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The title of THIS diary in the overview diary of this series was:  The technical enablers of modern biology

An overview of microbiological theory and practice

Microbiology has been empowered by a combination of physical, chemical,  biological , and mathematical techniques. It is the most complex of the sciences, studying the most complex thing in the universe: life.

Below the fold, this first diary in a series will give the 50,000 foot view of the technology behind modern biology.

Biology has gone from being zoology (classify and name) to being engineering (modifying genomes, modulating cell signaling networks with drugs) and information technology. This happened quite recently. The genetic code (what DNA triplet codes for what amino acid) was not worked out until 1965. In 1970, very little was understood about the molecular details of cell biology. Organelles (parts of the cell visibly different in an optical microscope) had names; but, in most cases, no one knew their functions.

Today, we have databases of complete genomes for hundreds of species. We have open source databases of atomic-scale models of tens of thousands of the protein molecules that make up the components of the cell. We know the function and the molecular components of all the organelles. (And the components are unbelievably complicated; e.g., each nuclear pore complex contains over 900 protein components.) We have circuit diagrams of the immense number of biochemical signaling pathways that keep the cell stable (in homeostasis), e.g., the intensely-studied  p53 cancer gene pathway.

We now understand that only 1-2% of our DNA actually codes for expressing proteins (exons), while the bulk of the genome is silent (introns), but is not "junk DNA". We now know that a human genome has code for about 30,000 proteins (each of which can have variants due to "alternative splicing". We understand that there are even more information and control systems, besides DNA: epigenetics (methylation, etc. of DNA), alternative splicing (how exons are assembled into whole proteins), and small interfering RNA (siRNAs) (parts of the introns that are actually control circuitry). The HapMap (Haplotype genome Map) Project has shown that, within the human species, properties of the genetic code previously thought to be static, such as the number of copies of a specific gene and the chromosomal location of that gene can vary (so-called Copy Number Variation) from one individual to the next.

While understanding exactly how various proteins do their jobs (so that we can cure diseases) is still a complex, Nobel-prize level of research, it is a well-explored field. The "wild west" of biological science is now morphology - how the time sequencing, spatial localization, and expression levels of protein and other signaling molecules give rise to the complex structures of, say, the heart or the brain or the developing fetus.

With that tour of the horizon, let's get down to the nuts and bolts of the technology.

Protein - Theoretical and Practical Advances to date

The first biologically-famous structure determined by X-rays was the DNA double helix (1953). These determinations used to be difficult science, as is attested to by the over-representation of protein crystallographers in the Nobel laureate list. Today, technique has advanced so far that a graduate student can determine a new structure in a few months. Today's student has access to perfected hanging-drop crystallization techniques, heavy-atom replacement for solving phase problems, high-intensity beam lines from synchrotrons, and off-the-shelf computer applications for solving structures.

Protein structures for all species pour into the databases at thousands per year. Even you can get into the act with Protein Folding at Home. At this website, volunteers donate compute cycles to run simulations of how proteins fold as they emerge from their ribosomal assembly line. Theorists have determined that there are only a few thousand generic "fold families"  to which all proteins can be assigned. (The slides "chap2_motif.ppt" from this directory at TU Norway discuss folds and families.) Are protein structures like words in a language, where most people get by with less than a ten thousand word vocabulary?

One result about proteins that I found fascinating from a "Darwin vs the fundies" POV is that somewhere between 10% and 30% of all proteins are misfolded upon synthesis. Cells have special protein machinery called "chaperones". These are containers that capture the dangerous/non-functional proteins and put them in a chemical environment that is designed to lead to correct folding.

Think about that. The "perfect" machinery of every living cell has a 10-30% error rate; and even after chaperoning, a non-trivial percentage of protein goes straight from the production line to the cellular trash bin (the proteasome). Protein misfolding is the cause of horrible diseases, like Alzheimers and Mad Cow; so, the existence and failure of chaperones is not some obscure fact that can be ignored.

DNA - Practical Advances to date

Most people know that Watson, Crick, and Franklin discovered the structure of DNA. Fewer know that the exact year was 1953. Fewer still know that the three-base code that translates DNA into protein was not deciphered until 1965 or that high-speed sequencing (Sanger, Maxam-Gilbert) was not invented until 1975. About the same time, biologists succeeded in using bacterial plasmids to transfer genetic material between organisms, creating the first artificial, human-made "recombinant DNA".

Unless you are a biologist, you probably haven't heard of "restriction enzymes"; but these enzymes are a critical tool in genetics. A restriction enzyme is a molecular scissors that cuts only at a specific place in a specific DNA sequence. The first one was discovered in 1955 - another Nobel Prize. Today, companies make a business out of discovering, cataloging, manufacturing, and selling microgram quantities of such enzymes to research labs. With these scissors, DNA can be cut and spliced in anyway you desire.

Here is another political aside. The possiblity that the current 3-letter DNA code evolved from an earlier 2-letter code is an active area of investigation. This research is motivated by the fact that, in a large percentage of the 3-letter code, the third letter is redundant; i.e., the same amino acid is coded for any DNA base in position three.

Isn't this a fun factoid? Suppose you run into a fundie who says, "I accept there is a genetic code, but I don't accept evolution." You can ask him, in reply, if he accepts the possiblity that the genetic code itself evolved.

Another important tool is Polymerase Chain Reaction (or PCR) - another Nobel prize, invented in 1985. PCR uses a naturally-occuring DNA polymerase (an enzyme that joins individual bases of DNA into a DNA polymer or chain). PCR can amplify minute traces of DNA into large quantities suitable for laboratory sequencing (to discover what proteins some new species is making or to discover whose blood is on the murder weapon).

The most recent advance in methodology, taking the bio world by storm since about 2000, has been "RNA interference" or RNAi. Again, RNAi technology is another re-purposing of a naturally occurring system. In living cells, the RNAi system is designed to destroy invading viral DNA. The system contains components that chop up free-floating double-stranded DNA (which does not belong outside a cell nucleus) into pieces whose length is long enough to represent a high likelihood of uniquely matching only the viral DNA. These pieces are then fitted into another RNAi component, "dicer". Dicer binds to matching sequences of DNA, and destroys them. It is a anti-DNA guided missile. It is used to "knockout" genes (i.e., destroy them) so that the effect of that single gene can be observed.

DNA - Theoretical Advances to date

After producing huge amounts of sequence data, we began to analyze it and to compare genomes between species and between individuals of the same species. This led to some important empirical data.

The first fact worth mentioning is that all species use the same genetic code. The second fact is that the slow changes of this code between species gives us a "molecular clock" for measuring the "distance" between species, based on mutations in the genetic code. And, it turns out that classifying species relationships by DNA distance gives almost the same "tree of life" as the Linnaean taxonomists and zoologists determined by observing physical features. Slight differences have usually been resolved in favor of the DNA evidence.

Political aside: Everyone has heard that humans share 99% of their DNA with chimpanzees; but what's even more telling in favor of evolution is that most of the 6,000 genes in common yeast have their counterparts in humans. That is, we share 25% of our genes with brewer's yeast.

Interestingly, mitochondria have their own separate genetic code. Again, this code, too, is constant across all species. By examining the number of mitochondrial genes as a function of species, it has been determined that, over evolutionary time, genes have migrated out of the mitochondria and into the nuclear DNA, changing their code in the process. The two facts, of different codes and of the ongoing shrinkage of the mitochondrial genome, are evidence for the "endosymbiont hypothesis". Here is a figure and some further discussion of this important hypothesis.

This hypothesis suggests that one unique event created the cell nucleus, and another the mitochondria. In this unique event, one bacteria (probably a macrophage) enveloped another bacteria; but the eater was unable to digest his meal. Instead, the two creatures settled into a symbiosis (like lichen); with the digestee becoming the nucleus or mitochondrion of the digestor. The progeny of this cell  evolved into all the multi-celled eukaryotic organisms.

Another important fact is that mutation rates are not unvarying across a genome. The mutation rates are a function of how "critical" a specific amino acid is to the correct operation of the protein. This demonstrates the default state for mutation is "on", and natural selection operates only at vital points in the genome.

In the overview, protein folds were mentioned. It turns out that the components of the business end (i.e., active site) of enzymes tend to occur at the "bends" (joints of the folds) in between the various structural elements (alpha helices, beta sheets)  of a protein. Looking across species at the sequence of a single enzyme (protein), it is amazing to watch the genetic code for individual amino acids in the structural elements mutate, while the amino acids in the active site are preserved by natural selection.

With this principle in hand, scientists applied it to mapping the mutation rate of introns; and that is how they discovered the non-coding RNA in the introns. Pieces of introns are preserved because they are doing a critical regulatory jobs. Recently, statistical analysis showed a higher mutation rate for "off-line DNA" (that is, DNA not unrolled from its storage "reels" - i.e., histones -  for expression) than for "on-line", unrolled DNA.

Political aside: The juxtaposition of constant, slow change everywhere that mutations are irrelevant, with rock-solid stability at the critical points in the DNA - found time after time in species after species - is the most powerful evidence that natural selection exists which one could ever demand.

Another empirical finding has been huge numbers of duplicate genes scattered around the genome. It is now understood that, due to the elaborate layering of control systems, it is possible to make a duplicate copy of an entire gene. Once there are two copies, one can diverge into a new gene without destroying production of the original gene product. This finding demonstrates how it is possible for incompletely changed copies of a gene to survive through generations without killing the carrier. It also demonstrates that mutations can be larger than a single base change. (Quite often, duplications are carried out by transposase enzymes involved in Horizontal Gene Transfer; but that's a digression.)

Does all this technology rise to the level of "micro-agriculture"?

The title of this diary series is "The Micro-agricultural revolution". There has been some legitimate pushback against my claim that we are on the verge of such a revolution reaching the public. That claim has two components (the methods and their widespread use for commercial purposes) which I would like to examine separately.

As to the methods, I would say that, in this short-order Cook's tour, we have seen that a large number of "bits" of cellular machinery have been torn lose from their parent "animal" and used for human purpose. That is, we are using the piece parts of the whole micro-animal in the same way that agricultural civilizations used hair, leather, and bone or milk, meat, and eggs.

One technology I did not mention yet is so-called "cell-free systems". In these systems, the entire protein manufacturing machinery of a cell is delicately separated out. This "naked" protein production system can be placed in a lab flask and fed any bit of DNA. It will produce nothing but the single protein in the DNA snippet, until the c-f system expires from natural wear and tear in a day or two. If doing this equivalent of getting a dead horse's leg to pull a wagon is not micro-agriculture, I am at a loss for a definition of such.

As to widespread use, I would draw an analogy. In the early days of individual UNIX workstations, half the computing power sold went into designing the next generation of workstations. It was only when Moore's Law brought the performance down to everyday prices that workstation applications became cheap and widespread.

I would argue that, today, most of the biological tools sold go into research labs designing the next generation of biological tools. But, as the $1,000 genome meets up with the ability to mass produce protein on demand, there will be one of those "hockey stick curves" in the commercial applicability of all these technologies.

At the edge of the world of biological science

Before you think that biology has jumped completely on the reductionist bandwagon - that is,  life is just inorganic machinery, blind, unthinking, etc. - there is a huge amount of work at the micro- and macro- frontiers of the discipline. Sort of the same way that all the real action in physics is at the extremes of sub-atomic particles or astrophysics.

The small-scale issue about biology is that we simply have no theory of why organic molecules can make such tiny working machines. It is astounding in its own way (the following blockquote is scientific, not political):

Between the nano- and micrometre scales, the collective behaviour of matter can give rise to startling emergent properties that hint at the nexus between biology and physics.

Up to about 30 nanometres, there is little difference between gold and niobium. It’s beyond this point that the electrons in niobium start binding together into the coupled electrons known as ‘Cooper pairs’. By the time we reach the micrometer scale, these pairs have congregated in their billions to form a single quantum state, transforming the crystal into an entirely new metallic state — that of a superconductor, which conducts without resistance, excludes magnetic fields and has the ability to levitate magnets.

In assemblies of softer, organic molecules, a tenth of a micrometre is big enough for the emergence of life. Self-sustaining microbes little more than 200 nanometres in size have recently been discovered. Although we understand the principles that govern the superconductor, we have not yet grasped those that govern the emergence of life on roughly the same spatial scale.

- P. Coleman, "Frontiers at your fingertips", Nature, 22 Mar 07, p. 379.

The large scale issue is about morphology. That is, how do all these proteins, controlled by all these genes, differentiate into this hugely complex organisms, which then maintain themselves in homeostatsis for decades (mammals) to centuries (trees)? The Complex Adaptive Systems people, like the Santa Fe Institute, are investigating these questions. Needless to say, the inclusion of such material in this particular diary series would simply make it so complicated as to be un-readable. Perhaps another time.

Political aside:  the renewed discussion between the hard-core "genes only" crowd and the "structuralist" school of morphology is one of the "controversies" that has been pointed to by "teach the controversy" creationists. No space for that in this diary. I'll come back to it in Diary 3 (The end of DNA dictatorship).

Ethical implications of the technology

Whether or not this "revolution" is a good thing is an entirely different argument. There is already a huge fight about whether the comparison of DNA from different human beings (the so-called Halotype Map Project or HapMap) will inevitably lead to racism, ethnically-targetted diseases/weapons, etc. One other "terrorist" worry to be discussed in a later diary is "synthetic biology".

Then, there is the implication of the increasing corporatization of academic research. Government has paid huge sums of money for this research, and yet, the professors (often in cahoots with corporate funders) are encouraged by the government to grab the patents we paid for and start their own companies - while paying ZERO royalties back to the public. (Meanwhile, universities have nasty Intellecutal Property offices which want their pound of the public's IP flesh.) Now, I am the last to want to restrict science; but the current situation is just robbery of the public treasury.

At least, the raw data itself is in the public domain (e.g., the various databanks mentioned above). There are also public domain tools for searching these databases, usually found on the database site itself. At least the public gets to see what it paid for and to use some of the tools we paid to create.

One final political point. Microbiology is simultaneously very concrete (atom-level analysis of DNA and proteins) and very abstract (statistical matching of gene similarity). The problem is that the concreteness takes place at such tiny dimensions that the entire abstract apparatus of physical science interposes itself between the phenomena and the facts in question. That is, there is very little "common sense" in molecular biology. Hence, the entire endeavor of molecular biology and genetics comes across to the average person as an opaque and threatening high-priesthood that is attacking "good folks" sacred way of life.

The increasing divide between what science knows and can do versus what the population understands about science and wants done is a recipe for political disaster.  

What the masses refuse to recognize is the fortuitousness that pervades reality. They are predisposed to all ideologies because they explain facts as mere examples of laws and eliminate coincidences by inventing an embracing omnipotence which is supposed to be at the root of every accident. Totalitarian propaganda thrives on this escape from reality into fiction, from coincidence into consistency...

- Hannah Arendt, "The Origins of Totalitarianism"

----------------------

In closing, an Apology

Please think of this diary series as a popularized, idiosyncratic ramble through biology. Textbooks on this topic run to thousands of pages and require more than one complicated illustration per page. Even as a bad joke, I cannot pretend to be saying anything at a level above a "cocktail party" conversation by a techie for a politically-oriented audience. I just hope that, coupled with the links given, these diaries will convince politically-oriented people that what ordinary people know (or, worse, don't know) about science is of extreme importance at this moment in history.

Originally posted to arendt on Mon Apr 06, 2009 at 04:14 PM PDT.

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Comment Preferences

  •  Tip jar (and request for feedback) (15+ / 0-)

    Please let me know if this is completely boring or completely over your head.

    •  Great Diary (1+ / 0-)
      Recommended by:
      Larsstephens

      Very enlightening not to heavy not to light.

    •  Excellent diary (0+ / 0-)

      Two comments though, the bulk of the silent DNA, which is not junk DNA as you pointed out, is not necessarily even introns, its much stranger than that. A lot of the DNA is actually the silenced remains of transposons and retrotransposons that were shut down by the host genome but remain in the genome as ghosts of there former parasitic selves. Why doesn't selection remove them from the genome over time? It's not really clear.

      Also, for RNAi, it's just a technical point since the term "gene knock-out" gets thrown around sometimes in the popular press, but Dicer doesn't actually target the DNA, it chews up the RNA made from a given gene. The DNA is still there, so in reality, when people do RNAi against a gene they aren't making a "knock-out" (which is a process in and of itself where you literally remove the DNA of a gene), they are making a "knock-down". It's an important distinction because knock-outs are permanent, but knock-downs can be transient.

      Thanks for the diary.

  •  Fascinating topics (5+ / 0-)

    But then I was a Biochem undergrad major in the era just before recombinant DNA became widely useful.  

    I love that you're tackling it, but perhaps as a suggestion smaller, more focused topics would make for less intimidating reading for the lay reader.

    Love your writing style, btw.  Very good for popular science in covering a difficult topic.  

    Dear Republicans: You can't repeat a lie enough to make it true.

    by Dallasdoc on Mon Apr 06, 2009 at 04:25:37 PM PDT

    •  Unfortunately, these ARE the smaller topics... (8+ / 0-)

      if I used more smaller topics, I wouldn't have a six diary series; I'd have a 25 diary series.

      After I started writing this first one, I realized that I had volunteered to empty the ocean with a teaspoon. But, having made the commitment, I'm going to do exactly six. It took me two days of research and writing and collecting reference URLs just to get this diary up.

      Like most of Kos, I am here for the politics. I just want the political folks to appreciate that not all scientists are nerds who can't tie their shoes. Its just that the science is moving so fast, there is very little time for other activities (like politics).

      The Bush Gang completely destroyed the interface between science and politics. Basically, it put politics and religion in charge of things that science used to be responsible for. We desperately need to get the right people back in the science jobs. The problem is getting heard over the noise about the economy, the Constitution, and the various wars.

      •  I'll look forward to reading them (4+ / 0-)
        Recommended by:
        sberel, arendt, allep10, Larsstephens

        Since I scaled up to multi-cellular organisms in my graduate work I've left my knowledge of these areas far behind.  You'll provide a wonderful update to my knowledge.

        Just curious, are you going to get into soil microbiology?  I've become interested in the effects of biochar on mycorrhizal growth and related topics, but can't find a good primer.

        Dear Republicans: You can't repeat a lie enough to make it true.

        by Dallasdoc on Mon Apr 06, 2009 at 04:38:08 PM PDT

        [ Parent ]

        •  Multi-cellular is so complicated... (3+ / 0-)
          Recommended by:
          sberel, Dallasdoc, Larsstephens

          I don't want to think about how you do experiments. I talked to some people at a dental research lab who had figured out how to make an entire tooth differentiate from a single cell. It evolved some elaborate 3D matrix of signaling chemicals applied at just the right times in just the right gradients and places.

          ----

          Its unfortunate that stuff like soil microbiology isn't sexy for most geeks. They all want to win a Nobel prize for curing cancer or Alzheimers. That lack of sexiness may be why Big Ag owns all the crop science IP.

          As for a primer, I suspect that, like every other microbiology discipline, its moving so fast that there aren't any current primers.

          My area of interest has always been brain function. I did some MRI, and my wife is a psychologist. That's about as far as you can get from soil, I think.

          •  Local land use decisions are made in ignorance of (4+ / 0-)
            Recommended by:
            OHdog, arendt, allep10, Larsstephens

            soil science, almost always.  People around here treat conversion of a forest to a housing development as if all you needed to do was knock down the houses someday, and the forest would grow back just like it was.  They  have absolutely no clue about the importance of what goes on in soil even at the macroscopic level, much less the complex microbiology.  I'm not a soil scientist, but I've read just enough of the science in my environmental policy/management work to know how critical it is.  I try to spread the word, but it's a slow slog.

            •  We've been paving good farm land for 50 yrs... (3+ / 0-)
              Recommended by:
              OHdog, allep10, Larsstephens

              just because of suburban sprawl.

              You are absolutely right. The soil doesn't bounce back. Outside of the Dust Bowl, America has never had to deal with lack of soil fertility. That era is coming to an end, as the Central Valley in CA is on the verge of "salting out" - if the drought doesn't get it first.

              •  Here's an article about the pipedream (2+ / 0-)
                Recommended by:
                arendt, Larsstephens

                of expecting to move agriculture northward in the wake of global warming:

                Climate Change and Famine: II Soil
                .......
                arendt: Great diary. I was a biology major in the latter half of the 1970's at a school in which the biology department didn't teach anything above single-celled organisms. The pressure to support genetic engineering was overpowering. I opposed it. I think GM crop science has the potential to destroy our food genomes by contamination with foreign genes gone out of control. Svaalbard is a good idea, but putting the genie back in the bottle is impossible.

                Monsanto GM-corn harvest fails massively in South Africa

                Just because we can do something, doesn't mean it's a good thing to do.

                I'm not dissing you. I look forward to catching up on where the science has gone since I left the field. I just think that, like the banksters' lack of self-restraint in taking on risk, there is not enough thought about potential bad consequences of GM.

                •  Interesting points - a teensy bit tangential... (4+ / 0-)

                  but I will take any comments I can get.

                  ----

                  That is a very interesting point about soil fertility in the Northern part of the continent. I live in New England, and the soil here sucks. New Hampshire looks like one big glacial scour pit (Lake Winnipisauke is a 50 mile long gouge in a granite basin.) If its this bad here, its probably worse in Canada. Never thought about the soil before. Thanks (I guess) for educating me about one more reason we are doomed.

                  ----

                  Mentioning Monsanto and "thinking of potential bad consequences" in the same paragraph is about like mentioning John Bolton and the concept of "diplomacy" in the same sentence. :-) Monsanto, where "suicide seeds" is a good product concept.

                  Having said that, the problem is that the research for and the application of the crop science REALLY IS controlled by these sociopathic Big Ag corporations, and that is not a good thing. ADM has been buying both sides of the political aisle for decades. And even a huge internal whistleblower scandal barely registered in the public's consciousness at the time, and is now completely forgotten.

                  ----

                  I know you aren't dissing. I think GM has gotten a deservedly bad reputation; but in the US, Big Ag has blocked laws that act on that reputation. I'm not sure what the ending was in that lawsuit about the organic farmer sued by Monsanto because Monsanto's genes wound up jumping into the weeds on the farmer's land. He countersued for their contaminating his organic crops.

                  Thanks again for the comments.

                  •  Here's (5+ / 0-)

                    Percy Schmeiser's website.

                    In Monsanto v. Schmeiser: ....“genetic engineering crop contamination” ..... was, in explicit fact, not considered by the courts. The patent infringement finding was based solely on the determination that Schmeiser had recognized the cross-contamination, and knowingly went on to collect the crossbred seed, then replant and harvest it the next year. No punitive damages or the costs of the technology use fee were awarded to Monsanto, as the Supreme Court also ruled 9-0 in Schmeiser's favor that his profits were exactly the same with or without the presence of the Roundup Ready Canola."

                    In Schmeiser v. Monsanto: "Monsanto has agreed to pay all the clean-up costs of the Roundup Ready canola that contaminated Schmeiser's fields. Also part of the agreement was that there was no gag-order on the settlement and that Monsanto could be sued again if further contamination occurred. Schmeiser believes this precedent setting agreement ensures that farmers will be entitled to reimbursement when their fields become contaminated with unwanted Roundup Ready canola or any other unwanted GMO plants."

  •  Thanks! I agree that we'd be much better off (3+ / 0-)
    Recommended by:
    OHdog, arendt, Larsstephens

    if the people who make decisions in the public sector (as well as those of us who react to those decisions!) had at least some science literacy.  So much more is known now then what they encountered in their high school science classes!  Thank you for taking on this big task, and for doing such a good job with it.  I'm enjoying them.

    As for feedback, I suspect that the series is getting more traffic than the number of comments suggests.  Many are probably skimming the text, learning something, but not feeling like they know enough to comment.

    A silly-sounding suggestion - add a couple of pictures.  A diagram or two (showing, say, what a protein looks like unfolded vs. folded) might make all the text a little less intimidating.  (I, for one, am always attracted by a good diagram.  But then, I'm widely acknowledged to be a little odd...)

    •  Adding pictures requires... (1+ / 0-)
      Recommended by:
      Larsstephens

      something I'm not willing to do because I'm paranoid.

      Kos demands that you use specific photo sites. I haven't had time to read the fine print on privacy at those sites. Unless they guarantee my privacy, I won't use them. As you can imagine, it would not help my science career to be seen as some outspoken leftwing politico who blogs on a highly partisan site.

      But, I have put links to figures into the text. Maybe I should just have the highlight text say "CLICK HERE FOR FIGURE". Do you think that would work?

      ----
      I am heartened by your support for the idea that politicians be scientifically literate. I think we first have to do something about the awesome levels of corruption in politics before we will get scientists to take low-level positions in politics.

      •  I work at the local- to sub-state-regional (2+ / 0-)
        Recommended by:
        arendt, Larsstephens

        level, assisting with, among other things, figuring out the connections between the different system elements and how to prioritize among an overwhelming number of things that need to be done.  Although it's largely policy and process facilitation, I'm a geologist by training; that systems-based physical science background is extremely helpful.

        In any event, I think that its at this local level that we can make the biggest difference.  I can meet face-to-face with a decision maker, build a good working relationship over time, and have an actual impact on that person's understanding of the situation.  In contrast, I don't feel like I have any influence at the national level, other than doing what little I can to try and get the better people elected.

        Your work as an educator is critical - we need to increase the science-literacy of students if we are to have science-literate decision makers in the future!

        •  I agree that local officials are more... (2+ / 0-)
          Recommended by:
          OHdog, Larsstephens

          accessible and receptive. Nationally, its "pay to play". Localism is also a strength of Kossacks.

          If you say "systems based physical science" to 90% of Americans, they will think you are either "a suit" trying to snow them, or an elitist wanker like Diane, the waitress on the old "Cheers" TV show.

          The thing about science literacy is that the media has to stop making science about nothing more than hi-tech violence or dweeby, incompetent nerds. So, its all wrapped up in corporate control of the media - and the 30 year project to dumb down America.

          I have often pondered why, with hundreds of cable channels, there is no publicly-sponsored remedial or supplementary education programming. When I would travel in Asia, there was always a channel of classes.

    •  Thanks (1+ / 0-)
      Recommended by:
      Larsstephens

      I'd like to repeat what everyone here has said already, I think this is a great diary, and I'm looking forward to the next in the series. As a biology major, I can say that many students and scientists who I've met are really eager to help advance the cause of scientific literacy, and get non-scientists involved and excited about the process, so kudos. As for pictures, if you use some of those on the Wikipedia page you ought to be fine, everything there is public domain. Once again, great diary!

  •  I feel a diary rescue is in order... (1+ / 0-)
    Recommended by:
    arendt

    Excellent writing about a
    difficult topic that is ever
    growing in utmost importance
    to all of us.

    I am looking forward to all
    26 future installments. Subscribed.

    Your links worked (lol) and
    you took the time and effort to respond
    to those who read it and commented.

    I would have tipped and recommended
    you just for Hannah.

    Doesn't your cable system carry
    the Research Channel?

    I watch it an awful lot-
    it is very informative and enlightening,
    and also at times unintentionally hilarious
    as only the most truly earnest academians can be.

    There is also probably a bit too much of the old
    corporate sponsored astroturfed and greenwashed
    "consent engineering", but no worse than PBS.  

    The local university runs it sporadically
    on their little slice of the 'public' cable
    spectrum for distance/remote education classes.  

    •  First I've heard of Research Channel... (2+ / 0-)
      Recommended by:
      Larsstephens, bluebuckaroo

      According to their website, its carried on a few small town channels (and upscale places like Cambridge and Newton) in Massachusetts. My crappy provider,Comcast, has it in some towns but not in mine. I will go nag them for it.

      Thanks for the recommendation.

      Thanks for busting me about 26 installments, NOT. :-)

      Science is a tough sell anywhere, but especially at practical, results-oriented DKos. I tried to make it relevant with the "political asides"; but not much traffic.

      Your comments are appreciated.

    •  Any friend of Hannah's is a friend of mine n/t (1+ / 0-)
      Recommended by:
      Larsstephens
  •  Fantastic effort (1+ / 0-)
    Recommended by:
    Larsstephens

    however the complexity of the topic is such that I think the lay reader is unlikely to be able to comprehend it. For those interested in learning about modern biology I would recommend the book "The Eighth Day of Creation". It describes the events and scientific principles that led to the discovery of molecular biology and biotechnology and it reads like a thriller. Can't recommend it enough. I have you subscribed now and I am looking forward to the rest of the series.

    "Everybody does better, when everybody does better" - Paul Wellstone 1997

    by yuriwho on Tue Apr 07, 2009 at 09:19:08 PM PDT

  •  Thank you so much for this diary! (2+ / 0-)
    Recommended by:
    yuriwho, Larsstephens

    I love and am fascinated by science, but unable deal with the math and "insider" terminology.  Your diary is amazing, and perfect, for an educated-but-math-illiterate like me.

    Science is a tough sell anywhere, but especially at practical, results-oriented DKos. I tried to make it relevant with the "political asides"; but not much traffic.

    Now I feel bad for not finding your diaries sooner. I tend only to read the main entries, not the diaries, and never thought to find such a wonderful science series.

    I'll keep an eye out for the next installment :)

    Thanks again!

  •  Would it be possible to add another tip jar? (1+ / 0-)
    Recommended by:
    Larsstephens

    Now that you've been linked to by the diary rescue? Idk, I'm new here, hope I'm not wasting your time. Thanks!

  •  Appreciate the effort. (2+ / 0-)
    Recommended by:
    Xapulin, Larsstephens

    I am working on my credential to teach HS Biology, and I passed the subject competency exams without breaking a sweat, but you've pointed out a few new pathways for me to look down that I did not learn about while at MIT (over 10 years ago). It didn't help that I tried to keep my studies focused on the complexity / emergent behavior side of things - eg. ecology, environmental economics, climate change. Knowing the general landscape of microbiology is very useful even for those of us who generally prefer organism / ecosystem level inquiry. I will be reading your followup diaries very closely.

    We can't cover everything at the HS level of course, but I think it's really important to convey just how vibrant and exciting so many sub disciplines of Biology are right now. It's so very far from a dead field, and a presentation in the forms of calcified "facts" deprives students of the sense of their potential ownership of future discoveries.

    So please keep these diaries coming and keep highlighting the cutting edge / politically interesting points and I'll try to weave some of it into my early lesson plan drafts where appropriate.

    •  Biology is unbelievably exciting right now (2+ / 0-)
      Recommended by:
      Larsstephens, Olon

      I was in computers for a long time; but that tech is as mature as Detroit. The cutting edge of science is in molecular biology (which I may have mistakenly referred to as microbiology - pretty big oops for a whole diary series).

  •  Excellent. (4+ / 0-)
    Recommended by:
    gogol, arendt, Larsstephens, Olon

    I remember at the time of the OJ trial trying to explain restriction fragment lp's to a couple very bright people with not much science background, and thinking how in the hell is a jury picked at random off the street going to make any sense of this?

    What's so hard about Peace, Love, and Truth and Progress?

    by melvin on Wed Apr 08, 2009 at 01:24:50 AM PDT

  •  wow. thanks for the diary (1+ / 0-)
    Recommended by:
    Larsstephens

    Informative and readable. You have done a public service and I thank you

    c

  •  arendt, thanks for the diary. (1+ / 0-)
    Recommended by:
    Larsstephens

    I am a lay, lay person but your essay is fascinating.

    Too late to rec or tip, but not too late to appreciate your work and scholarship.

    WOW.

  •  Glad this was rescued (1+ / 0-)
    Recommended by:
    Larsstephens

    There's a lot of good information here.

    One comment: the professors taking royalties based on the results of taxpayer-funded research is yet another destruction of the public weal we owe to Clinton. It was under his administration's prompting that the patent laws were changed to cover gene sequencing. Now, this is absurd on its face. No one will pay royalties for every millimeter of hair or nail growth, or when they have offspring, yet, this was the logical end of the law.

    Radarlady

  •  Ah, you should mention metagenomics (3+ / 0-)
    Recommended by:
    Larsstephens, Olon, RationalismWorks

    at some point.  Maybe you'll get there. One of the newer strategies to study the components of microbial systems is to take a sample of them--from seawater, puddles, soil, gut...and beyond--and analyze their DNA in bulk to see what's in there.  Many of the organisms are difficult or impossible to culture at this point, so it's a bit haphazard but still informative.

    "The New Science of Metagenomics – Report-in-Brief" report especially useful as a good primer on metagenomics for non-biologists.  It is a PDF, btw.

    Personally I fondly remember my first Winogradsky column.  I thought the purple bacteria were fascinating :)

    Darwinic pilgrims claim the image fills them with an overwhelming feeling of logic. --The Onion

    by mem from somerville on Wed Apr 08, 2009 at 05:51:37 AM PDT

  •  Just want to say (1+ / 0-)
    Recommended by:
    Larsstephens

    Thanks.  A delightful quick review, given that I lost my weekly access to Science in 1994 and no longer remember what half the articles I have stashed away really mean.

    The knowledge and possibilities of modern microbiology are exciting.  The ethical implications of our funding and control systems, however, are frightening.  This kind of knowledge represents immense power, and we have placed that power fully in the hands of those who are least suitable to control it. Only fools put nuclear warheads in the hands of psychopaths . . . but, uh, wait, we just finished that episode, didn't we?

  •  political relevance of microbiology (3+ / 0-)
    Recommended by:
    arendt, Larsstephens, Olon

    Great diary! Very well-written, and you make the subject understandable. My degrees were in microbiology - some time between the discovery of the deciphering of the 3 base code and the elucidation of the functions of organelles. After spending some time doing graduate level research on the mating behavior of slime molds ( really!), I became a science teacher in the public schools.  I especially like the way you highlight the political relevance of this subject. In Texas, we are currently in a struggle with the fundamentalists who dominate our State Board of Education, who recently got language into our biology curriculum that we must teach " all  sides" of the evolution issue. The complexity of the cell is a favorite argument of theirs, and it's good to be able to say that cells have a 30% error rate!

    Good thing we've still got politics in Texas -- finest form of free entertainment ever invented.- Molly Ivins

    by loblolly on Wed Apr 08, 2009 at 07:27:29 AM PDT

  •  Ray for Arendt! (1+ / 0-)
    Recommended by:
    Larsstephens

    Wow!  Thank you so much! It's so great that folks like you are trying to keep us knuckle-draggers at the edge of the loop. I can't say that I came close to digesting most of what you said, but I got the drift, and points along the way. As one trained in social science (scuse oxymoron), I came to the conclusion that any science matrix/theory that uses less than 10 variable (typical in social science) is out to lunch.
       The pace in your field is breath-taking. An area of special interest to me is instinct genetics. I hope at some point you might blog on this. Years ago a molecular bio friend and I talked idly of exploring the genetics accounting for how a species of wasp always laid 3 eggs; never 2 or 4.  Cold the wasp count?  by now I expect you folks know that and a great deal more.
    Many thanks again! and me Hannah's friend too.

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