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New study brings into question link between a kind of bacteria and environment
4

New study brings into question link between a kind of bacteria and environment

New study brings into question link between a kind of bacteria and environment

(OP)
A new study by the University of Indiana in collaboration with Cal Tech and Scripts Institute has found that a microscopic creature that was previously thought to exist only in oxygen-rich environments is thriving in an oxygen-deficient/methane-rich environment. This critter is a major factor in the historical atmospheric "record". Makes you wonder how many of the things we "know" about the atmospheric record are 100% the result of faulty correlations.

This is science. The researchers expected an outcome, found a different outcome, adjusted their hypothesis to match observed data, tested the new hypotheses. Really great work.

David Simpson, PE
MuleShoe Engineering

In questions of science, the authority of a thousand is not worth the humble reasoning of a single individual. ùGalileo Galilei, Italian Physicist

RE: New study brings into question link between a kind of bacteria and environment

How does that change what was in my science book? Or what people have learned?

Some of these discoveries should be news, yet, what I hear is another murder, a bombing, and someone was arrested.

Any idea why it has such a large range of enviroments?

RE: New study brings into question link between a kind of bacteria and environment

(OP)
These bugs in the fossil records are used as part of the computer models that predict historical CO2 and global temperatures. The discovery is a pretty big deal. In the story one of the researchers guessed that the bugs like a fairly solid sea bottom which tend to not exist in boggy, oxygen-poor environments.

David Simpson, PE
MuleShoe Engineering

In questions of science, the authority of a thousand is not worth the humble reasoning of a single individual. ùGalileo Galilei, Italian Physicist

RE: New study brings into question link between a kind of bacteria and environment

(OP)
The "bacteria" was mine. They called them "microscopic organisms".

David Simpson, PE
MuleShoe Engineering

In questions of science, the authority of a thousand is not worth the humble reasoning of a single individual. ùGalileo Galilei, Italian Physicist

RE: New study brings into question link between a kind of bacteria and environment

-----(the joke)--->

neutral

RE: New study brings into question link between a kind of bacteria and environment

(OP)
Interesting. Your short posts are no more comprehensible than your long ones.

David Simpson, PE
MuleShoe Engineering

In questions of science, the authority of a thousand is not worth the humble reasoning of a single individual. ùGalileo Galilei, Italian Physicist

RE: New study brings into question link between a kind of bacteria and environment

If some of the data and parameters of the climate models used to forecast Global Climate Change are based on assumptions nullified by this discovery, why isn't it getting more attention?

RE: New study brings into question link between a kind of bacteria and environment

because it might not be in line with the mantra

another day in paradise, or is paradise one day closer ?

RE: New study brings into question link between a kind of bacteria and environment

(OP)
I've promised not to write anything about ACC or AGW until 2016.

David Simpson, PE
MuleShoe Engineering

In questions of science, the authority of a thousand is not worth the humble reasoning of a single individual. ùGalileo Galilei, Italian Physicist

RE: New study brings into question link between a kind of bacteria and environment

Anything that compels us to learn and understand more is good. Research and resulting enlightenment driven by concern about climate is good. Dogma bad.

RE: New study brings into question link between a kind of bacteria and environment

(OP)
That was my reason for starting this thread TheTick. I love to see a scientist find a fact that violates his hypotheses and respond by revising the hypotheses instead of sweeping the new fact under some rug.

David Simpson, PE
MuleShoe Engineering

In questions of science, the authority of a thousand is not worth the humble reasoning of a single individual. ùGalileo Galilei, Italian Physicist

RE: New study brings into question link between a kind of bacteria and environment

"to make the punishment fit the crime" ... to make the facts fit the theory ?

another day in paradise, or is paradise one day closer ?

RE: New study brings into question link between a kind of bacteria and environment

Amen, Dave!

RE: New study brings into question link between a kind of bacteria and environment

Can someone link the actual paper? I can't seem to find a link to it in the press release. I know it's somewhere because how else could someone use this as an example of good science without looking at the method and results from the actual paper. I'm probably just blind and can't find it. I did a google scholar search as well.

zdas04, can you link a copy of the paper? I'd be interested in reading it.

RE: New study brings into question link between a kind of bacteria and environment

(OP)
The note at the bottom of the article Note "The above story is based on materials provided by Indiana State University." seems to indicate that it is not yet published. You might want to contact the researchers mentioned in the article.

David Simpson, PE
MuleShoe Engineering

In questions of science, the authority of a thousand is not worth the humble reasoning of a single individual. ùGalileo Galilei, Italian Physicist

RE: New study brings into question link between a kind of bacteria and environment

Obviously, there's a conspiracy to suppress the facts, or is there? Here's the Indiana Uni newsblurb. http://www.indstate.edu/news/news.php?newsid=4195 But, note that they are talking about ONE specific species of Benthic Foraminifera, because it's certainly known that Benthic Foraminifera, in general, do live on Oxygen Minimum Zones (OMZs):

Bathymetric preference of four major genera of rectilinear benthic foraminifera within oxygen minimum zone in Arabian Sea off central west coast of India

Live (Rose Bengal stained) and dead benthic foraminifera from the oxygen minimum zone of the Pakistan continental margin (Arabian Sea)

Benthic foraminifera associated with cold methane seeps on the northern California margin: Ecology and stable isotopic composition Note that Rathburn of IndU is a co-author of this paper.

THE DISTRIBUTION AND ECOLOGY OF LIVING (STAINED) BENTHIC FORAMINIFERA ACROSS AN OXYGEN MINIMUM ZONE IN THE SOUTHERN CALIFORNIA BIGHT Rathburn and Burkett are authors of this one

THE ECOLOGY OF BENTHIC FORAMINIFERA LIVING IN AN OXYGEN MINIMUM ZONE ON THE EASTERN PACIFIC MARGIN

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RE: New study brings into question link between a kind of bacteria and environment

(OP)
I certainly am not talking about anything like that. I just found it refreshing that the group found data that didn't fit the hypotheses and worked to fix the hypotheses instead of ignoring the inconvenient data. I have no idea how important the finding is or isn't. I was just impressed with the honesty.

David Simpson, PE
MuleShoe Engineering

In questions of science, the authority of a thousand is not worth the humble reasoning of a single individual. ùGalileo Galilei, Italian Physicist

RE: New study brings into question link between a kind of bacteria and environment

Some of you are talking about this press release about research that hasn’t been published yet as an example of good science. How could you possibly know whether this research is good science based off a press release?

Don’t get me wrong, this research sounds very interesting and I look forward to the paper when it’s released. But there is absolutely no possible way for me (or anyone) to honestly comment on the content of the research when we haven’t seen the research.

So this then begs the question, why post it? If you honestly just wanted to post about a paper that found something that violated the researcher’s original hypothesis than certainly you could find a better example. You know, one that is actually published so that you could go through and confirm it was an example of good science.

Your reason for posting it wouldn’t be because you (mistakenly) believe the implications of the research work against the current understanding of climate science, would it? No! You’re on a “pause” from that conversation until 2016.

..but that certainly seems to be what tinfoil took from it. I actually wanted to avoid this discussion but tinfoil’s comment (and the implied message of zda04’s original post) is completely unsupported and speaks to a lack of understanding of the science that needs correcting.

The first thing to realize is that paleoclimatology is based off a number of different, independent proxies. Study of forams and diatoms is only one such proxy. Even if this research determines that all paleoclimatology based off forams is flawed (which is highly unlikely, see below) than it is still not a magic bullet against paleoclimate.

The second thing to realize is how forams are used to reconstruct past climate states and past temperatures. Forams are used for two main things:
1) The oxygen isotope composition of the shells
2) The changing in particular species that result from environmental factors

Composition of Shells
Scientists use the shells of foram to study the isotopes and element ratios. The ratios can then be used to infer the temperature and date of the environment. The key here being that it is the composition of the shells that is used for as a temperature proxy, not their relative density or kind of species. Discovering that a certain species of foram can live in environment with low levels of dissolved oxygen would not appear to impact the current practice of using shell composition as a temperature proxy.

Change/Abundance of a Specific Species
Certain species do well in cold water, others in warm water. Certain species do well in low oxygen environment, other in high oxygen environments. As climate shifts, so does the concentration of various species of foram. This paper appears to make no comment on an anomaly related to the temperature dependency of the species. It does finds that a certain species, thought to only exist in high oxygen environments, has been discovered in low oxygen environments as well. This could be extrapolated to mean that estimates of the oxygen content at different stages in the Earth’s past could be put into question but that requires more investigation. Even if true, what impact on paleoclimatology would that have? Furthermore, would that completely change climate science as we know it? Would it invalidate the findings of the IPCC? Almost certainly not.

“But…but…the press release made it sound like an upcoming paper was a game changer for all of climate science!” Yes. That’s the job of a press release. And that’s why using a press release for a yet to be published paper as an example of good science is bad logic.

RE: New study brings into question link between a kind of bacteria and environment

(OP)
I have to admit that I didn't read your whole post, I got tired. I did get down to the "why post it" question. I have to say "why not post it?" I wasn't trying to convince anyone of anything. I felt uplifted reading about some folks whose first reaction to unexpected data was to reconsider part of their theory. Just a feel good piece. If they ever get to the point of publishing something with the intention of influencing a field of study, then that work will have to be evaluated on its own merit. You can pick your "feel good" pieces. I'll pick mine.

And please refrain from assigning motives to my actions. You are simply not qualified to read my mind.

David Simpson, PE
MuleShoe Engineering

In questions of science, the authority of a thousand is not worth the humble reasoning of a single individual. ùGalileo Galilei, Italian Physicist

RE: New study brings into question link between a kind of bacteria and environment

Here's the paper that I would select:

https://www.aip.org/history/gap/PDF/compton.pdf

The author states in the publication itself that his own previous hypothesis regarding the application of classical physics was clearly flawed. The objective analysis that was subsequently performed by this researcher demonstrated a quantum mechanical solution fit the data beautifully, and this work won Arthur Compton the Nobel Prize in physics in 1927. It is one of the best examples I can cite that clearly illustrates the scientific approach zdas mentioned in his opening post.

Maui

RE: New study brings into question link between a kind of bacteria and environment

Perhaps I misread your intention but I can hardly be faulted for doing so given the content of this thread:
  • You used a press release about an unpublished paper, which research you've never seen or gone through, as an example of good science. Why would you use a press release as an example of good science? How could you possibly know whether it’s good science when the paper and research has not been released yet?
  • Your title suggests the point of the thread is that a "new study brings into question link between a kind of bacteria and environment".
  • The dialogue between TheTick and yourself appears to carry a tacit assumption that all research that changes our current understating of climate science is good science (despite the fact no one here has any clue whether this is good science or not) and any research that agrees with the current understanding of climate science is dogma. (by the way, that assumption is dogma)
  • The last two sentences in your first paragraph flat out state that you (mistakenly) believe that this research will put into question climate science.
To claim that this thread is purely about celebrating an example of good science (when you have no idea whether it is good science or not) and not at all about suggesting that the current understanding of climate science may be weakened by this press release (even though your title and most of your original post is dedicated to stating exactly that) appears a little bizarre, to say the least.

What’s more, a while ago I referred you to a piece of science (that was actually published and publically available) where the researcher’s results were opposite to his original hypothesis. He didn’t sweep the results under the rug but, instead, accepted the results and changed his opinion on the subject. You were not so receptive of that at the time.

That research was the Berkley Earth Surface Temperature (BEST) data set (and Influence of Urban Heating on the Global Temperature Land Average). The researcher was Richard Mueller.

RE: New study brings into question link between a kind of bacteria and environment

You read to much into this, rconnor. This isn't about whether climate science as a whole is "good science" or "bad science".

My post certainly wasn't a critique of the validity of climate science, but simply a statement that anything that compels us to add to our knowledge is good. Knowledge will stand, regardless of the motivation behind finding that knowledge.

RE: New study brings into question link between a kind of bacteria and environment

(OP)
Maui,
Perfect example. Wish you didn't have to go back to 1927 to find it (sorry, I couldn't stop myself), but it is a great example of doing science right.

Rconnor,
Pleas chill. I never said that that story was the only example of people changing their hypothesis to fit the data, I just thought the story was illuminating and uplifting. Sorry it wasn't pal-reviewed in Nature. No, I'm not really sorry. I don't care if they ever publish the paper. I don't care if they backtrack and publish a paper that ignores the critters that thrived in the methane-rich environment.

The human interest story that was published made me feel good about science for a few minutes. Then I read a pal-reviewed "study" with a headline that said that hydraulic fracture stimulation had caused thousands of earthquakes while the actual paper said that we are seeing an increase in seismic events from salt water injection wells and that data from Oklahoma does not support the conclusion that frac'ing has ever caused an earthquake. Then I read another pal-reviewed study that the title claimed that cancer incidence was higher in the vicinity of the Barnett Shale (DFW area) than in a county with a few thousand people, but no shale gas--I opened that one and found that they were comparing total number of cancers in a population of 6.5 million to the total number in a population of under 50,000, not per capita, total. Then I had to ask a group of scientists to remove their acknowledgement of my contribution to a study on methane emissions from pneumatic equipment because they ignored over 70% of their own data to develop a conclusion that fit their agenda. Forgive me for posting a link to STORY ABOUT PEOPLE OF SCIENCE BEHAVING PROPERLY.

I have read quite a bit about BEST, and think that that team is working very hard to eradicate many of the worst sins in the Historical record. They don't claim to be getting rid of all of them, they are quite honest in their claims and I look forward to future temperature records without arbitrary, un-labeled edits.

David Simpson, PE
MuleShoe Engineering

In questions of science, the authority of a thousand is not worth the humble reasoning of a single individual. ùGalileo Galilei, Italian Physicist

RE: New study brings into question link between a kind of bacteria and environment

I await rconner's reply, pounding the desk with his shoe and proclaiming unto the masses that we should ignore news releases, since "the science is settled".

RE: New study brings into question link between a kind of bacteria and environment

That's the thing about science, that theory may never be proven. That theory may only be disproven, or remain in a state of limbo.

Science is never settled. It is just that the theory is in a stable state of limbo.

Anyone who states science is settled, is in essence trying to sell you a bridge in some part of New York.

RE: New study brings into question link between a kind of bacteria and environment

TheTick, fair enough. I certainly agree with your final sentence.

zdas04, my issue isn’t really that it hasn’t been peer-reviewed yet, my issue is that it hasn’t been zdas04-reviewed yet (which is apparently the true litmus test of scientific accuracy). I cannot understand how someone as skeptical of you could promote a piece of scientific research without seeing (or understanding) the research yourself. Just because they changed their minds does not inherently make it good science. Just because it agrees with or challenges the current understanding of climate science does not inherently make it good science. Good scientific practice makes good science. Since none of us have reviewed the methods, data and results, none of us can tell if its good scientific practice or not.

And I’m glad that you like BEST data. Given how hard this team has been working to “eradicate many of the worst sins in the Historical record”, how much has their data been diverging away from the other sinful data sets and closer towards the truth? What does BEST say about UHI?

btrueblood, what a base-level straw man. I’m quite disappointed as your usually someone who's contributions to the climate science debate I respect. Certainly you understand the difference between saying "the science is settled" and "this press release does very little to undermine the current understanding of climate science".

Furthermore, certainly you understand that there is a difference between “the science will not change at all, ever” and “there is compelling evidence such that a complete overturning of the fundamental concepts is unlikely”. When people say “the science is settled” they don’t mean the former, they mean something much closer to the latter.

RE: New study brings into question link between a kind of bacteria and environment

(OP)
I have replaced a decent hypothesis with a worse hypothesis to fit new data on occasion. A few times when this happened I abandoned the avenue of investigation. Other times I found that the old data did not fit the new hypothesis and had to develop a third (or 53rd) explanation that included all the data. My research has been on little stuff (how to make a downhole jet pump immune from cavitation, how do I cost effectively get gas out of a liquid stream, how can I prevent oil loss in an oil flooded screw compressor), but even at my piddly scale I have to start with an understanding of the initial state and describe (usually in a project proposal) how my intervention will get to the (desired) end state. When the data doesn't match the hypothesis then the hypothesis is wrong. The flooded screw example above required 15 cycles through this morass before the hypothesis matched all the data and the predictions matched actual outcomes.

The act of revisiting the theory in light of unexpected data is good science. Whether their process and data acquisition protocols were proper will come out if they ever write a paper on it (which they certainly will in this publish or perish environment). I will wait to see if I believe their conclusions until I see them.

David Simpson, PE
MuleShoe Engineering

In questions of science, the authority of a thousand is not worth the humble reasoning of a single individual. ùGalileo Galilei, Italian Physicist

RE: New study brings into question link between a kind of bacteria and environment

Maybe the takeaway is that this discussion is proof that science has been to some degree corrupted by dogma/politics, and the apparent sight of someone practicing cool, dispassionate science caused a stir of hopeful excitement.

RE: New study brings into question link between a kind of bacteria and environment

(OP)
I can get behind that statement.

David Simpson, PE
MuleShoe Engineering

In questions of science, the authority of a thousand is not worth the humble reasoning of a single individual. ùGalileo Galilei, Italian Physicist

RE: New study brings into question link between a kind of bacteria and environment

"Maybe the takeaway is that this discussion is proof that science has been to some degree corrupted by dogma/politics"

Sorry, where is the "proof" of that in this discussion?

My issue is that people may be confusing science that disagrees with their dogma/politics with science that is corrupted by dogma/politics. Especially considering the lack of evidence they present to help differentiate between the two.

RE: New study brings into question link between a kind of bacteria and environment

(OP)
I posted three examples above. All three crossed my desk the same week. My desk is a pretty small thing. I have no way of knowing how many are out there, but those three were blatant manipulation of data to fit an agenda.

David Simpson, PE
MuleShoe Engineering

In questions of science, the authority of a thousand is not worth the humble reasoning of a single individual. ùGalileo Galilei, Italian Physicist

RE: New study brings into question link between a kind of bacteria and environment

Oh, you mean those three anecdotes. Remind me again, as you've changed your signature quote, what's the plural of anecdote?

RE: New study brings into question link between a kind of bacteria and environment

(OP)
Well it is not data, you got me there. I have not done an objective evaluation of peer reviewed literature. I simply saw a several examples of bad science being published and it caused me dismay. There is nothing to say that the next 3 or 30 or 300 papers would show the same disdain for fact.

My concern is that a peer reviewer would pass on a paper that compares the count of cancers in a population of 50k to a population of 7 million. Had they compared per capita numbers then the counts may have been scalable, totals were not, but it was published.

I'm concerned that a first tier journal would sanction a study that had 70% null values, 10% real data, and 20% verifyably malfunctioning devices and then create an "average exhaust emissions" using a simple average of the non-null values, and then assigning that silly number to the 70% null values before bulking the study up to a national emissions number. This outrageous value has been published several thousand times since the horrible science appeared in the journal.

I had a paper peer reviewed and published in a second tier magazine recently, the peer reviewers mentioned several commas that were misplaced in the reviewer's opinion. There was one figure that looked like it was hand drawn (because it was) that one guy thought looked unprofessional. Two of the references had had their URL garbled in the translation from Word to .PDF. No mention in the peer review of busted references, I don't think the reviewers even opened the links to see if I properly represented the referenced papers. Not sure what a peer review means in that world.

Just anecdotes. No data here.

David Simpson, PE
MuleShoe Engineering

In questions of science, the authority of a thousand is not worth the humble reasoning of a single individual. ùGalileo Galilei, Italian Physicist

RE: New study brings into question link between a kind of bacteria and environment

Consitering that most people don't have to have any data to make a decision, and I suspect that number much lower in engineers. It is no doubt silly decisions will be made in society.
Also consitering that no one likes to admit they are wrong, it is no suprise that we travel down strange paths.

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