As you can see, I am an Engineer, and I almost know nothing about Biology and Medicine, however reading this article was really informative and it was very clear even for someone like me.
I liked the following parts the most:
"Thus, to imagine that the raison d’être of pathogenic or opportunistic bacteria is to survive by “harming” their host is simplistic, to say the least. The alternative viewpoint, which remains surprisingly uncommon in scientific literature and textbooks, is that some bacteria that had been stranded in the human body were driven to gradually evolve and adapt to such a hostile environment"
"Who attacks whom, that is the question! Indeed, the fact that we, humans, have more bacterial cells than our own cells has prompted the rhetorical question, “who parasitizes whom?”"
Competing interests
None declared
Countering anthropocentrism
Merry Youle, Writer/editor
11 August 2009
I was delighted by this excellent (open access!) commentary expressing a much needed perspective. The ideas expressed are very pertinent to all of biology, yet are all too often dismissed as trivial. Our anthropocentrism is deep, pervasive, unquestioned. The distortions in our way of seeing the rest of the planet seem to be particularly strong when it comes to microbes (including viruses). We miss so much by seeing them only in terms of their impact on our lives or their potential usefulness to us. As Aziz points out, this myopia has led to the skewed selection of genomes for sequencing, and thus the terra incognita remaining within the Tree of Life even as we approach 1,000 sequenced microbial genomes. Fortunately, biocentrism is increasing, thanks in part to the publication of articles such as this.
When I read the article for the first time, I was shocked! The article is providing a very different perspective, at least different than what I always dreamed of as a pharmacy student, to terminate harmful bacteria by designing an effective, highly selective chemotherapeutic!
What I got from the article is that the current human-centered view for microbiology has three major drawbacks: 1) Compared to medical microbiology, environmental microbiology is way underestimated, to medical students for example 2) It's clouding the overall view regarding bacterial evolution, because we stay focused on just m.o. of medical interest apart from their relatives from non-pathogenic bacteria 3) It's not providing us with the big picture of pathogenesis.
In fact, I spent all my life thinking that revolutionary ideas are THE ONLY ones accepted from publication and funding agencies, not resisted!!! But when Dr. Aziz mentioned Galileo's example, I get it (I was not aware of the H. pylori fight! A very interesting story).
The writing style is exciting; keeping one alerted the entire article. The idea is new, not tracked before. Also gathering all those thoughts & examples and organizing them is really amazing (I liked the PCR Taq-polymerase example the most). Regarding arguments listed, I believe that they are logical, the tabular form is very interesting and the final balancing paragraph -the conclusion- is saying it all. The "competing interests" part is fantastic! I do agree with "controlled vocabulary" for protein annotation, it's quite hard to search for a protein with current annotations. I'm also a big fan of the questions part, an excellent idea to open up discussion topics, especially for those who are not-natural-born brainstormers like myself!
I have one "undergraduate" comment: If we didn't use the nomenclature "Eukaryotes and prokaryotes", what should it be?
I thank Dr. Aziz for such an interesting, criticizing article that made us –pharmacy students- see microbiology from a very different perspective and hope him the best.
Competing interests
None declared
Thanks + Answer
Ramy Karam Aziz, Faculty of Pharmacy, Cairo University
20 August 2009
It is certainly a pleasure to see comments by a networks engineer, a science editor, and one of my undergraduate students, especially that online commenting on scientific articles is not yet as popular as commenting on blog posts. This is particularly encouraging because I was hoping that the article can reach a wide audience, not just microbiologists and ID specialists.
As an answer to Mariam's "undergraduate" question: In the cited references 21 and 23, Norman Pace* leads a campaign to use the terms Bacteria and Arachaea as two different groups, and to avoid using the term prokaryote/procaryote. His call does not go unchallenged (see for example references 22 and 24). We definitely still use a lot of scientifically inaccurate terms (including the term microorganisms itself), and it is up to you to decide which one to use. One day we may end up with five or more domains of life, and things will then change... _______ * http://pacelab.colorado.edu/PIpage.html
Competing interests
I am the author of this article.
What is a pathogen?
Xandra Smith, Danisco
5 September 2009
I agree with the author that the study of microbes should be all inclusive and not focus mainly on those that interact with humans, whether in a beneficial or harmful way. However, describing bacteria as having a pathogenic lifestyle is in itself, anthropomorphic. Many bacteria considered pathogens are not generally harmful to humans, but are in the wrong place or in the right place at the wrong time. Using your example, legionellae are not normally present in human macrophages, but in protozoa i.e. they are in the wrong place. Bacterial diarrheal disease in neonates may be caused by coliforms, which are commensal to the gastrointestinal tract, but usually only become established at later time points. Due to alterations in human behaviors; e.g. formula feeding; these bacteria are in the right place at the wrong time. Using your analogy of humans in a forest, if there are few humans and a large forest then a nomadic lifestyle will reduce negative impacts of the humans on the forest. However if the humans are prevented from moving around or increase drastically in number then the negative impacts will be far greater and the forest may not be able to recover.
Competing interests
None
Correction
Ramy Karam Aziz, Cairo University
28 December 2009
I have been emailed by a reader about a typographical mistake.
The end of the first paragraph of the Introduction section should read: "for years[4]" instead of "for year[4]".
Below is the original reader's email, sent on 11 Sep 2009:
" Dear Dr Aziz,
Thanks very much for your paper on anthropomorphism in microbiology. It was a very enjoyable read, as well as making an important point about the universe. Congratulations!
There is a typo at the end of the first paragraph of the introduction: it reads "a landmark discovery that was resisted for year[4]." That should be years.
That is all, Best wishes Douglas Carnall "
Competing interests
I am the author of this article.
I agree
Ramy Karam Aziz, Cairo University
28 December 2009
Dear Xandra, thanks for your comment "However, describing bacteria as having a pathogenic lifestyle is in itself, anthropomorphic." I certainly agree. There are many anthropocentric/anthropomorphic terms in the article, including the term 'microbes' itself. I just had to use some conventional terms to avoid being fully (mis-)understood!
"Many bacteria considered pathogens are not generally harmful to humans, but are in the wrong place or in the right place at the wrong time." I agree too. I referred to this particular point in this commentary: A hundred-year-old insight into the gut microbiome!
Network Architect
8 August 2009
As you can see, I am an Engineer, and I almost know nothing about Biology and Medicine, however reading this article was really informative and it was very clear even for someone like me.
I liked the following parts the most:
"Thus, to imagine that the raison d’être of pathogenic or opportunistic bacteria is to survive by “harming” their host is simplistic, to say the least. The alternative viewpoint, which remains surprisingly uncommon in scientific literature and textbooks, is that some bacteria that had been stranded in the human body were driven to gradually evolve and adapt to such a hostile environment"
"Who attacks whom, that is the question! Indeed, the fact that we, humans, have more bacterial cells than our own cells has prompted the rhetorical question, “who parasitizes whom?”"
Competing interests
None declared
Countering anthropocentrism
11 August 2009
I was delighted by this excellent (open access!) commentary expressing a much needed perspective. The ideas expressed are very pertinent to all of biology, yet are all too often dismissed as trivial. Our anthropocentrism is deep, pervasive, unquestioned. The distortions in our way of seeing the rest of the planet seem to be particularly strong when it comes to microbes (including viruses). We miss so much by seeing them only in terms of their impact on our lives or their potential usefulness to us. As Aziz points out, this myopia has led to the skewed selection of genomes for sequencing, and thus the terra incognita remaining within the Tree of Life even as we approach 1,000 sequenced microbial genomes. Fortunately, biocentrism is increasing, thanks in part to the publication of articles such as this.
Competing interests
None
Exciting article.
17 August 2009
When I read the article for the first time, I was shocked! The article is providing a very different perspective, at least different than what I always dreamed of as a pharmacy student, to terminate harmful bacteria by designing an effective, highly selective chemotherapeutic!
What I got from the article is that the current human-centered view for microbiology has three major drawbacks: 1) Compared to medical microbiology, environmental microbiology is way underestimated, to medical students for example 2) It's clouding the overall view regarding bacterial evolution, because we stay focused on just m.o. of medical interest apart from their relatives from non-pathogenic bacteria 3) It's not providing us with the big picture of pathogenesis.
In fact, I spent all my life thinking that revolutionary ideas are THE ONLY ones accepted from publication and funding agencies, not resisted!!! But when Dr. Aziz mentioned Galileo's example, I get it (I was not aware of the H. pylori fight! A very interesting story).
The writing style is exciting; keeping one alerted the entire article. The idea is new, not tracked before. Also gathering all those thoughts & examples and organizing them is really amazing (I liked the PCR Taq-polymerase example the most). Regarding arguments listed, I believe that they are logical, the tabular form is very interesting and the final balancing paragraph -the conclusion- is saying it all. The "competing interests" part is fantastic! I do agree with "controlled vocabulary" for protein annotation, it's quite hard to search for a protein with current annotations. I'm also a big fan of the questions part, an excellent idea to open up discussion topics, especially for those who are not-natural-born brainstormers like myself!
I have one "undergraduate" comment: If we didn't use the nomenclature "Eukaryotes and prokaryotes", what should it be?
I thank Dr. Aziz for such an interesting, criticizing article that made us –pharmacy students- see microbiology from a very different perspective and hope him the best.
Competing interests
None declared
Thanks + Answer
20 August 2009
It is certainly a pleasure to see comments by a networks engineer, a science editor, and one of my undergraduate students, especially that online commenting on scientific articles is not yet as popular as commenting on blog posts. This is particularly encouraging because I was hoping that the article can reach a wide audience, not just microbiologists and ID specialists.
As an answer to Mariam's "undergraduate" question: In the cited references 21 and 23, Norman Pace* leads a campaign to use the terms Bacteria and Arachaea as two different groups, and to avoid using the term prokaryote/procaryote. His call does not go unchallenged (see for example references 22 and 24). We definitely still use a lot of scientifically inaccurate terms (including the term microorganisms itself), and it is up to you to decide which one to use. One day we may end up with five or more domains of life, and things will then change...
_______
* http://pacelab.colorado.edu/PIpage.html
Competing interests
I am the author of this article.
What is a pathogen?
5 September 2009
I agree with the author that the study of microbes should be all inclusive and not focus mainly on those that interact with humans, whether in a beneficial or harmful way. However, describing bacteria as having a pathogenic lifestyle is in itself, anthropomorphic. Many bacteria considered pathogens are not generally harmful to humans, but are in the wrong place or in the right place at the wrong time. Using your example, legionellae are not normally present in human macrophages, but in protozoa i.e. they are in the wrong place. Bacterial diarrheal disease in neonates may be caused by coliforms, which are commensal to the gastrointestinal tract, but usually only become established at later time points. Due to alterations in human behaviors; e.g. formula feeding; these bacteria are in the right place at the wrong time. Using your analogy of humans in a forest, if there are few humans and a large forest then a nomadic lifestyle will reduce negative impacts of the humans on the forest. However if the humans are prevented from moving around or increase drastically in number then the negative impacts will be far greater and the forest may not be able to recover.
Competing interests
None
Correction
28 December 2009
I have been emailed by a reader about a typographical mistake.
The end of the first paragraph of the Introduction section should read: "for years[4]" instead of "for year[4]".
Below is the original reader's email, sent on 11 Sep 2009:
"
Dear Dr Aziz,
Thanks very much for your paper on anthropomorphism in microbiology. It was a very enjoyable read, as well as making an important point about the universe. Congratulations!
There is a typo at the end of the first paragraph of the introduction: it reads "a landmark discovery that was resisted for year[4]." That should be years.
That is all,
Best wishes
Douglas Carnall
"
Competing interests
I am the author of this article.
I agree
28 December 2009
Dear Xandra,
thanks for your comment
"However, describing bacteria as having a pathogenic lifestyle is in itself, anthropomorphic."
I certainly agree. There are many anthropocentric/anthropomorphic terms in the article, including the term 'microbes' itself. I just had to use some conventional terms to avoid being fully (mis-)understood!
"Many bacteria considered pathogens are not generally harmful to humans, but are in the wrong place or in the right place at the wrong time."
I agree too. I referred to this particular point in this commentary: A hundred-year-old insight into the gut microbiome!
Thank you again for the critical reading
RKA
Competing interests
I am the author of this article.