Foundations of Biology

Stephen Hawking: A brief examination of the recent warning over alien civilizations

Posted in Complexity, Foundations of Biology, General, New Ideas, Recreation on May 4th, 2010 by Hector Zenil – 1 Comment

Stephen Hawking asserts that while aliens almost certainly exist, humans should avoid making contact.

The original story published by BBC News can be found here.

He claims: “We only have to look at ourselves to see how intelligent life might develop into something we wouldn’t want to meet.”

Stephen Hawking recent assertion looks like an interesting time to bring up the question of intelligent life, meaning and purpose.

Let’s examine what Hawking’s argument implies, assuming that intelligent life, other than human, exists elsewhere in the universe:

1. Aliens come from an Earth-like planet.
2. The Earth has something the aliens do not.
3. The Earth has something aliens need or want.

Each point may be not necessarily independent of each other, each may be chained or added to the other. Point 2 may imply Point 1. However, Earth-like planets are likely to be quite common, as the current research on exoplanets seems to suggest. While Point 1 is chauvinistic, Point 3–the notion that Earth possesses something special– is egocentric. Concerning Point 2 again: as a sort of example, many cities on Earth are in need of potable water. Does that mean they can just go looking for it in another city?

If we think that aliens are looking for a planet with an atmosphere like ours, we are already making a very strong assumption that requires further support. To assume that their planet has the same atmosphere as ours and that they would consequently need a planet exactly like it, is to make a strong claim–and a highly implausible one at that. We may think that water is the most precious element in the universe, but it might just be lethal to an alien civilization. If it is true that we can only imagine them in the basis of the kind of life and it diversity on Earth, it is also true that we know nothing about them, if they really do exist.

If humans find life elsewhere, and if it is not related to Earth’s life, it is likely to be unrecognizable. After all we have experience of a very large range of life forms here on Earth, and we find some of them already alien enough. “Extremophiles” is the name we give to Earth species that can survive in places that would quickly kill humans and other “normal” life-forms.

As for needing a work force, it doesn’t make sense that aliens would seek it here. Humans are highly unproductive. And aliens with the technological capabilities to travel to Earth are likely to have had long experience building the kinds of machines that humans have only recently got around to building and improving. Advanced intelligent aliens most likely make extensive use of robots, if they are not some kind of cybernetic beings themselves.

Though assuming that aliens and humans are alike in their biochemical constitution may be chauvinistic and misguided, the supposition that our intelligences are similar has a more solid basis, especially since we also assume that the alien civilization in question has built spaceships, travels in space and is looking for other civilizations. According to Stephen Wolfram’s Principle of Computational Equivalence (PCE), there is a good chance that if non-trivial life forms exist they will have or develop the same degree of sophistication (e.g. intelligence) than ours. Wolfram’s PCE would also suggest that once primitive life has developed it will eventually achieve its maximal degree of sophistication, which would be the maximal possible degree of sophistication. In other words, if life is around, intelligent life is as likely as life.

We used to say that aliens are likely to be much more advanced than humans. Why so? Because the universe has a 15 billion year history. Characterizing a civilization that has been around for about 2 million years and has only begun developing technology in the last few hundred as ‘advanced’ is beyond naive, it is statistically implausible. As Carl Sagan pointed out, every intelligent civilization seems to reach a period when its own technological power is capable of destroying itself. This is the stage which human civilization reached about 70 years ago (and still is), with the invention of atomic bombs. The longevity of said aliens’ civilization means that they have managed to make good use of the resources of their host planet. Even assuming they have reached the point where they have exhausted their resources, we have to concede that they have probably been good, ecologically responsible stewards of their planet. Of course it is still possible, despite all this, that these aliens may wish to colonize a new planet in order to exploit its resources rather than simply seizing what they find and taking it away with them.

Water is one of the most common elements in the universe, or it is quiet easy to synthesize it (see the chemical recipe here). If they just need a rock revolving around a star at a distance such that life can be sustained, there are certainly many more possibilities than coming to Earth. Think about it. The human civilization is much closer to achieving the terraformation of Mars (reengineering Mars soil and atmosphere to make it Earth-life friendly), given its current and near future capabilities than traveling abroad to conquer, if not cohabit with another civilization.

Now, from a practical standpoint, the notion that we could hide away in a corner of the universe is nonsense, to say the least, if we are not somehow already hidden due to the size of the universe itself. The Earth has been broadcasting to space since radio signals were invented. Messages have been kept symbolical on purpose. So in the worst case scenario, assuming Hawking is right and our signals are likely to be picked up by an alien civilization willing to take us on, hiding is just rubbish because we can’t. As Seth Shostak says, the first thing to do would be to shut down the BBC, NBC, CBS and the radars at all airports. Not unless we install a kind of Dyson sphere around the Earth or stop broadcasting altogether. Now, the only way to make sense out of Hawking particular comment in this regard, is taking into consideration time scales. If it is true that Earth has been broadcasting to the space during the last 50 or more years, it is also true that someday in the future it may reach a technological state that allows it to avoid, purposely or not, doing so. So it may be the case that civilizations decide to hide themselves after a short period of broadcasting history.

The advice to hide from aliens implies of course that they are destructive, or that the contact between our civilizations may be destructive, and this brings us back to the question of their longevity. If they were indeed destructive they would have annihilated themselves. As Hawking does right, consider the human case.

But if Hawking is right, we would probably have nothing to be scared of. If an alien civilization wants us dead we will either barely notice it when that happens or that won’t ever happen if it hasn’t happened already. The chances of a destructive civilization to exist seem lower than the chances of a pacific civilization to extend their existence time period in the universe history. The former would have likely already destroyed itself while the latter may have better chances. Caution would not hurt though. We ought to keep an eye on ourselves and how we develop, and that means using our resources more intelligently and not necessarily manufacturing more bombs. But being scared definitely says much more about us than anyone else because we simply know nothing about them, nor we can pretend to know what are their intentions, if any.

But of course in the matter of encounters between civilizations in space, every possibility is time-scale dependent. Imagine for an instant that two alien civilizations are at war. We would certainly be well advised to keep away from the conflict. We may be justified in thinking that if we were in the way when either of the parties ran short of resources to prosecute their war, they would most likely help themselves to anything we had that could be of use. But think a little further. The odds of encountering two civilizations actually engaged in warfare are rather small.

Civilizations making war would either annihilate each other, or if they don’t, then one party would end up achieving hegemonic status. It would seem logical that periods of peace are much longer than periods of war. In the first place civilizations that contemplate war must be both smart enough and hostile enough, and reaching these thresholds of achievement and antagonism takes time–peacetime.

As Hawking claims, many of the life forms in the universe are probably just microbes, but unlike Hawking I believe that if civilizations do exist they’d have little time to make war, even assuming they wanted to. Once again, one has only to think of the Earth to reach this conclusion. If the Cold War had not remained cold, we either wouldn’t be here or else we’d all now be ruled by a single country–as has been pretty much the case (despite there being no actual war) over the last few decades, with the emergence of a current single superpower (with a partial sharing of the global power, and other powers emerging). But when superpowers emerge these days, they are more interested in keeping the peace because they have reached a stage where they depend on each other, chiefly because trade and commerce have become globalized. It turns out that the human world has become much more cooperative than we might have expected. But this is not by chance; it seems to be a common path. Not that one can be absolutely certain, though. Only by witnessing other civilizations could we safely make generalizations. And yet logic dictates that the opposite path–the path of belligerence–would be unlikely.

What I think is that if civilizations were to find each other they are more likely to be interested in each other’s culture and knowledge, than in each other’s natural resources–either because natural resources can be found in many places, or even created by civilizations that are sufficiently advanced, or else because they are simply not needed, curiosity about the universe being the sole motive behind exploration. Which would mean that civilizations would preserve ‘alien’ civilizations to enrich themselves, just as anthropologists and ethnologists do on Earth. To make my point in terms of Hawking, aliens are more likely to be like modern scientists than like the barbaric Europeans who colonized the Americas.

Evaluating the complexity of a living organism by its algorithmic complexity

Posted in Algorithmic information theory, Complexity, Foundations of Biology, General, New Ideas on September 26th, 2009 by Hector Zenil – 6 Comments

One of the greatest scientific achievements of the last century was the understanding of life in terms of information. We know today that the information for synthesizing the molecules that allow organisms to survive and replicate is encoded in the DNA. In the cell, DNA is copied to messenger RNA, and triplet codons in the messenger RNA are decoded in the process of translation to synthesize polymers of the natural 20 amino acids.

Humans have been intrigued by the origin and mechanisms underlying complexity in nature coming from information contained in repositories such as the DNA. Darwin’s theory of evolution suggests that this complexity could evolve by natural selection acting successively on numerous small, heritable modifications.

Darwin’s theory represents a great leap forward in our understanding of the fundamental processes behind life. However, there is a tendency to assume that evolution os the sole factor in designing nature while it may not actually be the main driving force behind the complexity of living organisms [If you wish to know more about the theory of evolution by means of natural selection, three respectable British institutions have set up special websites in celebration of Darwin's 200th. anniversary: the University of Cambridge (with the original scanned text and even an audio version in mp3 format), the Open University and the BBC].

Nature seems to use a specific toolkit of body features rather than totally random shapes. Like units of Lego, Nature assembles its forms from a limited set of elements. For example, despite the variety of living forms on the Earth, they do all seem to have a front-to-back line down the center of the body, and extremities (if any) on the sides, from flies who have a head at one end and a tail at the other, to worms, snakes and humans. Despite the randomness that may undermine any shared regularity among all animals in combinatoric terms, on a certain level, from a certain perspective, we are all similar in shape and features. Why didn’t evolution attempt other, completely different forms? And if it did, why were so few of them successful? Given the improbability of  several other shapes having been put into circulation without any of them winning out save the ones we all know, we could conclude that evolution never did attempt such a path, instead keeping to a small pool of tried and tested basic units whose survival has never been in jeopardy. There are some symmetries and general features that many animals share (more than can be explained by inheritance) that are not so easily explained in purely evolutionist terms. A remarkable example is the resemblance of all animals in their embryonic phase.

Two teams of biologists (Walter Jakob Gehring and colleagues at the University of Basel, Switzerland, and Matthew Scott and Amy Weiner working with Thomas Kaufman at Indiana University, Bloomington) seem to have independently discovered toolkits that Nature appears to use that they have called homeobox containing genes.

This discovery indicates that organisms use a set of very simple rules passed along to them (thus reducing the amount of randomness involved) to build a wide variety of forms from just a few basic possible body parts. To oversimplify somewhat, one can for instance imagine being able to copy/paste a code segment (the homeobox) and cause a leg to grow in the place where an antenna would normally be in an ant.

This begins to sound much more like the footprint of computation rather than a special feature characterizing life, since it turns out that a few simple rules are responsible for the assembly of complex parts. Moreoever, this is consonant with what in Wolfram’s scheme of things life’s guiding force is said to be, viz. computation. And with what Chaitin has proposed as an algorithmic approach to life and evolution, as well as with my own research, which is an attempt to discover Nature’s basic hidden algorithmic nature.  All the operations involved in the replication process of organisms– replacing, copying, appending, joining, splitting–would seem to suggest the algorithmic nature of the process itself. A computational process.

Based on my own research interests it is my strong belief that though by no means wrong, Darwin’s theory of evolution belongs within a larger theory of information and computation, according to which life has managed to speed up its rate of change by channeling information efficiently between generations, together with a rich exchange of information with the outside by a process that while seemingly random, is in fact the consequence of interaction with other algorithmic processes.

Think a bit further about it. Evolution seems deeply connected to biology on Earth, but as part of a larger computation theory it might be applied anywhere in the universe just as the laws of physics do. Evolution may be formulated and explained as a problem of information transmission and channeling, pure communication between 2 points in time. If you want to efficiently gather and transmit information it may turn out that biological evolution may be not the cause but the consequence.

The theory of algorithmic information (or simply AIT) on the other hand does not require a random initial configuration (unfortunately perhaps, nor any divine intervention) to have a program, when run, produce complicated output. This is in keeping with Wolfram’s finding that all over the computational universe there are simple programs with simple inputs generating complex output, what in NKS terms is called ‘intrinsic randomness’, yet is purely deterministic. Nor does AIT require the introduction of randomness during the computation itself. In other words, it seems that randomness plays no necessary role in producing complex organisms. Evolution seems to underlie change, its pace and direction, but it does not seem to constitute the driving force behind life.

Evolution seems to be taking advantage of the algorithmic properties of living systems to fabricate new forms of life. To facilitate understanding of these body patterns the University of Utah has set up an illustrative website. Incidentally, this genetic toolkit based on the homeobox concept is surprisingly well captured in the Spore video game.

In a recent article Greg Chaitin has proposed (Speculations on biology, information and complexity) that some of the properties of DNA and the accumulation of information in DNA may be better explained from a software perspective, as a computer program in constant development. When writing software, subroutines are used here and there all the time, and one usually creates an extra module or patch rather than rewrite a subroutine from scratch. This may correspond to what we see in DNA as redundant sections and ‘unused’ sections.

In Chaitin’s opinion, DNA is essentially a programming language for building an organism and then running that organism. One may therefore be able to characterize the complexity of an organism by measuring the program-size complexity of its DNA. This seems to work well for the length of DNA, since the longest known sequence of DNA belongs to what is certainly the most sophisticated organism on this planet, i.e. homo sapiens.
Chaitin proposes the following analogy:

program -> COMPUTER -> output
DNA ->

However, we encounter problems when attempting to view the process of animal replication in the same algorithmic terms. If, as the sophistication of homo sapiens would suggest, human DNA is the most complex repository of information, and given that DNA represents the shortest encoding capable of reproducing the organism itself, we would expect the replication runtime of human DNA to be of the same order relative to other animals’ replication times. But this is not the case. A gestation period table is available here. So what are we to make of the fact that the right complexity measure for living beings (the logical depth of an object as the actual measure of the organizational complexity of a living organism) does not produce the expected gestation times? One would expect the human gestation period to be the longest, but it is not.

Charles Bennett defined the logical depth of an object as the time required by a universal computer to produce the object from its shortest description, i.e. the decompression time taken by the DNA from the fertilized egg of an animal (seen as a universal computer) to produce another organism of the same type. There seems to be more at stake, however, when trying to apply the concept to Chaitin’s replication analogy– issues ranging from when to determine the end of the replication (the gestation period?), to better times to give birth, to gestation times inherited from ancestral species, to the average size of organisms (elephants and giraffes seem to have the longest periods). Some hypotheses on period differences can be found here for example.

If living organisms can be characterized in algorithmic terms as we think they can, we should be able to introduce all these variables and still get the expected values for the complexity measurement of an organism– seen as a computer program–reproducing another organism from its shortest encoding (the DNA being an approximation of it). A complete model encompassing the theory of evolution has yet to emerge. It seems to be on the horizon of AIT, as another application to biology, one that provides a mathematical explanation of life.

In summary:
So far, what we know is that DNA is the place where the information for replicating an animal is to be found. What’s being proposed above is that the information content in the DNA can be actually measured and effectively approximated as a distance measure of the complexity of an organism. If one can quantify these values one could, for instance, actually quantify an evolutionary step in mathematical terms.
Also, evolution is not usually seen as part of a computational theory, but as an special feature of life. I think otherwise.
Randomness has hitherto been thought to play a major role in evolution as it is mutation that drives the evolutionary process. But I suggest that this is not the case. It is just another part of the deterministic computation, as algorithmic information theory suggests.
Finally, evolution has been thought of in terms of very small steps rather than building blocks and building over them as other scientists have found (which would explain why the theory of evolution has been bedeviled by questions which have not thus far been satisfactorily answered). This favors my computational view of the process of life, because it is based on what in software technology is seen as a subroutine orientation programming paradigm.

In summary:

  • So far, what we know is that the DNA is the place where the information for replicating an animal is to be found. What’s being proposed above is that the information content in the DNA can be actually effectively approximated by means of its program-size complexity and logical depth to define a measure of the complexity of an organism. If one can quantify these values one could, for example, actually quantify an evolutionary step in mathematical terms. This would represent a first step toward encompassing Darwin’s theory of evolution within an algorithmic mathematical theory of life. Evolution is not usually seen as part of a computational theory, but as a special feature of life. The above suggests otherwise.
  • Randomness has hitherto been thought to play a major role in the evolution of species, as it is mutation that drives the evolutionary process. But I suggest that this is not the case. Rather I suggest that what appears to be random is actually part of a deterministic computation, which means that randomness plays no significant part in the process, while computation does.
  • Finally, evolution has hitherto been thought of as a process that advances by very small steps, rather than one that is capable of quickly building over blocks of code, as it might be actually the case. This new understanding favors the computational view I am putting forward here as playing a main role in the process of life, because it is based on what in software technology is the practice of a subroutine orientation programming paradigm: code reuse.

NKS upon Morphogenesis

Posted in Foundations of Biology on August 7th, 2006 by Hector Zenil – Be the first to comment

Stephen Wolfram’s NKS approach to the Reaction-Diffusion Process can be found at:

A beautiful compound of different animals’  markings can be found in the following NKS book page:

Turing on Morphogenesis

Posted in Foundations of Biology on August 7th, 2006 by Hector Zenil – Be the first to comment

Shortly before his death Turing did research on Biology, specifically on the  formation of patterns. He proposed that under certain conditions diffusion can destabilize a chemical system and cause spatial patterns.

His original paper on the subject can be found at the Turing Archive [].

More information can be found if you search  for “Gierer and Meinhardt” on pattern formation. Here is an interesting introduction to the topic written by P.T. Saunders:

Collected Works of A.M. Turing
P.T. Saunders, Editor


Turing’s work in biology illustrated just as clearly as his other work his ability to identify a fundamental problem and to approach it in a highly original way, drawing remarkably little from what others had done. He chose to work on the problem of form at a time when the majority of biologists were primarily interested in other questions. There are very few references in these papers, and most of them are for confirmation of details rather than for ideas which he was following up. In biology, as in almost everything else he did within science — or out of it — Turing was not content to accept a framework set up by others.

Even the fact that the mathematics in these papers is different from what he used in his other work is significant. For while it is not uncommon for a newcomer to make an important contribution to a subject, this is usually because he brings to it techniques and ideas which he has been using in his previous field but which are not known in the new one. Now much of Turing’s career up to this point had been concerned with computers, from the hypothetical Turing machine to the real life Colossus, and this might have been expected to have led him to see the development of an organism from egg to adult as being programmed in the genes and to set out to study the structure of the programs. This would also have been in the spirit of the times, because the combining of Darwinian natural selection and Mendelian genetics into the synthetic theory of evolution had only been completed about ten years earlier, and it was in the very next year that Crick and Watson discovered the structure of DNA. Alternatively, Turing’s experience in computing might have suggested to him something like what are now called cellular automata, models in which the fate of a cell is determined by the states of its neighbours through some simple algorithm, in a way that is very reminiscent of the Turing machine.

For Turing, however, the fundamental problem of biology had always been to account for pattern and form, and the dramatic progress that was being made at that time in genetics did not alter his view. And because he believed that the solution was to be found in physics and chemistry it was to these subjects and the sort of mathematics that could be applied to them that he turned. In my view, he was right, but even someone who disagrees must be impressed by the way in which he went directly to what he saw as the most important problem and set out to attack it with the tools that he judged appropriate to the task, rather than those which were easiest to hand or which others were already using. What is more, he understood the full significance of the problem in a way that many biologists did not and still do not. We can see this in the joint manuscript with Wardlaw which is included in this volume, but it is clear just from the comment he made to Robin Gandy (Hodges 1983, p. 431) that his new ideas were “intended to defeat the argument from design”.

This single remark sums up one of the most crucial issues in contemporary biology. The argument from design was originally put forward as a scientific proof of the existence of God. The best known statement of it is William Paley’s (1802) famous metaphor of a watchmaker. If we see a stone on some waste ground we do not wonder about it. If, on the other hand, we were to find a watch, with all its many parts combining so beautifully to achieve its purpose of keeping accurate time, we would be bound to infer that it had been designed and constructed by an intelligent being. Similarly, so the argument runs, when we look at an organism, and above all at a human being, how can we not believe that there must be an intelligent Creator?

Turing was not, of course, trying to refute Paley; that had been done almost a century earlier by Charles Darwin. But the argument from design had survived, and was, and indeed remains, still a potent force in biology. For the essence of Darwin’s theory is that organisms are created by natural selection out of random variations. Almost any small variation can occur; whether it persists and so features in evolution depends on whether it is selected. Consequently we explain how a certain feature has evolved by saying what advantage it gives to the organism, i.e. what purpose it serves, just as if we were explaining why the Creator has designed the organism in that way. Natural selection thus takes over the role of the Creator, and becomes “The Blind Watchmaker” (Dawkins 1986).

Not all biologists, however, have accepted this view. One of the strongest dissenters was D’Arcy Thompson (1917), who insisted that biological form is to be explained chiefly in the same way as inorganic form, i.e., as the result of physical and chemical processes. The primary task of the biologist is to discover the set of forms that are likely to appear. Only then is it worth asking which of them will be selected. Turing, who had been very much influenced by D’Arcy Thompson, set out to put the program into practice. Instead of asking why a certain arrangement of leaves is especially advantageous to a plant, he tried to show that it was a natural consequence of the process by which the leaves are produced. He did not in fact achieve his immediate aim, and indeed more than thirty-five years later the problem of phyllotaxis has still not been solved. On the other hand, the reaction-diffusion model has been applied to many other problems of pattern and form and Turing structures (as they are now called) have been observed experimentally (Castets at al. 1990), so Turing’s idea had been vindicated.

Turing’s approach to Biology

Posted in Computer Science, Foundations of Biology on August 7th, 2006 by Hector Zenil – Be the first to comment

Where do the spots on animals come from?
Turing’s answer to this question as well as much more on Turing and modern Fibonacci phyllotaxis is  presented and analysed by Jonathan Swintons in his Deodans’ blog