Controversy Over World’s Oldest Traces Of Life

ScienceDaily (Feb. 28, 2009) —
The argument over whether an outcrop of rock in South West Greenland contains the earliest known traces of life on Earth has been reignited, in a study published in the Journal of the Geological Society. The research, led by Martin J. Whitehouse at the Swedish Museum of Natural History, argues that the controversial rocks "cannot host evidence of Earth’s oldest life," reopening the debate over where the oldest traces of life are located.

NEW EPISODE: Futures in Biotech 39: Food, Genetically Modified

Dr. Lisa Weasel discusses the controversies that surround GM foods
Host: Dr. Marc Pelletier
Guest:Dr. Lisa Weasel; Associate Professor of Biology at Portland State University in Oregon, and a member of Governor Ted Kulongoski’s task force on developing public policy for bio-pharmaceutical crops in Oregon. So if we can design crops that reduce pesticides, grow more effectively in poor soil, bring nutrients such as vitamins A to populations with high incidences of blindness, or even just taste better, why are we hesitating? Why isn't there a wide consumer acceptance of genetically modified (GM) foods?

BIO LAB EXPERIMENT WALK THROUGH VIDEOS - Mike White's Entire Collection - Inserting GFP into bacteria, Mixing Agar, and More!

A big thank you to Dr. Mike White for posting these videos! and a thanks to Frank on the DIY Bio mailing list for telling us about this! Enjoy!



Inserting GFP into bacteria


Transforming carrot explants with green fluorescent protein


Surface Sterilizing Carrot Seeds


Planting and germinating carrot seeds


Washing carrot seeds and placing in germination medium


Placing seeds in germination medium


Placing seeds in germination medium 2


Analysis of Seed Germination Data


NUTRIENT AGAR

Preparing tissue culture media


Weighing Agar


Mixing Nutrient Agar


Nutrient agar after mixing


Pouring Agar Plates


SUBCULTURING BACTERIA

Subculturing Bacterial Stock


Transferring Bacteria to Fresh Medium


Agrobacterium Mechanism

Molecular Biology's Central Dogma

Compilation of "true" to size, shape and speed animations provided by the Howard Hughes Medical Institute showing each part of the Central Dogma of Molecular Biology using the Human globin gene as an example--all in one video

Bird identification

When we visited CCBER I mentioned museums being put to uses that are only limited by your imagination. I'm sure the original curators of the Smithsonian would never have imagined that their prized bird collections would one day be used to identify fragments of bird that had passed through a jet engine (particularly since many of the collections probably predate the jet engine).

But today the Smithsonian houses the 'Feather Identification Lab' where a staff of four analyze the remains of over 4,000 bird-plane collisions a year. The New York Times had a nice article on the lab: Identifying the Bird, When Not Much Bird Is Left.

Although you might think that these days it could all be done by DNA analysis instead of experts looking at feathers the article illustrates that DNA analysis will only take you so far. In one recent case the DNA from a bird strike at 1,500 feet came back as a deer. It required a human expert to identify the feather as coming from a black vulture - explaining the presence of deer DNA in the engine.

Databases and Algorithms for Pathway Bioinformatics presented by Peter D. Karp

LINK TO SOURCE

This talk will provide an overview of the BioCyc collection of 370 Pathway/Genome Databases that is available at URL BioCyc.org, and of the Pathway Tools software that underlies BioCyc. The BioCyc collection includes the EcoCyc DB, which describes the metabolic and genetic regulatory network of Escherichia coli, and the MetaCyc DB, which describes 1000+ metabolic pathways that were experimentally elucidated in more than 1200 organisms.

Pathway Tools includes a large biological ontology that facilitates the representation of complex biological knowledge with high fidelity; a set of inference modules for inferring new layers of biological information above an annotated genome, including inferring the metabolic pathway map of an organism, predicting which genes fill missing reactions in the predicted pathways, and predicting the operons of the organism; and visualization tools that support web publishing, querying, and analyses of these data. Pathway databases provide a rich environment for data mining - Association for Computing Machinery (ACM)

Bio
Peter D Karp - Peter D. Karp is director of the Bioinformatics Research Group at SRI International. Dr. Karp is the bioinformatics architect of the EcoCyc and MetaCyc databases. He has developed algorithms for visualization of metabolic pathways, and for prediction of metabolic pathways from genome data. His research interests include metabolic pathway bioinformatics, genome annotation, scientific visualization, biological ontologies, and database interoperation. Dr. Karp has worked in the Artificial Intelligence Center at SRI International since 1991, where he directs the Bioinformatics Research Group. Dr. Karp has authored more than 90 publications in bioinformatics and computer science. He received the Ph.D. degree in Computer Science from Stanford University in 1989.

Model Organism: Videos of the Nobel Prize-winning worm Caenorhabditis elegans!

Here is a visual introduction to the Nobel Prize-winning worm Caenorhabditis elegans. This page has links to timelapse films made by C. elegans researchers worldwide.

The movies can be viewed with the free version of Quicktime.

Contents:

Embryos

RNAi Screens

Larvae and Adults

Techniques

4D Movies

For more information about the worms, see the C. elegans web page and Wormbase.

The Dark Side of Gender Preference

In China, 120 boys are born for every 100 girls. Experts think that the recent trend (since 1980) is the result of China’s “one-child” population-control policy, combined with a traditional society in which the eldest boy inherits the family land and is responsible for taking care of aging parents. So if a couple is planning on having just one child, usually they will decide it should be a boy. The boy/girl sex ratio is highest in rural areas; in cities, the earning power of women tends to be accompanied by a more normal sex ratio.

What can be done about it? One approach is educational programs to encourage couples to value daughters equally with sons; another is to allow families whose first child is a girl to have a second child; still another is to encourage young couples to live with her parents rather than his. The government is even offering cash payments for girls in some regions.

Toucan time

I put all the toucans on one page for convenience. If you click the image you should get a larger version - or if you click here you can get them as a pdf file that you can enlarge. Seeing all 16 toucans will actually help in picking characters but make it harder to construct the phylogeny. If you want to go hardcore you could construct the table of character states and then use a computer program to work out the most parsimonious tree.

There are numerous programs that can do this. The problem is that many of them do a great many things so can be difficult to get started with. I tried to find one that can do what we require here and SimpleClade looks like it will be up to the task.

Beth Shapiro: How to Clone a Dodo (Video)

Summary
Rhodes Scholar and acclaimed researcher of ancient DNA Beth Shapiro discusses her research findings. She explains why Jurassic Park couldn't work, the lack of genetic diversity in Bison and how mosquitoes can live in the arctic.

"How to make a Dodo," is part of the 2008 Chautauqua Institution's Darwin and Linnaeus: Their Impact on Our View of the Natural World.

The Jumping Genome: Changing Ideas about Heredity and Evolution with Nina Fedoroff (VIDEO)

The Jumping Genome: Changing Ideas about Heredity and Evolution with Nina Fedoroff.

Genetics traces its origins to monk Gregor Mendel's experiments on common pea plants. The 20th century witnessed the explosive growth of genetics from the naming of genes to the identification of DNA as the stuff of heredity by Nobel Laureates Watson and Crick to the sequencing of whole genomes. Fedoroff's lecture explores the revolutions in ideas of genes and chromosomes from beads on a string to the jumping corn genes of Nobel Laureate Barbara McClintock to contemporary ideas of a dynamic genome - Santa Fe Institute

Quick Graphic Diagrams of improtant processes in Bio Technology (brought to you by The National Health Museum)

The National Health Museum's Graphics Gallery (click here) is a series of labeled diagrams with explanations representing the important processes of biotechnology. Each diagram is followed by a summary of information, providing a context for the process illustrated. The entire resource as been posted below for your convenience.

From Gene to Function

The major actors of molecular biology: the nucleic acids, DNA and RNA.
How they carry and transfer genetic information from one cell generation to the next and translate this coded information into active proteins.

• Hammerling's Acetabularia
• Hershey-Chase Blender Experiment
• Central Dogma of Molecular Biology
• Structure of DNA
• DNA Molecule - Two Views
• Possible Models for DNA Replication
• DNA Replicating Itself
• Collaboration of Proteins During Replication
• RNA and DNA
• RNA Synthesis and Processing
• Induction of the lac Operon
• Protein Synthesis
• The Genetic Code
• Base Pair
• Base Pair - A More Detailed View
• Cloning from Adult Vertebrate Cells
• Codon
• DNA (Deoxyribonucleic Acid)
• DNA - A More Detailed View
• DNA Replication
• Exon
• Exon - A More Detailed View
• Intron
• Repressor Protein Switching Genes On and Off
• RNA - (ribonucleic acid)
• RNA - A More Detailed View
• Initiation of Transcription by RNA Polymerase
• mRNA (Messenger RNA)
• Control of the Human B-Globin Gene
• Regulatory Protein Coordinating Gene Expression
• Steps Leading from Gene to Protein
• Control of Gene Expression
• Importance of Combinatorial Gene Control

Building Blocks

From atoms to molecules and cells to tissues, a study of structure and function.

Biochemistry:

• Covalent and Ionic Bonds
• Chemical Bonds and Groups Part 1
• Chemical Bonds and Groups Part 2
• Chemical Properties of Water Part 1
• Chemical Properties of Water Part 2
• Enzyme
• Families of Small Organic Molecules
• Types of Weak Non-covalent Bonds Part 1
• Types of Weak Non-covalent Bonds Part 2
• Macromolecules in Cells
• Molecules Drawn to Scale
• Binding Site of a Protein
• Outline of Sugar Types Found in Cells Part 1
• Outline of Sugar Types Found in Cells Part 2
• Fatty Acids and other Lipids Part 1
• Fatty Acids and other Lipids Part 2
• Amino Acid
• Amino Acids found in Proteins Part 1
• Amino Acids found in Proteins Part 2
• Nucleotide
• Nucleotide - A More Detailed View
• Survey of Nucleotides Part 1
• Survey of Nucleotides Part 2
• Protein
• Protein Structure

Cells:

• Blastocyst
• Cell
• Internal Membranes and Cytosol
• Nucleus
• Relative Sizes of Cells and their Components
• Ribosomes

Tissues:

• Mammalian Differentiated Cell Types Part 1
• Mammalian Differentiated Cell Types Part 2
• Plant Cells and Tissues Part 1
• Plant Cells and Tissues Part 2

Chromosomes and Cell Division

Eucaryotic cell duplication: how chromosomes and genes transmit the information from one mother cell to subsequent generations.

• Comparative Scale of Mapping
• Human Chromosomes
• Nucleosome
• Genes
• Mutation of Chromosomes
• Mitosis
• Mitosis: labeled diagram
• Meiosis
• Comparison of meiosis and mitosis
• Sequences of Base Pairs Mapping
• Crossing-over and Recombination During Meiosis
• Levels of Chromatin Packing
• Chromosome
• Metaphase
• Mutations

Biological Engineering

From the existing techniques of DNA cloning to gene therapy: understanding the present and a look at the future of genetic engineering.

• Biotechnology - The Present and The Future
• Nucleic Acid Hybridization
• Restriction Enzyme: Action of EcoRI
• Inserting DNA into Plasmid
• Cloning into a plasmid
• Transfer and Cloning of the Insulin Gene
• Cloning into a YAC
• Monoclonal Antibody Production
• Polymerase Chain Reaction
• Transgenic Mice

• Cell Breakage and Fractionation Part 1
• Cell Breakage and Fractionation Part 2
• Cytogenetic Map
• FISH - fluorescence in situ hybridization
• Means of Protein Separation
• Microarray Technology
• Microdissection
• SKY (spectral karyotype)
• Southern Blotting: Gel Transfer
• Construction of a Human Genomic Library
• Use of PCR in Forensic Science

Genetics

From Mendel to hemophilia: introduction to the major principles of heredity. biological inheritance influences what and who we are.

• Mendel: Experiment 1
• Recessive and Dominant Inheritance
• Sex Linked Inheritance: Drosophilia
• X-linked inheritance: Hemophilia
• Autosome
• Demo that DNA is Genetic Material
• Gene
• Gene - A More Detailed View
• Haploid, Diploid Cycle
• Deletion
• Duplication
• Insertion
• Pedigree
• Polydactyly
• Sex Chromosomes
• Translocation

Viruses

Genetic messengers surrounded by a protein coat.

• Examples of Viruses
• Influenza A Virus Replication
• Diagram of a Retrovirus
• Retrovirus Replication
• Overlapping Protein Codes
• Adenovirus
• Life Cycle of a Bacteriophage
• Life Cycle of a Retrovirus
• HIV (Human Immunodeficiency Virus)

Cell Processes

Cells and how they operate

Communication:

• Forms of Cell Signaling
• Extracellular Signals

Energy:

• A Simplified Diagram of Cell Metabolism
• An Outline of Glycolysis
• Details of the 10 Steps of Glycolysis - Part 1 (steps 1 - 5)
• Details of the 10 Steps of Glycolysis - Part 2 (steps 6 - final result)
• Anaerobic Breakdown of Pyruvate
• A Simple Overview of the Citric Acid Cycle
• The Complete Citric Acid Cycle - Part 1 (overview and steps 1 and 2)
• The Complete Citric Acid Cycle - Part 2 (steps 3 through 8)
• Glycolysis and Citric Acid Precursors
• Carbon-fixation Cycle
• Catabolic and Anabolic Pathways
• Interconversions of Energy
• Photosynthesis and Respiration
• Floating Ball Anologies for Enzyme Catalysis
• Interconversion of ATP and ADP
• Synthesis of Biological Polymers
• Cellular Oxidation vs. Burning of Sugar
• Production of Acetyl CoA

Immunity:

• Antibodies
• Antibody - Another View
• An Antibody Molecule
• Carbohydrade Recognition at Infection Site

Specialized Processes:

• Propagation of an Action Potential
• Conversion of Signal: Electrical to Chemical
• Cytoskeleton Filaments
• Myosin and Actin Model
• Cell Proliferation
• Collagen and Elastin

Transportation:

• Exocytosis
• Functions of Plasma Membrane Proteins
• Import and Export
• Main Mechanism to Import Proteins
• Membrane Permeability
• Osmotic Swelling
• Passive and Active Transport

Freaky frogfish

It's been a while since we had a crazy critter here - although we did see some bizarre plants on Saturday.

This new species of frogfish uses its leg like pectoral fins to crawl - that is when it isn't bouncing around like a rubber ball. See yesterdays University of Washington press release for information and some great photos and video.

Members of Histiophryne psychedelica, or H. psychedelica, don't so much swim as hop. Each time they strike the seafloor they use their fins to push off and they expel water from tiny gill openings on their sides to jet themselves forward. With tails curled tightly to one side --which surely limits their ability to steer -- they look like inflated rubber balls bouncing hither and thither.

"Play Fold.it, the “Tetris-On-Steroids” game that solves protein folding" Quoted from John Clien's blog "88 Proof Synth Bio." Great find John!

You can see John's blog post about the game here: http://88proof.com/synthetic_biology/blog/archives/247 I pasted his post below for your convenience. John writes:

"“Protein folding” is what again?

It’s this: Foldit (curiously, at the web address: “fold.it”). And it’s fun to play. Addictive, really. Check out the picture:

After I had been playing a while, my 8-year old niece came over to my laptop to see what the cute sound-effects were all about. After a minute of watching, she said: “Tell me the web site, I want to play too!” Yeah, no kidding.

“Foldit is a revolutionary new computer game enabling you to contribute to important scientific research,” according to the Fold.it website. The game tracks the score of your protein’s folds, and a higher score ranks higher against other users who are also folding the same protein.

Foldit runs on Microsoft Windows, Mac OS/X, and Linux. There are “introductory puzzles” which teach the basics — each puzzle gets harder and builds on the previous puzzles. At first, I had no idea what I was doing. After finishing the introductory puzzles, I started on a real protein folding challenge. As you can see in the picture my rank is still at 119 out of 300 or so.. I’ve still got some folding to do.

It’s educational, since I haven’t run protein folding simulations by hand before. Most of the biological details are hidden from the game player. The gamer focuses on increasing the score and getting rid of the red warning colors, and enjoying the “Rank Up!” announcements."

For Thursday

On Thursday we will carry out an exercise in class that involves constructing cladograms.

This link will serve as a refresher to the ideas behind cladistic analysis that we discussed earlier in the quarter and illustrates a simple mechanism for constructing a cladogram for taxon provided it doesn't have too many species. Please read this before Thursday.

Once the number of species becomes large the task of calculating the most parsiomonious tree rapidly becomes unmanageable. Fortunately computers are very good at this and there are numerous programs available which can be used, this site lists 386 phylogeny packages!

WHOA! Futures in Bio Tech Audiocast episodes!

http://www.futuresinbiotech.com/

This netcast explores the rapidely changing world of biotech, with a penchant towards getting a better understanding of who we are and where we are going. The living world will soon be a true substrate for engineering. Our world will change, and so will we. We bring a first hand account from the scientists that are moving us into this new technological era - the era of biotech. Produced by Marc Pelletier and Leo Laporte @ TWiT.Tv

There are currently 26 episodes from June 2006 to today! To listen to the videos
Click on the embeded audio players below. But note that only 2009-2008 videos are shown. To get to the older episodes you will have to http://www.twit.tv/FIB

PART 1 of 2: Futures in Biotech 37: Just A Touch Of Green - Published on Dec 29, 2008 GREEN FLUORESCENT PROTEIN DISCOVERY and HOW ORGANISMS SENSE TOUCH

Marty Chalfie, 2008 Nobel Laureate in Chemistry This episode covers how Marty Chalfie discovered the molecular machinery that senses touch. In Part II, Chalfie describes how he developed one of the most important tools of modern molecular biology, one that allows us to see inside a living cells, down to the protein level. With green fluorescent protein, or GFP, we can now track the life of a protein, from when the gene that makes the protein is turned on, to where it goes, to where it dies. Audible Pick: The Snows of Kilimanjaro and Other Stories, Abridged, By Ernest Hemingway, Narrated by Stacy Keach. Transcripts to the shows are now available on the FiB Extras blog thanks tom.price@podsinprint.com, PodsinPrint Also thanks to Phil Pelletier and Will Hall for the great themes. Thanks to Cachefly for providing the bandwidth for this netcast. Running time: 57:56

PART 2 of 2: Futures in Biotech 38: It Is Easy Being Green - Published on Jan 31, 2009

PART 2: Dr. Martin Chalfie; Professor and Chair of the Department of Biological Sciences, Colombia University, New York, NY. This is Part II of our conversation with Dr. Martin Chalfie. In this episode Dr. Chalfie shares the historical account of his contribution to the 2008 Nobel Prize in Chemistry: How he transformed a green fluorescent jellyfish protein into the most important biological marker used today, one that allows us to track the life of recombinant protein in a living cell. 2008 Nobel Prize in Chemistry Interview with Awardees Audible pick: The Ten Most Beautiful Experiments, by George Johnson, Narrated by dion Graham. To sign up for a free audiobook, visit Audible.com/biotech. Transcripts to the shows are now available on the FiB Extras blog thanks tom.price@podsinprint.com, PodsinPrint Also thanks to Phil Pelletier and Will Hall for the great themes. Thanks to Cachefly for providing the bandwidth for this netcast. Running time: 51:40


Futures in Biotech 36: Avoiding Death, Not Taxes with Dr. Cynthia Kenyon
Published on Nov 24, 2008

Host: Marc Pelletier Guest: Dr. Cynthia Kenyon; Professor, Department of Biochemistry and Biophysics, University of California San Francisco, Director of the Larry L. Hillblom Center for the Biology of Aging. We are back into a world leading lab to discuss the genetics of aging. Can it be controlled? You bet, and the implications are enormous. When these findings translate to the clinic, it will truly be a game changer for humanity. Some interesting links: sirtrispharma Elixir Sirtris Audible Pick: Prey by Michael Crichton. For a 30 day free trial visit GotoMeeting Transcripts to the shows are now available on the FiB Extras blog thanks tom.price@podsinprint.com, PodsinPrint Also thanks to Phil Pelletier and Will Hall for the great themes. Thanks to Cachefly for providing the bandwidth for this netcast. Running time: 1:01:21

Futures in Biotech 35: The Brain Machine Interface
Published on Oct 27, 2008

Host: Marc Pelletier Dr. Justin Sanchez discusses technologies that enable direct brain to computer interfacing, just think… Guest: Dr. Justin C. Sanchez, Director of the Neuroprosthetics Research Group, Assistant Professor, Department of Pediatrics, Division of Neurology, Department of Neuroscience, Department of Biomedical Engineering, University of Florida. I really had no idea that the technologies that Justin has developed existed other than in science fiction. The possibilities are endless, and could change everything from computing, to flying planes, to simply changing the channel… I will keep these notes short, and let Justin explain. Find more, including videos at: The Neuroprosthetics Research Group Transcripts to the shows are now available on the FiB Extras blog thanks tom.price@podsinprint.com, PodsinPrint. Also thanks to Phil Pelletier and Will Hall for the great themes. Thanks to Cachefly for providing the bandwidth for this netcast. Running time: 50:11

Futures in Biotech 34: A Great Historical Document - The Human Genome
Published on Sep 12, 2008

Host: Marc Pelletier Mark Gerstein endeavors to make sense our genome on its past and present course. Guest: Mark Gerstein, the Albert L. Williams Professor of Biomedical Informatics, a professor of Molecular Biophysics and Biochemistry and professor of Computer Science at Yale University Gerstein Lab. In past shows, we've had Lee hood, the inventor of the DNA sequencer, and George Church who was among those personally involved in initiating the Human project. But getting the code and really understanding these human blueprints are entirely different problems. Our guest today, Mark Gerstein, is trying to make sense of it all, and his work amoung other things has revealed that the genome is more than just a blueprint, or list of parts, but a rich historical text about our past. BLAST this sequence: atgttcc tgtccttccc caccaccaag acctacttcc cgcacttcga cctgagccac ggctctgccc aggttaaggg ccacggcaag aaggtggccg acgcgctgac caacgccgtg gcgcacgtgg acgacatgcc caacgcgctg tccgccctga gcgacctgca cgcgcacaag cttcgggtgg acccggtcaa cttcaagctc ctaa Instructions: Copy and Paste the DNA sequence into the query window, and hit the blast button. What does this encode? Interesting: Try again selecting the NON-HUMAN database. What organism is the exact same gene found in? Why? Audible pick of the week: Legacy of Ashes: The History of the CIA, Unabridged, By Tim Weiner, Narrated by Stefan Rudnicki. For your free audio book visit Audible.com/biotech. TWiT T-Shirts from Lori LeBeau Walsh. Transcripts to the shows are now available on the FiB Blog thanks to the kind folks at PodsinPrint. Also thanks to Philippe Pelletier and Will Hall for the great themes. Thanks to Cachefly for providing the bandwidth for this netcast. Running time: 55:35


Futures in Biotech 33: Dr. Milner’s Explorations Into The Human Mind
Published on Jul 23, 2008

Host: Marc Pelletier Dr. Brenda Milner describes the experiments that led to a revolution in modern neuroscience. Guest: Dr. Brenda Milner; Dorothy J. Killam Professor of Psychology, Montreal Neurological Institute and Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada. Throughout her 58 years at the Montreal Neurological Institute, Dr. Milner has explored the inner workings of the human mind, and helped define the structures that give us our exquisite memory and ability for leaning. Her groundbreaking work has influenced generations of psychologists and neuroscientists, and through her unbridled curiosity has revealed many facets to the human mind that were previously unknown. Gairdner Foundation Gairdner News Dr. Milner on Wikipedia Audible pick of the week: Starswarm by Dr. Jerry Pournelle, narrated by Lloyd James. For your free audio book visit Audible.com/biotech. Transcripts to the shows are now available on the FiB Blog thanks to the kind folks at PodsinPrint. Thanks to Cachefly for providing the bandwidth for this netcast. Running time: 1:12:37

Futures in Biotech 32: Controlling HIV Evolution
Published on Jun 07, 2008

Host: Marc Pelletier Dr. Ronald Collman talks about exciting new discoveries on HIV, the virus that has taken 25 million lives. Guest: Dr. Ronald Collman, professor of medicine in microbiology, virus/cell/molecular core director, Penn Center for AIDS Research, University of Pennsylvania. It looks like the summer of 2008 will be an amazing summer for science. The Phoenix Mars Mission and NASA have successfully landed their probe on the Martian arctic, in search for the conditions that can sustain life (FiB24), the personal genome project, run by Dr. George Church, is braving us forward into a new era human genomics (FiB29), and lastly, the Large Hadron Collider (LHC) is getting readied to explore the origins of the Big Bang, and may just unravel the ultimate theory of everything (FiB31). Nevertheless, a large cloud hangs over humanity, which has taken over 25 million lives (warning: hardcore biotech discussion). Dr. Ronald Collman describes the molecular structure, pathology, and with great insight, the incredible discoveries that might just help us conquer HIV. Software pick: Papers Audible pick: Freakonomics: A Rogue Economist Explores the Hidden Side of Everything by Steven D. Levitt and Stephen J. Dubner. For your free audio book visit Audible.com/biotech. Transcripts to the shows are now available on the FiB Blog thanks to the kind folks at PodsinPrint Thanks to Cachefly for providing the bandwidth for this netcast. Also thanks to Will Hall for the great theme. Running time: 49:46

Futures in Biotech 31: The Eensy-Weensy Teenie Weenie Big Bang
Published on May 03, 2008

Host: Marc Pelletier Guest: Dr. Michio Kaku, Henry Semat Professor of Theoretical Physics at the Graduate Center of the City University of New York. In this episode, we are very fortunate to have Dr. Michio Kaku. He is the co-founder of String Field Theory, and a Professor of Theoretical Physics at City Univerity in NY. In our discussion he talks about everything, literally: the theory of EVERYTHING! I must say, if we are going to have a true understanding of the living world, it will demand an understanding our universe and how it 's assembled. You can't separate out the laws of physics from biology, they go hand in hand. Dr. Kaku also talks about the current teleportation experiments to the space shuttle, and how we might some day be able to teleport DNA. Seriously, that is some BIOTECH!!! Dr. Kaku's Book: Physics of the Impossible: A Scientific Exploration into the World of Phasers, Force Fields, Teleportation, and Time Travel Our Audible Pick of the week: Born Standing UP: A Comic's Life by Steve Martin. For your free audio book visit Audible.com/biotech. Transcripts to the shows are now available on the FiB Blog thanks to the kind folks at PodsinPrint Thanks to Cachefly for providing the bandwidth for this netcast. Also thanks to Will Hall for the great theme. Running time: 54:23

SEE THE REMAINING AUDIOCASTS HERE: http://odeo.com/channels/109055-Futures-in-Biotech/episodes

Science Versus the Biological Clock (VIDEO) - MUST WATCH

Down with IGF1, The Grim Reaper Hormone! Power to Sadaf16 the fountain of youth Gene.
This is amazing. There is a whole network of Aging Genes. You can change individual genes and have huge effects on lifespan.

Science Versus the Biological Clock at the 2007 Aspen Health Forum with discussants William Colby, Cynthia Kenyon and Stephanie Lederman. Nigel Cameron moderates the discussion.

Despite advances in medical research, we're all getting older - but that hasn't stopped the scientific search for the Fountain of Youth. Experts such as those on our panel are discovering genes central to the aging process. Their research may make it possible to slow the process of aging, but in the meantime we face a burgeoning population of older adults. This demographic shift has the potential to change medical research, health care, and our nation as a whole - Aspen Institute

Nina Fedoroff explains the history of Genetically Modified Foods (VIDEO)

Genetically Modified Foods with Nina Fedoroff.
Fedoroff's lecture examines the history of food plants, describes the differences between previous and present methods of modifying them, and addresses common food safety and biodiversity concerns about GM crops and foods - Santa Fe Institute

Nina Federoff - Nina Federoff is the Evan Pugh Professor and Willaman Professor of Life Sciences at Pennsylvania State University. She is also an External Professor at the Santa Fe Institute.
Panacea... WIKI: In Greek mythology, Panacea was the goddess of healing. She was the daughter of Asclepius, god of medicine, and the granddaughter of Apollo, god of healing (among other things). Panacea was said to have a poultice or potion with which she healed the sick. This brought about the concept of the panacea in medicine. 'Panacea' is also the term for heal-all herbs, and an Asterix character.

Three seminars and an opportunity

CCBER's Mark Holmgren will be speaking at the Restoration Seminar on:
Vertebrate and Wetland Resources of the Goleta Slough
Monday February 23 6-7pm, Rm 1013, Harder South.

Susan Foster, Department of Biology, Clark University
Ancestral Plasticity and Evolutionary Diversification: The Stickleback Adaptive Radiation
Date: Monday, February 23, 2009
Time: 4 p.m. - 5 p.m.

Helen Poynton, Postdoctoral Fellow,U.S. Environmental Protection Agency
Wednesday, Feb. 25, 12:30 - 1:30 p.m. Bren Hall 1414
Small, Smaller, Nano! A Daphnia Magna DNA Microarray for Biomarker Discovery and Environmental Monitoring of Metal-based Nanomaterials.

Snowy Plovers Docent Volunteers Needed at Coal Oil Point Reserve!
The next training is at the Reserve Office at Coal Oil Point Reserve,
Saturday, March 7th, 9AM-1:30PM
To register, please contact the Program Coordinator, Jennifer Stroh:
office: 805-893-3703
stroh@lifesci.ucsb.edu

Genetic Screening Tests

What a difference a decade makes. Back in 2000, most U.S. states screened newborn infants for just four genetic disorders. Today, all 50 states screen for at least 21 of the 29 serious genetic or functional disorders that the American College of Medical Genetics recommends for testing. The list includes cystic fibrosis, sickle cell anemia, hypothyroidism, phenylketonuria, and a host of other conditions so rare you’ve never heard of them.

A list of the screening programs and tests provided by all 50 states can be found on the National Newborn Screening and Genetics Resource Center website. For information about the recommended tests, go to the March of Dimes website.

Magic pill

Whilst on the subject of herbal and vitamin supplements, which we almost were, there was a very impressive huge study published this week that looked at the effect of vitamin supplements in postmenopausal women. The bottom line: no effect on health. Nothing. Nada. Zilch.

In a way this is surprising because the study was so large and looked at so many aspects of health that it had a lot of statistical power to detect even a small effect. The study involved more than 160,000 women roughly split between those that took regular multivitamins and those that didn't. Eight years later they looked at a variety of disease incidences, including cancer (almost 10,000 cases) and cruder measures such as total mortality (again almost 10,000 deaths). Not even a hint of a difference.

Combined with other recent studies showing no effect of multivitamins in men and in children the evidence is pretty clear that the twenty BILLION dollars Americans spend each year on multivitamins is a waste of money.

Eat healthy. Exercise. Don't smoke. Wear a seat belt. Statistically these things are proven to be likely to add years to your life (individual results may vary of course). It's pretty simple but the allure of a magic pill continues to sucker people in.

News Report on a DNA SYNTHESIS Company (Video Feb 2008)

This video is a full year old, so tech has progressed. But here's an overview of the technology last year from a company called DNA 2.0.

More Music Video Bio = Ohio State U BioRap (DNA Replication and Protein Synthesis with a Beat)

There a lots and lots of student produced Bio Music Videos on the web, but most of them are silly and not very well done. This one was actually rather fun and a bit catchy. The refrain is a bit inaccurate, but they talk about RNA in the verses. Great if you have students that love rap. It is from some students over at The Center for Life Sciences Education at the Ohio State University.

TOUR OF THE LAB! SynBERC-Knight&Endy Britney Spears Video

Want to go and visit the MIT Lab? Of course! But you live too far away from Boston don't you. Don't Worry. Britney Spears was kind enough to make a video for us! We get our own personal tour and we get introduced to everyone. Thanks Britney for being so scientific!

Building the perfect Synth Biology Course... Working Lunch Session - SynBERC (MIT) - 20 March 2007

Thinking about how to best teach yourself Synth Biology? Listen to the SynBERC working lunch session at MIT about the perfect Synth Bio course.

IN THIS LUNCH:
Natalie Kuldell leads a discussion on education in synthetic biology including the following topics...

• What curriculum exists (and an open discussion of their efficacy)
• What communities would benefit/find usefulness in the materials
• What content should be taught (a big topic)
• How to best convey material (comic 2.0 vs web tutorials vs SB majors vs textbook etc.)
• What's holding us back (maybe...this might be part of all the rest of the topics and doesn't need a separate header).

See the OpenWetWare page for this lunch.

ABOUT THESE LUNCHES:
Synthetic Biology Working Group lunches are an opportunity for anyone in the Boston-area who is interested in synthetic biology to get together and discuss current issues and topics in the field. Each lunch discussion is led by someone (selected at the end of lunch the previous week) and focuses on a particular topic. The style of the lunch is really meant to be a discussion rather than a presentation. Therefore, discussion leaders frequently give a chalk talk or only have a handful of slides to help structure discussion. More info at OpenWetWare.

PROTEIN SYNTHESIS AND DNA (Low Quality Video)

Low quality video but informative review from the people at Biowiki.
DNA Transcription


Protein Synthesis


DNA RNA Structure


DNA Structure

Introduction to Systems Biology (Video Feb 2009)

NEW VIDEO LECTURE FROM THE NIH ABOUT SYSTEMS BIOLOGY (POSTED FEB 2009).

Craig Venter Talks About Joining 3.5 Billion Years of Microbial Invention (VIDEO)

Joining 3.5 Billion Years of Microbial Invention featuring biologist J. Craig Venter. Biologist, author and businessman Craig Venter discusses his work mapping and synthesizing genomes. Venter recalls his work mapping the human genome and expands on his current work which includes categorizing new genes and species of microbes from ocean water. Venter also explains how microbial research can be used for metabolic engineering and alternative energy sources.

Lotusland

The picture above is from Lotusland and was at the Botany Photo of the Day site. Well worth an occasional, if not daily, visit. Send me any good pictures you took at Lotusland today and I'll post them here for everyone to enjoy,

Here are two articles about the Lotusland gardens and their founder, Ganna Walska, Forget About Rubies – She Wanted Cycads from the Christian Science Monitor and What The Diva Wrought, published in the Wall Street Journal. This last article is hosted at the Lotusland website so click the links on the left for further information.

Saturday Movie Night brought to us by Miss Baker's Biology Class! Sir David Attenborough narrates the story of Charles Darwin. (FEB 2009)

This episode was produced by the BBC so the quality is of course excellent! And Sir David Attenborough does a wonderful job narrating the story. An absolute pleasure to watch. The BBC also has a great website with more information and interviews. http://www.bbc.co.uk/darwin/ And, for those living in the UK or IRELAND, you are able to receive a free tree of life poster from the BBC.

I want to give a big thank you to Miss Stacy Baker, for finding this series for us. Stacy is an amazing High School teacher! She teaches ninth grade AP biology to students at Calverton School in Huntingtown, Maryland and she and her class run two fantastic blogs...B(io)log(y) Videos & Slideshows and http://www.missbakersbiologyclass.com/blog/


So without further ado... Here is Sir David...

The Genius of Charles Darwin.
"The Tree of Life". Here, Sir David Attenborough narrates his latest series on the natural world. This special sequence of edited video clips marks 200 years since the birth of Charles Darwin, the man who changed the way we think about life on earth.

Attenborough On Evolution (1 of 5)

Attenborough On Evolution (2 of 5)

Attenborough On Evolution (3 of 5)

Attenborough On Evolution (4 of 5)

Attenborough On Evolution (5 of 5)

Jonathan Cline teaches us about the next generation tech for DNA Sequencing via his most excellent Synth Bio blog 88 PROOF.

THANK YOU JONATHAN! This is absolutely amazing. You can check out Jonathan's Synth Biology blog here: http://88proof.com/synthetic_biology/blog/ I just discovered it and it is an absolute DIY BIO gold mine! We have really struck it rich this time! I am serious! 88 PROOF is a must read!

Posted by JonathanCline on October 24, 2008

Let’s say an organism is successfully modified and seems to be performing a portion of it’s synthetically designed biological tasks. Several questions are raised: has the organism evolved, during replication, from it’s original design? Is the organism’s DNA actually the same as the desired engineered DNA? Is there some mistake in the new organism’s DNA which could be improved? If the organism doesn’t function properly, is it because of the designers’ mistake, or is it because of the random chance in nature?

These questions are usually answered by verifying the DNA of the organism — sequencing. Today, verifying the organism’s sequence in a normal lab is done by a long process of diffusing the DNA through a gel and taking a UV picture of the result. This is rather old (and annoying) technology. Yet DNA sequencing is difficult because working with DNA poses several big technical problems. What is the next generation technology for DNA sequencing which could improve this?

Here are some examples and some cool videos as well:

Pacific Biosciences

Pacific Biosciences is attempting to use nanotechnology to monitor individual molecules of DNA during replication.

454 Life Sciences

A video seminar, 454 Sequencing: Enabling Science, Genome Characterization using High Throughput Sequencing, Dr. Michael Snyder, Yale University, is offered by 454.

Applied Biosystems

A webcast seminar, Fundamentals of 2 Base Encoding and Color Space, Michael D. Rhodes Ph.D.
Sr. Applications Manager, High Throughput Discovery, at appliedbiosystems.com, summaries sequencing by using ligase.

Summary

Different approaches to DNA sequencing have different tradeoffs. The small-laboratory-DIY-guy would prefer low operational cost for sequencing small organisms in a relatively short amount of time, perhaps trading off accuracy (lack of sequencing errors) to lower cost. The industrial need is for massively parallel operation and highly accurate measurements, or minimizing total cost of sequencing a human genome. Most solutions today attempt to solve the industry problems — focused mainly on sequencing human genomes.

The technological history of DNA sequencing, which uses DNA electrophoresis separation, is summarized well in History and principles of conductive media for standard DNA electrophoresis, Jonathan R. Brody and Scott E. Kern, Analytical Biochemistry, Volume 333, Issue 1, 1 October 2004. The “best” that Gel Electrophoresis can perform is detailed in the following protocol, Agarose Gel Electrophoresis Protocol, Salt Buffer for Rapid Electrophoresis (developed by Brody and Kern), using sodium boric acid (Borax, Na2B4O7) and other reagents easily acquired from Faster Better Media, LLC.

Obama talks about the commitment to Science, Innovation, and Discovery. May he inspire the scientist in us all.

Obama's speeches on Science was a big inspiration for this blog. Learning and practicing Science is giving back, not just to your community, not just to your state, not just to your nation, but to humans all over the world. And, if Biology teaches us anything it is that we are indeed more alike than we are different. We are truly brothers and sister in this world.Thank you to Miss Baker for sharing this video.
"We must add the fuel of interest to the fire of genius in the discovery of new and useful things" - Abraham Lincoln.

Blood cell birth

Fluorescence imaging technology lets us see the inner workings of Blood cell birth.

Cells with clear endothelial morphology shown giving rise to blood cells. Left panel: phase contrast. Right panel: fluorescence detecting HIstone 2B-Venues expression.

1st pause in video: single mesodermal cell starting the colony
2nd pause: all cells in the colony exhibit a clear endothelial sheet mrophology
3rd pause: some cells lose tight integration into the endothelial sheet but keep adhering to endothelial cells
4th pause: Blood cells detach and are free-floating.

The arrow is following the starting cell and one daughter cell after each cell division until the end of the video