Talk:Pardis Sabeti

Articles for Deletion Discussion

http://wiki.riteme.site/wiki/Wikipedia:Articles_for_deletion/Pardis_Sabeti Dimdamdocdim (talk) 21:35, 6 February 2008 (UTC)

This person is a junior post-doctoral scientist and can hardly be considered notable. It is true she has received a lot of interest from journalists. Speedy deletion Dimdamdocdim (talk) 10:47, 29 January 2008 (UTC)

speedy of course is for no claim to notability whatsoever & does not fit. I think the awards make a discussion at afd advisable. Personally I don't think shes notable, but she does meet the geneal WP:N requirement. DGG (talk) 18:04, 29 January 2008 (UTC)

She may very well be a genius... give her time! ;) 24.202.94.76 (talk) —Preceding comment was added at 04:23, 18 July 2008 (UTC)

She's one of the top 100 living geniuses according to the Daily Telegraph (see links)... if that isn't notability, I don't know what is! (Previous unsigned comment made at 05:51, 13 February 2008 140.180.8.29 (princeton.edu ip))

Its not the daily telegraph, but a list compiled by 6 members of a consulting firm which was picked up on the telegraph website, so that doesn't say too much. 76.24.31.136 (talk) 03:42, 13 April 2008 (UTC)

I guess that proves my point, she is ludicrously over promoted, the picture of her at the world economic forum is more of the same - the fact that she accepted an invitation to the WEF demonstrates the point beyond doubt. To describe her as one of the top 100 living geniuses is absurd as anyone with the slightest familiarity with the breadth and complexity of natural science and mathematics could testify Dimdamdocdim (talk) 11:44, 13 February 2008 (UTC)

I just read her editorial in the NEJM. Daily JP, Sabeti P., A malaria fingerprint in the human genome? N Engl J Med. 2008 Apr 24;358(17):1855-6.

She's hot. Nbauman (talk)

Novelty of her test

Statistical tests for natural selection have been around for ages. Hitchhikings been known about for ages. Can someone who knows about this area clarify why her tests important - whats new about it etc. Tootootoot (talk) 00:34, 6 August 2008 (UTC

There are different tests of selection each of which have different properties in terms of the pattern of selection they define. The tests that are proposed by Sabeti find very recent patterns of selection.130.60.48.3 (talk) 09:59, 6 June 2012 (UTC)

Froth

All the stuff about her being a genius is a bit demeaning to the article and to her. She's obviously a bright young researcher but there's not much evidence to distinguish her beyond that. To cast her as a modern Einstein or Darwin is really pretty silly. I think this probably led to sarcastic edits which I have removed.Tootootoot (talk) 00:42, 6 August 2008 (UTC)

Did you read the Science magazine article which is cited in this entry? That's the source of some of the stuff you deleted, including her mathematics background. Why don't you accept Science as a reliable source? Nbauman (talk) 01:38, 6 August 2008 (UTC)

It says she's interested in maths, she enjoys it, but the article implies she read medicine. I'm happy to revert it if there is evidence she has a maths background - i.e. has studied mathematics at university level.

Tootootoot (talk) 19:23, 7 August 2008 (UTC)

Still Problematic

The subject seems to be an up-and-coming young researcher, but anyone who gives the article more than a cursory examination will see that its over-promotional tone is out of context for WP articles (WP:PEACOCK). A few specifics:

• Many of the technical claims seem to rest on Sabeti et al cited in the article, but if you check this publication, you find it is a "consortium" publication (not uncommon in biology these days) from many labs. Importantly, there are over 250 authors for this paper! The article implies that this is mainly Sabeti's work, which is grossly misleading, especially since the paper's author list indicates Sabeti is not one of the principal investigators.
• Having the UK Telegraph "list of geniuses" in the lead-in actually strikes me as demeaning Sabeti, considering some of the nonsensical entries like ranking speculator/activist George Soros above theoretical physicist Stephen Hawking. This list seems to speak more to celebrity than genius and should probably be relegated to the bibliography.
• The work on the Lassa fever genes would seem to be significant, but the article cites a fluff-piece in Science instead of the corresponding publication. We are left wondering how to find this publication.

It would be nice to see an accurate, de-peacocked, more sober description of Sabeti in this article. Respectfully, Agricola44 (talk) 16:13, 22 April 2009 (UTC).

Revisions and Reversions

The article was previously shortened, and given language that is more appropriate to the topic by Kattenstoet. Nbauman removed these edits, and reverted to language which contains fluff. I have removed the edits (my comments as to why apparently were not recorded the first time) as the current, shortened version frames the subject's work more appropriately. I think it has removed a large portion of the puffery/fluff objections. —Preceding unsigned comment added by Rlrogers (talk • contribs) 00:06, 22 July 2009 (UTC)

The previous text did not contain an accurate description of the test Sabeti designed, it included meaningless fluff (the "whopping signal" was a quote from sabeti in a news story, and not an objective description of the work, as previously described). Also, by attempting to explain how, in general, tests for selection work, the older text left the impression that Sabeti was responsible for developing the general approach to detecting selection, rather than modifying previously existing tests for a subtly new purpoes. A general explanation of how tests for selection work should be on a page dedicated to tests for selection. Sincerely, kattenstoet —Preceding undated comment added 05:38, 22 July 2009 (UTC).

Do you agree that Science magazine is a WP:RS? --Nbauman (talk) 05:45, 22 July 2009 (UTC)

Science magazine is a WP:RS, but the "whopping signal" was a quote from Sabeti touting her own work, and not an objective 3rd party description. Such press-release material is not appropriate for Wikipedia, whether Science magazine has chosen to run it or not. kattenstoet. —Preceding undated comment added 15:28, 22 July 2009 (UTC).

News reports, and even biology books, use quotes from scientists all the time. That's the way Sabeti described her own work. The job of Science magazine, or any news magazine, is to evaluate the claims and not print anything that exaggerates her work. Science magazine has several levels of reviewers, even in the News and Comments section. Science magazine isn't a press release. If they wrote a "whopping signal," it's because their reporter, who has a master's in biology, thought it was accurate after researching the subject, and his editors agreed. So Science magazine, which is a WP:RS, decided that it was a reasonable, clear and accurate way to describe her work, and not an exaggeration.

I think it's a good description because it explains to non-specialists what Sabeti was doing. Wikipedia is written for non-specialists, according to WP:MTAA and other WP rules.

Science quoted a scientist talking the way scientists talk. What is the Wikipedia rule that says we can't use that? --Nbauman (talk) 23:08, 22 July 2009 (UTC)

It's not a violation of wikipedia rules that's the issue - it's a matter of whether the quote accurately represents the source material. In this case, despite its use by a Science reporter, the description is misleading, as it implies that Sabeti discovered these alleles, their role in malaria resistance, and their history of positive selection, when none of these are true (for example, a paper from Sarah Tishkoff, published a year before Sabeti's, convincingly established selection at G6PD). While Science is a WP:RS, even WP:RS's make mistakes, and they should not be relied upon when they are wrong. kattenstoet. —Preceding undated comment added 03:56, 23 July 2009 (UTC).

I don't think the article implies that she discovered these alleles, their role in malaria resistance, or their history of positive selection. I read it and I didn't come away believing that. (Although if you wanted to rewrite the paraphrase to make that clear, instead of deleting it, that would be acceptable.) The article says that these tests were already developed and she improved them: "Some earlier selection tests looked at both variant frequencies and haplotypes in humans, but they weren't very sensitive."

The Science story quotes 2 researchers who think Sabeti's work is significant:

"This test is one of the most exciting developments in the field in the past few years," says Chris Tyler-Smith, a genome researcher at the Wellcome Trust Sanger Institute in Hinxton, U.K. Evolutionary biologist Martin Kreitman of the University of Chicago, who had developed a similar test but was beaten into print by a few months, says he has "nothing but praise for her contributions."

You're entitled to your opinion, but I don't know who you are. Do you know more about genomics than Tyler-Smith and Kreitman? Is there an equally knowledgeable geneticist on record supporting what you say? WP:RS

Wikipedia has rules WP:DR for resolving these editing disputes. The way to resolve it is to restore this section paraphrasing Science magazine, and, if you think Science is exaggerated or misleading, for you to add a comment from a verifiable, reliable authority who will give the other side.

WP:NPOV requires that you don't just blank out sections you disagree with. You add contrasting view points so that the WP entry gives both sides.

So the burden on you right now is to provide a WP:RS who supports your position that Sabeti's work isn't that significant. That would be a welcome contribution to the entry. --Nbauman (talk) 14:24, 23 July 2009 (UTC)

I'm sorry not to have followed wikipedia protocol to the letter. I am still learning them.

But you are misrepresenting my comments. I never said that Sabeti's work was not significant, nor did I make edits that downplayed its significance. Quite the contrary. I am a reasonably prominent researcher in the field, know Sabeti well, and like her work. I (and many others who read this page) felt that the frivolous language used in the previous version did not do justice to her work. I based my edits on your previous version and the WP:RS's you cite. --Kattenstoet (talk) 14:46, 23 July 2009 (UTC)

The question is whether, under Wikipedia rules, you have the right to blank out the entire section paraphrasing Science magazine. I don't think you do. If you disagree with it, you have to explain why you disagree with it, and (preferably) propose changes.

If I understand you correctly, you agree that the Science magazine article is accurate, and that the paraphrase was accurate. Your objection is to the style. You also believe that some readers might not correctly understand the distinction between what was already done, and what Sabeti added to it. Is that correct? --Nbauman (talk) 16:50, 23 July 2009 (UTC)

I was being polite. The previous version was riddled with factural inaccuracies and imprecise (and therefore misleading) language:

"Sabeti addressed the problem of telling whether a mutation is due to natural selection or just random."

Mutations are errors in the replication of DNA. All mutations are random - none of them are not to natural selection. Some mutations rise to high frequency in populations as a result of natural selection, other rise to high frequency through genetic drift. Sabeti's test attempted to identify mutations that had been subject to positive selection (there are many other kinds of natural selection).

"When humans are exposed to diseases, like malaria and Lassa fever, they evolve traits that resist those diseases, such as sickle cell trait."

Humans do not evolve traits like science cell anemia because they are exposed to diseases. Rather, in these cases, genetic diseases that occur through random mutations rise to high frequency in the population because they confer resistance to infectious diseases.

"Biologists can tell from comparing DNA sequences in populations whether mutations were due to natural selection, but those methods wouldn't work for evolutionary changes during the last 10,000 years, when diseases like malaria arose."

Again, mutations are not due to natural selection. And Biologists can never TELL whether a mutation rose to high frequency because of natural selection, as we were not there to observe history. They can merely make an inference. And it's unclear what is meant by "those methods". Sabeti was using DNA sequences just like everyone else.

"Sabeti took advantage of the fact that genes on the same place in the chromosome are inherited together."

This is simplifying to the point of inaccuracy. First, we are talking about polymorphisms here, and not genes. And the point is that polymorphisms that are near each other tend to (but not always) be inherited together.

"If a particular variation is subject to natural selection, its frequency will increase, along with the frequency of genes that have hitchhiked along with it. She developed a test that would use this principle to tell whether recent changes were due to natural selection or just chance."

Here a technical term - hitchiked - is being used without explanation. Furthermore, Sabeti's test is not about hitchiking per se (there were plenty of tests based on hitchhiking before). Rather her test is based on the idea that the size of the region that has hitchiked along with a particular allele is a measure of how rapidly it rose to high frequency. The bigger the region that went along with it, the newer the selective event.

She applied this test to malaria variants, and saw a "whopping signal" of positive selection.

What are "malaria variants"? It sounds like she applied the test to the Plasmodium genome. Rather she applied the test to polymorphisms in the human population that were known to alter susceptibility to malaria. It's an important distinction.

"This research was published in Nature. She later identified 2 genes, LARGE and DMD, that protect against Lassa fever, and show strong signals of natural selection in West Africans."

First, the "genes" do not protect against Lassa fever, particular variants of the gene do. And Sabeti did not, as the sentence implies, discover the protective role of these genes. Rather she showed that their prevelance in the human population was likely a result of positive selection for resistance to Lassa fever. It's a huge differences.

Sabeti has done interesting and noteworthy work. We tried to hire her at my institution. I am not in any way trying to denigrate her work. Rather I am trying to make sure that it is described clearly and accurately. --Kattenstoet (talk) 21:40, 23 July 2009 (UTC)

Too technical, too much of a CV

Problem with this entry -- Wikipedia is written for the non-specialist, say, a high school biology student. Most of this entry is written for the specialist. It's like a CV.

If you're considering giving her a grant, you might be concerned that she got a Packard award and an NIH Innovator award. If you're trying to learn biology, and learn about what she's doing, those awards mean nothing.

The section on "Research" is so technical that I had to read it three times to understand it, and I already know what she's doing. There's no excuse for having it so technical, because her work has been written up in many popular magazines, or even in the news sections of professional journals like Science, where they've explained her work in simple layman's language and show you how to do it.

Earlier version of this article did have less technical explanations of her work, but it was deleted. https://wiki.riteme.site/w/index.php?title=Pardis_Sabeti&oldid=303145025 As the entry progresses, it gets more and more technical (violating WP guidelines).

It's particularly a shame because evolutionary genetics is so important, and this entry should be used to explain evolutionary genetics to non-specialists. --Nbauman (talk) 05:45, 5 September 2014 (UTC)

Proposed Edits Regarding Pardis Sabeti

Hello, I am an employee of Pardis Sabeti's at the Broad Institute. I have disclosed this conflict of interest on my user page as well.

Proposed Edits for Multiple Sections

1. I propose updating the Early life and education section by deleting a few words and full sentences to better reflect Pardis's background and for easier readability and more focus. I also propose these edits to fix grammatical errors. Here is the proposed text:

Sabeti was born in 1975 in Tehran, Iran, to Nasrin and Parviz Sabeti. Her father came from a Baháʼí Faith family but never officially joined as a member and was the deputy in SAVAK, Iran's intelligence agency, and a high ranking security official in Shah's regime.

Her family fled Iran in October 1978, shortly before the Iranian Revolution, when Sabeti was two years old, and found sanctuary in Florida.

Sabeti went to Trinity Preparatory School. In high school, she was a National Merit Scholar, class president, valedictorian, and member of the Varsity tennis team. She additionally attributes part of her inspiration towards infectious disease research to the 1995 movie Outbreak.

Sabeti attended the Massachusetts Institute of Technology (MIT), where she was a member of the varsity tennis team and class president, graduating in 1997 with a bachelor’s degree in biology and a "perfect 5.0 average." At MIT, she began her research career in David Bartel's laboratory and was advised by Eric Lander, and was a teaching assistant for undergraduate courses in genetics and biochemistry. She created the MIT Freshman Leadership Program and pioneered the school's larger pre-orientation programming.

Sabeti was selected as a Rhodes Scholar and completed a masters in human biology followed by doctorate work in evolutionary genetics in 2002, at New College, Oxford, earning an M.Sc. and D.Phil. She went on to complete a Doctor of Medicine (M.D.) at Harvard Medical School in 2006 summa cum laude, being the third woman to receive this honor since the school had begun accepting female students. The Paul & Daisy Soros Fellowships for New Americans supported her medical studies. Initially, Sabeti planned to enter medicine and become a doctor, she decided to pursue research instead after completing medical school and discovering she preferred research to medicine.

2. I propose updating the Human Genetics part of the Career and research section to add updates to her work in this field in recent years. I also propose these edits to fix grammatical errors. Here is the proposed text:

As a graduate student at Oxford and postdoctoral fellow with Eric Lander at the Broad Institute, Sabeti developed a family of statistical tests that identify regions of the genome under positive natural selection, by identifying common genetic variants found on unusually long haplotypes. Her tests, extended haplotype homozygosity (EHH), the long-range haplotype (LRH) test, and cross population extended haplotype homozygosity (XP-EHH), are designed to detect advantageous mutations whose frequency in human populations has risen rapidly over the last 10,000 years. As a faculty member at Harvard, Sabeti and her group have developed a statistical test to pinpoint signals of selection, the Composite of Multiple Signals (CMS) as well as methods to quantify changes that occur in non-coding regions of the human genome. Her team also developed methods for delivering gene therapies to specific cells by using nonpathogenic adeno-associated viruses.

Sources: https://pubmed.ncbi.nlm.nih.gov/27259153/ https://pubmed.ncbi.nlm.nih.gov/34534445/ https://pubmed.ncbi.nlm.nih.gov/34506722/ https://pubmed.ncbi.nlm.nih.gov/36417917/

3. I propose updating the Infectious Disease part of the Career and research section to add updates to her work in this field in recent years. I also propose these edits to fix grammatical errors. Here is the proposed text:

In 2014, having worked for a decade together in West Africa on Lassa fever and other infectious diseases, Sabeti and Christian Happi, a Cameroonian-Nigerian geneticist, and their teams launched the African Center of Excellence for Genomics of Infectious Disease (ACEGID) to enhance pathogen surveillance and education in Africa.[44] Their efforts in the Ebola outbreak in West Africa helped identify the first cases in Sierra Leone and Nigeria, and advanced genomic sequencing technology to identify a single point of infection from an animal reservoir to a human.[45] RNA changes further suggested that the first human infection was followed by exclusive human to human transmissions.[46] They also showed the virus was mutating to be able to infect human cells more easily.

Sabeti's team continued to support outbreak response, developing and deploying genomic and computational tools to elucidate the origins, evolution, and community transmission of viruses. During the Zika epidemic in 2016, Sabeti's team assembled the largest sequencing study of the virus and showed the virus was circulating undetected for many months.[47] During the 2018 Lassa fever outbreak in Nigeria, her and Happi's team rapidly sequenced the virus on ground in the country, providing real-time feedback to the Nigeria CDC on the origins and spread of the outbreak. During COVID-19, her team led genomic investigations that elucidated the first superspreader events, variants of concern, and transmission from vaccinated individuals. Sabeti’s team has also developed molecular diagnostics that use CRISPR enzymes to detect genetic material from specific viruses and bacteria in patient samples. These diagnostic tools include CARMEN, which detects multiple pathogens in multiple patient samples, and SHINE, which is designed to be a point of care test. In 2019, Sabeti and Happi's teams were awarded funding from the TED Audacious Project to build Sentinel, a pandemic pre-emption and response system."[48][49]

Sources: https://www.nature.com/articles/s41586-020-2279-8 https://pubmed.ncbi.nlm.nih.gov/29700266/ https://www.nature.com/articles/s41467-020-19097-x Gngn123 (talk) 19:20, 18 September 2024 (UTC)