Thunderf00t's Research

Uploaded by C0nc0rdance on 04.11.2011

Now that Thunderf00t aka Phil Mason has made the decision to reveal his personal information,
we can finally talk about his research.
Some have characterized him as a glorified technician because he's not listed under faculty,
but rather under staff, on the website of the university by which he was employed. In
fact, nothing could be further from the truth. A professor is usually someone who runs a
lab but doesn't usually have time to generate data or conduct research. A professor, or
principal investigator, spends most of their time writing grant proposals, papers, and
in some cases teaching and in adminstrative roles in their own research and within the
What Thunderf00t is or was is much closer to a research fellow, someone employed to
do nothing but research. Staff, not faculty, but clearly an independent and productive
researcher. Someone who has had a positive impact on human scientific knowledge.
Here are his papers in PubMed, so far as I can tell, and I have to warn you that there
are at least two people with nearly the same name doing very similar work, so I'm having
to make some guesses. If I've gotten this right, he has 34 publications, starting in
2003. He's first author on 20 of them, which means that he contributed to the work more
than any of the other authors. The pubs are generally in physical chemistry journals of
the second or third tier. Meaning they're the kind of journals for routine but important
work. He does have one first author in the Proceedings of the National Academy of Science,
which is a definite prestige journal. To just summarize his publication record, it's tenure
level research for a very specific field of physical chemistry. He's been consistently
productive in high quality publications for over 9 years. He could absolutely take this
CV and be a serious contender for an associate professor spot at a top university.
His research focuses on molecular modeling from neutron scatter data, which I'll try
to explain as best I understand it. This is way outside my own field so I may be completely
Neutron scattering is a way of studying the physical structure of matter. You take a sample,
usually a powder, and place it near a nuclear reactor or source of energetic neutrons. Neutrons
are neutral but massive, so when they go shooting through the sample, they'll sometimes collide
with the nuclei of atoms in the substance and be deflected from straight-through lines.
The same process can be done with X-rays, and that's how the structure of DNA was finally
In Dr. Mason's (and yes, he is a PhD, so Dr. Mason is the respectful name) case, he is
often studying the way that a dissolved substance, like fluoride, interacts with the solution
that it's in. Where are the solutes in relation to the solvent? One area he seems to come
back to often is the nature of water and guanidinium interaction. Guanidinium is important in my
field of molecular biology, because it's what is known as a chaotropic salt. We use it to
mess up the structure of proteins either to study them or just to make them fall out of
solution. Dr. Mason is helping to explain how they perform that useful function.
By reading out the deflection of neutrons, he has observed the stacking or arrangement
of these solute molecules with water or other solvent. He then creates a simulation of the
laws that govern their behavior, and tests the experimental observations against the
simulation. If they match, then we'll know how these things behave in solution.
Are there applications for this work? Absolutely. Think about the oil spill in the Gulf of Mexico.
What kind of modification could we make to the petroleum to encourage it to either form
little globules or to break up that surface tension? In the case of drugs or industrial
chemicals, can we optimize the chemical composition of a solvent or buffer so that the water-loving
structures remain stable over time, increasing shelf life or availability for reaction.
It is a very abstract field of research, studying the structure of solutions of salts in water,
but it's a peek into the fundamental nature of matter and solvation. That's solvation,
by the way... SOOOOLvation, the nature of solutions... not to be confused with the religious
Not everyone likes Thunderf00t. I understand, he's a very bold character, he doesn't pull
any punches. Ultimately, though, he's just a guy with some strongly held positions. People
like to watch his videos, and he communicates science very well, and that's given him a
certain celebrity. With that celebrity will naturally come criticism and personal attacks.
The one thing that you can't say about Thunderf00t, no matter how much you dislike him is that
his work is unimportant or unimpressive. His contributions to scientific knowledge are
respect-worthy, even if you don't like his work here on YouTube.
Thanks for watching.
1: Mason PE, Neilson GW, Price D, Saboungi ML, Brady JW. Simulation and Neutron
Diffraction Studies of Small Biomolecules in Water. Food Biophys. 2011
Jun;6(2):210-216. PubMed PMID: 21921996; PubMed Central PMCID: PMC3171504.
2: Tavagnacco L, Schnupf U, Mason PE, Saboungi ML, Cesa`ro A, Brady JW. Molecular
Dynamics Simulation Studies of Caffeine Aggregation in Aqueous Solution. J Phys
Chem B. 2011 Sep 22;115(37):10957-10966. Epub 2011 Aug 30. PubMed PMID: 21812485;
PubMed Central PMCID: PMC3189405.
3: Mason PE, Lerbret A, Saboungi ML, Neilson GW, Dempsey CE, Brady JW. Glucose
interactions with a model peptide. Proteins. 2011 Jul;79(7):2224-32. doi:
10.1002/prot.23047. Epub 2011 May 13. PubMed PMID: 21574187; PubMed Central
PMCID: PMC3171503.
4: Tavagnacco L, Mason PE, Schnupf U, Pitici F, Zhong L, Himmel ME, Crowley M,
Cesàro A, Brady JW. Sugar-binding sites on the surface of the
carbohydrate-binding module of CBH I from Trichoderma reesei. Carbohydr Res. 2011
May 1;346(6):839-46. Epub 2011 Jan 23. PubMed PMID: 21377658.
5: Dempsey CE, Mason PE, Jungwirth P. Complex ion effects on polypeptide
conformational stability: chloride and sulfate salts of guanidinium and
tetrapropylammonium. J Am Chem Soc. 2011 May 18;133(19):7300-3. Epub 2011 Apr 26.
PubMed PMID: 21520945.
6: Mason PE. Molecular dynamics study on the microscopic details of the
evaporation of water. J Phys Chem A. 2011 Jun 16;115(23):6054-8. Epub 2011 Feb
15. PubMed PMID: 21322537.
7: Lerbret A, Lelong G, Mason PE, Saboungi ML, Brady JW. Molecular dynamics and
neutron scattering study of glucose solutions confined in MCM-41. J Phys Chem B.
2011 Feb 10;115(5):910-8. Epub 2011 Jan 10. PubMed PMID: 21214282; PubMed Central
PMCID: PMC3033472.
8: Mason PE, Heyda J, Fischer HE, Jungwirth P. Specific interactions of ammonium
functionalities in amino acids with aqueous fluoride and iodide. J Phys Chem B.
2010 Nov 4;114(43):13853-60. PubMed PMID: 20939557.
9: Mason PE, Neilson GW, Dempsey CE, Price DL, Saboungi ML, Brady JW. Observation
of pyridine aggregation in aqueous solution using neutron scattering experiments
and MD simulations. J Phys Chem B. 2010 Apr 29;114(16):5412-9. PubMed PMID:
20369858; PubMed Central PMCID: PMC3168782.
10: Heyda J, Mason PE, Jungwirth P. Attractive interactions between side chains
of histidine-histidine and histidine-arginine-based cationic dipeptides in water.
J Phys Chem B. 2010 Jul 8;114(26):8744-9. PubMed PMID: 20540588.
11: Mason PE, Dempsey CE, Neilson GW, Kline SR, Brady JW. Preferential
interactions of guanidinum ions with aromatic groups over aliphatic groups. J Am
Chem Soc. 2009 Nov 25;131(46):16689-96. PubMed PMID: 19874022; PubMed Central
PMCID: PMC2784182.
12: Lerbret A, Mason PE, Venable RM, Cesàro A, Saboungi ML, Pastor RW, Brady JW.
Molecular dynamics studies of the conformation of sorbitol. Carbohydr Res. 2009
Nov 2;344(16):2229-35. Epub 2009 Aug 8. PubMed PMID: 19744646; PubMed Central
PMCID: PMC2779705.
13: Mason PE, Dempsey CE, Vrbka L, Heyda J, Brady JW, Jungwirth P. Specificity of
ion-protein interactions: complementary and competitive effects of
tetrapropylammonium, guanidinium, sulfate, and chloride ions. J Phys Chem B. 2009
Mar 12;113(10):3227-34. PubMed PMID: 19708168.
14: Vondrásek J, Mason PE, Heyda J, Collins KD, Jungwirth P. The molecular origin
of like-charge arginine-arginine pairing in water. J Phys Chem B. 2009 Jul
9;113(27):9041-5. PubMed PMID: 19354258.
15: Mason PE, Schildt DC, Strein TG. In-capillary determination of creatinine
with electrophoretically mediated microanalysis: characterization of the effects
of reagent zone and buffer conditions. J Chromatogr A. 2009 Jan 2;1216(1):154-8.
Epub 2008 Nov 19. PubMed PMID: 19046749; PubMed Central PMCID: PMC2657084.
16: Mason PE, Ansell S, Neilson GW, Brady JW. Be2+ hydration in concentrated
aqueous solutions of BeCl2. J Phys Chem B. 2008 Feb 21;112(7):1935-9. Epub 2008
Jan 25. PubMed PMID: 18217749.
17: Dempsey CE, Mason PE, Brady JW, Neilson GW. The reversal by sulfate of the
denaturant activity of guanidinium. J Am Chem Soc. 2007 Dec 26;129(51):15895-902.
Epub 2007 Dec 4. PubMed PMID: 18052164.
18: Mason PE, Brady JW. "Tetrahedrality" and the relationship between collective
structure and radial distribution functions in liquid water. J Phys Chem B. 2007
May 24;111(20):5669-79. Epub 2007 May 1. PubMed PMID: 17469865.
19: Mason PE, Brady JW, Neilson GW, Dempsey CE. The interaction of guanidinium
ions with a model peptide. Biophys J. 2007 Jul 1;93(1):L04-6. Epub 2007 Apr 20.
PubMed PMID: 17449674; PubMed Central PMCID: PMC1914420.
20: Mason PE, Neilson GW, Enderby JE, Saboungi ML, Cuello G, Brady JW. Neutron
diffraction and simulation studies of the exocyclic hydroxymethyl conformation of
glucose. J Chem Phys. 2006 Dec 14;125(22):224505. PubMed PMID: 17176147.
21: Mason PE, Neilson GW, Dempsey CE, Brady JW. Neutron diffraction and
simulation studies of CsNO3 and Cs2CO3 solutions. J Am Chem Soc. 2006 Nov
29;128(47):15136-44. PubMed PMID: 17117865.
22: Mason PE, Ansell S, Neilson GW. Neutron diffraction studies of electrolytes
in null water: a direct determination of the first hydration zone of ions. J Phys
Condens Matter. 2006 Sep 20;18(37):8437-47. Epub 2006 Aug 30. PubMed PMID:
23: Mason PE, Neilson GW, Enderby JE, Saboungi ML, Brady JW. Structure of aqueous
glucose solutions as determined by neutron diffraction with isotopic substitution
experiments and molecular dynamics calculations. J Phys Chem B. 2005 Jul
14;109(27):13104-11. PubMed PMID: 16852630.
24: Mason PE, Neilson GW, Kline SR, Dempsey CE, Brady JW. Nanometer-scale ion
aggregates in aqueous electrolyte solutions: guanidinium carbonate. J Phys Chem
B. 2006 Jul 13;110(27):13477-83. PubMed PMID: 16821873.
25: Ansell S, Barnes AC, Mason PE, Neilson GW, Ramos S. X-ray and neutron
scattering studies of the hydration structure of alkali ions in concentrated
aqueous solutions. Biophys Chem. 2006 Dec 1;124(3):171-9. Epub 2006 May 11.
PubMed PMID: 16815625.
26: Dempsey CE, Mason PE. Insight into indole interactions from alkali metal
chloride effects on a tryptophan zipper beta-hairpin peptide. J Am Chem Soc. 2006
Mar 8;128(9):2762-3. PubMed PMID: 16506730.
27: Mason PE, Neilson GW, Enderby JE, Saboungi ML, Brady JW. Determination of a
hydroxyl conformation in aqueous xylose using neutron scattering and molecular
dynamics. J Phys Chem B. 2006 Feb 23;110(7):2981-3. PubMed PMID: 16494297.
28: Mason PE, Dempsey CE, Neilson GW, Brady JW. Nanometer-scale ion aggregates in
aqueous electrolyte solutions: guanidinium sulfate and guanidinium thiocyanate. J
Phys Chem B. 2005 Dec 22;109(50):24185-96. PubMed PMID: 16375411.
29: Matthews JF, Skopec CE, Mason PE, Zuccato P, Torget RW, Sugiyama J, Himmel
ME, Brady JW. Computer simulation studies of microcrystalline cellulose Ibeta.
Carbohydr Res. 2006 Jan 16;341(1):138-52. Epub 2005 Nov 17. PubMed PMID:
30: Salmon PS, Martin RA, Mason PE, Cuello GJ. Topological versus chemical
ordering in network glasses at intermediate and extended length scales. Nature.
2005 May 5;435(7038):75-8. PubMed PMID: 15875017.
31: Huang F, Switek KA, Zakharov LN, Fronczek FR, Slebodnick C, Lam M, Golen JA,
Bryant WS, Mason PE, Rheingold AL, Ashraf-Khorassani M, Gibson HW.
Bis(m-phenylene)-32-crown-10-based cryptands, powerful hosts for paraquat
derivatives. J Org Chem. 2005 Apr 15;70(8):3231-41. PubMed PMID: 15822986.
32: Dempsey CE, Piggot TJ, Mason PE. Dissecting contributions to the denaturant
sensitivities of proteins. Biochemistry. 2005 Jan 18;44(2):775-81. PubMed PMID:
33: Mason PE, Neilson GW, Enderby JE, Saboungi ML, Dempsey CE, MacKerell AD Jr,
Brady JW. The structure of aqueous guanidinium chloride solutions. J Am Chem Soc.
2004 Sep 22;126(37):11462-70. PubMed PMID: 15366892.
34: Mason PE, Neilson GW, Dempsey CE, Barnes AC, Cruickshank JM. The hydration
structure of guanidinium and thiocyanate ions: implications for protein stability
in aqueous solution. Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4557-61. Epub
2003 Apr 8. PubMed PMID: 12684536; PubMed Central PMCID: PMC404697.