March 26, 2016 | David F. Coppedge

Minimal Cell Challenges Naturalism

Origin of life theorists face a much higher “Mount Improbable” seeing a minimal cell with 473 genes.

Craig Venter’s team has published results of their latest attempt to strip down a living cell to bare essentials (the organism must be free-living, not parasitic). They’re calling it “Syn 3.0.” After years determining what a version of Mycoplasma mycoides bacterium could do without, they came up with a “synthetic” cell containing 473 genes deemed essential. They could not determine the function for 149 of the genes.

It’s the talk of the town in science news circles, because Syn 3.0 is much more complex than any proposed protocell emerging from a chemical soup. On his blog Darwin’s God, Cornelius Hunter remarks, “Mycoplasma mycoides Just Destroyed Evolution.” Here are some media headlines:

  • Artificial cell designed in lab reveals genes essential to life (New Scientist)
  • Synthetic bug given ‘fewest genes’ (BBC News)
  • Creation of minimal cell with just the genes needed for independent life (Science Daily)
  • ‘Minimal’ cell raises stakes in race to harness synthetic life (Nature News)
  • Tiny Artificial Life: Lab-Made Bacterium Sports Smallest Genome Yet (Live Science)
  • Microbe with stripped-down DNA may hint at secrets of life (PhysOrg)

Science Magazine published the original research by Hutchinson, Venter et al.  Commenting on the paper for Science, Robert F. Service says the organism has “fewest genes” but “many mysteries.” Venter’s team first tried to strip down their earlier bug, Syn 1.0, but the complexity of the cell stumped them.

In their current work, Venter, along with project leader Clyde Hutchison at JCVI, set out to determine the minimal set of genes needed for life by stripping nonessential genes from Syn 1.0. They initially formed two teams, each with the same task: using all available genomic knowledge to design a bacterial chromosome with the hypothetical minimum genome. Both proposals were then synthesized and transplanted into M. capricolum to see whether either would produce a viable organism.

“The big news is we failed,” Venter says. “I was surprised.” Neither chromosome produced a living microbe. It’s clear, Venter says, that “our current knowledge of biology is not sufficient to sit down and design a living organism and build it.

They started over with a “top-down” approach. Beginning with Syn 1.0, they systematically stripped out anything the bacterium could live without. They got it down to 473 genes, about half the size of their Syn 1.0 organism.

The big news is that so many genes are essential, and that 149 of the essential genes have unknown functions. New Scientist quotes a biochemist in the UK:

Finding so many genes without a known function is unsettling, but it’s exciting because it’s left us with much still to learn,” says Alistair Elfick, a bioengineer at the University of Edinburgh, UK….

If we’re already playing God, we’re not doing a particularly good job of it,” Elfick says. “Simply streamlining what’s already in nature doesn’t seem very God-like and, if anything, is a very humbling exercise.

Venter also felt the humility vibes, according to Live Science:

“We’re showing how complex life is even in the simplest of organisms,” said Craig Venter, founder and CEO of the J. Craig Venter Institute (JCVI), where the study was completed. “These findings are very humbling in that regard.”

From an intelligent design perspective, Ann Gauger explains in Evolution News & Views why this organism (and any protocell) is irreducibly complex:

All of this leads to an obvious question. This little bacterium has to be able to copy its DNA, transcribe and translate it into protein, plus be able to coordinate all the steps involved in cell division. It has to be able to make all the things it can’t get from its environment. That’s a lot of information to be stored and used appropriately. Hence 473 genes.

This puts pressure on the origin-of-life field.

But where did the cell come from in the first place? It’s a chicken-and-egg problem. Given the number of things the cell has to do to be a functioning organism, where does one begin? DNA or RNA alone is not enough, because protein is needed to copy the DNA and to carry out basic cellular processes. But protein is not enough by itself either. DNA is needed to stably inherit the genetic information about how to make proteins.

It’s like a car, Gauger says. It needs “engine, a transmission, a drive shaft, a steering wheel, axles and wheels, plus a chassis to hold it all together,” to say nothing of gas and a starter. If you get only one or two of those things, you have a piece of junk, not a transportation machine.

Take just protein synthesis. An article on PhysOrg explains that having the building blocks is not enough. The protein recipe “requires precise timing” as well. The steps are “precisely choreographed” analogous to a ballet or a recipe in the kitchen.

In fact, details about the splicing step just came to light in a paper in Science Magazine. Just one subcomplex “must dock onto the rest of the spliceosome and hints at the structural changes the complex must go through to form the mature spliceosome.” This matures the messenger RNA before it goes into the ribosome to be translated into a protein. Summarizing the find for Science, Jamie H. D. Cate calls it a “big bang in spliceosome structural biology.” Splicing occurs in eukaryotes, which evolutionists think evolved later than bacteria. Even so, numerous proteins are involved in handling DNA and RNA in the simplest living organisms, including Syn 3.0.

According to PhysOrg, lead author Hutchinson said that the genome in their minimal cell is “as small as we can get it and still have an organism that is … useful.” Even so, the bacterium lives in the comparative comfort and safety of the lab. Would it survive in the wild? Most cells live in ecological communities with other cells in complex food webs. How would the first protocell get along in a sterile world before life?

Live Science posted a somewhat humorous slide show about theories for the origin of life – humorous, because none of them work. Opening with Darwin and Oparin’s speculation about a primordial soup, Charles Q. Choi’s list includes:

  1. Electric spark (Miller experiment)
  2. Clay (Alexander Cairns-Smith’s favorite hypothesis)
  3. Deep-sea vents (Michael Russell’s model)
  4. Chilly start (obviously at odds with the above models, but needed to protect from UV rays)
  5. RNA World (a dead idea according to leading theorists)
  6. Simpler beginnings (“garbage bag world” or “lipid world”)
  7. Panspermia (Francis Crick’s escape; it just pushes the question farther out to space)

Each of these models has its supporters and detractors. Some are mutually exclusive. One party tries to start with metabolism, but no genetics. Another tries to start with genetics (RNA World), but no protein. Some like it hot, some like it cold. RNA was the leading hope that a molecule could emerge by chance that could begin evolving by Darwinian natural selection. Without natural selection, all agree that lucky accidents would have to occur by chance.

Susan Mazur rubbed shoulders with the leading origin-of-life theorists in the world at their conferences and institutions. Her 2014 book, The Origin of Life Circus, contains eye-opening interviews with the biggest authorities. All of them disown the well-known “RNA World” scenario, at least in its original formulation, despite its continuing presence in the media. Some think RNA had a role in combination with other molecules like proteins. But relying on proteins and other molecules undermines the whole reason for the RNA World, to try to account for metabolism and genetics in one molecule. Steven Benner, for instance, lists four paradoxes of RNA: (1) the building blocks tend to form tar, (2) RNA can’t form in water, (3) RNA polymerization goes against thermodynamics, (4) ribozymes are more likely to destroy RNA than build it (pp. 155-156). The bottom line is that RNA could not have worked alone. It needed proteins as helpers, as well as a container or membrane to hold everything together.

The problem with proteins and polynucleotides is getting the sequence right. Even if they could join up easily (which they don’t), unless they can actually do something, they cannot be building blocks to a living organism. As many have pointed out (including our online book), the probability of getting functional sequences under ideal conditions is infinitesimally small. If one usable protein would never form on Earth in the entire history of the universe, how much less 473 proteins in Venter’s minimal living cell? Each person interviewed in Mazur’s book sang the same refrain: we have no idea how life arose.

Materialists, come to your senses. It’s hard to kick against the goads. The reality of life is telling you something. It’s shouting. Why resist any longer? You respect evidence, don’t you? Faith in the impossible runs against your values. Follow the evidence where it leads. It’s the scientific thing to do.

 

 

 

 

 

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