Biotechnology in the News (BITN)


Biotechnology for the general public.

Dolly, the cloned sheep


Dolly, the cloned sheep (with her mother).

Dolly was a major news story -- the first mammal cloned from an adult cell.

For figure credit, see the
page on Cloning and stem cells.
 

BITN
topics
DNA and the genome
Cloning and stem cells
Agricultural biotechnology (GM foods) and Gene therapy
Prions (BSE, CJD, etc)
Influenza (Bird flu)
Other topics (more briefly noted)
   Topics include:    Aging    Alzheimer's disease    Anthrax    Antibiotics    Art    Bio-inspiration (biomimetics)    Brain (autism, schizophrenia)    Cancer    Diabetes    Ebola and Marburg (and Lassa)    Emerging diseases (general)    Ethical and social issues; the nature of science    HIV (AIDS)    Hormone replacement therapy    HPV (Human papillomavirus)    Malaria    Measles    Polio    Protein Folding -- and diseases    RNAi (RNA interference or silencing)    SARS, MERS (coronaviruses)    Smallpox    Sudden Oak Death    Synthetic biology    TGN1412: The clinical trial disaster    Vaccines (general)    Zika
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BITN
resources
Some resources that may be useful for your own explorations of biotechnology. The sections listed here are below, under the general heading BITN Resources.
Introduction
Magazines and journals
Local libraries
Local research
Web sites (Spanish)
Books
Glossaries (Spanish)
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BITN
course
Some background information on the original BITN class, which led to this set of pages. The sections listed here are below, under the general heading BITN course.
Overview: goals and general plan
Intended audience; level of discussion
Scope of "biotechnology" -- and of the course
Limitations
Course format
Course outline
Homework; textbook; student responsibilities
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Other featured pages
The BITN pages are part of a larger site, with materials over a range of science. Home page. Among featured pages that may be of general interest...

Musings is an informal newsletter mainly highlighting recent science. It is intended as both fun and instructive. Items are posted a few times each week. See the Introduction on the Musings page for more information.

Unusual microbes. A brief discussion of some of the oddities of the microbial world, organisms that capture our imagination by being different.

Books: Suggestions for general science reading is an annotated book list. Most are about science of one kind or another, and much is for the general audience. The list includes some books of historic interest.

Some pages of specific course-related content that may be of wider interest are:
* Metric prefixes, from yotta to yocto
* Significant figures - a beginner's guide
* ChemSketch - An Introductory Guide.
* Chemistry practice problems. Links to practice quizzes, self-help worksheets, and more -- for a range of topics in general and organic chemistry.
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Other
General information about this site and general resources:

List of pages of Internet resources. This page lists my other web pages of internet resources. They include resources for classes in chemistry and molecular biology, and much more. Some of these items will be referred to along the way, but you may want to just browse.

Library matters. Information about library resources, with some focus on the UC Library system. However, much of the information is general, especially about electronic resources. For example, it has information about doing searches of the scientific literature, to find articles on a topic that interests you. Major topic areas there include: UC Berkeley library; electronic journals; journal articles; PubMed (Medline) searches; citation searches.
Classic papers
FAQ - Frequently asked questions about this web site
Contact information

Some of the featured pages are listed in the next block.
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BITN resources. Some resources that may be useful for your own explorations of biotechnology.


Introduction

BITN is an informal course, without grades. There are no assignments, but a premise of the course is that you do hear about science items from the news. Whatever news sources you normally use are fine; having diverse sources in the class is great.

These BITN pages play two roles. Broadly, they may suggest some regular news sources for you -- particularly in the sections immediately below. More specifically, the other BITN pages provide information and resources for selected topics. Some topics have individual pages; some of these were the topics chosen for the first BITN class. The idea was to provide some discussion of the material for these class topics, and a range of suggested resources (web sites and other) for getting further information. A range of miscellaneous topics is more briefly noted on one page of "other". See top of page for links to these topic pages.

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Magazines and journals

The following is a list of some magazines (journals) of possible interest. They all have web sites, with some availability of contents to the public. Some may be in your public library.

The following three science magazines are intended for a general audience. Their web sites allow free access to selected articles, and also have some news items, so exploring the web site without a subscription can be of some use.
* Science News (bi-weekly). https://www.sciencenews.org/. Items are usually quite short, but also quite current and high quality as far as they go.
* Scientific American (monthly). https://www.ScientificAmerican.com.
* Discover (monthly). http://discovermagazine.com.

New Scientist (weekly) is a British magazine also intended for the general audience. It is becoming increasingly popular in the United States. Some articles are available from their web site: https://www.newscientist.com/.

The Scientist is a monthly news magazine (biweekly prior to 2006), generally aimed at biologists, but with much of the content at a level suitable for "general audience". It includes news of scientific developments, as well as commentary. I find it to be well written and informative. Online: http://www.the-scientist.com/.

Journal of the American Medical Association (JAMA) and New England Journal of Medicine (NEJM) are major American medical journals, whose readership includes the general public. As above, some things are available at the web site even without subscription, but more is available if you use a UC terminal.
* JAMA (weekly): http://jama.jamanetwork.com/journal.aspx
* NEJM (weekly): http://www.nejm.org/

The following two scientific journals publish primary research articles. However, they also have several pages of news stories at the front of each issue, with both scientific and policy content. Both are multidisciplinary, covering the full range of science. Science, published by the American Society for the Advancement of Science (AAAS), is found in some public libraries. The web sites for both allow free access to selected items. Those using computers at UC Berkeley can access these journals, full coverage, through the university subscriptions.
* Nature (weekly). http://www.nature.com/index.html
* Science (weekly). http://www.sciencemag.org

Science allows free access to research articles -- but not other content, including news stories -- at their site after one year; however, the site goes back only to 1997. Full online coverage of older volumes, back to Vol 1, is available through JSTOR; see below.

The Nature web site includes "web focus" sections, with links to many articles on a topic of interest. I refer to some specific focus sections on BITN pages for specific topics. The following link is to the index of focus sections for the biological sciences: http://www.nature.com/nature/focus/index_biologicalsciences.html. It is not always clear which of the focus sections allow free access to anyone, and which require registration or subscription. I suspect it changes over time, too. If you use a UC Berkeley library computer, you will have full access. If not, explore and see; you will usually get at least some access. The index does show some focus sites marked as free.

JSTOR. http://www.jstor.org. JStor is an interesting collection of journals. It is not specifically for science, but very broad. The science journals they have tend to be those with multidisciplinary coverage, such as Science and PNAS (Proceedings of the National Academy of Science, USA). However, they also have done some focused projects, such as ecology journals. What makes JStor particularly interesting is that some of their collections include very extensive back files. For example, their collections of Science and PNAS go back to Vol 1 -- over 100 years in the case of Science. Their collection of journals from the Royal Society of London goes back to the mid 17th century. JStor requires a subscription for full access, but most major universities in the US, and many throughout the world, do subscribe, so it is worth a try and worth looking around. (This site is also included in the section of my Library Matters page for More sources of journals online and on my Classic papers page. The former includes details of how to find articles by Isaac Newton in the JStor collection.)

The Electronic Journal of Biotechnology (EJB) is an open-access web-only journal, of particular relevance to our topic of Agricultural biotechnology (GM foods), although its coverage is broader than that. It is a scientific research journal, but they try to make much of the material accessible to the general reader. EJB, based in Chile, has a Latin American emphasis. It is now published four times a year, and the entire back collection, to 1998, is online. http://www.ejbiotechnology.info.

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Local libraries

Here is some information about which of the magazines and journals listed above are available in selected local libraries. I think it was correct information when acquired, but both library subscriptions and the rules for online access change. Please let me know of corrections -- or additions.

UC Berkeley has subscriptions to most of these, and most of them include online access. If you use the computer terminals in any UC library, you will be able to access most of the sources listed that require subscription. (This is least likely to hold for some of the "general audience" magazines.) I have mentioned the UC access above for some journals.

Berkeley Public Library (BPL; Central branch). Discover, JAMA, Nature, NEJM, New Scientist, Science, Science News, Scientific American.

El Cerrito. Discover, Scientific American. (The El Cerrito library is a branch of the Contra Costa County Library system.)

Albany. Discover, Scientific American. (The Albany library is a branch of the Alameda County Library system.)

For general information on using these libraries, especially their electronic resources, see my page Library Matters.

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Local research

The San Francisco Bay Area is arguably where biotechnology began. It is the home of major universities, national labs, and biotech companies big and small. Links to some of these are shown on my Internet resources: Miscellaneous page. Of particular relevance are the sections Colleges and universities (local, and beyond) and Of local interest....

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Web sites

This section lists some web sites with topic-content for many topics. (Web sites for specific topics are listed with those topics.)

There are some web sites that specialize in science news. Some of them will even e-mail you a daily or weekly dose of science news. I have listed some of them on my page of Internet Resources - Miscellaneous, under the heading Science: News, Discussion forums, General.

Understanding Genetics -- from "The Tech" (the Tech Museum of Innovation, San Jose, Calif). http://genetics.thetech.org/.

An NIH educational site... A Revolution in Progress: Human Genetics and Medical Research. Starts with the basics of inheritance, and then discusses the modern technologies, such as genetic engineering and gene therapy. Includes some case studies of how genes for certain diseases were discovered. Intended for the general public. https://history.nih.gov/exhibits/genetics/introf.htm.

Mill Hill Essays, http://www.historyofnimr.org.uk/mill-hill-essays/. A series of essays on a range of biological issues, from the National Institute for Medical Research in England. Topics for 2013 include: Cellular Alchemy: the science of reprogramming cells; Bacteria maketh the man; Plasmodium knowlesi malaria infections in Malaysia: The last parasite standing?; (E)MERGE; Beyond the DNA code; The jellyfish revolution; Are we too clean for our own good? -- and more. A 2002 essay on Rosalind Franklin essay is listed for BITN: DNA and the genome. (I am not sure new essays are still being published. However, the archives seem complete at the URL shown here.)

ActionBioscience, http://www.actionbioscience.org. An educational site, intended for a wide range of students. Much of the site is organized around "The bioscience challenges: How do these issues affect your life?". The six focus areas are: biodiversity, environment, genomics, biotechnology, evolution, new frontiers (Why is it the age of biology?). Topic areas under Genomics include: Understanding genomes, Genetic information and privacy, Ethics in genomics, Applications of genomic mapping, Genetic manipulation. Topic areas under Biotechnology include: Technology and ethics, Cloning, Genetically modified organisms, Medical biotechnology. These topics overlap, and articles on stem cells and gene therapy are in various places. The site is intended to present a range of views on controversial issues, but does seem to have something of an environmentalist slant. Some articles are accompanied by lesson plans for teachers. Also in Spanish. ActionBioscience is from AIBS (American Institute of Biological Sciences), which is listed as a general biology resource on the page Internet resources: Biology - Miscellaneous.

Malcolm Campbell, Davidson College, has much instructional material on the web, much of it describing methods used in molecular biology. These pages include: http://www.bio.davidson.edu/courses/genomics/methodslist.html and http://www.bio.davidson.edu/courses/movies.html. For example... the former contains a useful description of how to knock out genes in mice, which I refer to later under Agricultural biotechnology (GM foods) and Gene therapy. And the latter contains a nice animation of DNA microarrays showing one major method used to compare how a genome is expressed under different conditions.

A report The Application of Biotechnology to Industrial Sustainability, from the Organization for Economic Co-operation and Development (OECD). 2001. http://www.oecd-ilibrary.org/environment/the-application-of-biotechnology-to-industrial-sustainability_9789264195639-en. The report discusses specific applications where they project that use of biotechnology will be beneficial to the new buzzword goal of sustainability. Caution... Analyses of this type have a tendency to make very optimistic economic assumptions.

You may find links of interest on my other pages of Internet Resources, either for other specific courses or the miscellaneous pages. All of these are available from the List of pages of Internet resources.

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Books

D P Clark & L D Russell, Molecular Biology made simple and fun. Cache River Press, 3/e, 2005. ISBN 1-889899-07-0. Available in UCB Library. I highly recommend this book as a general introduction to molecular biology. It is intended for both a general audience and a wide range of science students. It presents the basics of molecular biology in a way that is readable and fun, yet scientifically quite sound. 4th edition, 2010: ISBN 978-1889899091.

E C Minkoff & P J Baker, Biology Today - An Issues Approach. Garland, 3/e, 2004. ISBN 978-0815341574. The second edition, 2001, is available in UCB Library. This is a college level biology textbook, but one that is organized largely around topics of current interest, rather than by the traditional biology subtopics. The book has been used at UCB for a non-majors biology course.

H Gest, Microbes - An invisible universe. ASM Press, 2003. ISBN 1-55581-264-3. Available in UCB Library. This nice little book was originally written for a college course to introduce microbiology to nonscientists. It succeeds; I recommend it highly. It has a reasonable dose of history, but most importantly describes the range of microbes and their many roles. It is certainly not a "DNA book"; it provides an important perspective on microbes as organisms.

F M Harold, The Way of the Cell - Molecules, Organisms and the Order of Life. Oxford, 2001. ISBN 0-19-513512-1. A popular account of cells -- the fundamental unit of life. If you are relatively new to biology, Harold's book can be a good overview of living systems at all levels. If you are familiar with much of the biology, this book is a delightful attempt to integrate and find the "big ideas".

For more, see my page of Books: Suggestions for general science reading. The books listed above are included there, along with others over a range of science.

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Glossaries

Talking glossary of genetic terms, from the National Human Genome Research Institute: https://www.genome.gov/glossary/index.cfm. Excellent resource for many biotech topics. Good links to more detailed information for many topics. Also available in Spanish.

I have listed two general biology web sites on my Internet resources: Biology - Miscellaneous page, in the Biology: Books and glossaries section. Both of those pages include a wide range of general biology information, organized around a "Bio 1" type course. Both sites include good glossaries.

The small DNA helix shown below is modified from a DNA figure in the Glossary at M J Farabee's On Line Biology Book, noted above.

I have a Glossary that I started for the Intro Organic/Biochem class (X402), but now use for terms for any course. I started it with the idea of adding things that come up which did not seem readily available in other course materials. So, if you have questions about terms, ask me about them, and I will consider adding them to the glossary.

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BITN course. Some background information on the original BITN class, which led to this set of pages.


Overview: goals and general plan

The human genome, stem cells and cloning, gene therapy and genetically modified organisms. Just some examples of headline stories from the recent news that involve biotechnology. Many issues are involved in these stories, including scientific information and social values. The primary goal of this course is to promote understanding of the scientific issues behind biotech stories such as these.

In this course we will examine selected biotech topics from the news. We will try to help you understand some of the biological background, and we will discuss the current status of the science. Many topics in the news are in their early stages -- which is precisely why they are news. We will try to help you understand how complex fields develop, and how one should deal with preliminary and contradictory news stories.

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Intended audience; level of discussion

The class is intended for the general public. No background in science is required. We might even say that the course is simply for those who read or hear biotechnology stories, and want to know more about what is behind them.

You may have heard of "DNA", or seen some representation of its double-helix structure (see right). You may know that it has something to do with genes, or with determining how an organism develops. That is, you have some general awareness of DNA -- what it looks like, and perhaps that it "carries information". If you know that much, that is great. It is not important that you know anything else about what DNA is or how it works. We will introduce some parts of those issues as they become relevant. DNA helix

For figure credit, see the
Resources section for Glossaries, above.

Discussion will be at various levels, with the general goal of promoting public understanding of the science, and of the scientific issues involved. We will sometimes discuss basic background, sometimes recent results, and sometimes (often!) discuss areas of uncertainty.

In deciding how much scientific detail to present, we will be guided by trying to present what is needed to understand the ideas that we are discussing. We will try to avoid going into more detailed levels of explanation.

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Scope of "biotechnology" -- and of the course

Biotechnology is, broadly, the application of biology. It thus covers a wide range of activities, some traditional and some very new. Biotechnological processes such as the making of bread and of alcoholic beverages have been carried out for thousands of years. Recent decades have brought an explosion in our understanding of biology and in its application.

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Limitations

We can't discuss or solve everything in a few hours. To help define what we will discuss, I think it may be useful to offer the following "limitations".

Our emphasis is science, not social policy. We will try to discuss some of the scientific issues behind stories in the news. Of course, there are other aspects to these stories, including personal values and politics. Ultimate decisions will -- and should -- be based on all these considerations, but our primary emphasis in this class is the science.

We will not resolve controversial issues. This follows in part from the previous point. However, we will not even resolve all the scientific issues. It is the nature of science that we have more questions than answers. Science is a process of seeking answers. If we are able to bring out questions, and discuss some work leading to answers, I think we have made progress. But we will make no claim to being comprehensive.

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Course format

Six classes, two hours each. We will start at 7 pm promptly, take a 10 minute break around 8, and finish about 8:50.

Class will be informal. I will always have a plan, but we do not need to stick with it exactly. I will have some "lecture" material prepared, but the lecture style is informal, and questions and discussion are encouraged along the way.

I have chosen three "core topics" for the course. Each of these is a "big story" which, in one way or the other, has been and is likely to be in the news. We will schedule two class periods for each of these topics. See Course outline, below.

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Course outline

A tentative and approximate course outline, by class, follows.

Classes 1-2. DNA and the genome. The human genome. DNA sequencing and genomics. How is DNA sequenced? How is the information used? Pharmacogenetics -- the tailoring of drug treatments to an individual's specific genetic makeup -- as one example.

Classes 3-4. Cloning and stem cells. What are stem cells, and why might they be useful? What are the different kinds of stem cells, and why do scientists disagree about which ones are useful? Cloning animals... the basic procedure -- and what the problems are. Dolly the sheep; cloned humans. How is the stem cell story related to cloning?

Classes 5-6. Agricultural biotechnology (GM foods) and gene therapy. How does one change a gene? Why would one do so? Why is this controversial?


There is something of a contradiction in providing a plan for a class which is to be strongly influenced by current news and by student interest. Nevertheless, we do want some basic plan, so those considering the course have some idea what to expect. Further, the plan serves as a reference point. If we choose to spend time on some other topic, we can see what effect that will have on the schedule.

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Homework; textbook; student responsibilities

This is intended as an informal course for the general public. There will be no tests and no grades, and no academic credit. (Continuing education units -- ceus -- are available.)

There is no textbook, and there are no required readings or assignments.

Consistent with that, there is no formal homework, and there are no formal student responsibilities. However, the broad goal of the course is to help you understand the news. Thus I encourage you to explore the real news as the course proceeds, and to share things you come across with the class.

The top of this page lists all BITN resources available here. They include information about specific topics, as well as suggestions for news sources, in addition to the common obvious ones, such as regular newspapers and broadcast media. The topic pages often contain some information to help you follow up on some of our topics. There is no obligation that you do any such follow-up, but I would be delighted to hear that some of you have at least followed up some on even one topic that particularly interests you.


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Last update: January 04, 2017