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_ihaque

695 karma · joined January 21, 2013

CTO at Kimia Therapeutics: https://kimiatx.com

https://bsky.app/profile/ihaque.bsky.social

https://twitter.com/imranshaque

https://ihaque.org

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_ihaque··on Extreme Heat conference cancelled due to extreme heat warning
This is an uncharitable take on the original comment which literally said:

> the fact this is how hot it will be from now on

That sounds to me like an acknowledgement that, in fact, the climate has changed.

_ihaque··on The nuclear-physics infrastructure behind PET scans
> Isotopes of a given element have the same number of protons (92 for uranium), but different numbers of neutrons (143 for U-235 and 146 for U-238), meaning they behave the same chemically but differ in mass or radiation emissions.

A fun but off-topic note: "behave the same chemically" is only approximately true. For heavy atoms like the ones discussed in the article, it's basically true. But for hydrogen, adding one neutron doubles its mass and you can get real effects on chemical reaction rates.

https://en.wikipedia.org/wiki/Kinetic_isotope_effect

And of course, an obligatory "In The Pipeline" link on how it's used in drug discovery: https://www.science.org/content/blog-post/isotopes-get-your-...

_ihaque··on My fan worked fine, so I gave it WiFi
Based on the description of the wiring to the motor (24V, GND, POT1, POT2, NC), it doesn't sound like the original setup would have been drawing much power through the pot either -- there's probably something else on the other end of that wire that is doing modulation based on the sense resistance, and the motor is itself drawing power from the 24V line. So while it's true that there should be a check for the allowable limits on the digipot, I don't think it's actually being used to sink much power.
_ihaque··on Intel Arc Celestial dGPU seems to be first casualty of Nvidia partnership
https://chipsandcheese.com/p/intels-battlemage-architecture
_ihaque··on The Bootstrap Load
The linked article doesn't say that much about what the bootstrap load is or how it worked, but luckily for us @kens wrote a whole article about it: https://www.righto.com/2020/10/how-bootstrap-load-made-histo...
_ihaque··on Researchers find a way to make the HIV virus visible within white blood cells
If this (or, more accurately, a drug developed downstream of this technology) worked, they absolutely would.

A great example of this in relatively recent history is the treatment of hepatitis C. The treatments pre-circa-2011 were pretty crappy: interferon/ribavirin had poor cure rates and bad side effects. But it was still better than hepatitis destroying your liver, so people dealt with it.

Then, in 2011, as the culmination of years of trials, telaprevir (from Vertex/J&J) [1] and boceprevir (Schering-Plough/Merck) [2] were approved and were DRAMATICALLY BETTER than interferon/ribavirin.

...and then just two years later both of these drugs got nuked by the approval of sofosbuvir (aka Sovaldi, from Pharmasset/Gilead) [3], which has _cure_ rates in excess of 90%. Telaprevir and boceprevir were pulled from the market because there was simply no more market for them once sofosbuvir hit. Scientific competition at its finest.

There is absolutely a dark side to pharmaceutical pricing and licensing, but please don't let the existence of that dark side cloud your vision of the transformative impact that those of us in biotech R&D want to have (and in many cases, have had). I was at Vertex when the early trial data on telaprevir started coming out and it became clear that we might be able to offer patients real hope who did not have it before.

[1] https://en.wikipedia.org/wiki/Telaprevir [2] https://en.wikipedia.org/wiki/Boceprevir [3] https://en.wikipedia.org/wiki/Sofosbuvir

_ihaque··on A toy RTOS inside Super Mario Bros. using emulator save states
I think you mean SMT (simultaneous multithreading), as opposed to SMP (symmetric multiprocessing)?
_ihaque··on Eli Lilly will soon release key data on its weight loss pill orforglipron
Those wondering about the mouthful of a name that is "orforglipron" may be interested in the INN (international nonproprietary name) standard for generic drugs. That name is a "generic" or "nonproprietary" name.

Those typically have a "stem" which indicate the mechanism by which the drug works. In this case, it's "-glipron", which you can parse as "glipr" -- GLP-1 receptor -- and "on" -- it's an "agonist", or something that turns "on" the receptor. So "-glipron"s are drugs which agonize, or activate, the GLP-1 receptor. There are other gliprons in trials, including danuglipron (https://en.wikipedia.org/wiki/Danuglipron) from Pfizer, and many others that don't have assigned INNs.

Semaglutide and liraglutide also agonize GLP-1, so why aren't they gliprons? Because chemically they are analogs of the naturally occurring GLP-1 peptide, so they get the -glutide (GLUcagon-like pepTIDE) stem.

I don't know why tirzepatide got that name. It's a peptide, so "-tide" makes sense, but it's actually listed as a "various" exception in the master document of INNs: https://iris.who.int/bitstream/handle/10665/379226/978924009....

_ihaque··on Eli Lilly will soon release key data on its weight loss pill orforglipron
No, it's not a reformulation of tirzepatide. Orforglipron is a small molecule with a molecular mass of 883 g/mol and tirzepatide is a large molecule peptide six tims larger, with a molecular mass of 4813 g/mol.

The Wikipedia pages are decent -- the picture makes it fairly obvious how much smaller orforglipron is than tirzepatide even if you don't know how to read chemical structures; just count atoms!

https://en.wikipedia.org/wiki/Orforglipron

https://en.wikipedia.org/wiki/Tirzepatide

_ihaque··on Why Recursion Pharmaceuticals abandoned cell painting for brightfield imaging
We definitely do (as in, I myself have) hire folks from "cold" inbound applications.
_ihaque··on Why Recursion Pharmaceuticals abandoned cell painting for brightfield imaging
Not that I know of! Note that the positions we list are typically in different teams so it's worth reading the descriptions to make sure you're picking whichever one is most appropriate to your experience+interests (and, as a corollary, if you weren't a fit for a previous position, you may be one for one that comes up in the future).
_ihaque··on Why Recursion Pharmaceuticals abandoned cell painting for brightfield imaging
I should point out that we are hiring! Software engineering, data science/ML, and IT positions are available in Salt Lake City, Toronto, New York, and London:

https://job-boards.greenhouse.io/recursionpharmaceuticals

_ihaque··on Why Recursion Pharmaceuticals abandoned cell painting for brightfield imaging
Yes, we (and plenty of others) have prior data showing that perturbations (things that you can do to cells, like knocking out genes or putting drug-candidates on them) have different effects at different times, so we are excited to see the potential for time course imaging.

Note that "video" is a little different here than the way we all usually think of it - think "minutes or hours between frames" not "frames per second".

_ihaque··on Why Recursion Pharmaceuticals abandoned cell painting for brightfield imaging
My team did part of the work described in TFA, AMA.
_ihaque··on Blood test for colon cancer screening approved by US regulators
These are tests of circulating cell-free DNA (cfDNA), not circulating cells. The fraction of circulating _cancer cells_ is too low (outside of blood cancers or metastatic cancers) to be technically feasible to detect; ditto in pregnancy. By contrast, while there isn't much cfDNA (DNA fragments floating around in blood plasma outside of cells) -- on the order of 1-10 ng/mL -- there's enough to extract reliably, and critically, the fraction of that that is tumor-derived (or fetally-derived, for prenatal testing) can be high. It's already high single to low double digit percent at 10-12 weeks of gestation, and can go much higher in some cancers.

But the biggest challenge for these tests is that this "tumor fraction" can be very very low in early stage cancers, which is why stage I sensitivity tends to be quite poor.

_ihaque··on Standard cells: Looking at individual gates in the Pentium processor
Biological microscopes illuminate the sample from below, as the samples are typically transparent. Metallurgical microscopes illuminate reflective samples from above.

*"Below" meaning "on the opposite side from the objective" - you illuminate _through_ the sample.

_ihaque··on Launch HN: Volta Labs (YC W19) – Easier sample prep for genomics
Hi Udayan - nice to see another shot at electrowetting microfluidics in this space.

1. How does your technology or product offering distinguish itself from prior attempts like NeoPrep (née Advanced Liquid Logic) from Illumina or Voltrax from ONT?

2. How "hackable" is the offering for power users to implement custom protocols on the instrument and consumables?

_ihaque··on Helium is essential but nonrenewable and difficult to recycle
Neon is produced from (cryogenic) separation of air, so, yes?
_ihaque··on IRS to begin trial of its own free tax-filing system
For anyone interested in why the system looks the way it does, I recommend patio11's insightful recent blog post, which is nominally about payroll systems but ends up discussing the history of taxation in the US because that's the origination of many of these systems: https://www.bitsaboutmoney.com/archive/payroll-providers-pow...

A relevant quotation for much of the discussion here:

> And, relevant to the question of whether Intuit controls U.S. tax policy: it can’t, because that would imply they have wrested control from Norquist. Norquist considers a public filing option a tax increase by stealth and opposes it automatically.

_ihaque··on Desalination can beat batteries for excess energy
Level 2? Certainly not.

A typical L2 charger will provide in the range of 6-10kW (AC, marginally less ends up going to the battery after conversion losses). 10kW is only 13hp; forget acceleration - the car draws more than that at highway speeds.

(You can come at this result another way too - an L2 charge may take 6-10hr to refill the battery from empty. But the car would not be able to drive 6-10hr at highway speed starting at 100% charge! So the L2 must be delivering less power than the car consumes at cruising speed.)

_ihaque··on Don't waste money on a math coprocessor they said
I believe the 387 was an actual coprocessor; the _487_ may be what you're thinking of -- the 487SX contained a whole 486DX inside and just disabled the host processor [1].

[1] https://en.wikipedia.org/wiki/X87#80487

_ihaque··on Cystic fibrosis treatment wins Breakthrough Prize
Surprisingly, sort of.

It won't alter the underlying genetic condition, but there has been at least one case report that taking these CFTR modulators during pregnancy can improve the condition of the fetus/newborn:

https://www.sciencedirect.com/science/article/pii/S156919932...

https://med.stanford.edu/news/all-news/2023/07/cystic-fibros...

_ihaque··on A supercapacitor made from cement
Energy in a capacitor is (1/2)CV^2 - so 12x the voltage would be 144x the energy.
_ihaque··on Commercial quantum computer identifies molecular candidate for better solar cell
H4 certainly sounds strange to me (and as other commenters have pointed out, this is a toy example, not a real molecule), but there are weird bond structures out there in real molecules that violate "at minimum, two electrons shared between the two atoms": https://en.wikipedia.org/wiki/Three-center_two-electron_bond.

(The 3C-2E bonds in diborane are not linear, so that doesn't seem like what could be happening here.)

_ihaque··on Confessions of a Bitcoin Widow
One would use a scheme like Shamir's secret sharing [1], not literally cutting the exact bits of the key into strips.

> To unlock the secret via Shamir's secret sharing, a minimum number of shares are needed. This is called the threshold, and is used to denote the minimum number of shares needed to unlock the secret. An adversary who discovers any number of shares less than the threshold will not have any additional information about the secured secret-- this is called perfect secrecy. In this sense, SSS is a generalisation of the one-time pad (which is effectively SSS with a two-share threshold and two shares in total).

[1] https://en.wikipedia.org/wiki/Shamir%27s_Secret_Sharing

_ihaque··on 'Useless specks of dust' turn out to be building blocks of vertebrate genomes
> As it implies the close spacing is for some kind of mechanical/electrical mechanism within the core of every cell’s nucelus.

It is interesting, but not for the reasons you may be imagining. And not a mysterious electrical mechanism.

It's well-known in the field that (e.g., in humans), chromosomes fold in on themselves in structured ways [1,2]. The functional consequence is not precisely mechanical or electrical -- rather, these folds bring regulatory domains close in 3D space to the sequences which they regulate (which may be far in 1-D sequence distance). These can be elements like "enhancers", which increase the level of transcription (DNA->RNA copying, the first step of gene expression); "insulators", which break up coherent blocks of gene regulation, etc. One of the mediating mechanisms is that regulatory proteins bind to these particular sequences; bringing them together in 3D space allows the assembly of a protein complex that actually carries out the relevant process (eg, transcription).

So, what's interesting here? There is extensive evidence of these contacts within mammalian chromosomes, but limited evidence _between_ different chromosomes. Insofar as the paper shows that mammalian macrochromosomes have homology to multiple reptile/avian microchromosomes (really, to their most recent common ancestor), it may be (speculation alert) that intra-chromosome contacts recapitulate contacts and organization seen in the ancestral microchromosomes.

(There are also "simple" interactions like wrapping of DNA on protein complexes called nucleosomes, like string on beads, but that's less interesting in this context.)

[1] https://en.wikipedia.org/wiki/Nuclear_organization#DNA_loopi... [2] https://en.wikipedia.org/wiki/Nuclear_organization#Chromosom...

_ihaque··on Chemical space is really big (2014)
Even at 500Da or less, it's much, much larger than that.

You may be interested in the work of Jean-Louis Reymond's group, who have done more or less exactly what you suggest: https://gdb.unibe.ch/downloads/

GDB-11, with 11 heavy atoms, has 26.4M structures (110.9M stereoisomers -- molecules aren't 2D). Going up to 13 gives you 970M molecules. Going up to 17 (still mostly below 250Da) is 166,400M.

There's a lot of space up there below 500Da.

_ihaque··on Be in a field where tech is the limit
Sorry @RhysU! My intention wasn't to poo on financial careers. A lot of* what happens in finance is in fact useful and certainly technically interesting.

My point was that _if_ one's primary goal is to get the highest comp possible, it's probably better to go into finance than biotech. No bones about that; we don't pay as well. But that does not mean that biotech universally pays _badly_ for technical skills, as casual readers might assume based on reading this thread. My point was that if someone is both technically-minded and interested in the mission in biotech, it's worth taking a closer look, especially at the wave of companies from the last ten years bringing tech and biotech together.

* Not everything, I'm sure, but neither is everything in biotech!

_ihaque··on Be in a field where tech is the limit
There are a lot of comments in this thread discussing biotech salaries. They're not universally true. Source: I'm the VP of data science at Recursion, a biotech company focused on drug discovery, so I manage or have visibility into hiring in the domains that most people on this site would likely be interested in.

The biotech industry (which is made up of at least three rather different verticals: tools, diagnostics, and therapeutics) is changing quite a bit today. There are certainly companies that have less of a technology or data emphasis or who are still trying to figure out the value those could bring, and those companies are far less likely to pay well in SW/DS roles. There are others that either from their inception or more recently realize the value these approaches can deliver and compensate accordingly. I personally find the new wave of biotech startups that are focused on being hybrids of experimental and computational capabilities extremely exciting (which is why I'm at one) and these are the firms where software and mathematical skill sets are most likely to be valued.

You'll probably still make more on Wall Street than you would in biotech. But you don't have to be _badly_ paid in order to work on a meaningful mission. OP is, IMO, correct that biology is entering a phase in which computational skills are a rate-limiting factor in our ability to make advances (note: not _the_ limit -- experiment is still absolutely critical), and it's a super exciting and impactful field to be in.

Shameless plug: Recursion is hiring a TON of positions in data science and machine learning, engineering, and elsewhere. Check us out: https://www.recursion.com/careers. (Contact info is in my bio.)

_ihaque··on Periodical cicada Brood X will emerge in 15 states in 2021
(For those who didn't click, note that What-If #120 is "Excerpts from What If articles written in a world which, thankfully, is not the one we live in")
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