Mark Dörr

Center for Fundamental Living Technology
Department of Physics and Chemistry
University of Southern Denmark
Campusvej 55
5230 Odense M
Denmark

 

FAX: +45 6550 4470
PHONE: +45 6550 2559 or +45 6550 4321
Email: mark ismeralda.org or markd ifk.sdu.dk
Web: personal homepage

Research Interests

  • Complex chemical networks
  • pattern forming reactios
  • oszillating reactions
  • DNA/RNA/PNA/XNA replication
  • hylozoism

Curriculum vitae - or questions - of Mark Dörr

My curriculum vitae is not a series of numbers and dates, it is solely question driven. If You are interested in these questions, please take Your time with reading. I started to ask fundamental scientific questions during my first years at the gymnasium and there it became obvious to study chemistry, biology and physics. In 1990 I began my studies at the University of Mainz, starting with chemistry (Vordiplom) and biology (Vordiplom), but also listening to lectures in physics and mathematics.

Question: What do we know about “biogenisis” - the origin of life ?

In October 1995 I started my first scientific project in the working group of Dr. Andreas Schwienhorst, Institut für Molekulare Biotechnologie (IMB), Jena, Germany. The topic was a site-directed mutagenesis of a group I intron ribozyme – one type of the well known "self-splicing RNA introns", discovered by Thomas R. Cech (Nobel prize 1989 for this discovery)1 to get some deeper insight into the catalytic core of the ribozyme. Basic molecular biological operations, like PCR, DNA/RNA purification, and site-directed mutagenesis were used. Dr. Andreas Schwienhorst was a member of Prof. Manfred Eigen's group (Göttingen) and he brought some of Manfred Eigens spirit to his own young group. In a very intense time, I learned to know some of the at that time state of the art artificial evolutionary systems. The discussions in his young and exciting group lead to a further and deeper studies of the ideas related to “theories concerning the origin of life and complex (chemical) systems/networks”.

Question: How do we develop methods and probes for studying (bio-)molecules ?

In 1997, during a research project in the laboratory of Prof. Charles Glabe, Department of Biochemistry at the University of California, Irvine, I used their semi-automated technique to do large scale peptide synthesis of fluorine labelled peptides. The sequences of these peptides were derived from the membrane protein bindin – a protein responsible for the fusion of sperm and egg. Returning to Jena, Germany, we used these peptides in the working group of Dr. Anne Ulrich, Institut für Molekularbiologie, Jena, to study the orientation of the peptides in ordered lipid layers, using solid state magic angle spinning NMR. The results of this work has been published in my diploma thesis, entitled “Darstellung und Charakterisierung Fluor-markierter Peptide als biologische Modellsubstanzen für die NMR-Spektroskopie”.

Question: What are possible scenarios of prebiotic chemistry ?

With the start of my PhD thesis in 1999 I joined the nitrogen fixation project in the working group of Prof. Wolfgang Weigand, Institut für Analytische und Anorganische Chemie, Jena. Inspired by ideas of Günter Wächterershäuser's “iron sulfide world” Prof. Weigand hypothesised about the possibility of iron sulfide as an primordial catalyst in nitrogen fixation reactions on the early earth. In his group I helped to develop the nitrogen fixation apparatus, the process automation software and the isotope trace analysis of the resulting ammonia. With this apparatus, molecular nitrogen was reduced to ammonia on an iron sulfide surface under probable primordial conditions (aqueous solution, 80°C, oxygen free atmosphere, atmospheric pressure). Isotope ratio mass spectrometry (IRMS) was applied for the analysis of 15N-labelled ammonia. To increase the reactivity of iron sulfide, I developed iron sulfide nanoparticles via inverse micelles technique. These nanoparticles were characterized by scanning electron microscopy (SEM), by transmission electron microscopy (TEM), and by energy dispersive X-ray analysis (EDX). The greater part of this research was embedded in the “Sonderforschungsberich (SFB) 436” of the “Deutsche Forschungsgemeinschaft (DFG). The results of this work are published in my PhD thesis, entitled “Aktivierung von Stickstoff an Eisensulfidoberflächen – ein präbiotisches Nitrogenase-Modell?”3 These experiments attracted worldwide scientific attention and several journals4 as well as television and radio broadcasting stations gave an account of the results; the work was also awarded by the “Thüringer Forschungspreis 2003” (Thuringian basic-research price, 2003). In the last stage of this project, I developed immobilized iron sulfide particles on an Al2O3 and SiO2 support.

Question: Are peptide nucleic acids (PNAs) a good candidate for an early genetic code ? How did the early genetic code look alike and how was it possible to make a simple genotype-phenotype coupling ?

In March 2005 my family and I moved to Copenhagen to start a post-doctoral position as a (bio-)chemist in Prof. Peter Egil Nielsen's laboratory at the Panum Institute, University of Copenhagen (“Institut for Cellulær og Molekylær Medicin”). The aim of the still ongoing project is a ribosome-free, PNA based translation system for protocells (including the synthesis of modified PNA's and peptides). The project is funded by a grant of the European Community within the SynthCells Project (a FP6-2005-NEST-PATH (SYNTHETIC BIOLOGY) STREP project, Framework Programme 6 (FP6) of the European Union, No.: 043359) . Additionally, together with my colleagues Dr. Goran Goranovic and Dr. Anjana Sen I worked on a PNA-lipid project, investigating the distribution of modified PNAs in a lipid-water phase; and a PNA-DNA replication system project for microfluidic evolution experiments (these two projects are related to the Programmable Artificial Cell Evolution-(PACE) Project of the EU-FP6).

Questions: Is it possible to build a protocell with our current knowledge ?

With this question I applied for a second post-doctoral position at the “Center for fundamental living technologies” (FlinT) at the University of Southern Denmark, Odense in the working group of Prof. Steen Rasmussen. In this group a protocell model was developed (s. www.sdu.dk/flint). I am responsible for the synthesis of some of the protocell building blocks and RNA ligation reactions.

Current question:

What is the simplest chemical network that exhibits evolovability (“Darwinian like” evolution) ?

What classes or arrangements of molecules are able to build, based on their own history new “emergent” properties (i.e. properties that cannot explained by the properties of sum of their components) ? Is it a common property of matter that it achieves “emergent properties” if its arrangement reaches a certain threshold ?

List of Publications 2002-2011

[1] Weigand, W., Dörr M., Robl C., Kreisel, G., Grunert, R., Käßbohrer J., Brand W., Werner R., Popp J., Tarcea, N.;Formation of Ammonia from Dinitrogen under Primordial Conditions. Proceedings of the Second European Workshop on Exo/Astrobiology, Graz, 209, (2002)

[2] Dörr, M.; Kässbohrer, J.; Grunert, R.; Kreisel, G.; Brand, W.A.; Werner R.A.; Geilmann, H.; Apfel, C.; Robl, C. & Weigand, W.; A possible prebiotic formation of ammonia from dinitrogen on iron sulfide surfaces. Angewandte Chemie, Int. Ed. Engl., (2003), 42, 1540-1543. 

[3] Dörr, M.; Kreisel; G., Völksch; G. & Weigand, W.; Herstellung von Eisen(II)-sulfid-Nano- und Mikropartikeln in inversen Micellen.1 ; Zeitschrift für Anorganische und Allgemeine Chemie, (2003), 629, 1113-1115.

[4] Kreisel, G.; Wolf, C.; Weigand, W. & Dörr, M.; Ammoniak aus Stickstoff unter präbiotischen Bedingungen.2; Chemie in unserer Zeit, (2003), 37, 306-313. 

[5] Dörr M.; Alpermann, T. & Weigand W. ; Question 1: the FeS/H2S system as a possible primordial source of redox energy ; Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life (2007), 37(4-5), 329-33.

[6] Dörr, M.; Deuterium; In: Encyclopedia of Astrobiology. / ed. Muriel Gargaud. Heidelberg : Springer Verlag, 2010. [accepted] (plus seven smaller contributions)

[7] Maurer, S.E.; DeClue, M.; Albertsen, A.N.; Dörr, M.; Kuiper, D.S.; Ziock, H.; Rasmussen,S., Boncella, J. M. and Monnard, P.-A.; Interactions between catalyst and amphiphilic structures and their implications for a protocell model; ChemPhysChem ; 2010 [accepted]

[8] Fellermann, H.; Dörr, M.; Hanczyc, M.; Maurer, S.E.; Merkle, D. ; Monnard, P.A.; Støy, K.; Rasmussen, S. [Editors]; Proceedings of the Twelfth International Conference on the Simulation and Synthesis of Living Systems; August 2010

[9] Dörr M.; Monnard, P.-A.; Non-enzymatic, template-directed nucleic acid replication: Relevance to the origins of information transfer and to novel synthetic methodologies; Current Organic Synthesis; Invited Review [submitted]

[10] Wieczorek R.; Dörr, M.; Luisi, P.-L.; Monnard, P.-A.; Dipeptide catalysed polymerisation of RNA. [working title in preparation]

[11] Dörr, M.; Löffler, P.M.G.; Monnard, P.-A.; RNA monomer polymerisation versus oligomer condensation –Strategies to reach catalytically active RNA lengths in the eutectic ice phase. [working title, in preparation]

The publication gap between 2008 and 2010 had personal and private reasons.

Oral contributions – 2001-2011

[1] Dörr, M. „Aktivierung kleiner Moleküle an Übergangsmetall-Schwefel-Verbindungen“.3

Talk at “DFG-SFB 436 Meeting”; Thalbürgel, Germany; 27.4.2001

[2] Dörr, M., Wolf, C. „Reduktion an Metallsulfiden“.4

Talk at “DFG-SFB 436 Meeting”; Thalbürgel, Germany; 26.4.2002

[3] Dörr, M. „Eine mögliche präbiotische Bildung von Ammoniak aus molekularem Stickstoff auf Eisensulfidoberflächen“.5 Talk at the first “Mitteldeutschen Anorganiker Nachwuchs Symposium (MANS)”; Chemnitz, Germany; 22.9.2003

[4] Dörr, M. „Aktivierung von Stickstoff an Eisensulfidoberflächen – ein präbiotisches Nitrogenase – Modell“6 Guest lecture at the “Institut für Anorganische Chemie Wien”, Vienna, Austria; 3.12.2004

[5] Dörr, M., Löffler, P.M.G., Monnard P.-A.;

“Possible role of ice in the synthesis of polymeric compounds”; invited talk at the Committee On Space Research (COSPAR) 2010 in Bremen, Germany; 18.7.-25.7.2010

[6] Dörr, M., Löffler, P.M.G., Monnard P.-A.; “Possible role of ice in the synthesis of polymeric RNA”;

accepted talk at the 12th International Conference on the Synthesis and Simulation of Living Systems (AlifeXII) 2010, Odense, Denmark; 9.8.-23.8.2010

Posters

[1] Wolf, C.; Kreisel, G.; Dörr, M.; Weigand W.; „Primordial Formation of Ammonia from Dinitrogen on Iron Sulfide Surface”. Poster at the Conference „Fe/S proteins – Biogenesis, Structure, Function, Pathogenesis and Evolution“, Philipps-Universität Marburg, Germany; September, 11th -14th 2002

[2] Weigand W.; Dörr M.; Kreisel G.; Wolf C. “Primordial Formation of Ammonia from Dinitrogen on Iron Sulfide Surface”. Poster at the Second European Workshop on Exo/Astrobiology, Graz, Austria; September, 16th -19th 2002

[3] Weigand W.; Dörr M.; Kreisel B.; Wolf C. “Primordial Formation of Ammonia from Dinitrogen on Iron Sulfide Surface”. Poster at 12. Vortragstagung der GDCh-FG Wöhler-Vereinigung für Anorganische Chemie, Marburg, Germany; September, 15th-17th 2004

[4] Dörr, Mark ; Maurer, S. E. ; Monnard, P.-A.'“Polymerisation of activated RNA in eutectic ice phases”. Poster at conference: Emergence in Chemical Systems, No. 2, Anchorage, United States, June 22th – June, 26th 2009.

[5] Dörr, Mark ; Löffler, P.M.G ; Monnard, P.-A.“Ligation of oligomers in the eutectic ice phase”. Poster at conference: ORIGINS 2011, Montpellier, France, July 1st – July 7th 2011.

FootnotesThomas R. Cech's discovery supported the theory of the Leslie Orgels "RNA-world" - RNA might have been the ancestor molecule of DNA.
"Synthesis and Characterization of Fluorine-marked Peptides as Biological Model Compouds for NMR Spectroscopy"
"Activation of Nitrogen on Iron Sulfide Surfaces - a prebiotic Model of Nitrogenase?"
Science (2003), 300, 215; ChemEng News (April 7, 2003) 11
 

1“Synthesis of Iron(II)-sulfid-Nano- and Microparticles in reverse Micelles.”
2“Ammonia from Nitrogen under Prebiotic Conditions”
3“Activation of small molecules on transition-metal sulphur compounds.”
4“Reduction on metal sulfides”
5“A possible prebiotic formation of ammonia from molecular nitrogen on iron sulfide surfaces.”
6“Activation of nitrogen on iron sulfide surfaces – a prebiotic nitrogenase model.”