The Joshua Files - a complete box set: Books 1-5 of the young adult sci-fi adventure series plus techno-thriller prequel

by M. G. Harris

  “Of known length?” ventured Marie-Carmen.

  Jackson grinned. “Exactly. Now, let’s just hope that this one isn’t too long, or your friend’s gonna be mad at me for using up time on her sequencer!”

  ***

  Three hours later, Jackson removed a CD from the DNA sequencer. Now to cross-reference the data against all known gene sequences in the world’s most recently updated data banks. Outside the faculty, Marie-Carmen was waiting in her car. With an air of triumph, Jackson slapped the CD against the window.

  “There’s an open reading frame.”

  “A what, now?”

  Jackson dropped into the passenger seat. “Open reading frame: it’s what we call the part of the gene which the cell machinery would translate into a protein. The rest of the gene is a set of instructions which tell the cell when to make that protein, and how much. Think of it like the introduction and index of a book; it takes up space and has important information, but the real ‘story’ is in the open reading frame. What’s weird,” he continued, “is that I don’t recognize the sequence at all.”

  “Is that so unusual?” she asked, diverting the car to a nearby store selling tortas – large rolls spread with refried bean paste, stuffed with ham, cheese, pickled chilies and salad.

  “When you work with a particular sequence of DNA, or a family of those sequences, you get a feel for it. Like I told you last night: you get to recognize portions. The same stuff pops up again and again all over the genome you know. You’d be surprised. Well, I got nothing from this sequence. It’s like nothing PJ or I work on. But I really need to look for it properly in a gene data bank. Those are updated all the time – if anyone else in the world has published a sequence like this, I’ll find it.”

  “What if they haven’t?”

  “It’s not just the human genome that has been entirely sequenced by now. Lots of other organisms, too. For this to be unpublished, even as a sequence of unknown function, would mean that it was from some bizarre organism. Or else that it was from a very rare gene. A really rare gene might not have been picked up by anyone yet. The human genome project only sequenced a few peoples’ genes. It wasn’t the most representative of samples.”

  “You mean there could be entire genes that only some people would have?” asked Marie-Carmen.

  “It’s unlikely, sure. Most species have the same genes, just different forms of the genes. That’s part of what makes individuals different. So it wouldn’t be entirely out of the question. For example, like I told you, joust, the gene I work on, and PJ’s gene also, are ‘jumping genes’. They didn’t originate in the fruit fly. At some point during evolution, they just appeared in the fruit fly’s DNA.”

  “From where?”

  “Probably a virus. Joust and phoenix are retrotransposons – in their DNA structure they look a bit like some retroviruses, like the kind of virus that causes AIDS. The human genome is riddled with those kinds of mobile genetic elements. They wouldn’t necessarily actually work as genes. And they wouldn’t be in every person.”

  “What do you mean – they wouldn’t ‘work as genes’?”

  Jackson thought for a moment.

  “Imagine a gene as a freight train carriage. It can’t produce a result – deliver its load – without an engine carriage, a driver, the train signals, a whole load of equipment and events which need to happen to make the delivery. If any of those are disrupted; like, for example, if the signal lights are worn out, or the engine isn’t working, then the freight doesn’t get delivered properly, or at all. The freight carriage, engine carriage, driver, can all be there. It’s just that something crucial, one element is missing. That’s how it can be with a gene. Most of what you need to be there could be there, but just the wrong bit missing or altered and . . .”

  “No delivery.”

  Jackson nodded. “Right – the gene doesn’t make a protein. Joust and phoenix look like a lot of ‘jumping genes’ – they look like they mightn’t work. Yet, they do. They make really interesting proteins. Also, not all fruit flies have joust, or maize have phoenix.”

  Marie-Carmen pondered for a second. “Maybe Pedro Juan found a new ‘jumping gene’?”

  “Maybe he did.”

  They sat side-by-side in front of the large flat screen monitor of a computer in the university library. Jackson loaded the CD with the freshly-sequenced DNA, then cut and pasted a section of the DNA sequence code into another browser window.

  “This website has ‘BLAST’,” he explained. “A computer program that will search for your sequence in a huge gene data bank and process the result. I’m only checking for things that match up with the open reading frame; the bit which codes for the amino acids, the protein-y part. In fact a protein this small,” he paused to count up the letters in the sequence; “only fifteen amino acids, is known as a ‘peptide’.”

  “You’re going peptide-hunting?”

  “BLAST will show us all the similar sequences, in all species.”

  They waited for two minutes, Jackson impatiently refreshing the browser window every few seconds.

  After this time, the program returned the result.

  No significant similarities found.

  Jackson sat back, shocked. “Wow.”

  “That just means that no-one’s published it, right? It doesn’t mean they don’t know about it. People could be working on it.”

  Jackson thought for a minute. “You’re right. Maybe instead of publishing, they patented it. That would mean we should be able to find some reference to it in the patent databases.”

  He brought up another browser window, typing in the Web address of a patent search engine. He copied a section of the DNA code from PJ’s molecule and entered it into the search box.

  Again, the search returned no results.

  Jackson was pensive. “You mind if I check my email?” he asked.

  Marie-Carmen shrugged. “Go ahead.”

  Among twenty-five new messages was one dated that day, from PJ.

  “That’s weird,” Jackson said. “This was sent after PJ met me. I don’t think he could have sent it. Maybe his email account has been hacked?”

  “Unless he set up some kind of automatic email,” Marie-Carmen suggested. “You know, like when you use the vacation settings on your email? You can configure it to send an automatic email. Unless you change the settings back.”

  “Can you set it to send a specific email to a specific person?”

  “It’s not difficult.”

  Jackson clicked on the email. “If PJ figured out that someone was onto him, maybe he did set something up to send automatically. He sure-as-hell covered himself.”

  He sensed, suddenly, an intake of breath from Marie-Carmen. Then Jackson saw what had alarmed her.

  A warning icon had appeared in the bottom right hand corner of the screen: “Warning. Someone is trying to trace your IP address.”

  “And now,” murmured Marie-Carmen, “they’ll be onto us. Those searches you did must have tripped someone’s IP tracing system. Your IP address is the address of your machine as it appears on the Internet.”

  “I know what an IP address is,” Jackson said. “But someone can actually trace your computer’s address down from a Web search?”

  “Sure. You performed those searches on the Web, openly. A Web search is a query, a string of characters that is sent out as a request across the Internet. Whatever you search for will form part of that query. That search bounces the Internet; a message, waiting for an answer from the search engine.

  “If someone else put a program out in the Internet, sniffing out searches with specific characters in the search string, they could easily trace the origin of that search; the IP address of this computer. They could quite easily trace that search down to this library.”

  Thoughtfully she continued, “I’m guessing the same thing happened to Pedro Juan. It led them to him. Jackson, we have to go. If they’re in Mexico City, it won’t take them long to get here.”


  With that, Marie-Carmen picked up her bag, removed Jackson’s CD and methodically deleted all references to the work they had done that day.

  Jackson sat back, saying nothing. He was beginning to understand why PJ had given him just one phone number as an escape route.

  On the way back to Marie-Carmen’s apartment, they stopped at a shopping mall, where Jackson picked up a cheap laptop to replace the one he’d left in his suitcase in the rental car he’d been forced to abandon. Afterwards, Marie-Carmen insisted he buy some decent clothes. To her amusement, Jackson had taken less than eight minutes to pick out three polo shirts, jeans, chinos, black jeans and a pair of dark brown, leather brogues.

  “What?” he said finally, unable to bear her obvious and barely contained mirth.

  “It’s just – you are so conservative! Look at you; I bet that’s all you ever wear.”

  “For your information, it’s a successful combination, and it doesn’t take any planning. Low overhead, see?”

  Marie-Carmen continued to smile, a hint of flirtation playing about her lips. “I didn’t mean to offend your ego. You should let your girlfriend take you shopping sometime.”

  “If I had a girlfriend, I’d just let her pick up whatever she wanted to see me in.”

  “And you’d wear it?” she asked, in fascination.

  “If it made her happy, sure. What do I care?”

  “You’d never hear a Mexican guy talk that way.”

  “Why not?”

  “Because clothes send a signal. They are a kind of code. Mexican men like to be in charge of those kind of signals.”

  Jackson stopped in his tracks. “You know what? Maybe you’re onto something.”

  “Meaning what?”

  “The DNA sequence, Marie-Carmen. What if it isn’t meant to be a real, biological sequence, but a code we’re meant to be able to read; a message?”

  Beltran Sequence

  Later in Marie-Carmen’s apartment, they sat together at her computer. Earlier in the day their physical proximity might have been pleasantly distracting. Now however, Jackson was overtaken by the enthusiasm that always gripped him when discussing his work. It was strong enough to displace almost everything else that preoccupied him.

  “DNA is a biological molecule made up of four types of building blocks. We assign each of these a letter: A, C, G, T. A DNA sequence reads as a long string of various combinations of ACGT.”

  “Difficult to convey much meaning with those four letters.”

  “Precisely. But that DNA code is ‘read’ by the machinery of the cell, and translated into a code for making proteins. It takes three letters in the DNA code to code for one amino acid. For example, the DNA triplet codon ‘AAA’ is translated by the cell into an amino acid named ‘lysine’. Proteins are made from around twenty different building blocks; each represented by a single letter code. With twenty letters, you can make a lot of words in English.”

  “Or Spanish. After all, it is Pedro Juan’s code.”

  “We’ll check both.”

  They watched as Jackson opened a Web browser window to a Web site entitled “ExPASy”. He stopped for a second.

  “Wait up. Can the IP tracing whozit get to us here?”

  Marie-Carmen smirked. “The ‘IP tracing whozit’?”

  “Don’t make fun.”

  “Not make fun of you?” she mused. “Then how would I pass the time? But the answer to your question, by the way, is ‘wait and see’. I have a level of control over my own computer that I don’t have over the one at the University. And I’m even more paranoid. Mayan archaeology is pretty competitive.”

  Jackson nodded slowly. “OK then. Here goes.”

  He pasted the DNA sequence into the box under the words ‘DNA Translate tool’ and watched the website return the translation of the DNA into a protein sequence.

  They scrutinized the resulting string of fifteen letters for a few seconds. Jackson clicked the ‘Print’ button. A nearby printer stirred to life.

  “It doesn’t look very promising. You see anything in Spanish?”

  “Nope. Nor English. Maybe it’s an anagram?”

  “Good thinking.” He opened another browser window to Google. “Let’s throw this at an anagram decoder.” Jackson pasted the amino acid letter sequence into the anagram tool’s box. This time, after a few seconds, the screen began to fill with a long list of possible anagrams, in alphabetical order. The possibilities streamed past, seemingly interminable pages of them. Patiently, they scanned the entire list. Finally, Jackson leaned back, heavily.

  “This is stupid. PJ wouldn’t do this. It’s too vague; there are too many permutations.”

  Sighing, he opened another browser at the email login page. He looked again at the email sitting in his Inbox, from PJ and tried to open it. The virus warning message came up. Just then, Jackson’s cell phone, which had been charging since last night, began to buzz. A yellow flashing light indicated a call from his boss’s lab. He hesitated, then let the call go to voicemail.

  “Look at that,” Marie-Carmen exclaimed, staring at the computer screen. “It’s just one of those automatic virus emails. You’re sure it’s from Pedro Juan?”

  Jackson pondered. “Could be. Or maybe the warning just came up because it’s got an exe file attached. Viruses often have an attached exe file; that alone is enough to set off the antivirus warning. But maybe he meant to send me a program that would run by itself.”

  “You want to run something that could be a virus on my computer?”

  Jackson gave Marie-Carmen a lopsided grin. “Would you mind very much? After all, I’m already in to you for a new VW Beetle.”

  “Don’t forget it!”

  “I’ll admit it’s weighing on my mind. Some of us are still just graduate students, you know.”

  Marie-Carmen leaned across Jackson, taking the mouse in her hand. Jackson caught his breath for a second as her fingers brushed his aside.

  “Some of us didn’t throw away our teenage years on a snowboard.”

  “Wait until I teach you, you’re going to have such a different perspective.”

  “Fine, snow bum, we’ll run Pedro Juan’s program.”

  He double-clicked on the email’s attachment. The entire screen suddenly went black; then, a small animation beginning as a colorful blob began to grow larger, magnifying to the size of the full screen.

  Marie-Carmen whispered, “What is it?”

  “A 3D animation of a protein structure. I wonder . . .” Jackson muttered, staring at the screen in fixed concentration. “I think that’s a three-dimensional structural model of Pedro Juan’s phoenix protein. He’s got a lot further with this research than I’d imagined.”

  “How can you tell?”

  Jackson pointed to the animation, under which a stream of text was beginning to appear. “This is a recording of an experiment; a computer modeling experiment. What we see represents just a fraction of the time the experiment actually took. PJ’s been looking for amino acid sequences which bind to this protein. It’s a really new technique. From the target protein – the joust or phoenix, for example – you calculate the most likely binding sites. Then you use ask the computer to create a virtual peptide – a short stretch of amino acids – which has the right shape to fit such a site. Finally, you ask the software to test each one in a virtual reality binding reaction. It takes hours. The computer suggests possible, three-dimensional matches; sequences which could, in theory, bind to the protein sequence you’re looking at.”

  “Does the match have to be perfect?”

  “In biology, you need a fairly good match. An analogy would be a computer program which matches an outfit to a really fussy dresser. It takes up so much computer power that you have to use a supercomputer to do it. Costs a fortune to get time on a program like this. And plenty of people don’t think it works.”

  As they talked, from the string of texts which were streaming rapidly under the animated structure, one emerged, enlarged, trans
formed into a bright blue- and pink- colored three-dimensional model and aligned itself against a portion of the much larger model of PJ Beltran’s protein.

  “Look. It found a match.” Looking around for the printer, Jackson pulled out the printout of the amino acid sequence. He examined it for a few seconds, before tapping the paper. “I’ll bet you a new Beetle that PJ’s DNA sample – let’s call it the BELTRAN sequence – is actually the gene for this peptide.” He touched a finger to the blue-and-pink colored animated structure that had just materialized on the screen. The two animations now rotated together slowly, as if locked in a tight embrace.

  Marie-Carmen rose to her feet. “Would you like something to eat? Some quesadillas?”

  Jackson continued to stare, transfixed, at the screen. “Please!”

  She paused by the kitchen door. “You know I’m not taking that bet, right?”

  “Why would you? You know I’m right.”

  He was still glued to the screen when Marie-Carmen returned. She picked up a lime-green iPod nano that was lying, headphones attached, on a sideboard made of rustic, antique pine, and pulled out the headphones. She docked the iPod, selecting a tune. The sound of melancholy piano music filled the room. It sounded vaguely familiar.

  “Beethoven?”

  Marie-Carmen grinned. “Sonata twenty-five, second movement. You didn’t give it a chance in the car yesterday. It’s better than Eminem.”

  “Are you kidding? Beethoven was an eighteenth-century Eminem.”

  Her grin broadened. On the table, next to his right hand, she placed a blue-and-white patterned plate containing six folded tortillas filled with melted cheese. Jackson took one of the quesadillas. They were made from maize tortillas, the stringy melted cheese inside spiced up with pickled carrots and jalapeno peppers drizzled with oil. He picked up a pen and jabbed at the screen.