Expert Assessment Part 3: Analysis of Potential Bias

Analysis of Potential Bias:



1.) Bias Through Selection and Omission:

This article mostly shows the bad parts of the drug herceptin as well as the tests that show whether or not it is needed. The two other supporting articles pretty much agree with this statement, however, not quite as harshly. The main article seems to have its points clear more than the other two articles

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2.) Bias through Placement:

This article was placed on the front page of the New York Times. This could make the article seem more important than it may be. It may aslo encourage people to be against this treatment because of the importance set on the negatives of this drugs rather than positives in this article.



3.) Bias by Headline:

The title of this article makes the results of the tests of the drugs look unorganized and confused, which could give people a negative impression of the scientists that ran this experiment. This is bias because by making the tests look unorganized, the author is making the readers doubt the ethics of the experiment and they are more likely to be against it.

4.) Bias by Photos, Captions, and Camera Angles: 

This article had only two pictures, both of which were of people that were involved with the research. There was not bias in the pictures, because they were simply photos of the scientists.

5.) Bias through use of Names and Titles:

The main example of a patient with receiving this treatment is a doctor. This is bias because, at the end of the article, the doctor decides not to get the treatment. This might make other people choosing whether or not to get the treatment choose not to, since a doctor, who knows what they are talking about, chose not to get the treatment.

6.) Bias through Statistics and Crowd Counts:

There are several crowd counts about results of the treatment, all of which seem to be accurate and with out bias.

7.) Bias by Source Control:

All of the quotes concerning the technicalities of the drug treatment are from doctors, which makes it seem like their information is from a legitimate source.

8.) Bias by Word Choice and Tone:

There is bias by word choice in the last bit of the article, when the doctor chooses traditional chemotherapy in stead of this new drug. The article says, “… the studies, along with Dr. Winer’s clinical perspective, did not convince her that the drug would help.” This tone is suggesting that since a doctor with a doctor’s perspective was not convinced to get the treatment, no one else should get the treatment, either.

Expert Assessment Part 2: Background Research

Other Article Summaries:

The first article was from the San Francisco Chronicle and is about the financial aspect of the drug. Herceptin is very costly and has made a very large profit. It also talks about a man named Roche Holding who is currently attempting to get a drug, similar to herceptin, approved by the FDA. Also, it talks about several statistics that involve the accuracy of the tests as well as the success of the actual drug. It also mentions the DM1 drug that was added to herceptin, even though it was proven to be toxic and not very successful when it was used as a drug for chemotherapy, several years ago.

The second article is very in depth and talks about both the positives and negatives of testing for the HER2 protein as well as the actual medication, Herceptin. Treatment with herceptin to tumors with high levels of HER2 seems to have promising results but some situations that occur during the clinical trials with advanced breast cancer patients lack some explanations. For example, they do not know why patients react better when the drug is given with chemotherapy. Also, they do not know why less than half of the cases responded to it on just the drug by alone. Test results are also varied. Someone who takes the test and gets a positive result may take it again and get a negative result. One type of testing called fluorescent in situ hybridization (FISH) analysis is usually more accurate. However, it is also more time consuming, expensive, and therefore is not as oftenly used. Some hospitals use only FISH testing. But normally, FISH is only used to clarify unclear test results. Dr. John Kennedy thinks that FISH testing should always be used since it is more accurate.




Article #1:
Doherty, Dermot. "Roche to Seek Early Approval of Breast Cancer Drug (Update3)." San Francisco Chronicle. 15 Apr. 2010. Web. Apr. 2010. .



Article #2:
 "HER2 Testing and Its Role in Breast Cancer." Ethiopian News and Opinion Journal. 16 Apr. 2010. Web. Apr. 2010.

Expert Assessment Part 1: Article Summary

Cancer Fight: Unclear Tests for New Drug



Purpose:

- The purpose of this article is to show the many complications that can happen when testing for HER2 tumors. Also, it talks about the possibility of a drug, called herceptin, which could possibly cure tumors that have high levels of HER2. The drug, herceptin, is not positively promoted in this article.

Key Information:

- Some breast cancer tumors have extra copies of a protein known as HER2. The drug herceptin blocks this protein, which, in turn, hinders the growth of the tumor. However, the drug only works if the tumor does have extra copies of the HER2 protein. The test to see if there are extra copies is not very reliable.
- When herceptin is used with a tumor that does have high levels of HER2, it can cause flu-like symptoms and can rarely cause severe heart damage and/or death. If used on a tumor without high levels of HER2, herceptin can be very toxic.

- Testing for extra copies can vary greatly from lab to lab. Therefore, most of the statistics that involve false positives, etc., are not readily available. Some tumors have parts that do have high levels of HER2 and may also have parts that don’t, so sometimes a false positive may be correct.

Key Conclusion:

- Herceptin would be a much more promising cancer treatment, if the test to see if there were high levels of HER2 was more reliable. If, the tests for extra copies of HER2 are revised and have a higher rate of accuracy, I believe that Herceptin should be used as a treatment for HER2 positive tumors.

How this class helped me to better understand this article:
- I thought that this article related to what we discussed in class, because it talked about proteins, genetic testing, and cancer. We discussed proteins a lot and how too many or too few copies of a specific protein can be dangerous and can cause certain diseases to become better or worse. We also talked about genetic testing and how sometimes they are not very reliable.





LIST OF PEOPLE AND AGENCIES REFERENCED BY THE AUTHOR:

People:
- Dr. Linda Griffith: Patient

- Dr. Antonio Wolff: Breast Cancer Specialist at John Hopkins
- Krysta Pellegrino: FDA spokeswoman

- Dr. Jeffrey Bloss: Vice President of North America Medical Affairs at GlaxoSmithKline

- Dr. Edith Perez: Breast Cancer Specialist at the Mayo Clinic in Jacksonville FL

- Alberto Gutierrez: Overseer of Diagnostic Products at the FDA

- Dr. Eric Winer: Dr. Griffith’s doctor

- Dr. Elizabeth Hammond: Pathologist at Intermountain Healthcare in Utah

- Sheila Maloney: Breast Cancer Survivor


Agencies:

- Center for Gynepathology Research at MIT

- Genentech: Maker of the drug, Herceptin

- Food and Drug Administration

- College of American Pathology

- American Society of Clinical Oncology

- The College of American Pathologists


TYPE OF ARTICLE:

- Report on Potential New Cure or Innovation
-
-This article reports on the potential of the new drug Herceptin


-Report on New Research Development

 -This article talks about the most recent discoveries of the problems with the tests that detect extra copies of HER2 proteins in cancerous tumors

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Citation:
Kolata, Gina. "Cancer Fight: Unclear Tests for New Drug." New York Times. 19 Apr. 2010. Web. Apr. 2010. .

"Imitators That Hide in Plain Sight, and Stay Alive."

- Henry Bates studied animal species in the Amazon jungle for eleven years from 1848 to 1859.

- Darwin’s “On the Origin of Species” was able to help Bates provide evidence of natural selection based on what he had seen in the jungle.

- What interested Bates greatly, was the ability of some animals to resemble other living or inanimate objects.

- “He observed flies that looked like bees, beetles that looked like wasps, even caterpillars that looked like pit vipers. He referred to these as ‘analogous resemblances’ or ‘mimetic analogies.’”

- Today, this phenomenon is known as Batesian mimicry. It is thought to have happened because of natural selection. Animals that did not look “tasty” or resembled other poisonous species were less likely to be eaten and had a better chance of survival and lived longer lives.

Reflection:

I found this article interesting because it directly related to Natural Selection. If you look unappetizing, you’re less likely to be eaten. In a world of “survival of the fittest” this would come in handy so that, even if a species was not harmful, if it look like it was, predators would avoid it. In conclusion, this article helped me to understand one aspect of Natural Selection.

http://www.nytimes.com/2010/02/16/science/16crea.html Carroll, Sean B. "Imitators That Hide in Plain Sight, and Stay Alive." New York Times 15 Feb. 2010: 1-3. Web. 20 Feb. 2010. .

"Rising Threat of Infections Unfazed by Antibiotics."

- Acinetobacter baumannii is one category of bacteria that is estimated to already be killing tens of thousands of hospital patients each year.

- There are medicines that treat Acinetobacter baumannii, but new treatments are not being heavily researched and in that time, the bacteria is evolving and not responding to the current treatments.

- Dr. Louis B. Rice, an infectious-disease specialist at the Louis Stokes Cleveland V.A. Medical Center and at Case Western Reserve University said, “There are strains out there, and they are becoming more and more common, that are resistant to virtually every antibiotic we have.”

- This strain of bacteria can cause pneumonia and infection to the urinary tract, bloodstream, and other parts of the body. The cell structure of the bacteria is what makes it more difficult to attack with antibodies than other infectious bacteria.

- The drugs that are currently being used to treat this strain of bacteria are colistin and polymyxin B. However, they are not used often because they have been known to cause kidney and nerve damage. Since they are not used often, the bacteria has not had a chance to evolve resistance to them yet. They are still trying to find better treatments, though.

Reflection:

This article relates to our class because it is similar to the strain of AIDs we studied that evolves to become resistant to the medicines designed to treat it. If doctors could foresee how a disease or infection would evolve, they could come up with better treatments. If this happened, people would have a higher chance of surviving infections, cancer, or AIDs. In conclusion, this article helped me to better understand the evolution of strains of bacteria to become resistant to treatments.

http://www.nytimes.com/2010/02/27/business/27germ.html

Pollack, Andrew. "Rising Threat of Infections Unfazed by Antibiotics." New York Times 27 Feb. 2010. Web. 3 Mar. 2010. .

"Vast Genetic Diversity Found Among Africans."

- Recent studies have shown that there is a greater genetic differences between two Africans, such as the Bushmen and Bantus, whom speak different languages than the genetic differences between a European and an Asian.


- Africans are so genetically different, because they have lived in one place, with many different kinds of environments, that they have had a much longer time to obtain these genetic differences than Europeans and Asians have.


- All human genomes are almost identical.

- The small differences in the nucleotide bases of the DNA make up for most of the visible differences.

Reflection:

I found it really interesting that African people have much greater genetic differences than Europeans and Asians do since they have had longer in one environment to acquire all the differences.
 I also found it interesting that the large number of nucleotide bases in our genomes are what allows all humans to have very similar genomes while the small differences are all that really shine through.

 I was able to understand that even though everyone’s genomes are very similar, our SNPs are what allow us to all be different and individual, even in the little ways.
 I was able to understand how the Africans could be so genetically different because of time and evolution.

http://articles.sfgate.com/2010-02-18/news/17927011_1_bushmen-genetic-diversity-decoded

Ritter, Marcus. "Vast Genetic Diversity Found Among Africans." SFGate 18 Feb. 2010. Web. .

"Disease Cause Is Pinpointed With Genome."

- At one time, a single person’s genome was about $50,000 to decode. Now, it is about $5,000. Over the years, genome sequencing has also gotten much more effective since we can now do more with the results.

- The Human Genome Project (a three million dollar project) was based on a possible shortcut that is now seeming to be incorrect.

- The geneticists that are involved in the project assumed that mutations that caused common diseases were more frequent. Now, they believe that natural selection has ‘weeded out’ most of the bad mutations before they become too common.

- Right now, multigenerational families are next in line for genome sequencing.

- Geneticists are currently looking into how genes are passed from parent to child, where the mutations are, why the genes mutate where and when they do, and how often they occur.

KEY CONCLUSION:

Genome sequencing has come a long way since the beginning of the Human Genome Project. Geneticists are now know more from the results which makes the whole process much more efficient. This article helped me understand genome sequencing and relate it to what we learned in class (genes and genomes). Also, the geneticists believe that natural selection has made many of the genetic mutations in common diseases that ‘weed out’ any flawed genes before they become too common.

http://www.nytimes.com/2010/03/11/health/research/11gene.html

Wade, Nicholas. "Disease Cause Is Pinpointed With Genome." The New York Times 10 Mar. 2010. Web. 17 Mar. 2010. .

"Speed Reading of DNA May Help Cancer Treatment."


- Mitochondrial DNA is passed only through the mother. It has easily identifiable DNA, since the genome only has 16,000 units compared to the 3 million units of nuclear DNA.


- Sequencing mitochondrial DNA is a lot less expensive than nuclear DNA and can also be found in much smaller samples of blood.


- In over 80% of cancer cases, the patients have mutations in their mitochondrial DNA. Doctors believe that if they can find the mutations they could get a sense of where they begin and when they end.


- These reformed portions of DNA possibly could monitor the success of a cancer treatment to see whether or not the cancer is completely gone.



Reflection:

This was an eye-opening article because if scientists were able to quickly read through a cell’s DNA, it would be easier for them to read and monitor cancer treatments on a cellular level.

 I was able to understand this article since we studied the concept of DNA and since I was aware of how expensive and difficult decoding a genome is, as well as the benefits and risks of such a project.
 Also, I was able to understand this article since I knew the different parts of the cell, such as mitochondria.




http://www.nytimes.com/2010/03/09/science/09gene.html

Wade, Nicholos. "Speed Reading of DNA May Help Cancer Treatment." The New York Times 8 Mar. 2010. Web. 18 Mar. 2010. .

Gene Variant Might Guard Against Alzheimer’s

➢ A type of a gene known as the CETP gene is now thought to lessen one’s odds of getting Alzheimer’s.


➢ In a study of 523 people, 105 people carried 2 copies of the CETP gene while 235 carried one copy of the CETP gene. The remainder did not carry copies of the CETP gene.


➢ Over the span of four years, out of the 523 people (who were about 78, years old), the people with two copies of the CETP gene only had a 1/3 chance of getting Alzheimer’s.


➢ Also, people who had the CETP seemed to have lower HDL cholesterol levels, as well.



➢ While the majority of the population does not have this gene it seems to have positive effects when it comes to the prevention of Alzheimer’s.

Reflection:

I found this article interesting, because I have family members suffering from Alzheimer’s and I wanted to know more about it. In the article, it was stated that while 2 copies of this gene have a good effect, 1 or none seem to have no effect. This seems to be a case of complete dominance where the CETP gene is recessive. During class, we learned about dominance, how proteins function, and how that can affect an organism’s phenotype and genotype. This article was helpful for me because I could connect it to what we leaned in class.

Seppa, Nathan. "Gene Variant Might Guard Against Alzheimer's." U.S. News and World Report. 12 Jan. 2010. Web. 7 Feb. 2010.

http://www.usnews.com/science/articles/2010/01/12/gene-variant-might-guard-against-alzheimers-other-dementia.html

"From a Songbird, New Insights Into the Brain "

- Zebra finches are a species of songbird. The male learns one song from their fathers and they repeat it throughout their entire lives.


- Scientists are studying this phenomenon to learn more about how language is developed in the human brain.

- If someone has a genetic mutation in a gene, known as FOXP2, they will have speech defects. Finches that have similar mutations in one of their genes cannot sing.

- Because of this, many scientists believe that humans and zebra finches have a similar language development processes.


-When the zebra finch listens to a song, the genes in it’s brain make several copies of the genes, which change other genes (instead of making proteins) that are involved in listening. Scientists believe this how the finches learn their song.

Reflection:


 I found this article very interesting because of the many similarities between the developmental skills and the brains of zebra finches and humans. I was better able to understand how and why the scientists think that they are so similar since we studied evolution and how we learned that everything is related and no species is really very different from each other on the genetic level. Also, I was better able to understand this article since we studied genetics and learned that all genomes of every single living thing are really very similar, no matter what they are.

 In conclusion, I would be interested in finding out if the language development part of the brain in zebra finches and humans are as similar as scientists think they may be.

Wade, Nicholas. "From a Songbird, New Insights Into the Brain." The New York Times. 5 Apr. 2010. Web. 8 Apr. 2010.

http://www.nytimes.com/2010/04/06/science/06bird.html?partner=rss&emc=rss

Human Culture, an Evolutionary Force

This video talks about cultural evolution:

http://www.youtube.com/watch?v=jk7aDGntUbw

It also relates to the other article, "From a Songbird, New Insights Into the Brain".

- People have begun to think that the way a certain group of people live, changes the way humans change and develop over long periods of time.


- There are three major gene changes that biologists use to support this point:


1) Extra copies of the amylase gene:


- Amylase is an enzyme that breaks down starch. In societies where more starch is consumed, people will have more copies of the amylase gene.


- More copies are frequently found in farming communities, rather than hunting or fishing communities.

2) Genes that affect bone growth:

-After living a settled life became more common, the human skeleton began to become lighter and less sturdy.

3) The EDAR gene:


-This gene controls hair growth. One form, causes very thick hair and is found more commonly among East Asians and Native Americans rather than in Europeans or Africans.


-3 reasons that this may be so is:

1. To retain heat in colder climates

2. People may have found it more attractive in their partners

3. When the gene is turned on thicker hair seems to controls part of the immune system

Reflection:

I found it interesting that the way people live and act, affect the way that their genetics change over time. When a certain way of living stops, so do the genes that benefited that way of living. When a new way of living starts, genes slowly begin to develop to benefit the new way of living. I understood this article because I understood that there are many different probable causes for genetic changes because of all the different selective pressures present in the world.

Wade, Nicholas. "Human Culture, an Evolutionary Force." New York Times. 1 Mar. 2010. Web. 21 Mar. 2010.

"Mammoth Hemoglobin Offers More Clues to Its Arctic Evolution."

Mammoth Hemoglobin Offers More Clues to Its Arctic Evolution





- In Canada, scientists have reconstructed a woolly mammoth’s hemoglobin. This started at a molecular evolutionary level. They first looked at hemoglobin genes that were active in woolly mammoths. People have 4 hemoglobin chains- alpha, beta, gamma, and delta.
- Mammoths have a combined strand of the beta and the delta chains along with the alpha chains. These barely differ from Asian elephants today.
-With this figured out, the scientists produced functioning hemoglobin molecules from a mammoth.

- With this sort of information in our hands, questions about genetic histories of the mammoth as well as questions about the differences between ancient woolly mammoths and today’s elephants can now be answered.

Reflection:
I was very fascinated by this article, because it is really amazing that we have the technology to do this sort experiment. Through new genetic techniques, scientists have finally been able to answer age- old questions about how and when mammoths and elephants split off from each other. They have also been able to come closer to creating a complete genome of a woolly mammoth.

 I understood this article since we talked about hemoglobin when we were studying sickle cell anemia and its effect on the hemoglobin cells in the body.


Wade, Nicholas. "Mammoth Hemoglobin Offers More Clues to Its Arctic Evolution."