Final thoughts (100 years, part VII)

To end my series of posts on the man and the book (D’Arcy Thomspon and On Growth and Form respectively, the latter a book with over 1000 pages), I wanted to share a few more quotes from and about him that I found interesting enough to type out:

“In his figure and bearded face there was majestic presence; in is hospitality there were openness, kindness and joviality; in his ever quick wit were the homely, the sophisticated and, at times, the salty… in status he became a very doyen among professors the world over; in his enquiring mind he was like those of whose toungue and temper he was a master, the Athenians of old, eager ‘to tell or hear some new thing'” – Professor Peacock (1)

  1. With the name Professor Peacock, I can’t help but imagine a flamboyant, multicolour-labcoat-wearing, frizzle-haired man…
  2. I hope the meaning of the word salty has changed over time…

There is a certain fascination in such ignorance; and we learn without discouragement that Science is “plutot destine a etudier qu’a connaitre, a chercher qu’a trouve la verite.” (2)
(Rather than destined to study for knowledge, (we are) searching to find the truth.)

#IgnoranceIsBliss?

In my opinion the teaching of mechanics will still have to begin with Newtonian force, just as optics begins in the sensation of colour and thermodynamics with the sensation of warmth, despite the fact that a more precise basis is substituted later on. (3)

As a self-proclaimed science communicator, it is often difficult to judge how much to simplify things. On the other hand, making things relatable to everyday experiences does not necessarily mean telling untruths. Classical physics may not be valid for every single situation, but it is often enough to describe what is happening without needing to resort to more complicated relative physics. And you don’t have to start quoting wavelengths when a colour description would do just as well. Fill in the details later, if necessary.


Some quotes on evolution and natural selection:

And we then, I think, draw near to the conclusion that what is true of these is universally true, and that the great function of natural selection is not to originate, but to remove. (4)

Unless indeed we use the term Natural Selection in a sense so wide as to deprive it of any purely biological significance; and so recognise as a sort of natural selection whatsoever nexus of causes suffices to differentiate between the likely and the unlikely, the scarce and the frequent, the easy and the hard: and leads accordingly, under the peculiar conditions, limitations and restraints which we call “ordinary circumstances,” one type of crystal, one form of cloud, one chemical compound, to be of frequent occurrence and another to be rare. (5)


We can move matter, that is all we can do to it. (6)

On a fundamental level, are we really able to build things? Aren’t we just rearranging the building blocks?

I know that in the study of material things, number, order and position are the threefold clue to exact knowledge; that these three, in mathematician’s hands, furnish the “first outlines for a sketch of the universe“, that by square and circle we are helped, like Emile Verhaeren’s carpenter, to conceive “Les lois indubitable et fecondes qui sont la regle et la clarte du monde.” (7)

(The unquestionable and fruitful laws that rule and clarify the world.)

For the harmony of the world is made manifest in Form and Number, and the heart and soul and all the poetry of Natural Philosophy are embodied in the concept of mathematical beauty. (8)

Delight in beauty is one of the pleasures of the imagination … (9)

#MathIsLife. Thank you, D’Arcy, for the 1000+ pages of mind-expanding, educational and philosophical topics.

ms50127_4


Sources:

(1) D’Arcy Thompson and his zoology museum in Dundee – booklet by Matthew Jarron and Cathy Caudwell, 2015 reprint

(2) On Growth and Form – p. 19

(3) Max Planck

(4) On Growth and Form – p. 269-270

(5) On Growth and Form – p. 849

(6) Oliver Lodge

(7) On Growth and Form – p. 1096

(8) On Growth and Form – p. 1096-1097

(9) On Growth and Form – p. 959

(2, 4-6, 8-9) from D’Arcy Thompson, On Growth and Form,  Cambridge university press, 1992 (unaltered from 1942 edition)

When size matters (100 years, Part VI)

Neat process diagrams of metabolism always gave the impression of some orderly molecular conveyer belt, but the truth was, life was powered by nothing at the deepest level but a sequence of chance collisions. (1)

Zoom down far enough (but not too far – or the Aladdin merchant might complain) and all matter is just a soup of interacting molecules. Chance encounters and interactions, but with a high enough probability to happen. In essence, life is a series of molecular interactions (that, in turn, are atomic interactions and so on and so on…)

The form of the cellular framework of plants and also of animals depends, in its essential features, upon the forces of molecular physics. (2)

Quite often, we can ignore those small-scale phenomena, but only as long as the system we are describing is large enough. As in physics, in biological systems size does matter (*insert ambiguous joke here*). We have to adapt the governing physical rules depending on the scale that we are observing. Do we consider every quantum-biological detail, can we use a cell as the smallest entity or even use whole organisms as the smallest functional entity?

Life has a range of magnitude narrow indeed compared to with which physical science deals; but it is wide enough to include three such discrepant conditions as those in which a man, an insect and a bacillus have their being and play their several roles. Man is ruled by gravitation, and rests on mother earth. A water-beetle finds the surface of a pool a matter of life and death, a perilous entanglement or an indispensable support. In a third world, where the bacillus lives, gravitation is forgotten, and the viscosity of the liquid, the resistance defined by Stoke’s law, the molecular shocks of the Brownian movement, doubtless also the electric charges of the ionised medium, make up the physical environment and have their potent and immediate influence on the organism. (3)

Observing life at the smallest scales (by which I mean cells and unicellular organisms) at least has the advantage the rules driving form and structure can, at least in many cases, be considered relatively simple: surface-tension.

In either case, we shall find a great tendency in small organisms to assume either the spherical form or other simple forms related to ordinary inanimate surface-tension phenomena, which forms do not recur in the external morphology of large animals. (4)

While on the topic of size, as many things in the universe: size is relative. I have noticed in conversations with colleagues and supervisors that what is considered small or large, definitely depends on the point of perspective (and often: whatever the size is that that person typically studies). I could assume that for a zoologist, a mouse is a small animal, but tell a microscopist they have to image an area of 1 mm² and the task seems monstrous. For a particle physicist, a micrometre is immense, but for an astrophysicist, the sun is actually quite close.

We are accustomed to think of magnitude as a purely relative matter. We call a thing big or little with reference with what it is wont to be, as when we speak of a small elephant of a large rat; and we are apt accordingly to suppose that size makes no other or more essential difference. (5)

Undoubtedly philosophers are in the right when they tell us that nothing is great and little otherwise than by comparison. (6)

There is no absolute scale of size in the Universe, for it is boundless towards the great and also boundless towards the small. (5)

That’s the amazing thing about science: we strive to understand the universe on all scales. The universe is mindblowing in its size, in both directions on the length scale.

We distinguish, and can never help distinguishing, between the things which are at our own scale and order, to which our minds are accustomed and our senses attuned, and those remote phenomena which ordinary standards fail to measure, in regions where there is no habitable city for the mind of man. (7)

Good thing we have scientists, amazing minds, capable of studying, visualising and even starting to understand the universe on all its scales…

Ms48534_13
My mind might be boggled, but here’s a man that looks like his mind contains the universe. (D’Arcy in his 80s)

(1) Permutation city – Greg Egan, p. 67

(2) Wildeman

(3) On Growth and Form – p. 77

(4) On Growth and Form – p. 57

(5) Gulliver

(6) On Growth and Form – p. 24

(7) On Growth and Form – p. 21

(3-4, 6-7) from D’Arcy Thompson, On Growth and Form,  Cambridge university press, 1992 (unaltered from 1942 edition)

Let’s get physical (100 years, Part V)

[…] of the construction and growth and working of the body, as of all else that is of the earth earthy, physical science is, in my humble opinion, our only teacher and guide. (1)

You might have seen the xkdc comic ranking different scientific disciplines by their purity (and if you haven’t, it’s just a bit of scrolling away). The idea it portrays is that all sciences are basically applied physics (which is in turn applied mathematics). In other words: if you go deep enough to a subject, you eventually end up explaining in with principles from physics. And this is the same principle D’Arcy explores in his book. That has over 1000 pages, did you know that?

purity

A famous D’Arcy quote states that the study of numerical and structural parameters are the key to understanding the Universe:

I know that the study of material things number, order and position are the threefold clue to exact knowledge, and that these three, in the mathematician’s hands, furnish the ‘first outlines for a sketch of the Universe.’ (2)

You can ask the average high school student about mathematics, and the usual response would probably be something in the lines of: “Ugh, I’ll never use this for anything.” Sometimes, it might be difficult to see the every-day use of mathematics, or even the not-so-everyday use. But in reality, the possibilities are endless (given that we are open to having long lists of endless equations that need a supercomputer to solve – probably).

We are apt to think of mathematical definitions as too strict and rigid for common use, but their rigour is combined with all but endless freedom. The precise definition of an ellipse introduces us to all the ellipses in the world; the definition of a ‘conic section’ enlarges our concept, and a ‘curve of higher order’ all the more extends our range of freedom.

It might not be straightforward to see how mathematics (or physics for that matter) would help a biologist in the understanding of natural processes. However, there are a few examples of how physical properties, forces or phenomena are used in biology, such as helping bone repair:

The soles of our boots wear thin, but the soles of our feet grow thick the more we walk upon them: for it would seem that the living cells are “stimulated” by pressure, or by what we call “exercise,” to increase and multiply. The surgeon knows, when he bandages a broken limb, that his bandage is doing something more than merely keeping the part together: and that the even, constant pressure which he skilfully applies is a direct encouragement of the growth and an active agent in the process of repair. (4)

Nowadays the link between physics and biology is more accepted that a century ago, leading to new research fields such as biomechanics, mechanobiology and “physics of cancer”. I have eluded to some of the links between cancer and physics in previous posts (Physics of Cancer, Part I and II). Mathematical models are commonly used to better understand biological processes, including signalling pathways, tissue formation and growth and changes occurring in cancer.

This goes to show (again) that “interdisciplinary” is not just a fancy buzzword, it is a core principle of scientific research. While I must admit from own experience that carrying out interdisciplinary research might not be the easiest path, the potential discoveries and applications are even more endless. And while it might seem mind-boggling, I would argue that mind-bogglement is a good thing, stretching the potential of our minds and our understanding of the universe. And as far as I can read, D’Arcy agrees:

… if you dream, as some of you, I doubt not, have a right to dream, of future discoveries and inventions, let me tell you that the fertile field of discovery lies for the most part on those borderlands where one science meets another. There is a cry in the land for specialisation … but depend on it, that the specialist who is not reinforced by a breadth of knowledge beyond his own speciality is apt very soon to find himself only the highly trained assistant to some other man … Try also to understand that though the sciences are defined from one another in books, there runs through them all what philosophers used to call the commune vinculum, a golden interweaving link, to their mutual support and interpretation. (5)

So I guess my point is (if there even was a point in this post, apart from that the book has like over 1000 pages, in case you didn’t know): if you are a biologist, don’t be afraid to break some sweat and get physical. And the opposite goes for physicists. You might want to get a bit chemical as well, while you’re at it.

The Homo Universalis is back!

ogf-fig-237
Featured image: math and shells.

(1) On Growth and Form, p 13.

(2) On Growth and Form, p. 1096

(3) On Growth and Form, p. 1027

(4) On Growth and Form, p. 985

(5) D’Arcy Thompson and his zoology museum in Dundee – booklet by Matthew Jarron and Cathy Caudwell, 2015 reprint

(1-4) from D’Arcy Thompson, On Growth and Form,  Cambridge university press, 1992 (unaltered from 1942 edition)

If only it were so simple (100 years, part IV)

Ever since I have been enquiring into the works of Nature I have always loved and admired the Simplicity of her Ways. (1)

In his book (yes, it’s about that again), D’Arcy supports his ideas through examples, through observations on biological systems that he can either explain through mathematical equations or directly compare to purely physical phenomena such as bubble formation. You might think that these are grave simplifications.

However, even in biology, which some people might call a “complex science”, simplifications are often used. Using cell culture rather than tissue. Isolating a single player in a pathway to see what its effect is. And quite often, a simplification holds true within the limits that have been set up to define it.

As was pointed out to me recently, the definition of “complex” is that something is “composed of many interconnected parts”. Meaning that this is not necessarily the antonym to “simple”. But “complex” is often seen to mean the same thing as “difficult”, even if that’s not necessarily the definition. In any case, it is definitely not so that physics is a “simple science”:

But even the ordinary laws of the physical forces are by no means simple and plain. (2)

It makes sense to break down a complex system into its individual components and analyse these, perhaps more simple concepts, separately. There is great value in simplifying things. First of all, there is a certain beauty in simplicity:

Very great and wonderful things are done by means of a mechanism (whether natural or artificial) of extreme simplicity. A pool of water, by virtue of its surface, is an admirable mechanism for the making of waves; with a lump of ice in it, it becomes an efficient and self-contained mechanism for the making of currents. Music itself is made of simple things – a reed, a pipe, a string. The great cosmic mechanisms are stupendous in their simplicity; and, in point of fact, every great or little aggregate of heterogeneous matter involves, ipso facto, the essentials of a mechanism. (3)

When reading this paragraph, two things jumped out at me. Two weeks ago, I was at the annual meeting of the British Society for Cell Biology (joint with other associations) and heard an interesting talk by Manuel Théry. Part of his story relied on putting boundaries on a system. Without boundaries, whatever we would like to study just gets too complicated, and we are unable to understand what is happening. For example, when explaining how waves originate, it is much easier to use a system where water is confined in a box. We can then directly observe the wave patterns that start to occur and understand their interactions.

And then this: “Music itself is made of simple things – a reed, a pipe, a string. The great cosmic mechanisms are stupendous in their simplicity.” D’Arcy sure knew his way around words.

Simplifying also heavily increases our understanding of the principles of life, the universe and everything. When you think about it, it is used so often, you hardly even notice that certain simplifications have been made. D’Arcy points this out as well:

The stock-in-trade of mathematical physics, in all the subjects with which that science deals, is for the most part made up of simple, or simplified, cases of phenomena which in their actual and concrete manifestations are usual too complex for mathematical analysis; hence, even in physics, the full mechanical explanation is seldom if ever more than the “cadre idéal” towards which our never-finished picture extends. (4)

When considering biological systems, he states the following:

The fact that the germ-cell develops into a very complex structure is no absolute proof that the cell itself is structurally a very complicated mechanism: nor yet does it prove, though this is somewhat less obvious, that the forces at work or latent within it are especially numerous and complex. If we blow into a bowl of soapsuds and raised a great mass of many-hued and variously shaped bubbles, if we explode a rocket and watch the regular and beautiful configurations of its falling streamers, if we consider the wonders of a limestone cavern which a filtering stream has filled with stalactites, we soon perceive that in all these cases we have begun with an initial system of very slight complexity, whose structure in no way foreshadowed the result, and whose comparatively simple intrinsic forces only play their part by complex interaction with the equally simple forces of the surrounding medium. (5)

For many biological and non-biological systems, the initial conditions might not seem complex. It is by interactions between other – perhaps on their own relatively simple – environmental conditions, other simple systems, that it grows out to be complex. Obviously, as in the definition. But a complex system is more difficult to understand conceptually, more difficult to model. And that brings us the value of simplification, looking at smaller, simpler systems that more closely resemble the “cadre idéal”, allow us to pick apart the different players in a larger system. If we understand their individual behaviour, perhaps this can shed light on the collective behaviour.

As we analyse a thing into its parts or into its properties, we tend to magnify these, to exaggerate their apparent independence, and to hide from ourselves (at least for a time) the essential integrity and individuality of the composite whole. We divide the body into its organs, the skeleton into its bones, as in very much the same fashion we make a subjective analysis of the mind, according to the teachings of psychology, into component factors: but we know very well that the judgment and knowledge, courage or gentleness, love or fear, have no separate existence, but are somehow mere manifestations, or imaginary coefficients, of a most complex integral. (6)

As far as D’Arcy goes in his book, his simplifications hold true:

And so far as we have gone, and so far as we can discern, we see no sign of the guiding principles failing us, or of the simple laws ceasing to hold good. (7)

Of course, this does not automatically lead to complete understanding. We only get that tiny bit closer to seeing the bigger – and smaller – picture:

We learn and learn, but will never know all, about the smallest, humblest, thing. (8)

Because we must never forget that adding together those simplifications does not automatically lead to the answer to the complete problem (and I find this oddly poetic):

The biologist, as well as the philosopher, learns to recognise that the whole is not merely the sum of its parts. It is this, and much more than this. (9)

To end, D’Arcy also makes note of things beyond his comprehension:

It may be that all the laws of energy, and all the properties of matter, and all the chemistry of all the colloids are as powerless to explain the body as they are impotent to comprehend the soul. For my part, I think it is not so. (10)

ogf-fig-135
Contact surfaces between four cells, or bubbles. This has nothing to do with the soul. It does have to do with how we can often simplify cells to their “shells”, and for certain principles this approximation holds true.

Sources:

(1) Dr. George Martine, Medical essays and Observations, Edinburgh, 1747.

(2) On Growth and Form, p. 19

(3) On Growth and Form, p. 292

(4) On Growth and Form, p.  643-644

(5) On Growth and Form, p. 289

(6) On Growth and Form, p1018

(7) On Growth and Form, p. 644

(8) On Growth and Form, p. 19

(9) On Growth and Form, p1019

(10) On Growth and Form, p. 13

(2-10) from D’Arcy Thompson, On Growth and Form,  Cambridge university press, 1992 (unaltered from 1942 edition)

Physics, but not vs evolution (100 years, part III)

As you may well know, because you have read it here or heard it elsewhere, this year is the 100 year anniversary of D’Arcy Thompson’s On Growth and Form. The book is over 1000 pages long, and while extremely interesting, it can be quite a task to get through. Therefore, I figured I’d share some of the thoughts I had while reading – and to be honest, this was sometimes diagonally – through this masterwork.

To place this and future posts within context, I will first focus on how its main premise (physical forces as the driver of morphology) fits into the context of the time where the general sentiment was:

No other explanation of living forms is allowed than heredity, and any which is founded on another basis much be rejected… (1)

But that is not to say that no one in the scientific community was open to the idea that physics had some part to play:

To think that heredity will build organic beings without mechanical means is a piece of unscientific mysticism. (1)

It seems D’Arcy Thompson’s book was the first major publication on this idea, and his book is an inspiration for biomathematicians and biophysicists today. Or at least it is thought-provoking: throughout the book he underlines through several – 1000 pages worth of –  analogous observations from the material (non-living) and biological (living) world his theory, that the way biological systems grow, and the shape and size they eventually take, is driven by physical principles:

Cell and tissue, shell and bone, leaf and flower, are so many portions of matter, and it is in obedience to the laws of physics that their particles have been moved, moulded and conformed. … Their problems of form are in the first instance mathematical problems, their problems of growth are essentially physical problems. (2)

It is important to point out that he never claimed that physics is the only driving force of the shape and size of living things, just that it is one of the drivers, and that heredity is extremely important in understanding the processes of biology in its own right. But if outlining the physics of growth and form takes over a thousand pages, we should almost be thankful that heredity was taken out of the picture:

We rule “heredity” or any such concept out of our present account, however true, however important, however indispensable in another setting of the story, such a concept may be. (3)

Ruling it out of the picture doesn’t stop D’Arcy from occasionally musing on the limitations of heredity:

That things not only alter but improve is an article of faith, and the boldest of evolutionary conceptions. How far it be true were very hard to say; but I for one imagine that a pterodactyl flew no less well than does an albatross, and that Old Red Sandstone fishes swam as well and easily as the fishes of our own seas. (4)

This goes to show that while D’Arcy did not consider evolutionary theory in his story, it was not something he hadn’t thought about. He regularly quotes Darwin (I’m working through The Origin of Species myself at the moment… at least D’Arcy’s book had some pictures!) and as a professor in zoology, it stands to reason that he was knowledgeable on the subject.  Throughout his career, he published around 300 articles and books, and some day I’ll go through all of them to show he has written more on heredity.

To conclude, while On Growth and Form outlines an alternative theory to explain the morphology of biological systems, it is in no way trying to replace or contradict the theory of evolution or any idea of genetics-driven development. I’ll wrap up with one of D’Arcy’s final thoughts:

And though I have tried throughout this book to lay the emphasis on the direct action of causes other than heredity, in short to circumscribe the employment of the latter as a working hypothesis in morphology, there can still be no question whatsoever that heredity is a vastly important as well as a mysterious thing; it is one of the great factors in biology, however we may attempt to figure to ourselves, or howsoever we may fail even to imagine, its underlying physical explanation.  (5)

Well, that’s all folks. More on growing and forming next time! Have I mentioned that this book is over a thousand pages long?

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D’Arcy in his twenties (University of Dundee Archive Services)

Sources:

(1) Haller, 1888

(2) On Growth and Form, p. 10

(3) On Growth and Form, p. 284

(4) On Growth and Form, p. 873

(5) On Growth and Form, p. 1023

(2-5) from D’Arcy Thompson, On Growth and Form,  Cambridge university press, 1992 (unaltered from 1942 edition)

Physics of Cancer (1)

If you are confused by the title, that’s okay. Usually, when we read something about cancer, it is about something biology-related, for example about specific mutations or the environmental conditions that increase cancer risk. A lot of research is happening with regards to the biology and biochemistry of cancer: which tumour suppressor genes are mutated in certain cancers, what are the effects cancer has on someone’s health, what drugs can we use to treat a cancer, … ? But, perhaps surprisingly, studying the physics of cancer also has its merit. Why, it’s a whole field in itself!

So I’d like to talk a little bit about this topic, the physics of cancer, and in this first part, I will focus on how physical forces can change the behaviour of cells (and how this might be involved with disease).

Cells not only sense their biological environment, they also feel their physical environment. They sense the stiffness of the cells and protein structures around them, they sense how other cells are pushing and pulling on them, and then they react to it. And these mechanisms could actually be quite important for the development and progression of cancer.

Recent research showed that the cells surrounding a tumour are under mechanical stress because of the growth of the tumour. As a tumour grows, it pushes on its environment. So the – initially healthy – cells in its direct surroundings, feel a pressure. In this specific study, they showed that this pressure caused the cells to start a mechanical response pathway leading to the upregulation of a protein β-catenin. This protein is involved in activating certain pathways involved in cell proliferation.

Which is exactly what its upregulation leads to in cancer. In the case of colorectal cancer (which, if you remember, I am particularly interested in), a mutation of Apc (adenomatous polyposis coli, in case you were wondering) also leads to an accumulation of β-catenin amongst other things. The APC protein has been linked to many functions, but the best known is its involvement in forming a complex that binds to β-catenin and tagging it for destruction. That way the proteins involved in protein recycling know that the β-catenin proteins can be cut up. But when APC is mutated, β-catenin gets tagged and starts piling up and doing some of its jobs a little bit too well, including inducing proliferation pathways.

So back to the study, if healthy cells are experiencing a constant pressure (due to a big bad tumour growing into their space, or – as they tested in the study – artificially caused pressure), they start acting more “cancer-like”. This suggests that mechanical activation of a tumorigenic pathway, in this case, the β-catenin pathway, is a potential method for transforming cells.

This is just one example of how physics and cancer are potentially related. As a side note, I myself am also interested in how cells respond the mechanical stresses, which prompted me to do an experiment where I placed weights on top of cells.

 

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Feeling the pump.

 

This subject was the topic of my first FameLab performance, which ended in a little song (to the tune of “Friday I’m in Love” by the Cure). It’s sung from the perspective of a cell that is stuck next to a growing tumour:

Hello there, I am a cell.
Feeling healthy, fit and well.
Life is good, yes, life is swell.
But my neighbour’s got it worse.

Something about him does not belong.
The way he pushes is just wrong.
They say in him the force is strong,
they say he’s got the force.

He takes up so much space.
And is always getting up in my face.
It’s putting me in a stressful space.

You could say he’s left his mark.
It’s like swimming with a shark.
He’s pushing me towards the dark,
the dark side of the Force,
the dark side of the Force.

Oh, have a mentioned that I like Star Wars?

There’s plenty of room at the bottom to listen

If you are in any way familiar with the world of electronics, electrical engineering or anything with the catchword “nano” in it (except perhaps the ipod nano, though actually it is a prime example of my Moore’s law point later on), you’ve heard of Feynman’s famous words:

“There is plenty of room at the bottom”

If you’re not, here’s the jest of it:

In December 1959, Richard P. Feynman presented a talk to the American Physical Society in Pasadena,  California, commenting on the wondrous world of miniaturisation. He explains that even though they progressed so far by that time, there is so much more room to improve. Things can still be made so much smaller.

 It is a staggeringly small world that is below. In the year 2000, when they look back at this age, they will wonder why it was not until the year 1960 that anybody began seriously to move in this direction. Why cannot we write the entire 24 volumes of the Encyclopedia Brittanica on the head of a pin?

And we’ve done it. We can manipulate single atoms. And we can image single atoms. Isn’t science grand?

When I was doing a course in nanotechnology, Feynman was often quoted in one breath together with Moore. Moore’s law, which dates back to 1965, postulates that every two years, the amount of transistors (an semiconductor element that is very important in computing) that can fit on an integrated circuit will double every two years. This prediction has been surprisingly well met;  most direct consequence is that the size of computers and electronic components keep getting smaller (remember, ipod nano). But there is a limit, transistors can only be so small; single atom transistors are not impossible (and currently in research stage), but after that, we cannot go any smaller.

Has research reached it’s lower limit? As I’ve stated, we are able to manipulate single atoms, we can build single atom electronics, and in the field of optics we are pretty much at the lower limit as well with superresolution microscopy and single molecule imaging and with electron microscopy to unravel the world at an atomic scale.

What is left to improve?*

* I’m not claiming research in these areas are futile. Obviously there is so much more to do in optics, electronics, atomic force microscopy, … Obviously there is so much more to learn. I just want to point out that size-wise, we have pushed these fields pretty much to their (lower) limit. So maybe it is worth exploring other fields as well? 

There are different ways to study something. For example, let’s take cancer cells. We can look at them, through a microscope, and if we want at very high resolution, to unravel the differences between cancerous cells and their healthy counterpart. We can feel them, well not us directly but through techniques such as atomic force microscopy, which also can provide very high resolution, to investigate the effects of different mutations. Additionally we can listen. Well, not us directly, but by using ultrasound. Now there’s a field with plenty of room on the bottom.

Conventional ultrasound, for example the type that is used to look at babies in wombs, uses frequencies from over 20 kHz (which is the maximum frequency of sound that is audible to us, hence ultrasound) to a few MHz and provides a resolution usually no less than 100 µm. Compared to optics, this is nothing. However, ultrasound has quite some advantages over optics. Higher penetration depth, no lasers (pew pew pew), possibility of quantifying a lot of useful things like mechanical properties, just to name a few. And it has plenty of room at the bottom, we are now where near the limit yet!

We can increase the frequency up to 47 MHz (what I use routinely), or 150 MHz or even up to 1000 MHz. It’s called high-frequency ultrasound. Or super-high ultrasound. Things get really interesting then. You can image cells. You can do superresolution imaging.

There are really exciting things going on in the field of ultrasonics, and I’m not just saying that because I’m looking more into it for my own research at the moment. Researchers were recently able to image the rat brain at a previously unseen resolution (see the pretty picture below). Other groups are extracting information from single cells using ultrasound that can’t be obtained using optical techniques. And that is just mentioning a few of the many recent advances.

In any case, my point is that we might be plateauing with regards to improving resolution on optics or miniaturising our electronics, but there is still plenty of room at the bottom to listen !

 

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High resolution image of vessels in a rat brain. Red/blue shows directionality of the blood, brightness gives an indication of speed. Photo credit: ESPCI/INSERM/CNRS.

 

The existential crisis of being an interdisciplinary scientist.

Two days ago, I was called a physicist.

Not that I find that an insult, quite the contrary. I have been called a physicist before, just not by another physicist. My working environment consists almost solely of biologists, of all sorts and kinds, and on occasion when I walk in a room or join a table, a conversation much like this one would start:

“You’re a physicist, right?”

“Not really, well sort of, I guess.”

“So, is it better wrap food with the shiny part of aluminium foil on the inside.” Or another physicky question I don’t actually know the answer to.

But the thing is, I would never describe myself as a physicist. And I always had the impression that even if biologists would describe me as a physicist, physicist would rather describe me as a biologist. I don’t consider myself a biologist either.

So when two days ago a physicist said to me: “I see you as a physicist,” I got catapulted into an existential crisis.

Who am I? is a philosophical question and difficult enough. Now I was asking myself asking: What am I?

Yeah, human. A bunch of cells organised into tissues and organs and a body. A set of connections and bioelectrical signals making up a consciousness. But I don’t think that will qualify as a good answer at, say, a future job interview.

I have recently described myself – during my debut as a stand-up comedian(*) – as an inbetweener (no, not one of these). My research lies on the interface between biology/life science and physics/engineering. The whole point of the project I’m in, is to create a new cohort of interdisciplinary scientists that are able to talk to both biologists or clinicians, and physicists, essentially bridging the gap between both worlds. If you’re wondering why interdisciplinary research is even worth pursuing, a recent Nature special does a pretty good job describing the advantages (and current issues). Note that one of the ways to promote interdisciplinary research is: “Invest in interdisciplinary PhD cohorts, co-supervised by academics from diverse departments or faculties.” Exactly.

But my point is that, most of the time, people undertaking interdisciplinary research have a solid background in one particular field. You might have heard of physicists merging into biology or biologists dabbling in physics. Most of the people in my program fall in this category, they are either physicists or biologists and doing research on the interface.

But not me. I started out interdisciplinary. I usually describe myself as a bio-engineer, even though that’s not really what my MSc diploma says (but no matter what I say -“nanotechnologist, “bionanotechnologist” or “bio-engineer” – it almost always merits further explanation and I feel the latter describes me best). Unfortunately, a test linked to that recent Nature special tells me that “I am not truly an interdisciplinary scientist, I am able to talk about different subject but to not have the core understanding of all of them.” If this is correct – assuming online tests have some fraction of truth – shouldn’t I then have a core understanding in one field? What would that field even be?

I sometimes *jokingly* say that as a bio-engineer, I know a bit about a lot of different things, but never a lot about one thing. I then *jokingly* say that this is *very useful*. This sarcasm is quite often true; I’m constantly reminded of gaps in my knowledge. Fortunately, I am occasionally reminded of the advantages of my background. I know of a lot of things. I’m capable of absorbing a lot of information in relatively short amounts of time because I have a basic understanding of the lingo and concepts in all these various fields. I have a certain way of approaching a problem. As I have pointed out in a previous post, I am an engineer, trust me, and that comes with a certain mindset and way of thinking, and probably the type of mind that has difficulty asking for help and is socially awkward. Hmm, *very useful*.

Which leads to another existential question: Did I study engineering because I have an engineering-type mind, or did studying engineering develop my engineery mind? It’s the nature-nurture debate. And the answer is probably also: most likely a combination of both.

Maybe all interdisciplinary scientists go through existential crises sometimes, because they’re never really sure where they fit in best. Luckily not fitting in isn’t always a bad thing.

I’m not sure if I made any progress on answering the question What am I?, but I’m thinking about myself and I guess that’s part of a PhD as well; it’s not only about science, it’s also a path of self-discovery.

In other news, I seem to have had an overdose of Mars in the past few weeks: I finished reading Brian Cox’s Human Universe, where he states that space exploration and sending humans to Mars is basically a must (if you consider how much advancement moon exploration has helped our advance), they have discovered evidence of water on mars (Dont’t drink the water. Don’t even touch it. Not one drop.), I saw The Martian the day before NASA published a document outlining their strategy to send people up there. It makes me wish I never gave up on my dream to become an astronaut (when I was about 8, and realised that there’s no way someone scared of dogs could be a vet).

(*) I have no real plans of becoming a stand-up comedian, it was just a really awesome and scary thing I tried recently.

Wasteful waiting

from xkcd

Sometimes doing research involves quite a lot of waiting. I’ve made a little graph to illustrate:

There is absolutely no point to the Torosaurus, except that it's adorable.
There is absolutely no point to the Torosaurus, except that it’s adorable.

The trick is to find productive (no, not office chair sword fights) things to do. Seeping could be useful, especially for overnight protocol steps. Or reading papers. Or doing other experiments. Or having inspiring coffee meetings. Or doing a little morning stretch.

Waiting time is not necessarily a waste of time. The French sculptor Auguste Rodin once said:

Nothing is a waste of time if you use the experience wisely.”

Yes, I did just find that through searching google for a “waste of time quote”, but nevertheless, take advantage of down time. Rest, think, talk, dream, experiment, blog (meta). Do anything, except waste it.

Competition, conversation and collaboration

Last weekend I moved to Basel for a two month impersonation of “guest researcher” in a nanobiology lab.

Before I even get to the point, I want to say that Basel is awesome. Except for the evening I arrived, the weather has been the perfect example of “Spring is in the air” and Basel’s traditional emblem and guardian creature is a Basilisk. First of all, this city has a guardian creature. Second of all, this creature appears in one of my favourite books (I was going to say in my favourite septology but I’m pretty sure that’s not a word, so I decided to refer to Newt Scamander’s Fantastic Beasts and where to find them instead). A quick look at the various statues scattered around the city – most of them spouting water – as well as the wikipedia page – I’m such a professional -, taught me that unlike my expectations of a giant snake living in sewage under girls bathrooms, a basilisk looks more like a dragon with a bird’s head. It does still have Medusa-like statue making abilities or killing-at-a-glance powers (depending on the source) and a weakness for weasels/Weasleys. Come to think of it, I’m pretty sure the emblem of Dundee involves dragons and that of Scotland in general has a unicorn. I sure know how to pick my magical creatures. (That of my home town is a boring old swan though…)

In any case, moving to a new lab, albeit for only two months, reminds me of one of the things I love about being in science (as far as I can call my current career “being in science”. A friend of mine basically covered this same topic in her blog recently and I’ll probably just plagiarise repeat some of what she said, but one of the things I love is moving around for conferences, lab visits or even just a new job (as I have for my PhD) to not only explore the world but also explore the minds of all the amazing people I encounter. I might be because I’m still quite young (no need to settle down yet), adventurous at heart (always moved around a bit) and get amazing opportunities (an international and interdisciplinary PhD), but I also believe that the future of science lies in international, collaborative and interdisciplinary research. Also, it’s surprisingly refreshing to pack all you basic needs in one suitcase and just step on a plane.

The thing is, I’ve heard disconcerting stories about research groups not willing to present unpublished work at conferences in fear their ideas will be stolen. Or people naming collaborators as reviewers when submitting papers, while steering clear of their competitors. Science seems to exist in an atmosphere of suspicion and nepotism (though I like the Dutch word vriendjespolitiek – literally friends politics – better) where results and ideas are only shared with collaborators but hidden from competitors.

Of course there’s merit in a bit of healthy competition, it drives people to be ambitious and bring out the best in themselves, but as it is becoming increasingly clear that science is no longer a one-man’s-job (though my friend that I mentioned earlier is well on her way of becoming a homo universalis), I am supporter of more collaborative and open science. I for one have had great ideas by conversing with other people, inside and outside my field of research (and so we bring in the aspect of interdisciplinary research as well). Bouncing ideas off each other, seeing different points of view and geeking out during lunch breaks brings out the best of us, or at least of me.

Well, in any case, I am glad to be here in Basel, these first few days have already been amazing and mind opening and I’m sure there are many more inspiring moments to come.

I’ll leave you with this quite funny looking basilisk. It doesn’t have any jet black scales or horcrux-destroying fangs, but I’d still not look in the eye…