The Drunk Under the Streetlight

A policeman came across a drunk on a dark road scrounging around on the ground under a streetlight.

"What are you doing?"
"Looking for my wallet, I lost it in that ditch over there."
"Why are you looking for it here?"
"The lighting is better."

I'd like to go back to a phage display project because it encompasses the fundamental flaw of science as it is conducted in the biology, medical world. Unlike other sciences, we have a low standard. W are wrong most of the time. The unofficial measurement, wrong 90% of the time, did not raise much protest.

Dr. Nicklin is one of the scientists who worked on the GETRAPL project. The paper is titled:

Development of efficient viral vectors selective for vascular smooth muscle cells.

And it's findings are false. Here is why.

Nicklin et. al. performed phage display as instructed by the kit purchased from New England Biolabs and they came up with a list of peptide sequences. It was decided that a peptide of 7 amino acids would bind to and deliver their DNA to a specific cells type. Once the peptide was discovered it could be used to deliver the viral vector to the cell where the vector will then enter the cell and increase gene therapy activity.

Many assumptions have been made but we will focus on one thing, phage display. The following is the list of peptides the turned up when using the phage display kit.

Peptide Frequency Peptide Frequency Peptide Frequency
AAPMQVT 1 KVTTTRV 1 TARQDSI 1
AKPSPFP 1 LAKHPDS 1 TGHHIFY 1
ALQBKPI 1 LERGPYG 1 THLSRTP 1
AMPYAPR 1 LVPPSGT 1 TLSNYSQ 1
ANMSLLT 1 MGPPSTP 1 TNGLRTA 1
ANSKLSP 1 MPPGYPH 1 TPPQSTG 1
APATSIG 1 NALKFSA 1 TPTIHKT 1
APQPWLM 1 NPFYSLR 1 TPVQQVA 1
ASTQQPT 1 QLTMFPS 1 TQEYRSA 1
DLRIAAS 1 QPNNHAH 1 TQMRQPP 1
EGLPANP 1 QQQHPFK 1 TQPPIRT 1
EYHHYNK 2 SAPERFS 1 TSPIPPK 1
EYTHTPY 1 SFGENSI 1 TTPRFIL 1
FPGKQTT 1 SGSPPSV 1 TTTLRPS 1
GETRAPL 5 SLPDPIH 1 TYATDRR 1
GHSHSHS 1 SLRPSID 1 TYSQSMT 1
GPGPNIS 1 SMPKLIN 1 VKPBTGA 1
GPNQVEW 1 SNAQSMR 1 VLPRASY 1
GSTQPPW 1 SNMAQHR 1 VNPVNTH 1
HLHTIGR 1 SPIRHVH 1 VSAQTRQ 1
HPFILKP 1 SPQLPQL 1 WAPPPAG 1
HPPBVSS 1 SQSPFFP 1 WNLQPPQ 1
HSFPHAP 1 SSHGSLS 1 WPNTYRL 1
HVLWTPP 1 SSQYAHL 1 YHPMSSL 1
IRPPSII 1 SWLPHNA 1 YLKPPGP 1
KLVASNP 1 SYMYKPQ 1

The two peptides of interest recur twice (EYY) and five times (GET). Had the New England Biolabs provided a database of sequences from other panning experiments, Nicklin would have known these sequences are contaminants from the NEB library. The observance of these sequences is to be expected. They are an annoyance and not the holy grail of DNA delivery for gene therapy. What we have here is a limited data set, kit science, and a hope that something shows up. The kits cost $300 dollars each and thus they provide the streetlight that can be used to search for the wallet in the ditch.

The peptide sequences that were "discovered" in this project are the proverbial prism in this modern day N-Ray story.

Once you have "something" the leadership can get to work. You now have a solution and the corrective measure that can be organized and managed. Leadership knows how to organize and manage. They hire team leaders and project managers and directors and even a few white lab coat kids to run the assays in the lab. And they are kids. They will take that useless phage contaminant and make the assays tell the predetermined story. The only question they ever had was how far the bars on their charts would be separated.

Management has found a nice comfortable streetlight. But the wallet is over in the ditch, under water behind a patch of thick weeds 3 feet high. It is hidden in a big way. 20 yards away the leadership stands with their hands in their pockets directing low paid grunts to look harder. Failure in this system is a guarantee. In order to not face failure, hope is put in its place. Hope keeps the project lumbering on and costing countless wasted man-hours and plenty of money.

A recent comment on the state of medical research from Roy Mankovitz.

I have a background­, and publicatio­ns, in the field of rocket science, having designed control systems for planetary landers and deep space probes. As most folks know, we have had a phenomenal record of getting it mostly right.

Well, with respect to science, research is research, but when I finally starting poking around in the area of medical research, spending decades reading and analyzing thousands of studies, I was horrified. It seems they get it mostly wrong.

We do and this is one example. I worked in a different part of the world but I did the same project. The NEB libraries were the same, the cell target was different, the peptide sequences were the same (we found EYHHYNK)and we made the same charts. We used the streetlight approach because it was within our understanding (so we thought) and we found what we wanted. We found the same peptides Nicklin did. Our bosses were satisfied for the time being and kept our project aimlessly moving forward. We too eventually gave up and found new jobs.