Hessam Akhlaghpour
@theHessam
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postdoc in Maimon lab @RockefellerUniv | alumnus of @PrincetonNeuro | Check out my blog: | @hessamBeFarsi به فارسی
New York, NY
Joined July 2013
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Pinned Tweet
It's officially published in the Journal of Theoretical Biology! An RNA-Based Theory of Natural Universal Computation.
free-access link for next 50 days:
In it, I raise a theoretical challenge that I believe is overlooked in neuroscience and biology...👇
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This past weekend, I re-read “No Good Men Among the Living: America, the Taliban, and the War through Afghan Eyes” by
@Anand_Gopal_
for the 2nd time.
What an amazing and insightful book. Here is one of the most eye-opening things I learned from it: 🧵
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The Taliban are in power today, not "despite 20 years of US presence", but precisely because of the form of US presence and the political order that ensued. It is a mess we created, not one that we failed to fix out of incompetency or lack of resources.
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Here was the dilemma. The US was there to "fight terrorism". But without the Taliban or AlQaeda there, there was no enemy. They needed targets to bomb, homes to raid, and people to imprison. This created an incentive for local politicians to “create enemies where there were none”
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When I was a child my father taught me that if you see someone being bullied at school, speak up and defend them. If you then get bullied in response, that is unfortunate, but at least you were not a coward.
Here is my letter to the eLife board in defense of Michael Eisen.
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In one telling case, January 2002, two competing political groups of pro-American Afghan political officials were simultaneously massacred, arrested, and tortured by US marines. Each group had falsely tipped off the Americans, portraying the other group as Talibs.
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...and report their political rivals to US intelligence branding them as terrorists. These false intelligence reports were typically rewarded with money, business contracts, and more access to American troops which meant more political power to wield US military in their favor.
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Excited to finally share this preprint:
"A Theory of Natural Universal Computation Through RNA"
summary thread below: 1/n
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Within months after the US-led invasion in 2001, the Taliban effectively vanished. Al-Qaeda leaders fled to Pakistan, but the Taliban - realizing they had no chance of victory - accepted the new order. They acknowledged Karzai as interim president, surrendered arms, and ...
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Soon Afghanistan was riddled with a bunch of regional repressive strongmen, like Gul Agha Sherzai and Jan Mohammad Khan, who fed their enemies and dissidents to the target-hungry American war machine and buffed up their own private militia with US dollars.
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US troops raided homes and detained and tortured village elders and tribal leaders, many of whom were sympathetic to the US. This violence had nothing to do with the Taliban and everything to do with local politics which grew more sectarian in such circumstances.
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The book covers the story of a former Talib that renounced all former ties with the group and set up a local business. Police repeatedly beat him, threatened him with torture and took all his savings. He and his fellow villagers ultimately joined the Taliban.
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It was in this atmosphere of resentment and that the Taliban re-emerged in 2004 and grew in the years to come.
The repression led to more resentment. The resentment led some to seek revenge against the US and Afghan government by joining the Taliban.
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Many of the pre-Taliban war criminals had rose to power again, with full US backing, pretending to fight terrorists. Police forces morphed into the same militias and gangs of the civil war days. They'd ransack shops and homes, loot travelers, and in some cases rape and murder.
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retreated from politics with no plans to return. They even denounced fund-raising efforts by religious clerics in Pakistan to revive the Taliban. It wasn’t a just scheme to hold-out in hiding. They genuinely ceased to exist.
So what led to revival of Taliban several years later?
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The resurgence of the Taliban made the US even more dependent on private Afghan militiamen (which ironically would sometimes pay the Taliban to withhold their attacks - meaning that the US indirectly paid the Taliban for security).
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Things were different in places with less US military presence. In northern Afghanistan or Istalif, for example, political rivals could not call in US troops to settle their feuds. American troops in the south brought instability, violence, and cycles of revenge.
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I have been following the discourse surrounding MMT among academic economists and it’s astonishing how dismissive the field is toward any paradigm-shifting ideas.
#MMT
is producing insightful & valuable work. They’re starting to get some recognition among the public. But...
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Current postdoc here. The uncertainty about the future and geographic instability in your 30s is the absolute worst.
Experimental biology/neuroscience is incredibly exploitative and puts too much of the risk inherent to science on the shoulders of early career scientists.
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I’m all ears for what current postdocs are saying would make their experiences better.
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Here is the Farsi version of the thread:
در چند روز گذشته کتاب آناند گوپال را برای بار دوم خواندم. کتاب بینظیری است در شرح وضعیت افغانستان پس از حملهی آمریکا. هیچی جای متن اصلی را نمیگیرد. ولی بعضی از جالبترین چیزهایی که ازش آموختم را برایتان مینویسم.
#رشتو
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Here, I make the case that neural networks and dynamical systems are computationally weak and are probably unable to explain how biology computes.
Let me know if you disagree or if this changed your mind. I would be more than happy to discuss.
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I think this is a study that every neuroscientist should at least know about. So here's my short summary of two fascinating papers by
@scthornquist
et al.
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It never ceases to amaze me how uncoordinated, yet coordinated, US media can be. The Biden administration vetoed Israel-Gaza cease-fires *three times* in a week. Which major media outlets have covered any of these vetoes?
🧵
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“his approach [has] been detrimental to the cohesion of the community we are trying to build.”
What kind of community are you trying to build eLife? Cohesion around what? Spell it out for us please.
The Board of eLife has made the decision to replace our Editor-in-Chief. Read more in the full statement .
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Me, 60 years later, still trying to teach these motherfuckers to count.
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About 30 people are blocking the garages. Cars honk by in support. Rain is starting but no one is leaving. They plan to stay here until they shut it down.
#AbolishICE
#OccupyICENYC
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@nytopinion
hah. Starving a nation is to teach their leaders a lesson is really funny. Here's what happened when the sanctions started first in 2006:
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Proboscis ✔️
Ocelli ✔️
Antennas ✔️
Aristas ✔️
Oversized ommatidia ✔️
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Here is a video of my recent talk at UCLA.
If you want to hear an overview about what I think is the most exciting problem in biology, check it out below: (It's only 24 minutes excluding Q&A).
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have reported it:
Reuters
AP
AlJazeera
Haaretz
DW
France 24
Jerusalem Post
Guardian
the Independent
completely avoided reporting it:
New York Times
MSNBC
CBC
CNN
Washington Post
Wall Street Journal
Vice News
Bloomberg
NPR
Notice a pattern?
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I know they don’t read the literature because anyone who has spent the slightest amount of time on the subject knows that MMT doesn’t claim there are no constraints to govt spending. Yet, the here’s a tweet from a famous economist
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But MMT ran with it: central banks could "print money" to pay for any amount of spending. At the limit, they had a motto: there is no constraint on how much the government can spend. This is an absurd limit, wrong and backwards: CB reserves are just another form of borrowing
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They could. But my extensive experience working with them tells me they don’t want to.
Could fruit flies reveal the hidden mechanisms of the mind?
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But the response from mainstream economists has been ridicule (eg tweet below) and distortion.
For some reason, they don’t even think it’s worth their time to engage with it at a serious level.
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@AdyBarkan
Yep. Here is a list of sources that did and didn’t report that Biden has blocked UN cease-fires this week. US corporate media intentionally omit it, but it’s covered everywhere else.
have reported it:
Reuters
AP
AlJazeera
Haaretz
DW
France 24
Jerusalem Post
Guardian
the Independent
completely avoided reporting it:
New York Times
MSNBC
CBC
CNN
Washington Post
Wall Street Journal
Vice News
Bloomberg
NPR
Notice a pattern?
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I started a blog where I will be rambling about science, computation, and some other random things.
Here is my first post:
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damn it feels good to get cited *before* your paper gets published. (especially when you’re having a tough time getting it accepted)
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There’s no effective difference between when the Fed sells bonds and when the Treasury sells bonds.
We call the latter “borrowing” and the former “open market operations”.
See t=3:50 for explanation
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The Islamic regime is about to execute another protester
#MahanSadarat
for allegedly "wielding a knife" without even hurting anyone. They have no shame in making up charges and, in fact, Mahan says he never had a knife. So why don't they go all out and accuse him of murder?
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بیدادگاه اتهام «کشیدن سلاح سرد» را بر اساس ادعاهای واهی یک «شاکی خصوصی» مطرح کرده است! اما حتی در این اتهامات واهی هم ماهان به شرکت در اقدامی که به آسیب جدی کسی منجر بشود متهم نشده است. با این حال میخواهند جان #ماهان_صدرات را بگیرند.
#مهسا_امینی #ماهان_صدرات_مدنی
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And if you get unlucky and for whatever reason your experiments don't yield the results people want to see, you are compelled to leave academia.
It's such a strange system. We lose so many passionate and skillful scientists every year. Does any industry work like that?
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1/2) Attention neuro twitter! Athena Akrami is starting a lab at UCL, London, from October 2018.
She is looking for talented students/postdocs with strong quantitative backgrounds but also willing to work on experiments (ephys, opto, imaging).
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Stressing out and confused about an uncertain future when I see this uplifting message from friends in the lab
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The "universal approximation theorem" implies that feed forward neural networks can be used to model any function. Just like universal computers. Right?... Wrong!
The theorem says that you can approximate any *continuous* function over a *compact* domain with feed forward nets.
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really hard to focus at work when thousands of kids are being starved, incinerated, or trapped to death under rubble by bombs manufactured in your country’s economy while everyone at the top is like “it’s sad we didn’t want this but we have no choice”
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So serious question in good faith for the academic critics: is this wrong? Can you explain why? If not, will you at least recognize that MMT has brought new insights to your field?
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I hope this summary is exciting enough to get some of you to read the paper. Even if the RNA-based theory is disproved, the fact that universal computation is within the reach of molecular biology means that we'd need to search for it elsewhere.
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Really cool preprint (only 6 pages) exploring the idea that RNA/DNA sequences may be directly converted to neuronal signaling in the brain:
(and they refer to my paper 😇)
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It all clicked in once I learned about lambda-calculus/combinatory-logic and realized that RNA secondary structure solves the [otherwise difficult] problem of parenthesis matching.
5/
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So where’s the neural network for this little fella?
Lacrymaria Olor is an unicellular microorganism able to stretch its "neck" to about 7-10x its body length. With no eyes, it also looks like it knows where prey are located. This is a normal speed clip [source, full video: ]
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@nytopinion
wait... what is the lesson supposed to be again? To stop a nuclear weapons program that doesn't exist?
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It’s quite elegant how a new paradigm follows from recognizing a simple symmetry: the symmetry between the Treasury and the Federal Reserve (Central Bank).
This is a very concrete claim. It is central to MMT. It’s novel. Didn’t exist in the field before MMT.
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Thur, Feb 6
A giant fly landed next to me as I was flipping flies. I skillfully caught it using my special postdoc level experience. I treated her with a drop of 95% ethanol. She came back for more. I gave her more. She got drunk and uncoordinated for 4 hrs. Then I set her free.
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It's not just that. Some of my friends (US citizens and GC holders) entered the US last night. They took their phones, their passwords, all of their social media handles, kept the phones for hours, question family information and really treated them with disrespect.
BREAKING: US CUSTOMS & BORDER PROTECTION NATIONALLY HAVE BEEN ORDERED TO DETAIN & "REPORT" ALL IRANIANS ENTERING THE COUNTRY DEEMED POTENTIALLY SUSPICIOUS OR "ADVERSARIAL" REGARDLESS OF CITIZENSHIP STATUS. 60+ Iranis held last night at the US/Canada border for 11+ hrs / thread
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been pregnant with twins for about two years now. When New York goes into quarantine mode I'll finally have the time to go into labor and upload them both to bioRxiv.
One is a stats framework for hypothesis testing. The other, a crazy theory on molecular computation. Stay tuned.
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Every computation system has a scope: a set of problems it can solve. Some computation systems are capable of solving all computable problems. These are called "universal computers". Turing Machines are a popularized example but others exist that don't look anything like TMs
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I wrote something on how practically every usage of statistical significance (p-values) is rationally flawed.
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I can't wait to share my latest research alongside such a remarkable panel of individuals whose work I deeply respect and admire. (
@ctmurphy1
@Puthanveettil_S
@JasonSynaptic
)
If you're attending
@LEARNMEM
and want to discuss RNA computation come find me!
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scientific papers typically appear more complicated than they need to be. It's very difficult for anyone outside of science to read a paper and understand it. But the actual content is usually easy to explain verbally.
This study shows it's getting worse.
Scientific papers are getting less readable: fewer common words; more jargon
NB: For upper right figure, higher scores indicate lower readability.
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As far as we know, none of our current models in biology achieve universal computation. Not neural nets. Not molecular networks. Only structurally unstable dynamical systems (which are physically/biologically irrelevant) have been shown to simulate TMs.
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And the same’s true for buying bonds. Everything else follows from accepting this symmetry.
Something that convinced me that they’re right is that the bonds held by the Fed are not a liability for the treasury. In other words The treasury never owes the fed money.
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When bonds held by the Fed mature, they are forgiven or roll over to new bonds. That’s just a fact, not a theory.
So when the Fed buys bonds in its day to day operations, it is as if the Treasury pays its “debt” through the money created by the Fed.
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Our message to
@SenSchumer
. I hope he hears it. Part 1/3
“Chuck Schumer had been consistently hawkish on Iran. He has refused to call out Trump’s actions despite our constant pleas.”
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I wrote a short piece on "when biology isn't messy". It ends with a question that I hope is thought-provoking. Let me know your thoughts!
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All the bits and pieces are in place for my new research project. Fruit flies on spherical treadmills are awesome.
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Muskification:
[mʌskɪfɪˈkeɪʃən]
(n.) The act of attributing an organization’s progress to its leader’s ingenuity and skill rather than to that of its workers/scientists/engineers or to public investment and infrastructure or to negative factors like coercion and control.
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I argue that an undiscovered universal computation system exists in biology. Why would evolution have missed the chance to create it? It would immensely benefit organisms that struggle to survive and reproduce and can be used in cognition, cell-behavior, and development.
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Ali’s brother just tested positive. So did everyone else in their medical team. But they are all still going to work because they have no one to take their place in the hospital.
Dude is my little brother, a 2nd year resident at Mt.Sinai pulling long hours taking care of Corona patients.
Trump can call Iranians names and ban us from US entry. We respond with unconditional kindness and care. We are all in this together and we will survive.
Dude is my hero
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My friends outside of the field are shocked when they hear that we do 6, 7, sometimes up to 10 years (!) of postdoc before even having a *chance* at a faculty position.
Even if all goes well, you have very little influence (or even prior knowledge) which city you end up in.
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It actually isn't difficult to stumble upon universal computation by accident (e.g.Conway's game of life, or rule 110). It can be done through simple rules. The key ingredient, though, is memory expansion: the ability to expand memory usage *during* computation
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A very common complaint that I see from the critics is that MMT is elusive and there are always people who say “you just haven’t fully understood it”.
Reis says it in the thread above. Krugman says it here.
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I've been saying that MMT involves a lot of Calvinball -- constantly changing the rule in mid-game. Try to pin its advocates down on, well, anything, and they insist that you haven't understood their deep insights 1/
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So the fruit fly connectome came out today. Now all we have to do to “understand” the brain is to memorize all the connections. We decided to split it up across our most talented lab members (yes, myself included) and then we will collectively know how fruit flies think.
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This is pretty dope. Couldn’t believe it at first but apparently it’s a well known phenomenon called an “ant mill” first described 100 years ago.
Amazing: a bug in Nature’s code.
🐜🐜🐜 use pheromones to follow trails. If a trail loops, they get locked running in a circle and die from exhaustion.
via
@Mehdi_Moussaid
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It's my 2nd month working on flies and I already have exciting behavioral findings. Fly experiments are fast and fun.
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Excited to be part of this symposium at UCLA next week. My talk will be about "surprising parallels between RNA biology and combinatory logic."
Looking forward to all the other talks and discussions!
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Me, my former advisor
@IlanaWitten
, and an experimental subject [published with full consent of the subject].
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One day, when all this is over, I will find this man, hug him, and probably weep in his arms. For turning is pain into empathy for the pain of others. I have seen his other interviews. Whatever he has in his heart I feel that same thing in mine.
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If you’re attending
@CosyneMeeting
and interested in insect path integration, I will be presenting a poster Thursday night on a new setup I am excited about.
If you want to discuss molecular computation and the limits of neural net models, find me anytime during the conference!
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For instance, here is an RNA program (!) I designed to compute addition of any two arbitrarily large number in logarithmic time.
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But there are very concrete and simple claims in MMT that an economist should be able to understand and directly criticize. I’d love to see a solid refutation so let me try to make it easy.
A central idea to MMT (both historically and conceptually) is that...
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...and I argue that the common belief that it has already been solved by our models of biological computation is incorrect.
I then propose a class of models that solve this challenge with RNA and that may guide us in finding life's universal computer, if it exists.
👇
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In this 90 min video (60 min if you play at 1.5x), I present my recent paper on RNA-based natural computation. Thanks to the hosts for their thoughtful questions and the engaging discussions!
New episode:
@theHessam
takes us through his fascinating and elegant work which bridges molecular biology and theoretical computer science to show how RNA has the potential for universal _natural_ computation. Thanks for the great discussion Hessam!
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The models in this paper use simple operation rules on RNA strands that mimic combinatory logic/λ-calculus.
Here is one set of operation rules that achieves universal computation. This mimics left-associative CL.
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Striving to be more like Darwin every day
#OnThisDay
in 1861, Charles Darwin wrote to his friend "But I am very poorly today and very stupid and hate everybody and everything."
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.
@veritasium
just dropped a fantastic video on non-repeating tilings and quasicrystals.
Made me think of Schrodinger’s prediction that life’s hereditary info. must be in an “aperiodic crystal”. (Not sure if this is a exactly what Schrodinger had in mind)
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I hope people read the text and - most of all - hope that it inspires new research directions and ultimately leads to biological discovery.
I am eager to hear your thoughts (critical thoughts especially). And many thanks to all who share it.
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RNA predated DNA and proteins. And we currently don't know what most of our RNA are even doing (see ) There's a very heated debate in the literature on the functional extent of non-protein-coding RNA (see for a start).
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@SGhasseminejad
Translation: "I support sanctions and conflict against Iran because I care more about punishing the rulers who tortured me than not harming the Iranian people. And I will defame Iranian expats who disagree with me on this even if they were subject to the same oppression".
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So where is life's universal computer? An obvious place to look at is the molecular biology of polynucleotides (RNA/DNA).
I have been struggling for a long time to show that an RNA-based system can be TM-equivalent, without assuming extraordinarily complex molecular machines
6/
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For Goniurellia tridens this is unmistakablly its strategy. I think other flies may be using this strategy but Goniurellia tridens has perfected it.
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Over 10 years in neuroscience and I just learned yesterday that intracellular receptors are a thing.
This was such a neat paper, with beautifully controlled experiments at every step.
Check out our latest paper in
@ScienceMagazine
about the mechanism of
#psychedelic
-induced neuroplasticity. Fantastic collaboration between
@UCDavisIPN
labs
@DEOlsonLab
,
@LinTianPhD
,
@johnalangray
, as well as
@MccorvyL
!
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Fruit flies are smart. They know what’s going on. I know because I saw a fruit fly give me that look when I was about to start an experiment today.
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Imagine thinking that the problem is choosing the right people to “rule the world”
And then imagine thinking these guys are the ones
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|———————|
| SCIENCE CAN
| BE DONE
| WITHOUT
| HIERARCHY
|———————|
||
(\__/) ||
(•ㅅ•) ||
/ づ
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This is harmful advice. For all those professors out there seeing this: the power dynamics are already tilted in your favor. Don’t e-mail like a boss. Be fine with not getting your way, especially when talking to students and postdocs.
Email like a boss... interesting to think about how wording changes the dynamics so much
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The most practically relevant version of the trolley problem. Applicable to almost any important political cause in human history.
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I thought I would have got over this by now but as a third year postdoc I feel most like a scientist when I am mixing a solution in a beaker
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The deliberate omission is so obvious it is almost comical. NPR has an article about the security council virtual meeting but then left out the most important fact: that Biden blocked the resolution. It is as if it was in the article but was taken out.
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