Novacene: the future of humanity is digital?

As it says on the cover of the book, James Lovelock may well be “the great scientific visionary of our age“. He is probably best known for the Gaia Hypothesis, but he made several other major contributions. While working for NASA, he was the first to propose looking for chemical biomarkers in the atmosphere of other planets as a sign of extraterrestrial life, a method that has been extensively used and led to a number of interesting results, some of them very recent. He has argued for climate engineering methods, to fight global warming, and a strong supporter of nuclear energy, by far the safest and less polluting form of energy currently available.

Lovelock has been an outspoken environmentalist, a strong voice against global warming, and the creator of the Gaia Hypothesis, the idea that all organisms on Earth are part of a synergistic and self-regulating system that seeks to maintain the conditions for life on Earth. The ideas he puts forward in this book are, therefore, surprising. To him, we are leaving the Anthropocene (a geological epoch, characterized by the profound effect of men on the Earth environment, still not recognized as a separate epoch by mainstream science) and entering the Novacene, an epoch where digital intelligence will become the most important form of life on Earth and near space.

Although it may seem like a position inconsistent with his previous arguments about the nature of life on Earth, I find the argument for the Novacene era convincing and coherent. Again, Lovelock appears as a visionary, extrapolating to its ultimate conclusion the trend of technological development that started with the industrial revolution.

As he says, “The intelligence that launches the age that follows the Anthropocene will not be human; it will be something wholly different from anything we can now conceive.”

To me, his argument that artificial intelligence, digital intelligence, will be our future, our offspring, is convincing. It will be as different from us as we are from the first animals that appeared hundreds of millions ago, which were also very different from the cells that started life on Earth. Four billion years after the first lifeforms appeared on Earth, life will finally create a new physical support, that does not depend on DNA, water, or an Earth-like environment and is adequate for space.

Could Venus possibly harbor life?

Two recently published papers, including one in Nature Astronomy (about the discovery itself) and this one in Astrobiology (describing a possible life cycle), report the existence of phosphine in the upper atmosphere of Venus, a gas that cannot be easily generated by non-biological processes in the conditions believed to exist in that planet. Phosphine may, indeed, turn out to be a biosignature, an indicator of the possible existence of micro-organisms in a planet that was considered, up to now, barren. Search for life in our solar system has been concentrated in other bodies, more likely to host micro-organisms, like Mars of the icy moons of outer planets.

The findings have been reported in many media outlets, including the NY Times and The Economist, raising interesting questions about the prevalence of life in the universe and the possible existence of life in one of our nearest neighbor planets. If the biological origin of phosphine were to be confirmed, it would qualify as the discovery of the century, maybe the most important discovery in the history of science! We are, however, far from that point. A number of things may make this finding another false alarm. Still, it is quite exciting that what has been considered a possible sign of life has been found so close to us and even a negative result would increase our knowledge about the chemical processes that generate this compound until now believed to be a reliable biomarker.

This turns out to be a first step, not a final result. Quoting from the Nature Astronomy paper:

Even if confirmed, we emphasize that the detection of PH3 is not robust evidence for life, only for anomalous and unexplained chemistry. There are substantial conceptual problems for the idea of life in Venus’s clouds—the environment is extremely dehydrating as well as hyperacidic. However, we have ruled out many chemical routes to PH3, with the most likely ones falling short by four to eight orders of magnitude (Extended Data Fig. 10). To further discriminate between unknown photochemical and/or geological processes as the source of Venusian PH3, or to determine whether there is life in the clouds of Venus, substantial modelling and experimentation will be important. Ultimately, a solution could come from revisiting Venus for in situ measurements or aerosol return.

The mind of a fly

Researchers from the Howard Hughes Medical Institute, Google and other institutions have published the neuron level connectome of a significant part of the brain of the fruit fly, what they called the hemibrain. This may become one of the most significant advances in our understanding of the detailed structure of complex brains, since the 302 neurons connectome of C. elegans was published in 1986, by a team headed by Sydney Brenner, in an famous article with the somewhat whimsical subtitle of The mind of a worm. Both methods used an approach based on the slicing of the brains in very thin slices, followed by the use of scanning electron microscopy and the processing of the resulting images in order to obtain the 3D structure of the brain.

The neuron-level connectome of C. elegans was obtained after a painstaking effort that lasted decades, of manual annotation of the images obtained from the thousands of slices imaged using electron microscopy. As the brain of Drosophila melanogaster, the fruit fly, is thousands of times more complex, such an effort would have required several centuries if done by hand. Therefore, Google’s machine learning algorithms have been trained to identify sections of neurons, including axons, bodies and dendritic trees, as well as synapses and other components. After extensive training, the millions of images that resulted from the serial electron microscopy procedure were automatically annotated by the machine learning algorithms, enabling the team to complete in just a few years the detailed neuron-level connectome of a significant section of the fly brain, which includes roughly 25000 neurons and 20 million synapses.

The results, published in the first of a number of articles, can be freely analyzed by anyone interested in the way a fly thinks. A Google account can be used to log in to the neuPrint explorer and an interactive exploration of the 3D electron microscopy images is also available with neuroglancer. Extensive non-technical coverage by the media is also widely available. See, for instance, the article in The Economist or the piece in The Verge.

Image from the HHMI Janelia Research Campus site.

DNA as an efficient data storage medium

In an article recently published in the journal Science, Yaniv Erlich and Dina Zielinski showed that it is possible to store high density digital information in DNA molecules and reliably retrieve it. As they report, they stored a complete operating system, a movie, and other files with a total of more than 2MB, and managed to retrieve all the information with zero errors.

One of the critical factors of success is to use the appropriate coding methods: “Biochemical constraints dictate that DNA sequences with high GC content or long homopolymer runs (e.g., AAAAAA…) are undesirable, as they are difficult to synthesize and prone to sequencing errors.” 

Using the so-called DNA fountain strategy, they managed to overcome the limitations that arise from biochemical constraints and recovery errors. As they report in the Science article “We devised a strategy for DNA storage, called DNA Fountain, that approaches the Shannon capacity while providing robustness against data corruption. Our strategy harnesses fountain codes , which have been developed for reliable and effective unicasting of information over channels that are subject to dropouts, such as mobile TV (20). In our design, we carefully adapted the power of fountain codes to overcome both oligo dropouts and the biochemical constraints of DNA storage.”

The encoded data was written using DNA synthesis and the information was retrieved by performing PCR and sequencing the resulting DNA using Illumina sequencers.

Other studies, including the pioneering one by Church, in 2012, predicted that DNA storage could theoretically achieve a maximum information density of 680 Peta bytes per gram of DNA. The authors managed to perfectly retrieve the information from a physical density of 215 Peta bytes per gram. For comparison, a flash memory with about one gram can carry, at the moment, up to 128GB, a density 3 orders of magnitude lower.

The authors report that the cost of storage and retrieval, which was $3500/Mbyte, still represents a major bottleneck.

Arrival of the Fittest: why are biological systems so robust?

In his 2014 book, Arrival of the Fittest, Andreas Wagner addresses important open questions in evolution: how are useful innovations created in biological systems, enabling natural selection to perform its magic of creating ever more complex organisms? Why is it that changes in these complex systems do not lead only to non-working systems? What is the origin of variation upon which natural selection acts?

Wagner’s main point is that “Natural selection can preserve innovations, but it cannot create them. Nature’s many innovations—some uncannily perfect—call for natural principles that accelerate life’s ability to innovate, its innovability.”51bwxg5grcl-_sx324_bo1204203200_

In fact, natural selection can apply selective pressure, selecting organisms that have useful phenotypic variations, caused by the underlying genetic variations. However, for this to happen, genetic mutations and variations have to occur and, with high enough frequency, they have to lead to viable and more fit organisms.

In most man-made systems, almost all changes in the original design lead to systems that do not work, or that perform much worse than the original. Performing almost any random change in a plane, in a computer or in a program leads to a system that either performs worst than the original, or else, that fails catastrophically. Biological systems seem much more resilient, though. In this book, Wagner explores several types of (conceptual) biological networks: metabolic networks, protein interaction networks and gene regulatory networks.

Each node in these networks corresponds to one specific biological function: in the first case, a metabolic network, where chemical entities interact; in the second case, a protein interaction network, where proteins interact to create complex functions; and in the third case, a gene regulatory network, where genes regulate the expression of other genes. Two nodes in such networks are neighbors if they differ in only one DNA position, in the genotype that encodes the network.

He concludes that these networks are robust to mutations and, therefore, to innovations. In particular, he shows that you can traverse these networks, from node to neighboring node, while keeping the biological function unchanged, only slightly degraded, or even improved. Unlike man-made systems, biological systems are robust to change, and nature can experiment tweaking them, in the process creating innovation and increasingly complex systems. This how the amazingly complex richness of life has been created in a mere four billion years.

 

Writing a Human Genome from scratch: the Genome Project-write

The Genome Project-write has released a white paper, with a clear proposal of the steps and timeline that will be required to design and assemble a human genome from scratch.

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The project is a large scale project, involving a significant number of institutions, and many well-known researchers, including George Church and Jef Boeke. According to the project web page:

“Writing DNA is the future of science and medicine, and holds the promise of pulling us forward into a better future. While reading DNA code has continued to advance, our capability to write DNA code remains limited, which in turn restricts our ability to understand and manipulate biological systems. GP-write will enable scientists to move beyond observation to action, and facilitate the use of biological engineering to address many of the global problems facing humanity.”

The idea is to use existing technologies for DNA synthesis to accelerate research in a wide spectrum of life-sciences. The synthesis of human genomes may make it possible to understand the phenotypic results of specific genome sequences and will contribute to improve the quality of synthetic biology tools.

Special attention will be paid to the complex ethical, legal and social issues that are a consequence of the project.

The project has received wide coverage, in a number of news sources, including popular science sites such as Statnews and the journal Science.

Reaching “longevity escape velocity”…

The concept that we may one day reach “longevity escape velocity“, a point in time when life expectancy increases by more than one year, every year, is not new. Many people believe that advances in medical and biological sciences will one day create the possibility that humans will live, if not forever, at least for millennia.

An interesting and very informative article in The Economist surveys some of the many ongoing efforts towards extending human longevity.

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The “low tech” approach is based on the idea that calorie restriction (CR), the consistent ingestion of significantly less calories that what is normal, will significantly prolong life. Although the evidence is scant that CR is effective in normal humans, there exists some evidence that, under this regimen, other animals (and unicellular organisms) tend to live longer. The idea is that even a life extension of a few years may take you past the threshold where medical science may extend your life for centuries. So, a Pascal’s Wager makes sense: a few decades of sacrifice, in exchange for centuries of happy life.

More high-tech approaches include genetic manipulation and the development of special drugs that may delay ageing, such as metformim, resveratrol, or rapamycin. Clinical trials are at present very limited, because ageing is not considered a disease  and, as such, anti-ageing drugs cannot get regulatory approval. Self-experimentation seems to be very common in the field, though.

Interest in this type of research is likely to increase, as the population of developed countries ages, and the prospect of significant increase of life expectancy becomes more real. Believers in the singularity have one more incentive. After all, you only need to live enough to get to the singularity.

Next challenge: a synthetic human?

A group of researchers is calling for the next challenge in genetics: create an entirely synthetic human genome. The Human Genome Project Write (HGP-write) aims at creating a human genome from scratch, using the information available from thousands of sequenced human genomes.

Creating a DNA sequence that corresponds to a viable human being is quite an achievable challenge with existing technology. The large number of sequenced human genomes provide an excellent blueprint for that such a genome could be. Poorly understood or hard to sequence regions provide considerable challenges, but they should not be impossible to tackle. More difficult would be to create viable cell lines out of the synthesised DNA, or even viable embryos.

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As IEEE Sprectrum reports, the subject has received considerable attention in the media, namely in the NY Times. The authors of the proposal have already said that they do not intend to create synthetic humans, but only advance the state of the art in genetics research. Their objective is to understand better the human genome, by building a human (and other) genome from scratch. However, one never knows where a road leads, only where it starts from.

 

A new and improved tree of life brings some surprising results

In a recent article, published in the journal Nature Microbiology, a group of researchers from UC Berkeley, in collaboration with other universities and institutes, proposed a new version of the tree of life, which dramatically changes our view of the relationships between the species inhabiting planet Earth.

Many depictions of the tree of life tend to focus on the enormous and well known diversity of eukaryotes, a group of organisms composed of complex cells that includes all animals, plants and fungi.

This version of the tree of life, now published, uses metagenomics analysis of genomic data from many organisms little known before, together with published sequences of genomic data, to infer a significantly different version of the tree of life. This new view reveals the dominance of bacterial diversification.  A full scale version of the proposed tree of life enables you to find our own ancestors, in the extreme bottom right of the figure, the Opisthokont group of organisms. The Opisthokonts include both the animal and fungus kingdoms,  together with other eukaryotic microorganisms. Opisthokont flagelate cells, such as the sperm of most animals and the spores of the chytrid fungi, propel themselves using a single posterior flagellum, a feature that gives the group its name. At the level of resolution used in the study, humans and mushrooms are so close that they cannot be told apart.

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This version of the tree of life maintains the three great trunks that Carl Woese and his colleagues published in the first “universal tree of life”, in the seventies.

Our own trunk, known as eukaryotes, includes animals, plants, fungi and protozoans. A second trunk included many familiar bacteria like Escherichia coli. The third trunk, the Archaea, includes little-known microbes that live in extreme places like hot springs and oxygen-free wetlands.

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However, this more extensive and detailed analysis, based on extensive genomic data, provides a more global view of the evolutionary process that has shaped life on Earth for the last four billion years.

Images from the article in Nature Microbiology, by Hug et. al., and the work of Woese et al.