Spring 2010: Volume 3, Issue 2

The Amherst

ELEMENT Volume 3, Issue 2

Spring 2010

From The Editors: We are pleased and proud to bring you the Spring 2010 issue of The Amherst Element. We wish to thank all of our fabulous contributors who made this issue not only possible but a pleasure to compile.

The submissions we received this semester would have made Charles Darwin proud. These articles range from offering a wholly new take on evolution (A Snapshot of a Contemporary View on Evolution: Can Darwin be Evaluated Through a Newtonian Scope?, page 15) to suggesting how the agency-detection mechanism in humans could have led to the development of human religions (Gods, Genes, Brains, and Baseball: Evolutionary Psychology Sheds Light on the Development of The Human Religious Mind, page 10). Those of you who are curious as to why white-headed raptors frequent lake shores ought to read Feathers, fish, and phylogenies: exploring why different species look the same (page 17). And those who wish to comprehend the mind’s appreciation of beauty may enjoy Why Bother Learning? Evolution and Human Nature (page 13).

We also received a diverse set of articles on the human mind for this issue. Decoding humans’ perception of time (page 11) will not help you interpret the phrase “The due date has been moved forward one day” any better, but it will give you an excellent idea of how humans use their spatial perspectives to visualize time.

Those who followed the Terri Schiavo case may be chilled to learn that not all patients in a vegetative state are truly unconscious (New Findings of Brain Activity in Disorders of Consciousness, page 5). But for vegetative individuals and for those suffering paralysis, devices are on the way that will soon allow them to communicate with the outside world (Mixing Mind with Machine: Tapping the Brain-Computer Interface, page 8).

Vitamin D might not directly relate to the mind, but it is crucial to bone development (and hard to come by in the Northeastern US). For an evaluation of the myths and facts surrounding this dietary supplement, check out Vitamin D: “Wonder Drug”? (page 4).

Finally, our issue features two original research articles. Emine Aluntas ‘11 discusses the unsolved problems of the Standard Model of physics and describes her summer research at the Large Hadron Collider in Mysteries of the Large Hadron Collider (page 20). In Aph-1 and Presenilins: a Tailless Tale? (page 22) Rebecca Resnick ‘10 describes her thesis research into a pathway crucial for C. elegans development. We hope you enjoy learning about their work as much as we did.

Although many of this issue’s articles focus on Biology and Neuroscience, The Amherst Element is in no way limited to these disciplines. If you have something to say about an interesting topic in Chemistry, Physics, Psychology, Geology, Computer Science, Mathematics, or other fields of scientific inquiry, we’d love to hear from you! Submissions can pertain to research you have personally contributed to, like a summer project or honors thesis, or be based on recent scientific publications, or the relationship between science and society. We also welcome all members of the Five College community to participate in editing and doing layout for The Amherst Element (no experience necessary). For more information about how to get involved, e-mail us at TheAmherstElement@gmail.com.

Sincerely,

The Amherst Element, Vol 3, Issue 2. Spring 2010

Christina Wright

Emma Fink

Table of Contents

The Amherst Element Staff Editors-in-Chief Emma Fink Christina Wright

Staff-Writer Liaison Ambika Kamath

Chief Layout Editor Mingzi Shao

Associate Copy Editors Emine Altunas Whitney Hang Ambika Kamath Afua Nti Kayleigh O’Keeffe Idrees Syed

Thesis Student Liason

Cover Feature 17

Feathers, Fish, and Phylogenies: Exploring Why Different Species Look the Same.

Ambika Kamath ‘11

Letters 4

Vitamin D: “Wonder Drug”?

Katherine Savage ‘12

Brian Smith ‘12

5

New Findings of Brain Activity in Disorders of Consciousness

8

Mixing Mind with Machine: Tapping the Brain-Computer Interface

10

Gods, Genes, Brains, and Baseball: Evolutionary Psychology Sheds Light on the Development of The Human Religious Mind

Sophia Cai

Layout Ambika Kamath Whitney Hang

Special thanks to David Vaimberg.

Laura Mahr ‘13

Whitney Hang ‘13

Alexandra Arvanitis ‘11

11

Decoding Humans’ Perception of Time

13

Why Bother Learning? Evolution and Human Nature

15

A Snapshot of a Contemporary View on Evolution: Can Darwin be Evaluated Through a Newtonian Scope?

20

Keelin O’Connor ‘12 (Smith)

Mysteries of the Large Hadron Collider

Get Involved!

Send questions, comments, letters, or submissions to TheAmherstElement@ gmail.com.

Christina Wright ‘11

Emine Altunas ‘11

Thesis Research 22

Aph-1 and Presenilins: a Tailless Tale?

Rebecca Resnick ‘10

The opinions and ideas expressed in The Element are those of the individual writers and do not necessarily reflect the views of The Element or Amherst College. The editorials are a product of the opinions of the current editors-in-chief of The Element. The Element does not discriminate on the basis of gender, race, ethnicity, sexual orientation, scientific background, or age.

Research findings published in The Element are not intended for wide distribution or for the reader’s profit. As a member of the Amherst community, please use the information and data presented in The Element judiciously.

Cover image: The African Fish Eagle (Haliaeetus vocifer) in Kruger National Park, South Africa.

The Amherst Element, Vol 3, Issue 2. Spring 2010

Letters

Vitamin D: “Wonder Drug”?

Katherine Savage Have you every wondered or wished for a miracle drug: a treatment that could treat multiple illnesses, while supporting your immune system and strengthening your bones? Some researchers believe such a drug exists. The name for this alleged panacea: Vitamin D. Vitamin D, which is sometimes referred to as the “sunshine vitamin,” is an essential nutrient found in most dairy products (especially fortified milk) and some types of seafood including fish and oysters. It is a common misconception that we receive Vitamin D from UV light from the sun. Rather, sunlight exposure triggers the production of Vitamin D in the body. Ten to fifteen minutes in the sun, three times a week, is sufficient for our bodies to generate the required amount of Vitamin D.1 Vitamin D exists in two forms. The Merck Manual of Medical Information nicely summarizes these forms: “Vitamin D2 (ergocalciferol) Figure 1. Editorial Cartoon from The Onion Source: http://www.theonion. is found in yeast that has been exposed to ultraviolet light (irradiated), com/articles/editorial-cartoon-october12-2009,12417/ and vitamin D3 (cholecalciferol) is found in fish liver oils and egg yolk.”2 But don’t be tempted to run to the nearest pharmacy and stock up The human body requires both forms to maintain a healthy diet. on Vitamin D supplements. Vitamin D’s true effects have not yet been Vitamin D3 is produced in the skin when exposed to ultraviolet light, such sufficiently studied.

It can be difficult for researchers and health care as sunlight. The liver and kidney convert and modify these vitamins into professionals to determine and isolate the effects of Vitamin D amidst hormones and forms that can be transported by the blood, thus allowing 2 the effects of other vitamins in the body. Additionally, although people these nutrients to reach tissues throughout the body. often perceive them as benign, vitamins, like all drugs, can have serious The best-understood role of Vitamin D is to maintain strong, healthy negative side effects when not taken in the proper dosage. For example, bones by promoting calcium absorption. New research suggests that it can excess consumption of Vitamin D can raise blood calcium levels, causing reduce the risk of coronary heart disease, diabetes, arthritis, and multiple 1 kidney stones and permanent damage to the kidney caused by calcification.5 sclerosis. Though most health care professionals agree on Vitamin D’s Further research is necessary before health care professionals can reach health benefits, there has not been enough scientific research to suggest the more definitive conclusions on the pros and cons of this so-called “wonder proper dosage. Few clinical trials have studied the ideal level of intake of this drug”.

Key among research aims is determining the “ideal dose” of Vitamin “wonder drug” and most of the existing recommendations derive from 3 D and based on the results of Dr. Manson’s studies and other research being retrospective observational studies. The absence of randomized, placeboconducted, the Institute of Medicine is currently reevaluating the dailycontrolled and double-blinded experiments makes a conclusive evaluation of 3 recommended intake of Vitamin D. Vitamin D’s beneficial and detrimental effects difficult.

Tara Parker-Pope, a medical writer for the NY Times, stated: “Since most of the data on Vitamin D comes from observational research, it may References be that high doses of the nutrient don’t really make people healthier, but that healthy people simply do the sorts of things that happen to raise vitamin 1. Vorvick, Linda, MD. “Vitamin D.” Medline Plus Medical Encyclopedia. 2009. <http://www.nlm.nih.gov/medlineplus/ency/article/002405.htm>.

D.”4 This suggests that a correlation, and not a causal effect, exists between 2.

The Merck Manual of Medical Information. Robert Berkow M.D. ‘ed’, being healthy and having high levels of Vitamin D. Dr. JoAnn E. Manson, Whitehouse Station, NJ: Merck Research Laboratories, 1997. a professor at Harvard University and chief of preventative medicine at 3.

“Largest Study of Vitamin D and Omega-3s set to begin soon at Brigham and Women’s Hospital in Boston is focusing her research on this Brigham and Women’s Hospital” Brigham and Women’s Hospital- Press particular question. In addition to her research on Vitamin D, she is also Releases (23 June 2009). studying the benefits of fish-oil supplements, which contain omega-3 fatty acids (The effects of which are currently unsubstantiated by rigorous 4. Parker-Pope, Tara. “Health Benefits of Vitamin D- Sound Science, or Hype?” New York Times (2010). <http://www.nytimes. scientific investigations.) She is also co-leading the largest randomized com/2010/02/02/health/02well.html>. research trial on the use of Vitamin D and omega-3s in the primary 5.

Turbo, Richard. “Vitamin D: Vital Role in your Health.” MedicineNet. prevention of chronic disease. Dr. Manson reported: “What is most exciting com (2004). <http://medicinenet.com/script/main/art.asp?articlekey is that these low-cost supplements have the potential of tremendously =54223&page=2.>. reducing the burden of chronic disease in this country and throughout the 6 world if they are shown to be effective.”

The Amherst Element, Vol 3, Issue 2. Spring 2010

Letters

New Findings of Brain Activity in Disorders of Consciousness Brian Smith Introduction In mid-March of 2005, national attention fell on the life of Terri Schiavo, a patient who was presumed to be in a Persistent Vegetative State (PVS). The debate as to whether or not to keep her on life support drew national attention and sparked numerous disputes. While Schiavo’s parents believed she was still conscious of her surroundings, her husband thought otherwise. After weeks of legal battles, Terri Schiavo’s life support was discontinued, and she passed away less than two weeks later.2 The case of Terri Schiavo raises the question of whether or not patients in vegetative states are aware of the world around them.

Could it be that Schiavo was simply incapable of communicating, and that, in reality, she was completely conscious, or was her brain simply unable to process her surroundings? In Schiavo’s case, this question will likely never be answered, but recent studies have found that not every patient in a vegetative state is unconscious.

In 1983, Rom Houben, a Belgian man, was involved in a car accident, leaving him paralyzed, as well as in what the doctors thought was a coma. However, Houben was fully conscious but unable to communicate. With a working brain and a defunct body, Houben was only left with his thoughts, and it was not until 23 years later that doctors discovered his state of consciousness by using high-tech brain scans, such as functional Magnetic Resonance Imaging (fMRI).3,4,5 It has become increasingly apparent that patients deemed to be in a vegetative state should be given a closer look. In November of 2009, an article published in the New England Journal of Medicine titled “Willful Modulation of Brain Activity in Disorders of Consciousness” (Monti et al. 2010), shed light on the diagnoses of these patients and found rather intriguing results that could eventually help vegetative-state patients to communicate.

The study had two main aims in the clinical assessment of patients in a vegetative or minimally conscious state. One goal was to determine whether the patient retained the capacity for purposeful response to stimulation, even if this response was inconsistent. This would suggest partial awareness from the patient, distinguishing patients considered to be in a vegetative state from those recognized as being in a minimally conscious state. This is important not only to gain knowledge on treatment and care of these patients, but also to formulate legal and ethical guidelines in regards to their welfare.

While making an assessment on a patient’s level of consciousness is extremely important, it is unclear as to whether or not the patient’s responses are reflexive or voluntary.

Unfortunately, this has led to a high percentage of diagnostic errors, with 40% of this group of patients being misdiagnosed.6 The second goal of Monti et al.’s study was to extract responses from the patients in the form of any type of reproducible communication.

This would not only be a major milestone for the patient, but it would also help in clarifying the patient’s state of consciousness.

Methods Fifty-four patients with severe brain injuries (23 vegetative state, 31 minimally conscious state) were evaluated on motor and spatial imagery tasks using functional Magnetic Resonance Imaging (fMRI). This involved taking images of the brain while asking specific questions to the patients in order to see what areas of the brain where activated during the questioning. The results of fMRI scans of 16 healthy control subjects (9 men and 7 women), who were asked the same questions, were then used to make comparisons with the group of patients with impaired consciousness.

Imagery Tasks

Every patient and control subject in this study was asked to perform two imagery tasks while in the fMRI scanner. The first task, which tested the patient’s motor imagery, involved asking the patients to imagine that they were playing tennis. The second task, which tested the patient’s spatial imagery, involved asking the patients to imagine walking the streets of a familiar city or walking from room to room in their house. (Figure 1.)1

Communication Task

This task only involved the 16 control subjects and 1 patient, as the task constituted modulating brain activity. Each test subject underwent fMRI while attempting to answer yes-or-no questions by using mental imagery. For instance, if the question “do you have any brothers?” was asked, the subject could think of either spatial or motor activity, which would correspond to an answer of “yes” or “no.” (Figure 2.)1 Results

Responses to the Imagery Tasks

Five of the 54 patients (23 of whom had non-traumatic brain injuries) who were tested were found to be able to modulate their brain activity. In all of these patients, the fMRI results showed that motor imagery was associated with activation of the supplementary motor area. The scans of 4 of the 5 patients showed activation in the parahippocampal gyrus in the brain, which plays an important role in memory retention. The results were almost identical to those of the control subjects. All of the 5 patients that showed brain modulation had previously experienced a traumatic brain injury, and the 4 of them had been considered to be in a vegetative state.

Responses to the Communication Task

All 16 control subjects correctly answered their questions in the communication scans. A comparison between the localizer scans and the communication scans verified this accuracy, as the patterns produced by the responses were very similar. The distinction found

The Amherst Element, Vol 3, Issue 2. Spring 2010

Letters

Figure 1.1 Imagery Tasks.

This figure compares fMRI scans of one healthy control with five patients with traumatic brain injury.

The scans show the activated areas of the brain associated with spatial imagery tasks (yellow and red areas) and motor imagery tasks (green and blue areas). The five patients show very similar results to the healthy control, giving reason to believe that they can modulate their brain activity despite being diagnosed as in a vegetative state. between the different tasks was also verified, as there was activity in the supplemental motor are for motor imagery and activity in the parahippocampal gyrus for spatial navigation.

The one patient that partook in the communication task went through the same tests as the healthy control subjects. Of the six questions that were asked to the patient, five were found to produce matching scanner images with those of the healthy control subjects.

Discussion While 5 of the 54 patients who had traumatic brain injuries were able to modulate their brain activity by performing imagery tasks, none of the 23 patients with non-traumatic brain injuries were able to produce voluntary brain activity. Due to the fact that 4 out the 5 patients who could modulate their brain activity were admitted to the hospital in a vegetative state, this new information may mean that there is a small chance that a patient who appears to be in a vegetative state could actually be consciously aware.

One of the five patients who showed evidence of consciousness on the fMRI scans was found to be able to accurately answer simple “yes or no” questions using the imagery technique. Whereas all other

The Amherst Element, Vol 3, Issue 2. Spring 2010

means of detecting the patient’s awareness pointed to a vegetative state, these scans proved the patient to be in a minimally conscious state.

This patient only failed to answer one of the six questions asked, as there was no brain activation in the areas of interest. This fact might be due to several reasons—the patient might have fallen asleep, lost consciousness, or simply not have heard the question.

The 49 patients that were not able to modulate their brain activity showed no significant fMRI changes during the imagery tasks. This could have been due to technical limitations in measuring smallerthan-normal changes in the brain scan, or else because of the limited cognitive abilities of the patients. Some patients could have been unconscious, either permanently or transiently, during the study. Other patients who were in a minimally conscious state may have had deficits in language comprehension, working memory, decision-making, or executive function.

While results from this study show that fMRI has the potential to give a clearer clinical assessment of the awareness of a patient, it also sheds light on how often patients with severe brain injuries are misdiagnosed. There were 23 patients in the study who were diagnosed as being in a vegetative state, and 4 of these patients were found to

Letters be able to willfully modulate their brain activity. When behavioral examinations were performed on two of these patients after the scans, there was some behavioral evidence of awareness, which was not noticed in these patients before. Since this study could lead to a better chance of correctly diagnosing patients with disorders of consciousness, its importance becomes more obvious.

The two other patients who could modulate their brain activity continued to show no sign of awareness outside of the fMRI results.

This indicates that some patients may have an extremely limited amount of motor capabilities, at such a level that they may not be able to physically demonstrate their awareness. This suggests that fMRI can be an important diagnostic tool for these vegetative patients. One patient gained the ability to communicate solely by modulating brain activity, which was not possible to establish at the bedside.

Future extensions of this study could delve into more important clinical questions. Asking patients if they are experiencing any pain, or any other patient-benefitting question could determine whether the patient should be put on medication or if there is something that can be done to make the patient more comfortable. Future technology could use this technique to help these patients express thoughts, control their environment, and improve their quality of life.

Conclusion This study provides much-needed insight into the world of consciousness disorders. Patients who were once considered to be in a vegetative state may now be able to be correctly diagnosed. The possibility of becoming stuck in one’s own body is a frightening thought, but the unfortunate reality is that there are rare instances when it happens. For these patients, the opportunity to express themselves, sometimes after years or even decades of silence, provides the ultimate sense of relief and gratitude.

The effects of this research have already made a difference for many patients. One patient in particular, the aforementioned Rom Houben, has been the topic of a multitude of media feel-good stories.

Not only has he been able to regain his ability to communicate, he has been able to tell his story in vivid detail with the aid of a computer.

It can be assumed that there are many other people like Mr. Houben, who are trapped inside their own bodies and are incapable of outward communication. The use of fMRI brain scans like the ones in this study could help reassess the diagnoses that are placed on these patients, in turn giving valuable insight into the minds of some of the most misunderstood human beings.

References

1.

2.

3.

4.

5.

Figure 2.1 Communication Scans.

This figure compares the activity patterns in the brains of a healthy control and a patient during an fMRI. Panels A and B show that the observed activity pattern (orange) closely resembled the patterns observed in the motor-imagery localizer scan, which indicates a “yes” response. Panels C and D show the observed activity pattern (blue) closely resembled the patterns observed in the spatial-imagery localizer scan, which indicates a “no” response.

6.

Monti, M. M., Vanhaudenhuyse, A., Coleman, M. R., Boly, M., Pickard, J. D., Tshibanda, L., Owen, A. M., Laureys, S. 2010. Willful Modulation of Brain Activity in Disorders of Consciousness. New England Journal of Medicine.. 362: 579-589.

The Terri Schindler Schaivo Foundation. http://www.terrisfight.org/ Paralysed Belgian misdiagnosed as in coma for 23 years. BBC News Online. 2009. http://news.bbc.co.uk/ Paddock, Catharine. Belgian Man Trapped In Coma For 23 Years Was Conscious Throughout. Medical News Today. 2009. http://www.medicalnewstoday.com/ Diagnostic accuracy of the vegetative and minimally conscious state: Clinical consensus versus standardized neurobehavioral assessment.

Schnakers C, Vanhaudenhuyse A, Giacino J, Ventura M, Boly M, Majerus S, Moonen G, Laureys S. BMC Neurology. 2009. 9:35 (21 July 2009).

Childs NL, Mercer WN, Childs HW. Accuracy of diagnosis of persistent vegetative state. Neurology 1993; 43:14651467.

The Amherst Element, Vol 3, Issue 2. Spring 2010

Letters

Mixing Mind and Machine: Tapping the brain-computer interface Christina Wright Science fiction has popularized the concept of the brain-computer interface, a direct communication pathway between the mind and a technological device. It’s easy to see where the charm comes in. What college student hasn’t wished for a neural implant with which he could store biology terms before his big midterm? Or a USB drive that would allow him to share memories with his friends? Although many consider cyborgs to be confined to the universe of Star Wars or Battlestar Galactica, for the physically disabled, the brain-computer interface is not just an interesting idea, but a rapidly-materializing reality.

Electronic devices that interact with the body are hardly new.

Perhaps the best-known electromechanical device, the pacemaker, was developed in the 1950s and continues to receive widespread use.

Cochlear implants, which gained FDA approval in the 1980s, currently serve as many as 60,000 people in the United States and 180,000 worldwide. These devices work by harnessing the ear’s tonotopic map – the spatial arrangement of neurons that fire in response to mechanical waves of various frequencies – to aid in detecting sounds. An array of electrodes is implanted within the cochlea and is linked (through a transmitter) to an external speech processor; stimulation of different cochlear electrodes mimics the sounds a non-deaf person would hear.

The cochlear implant and its cousin, the still-in-testing artificial retina1, have shown scientists that it is possible to pass information from the outside world into the nervous system in a form that the mind can comprehend.

However, for sufferers of devastating conditions such as locked-in syndrome, in which patients are totally paralyzed but retain full awareness of their surroundings, the issue is not getting the information in, but communicating with the outside world.

As many as 5000 individuals per year are diagnosed with locked-in syndrome, which may be caused either by damage to the lower brain or brainstem or by Amyotrophic Lateral Sclerosis (ALS), a disease of the nerve cells that control voluntary muscle movement. Often the voluntary muscles controlling the eyes remain intact, and communication is possible through devices such as an eyegaze computer. Scientists are seeking new approaches that will enable effective and rapid communication for individuals whose paralysis extends to the eyes (total locked-in syndrome), and the braincomputer interface (BCI) seems the best hope for success.

Scientists in Frank Guenther’s laboratory at Boston University, working in collaboration with Phillip Kennedy, a leader in neural

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implantation science and the founder of Neural Signals, Inc., are attempting to develop a BCI that will translate neural signals into actual speech. The approach involves the implantation of an electrode into a region of the left-precental gyrus, an area of the brain associated with speech.2 So far, this procedure has been performed in one man, Erik Ramsey, who suffered a stroke following a car accident at the age of 16.

The process of electrode placement is complex and patient-specific, requiring multiple pre-surgery MRIs. The implanted electrodes are extremely thin gold wires, coiled into flexible springs so that the ends will remain in place when the brain moves relative to the skull. The wires are encased in a cone-shaped glass micropipette tip that contains an opening to facilitate the entry of axons. Nerve growth factors – chemicals that stimulate neural proliferation – are applied to the glass tip, and these also stimulate neural processes to enter the micropipette, holding the electrode in place within the brain.3 The special nature of the electrode implant – in particular, encasing it in glass – is important if the electrode is to remain functional for more than a year. Gliosis, or neural scar tissue formation, is a major problem with brain implantation, arising from direct exposure of a metal electrode to cells or electrode movement in the brain. Gliosis can cause implant sensitivity to be drastically reduced, meaning that an implanted device may rapidly lose its ability to read from within the brain.3 Once the electrode is placed and the patient has recovered, feature-extraction algorithms are used to dissect the signals surrounding the electrode.4 These algorithms identify specific and relevant features that encode messages from the patient, such as the firing pattern of a specific neuron – in this case, the patterns of activity detected in neurons related to speech.

Naturally neurons within range of the electrode must be first identified; in Ramsey’s case, forty-one were found to be speech-relevant.3 Following feature extraction, a second type of algorithm known as a translation algorithm makes sense of the signal features previously extracted. These algorithms are capable of adjusting to the user’s typical range of firing rates and intensities and of adapting to shortterm variations in performance, such as those induced by illness, time of day, or hormone levels.4 Then comes the complicated task of training the patient to use his implant. Just like learning to walk, tuning any BCI requires training and feedback. Complex BCIs cannot simply “mind-read”; their use is

Letters an acquired skill that requires adaptation of the brain’s natural activity.4 The ideal processing and translation algorithm should help this process, taking into account changes in the use of the BCI over the long-term and using it to improve BCI operation.

So far, the Guenther lab has succeeded in decoding vowel sounds but not the full plethora of syllables that constitutes true speech.2,3 Dr. Guenther is hopeful that the use of a new device, which can read from many more neurons, will allow scientists to extract signals controlling more complicated consonant sounds. Still, Dr. Kennedy predicts that it will be many years before fast, fluid speech is achieved through a prosthetic implant.

For paralyzed individuals who wish to communicate via the internet, the BrainGate System, initially developed by Cyberkinetics Neurotechnology Systems in collaboration with researchers from Massachusetts General Hospital and Brown University, may suffice as a communication medium in lieu of real-time speech. The device is a small silicon computer chip with 96 electrodes, implanted above the motor cortex, which can monitor neuron signaling involved in movement. Patients implanted with this device can move a cursor across the computer screen, check their e-mail, and play Pong without actually lifting a finger. Technology such as this may be the key to the development of prosthetic devices such as artificial limbs that are under neural control.5 Electrode implantation is not without downsides. Like any foreign device in the body, electrodes increase the possibility of immune response, inflammation, and infection. Assessing patient understanding about the surgery is a challenge with locked-in patients, who may be unable to communicate their agreement or comprehension of the procedures involved. The ethical complexities associated with gaining informed patient consent6 may hamper researchers seeking funding and approval for experimental implants.

Adam Wilson, a graduate student at the University of WisconsinMadison, has found an alternative to the approach of an electrode implant. His widely-publicized April 2009 Twitter post (“SPELLING WITH MY BRAIN”) could herald a revolution for paralyzed individuals struggling to communicate with the outside world.

The UWM system (which researchers have jokingly nicknamed the Brain-Twitter interface) and many similar systems use a combination of computer science and electroencephalography (EEG). Instead of surgically implanted wires, electrodes are placed on the scalp to record the electrical activity produced by firing neurons within the brain. Of course, each electrode is bombarded by the synchronous activity of thousands or even millions of firing neurons, so attaining specificity comparable to that of an intracranial electrode is impossible.

Instead, scientists use EEGs to measure brain waves and neural activity on a broader scale. The appearance of a special brain wave called the P300 event-related potential (ERP) is most commonly used to inform the computer that the user’s letter of interest has appeared.

The P300 signal, which appears 300 ms after the correct letter is flashed, is linked to an individual’s attentiveness to a stimulus but not to the stimulus’s physical characteristics.7 The brain emits different wave patterns when the letter of interest lights up, and electrodes placed on the user’s head detect these wave differences causing the computer to record the letter on a word processor – or a Twitter post.

The advantage of the UWM approach and that of Intendix, its

commercial twin that will launch this year, is its non-invasive approach; the electroencephalogram (EEG) recordings are painless and external to the brain. Unfortunately, the process of sending a message is laborious, with the fastest users achieving a speed of 10 letters per minute: certainly not ideal when one considers that the average typing speed for adults is on the order of 60 words per minute.

Judging by the rapidity with which BCIs are gaining popularity, the use of neural implants for paralyzed or locked-in patients is sure to skyrocket in the coming years. Locked-in patients are not the only ones for whom researchers are targeting BCIs; brain-controlled prosthetic arms might one day help amputees to move, and scientists have even looked into silicon chips as artificial hippocampal replacements for individuals suffering from Alzheimer’s or memory loss.

Quite distinct from the already-contentious issue of patient consent for invasive procedures, the potential blurring of human body and mind with machine sparks a new, ironically mind-boggling set of ethical questions. Among these are issues of privacy (could devices that extract information from the mind also be used for tracking or control?), the morality of using of such devices for physical and sensory enhancement (such as infrared vision), the moral responsibility of individuals with malfunctioning BCIs, and the question of when to draw the line between human and machine.8 If genetic modification has locked biologists in a twenty-year ethical battle, BCIs have at least as much potential to incite controversy in future years.

Perhaps fortunately, the complications associated with implanted BCIs make them a more difficult route toward bodily enhancement than genetic modification. Even their use for improving the quality of life of the disabled suffers from obvious limitations. Furthermore, although results look promising, as of now, invasive BCIs have been tested on a relatively small number of individuals. Noninvasive BCIs, while safer, are still limited in the scope and speed of user activity.

In short, it will probably be a number of years before Darth Vader walks down the street. And when he does, you’ll probably want to go to the Neural Devices store around the corner and ask about that memory chip.

References 1. Miller, G. (2008). Engineering a fix for broken nervous systems.

Science. 322(5903).

2. Guenther, F., et al (2009). A wireless brain-machine interface for real-time speech synthesis. PLoS ONE.4(12): e8218.

3. Schnabel, J. (2008). Neural implant aims to restore speech to the paralyzed. The Dana Foundation.

4. Wolpawa, J.R., Birbaumer, N., McFarlanda, D.J., Pfurtscheller, G., Vaughan, T.M. (2002). Brain-computer interfaces for communication and control. Clinical Neurophysiology. 113.

5. BrainGate: http://www.braingate.com 6. Haselager, P., Vlek, R., Hill, J., Nijboer, F. (2009). A note on the ethical aspects of BCI. Neural Networks. 22(9).

7. Daly, J.J., Wolpaw, J.R. (2008). Brain-computer interfaces in neurological rehabilitation. The Lancet Neurology. 7(11).

8. Schermer, M. (2009). The mind and the machine. On the conceptual and moral implication of brain-machine interaction.

Nanoethics. 3(3): 217-230.

The Amherst Element, Vol 3, Issue 2. Spring 2010

Letters

Gods, Genes, Brains, and Baseball: Evolutionary Psychology Sheds Light on the Development of The Human Religious Mind Laura Mahr The baseball team is doing pushups on the field, counting them off in unison. The parishioners sit and stand together in the church, reciting the liturgies of their faith. These are two very different scenarios—the one secular, the other sacred (although in America it is sometimes debatable which is the sacred)—with important similarities. A recent article1 by Matt Rossano argues that some of the same mental features and selective pressures underlie a baseball practice and a Sunday morning in church.

Religion is a universal and—in terms of time, energy and resources—costly phenomenon, and as such it cries out for an evolutionary explanation. (Religion can be defined here as behavior based on the belief in supernatural agents.)

The basic question is this: how would genes associated with religious behavior increase their chances of out-reproducing other genes in the human gene pool? Rossano comes at the question from a fresh angle. He asks what features of mind are necessary for religion and how natural selection would have favored them in our evolutionary past. The two most important are social bonding and agency detection.

Is That a Tiger or the Wind?

Religion is all about agency. Gods are always doing things: creating the world, punishing sinners, dispensing revelations.

Human beings, too, are usually doing things, and it is useful to be able to predict what those things will be. That ability both requires the idea that another hunter has a mind like your own and confers a substantial selective advantage. You can tell if he is willing to help you bring down a large prey animal—or if he is coming to kill you.

Because of its utility, the agency-detection mechanism evolved a hair-trigger. Rustling leaves might just be the wind—or they might mean a tiger is getting ready to pounce from the bushes. The human who spins around at every rustling leaf has a better chance of surviving when, once in one thousand times, the sounds are in fact caused by a hungry tiger. Over-reaction costs seconds; under-reaction costs lives. Therefore, genes that code for over-assigning agency are more likely to be passed on to the offspring of their human carriers.

Rossano, among others 2,3, views the human tendency to over-apply agency as a fundamental feature of the religious mind.

Shamanistic cultures have seen natural events—earthquakes, disease, weather—as the results of spirit actions for tens of thousands of years. 4 It is not hard to see why. When the

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theory of other minds so well explains events on a small, social scale, why posit a new theory to explain events on a larger, natural scale? Such a theory will not help either bodies or genes survive or reproduce. (Thinking that lightning intends to kill you is sufficient motivation to avoid trees during thunderstorms, even if it is incorrect to personify a storm.) And without the ability to postulate supernatural beings, religion would be—literally—unthinkable.

I Love You, Man Much as some Protestants insist otherwise, religion is not just between you and God; explaining how the concept of supernatural agents evolved does not come close to explaining the religious community. It is necessary, not sufficient. Of course, no one yet knows what is sufficient, but Rossano has a model to offer. Religion cannot be considered simply as an offshoot of a mental module with survival value, but must be thought of as a cultural innovation with survival value in itself.

Human beings are social. From prehistory to the present, arguably our greatest assets and our greatest threats have come from each other. The social cohesion of a group has always offered great rewards for the survival of individual genes that code for social behavior—their human carriers would reap the benefits of group life and survive long enough to reproduce and pass on the genes that made it possible.

Genes for behaviors enhancing social cohesion could then be expected to predominate in humans.

Studies 5, 6 reveal that some nonhuman primates engage in social bonding behaviors like grooming, group hooting, and embracing. Such rituals, especially when they involve rhythmic dancing and chanting or intoxicants (take a look at the Social Quad), release brain opioids that may be critical to bonding. 2 Religious rituals probably grew out of such secular (or pre-religious) bonding behaviors; the tendency to postulate supernatural gods most likely came in later in evolutionary history. (As evidence for this view, one can cite the fact that the emotional centers are in an “older,” “deeper” area of the brain than the cognitive centers that underlie agency detection.)

Groups of hunter-gatherers that bonded through religion may have been more cohesive, especially with the development of the idea of ever-vigilant supernatural policemen—members of the group would be less likely to cheat and hurt each other and thereby weaken social bonds.

Letters God and Babe Ruth When the members of the baseball team exercise and chant together, their brains are releasing bonding opioids.

When the crowded mosque bows as one toward Mecca, the same thing is happening. Social bonding and agency detection are vital in both settings, and both probably underpin all past and present forms of human religion. They will be included, and of course expanded upon, in every model of religion. So when Babe Ruth pointed to the sky after hitting a home run, he was doing more than infuriating Red Sox fans—he was illustrating the conclusions of evolutionary psychology.

References 1. Rossano, Matt J. (2006). “The Religious Mind and the Evolution of Religion.”Review of General Psychology, 10, 346364.

2. Hayden, B. (2003). Shamans, Sorcerers, and Saints.Washington, D.C.: Smithsonian Institute Books.

3. McClenon, J. (1997). “Shamanic Healing, Human Evolution and the Origin o Religion.” Journal for the Scientific Study of Religion, 36, 345-354.

4. Clottes, J., & Lewis-Williams, D. (1998). The Shamans of Prehistory: Trance and Magic in Painted Caves.New York: Abrams Press.

5. Watanabe, J.M., & Smuts, B. B. (1999). “Explaining Religion Without Explaining ItAway: Trust, Truth, and the Evolution of Cooperation in Roy A. Rapaport’s ‘The Obvious Aspects of Ritual.’ American Anthropologist, 101, 98-112.

6. Goodall, J. (1986). The Chimpanzees of Gombe. Cambridge, MA: Harvard University Press.

Decoding Humans’ Perception of Time Whitney Hang Humans use their spatial experiences to “visualize” time. Therefore, manipulating their interpretation of space also changes their understanding of time.

It is the final week of school. All of your friends are stressed out, trying to finish their work. During a quick study break, you see an e-mail from your professor for whom you have a paper due on Thursday. The e-mail reads: “The due date for the final paper has been moved forward one day.”

Does this mean that the paper is now due on Wednesday or Friday? It is during dire moments like these that you wish you understood how humans, particularly your professor, perceive time.

Because time is so abstract, people regularly use space, a more concrete concept, to represent time. In his latest book The Stuff of Thought, Steven Pinker explores the reasons behind the ambiguity of moving “forward” a deadline. When interpreting stationary time, people use the time orientation metaphor where the observer, located at the present, has the future in front of him and the past behind him. The time orientation metaphor gives rise to such sayings as “that’s all behind us” and “we’re looking ahead.” However, once metaphorical motion is considered, there are two ways in which the time orientation metaphor can be perceived. 1 First is the ego-moving perspective, in which the observer sees himself moving forward through stationary time, such

as in the sayings “there’s trouble down the road” and “we passed the deadline.” If the professor has this point of view, the due date would be moved forward in the direction of motion (towards the future), which is from Thursday to Friday. The second option is the time-moving perspective, in which the observer sees time approaching him, such as when we say “the deadline is approaching.” The due date is again moved forward in the direction of motion, but since time is moving past the observer (towards the past) in this view, forward refers to a switch from Thursday to Wednesday. 1 Boroditsky and Ramscar, researchers at the Massachusetts Institute of Technology and the University of Edinburgh, set out to determine whether moving through space, a more concrete experience, influences people’s perception of the time orientation metaphor. Previous studies showed that in a neutral environment people favor neither the ego-moving perspective nor the time-moving perspective, thus they would be just as likely to say that the due date has been moved to Friday as they are to say it has been moved to Wednesday.

Boroditsky and Ramscar hypothesized that if perception of time is related to movement through space, then manipulating The Amherst Element, Vol 3, Issue 2. Spring 2010

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Letters how people think about space should also influence their perception of time. 2 To test their hypothesis, Boroditsky and Ramscar separated their experiment into four studies. In the first study, they asked a pool of undergraduates the question, “Next Wednesday’s meeting has been moved forward two days. What day is the meeting now that it has been rescheduled?” Before asking the question, they told half of the pool to imagine moving themselves through space in an office chair and the other half of the pool to think about pulling an office chair towards them. This study focused on whether imagining themselves moving through space (akin to the ego-moving perspective) or imagining objects coming toward them (akin to the timemoving perspective) caused participants to favor one of the perceptions of the time orientation metaphor. 2 Of the people who imagined the office chair approaching them, 67% answered with the mindset of time approaching them (the time-moving perspective), meaning the meeting initially on Wednesday is now on Monday. On the other hand, those asked to imagine themselves moving in the office chair were more likely to adopt the ego-moving perspective and answered that the meeting is now on Friday. These findings supported the original hypothesis and incited Boroditsky and Ramscar to further their study. 2 In the second part of the study, Boroditsky and Ramscar tested whether people unconsciously changed their perception of time during everyday spatial-related activities, such as waiting in a lunch line. To do so, they asked people in a lunch line the question about Wednesday’s meeting and recorded how far along the line the people were. The results showed that spatial motion affects people’s perception of time, as those who were further along in line, and thus experienced more forward spatial motion, were more likely to adopt the ego-moving perspective. 2 The third study tested whether physical spatial motion is necessary to influence a person’s perception of time or if mere spatial thinking is enough. The researchers asked the same question to people at an airport who had either just landed, were waiting for someone to arrive, or were waiting to depart. Those who had just landed had physically moved through space, those waiting to depart were thinking about spatial motion, and those who were waiting for someone to arrive had not experienced spatial motion, nor were they thinking about it. People who had just landed were more apt to adopt the ego-moving perspective (and say that the meeting was now on Friday) than others. But even more interestingly, those who merely thought about spatial motion were also likely to assume the ego-moving perspective, though not as often as those who had actually experienced spatial motion. 2 These results prompted a final study to determine whether those who had just landed were more likely to adopt the ego-moving perspective than those who were about to depart because they had actually experienced spatial motion or because they had thought about spatial motion for a longer

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period of time. In this final study, the researchers posed the question to train passengers. The researchers also recorded how long the passenger had been on the train and how much further they had to travel to their destination. All of the passengers were engaged in the same spatial experience (sitting on the train), but their attachment to thinking about spatial motion varied based on whether they had just boarded the train, were in the middle of their journey, or were about to arrive. Passengers are more likely to think about their journey when they have either just boarded the train or are about to arrive at their destination, so according to the researchers’ hypothesis, these passengers were more likely to adopt the ego-moving perspective on time. The results support their hypothesis, which finalizes the relationship between people’s spatial motion experiences and their perception of time. 2 Now, if you put yourself back into the shoes of a stressed out college student (which may not take much effort), and you reread you professor’s email stating that the due date for your final paper has been moved forward one day, do you know if the paper is due Wednesday or Friday? Probably not, but you know you have two options: take the time-moving perspective on time and potentially turn in your paper a day early, or potentially turn in your paper late and use the excuse that you merely have an ego-moving perspective on time.

References 1. Pinker, S. 2007. The Stuff of Thought. New York: Penguin Group.

2. Boroditsky, L. and Ramscar, M. 2002. “The Roles of Body and Mind in Abstract Thought.” Psychological Science 13: 185-89.

Letters

Why bother learning? Evolution and human nature alexandra arvanitis What is human nature? Good, bad, indifferent, corruptible?

Philosophers, priests, and poets have debated human nature for millennia, and no one has ever come up with a satisfactory answer—at least as far as its qualities are concerned. But when it comes to its origins, biologists, at least, are fortunate to have a few more answers.

Studies over the past forty to fifty years have shown that understanding the mechanisms of development, function, and evolution of animal behaviors can help us to understand their counterparts in human behavior, by exposing the evolutionary pressures that result in the mental instincts of both animals and humans.

The architecture of the brain In a 2005 article for the Handbook of Evolutionary Psychology, John Tooby and Leda Cosmides take an adaptationist perspective to the old question of nature vs. nurture, demonstrating that the two theories of human development are not only not mutually exclusive, but in fact seem to work in harmony. The reason for this, they argue, lies in the architecture of the human brain itself, and how it leads to “learning” behaviors: “logic,” they say, “forces us to conclude that there had to be, at some point in the causal chain, a program that caused learning but that was itself unlearned.”1 In other words, there is something in the “hardware” of the brain (as opposed to, as Tooby and Cosmides put it, the hardware of a three-pound cauliflower) that allowed the “software” of learning programs to arise.

Their point, of course, is that “learning is not an alternative explanation to the claim that natural selection shaped the behavior”2 because the ability to learn and the degree to which a person (or any other organism) can learn is a trait that is naturally selected for. In other words, given the reproductive pressures acting on humans, the ability to learn to the high degree we call sentience was reproductively advantageous, whereas in birds (for example) resources that we use to power our energy-costly brains were from a reproductive standpoint put to better use in other areas (such as into muscles for long-distance migration or high-maintenance displays of feathers to attract mates).

Just as a bird builds a nest because of instinct, we—human beings—learn because we have an instinct to do so. Learning and

acquiring (certain types of) knowledge conferred and continues to confer a reproductive advantage on the humans who possess and act on it, just as the instinct to acquire twigs and build nests conferred and continues to confer a reproductive advantage on the birds who possess and act on it.

Just another organ Steven Pinker, also writing for the Handbook of Evolutionary Psychology, makes a similar point. Regarding his youthful dissatisfaction with the field of psychology, he writes, “a student rarely enjoyed the flash of insight which tapped deeper principles to show why something had to be the way it is, as opposed to some other way it could have been”3 and asks, “couldn’t other areas of psychology…benefit from an understanding of the problems our mental faculties solve—in a word, what are they for?”4 The same idea underlies both his complaint and his question: the search for ultimate, rather than proximate, explanations of elements of human psychology.

Moreover, Pinker directly relates the evolution of psychological and behavioral traits in humans to the evolution of every other distinctive feature of every other organism on the planet: “the appeal to function in evolutionary psychology is itself constrained by an external body of principles—those of the modern, replicator-centered theory of evolutionary biology.”5 Elaborating on this relationship, he declares that “an explanatory hypothesis for some emotion or cognitive faculty must begin with a theory of how that faculty would, on average, have enhanced the reproductive chances of the bearer of that faculty in an ancestral environment.”6 In addition, he insists on extra-psychological (e.g. physical, chemical, physiological, etc.) explanations for the usefulness of the psychological trait, giving the example of a psychological trait to fear snakes as being grounded in the chemical effect of snake venom on human physiology.

What is notable here is the fact that Pinker treats human psychology— human consciousness and human cognitive ability—just like any other physical characteristic: as something evolved because of specific selective pressures that encouraged it, or encouraged a trait of which it is a side effect. This is similar to Tooby and Cosmides’ argument, The Amherst Element, Vol 3, Issue 2. Spring 2010

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which could be summarized as saying that human psychology is at least partially dependent on certain evolved, physical connections between neurons that cause certain advantageous behavioral affects.

A beautiful mind Of course, Tooby and Cosmides’s point about the evolutionary advantage conferred by the ability to learn and to acquire knowledge is not unique to the twenty-first century. Nor is Pinker’s point that, in contrast to other psychological traits, “[it is] not clear what the adaptive function of music is, or of religion.”7 In fact, both were addressed and synthesized in a 1965 BBC narrative by Nicholas Humphrey, called The Illusion of Beauty. Humphrey suggests that human appreciation of beauty arises from the mind’s need to learn how to categorize and classify the world around it—the ability to notice pertinent differences between generally similar objects. In doing so, he theorizes a concept of beauty based around repetition with minor and/or cumulative differences, suggesting that humans find this attention to theme and variation pleasurable because it is necessary for the development of the human mind. This is similar to how humans find the consumption of fat, salt, and sugar pleasurable because they are necessary for the development of the human body.

Moreover, Humphrey suggests, just as junk food hijacks the gastronomic pleasure response, things like music and art hijack the psychological one. The difference, he cedes, is that while one can overdo it on junk food—taking in too much of elements that are so appealing because they were once so scarce—it is difficult to overdo it on mental training.

Though, one may be tempted to point out that a human who is so overwhelmed by the pleasure of, say, Beethoven’s symphonies that he sits and studies them all day without engaging in meaningful social interaction (and is therefore socially or psychologically

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unappealing to potential mates) is rather unlikely to reproduce.

Similarly, a man who is so overwhelmed by the taste of his food that he overeats and becomes obese (and is therefore physically unappealing to potential mates).

In either case, Humphrey’s point can be broadly applied to the whole exercise of understanding the evolution of human behavior through understanding the evolution of animal behavioral and even somatic characteristics. Perhaps the “flash of insight” that Pinker longs for is praised and sought after because it indicates a successful categorization on a basic level—a categorization arising out of understanding a particular similarity between seemingly different human and animal evolution. Perhaps Tooby and Cosmides’s drive to resolve the debate between nature and nurture—to defuse the tension, to come to a solution that integrates key elements of both theories—is desirable because it encourages humans to resolve apparent inconsistencies or tensions in their attempts to categorize their environments, thus leading to more accurate (and presumably, therefore, more useful) categories.

Both humans and animals inherit the physical and psychological traits that gave their forbears a reproductive advantage over the competition; the only question is how deep beneath the surface the origins of those first advantages lie.

References 1. Tooby, John, and Leda Cosmides. “Nature and nurture: an adaptationist perspective.” In The Handbook of Evolutionary Psychology, edited by David M. Buss, 30-36. Hoboken, NJ: John Wiley & Sons, 2005. 31 2. Tooby and Cosmides 32 3. Pinker, Steven. “Foreword.” In The Handbook of Evolutionary Psychology, edited by David M. Buss, xi-xvi . Hoboken, N.J: John Wiley & Sons, 2005. Xi 4. Pinker xiii 5. Pinker xiv 6. Pinker xiv 7. Pinker xv

Letters

A Snapshot of a Contemporary View on Evolution: Can Darwin be Evaluated Through a Newtonian Scope?

Keelin O’Conner Now that Charles Darwin’s commemorative work, On the Origin of Species, is over 150 years old, questions regarding his work reflect the present scientific community’s aim towards physical reductionism. Examining an abstract way of getting to the core of evolutionary theory may be a useful way to honor both Darwin’s legacy “Long before having arrived at this part of my work, a crowd of difficulties will have occurred to the reader. Some of them are so grave that to this day I can never reflect on them without being stag gered…” 1 Charles Darwin published these remarks on the “Difficulties on Theory” in 1859 in the sixth chapter of his book, On the Origin of Species. In the chapter, Darwin’s main focus is to expound upon what he believes to be potential areas of discontent in his theory of natural selection. Though modern science might not yet be able to satisfy his every qualm regarding natural selection, the past 150 years of work since the original publication of On the Origin of Species have elucidated many of his noted “difficulties.”1 We might measure the past 150 years in terms of the progress made in addressing Darwin’s own queries into how natural selection works: we could start with the recovery of Mendelian genetics and work our way towards game theory and the workings of population equilibria. However, in the true spirit of inquiry, we might instead choose to measure the time between Darwin’s initial publication and today by evaluating how our own questions regarding his work have changed.

An interesting, and possibly less publicized, line of inquiry regarding evolutionary theory is born from reductionism. 2 Reductionism is a view that relies upon physical law to account for any phenomena. When applied to biology— and further to evolutionary theory—reductionism seeks to explain biological processes in terms of bare-boned physics. 3 The reductionist, then, would consider evolution in terms of the processes and phenomena by which it occurs, and would then—theoretically—break these down until each aspect, each step, could be explained through physical law.

The task taken up by many contemporary evolutionary reductionists is to explain the drivers of evolution—natural selection, genetic drift, and random mutation, to name a few—through analogy in terms of forces of classical Newtonian physics. 4 The abstraction of this idea seems unquestionable, and

the possibility of it working out is certainly debatable. In order to represent something like natural selection through a Newtonian scope, a reconciliation of sorts is required: an explanation of a biological occurrence must be satisfied within the criteria of Newtonian forces. Newtonian forces are the pushes and pulls of the physical world, which may be understood or characterized by four criteria: (1) Effect: there must be a consequence of the application of a Newtonian force—it makes things happen (2) Direction: A Newtonian force is applied in a given, specifiable direction (3) Magnitude: A Newtonian force is measurable in terms of a quantifiable strength (4) Source: a Newtonian force must originate from another physical force. 4 In the spirit of classical Newtonianism, we might imagine an effect of a force to be an apple hitting someone on the head, the direction of the apple’s fall to be toward the ground—more immediately toward the person sitting under the tree—the magnitude of the force of the fall would be the weight of the apple, and its causal physical source could be accounted for by any number of things we might wish to imagine—say a bird landed on it to cause it to fall from the tree. The task of the reductionist is to apply an explanatory account of an evolutionary driver (natural selection, genetic drift, random mutation, etc.) within the four criteria as has been done in the case of the apple falling from the tree. Can it be done? Could doing so in any way elucidate what we do not yet understand about evolution and its causes?

Is it useful to think of e volutionary drivers as things that act?

Adversaries of the Newtonian analogy cite natural selection, genetic drift, and random mutation as statistical “summaries of information” resulting from the events of the living world. Biologists Walsh, Lewens, Matthen, and Ariew employ an analogy to “overall life expectancy” to explain the statistical nature of natural selection and other evolutionary drivers. Evolutionary drivers, like an overall The Amherst Element, Vol 3, Issue 2. Spring 2010

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Letters life expectancy estimate, do not cause things to happen; rather, they are statistically explainable events predicted by the ways of the living world. In contrast to this view—that the behavior of evolutionary drivers may be summarized by statistical foresight—proponents of the Newtonian application argue that drivers of evolution mimic Newtonian forces in that they may be viewed as additive causes of sur vival.

That is, proponents of the Newtonian analogy argue that evolutionary drivers may contribute to an individual’s overall fitness in varying degrees—much like a magnitude and direction of an applied physical force might cause a billiard ball to roll for a given distance.5 The mere characterization of biological events in Newtonian terms does not sit well with many biologists who uphold a statistical view on the obser ved trends of life. Applying the force analogy as a way of explaining the obser ved behavior of evolutionary drivers is seen by some biologists to be a misrepresentation of statistical information. Thus, the very attempt made by some biological theorists to actually define evolutionary drivers in terms of the four force criteria is fodder for even further debate. This controversy is most notable when it comes to applying directional criterion. 4 Can evolutionary drivers be characterized by a direction?

If the Newtonian analogy is to be applied to something like genetic drift or natural selection, then these must be reconcilable with the criteria noted above. Though there is debate centered on applying the magnitude, causal, and effectual criteria of Newtonian forces to evolutionary drivers, the most controversial of applications seems to be in the case of the directional criterion. Many biological philosophers hold that any way in which the Newtonian directional criterion can be applied to an evolutionary driver would make nearly anything meet the directional criterion.

Newtonian forces act in fields of space and time—the attempt to apply, say, genetic drift to a directional field has resulted in construction of a “phenotypic space,” in which a population’s genome is thought (by some biological theorists) to move. Those in favor of applying the directional criterion to evolutionary drivers say that a population’s genotype (or genetic constitution) moves in “phenotypic space” towards homozygosity (where each possible combination of genes is either all one type or another)—a trend noted in population genetics. On the other hand, some argue that if “phenotypic space” is to be a valid medium for direction, what is there to stop fatigue from being characterized as a Newtonian force acting in a field of drowsiness? 4 Perhaps evolutionary biology cannot be broken down in terms of Newtonian physics—maybe Newton just does not belong in an account for Darwin’s work. I for one think that the reductionist debate illuminates a gap evocative of questions and more work to reconcile our current understanding of the physical world with our obser vations of the dynamics of life. Defining what we have obser ved about biology in

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terms of what we know about physics seems to be a bit of a semantic labor—requiring the weakening of the definition of “direction,” as it applies to Newtonian vectors, or potentially attributing the nuance of “cause,” or “force” to what could be otherwise a statistically accountable trend like genetic drift. If we want a bottom line account of how physical law is behind biological trends perhaps we should look for consistencies between the two disciplines. For instance, how are trends in biology consistent with physical laws of energy, entropy and equilibrium? In what ways could certain biological population trends be consistent with laws of physical equilibrium? Are there any ways in which the occurrence of a given mutation event could be consistent with the decrease of energy of a biological system?

No matter the approach, by merely appreciating the contemporary, philosophical, and abstract nature of some of the questions arising from Darwin’s work, we follow in a 150 year old tradition of questioning and exploring ways to understand the implications of biological trends.

References 1. Charles Darwin, On the Origin of Species, ed. David Quammen (New York: Sterling Publishing Company, Inc., 2008), 174.

2. Olding, A. “Reductionism and Natural Selection.”

Synthese 65, no. 3 (December 1985): 407-410. Academic search Premier, JSTORhost 3. Rosenberg, Alex, and D. M. Kaplan. “How to Reconcile Physicalism and Antireductionism about Biology.” Philosophy of Science 72, no. 1 (January 2005): 43-68. Academic Search Premier, EBSCOhost.

4. Filler, Joshua. “Newtonian Forces and Evolutionary Biology: A Problem and Solution for Extending the Force Interpretation.” Philosophy of Science 76, no. 5 (December 2009): 774-783. Academic Search Premier, EBSCOhost.

5. Stephens, Christopher. “Selection, Drift, and the “Forces” of Evolution.” Philosophy of Science 71, no. 4 (October 2004): 550-570. Academic Search Premier, EBSCOhost.

Letters

Feathers, fish, and phylogenies: exploring why different species look the same Ambika Kamath For a biologist in the eagles in India. * It turned out making, the most exciting that I had seen a Brahminy aspect of traveling is Kites (Haliastur indus), and my observing the huge diversity mistake was justifiable, for of organisms found on earth.

Brahminy Kites are also brownHowever, making sense of bodied, white-headed birds this diversity—why it exists, of prey that are found mostly how it is organized, and how near large bodies of water to remember the name of that and whose diet includes fish. bizarre orange spider you And then in Baja California, saw just three days ago—is a Mexico, a few weeks later, I saw central challenge in biology. two ospreys (Pandion haliaetus; A first step in the process of Figure 1a) perched on sand grappling with huge volumes dunes by the beach—brownof biodiversity is realizing bodied, white-headed, fishhow similar two organisms eating birds of prey yet again! from different corners of And if I tell you that bald the world can be. Traveling eagles (Haliaeetus leucocephalus) in the southern U.S., South are also fish-eating raptors, Africa, India, and Mexico I bet you can guess exactly over the last year, I have seen what they look like, even if more cool creatures and funky you haven’t seen one. biological phenomena than I T he obser vant reader could have hoped for. The would have noticed that at pattern that struck me most least two of the four raptors forcefully, however, was how discussed above are closely the similarities kept cropping related: the African Fish Eagle up, despite a conscious effort and the Bald Eagle share the on my part to appreciate first part of their scientific different ecosystems for name, denoting that they their uniqueness. belong to the same genus, Consider the example of Haliaeetus. This observation fish-eating birds of prey. The points to one reason that two African Fish Eagle (Haliaeetus species can look similar— vocifer) is a fairly common Figure 1: Two fish eating birds: a) the Osprey (Pandion haliaetus) in the two species might have sight around the waterholes the Cabo Pulmo National Marine Park, Mexico (top) b) the Pied inherited the properties they of Kruger National Park in Kingfisher (Ceryle rudis) in the Kruger National Park, South Africa share from their common north-east South Africa. The (bottom). ancestor. T hinking about striking contrast between its shared ancestry is essentially black-and-brown body and like thinking about why you bright white head makes this fish eagle easy to distinguish from other raptors (cover image). When, upon returning * That is not entirely true—there is one. However, the White-bellied home to India, I saw a similarly patterned and colored bird- Sea Eagle (Haliaeetus leucogaster), as its name suggests, occupies of-prey by a large pond, I dismissed it as yet another fish mostly coastal habitats, and I was quite far inland when I saw this eagle. This turned out to be a mistake, since there are no fish bird.

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Letters would readily conclude that the fish-eating birds-of-prey are all closely related to each Haliastur indus (Brahminy Kite) A other. Why is this a problem? Consider the fact that both fish-eagles and kingfishers eat Haliastur sphenurus (Whistling Kite) fish; I am certain you will agree, based on Figure 1, that fish-eagles are likely more closely Milvus migrans (Black Kite) related to other eagles than to kingfishers. This Milvus milvus (Red Kite) implies that piscivory evolved independently in these two groups of birds. Similarly, it is conceivable that the evolution of piscivory Haliaeetus (Fish Eagles) occurred independently in the African Fish Eagle and the Brahminy Kite, and the two raptors may not be closely related at all. But, you counter, these two species both look AND behave similarly (while kingfishers look nothing like fish eagles; Figure 1b), so maybe they are closely related after all. Suppose, B however, that raptors with white heads are more successful at catching fish than raptors Accipitridae (Hawks and Eagles) with brown heads. One would then expect this color pattern to evolve by natural selection (perhaps independently) in all fish-eating birds of prey. One would therefore not be surprised if our examples of white-headed fish-eating raptors were in fact not closely related to each other. This reason for two Pandionidae (Osprey, species looking similar—that they experience Pandion haliaetus) similar pressures from natural selection leading to morphological or behavioral similarity—is Sagittariidae (Secretary Bird, known as convergent evolution.

Sagittarius serpentarius) It turns out that the genus Haliaeetus Figure 2: Phylogenies adapted from Griffiths et al. 1 showing a) the relationship comprises eight species of fish-eating eagles, between Haliastur, Milvus, and Haliaeetus and b) the relationship between seven of which have brown bodies and white Accipitridae and Pandionidae. heads. The Brahminy Kite, Haliastur indus, is not very closely related to these fish-eagles, but is not too far either. Look at the phylogeny, and your brother might look and behave similarly, except on derived from DNA sequence data, 1 in Figure an evolutionary time scale.

2a, and trace the branch back from the Brahminy Kite: the So does that mean that all species of fish-eating raptors first intersection we reach branches off to the Whistling are closely related, and both the behavior of eating fish (or Kite, Haliastur sphenurus, which means that the Brahminy piscivory) and the color patterns of a white head and brown Kite is most closely related to the Whistling Kite. Tracing body evolved just once? How does one go about answering such further back, one discovers that the genus Haliastur is most a question? One turns to a phylogeny—a branching “tree” closely related to the genus Milvus, which includes the Red that represents a hypothesis for how a group of species are Kite (Milvus milvus) and the Black Kite (Milvus migrans). None related to each other. These hypothesis trees are constructed of the three species most closely related to the Brahminy from data that describe the species of interest in some way. Kite feed mostly on fish or have white heads. 2 Going back One could collect morphological data (do these species of even further, the group of species that include the genera butterflies have spotted or striped wings?), behavioral data Milvus and Haliastur is most closely related to the genus of (are they active at dawn or dusk?), or, as is now ubiquitous, fish-eagles, Haliaeetus.

DNA sequence data (do they have the nucleotide adenine or These relationships give rise to several possibilities nucleotide guanine at a particular spot in a particular gene?). regarding when and in which species piscivory and white One would then compare this data for different species, heads evolved. A common way of deciding among these and group species by similarity, inferring that more similar different possibilities involves counting up the number of species are more closely related. evolutionary changes that must occur for a given possibility to It is easy to see that if we created a phylogeny of raptors be true. Under the reasonable assumption that the occurrence using either preferred diet or coloration to group species, we

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Letters of more changes is less likely than the occurrence of few changes, one concludes that the scenario necessitating the fewest changes is probably true. For example, it is possible that these eight species of fish-eating, white-headed raptors in Haliaeetus and Haliastur evolved these traits separately, a scenario involving eight evolutionary events. A far more parsimonious possibility, requiring just four evolutionary changes, is that piscivory and white heads evolved in the common ancestor of Haliaeetus, Haliastur, and Milvus, and that these traits were subsequently lost in the Whistling, Red, and Black Kite. The most parsimonious explanation, however, would involve two evolutionary changes—piscivory and white heads evolved once in the ancestor of all Haliaeetus fish-eagles and once, convergently, in Haliastur indus.

A more convincing case for the convergence of fisheating behavior and white-and-brown coloration is made by the Osprey. Pandion haliaetus is not even in the same family as hawks and eagles—scores of other eagles that do not eat fish or have white heads are more closely related to fish eagles than the osprey. Looking across the family of hawks and eagles, Accipitridae, there is one more example of a fish-eating, white-headed raptor—the Black-collared Hawk, Busarellus nigricollis, from South America 2—whose behavior and coloration have almost certainly evolved convergently.

However, there are several white-headed raptors (the Blackand-white Hawk Eagle, the pale morph of Wahlberg’s Eagle, and several hawks in the genus Leucopternis) that do not eat fish, and several fish-eaters (in the genus Buteo) that have dark heads 2, suggesting that there is more at work than a simple association between eating fish and having a white head. For instance, perhaps all white-headed raptors live in environments with similar light conditions in which having a white head is helpful for catching any sort of prey.

Nevertheless, the association between white heads and piscivory is compelling enough to warrant further investigation.

But what sort of investigation? The most definitive evidence either for or against any hypothesis explaining the association would come from an experiment. For instance, consider the hypothesis constructed earlier—that raptors with white heads are more successful at catching fish than raptors with dark heads, because white heads are better camouflaged against the sun when viewed from the water by a fish than brown heads. One could test this hypothesis by catching, say, 50 African Fish Eagles, painting the heads of 25 of them brown and the other 25 white, releasing them and then measuring how many fish they catch. The group with white paint on their heads act as a control, since it is quite possible that painting a bird’s head, irrespective of the color, might affect its abilities to catch fish. If our hypothesis were true, then birds whose heads have been painted brown would catch significantly fewer fish than birds with white paint on their heads or unpainted birds. Let me know if you ever get around to carrying out this experiment; personally, the thought of catching these 3 kg birds with a 2 m wingspan and undoubtedly sharp talons and beak, let alone painting

their heads, makes me slightly nervous.

This little investigative journey is precisely the sort of reasoning that being outdoors (“in the field” in biologistspeak) often prompts. And what makes field biology so much fun is that the sparks that set this reasoning into motion are everywhere around you and are usually entirely unrelated to whatever you are meant to be studying, making field work really good brain exercise. So the next time you’re outdoors, pay special attention to how the organisms around you look and behave, and you might end up following a path of reasoning that concludes with needing to paint an eagle!

Acknowledgements Thanks to Professors Jill Miller and Rachel Levin for a discussion about why white heads might be adaptive in fish-eating raptors and how to test this hypothesis (which occurred when we were in the field collecting leaves and flowers from plants in the tomato family). Thanks to Professor Ethan Temeles for suggesting the phenomenal Handbook of the Birds of the World as a source of descriptions of raptors and information on their foraging behavior.

References 1.Griffiths, C.S., G.F. Barrowclough, J.G. Groth, L.A. Mertz.

2007. Phylogeny, diversity, and classification of the Accipitridae based on DNA sequences of the RAG-1 exon. Journal of Avian Biology 38: 587-602.

2. del Hoyo, J., A. Elliott, J. Sargatal (eds.). 1994. Handbook of the Birds of the World, Volume 2. New World Vultures to Guineafowl. Lynx Edicions, Barcelona

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Letters

Mysteries of the Large Hadron Collider Emine Altuntas

When in November of 2009, the Large Hadron Collider (LHC) recorded the first proton-proton collisions at the injection energy of 450 GeV per particle, physicists felt relieved, especially after the unfortunate month of September of 2008. On September 19, 2008, the LHC operations were halted for at least a year, when it was discovered that there was a faulty magnet connection that had quenched around 100 of the LHC’s super-cooled magnets, causing them to heat up almost 100 degrees Celsius. In the year following this disappointing failure, the numerous delays in the operation of the LHC caused anxiety among physicists. Many worried that the most complex machine built by man would never be able to operate as desired. Thus the cheering of physicists was expected when the LHC pushed the energy of its particle beams higher almost every couple of days last November. Physicists around the world are excited at the prospect that the experiments conducted at the LHC will finally confirm or reject the various disputed aspects of the Standard Model, the fundamental theory of all interactions.

2. What is dark matter? What is dark energy?

Only 4% of the universe is composed of observable matter, and we know virtually nothing about the remaining 96 %, which is made up of dark energy and dark matter. All those magnificent pictures taken by the Hubble telescope are composed of this minuscule 4% – so just try to imagine what the remaining 96% could “look” like. Although dark energy, which accounts for 73% of the total mass of the universe, cannot be observed directly, it is responsible for speeding up the expansion of the Universe. It was this phenomenon, which can be detected in astronomical observations that enabled us to discover dark energy. Dark matter, on the other hand, has mass – hence the name – and has direct effects on the observable portion of the universe. As you are reading this article, you do not feel the effects of the dark matter, but our galaxy and the other galaxy clusters do. Almost 90% of our galaxy is made up of dark matter, without which our galaxy may not have formed the conditions required for our existence. At this stage, physicists can only speculate

The Unsolved Problems of Physics and the LHC The LHC carries a considerable significance for new physics beyond the Standard Model, which, despite its remarkable framework, cannot explain either gravity or dark matter, what the large portion 23% of the total universe is made up from. More importantly, the Higgs boson, one of the most important particles that the Standard Model predicts, has yet to be observed. The so-called Big Bang machine’s experiments, the largest of which are ATLAS and CMS, make a promise for shedding light on these quagmires. The most important of these unsolved problems of physics are: 1. How do particles acquire mass? Why do we have mass? What is the origin of mass in the universe?

Mass is a physical concept that we are yet to understand from a theoretical perspective. The Higgs mechanism predicts the existence of the extra particle, the Higgs Boson, that provides all the other particles with mass. According to the theory, the Higgs boson has an all-pervading field, called the Higgs field, which gives mass to particles through its interactions with them. The Higgs mechanism is analogous to President Marx entering the Valentine Hall and crossing through; since all the students are strongly attracted to him they will cluster round him.

As he moves, the students he moves towards will be attracted towards him and the ones left behind will return to their previous spacing. Since there will always be a cluster of people around him, he will acquire a greater mass than the usual student. However, the predicted Higgs boson has yet to be observed experimentally. The Atlas and CMS are general-purpose experiments of the LHC that will be conducting the hunt for the Higgs boson.

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about dark energy and dark matter. Thus another purpose of the LHC experiments is to reach the high energies required to investigate the formation of dark matter

3. Who lost the antimatter?

We live in a Universe almost entirely composed of ordinary matter although, in theory, half of the universe should be composed of antimatter.

We know that through the process known as annihilation, a particle of ordinary matter and its anti-particle disappear in a flash, while their mass is transformed into energy. The Big Bang theory predicts that equal amounts of matter and antimatter were present at the beginning of the universe. Based on this highly respected prediction, we would expect that

Letters equal amounts of matter and antimatter would have annihilated each other, so equal amounts would remain. Or else we would predict that all of matter and anti-matter should have completely annihilated each another after the birth of our Universe. One of the main purposes of the LHC is to investigate the fate of the antimatter – why it is not present in today’s universe? Perhaps the energies at the scale of the Big Bang are governed by a completely different set of physics laws that we cannot predict based on our experiences from the current universe.

The LHC operates at the energy scales of 14TeV and will be upgraded to even higher scales in order to recreate the conditions of the Big Bang.

My Summer Work at LHC For more than 30 years, CERN has been running its Summer Student Program, which enables undergraduate and graduate students to directly participate in many groundbreaking experiments. I was one of the 2009 program students and one of the three recipients of the Engin Arik Fellowship, founded in the memory of the eponymous and renowned particle physicist who died in a plane crash in 2007.

One part of the CERN Summer Program is a series of approximately two month long daily lectures on topics ranging from Standard Model to the building of accelerators given by leading particle physicists as well as engineers and computer scientists. In the second part, each student joins a research team. My research team’s project concerned the upgrading of Resistive Plate Chambers (RPC), which are large-area gaseous detectors installed at the Large Hadron Collider (LHC) experiments (CMS, ATLAS, ALICE) in order to identify the associated muon tracks via the detection of relevant bunch crossing.

RPC’s have been introduced as an alternative to the “Localized discharge spark counters” in 1981. As the RPCs achieved a time resolution of the order of 1 nanosecond as opposed to the “Localized discharge spark counters” time resolution of 25 picoseconds , they have found wide acceptance in High Energy Physics.

LHC and RPC’s The very large pulse height, reduced cost per unit area, and good (about 1 ns) time resolution are the main features that have rendered RPCs highly affordable and preferable in the construction of the LHC experiments. RPCs are widely used as part of the muon detectors for triggering purposes at the LHC experiments. They are expected to operate even at the high rate of background radiation,anticipated to be up to 1000 Hz/cm2.

In the LHC experiments RPCs are operated with a gas mixture of approximately 94.7% C2H2F4, 5% iC4H10 and 0.3% SF6. The gas mixture is supplied with water vapor to stabilize the relative humidity at about 45% (i.e. 8000-12000 ppmV) and the resistivity of the Bakelite electrodes. For the LHC RPC configurations, a closed-loop (90-95%) gas circulation is necessary due to the large detector volume and relatively

expensive price of the gas mixture used. At the LHC, where RPCs are operated in a high radiation environment, large amounts of impurities that are potentially harmful to the operation and construction material of the chambers have been detected in the return gas. These impurities have been observed to develop as the ionized and fragmented gas molecules recombine to new, stable and reactive compounds after the gas amplification process. Conceivably, these impurities minimize the stable operation of the detectors and produce harmful conditions for the gas system and the materials that construct detectors. The effects of these impurities are expected to increase with the ten-fold increase of the luminosity of the LHC upgrade project.

The operation of RPCs could be carried in openloop gas system and thus remove any impurities; however for economic reasons the gas must be circulated, preferably with a 90-95% closed-loop system. Therefore, purification of the impurities is essential.

For this purpose, full size RPC chambers are irradiated in the CERN Gamma Irradiation Facility (or the GIF, as my research team called it), which simulates the high radiation environment of the LHC. The impurities generated in the system are identified using analytical techniques, and subsequently the performance of a variety of impurity absorbers is tested at the GIF gas system.

My summer work was carried out as part of ongoing research into the study of formation and effects of gas impurities in Resistive Plate Chambers (RPC) at the GIF. The main objective of my summer project was to study the impurity absorbers’ performance, the safe operation techniques and conditions of the chambers in high radiation environment. Since the test facility at the GIF has not been operating under a closed-loop gas circulation my summer project focused on the switch to the closed-loop gas circulation configuration. As a team of three summer students, we carried out the construction of the humidity and temperature control system, regeneration and installation of purifiers at the GIF, calibration of the analytical instruments, namely the Gas Chromatograph and Mass Spectrometer, and coding of a ROOT data analysis program.

References 1. http://www.hep.ucl.ac.uk/~djm/higgsa.html 2. Evans, Lyndon. 2009. Milan, Italy. The Large Hadron Collider: a Marvel of Technology.

3. Capeans, Glushkov, Guida. 2008. Studies of Purification of the LHC RPC Gas Mixture.

4. Guida et. Al. 2008. Results about HF Production and Bakelite Analysis for the CMS Resistive Plate Chambers.

5. Capeans et. al. 2008. Studies of purification of the Resistive Plate Chamber gas mixture for the Large Hadron Collider experiments.

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Thesis Research

Aph-1 and Presenilins: a Tailless Tale?

Rebecca Resnick How does an embryo know how to make your arms grow 12 and hop-1 are thought to be biochemically interchangeable. from your shoulders instead of your head? And how does it When both presenilin genes are knocked out, the worms have choose which cells become nerves, or muscles, or skin? Obviously a much more dramatic phenotype: they are sterile or give all dead this is a complicated process, but embryos.7 These are phenotypes one major player is the Notch characteristic of Notch signaling pathway. Cells can talk mutants. This means that in an to each other through Notch otherwise normal worm, only signaling to determine who one presenilin is necessary for becomes what. This process sufficient Notch signaling to is so important that almost all occur, further supporting the multicellular animals have it, from idea that the two proteins are the nearly microscopic soil worm biochemically interchangeable.

Caenorhabditis elegans to humans.

Aph-1, another Notch signaling occurs component of the γ-secretase between two adjacent or nearby complex, is also required for cells where both the signal and γ-secretase function. C. elegans receptor are membrane-bound, aph-1 has seven regions that cell-surface proteins. When the span the membrane of the cell, signal binds to the receptor, followed by a tail (Figure 2), and the extracellular portion of the a null mutation in aph-1 results receptor is cleaved. This allows the in all dead embryos. While γ-secretase complex to bind and Figure 1: Caenorhabditis elegans (photo courtesy of Caroline null mutations completely cleave the intracellular portion Goutte) abolish gene function, alleles of the receptor. The resulting with leaky mutations produce Notch intracellular fragment translocates to the nucleus, changing a small amount of gene product that is less than wild-type. The transcription to activate genes necessary for cellular specification.1 leaky mutation aph-1(zu147) introduces a stop codon before the My research focuses on the γ-secretase complex, which is tail portion of the protein, thereby shortening it. This allows a comprised of 4 proteins: aph-1, aph-2, pen-2, and presenilin. 2 low level of Notch signaling to occur, leading to about 1% of Presenilins get their name from their role in early-onset familial the embryos of aph-1(zu147) worms surviving to adulthood.

Alzheimer’s Disease. Increasing our understanding of γ-secretase We hypothesized that combining aph-1(zu147) with a could help inform the design of treatments for Alzheimer’s. presenilin mutation would reduce overall levels of Notch To study the γ-secretase complex, we use the tiny signaling, increasing embryonic lethality. For an aph-1(zu147) nematode worm C. elegans as a model system (Figure 1). sel-12- double mutant, we found that this was in fact the case.

Worm γ-secretase is similar enough to human γ-secretase that Crippling aph-1 and removing sel-12 led to such low levels the human proteins can function in the worm.3,4,5 C. elegans of Notch signaling that no embryos could survive. This led us worms are hermaphrodites that self-fertilize, making them an to believe that mutating hop-1 in aph-1(zu147) would have the excellent system for genetic analysis since a mother produces same effect, since hop-1 and sel-12 are thought to be equivalent. many offspring that contain only her genetic information. To our surprise, an aph-1(zu147) hop-1- double mutant, far from C. elegans has two presenilins, hop-1 and sel-12, either of which giving all dead embryos, instead gives all live ones! (Figure 2) The can be part of the γ-secretase complex. A mutation that knocks hop-1- mutation functions to suppress the aph-1(zu147) embryonic out hop-1 function (a null mutation) has no effect on the worm lethality. This creates a situation where hop-1 and sel-12, rather whatsoever, because sel-12 can take over for it. A null mutation in than being interchangeable, have completely opposite effects. sel-12 affects only vulval morphogenesis, one area where Notch This result led us to propose two potential models of signaling is necessary. This is due to the timing of expression interaction. The first is that HOP-1 protein, encoded by the hop-1 rather than the inability of hop-1 to replace sel-12 in γ-secretase. gene, requires the tail portion of APH-1 to function, while SEL-12 When hop-1 is expressed with a sel-12 promoter, it rescues the protein does not. In an aph-1(zu147) sel-12- double mutant, there is vulval defect of a sel-12 mutant.6,7 Because of this effect, sel- only HOP-1 protein and no APH-1 tail, so signaling does not occur.

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Thesis Research In an aph-1(zu147) hop-1- double mutant there is only SEL-12 protein, which according to this model doesn’t need the tail. This leads to normal levels of signaling and all live embryos. In an aph-1(zu147) mutant where both presenilins are present, there is a competition between the two (Figure 3). HOP-1-containing complexes form but don’t function, meaning they keep SEL-12-containing complexes from forming by using up some of the available APH-1 protein. This leads to very low levels of signaling and only 1% of embryos surviving to adulthood.

Another potential model is that HOP-1 protein requires wild-type expression levels of aph-1 to function. Aph-1(zu147) has very low expression levels because the mutation causes the mRNA to be recognized as defective and destroyed by a cellular pathway called nonsense-mediated decay. If HOP1 protein required wild-type amounts of APH-1 in order to form complexes, but SEL-12 protein did not, then an aph-1(zu147) hop-1- double mutant, which only had SEL-12 protein, would be viable whereas an aph-1(zu147) sel-12- double mutant would not be.

We took advantage of genetic mutations that affect mRNA levels of aph-1 and hop-1 to attempt to distinguish between these two models. Although we found evidence Figure 2: Result of presenilin mutations in an aph-1(zu147) background for and against both models and further experiments are necessary to determine the actual pattern of interactions, References we now have a better understanding of how presenilins 1. Nichols, J.T., Miyamoto, A. & Weinmaster, G. function. Hopefully this work will help to further elucidate Notch Signaling: Constantly on the Move. Traffic the function of γ-secretase and its role in Notch signaling.

8, 959-969 (2007).

2. Edbauer, D. et al. Reconstitution of γ-secretase activity. Nat Cell Biol 5, 486-488 (2003).

3. Levitan, D., Yu, G., St. George Hyslop, P. & Goutte, C. APH-2/Nicastrin Functions in LIN12/Notch Signaling in the Caenorhabditis elegans Somatic Gonad. Developmental Biology 240, 654-661 (2001).

4. Levitan, D. et al. Assessment of normal and mutant human presenilin function in Caenorhabditis elegans. Proceedings of the National Academy of Sciences of the United States of America 93, 1494014944 (1996).

5. Francis, R. et al. aph-1 and pen-2 Are Required for Notch Pathway Signaling, [gamma]-Secretase Cleavage of ΒAPP, and Presenilin Protein Accumulation. Developmental Cell 3, 85-97 (2002).

6. Levitan, D. & Greenwald, I. Facilitation of lin12-mediated signalling by sel-12, a Caenorhabditis elegans S182 Alzheimer’s disease gene. Nature 377, 351-354 (1995).

7. Li, X. & Greenwald, I. HOP-1, a Caenorhabditis Figure 2: Result of presenilin mutations in an aph-1(zu147) background elegans presenilin, appears to be functionally redundant with SEL-12 presenilin and to facilitate LIN-12 and GLP-1 signaling. Proceedings of the The author would like to acknowledge Professor Caroline Goutte, her thesis National Academy of Sciences of the United States of advisor, and Valerie Hale, whose experiments formed the framework for her thesis.

America 94, 12204-12209 (1997).

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News-In-Brief The Amherst Element Staff Mamma elephant to baby elephant: eat your grass or the bees will come after you…

Scientists from the United Kingdom have identified the first alarm call in African Elephants. And what, you might ask, are these 20,000 lb animals afraid of ? The answer: bees. In the presence of a swarm of bees, African elephants shake their heads, run, and produce a vocalization known as a “bee rumble.” On recording the “rumble” and playing it back to different herds of elephants, they found that six out of ten herds fled immediately.

Chimpanzees grieve too.

Chimpanzees grieve over their dead relatives, a behavior seen before only in humans and elephants. Zookeepers in the United Kingdom allowed an ill chimpanzee, Pansy, to remain with her fellow chimps when she died. Pansy’s daughter Rosie stayed by her dead body the whole night, and the chimpanzees in the group remained unusually subdued for a week. In another incident, a wild mother chimpanzee in Guinea was seen carrying her dead infant for over 60 days, both grooming it herself and allowing other chimps in the group to handle and groom it. A different expression of grief than in humans, but grief nonetheless.

Football-shaped dark matter is exactly what the physicists were hoping for.

Dark matter is all that stuff in the universe that you can’t see but that must be out there to hold the universe together. Scientists from Japan, using images from the Subaru telescope in Hawaii, have managed to figure out what dark matter “looks like.” They used a technique called gravitational lensing, which is based on the fact that light can bend when it passes really heavy objects. It turns out that

the lumps of dark matter are shaped like footballs, which proves that dark matter doesn’t interact with regular matter. Physicists can breathe a sigh of relief, for this evidence does in fact support models based on the Big Bang origin of the universe.

Forbidden liaisons: a prehistoric Romeo and Juliet Genetic data from human populations in Africa, Europe, Asia, Oceana, and the Americas reveals that interbreeding may have occurred between Neanderthals and humans. From projections of genetic mutations, researchers estimate that interbreeding occurred twice: once 60,000 years ago in the eastern Mediterranean, and again 45,000 years ago in eastern Asia.

Inbreeding: It’s not worth your time…or life For males of the spider Argiope bruennichi sex is dangerous: three out of four times, males end up as their mates’ meal. However, Klaas Welke and Jutta Schneider recently reported that the cannibalism rate is halved for brother-sister pairings, likely resulting from shortened coital duration. Since inbreeding often decreases offspring fitness, it seems that the male spiders balance their decreased chance of reproductive success for incestual trysts against their risk of being eaten by adjusting the amount of time they spend mating.

Failed that drug test? There may be another answer.

A new study shows that mice, and probably humans and other mammals, can synthesize morphine. A team led by Meinhart Zenk injected a mouse with a morphine precursor, THP, which naturally occurs in human brain cells. Using supersensitive mass spectrometry, they recovered molecular intermediates and showed that mouse cells could direct the complete synthesis of morphine. The natural role of morphine in the body and where it is made remain unknown, although the fact that the mammalian pathway differs slightly from that in poppy plants suggests that morphine is important to multiple branches of life.