Lecture 2 Scientific method PDF

Scientific method Ent 104 Johnson Scientific method Observation Hypotheses Experiment Reject or fail to reject hypotheses Refine hypothesis and repeat Scientific Experiments Test of a hypothesis Treatment vs control Manipulation of a situation such that: One variable is different Any change is attri...

Scientific method Ent 104 Johnson Scientific method Observation Hypotheses Experiment Reject or fail to reject hypotheses Refine hypothesis and repeat Scientific Experiments Test of a hypothesis Treatment vs control Manipulation of a situation such that: One variable is different Any change is attributed to that variable Case history: Kin Selection Inclusive fitness theory Genes can spread via Offspring Relative’s offspring Must record direct and indirect fitness Relatedness asymmetries are important for determining social behavior Individuals help their closest relatives the most Worker Policing Observation: workers eat other workers eggs Hypotheses / Predictions: Workers are more related to sister’s sons than to queen’s sons in colonies with one singly mated queen Should favour worker production of males Workers should not police Workers are more related to queen’s sons than to their sister’s sons in multiply mated colonies Should favour queen production of males Workers should police. Experiment Honey bee queens are multiply mated So, Workers should eat worker eggs Treatment vs control The treatment has one difference with the control If the dependent variable changes then we conclude the one difference caused it Add queen eggs and workers eggs to the same nests and record rates of removal Everything in the nest is the same except for the origin of the egg Eggs remaining Policing Results: egg removal rates in Apis mellifera 100 90 80 70 60 50 40 30 20 10 0 Queen laid Worker laid 1 3 5 7 9 11 13 15 17 19 21 23 25 Days Ratnieks and Visscher 1989 Confounding variables A confounding variable is something that co-occurs with the treatment variable Hence, we may not have produced one difference between treatment and control Common confounding variables: Age & experience Genotype & environment Egg confounding variable Maybe the worker eggs are removed because they are worse than the queen eggs? Less likely to hatch Produce young of lower quality Observation: Workers eggs are smaller, more misshapen Experiment Keep workers from removing the worker eggs and check on hatching rate Hatch them in an incubator Policing results 2: egg viability % Egg Survival 100 80 60 40 20 0 Queen eggs Worker eggs Ratnieks and Visscher 1989 End of study This is the end of Ratnieks and Visscher 1989 Published in a very prestigious journal as a rock solid demonstration of the importance of kin selection in understanding social behavior However… Lots of species with a singly mated queen police! Even clonal species! Workers are more related to their sisters sons than to their mothers in a single mated colony What does this mean for worker policing via kin selection? Kikua and Tsuji 1999 Iwanishi et al 2003 Pirk et al 2003 Hartmann et al 2003 (clonal species) Alternative Hypotheses 1. Kin selection: Relatedness asymmetry Nepotism active within the group 2. Superorganism Colony efficiency Nepotism resolved within the group Prediction Table Policing Kin selection Superorganism Multiply mated Yes Yes Singly mated No Yes Kin selection makes a number of predictions, all of which should be true to support the kin selection hypothesis Can’t prove one half the argument and move on Superorganism tests Hypothesis: Queen is specialized for reproduction Queen eggs should have higher viability than worker eggs Hence, worker’s police to improve colony level efficiency Variation in Experimental tests: Real nest 100 90 80 70 60 50 40 30 20 10 0 % Eggs hatching % Eggs hatching Incubator Queen eggs Worker eggs 100 90 80 70 60 50 40 30 20 10 0 Queen laid Worker laid Pirk et al 2004 What went wrong? In Ratnieks and Visscher 1989 they took the animals outside their natural context Raised eggs in an incubator In the real nest, howver, the pattern was very different from the incubator How common is this? Super common Experimental Artifact An experimental artifact is when a result is dependent on an artificial situation Hence, the result is not useful in the real world Common examples: In vitro vs in vivo Lab vs field Bioassays of all sorts Correlation not causation Just because something happens with a pattern (in time or place) that matches your expectation doesn’t mean it caused it The chosen male on a lek is: The loudest The biggest The most colorful How could we tell which is important? We could make the biggest male: Dull and quiet Not mutually exclusive The chosen male on a lek is: The loudest The biggest The most colorful They could all be true Case history 2: Honey bee DOL Honey bee specialize by age Each age group is called a caste and does a particular set of jobs Each caste has a distinct physiology and hormonal basis Hormones control differential gene expression between castes Cell cleaner Nurse Nectar processor / nest builder Forager Days 1-4 Days 4-12 Days 12-21 Days 21+ Messiness of the real world Throw away caste idea Amdam and coauthors Hypothesis: Foragers only live a short time No point investing in a forager immune system Immune system is costly so removing it makes foragers less costly to the colony Prediction: Foragers should adaptatively down regulate their immune system Experiments / Evidence Antioxidants lower in foragers White blood cells lower in foragers Gene expression of AMPs lower in foragers What didn’t they show? Does the forager immune system not work? Scientific method is rarely followed from start to finish In this case, the function of forager immune systems, the basic pattern to be explained, was never actually measured Often difficult to measure the real world pattern so proxies or bioassay are used instead Proxies of the immune system were measured: Immune cells, gene expression of immune genes etc Experiments Subsequent experiments were done infecting nurses and foragers with various pathogens Fungi, bacteria, viruses, etc Survivorship, gene expression, and metabolic activity were measured Results Foragers actually have the strongest immune systems How? Their system works differently Immunity is complex Many possible approaches to using different components Foragers are not expressing AMPs They already have the proteins! Bull et al 2012 Conclusions Science is a process At the vanguard Many ups and downs Many retractions Some lines of inquiry build Consensus emerges slowly Never really finished