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		<title>Ancient Bacteria</title>
		<link>http://blog.essayweb.net/2010/09/22/ancient-bacteria/</link>
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		<pubDate>Wed, 22 Sep 2010 07:28:34 +0000</pubDate>
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				<category><![CDATA[biology]]></category>
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		<description><![CDATA[Ancient DNA: Is it possible to revive bacterial spores that are millions of years old, or extract intact DNA from fossils that are millions of years old? Here is a summary of some of the work done in this area, as well as general comments about the plausibility.]]></description>
			<content:encoded><![CDATA[<p>Here’s an interesting question: how long can living organisms survive in hibernation? We know that many animals such as bears, squirrels and bats hibernate seasonally, but I am talking about bacteria, which can enter a state of suspended animation and survive for very long periods. By “very long” I mean possibly millions of years. Hundreds of millions of years.</p>
<p>This question is interesting for several reasons. First, just what kind of chemistry does it take to do that? We know that DNA degrades over time. The random influences of temperature, radiation, or environmental chemistry ought to degrade any huge and complex molecule over such long time spans. How could bacterial DNA survive intact for millions of years?</p>
<p>Second, if it is true that bacteria can survive so long, what a remarkable opportunity this would be to investigate the process of evolution! Consider the organisms alive today. Although it is generally believed that archeobacteria found in certain inhospitable environments (such as mid-ocean ridges, or deep beneath the Earth) are the oldest forms of life, they can offer only limited insight into what early life might have been like. All forms of life continue to evolve, including archeobacteria. Although such bacteria look very primitive to us, they have also evolved and changed continuously for 3-4 billion years. Who knows what they looked like 3 billion years ago? Or even 100 million years ago? How could we know, unless we found a 100 million year old bacterial spore, and were able to sequence it? Since bacteria do not reproduce while in the spore state, they are not evolving. Their DNA is essentially unchanged. Such an organism could provide a 100 million year old snapshot of evolution, frozen in time. If we could then sequence its genome and compare it to similar life forms today, we would see how a hundred million years of evolution have brought about their changes.</p>
<p>It is also interesting from the point of view of <a href="http://en.wikipedia.org/wiki/Panspermia" target="_blank">panspermia</a> – the hypothesis that life was seeded to Earth from space. Or even the reverse – life from Earth reaching other planets or other extraterrestrial habitable environments. We know that certain things (like large impact events) can propel material into space at speeds exceeding escape velocity. However, because of the immense distances involved, such material could take thousands of years to reach another solar planet, or millions of years to reach nearby stars. But if there are bacteria that can hibernate for millions of years, then such ideas become more practical.</p>
<p>I was reminded of these questions today when I read a story on <em>New Scientist </em><a href="http://www.newscientist.com/article/dn19475-arctic-bugs-may-have-the-longest-lifecycle-on-earth.html" target="_blank">about bacteria found on the sea floor</a> near Svalbard, an island off the coast of Norway. These are arctic bacteria, so you’d expect them to grow at cold temperatures. However, when the scientists incubated them, they had a surprise. In addition to the expected growth peak at about 20 °C, they observed a second growth peak at 55 °C.</p>
<p>Obviously, the sample contained different types of bacteria, one of which was thermophilic, with spore activation at 50 °C and peak growth at 55 °C. Why do these bacteria exist on the arctic sea floor, where the temperature never reaches 55 °C?</p>
<p>The DNA of these bacteria showed that they resemble bacteria known to exist deep under the Earth’s crust, where the temperatures are warmer. Typically, such bacteria are found associated with petroleum deposits. This might just be coincidence though, since most of our drilling underneath the sea floor is to look for oil. At any rate, the conditions in their normal habitat are hot and anoxic. So what were they doing on the arctic sea floor?</p>
<p>The temperature at the deep sea floor is near zero. It continues to rise in the Earth below the sea bed, at a rate of about 2-3 °C per 100 meters depth. So the normal habitat of these bacteria, with a peak growth rate at 55 °C, would be about 2 to 3 kilometers beneath the sea floor. Note that there are bacterial species that live at different depths below the sea floor – <a href="http://en.wikipedia.org/wiki/Mesophile" target="_blank">mesophiles</a>, <a href="http://en.wikipedia.org/wiki/Thermophile" target="_blank">thermophiles</a> (like these bacteria), and <a href="http://en.wikipedia.org/wiki/Hyperthermophile" target="_blank">hyperthermophiles</a> (in even deeper and more ancient sediments). It has been estimated that about 1/2 to 5/6 of the Earth’s entire bacterial biomass lives in the Earth beneath the sea floor[<a href="#1" target="_self">ref 1</a>]. Some studies estimate that 1/10 to 1/3 of the Earth’s entire biomass is contained in these sub-sea-floor bacteria. So we are talking about very large bacterial populations, and an extremely diversified ecosystem.</p>
<p>There are a few different ways in which bacteria from deep sub-sea-floor regions could move to the ocean floors, and vice versa. The ocean floor constantly accumulates sediment, and therefore anything on the sea floor will be eventually buried deep beneath the sea floor. But this process takes millions of years, even hundreds of millions of years. So if these bacteria are in their normal life cycle, it would take up to a hundred million years for them to be buried deep enough to have a satisfactory environmental temperature in which to germinate. Can they live that long?</p>
<p>Another, somewhat faster process, involves the circulation of ocean water into the deep sediments below the sea floor. This takes about a million years, which is much faster the burying of sediments, but still pretty long. This could give the microbes a boost, take them at least part way through their journey down to 2500 meters. It could also explain how they happened to end up on the sea floor, through the deep sea bed circulation.</p>
<p>The article itself [PDF of the full article <a href="http://www.microbial-ecology.net/pdf_download_free/264.pdf" target="_blank">can be found here</a>] concludes that the bacteria are engaged in their normal life cycle. Depending upon which cycle we are talking about (burial under accumulating sediments until they reach their target depth, or movement through oceanic sub-sea-floor circulation, or some combination of the two), this would mean that the normal life cycle for these bacteria ranges from a million to possibly a hundred million years.</p>
<p>There are other putative examples of extremely long-living bacteria, but the claims tend to break down upon further examination. For example, Vreeland and others found a species of Bacillus enclosed in the brine inside a salt crystal in the Salado salt formation in New Mexico [<a href="http://www.dna.gfy.ku.dk/course/papers/F1a.vreeland.pdf" target="_blank">full PDF here</a>]. These crystals are from the Permian, 250 million years old. Their team was able to successfully revive the bacterial spores and grow them in culture, and named them Bacillus strain 2-9-3, subsequently called <em>B. permians</em>. However, it was not clear whether these are actually 250 million year old bacterial spores trapped inside the salt crystal, or if they are bacteria that only recently migrated into the salt crystal.</p>
<div id="attachment_203" class="wp-caption aligncenter" style="width: 360px"><a href="http://blog.essayweb.net/wp-content/uploads/2010/09/crystal.png"><img class="size-full wp-image-203" title="crystal" src="http://blog.essayweb.net/wp-content/uploads/2010/09/crystal.png" alt="" width="350" height="315" /></a><p class="wp-caption-text">Salt crystal from which B. Permians was extracted.</p></div>
<p>There are some studies that cast doubt on the age of the bacteria. The gene for the 16S ribosomal subunit was sequenced, and has been compared to the same gene from modern day halophilic bacteria. One study reports that “The <em>B. permians</em> sequence differs from that of <em>S. marismortui</em> by only one transition and one transversion out of the 1,555 aligned and unambiguously determined nucleotides” [<a href="#2" target="_self">ref 2</a>].  <em>S. marismortui</em> is a moderately halophilic species from the Dead Sea. It seems very unlikely that a 250 million year old bacterium would differ from a modern species by only 2 mutations on that gene. Phylogenetic studies comparing <em>B. permians</em> to closely related organisms do not place <em>B. permians</em> at an ancestral position in the phylogenetic tree. So at best, there are serious doubts about the 250 million year claim.</p>
<p>Another example is the claim by <a href="http://www.ncbi.nlm.nih.gov/pubmed/8031102" target="_blank">Cano et al</a> that they revived spores from many bacterial species found in the stomach of a bee that had been trapped in amber. The amber was mined in the Dominican Republic, and is 25-40 million years old. One of these strains was identified as <em>Bacillus sphaericus</em>, which is a common species even today, and is often found inside the bodies of insects. <em>B. sphaericus</em> is listed as a single species, but like many bacteria, it is really a complex of several different subgroups. There are at least 5 recognizable DNA subgroups in various strains of <em>B. sphaericus</em>. The type isolated from the ancient amber was named BCA16, and eventually 1482 base pairs from its 16S ribosomal subunit gene were sequenced. These have been compared to various types of modern <em>B. sphaericus</em>.</p>
<p>There is about 80% similarity to one modern strain – NRS 592 [<a href="#3" target="_self">ref 3</a>]. This sort of leaves the question open – it’s not possible to definitely conclude that the spores found in the amber are millions of years old, but it’s not possible to rule it out either. Interestingly, the NRS 592 type that is most similar to the ancient strain is not primarily an insect pathogen. Other types of <em>B. sphaericus</em> which are known to be insect pathogens today share much smaller similarities to BCA16.</p>
<p>Another species isolated from ancient amber by Cano and his group was tentatively named <em>Staphylococcus succinus</em> [<a href="http://ijs.sgmjournals.org/cgi/reprint/48/2/511" target="_blank">full PDF here</a>]. The 16S ribosomal subunit gene for this bacterium differs from its closest modern day homologue (a urinary tract pathogen called <em>Staphylococcus saprophyticus</em>) by 19 substitutions out of 1525 aligned base pairs. This is certainly far larger than the reported homology for <em>B. permians</em>, which is supposed to be even older (250 million years). I don’t know if this is enough to support the ancient origin of <em>S. succinus</em>, but it certainly seems to deny the claim for <em>B. permians</em>. If a 25-35 million year old bacterial spore differs from modern species by 19 substitutions on that gene, how could a 250 million year old spore only differ from modern relatives by only 2 substitutions on the same gene?</p>
<p>There are a number of other similar claims, which I will not cover. Here are some of the papers if you are interested:</p>
<p><strong>DNA sequences from a fossil termite in Oligo-Miocene amber and their phylogenetic implications.</strong> DeSalle R, Gatesy J, Wheeler W, Grimaldi D. <em>Science</em> 1992 Sep 25; 257 (5078): 1933-6.</p>
<p style="padding-left: 30px;">This was one of the first papers about supposedly ancient DNA (25-30 million years old). Unlike the previous examples, this is not bacterial DNA, this is from a termite, which makes it harder to believe. On one hand, the fossil was preserved in amber, which is good. On the other hand, it’s not a spore, it’s a whole multicellular organism, which makes it hard to believe that the DNA could survive that long. The 18S ribosomal subunit gene was sequenced, and was found to be similar to modern termites and roaches.</p>
<p><strong>Amplification and sequencing of DNA from a 120-135-million-year-old weevil.</strong> Cano RJ, Poinar HN, Pieniazek NJ, Acra A, Poinar GO Jr. <em>Nature</em> 1993 Jun 10; 363(6429): 536-8.</p>
<p style="padding-left: 30px;">This one is from another insect, the weevil. This is even older, the weevil was found in Lebanese amber that is 120-135 million years old. Both 16S and 18S ribosomal unit genes were sequenced. Two short fragments from the 18S show that it’s possibly from some extinct weevil.</p>
<p><strong>PCR jumping in clones of 30-million-year-old DNA fragments from amber preserved termites (Mastotermes electrodominicus).</strong> DeSalle R, Barcia M, Wray C. <em>Experientia</em> 1993 Oct 15; 49(10): 906-9.</p>
<p style="padding-left: 30px;">More from the DeSalle group, also 30 million year old termites preserved in amber.</p>
<p>Here are some papers that talk more generically about extracting ancient DNA:</p>
<ol>
<li><strong>Very old DNA.</strong> DeSalle R, Grimaldi D. <em>Curr Opin Genet Dev</em> 1994 Dec; 4(6): 810-5.</li>
<li><strong>Ancient DNA: using molecular biology to explore the past.</strong> Brown TA, Brown KA. <em>Bioessays</em> 1994 Oct; 16(10): 719-26.</li>
<li><strong>Implications of ancient DNA for phylogenetic studies.</strong> DeSalle R <em>Experientia</em> 1994 Jun 15; 50(6): 543-50.</li>
<li><strong>Rapid isolation of DNA from fossil and museum specimens suitable for PCR.</strong> Cano RJ, Poinar HN. <em>Biotechniques</em> 1993 Sep; 15(3): 432-4, 436.</li>
<li><strong>The range of life in amber: significance and implications in DNA studies.</strong> Poinar GO Jr. <em>Experientia</em> 1994 Jun 15; 50(6): 536-42.</li>
</ol>
<p>So how plausible are these accounts of finding ancient DNA and being able to sequence it? Many modern microbiologists consider it very implausible. The main reason is that DNA is a very large and complex molecule, which degrades rapidly in the environment. The problem is radioactivity in the soil and rocks. Even small levels of radioactivity which are naturally found everywhere, should degrade DNA within a few hundreds of years. Bacterial spores contain no active DNA repair enzymes. How could the DNA survive that long?</p>
<p>A bacterial spore is a remarkably hardy entity. The thick walls offer considerable protection to the contents. The core, which contains the nuclear material and other cellular machinery is very low in water content, which also helps in preserving the material.</p>
<p><a href="http://blog.essayweb.net/wp-content/uploads/2010/09/sporestructure1.png"><img class="aligncenter size-full wp-image-209" title="sporestructure" src="http://blog.essayweb.net/wp-content/uploads/2010/09/sporestructure1.png" alt="" width="400" height="400" /></a></p>
<p>We know that live bacteria can take a lot of abuse. For example, <em><a href="http://en.wikipedia.org/wiki/Deinococcus_radiodurans" target="_blank">Deinococcus radiodurans</a></em> can stand cold, vacuum, acid, dehydration, and massive amounts of radiation. It has been shown to tolerate 10,000 grays of radiation (5 grays are lethal to humans). It’s not obvious why such an organism should evolve – after all, there are no habitats on Earth with such extreme radioactivity. The highest natural radiation is found in some areas of Iran, and it’s only about 260 milligrays per year. A year is far in excess of a bacterium’s lifetime, and even so the total cumulative radiation in a year would be far below the capacity of this organism to tolerate.</p>
<p>Some people have suggested that resistance to radiation and resistance to drying use the <a href="http://jb.asm.org/cgi/reprint/178/3/633?view=long&amp;pmid=8550493" target="_blank">same mechanism</a>, so the bacteria were really selected for resistance to drying, and resistance to radiation was just a side effect. This is certainly possible, but the fact remains that many of the mechanisms for the resistance depend upon the organism being alive and active. <em>D. radiodurans</em>, for example, has multiple copies of its genome for redundancy, and very active DNA repair enzymes. It has special mechanisms for annealing split strands. However, these are all active mechanisms, and don’t occur in bacterial spores.</p>
<p>What about passive mechanisms? We know that in <em>D. radiodurans</em>, the DNA is very tightly coiled into toroids. Does this confer some extra resistance? Some studies have found high levels of manganese associated with the DNA. Manganese complexes can act as antioxidants. Some researchers have also suggested that the chief damage from ionizing radiation is <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1828145/?tool=pmcentrez" target="_blank">not to the DNA, but rather to the associated proteins</a>. Manganese complexes could be protecting the proteins. These passive mechanisms would work in bacterial spores, but are they enough to ensure survival for millions of years? Who knows.</p>
<p>The amber fossils may be similarly protected. We know that amber slows down the degradation of biological material. This has been shown in studies on proteins. Proteins in all life forms on Earth are made of amino acids which are “left handed”, that is, they are levorotatory stereoisomers. However, simply over time, all amino acids racemize – spontaneously convert from one stereoisomer to the other. In living organisms, this is not a problem, because proteins are constantly being destroyed and replaced. Since all new proteins are formed with levorotatory amino acids, this is the predominant stereoisomer seen in living organisms.</p>
<p>However, after the cell dies, no new proteins are being synthesized. In time, all the remaining amino acids racemize, and after an extended period of time, the amino acids will be about half and half – roughly 50% in the levo form, and the other 50% in the dextro form. But it has been shown that this process of racemization <a href="http://onlinelibrary.wiley.com/doi/10.1111/j.1475-4754.1997.tb00806.x/abstract" target="_blank">is significantly slowed down if the organic material is preserved in amber</a>. So if amber can protect proteins, perhaps it can protect DNA as well. Again, the question is for how long, and under what conditions. Could DNA protected by amber, then buried in inert rock or inside a salt crystal, with a low ambient radioactivity level survive for a long time? For millions of years? How about a whole bacterial spore, presumably with manganese complexes, or something functionally equivalent that preserves it?</p>
<p>I don’t think this question has been answered yet, but it seems like people are slowly chipping away at the notion that DNA (or bacterial spores) couldn’t survive beyond a few hundred years.</p>
<p>References:</p>
<p><a name="1"></a>1. <strong>Leg 201 synthesis: Controls on microbial communities in deeply buried sediments.</strong> Jørgensen, B.B., D’Hondt, S.L., and Miller, D.J. (Eds.). <em>Proceedings of the Ocean Drilling Program, Scientific Results</em> Volume 201. [<a href="http://www-odp.tamu.edu/publications/201_SR/VOLUME/SYNTH/SYNTH.PDF" target="_blank">PDF</a>]</p>
<p><a name="2"></a>2. <strong>The Permian Bacterium that Isn&#8217;t.</strong> Graur, D and Pupko, T. Mol. Bio and Evolution. (2001) 18(6): 1143-1146. [<a href="http://mbe.oxfordjournals.org/content/18/6/1143.full.pdf+html" target="_blank">PDF</a>]</p>
<p><a name="3"></a>3. <strong>DNA similarity analysis of a putative ancient bacterial isolate obtained from amber.</strong> Yousten, AA and Rippere, KE. FEMS Microbiol Letters. 152 (1997): 345-347. [<a href="http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.1997.tb10450.x/pdf" target="_blank">PDF</a>]</p>
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		<title>On &#8220;Science Turns Authoritarian&#8221;</title>
		<link>http://blog.essayweb.net/2010/07/28/on-science-turns-authoritarian/</link>
		<comments>http://blog.essayweb.net/2010/07/28/on-science-turns-authoritarian/#comments</comments>
		<pubDate>Thu, 29 Jul 2010 03:30:14 +0000</pubDate>
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				<category><![CDATA[science]]></category>

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		<description><![CDATA[Comments on "Science Turns Authoritarian" by Kenneth Green from the American Enterprise Institute. More political propaganda by a very unscientific man.]]></description>
			<content:encoded><![CDATA[<p>I read an <a href="http://www.american.com/archive/2010/july/science-turns-authoritarian" target="_blank">article in <em>The American</em></a> claiming that science is losing its credibility because it has adopted an &#8220;authoritarian tone&#8221;. The author, Kenneth P. Green, asserts that science used to be in the business of simply stating facts neutrally; but now it has become increasingly assertive about drawing conclusions from the facts, that is, telling us what we ought to be doing.</p>
<p>For those unfamiliar with the magazine, <em>The American</em> is published by the American Enterprise Institute, a right wing think tank. While I have no idea how scholarly they pretend to be, this particular article is so full of errors and strawmen that it demolishes any credibility they may have as a serious think tank.</p>
<p>Here is the gist of it. They performed an &#8220;experiment&#8221;, in which they searched for certain phrases in the Lexis/Nexis database. The phrases were:</p>
<ul>
<li>science says we must</li>
<li>science says we should</li>
<li>science tells us we must</li>
<li>science tells us we should</li>
<li>science commands</li>
<li>science requires</li>
<li>science dictates</li>
<li>science compels</li>
</ul>
<p>They narrowed the search by date, and reported cumulative results for each year, from 1980 to 2009, and graphed them. Here is the graph:</p>
<div id="attachment_185" class="wp-caption aligncenter" style="width: 510px"><a href="http://blog.essayweb.net/wp-content/uploads/2010/07/lexis.gif"><img class="size-full wp-image-185" title="Search of Lexis/Nexis Database" src="http://blog.essayweb.net/wp-content/uploads/2010/07/lexis.gif" alt="" width="500" height="421" /></a><p class="wp-caption-text">adapted from article at American Enterprise Institute</p></div>
<p>The steep green line at the top is the cumulative total for all phrases. The next two lines, which show a significant increase over the years are for &#8220;science tells us we should&#8221; in purple, and &#8220;science requires&#8221; in brown. The rest of the lines are scrunched up at the bottom and do not show any sharp increases in the frequency of those phrases.</p>
<p>From this molehill of &#8220;experiment&#8221;, the author derives far reaching conclusions. He says that the graph shows that the occurrence of these phrases has increased sharply over the years since 1980, which reflects an increasingly &#8220;authoritarian&#8221; slant to science. He says:</p>
<p><span style="color: #339966;">&#8220;In other words, around the end of the 1980s, science (at least science reporting) took on a distinctly authoritarian tone. Whether because of funding availability or a desire by some senior academics for greater relevance, or just the spread of activism through the university, scientists stopped speaking objectively and started telling people what to do.&#8221;</span></p>
<p>Now consider how laughably unscientific this experiment is. If you have children in middle school, consider if your average 10-14 years old could have designed a better experiment. Then understand that Mr. Kenneth P. Green, resident scholar at American Enterprise Institute failed.</p>
<p>I&#8217;ve described some problems with their &#8220;experiment&#8221; below.</p>
<h2>The Graph is Meaningless Unless Normalized</h2>
<p>It&#8217;s a fair bet that between the period covered by the graph (1980-2009), the size of the Lexis/Nexis database grew tremendously. Recall that back in 1980, people used 300 baud modems, and hard drives in gigabyte sizes arrived from IBM on a palette, and cost thousands of dollars. The web as such barely existed. Now consider the situation today, when 2 terabyte drives are available by mail order for a couple hundred bucks. Obviously, databases have grown. A lot more is being stored in the Lexis/Nexis database today than used to be the case in 1980. Here&#8217;s <a href="http://www.fundinguniverse.com/company-histories/LEXISNEXIS-Group-Company-History.html" target="_blank">a brief history of Lexis/Nexis</a>, showing how they have grown by incorporating more and more publications into their database.</p>
<p>Anyone interested can do their own search, but 2 minutes on Google turned up these facts:</p>
<ul>
<li>By <a href="http://www.fundinguniverse.com/company-histories/LEXISNEXIS-Group-Company-History.html" target="_blank">1983</a>, the LEXIS database had 12.5 million pages, including the full text of federal and state laws, court decisions, and much of British and French law.</li>
<li><a href="http://en.wikipedia.org/wiki/LexisNexis" target="_blank">Today</a>, to serve its user population of about 5 million subscribers, LexisNexis hosts over 100 terabytes of content on its 11 mainframes (supported by over 300 midrange UNIX servers and nearly 1,000 Windows NT servers) at its main datacenter in Miamisburg, Ohio.</li>
</ul>
<p>This is not even going as far back as 1980, the date the author uses, when the database would have been even smaller. In 1983, it was 12.5 million pages. Even at a generous 100 kilobyte per document (100 kilobytes is a good sized novella), the size of the database was about 1 terabyte in 1983. Realistically, it was probably much smaller than 1 terabyte. Terabyte size databases were exceedingly rare in 1983. Today it is 100 times larger. This is because Lexis/Nexis is indexing a vast number of magazines, journals, legal documents and other texts today, than it was in 1980.</p>
<p>With a much larger number of publications being indexed today, it&#8217;s no surprise that any given search phrase produces more hits. This is why graphs such as these are completely and utterly useless. If the author had even a little bit of common sense, he would have taken the trouble to contact Lexis/Nexis, and ask them specifically &#8220;how many gigabytes per year do you add to your database today? How many gigabytes per year were you adding to your database in 1980?&#8221; If the difference between 1980 and today is 10 fold, then simply divide today&#8217;s numbers by 10 to obtain a normalized result for today. If you want to plot a point for every year between 1980 and 2009, then you need to ask the same question for each year &#8211; how many gigabytes of data per year were you adding in 1989? In 1990? In 1991?&#8221;</p>
<p>If this was too much trouble, I can suggest a simpler test, which is not as accurate but better than nothing. Pick a phrase that has nothing to do with science, such as &#8220;I like cookies&#8221;. Do a search for it in the same way, year by year. I am willing to bet cookies to peanuts that he will find the exact same result &#8211; that the frequency of occurrence of this phrase increases yearly. This is simply a result of the increasing number of resources indexed by the database, and has nothing to do with whether cookies are really more popular today than in 1980.</p>
<p>So pick half a dozen such non-science phrases. &#8220;I like cookies&#8221;. &#8220;Cars are fun&#8221;. Whatever. Get some numbers for how <em>those</em> phrases have changed in frequency, then normalize to those numbers. Better than nothing.</p>
<h2>Results Show the Opposite of What Author Claims</h2>
<p>Mr. Green makes fleeting reference to the increasing size of the database:</p>
<p><span style="color: #339966;">&#8220;Some of this may simply reflect the general growth of media output and the growth of new media, but if that were the case, we would expect all of the terms to have shown similar growth, which they do not.&#8221;</span></p>
<p>He gets zero points from me for this. No, we wouldn&#8217;t expect all phrases to show similar &#8220;growth&#8221;. First, as I explained above, no &#8220;growth&#8221; was demonstrated. You cannot demonstrate growth unless you normalize the numbers, which he failed to do. However, <em>if</em> he had normalized the numbers, even then, any growth (or shrinkage) does not need to be even. Language is an evolving thing. Over time, some phrases become popular. Others become archaic or obsolete. This graph stretches 30 years, over a generation long. That&#8217;s plenty of time to see statistical effects in the popularity of phrases.</p>
<p>But the funny thing is that even if you grant him his point, it shows exactly the opposite of what he claims. What are the phrases that are becoming more popular, according to his graph? They are:</p>
<ul>
<li>science tells us we should</li>
<li>science requires</li>
</ul>
<p>Compare that to which phrases are at the bottom, that did not become more popular:</p>
<ul>
<li>science commands</li>
<li>science dictates</li>
<li>science compels</li>
</ul>
<p>Which is more authoritarian? &#8220;Science commands&#8221;? Or &#8220;science tells us we should&#8221;? The fact is that the most authoritarian phrases (commands, compels, dictates) are the ones that have <strong>grown the least</strong> in popularity. If anything this is a sign of <strong>decreasing authoritarianism</strong> in science. If he had bothered to normalize his numbers, these phrases would probably all have negative growth. But somehow he misses all that and just merrily goes on his way.</p>
<p>Some of the phrases are particularly poorly chosen, such as &#8220;science requires&#8221;. This could easily be part of a statement such as &#8220;&#8230; credit in science requires that you take three 101 levels courses in physics, chemistry and biology &#8230;&#8221; which doesn&#8217;t have a darn thing to do with the &#8220;authoritarianism&#8221; of science, just some school listing its requirements. Or it could be &#8220;<a href="http://www.iep.utm.edu/requires/">what science requires of time</a>&#8220;, meaning what are the scientific constraints on our understanding of time that need to be taken into account. Again, not an &#8220;authoritarian&#8221; directive telling people they better not smoke or they&#8217;ll get lung cancer, or they better watch the greenhouse gases (Mr. Green&#8217;s pet peeve) or the Earth will get hot. Or &#8220;<a href="http://abcnews.go.com/Technology/story?id=99484&amp;page=1" target="_blank">Mercury Mission Shows Science Requires Patience</a>&#8220;.  This is precisely the content that&#8217;s getting indexed in Lexis/Nexis, and is showing up on the graph.</p>
<p>One click on Google turns up a hundred thousand hits, and from what I can see precious few have anything to do with Mr. Green&#8217;s thesis about authoritarianism. If you pick such a commonly used phrase, of course you&#8217;ll see its use spike as more material is indexed. But it says nothing about authoritarianism in science.</p>
<h2>The Lexis/Nexis Database Doesn&#8217;t Represent What Scientists Say</h2>
<p>The Lexis/Nexis database consists of popular magazines, TV reports, business journals, legal documents, and other texts of this nature. What it does <strong>not include</strong> are scientific journals. In other words, the material in the Lexis/Nexis database represents the words of journalists, not so much scientists. If you want to see what scientists actually say, better databases would be those which index scientific journals.</p>
<p>So really what he&#8217;s claiming is that journalists are using these phrases more often than they used to, that journalists are becoming more &#8220;authoritarian&#8221; about science. Perhaps in some cases the journalists are actually quoting scientists, but certainly not in all. Journalists also editorialize the words of those they interview. They also present their own viewpoints. Without any effort to differentiate between what the scientists said and what the journalists said, how could you draw any conclusions about scientists? You wouldn&#8217;t, if you cared about the truth. Obviously, Mr. Green is not so burdened. He has an agenda to push, and he gets busy pushing it.</p>
<h2>The Agenda</h2>
<p>So what is Mr. Green trying to do? He works for the American Enterprise Institute, a right wing think tank. They produce reports that are cited by right wing politicians, to support right wing agendas. The science he particularly hates is climate science, specifically global warming. He mentions it specifically:</p>
<p><span style="color: #339966;">&#8220;The climate community is probably the biggest user of the authoritarian voice, with frequent pronouncements that “the science says we must limit atmospheric carbon dioxide concentrations to 350 parts per million,” or some dire outcome will eventuate.&#8221;</span></p>
<p>This is what he&#8217;s fighting against. Apparently, he&#8217;s not happy with the gl0bal warming reports, and he doesn&#8217;t want any legislative actions taken. So what is he really saying?</p>
<p>When he says &#8220;science should be neutral&#8221;, what it amounts to is that scientists should just state the facts as they see them, and then shut up. In particular, they should never make any suggestions about what ought to be done. They should have no political voice.</p>
<p>Who then has the political voice? Who makes the decisions? If the scientists shut up, then it&#8217;ll be the non-scientists making the decisions. In other words, in the most complex technical matters, when it really helps to have an understanding of science to know what you&#8217;re talking about, he wants to silence the most technically qualified people. He wants the only people who are allowed to make &#8220;ought&#8221; statements to be the most clueless &#8211; hacks like himself, politicians of all stripes, whatever. So long as they&#8217;re not scientists.</p>
<p>This sort of viewpoint, overwhelmingly silly though it may be, comes from a very real resentment that people like Mr. Green have. Science is outside their understanding, specially highly technical matters such as climate science, where you need a technical understanding of an immense body of data to even sound half-intelligent. Being unable to use science himself, Mr. Green wants to deny it to his opposition as well. He wants to have a shouting match between people as clueless as himself, with the scientists all locked out of the discourse, because if they participate, they&#8217;re &#8220;tainting&#8221; science, don&#8217;t you know.</p>
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		<title>Deepwater Horizon Oil Spill</title>
		<link>http://blog.essayweb.net/2010/05/19/deepwater-horizon-oil-spill/</link>
		<comments>http://blog.essayweb.net/2010/05/19/deepwater-horizon-oil-spill/#comments</comments>
		<pubDate>Wed, 19 May 2010 15:39:05 +0000</pubDate>
		<dc:creator>Admin</dc:creator>
				<category><![CDATA[current news]]></category>
		<category><![CDATA[science]]></category>
		<category><![CDATA[Deepwater Horizon]]></category>
		<category><![CDATA[Ocean Currents]]></category>
		<category><![CDATA[Oil Spill]]></category>

		<guid isPermaLink="false">http://blog.essayweb.net/?p=146</guid>
		<description><![CDATA[The Deepwater Horizon Oil Spill explained. Where will the oil end up? Prevailing wind and water currents in the Gulf of Mexico determine which coastlines are most at threat.]]></description>
			<content:encoded><![CDATA[<p>This <a title="Deepwater Horizon" href="http://en.wikipedia.org/wiki/Deepwater_Horizon" target="_blank">oil spill in the Gulf of Mexico</a> has been in the news a lot lately. Recently, I came across this satellite photograph from NASA, which shows the oil heading southeast in a long stream. There’s a lot of speculation on what will happen in the days to come if the spill isn’t capped soon. Where will the oil go? Which areas will be affected?</p>
<p><a href="http://blog.essayweb.net/wp-content/uploads/2010/05/satellite.jpg"><img class="aligncenter size-medium wp-image-147" title="Satellite Photo Showing Spill" src="http://blog.essayweb.net/wp-content/uploads/2010/05/satellite-300x288.jpg" alt="Satellite Photo Showing Spill" width="300" height="288" /></a>Here&#8217;s a map showing the topology of the sea floor where the Deepwater Horizon was located. As you can see, the site is near a steep incline, where the continental shelf drops off sharply towards the sea floor. The depth of the sea floor was around 5000 feet.</p>
<p><a href="http://blog.essayweb.net/wp-content/uploads/2010/05/gmap-c.jpg"><img class="aligncenter size-medium wp-image-159" title="Sea Floor at Deepwater Horizon" src="http://blog.essayweb.net/wp-content/uploads/2010/05/gmap-c-300x210.jpg" alt="Sea Floor at Deepwater Horizon" width="300" height="210" /></a></p>
<p>I’ve come across a bunch of comments at various websites, with some people saying “oh well, the oceans are huge, so what if we have a spill? If you consider the amount of oil compared to the vast volume of the oceans, it is so tiny it doesn’t matter”. This kind of talk seems singularly uninformed at best and deliberate distortion of the facts at worst to me. It’s clearly obvious if you follow the news at all, that the spill isn’t being distributed evenly among the oceans. Tar balls and oil are appearing on the Louisiana coast. And as the satellite picture from NASA shows, the oil is definitely being channeled in a very specific direction. So I thought to write this note to explain what is happening, and what we might expect in the days to come.</p>
<p>In order to understand what’s happening to the oil as it leaks out, we need to understand water currents and wind directions in the Gulf of Mexico.  These can be summarized as follows:</p>
<ol>
<li>There is a deep water current that enters the Gulf of Mexico from the south, loops through the Gulf, and then exits through the Florida Strait and curves northwards along the east coast of the US, as the Gulf Stream.</li>
<li>The prevailing winds in this area are the Westerlies, or anti-trade winds, which blow from south west to north east. Winds do not affect deep waters, but they do in fact produce currents in surface waters. It might seem intuitively right that the surface water current should be in the same direction as the wind, but this is not so. In fact, surface water currents flow in a direction 90 degrees to the right of the wind direction, because of a phenomenon known as <a title="Eckman Transport" href="http://essayweb.net/geology/quicknotes/ocean_currents.shtml#eckman" target="_blank">Eckman Transport</a>. Since the prevailing winds in this region are southwest to northeast, surface currents induced by the winds flow northwest to southeast.</li>
<li>The movement of the oil itself is subject to the <a title="Coriolis Effect" href="http://essayweb.net/geology/quicknotes/coriolis.shtml" target="_blank">Coriolis Effect</a>. This is an effect which happens due to the west to east rotation of the Earth. Air or water or oil flowing in a fluid medium is affected in that its path curves westwards if the flow is towards the equator, and curves eastwards if the flow is away from the equator.</li>
<li>The oil leak is occurring at the bottom of the ocean. The oil rig collapsed to the sea floor. The leaks are in the valve at the sea bed, and also in the riser pipe which is now lying collapsed on the sea floor. So the oil is being released at the sea floor, and then rising slowly to the surface. Therefore, since this oil is traversing the entire depth of the sea, from the sea floor to the surface, it is affected by both deep water and surface currents.</li>
</ol>
<p>You can see these things in this diagram I made:</p>
<p><a href="http://blog.essayweb.net/wp-content/uploads/2010/05/oilspill_corrected.png"><img class="aligncenter size-medium wp-image-157" title="Deepwater Horizon Oil Slick" src="http://blog.essayweb.net/wp-content/uploads/2010/05/oilspill_corrected-300x210.png" alt="Deepwater Horizon Oil Slick" width="300" height="210" /></a></p>
<p>Notice the deep water current displayed in tan. This current enters the Gulf of Mexico from the south, loops around the Gulf, and then exits around Florida, only to swing back north and proceed along the eastern seaboard as the Gulf Stream.</p>
<p>Next, consider the winds, shown in yellow on the map. These are the <a title="Westerlies" href="http://essayweb.net/geology/quicknotes/coriolis.shtml#permanentwinds" target="_blank">Westerlies, or anti-trade winds</a>. At these latitudes, they blow from southwest to northeast (as an aside, this is why “weather” in the form of storms tends to move from southwest to northeast in the continental US). Because of these winds, the movement of surface water is from northwest to southeast, as shown by the orange arrow. This is because of Eckman Transport, which tends to push water 90 degrees to the right of the wind direction. Remember, this represents surface water only, since the wind does not affect deep water.</p>
<p>Now in the light of these factors, look at how this oil slick has evolved over time:</p>
<p><a href="http://blog.essayweb.net/wp-content/uploads/2010/05/evolution-c_small.jpg"><img class="aligncenter size-full wp-image-158" title="Evolution of Oil Slick" src="http://blog.essayweb.net/wp-content/uploads/2010/05/evolution-c_small.jpg" alt="Evolution of Oil Slick" width="300" height="1243" /></a></p>
<p>These are four satellite images taken by NASA, from May 9th, 10th, 11th and 17th. Note that the images have not been equally scaled. Specifically, I zoomed out on the May 17th image to include the long tail.</p>
<p>As you can see, the slick slowly elongates in a north-south direction, and develops a &#8220;tail&#8221; pointing south. Between May 11 and May 17, the tail grows enormously, curving southeast. What could explain this effect?</p>
<p>If you look at the diagram I made earlier, you can see that the slick was slightly north of the loop current. The position of the loop current isn&#8217;t fixed, it has some daily/weekly variation. During early May, satellite imaging showed that the northernmost extent of the loop current was about 50 miles south of the oil spill, though the strongest currents were about 80 miles south. Since then, as we&#8217;ve seen in the satellite maps, the spill has extended far southwards. The satellite image from May 17th shows the slick extending 100+ miles south of its origin. This would put it well within the range of loop current, even if the loop current has shifted somewhat in this time.</p>
<p>So far, BP is still saying that the oil has not entered the loop current. There is still some doubt about this, but <a href="http://articles.sun-sentinel.com/2010-05-18/news/fl-oil-spill-florida-current-20100517_1_spill-bp-oil" target="_blank">some scientists think it may already have entered the loop</a> circulation. We will probably know for sure in a day or two.</p>
<p>Here is how I think the slick has proceeded:</p>
<ul>
<li>Oil leaking from the sea floor rose up and encountered local currents. Since the leak origin was fairly close to the shore where currents are quite turbulent, it initially spread pretty randomly, forming a large patch offshore.</li>
<li>As oil continued to pump out from the leak and the volume of the leak increased, some of it drifted southwards. It acquired a slight easterly curve, because surface currents move in a direction 90 degrees to the right of the prevailing winds, due to Eckman Transport. The prevailing winds in this area are the anti-trade winds, or westerlies, which blow from southwest to northeast.</li>
<li>This could very well explain the southeastward trajectory of the slick, without needing to invoke the loop current. However, the fact that it&#8217;s spread so far south and is either in or very close to loop current trajectory, means that there is a good chance that at least the tail end of it is being pulled along by the loop current, which would carry it eastwards at this point. The sudden sharp bend it makes at the very southern end also suggests that something else happened at this point &#8211; perhaps that something else was the slick being drawn into the loop current.</li>
</ul>
<p>If the slick hasn&#8217;t been drawn into the loop current, it seems almost certain that it will, since it&#8217;s so very close.</p>
<p><strong>Future Expectations</strong></p>
<p>The size of the spill is under debate. BP has stated that it’s about 5000 barrels per day, but independent estimates from other scientists say that it could be as much as 70,000 barrels per day. The fate of the spill depends upon its size, which means how much oil is being spilled per day, and how many days it continues to flow before it’s capped.</p>
<p>If a substantial amount of oil leaks out, where will it go? As you can see in the maps, the deep water currents loop around the Gulf, and head north along the Gulf Stream, which passes by the east coast of the US. Oil that gets caught in this current and doesn’t make it to the surface until much later may therefore follow this path and only surface off the east coast of Georgia or the Carolinas. But this would take a lot of oil, and perhaps there won’t be so much.</p>
<p>The more immediate danger is to the Florida Keys and the Bahamas, as well as the north coast of Cuba. Because the loop current stays pretty far away from the west coast of Florida, it seems unlikely that much oil could end up there. But it comes very close to land when the current passes out of the Florida Strait. It has to pass through a triangle formed by the Keys to the north, Cuba to the south, and the Bahamas to the east. Those are the likely danger spots.</p>
<p>If there are strong winds in this period, driving strong surface currents, then the Bahamas and Cuba are probably even worse off, since wind-driven surface currents will be in a southeasterly direction. By the same token, if the oil makes it into the Gulf Stream and heads up the east coast of the US, winds may cause the coasts of Georgia and the Carolinas to be spared, since surface currents would push the oil away from the shores.</p>
<p>It’s also important to remember that the paths of these currents and even the wind directions aren’t always constant. There is day to day variation, as well as seasonal variation now that summer is coming. So these predictions are only approximate.</p>
<p>I also wrote a short article on ocean currents which <a title="Ocean Currents" href="http://essayweb.net/geology/quicknotes/ocean_currents.shtml" target="_self">you can read here</a>, if you’re interested.</p>
<p><strong>EDIT</strong>: There were some news stories recently that tar balls have washed up in the Florida Keys. These are <em>not </em>from the Deepwater Horizon spill. As you can see from the maps, the spill hasn&#8217;t reached anywhere near the Florida Keys so far. The Gulf of Mexico has a lot of oil rigs and many spills have happened here before, so it&#8217;s not uncommon for tar balls to show up on any of these coasts.</p>
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