Category Archives: projects

2 August 2020
english, epistemology, projects, resources, science

Units, please

Whenever I see scientific code without units I scream inside my heart.

Everytime you write simulations of physical phenomena (often using numpy or matlab), make sure to always have variables where the units are clear, e.g. :

lambda_m = 633e-9 #wavelentgh in meters
c_mps = 3e8 #speed of light in meters per seconds
freq_Hz = c_mps/lambda_m

Failure to keep good track of the units has led to disasters. Yet complete lack of clarity  happens more often than not – just look at the code of a random scientist on github to witness the extent of the damage.

The reason why I am adamant about this is because a lot of time is wasted trying to debug code where it there’s a silly unit mismatch, and because we are doing physics.

Math versus physics

Why is coding without units such a terrible practice? It all boils down to the fact that computing is mostly about math and logic, and therefore not geared towards physical quantities. There is beauty in mathematical abstraction, but sometimes it doesn’t mean anything.

Take a mathematical statement that should be true:

1+1=2

Now ask yourself: what does it mean? If I add one orange to one apple:

1 orange + 1 apple = ?

It might sound silly but it’s actually pretty deep. You cannot add quantities which are not congruent. Yes, you may say that by adding one fruit with another fruit you get two fruits, but you’re cheating then.

This is somehow why object-oriented programming was invented: with the notion of “classes”, you can add entities which are compatible, through the game of function overloading and other niceties. In an ideal world, physical quantities in simulations should all have their own class, where the units would be defined.

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21 July 2020
english, projects, resources, science, science life

Effective online presentations

Thomas Danthony https://thomasdanthony.com/

respect the flow

Nowadays, many conferences and workshops are going online because of the pandemic, and we all are ill-prepared for this kind of shift forced upon us. Delivering an online presentation is very different from delivering an in-person presentation, for a few reasons, and we need cognizant of the nuances.

While many talks are indeed disastrous (people lack proper training), going to a conference is often not only about the content of the talks (you could just read the papers), but about visual and vocal cues which are often absent from literature. These cues help you figure out what are the important points and make clear what what other people are interested in.

Therefore, it is important to establish and maintain contact with the audience. For this, there are many things we can learn from news anchor: they also talk to the camera, they have dedicated studios and they alternate between speaking and news content.

I attended an online workshop by Jean-Luc Doumont on delivering an online presentation, and I found it useful. Here are some of my takeaways.

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11 July 2020
english, epistemology, projects, resources, science, science life

It’s getting pretty crammed at the bottom

Let us represent a dot by a small spot of one metal, the next dash by an adjacent spot of another metal, and so on. Suppose, to be conservative, that a bit of information is going to require a little cube of atoms 5 x 5 x 5 – that is 125 atoms. Perhaps we need a hundred and some odd atoms to make sure that the information is not lost through diffusion, or through some other process.
– Richard Feynman

Spoiler alert: we are nearly there!

* *

These very old line (1959) fro Feynman’s famous speech “There’s Plenty of Room at the Bottom” is still valid, though nowadays are getting very close to the bottom!

With my colleague Gautam Gunjala, we published an article in Berkeley Science Review on the ongoing contributions of UC Berkeley and Berkeley Lab to photolithography, the process of making microchips: Room to Shrink.

Photolithography is how you make tiny circuits

It was supposed to be part of the BSR Issue 38 (Spring 2020) but I guess it got covided.

Here are other pieces from yours truly on the topic:

Also:

The topic is getting red hot politically:
Lawmakers Propose Multibillion Dollar Semiconductor R&D Push  (American Institute of Physics, June 24, 2020)

if not down right nasty:
Trump administration pressed Dutch hard to cancel China chip-equipment sale: sources (Reuters, January 2, 2020)

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22 June 2020
english, mood, projects

Broken Berkeley social scene

I haven’t had a drink in a bar for four months now, so I’m trying to remember where are all the places I used to go… All these great places that I miss dearly (if you’re looking for things to do in the meantime, check out you hikes in the East Bay and the Bay Area.)

Berkeley Art Museum / Pacific Film Archive during the Covid-19 pandemic

Theatres

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4 June 2020
english, epistemology, projects, resources, science life

Graph alignment chart

There are many ways to document research, and some are better than others.

Make beautiful graphs : only start to write when you have the best data our group can get.
– Paul Alivisatos

Here’s my graph alignment chart, curated from personal experience.

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20 April 2020
english, epistemology, projects, resources, science, science life, skepticality

Earth Day

Today is Earth Day, a celebration of Earth and the environment started fifty years ago. This year, as the covid-19 pandemic upends the regular unfolding of the world, we can step back and ask how what we learn from the current crisis can help us scientists make science better and more efficient to curb climate change and its consequences.

 

Here’s a set of eight question to ponder about this, and some preliminary thoughts gleaned during a forum@ESA.

1. The interdependence of the supply chain has become very apparent. Can we make the case for renewable energy in terms of resilience of systems?

Solar energy is the only form of energy available everywhere on the planet: all others need to be transported and transferred. Geothermal energy should also be tapped (it is essentially low grade solar energy!)

2. The dramatic reduction of activity in urban centers has brought back clean air in some cities for the first time in decades. Can we envision a world without emission, from energy production to energy use?

Cars on the road have the most impact – we need to switch to switch transportation modes. We could have electrical energy on tracks, some flavor of autonomous driving could quickly provide modular transportation schemes. We also need to change how some cities are built, to make it easier to have common transportation (relative location of schools, business and housing)

3. The current covid-19 crisis is global, and scientists have broken paywalls and started new collaborations with their peers around the globe. What can we learn from this, and promote meaningful collaborations?

Open Access is on the rise (Project DEAL, Plan S,  White House Open Access plan.) Wikipedia is a great resource, completely under-used; it seems that it stems from the issue of ownership (who gets to write on who? and who gets the credit for this work?) We can also rethink research tools, to make them more efficient and more collaborative. The way academia is organized (race to tenure, etc.) may hamper collaboration and therefore innovation.

4. The global economy has been hit severely, and it will be important to promote new economic activity when the outbreak will be over. How can energy technologies inform policies and shape capital projects?

We could build mass transportation system, with initiatives similar to the New Deal (infrastructure is manual labor intensive.) Science can help to find which are the most effective or efficient ways (data science and machine learning.) Scientists could work in tandem with civil engineers, maybe using their school network to reconnect. There should be incentives for scientists to do so.

5. The disruption school year has taken a toll on kids and parents alike. How can scientists engage with students, when the distance is measured in bits per seconds rather than miles?

It would be good to reuse and repurpose older devices. There could be an open OS for discarded devices that would provide minimal functions (video conferencing, calculator, etc.) Scientists should also learn to mentor without physical presence (though one-on-one interaction is important), and therefore allow more frequent interactions, over larger distances.

6. When resources are lacking – masks, ventilators,– engineers and scientists devise creative ways to fill the need using available resources and altering them. How could we repurpose existing facilities to help with climate change?

7. The shelter-in-place is difficult to negotiate, but as anthropogenic emission of CO2 affects the environment, it may become routine. How can we fix the harm done using science and technology?

8. There is a lot of contradictory information being circulated around the epidemic. How can scientists help disseminate information and prevent the spread of alternative facts?

 

In addition, here are some historical and current resources on Climate Change:

I also made a thread about Berkeley Lab Art Rosenfeld on his Art of Energy Efficiency.

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20 March 2020
english, projects, resources

Hikes in the East Bay and the Bay Area

Because wee need to socially distance, perhaps most interesting right now are the nice places to hike nearby (East Bay/regional parks; stay away from state parks as they tend to be crowded and closed subsequently.)

Hikes in the East Bay

They’re all less than 30 min drive from Berkeley. Some can be reached by walking or cycling.
  • Cesar Chavez park (Berkeley Marina, 30min hike), stunning at sunset, great walks
  • Fire Trail (Berkeley), entrance a little before Botanical garden (3h hike)
  • Tilden Park (Berkeley hills): wild cat canyon hike, inspiration point (1h20 hike)
  • Lake Anza (Berkeley hills): 30 min hike; It is gorgeous, and a place of quiet; excellent if you want to bring a book
  • Huckleberry preserve (Berkeley/Oakland skyline boulevard, 1h hike)
  • Mountain View cemetery (Oakland, 1h): great views of the bay, solemn setting but not spooky.
  • Pinole Point (Richmond, 1h30 hike), wonderful at sunset
  • Redwood regional park (1–2 hours) many trails, very varied landscapes
  • Pinehurst East Ridge (start from Pinehurst Staging area – map)
  • Briones Crest trail loop (Orinda, 4 hours, or Lafayette Ridge staging area is open. It’s a very long hike, and portions can be steep. Plan at least 3h!)
  • Mt Diablo (Walnut Creek): stunning view of the highest peak in the Bay
  • Angel island (daylong hike, you need to take the ferry from Tiburon) might be closed

East Bay hikes

Hikes in the greater Bay Area

You’ll need to drive a littlemore, but these are splendid hikes:

  • Mt Tamalpais (Marin county, 1h30): beautiful hikes to the top.
  • Cataract Falls (one of the best hikes, map, on the dipsea trail, seems closed too)
  • Dipsea trail (from Mill Valley to Stinson Beach, 4h. beware: it seems closed, because it is too popular)
  • Pt. Reyes & Pt. Reyes Lighthouse (seems closed)
  • Russian River (usually you can rent canoes from late May to October, to go down the 10 mile stretch from Forestville to Gerneville. Maybe they’ll open. I LOVE this one. In the meantime, you may be able to enjoy wading in the river in a few locations; the drive is also quite nice)
  • Bodega Bay Trailhead (1h from Berkeley, gorgeous sights of the ocean. A fav!)
  • Mount St Helena (North of Napa, map, it seems closed for the time being:-/)
  • Half Moon Bay (South bay, 45min from Berkeley – nice beaches, and the boardwalk is very beautiful. Start from Miramar and head South)

and here’s a few more: Best beginner hikes in the Bay Area!

* * *

Additional suggestions:

  • Walking around lake Chabot.
  • Tilden Park at full moon. Get the code for EBMUD lock for $5!
  • Pt Reyes has 7 distinct ecosystems — totally great!
  • Don’t miss Indian Rock in Berkeley, and the Mountain View Cemetery in Oakland
  • Castle Rock in the southbay is a great place for hike
  • if you happen to be on Highway 92 near Half-Moon Bay, don’t forget to stop at Sam’s Chowder
  • Lake Almaden has nice, easy walks great for kids

You can also discover a lot of crazy place in Berkeley by just walking around in the streets:

https://www.berkeleyside.com/tag/quirky-berkeley

https://www.newyorker.com/business/currency/things-quirky-berkeley

Your favorite places, inspired by Berkeley Rep’s Place/Settings

Part 2: Your favorite places, inspired by Berkeley Rep’s Place/Settings

12 January 2020
english, epistemology, projects, resources, science

Most notable science and technology from the last 20 years, and predictions for the next 20

Here is a selection of the most notable advances in science and technology over the last twenty years.

I’ve collected these from people working around me (there may be a Berkeley Lab or Optics bias!) or by looking at what around me had made life different (a  an Academic life or California bias!) They are listed in no particular order, but the ordering tries to highlight some relationship between the topics.

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9 January 2020
english, mood, projects, science

ALS-U CD-3A

We were awarded CD-3A, yay!
Amazing team, and amazing project:)

On Dec. 23 the DOE granted approval for a key funding step that will allow the project to start construction on a new inner electron storage ring. Known as an accumulator ring, this inner ring will feed the upgraded facility’s main light-producing storage ring, and is a part of the upgrade project (ALS-U)

[…]

Powerful arrays of magnets bend the beam of electrons, causing it to emit light that is channeled down dozens of beamlines for experiments in a wide range of scientific areas – from physics, medicine, and chemistry to biology and geology. More than 2,000 scientists from around the world conduct experiments at the facility each year.

[…]

The ALS-U project will keep the facility at the forefront of research using “soft” X-rays, which are well-suited to studies of the chemical, electronic, and magnetic properties of materials. Soft X-rays can be used in studies involving lighter elements like carbon, oxygen, and nitrogen, and have a lower energy than “hard” X-rays that can penetrate deeper into samples.

It will also expand access to “tender” X-rays, which occupy an energy range between hard and soft X-rays and can be useful for studies of earth, environmental, energy, and condensed-matter sciences.

Milestone in Advanced Light Source Upgrade Project Will Bring in a New Ring

5 November 2019
english, mood, projects, resources, science, science life, skepticality

Science and politics – Part 1

On October 30th, 2019 I’ve organized an event at Manny’s (3092 16th St, San Francisco) on Science and Politics, with accomplished scientists Elaine DiMasi and Michael Eisen who chose to run for congress, in the wake of the 2016 US election, the Women’s March and the March for Science.

Dr. Michael Eisen and and Dr. Elaine DiMasi, who respectively ran for US Senate (CA) and US House of Representative (NY-1) , at Manny’s in San Francisco on October 30th, 2019

The setting was well suited for the speakers (Manny’s has held event for 17 out of the 20 Democratic candidates to the US Presidential election), and the two accomplished scientists shared many thoughts on their unsuccessful run. Needless to say, getting into the political arena is not an easy task, and it takes a lot of courage.

A man’s life is interesting primarily when he has failed — I well know.
For it’s a sign that he tried to surpass himself
— George Clemenceau

Of the wave of scientists who ran in 2018, few were elected, but it’s is hard to change a political machine that has been here for many decades on the first attempt.Trial, error, re-calibrate, try again. I hope to shortly provide a summary of lessons learned in a “Part 2” (I have a recordings of the event, but it’s low quality.)

While there is a lot of work done in the realm of science policy (how to inform our representative and make sure they make evidence-based decision)—groups such as the Union of Concerned Scientists, Engineers and Scientists Acting Locally (ESAL) or closer to me the Berkeley Science Policy Group and interesting programs such as the AAAS Science & Technology Policy Fellowships— very few scientists do engage politics frontally, as candidates.

While other countries do have trained scientists at their helm (Angela Merkel from Germany and Xi Jinping from China are both doctors in Chemistry, and their respective term have been relatively successful up to this point), other countries not so much. Currently, Rep Bill Foster (D-Il), Steve Englebright (NY state assembly) and Dan Kalb (Oakland City Council) are scientists in public offices; Vern Ehlers and Rush D. Holt were the first physicists to be elected in congress (party did not matter so much, Ehlers being a Republican and Holt a Democrat; see College Professors Who Have Served in Congress – The Chronicle of Higher Education (June 2014) for a partial list)

Interestingly, a few rising stars (or shining bright already!) of the Congress are professors (but not scientists): Katie Porter, Kirsten Sinema, Elizabeth Warren. Jess Phenix is a geologist who has ran for the House of Representative; she has still been unsuccessful, but her time might come.
https://vis.sciencemag.org/midterm-science-candidates/

(edit 11/8/2019: note that Olivier Ezratty published a post on “Do we need more scientists and engineers in politics“, quite thorough (in French.) And if you speak French there’s this podcast on Les sciences peuvent-elles aider la démocratie?  (“Can sciences help democracy”) featuring Philippe Kourilsky (author of De la science et de la démocratie) – I was a bit disappointed: it’s mostly about scientists helping democratically elected leaders, not participating in it, but at least there’s some conversation.

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