User:SteveChervitzTrutane

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Welcome to my Wikipedia user page!

Stephen Chervitz Trutane is my official, legal name though it was originally Stephen Allen Chervitz, as described here. So you might know me as having the surname Trutane or as Chervitz, depending on what era of my life or circle of friends you know me from. I respond to either, so use whichever one you want. For simplicity, you can just call me "Steve".

Bio[edit]

By day, I'm a bioinformatics software engineer at Personalis, enabling precision medicine for immuno-oncology by providing tools to annotate and help interpret variations in human genomes from individuals and their tumors. I also worked on genome analysis software at Omicia and before that at Affymetrix where I helped annotate DNA microarray probe sets for end-user scientists via the NetAffx web portal. I came to Affy in Nov 2000 when it acquired Neomorphic (archived), which I joined in Sep 1998. So computers and biological "omics" data are my friends.

I have a B.A. in biology from Macalester College and a Ph.D. from CU Boulder's MCDB department, working under Prof. Joseph Falke in the biochemistry department doing wet-lab molecular biology experiments on a chemoreceptor that mediates bacterial chemotaxis. I did ample amounts of site-directed mutagenesis and in vitro signal transduction assays, as well as 3D molecular graphics visualization and protein structure analysis and other fun stuff (like teaching myself C).

After Boulder, I shifted directions into the world of genomics (or post-genomics) joining David Botstein's lab (while he was at Stanford) working on the Saccharomyces Genome Database (S. cerevisiae a.k.a. baker's yeast, was the first eukaryote to have it's genome completely sequenced, which happened in April 1996, about 3 months after I started with SGD). While at SGD, I developed lots of Perl modules for working with bioinformatics data and contributed most of this code to the open source BioPerl project, which was just getting started around this time, as noted in the early BioPerl history.

I am no longer actively involved with BioPerl development, but continue to be a fan of the Open Bioinformatics Foundation (and open source software for science generally). Other projects I've been involved with include BioDAS, GenoViz, and HCLS projects. I'm on the board of the FGED Society (since 2002) and have continued volunteering with them as their secretary and webmaster since 2010.

In my spare time, I'm either hanging out with my family, training for or organizing triathlons, promoting health and fitness, tweeting, contributing to Wikipedia (my stats), or trying to help humanity with the organization I founded, TeamHuman.org. Wikipedia, I feel, is well-aligned with the "promoting a shared understanding" goal of TeamHuman.org.

Other online hangouts[edit]


Steve Chervitz Trutane in April 2012
Unified login: SteveChervitzTrutane is the unique login of this user for all public Wikimedia projects.
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Support Wikipedia!

My Wikipedia story: When I was a kid I used to browse a physical encyclopedia (I think it was a World Book Encyclopedia ca. 1974), reading random pages here and there. One day when I was 13 or 14 years old, I came across a page that changed my life, specifically a section describing molecular biology. It blew me away that we humans have figured out the genetic code, a code that nearly all cells on earth use for creating proteins from DNA. My teachers had never mentioned the topic at all! The rest of my life has essentially been following up on what I stumbled up on that day, pursuing a Ph.D. and now working at a genome analysis company.

I've been contributing to English wikipedia sporadically for the past few years and enjoy the feeling that I'm creating a knowledge resource that will be read and augmented by others, and persist over time. Perhaps I will add content that will inspire someone else and alter the course of their life as mine was altered long ago by that static encyclopedia. It almost feels like I'm giving back to the encyclopedia gods that led me to where I am today. Sure, wikipedia has issues, but I have seen it evolve and self-correct over time via community input, keeping up with our evolving state of knowledge in real time -- and it's available worldwide via the internet for free. Awesome.

Wikipedia Contributions[edit]

Here are a few highlights of my contributions. This listing isn't necessarily current, so check here for what I've been up to.

I still consider myself to be cutting my teeth as a Wikipedia editor (though Wikipedia considers me established enough to edit some semi-protected pages, such as Barack Obama, which I have edited on occasion). Many of my Wikipedia contributions focus on my domains of expertise: Molecular and cellular biologyBioinformaticsGenomicsFunctional genomicsGenes

However, I have wide-ranging interests so you may find my edits outside these areas, in odd corners of Wikipedia.

Some pages I've created[edit]

Some pages I've contributed substantially to[edit]

  • Science
    • Genome annotation (I wrote a page related to this on the original Wikiomics (archived), later folded into OpenWetWare.)
    • Retrotransposon (Verified and added citation supporting claim that 42% of the human genome is made up of these buggers.)
    • Genetic Information Nondiscrimination Act and Genetic discrimination
    • War on Cancer (I've greatly expanded this from stub state starting in Oct 2008. Continues to be a work in progress.)
      • I initially redirected it to Nat'l Cancer Act of '71, then decided it was better to redirect the other way around.
      • On 2 Oct 2009, I participated in the Lance Armstrong Foundation's "LIVESTRONG Day" by registering a virtual event where did my part to raise cancer awareness by inviting people to the WoC wikipedia page. Not sure if anyone noticed.
      • Some google stats on WoC searches as of 2 Oct 09: the WP page is now on the first page of results, though near the bottom. I take this as a sign of progress of my efforts, as the WoC page has usually been quite distant from the top when I've checked earlier this year. Total google WoC hits on 2 Oct 09: 45M (unquoted), 135k (quoted). Update 3 Nov 2009: WoC page is now #2 out of 47.5M total (unquoted) and #3 out of 327K (quoted). Hot topic! Update 13 Nov 2009: WoC page is now #1 out of 52.3M total (unquoted) and #2 out of 142K (quoted -- the previous 327k seems anomalous).
    • Gene expression techniques
    • Genetic disorder
    • Cancer and inflammation (discussion I had on a now-archived Cancer talk page with JFW and User:Franamax)
      • JFW is looking for more authoritative references describing a 'grand unified' theory for how inflammation relates to cancer before putting anything about it in the cancer article.
      • I think the cancer-inflammation field is rich enough that it deserves its own page & plan to create when I get a chance.
      • This would avoid provide a common, main article to link to from either cancer or inflammation.
      • Cancer article is quite big: 96kb as of 12 May 2012
    • FGED Society (Major re-write, page rename. Formerly known as 'MGED')
    • Affymetrix (My former employer)
    • Treatment of cancer (my proposal to rename this page from Management of cancer was approved... nearly 7 years after my proposal. I hope there were no cancer patients waiting on that change :o).
  • Non-science
    • Jack LaLanne
    • Joe Ranft (Added death section after watching Cars.)
      • Some of my original contribution on Joe's page has since been removed on the basis of being WP:OR or WP:POV. I'm not sure about this removal, since I'm pointing out a coincidental fact between the circumstances of his death and a major theme of the movie he was making when he died. Here's what I said: The road on which Joe died, Highway 1, is akin to Route 66 featured in Cars in the way it "works/moves with the land" (quote from movie). Meandering along the scenic California coastline, Highway 1 is a very much a road where appreciating the journey is as important as reaching one's destination, a theme of Cars. Maybe I'll bring this up on Joe's talk page.
    • Scat singing (In the "Origin" section, I added the Jelly Roll Morton quote from Alan Lomax interview.)
    • Cantillation and Hebrew language (Posted links to audio example of cantillation I uploaded to Wikimedia Commons. Had to convert the mp3 I got from Cantor Seth into Ogg format. A little tricky.)

Assorted contributions[edit]

  • Douglas Adams (Speculated on his talk page that that his 'trilogy of five books' joke derives from a Monty Python skit.)
  • Crips (Added statement and citations about the roots of gang activity in So Central LA. Important issue and article. Definitely could use expansion.)
  • The Jedi Code (Found it in one of my son's books I Am A Jedi by Qui-Gon Jinn and saw that it was not in -- or had been deleted from -- the Jedi page.)
    • OK, the code has been removed once again from the article. Not clear what's the beef. Here's the version of the article with the Jedi code as I added it.
    • The definitive article about the Jedi Code can be found in Wookiepedia.
    • My attempt to add the Wookiepedia citation to the Jediism article was reverted as being an unreliable source. However, being a wiki, Wookiepedia's reliability should improve over time, eh?
    • I still feel that the actual Jedi Code itself should appear in Wikipedia, perhaps on a dedicated page. It could cover alternative versions of the code has it has appeared in different places. One day, when the Force feels strong, I'll attempt it.
  • 'Ghouls' vs. 'Zombies' (See my 'Ghouls' sub-section on this archived page -- this discussion page gets archived a lot.)
  • Drupe (Minor update to include Cashew among the list of plants the produce drupes)
  • Septuple meter (Added Led Zeppelin's "The Ocean," the main riff of which has one bar of 4
    4
    and one bar of 7
    8
    .)
    • This piece can also be counted as a single bar of 15
      8
      , but that is not the most 'reduced' form towards which musical types seem to strive.
    • It was originally included in the "List of musical works in unusual time signatures" (MWUTS) page but got removed, probably because it lacked a decent citable source describing the time signature.
    • Researching this has revealed some insight into Wikipedia culture as it seems one Wikipedian decided to maintain the MWUTS page outside of Wikipedia after pushback from other editors regarding the reliability of sources. This person maintained his list at dkap.info/oddtime.php from May 2009 till April 2017. Here the last archived copy of it.
    • What's the lesson here? If editors feel the need to leave Wikipedia over disputes with other editors, that seems like a bad result indicating a problem with the system. Perhaps the dkap.info author's contribution could have been maintained on a talk page or in his sandbox, or added to the article with a "citation needed" flag. As it is, Wikipedia lost the energy of a knowledgeable person -- an unfortunate outcome.
    • Btw, there are some interesting works listed on that MWUTS page, such as the progressive metal "Schism" in 6+12
      8
      time (which must be an average of the various time changes in that song).
  • A Magnificient Text Book Of Pharmacovigillance
    • I found a "text book" example of plagiarism from Wikipedia, noted on the talk page of Contract research organization.
    • In addition to having more than one typo in the title of the book, the authors also lifted one of the citation anchors "[4]" appearing in the Wikipedia article!
    • Unattributed use of text like this from Wikipedia is widespread, I suspect. I found other web pages that contained lifted verbiage from the CRO page, such as this.
    • While a form of flattery, such copying can be problematic when errors are copied from Wikipedia articles. After the errors are fixed in Wikipedia, the untold copies are not. There's no way to track these copies other than by Google searching.
    • It would be cool to have a way to signal 3rd party websites that the Wikipedia text they copied has been changed, signaling that the copied text may contain an error or other fix.
  • 2019–20 coronavirus pandemic - (Added citation about cytokine storms on 19 Mar 2020)
    • I also noted the pandemic in the history section of the Cytokine release syndrome article, along with citations for cytokine storms as a cause of death due to COVID-19. The history section of CRS was subsequently (May 2020) moved to the Cytokine storm page.
    • Cytokines comprise a fascinatingly complex system of immuno-modulators that's a hot topic of biomedical research. Here's a figure (I tweeted via @Awesomics, Nov 2018), that provides a glimpse of this complexity.

Sandbox[edit]

potential contributions (my sandbox area)

Licensing terms of my contributions[edit]

Dual licensed with the Creative Commons Attribution License version 3.0 CC some rights reserved.svg
I agree to dual-license my text contributions, unless otherwise stated, under Wikipedia's copyright terms and the Creative Commons Attribution license version 3.0. Please be aware that other contributors might not do the same, so if you want to use my contributions under the Creative Commons terms, please check the CC dual-license and Multi-licensing guides.


NOTE: I actually don't have a strong preference to dual license my contributions with CC. I'm fine with Wikimedia All Licensing. The only beef I have with Wikimedia licensing is that adding that template to my user page causes the complete contents of the page to be collapsed under a "More information. Licensing rights" box when using the Wikipedia mobile app. It doesn't behave that way in a web browser, so it may be a bug in the app (as of 9 May 2020). Nevertheless, I don't want to require users to expand a box in order to simply read my page...

Wikipedia Picks[edit]

Some notable content I've come across in my Wikipedia travels. This is completely random and non-exhaustive. May grow over time... or not.

For the officially curated list of "Wikipedia picks," see the archives of the daily feature article and picture that appear on the Main Page.

Images of note[edit]

Pages of note[edit]

A mix of unrelated yet noteworthy topics.

  • SGR 1806-20 - "A starquake [on this magnetar] ... released more energy in one-tenth of a second (1.3×1039 J) than our sun has released in 100,000 years".
    • Lets hope this doesn't ever happen w/in 3 parsecs of Earth :-O
  • Psalter world map - "mysterious as parts of the world once marked with sea monsters and dragons by 13th-century mapmakers." ref
  • Canine cancer detection - Putting man's best friend's sniffer to medical use: "dogs can detect some substances in the region of parts per trillion..."
  • Talk page of Mansplaining - Amazing the amount of collective energy spent here. Probably no mansplaining taking place there, since most Wikipedians are men, you know ;).
    • Q: How does a mainsplainer get his water? A: Well, actually...
  • Nu metal - amazing amount of vitriol in the "Criticism and controversy" section, harkening the disco sucks backlash of the previous generation, and even ragtime backlash at the beginning of the 20th century, which got slammed both coming and going.
  • Brouhaha - helpfully offers some interesting examples so deemed.
  • Notable numbers: 4294967295 and 2147483647 (number) - How many numbers have their own wikipedia pages? Is that question even answerable?

  • Kármán vortex street as an explanation for the Dyatlov Pass incident
    • Personally, I'm leaning towards the infrasound explanation. I'd like to experience that natural phenomenon myself... in the daytime.
  • Man versus Horse Marathon - Seems like the horses shouldn't be handicapped by having to run with a human on their back,
    • or the humans should have to carry a heavy backpack.
    • Slate story mentioning this contest and describing the "runner" theory of human evolution: All Men Can't Jump
  • Phrases from The Hitchhiker's Guide to the Galaxy
    • Contains a classic Adams quote: "I may be a sorry case, but I don't write jokes in base 13."
  • Ray Dorset quote: "I should be retired, but my brain is like that of an 18 year old."
  • Anti-pattern - Quite a few of these, and not just for software engineering.
    • Great pedagogical value. I added some proposals to the Talk page.
  • Talk about Roseanne Barr's infamous tweet, and whether it warrants inclusion on Valerie Jarrett's page.
  • RMS Titanic - Sank on Tax Day 1912 (the year before US federal income taxes actually started), and many died as a result of insufficient lifeboat passenger capacity stemming from "outdated maritime safety regulations."
    • Good example of what can happen when an industry moves faster than our ability to regulate it.
    • Subsequent maritime disasters with major fatalities, SS Eastland in 1915 and RMS Empress of Ireland in 1914, stemmed from regulatory over-correction in the 'wake' of the Titanic disaster.
  • Does Anybody Really Know What Time It Is?
  • Immunotherapy includes helminthic therapy (i.e. infection with whipworms & hookworms)
    • Though the mechanism of how these helminths modulate the immune response, is unknown.
  • Matthew 5:5, the third of the Beatitudes ("blessed are the meek..."), contains an interesting linguistic note regarding the Greek word typically translated as 'meek':
    • it is not suggesting weakness but instead the way power is handled.
    • It is "strength under control". The English language does not have a word that translates conveying both gentleness and power together.
    • Makes one wonder how many other original terms used in the Bible are difficult to translate.
  • June 1962 Alcatraz escape attempt
    • Flagged as "appears to contradict itself on whether the escape attempt succeeded or failed." The U.S. Marshals Service investigation remains open to this day.
  • DevOps - Riddled with many editorial flags, mostly "unreliable source" or "citation needed".
    • 'DevOps' means different things to different people in the industry and there is apparently no definitive authority on the topic.
    • Irony here is that many Wikipedians would probably describe their day jobs as being in devops, I would bet.
    • Relevant article by an IT SME: DevOps vs DevSecOps (10 Mar 2021)

  • Arrow of time - a consequence of the entropy-maximizing Second law of thermodynamics and the resulting irreversibility of natural processes.
  • Meaning of life - find enlightenment through Wikipedia. 🙏
  • Ineos 1:59 Challenge - Kipchoge's successful achievement of a sub-2-hour marathon is not recognized as an official world record, but did make it into the Guinness World Records.
    • How long before he or someone else makes it official? Could depend on the legalization of high-tech running shoes like he used.
    • Nike's 'AlphaFly' shoes like Eliud used are banned, but Nike's new 'VaporFly' shoes are officially legal.
  • Superoxide dismutase - My favorite enzyme as it plays a vital role in antioxidant defense in nearly all living cells exposed to oxygen.
    • It's the most catalytically efficient enzyme known with a reaction rate that is limited only by how fast the reactants can diffuse (kcat/KM = ~7 x 109 M−1s−1).
    • It's a metalloprotein that relies on interesting metal ions for catalysis: Cu-Zn, Mn, Fe, or Ni (underscoring the importance of a diverse, micronutrient-rich diet).
    • It's so important for life that the human genome has three different versions of it, customized for different cellular locales: cytoplasmic (SOD1), mitochondrial (SOD2), and extracellular (SOD3).
    • Mutations in SOD genes are implicated in notable diseases, such as Lou Gehrig's disease.
    • An interesting research question is whether supercentenarians have protective levels of SOD proteins, or SOD genetic variants, or SOD-regulatory gene variants.
      • A July 2020 study from Japan (open access) that looked at a number of relevant biomarkers (protein levels) did not find significant association of extracellular (EC) SOD3 with the super-old.
      • Note that they excluded individuals with the SOD3 R213G variant which is associated with high plasma levels of EC-SOD and an elevated risk for incidental ischemic heart disease, so there is a connection between SOD levels and cardiovascular health, but it's not a simple "more is better" relationship.
      • Also see this July 2000 Italian study that tested for genetic markers associated with longevity (it's also OA). It looked at SOD1 and SOD2 and did not find any significant associations. Also covers the importance of correcting for multiple hypothesis testing.

  • Protocadherins - a.k.a "Pcdhs" = neural adhesion proteins, thought to provide an address code system for the developing nervous system.
    • "different subsets of Pcdhs genes are differentially expressed in individual neurons, a vast cell surface diversity may arise from this combinatorial expression... Pcdhs may provide a synaptic-address code for neuronal connectivity or a single-cell barcode for self-recognition/self-avoidance.
    • The Pcdh genes have an interesting "locus region" organization akin to the T-cell & B-cell receptor genes, which also depend on combinatorial complexity for their function. For example PCDHA@.
    • Ubiquitously expressed in the brain (among other tissues), they play a big role in building the human brain -- the most advanced machine in the known universe. Keep an eye on these guys!
  • Normcore fashion
  • Red pill and blue pill
  • Scot Halpin - "who sojourned into the realm of the gods and returned anointed."
    • The 19yo from Iowa who answered Pete Townshend's call at the Cow Palace in 1973 after Keith Moon had trouble maintaining consciousness: ''"Can anybody here play the drums? I mean somebody good!"
    • The Who paid tribute to him after he passed away in 2008.
  • Political gaffe - The idea for an article dedicated to gaffes made by politicians was born on Dan Quayle's talk page.
  • Vermin Supreme - Could use some background on the origin of this moniker.
    • The talk page had a request from Mr. Supreme to have his real name removed, which was honored.
  • Pejorative terms for people (category)
    • Quite a litany of negative lingo. Likely outweighs the set of positive terms for people -- is there even such a category?
    • Here's a few positive terms to get the ball rolling: mensch (but not gutmensch), saint, gentleman and a scholar, samaritan, dear, star, savior, treasure, go-to guy, right-hand-man, angel, up-standing citizen.
    • Social justice warrior (SJW) has an interesting history: it started out positive in the 1990s, then became a pejorative in 2011 as a result of social media activity (Twitter).
    • The extensive & well-referenced list of nicknames used by Donald Trump falls in a sub-category of the pejorative terms for people category.

  • Collagen, the structural protein "glue" that holds our bodies together, deserves many kudos:
    • It's the main component of connective tissue (cartilage, bone, ligaments, tendons, skin) and also abundant in many other body parts.
    • It's the most abundant protein in mammals, accounting for 25% to 35% of whole-body protein content.
    • Has an interesting protein structure: three left-handed procollagen polypeptides coil together forming a right-handed triple helical tropocollagen which themselves bind together to form a fibril and those come together to form a collagen fibre.
    • Has an unusual amino acid composition and sequence containing two uncommon derivative amino acids: hydroxyproline and hydroxylysine that require vitamin C to be produced -- explaining why deficiency of that vitamin leads to scurvy.
    • Genetic defects in collagen structure or processing can lead to diseases such as Ehlers–Danlos_syndromes.
  • List of Internet phenomena
    • Vast array of culturally interesting topics.
    • And an impressive list of references (428 as of 25 Jan 2021) - the largest I've seen in Wikipedia.
  • Unusual articles - articles that have met the standard of unusualness.
  • Imprinted brain hypothesis
    • An intriguing genomic imprinting theory that lacks scientific support.
    • The Main Page on 5-6 Mar 2021 claimed "that the proposers of the imprinted brain hypothesis, which claims that autistic and schizotypal traits are opposites, had no background in behavioural genetics before proposing it," - but I don't see any such claim in the article.
  • Trump derangement syndrome a.k.a. "TDS"

Users of note[edit]

Alphabetical, but definitely not an exhaustive list here. There are tons of notable Wikipedians out there. What follows is a teensy list of a few folks that just happened to catch my attention for one reason or another.