Traveler J - "Catalyst (Find Him)" [02/08/2007]

Luminous · Post by **Luminous** » Wed Feb 21, 2007 12:49 pm

Thanks for finding the TinyUrl. You did a great job. I don't know much about genetics either. TOSG amazes me the way he decipers that stuff.

theresascraps wrote:Do you think the chalkboard letters might spell out Cassie?

OMG that's my laugh for the day. I seriously doubt it, but that would be so funny. Maybe its an anagram? But Hmmmm - Maybe Cassie is the girl in Walters first video clip? No let's not go there . . .

About the photos: I went another direction with my thoughts on the picture of the baby. Maybe this child or its parents were subjected to exposure to this toxic gene that Traveler J has referred to.

Maybe this baby was actually created in a test tube, and the bent leg bone is a birth defect caused by genetic engineering?

McPackage · Post by **McPackage** » Wed Feb 21, 2007 12:57 pm

There are words below the photographs in the video, but I think they're way too small to decypher.

Luminous · Post by **Luminous** » Wed Feb 21, 2007 7:14 pm

McPackage wrote:There are words below the photographs in the video, but I think they're way too small to decypher.

I think you are right about that, but I'd like to take a look anyway. Hopefully someone can download the video and post an image capture.

Does anyone besides me think its strange that the baby appears to be floating in mid air?

Luminous · Post by **Luminous** » Wed Feb 21, 2007 7:22 pm

TOSG wrote:Okay, here's my explanation. I wish that I had some brilliant, razor-like solution, but I'm afraid that I just used logic and persistence, with a few guiding principles.

1) Looking at a BLAST (http://130.14.29.110/BLAST/ ; look at "nblast") alignment of the sequence, I saw that there were three large regions of human DNA, and two regions of DNA sequence that did not match with any known DNA source.

2) So, I hypothesized, as before, that the unmatched DNA was likely where the message was encoded (as Walter could have free reign to encode any message he liked there, rather than being constrained to a given sequence of human DNA).

3) Thus, I manually removed most of the regions that had homology with the human DNA, so I could focus on the (in my estimation) important part of the sequence.

4) So, I made a restriction map of this sequence (on the NEBCutter 2.0 program), showing all the restriction enzymes that cut the sequence.

5) I noticed that BamHI was a double-cutter of this sequence (BamHI is a commonly used enzyme, so that tipped me off), and removed the rest of two of the human DNA regions. So, I cut the DNA with that.

6) I then looked at this fragment in NEBCutter, again.

7) Given the clue that TaqI might be used (see my previous post), I searched for that, and found that it cut three times.

I counted up that Walter had given instructions for decoding 61 letters, so I looked for a DNA fragment that was 61*3 = 183 bases long.

9) Awesome! I found that two of the TaqI cut sites combined to leave behind a 183-base pair sequence!

10) I put this sequence into a protein translator, and then grinded away at decoding the letters, according to the same principles as last time.

So, there you have it! Probably not the most elegant way to do it, but it worked, and pretty fast.

For the curious, the DNA sequence is: cgacatatgagcatggcgaccagcaccttcagtgcgcagtgtggcccggagcatcattacctggctgaa
cattcttctatttttaatggcgtcttcagccagcagcttaaaaacaaccttatctactttccctcctcctactttccctcctcccgcttgagggtaggccccatcccccccttt

And the protein sequence is: R H M S M A T S T F S A Q C G P E H H Y L A E H S S I F N G V F S Q Q L K N N L I Y F P S S Y F P S S R L R V G P I P P F

This is like a foreign language to me. I am not up to speed on genetics. Can you suggest some basic reading to get me started?

trainer101 · Post by **trainer101** » Wed Feb 21, 2007 8:40 pm

The level of intelligence of the members of this forum never ceases to amaze me. You guys are awsome!

The J Team - I like it.

TOSG · Post by **TOSG** » Wed Feb 21, 2007 9:05 pm

Luminous wrote:
This is like a foreign language to me. I am not up to speed on genetics. Can you suggest some basic reading to get me started?

Hmm...that's a tough one. I'm a biochemistry major (and do this kind of thing in the lab almost every day...well, cloning, not solving cool puzzles, unfortunately), so I've been exposed to most of this in a classroom setting. Textbooks are a good resource, but I can imagine that might be a little rough.

Wikipedia might be your best bet.

You're also welcome to PM me if you have questions about anything in particular.

Luminous · Post by **Luminous** » Wed Feb 21, 2007 10:21 pm

Next Steps:
Find Walter's true identity.
WalterDW tells us in his telegram ( http://tinyurl.com/33R59P )
that our next step is to uncover his true identity. In order to do this, he says we will have to "shift our perspective on the sequence that got us here". Most likely, the DNA sequence TOSG decoded:

cgacatatgagcatggcgaccagcaccttcagtgcgcagtgtggcccggagcatcattacctggctgaa
cattcttctatttttaatggcgtcttcagccagcagcttaaaaacaaccttatctactttccctcctcctactttccctcctcccgcttgagggtaggccccatcccccccttt

which lead us to the tinyurl above.

I don't know much about these things, but does this mean we now need to look at the RNA sequence? If so, how do we do this?

We have also been given other clues that need to be analyzed - the letters that are stamped on the telegram,

wnhwyry
aaanay
aagwehjjh
nauaj

and possibly the cutoff numbers at the top of the telegram
(looks like 11226 or 11228)

Then there are some strange markings hidden in frames within the "a proper introduction" video http://youtube.com/watch?v=SrU0Im9LjNY

theresascraps · Post by **theresascraps** » Wed Feb 21, 2007 10:30 pm

Well hmmm......I need to figure out how to get still images of those frames. i want to find the next piece of the puzzle....

Theresa

TOSG · Post by **TOSG** » Wed Feb 21, 2007 10:57 pm

Some ideas about the latest puzzle:

Walter tells us to shift our perspective on the sequence that got us here. As you may know, DNA can be translated into protein in a number of ways: the sequence can be read in either direction (actually, that's kind of an oversimplification, but for these purposes, it's valid), and from three different "frames." Since three-letter codons dictate which amino acid gets incorporated, by starting at position one, two, or three of a sequence (or any multiple of three thereafter), you will specify very different three-letter codons as you read across.

A good program for converting raw DNA sequence into variously-framed protein sequences is here: http://www.expasy.ch/tools/dna.html . Decode the one-letter amino acid abbreviations here: http://www.ncbi.nlm.nih.gov/Class/MLACo ... tions.html .

The "STOP" codes in WD's "telegram" might be significant. They may correspond in some manner to stop codons in the protein sequence.

I tried a few things and came up dry. I'll give it some thought later, but I encourage you guys to try out some of this stuff in the mean time.

theresascraps · Post by **theresascraps** » Wed Feb 21, 2007 11:00 pm

Oh I will try it out, but I have an English degree, give me an anagram anytime and I can go to town. Gene sequencing....not so much.... you are the man TOSG (or lady)....You rock!!!

Theresa

Luminous · Post by **Luminous** » Thu Feb 22, 2007 12:27 am

I don't know if this helps any, but since TOSG mentioned the STOP's in the telegram might mean something, so I decided to count the words and letters in between the stops:

MY NEW ACQUAINTANCES [3 words, 18 letters] no stop
I FEAR THAT I HAVE NO CHOICE BUT TO TRUST YOU [11 words, 34 letters] stop
IT LOOKS LIKE YOU SOMEHOW MANAGED TO PROPERLY CUT THE DNA [11 words, 47 letters] stop
I AM SURPRISED [3 words, 12 letters] stop
THE FIRST CUT MAY BE THE DEEPEST, BUT THE SECOND ENZYME WAS MORE SIGNIFICANT [14 words, 62 letters] stop
I SUPPOSE THAT IT IS TIME THAT I LET YOU KNOW MY FULL IDENTITY [14 words, 49 letters] stop
TO FIND IT YOU WILL HAVE TO SHIFT YOUR PERSPECTIVE ON THE SEQUENCE THAT GOT YOU HERE [17 words, 68 letters stop]

What I noticed was the first line is 3 words (no stop after that but it seems like a break, so I counted it as one.)
The first sentence is 11 words
The second sentence is 11 words
The third sentence is 3 words
The fourth sentence is 14 words (3 + 11)
The fifth sentence is also 14 words (3 + 11)
The last line is 17 words (3 + 3 + 11)

There seems to be a pattern of 11's and 3's. This caught my attention because the note Daniel found in the "Jonas Sucks" video has 11 x's and 3 y's on it. 11's and 3's seem to be trendy. Something else I noticed although I'm not sure it matters - the "Shift in perspective" Walter speaks of establishes a parallax - the name of the new OpAphid arc.

janesalteredstates · Post by **janesalteredstates** » Thu Feb 22, 2007 5:22 am

Ok, here are the screen shots of the three scratches at the end of "A Proper Introduction."

janesalteredstates · Post by **janesalteredstates** » Thu Feb 22, 2007 5:30 am

They look like symbols that have been partially erased... on a chalkboard?

Also, it is a sequence. Obviously, hehe.

And, I am with whoever feels they are reading a foreign language. I can decipher codes as long as I have the key.

Incidentally, I am a History major minoring in Sociology, concentration is on Latin America. So... yeah. I'm a big help.

(er... I mean, one of my personalities is... oh forget it.)

theresascraps · Post by **theresascraps** » Thu Feb 22, 2007 11:27 am

I think we need to see why 3 and 11 are important numbers. that really seems to tie this all together. Something about those numbers and what they mean genetically.

Theresa

autumneternal · Post by **autumneternal** » Thu Feb 22, 2007 12:51 pm

janesalteredstates wrote:Ok, here are the screen shots of the three scratches at the end of "A Proper Introduction."

I've just been watching you guys on the J Team do your thing, but I had to point out, (and you may already know), but the 'scratches' from the above screenshots are sideways stencils of letters. The 'S' is obvious. The other two letters are 'A'.