Cell biology Origin Of Life

“1st International Symposium on Building a Synthetic Cell,” Netherlands, August 28–29

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The world-class symposium features several controversies long the lines of 1) Should we build a synthetic cell and 2) Aren’t we really doing that under another name anyway? Suzan Mazur reports at her blog, Oscillations:

The late Carl Woese, who was awarded the Leeuwenhoek Medal by the Royal Netherlands Academy of Arts and Sciences (1992), opposed the idea of making a synthetic cell, telling me in a 2012 interview weeks before he died that he thought the push for a synthetic cell was all about “Power” and scientists “thinking they’re God.”

The Dutch conference promo never actually defines life. It does, however, address why the country has decided to build a synthetic cell. It repeats the mantra that the initiative is all about trying to understand how life works, adding that part of the plan is to “gain insight” into what the conditions were that first enabled life to emerge on Earth, which may also be relevant elsewhere in the universe. Plus the Dutch, like most invested parties, have an interest in seeing spinoffs from the research.

Motive-wise, nothing really new here. What is new is the Dutch drive to get the job done. To show they mean business, they’ve invited some pretty serious scientists to the Delft discussions.

Some names and positions to watch for:

Of considerable note among the Dutch presenters is Cees Dekker, who in 2014 was decorated by King Willem-Alexander for his “pioneering work of great social relevance”: Knight of the Order of the Netherlands Lion. Cees Dekker is a physicist at Delft whose research interests include the biophysics of DNA and synthetic cells.

According to physicist Eberhard Bodenschatz, director of Max Panck Institute for Dynamics and Self-Organization, Gottingen, who addressed the NSF synthetic cell meeting in May—the Dutch and Max Planck synthetic cell initiatives are very similar, except that the Dutch have now added a genome to their synthetic cell scheme and the Germans have not. The Germans want to see how far self-organization will take them.

Eugene Koonin

“Extraordinary professor” Pieter Rein ten Wolde, from AMOLF (Dutch Foundation for Fundamental Research on Matter), will also share highlights of his research at the Delft gathering. His Biochemical Network group at AMOLF is looking to “unravel the design principles” of biochemical networks through database analyses, theory and computer simulation.

Eugene Koonin is coming.

Koonin has demonstrated the ability to unite various tribes of evolutionary science and articulate a way forward. And he has set the record straight on natural selection, even if his co-author(s) may be stuck in selfish Dawkins-speak. Suzan Mazur, “Who’s Who at the Dutch Synthetic Cell Symposium” at Oscillations

Mazur hopes they’ll live-stream the conference.

It would be interesting if some serious predictions or wagers emerged, so that they can be tested years later. See this wager, for example: At New Scientist: The neuroscientists’ bet that a signature of human consciousness will be found in the brain has only five years to go… No one really loses if they discover that they might be on the wrong track in terms of what they are trying to do.

Origin of Life Circus

Suzan Mazur is the author of The Origin of Life Circus

See also: The minimal cell: How is research coming on a simple, self-replicating “artificial” cell?

Suzan Mazur on mechanobiology, the next level of understanding of the cell

Cells are chock full of information systems, not just DNA

and

Origin of life: What we do and don’t know about the origin of life.

5 Replies to ““1st International Symposium on Building a Synthetic Cell,” Netherlands, August 28–29

  1. 1
    AaronS1978 says:

    So in short this is a meeting on how to create a living cell from scratch, certain would boast that we figured it out already, but haven’t produced a result. My question is for us God believers, what would it mean if they actually succeeded in producing a synthetic cell? Would that take away from the idea of the soul and also the idea that the existence of life is a special event?

    I know A lot of this has to do with disapproving vitalism which deeply saddens me because that is driven by a very materialistic mindset.
    But this is a question I’ve had for a while and I was wondering if anybody would be able to address it especially if it happened to be at science was successful at producing a synthetic sell and how quickly they would put the atheistist materialistic flag into that victory

  2. 2
    AaronS1978 says:

    Also wouldn’t this impact our view on the consciousness and how it arises ? It is just something that bothers me because if they succeeded they would have created life from nonliving matter and that also would have implications on our view of the consciousness. Any thoughts?

  3. 3
    bornagain77 says:

    AaronS1978 “Any thoughts?”

    Here are a few:

    The “Hard Problem” of Life – Sara Imari Walker, Paul C.W. Davies
    (Submitted on 23 Jun 2016)
    Chalmer’s famously identified pinpointing an explanation for our subjective experience as the “hard problem of consciousness”. He argued that subjective experience constitutes a “hard problem” in the sense that its explanation will ultimately require new physical laws or principles. Here, we propose a corresponding “hard problem of life” as the problem of how `information’ can affect the world. In this essay we motivate both why the problem of information as a causal agent is central to explaining life, and why it is hard – that is, why we suspect that a full resolution of the hard problem of life will, similar to as has been proposed for the hard problem of consciousness, ultimately not be reducible to known physical principles.
    http://arxiv.org/abs/1606.07184v1
    pdf
    The “Hard Problem” of Life – Sara Imari Walker and Paul C.W. Davies = June 23, 2016
    Excerpt:. In the case of consciousness, it seems evident that certain aspects will ultimately defy reductionist explanation, the most important being the phenomenon of qualia – roughly speaking our subjective experience as observers. It is a priori far from obvious why we should have experiences such as the sensation of the smell of coffee or the blueness of the sky. Subjective experience isn’t necessary for the evolution of intelligence (we could for example be zombies in the philosophical sense and appear to function just as well from the outside with nothing going on inside). Even if we do succeed in eventually uncovering a complete mechanistic understanding of the wiring and firing of every neuron in the brain, it might tell us nothing about thoughts, feelings and what it is like to experience something. Our phenomenal experiences are the only aspect of consciousness that appears as though it cannot, even in principle, be reduced to known physical principles. This led Chalmers to identify pinpointing an explanation for our subjective experience as the “hard problem of consciousness” [5]. The corresponding “easy problems” (in practice not so easy) are associated with mapping the neural correlates of various experiences. By focusing attention on the problem of subjective experience, Chalmers highlighted the truly inexplicable aspect of consciousness, based on our current understanding.
    ,,,in the same way that Chalmers identified qualia as central to the hard problem of consciousness. To that end we propose that the hard problem of life is the problem of how ‘information’ can affect the world. In this essay we motivate both why the problem of information is central to explaining life and why it is hard, that is, why we suspect that a full resolution of the hard problem will not ultimately be reducible to known physical principles.,,,
    ,,, There are some indications for a potentially deep connection between information theory (which is not cast as a physical theory and instead quantifies the efficacy of communication through noisy channels), and thermodynamics, which is a branch of physics(5) due to the mathematical relationship between Shannon and Boltzmann entropies. Substantial work over the last decade has attempted to make this connection explicit, we point the reader to [22, 20] for recent reviews. Schrodinger was aware of this link in his deliberations on biology, and famously coined the term “negentropy” to describe life’s ability to seemingly violate the 2nd law of thermodynamics(6) . Yet he felt that something was missing, and that thermodynamic considerations alone are insufficient to explain life [26]:

    “. . .living matter, while not eluding the ”laws of physics” as established up to date, is likely to involve ”other laws of physics” hitherto unknown . . . ”
    – Erwin Schrodinger

    We suggest one approach to get at these “other laws” is to focus on the connection between the concept of “information” and the equally ill-defined concept of “causation” [34, 17, 9]. Both concepts are implicated in the failure of our current physical theories to account for complex states of the world without resorting to very special initial conditions. In particular, we posit that the manner in which biological systems implement state-dependent dynamics is by utilizing information encoded locally in the current state of the system, that is, by attributing causal efficacy to information. It is widely recognized that coarse-graining (which would define the relevant ‘informational’ degrees of freedom) plays a foundational role in how biological systems are structured [12], by defining the biologically relevant macrovariables (see e.g. Chapters by Flack, Dedeo and by Wolpert et al. in this volume). However, it is not clear how those macrostates arise, if they are objective or subjective [27], or whether they are in fact a fundamental aspect of biological organization – intrinsic to the dynamics (i.e. such that macrostates are causal) rather than merely a useful phenomenological descriptor. A framework in which coarse-grained information-encoding macrostates are causal holds promise for resolving many of the problems discussed herein. This is the key aspect of the hard problem of life.
    Conclusions:
    There are many difficult open problems in understanding the origin of life – such as the ‘tar paradox’ [2] and the fact that prebiotic chemistry is just plain hard to do. These problems differ qualitatively from the ‘hard problem of life’ as identified here. Most open problems associated with life’s origin such as these, while challenging right now, will likely ultimately reduce to known principles of physics and chemistry and therefore constitute by our definition “easy problems”. Here we have attempted to identify a core feature of life that won’t similarly be solved based on current paradigms – namely, that life seems distinct from other physical systems in how information affects the world (that is, that macrostates are causal).,,,
    To quote Einstein, ‘One can best feel in dealing with living things how primitive physics still is.’
    ( A. Einstein, letter to L. Szilard quoted in [25]).
    http://arxiv.org/pdf/1606.07184v1.pdf

    Darwinian Materialism vs. Quantum Biology – video
    https://youtu.be/LHdD2Am1g5Y

    A few more thoughts:

    An Open Letter to My Colleagues – James Tour – 2017
    Excerpt: We synthetic chemists should state the obvious. The appearance of life on earth is a mystery. We are nowhere near solving this problem. The proposals offered thus far to explain life’s origin make no scientific sense.
    Beyond our planet, all the others that have been probed are lifeless, a result in accord with our chemical expectations. The laws of physics and chemistry’s Periodic Table are universal, suggesting that life based upon amino acids, nucleotides, saccharides and lipids is an anomaly. Life should not exist anywhere in our universe. Life should not even exist on the surface of the earth.17
    http://inference-review.com/ar.....colleagues

    “We have no idea how the molecules that compose living systems could have been devised such that they would work in concert to fulfill biology’s functions. We have no idea how the basic set of molecules, carbohydrates, nucleic acids, lipids, and proteins, were made and how they could have coupled into the proper sequences, and then transformed into the ordered assemblies until there was the construction of a complex biological system, and eventually to that first cell.
    Nobody has any idea how this was done when using our commonly understood mechanisms of chemical science. Those that say they understand are generally wholly uninformed regarding chemical synthesis. Those that say “Oh, this is well worked out,” they know nothing, nothing about chemical synthesis – Nothing!
    Further cluelessness – From a synthetic chemical perspective, neither I nor any of my colleagues can fathom a prebiotic molecular route to construction of a complex system. We cannot figure out the prebiotic routes to the basic building blocks of life: carbohydrates, nucleic acids, lipids, and proteins. Chemists are collectively bewildered. Hence I say that no chemist understands prebiotic synthesis of the requisite building blocks let alone their assembly into a complex system.
    That’s how clueless we are. I’ve asked all of my colleagues – National Academy members, Nobel Prize winners -I sit with them in offices; nobody understands this. So if your professors say it’s all worked out, your teachers say it’s all worked out, they don’t know what they’re talking about. It is not worked out. You cannot just refer this to somebody else; they don’t know what they’re talking about.”
    James Tour – one of the top ten leading chemists in the world
    The Origin of Life: An Inside Story – March 2016 Lecture with James Tour
    https://www.youtube.com/watch?v=_zQXgJ-dXM4

    Origin of life both one of the hardest and most important problems in science – November 2011
    Excerpt: ‘Despite many interesting results to its credit, when judged by the straightforward criterion of reaching (or even approaching) the ultimate goal, the origin of life field is a failure – we still do not have even a plausible coherent model, let alone a validated scenario, for the emergence of life on Earth. Certainly, this is due not to a lack of experimental and theoretical effort, but to the extraordinary intrinsic difficulty and complexity of the problem. A succession of exceedingly unlikely steps is essential for the origin of life, from the synthesis and accumulation of nucleotides to the origin of translation; through the multiplication of probabilities, these make the final outcome seem almost like a miracle.’
    – Eugene V. Koonin, molecular biologist
    http://www.uncommondescent.com.....lution-is/

    Origin of Life: An Inside Story – Professor James Tour – May 1, 2016
    Excerpt: “All right, now let’s assemble the Dream Team. We’ve got good professors here, so let’s assemble the Dream Team. Let’s further assume that the world’s top 100 synthetic chemists, top 100 biochemists and top 100 evolutionary biologists combined forces into a limitlessly funded Dream Team. The Dream Team has all the carbohydrates, lipids, amino acids and nucleic acids stored in freezers in their laboratories… All of them are in 100% enantiomer purity. [Let’s] even give the team all the reagents they wish, the most advanced laboratories, and the analytical facilities, and complete scientific literature, and synthetic and natural non-living coupling agents. Mobilize the Dream Team to assemble the building blocks into a living system – nothing complex, just a single cell. The members scratch their heads and walk away, frustrated…
    So let’s help the Dream Team out by providing the polymerized forms: polypeptides, all the enzymes they desire, the polysaccharides, DNA and RNA in any sequence they desire, cleanly assembled. The level of sophistication in even the simplest of possible living cells is so chemically complex that we are even more clueless now than with anything discussed regarding prebiotic chemistry or macroevolution. The Dream Team will not know where to start. Moving all this off Earth does not solve the problem, because our physical laws are universal.
    You see the problem for the chemists? Welcome to my world. This is what I’m confronted with, every day.“
    James Tour – leading Chemist
    http://www.uncommondescent.com.....nt-design/

  4. 4
    The creationist says:

    The magicians will not be creating life. That was the one thing they couldn’t do in response to Moses.

  5. 5
    DATCG says:

    Cats out of the Genome bag so to speak.

    Nations around the world are rushing to be first in this area and if we(America and the West) do not do it, someone else will like China.

    People won’t like it, but it’s Defense related to, partly funded by DARPA in some cases. So if DARPA is doing this, so is China’s military.

    Mazur reported on American synthetic cell progress for American scientist July 2018…

    https://oscillations.net/2018/07/12/national-science-foundation-funds-synthetic-cell-development/

    News may have already posted this.

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