Rock absorbing nutrients?

[EnterName]

I’m generalizing to all creatures in our tanks that are taking up ammonia or nitrate as a source of N, unless I see any evidence otherwise. Not only do studies support it for some creatures, the idea that an organism would prefer nitrate seems almost implausible to me.

It would be like a person tasked with collecting a large number of apples. One could collect those within reach from the ground, or one could climb a different tree to get identical apples that are 20 feet up, each in a different tree.

I said nothing about how much of what they take up. No reefer has such info for their tanks and the creatures in it. It would be extremely complicated to get such info in an operating reef tank.

It is certainly true there is competition for ammonia, and it is exactly why I am against dosing nitrifying bacteria or adding media for purposes of housing them.

I think this is exactly where the generalisation becomes problematic. The extra energetic cost of nitrate assimilation is real but apparently it doesn’t automatically determine preference.

Pseudo-nitzschia australis has been experimentally shown to have a “clear preference for nitrate at equivalent concentrations” over ammonium and other N sources. There’s also Phaeocystis globosa, where nitrate was the favoured nitrogen source for growth across three tested strains, despite ammonium being energetically cheaper to assimilate.

So perhaps the apple analogy is a little too simple for biology. Sometimes the organism apparently does climb the taller tree.

https://hero.epa.gov/reference/8778397/

https://www.tandfonline.com/doi/full/10.1080/09670262.2011.602430


Edit: There’s also a third possibility the generalisation overlooks, organisms that assimilate nitrate and ammonium simultaneously rather than simply using ammonium first and switching to nitrate once it’s depleted. There seem to be plenty of examples of this in the literature. Some apparently pick apples from both trees at the same time.

https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1529-8817.1976.tb00508.x

From your own source (Bird 1976):

They even acknowledge that their methods are insufficient to determine if there is still a preference.
I wouldn't use a paper to prove a point when the paper itself says it cannot be used to prove that point.

 

[BeanAnimal]

I think this is exactly where the generalisation becomes problematic.

Two organisms found in toxic ocean blooms are edge cases, not representative of our aquariums, and already covered by both EnterName's position and Randy's. Now arriving after two pages of narrowing deflections, it still doesn't touch what EnterName actually said. His position and Randy's generalization stand. That's been the point all along.

You used semantics to build a pedantic argument against a post that was accurate from the start. You were chased for two pages as you deflected numerous pieces of evidence. Now it gets reframed as "difficult questions." Ridiculous. It answers a question you framed yourself to set up EnterName to begin with.

@EnterName I’m not trying to make you look bad. I’ve asked you difficult questions, just as I’ve asked Randy plenty of difficult questions. If questioning conclusions or asking for clarification is being interpreted as an attempt to make someone “look bad”, I’m not sure how we’re supposed to have a technical discussion. Bit sad really when difficult questions have to be reframed as personal attacks instead of just being answered as difficult questions.

"Difficult questions" is doing a lot of work here. It’s gaslighting. EnterName didn't say you asked hard questions. He said you ignored his arguments and made a second attempt to frame him. The evidence shows that to be true.

What actually happened is pedantry dressed up as accountability, two pages of narrowing and reframing, followed by edge-case citations you set up the argument to require in the first place.

Calling that a technical discussion were you portray yourself as holding people accountable with difficult questions s is a reframe of what actually occurred, and casting yourself as the one under attack for having it is one more reversal on top of the rest.

And yet here we are again, another entire post analysing me instead of discussing the actual subject. You’ve made your opinion of me and how I participate in discussions abundantly clear, Bean. I’ve heard it repeatedly. At this point, continuing the running commentary is doing more to derail the thread than the questions you keep accusing me of derailing it with. Can we get back to the actual topic now?

We are here because of your serial deflections. It's a fair label because the deflections are repetitive. Several other people were chasing them before I got here. You framed that as conspiratorial.

The topic becomes whatever people chase you to. Demanding we get back to it only serves to portray you as the victim instead of the force derailing the thread to begin with. It's just another self-serving reframe.

You're rewriting the thread to cast me as the problem. The record says otherwise. This is also a recurring pattern.

 

[sixty_reefer]

And all your questions have been answered kindly, with appropriate sources and zero attempts to avoid them. I even double-checked that I got everything you asked about, as you'll remember.

Framing me as not accepting "difficult" questions, when all I've done so far is take my time to answer them and even double-check that I included everything you asked for, is unprofessional, dishonest, and an uncalled-for level of hostility. I will not participate in that level of hostility.

None of the other points I made in my previous response were addressed. Technical discussions require everyone involved to participate in good faith and address the counterarguments being made. I would very much welcome it if we could actually get to the technical and scientific part of the discussion. I have been awaiting actual counterarguments to the various points I made, or an acknowledgement that the discussion is resolved.

I think it’s probably best that we agree to disagree and leave it there. We clearly have different interpretations of what has been said, what has been answered and where the burden of evidence lies. I don’t think going back and forth over those differences is going to move the technical discussion forward, so I’m happy to leave our disagreement as it stands.

 

[EnterName]

I’m generalizing to all creatures in our tanks that are taking up ammonia or nitrate as a source of N, unless I see any evidence otherwise. Not only do studies support it for some creatures, the idea that an organism would prefer nitrate seems almost implausible to me.

It would be like a person tasked with collecting a large number of apples. One could collect those within reach from the ground, or one could climb a different tree to get identical apples that are 20 feet up, each in a different tree.

I said nothing about how much of what they take up. No reefer has such info for their tanks and the creatures in it. It would be extremely complicated to get such info in an operating reef tank.

It is certainly true there is competition for ammonia, and it is exactly why I am against dosing nitrifying bacteria or adding media for purposes of housing them.

I think this is exactly where the generalisation becomes problematic. The extra energetic cost of nitrate assimilation is real but apparently it doesn’t automatically determine preference.

Pseudo-nitzschia australis has been experimentally shown to have a “clear preference for nitrate at equivalent concentrations” over ammonium and other N sources. There’s also Phaeocystis globosa, where nitrate was the favoured nitrogen source for growth across three tested strains, despite ammonium being energetically cheaper to assimilate.

So perhaps the apple analogy is a little too simple for biology. Sometimes the organism apparently does climb the taller tree.

https://hero.epa.gov/reference/8778397/

https://www.tandfonline.com/doi/full/10.1080/09670262.2011.602430


Edit: There’s also a third possibility the generalisation overlooks, organisms that assimilate nitrate and ammonium simultaneously rather than simply using ammonium first and switching to nitrate once it’s depleted. There seem to be plenty of examples of this in the literature. Some apparently pick apples from both trees at the same time.

https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1529-8817.1976.tb00508.x

Cochlan et al. 2008 speaks about freshly nitrate depleted P.-nitzschia australis within a 20min window. You may recall the nitrate storage in vacuoles which is a storage not a full assimilation. So it was shown that nitrate depleted diatoms of this species take up nitrate fast, but not if it's full assimilation or if they can keep that speed.

They also grew the cells in water with NO3 as the sole nitrogen source and tested minutes after depletion. Nitrate transporters and nitrate reductase are substrate-induced and ammonium-repressed, so the cells were maximally primed for the exact substrate that "won".

If you take a look at section 2.3. they never offered ammonia and nitrate simultaneously and in the discussion section the authors acknowledge that their study didn't account for substrate interactions like the repressive effect of ammonium on the required enzymes.

I'm not saying there aren't any organisms that may prefer nitrate, but I wouldn't have chosen this paper as evidence when it points out that it cannot be used for that purpose.

 

[sixty_reefer]

From your own source (Bird 1976):

They even acknowledge that their methods are insufficient to determine if there is still a preference.
I wouldn't use a paper to prove a point when the paper itself says it cannot be used to prove that point.

Could you read that quote again? I don’t think it says what you think it says.

 

[sixty_reefer]

@EnterName, we can stop here and agree to disagree or we can move on to the second part of the discussion, whether feeding preference and assimilation can actually be inferred from growth. They are different biological measurements and one does not necessarily predict the other. I think that distinction has been getting generalised throughout this discussion also.

 

[EnterName]

From your own source (Bird 1976):

They even acknowledge that their methods are insufficient to determine if there is still a preference.
I wouldn't use a paper to prove a point when the paper itself says it cannot be used to prove that point.

Could you read that quote again? I don’t think it says what you think it says.

It's possible that there is still a preference (yes even if it isn't discernible from the data).

It says what I was trying to articulate: They haven't ruled out that there might be a preference. They are aware of the limitations of their applied methodology and are very careful about the conclusion they draw from their observations.

I'm not really questioning that there might be organisms that prefer nitrate over ammonia, I just don't think it's the best paper to use as evidence for that particular claim.

 

[BeanAnimal]

I think it’s probably best that we agree to disagree and leave it there. We clearly have different interpretations of what has been said, what has been answered and where the burden of evidence lies. I don’t think going back and forth over those differences is going to move the technical discussion forward, so I’m happy to leave our disagreement as it stands.

There's no difference in interpretation here, that's gaslighting, all of us this time, not just EnterName. Everything is a reframe away from accountability. There was no technical discussion to leave.

You made a pedantic demand for accountability based on semantics, then did exactly what you were demanding, made a broad claim that you can’t support and have spent pages deflecting, reframing and narrowing to not be wrong.

"Agree to disagree" isn't an exit from a discussion. It's an exit from being caught and held accountable.

@EnterName, we can stop here and agree to disagree or we can move on to the second part of the discussion, whether feeding preference and assimilation can actually be inferred from growth. They are different biological measurements and one does not necessarily predict the other. I think that distinction has been getting generalised throughout this discussion also.

That's not two options, it's an exit disguised as one, after already exiting two post prior. Word games.

You're not offering to "stop or move on", you're railroading the topic past the part you just lost, straight into a new frame you get to define on your own terms.

You never answered EnterName's point that your own citation admits it can't prove the claim. You've reframed and abandoned the entire context of everything that's transpired so far and want this to appear as a "technical conversation" when it is still one deflection and reframe after the next being chased.

"Feeding preference versus assimilation" isn't the real discussion. It's the next diversion, fog, packaged to look like progress and reframe this as a good-faith discussion, when it is everything but that.

 

[EnterName]

@EnterName, we can stop here and agree to disagree or we can move on to the second part of the discussion, whether feeding preference and assimilation can actually be inferred from growth. They are different biological measurements and one does not necessarily predict the other. I think that distinction has been getting generalised throughout this discussion also.

You can move on as you wish, I won't stop you.

Just know that I never claimed anything about growth or drawing conclusions from growth so the topic is moving far away from your initial "criticism" of my post without having ever touched the evidence that I or others provided.

It's a continuous cycle of attacking a point, getting a detailed answer supported by research, and then skipping over important aspects of the presented evidence just to move forward to something else or starting again without even acknowledging any previously made points.

This isn't a scientific debate anymore.

 

[BeanAnimal]

This isn't a scientific debate anymore.

It never was to begin with. You and others have operated in good-faith despite the circumstances and pattern that has emerged here and elsewhere. These thread derailments aren't your fault and you are not being unreasonable by any meaningful definition, no matter the framing after the fact. You have been far more accommodating to this nonsense than most.

Thank you for the information and patience you have brought to the table, despite the circumstances presented.

 

[Randy Holmes-Farley Verified Community Expert]

I think this is exactly where the generalisation becomes problematic. The extra energetic cost of nitrate assimilation is real but apparently it doesn’t automatically determine preference.

Pseudo-nitzschia australis has been experimentally shown to have a “clear preference for nitrate at equivalent concentrations” over ammonium and other N sources. There’s also Phaeocystis globosa, where nitrate was the favoured nitrogen source for growth across three tested strains, despite ammonium being energetically cheaper to assimilate.

So perhaps the apple analogy is a little too simple for biology. Sometimes the organism apparently does climb the taller tree.

https://hero.epa.gov/reference/8778397/

https://www.tandfonline.com/doi/full/10.1080/09670262.2011.602430


Edit: There’s also a third possibility the generalisation overlooks, organisms that assimilate nitrate and ammonium simultaneously rather than simply using ammonium first and switching to nitrate once it’s depleted. There seem to be plenty of examples of this in the literature. Some apparently pick apples from both trees at the same time.

https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1529-8817.1976.tb00508.x

I stand by my generalization and analogy. Could there be deviation from it? Sure. Are your posted links actual deviations? I suspect not.

Let's look at the first one you posted. The diatoms were cultured using ONLY nitrate as the N source. Then they instantly check relative uptake capability for it and other N sources. Seems wildly inappropriate to me, and they note the issue. Even so, the preference for nitrate is small.


Table 1. Kinetic parameters for N uptake by Pseudo-nitzschia australis previously maintained on nitrate as the sole N source.
...
As mentioned above, kinetic parameters may vary as a function of the pre-conditioned substrate used for growth, and the reader should be cautioned that all P. australis cells used in the present study were pre-conditioned on NO3. This could potentially affect the kinetic parameters reported here.

Let's look at the second one posted. There is NO experiment testing the uptake preference of these organisms for ammonia vs nitrate. It only looks at solitary cell growth and colony formation. I make no assertions about how different N sources might impact growth forms, and how the growth forms may grow at different rates.

Comparatively few colonies developed when ammonium or urea were provided as N sources, whereas solitary cell abundances increased with time for all three strains, irrespective of nitrogen source. Furthermore, the final biomass of CCMP 627 grown in urea was greater than that grown in nitrate, strongly suggesting that the growth of P. globosa solitary cells was largely independent of nitrogen source.

 

[Randy Holmes-Farley Verified Community Expert]

Edit: There’s also a third possibility the generalisation overlooks, organisms that assimilate nitrate and ammonium simultaneously rather than simply using ammonium first and switching to nitrate once it’s depleted. There seem to be plenty of examples of this in the literature. Some apparently pick apples from both trees at the same time.

https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1529-8817.1976.tb00508.x

Certainly organisms can take up both. I'm sure tank creatures do. If they can take up one or the other, and are not getting what they need from the preferred one, whatever that is, they will take up others.

Same is true for phosphate.

Organisms take up MANY forms of N and P. They can and do.

 

[Randy Holmes-Farley Verified Community Expert]

But that doesn’t really define the bounds. A fish is an organism we keep too. Does a fish prefer ammonium over nitrate? That’s exactly why I’m asking which organisms the generalisation is actually referring to.

Do you have reason to think fish prefer to uptake nitrate over ammonia?

If not, then why mention it?
Fish very readily take up ammonia, but not so much nitrate.

 

[sixty_reefer]

Certainly organisms can take up both. I'm sure tank creatures do. If they can take up one or the other, and are not getting what they need from the preferred one, whatever that is, they will take up others.

Same is true for phosphate.

Organisms take up MANY forms of N and P. They can and do.

Randy, that’s a significant modification of your original generalisation:

“All experiments that I have seen suggest the organisms we keep prefer ammonia over nitrate.”

You’re now acknowledging that organisms can use both, deviations exist and nitrogen source use depends on availability and circumstances. That’s essentially the point I’ve been making.

 

[sixty_reefer]

Do you have reason to think fish prefer to uptake nitrate over ammonia?

If not, then why mention it?
Fish very readily take up ammonia, but not so much nitrate.

I mentioned fish to define the bounds of your generalisation, not because I claimed fish prefer nitrate. “The organisms we keep” includes fish, so asking whether your generalisation applies to them is directly relevant. Asking me whether I have evidence that fish prefer nitrate doesn’t answer which organisms your generalisation actually covers imo.