Talk:Molecular paleontology

Untitled

Hello all,

We are trying to create the article page for "Molecular paleontology". Below is a suggested outline, as well as references that we are thinking of using. Let us know if there are any other things that could help us develop this article page better.

Outline for Molecular Paleontology

   1.1 Overview of Molecular Paleontology
   1.2 History of Molecular Paleontology
   1.3 Applications of Molecular Paleontology
   1.4 Methods
       1.4.1 Techniques for Sequencing DNA preserved in fossils
       1.4.2 Techniques involved in isolating and amplifying ancient DNA
       1.4.3 Environmental Conditions Needed to Preserve DNA for Long Periods of Time
   1.5 Notable Achievements
   1.6 Challenges
   1.7 See also:
   1.8 Further Readings
   1.9 Links
   1.10 First Look at Usefulness of References
   1.11 References

First Look at Usefulness of References

• "Molecular paleontology" - Defines molecular paleontology (MP), describes limitations on MP and challenges, explores approaches to MP.

• "A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA" - A review of the origins and growth in MP; explains challenges overcome in MP.

• Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification - Techniques for DNA extraction and amplification of DNA from 4 to 13,000 years old. DNA from two extinct animals (Giant Ground Sloth and the Marsupial Wolf) are analyzed.

• Ancient DNA DNA decay and retreival, assessment of preservation, neanderthals

• Review Paper, Ancient DNA - Apparently, Molecular Paleontologists are not the most creative with their paper names. Review of history of collecting Ancient DNA, Degradation, contamination, and other challenges.
• Resurrecting ancient animal genomes: The extinct moa and more - Hair proves itself extremely useful in MP due to low levels of contamination. The Wooly Mammoth genome is completed using hair. 2012 article.

• "Analysis of one million base pairs of Neanderthal DNA." - Early analysis of 38,000 year old neanderthal genome suggests humans and neanderthals diverged 500,000 years ago.

• THE FUTURE OF MOLECULAR PALEONTOLOGY." - A review of the history and outlook of Molecular Paleontology

• Reconstructing Deep-Time Biology with Molecular Fossils - This chapter of this book explores information gathering from Molecular Fossils with largely non-DNA methods. Reviews sampling strategies and preparative methods and extraction, as well as analytical methods and interpretation.

• Molecular Palaeontology - This is a Secondary Article, however it does include a great overview of the different methods used, as well as original sources.

• Molecular paleontology: a biochemical model of the ancestral ribosome - An example of molecular paleontology being used to develop a model. Thought that this could just be added to "suggested reading" section.

References

Cchandu1 (talk) 21:18, 11 March 2014 (UTC)

Comments from Amontei2

Great start! I think using the outline above will provide viewers with a variety of resources and explanations about Molecular Paleontology. Since the article still under construction, I would recommend adding some images of the techniques you will be describing to make it easier for beginners to understand. A couple questions/suggestions I have while going over the article are as follows:

• I see you have explained what Molecular paleontology is, wouldn't that be considered under the overview section? If not what would be under that section?
• Since history and science are closely related in this field, I thing viewers would appreciate to have a larger history section. Maybe you could list the most famous/interesting discoveries made in the last years (you could do a chronological time line graph, for example). Your reference number 8 (in the talk page- here is the link: http://palaeo-electronica.org/2002_2/editor/r_and_p.htm) is loaded with the history of many discoveries and future prospective in the field, and I think you should utilize this source to the max!

Overall, I think you are on the right track and you have plenty of room to expand :)Amontei2 (talk) 19:53, 28 March 2014 (UTC)

I think the timeline is a great idea! Maybe even for the achievements section? Gkaltam (talk) 01:24, 29 March 2014 (UTC)

Yes! That would also look very nice! I just saw your comments and I also agree with your suggestions in regards to the rearrangements. Amontei2 (talk) 23:38, 29 March 2014 (UTC)

Thank you for you input. All great suggestions. I agree that the Overview section is redundant, and the chronological timeline is also a great idea! We will look more into this. PaleoBioJackie (talk) 09:03, 31 March 2014 (UTC)

Thanks for your suggestions, will definitely look more into the overview section, as well as expanding the history section. Cchandu1 (talk) 18:48, 7 April 2014 (UTC)

Hi there! The changes look really good, the article is looking great!Amontei2 (talk) 11:02, 9 April 2014 (UTC)

Comments from Gkaltam

Hi all!

I really like your outline, and the language used in your article. It is nice and easy to understand. However, I think that in the methods section, the amplification subsection should come before the sequencing section since that is how the method goes. It would make the article flow better I think. I also think the Challenges section may want to come before the notable achievements section.

In addition, perhaps make a distinction in the type of DNA testing that is being used, like nuclear vs. mitochondrial. If the specimen is hair, it is most likely mitochondrial testing because there are no nuclei in hair. Also, be careful about the wording in the environmental conditions section because it seems very similar to the article that is referenced.

Finding some more sources may be beneficial in filling out the rest of the article nicely. Nice job so far though! Gkaltam (talk) 01:23, 29 March 2014 (UTC)

Thank you for your input Gkaltam! I agree that a rearrangement is in order, I will adjust accordingly. I will look into the section you mentioned, I definitely don't want to have any hints of plagiarism in our article. Good point to in making sure to differentiate between mitochondrial and nuclear DNA. Thanks again!PaleoBioJackie (talk) 09:04, 31 March 2014 (UTC)

We will definitely look into rearranging. Thank you for your comments! Cchandu1 (talk) 18:48, 7 April 2014 (UTC)

We rearranged the sections so that the Amplification section comes before the Sequencing section. Thank you for your suggestion on that. As for the notable achievements sections, it seems to be more of a part of the history section so it has been removed for now. Cchandu1 (talk) 04:11, 9 April 2014 (UTC)

Your article is looking better and better every time I see it. Is there a way to maybe put the timeline in more a table setting? It may make it look a little bit neater.Gkaltam (talk) 19:52, 13 April 2014 (UTC)

I love this idea, I will look into it. Thanks! PaleoBioJackie (talk) 22:31, 15 April 2014 (UTC)

Your page looks like it deserves Good Article status! Great job!Gkaltam (talk) 00:24, 5 May 2014 (UTC)

Comments from Klortho

Hi, I think you guys are off to a great start! I know it was a lot of trouble getting the article launched, and congratulations on that.

• General comments
  • Kudos for writing at a very easy-to-understand level. The #1 problem I see with articles for this class is that they are too technical. You guys have really done a good job on this score.
  • You probably don't need a separate "Overview" section. That's what the lead is for.
  • Not enough wikilinks. There are lots of terms throughout the article that should be turned into links.
  • More content, please! You are off to a good start, but should maybe have a bit more content than this by now. For instance, there's nothing (except in the figure caption) about Neanderthals -- that's a big omission, isn't it?
  • I have to say that I am not crazy about your overall outline, but that I don't have a specific alternative suggestion. I like "History", but I'm not sure that Applications / Methods / and the rest is the right way to break up the rest of the content. Maybe you could poke around for other WP articles that cover similar topics, or maybe you could ask Keilana - she would probably have some ideas.

• The lead
  • It is not clear to me how the sentence, "The study of ancient DNA has been found to yield substantial insights into evolutionary events, species' diasporas, population bottlenecks, and can quantify the level of relatedness between any two organisms", is supported by your reference #2 (Shapiro and Hofreiter). I'm not saying that it isn't, but I skimmed the article, and can't find anything. Could you clarify that here, or else rewrite the sentence, or add another reference?

• History
  • Don't use abbreviations like "mtDNA" without first introducing them. You could put this abbreviation in parentheses after the first occurrence of "mitochondrial DNA".
  • Similarly, "3-4 Myr" → "three to four million years ago".

• Applications
  • "De-extinction" → headings should never be hyperlinks. Also, unless you plan to have other applications, then you shouldn't have just one subsection under a main section; you should get rid of the extraneous heading level.
  • Could you elaborate on how exactly de-extinction is achieved through the tools of molecular paleontology? I know you are talking about cloning, but you never explicitly state it.
  • Also, more details would be nice: how is cloning done? How does this kind of cloning differ from run-of-the-mill cloning? Etc. Maybe you plan to cover that in the Methods section; that would be fine.
  • Why are the ethics controversial? What are the issues? More content, please!

• Methods. Could the subheadings here be shorter? They are a bit too long.

• Notable achievements. I am not sure that you need this section. I would think that these could be included in the "History" section. But, see my comment above about maybe redoing the outline.

Klortho (talk) 02:50, 31 March 2014 (UTC)

Klortho, thank you for taking the time to review our article. I look forward to implementing all of these ideas. PaleoBioJackie (talk) 09:08, 31 March 2014 (UTC)

Thank you for these comments and we will definitely be using them to help develop the page more.Cchandu1 (talk) 18:48, 7 April 2014 (UTC)

Just wanted to update. The Introduction section was redone because the reference was incorrect. The methods section was expanded, as well as made the headings sorters. We are continuing to add in more images and restructuring the page. Cchandu1 (talk) 21:40, 22 April 2014 (UTC)

Comments from CarpeDiem90

Hey all, I think you guys did a wonderful job on the article. After reading through the comments from the first peer review, you have expanded the article in great depth and have a well thought-out outline/layout for improving the article. Here is what I like/my comments about the article:

• Great flow-through - However, I think it would be better if you would add the "applications" section after the "methods" section. That way the reader knows that these methods and techniques are used in molecular paleontology and then they can read about how these methods are application in real life situtations.

• Great external links/paragraph incitation techniques. I especially like that you have certain key words that are linked to other wikipedia articles since the audience may/may not know the definitions of the word

• The images are appropriate for the article - however I do think the images are a bit blurry and see if you can find more clearer pictures to use in the article.

• More references could greatly expand the article.

Overall, an exceptional job after a first review on the article!

CarpeDiem90 (talk) 13:37, 15 April 2014 (UTC)

Thank you CarpeDiem90, I definitely agree with the Applications reordering. I have been trying to figure out how to introduce some concepts talked about there and that would be a great way to do it. Thank you for your input. We are continuing to expand the article and add references. Please let us know if you have any other ideas. PaleoBioJackie (talk) 22:29, 15 April 2014 (UTC)

The article looks great guys!! I really loved how well it all came together in the end! Great job! CarpeDiem90 (talk) 01:40, 7 May 2014 (UTC)

Comments from mmehta10

Hello!

I think you have done a fantastic job on this article overall! I really liked that you added some history and timeline as this creates a great impact around the efforts and accomplishments made in the field. I also liked that you have wiki-linked words such as "racemization" as I did not have previous knowledge about that. There are just a few things I'd like to mention that stuck out while reviewing the article, these are:-

• Applications: Wiki-link "Neanderthal" just once since it is used quite a bit in the article.
• Techniques: At least a line or two introducing 'Isolation' and 'Sequencing' with appropriate wikilinks so that people can indulge in those for further details about individual techniques.
• References: Prüfer, Kay et al doi:10.1038/nature12886 reference appears twice so this can perhaps be clubbed to avoid repetitions.

Also if I may, I'd like to suggest possibly adding a section with information about some "Future Directions of Molecular Paleontology"?

Keep up the good work guys! Mmehta10 (talk) 23:40, 15 April 2014 (UTC)

Thank you for your comments! They were definitely helpful, especially for catching the references and wiki-linking neanderthal. Changes have been made and were definitely still working on the techniques section. Adding a Section for "Future Directions" is definitely seems like a good suggestion and, if time permits, we'll see about adding it. Thanks again! Cchandu1 (talk) 05:04, 16 April 2014 (UTC)

Great ideas, mmehta10! Thanks for catching the double reference. We will make your suggested changes to the article. PaleoBioJackie (talk) 23:05, 21 April 2014 (UTC)

Thanks for adding more information under techniques. The article looks even more interesting that before! Great job team! Mmehta10 (talk) 03:27, 23 April 2014 (UTC)

Thank you.Cchandu1 (talk) 22:03, 6 May 2014 (UTC)

I think it's time for this article to receive a high quality scale by Wikipedia!Mmehta10 (talk) 01:14, 7 May 2014 (UTC)

Comments from Graeme

I think that you have picked a great topic. It has a lot to cover. I have heard quite a few stories about topic covered in this in the last year. Anyway to actually comment on the article: There are still more subtopics to cover.

• Are there other molecules in this topic apart from DNA? I am sure I have heard about detection of pigmentation, included by detecting copper or other metals present in metalloproteins.
• There is a tag at the end of the lead still (check).
• There are time dependent statements like "grown tremendously in the last decade" - much better to say which decade, as when someone reads this in 2020 it will be out of date, see Wikipedia:DATED.
• When you are writing a summary of something we already have an article you can put {{main|de-extinction}} under the headng giving
  Main article: de-extinction
  .
• please link Denisovans in the characterization of new species section.
• We could also have links to DNA preservation (even if is not written yet). degraded DNA could be redirected to Ancient DNA which covers some similar ground. With Mitochondrial DNA link it the first time you use it. Also link amino acid analysis and immunological method (though I don't know which article), Palaeobotanist (fix your spelling).
• mitochondrian misspelling of mitochondria. Graeme Bartlett (talk) 08:32, 16 April 2014 (UTC)

Thank you for your comments. Especially for the additional wiki-links and spelling mishaps. Definitely working on making all of the changes you suggested and I also recall reading about metal detection so I will try to add something in about that. Thanks again and if there are any other suggestion, please let us know! Cchandu1 (talk) 23:13, 18 April 2014 (UTC)

Thank you, Graeme, for taking the time to write some really quality comments. Your comment about not dating the article and considering future readers was not something I had considered previously. We will continue to improve the article and address all of your concerns. I am interested in considering other molecules in this topic apart from DNA, I will do some more research on this. PaleoBioJackie (talk) 23:03, 21 April 2014 (UTC)

Reordering a little bit

I am going to start reordering the article over the next few minutes. I hope the overall effect will be an easier to understand article structure. PaleoBioJackie (talk) 19:21, 22 April 2014 (UTC)

This topic is so vast! There is so much more that one could write. PaleoBioJackie (talk) 06:08, 23 April 2014 (UTC)

Comments from Neelix

Thank you for doing such great work on this article. Here are recommendations for further improvement:

1. The title of the article should only be bolded once in the lead.
2. There should be no need to include any citations in the lead as the lead should only be a summary of the body.
3. In order to be considerate of users with visual impairment, it would be beneficial to add alternative text to the images.
4. This article currently has only one incoming link from another Wikipedia article. I would recommend linking to this article from other articles, either manually or by adding a link to a relevant navbox or sidebar. You may wish to consider whether or not this template would be suitable. Neelix (talk) 21:06, 27 April 2014 (UTC)
5. The article would look better if the lead image was moved to the top of the article so that the image and text of the lead were side-by-side.
6. All information should be sourced; the statements in the "Discovery and Characterization of New Species" section are currently unsourced, as are other statements in the article.
7. There should be no capitalization in the section headings except what is required for paragraphical content; "Limitations and Challenges", for example, should read "Limitations and challenges".

Wikipedia is a better place because of your contributions. I hope that you will contact me if you have any questions about the above. Neelix (talk) 21:06, 27 April 2014 (UTC)

Thank you for your recommendations! We have already started to incorporate some of them such as having the title bolded only once, as well as moving the lead image. Changing the capitalization of the section headings also helped make the page look more uniform.

As for including the citations in the lead, it was done to ensure that everything was sourced and that there would be no conflicts arise due to this. Thank you for pointing out the missing sources in the Discovery section, we will definitely look into that. We will continue to work on improving the page and if you have any additional recommendations please let us know.

Thank you. Cchandu1 (talk) 18:21, 29 April 2014 (UTC)

Thanks, Neelix! This is exactly the type of advice I was feeling we needed. The formatting and linking insight is great, I am looking forward to incorporating each of your suggestions. PaleoBioJackie (talk) 10:05, 30 April 2014 (UTC)

Neelix, we have incorporated all of your suggestions except for the citations in the lead. I would like a new reader to be able to quickly find the reference, even if it is for a basic concept that is also referenced later in the article. If you feel strongly about this please let us know. I am continuing to work on the "Discovery and characterization of new species" section. Please let us know if you might have any further suggestions. PaleoBioJackie (talk) 20:22, 6 May 2014 (UTC)

Comments from Mnemcek (peer review 3)

Great article! There is not much more I'd like to add, other than a few minor suggestions. I would like to comment on the Applications section. I thought the authors have done a great job in presenting the possible applications while staying unbiased, especially in presenting the "de-extinction" possibilities. I also really like the limitations section, as you go into detail about what could cause issues in this process and even some ways to fix these issues.

Just a few small suggestions:

• the title of the article is listed as "Molecular paleontology" but it is referred to as Molecular Paleontology in the second paragraph -- this inconsistency may be confusing to some readers
• In the second paragraph, the "biotechnological techniques" are listed in the order of DNA sequencing, isolation, and amplification. This is a very picky suggestion, but I would change the order to DNA isolation, amplification, and then sequencing, as this it the logical order that a researcher might perform these steps
• Consider adding a Wiki link for paleobotanists (in the Timeline section) to the Paleobotany page. Also, check the spelling (palaeobotanists or paleobotanists?)
• Also consider a Wikilink to the Neanderthal Genome Project (in the Timeline section) to give a more in-depth context to this subject
• Your "See Also" section includes several informative and important links, but there might be more applicable links to add in this section (maybe some specific genetic histories of certain countries or regions)

Mnemcek (talk) 03:31, 30 April 2014 (UTC)

Thanks Mnemcek! I appreciate you taking the time to review our article. I agree with all of your suggestions, especially your point about the ordering of isolation, amplification, and sequencing. I am not sure how we missed that. PaleoBioJackie (talk) 10:08, 30 April 2014 (UTC)

Hi Mnemcek, I think we have made most of your suggested changes. Please let us know if there is anything else you think of that we could do to improve! PaleoBioJackie (talk) 20:15, 6 May 2014 (UTC)

Thank you Mnemcek! We have definitely worked on incorporating your suggestions. In regards to the spelling of paleobotanists, it can apparently be spelled both as paleobotanists or palaeobotanists (which I myself had previously not known). We've added a note that it can be spelled both ways and also once you click on the wiki-link the next page explains that it can be spelled both ways as well. Cchandu1 (talk) 22:22, 6 May 2014 (UTC)

Ideas for further improvement

As this project wraps up today, I am satisfied with the article overall. To someone looking to further improve this article, I have a few ideas on some worthwhile contributions. It would be a nice addition to space the events in the timeline linearly, with each year taking up the same amount of space, such that one could easily see how significant achievements within the field have sped up in the last decade or two. There is so much more content that could be added, particularly in the techniques section, and in the history section. More specifically, more content regarding the Neanderthal Genome Project, the sequencing of the wooly mammoth, and also aspects of molecular paleontology more focused on lipids, proteins, carbohydrates, and the DNA's diagenetic products. PaleoBioJackie (talk) 20:39, 6 May 2014 (UTC)

It was definitely a great experience working on this article page! As time goes and new discoveries and breakthroughs are made in this field, it will be very exciting to see this page continue to grow. There are still other sections that could be added such as new or future directions being taken, as well as additional limitations to be encountered. I would like to add a thank you note to everyone who has, as well as future contributors, helped us work on this article page! Overall, I hope that this page, as well as others, will continue to develop as time goes on. Cchandu1 (talk) 23:37, 6 May 2014 (UTC)

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New publication describing how biological cells and tissues preserve chemically

Here is a recent, peer-reviewed publication describing, for the first time with in-depth chemistry, how biological cells and soft tissues preserve into the fossil record. Since this page is on molecular paleontology, I think the information from this publication may be desirable to add. Here is the link to the actual article:

https://www.sciencedirect.com/science/article/pii/S0012825223000569#f0040

And here is a link to a news article that describes the peer-reviewed article in layman's terms:

https://phys.org/news/2023-05-dinosaur-tissues-deep.html 184.170.72.76 (talk) 05:41, 8 May 2023 (UTC)