Talk:Jonathan Rothberg

edits for neutrality and references

Hi, I have cleaned up the article to a more neutral point of view and added additional references. Ftroxell (talk) 02:40, 25 February 2011 (UTC)

Hi, still the passages with "Jonathan" appear to be written by someone with close connections to him; there have been no changes in this regard since my re-adding of the COI tag. Ftroxell, do you know Dr. Rothberg in person? If yes, the tag should stay there until all passages that might cause concern have been removed/rewritten. Also, a publication list seems not to be standard in Wikipedia.--Biologos (talk) 11:04, 25 February 2011 (UTC)

a

This article seems to be mostly a copy-paste job from the Baylor website on Rothberg: http://www.bcm.edu/news/packages/rothberg-bio.cfm PhineasG (talk) 13:54, 10 May 2008 (UTC)

Edits to improve article based on COI and rewrite tags

Hi, I deleted some duplicate information and made the whole thing look more encyclopedic. There are still some peacock terms and unsourced assertions left, I think.--Biologos (talk) 10:28, 14 October 2010 (UTC)

External links modified

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External links modified

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New content

The content added here was badly sourced and very promotional. Not an improvement. Jytdog (talk) 15:22, 26 June 2018 (UTC)

That content was from Draft:Jonathan_Rothberg. Jytdog (talk) 15:24, 26 June 2018 (UTC)

Hello,

It was not my intention to write promotional content and I would very much like to reach an agreement on the appropriate tone and level of detail for this page. My thought process in the edit (Draft:Jonathan_Rothberg) was to provide greater objective detail on the scientific and business dealings of Rothberg's career, as these provide context for his professional life and are the primary reason for his notability.

I made efforts to write with an objective style and to provide additional citations, increasing the number of references from 13 to 91 (the notification at the top of the current page reads: "This biography of a living person needs additional citations for verification. Please help by adding reliable sources."). The vast majority of the sources I added were secondary, comprising mostly of newspaper articles and scientific publications, with several exceptions that have since been pointed out to me by Jytdog. I am completely willing to redact these in accordance with Wikipedia's policies on Original Research, and to otherwise modify the prose so as to be more objective.

I would greatly appreciate specific guidance on how to adjust the edits I've made to be in accordance with Wikipedia's standards. I understand that some of the content may be considered Original Research or is outside the scope of Rothberg's personal biography. I will work to reduce and improve content in both of these areas but welcome any comments.

Wconard1965 (User_talk:Wconard1965) 17:29, 26 June 2018 (UTC)

New content: requested edits

Opening paragraph:

Jonathan M. Rothberg (born 1963) is an American scientist and entrepreneur. He is the founder of CuraGen, 454 Life Sciences, RainDance Technologies, Ion Torrent Systems, Butterfly Network, and the medical device incubator 4Catalyzer. Rothberg is best known for his contributions to next-generation DNA sequencing. He was awarded the National Medal of Technology and Innovation by President Barack Obama in 2015 for his “pioneering inventions and commercialization of next-generation DNA sequencing technologies, making access to genomic information easier, faster and more cost-effective for researchers around the world." Wconard1965 (talk) 18:27, 2 July 2018 (UTC)

References

Edit request reply 02-JUL-2018

Partially implemented

1. N The lead is not the best place for quotations to go, as it should be a space where the main topics of the article are summarized.
2. N The claims regarding CuraGen, 454 Life Sciences and Ion Torrent Systems are already in the article.
3. Y The citation given for RainDance Technologies was added to the location of the mention of this company in the article. The citation needed inline maintenance template added for this claim was removed.
4. Y The claim regarding the Butterfly Network was added to the main body of text.
5. Y The claim regarding the subject receiving the National Medal of Technology and Innovation was added to the article.
6. N The passages of text already existing in the article and shown in the table below were found to be insufficiently paraphrased from the source material. These passages were removed from the article. (See WP:CLOSEPARAPHRASE.)

Regards,  spintendo  20:05, 2 July 2018 (UTC)

Comparison of texts

Text as it appeared in the Wikipedia article Jonathan Rothberg	Text as it appears in the Source material
He went on to Yale University and earned an MS, M.Phil., and Ph.D. in biology. His thesis at Yale focused on decoding a gene called slit responsible for wiring the nervous system. This work resulted in a cover article in the journal Cell in 1988.	After completing college, Dr. Rothberg attended Yale University, earning a PhD in biology. His thesis work — decoding a gene responsible for wiring the nervous system — appeared on the cover of the prestigious journal Cell.
CuraGen focused on how the proteins encoded in a genome function together, and published the first global proteomic maps of a eukaryotic cell and a metazoan organism (featured on the covers of Nature and Science) and developed drugs for the treatment of metastatic skin and breast cancer.	At CuraGen he was the first to completely map out how the proteins encoded in a genome functioned together (featured on the covers of Nature and Science) and develop drugs for the treatment of metastatic skin and breast cancer.

Notes

References

Requested Edit: Recognition

Replace Recognition section with following content:

• 2015: The National Medal of Technology and Innovation for "pioneering inventions and commercialization of next generation DNA sequencing technologies, making access to genomic information easier, faster, and more cost-effective for researchers around the world."
• 2015: The World Economic Forum’s Technology Pioneer, for Butterfly Network Ultrasound on a chip
• 2014: John A. Quinn Lecture in Chemical Engineering, University of Pennsylvania
• 2012: Wilbur Cross Medal for most distinguished alumni, Yale University
• 2011: DGKL Biochemical Analysis Prize for development of massively parallel DNA sequencing
• 2011: Doctor of Science Honoris Causa Mount Sinai School of Medicine for inventing massively parallel DNA sequencing
• 2010: The World Economic Forum’s Technology Pioneer, for the Ion Torrent Semiconductor Sequencing
• 2010: Connecticut Medal of Technology for inventing Next-Generation sequencing
• 2009: $2.2 Million NIH/NHGRI technology development award to ION for the $1,000 genome
• 2008: The World Economic Forum’s Technology Pioneer, for the Raindance microfluidics system
• 2007: The World Economic Forum’s Technology Pioneer, for 454 Life Sciences' invention of Next-Gen Sequencing
• 2006: R & D 100 Awards to 454 Life Sciences
• 2005: Wall Street Journal 2005 Technology Innovation Awards, Gold Medal Winner for inventing Next Generation sequencing
• 2005: Member Connecticut Academy of Science and Engineering
• 2004: National Academy of Engineering
• 2000: The Irvington Institute’s Corporate Leadership Award in Science
• 1998: Ernst and Young Entrepreneur of the Year
• 1991: John Spangler Nicholas Prize for the outstanding Doctoral candidate Wconard1965 (talk) 17:11, 5 July 2018 (UTC)

References

Reply to edit request 05-JUL-2018

Below you will see where proposals from your request have been quoted with reviewer decisions and feedback inserted underneath, either accepting, declining or otherwise commenting upon your proposal(s). Please read the enclosed notes for information on each request.  spintendo  19:56, 5 July 2018 (UTC)

Review of edit request 05-JUL-2018

2015: The National Medal of Technology and Innovation for "pioneering inventions and commercialization of next generation DNA sequencing technologies, making access to genomic information easier, faster, and more cost-effective for researchers around the world." 2010: Connecticut Medal of Technology for inventing Next-Generation sequencing  Already done. ___________ 2014: John A. Quinn Lecture in Chemical Engineering, University of Pennsylvania. 2011: Doctor of Science Honoris Causa Mount Sinai School of Medicine for inventing massively parallel DNA sequencing. 2000: The Irvington Institute’s Corporate Leadership Award in Science.  Not approved. ___________ 2012: Wilbur Cross Medal for most distinguished alumni, Yale University  Approved. ___________ 2011: DGKL Biochemical Analysis Prize for development of massively parallel DNA sequencing. 1991: John Spangler Nicholas Prize for the outstanding Doctoral candidate.  Not approved. ___________ 2009: $2.2 Million NIH/NHGRI technology development award to ION for the $1,000 genome. 2008: The World Economic Forum’s Technology Pioneer, for the Raindance microfluidics system. 2007: The World Economic Forum’s Technology Pioneer, for 454 Life Sciences' invention of Next-Gen Sequencing. 2010: The World Economic Forum’s Technology Pioneer, for the Ion Torrent Semiconductor Sequencing. 2015: The World Economic Forum’s Technology Pioneer, for Butterfly Network Ultrasound on a chip.  Not approved. ___________ 2006: R & D 100 Awards to 454 Life Sciences. 2005: Wall Street Journal 2005 Technology Innovation Awards, Gold Medal Winner for inventing Next Generation sequencing. 1998: Ernst and Young Entrepreneur of the Year.  Not approved. ___________ 2005: Member Connecticut Academy of Science and Engineering. 2004: National Academy of Engineering.  Not approved. ___________

Requested Edit: 7/23/18

"I'd propose that each company have its own subheading for easy page navigation (as I've done below). Additionally I'd like to propose the following additions to the CuraGen and 454 sections:"

Career and Research ==

CuraGen===

In 1991 Rothberg founded his first company, CuraGen, from his basement with financial backing from his family. CuraGen's goal was to use newly emerging data from the Human Genome Project, which had launched shortly before, to discover drug targets and diagnostic tests using robot-automated workflows.

CuraGen went public in 1999, and in 2000 was valued at US$5 billion. In 2001, CuraGen partnered with Bayer in a $1.5 billion agreement, one of the largest of its time, to develop drugs to treat obesity and Alzheimer's.

CuraGen's rise tracked the genomics bubble of the early 2000s. With access to newly available human genome data, pharmaceutical companies invested heavily in genomics with hopes of guiding drug disdocvery, largely before genomics had proven its efficacy in therapeutic R&D. CuraGen's lead drug to treat chemotherapy side-effects failed in phase II, causing CuraGen's shares to plummit, and Rothberg was forced out in 2004. CuraGen was acquired by Celldex Therapeutics in 2009 for $95 million.

454 Life Sciences===

While at CuraGen, Rothberg observed the enormous demand for faster, cheaper genome sequencing technologies; in 2000 the Human Genome Project released the first complete draft of a human genome after 13 years and $2.7 billion in development cost. Rothberg's second company, 454 Life Sciences, spun out of CuraGen to develop a sequencing machine that would reduce the cost and time required to sequence genomes.

Rothberg and colleagues at 454 developed a massively parallel sequencing machine capable of reading 300 million bases per day. The device contained a single glass slide with 1.6 million wells, each approximately 50 microns wide and 55 microns deep, where individual sequencing reactions were processed in parallel. 454 sequencing had several advantages over traditional conventional Sanger sequencing, such as its lower cost, higher throughput, and simplified sample preparation, eliminating the need to separate strands by size. 454's device performed sequencing by synthesizing a growing DNA strand rather than the chain termination used in Sanger sequencing.

Rothberg used the 454 sequencer to undertake a variety of projects. In 2006, Rothberg and Dr. Svante Pääbo of the Max Planck Institute for Evolutionary Antropology in Leipzig, Germany initiated the Neanderthal Genome Project to recover a full genome of Neanderthal. Pääbo’s team and researchers from 454 sequenced one million base pairs of Neanderthal DNA from less than 200 milligrams of material of a sample estimated to be 38,000 years old, demonstrating the feasibility of sequencing all three billion bases in the Neanderthal genome.

Rothberg collaborated with Dr. Matthew Meyerson in 2006 to study the genetic basis of a patient’s drug response by applying next-generation sequencing to a lung cancer tumor. Meyerson hoped that sequencing of tumor samples would provide insight into which patients respond to which drugs by uncovering the specific mutations present. "I imagine in a few years all cancer patients will have their tumors characterized by single-molecule sequencing if the technology continues to decrease in cost," Meyerson said of the study.

In May 2007, Rothberg and colleagues used a 454 device to sequence Dr. James Watson’s complete genome, marking the first individual genome to be sequenced using next-generation rapid-sequencing technology, and the "first individual genome to be sequenced for less than $1 million". Watson's complete genome was announced two weeks after J. Craig Venter published his own genome on the public GenBank database, having sequenced himself using previous-generation machines at a cost of $100 million.

Roche Diagnostics acquired 454 Life Sciences for $154.9 million in late March 2007. In October 2013, Roche shut down 454 when the technology became non-competitive with the introduction of faster and less expensive sequencing machines from competitors including Illumina and Ion Torrent.

References

Wconard1965 (talk) 17:57, 23 July 2018 (UTC)

I will leave it to someone else to respond formally. This has improved a lot in parts; some of the content is use-able; some is not. The 3 paragraphs about work with 454's sequencing is assembled from primary sources. We don't do that in Wikipedia. Jytdog (talk) 19:22, 23 July 2018 (UTC)

Jytdog Much of this proposal has information already existing in the article (6 different sections) but it is worded differently. If you could briefly mention which of these re-worded parts are improved, I can do the work of implementing them. I had prepared a rough draft of my response indicating which parts are already included. I just need to know which ones are worded better than I can go ahead and implement.

Review of edit request 23-JUL-2018

In 1991 Rothberg founded his first company, CuraGen, from his basement with financial backing from his family.  Already mentioned. ___________ CuraGen's goal was to use newly emerging data from the Human Genome Project, which had launched shortly before, to discover drug targets and diagnostic tests using robot-automated workflows.  Not approved. ___________ CuraGen went public in 1999, and in 2000 was valued at US$5 billion. In 2001, CuraGen partnered with Bayer in a $1.5 billion agreement, one of the largest of its time, to develop drugs to treat obesity and Alzheimer's. ? Clarification needed. ___________ CuraGen's rise tracked the genomics bubble of the early 2000s. With access to newly available human genome data, pharmaceutical companies invested heavily in genomics with hopes of guiding drug discovery, largely before genomics had proven its efficacy in therapeutic R&D.  Not approved. ___________ CuraGen's lead drug to treat chemotherapy side-effects failed in phase II, causing CuraGen's shares to plummit, and Rothberg was forced out in 2004. CuraGen was acquired by Celldex Therapeutics in 2009 for $95 million.  Already mentioned. ___________ 454 Life Sciences: While at CuraGen, Rothberg observed the enormous demand for faster, cheaper genome sequencing technologies;  Not approved. ___________ in 2000 the Human Genome Project released the first complete draft of a human genome after 13 years and $2.7 billion in development cost.  Not approved. ___________ Rothberg's second company, 454 Life Sciences, spun out of CuraGen to develop a sequencing machine that would reduce the cost and time required to sequence genomes.  Already mentioned. ___________ Rothberg and colleagues at 454 developed a massively parallel sequencing machine capable of reading 300 million bases per day.[8] The device contained a single glass slide with 1.6 million wells, each approximately 50 microns wide and 55 microns deep, where individual sequencing reactions were processed in parallel. 454 sequencing had several advantages over traditional conventional Sanger sequencing, such as its lower cost, higher throughput, and simplified sample preparation, eliminating the need to separate strands by size. 454's device performed sequencing by synthesizing a growing DNA strand rather than the chain termination used in Sanger sequencing.  Not approved. ___________ Rothberg used the 454 sequencer to undertake a variety of projects. In 2006, Rothberg and Dr. Svante Pääbo of the Max Planck Institute for Evolutionary Antropology in Leipzig, Germany initiated the Neanderthal Genome Project to recover a full genome of Neanderthal. Pääbo’s team and researchers from 454 sequenced one million base pairs of Neanderthal DNA from less than 200 milligrams of material of a sample estimated to be 38,000 years old, demonstrating the feasibility of sequencing all three billion bases in the Neanderthal genome.  Already mentioned. ___________ Rothberg collaborated with Dr. Matthew Meyerson in 2006 to study the genetic basis of a patient’s drug response by applying next-generation sequencing to a lung cancer tumor.  Approved. ___________ Meyerson hoped that sequencing of tumor samples would provide insight into which patients respond to which drugs by uncovering the specific mutations present. "I imagine in a few years all cancer patients will have their tumors characterized by single-molecule sequencing if the technology continues to decrease in cost," Meyerson said of the study.  Not approved. ___________ In May 2007, Rothberg and colleagues used a 454 device to sequence Dr. James Watson’s complete genome, marking the first individual genome to be sequenced using next-generation rapid-sequencing technology, and the "first individual genome to be sequenced for less than $1 million".  Already mentioned. ___________ Watson's complete genome was announced two weeks after J. Craig Venter published his own genome on the public GenBank database, having sequenced himself using previous-generation machines at a cost of $100 million.  Not approved. ___________ Roche Diagnostics acquired 454 Life Sciences for $154.9 million in late March 2007.[17] In October 2013, Roche shut down 454 when the technology became non-competitive with the introduction of faster and less expensive sequencing machines from competitors including Illumina and Ion Torrent.  Already mentioned. ___________

 spintendo  19:52, 23 July 2018 (UTC)

I just meant compared to earlier drafts that Wconard1965 had proposed and I had looked at it, in their sandbox. Please do your thing, Spintendo, I will follow and do mine afterward. Easier that way. Jytdog (talk) 19:57, 23 July 2018 (UTC)

Thank you both for your feedback. Spintendo, regarding note three (Bayer deal), I would argue that the huge size of the deal was an indication of an interesting larger trend: namely the sudden and massive hype genomics companies received from drug developers at the turn of the century. Pharma companies saw so much potential in genomics that they were willing to make some of the biggest biotech deals ever without any promise that the genomics technologies were capable of providing actionable insight into therapeutic R&D. The Bayer deal, and more broadly CuraGen's story, is interesting for much the same reason that any failed dotcom bubble company is worth its own page. Wconard1965 (talk) 21:04, 23 July 2018 (UTC)

I see your point about the potential here, based for example on something like Pets.com, which I think is what you were referring to when you mentioned the dot.com bubble. As it is in that article, I think that placing the information here in a separate Curagen article would work better than placing it under Rothberg's article. As for the claims which are already in the article, some of these were worded better than they are now, but only slightly so:

Comparisons of Already-Mentioned Claims
Versus Their Edit-Requested Equivalents

#	The claim as it currently appears in the Wikipedia article	The same claim as it appears in the most-recent edit request
1	While a graduate student at Yale in 1991, he founded CuraGen, one of the first genomics companies.	In 1991 Rothberg founded his first company, CuraGen, from his basement with financial backing from his family.
2	However, after never bringing a drug to market, CellDex Therapeutics acquired CuraGen in 2009 and reduced it to only five employees by October.	CuraGen's lead drug to treat chemotherapy side-effects failed in phase II, causing CuraGen's shares to plummit, and Rothberg was forced out in 2004. CuraGen was acquired by Celldex Therapeutics in 2009 for $95 million.
3	In 2000, 454 Life Sciences was founded as a subsidiary of Curagen; Rothberg was the CEO of Curagen at the time (...) Rothberg brought to market a machine for massively parallel DNA sequencing.	Rothberg's second company, 454 Life Sciences, spun out of CuraGen to develop a sequencing machine that would reduce the cost and time required to sequence genomes.
4	454 Life Sciences and the Baylor College of Medicine Genome Center was the first to complete and make public the sequence of an individual human genome (James D. Watson).	In May 2007, Rothberg and colleagues used a 454 device to sequence Dr. James Watson’s complete genome, marking the first individual genome to be sequenced using next-generation rapid-sequencing technology, and the "first individual genome to be sequenced for less than $1 million".
5	Rothberg initiated the Neanderthal Genome Project in collaboration with Svante Pääbo's group.	In 2006, Rothberg and Dr. Svante Pääbo of the Max Planck Institute for Evolutionary Antropology in Leipzig, Germany initiated the Neanderthal Genome Project to recover a full genome of Neanderthal. Pääbo’s team and researchers from 454 sequenced one million base pairs of Neanderthal DNA from less than 200 milligrams of material of a sample estimated to be 38,000 years old, demonstrating the feasibility of sequencing all three billion bases in the Neanderthal genome.
6	It (454 Life Sciences) was acquired by Roche Diagnostics in 2007 then closed down by Roche in 2013 after other approaches to sequencing rendered the underlying technology noncompetitive.	Roche Diagnostics acquired 454 Life Sciences for $154.9 million in late March 2007. In October 2013, Roche shut down 454 when the technology became non-competitive with the introduction of faster and less expensive sequencing machines from competitors including Illumina and Ion Torrent.

As you can see, the text is expanded in almost all of the edit requested versions. But all of those expansions are not necessarily better. Take for instance:

• Row 3, where a claim of cost effectiveness is made for a technology used successfully with two notable projects
• Row 5, where genome project minutiae is covered in detail.
• Row 6, where an added claim is made about the "faster and less expensive sequencing machines" manufactured by Mr. Rothberg's present company.

These details seem to be much more than what is needed to convey the information simply. In any event, I believe one of the remaining sentences could be rewritten (row 2) to offer a compromise between the standing version on the left and the requested version on the right.  spintendo  01:19, 26 July 2018 (UTC)

Notes

Request edit

Spintendo, thank you for your edits. I appreciate your Spartan concision, but I do wonder if it would ever be possible to write this page in such a way that resembled a well fleshed-out page such as Niel deGrasse Tyson's, for example. This was my intention in writing the draft page, and while Jytdog has made it clear that much of the content does not adhere to Wikipedia's standards on OR and promotional content, my hope was to put down something that read more like a biography page and less like a list of bullet points. I am more than happy to work with editors to shop this further but want to know if there is any path I can take to create a more complete page. Thank you, Wconard1965 (talk) 13:43, 9 August 2018 (UTC)

Reply

Page view comparison of Neil deGrasse Tyson (blue) and Jonathan Rothberg (green) Wikipedia articles over a two-year period, from August 2016 to August 2018. On average, the Tyson article receives about 156,000 more page views a month than the Rothberg article does.

The level of notoriety which an article's subject attains can affect how "well fleshed-out" an article is. Even though Wikipedia's content considerations are based largely on verifiability and what Wikipedia is Not, a large portion of what is deemed acceptable is driven by a subject's notoriety. Whether or not someone chooses to attend church every Sunday is a detail which has been deemed acceptable in articles about well known people while also deemed unacceptable in lesser known people (despite these considerations being equal for the most part).

If this seems arbitrarily unfair, it may be because it is, but a person's notoriety can work itself out in more egalitarian ways. For instance, when a subject is more well-known, their article garners more page views. This increased visibility draws more editors to edit, increasing the size and the scope of the information presented. In this manner, the subject's notoriety organically drives an article's growth. Replicating this expansion synthetically (using one or two editors to add all the information at once) may be quicker, but would undoubtedly ring hollow to many editors noting that an article which reaches synthetically in one swift stroke the same level of detail achieved organically by others has an unfair advantage (the advantages discussed in the previous paragraph notwithstanding). As shown in the chart comparing the two articles you mentioned over a two year period, they have very different page view numbers, which impacts the quality quantity of information shown in both of them.

In comparison, the Tyson article was essentially a stub for the first few years, eventually growing beyond stub status to reach a better form by 2011, a full 6 years after being created. Each time the article grew roughly corresponds to when Tyson either released new books, made television appearances, narrated new documentaries or hosted television series, all which increased his notoriety. I can understand the desire to have one article resemble another, but based on notoriety, these two really are apples and oranges. A more apt comparison would be to the Tyson article in 2007, as the article then looks much more like how the Rothberg article looks now. That was before many of Tyson's media appearances occurred.  spintendo  14:38, 13 August 2018 (UTC)