\

Resource Handbook $.50

DIGITAL EQUIPMENT CORPORATION

| BCUCCIIC

t HUNTINGTON II Simulation Program GENE 1

computers are for kids EduSystems—expandable, economical

DIGITAL EQUIPMENT CORPORATION EDUCATIONAL PUBLICATIONS

A partial list of the publications in the continuing series of curric- ulum material published by Digital for use with EduSystems and RSTS are listed below. Please inquire directly for prices on classroom quantities.

Additional publications may be obtained from:

Software Distribution Center Digital Equipment Corporation

Maynard, Massachusetts 01754

Populution: Self teaching BASIC Workbook $2.00 BASIC Matrix Operations, Project Solo $1.00 Problems for Computer Mathematics $i. 25 Advanced Problems for Computer Mathematics 2.00 BASIC Application Programs Mathematics I $1.00 Mathematics II 1.00 Science 1.00 Business and Social Studies 1.00 Plotting 1.00 Huntington I Application Programs MATHEMATICS $2.00 TEACHER ASSISTANCE 1.00 Huntington I Simulation Programs BIOLOGY $1.00 CHEMISTRY 2.00 EARTH SCIENCE 1.00 PHYSICS 2.00 SOCIAL STUDIES 1.00 Huntington II Simulation Modules Student Workbook $0.30 Teacher's Guide 30 Resource Handbook -50 Program Paper Tape L£.90

a, “» 3 Pe Se ¥

A SIMPLE GENETICS PROGRAM

Developed and programmed by:

Ludwig Braun Polytechnic Institute of Brooklyn

Teacher support material written by:

Kirsten Moy Polytechnic Institute of Brooklyn

HUNTINGTON TWO COMPUTER PROJECT 1 June 1971 Copyright C 1971, State University of New York

The work of the Huntington Two Computer Project is partially supported by the National Science Foundation, Grant GW-5883.

Exclusive publishing rights granted to Digital Equipment Corporation. REPRODUCTION NOT PERMITTED

TIRE Gan,

Yn

GENE1

TABLE OF CONTENTS

f ;

13 = teemed Pications: ta sdss ors bal wee td ieite A «A

II. Description of the Experiment- ---+-+.. 2

III. Rationale for the GENE] Unit ---.-.-.. 2

IV. Goals for GENEL a, ae ae eee ee ee ee ee ees ee oe see eae 2

V. Basic Use of the GENE] Program ---+-+-- 3

VI. Further Instructional Uses of the GENE] Program , ,

6 & eee ee

VII. Follow-up Discussion Questions -+-+-+.-+.-- 4

Vill. Semele igs < «6 ee ee eS

1x. -Peageae tithing: (6 66s 4 ws se

IDENTIFICATION Subject Area: Science - Biology

Mathematics - Probability and Statistics Specific Topic: A simulation of the inheritance of genetic traits Abstract: A computer simulation of the inheritance of genetic traits for a varying number of offspring demonstrates the statistical nature of the Mendelian Laws. Grade Level: 11 or 12 Coordinated Computer Program: GENE1l Computer Lanugage: BASIC Special Language Features Used: RANDOMIZE, Strings Text References:

Beadle, George and Muriel, The Language of Life, Garden City, New York: Doubleday & Co., Inc., 1966.

Johnson, W. H., General Biology, New York: Holt, Rinehart & Winston, 1961.

=

Il.

Description of the Experiment

This computer simulation of the inheritance of specific genetic traits is built upon the Mendelian assumptions that: 1) genetic traits are non-sex-linked and independent; 2) each allele of a trait has an equal probability of being transmitted from the parent to the offspring; and 3) one allele is clearly dominant, while the other is clearly recessive.

The model is probabilistic and operates in the following way:

The student inputs the two alleles of the genetic trait selected, specifying which of the two is dominant and

which recessive. The next assigns a dominant or recessive classification to each of the two genes involved for each parent. The student then specifies the number of offspring, n, that he wishes to consider for a particular run.

The program will generate two random numbers, one for each parent. Jn both cases, the program assigns the first gene of a parent to the offspring if the random number generated is greater than 0.5, the second gene if the number is less than or equal to 0.5. The machine then prints out the two genes received by a particular offspring, as well as his phenotype. * The program is executed n times (where the number n is specified by the user).

ITI. Rationale for the GENE] Unit

IV.

In his initial experiments, Mendel harvested, classified, and planted approximately 7200 seeds of the common garden pea. In his studics of the fruit fly, Thomas Hunt Morgan examined and recorded the eye color of over 4200 flies for one experiment alone. Clearly, men cannot be treated experimentally like a patch of garden peas or a bottle of Drosphila. Moreover, the Mendelian laws are statistical statements and require a large data base for their verification. What the student cannot do in the laboratory, he can simulate on a computer with the GENE] program.

Goals for GENEL

After completing the GENE1 study unit, the student should:

Have a deeper understanding of the statistical nature of the Mendelian Laws.

* The phenotype is specified by the dominant gene.

Be able to develop the phenotype and genotype ratios for succeeding generations.

Be able to explain why the model is only an approximation of the process of gene inheritance.

Have a better understanding of the nature of computer modeling.

V5 Basic Use of the GENE] Program

Preparatory Activities:

1) The class may choose to begin with a brief meteors of genetic research and discovery.

2) The students should be familiar with the physical mechanism of genetic inheritance.

3) They should know the Mendelian Laws and be aware that the laws are statistical in nature.

4) The class should discuss the operation of the model: the assumptions made; the equations used; the procedures for running the program.

5) They should outline strategies for varying n, the number of offspring, as well as the gene combinations of the parents. Plans for simulating the genetic inheritance in the second and third generations should be developed.

Use of the Program:

1) The program can be used to situlate Mendel's original experiments with the garden pea. By using an increas- ingly large data base, the student can discover geno- type and phenotype ratios comparable to Mendel's.

2) The: program allows an exploration of the possibilities of genetic inheritance within a given family. If the genotypes of both parents with respect to a specific trait are known,** what are the genetic possibilities for their grandchildren (assuming we have additional knowledge of

the genetic makeup of those marrying into the family)?

3) The program can also be used to demonstrate elementary principles in probability and statistics. What, for instance, is the probability that parents who both have dominant-recessive genotypes for a certain trait will have a child with a dominant-dominant genotype?

* Remember: Four genetic combinations possible for each parent: D-D, R-D, D-R, R-R.

VI. Further Instructional Uses of the GENE1 Program ali tai ep chs acct Rit eerie Adana ~ Made

1) The GENE] program would gain additional usefulness if it could be modified to deal with: a) linked traits and sex-linked traits; b) several traits at the same time; and c) multipli-determined traits. The class may choose to effect one or more of these modifications with the assistance of someone familiar with the BASIC language.

2) With one or more of the modifications suggested in 1), the GENEl program would be especially useful for simulating experiments in plant and animal hybridization. Such computer simulations would find a place easily in studies on animal husbandry, agricultural research, and techniques of dealing with the world food shortage.

VIL. Follow-up Discussion Questions

1) Explain the Medelian Laws in terms of the actual mechanism of gene inheritance.

2) Why is no human being (except for identical twins) exactly like another?

3) Why do mothers only carry such sex-linked defects as color- blindness and hemophilia, while their sons show it?

4) Can blood tests be used legitimately to establish whether an individual is a parent of a particular child? Support your conclusion.

5) What are the primary causes for genetic mutations? How often do mutations occur, on the average? What fraction of these mutations is beneficial? lethal?

6) Is eugenics legislation with respect to any traits justified in light of our current knowledge of heredity?

VIII. Sample Runs

Eight sample runs of GENE] are listed on the following pages. Several comments are appropriate with respect to these runs:

1) In all of these runs, the traits chosen to be studied are brown and blue eye color.

2) In runs 1 and 2, the genotype and phenotype of each offspring is reported, as well as the genotype and phenotype ratios; while in runs 3-7, only the genotype and phenotype ratios are reported. In runs 1 and 2, less than 200 offspring are studied,

3)

4)

5)

6)

and the program permits the user to decide whether or not a detailed report on individual offspring will be printed. If 200 or more offspring are to be studied, the program will not generate this report on individual offspring, in order to conserve printing time. If it is desirable to generate such a report for larger numbers of offspring, the program may be modified by changing line 270 (e.g., if a detailed report on 500 offspring is desired, line 270 should be changed to:

270 + LET R = 500).

For the parental genotypes of runs 1-6, the Mendelian ratios are: genotype ratio = 1:2:1; phenotype ratio = 3:1. With only 10 offspring, in runs 1 and 2, these ratios are significantly different from the theoretical values, because of the small number of offspring -- and the consequently poor statistics.

In runs 3 - 6, there are increasing numbers of offspring, and the genotype and phenotype ratios approach more and more closely the theoretical values, until, in runs 5 and 6, the actual and theoretical ratios differ by about 32%.

On run 7, the genotype of the female parent is changed from the brown - blue of the preceding runs to brown- brown. The theoretical ratios are: genotype = 1:1:0; phenotype = 1:0; with the actual ratios within about 4% of these values.

Run 8 is one example of the result of a run when the parental traits are such that all of the offspring have identical

traits (the cases where: both parents are dominant-dominant,

and all offspring are dominant-dominant; both parents are recessive-recessive, and all offspring are recessive-recessive; and finally, where one parent is dominant-dominant and the other is recessive-recessive, and all offspring are hybrid).

Although the sample runs use the traits brown and blue, the user could specify round and wrinkled, or yellow and green (for peas), or tasters and non-tasters, or attached and de- tached ear lobes (for humans), or any other pair of non-sex- linked, independent alleles for any species.

a @

ti.

oF «

E

WiAT ARE THE TWO TRAITS TO BE STUDIED? DOMINANT TRAIT? BROWN

RECESSIVE TRAIT? BLUE

RAE A OK IK AK

GENOTYPE OF FEMALE PARENT? BROWN» BLUE

GENOTYPE OF MALE PARENT? BdOWN» BLUE

HOW MANY OFFSPRING DO YOU WANT TO STUDY? 10

DETALLED REPOXRTCYES On NO)? YES

OFFSPRING NO« ------ GENOTYPE------ GENE 1 GENE 2

a me EE 1 BLUE BLUE

2 BROWN - BROWN

3 BROWN BROWN

4 BLUE BuO Wi

5 BROWN BLUE

6 BROWN BLUE

7 BLUE BROWN

6 BLUE BROWN

J BLUE BLUE

10 BLUE BROWN

Ae 2K 2S ik 3 2K 2K 2K 2K 2K OK Ok

GENOTYPE RATIO eat PHENOTYPE RATIO 42 1

PEPER AEER ERE

PHENOTYrE

bniOWN BudWn BrOwNn ButOwn B.tO WN BaOWNn BuiOwN BLUE

BraowN

RUN 2

WANT ANOTHER RUN? YES

ARIK AK 2K OK 3%

GENOTYPE OF FEMALE PAKENT? BriOWNs BLUE

GENOTYPE OF MALE PAKENT? BnOWNs BLUE

HOW MANY OFFSPRING DO YOU WANT TO sTUDY? 10 DETAILED REPORTCYES OH NOD? YES

GOFF SPHING NO « <“==-<-GENGT IF <<" << PHENOTYri

GENE 1 GENE e2

1 BuOwWN BLUE BROWN 2 BLUE BLUE BLUE 3 BiiQWN BLUE BuO.WN 4 BLUE BLUE BLUE e) BROWN BLUE BuOQUuNn 6 BROWN BitO WN BROWN 7 B1tO WN' BrOWN Brown 6 BrOWN 5n0 WN BROWN = BLUE BitOWN BrO WN LU BLUE BHOWN BAOWN AR A AE 2S OK AK 2k 2K 2k Ok 2K

GENOTYPE KATIO PHENOTYPE KATI

Heo HH HEE EEE #

0 dt

1666667 &

1

°6666667

Veh : EGR Mater Meh Sm CIs OU fry Sa OE 7G Ae JS THEA Ch eis S)

2 > 8 -

Coli . &

e

WANT ANOTHEK RUN? YES aaK A KK

GENOTYPE OF FEMALE PARENI? SROWN» BLUE GENOTYPE OF MALE PARENT? BsOWNs BLUE

HOW MANY OFFSPRING DO YOU WANT TO, STUDY? 100

DETAILED REPORTCYES On NOD? NO

2 ak og 2 AK AK GENOTYPE RATIO L 3 Se255294 3 146647054 PHENOTYPE RATIO 2e571l4eay = 1

tit tt HAH EE EEE

WANT ANOTHER RUN? YES RUN 4

28K 2k 2K KK

GENOTYPE OF FEMALE PAKENT? BiOWNs BLUE GzENOTYr& OF MALE PARENT? BROWN» BLUE HOW MANY OF ForniNG DO YOU WANT TO STUDY? Suv

HATLOS ONLY WILL BE TYPED, BECAUSE OF LAKGE NOe OF OFFSPHING.

Re 2 36 2k a 2 ok KK GENOTYPE RATIO Ls 1e741007 & 25561151 PHENOTYPE nATiO SecUl6ol : 1

EHH RHER ERE

WANT ANOTHESM RUN? YES RUN 5 DSSS HE OE 3S 2s

GEANOTYrk OF FEMALE PARENT? BAOWNs BLUE GENOTirPi OF MALE PARENT? BROWN» BLUE nOW MANY OFForPiING DO YOU WANT TO STUDY? 1000

mATLOS ONLY WILL BE TYrEDs BECAUSE OF LAnGE NOs OF OF For niINGe

ARK AE 2K OK 26 2 OK 2K 2K 2K OK

GENOTIPH «ATLO 1 8 e2eU52546 $ 1-U1e1Y¥5 PnENOTYPE wATLO 3eU16U64 : 1 HEHE EH EEE

RUN 6 WANT ANOTHEX nUN? YES RK AK 2K 2K OK GENOTYPE OF FEMALE. PARENT? BnOWNs BLUE

GENOTYPE OF MALE PARENT? BROWN» BLUE

oD “a

HOW MANY OFFSPRING DO YOU WANT TO STUDY? 1UUVO

RATIOS ONLY WILL BE TYrEDs BECAUSE OF LARGE NOe OF OFF SrHING.

2k CK 2c ae kK a 2K > 26 2 GENOTYPE RATIO 1 8 2eV66611 & 14039852 PHENOTYPE «ATIO aeY51005 ¢-1

hbeeRHEHBEEE WANT ANOTHER RUN? YES RUN 7 FROK Oe IK AS OK

GENOTYr& OF FEMALE PARENT? BAOWNs BAO WN

GENOTYFE OF MALE PARENT? BbrOWNs BLUE HOW. MANY OFFSPHING DO YOU WANT Yfo STUDY? luv DEVALLED KEPORTCYES OK NOD)? NO eK Dk 2s OK OK 2K OK ot OK Ok oK GENOTYPE naAlrloO i$ s¥960 7643. 5-0 PHENOTYPE HALIC M30 Pen ta Rea ae tp Ht WANT ANOTHER RUN? YES vs

seeks ok A OK On 8

GENOTYPE OF FEMALE rAnENT? BuOWNs BXOWN GENOTYPE OF MALE PANENS? BLUEs BLUE

BECAUSE tot PARENTS AsciE PURE GeNnOlirkss ALL OFF SruilNG Aue BxiOWwNe-BLUBs VHA Los mybudldDe

PH FO oF iF a OE tr tt #

CRD cowie

149 119 129 139 14% 159 169 179 189 199 2940 219 220 239 LAD 259

279 289 29H 39% 319 329 339 349 359 369 378 3893 399

439 3 410 420

439 445 450 463

?

IX. Program Listing

A listing of the program is included below. It is written in the

version of BASIC which existed on the Digital Equipment Corporation

TSS/8 in May 1971. The program, as listed, requires string capability and uses the RANDOMIZE command.

REM GENEL = A SIMPLE GENETICS PROGRAM

REM COPYRIGHT 1971, STATE UNIVERSITY OF NEW YORK

REM ASsBS = FEMALE PARFNT'S GENES

REM Z$sY$ = MALE PARENT'S. GENES

REM G$sH%S - CHILD'S INHERITED GENES 3 P$ - CHILD'S PHENOTYPE REM D&s2RS - DOMINANT AND RECESSIVE GENESs RESPECTIVELY

REM TS - DETAILED REPORT FLAG

REM Si: TOTAL NUMBER OF CHILDREN WITH PURE DOMINANT GENES

REM REM REM REM REM REM REM REM REM LET REM

S2: TOTAL NUMSER OF CHILDREN WITH PURE RECESSIVE GENES

S3: TOTAL NUMBER OF CHILDREN WITH DOMINANT PHENOTYPE (IeEe PURE DOMINANTS PLUS HYBRIDS)

DEVELOPED AND PROGRAMMED BY Le BRAUNs MAY 1971

LATEST REVISION: 8-27-72

CONVERT FOLLOWING TWO LINES TO DIMENSIONS IF NECESSARY

DIM A$C14)5BSC19)5sDEC19)sRSC19)sYSC19)5Z5C108)

DIM G$C19)5sHSC19)5P$(19)5TSC19)

CHANGE NEXT LINE TO INCREASE UPPER LIMIT ON REPORTING

R=200

INPUT DOMINANT AND RECESSIVE TRAITS

PRINT "WHAT ARE THE TWO TRAITS TO BE STUDIFD?"

PRINT "DOMINANT TRAIT'*S

INPUT D$

PRINT "RECESSIVE TRAIT"s$

INPUT R$

IF DS=RS THEN 2996

PRINT

PRINT ‘sexes te t%**

PRINT

REM INPUT THE GENOTYPES OF ROTH PARENTS

PRINT "GENOTYPE OF FEMALE PARENT'S

INPUT A$sB$

IF AS$=D%$ THEN 459 IF AS=R$ THEN 459

PRINT "FEMALE GENOTYPE INCLUDES INCORRECT TRAITe RE-ENTER." GOTO 3998 | IF BS=D$ THEN 479

IF BS <> RS THEN 439

10

A479 PRINT

480 PRINT "GENOTYPE OF MALE PARENT"

49% INPUT Z$sY$

509 IF Z$=D$ THEN 549

510 IF Z$=R$ THEN 549 |

520 PRINT "MALE GENOTYPE INCLUDES INCORRECT TRAIT. RE-FNTER."

53 GOTO 480

543 IF Y$=D$ THEN 580

559 IF Y$ <> R$ THEN 529 ©

569 REM IF BOTH PARENTS ARE PURE GENOTYPES» DO NOT RUN THE RANDOM

579 REM EXPERIMENTSs BUT INDICATE RESULTS AS A SPECIAL CASE.

580 PRINT |

590 IF AS <> BS THEN 7409

609 IF YS <> Z$ THEN 799

610 PRINT "BECAUSE THE PARENTS ARE PURE GENOTYPES, ALL OFFSPRING ARE " 620 IF A$S=Y$ THEN 650

636 PRINT D$3"-"$R$5"s THAT IS» HYBRID."

640 GOTO 1340

650 IF A$S=R$ THEN 680

669 PRINT D$3"-"s3D$3", THAT ISs PURE DOMINANT."

670 GOTO 1342

680 PRINT RS3"=-"3R$3", THAT ISs PURE RECFSSIVE."

693 GOTO 1349

720 PRINT | 710 PRINT “HOW MANY OFFSPRING DO YOU WANT TO STUDY'S

720 INPUT N

739 PRINT

74Q REM LET Q=RND(-1)

759 RANDOMIZE

769 REM CHANGE HERE FOR DIFFERENT NUMBER OF REPORTED CASES

779 IF N<R+1 THEN 829

789 LET T$="NO"

799 PRINT “RATIOS ONLY WILL BE TYPED, BECAUSE OF "

890 PRINT "THE LARGE NUMBER OF OFFSPRING."

81% GOTO 920

829 PRINT "DETAILED REPORT (YES OR NO)"

839 INPUT TS ss 840. IF TS="NO" THEN 929 850 IF T$ <> "YES" THEN 820

ay ey

860 PRINT

879 PRINT

886 PRINT |

694 PRINT “OFFSPRING NOe"'s %------ GENOTYPE---<--=-", "PHENOTYPE" 9906 PRINT * ";"GENE 1"s"'GENE 2"

9190 PRINT “ss2eeeeeeeeee22SS22S5 ner srseeese2eeeseeeeeee2ee=e=e=e=e=="

11

Qa

929 936 94D 954 964 979 989 999 1909 1919 1929 14930

1949

1059

10866

1970 1989 1999 1199 1114 1129 1139 114% 1159 1160 11790 1180 1190 1299 12190 1226 1239 1249 1259 1266 1270 1289 12990 1399 13190 1329 133% 1349 13594 1369 1370 1386 1399 14959 1419

LET LET LET FOR REM LET IP LET GOT LET

51=9 S2=9 S3=9 I=1 TON SELECT RANDOMLY WHICH GENE CHILD WILL INHERIT R1=RNDCX) i1>e5 THEN 1910 GS$=A$ 0 1939 G$S=BS$

REM SELECT RANDOMLY WHICH GENE CHILD WILL INHERIT

LET IF LET GOT LET IF

R2=RNDCX) R2>e5 THEN 1978 HS$=Z$

O 14089

HS=YS

G$=D$ THEN 1140

IF HS$=D$ THEN 1172

REM LET LET GOT IF

REM LET LET REM LET if

IF BOTH PS=RS S2=S2+1 O 1299 HS <> D$ THEN 1170 |

IF ROTH INHERITED GENES DOMINANTsADD 1 TO NO« PURE DOMINANTS S1=S1+1

P$=D$

IF EITHER INHERITED GENE DOMINANT» ADD 1 TO DOMINANT PHENOTYPES S3=S3+1 TS="NO**

INHERITED GENES ARE RECESSIVEs ADD 1 TO NO- RECESSIVEFS

THEN 1229

PRINT IsGSsH$sP$

NEX PRI

PRINT

<a NT Pete OK eK ee

PRINT

IF

PRINT

GOT

PRINT “GENOTYPE RATIO !

S1>9 THEN 1299 “GENOTYPE RATIO 4) 0 13095

$3 CN=SiSe ieee St I"

3°°S (N<-S51-S2)/515 "3" S278

IF N>S3 THEN 1330

PRINT

GOT

PRINT

“PHENOTYPE RATIO oe 0 1346 “PHENOTYPE RATIO

qr

"PSS/7CN#S395 "8 3"

PRINT

PRINT

"eHeHH EERE REET

PRINT

PRINT INPUT

IF IF

END

"WANT ANOTHER RUN CYES OR NO)D'"S T$

TS="YES" THEN 354

TS <> "NO" THEN 1370

12