Talk:Bacteriophage/Draft

Article Checklist for "Bacteriophage/Draft"

Workgroup category or categories	Biology Workgroup [Categories OK]
Article status	Developed article: complete or nearly so
Underlinked article?	No
Basic cleanup done?	Yes
Checklist last edited by	Matt Innis (Talk) 10:48, 24 May 2007 (CDT)

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Approval area

David Tribe has nominated the version dated 11:47, 20 May 2007 of this article for approval. Other editors may also sign to support approval. The Biology Workgroup is overseeing this approval. Unless this notice is removed, the article will be approved on May 24, 2007.

David Tribe has made only typographical adjustments to the page and is not an author. However he is expert in the field and teaches senior year college courses in this topic. But the author is more expert than David Tribe

URL pointer first set at http://en.citizendium.org/wiki?title=Bacteriophage&oldid=100105406 18:09, 16 May 2007 (CDT) URL pointer updated http://en.citizendium.org/wiki?title=Bacteriophage&oldid=100107557 David Tribe 03:06, 20 May 2007 (CDT) URL updated http://en.citizendium.org/wiki?title=Bacteriophage&oldid=100107653 David Tribe 06:49, 20 May 2007 (CDT) URL updated http://en.citizendium.org/wiki?title=Bacteriophage&oldid=100108666 David Tribe 16:16, 21 May 2007 (CDT)

It seems there is an individual approval that ends today, May 24, 2007. I see that the person approving the article has not worked much on the article. It therefore stands approved with URL updated http://en.citizendium.org/wiki?title=Bacteriophage&oldid=100108666 --Matt Innis (Talk) 12:07, 24 May 2007 (CDT)

Images

The images within should be in the public domain. I was given the photos by colleagues from whom, if it came to that, I can request permissions. I can't immediately verify the false color T4 photo's provenance, so I removed it.

I've had to delete most these images:

• Image:Phage_lifecycle.gif
• Image:Lambda.jpg
• Image:T-_4_Phage.gif
• Image:Phage.gif

because of lack of source documentation for them. I hate doing that. If someone gives me a list of what exact images are still needed, I'll make an effort to find replacements we can fully document. The above four could in a snap be undeleted, too, if the source and copyright status can be verifiably documented. Stephen Ewen 15:39, 16 May 2007 (CDT)

Scientists comments on first reading

• You begin with "In 1896, M. E. Hankin reported that something in the waters of the Ganges and Jumna rivers in India had marked antibacterial action against cholera and could pass through a very fine porcelain filter (Adhya and Merril 2006)." Yet, you do not mention what the significance of that is, and you do not take adavantage of weaving a little mystery here. I happen to know, because my mother as a young woman was a cook in "Mr.Stanley"'s household, that the first virus was not identified then and that a notable characteritic for the early virologists was this ability to pass through porcelain. I do not think this is universal knowlege.

• This article looks great and I am probably as good non-expert person to review it as anyone, I am going to quote a sentence that confuses me.

"One of the densest natural sources for phages and other viruses is sea water, where up to 107 phages per ml (or, at least, of virus-like particles)(Wommack & Colwell 2000). Whitman et al. (1998) argue that there are between 1030 and 1031 prokaryotic cells on our planet." ?????Nancy Sculerati 18:28, 16 May 2007 (CDT)

• Question: quoting the text:"Twort's work was interrupted by the onset of World War I, and when he returned to the Brown Institution, he spent the rest of his career trying to grow bacteriophages on artificial medium." Please include the punchline! He failed I take it because he didn't try to grow them in bacteria? Or what?Nancy Sculerati 18:35, 16 May 2007 (CDT)

• "Duckworth (1976) provides a historical account of the discovery of bacteriophages." This is a non-sequitor. Perhaps you should put his article or book under further reading and place this descriptor next to it. Nancy Sculerati 18:32, 16 May 2007 (CDT) Oh, I see- the next part is a summary of his writing? I don't know this history, if I did I would help you, but I suggest that you simply tell the story rather than give a list of events. Why are thses events important?

• Similarly, with the list of fmilies, the classification. I think what is needed here is an expalanation of how the taxonomy works, what features are used to classify the phages and why are these features important. Maybe it was a historical thing, I don't know, but some concepts need to be conveyed here. And then I suggest that either you make a catalog of the families that are presently in this list and link that to the article, or you make a table of this list that is not just a list but is arrayed in a manner that conveys the concept of how bacteriophages are classified.Nancy Sculerati 18:44, 16 May 2007 (CDT)

• Third paragraph: If one phage per cell is assumed, I would expect the argument to arrive at the same number of phages as cells, but the number of cells is given as $10^{30}$ to $10^{31}$ and the number of phages as $10^{30}$ to $10^{32}$. I would expect "conservatively" to mean that the number of phages is if anything underestimated; maybe it was intended to mean the opposite here but I don't find that clear. --Catherine Woodgold 20:39, 20 May 2007 (CDT)

• It would be good to have a concluding paragraph that gives the reader a definite feeling that they've come to the end of an article. Here's an attempt at one — no doubt others can do better than this, though: "As we have seen, the study of bacteriophages is a flourishing science which has contributed to some of the fundamental discoveries of biology. In addition to contributing to pure science, promising uses in food safety, medicine and nanotechnology are on the horizon, if not already here. Who would have thought such a small particle would turn out to be of such importance?" --Catherine Woodgold 21:02, 20 May 2007 (CDT)

Non-scientists comments on first reading

• The historical account of the discovery of bacteriophages strikes me as lacking. It might be very interesting to get a bit inside the heads of the people who made these discoveries, to understand what drove them and how they viewed their successes and failures. Choice quotes from memoirs, etc, is a great technique by which to do that. Stephen Ewen 04:37, 17 May 2007 (CDT)

• The meaning of "This specificity means that a bacteriophage can only infect certain bacteria bearing receptors that they can bind to, which i.e. determines the phages hostrange" is unclear to me. Believing the problem is only one of wording, and hoping I changed no meaning, I reworded it to, "This specificity means that a bacteriophage can only infect bacteria that bear the certain types of receptors that they can bind to, which determines the phages hostrange. Stephen Ewen 18:49, 16 May 2007 (CDT)

fixed it, I hope.Nancy Sculerati 11:24, 17 May 2007 (CDT)

Excellent, Nancy. I completely and without effort grasp your re-wording and minor expansion. Stephen Ewen 13:42, 17 May 2007 (CDT)

• The section Major discoveries with phages might be better if explained in a narrative. Stephen Ewen 03:49, 17 May 2007 (CDT)

• The section "Structure": 1) This section would be better narrated as well, I think. 2) it would be helpful if I had points of reference with which to compare "from 24-200 nm". Since people learn using contrasts, compare this size with one or two common things from microbiology, and then how many would fit on a pin-head or a period, for example. 3) The statement "In the more complex phages, like T4" seems to lack context. Perhaps mention in the Intro or somewhere that phages range from the simplest, e.g., x, to ones like T4. Better, expand the classification section to show how they compare, and to contrast the features that more complex phages have that simpler ones do not. Stephen Ewen 04:20, 17 May 2007 (CDT)

• The section "Release of virons": "Host lysis is usually achieved through an enzyme called endolysin which attacks and breaks down the peptidoglycan, which is....". If a peptidoglycan can be described in a few words, it'd be helpful. Otherwise, I am lost on that point. Stephen Ewen 04:20, 17 May 2007 (CDT)

Congratulations

I like it, hope my copy edits and minor style tweaks are OK. I stuck at the lead with an unanswered question If we assume that there is one virus for every prokaryote host.... Why would we assume this exactly?Gareth Leng 09:38, 17 May 2007 (CDT)

On this point, there are number estimates on phage numbers in the oceans that indicate virus (phage) numbers exceed bacterial number. Couldn't this point be leveraged off these actual data rather than an assumption? David Tribe 21:24, 17 May 2007 (CDT)

If you can point me to a source that I'd be expected to be able to access from the electronic resources of a large university, I'd be happy to look it up, add it, and cite it. Stephen Ewen 03:29, 23 May 2007 (CDT)

Congratulations and apology

I made a number of additions, and some revisions, that -to me-make the article more of a narrative story. I read the references (what good ones!) supplied to do so, and hope that these changes have not hurt the accuracy of the article. Therein lies the "apology". Please change and revert without question anything that has impaired the sense of the article rather than clarified it. Nancy Sculerati 08:12, 19 May 2007 (CDT)

minor point (that I am too lazy to look up myself)-Tectiviridae has no descrfiption in the list.Nancy Sculerati 05:18, 20 May 2007 (CDT)

Image, Link

• This is usable if wanted and if we get the person's name: http://www.flickr.com/photos/ajc1/464055431/
• This seems like an interesting External link: http://www.rowland.harvard.edu/organization/past_research/bacteriophage/phageaction.html

Stephen Ewen 21:31, 20 May 2007 (CDT)

Some suggested edits

I enjoyed reading this article and learned lots of things I hadn't known.

One way to present the list of strains is as a table like this: User:Catherine Woodgold/listbox. "Classification" can be handled similarly or moved onto a separate "list" page. I agree with Stephen Ewen that the list of discoveries could be productively written into a narrative.

The section "Phage ecology" seems to me to disrupt the flow of the article where it is. I suggest either deleting this section and putting some of the information in "See also" and "External links" sections, or somehow combining it with the "Bacteriophage experimental evolution" subsection, although that might require moving the latter out of a "uses" section, or finding some other way to tie the information into a logical flow of the article.

Under Structure, I would delete the subheadings and elminate the parentheses in the first paragraph as follows: "Most phages are 24–200 nm in length, in comparison to a typical bacterium cell which may be about 1000 nm long, i.e. 1/1000th of a millimeter or 1 micron in length."

3. Tail: "At the end of the tail, some phages have a base plate and one or more tail fibers attached to it;" If the fibers are attached to the plate, I suggest changing "and" to "with". If, on the other hand, the fibers are attached to the tail, I suggest "Attached to the end of the tail of some phages are a base plate and one or more tail fibers;"

Section "Replication": Because "lytic" may be an unfamiliar word, I suggest moving the phrase "and most undergo a lytic lifecycle" later in the paragraph so it will be closer to the explanation of the meaning of "lysis". It could then look like this: "Bacteriophages are obligate parasites: to propagate, they must enter bacterial host cells. Once inside a host cell, phages hijack the host cell's DNA replication machinery and induce the host to manufacture more phages. Most bacteriophages undergo a lytic lifecycle: when enough phage offspring are produced..."

Section "Attachment": the 3rd and 5th sentence repeat some of the same information. I suggest reformulating the 3rd, 4th and 5th sentences to: "Each type of phage has only a certain set of features that it recognizes. This means that a bacteriophage can only enter bacteria that bear the certain types of receptors that they can bind to, and it is these portals of entry that determine the phage's "host range". Phages are said to have "specificity" for the bacteria that they do infect."

Section "Virion assembly": "...will spontaneously assemble with the tail." I think this is intended to mean that they spontaneously join, but it sounds as if it might mean that the capsid assembles itself spontaneously and so does the tail. I suggest "...will spontaneously join to the tail."

"The whole process takes about 15 minutes." Please specify: the process of assembling one virion? (Or the whole process from infection to lysis?)

I suggest also changing "salient" to "ambient" (2nd paragraph of "lysogenic life cycle").

Section "Nanotechnology": snails transform abalone into two crystalline structures? I think abalone are a mollusc; I don't see how an animal can be tranformed into a crystalline structure. Possibly it should say "abalone shells" instead of just "abalone"?

Larry, I'm delighted that you've changed "species" to "type". I had almost put "type" and wasn't sure which was better.

I've also made a couple of comments in the "first reading" section above; I hope they aren't missed because everything else in that section is several days old. - Catherine Woodgold 15:53, 21 May 2007 (CDT)