Big Data is a Day at the Beach

“So you’re saying we don’t know?”

“No, what I am saying is that we can’t know.”

The two friends were sitting on the grass under the shade of a drooping tree. They were enjoying the heat of the mid-day, staring out at the shimmering waters before them. The friends had spent the last few days in this agreeable way, and they both knew that they were just where they should be. 

On some of those days the two friends took to pondering the imponderables.

“Does anybody know?”

“Well, together we all sort of know, but no one knows.”

“Ok, now you’re just being ridiculous. I am going for a swim.”

With an exasperated huff, the friend got up and awkwardly shuffled his way across the hot sand in the direction of the water.

As the other friend sat staring out at the water, he contemplated what it was that he was seeing. Right now photons were emerging after banging around inside the sun for thousands of years. In unfathomable numbers, these packets of light energy streamed silently away from the sun, through the blackness of space, through the earth’s atmosphere, finally slamming into the surface of the water. Through reflection and refraction photons were scattering off the water, with only a lucky few quadrillion finding their way into his eyes where they caused a chemical reaction within his retina. 

He wondered how much of the vast amount of information encoded in the waves of photons washing across his retina was being recorded. Was there a memory lattice somewhere deep within the earth’s crust being reorganized in concert with the photonic reactions within his eyes?

He knew that some part of that information would surely be stored – What way was the wind blowing? How big were the waves rippling across the bay?  What chemicals were likely present in the water given the emission spectra? What and how many animals were likely swimming below those ripples? How many birds were flying across the sky? It was all science, but what was of interest to the net, or even how much of the information could be saved, were unknown to him.

He could of course simply think a little further to the right and find out what datasets were being collected, but current fashions espoused the value of disconnection from the net. 

“People should wonder and dream, this is our purpose in the net. We are not meant to subsist on daily rations of dried information. Go out into the world and feel.” In his mind’s eye he could hear the roars of agreement as the popular line of thinking spread through the net.

Where had this new trend really come from he wondered? Was there really any value to random human thought patterns from a disconnected mind, or was the net just trying to push for a little more data collection? There must be better ways to collect information than through imperfect biology. Maybe it was just a fad….  

He couldn’t be sure, which he guessed must in itself be the point. “What an oddly thrilling feeling, this not knowing,” he thought, as he got up and walked towards the water.

He felt the sand under his feet turn from hot and dry to wet and cool. He could smell the salty sea air. More data.

His mind strayed to the past. How many times had this kind of idyllic scene passed into the retinas of people before him? Maybe someone had stood right where he was and felt the water lapping at their feet. They would have taken in all of the deep information around them, just as he was and then…. He shuddered at the thought of all of that lost information, all of it just gone.

Thousands of years of perception boiled down to a few exabytes recorded in the preposterously inefficient encoding of written language. By modern comparison, even the people of the 21st century had managed to record pitifully little through the digital technology they had so embraced. With his sensory input alone he was probably generating an equivalent amount of data every minute as the whole of pre-digital era of human history.

“Did people used to know?”

His friend’s question snapped him out of his contemplation.

“We thought we did, but we were wrong.”

“Is there no way to simplify it?”

“Any simplification that you could understand would be so far from the truth that it wouldn’t really be useful.”

“Couldn’t I learn enough to understand it?”

“It would take an impossibly long time to learn even the underlying theories, it is just too much for one mind to ever comprehend.”

Standing waist deep as the small waves rolled past him, his friend stared back at him with an unsatisfied look.

“Individually we are just too limited, but together with each of us holding small pieces of the answer and with the net connecting us we really can know. Together we know.”

His friend sighed and turned towards the sun.

He watched as his friend slapped at the water, the light glinted off the water droplets flying through the air.

More data, he thought.

————————————————————–

With the growth of big data, an ever increasing volume of information is going to be gathered  from our bodies. This may lead to great scientific insights and new ways of understanding the world, but as this store of information grows exponentially, we may also find that the complexity of models that must be constructed to understand the world also increase exponentially. Will we soon find ourselves in a place where we have answers to the mysteries of the universe, but we don’t understand them?

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Nature Has No Allegiances: An Argument for Geoengineering

The earth does not owe us anything. The earth has no allegiances, it has no cares, and it does not love us.The earth is a collection of inanimate matter which happens to have the lucky conditions necessary to favour the emergence of highly organized and highly complex groupings of self-replicating molecular patterns, collectively known as life.  

The earth is staggeringly beautiful and all of its glorious biodiversity is absolutely something worth protecting, but we should not forget how we came to have such a beautiful and diverse planet. The history of the earth is not one of constant harmonious balance, but one of perpetual life and death competition.

In a recent post I talked about the tension of chaos and order in the universe. Nowhere is the interplay of chaos and order more apparent then in the natural world where a constant evolutionary race is ongoing between all of the interconnected species of the planet. Through chaotic evolution, life has bumbled into the current balance that is necessary to support life as we know it today, but it is dangerously delusional to think that the natural system will stay just as it is today, forever.

In recent times, human activities have had an exponentially increasing effect on the natural systems of the planet. In a very real sense, the build-up of greenhouse gases is stacking the scales in favour of chaos over order. We are putting more energy into the system, and we can’t be sure exactly what that is going to do. Our current trajectory foreshadows a chaotic implosion of the balanced life-support systems which we rely on for survival. Yes, the natural world will eventually reach a new equilibrium, but whether that is one conducive to human life on this planet is unclear.

We must start to take responsibility for the long term impact of our actions on the environment. More importantly, we must give up on the idea that the natural world is designed for us, and if we simply somehow  “go back to nature”, then we can get back to a fairy tale state of harmonious balance with nature.

Aside – At this point, I am tempted to go off on a tangent about whether or not the Universe has an interest in your personal well-being, and the role that belief should have in politics – but this will have to be an argument for another post. Suffice it to say that faith should have no place in politics. Regardless of our personal beliefs, I think the majority of thoughtful individuals can agree that our mechanisms of collective decision making ought to be organized around rational principles.

Doubling the amount of carbon dioxide in the atmosphere is going to have a drastic impact on the way the natural world functions. Scientists are now saying that the changes we are already seeing in global temperatures may be but a sign of things to come. Even if we were to stop putting CO2 into the atmosphere today, it’s thought that temperatures may continue to increase for hundreds of years. Given the speed of changes we are seeing already, I don’t think it is going to be possible for us to live through hundreds of years of this.

Amongst the overwhelming majority of scientists who accept the existence of climate change, the grave danger it poses is well accepted; yet still the only ‘solution’ that seems to be widely discussed is the cessation of activities that produce greenhouse gas as soon as possible.  I am becoming increasingly convinced that stopping fossil fuel use alone is not going to be able to reverse the effects of 200 years of greenhouse gas emissions.

To oversimplify a complex argument; I don’t think that the earth is going to “fix” itself. We are going to need other options, and it is time that we figure them out.

Geoengineering offers our only hope to reign in an unruly climate should some of the more dire predictions of climate scientists start to come true. Despite this, both from the environmental lobby and the wider media, I hear a conspicuous silence when it comes to the issue of geoengineering.

It would seem that the reason for this comes at least in part from a pseudo-spiritual belief that nature will somehow take care of us, if only we mend our mistaken industrial ways. This kind of philosophy is a dangerous bedfellow for climate scientists interested in  of populist support against climate change. Nature has no allegiance to us. It is in our hands to make wise decisions in the interest of our collective future. 

There is another argument sometimes put forward against geoengineering: That putting geoengineering on the table would take away the incentive to continue the fight against GHG emissions. This is a ridiculous argument, akin to suggesting that the existence of chemotherapy takes away the incentive to quit smoking.

Just like chemotherapy, geoengineering is an extreme and dangerous treatment for a disorder which we don’t fully understand. It is also a treatment which we would all rather avoid. Nonetheless, we know that doing nothing will allow an invisible disorder to become a visible disease, and one that might just kill the patient.

Unlike chemotherapy however, we still don’t have the scientific data to show what kind of geoengineering will work. It is time for this to change. The precautionary principle states that we cannot perform an intervention where we do not have confidence it will help more than it hurts. Several different geoengineering schemes have been proposed, but we are basically in the dark as to which ones might be effective, and which ones might be disastrous.The only way to know this is to do the science.

Let me be clear, I am not advocating that we go ahead and start on large scale geoengineering, but I do think that it is time that we start talking seriously about geoengineering, and it is time we give it serious funding to match. We need to decide what form of geoengineering we would use, and when it would be appropriate to use it – and we need to start working on these questions right now. Pretending that geoengineering doesn’t exist, or trying to outlaw its use is short-sighted, and potentially dangerous.

Geoengineering is not the cure we want, but it might be the one we need.

You can have the future but you can take nothing with you

As I spend more and more time awash in the techno-optimism of the great futurist forum that is r/Futurology, a thought has been bothering me lately. Make no mistake, I am very much an optimist about the power of technology, but I just think that we are missing an important counterpoint. Our mistake is that we imagine a totally transformed world, but we often place ourselves relatively unchanged within this world. 

I think we sometimes forget that the future can be as merciless as it is fantastic. The world of the future will be a remarkable place, but we are not necessarily going to like it.

To flesh out this view, I will start with an inverse example. Imagine an average person of 100 years ago instantly transported to the world of today. They would be met with a marvellous world of technology and possibility, the likes of which they could not have even imagined in 1913, but would they like it here?

Our traveller would certainly be astounded that we can instantly communicate with anyone in the world, but would they perhaps be equally dismayed by our inability to communicate with those in front of us? They would likely be amazed by our unprecedented access to the sum of human knowledge, but also likely disheartened by our lack of applied knowledge and skills that were so important to people of their time.

I think that the view of our social progress would be more or less dependent upon their personal views, but I would wager they would shocked by the race-mixing, gender-equal, homosexual-accepting, multi-cultural, and generally tolerant society that we have become. To expect that a person transported from 100 years ago would be entirely happy or even comfortable with our society as it is today is to place unrealistic expectations on our past, and essentially is to rewrite history.

The traveller would be impressed by all that we had learned about the way that the world works (the age of the universe, the quantum nature of reality, DNA, etc…) but I think that the impact of these revelations on a mind unready for them would ultimately be devastating. The traveller’s whole world view is based on a 1913 mindset and they are entirely unprepared for the godless and techno-centric new world of 2013.

If instead of bringing a traveller forward to our time, we project ourselves forward into the future (as futurists like to do), there is no reason to necessarily think that we would fit better into or be more happy with the world of tomorrow. The new world will be a remarkable place, but we probably wouldn’t like it.

If you buy a goldfish, take it home, and plunk it into it’s new home suddenly, the shock can be enough to kill it. If on the other hand, you place the fish in its bag on top of the water in the new tank, and give time for the water to slowly change then the fish can acclimate well to new conditions. We are the goldfish; immersed in the unseen philosophy and morality of our time. We can and will slowly acclimatize from one time to another, but the jump from one time to would likely be an unbearable culture shock.

So what are some of these fundamental changes that will make the future so foreign and potentially distasteful to someone of today? A few that I have been tinkering with are as follows:

  1. The proliferation of cheaper and cheaper consumer good and the melding of the real and the virtual will ultimately lead us to massively devalue physical goods. The idea of owning anything will become completely foreign because we will be able to so easily bring anything we imagine into existence. Through this we will eventually lose touch with physical reality altogether. 
  2. The fact that the vast majority of work will be done by machines will make the idea of work ethic quite quaint. As it becomes possible easily to sculpt our bodies and our minds to meet our desires, the very idea of work will dissolve away. The very idea of a purposeful life may eventually become an idea of the past.
  3. The exponential increase in the speed and volume of communication between human minds will eventually lead us to devalue individualism itself.  We will no longer see individual people as hard separate nodes, but rather as another part of a robust and redundant biological information network. As I pointed out in a previous post, as it becomes possible to reinstantiate individuals at will, we may stop caring about individuals at all. What care would gods have for the fate of men?

These are just a few ideas about how I think we might outgrow the the grand ideals of our time, that of hard work, material success, and the realization of our individual potential. What are some of the unseen philosophies which you think will change in the fullness of time?

For those that believe in an afterlife, it is often said that we can take nothing with us from this world into the next. It strikes me that the slow slide of now into the afternow is also a passing of sorts. The journey to the future is every bit as absolute as death, and is ultimately a journey that can strip us of everything that we thought we were.

You can have the future but you can take nothing with you. 

Selfish Information and the Depth of Disease

The last 100 years has seen a series of phenomenal breakthroughs in the biological understanding of disease. From the advent of antibiotics to the sequencing of the human genome, we have come a very long way in a short amount of time, but we still have a long way to go. This is a story about a fascinating disease, the understanding of which has revolutionized the way we think of infectious disease. This disease also speaks to the depth of scientific understanding and biological control that will be needed before we will be able to call disease a thing of the past.

Many diseases are caused by infectious pathogens which we are exposed to throughout our lives. A pathogen is usually defined as a microbe which causes a disease. For instance, if you eat some raw meat or unwashed vegetables and get sick, the pathogen causing your illness could likely be some form of the Salmonella bacterium.

Unfortunately, defining pathogens as microbes which cause disease starts to fall apart when you consider viruses, as these simple clumps of genetic material and protein cannot live on their own and are not really considered to be alive at all. Common colds and flus are caused by viruses which get transmitted to you from another infected person and then start reproducing in the cells lining your respiratory tract.

It is actually quite amazing how simple these viruses can be, with the smallest viruses having only a few genes. This means that a clump of matter with only a few thousand proteins and the equivalent of about 1 kilobyte of genetic information, have evolved the capacity to evade your immune system (at least temporarily), get into your cells, and turn them into virus factories. For comparison, each of your cells has a DNA code in the range of 750 megabytes of information and contains billions of proteins  

Given that viruses fall below the threshold for what we would define as life, a broader definition of a pathogen is needed.  Fundamentally, pathogens are simple self-reproducing patterns of biomolecules that have evolved to parasitize much more complex self-reproducing patterns of biomolecules like youPathogens have outsourced all of the complexity necessary for dealing with the environment and gathering energy to their hosts. Pathogens opt to steal energy  from your cells and channel it into their own selfish reproduction. Thus, an alternative definition of a pathogen might simply be any biological unit of parastic self-reproducing information.

As simple as viruses can be, it turns out that this is far from the simplest that a disease causing pattern of information can be.

To understand the next part of the story, I am going to need to explain a little bit about protein. To the uninitiated, the word protein might conjure up nebulous thoughts of some kind of nutrient that you get from steak and nuts. In actual fact, protein is not only found in meat, but is what makes up the nanomachines that are performing all of the behind the scenes magic going on in each and every one of your cells. They make up everything from the living skeleton that supports your cells, to the enzymes that break down your food, to the molecular pumps that move chemicals in and out of the cell. 

Literally, if anything is happening in your cells, its probably being done by protein.

Futurists imagine a world where we have developed the capacity to synthesize nanomachines that can fit inside of a cell and perform complex tasks, but the amazing fact is that this is already happening – right now… inside of you! At this very moment, millions of tiny protein robots are being synthesized to perform the plethora of tasks necessary to make you work. 

This process relies on very special biological robot replicators, known as ribosomes, which function to create more proteins for the cell. These ribosomes read strips of genetic information and string together the building blocks of protein, known as amino acids. Depending on the specific genetic code being read, the ribosome will incorporate the appropriate amino acid into a growing string of amino acids.

The amino acids are essentially just 20 differently shaped chemicals which can be strung together to create a strand of any sequence. As these shapes come together they will start to fold up into a tangled structure that is a protein. Eventually, long strings of amino acids form into larger and larger structures, resulting in the final functional structure of the protein. In its final form the protein becomes functional and will start to go about its job in the cell.

Protein Folding

How your body turns genetic information into bio-robots

With only ~20 building blocks to work from, the ribosome can generate the endless array of proteins, each with a different shape that suits its final function.

The process of protein folding is actually quite a complicated process, and despite intensive study of how it works we still cannot completely simulate it (even on super computers). You can play a game and help scientists understand the process of protein folding over at fold-it.

What we do know about protein folding, is that in some cases this process goes wrong and proteins become misfolded. The cell has evolved ways to deal with misfolded proteins by chewing them up. In some rare cases however, these proteins will not be degraded and they can build up within the cell. It is thought that this build up of misfolded protein is responsible for some of the damage associated with aging.

Because proteins have the capacity to stick to eachother, this means that in some very rare cases misfolded proteins have can somtimes transmit their misfolded state to other proteins like it. By helping similar proteins become misfolded they will set off a chain reaction, causing more and more accumulation of useless and possibly damaging forms of protein.

Protein misFoldingSome misfolded proteins can replicate their misfolded state within similar proteins, leading to a dangerous chain reaction. 

This type of misfolded protein chain reaction is precisely what happens in a disease known as Creutzfeld-Jakob Disorder (CJD). In CJD a protein called a prion becomes misfolded in such a way that it promotes further misfolding in other prion proteins. This sparks a chain-reaction, which results in the disease characterized by rapid onset of severe dementia and eventually results in death.

When this type of prion disease occurs in cows it is known as Bovine Spongiform Encephalopathy (BSE) or “mad-cow disease”. In the United Kingdom, it is estimated that 166 people contracted BSE by eating beef which was contaminated with misfolded prion proteins. These people developed a form of CJD, and subsequently died of the disease.

This means that the misfolded state of prion protein was somehow able to propogate from one species to another through eating! This type of transmissible prion diseases also occurs in deer populations, where it is known as chronic wasting disease, and sheep, where it is known as scrapie.

The fact that misfolded prions can transmit disease from one individual to another is actually quite mind-blowing. Prions do not carry no genetic information at all, in fact they don’t even need to have any special amino acids. The only information they need carry is an anomalous twist in their protein folding which can selfishly reproduce itself in the prions it encounters. 

Since, 1989 various changes in the handling of cattle and beef has prevented widespread outbreaks of CJD, but there remains a constant undercurrent of ‘classical’ CJD which occurs in around 1 in 1 million people. In these cases, the disease is not thought to be linked to eating beef, but rather is driven by random misfolding in prions already present in the body.

While some cases are linked to the presence of genetic mutations which might favour the misfolding of prions, known as familial CJD, this accounts for only about 10-15% of CJD cases. The majority of CJD cases are due to random misfolding of prion proteins leads to a chain reaction and just happens to kill around 1 in every million people.

This means that as far as it is currently understood, the cause of CJD is a purely sporadic event. Simply through the ongoing process of folding billions of proteins in millions of people, some of them are going to randomly go bad. And when prions go bad in just the wrong way they will set off a chain reaction that will kill the people who are attached to them. 

You might say to yourself that 1 in 1 million is not too bad of odds, but new research indicates that self-propogating protein misfolding may also be behind major diseases like Alzeimers and Parkinson’s Disease. There is a great article which talks about new research supporting this possibility in the most recent issue of Scientific American [paywall]. 

So what does all of this mean? CJD teaches us that an infectious pathogen can be as simple as an abherrent fold in a protein. This drives home the point that we must dissolve our expectations of what a disease causing agent must be. Any pattern which can copy itself (no matter how simple) can represent a potential danger to larger patterns of information like human beings.

This also underlines the depth of biology which is often missed given the hype around the DNA genome. Our DNA is not the only blueprint that is of importance to understanding our biology, there is vital information stored within the physical state of our living cells as well. It seems plausible that the amount of information encoded in the physical state of our cells may be even larger then that encoded by the DNA.  Until we can understand the physical interactions of all of the proteins in all of our cells we will not truly be able to understand the causes and develop treatments for many diseases. We are a long way from even simulating the entirety of a single cell, let alone actually tracking the interactions of the billions of proteins within a living cell. The idea of understanding the number of protein interactions within an entire body is an unfathomable dream at this point.

We have a long way to go.

This is why we need better computers.

This article is the first in what I hope to be a series about the advancement in the understanding and treatment of disease and how far we yet have to go before we will see an end to disease. How did I do? Was it too technical? Not technical enough? Leave a comment in the feedback section and let me know.