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jebus989

845 karma · joined November 8, 2013

Computational biology PhD.

blm.io

@benjaminlmoore

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jebus989··on How to sequence your own DNA at home
It's been around for a decade and was $1k in early access, so don't hold your breath.
jebus989··on How to sequence your own DNA at home
Per the article, ONT sells tiny sequencers that all this genre of "Omg I just sequenced my genome" posts use. They've been around for a decade or so. A commercial lab will give you 30x illumina sequencing for maybe 5% of the cost of this post.
jebus989··on Claude for Small Business
The good thing is we've learned this already from cloud. When one AWS region is degraded we all failover to other regions, and then other cloud providers, right? ...right?
jebus989··on Show HN: Mcp2cli – One CLI for every API, 96-99% fewer tokens than native MCP
Roll your own
jebus989··on Claude Sonnet 4.6
Even simpler it just takes screenshots (or at least that's what it was doing last time I used it)
jebus989··on Why a cancer scare around aspartame is mostly unfounded
> In complex systems, such as the human body, the only evidence of safety is time -- a very long time. The Stevia plant (though not the same as extract) has been used for centuries. Aspartame was (accidentally) created in the lab in 1965.

Time is not evidence of safety, that is an odd claim (see smoking tobacco), thankfully we have the scientific method to investigate hypotheses like "x is bad for you".

jebus989··on Why a cancer scare around aspartame is mostly unfounded
This is an example of the "appeal to nature" logical fallacy. You may be able to make a case that Stevia is healthier than Aspartame, but it should be based on evidence to that effect rather than because you like the idea that it has ingredients derived from organic material.
jebus989··on Ask HN: Any open source stack exchange clone
In the bioinformatics sphere there is this MIT-licensed Stack Exchange clone: https://github.com/ialbert/biostar-central
jebus989··on Ask HN: What are examples of common beliefs conclusively invalidated by data?
All crops are inclined to be grown in monocultures. That's because even if you'd get more yield pairing with other species — as in these studies — pragmatically the time and cost of sowing, harvesting and separating multiple species outweighs the theoretical yield gain per unit area of a monocrop.
jebus989··on Ask HN: What are examples of common beliefs conclusively invalidated by data?
These are indeed links but quite random ones. Mostly they are reporting that growing two things together in a field can give higher yields than growing a single thing. None seem to be related to GMOs, which could obviously also be grown with complimentary species to increase yield.
jebus989··on Ask HN: What are examples of common beliefs conclusively invalidated by data?
I'm not sure if this was an unfortunate accident but almost every banana worldwide is essentially genetically identical: https://en.wikipedia.org/wiki/Cavendish_banana
jebus989··on Ask HN: What are examples of common beliefs conclusively invalidated by data?
To re-iterate: there is no biodiversity in agriculture. As an example, "non-GMO" bananas are cloned from a single species the world over. If you'd be concerned about a single disease destroying genetically-identical crops worldwide, that happened with the Gros Michel cultivar in the 20th century. Competing GMO banana products would introduce more diversity than exists today.
jebus989··on Ask HN: What are examples of common beliefs conclusively invalidated by data?
There is no biodiversity in agriculture. Whether or not the seeds you purchased have been edited to add drought resistance or high vitamin A content or other fantastic benefits to humankind you are still growing a monoculture, just as you were with non-GMO crops.
jebus989··on Butyrylcholinesterase is a potential biomarker for Sudden Infant Death Syndrome
I agree, I'm guessing the highest (arguably avoidable) risk to a baby or child is driving them around in a car.
jebus989··on I'm Too Risk-Averse for Index Investing
Your points in order were:

1. There's no way to hedge against inflation (you didn't know TIPS existed)

2. Having learned about TIPS you assert they're illiquid and can't be traded easily (you didn't know about TIPS funds)

3. Having learnt about TIPS funds you don't the recent returns of a specific fund (you don't know that TIPS adjustments lag reported inflation numbers)

jebus989··on I'm Too Risk-Averse for Index Investing
Erm, just buy a TIPS fund like VIPSX from Vanguard.
jebus989··on I'm Too Risk-Averse for Index Investing
> You can't even hedge inflation without the stock market (or real estate, if you can afford the buy-in).

See also: treasury inflation-protected securities (TIPS).

jebus989··on Moderna mRNA sequence released to GitHub [pdf]
Proteins are written in standardised IUPAC amino acid codes that carry some semantic meaning, e.g. Alanine: A, Glycine: G etc. Also viral genomes often have overlapping transcription with shifted open reading frames. Biology is not as simple as you think.
jebus989··on An introduction to Tmux
Suspend?
jebus989··on CPAN is 20
Also CRAN, which is still meant to be pronounced C-RAN as an homage.
jebus989··on Functional Programming in the Real World (2003)
It's an academic webpage so by definition at least a decade since last updated.
jebus989··on Warren Buffett Just Wrote His Best Annual Letter
He talks about this in lots of annual letters. Reality is that Berkshire Hathaway undoubtedly has (a perception of) the lowest bus factor of any holdings group and Buffett has been priming for years to prevent shares tanking when he inevitably passes or steps down.

Aside: to those who enjoyed reading this annual letter I recommend "The Essays of Warren Buffett" — an arranged collection of edited previous letters by theme (though they are all also freely available online).

jebus989··on Show HN: New IDE and GUI for R language
Both sound good, maybe you could highlight these on your landing page? The picker for RColorBrewer palettes looks particularly handy!
jebus989··on Show HN: New IDE and GUI for R language
Making R available from Excel seems a good idea to ease the transition for newbies (like R commander) but what advantages does the standalone IDE have over RStudio or the default R.app?

Edit: actually I managed to click through to find this screenshot: http://fasterstat.com/Images/Desktop/12_R_gui.png which looks novel (can't currently watch the video unfortunately)

jebus989··on XKCD: Meeting
Randall's been sitting on this since 20 Nov 2014?
jebus989··on Our Director of Engineering on the new Wired.com
Post title is particularly horrible IMO, Ambroise STD Francois with uppercase transform ugh.
jebus989··on Twitter’s new R package for anomaly detection
Even the original twitter blog seems to have gone out of its way to make this seem more complex then it is...

Decomposition of time series is done with STL (stl function in stats package) and this is the first part of what they call "Seasonal Hybrid ESD (S-H-ESD)" (sounds impressive right?) which then apparently just involves taking the max absolute difference from the detrended sample mean in terms of standard deviations, remove it and repeat until you have your collection of x outliers. If they wanted to this could be explained in a few sentences, and the underlying code is really simple [0], but for whatever reason it's been written up as advanced analytics — as if decomposing a time series is a major challenge.

[0] https://github.com/twitter/AnomalyDetection/blob/master/R/de...

jebus989··on Elon Musk AMA
Unsure of how much editing you've done but I've made over 10,000 edits over the past 9 years and that's not been my experience (google my HN username + wikipedia).
jebus989··on Elon Musk AMA
Happy to continue to debate this point (possibly on another medium?) but no, a comment 437 days ago on HN saying "I once tried to edit but was reverted" is not evidence that too many rules have "murdered wikipedia", your original contention with which I took issue.
jebus989··on Elon Musk AMA
You're making leaps of logic based on the occasional HN anecdote. Numbers have been in decline since 2007, what percentage of those left over bickering about rules? Do you have any evidence for this given that IAR has been in place as a core principle throughout?

IAR can be and indeed is invoked all the time, making Wikipedia a bad example of how strict rule adherence stifles a community. It was quite a simple point that needn't warrant downvotes, italics and so many HN searches.

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