George Church Thu 22-Jun-2006 at 12:30.NRB 258 Lab-meeting

Warning: The following presentation style has been determined by the Surgeon General to be hazardous to your career. Do NOT try this at home.

The future of evolution

Thirsty?

An Inconvenient

Truth

An Inconvenient

Truthabout your

tuna sandwich

Every second the sun emits 2E45 photons. The earth gets 6E35 of these

(4E17 W = 4E4x human consumption). 1% of this is captured by

Prochlorococcus & it’s ilk. (100 Gton CO2/yr v. 5 for fossil fuels)

But.. > protozoa > copepods > krill >herring > 60 kg albacore >

trucks/canning

2E5 J/mol 200 W/m2 http://www.lifesciences.napier.ac.uk/teaching/Env/En9light.html

Albacore eat 25% of their own weight every day for 13 yr (= 0.1% efficiency)

Green constructive

biology

Solar-Powered Sea Slugs Rumpho et al. Plant

Physiology 2000

Hydrogen production by Cyanobacteria Dutta et al. Microbial Cell Factories 2005

Fast noninvasive activation and inhibition of neural and network activity by green algae channelrhodopsin. PNAS 2005Synthetic biology: engineering Escherichia coli to see light. Nature. 2005

In vitro-cultured meat production.Tissue Eng. 2005 11:659-62.

Old interfaces of Technology & Society

Issues - Reactions • Manhattan Project

• Animal testing

• Genetically Modified

Organisms (GMOs)

• Robots & Nanotech

New interfaces of Genomics & SocietiesIssues - Proactions

• Synthetic Pathogens - Surveillance of DNA resources• Global Warming - DOE BioEnergy/Ecology Project• Research Privacy - Personal Genome Project Consent

June 2006

Genographic Project 2005150,000 subjects 12 DNA loci each

Spencer Wells

Personal Genome Project (PGP) tour:3 subjects, 1 diplome each (225 volunteers)

IthacaBuffaloToronto

Lake OrionDetroit

Ann ArborCleveland

Harpers FerryOcean CityPhiladelphia

NYCNew HavenCoventry, RI

(Micro)Evolution Passé Mutation, drift, selection, migration

The Future of Evolution1. Lamarckism (acquired characteristics)

2. Intelligent Design

3. Panspermia (interplanetary)

4. Orthogenesis (too much of a good thing)

5. Transmutation (between species)

6. Saltation "Hopeful Monsters"

1a. Lamarckism (acquired characteristics)

Past CurrentInputVisible 4 to 7 E-5 E-12 to E6 metersHearing 10 to 20000 E-9 to E12 Hz Chemosenses 5 to 500 millions of compounds Touch 3000 0.1 nmHeat sensing 200 to 400 3 to E5 oK

MidputMemory span 20 5000 yearsMemory content 1E9 1E17 bitsCell therapy 0 most tissuesHeat tolerance 270 to 370 3 to E3 oK

OutputLocomotion speed 50 26720 km/hOcean depth 75 10912 metersAltitude 8E3 3E9 metersVoice 300 to 3500 10-20000 Hz

1b. Lamarckism (acquired characteristics)

Methacrylate + ethylene

glycol dimethacrylate

Drug assay using antibody mimics made by molecular imprinting. Nature. 1993 Feb 18;361(6413):645-7.

Can we do the same with aptamers?

Solidphase

DNA Nano to Macro Challenge From: 7 kbp natural ss-DNA

to: 1Mbp ds-DNA on nanogrids&/or selectable 3D structures

Rothemund Nature Mar-2006

Shih et al. Nature 2004

“BioBricks to Bricks”

$20K/g to $50/ton

Mitra, R. & Church, G.M. (1999) In situ localized amplification and contact replication of many individual

DNA molecules. NAR 27:e34; pp.1-6. Bioprinting: A Beginning Mironov, et al. Tissue engineering 12:631-4. 2006

Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson BO. In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng. 2005 91(5):643-8.

Rozen DE, Schneider D, Lenski RE Long-term experimental evolution in Escherichia coli. XIII. Phylogenetic history of a balanced polymorphism. J Mol Evol. 2005 61(2):171-80

Andries K, et al. (J&J) A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis. Science. 2005 307:223-7.

Shendure et al. Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome Science 2005 309:1728 (Select for secretion & ‘altruism’).

2. Intelligent Design & Genome Evolution

trp/tyrA pair of genomes shows the best co-growth

Reppas, Lin & Church ; Shendure et al. Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome(2005) Science 309:1728

SecondPassage

First Passage

Constructive ecosystems, evolution, I/O, sequencing

ID evolution: Next steps

1. Couple replicon fates (yeast, E.coli, phage, ribosome display)

Benhar I, et al.. Highly efficient selection of phage antibodies mediated by display of antigen as Lpp-OmpA' fusions on live

bacteria. J Mol Biol. 2000 301(4):893-904.

Richman SA, et al. Protein Eng Des Sel. 2006;19(6):255-64. Development of a novel strategy for engineering high-affinity

proteins by yeast display.

2. In vivo counters: E.g telomeres & integraseshttp://arep.med.harvard.edu/SBP/iGEM/iGEM_2004.ppt

3. Panspermia Universal DNA primers amplifying bacterial 16S rRNA/DNA variable regions

5’ GTGCCAGCMGCCGCGGTAA 515F primer >>5'AACTCTGTGCCAGCAGCCGCGGTAATTCCAGCT-------------------GTGAAGTCGTAACAAGGTAACCGTAGGGGA 3'TTGAGACACGGTCGTCGGCGCCATTAAGGTCGA-------------------CACTTCAGCATTGTTCCATTGGCATCCCCT << TTCAGCATTGTTCCAWYGGCAT 5'

1512 universal primer

Isenbarger, Finney, Church, Gilbert, Carr, Zuber, Ruvkun (Submitted to Astrobiology 2006)

2.7-year return trip to Mars, = 2 sieverts (J/kg) (enough to give 15% lethal cancers)

Deinococcus can survive 10,000-fold more.

4. Orthogenesis(too much of a good thing)

Bug=Safe

SUV=Safer

Armored car = Safe from Bugs

Irish Elk

GMOs vs. Natural Constructs Recombinant DNA molecules that are constructed outside living cells by joining natural or synthetic DNA segments to DNA molecules that can replicate in a living cell.http://www4.od.nih.gov/oba/rac/guidelines_02/NIH_Guidelines_Apr_02.htm#_Toc7261549 http://www.omri.org/OMRI_GMO_policy.html

U.S. National Organic Standards Board definition of genetic engineering & GMOs: "Made with techniques .. not possible under natural conditions or processes… It shall not include traditional breeding, conjugation, fermentation, hybridization, in-vitro fertilization, or tissue culture."

TILLING: Targeting Induced Local Lesions IN Genomeshttp://www.plantphysiol.org/cgi/content/full/123/2/439 Accelerated natural selection, engineered haplotypes…

Smart therapeutics example: Environmentally controlled invasion of cancer cells by engineered

bacteria. Anderson et al. J Mol Biol. 2006

Optical imaging: bacteria, viruses, and mammalian cells encoding light- emitting proteins reveal the locations of primary tumors & metastases in animals. Yu, et al. Anal. Bioanal. Chem. 2003.

accumulate in tumors at ratios in excess of 1000:1 compared with normal tissues. http://www.vionpharm.com/tapet_virulence.html

Regulated Capsule TonB, DapD

& new genetic codes for safety

5. Transmutation (between species)

Copolymer effects on microglia and T cells in the central nervous system of humanized mice. Eur J Immunol. 2005

Humanized liver in mice shows human-type metabolic responses to drugs. Am J Pathol. 2004 Sep;165(3):901-12.

Mueller D, et al. Transplanted human embryonic germ cell-derived neural stem cells replace neurons and oligodendrocytes in the forebrain of neonatal mice with excitotoxic brain damage. J Neurosci Res. 2005 Dec 1;82(5):592-608 : "the survival of transplanted hNSC .. was about five times greater in the lesioned brains compared with nonlesioned brains.. Neuronal cell loss in the QA-lesioned striatum was attenuated by the hNSCs. "

Combining two genomes in one cell: Stable cloning of the Synechocystis

genome in the Bacillus genome

Itaya, Fujita et al. PNAS 2005

(Micro)Evolution Passé Mutation, drift, selection, migration

The Future of Evolution1. Lamarckism (acquired characteristics)

2. Intelligent Design

3. Panspermia (interplanetary)

4. Orthogenesis (too much of a good thing)

5. Transmutation (between species)

6. Saltation "Hopeful Monsters"

What is Life?

What is big?

Time line of introduction of standardized quantitative measures

3000 BC Sumerian cubit = 518.5 mm & shekal = 8.36 g, (Egyptian pyramids were constructed to a precision of 15 mm in 235 m = 6e-5.)2100 BC time: year 360 days700-600 BC Coins (to measure value and commerce)1585 Stevin decimal weights, measures, coinage and arcs.1799 meter & kg1760-1880 first industrial revolution: Steam & thermodynamics E,H,S,T,P1870-1920 second industrial revolution: EM Maxwell (measures B,V,A,W) 1930-1980 third industrial revolution : atomic, space, digital1948 Shannon information entropy 1960 the International System of seven base units: meter, gram, second, degrees K, ampere, mole, and candela. 1953-present fourth industrial revolution : biopolymer sequencing beginning with insulin by Fred Sanger in 1953.

Life = Complexity?

High Order Low OrderLow Complexity High Complexity

Replicated complexity(replexity)

Replexity in

Replexity Out

Robotics: self-replication from random parts. Griffith S, Goldwater D, Jacobson JM (2005) http://www.nature.com.ezp1.harvard.edu/nature/journal/v437/n7059/extref/437636a-s1.mov

Minimal replicators

•Short nucleic acids (6-mers) can be shown to catalyze chemical ligation of 3-mers producing an autocatalytic cycle [Sie94].

•RNA molecules about 189 nucleotides long can be evolved in the lab to use triphosphates to copy up to 14 bases on an RNA template with errors of less than 1% per nucleotide. [Joh01].

• 110 kbp 153 genes in vitro minE.coli [Forester & Church]

Replexity examples

Estimates We can divide the rectangle encasing that molecule into cubes small enough to represent each atom’s position about as accurately as thermal motion will permit. So at 0.05 nm resolution, the minimal box of 16*8*3 nm divided in (0.05nm)^3 cubes would be about 3 million cubes. Since 2^22 = 3M, positioning merits 22 bits per atom (for X,Y,Z coordinates), plus 8 bits to define the atom type, i.e. C,N,O,P,S). So 30 bits * 1652 non-hydrogen atoms = 5E4 bits (max). Alternatively, assuming that tRNA folds spontaneously (aided by previously measured molecules, e.g. water, ions, chaperones, etc.) then the 3D structure of 4 (or so) bases and one phosphate-ribose unit would require about 600 bits plus 200 bits for the sequence (76 bases long) or about 1E3 bits total (min). There are intermediate cases where the spatial information bits specify the adjacent atoms, but one needs to be careful about errors propagating as your get further from the starting point of the coordinates.

Imagine that we are trying to communicate with a distant planet on how to make a copy of the simplest cell that we have on earth. We might start with a description of the individual molecules (as described above) and then specify either precisely or roughly where to place these as quasi-rigid bodies initially. To specify the 3D structure of the 500 nm diameter (Mycoplasma) cell (1e8 nm3) with 600 molecular types (each on average the size of the above example). The 1E8 nm3 cell divided by 4E2 nm3 blocks per macromolecule means 3E5 macromolecules. Each of these might need to be positioned with precision similar to the atoms in the tRNA example above 2^40 = 1E12 tiny cubes (plus a similar number of bits for three precise rotations). So 3E5 molecules * 80 bits = 24E6 bits plus 5E4 bits for each of the 600 molecular types = 30E6 bits, hence 54E6 bits total (max). (This is an improvement over the 1652*3E5*80=4E10 bits if we don’t exploit the fact that the molecules are semi-rigid modules). As a lower estimate, if the entire cell could self assemble, then the number of bits might be closer to 2000 bits for the 3D structure of all major monomers + (200 bits for each sequence + 20 bits to specify quantities of each)* 600 = 1E5 bits total (min).

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