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Cell Signaling Technologies – Detailed 3D model of human cells (digizyme.com)
163 points by ozten on Nov 11, 2020 | hide | past | favorite | 50 comments



For those just seeing a huge mess: This is a visualisation of most (everything?) we know about what's in a human cell. It shows molecules (except water some stuff dissolved in it) in their full 3D structure (to scale) . We can actually see the macro structure those can take, e.g. DNA (blue strand at the bottom) is actually a coiled coil, cell membranes (pale golden stuff) is a bilayer, etc.

It really shows how busy and complex life is.


It really is only a small amount of what we know. Look for example at the KEGG pathway list (https://www.genome.jp/kegg/pathway.html), which is a curated list of pathways (so also only a part of what we know, albeit a larger). And this visualization depicts a dozen or so of these pathways.


The Roche Biochemical Pathways posters are also a nice display of the complexity within biological systems: http://biochemical-pathways.com/#/map/1


That metabolic pathway diagram is utterly insane.


> It really shows how busy and complex life is.

...and it's "just" a cell, we have billions of them. Some die, some come into being every moment. The individual cells may depend on each other for survival, but it's still a mystery how all of this function and cling together into a big warm blob without falling apart into individual pieces.


One word: Amazing.

How was this done? Raytracing? If yes, what was the resolution of the spacial data?


Must be big, I see that the full-sized render is 2000x2400: http://www.digizyme.com/images/pf_cstlandscape_full.jpg?crc=...


Would love to experience a VR version of this


it's not everything at all, it's missing all the cell cycle circadian rhythm stuff


It's a tiny fraction of what we know.


It's a very interesting visualization, but probably not understandable without quite a bit of cell biology knowledge.

The scale seems wrong in some cases, though I'm not entirely sure. The mitochondria look far too small to me. For the ER which is similarly small it is quite clear that it's only showing a tiny subsection. In other parts the scale looks pretty good. And it does manage to convey how busy cells are a bit better than many visualizations.

For the audience here it might be worth emphasizing that these are pretty close zooms on cells, you can see individual proteins here. If you imagine an image of a cell, each visualization shown here is maybe a single pixel of that full image of a cell (I'm probably off by an order of magnitude here or two).


That is correct, the magnitudes seem to be squashed so they all are within the same magnitude. In reality the size differences are huge.


Very nice looking and informative. Here's another nice resource for molecular biology art: https://ccsb.scripps.edu/goodsell/


Some additional links:

- Drew Berry (https://www.drewberry.com/)

- Janet Iwasa (http://onemicron.com/)

- Irving Geis, one of the pioneers in biomolecular art (https://pdb101.rcsb.org/sci-art/geis-archive/about)


Drew I recognize from many of the truly remarkable animations from WEHI - https://www.youtube.com/user/WEHImovies/videos


for those who are ready for a deep dive - https://www.amazon.com/Fundamentals-Protein-Structure-Functi...


This is amazing. Life is technology to its finest. Nanomachines working together and keeping the whole cell machine running, all the cells working together to produce a machine that can walk an talk: Animals. Humans. Amazing....

Whenever I feel sad, reading about DNA, Ribosomal machines, and the complexity of a single cell makes me feel special. Life is the most complex organization of molecules and live emerges from the universe.. Its amazing to see we're all such a complex machine.


Life is literally alien technology.


The jury is still out on that one.


It wasn't designed by humans, which means it's alien, in a sense. IMO "alien technology reverse engineering" would sound much more badass than "biological research".


Awesome !

As a programmer starting to get acquainted with the stupendous complexity of life at the molecular level - I'm hoping there's many more of us in the months and years to come.

It's not possible to overstate the importance of this fact - all these structures and processes evolved - weren't designed - but evolved !

It's also incredible how scientists keep breaking through all kinds of scale related barriers to successfully study them


It's not possible to overstate the importance of this fact - all these structures and processes evolved - weren't designed - but evolved !

Why not: designed to evolve


It's just as likely that we're in a simulation. Or that God is a potato.

Without evidence, it's just not worth the time.

We have evidence of evolution. Every observation fits the model. If you can refute it, you'll win a Nobel prize.


Because there is no evidence to that and everything that is asserted without evidence can be dismissed without evidence.


Because there is no reason to think that. Evolution happens quickly enough to be observed and studied (and of course the underlying mechanisms are being studied as well), and we are doing that for a very long time now (hundreds of years - ask botanists), and so far not a single reason to think of designers has surfaced.


The question is how much of the machinery in the linked page can you take away and still have a system that supports an evolutionary process. Once you're at the MVP for evolution, the next question is how did we get there from the initial conditions on Earth.


The answer to the first question is known (most of it), and there are strong theories for the second.


Shitty design tbh. Just look at modern plants. Chlorophyll is immensely inefficient because it only filters the green part of light. A tree literally misses out on 80% of the energy provided by the sun. We did have purple photosynthesis for a quite a while but either competition or something else wiped them away minus some remaining bacteria families.

Or look at ATP, the power currency of all lifeforms we know off minus virii. Almost all bigger lifeforms converted to mitochondrial production but then you have things like slime mold that doesn't for some reason and plants which have both mitochondria and photosynthesis. The entire ATP system is a mess because it has it's fingers in every other process. Impossible to optimize because any change just kills the cell. If that is designed, it's garbage.


> Shitty design ... Chlorophyll is immensely inefficient

A simpler explanation is chlorophyll is balancing energy production vs. safety.

Instead, for a safe, steady energy output, the pigments of the photosystem had to be very finely tuned in a certain way. The pigments needed to absorb light at similar wavelengths to reduce the internal noise. But they also needed to absorb light at different rates to buffer against the external noise caused by swings in light intensity. The best light for the pigments to absorb, then, was in the steepest parts of the intensity curve for the solar spectrum — the red and blue parts of the spectrum.

https://www.quantamagazine.org/why-are-plants-green-to-reduc...


Purple is both red and blue, both from the steepest parts of the spectrum. The green part of the spectrum is literally nowhere near that.

And again, organisms with purple chlorophyll have and continue to exist, so it's not like it's impossible or produces very incompetitive lifeforms.



I think the shittier design is that it hasn't figured out a way to develop intelligence without hubris.


> optimize

For what? Along what metrics? To what end?

Evolution has no purpose. There's nothing to optimize for.


it does tend to optimise for survivability - not that it consciously intends to - but because survivability leads to survival, and survival in combination with lucky mutations leads to developing more survivability... and so on


I know what you're saying, I think, but there's a subtle point that often gets overlooked. There's no "it" there in evolution. Life is a chemical tautology, a molecular fever dream sandwiched between hard vacuum and magma, between cold sky and Sun. There is no purpose or goal, so there can be no optimization.

I think it was Alan Watts, "The way the oceans ways, the Universe peoples."

Since "it" has no goals, "it" can't optimize for anything, even survivability. That just happens.

- - - -

It's a matter of wonder that this apparently meaningless gyration of agitated molecules gives rise evidently to teleological entities, you and me friend, who can have goals.

The question before us is can we optimize for survivability, if that is our goal, or, if not, harmonize our goals with that goal (for those who do not shall surely perish, eh? Or do we take that on faith?)

How do you know what will work? It seems naive to me to criticize the only example we have, that has been successful so far for nearly four billion years and counting.


You can replace "Natural" in "Natural Selection" with "Divine" to say "Divine Selection" and that's fine. No scientist can gainsay you.

However, jumping in a scientifically-grounded discussion with "But what about design?" is kinda silly and unlikely to be useful.

Frankly, I think you're right, I believe God exists and created the Universe such that it includes evolution of life, and that this redounds to His glory. Hallelujah!


Just to add to the usual arguments against this, please take a look at this article

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

especially the "Primordial origin of biomolecules" section

You may also enjoy reading about the PAH world hypothesis

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


And then why not: the designer originated through evolution. Which in turn...


It's an interesting idea: if we eventually learn to control time, perhaps we are/become the telos of the Universe?

> His posthumously published book, The Phenomenon of Man, set forth a sweeping account of the unfolding of the cosmos and the evolution of matter to humanity, to ultimately a reunion with Christ. In the book, Teilhard abandoned literal interpretations of creation in the Book of Genesis in favor of allegorical and theological interpretations. The unfolding of the material cosmos is described from primordial particles to the development of life, human beings and the noosphere, and finally to his vision of the Omega Point in the future, which is "pulling" all creation towards it. He was a leading proponent of orthogenesis, the idea that evolution occurs in a directional, goal-driven way. Teilhard argued in Darwinian terms with respect to biology, and supported the synthetic model of evolution, but argued in Lamarckian terms for the development of culture, primarily through the vehicle of education.[15] Teilhard made a total commitment to the evolutionary process in the 1920s as the core of his spirituality, at a time when other religious thinkers felt evolutionary thinking challenged the structure of conventional Christian faith. He committed himself to what the evidence showed.[16]

> Teilhard made sense of the universe by assuming it had a vitalist evolutionary process.[17][18] He interprets complexity as the axis of evolution of matter into a geosphere, a biosphere, into consciousness (in man), and then to supreme consciousness (the Omega Point).

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


I worked in a Cell Biology lab for my graduate work and we did quite a bit of business with this company. They would send us really cool, informative posters, but these examples are really next level. I would love a large, high quality print of one of these, I’d frame it and put it up in my house.


Never thought I’d see my old workplace on the front page of HN. Congratulations everyone! :)


My next side project is completing the 101 bioengineering course from The Odin. I really want to have a basic understanding of what's going on in biology.

Someone here did something similar or can recommend some resources?


https://www.amazon.com/Fundamentals-Protein-Structure-Functi...

there's another book called cell biology by Alberts et al


Biochemistry by Jeremy M. Berg, John L. Tymoczko and Lubert Stryer is a widespread introduction to Biochemistry.


The title is misleading—Cell Signaling Technologies is a company. This appears to be Digizyme’s portfolio of work they have done for their client, Cell Signaling Technologies.


I have no idea what I'm looking at here, but showed it to a molycularbiologist student and she got pretty happy!


Incredible!


Agreed

But I don't even know enough to know how incredible it is

I studied Biology before but had issue remembering the names


A little context? Are these CGI?


Basically yes. But the proteins, sizes, shapes are based on real sizes/microscopy, with added depth, and with a lot of clutter removed.




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