Read the article and answer questions on "Scientific Literacy-RCAN 1" document
fRCAN-1 Scientific Literacy Assignment Purpose. The goal of this assignment is for you to be able to relate your classroom learning about Genetics to a real-world application of these concepts. The focus of this assignment is primary literature, which is formally reported & peer-reviewed research findings that are published in scientific journals. It takes a lot of practice to learn how to effectively read and analyze primary literature. Regardless of whether or not you plan to pursue Biology long-term, this exercise will definitely help you develop the critical thinking and problem-solving skills that are so valuable to employers in all sorts of careers. Being able to understand and critically assess data are important literacy skills for all people, regardless of major. Mastering these skills will empower you to make informed choices in your life. We also want you to be able to write about science in a clear, concise manner – this is an important skill for job applications and interviews. Ground Rules. You may DISCUSS this assignment with your classmates; however you may NOT copy directly or write the same words as your classmate. You may NOT consult the internet, websites, message boards, etc. TYPE your answers in a separate Answer Sheet (see attached document) (not this document!), being sure to reference the original question # when you write your answers. Your answers must be written in your own words. Please use complete sentences with proper grammar and spelling. A grading rubric at the end of the assignment is included so that you can see how you will be assessed. And as always, you may find it helpful to review the question prompt after you finish answering to ensure that you have indeed answered all components of the question fully. Don’t forget to put your name in your response document! 1. First, let’s think about what you already know about metabolism. For this question, you do not need to examine the figure or figure legend below. How does your diet impact weight loss / weight gain? What other factors impact how much you weigh? Legend: Regulator of Calcineurin 1 (RCAN1) encodes a protein that suppresses two distinctly different mechanisms of nonshivering thermogenesis (NST), meaning how an organism generates heat. Two independently derived Rcan1-KO mouse lines were used in our studies: one lacking exons 5 and 6 and the other deficient for the coding regions of exon 6 and 7. In both cases, the mutations result in no Rcan1 protein production. Initially, all mice were fed a normal fat diet. Starting at 8 weeks of age, WT and Rcan1-KO mice (n=15 each) were placed on a high-fat diet (HFD: 60% calories from fat) for 25 weeks. Animals were housed at 23°C under standard vivarium conditions under a 12:12-hr light:dark cycle. Animals were allowed free access to water and were fed ad libitum a high-fat diet (HFD) in which 60% of the calories derived from fat (Research diet D12492). Food consumption and body weight were recorded weekly. All animal procedures were carried out with the oversight and approval of the University’s Institutional Animal Care and Use Committee and conformed to the current Guide for the Care and Use of Laboratory Animals, published by the National Institutes of Health. Data information: Values shown are mean +/- SD. *P < 0.05; multiple t-tests. adapted from: rotter, d., peiris, h., grinsfelder, d. b., martin, a. m., burchfield, j., parra, v., ... & parks, b. w. (2018). regulator of calcineurin 1 helps coordinate whole‐body metabolism and thermogenesis. embo reports, 19(12), e44706.. a 2. what is the main question the authors are addressing in this figure? be sure to write your answer in the form of a question (not a statement). 3. write the hypothesis or hypotheses that the author is testing. 4. create a flowchart describing the methods. a generic example is shown below. be sure to include all major components of the method and label: a. independent variable(s) b. dependent variable(s) ind. var. exp. group n=? ctl. group n=? model organism (include any baseline manipulation) constant variables other constant variables or manipulation (e.g. time) dependent variable(s) 5. describe the results. be sure to describe results completely – not just one bar, part of a line, etc. you may need several sentences. be sure to address the statistical significance of the findings. 6. most studies use a smaller sample size with the hope of being able to generalize the findings for a larger population, potentially even other species. every study has limitations, some of which are avoidable by using an improved study design, and some of which are unavoidable due to logistical constraints. the following questions will guide you through the process of identifying possible limitations for this experiment. a. what model organism was used? think about how different you are genetically from your mother, sibling or cousin? in an inbred mouse line, how genetically different is a mouse from its mother, sibling, or cousin? are there advantages or disadvantages to these two situations? what limitation might be associated with this methodological choice if you wanted to apply this information to humans? would a different methodological choice reasonably address this limitation, or is it an unavoidable limitation given the advantages of the organism used? b. would a larger sample size have improved your confidence in the results? why or why not? consider how variable the data were (look at the error bars) and the statistical significance. a p value indicates the likelikhood that the results were obtained by random chance. convert the p value into a fraction. if you were to repeat this experiment 100 times, how many times would show the same result due to random chance? how many would show the same result because there is actually a difference between control and experimental groups? c. think about the dependent variable. what other factors (confounding variables) impact an individual’s weight aside from their genetic background? were these factors controlled for in the experiment? what limitation might be associated with this methodological choice of dependent variable? how would this impact interpretation of results? would a different methodological choice or an additional experiment reasonably address this limitation, or is it an unavoidable limitation? 7. future directions. what would a logical next step be for these researchers? if you were going to improve or build upon the study, what would you do? 8. applying genetics to the real world. your best friend is overweight, and she sees a commercial for a supplement that claims to inhibit rcan-1 activity and cause weight loss in obese patients. she is excited to try it, but asks you for your advice. would reading the above study on the rcan-1 knockout make you more or less likely to recommend that your friend try the supplement? are there reasons to consider other information aside from the data presented in the above study? think about how generalizable this study was and whether or not it is relevant to your friend. (describe in detail why or why not. there is not one correct answer here – rather, you will be graded on your ability to use sound arguments to defend your choices) how you will be graded. write your answers in a new word document (not papers!), being sure to reference the original question # when you write your answers. you must type your answers to the questions above (in complete sentences and your own words) and upload the final word document to blackboard (don’t forget to write your name!). you may draw the flowchart, but please take a picture of it and insert it into the word document. the following rubric will be used to grade your assignment. rubric question (weight) proficient (100%) emerging (85%) needs improvement (75%) not attempted (0%) what is the main question the authors are addressing (10%) question addresses all variables and accurately summarizes the main theme. question may not be written in the form of a question; however, it does include all variables (independent & dependent) question may or may not be written in the form of a question; it does not include all variables attempt to describe authors question was not made. write the hypothesis that the author is testing (10%) hypothesis contains both independent and dependent variables, is testable and falsifiable (e.g. if x is done, y will be observed) hypothesis may have one of the following issues: not testable, not falsifiable, no clear statement relating both independent and dependent variables, includes one, but not both, independent variable. hypothesis has two or more of the following issues: not testable, not falsifiable, no clear statement relating both independent and dependent variables, includes one, but not both, independent variable. attempt to describe hypothesis was not made create a brief flowchart that describes the method used for this experiment (15%) flow chart is simple, concise, and accurately describes samples and method, and clearly related dependent and independent variables. description of method may be verbose, copied directly from figure legend, or not contain a flow chart, but long sentences instead; may be missing details of the experiment that are small but essential description of method may be missing or substantially inaccurate in one or two key steps that enable the reader to understand the experiment method missing more than 2 key steps in the description of the experiment. what is(are) the independent variable(s)? (10%) all ivs are listed and accurately stated mixture of correct and incorrect information only incorrect information given no attempt to answer made. what is(are) the dependent variable(s)? (10%) all dvs are listed and accurately stated mixture of correct and incorrect information only incorrect information given dvs are: not clearly identified; not given; none are correct describe the results. (15%) all results are accurately described, including their statistical significance. most key results are explained accurately; however, minor results may be absent. statistical significance is considered. most key results are not explained or are inaccurate. minor results are not explained. statistical significance may or may not be considered. no key results are explained or are explained inaccurately. minor results are not explained. statistical significant is not considered. what are the limitations of this experiment? (10%) specific limitations are mentioned along with the potential impact on the interpretation of the data specific limitations are present but do not address the implications of those limitations; may not include limitation not mentioned by the authors vague limitations or a mixture of accurate / inaccurate limitations missing or inaccurate limitations future directions (10%) specific suggestions that logically build upon the current outcomes or that suggest a redesign to better test the same hypotheses. some specific suggestions are given, but answer is otherwise vague. or specific suggestions are given, but they either do 0.05;="" multiple="" t-tests.="" adapted="" from:="" rotter,="" d.,="" peiris,="" h.,="" grinsfelder,="" d.="" b.,="" martin,="" a.="" m.,="" burchfield,="" j.,="" parra,="" v.,="" ...="" &="" parks,="" b.="" w.="" (2018).="" regulator="" of="" calcineurin="" 1="" helps="" coordinate="" whole‐body="" metabolism="" and="" thermogenesis.="" embo="" reports,="" 19(12),="" e44706..="" a="" 2.="" what="" is="" the="" main="" question="" the="" authors="" are="" addressing="" in="" this="" figure?="" be="" sure="" to="" write="" your="" answer="" in="" the="" form="" of="" a="" question="" (not="" a="" statement).="" 3.="" write="" the="" hypothesis="" or="" hypotheses="" that="" the="" author="" is="" testing.="" 4.="" create="" a="" flowchart="" describing="" the="" methods.="" a="" generic="" example="" is="" shown="" below.="" be="" sure="" to="" include="" all="" major="" components="" of="" the="" method="" and="" label:="" a.="" independent="" variable(s)="" b.="" dependent="" variable(s)="" ind.="" var.="" exp.="" group="" n="?" ctl.="" group="" n="?" model="" organism="" (include="" any="" baseline="" manipulation)="" constant="" variables="" other="" constant="" variables="" or="" manipulation="" (e.g.="" time)="" dependent="" variable(s)="" 5.="" describe="" the="" results.="" be="" sure="" to="" describe="" results="" completely="" –="" not="" just="" one="" bar,="" part="" of="" a="" line,="" etc.="" you="" may="" need="" several="" sentences.="" be="" sure="" to="" address="" the="" statistical="" significance="" of="" the="" findings.="" 6.="" most="" studies="" use="" a="" smaller="" sample="" size="" with="" the="" hope="" of="" being="" able="" to="" generalize="" the="" findings="" for="" a="" larger="" population,="" potentially="" even="" other="" species.="" every="" study="" has="" limitations,="" some="" of="" which="" are="" avoidable="" by="" using="" an="" improved="" study="" design,="" and="" some="" of="" which="" are="" unavoidable="" due="" to="" logistical="" constraints.="" the="" following="" questions="" will="" guide="" you="" through="" the="" process="" of="" identifying="" possible="" limitations="" for="" this="" experiment.="" a.="" what="" model="" organism="" was="" used?="" think="" about="" how="" different="" you="" are="" genetically="" from="" your="" mother,="" sibling="" or="" cousin?="" in="" an="" inbred="" mouse="" line,="" how="" genetically="" different="" is="" a="" mouse="" from="" its="" mother,="" sibling,="" or="" cousin?="" are="" there="" advantages="" or="" disadvantages="" to="" these="" two="" situations?="" what="" limitation="" might="" be="" associated="" with="" this="" methodological="" choice="" if="" you="" wanted="" to="" apply="" this="" information="" to="" humans?="" would="" a="" different="" methodological="" choice="" reasonably="" address="" this="" limitation,="" or="" is="" it="" an="" unavoidable="" limitation="" given="" the="" advantages="" of="" the="" organism="" used?="" b.="" would="" a="" larger="" sample="" size="" have="" improved="" your="" confidence="" in="" the="" results?="" why="" or="" why="" not?="" consider="" how="" variable="" the="" data="" were="" (look="" at="" the="" error="" bars)="" and="" the="" statistical="" significance.="" a="" p="" value="" indicates="" the="" likelikhood="" that="" the="" results="" were="" obtained="" by="" random="" chance.="" convert="" the="" p="" value="" into="" a="" fraction.="" if="" you="" were="" to="" repeat="" this="" experiment="" 100="" times,="" how="" many="" times="" would="" show="" the="" same="" result="" due="" to="" random="" chance?="" how="" many="" would="" show="" the="" same="" result="" because="" there="" is="" actually="" a="" difference="" between="" control="" and="" experimental="" groups?="" c.="" think="" about="" the="" dependent="" variable.="" what="" other="" factors="" (confounding="" variables)="" impact="" an="" individual’s="" weight="" aside="" from="" their="" genetic="" background?="" were="" these="" factors="" controlled="" for="" in="" the="" experiment?="" what="" limitation="" might="" be="" associated="" with="" this="" methodological="" choice="" of="" dependent="" variable?="" how="" would="" this="" impact="" interpretation="" of="" results?="" would="" a="" different="" methodological="" choice="" or="" an="" additional="" experiment="" reasonably="" address="" this="" limitation,="" or="" is="" it="" an="" unavoidable="" limitation?="" 7.="" future="" directions.="" what="" would="" a="" logical="" next="" step="" be="" for="" these="" researchers?="" if="" you="" were="" going="" to="" improve="" or="" build="" upon="" the="" study,="" what="" would="" you="" do?="" 8.="" applying="" genetics="" to="" the="" real="" world.="" your="" best="" friend="" is="" overweight,="" and="" she="" sees="" a="" commercial="" for="" a="" supplement="" that="" claims="" to="" inhibit="" rcan-1="" activity="" and="" cause="" weight="" loss="" in="" obese="" patients.="" she="" is="" excited="" to="" try="" it,="" but="" asks="" you="" for="" your="" advice.="" would="" reading="" the="" above="" study="" on="" the="" rcan-1="" knockout="" make="" you="" more="" or="" less="" likely="" to="" recommend="" that="" your="" friend="" try="" the="" supplement?="" are="" there="" reasons="" to="" consider="" other="" information="" aside="" from="" the="" data="" presented="" in="" the="" above="" study?="" think="" about="" how="" generalizable="" this="" study="" was="" and="" whether="" or="" not="" it="" is="" relevant="" to="" your="" friend.="" (describe="" in="" detail="" why="" or="" why="" not.="" there="" is="" not="" one="" correct="" answer="" here="" –="" rather,="" you="" will="" be="" graded="" on="" your="" ability="" to="" use="" sound="" arguments="" to="" defend="" your="" choices)="" how="" you="" will="" be="" graded.="" write="" your="" answers="" in="" a="" new="" word="" document="" (not="" papers!),="" being="" sure="" to="" reference="" the="" original="" question="" #="" when="" you="" write="" your="" answers.="" you="" must="" type="" your="" answers="" to="" the="" questions="" above="" (in="" complete="" sentences="" and="" your="" own="" words)="" and="" upload="" the="" final="" word="" document="" to="" blackboard="" (don’t="" forget="" to="" write="" your="" name!).="" you="" may="" draw="" the="" flowchart,="" but="" please="" take="" a="" picture="" of="" it="" and="" insert="" it="" into="" the="" word="" document.="" the="" following="" rubric="" will="" be="" used="" to="" grade="" your="" assignment.="" rubric="" question="" (weight)="" proficient="" (100%)="" emerging="" (85%)="" needs="" improvement="" (75%)="" not="" attempted="" (0%)="" what="" is="" the="" main="" question="" the="" authors="" are="" addressing="" (10%)="" question="" addresses="" all="" variables="" and="" accurately="" summarizes="" the="" main="" theme.="" question="" may="" not="" be="" written="" in="" the="" form="" of="" a="" question;="" however,="" it="" does="" include="" all="" variables="" (independent="" &="" dependent)="" question="" may="" or="" may="" not="" be="" written="" in="" the="" form="" of="" a="" question;="" it="" does="" not="" include="" all="" variables="" attempt="" to="" describe="" authors="" question="" was="" not="" made.="" write="" the="" hypothesis="" that="" the="" author="" is="" testing="" (10%)="" hypothesis="" contains="" both="" independent="" and="" dependent="" variables,="" is="" testable="" and="" falsifiable="" (e.g.="" if="" x="" is="" done,="" y="" will="" be="" observed)="" hypothesis="" may="" have="" one="" of="" the="" following="" issues:="" not="" testable,="" not="" falsifiable,="" no="" clear="" statement="" relating="" both="" independent="" and="" dependent="" variables,="" includes="" one,="" but="" not="" both,="" independent="" variable.="" hypothesis="" has="" two="" or="" more="" of="" the="" following="" issues:="" not="" testable,="" not="" falsifiable,="" no="" clear="" statement="" relating="" both="" independent="" and="" dependent="" variables,="" includes="" one,="" but="" not="" both,="" independent="" variable.="" attempt="" to="" describe="" hypothesis="" was="" not="" made="" create="" a="" brief="" flowchart="" that="" describes="" the="" method="" used="" for="" this="" experiment="" (15%)="" flow="" chart="" is="" simple,="" concise,="" and="" accurately="" describes="" samples="" and="" method,="" and="" clearly="" related="" dependent="" and="" independent="" variables.="" description="" of="" method="" may="" be="" verbose,="" copied="" directly="" from="" figure="" legend,="" or="" not="" contain="" a="" flow="" chart,="" but="" long="" sentences="" instead;="" may="" be="" missing="" details="" of="" the="" experiment="" that="" are="" small="" but="" essential="" description="" of="" method="" may="" be="" missing="" or="" substantially="" inaccurate="" in="" one="" or="" two="" key="" steps="" that="" enable="" the="" reader="" to="" understand="" the="" experiment="" method="" missing="" more="" than="" 2="" key="" steps="" in="" the="" description="" of="" the="" experiment.="" what="" is(are)="" the="" independent="" variable(s)?="" (10%)="" all="" ivs="" are="" listed="" and="" accurately="" stated="" mixture="" of="" correct="" and="" incorrect="" information="" only="" incorrect="" information="" given="" no="" attempt="" to="" answer="" made.="" what="" is(are)="" the="" dependent="" variable(s)?="" (10%)="" all="" dvs="" are="" listed="" and="" accurately="" stated="" mixture="" of="" correct="" and="" incorrect="" information="" only="" incorrect="" information="" given="" dvs="" are:="" not="" clearly="" identified;="" not="" given;="" none="" are="" correct="" describe="" the="" results.="" (15%)="" all="" results="" are="" accurately="" described,="" including="" their="" statistical="" significance.="" most="" key="" results="" are="" explained="" accurately;="" however,="" minor="" results="" may="" be="" absent.="" statistical="" significance="" is="" considered.="" most="" key="" results="" are="" not="" explained="" or="" are="" inaccurate.="" minor="" results="" are="" not="" explained.="" statistical="" significance="" may="" or="" may="" not="" be="" considered.="" no="" key="" results="" are="" explained="" or="" are="" explained="" inaccurately.="" minor="" results="" are="" not="" explained.="" statistical="" significant="" is="" not="" considered.="" what="" are="" the="" limitations="" of="" this="" experiment?="" (10%)="" specific="" limitations="" are="" mentioned="" along="" with="" the="" potential="" impact="" on="" the="" interpretation="" of="" the="" data="" specific="" limitations="" are="" present="" but="" do="" not="" address="" the="" implications="" of="" those="" limitations;="" may="" not="" include="" limitation="" not="" mentioned="" by="" the="" authors="" vague="" limitations="" or="" a="" mixture="" of="" accurate="" inaccurate="" limitations="" missing="" or="" inaccurate="" limitations="" future="" directions="" (10%)="" specific="" suggestions="" that="" logically="" build="" upon="" the="" current="" outcomes="" or="" that="" suggest="" a="" redesign="" to="" better="" test="" the="" same="" hypotheses.="" some="" specific="" suggestions="" are="" given,="" but="" answer="" is="" otherwise="" vague.="" or="" specific="" suggestions="" are="" given,="" but="" they="" either="">