the whole range of the paper. This is especially the case with 'cutting edge' techniques. So while the reviewers maybe able to cover certain areas of the work they may simply be lost at sea with regards to the paper as a whole. While they are meant to write down and clarify their own limitations regarding the review, often they don't.

(2) The review process is only blind not double blind. The reviewers know the authors names of the papers they are reviewing. If you have ever met top flight scientists you will know that they are the most egotistical and nasty people you will ever come across. Certain scientists are hated and there are many bitter rivalries and feuds throughout science ... they are people after all and as such will happily put the knife in or skirt over a flaw.

(3) Due to time constraints many reviewers do a poor job and many more simply turn down the requests. So exactly whom are these people that do the reviewing. I can tell you that the commercial side is woefully under-represented, private companies don't spend money for no return.




http://en.wikipedia.org/wiki/Peer_review has a pretty reasonable overview of the process and its flaws.

btw - I didn't say that review doesn't matter, obviously oversight is essential, what I meant was that just because a paper has been reviewed it doesn't mean that it's right.

You can make jokes all you like, but the scientific process doesn't allow researchers to do what they want. Even outside of the commercial world they still have to write proposals and get funding. So its of little surprise that Hovanec's research hasn't been taken up ... there is simply no mileage and no point because it lacks a wider applicability ... perhaps some would consider this a flaw in the non-commercial world.

You are right by the way that commercial research is much more productive. That's no surprise when you consider that commercial research is narrow and directed - practically worthless outside of its specific frame of reference ... and more importantly it is parasitical on non-commercial research.

As an example - the Human genome project (the UK side at least) was a non commercial enterprise ... however, from that many parasitical commercial organisations have taken that work and gone on to patented genes etc ... those companies would never have managed to sequence the genome. Again how many commercial organisations could have made the CERN Particle accelerator and everything that has come from that ... much capitalised upon by commercial organisations.

So yes on face value commercial research is much more profitable, in reality it simply couldn't survive on its own.

As for who's vision we should follow, the commercial vision will always be for profit and against better long term sense. Using cars as an example, its amazing that something as pathetic as the ICE has managed to last so long. This isn't even going into the technological clutter insides everyones house that's basically just landfill waiting to happen.

It wasn't a commercial company that provided the means for us to be holding this discussion. TBL worked at CERN and the Internet comes from the military. In fact I think you'll be hard pushed to find anything truly worthwhile that was made or discovered using commercial funding - even most of our medical advancements were either the result of necessity via war or because of organisations like the NHS. Cancer research would be nowhere without the charity funded foundations.

As for Hovanec's paper. I've already pointed out its failings. Its focus was extremely narrow and the usefulness of the results questionable and limited. That he didn't find Nitrobacter says nothing about the wider world only about his set up and water chemistry. That he found Nitrospira-like bacteria again doesn't say much especially when you take into consideration that the 'LIKE' aspect is the same as someone pointing to you and saying you are a monkey-like person.

Also consider this. Depending upon the assay that he used he could have been looking for the presence of a specific gene or gene sequence responsible for the nitrification process ... however finding its presence doesn't mean that the gene was active.

That his paper is still cited shows little more than the limited, if not non-existent, research into the field of aquarium bacteria and this is hardly surprising considering its lack of wide applicability to the real world.
The reality is that scientists are finding it hard enough to find funding for identifying soil bacteria, let alone discovering what they are doing ... why are they more likely to find funding for aquaria bacteria?

Food for thought, did Hovanec patent the bacteria (I kind of doubt it being that it is described only as -like) or did he patent the gene sequence (partial or full?) or a process? Depending upon what he patented and it full reach, he may very well have made further research difficult or pointless.

This post has been edited by pastabake: Jun 23 2008, 11:23 AM

But there is! The only scientific paper looking at what bacteria deal with nitrite in an aquarium setting suggests it is not Nitrobacter. Surely if you were a copmany selling a bacteria solution with Nitrobacter in it you would want to publish a rebuttal? I know I wouldn't want the only science out there to suggest my product was less than ideal.



On a somewhat pedantic term, I don't think you can class that as public funded. Charity funded is still private monies.



The patent appears to be for a form of cultured bacteria with properties similar to the gene sequence he witnessed in the 1998 paper.

Linky

I think the main point is cost. It doesn't come cheap to run the experiment and tbo I doubt that the results would be any different under the same conditions and from a scientific point replication is all that counts. I'm most definitely not accusing Hovanec of falsifying his research. So while it is more than possible that another experiment using quite different water parameters could find the presence of Nitrobacter at the end of the day it wouldn't make any difference because under Hovanec's experimental conditions his results would still hold.

As an aside, Hovanecs research doesn't require a rebuttal from the Nitrobacter camp. As I pointed out his results were not conclusive primarily because they covered such a narrow range. In fact you would be hard pushed to seriously make the claim that Nitrobacter played absolutely no part in all or any aquaria nitrification processes. The way science works is by weight of evidence, and one or even a few papers with such limited focus are simply not enough. On the other hand, nitrobacter does have a proven track record albeit in water purification.

I'd read the patent previously but not being a molecularbiologist I couldn't be sure what exactly was being used to define the patented bacteria. From reading it again I am still unsure, but I suspect that through the use of 95%'s etc and a gene sequence that I bet specifically covers the genes responsible for the nitrification process the patent will basically make any further commercial research into nitrospira-LIKE bacteria pointless because I very much doubt that any new bacteria that you found wouldn't already be covered by the wide net of the patent.

Btw my distinction was commercial vs non commercial, so public or