SCIENTIFIC SLUG STAFF

Nicolas Lounsbury, Editor in Chief Computational Mathematics Casey Weiss, Director of Art Physical Anthropology Neuroscience Class of 2013 Class of 2014

Jessica Hodson, Writer & Editor Caitlin Celic, Writer Neuroscience Marine Biology Psychology Chemistry Minor Class of 2014 Class of 2015

Odile Bouchard, Writer & Artist Hanae Armitage, Writer & Editor Biology Biology Environmental Studies Class of 2014 Class of 2016

Titash Chatterjee, Writer Shivam Dave, Writer Biology Computer Science Chemistry Minor Class of 2016 Class of 2015

Quinn Cachola , Artist Alex Infanger, Anthropology Writer Physics Biology Class of 2016 Class of 2015

John Haytko, Cameron Mehrabian Writer , Writer Computer Science Cognitive Science Mathematics Class of 2013 Class of 2016

Nikki Usui, Artist David Shugar, Writer Art Physics Class of 2015 Class of 2014

Jahlela Hasle, Guest Writer & Editor Andrew Kornfeld, Writer & Artist Cognitive Science Psychology UC Berkeley Class of 2013 Neuroscience Class of 2013 Art by Odile Bouchard Interested in Science Journalism? Robert Irion, director of UCSC’s Science Communication Program, offers an under- graduate course each spring quarter: SCIC 160 / BIOE 188, Introduction to Science Writing. Students learn about news and feature writing for public audiences, culminat- ing in a magazine-length story about campus research. For details, contact the SciCom Program at [email protected] or x9-4475.

Life, which we once believed to be exceptional, may very

well be inevitable. »» p.23

»» p.17

»» p.10 »» p.7 »» p. 14 CONTENTS Scientific Slug

6 Seeing Green: Fluorescent Detection of Poisonous Urushiol By Jessica Hodson

8 The Rhythm Schism: Who’s got rhythm? By Caitlin Celic

»» p.23 10 Telomere Structures Unfold to Reveal Possible Anti-Cancer Therapy By Hanae Armitage

12 From Polar bears to Brown Bears: Genomic Footprints Reveal Patterns of Evolution By Titash Chatterjee

14 Can You Grasp This Concept? By Cameron Mehrabian

16 Solar Greenhouse: Two Birds »» p.8 With One Stone By David Shugar

19 A New Perspective on Sight and Technology By Shivam Dave

20 The Golden Age By John Haytko

22 Living Systems Happen By Andrew Kornfeld & Jahlela Hasle

»» p.13 6 BIOCHEMISTRY Seeing Green: Fluorescent Detection of Poisonous Urushiol By Jessica Hodson

Do you know how to spot bilayer and, after a series of enzymatic shiol. In her lab at UC Santa Cruz, Dr. poison oak? If it’s shiny, watch your breakdowns, attaches itself to proteins Braslau explores the practical applica- hiney, leaves of three, let it be. Not in the membrane. tions of radicals. bad. I’ll give you partial credit for that “This [altered protein] is the Radicals are reactive molecules answer -- it did once represent the cut- thing that your immune system sees with an odd number of electrons: they ting edge in poison oak detection. If and goes Intruder! Mount the defenses!” lack the partner electron they need you want full points though, talk to Dr. Braslau explains. to make a bond. In order to find their Rebecca Braslau. She can see traces missing piece, radicals attack the bonds of that shiny, dangerous oil in poison in other molecules and steal their elec- oak, called Urushiol, hours later and Urushiol is trons. This prompts a vicious cycle that miles away from any plant on the heel dangerous resembles the plot of virtually any epi- of your shoe. That’s right, Dr. Braslau because that sode of Game of Thrones. and her colleagues at UC Santa Cruz greasy carbon chain In the beginning, all is fine and have discovered a way to make Uru- looks a lot like the fats dandy (more or less) between the main shiol residue glow in UV light. families; they have stable bonds. Then Dr. Braslau’s work is classic in our cell membranes. one day someone’s head gets chopped -- she found a problem, she solved it. off. When a radical attacks a bond and The poison oak scattered all over the steals an electron, it creates another California wilderness threatens many radical. In Game of Thrones, when you of us: 50-70% of the adult American Whilst brazenly defending chop off someone’s head, their family population is allergic. Although most our honor, our immune system dam- gets a little upset and swears to avenge of us know to avoid the plants, we still ages our skin cells, provoking that their death. Unfortunately, revenge end up with it on our clothes, oblivi- itchy, oozy, crimson rash that we all doesn’t do much in the way of repair- ous to the oil lurking in the folds. It’s know and dread. ing bonds - quite the contrary - it creates not until the later onset of itchy skin For Dr. Braslau, the threat of more enemies. The same holds true for that we suspect up close and personal poison oak is especially acute. While radicals; they simply perpetuate the de- contact with Urushiol. she is extremely allergic, her geolo- struction. Urushiol in poison oak is part gist husband is not. He would go out As you might expect, due to of a family of compounds known as to survey land, come home, and unin- their reactive and destructive nature, Catechols. Catechols have a six carbon tentionally give her poison oak. One radicals harm living things. However, ring with two alcohol groups and, as time, she recalls, “He got it on his arm if directed carefully, their power can be Dr. Braslau puts it, “a long greasy car- and he slept with his arm around my harnessed for good. Dr. Braslau works bon chain.” Urushiol is dangerous be- torso...I got it from my neck all the way with nitroxides, carbon compounds cause that greasy carbon chain looks a down to my underwear, just all over with an unpaired electron spread over lot like the fats in our cell membranes. the front of me. It was horrible and a nitrogen atom and oxygen atom. When we get the oil on our skin, it he felt so bad, he had no idea he had Around the time of her particularly bad sneaks right through the membrane it there.” After spending three weeks run-in with Urushiol, Dr. Braslau had in agony with contact dermatitis (and been exploring some specific nitroxide this was not the first time), Dr. Braslau interactions. Two of them became the thought to herself, “I should be able to foundation for her fluorescent Urushiol do something about this.” discovery. As it turns out, her work with In one project she studied the radical chemistry put her in a unique interplay between nitroxides and fluo- position to solve her poison oak prob- rescent dye. When she bonded a nitrox- lem by creating a way to detect Uru- ide to a fluorescent dye, the unpaired radical electron quenched the dye’s

Scientific Slug | February, 2014 7 fluorescence. The resulting compound ing the two react! could have other biomedical uses: is called a pro-fluorescent nitroxide, Dr. Braslau’s pro-fluorescent Urushiol is related to catecholamine meaning that the fluorescence is -cur nitroxide plus boron mixture is like neurotransmitters in the brain such rently off but can be switched back vinegar, Urushiol is like baking soda. as epinephrine, norepinephrine and on when there is no longer a radical When this mixture comes into contact dopamine. This might mean that Dr. quenching the fluorescence. with Urushiol, it glows, so any ob- Braslau’s method could detect these In a separate project, Dr. server can locate the Urushiol with UV compounds. Effective identification of Braslau attempted to utilize com- light. As soon as she could, Dr. Braslau dopamine distribution, for example, pounds containing the element boron went out into the woods, dripped her could be instrumental in Alzheimer’s to generate radicals on carbon atoms, solution on some poison oak, pressed research. but was unsuccessful. Ideally, she it onto a paper towel, and held up a Although the Urushiol spray could create a carbon radical using a UV light. This is what she saw: project is moving at a relatively slow boron compound and a nitroxide. Dr. Braslau struggled to achieve this un- til she saw the research of Swiss col- league, Philippe Renaud. He reacted nitroxides with boron attached to a catechol, like Urushiol, and success- fully generated carbon radicals. Suddenly she had her big, as she describes it, Eureka! moment -- she could use a Urushiol-boron compound to generate carbon radicals with ni- troxides! These carbon radicals could then pair up with the nitroxide radi- Left: Classic Poison Oak with “leaves of three” cals to restore the quenched fluores- Right: Fluorescence from Urushiol left behind by Poison Oak seen in UV light cence. She went back into the lab to try it and “it worked...the first time, it was really exciting” she says. Her profound discovery not pace, Dr. Braslau has another practi- Catechols like Urushiol aid only illuminates a dangerous oil oth- cal applications project underway. She the generation of a carbon radical be- erwise invisible to the human eye, but hopes to develop an alternative to the cause their structure, due to the six- also lays down the foundation for the dangerous plasticizers found in PVC carbon benzene ring, easily carries the development of a spray anyone could pipes, electric cables, clothing, and extra electron that the nitroxide do- use at home or in the field. This is pos- medical fluid bags. nates. This stabilization makes it pos- sible because the reaction can be made The practicality of Dr. Braslau’s sible for the nitroxide to bond with the to occur in a safe solvent: acetone (nail work makes it wonderful. She took her Urushiol-boron compound and kick- polish remover) at room temperature profound scientific knowledge and ap- out a carbon radical. The carbon radi- and only takes a few minutes. Howev- plied it to a simple problem in her life, a cal then reacts with the pro-fluorescent er, Dr. Braslau wants to test the safety problem that thousands of other people nitroxide and switches on the fluores- of the fluorescent and boron-contain- share. As a result of her exploring radi- cence. There will only be a glow in the ing compounds before a spray goes to cal chemistry, we are all much less likely presence of Urushiol because it is the market. to have uncomfortable rashes in the fu- final ingredient needed for the - reac Unfortunately, product devel- ture. I’d say that’s a win. tion to take place. opment has stalled because Dr. Braslau This reaction is just like our fa- has not received any funding. Also, the vorite baking soda and vinegar volca- fluorescent dye used in the reaction, no. At first you just have vinegar and Dansyl, reacts somewhat with water. baking soda, not very exciting at all. This means that you might get a slight However, when you mix them togeth- glow if you have water on your shoe er you get an extremely pleasing bub- even when you haven’t touched any bling explosion. Theoretically, if you Urushiol. One of Dr. Braslau’s gradu- had invisible baking soda all over your ate students is searching for a better shoe you could use vinegar to find it: fluorescent dye, but progress is slow. wherever you see bubbles, you’re see- Interestingly, this method

Scientific Slug | February, 2014 8 MARINE BIOLOGY

The Rhythm Schism: Who’s got rhythm? By Caitlin Celic

Ask any musician or dancer, can’t be scientifically proven, but can will take your foot off the gas pedal and rhythm is something you feel. It’s an be inferred after learning about the place it on your brakes. We perceive the entrainment that links us to our exter- training process. Peter Cook was the environment and physically respond to nal surroundings. Something that en- primary trainer involved in this proj- it. This makes complete sense. In fact, gulfs us and we get lost in. The ability ect. He started by training Ronan to without such neural connections, we to coordinate our movement with an bob her head to various tempos of could not survive. external auditory stimulus, i.e senso- a metronome. Interestingly enough, If Ronan and animals alike have rimotor synchronization, is seemingly there was no progression in her ca- rhythmic capability, why isn’t it more innate. The phenomenon is not limited pability to bob her head in beat -- she obvious in nature? In humans, rhythm to hearing and can be propagated by either did it or didn’t. According to Pe- is universally recognized. Perhaps any sense. We see it throughout the ter, it was as if she had an epiphany or this is because of our cultural disposi- animal kingdom: wolves that hunt to- gether, dolphins that jump in cadence in wake of boats. Scientists originally believed auditory stimulated rhythm was only found in animals with com- plex vocalizations, like humans and birds that can talk. This is a theory known as the vocal learning and syn- chronization hypothesis. However, re- searchers at the Pinnipeds Cognition and Sensory Systems lab -- Peter Cook, Andrew Rouse, and Colleen Reich- muth -- challenged this hypothesis when they trained a clever California Art by Quinn Cachola sea lion named Ronan, to keep a beat. a light-bulb that went off in her head. tion to it -- we tap our foot, dance, and Their research suggests that rhythm He did not question her capability to play music. Rhythm is a part of being is something more widespread than perceive the rhythm. Rather, the chal- human. These animals have the innate originally thought. Perhaps rhythm is lenge was to get her to understand timing necessary for rhythm, but maybe something more fundamental. that he wanted her to bob her head all they lack is incentive. The last time You may remember the video to the beat. Researchers still question I went scuba diving, I didn’t hear any that went viral last year in which the whether the rhythmic perception was catchy pop music to dance to. Research Long Marine Lab’s sea lion Ronan, conscious. has provided the answer that keeping bobbed her head in rhythm to the Let’s take a step back and look a beat is a trained response. How and Backstreet Boys. As adorable as this is, at the basic brain functions behind sen- why the trained response actually oc- it contradicts the vocal learning and sorimotor synchronization. The cortex curs remains open and up for further synchronization hypothesis, since sea is the region of the brain where higher research. lions do not have complex vocaliza- order processing of sensory input oc- tions. Researchers at the Pinnipeds lab curs. Since all sensory cortices, i.e visu- note Ronan’s cognitive processing of al, audio, olfactory, etc., are connected the auditory stimulus when investi- to the motor cortex, sensorimotor syn- gating how she can keep a beat. Does chronization may occur. Take driving she recognize rhythm as a pattern? Is for instance: if you see the brake lights it something she can feel? The answers go on in the car in front of you, you

Scientific Slug | February, 2014 9

A Poem About Science

I guess you could say I am addicted to science. It is a hunger that persists An itch that won’t scratch. You would think getting a bachelor’s of science would tame my cravings, but it makes it worse. Much worse. Constant exposure to new ideas causes curiosity to grow so fast-- it rips. A spike in the graph. There will always be more questions. Never ending. I try to numb the sensation by reading scholarly articles. I will eventually fall asleep. Wake up. Go to class. Learn something already learned. Know something already known. Think something already thought. Boring. Uniform. Soul-crushing. I learn a finite amount of material throw it up on an exam. A letter tells me if I’m good enough or not. This is not real science. Science is a method, art, philosophy, experience, a way of life.

Ayn Stein

Scientific Slug | February, 2014 10 BIOCHEMISTRY

Telomere Structures Unfold to Reveal Possible Anti-Cancer Ther apy By Hanae Armitage

Scientists have long fought telomeres, play a key role in differ- makes new telomeric DNA, enabling cancer with their biggest, baddest re- entiating between chromosomes that the rapid divisions by keeping the ends search tactics — but big and bad only end naturally with telomeres, and healthy. However, the quick and nu- go so far. A new, potential approach chromosomes that have damaged merous cell divisions telomerase facili- involves working in a more concealed ends without telomeres. Scaled to fit tates can also play a darker role in hu- space: within the ends of our chromo- in your hand, a chromosome would man health. somes. Biochemist Michael Stone, an appear much like a shoelace, with the Over years of cancer research, assistant professor at the University telomere acting as the plastic tip that scientists have repeatedly come to the of California, Santa Cruz, and his col- keeps the lace from unraveling. same conclusion: telomerase is a fun- leagues are tackling cancer research Every time our cells divide damental contributor in creating most with, literally, a twist of biophysics. and copy, each telomere loses a bit of cancerous cells. The growth of a can- Stone’s lab probes inside the tips of its length. Shortening telomeres es- cer cell is uncontrolled and its lifespan, chromosomes to stretch and bend sentially act as an hourglass for the virtually immortal. Research has found DNA, watching how each strand re- life span of the cell. The chromosome overactive telomerase in 90% of cancer acts to invasive prodding. cells, perpetuating cell growth that de- Warping DNA requires spe- velops into tumors. cific and precise instruments. These By tweaking the telomeres’ adjustments in structure are so minus- structure, Stone’s lab at UCSC reaches cule, less than one billionth of a meter, outside the usual realm of techniques that only special microscopes can de- used to study DNA. “My lab is one of tect the changes. Stone’s lab is apply- the few groups in the world digging ing a pair of novel techniques — fluo- deep biophysically into the molecular rescence microscopy and “magnetic mechanisms of telomere length mainte- tweezers” — to contort DNA precisely nance, which is very important in medi- and, at the same time, account for each cal biology,” he says. infinitesimal change in structure. The magnetic tweezers and The magnetic tweezers and a fluorescence microscopy technique fluorescence microscopy duo are - stir called Förster Resonance Energy Trans- ring new ideas about how folded fer (FRET) may look like a convoluted structures in our cells may serve as duo to the untrained eye. But the basic the next major drug target for cancer ideas are simple: the “tweezers” pull therapies. divides and shrinks until it becomes a and twist on molecules of DNA, while “We have this unique niche health risk to the cell, at which point, it FRET measures the distances in real where we’re not only up on the biol- enters a death phase. Though “death time. ogy, but we also have these specialized phase” sounds fairly ominous, it’s The instruments reside in a techniques,” Stone says. “We study actually what’s keeping our cells in small, busy lab room. At first sight it’s how our genetic material behaves as check. Every cell division is an oppor- overwhelming, but it’s a purposeful just that, a material. That’s not the way tunity for chromosomal mutation. The clutter. What appears to be a haphazard we’re typically taught to think about cell’s limited lifespan, caused by telo- maze of varying sizes of glass is a pains- DNA.” mere shortening, restricts mutation takingly aligned series of laser-guiding The cells in our bodies carry a and genetic damage. lenses and mirrors. Correctly aligned, genetic blueprint tucked into compact Not all cells divide at the same the optics direct the laser that powers pieces of DNA called chromosomes. rate though. Some cells—like stem FRET. In other words, it’s the kind of A cap at the end of each chromosome cells—need to divide more rapidly to display best kept at arm’s length. protects the DNA from being dam- successfully function. In these kinds Near the tweezers, a computer aged. These protective ends, called of cells, an enzyme called telomerase screen displays images of the manipu-

Scientific Slug | February, 2014 11 lated DNA. With one end of the DNA molecule secured to a glass plate, sci- Scaled to fit in your hand, a chromosome would entists attach a magnetic bead to the appear much like a shoelace, with the telomere other end and place a larger magnet acting as the plastic tip that keeps the lace from above the bead. As the large magnet moves closer to the bead, the force on unraveling. the DNA increases, stretching it fur- ther. During this process, FRET mea- sures the fractional changes in length within single molecules by monitoring the interactions between a green do- found. In its folded, stable state, the G- than just the interests of my lab.” nor FRET dye and a red acceptor FRET quadruplex inhibits telomerase action, On a larger scale, Stone strives dye. The amount of energy transfer making it an intriguing candidate in to explore how the G-quadruplex in- between the two dyes directly corre- the cancer therapy world. fluences the broader biological roles sponds to the distance between them, Stone’s lab used the paired of telomeres. For example, the lab will making it one of the world’s smallest magnetic tweezers and FRET tech- study how replication in telomeres dif- measuring tapes. (refer to Ben’s pic- nique to explore the role of the G- fers compared to other segments of ture either FRET or beadfret). quadruplex in detail. The tweezers DNA. One salient feature of telomere stretch specifically dye-labeled DNA DNA is its high sequence repetition. molecules in the structure to reveal Repetitive sequences can lead to chal- the lengths at which folding and un- lenges in replication by confusing DNA folding occurs. The team has found polymerase, the replicating protein. A that the G-quadruplex is surprisingly repeat in DNA causes stalling or back- touchy. Disturbing a single nucleotide tracking, like a scratch on a CD makes could mean its demise. In that way, it’s the music skip or stutter. a lot like Jenga: tamper with one build- Stone and his team have stud- ing block and the whole thing collaps- ied the G-quadruplex for more than es. four years. With such a complex focal With such a temperamental point, the lab can be an arduous place to structure, the goal is to find a way to work. keep the G-quadruplex happily stable “I tell my younger students that and folded. Such a tactic could suggest you have to enjoy the process of science ways to design a new type of cancer to be a good scientist. You can’t be com- Photo by Hanae Armitage therapy. In the lab, scientists have ex- pletely results-focused,” says Stone. perimented with stabilizing molecules “Experiments are filled with challenges “Basically our lab married that keep the G-quadruplex folded, and difficulties. Taking these challenges these two techniques so we could ap- blocking overactive telomerase. Rep- in stride is just a part of the daily grind ply a very stable force and simultane- licating that success in cancerous cells of being a research scientist.” ously monitor it [the DNA structure] — and, ultimately, in patients — will He gestures to a photo of the on a very small scale,” says Xi Long, be a long road, Stone acknowledges. New York Yankees stadium pinned to the lead graduate student in Stone’s Stone’s lab is keen to share his office wall. “Major league baseball lab. the skills needed to develop and re- hitters fail way more than they suc- The researchers focus on what fine these techniques with other labs ceed,” Stone says. “In fact, the very best happens in the telomeres of the chro- and researchers. Keeping them secret hitters fail seven times out of ten. So if mosomes. They zero in on an unusual would eliminate the opportunity for you hit .300, you’re doing really well. structure of DNA known as a G-qua- colleagues to contribute their findings You might even be MVP of the league. druplex. With a structure just as com- to science on a larger scale, says Stone. Yet more times than not, you didn’t get plicated as its name, the G-quadruplex “Now, when we report on it in a hit. Science is like that. You need to is no simple query. It fascinates re- the literature and at meetings, people have resilience.” searchers because of its propensity to studying things different than telo- fold and unfold into different forms, mere structure are very excited about like origami on a molecular level. The the methodology,” says Stone. “There effects of these folded forms on the are many applications for this sort of level of telomerase activity are pro- technology, reaching much further

Scientific Slug | February, 2014 12 BIOLOGY

From Polar bears to Brown Bears: Genomic Footprints Reveal Patterns of Evolution By Titash Chatterjee

Why are some species’ ge- populations. They strive to outline the mitochondrial DNA (mtDNA), which nomes ultimately driven to extinction patterns of genetic change associated is always inherited from the mother, re- while others are not? How did popu- with certain events over past lineages searchers found that brown bears from lations of the past move around and and explain why our modern biodiver- the ABC Islands are very distinct and end up in their current habitats? An- sity is the way it is. Big omnivores like bigger than brown bears found on the swering these questions is like solving ancient brown bears are, “an interest- mainland. In fact, ABC’s brown bears a Rubik’s cube; one has to twist and ing proxy for how humans may have share almost the same mtDNA with contort the many pieces of evidence used the landscape...they are also very polar bears; therefore these two appear until the pattern is right. By analyzing genetically structured, which makes to be more closely related to each other ancient DNA and utilizing a novel ge- them interesting [to study patterns of than to other brown and black bears. nomic approach, UC Santa Cruz’s Pa- genetic change],” says Shapiro. Moreover, another group matched el- leogenomics Lab attempts to unravel the mystery behind the ancient evolu- tionary changes that led to population patterns of today. In practice, Paleogenomics, the study of genomes of the past, is the closest thing we have to time travel. It enables us to inspect the dynamics of communities that lived long before hu- mans. So far led by Associate Professor of Ecology and Evolution, Beth Shap- iro, the lab has studied a broad range of ancient DNA preserved in fossils, including: dodo, pathogen, woolly mammoth, and the Neanderthal. In- terestingly, the full mitochondrial DNA sequence of the close human rel- ative, the Neanderthal, was published in 2008 by UCSC Paleogenomics co- leader, Richard Green. Finally, the team just collaborated with research- ers from Denmark and Canada to ana- lyze a 700,000 year old horse genome Art by Quinn Cachola - the oldest genome ever sequenced. Along with Shapiro and first evated amounts of mtDNA from ex- There have also been talks about de- author James Cahill, the lab recently tinct and living brown bears to mtDNA extinction, which would require the resolved the confusion behind the evo- from a 105,000 year old polar bear fossil. complete genome of a species to bring lutionary relationship between polar However, nuclear DNA tells a different it back. It won’t be as easy as in Juras- bears and brown bears -- specifically, story -- researchers have traced nuclear sic Park, but scientists see it as a way to on the Admiralty, Baranof and Chi- DNA (inherited equally from each par- correct past extinctions. But paleogen- chagof (ABC) Islands of Alaska. The ent) to brown bear ancestry in both omicists don’t limit their curiosity to two bears have a very old link: whole brown and polar bears. extinct species. genome comparison suggests they di- In short, both bears have most- Recently, the UCSC Paleoge- verted from their common ancestor ly polar bear mtDNA, but brown bear nomics Lab has been working on trac- around the same time, 4-5 million years DNA on the rest of the genome. Addi- ing the genetic framework of bear ago. Previously, based on analysis of tionally, mtDNA suggests that the two

Scientific Slug | February, 2014 13 bears diverged from the common an- garded draft of the full human genome cestor, leading to origin of polar bears, sequence, inspired by the international 20,000 years ago. Nuclear DNA sug- Human Genome Project. gests it was 500,000 years ago. Cahill So how does genome sequenc- acknowledges that this unusual ge- ing work? First, the team obtained sam- netic pattern ultimately led to an am- ples like hair from wildlife agencies that biguous conclusion and many clash- routinely collect samples from individ- ing theories about bear lineage on the uals they track. Then, they degraded the ABC islands. samples to isolate DNA molecules by In order to align the conflict- exploiting its unique chemical proper- ing pieces of evidence together and get ties, and broke down the pieces of entire a more holistic picture of the situation, genomic DNA into random fragments the team shotgun-sequenced complete to store them as a sequencing library. genomes of two living brown bears, Conventionally, short DNA segments seven polar bears and a black bear. are analyzed using Sanger sequencing, Like the rapid random firing process Art by Nikki Usui developed by the father of genomics, of a shotgun, shotgun sequencing had maternal polar bear genes -- the Fred Sanger. Alternatively, the lab uti- breaks down the genomic DNA into small polar bear population was con- lized advanced technologies known as random fragments, sequences them, verted into brown bears over time. next generation sequencing. Research- and puts them back together based “Gradually, with every gener- ers use this technology to sequence on overlapping sequence reads. When ation...the genome [of this island pop- fragments longer than 1000 DNA base the group analyzed the whole genome ulation] becomes less and less polar. pair units; sometimes even complete ge- sequence of an ABC islands bear, they The vast majority of the ABC islands’ nomes. The individual fragments were found that it was 99% brown bear bear population genome is brown divided into two sets and sequenced at DNA and 1% polar bear DNA. How- bear, while they still have an echo of UC Berkeley and UCSC, resulting in a ever, only 93.5% of X chromosomes polar bear,” noted Cahill. huge 40 gigabyte text file. Then, using a had brown bears genes while 6.5% had Similar hybridization with previously published reference bear ge- polar bear genes -- the X chromosome polar bears has also been seen among nome sequence to guide the mapping of had ~6 times more polar bear genes Irish brown bears, so this theory of the genes, Cahill reassembled these in- than expected. This inheritance of X polar bear genome wipeout provides dividual fragments, putting together a chromosomes is likely to be maternal a molecular prediction for the future genome sequence of the sampled brown since females have two copies of them of polar bears. Cahill stresses that ad- and polar bears. This entire process took while males have one. This along with dressing the question of how past cli- six months, while the actual analysis of mtDNA, shows that ABC bears have matic fluctuations re-defined certain the sequence and conclusion drawing polar bear ancestors on their mother’s populations, helps us understand how took about a year. side of the family. As a result, the more today’s climate-sensitive arctic popu- Extraction and sequencing genes a bear inherits from its mother, lations will behave. Shapiro adds that, techniques in paleogenomics are still the more polar bear is in its genome. “One goal of this research is to learn improving rapidly. Despite the DNA So the rest of the genome, consisting why some species go extinct while oth- fragments’ better survival rate at colder mostly brown bear genes, must have ers don’t, and use that information in climates and the scarcity of fossils, Sha- come from the dad. present-day conservation efforts.” As piro is hopeful, “In the last year or so, Thus, Shapiro’s lab published indicators of arctic ecosystem health, we have gotten increasingly better at their solution to the puzzle: 26,000 polar bears are keystone species, thus extracting all of the DNA that is pre- - 12,000 years ago, during the last their distinctly small population size served in a sample. Even the very short ice age, a small population of polar and increased vulnerability to the fragments...” She predicts that eventu- bears colonized the sea ice near ABC climate-driven extinction of their ge- ally we will be able to recognize older islands. Polar bears are dependant on nome is alarming. and older paleogenomes that lived in extreme cold and seafood. As islands Comparative genomics has diverse habitats. got warmer and glaciers melted, these become a very powerful tool. The Shapiro comments on her feel- bears got stranded on the ABC is- analysis helps us understand evolu- ings about the advances in paleoge- lands while male brown bears (female tion, personal genomics for cancer nomics. “This will be wonderful. It’ll brown bears are not known to do so) treatment, and isolating genes with provide a wealth of new information for migrated to these more hospitable is- useful protein expression from oceanic evolutionary analysis.” lands. Over time, the polar bears and samples. UCSC is a leader in computa- immigrant brown bears gave rise to tional biology -- in 2000, it was the first viable hybrids that looked brown, but institution to publish the highly re-

Scientific Slug | February, 2014 14 COGNITIVE SCIENCE

Can You Grasp This Concept? By Cameron Mehrabian

personal experiences in order to fully a hypothesis. However, there lies great convey an idea. Describing an inter- evidence in validating this concept action as “warm” or a relationship as through the analysis of language. a “rollercoaster” conveys an intuitive understanding of ideas. Also ingrained Time flies… into our neural conduct is that we mentally mimic the actions of others Consider this example: just by observing them perform that action. The discovery of mirror neu- Next Wednesday’s meeting is rons, i.e. neurons that fire both when moved forward two days. observing and performing an action, has initiated interesting developments What day is it on? in evolutionary biology, cognitive sci- ence and many other fields of research. The way you answer this ques- The mirror neuron system addresses tion can elucidate how you understand possible explanations for many types abstract concepts such as time and of developed human behaviors, such Art by Miguel Hernandez space. Specifically, the way you under- as: how we understand the actions of stand the motion of time and how you others, experience phenomena like em- How do we imagine impossible ac- interpret, “moved forward,” will affect pathy, comprehend language, imagine tions? whether this sentence means to you that and conceptualize. The latter two ex- How does our mind make and/or rep- this meeting is on Monday or on Friday. amples are referred to as “simulation” resent meaning? in this field of cognitive research. The Cracking the Code Raymond Gibbs, a psycho- linguistic experimenter and professor Gibbs, a leading proponent of here at UC Santa Cruz, is attempting to the embodied simulation hypothesis, answer these controversial questions has found interesting ways to demon- by studying the way people use lan- strate how we simulate by analyzing guage. Gibbs and other cognitive sci- metaphorical interpretation and ex- entists argue that we use metaphor at pression. In particular, he has sought both a linguistic and conceptual level; to understand how humans resolve se- that metaphor is understood through mantic ambiguity, i.e. words that have embodied simulations. The Embodied many possible interpretations. His most Simulation hypothesis (ES) proposes significant claim is that concepts, espe- the idea that the body influences cog- cially abstract ones, are mentally repre- nition just as the mind influences the sented through metaphors. Art by Miguel Hernandez body; it is this relationship in which concepts form and meaning arises. mirror neuron system has greatly as- Words carry meaning... sisted our development, and through Two Peas in a Pod the ES hypothesis, we can attempt to Gibbs began to study this claim understand these facets of human cog- by analyzing how people interpret Language processing is an nition. poetry. In two of his experiments he intuitive action. Some words tend to presented a poem to each of his par- mean much more than their literal rep- Since embodied simulation ticipants and following the reading, he resentation and seem to draw upon cannot be directly observed, it remains inquired their personal interpretation

Scientific Slug | February, 2014 15 COGNITIVE SCIENCE

of the piece. In his first study, he gave wholesome illustration of Sally’s an- How does it all fit together? them options of possible metaphorical ger. themes for the poem, whereas in an- How we engage in meaning- other, he asked for their own personal In another study, Gibbs ful interpretation involves embodied interpretation of the reading. In both sought to observe the human body’s simulations. If the ES hypothesis holds experiments, he found that a large ma- role in understanding. Specifically, he true then this suggests we understand jority of his participants agreed upon wanted to observe whether human language by simulating in our minds the theme of the poem. bodies simulate action when interpret- what it would be like to experience the ing metaphoric language represen- information presented to us. In a subsequent study, Gibbs tative of physical movement. Gibbs attempted to show that metaphors claims that moving the human body in Language is imperative to how and idioms are more than just dead a way that is relevant to the metaphor we think and communicate. In most language, and indeed represent more can facilitate the understanding of the cases, the literal usage of words does than their literal depictions. He pro- metaphorical phrase. In order to show not efficiently describe the information posed that individuals undergo a this, Gibbs asked his participants to that the words are intended to convey. richer experience when interpreting memorize a specific symbol such as Let’s say that meaning is represented information, utilizing rhetorical lan- @, $, or % and associate it with an ac- by our experiences. Meaning could be guage opposed to its literal counter- tion such as chew, grasp or cough. He quite personal, varying across differ- part. Gibbs presented his participants then presented a symbol with a meta- ent cultures and languages. Thus, ex- with a story describing a couple pre- phorical phrase such as: chew on the panding our lexicon could allow us to paring for a dinner party, where the idea, grasp this concept, cough up a secret, organize and express our thoughts in a wife, Sally, does most of the work and and primed the phrase with either a more effective manner. If language and the husband contributes nothing. The matching symbol, a mismatching sym- meaning indeed work hand-in-hand, story climaxed with Sally getting very bol, or no symbol. He then measured then meaning requires metaphors that angry, which was either described as how long it took for the participants to prompt listeners to draw upon their Sally blew her lid (idiom) or Sally got understand a phrase by having them own personal experiences to fully fa- very angry (literal paraphrase). He then press a button once they felt like they cilitate their understanding. Metaphor examined the participants degree of understood it. Ultimately, he found is merely a human mechanism used to agreement with statements regarding that the amount of time it took to un- construct and organize information as Sally’s emotional reaction, her rea- derstand the phrase in the symbol- it is represented through the human’s son for doing so and the conduct of matching condition was significantly body, thoughts, and experiences. her expression. He found that in the faster than in both the mismatching case where the idiom was used, the and no prime condition. You see my point? reader rated the phrase higher. Thus, the idiom seemed to provide a more

Scientific Slug | February, 2014 16 PHYSICS

Solar Greenhouse: Two Birds With One Stone By David Shugar

eration and for plant growth. This is in energy available for photosynthesis. accomplished through using a unique However, due to the selective wave- dye, called LR305, which absorbs most- lengths that the dye absorbs and emits, ly green light and emits light in the red the panels can be installed on a green- spectrum. This dye can be mixed with house roof without greatly affecting plastic and used to create a thin film plant growth. Using solar panels for a of red colored plastic, which is often greenhouse roof also reduces land use called a Luminescent Solar Concentra- and substitutes a necessary closed roof, tor (LSC). Plants primarily absorb red offsetting some costs for the customer. and blue light for photosynthesis and This new integrative agriculture and reflect green light. This is why we see sustainable energy technology has in- plants as having a green color. The dye teresting promise for the greenhouse within the LSC absorbs mostly green farming market within California and light, therefore taking away light that around the world. Professor Sue Carter, Ph. D the plants don’t need it, while emitting light in the red spectrum, which can be I first learned about the project As I walked into the solar used by plants. The light absorbed by in winter quarter 2012 when I contacted greenhouse, the sunlight was tinted to the LSC, mostly unused by plants, is UCSC Professor of Applied Physics, Sue a red glow. Warm air circulated across also used to increase solar cell genera- Carter, to ask if there were any openings my face and I could smell the scent tion. in her Optoelectronic lab. She suggest- of the surrounding plants. My brain ed that I work with one of her graduate was still buzzing from the abstract The LSC concentrates and students, Ian Carbone, to assemble two math concepts I had just learned in waveguides light to the edges of the greenhouses at the UCSC Arboretum. my physics class, but as I started pay- film by promoting total internal re- I willingly volunteered for the project ing more attention to the plants in the flection. As photons strike the dye and helped build a control greenhouse greenhouse my mind began to relax. molecules in the LSC, they frequently made with clear glass and a solar green- bounce off at skewed angles and get house made with red-tinted LSC glass I felt lucky to have a unique trapped within the layer of the dyed that had strips of solar cells. After the opportunity that, as an applied phys- film. With the addition of strips of so- greenhouses were built, my project in- ics major, I was able to work on a proj- lar cells, the trapped photons are often cluded planting and growing various ect that bridged physics, biology and absorbed by solar cells. A film of the plant species such as tomatoes, spinach, renewable energy. Another plus was LSC material can be laminated onto strawberry, peppers, cucumbers, basil that I was often able to work outside! glass or clear plastic, with sections that and citrus trees. This was a simple, yet This drastically contrasts the research contain solar cells, to create an LSC so- surprisingly difficult task coming from done by most physicists, which is usu- lar panel. Within the current design, a physics background. ally done in indoor labs packed with solar cells only cover about 10% of the electronics, having little to no natural area of the panel, but the waveguiding I worked on this project with lighting. As a sustainability advocate, effect of LSC allows the solar genera- select undergraduates through the I also felt motivated to work on a re- tion to increase 40%! This gives more spring of 2012 to the spring of 2013. We newable energy technology that could energy for the expensive solar cell met often with Carter, as well as Profes- potentially be used on greenhouses material and makes the product much sor Micheal Loik from the Environmen- throughout the world. more economically feasible. tal Studies department. Working with students and experts from multiple dis- The solar greenhouse technol- Normally, plants underneath ciplines was very helpful and we were ogy works through simultaneously a panel that absorbs sunlight would often able to work together to solve utilizing sunlight for solar power gen- not grow as large due to the decrease questions for a common research goal.

Scientific Slug | February, 2014 17

...both mea- surements support the claims that the plants grown under the LSC material have functioning photosys- tems and are effectively able to gain energy through sunlight. Photo by David Shugar

Our research was focused on studying how the plants reacted to the altered light spectrum of the LSC. This was done through study- ing plant growth response and ana- lyzing parameters such as plant height, plant weight, leaf area, distances between nodes of leafs, amount of open flowers and fruit production. The data helped us understand the photomorphogen- esis, i.e. the light-mediated changes in plant growth and development. Plants have many pigments sen- Photo by David Shugar sitive to light and can detect the quantity, direction and duration of light within their environment. This can trigger the germination process, flowering cycles, the direc- tion of plant growth, stem elonga- tion, leaf size and shape. Due to the fact that the LSC material alters the light spectrum, we wanted to test the effect of photomorphogenesis. We generally observed that the plants had comparable biomass and fruit production, which supports the claim that plant growth under the LSC material is comparable to growth within a clear greenhouse. However, there were some nota- ble differences worth mentioning. Some plants, such as strawberries and tomatoes, flowered and fruited earlier when grown under the LSC material. This may be due to the in- crease of red and infrared radiation. Also, some plants like basil and certain flower species had slightly different colors - another possible result of the altered spectrum.

Scientific Slug | February, 2014 18

In addition to observing the plant physiology, we also wanted to study the photosynthesis process. Photosynthesis is the mechanism by which plants can use sunlight to gen- erate glucose from water and carbon dioxide. The production of glucose is fundamental to plant growth and fruit production. This conversion of light into usable biochemical energy occurs within photosystems I & II. Within the photosystems, chlorophyll molecules are the main pigments that convert light into useful energy for the plant. Art by Nikki Usui In order to study properties fluorescence and is lower than the more thoroughly controlled greenhouse of the photosystems, a property called dark adapted fluorescence. Studying at the Interdisciplinary Science build- the chlorophyll fluorescence can be the chlorophyll fluorescence can give ing. All the results support the claim used. Fluorescence is a term used for information about the photosystem ef- that the efficiency of photosynthesis is light that is re-emitted from a molecule ficiency. not greatly affected for plants growing after it has absorbed an initial pulse of under the LSC panels. With this being light. By measuring the fluorescence A common measurement that said, more research needs to be done. from chlorophyll molecules, aspects was taken was the light induced and Professor Loik, an expert of plant physi- of photosynthesis can be inferred. As dark adapted efficiency of photosyn- ology, suggested that there is a need light excites a plant’s chlorophyll mol- thesis; more specifically, photosystem for more tests, larger sample sizes and ecules in the photosystems, the ex- II. When testing the dark adapted ef- more data to more fully characterize ef- cited chlorophyll can transfer energy ficiency of photosystem II, the plants fect on LSC to plant health and photo- in three ways: excited chlorophyll can between the LSC and control green- synthesis. In a draft paper, presenting transfer energy for the photosynthesis house were near equal. This supports the results of this study, he also states processes, disperse energy as heat, or the claim that both plants have the that a systematic study of various pho- re-emit light as chlorophyll fluores- same maximum efficiency and that the tosynthetic pathways should be tested cence. These three processes happen LSC is not detrimental to the plants’ within “stem vs. root vs. fruit vs. seed in relation with one another; so if there photosystem II health. Within the light crops; monocots vs. dicots; woody vs. is relatively more chlorophyll fluores- induced photosystem II efficiency, herbaceous species; as well as compari- cence, then there will be relatively less the plants grown under the LSC had sons between cultivars, varieties, and energy used for photosynthesis or less similar to slightly higher measure- heirlooms within species” before more energy dispersed as heat. ments than in the clear greenhouse. conclusive claims can be made. These The slightly higher light induced initial tests, as well my other work test- In order to measure chloro- photosystem II efficiency may mean ing the biomass and fruit production phyll fluorescence, one needs a fluo- that the plants’ photosystem II were of the plants, provide insight useful to rometer device. A fluorometer sends slightly less saturated, which would support the future implementation of out a saturating pulse of light which make sense considering the LSC ab- this technology. excites the chlorophyll molecules, sorbs light. With this being said, both then detects how much light is emit- measurements support the claims that This project was a unique in- ted as fluorescence. If the leaves have the plants grown under the LSC ma- terdisciplinary learning experience in not been exposed to light for over 15 terial have functioning photosystems which me and my fellow collaborator’s minutes, the various photosystems are and are effectively able to gain energy research was able to give insight into “open”, which means that the light has through sunlight. This is additionally a potential product to be used to sup- more ability to saturate chlorophyll supported by the comparable biomass port agriculture and sustainable energy. molecules. In turn, this creates a maxi- and fruit production. Through this project I learned to apply mum fluorescence, known as dark the discipline of physics to larger topics adapted fluorescence. As leaves are Various chlorophyll fluores- of plant physiology and renewable en- exposed to light, more of the photosys- cence measurements were done at three ergy. I also want to thank all the support tems “close”, thus, lowering the ability locations: the UCSC Arboretum green- from professors and students who have for light to saturate chlorophyll mol- house, a commercial greenhouse at KB contributed to this research. ecules. This is called the light adapted farms in Watsonville, and a small, but

Scientific Slug | February, 2014 19 COMPUTER SCIENCE A New Perspective on Sight and Technology By Shivam Dave

Manduchi says, “There are achieved what he was trying to test. Vi- a lot of people who wake up and say sually impaired participants were sent they can apply their hardware and into a long corridor while pointing the software to help the blind, but they cellphone forward in order to look for don’t really know what a blind person the placed tag. As the participant got needs.” Prior to implementing actual closer to the tag a beeping noise was research, he made an effort to under- emitted. Compared to tests that were stand the community he has sought to more preliminary, he is now using help. smartphones like the iPhone in his re- Starting with a solution is not search. the way to go, but really delving into Manduchi recounts from his ex- what the problem is how it should be periences, “blind people use the iPhone Professor Roberto Manduchi Dott. Ric. addressed. The blind community is a lot. Not everybody, but a good num- diverse and has many different needs. ber.” Not only does the iPhone have a When Roberto Manduchi was Manduchi began by making blind camera, but also has the built in sensors asked what he was most proud of in friends and running user studies with required for the technology he is engi- his research, he smiled and said, “Oh the visually impaired. However, he neering. boy, not a lot.” Although he is hum- states this is an ongoing process as he Currently, Manduchi is work- ble about what he has worked on, his continues work on his research. ing with smartphones to help the blind research history speaks for itself. He take better pictures, give feedback, and comes from a background in computer ...they can apply continually aid them in taking pictures. vision, a field centered around the use Although some apps currently do this, of technology to process, and analyze their hardware Manduchi is striving to make this more real life images taken with a camera. and software to consistent for the blind community He has worked on Computer Vision at help the blind, but they through Optical Character Recognition Apple and NASA where he worked at don’t really know what and low-cost apps. the Jet Propulsion Laboratory. a blind person needs.” One app in particular computes At UC Santa Cruz Manduchi a proper position to hold the camera is working on using technology to as- and provides feedback to the user on sist those who are visually impaired. whether their pose is proper for the at- Specifically, he uses something almost As Manduchi understood the tempted picture. Analyzing what the all of us have: a cell phone. In his own blind community more and more he picture is composed of, an algorithm words, his lab is, “trying to devise began implementing the actual tech- “reads” its pixels and tells whether the technology to help people with vision nology. His specific field of research is image is a high enough quality. If the disabilities.” computer vision. Although technology image is readable it can then be inter- The demographic that Man- is advancing at such an alarming pace preted for the user. duchi wishes to help ranges from the and most people would expect to use Manduchi’s research with Com- blind to those with low vision. Blind the most current technology, he states, puter Vision and the blind is still a work people may be what people think of “sometimes low-tech really works the in progress. He continues to research when visual-impairment comes to best.” the people he wants to help, along with mind, but there are many more who In 2010, Manduchi published the smartphones that his research now have reduced vision. Although he work that used a Nokia N95 8GB to utilizes. Predicting where computer vi- has worked with different levels of scan small tags to direct those who are sion will be in 10 years is almost impos- computer vision in his career, prepar- visually impaired. Although the Nokia sible to say right now. One thing that is ing for this research was different that was not the most advanced cell phone almost certain is that Manduchi will be anything he had done before. or the most technologically current, it an important part of its future.

Scientific Slug | February, 2014 20 PHYSICS The Golden Age By John Haytko

mense amount of energy. While the ex- Think about four poorly co- act trigger leading to TGFs is currently ordinated hockey teams skating faster unknown, the key ingredient is en- and faster around a rink at the same ergy. There are two common methods time. Collisions are bound to happen, for accumulating the “seed” electrons and when they do, they inevitably cre- necessary. One method, also known as ate more collisions. In these “runaway “thermal runaway,” relies on the high- electron avalanches”, the newly rela- electric field generated by lightning, tivistic electrons occasionally collide which serves as a charging station by with other electrons in the air, creating accelerating electrons until they burst a self-propagating cycle in which each out of the high-electric field. If the electron collision makes more electrons electric field is large enough, the elec- relativistic. The relativistic electrons Professor David Smith, Ph. D trostatic force produced will outweigh eventually decelerate through colli- the opposing frictional forces; thus, sions with positive nuclei in the air. In Blink and you’ll miss it. Cur- allowing the electron to accelerate to turn, this deceleration produces visible rent research directed by Professor Da- highly relativistic1 speeds. The other Bremsstrahlung Radiation2. While this vid Smith is challenging our current method requires cosmic rays to intro- process may seem simple enough to be theories on how lightning operates. duce high-energy electrons into the readily common, TGFs are quite rare – Over the past twenty years, research mix. Both of these methods then lead with well over three million daily light- on the subject of Terrestrial Gamma to a relativistic runaway avalanche. ning events, only fifty produce TGFs. Ray Flashes (TGFs) has exploded so much that Professor Smith has brand- ed the future decade, “The Golden Age” for research on TGFs. Everything began with an acci- dent in 1994 when the satellite, BATSE, observed the first ever TGF related to thunderstorms. Originally, BATSE was launched with the mission to observe gamma rays from outer space; little did we know how much was happen- ing near the surface of our own plan- et. Researchers quickly began to note connections between these TGFs and other lightning related phenomena, namely several types of upper atmo- spheric lightning: sprites, elves, and jets. However, later on, the majority of detected TGFs were, in fact, found A computer simulation of relativistic electrons (magenta). to have originated at much lower alti- tudes. As researchers steadily lowered the target altitude for TGF formations, 1. Relativistic: Accurately described only by the theory of relativity. the mystery revolving around TGFs increased. 2. Bremsstrahlung Radiation: Electromagnetic radiation produced by the deceleration of a charged TGFs quickly became a hot particle when deflected by another charged particle, typically an electron by an atomic nucleus. The topic for research because of their im- moving particle loses kinetic energy, which is converted into a photon because energy is conserved.

Scientific Slug | February, 2014 21

Still, a critical piece of the Do TGFs occur in all lightning puzzle is missing. While researchers events? Is this radiation possibly dan- agree that the electron avalanche is a gerous to its surroundings? What con- substantive portion of the energy re- nections, if any, do TGFs carry to other quired for TGFs, there is still debate naturally occurring events? over what makes up the rest. On one While California may be hand, the relativistic feedback hypoth- known for Earthquakes rather than esis states that gamma rays occasion- Lightning, UC Santa Cruz has shown ally produce anti matter that would itself to be a deciding force on TGF travel downward, opposite the elec- research. Professor Smith and his fel- trons movement, and create new elec- low researchers have many plans for tron avalanches. On the other hand, the future including a crowd sourced the lightning leader hypothesis posits mobile app, further implementation that lightning bolts release additional of sounding balloons and an ADELE electron avalanches as they grow. clone carried on more aircrafts. With Since the original BATSE three spacecrafts currently active and sighting, TGF research has benefitted four encouraging missions projected immensely from improved technol- for the future, there are many reasons ogy. In 2002, the satellite, RHEESI, for us to be excited about his research launched and, although not specifical- over the coming years and hopefully it ly designed for TGFs, was able to better can live up to his belief in, “The Gold- measure TGFs arising from thunder- en Age.” storms. With its improved technol- ogy, RHEESI measured TGFs more frequently and with greater accuracy. Even more current, in 2009, with the help of UC Santa Cruz’s ADELE, the first TGFs were observed from a plane. Over the next decade, researchers will gain a wealth of data with which they will try to answer some long-standing questions.

Scientific Slug | February, 2014 22 BIOCHEMISTRY

Living Systems Happen By Andrew Kornfeld & Jahlela Hasle

parents of UC Santa Cruz science un- dergraduates was speaking at a fund- Two of the largest raiser for the UCSC science program. mysteries facing Deamer was also opening the audi- ence’s minds to incredible research be- science today ing conducted at UCSC. include the origin of life and the origin of con- Professor Deamer has com- sciousness,” stated David mitted his life’s work to rigorous sci- Deamer, Professor Emeritus entific experimentation of chemistry and biology, and is widely regarded of Chemistry at UCSC. as one of the world’s authorities on Professor Emeritus Dave Deamer, Ph. D the origin of living systems. While Deamer explores many questions, the foremost among them is fundamental: supernovae, the dramatic explosions at Imagine the most pristine en- the end of a star’s life. vironment ever created. No flaws, no How did life begin? The answer, it germs, no motes of dust. The hypo- would seem, lies in the basic chemical units that make up all living things. Modern scientists widely agree chondriac’s paradise. It is completely that every single carbon atom in our devoid of life, for life could never arise All living organisms on Earth bodies was once part of an exploding or perpetuate from this sterile environ- star somewhere in the universe. These ment. Without matter, there is no form, are made primarily from organic mole- cules -- specific combinations of atoms atoms, as either raw elements or mol- and without form, no organism could ecules, were then delivered during the hope to exist. While many of you that include carbon. Carbon’s preva- lence in life is no accident. The four formation of the earth on meteorites might think of a disinfected counter and comets. Understanding the type top, we are actually describing one of outer electrons that orbit its nucleus are constantly shared amongst other of “processing” these molecules under- nature’s most perfect laboratories, the went before being incorporated into life edge of a sulfur-ringed volcano. available electrons, either in other car- bons or atoms like oxygen and nitro- is the limit of our current knowledge. gen. In combination, these compounds What we do know, however, is that It seems unimaginable, but some of the molecules -- including ly- bubbling pits on the nascent earth create the building blocks for life: lip- ids, amino acids, nucleic acids, and sine and alanine (amino acids), and ad- like those found around Mount Mut- enine and guanine (nucleotides found novsky, in eastern Russia, may have sugars. With these, our bodies can cre- ate basic fats, proteins, and DNA, all in DNA) -- appear in homologous forms witnessed the very first life forms on in both carbonaceous meteorites and in our planet. In modern times, they the way up to more complex tissues, organs, and entire species. modern life. This means that some com- provide good models for these initial pounds found in space rocks are identi- conditions that may have spawned life cal to those found in you! and one UC Santa Cruz researcher is These atoms and molecules all over it. are vital for life, but how and where did they originate? Hydrogen, the Living organisms are defined in part by their ability to self-organize. “Two of the largest mysteries most simple and abundant element in the universe, has existed since the Big One example of this type of self-assem- facing science today include the ori- bly includes normal replication of cells gin of life and the origin of conscious- Bang. Helium and lithium formed in the aftermath as matter collected and in living systems. There are certain ness,” stated David Deamer, Professor abiotic molecules, such as those that ap- Emeritus of Chemistry at UCSC. It became more dense. Other heavier ele- ments, like carbon, nitrogen, and oxy- pear in cellular membranes that, when was the fall of 2010 and Professor De- placed in water, will “self assemble” to amer, surrounded by 40 or so proud gen were all created much later during

Scientific Slug | February, 2014 23

form membranes, a key component of BIOCHEMISTRY life. The trick is for these mol- ecules to become what is called ‘am- phipathic’ -- that is, one end has polar charge, while the other does not. You can imagine gluing a rubber eraser to a small magnet, and watching how the two ends interact with your fridge door. If we take this one step further, and collect many hundreds or thou- sands of these amphipathic molecules, the result is a continuous membrane- Supernova Remnant N 63A, Credit: NASA, ESA, like structure, with all of the magnetic HEIC, and The Hubble Heritage Team (STScI/AURA) ends facing out. This membrane for- mation may be the critical first step researcher in Deamer’s lab brings ex- between non-living and living. pertise in combinatorial chemistry to the table. Dr. Damer, who holds his In his laboratory on the Santa Ph.D in computer science, not only co- Cruz campus, Professor Deamer is incidentally shares 5 last name letters modeling these conditions by focusing with Dr. Deamer, but also shares a pas- on the four critical c’s for life: Com- sionate interest in the origin of life. His partments, Concentration, Cycles, work will be to produce large numbers and Combinatorial Chemistry. Here’s of parallel reactions using a concept the story: If you want to create life, in computer science and complexity you will need compartments (circular theory called “hill climbing”. Applied membranes) to store molecules in one in this context, hill climbing involves place so that they can undergo chem- the use of sheer numbers and the ma- ically-driven reactions. You also need nipulation of single variables that will enough molecules for those reactions increase the likelihood that at least one to have an effect, and one natural way of these reactions produces desired to concentrate molecules is through results. In this way, combinations that dry and wet cycles. Pour salt into a pot may previously have been overlooked of water, and it will dissolve into so- also gain proper scrutiny. lution. Boil all of the water away, and you are left with concentrated salt. The The next steps for Drs. De- same is true for any compound you amer and Damer are to combine their might use to create organic structures. knowledge of the 4 C’s necessary for Lastly, you need chance and big num- life, and take compounds similar to bers. One tablespoon of lipid (fat) can those found in asteroids to test them create one trillion compartments. With in sterile environments, like the sulfur numbers that high, it is only a matter pits on the side of Mount Mutnovsky. of time before combinatorial chemis- They hope to observe self-assembling try will produce pockets of molecules membranes and vesicles begin to in- with proto-life-like characteristics. We teract with one another through mol- now call these pockets ‘vesicles’, and ecules similar in structure to RNA. like a bubble within a bubble, vesicles Success will mean proof that living are capable of carrying signaling mole- systems happen spontaneously and cules, assembly proteins, or even parts naturally in complex biochemical sys- of other cells. tems. Life, which we once believed to be exceptional, may very well be inevi- Modeling these reactions is table. Art by Andrew Kornfeld tricky, but fortunately, a newly hired

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