BIOB50H3 Lecture Notes - Lecture 2: Scientific Control

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7 Oct 2015

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Ecology may seem like a soft science because they are still looking for the laws and it is a relatively young and complex science. The tools required for ecology are only now available and it is a rapidly developing and complex science. Some unique challenges: no two organisms or situations in nature are exactly the same. Natural. : organisms and ecosystems are dynamic they are constantly changing and developing. No two moments in time are exactly alike: we cannot truly account for the past. We don"t completely know what factors influenced the development of an individual, community or ecosystem that led it to its current state: we cannot measure or account for all variables, or even most of them. Sometimes we don"t even know what to measure: the world is changing rapidly at every scale. No ecosystem is pure or untouched by human alterations at this point.

Related Questions

What exactly was Hooker's response to Darwin's, Origin of Species? Thank you for your help. I need help deciphering what his opinions truly were.

Hooker, J. D. 1859. [Review of] On the origin of species. Gardeners' Chronicle (31 December): 1052. Part 1.

From the above expressions it will be inferred that we have risen from the perusal of Mr. DARWIN'S book much impressed with its importance, and have moreover found it to be so dependent on the phenomena of horticultural operations, for its facts and results, and so full of experiments that may be repeated and discussed by intelligent gardeners, and of ideas that may sooner fructify in their minds than in those of any other class of naturalists, that we shall be doing them (and we hope also science) a service by dwelling in some detail upon its contents. Thus much we may premise, that it is a book teeming with deep thoughts on numberless simple and complex phenomena of life; that its premises in almost all cases appear to be correct; that its reasoning is apparently close and sound, its style clear, and we need hardly add its subject and manner equally attractive and agreeable; it is also a perfectly ingenuous book, bold in expressions as in thought where the author adduces what he considers clear evidence in his favour, frank in the statement of objections to the hypotheses or conclusions founded on its facts and reasonings; and uniformly courteous to antagonistic doctrines. In fine, whatever may be thought of Mr. DARWIN'S ultimate conclusions, it cannot be denied that it would be difficult in the whole range of the literature of science to find a book so exclusively devoted to the development of theoretical inquiries, which at the same time is throughout so full of conscientious care, so fair in argument, and so considerate in tone. . . . Hitherto most [naturalists] have, as we have already observed, contented themselves with the hypothesis that they were independently created, and the minority have clung to the only other explanation hitherto conceived, that they have all been created by variation from a single first-created living organism, or a few such. Now it must be borne in mind that both these views are mere hypotheses in a scientific point of view; neither has any inherent or prescriptive right to a preference in the mind of the impartial inquirer; but the most superficial observation will show that the hypothesis of original creations is incapable of absolute proof, except the operation be witnessed by credible naturalists, and can only be supported by facts that are either not conclusive against the opposite doctrine, or may be regarded as equally favourable to it; and this hypothesis is hence placed at a disadvantage in comparison with that of the creation of species by variation, which takes its stand on the familiar fact that species do depart from the likeness of their progenitors, both in a wild and domestic state. On the other hand the hypothesis of creation by variation labours under the disadvantage of being founded upon a series of phenomena, the action of each of which individually, as explained by Mr. DARWIN, would appear to prevent the possibility of species retaining their characters for any length of time, and it therefore appears at first sight opposed to the undisputed fact, that many hundreds of animals and plants have transmitted their characters unchanged (or nearly so) through countless generations, and covered, even within the historic period, many square miles of country each with millions of its exact counterpart. To explain this anomaly and to raise this hypothesis of creations by variation to the rank of a scientific theory, is the object of Mr. DARWIN'S book, and to do this he has endeavoured to invent and prove such an intelligible rationale of the operation of variation, as will account for many species having been developed from a few in strict adaptation to existing conditions, and to show good cause how these apparently fleeting changelings may by the operation of natural laws be so far fixed as to reconcile both the naturalist and the common observer to the idea, that what in all his experience are immutable forms of life may have once worn another guise. The hypothesis itself is a very old one; it was, as all the world knows, strongly advocated by LAMARCK, and later still by the author of the "Vestiges of the Natural History of the Creation," but neither of these authors were able to suggest even a plausible method according to which Nature might have proceeded in producing suitable varieties, getting rid of intermediate forms, and giving a temporary stability to such as are recognised as species by all observers. Mr. DARWIN has been more successful, though whether completely so or not the future alone can show. We shall proceed to examine his method in another article.

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Case Study Section 4 â Nitrogen Metabolism Based on âA Sickeningly Sweet Baby Boy: A Case Study on Autosomal Recessive Inheritanceâ by Jacqueline Washington and Anne Zayaitz (National Center for Case Study Teaching in Science) The Patient: Mathew Miller is a 7-day-old infant that is rushed to the emergency room by his parents Emma and Jacob Miller, Mennonites from Lancaster County, PA. Emmaâs pregnancy and delivery with Mathew was normal but he started having trouble nursing and now has completely stopped feeding. By the time they reach the emergency room Mathewâs limbs were rigid and he had had a seizure. The initial examination showed no infection and his x-rays were normal. The family history collected by the Doctor revealed that Emma and Jacob had had a previous son, Samuel that died at 9 days-of-age. There also is a history of unexplained childhood mortality on both sides of the family; Emmaâs mother had two sisters who died in the first year of their lives and Jacobâs father had a sister who died at 7 months of age. Emma also points out to the Doctor that Mathewâs diaper has a funny smell to it. Blood and urine samples were taken for testing and skin biopsies from Mathew, Emma, and Jacob were taken and tested for enzyme activity. The tests results showed that:

â¢ Mathewâs urine had elevated levels of the branched chain amino acids and their Î±-keto acid derivatives (which caused the sweet smell in his diapers)

â¢ Both Emma and Jacobâs skin biopsies had nearly normal levels of branched chain amino acid metabolism/enzyme activity

â¢ Mathewâs enzyme activity was less than 2% of normal

Question 1: What is the most likely diagnosis for Mathew?

A. Argininemia

B. Diabetes mellitus '

C. Maple syrup urine disease

D. Phenylketonuria

Question2: What enzyme did the skin biopsy test measure?

A. Carbamoyl phosphate synthetase I

B. Alanine aminotransferase

C. Phenylalanine hydroxylase

D. Branched-chain Î±-keto acid dehydrogenase complex

Question 3: This enzyme functions VERY similarly to two other enzymes that we have discussed, what are they?

A. Phosphofructokinase-1 and fructose 1,6-bisphosphatase (FBPAse-1)

B. Pyruvate dehydrogenase complex and Î±-ketoglutarate dehydrogenase complex

C. Urease and arginase

D. Isocitrate dehydrogenase and malate dehydrogenase

Question 4: How did Mathew (and presumably Samuel) inherit the disease if both Emma and Jacob have normal enzyme activity levels?

A. Emma and Jacob must both be carriers for the disease but their one normal gene is enough to maintain enzyme activity levels.

B. The disease can happen spontaneously, there is no genetic link.

C. Jacob is not really the father of the boys.

D. The disease can skip generations.

Question 5: What would be the best diet for Mathew to follow to control his disease?

A. Atkinâs diet (low carbohydrates, high fat, and high protein)

B. Low protein

C. Low fat

D. No special diet will control the disease

Over the next 4 years Mathewâs metabolic disease is controlled by his special diet but he still suffers approximately 3 metabolic crises a year. These occur when amino acids accumulate in his blood leading to the swelling of his brain. Even something as simple as a cold or the flu can affect his amino acid levels and send his metabolism into crisis. Jacob and Emma decide that âWe cannot continue to live in constant fear that a minor infection or a simple cold or ear infection could kill our son. Even though we are doing everything we are supposed to, he is still getting sick and we are afraid we may lose Mathew.â They learn that some children with Mathewâs disease have undergone liver transplants and are effectively cured.

Question 6: How/why would a liver transplant effectively cure Mathewâs condition?

A. A new liver would be able to spread itâs genes throughout the body and correct the genetic disorder.

B. A new liver would more effectively respond to metabolic hormonal control.

C. A new liver would express the functional enzyme needed to metabolize the amino acids causing Mathewâs condition.

D. A new liver would produce more hemoglobin to transport oxygen more effectively.

The family is directed to Dr. Morton of Childrenâs Hospital of Pittsburgh, where transplant experts agree to list Mathew for a liver transplant. Jacob and Emma learn that children who receive a liver transplant have to take strong immunosuppressive drugs for the rest of their lives. It was also clear that there was a 40% possibility that Mathew could reject the liver and need a second transplant (which also might be rejected) or he could die from surgical complications.

Question 7: Assuming the liver transplant was successful and Mathew did not reject the new liver, what type of diet would Mathew be able to/need to eat?

A. He would still need to eat his special diet but he would be at less risk of a metabolic crisis

B. He could eat a normal diet

C. He would need to change to a high protein diet like Atkinâs

D. He would be on an all liquid diet

Question 8: Emma and Jacob decide they want to try to have another child. What would be the chance that this child would also have the disorder that Mathew and Samuel have/had?

A. 0 %

B. 25%

C. 50%

D. 75%

E. 100%

Question 9: If Mathew grew up, got married, and decided to have children, what would be the chance that his children would have the disorder? A. 0%, the liver transplant would have cured him

B. 25%

C. 50%

D. 100%

E. It would depend on his wife, if she was normal than there would be a 0% chance of his children having the disorder but 100% would be carriers, if she was a carrier than there would be a 50% chance of his children having the disorder and a 50% chance that they would be a carrier.

Question 10: The disorder is found in 1 in 200,000 infants throughout the US but 1 in 200 in the Amish and Mennonites of Lancaster County, PA. Why is there such a difference in the prevalence of the disease?

A. There are environmental factors associated with being Amish or Mennonites that increase the prevalence.

B. There is a large amount of genetic similarity within these populations because they tend to marry within the population so recessive disorders such as this are more likely.

C. The gene mutation is preferentially carried in Caucasians so when you average the prevalence across all races in the US the prevalence drops.

D. It is unknown why the prevalence is so much greater in Amish and Mennonites.

Based on âMorgan: A case of Diabetesâ by Lisa Rubin and Clyde Freeman Herreid (National Center for Case Study Teaching in Science)

The Patient:

Morgan Water is a 27-year old Native American that lives on a reservation in Oklahoma. Nearly Â¼ of Morganâs tribe has diabetes but she has no direct family history of diabetes, heart disease, or other serious conditions. She is however obese (BMI = 32) and leads a sedentary lifestyle. Morgan has been suffering from an increasing persistence of symptoms including unusual thirst, dizziness, blurred vision, and numbness in her right foot. The symptoms have been developing over several months but as she is planning her wedding she attributed them to nerves. She is finally persuaded to see her family doctor. Her non-fasting blood glucose level was elevated so the doctor has her return the next morning for a fasting blood sample so they could more accurately measure her blood glucose and insulin. Her blood results are below:

Test	Morganâs values	Normal range	Pre-Diabetic range	Diabetic range
Plasma glucose, mg/dl	260	70 -139	140 - 199	â¥ 200
Fasting glucose, mg/dl	140	â¤ 99	100 - 125	â¥ 126
A1C, %	7.6	~ 5	5.7 â 6.4	â¥ 6.5
Fasting Insulin, mIU/ml	34	2 - 10	10 - 20	â¥ 20

The recommendation of Morganâs doctor was to improve her exercise, good nutrition, and weight loss. He recommends meeting with a nutritionist to assist Morgan in her weight loss goals. When Morgan got home and told her family the diagnosis they however had LOTS of suggestions on how she can lose weight. Below is a description of the advice given to her by three family members.

Best friend Savannah:

âYou know how Iâve been losing weight? Well, Iâve been on the Atkinsâ Diet. I heard about it on TV. Itâs great! You get to eat steak, chicken wings, and all the good stuff. All you have to do is limit carbohydrate intake. You should definitely give it a try. This diet has been around for years and it has worked for lots of people, including me.â

*Note: Atkinâs Diet recommends: 10% carbohydrates, 55% fats, 35% protein

Brother Alan:

âI think the best thing for you to do is exercise and stop eating all of that pizza and candy and food filled with fat. Our people never used to eat that junk. I say eat meals that are nutritionally balanced and high in fiber and low in refined sugars and saturated fats. And run a lot. Stop sitting around the house.â

Grandfather:

âMorgan, it is true that it is best to live in harmony and balance â to eat a nutritionally balanced diet that includes carbohydrates, proteins, and âgoodâ fats to meet your bodyâs needs. That is good. But look to your heritage. Our people were never overweight before we started eating âcivilizedâ food. Look to our native diet. I think you should look to traditional herbal remedies for help. What Alan says is true. Exercise is good. But it is sometimes not enough. Our people have always looked to natural medicine for cures. They will lift your spirits and energize you. Then you will lose weight and you will be healthy again. I hear the herbs from the diet shop are safe and good. But you must take them like the medicine label says. It canât hurt to try them.â

*Note: these herbal supplements Morganâs grandfather is recommending contain the herb

ephedra (ephedrine).

Question 5:

Given Morganâs metabolic state, what is the primary fuel source for her cells currently?

A. Carbohydrates (glucose)

B. Fats

C. Proteins

D. It is a balance of all three

Question 6:

Metabolic ketoacidosis is a common problem with diabetics, which is caused by which of the following?

A. Excessive oxidation of fatty acids, leading to an accumulation of ketone bodies in the blood.

B. Excessive oxidation of glucose, leading to an accumulation of ketone bodies in the blood.

C. Excessive oxidation of proteins, leading to an accumulation of ammonia in the blood.

D. Hyperglycemia.

Question 7:

Which weight loss suggestion is designed to achieve some level of ketosis?

A. Atkins Diet

B. Exercise

C. High fiber diet

D. Herbal treatments

Question 8:

One major side effect of the herbal supplement can be hot flashes and increased perspiration due to increased thermogenesis, what is the likely cause of the heat production?

A. Increasing the activity of phosphfructokinase-1.

B. Increasing the activity of the pyruvate dehydrogenase complex.

C. Increasing the activity of citrate synthase.

D. Increasing the activity of uncoupling proteins.

Question 9:

Would substituting fiber and complex carbohydrates (larger % cellulose) for the simple sugars and starches (high sucrose and amylose/amylopectin) help Morgan lose weight, why?

A. Yes, because complex carbohydrates like cellulose are largely indigestible so they pass through

the digestive tract without being absorbed.

B. Yes, cellulose contains less glucose residues than amylose or amylopectin.

C. Yes, because the fructose in sucrose is much more responsible for weight gain than the glucose.

D. No, because cellulose, amylose, and amylopectin are all composed of glucose so it doesnât

matter.

Question 10:

Which weight loss suggestion will lead to an increased need for gluconeogenesis?

A. Atkins Diet

B. Exercise

C. High fiber diet

D. Herbal treatments

BIOB50H3 Lecture Notes - Lecture 2: Scientific Control

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