Friday, November 2, 2012

WAMP Step 3: Install MySQL

In the previous installments of this series (here and here), we set up and configured the Apache web server and the PHP scripting engine. Now we will add the database server, MySQL.

SQL databases implement the powerful relational database paradigm, a way of thinking about data that is based in the mathematics of set theory. This makes them (in theory) more powerful and safer than other kinds of databases that preceded them. While relational databases started life on mainframes, MySQL is an example of how the concept can be adapted to desktops. After all, your desktop is probably a more powerful computer than the 'big iron' mainframe of the 1960's!

Installing MySQL


MySQL started as the project of an independent company, which was subsequently acquired by Oracle. A free and open version is still available, called the "community" server.

The MySQL download for the Community Server is at http://www.mysql.com/downloads/mysql/. If you just got http://www.mysql.com/downloads/, you'll be offered a Windows installer that includes a whole bunch of additional software and connectors, over 200 MB of stuff! We don't need all of that to test out WordPress, which is the objective of this exercise. Just grab the installer for the Community Server.

Global Warming: a brief background

I'm writing this for an audience that isn't short on science or Google chops. I'll try to supply links where useful.

We're here to discuss global warming, and several levels of skepticism expressed about global warming.

  • What is global warming (GW), and does it really exist?
  • Is global warming anthropogenic (AGW)? That is to say - are human activities principally responsible for global warming?
  • Is global warming catastrophic (CAGW)? Are the changes severe, irreversible and creating misery for humans and other life on the planet?
A basic issue of terminology - the problem we'll be discussing is one of heat, and heat is measured by temperature. However, there is not a one-to-one correspondence between the two ideas.

Thursday, November 1, 2012

Podebrady, Poetry by Francis Klein, reviewed by Davd vun Kannon

Podebrady is a slim chapbook of poetry. The poems inside are, at times, a painfully intimate window into the author's heart. But they are also full of wisdom, beautiful words and images, and the painful intimacy is mostly the result of recognizing ourselves waiting in the mirror of these words.

I especially like the The Apple Press, and the last lines of Morning Laundry:


We are replaced by what we love.
We leave the green fields free and fallow. 

Klein is a published poet and an architect with a practice in Montclair, NJ. Podebrady is avaible from Amazon and Finishing Line Press.

Recommended.

Sunday, October 28, 2012

Nice Work If You Can Get It - Review

Nice Work If You Can Get It is a frothy bit of Broadway magic. The show features songs by George Gershwin, and a plot loosely (very loosely) based on his 1926 musical, Oh, Kay. Other material from the film Delicious, including the immortal love song Blah, Blah, Blah.

The show stars Matthew Broderick, Kellie O'hara and a great cast. I saw a matinee last Saturday with my wife, my son Daniel, and a friend of his. We all laughed and clapped up a storm.

The thin plot involves Broderick as Jimmy Winter, a dissolute young rich boy who prefers chorus girls to nice girls. But he's marrying a nice girl to secure his inheritance. Until he meets a bootlegging dame, Billie Bendix. Hilarity ensues.

Apres theater dinner at Barbetta was excellent.

Thursday, October 18, 2012

WAMP Step 2: Install PHP

As detailed in our previous post, we are building towards a WordPress installation on a desktop PC. In step 1, we successfully installed and tested the Apache web server.

As mentioned last time, some documents that are served by the web server to your web browser are static documents - just files sitting on the hard drive. Other documents are actually queries into a database, where the data has been dressed up and presented as a web page. Still other documents are mostly static, but with some customization by a script running on the server.

To support WordPress, we are going to need both a database and a script engine. A very popular scripting language for web pages is PHP, and that is what WordPress requires. The rest of this post will walk through installing PHP.


Wednesday, October 17, 2012

WAMP step 1: the Apache httpd server

Our goal in this process is to set up WordPress to serve the test content of a website and blog. Therefore the very first thing we are going to need is a web server.

I should say at the beginning that you don't need a web server to test basic web pages, you can write HTML files with any text editor, and then point your web browser at the file. You can teach yourself a lot of HTML and client-side JavaScript programming in this way. I think it is better to learn the fundamentals of how web pages work by typing it out for yourself instead of starting with a web development environment - you really understand what is going on.

Web servers deliver content to browsers. This content (web pages, music, images, etc.) is either a file on your machine's hard drive, or data stored in a database (on the hard drive). If it is data from the database, then a program (a script) must be run first to turn it into a document that is served out by the web server.

So even before we set up our Apache web server, we need to set up some space on our hard drive where this content will live. Importantly, we want this space to be independent of the Apache server file structure, so that we can back it up separately, and update Apache if necessary without moving our content. We could even change web servers entirely and our content would still be in the same place.

Setting Up WordPress on a Desktop

My wife is setting up her business and wants to have a website with blog, etc. Great! She'll be getting her domain name and contracting with a web hosting company - we haven't decided which at the moment.

For the blog support, I'm going to test WordPress, since it is very popular. Being the geek that I am, this means setting up WordPress on our home desktop machine.

WordPress (WP) runs on top of several other popular Web tools. Apache is a free web server, PHP is a free scripting engine, and MySQL is a free database. If these tools were running together on a machine using the Linux operating system the whole stack would go by the acronym LAMP. Since I'm using a Windows PC, it will be a WAMP stack for me.

While there are products that claim to install WP and all of these prerequisite pieces of software, I'm going to do it myself and write series of blog posts about the process.

Wish me luck!

ps - The process I will follow is based on Jessie Forrest's blog. Thank you Jessie for putting so much in one place! My posts will include a little background info and changes to the process Jessie posted a few years ago, based on the problems I encountered and how I solved them.

Friday, October 5, 2012

How can a virus see?

Proteorhodopsin genes in giant viruses

This is teh awesome! Rhodopsin is a key protein used in the eye, the first step in capturing light and turning it into sensory information. It can be found even in single celled creatures that swim towards or away from light as a feeding signal. Here, the virus is modifying the behavior of the infected cell with its own rhodopsin gene.

There are many examples of parasites modifying the behavior of their host. A creepy example (aren't all parasites creepy?) is the fungus that makes zombie ants leave their nest and climb up where they will get eaten, which helps the fungus spread.

So how do these giant viruses see with their rhodopsin gene? By making their host see for them. Giant viruses are very different from very small viruses, like the famous Ebola virus. Ebola is less than 20,000 nucleotides long (single stranded RNA) and makes only eight proteins, according to Wikipedia. In contrast, mimivirus has a genome of almost 1.2 million base pairs of DNA. While Ebola just replicates as fast as possible before destroying the host cell, giant viruses are more long lived parasites.

Thursday, October 4, 2012

Evolution: A view from the 21st Century by James A. Shapiro, reviewed by David vun Kannon

In this slim book, eminent bacteriologist James Shapiro attempts to communicate his view of the most important drivers of evolution for a non-specialist readership. The material is dense, mostly because the text does not rise much above an outline of all discovered processes of genetic variation, no matter how obscure.

Shapiro succeeds in conveying the idea that variations arising from genetic change other than uniformly distributed single nucleotide changes are the most important to understanding the diversity of life today. However, his other agendas, such as displacing Crick's Central Dogma of Biology, are not successful.

Let's deal with some of the positives of the book first.

Shapiro is writing for a wide audience, and does not shy away from addressing some issues related to the "Intelligent Design" controversy. Some in the ID community initially took Shapiro to be their friend, in the "enemy of my enemy" sense. However, Shapiro takes the age of the planet and the evolution of life as ground facts.

The book makes extensive use of online appendices and additional reference material. I read the book on the Nook e-reader from Barnes & Noble, and opening the book using the PC version of the Nook reader application made these materials easy to access. Much of the online reference material is linked directly to Pubmed. Online additional readings link mostly to articles from Scientific American - not the primary literature, but an accessible source for the expected audience. These articles span 60 years of publication and many are of historical interest only.

The book is very complete in its coverage of genomic change processes. And while Shapiro's main point is to focus on sources of variation other than point mutation, when it comes to discuss mutation, the book includes intriguing sources such as viruses (in which mutation can happen at much higher frequencies).

Most readers will probably be quite surprised by the importance of genomic processes other than mutation in shaping the course of evolution. Even if you've been following the developments as an interested non-professional, as I have, the variety of processes discussed is sure to teach you something new.

One insight I got was that the machinery that is used to guide protein production inevitably interacts with the machinery of cell duplication (in single celled organisms) and germ line continuation in metazoa. I failed to see previously how often the genome is opened up and read, and how that necessary process creates the chances for things to break and be repaired differently.

However, it must also be said that the book is far from perfect. Indeed, there are many irritations that spoil the enjoyment of learning.

Shapiro seems to feel that it is his job to carry forward the mantle of "unorthodox biologist" worn by Lynn Margulis and Barbara McClintock, among others. He takes several shots at "evolutionists" for missing the importance of jumping genes and symbiosis, while focusing on the population genetics of single random changes.

With all due credit to McClintock and Margulis, Shapiro's rhetorical stance is unhelpful. He does play into the hands of those that would willfully misrepresent his position by using loaded terms such as Darwinism and evolutionist, without defining them and apparently without concern with how these terms have been used in the popular press. If Shapiro means "evolutionary biologist" when he says evolutionist, he should use the less charged term.

Shapiro repeatedly uses a "microprocessor" metaphor that is painfully inappropriate. A computer CPU is a piece of hardware that can execute any series of instructions stored in memory, given a link to the first address of where to fetch the data. The information of the genome is the data, not the hardware that reads or  acts on the data. The closest thing in the cell to a CPU is the set of molecules that read, transcribe and translate, DNA into protein - the ribosome.

There are many ribosomes working in parallel in the cell, one of several failures of the analogy. As a system, the protein production and genetic machinery are more like a "production system" - a set of if-then rules that work in parallel. This is software, not hardware, but it fits better.

Scientists frequently stretch to find an analogy which will work for a lay reader, to help the reader understand their work. If that is what Shapiro was trying to do, it doesn't work. If he actually thinks the genome instantiated in a cell is a microcircuit, he is sadly mistaken about microelectronics.

Few, if any, people would call a microprocessor "aware", "intelligent", or capable of cognition, yet this book does use such aggressively telic language with respect to the cell and the genome. However, we should only be willing to talk about "cell cognition" if we are also willing to talk about "thermostat cognition". The feedback loops elaborated in the cell are only marginally more complex than your friendly household appliance.

Darwin comes in for some criticism that seems unnecessary, sort of like criticising Newton for not discussing relativity. Yes, Darwin's uniformitarianism was/is a simplification of what we know today, and did reflect philosophical debates of his time. So what? Does this need to be criticised or simply acknowledged?

Repeatedly when dismissing the random mutation of single nucleotides, Shapiro seems to confuse random with 'uniformly distributed' - or read that confusion onto others. We know that SNPs (single nucleotide polymorphisms) are not randomly distributed. They are more likely in some parts of the DNA string than in others. However, they are random, in the sense that we don't know in advance where a change will take place, even if we know they take place at different frequencies. As an analogy, we know that a sample of a radioactive element has a half-life, but we don't know which atom will decay next.

Shapiro seems unconcerned with the Darwinian distinction between selection and sources of variation, giving all the credit to the multiple sources of variation, and little or none to the various forms of selection that can act on an organism. There is also no discussion of the "evolution of evolvability" as a framework for understanding the many mechanisms that are cataloged in the book.

A weakness in the writing is to describe the genetic machinery as "indescribably complex" before launching into a description of it! Phrases like 'indescribably complex' are just more fodder for quote mining by creationists. Similarly, Shapiro's overall anti-reductionist stance obscures the fact that all of the data and research are based on a reductionist paradigm - the genetic machinery of the cell is entirely the arrangement of atoms and the forces acting upon them, as is everything else in the cell. There is no vital elixir or special sauce that defies reduction to these terms.

While referring to it several times, Shapiro never successfully attacks the Central Dogma of Biology, that information flows in the direction of DNA to RNA to protein, but not in reverse. There are ample examples given of proteins attaching to and regulating the genome, but those proteins are always created by the genome.

Relevance to the ID debate

The book does mention Intelligent Design. However, it also treats evolution as a fact. Natural genetic engineering, as Shapiro calls it, is the source of variation used by evolution. These large scale additions and rearrangements are the driver of metazoan evolution - not new sequences.

It has been the mistake of ID supporters to try to find an ally in Shapiro. Obviously, they did not read the whole book, or if they did their memory is quite selective as to its contents.

It should be mentioned that Shapiro published two papers with controversial ID figure Dr. Richard von Sternberg in 2005. Sternberg is thanked in the acknowledgements.

Shapiro also indulges in some 'bignum' argumentation. This is the sort of handwaving probability calculation that concludes that "there is not enough time" for base-by-base change to create the evolutionary results we see. This kind of reasoning has often been proved wrong, usually by pointing out that sexual reproduction allows many changes to be selected in parallel throughout a population and combined, and high rates of reproduction and HGT (horizontal gene transfer) accomplishing the same thing in bacteria.

Indeed, Shapiro's own discussion of viruses as sources of variation for other life does not examine the sources of variation in viruses - uncorrected random mutation.

The telic language, anti-"Darwinism", and "gee, its complicated" attitude are all ID friendly, but in the end Shapiro has a clear vision of who the Intelligent Designer is, and it is the cell itself.

Relation to the GA software paradigm

Much of conventional Genetic Algorithm software is explicitly point mutation based. Mutation and crossover are often the only operators used, and usually mutation is uniform along the genome. This is the strawman view of genetics that Shapiro criticizes most sharply.

I think the book can be read as a set of suggestions for improving our GA algorithm design if we want to achieve more than numerical optimization with GA. Here are some taking off points that I see:


  • exon/intron distinctions, and redundant representations
  • germ/soma distinctions
  • both of the above presuppose a more robust genotype/phenotype distinction
  • development of that phenotype aka evo-devo GAs
  • fitness testing at multiple points during a phenotype's lifetime
  • gene regulatory networks - genetic operators for regulation of the genome


In conclusion, a book well worth reading and thinking about, even with the annoyances and idiosyncrasies of the author.

Monday, October 1, 2012

Freestyles!

I wrote previously that my wife and I were attending the Arthur Murray "Freestyles" event that was held yesterday, so this post is report on that event.

Wow! It has a lot of fun, a whole day of dancing and socializing with our friends from the Arthur Murray dance studio in Montclair. At a Freestyles event, several Arthur Murray studios get together to give students a venue to perform for a judge, in order to receive impartial feedback. It is not a competitive event, and the emphasis for beginning students (like us) is on performing the syllabus figures for your level, either without additional choreography (closed) or with (open).

Yesterday's Freestyles was held at the Bridgewater Marriott, a centrally located venue for the Arthur Murray studios of Montclair, Kenilworth, Whitehouse Station, and Princeton. The event was well organized. The dancing was by 'heats' of several couples at once on the floor, all dancing the same dance, though each couple was dancing their own choice of steps. Each heat also had a variety of skill levels, and while there were no collisions it was clearly the responsibility of the better dancers and instructors to avoid the less skilled.

Blanka and I had chosen to dance four dances (Rumba, Cha-Cha, Foxtrot, and Tango) both together and with our instructors. As a result, we were each on the floor eight times, across twelve different heats. It was very nice that we were not in the same heat while dancing with our instructors, because we got to enjoy watching each other dance.

The actual dancing was wonderful, without much anxiety about forgetting steps, losing timing, or stepping on the dress of the lady next to me. We had practiced so much leading up to the event that it was almost second nature to dance the dances that we had chosen, and we did dance them 'freestyle', without repeating a set sequence.

As the day progressed, it was obvious that we had taken a very cautious approach to participating in the event. Many students danced multiple heats of the same dance, open and closed, for many more than four dances! There were 166 (!!) heats during the day, so we were sitting and cheering our friends on for most of the day. Next time, we'll know to push ourselves to dance more.

The day included lunch, dinner, a pro show by the instructors from each studio, and casual dancing after dinner. We were quite tired by the end of the evening, and I can't imagine where some of the instructors got their energy, dancing heat after heat with their students.

We had a great time.

Saturday, September 29, 2012

Getting the Most from your Arthur Murray Dance Package

My wife, Blanka, and I have been dancing at the Arthur Murray studio in Montclair, NJ for a little less than a year. It all began as a birthday present from her of a few private lessons, but it has grown into an important part of our life and growth within the Montclair community.

Put simply, the people and staff of the dance studio are wonderful. We have met so many people from different backgrounds that we otherwise would never have met. Our instructors, Gregory and Emma, are simply the best. They are fantastic at communicating quickly and clearly, and giving us maximum value in each 40 minute lesson.

If you are also interested in learning to dance through the Arthur Murray system, or you are in the process of comparing studios, here are a few of the things we have learned that will help you maximize your enjoyment, progress, and value of your purchase.
  • Buy a package of lessons if you can afford it. It helps lower the total cost and increases your commitment to continuing.
  • Stay an informed consumer, and manage your package to make sure you are learning the dances you want. Ask questions and give feedback. You're paying a lot of money to the studio, make sure you feel that you are getting your money's worth.
  • At the same time, I can't emphasize enough how helpful it has been for me to spend entire private lessons just on the basics of framing and leading that are fundamental to every dance. Creating a connection with another person on the dance floor is probably the best part of dancing! Don't cheat yourself out of it by making the mistake of focusing on memorizing steps. That will come at its own pace. The body awareness of your dance frame and the 'other' awareness of your lead (or follow) skills are the most important benefits of dancing - they will extend far into other parts of your life.
  • Take advantage of all the free training that Arthur Murray studios give you. Attend at least one group lesson and practice party a week.
  • Come early to your lesson and warm up. Practice time is also free! This is an important benefit that I don't see a lot of students taking advantage of. You'll get more out of your lesson time if you've warmed up and practiced a bit on your own beforehand.
  • Keep a dance journal. We were told that more serious students did this, and now that we do it also, we can see the benefits. It really helps to review what you've learned, and writing out the ideas by hand helps you remember them better. We haven't got to the point of videoing our steps, but it could happen!
  • Make friends and have fun. You are there to have fun, right? Moving to music is a pure, visceral joy. Everyone else is also there to have fun. Smile at all your dance partners in group lessons. Our studio is blessed with a diverse student body, and I think mutual encouragement is important to keeping everyone coming.


I hope your studio does not pressure you to participate in additional activities. These balls, festivals, showcases, or competitions are completely extra - do them if they make sense to you, at your comfort level. Don't respond to any high-pressure sales tactics, and if you experience such tactics from your instructor or the studio owner tell them directly that it is inappropriate when you've already committed to spending thousands of dollars with them. (I'm saying that I've experienced anything like this at our studio, but I have read some horror stories on the web...)

Tomorrow, Blanka and I dance in our first "Freestyles" and we are thrilled to do it, having passed up several earlier opportunities that were available to us. Now we are ready, and now we will have fun. We've geared up, bought some extra 'bling' for each of us and we're looking forward to showing off our skills and getting some constructive feedback on our progress. It is going to be a great, fun day! I hope you have a lot of fun days during your dance experience, and I hope these tips will help you.

Tuesday, June 19, 2012

Barhaminology: The Bioessentialist Manifesto

Over at his TheBestSchools.org blog, James Barham continues to entertain us with armchair philosophy. In this episode, his view of what biology is really all about.

Barham sets up two views, the Darwinian view, and the bioessentialist view. Guess which one he prefers?


The Darwinian View of Life
  • There is no deep difference between living and nonliving matter; therefore, it is idle to seek “essential” properties or a “definition” of life.
  • In any case, the most fundamental fact about a living thing is its ability to undergo natural selection.
The Bioessentialist View of Life
  • There is a fundamental difference in kind between living and nonliving systems; the main task of biology is to understand the distinctive nature of living matter.
  • The most fundamental fact about a living thing is its ability, by doing work selectively, to maintain itself in existence as the kind of physical system that it is.

Dismiss in passing Barham's purposeful confusion of Darwinism and materialism. Let's go to the videotape! Anyone remember the search for elan vital? It doesn't exist. Living things are made of the same atoms as non-living things. Use the same chemical reactions. Watch the same TV shows. Mr Barham seems to have forgotten that.


Oh, sorry, I didn't notice that the Darwinian was looking at 'matter' and the bioessentialist was looking at 'systems'. For a philosopher, Barham has a tough time setting up his comparisons.


"The main task of biology" - James Barham, armchair philosopher and web technician, has pronounced. It must be so.


"by doing work selectively," - selectively? A bacteria only eats half the available sugar? A virus only makes half the copies of itself that it could? Sperm cells only swim as much as they want? Barham might work selectively but it hardly qualifies as a definition of life.


(My own definition of life, FWIW: Life is a collection of molecules working together to avoid equilibrium for as long as possible.)


The essay is quite long and continues to be silly in the same vein. Genes are contrasted with proteins because metabolism is more important than reproduction. WTF? Since when was living forever an option? Metabolism explains the fossil record, biodiversity, the peacock's feathers and the panda's thumb?


Barham and his dog Marty are not, apparently, made of quarks descended from the Big Bang. Perhaps they were specially created 6,000 years ago. Who knew? Marty ain't made from no quarks! Reductionism is defeated.
For example, they are all explained at a more fundamental level by the Pauli exclusion principle.
Except when it is convenient.

In the case of a true machine, the functional order has nothing whatever to do with the matter out of which the machine is composed. It is imposed upon the matter entirely from without—by us. The material parts out of which a machine is made are supremely indifferent to the purpose the whole is designed by us to serve. Moreover, the stability of a machine resides in the rigidity—not the flexibility, much less the inherent intelligence—of its parts.
In contrast to what happens inside a machine, everything that goes on within a living being possesses an inherent purpose—namely, maintaining the organism in existence. That is the essential difference between living and nonliving things.

So living things are NOT machines. Just don't tell Polanyi and all those folks that want to argue that living things ARE machines, because machines are designed.


Don't quit the web job, James. Armchair philosophy, it ain't for you.

Friday, June 8, 2012

Someone Teach Ann Gauger to Google

Over at the blog of the Biologic Institute (the Discovery Institute's science-y wing), Ann Gauger has been writing regularly about molecules. Her April 30th post, Intricate Coordination, looked at the enzyme carbamoyl phosphate synthetase (CPS). Wow! CPS is complicated! It has two parts, three active sites, and an intramolecular tunnel. And here is Ann's take-away message:

How does a neo-Darwinian process evolve an enzyme like this? Even if enzymes that carried out the various partial reactions could have evolved separately, the coordination and combining of those domains into one huge enzyme is a feat of engineering beyond anything we can do. 

Well, how do we explain this?

First, by understanding that CPS is not a singular 'thing'. Like any biomolecule of any size, it comes in a variety of shapes and sizes throughout the different species of life. In fact, CPS performs an important role in the cell, and is therefore found across Bacteria, Archaea, and Eukarya. We can use CPS to draw a phylogeny, a tree of life. So the first part of an answer to Ann is yes, CPS does evolve. Evolution is the simplest explanation of the many versions of CPS found throughout living species.

Second, we can see that Ann's question is really a sense-of-wonder question. Parts, sites, a tunnel, a  lab under an extinct volcano, sharks with lasers, it is all so amazing. Yes, it is, even if it doesn't have those last two items. But "substrate channeling", as the cool kids call it, isn't unique to CPS. Lots of enzymes do it. Sometimes they use a tunnel of hydrophobic residues, sometimes hydrophillic residues. Sometimes the 'tunnel' is more of a path of favorable charges across the surface of the enzyme, sometimes it is a floppy arm that carries substrates from one place to another as it flops around. Not only has it evolved, it has evolved multiple times for different substrates.

These different functional mechanisms help to keep reactants from floating off into the cytoplasm, thereby increasing the speed and efficiency of an enzyme. AA residues facing into the tunnel can effect the speed with which molecules diffuse down its length, keeping the different parts of the reaction in sync. These qualify as huge selective pressures, so the second part of an answer to Ann is that evolution created these enzymes using the standard preference for higher functioning processes. Natural selection, you've heard of it, right?

Thirdly, we can understand the question to be one of, 'from what functional predecessor did CPS evolve?" If we look at CPS across the various species, it comes in two parts with separate functions, so right there we can see that these parts could have evolved separately, from less specialized or efficient predecessors. The larger of the two subunits, the part with two active sites, seems to have undergone a gene duplication event very early in its history. This subunit seems to have developed from a carbamate-kinase ancestor.

Putting it together, an answer to Ann's question is "Yes, CPS does evolve, by normal functional selection, from clear ancestors via well understood variational events."

"... a feat of engineering beyond anything we can do"? Ummm, no. Looking at the phylogeny, pretty much any branch is a sequence of exaptations, duplications, fusions, mutations, wash, rinse, repeat. Yeah, we can do that. As a matter of fact, we do do that. We've been poking at CPS for a while, pulling the genes apart, putting them back together, mutating it. It is the basic path to understanding how CPS works.

Now I will make a confession. I am not a biochemist or an evolutionary molecular biologist. But I do know how to use Google. Starting from "evolution carbamoyl phosphate synthetase" and ending with "evolution substrate channeling" I learned a lot about CPS very quickly, mostly with the help of papers published in the 1990's. Google is your friend. PubMed is your friend. 

Friends don't let friends blog stupid. Don't follow the path of Cornelius Hunter, he of the "Stuff's Complicated, Must Be Jeeebus" blog tic. Think about it, Ann.

Friday, June 1, 2012

No trend in tornadoes

This is my first post dipping a toe into the churning waters of climate change/global warming.

I saw a pretty visualization over at WUWT of tornado storm tracks, and decided to follow up with looking at the data myself. It is all available from the NOAA Storm Prediction Center site. (I normally go to WUWT for the comedy. The few earnest skeptics are mixed in with a vast number of loons.)

To estimate the energy of a single tornado, I multiplied the track length * the track width * (F+2)^1.5. This gave me a number I felt it was safe to add up across all tornadoes in a year.

Looking at all tornadoes, or at just the severe F4+F5 subset, I did not see any trend in the data when charted in Excel. That is my rough, first pass observation. There certainly are more tornado observations as time passes, but seeing many more small tornadoes isn't changing the big picture much.

Why might that be? Well, one thing that I can think of is that, as spectacular as tornadoes are, they don't actually account for a lot of energy. Or the GW effect might be to shift where and when the occur, not the strength when they do. Actual strength might be limited by some other constraint of atmospheric physics.

As I said above, there are many more tornadoes reported now compared to decades ago. Many commentators put this down to better observational data, the growth of populations in tornado prevalent areas, etc. If there is a GW aspect to number of tornadoes, it will be difficult to untangle from these issues.

Thursday, May 31, 2012

TheBestSchools.org joins the Discovery Institute link farm

For a while, Uncommon Descent's resident flack (Denyse O'Leary) has linked in several blog entries from TheBestSchools.org's blog. TBS appears to be a web resource targeted at Christians choosing a college. The main site mixes articles on the 10 Best Nursing Programs with interviews with folks such as William Lane Craig. The blog, however, seems to be the sole province of James Barham.

Well, it used to be the sole province of James Barham. Now Denyse herself has begun posting there, and Barham's posts have begun cross-posting between TBS and the Discovery Institute's Evolution News and Views site.

I had hopes for TBS, since it seemed to allow comments and Barham seemed to be a nice fellow posting on intellectually interesting topics. Alas, after I registered and tried to post a comment it went from moderation to deletion without seeing the light of day. At this point, I would consider TBS (the blog at least) to be just another corner of the DI link farm.


Tuesday, May 29, 2012

When there is no good news for ID, quote an old book

It is a slow news day over at UncommonDescent. Actually, every day is a slow news day there, since there are no ID scientists doing ID research publishable in peer reviewed journals. So the UD news desk, Denyse O'Leary, dips into the pages of John Sanford's Genetic Entropy for an extended quote.

During the last century, there was a great deal of effort invested in trying to use mutation to generate useful variation. This was especially true in my own area – plant breeding. When it was discovered that certain forms of radiation and certain chemicals were powerful mutagenic agents, millions and million of plants were mutagenized and screened for possible improvements. Assuming the Primary Axiom (that the secies are merely the product of random mutations plus natural selection), it would seem obvious that this would result in rapid "evolution" of our crops. For several decades this was the main thrust of crop improvement research. Vast numbers of mutants were produced and screened, collectively representing many billions of mutation events. A huge number of small, sterile, sick, deformed, aberrant plants were produced. However, from all this effort, essentially no meaningful crop improvement resulted. The entire effort was a failure, and was eventually abandoned. – Genetic Entropy & the Mystery of the Genome , page 25

It is an interesting quote, and I'd like to address the ideas in it by referencing the development of high-yielding varieties of wheat and rice during the Green Revolution, work which took place during the same approximate time as Sanford refers to.

First, let us note that Sanford is going to trade upon the ambiguity in his phrase "random mutations plus natural selection". RM+NS, as it is often abbreviated in internet dialogs, can mean either any kind of genomic variation and any kind of selective pressure, or only the substitution of exactly one nucleotide for another in DNA and the survival of the fittest. When making a claim against "Darwinism" or "evolutionism" opponents imply the first, broad meaning. When asked to defend a claim, they retreat to the narrow meaning.

No modern scientist thinks nucleotide substitution alone built the genomes of every species alive, and those extinct. Reading the genomes of many species has shown how  groups of genes have been duplicated as groups, sometimes across species boundaries. Importantly for the case of useful plants, the entire genome of plants such as wheat and potatos has been duplicated more than once. Each cell of a wheat plant has six complete copies of its genome! These large scale restructurings are responsible for the rapid change in plant and animal evolution, compared to bacterial evolution.

Second, if we look at the Green Revolution - the rapid expansion of crop productivity around the world since World War II - we see that the main driver was new kinds of wheat and rice. These new cultivars grew shorter stems, which were mechanically stronger than previous wild-type long stems. The strength of the stem was important when the seed head grew bigger. Without a strong stem, the plant fell over (lodged).

The short stems are the result of point mutations in the genome. We've known this for a long time. We know that the mutations affect the growth signal processes, stunting growth compared to the wild-type plant. So Sanford is flat wrong to suggest that we have never found beneficial mutations in plants. He has a fig leaf to hide behind in that these mutations were found in naturally growing variants of wheat and rice. They were not induced by human radiation or chemical experiments.

Since we now know the size of the wheat genome, we could calculate the expected time until discovery of a beneficial mutation, using the techniques of radiation and chemical mutagenesis. I'm going to guess it would be on the order of millions of years, if each batch of seeds has to be grown and tested for increased function.

This is an essential contrast between the small bodied, asexual evolution of bacteria and the large bodied, sexual evolution of plants and animals. We do see rapid response to chemical stresses, such as anti-biotic resistance, in bacteria because the population being stressed is trillions of individuals. We can't test a population of trillions of plants or animals. Perhaps Sanford hasn't thought about the implications of that, or perhaps he has and would prefer to obfuscate them.

The idea that exposing pollen grains to radiation would advance the species is 'hopeful monster' thinking. That said, it worked! Dwarf wheat and rice have fed billions of people. Sanford's pessimism is misplaced.

Wednesday, May 23, 2012

Graceland

Blanka and I drove down to Memphis last week to spend some time with my Dad and his wife Doris. We had a great time. It was the first time I had been in Memphis since childhood.
We visited two places on our own, Graceland, and the National Civil Rights Museum.

Graceland, as most of the planet knows, is the home of the second best musician to graduate from Humes High School. (My father being number one, of course.) There was plenty of over the top Elvis worship on display, but it was enjoyable and a good introduction to the music and times Elvis shaped.

A different take on the same period was the NCRM. The museum preserves the facade of the Lorraine Motel, the site of Dr. Martin Luther King Jr.'s assassination. The museum exhibits wind back and forth, and rise by carefully placed ramps until suddenly you are there, looking out of the window of room 307, right next to Dr. King's 306.

The museum is a powerful testimony to the civil rights struggle. One of the best parts, in my view, was the short film, "The Witness". Narrated for the most part by Rev. Billy Kyles, who was standing just a few feet from Dr. King when he was killed, the film gives the context for the events that brought Dr. King to Memphis.

The film is extremely effective and emotional. I highly recommend it. I purchased a copy in the museum store, and it has been uploaded to vimeo (not sure of the legality of that, though).

Friday, May 4, 2012

Superconductivity and Intelligent Design

I was reading a recent article on the very cool topic of topological insulators when it reminded me of an interesting period of time.

Superconductivity, the phenomenon of complete absence of electrical resistance, was first observed by Heike Kamerlingh Onnes in 1911. The observation was readily repeatable, and Onnes won the 1913 Nobel Prize in Physics for its discovery. However, for nearly 50 years there was no theoretical explanation that really satisfied the physics community. But during the 1950s the BCS theory of Cooper pairs of electrons acting as phonons was developed that described a mechanism for superconductivity.

Never, to my knowledge, did the physics community assume intelligent design was the answer for why superconductivity existed. There was not naturalistic explanation for 50 years, yet they never lobbied for a supernatural explanation as the 'default' or inference to the 'best' explanation. I wonder why that is?

Going Green

We just purchased a beautiful floor lamp at the Zen Shop in Riverside Square Mall.


The vertical poles are dark stained bamboo, and the panels are real cocoa (chocolate tree) leaves. It looks fantastic either lit or unlit. Unlit, the panels are an emerald green, darker than the image. Thank you Michelle for stocking this!

Blanka wanted something to celebrate returning from her Soul Coaching seminar in California, and this was it!

Wednesday, April 25, 2012

Hairpin RNA

Another entry in the "is function arbitrary" series...

One of the most commonplace motifs in RNA molecules is the hairpin. The basic idea is this: the 'primary' structure of a strand of RNA is the sequence of bases, GCAU. But function doesn't depend on the primary sequence. That sequence has to be folded up into three dimensions - the 'tertiary' structure. In between primary and tertiary, we have the secondary structure, which captures most of the bonding between nucleotides in a flat, 2D picture.

An RNA hairpin's primary structure is like a palindrome, the beginning and end are mirrors of each other. For example:

GUGCCACGAUUCAACGUGGCAC

Looks like:
(Credit Wikipedia, article 'Stem-Loop')

It just isn't that hard for these things to form by chance. An example such as the above, with an 8 base pair stem, has a 1 in 64,000 chance of forming in a random chain. That might not sound like a lot to us humans, but to molecules where gazillions can be held in a drop of water, a lot hairpins can form! 1 in 64K is way way lower than William Dembski's Universal Probability Bound of 1 in 10^150, so even he would agree that no "Intelligent Designer" is necessary.

So if 1 in 64K of short (11 base pair) primary sequences forms a hairpin secondary structure, how many of those show stability and biological function as a tertiary (3D) structure? A good question. "Function" can be based on the choice of the base pair at the bottom of the stem, the stem pairs, and the top. But it is clear that even small, simple molecules such as these can have significant function, as shown by the existence of ribozymes (enzymes made of RNA) such as the Hairpin or Hammerhead ribozyme.

Further, really important molecules such as transfer RNA are simply 4 hairpins stuck together like Lego blocks. This structure can be broken down into the "top half", consisting of two of the hairpins, and the "bottom half", the other two. These halves could have evolved independently and then acquired new functionality when they stuck together.

A key message of ID and pure creationist propaganda is that the system of replication used in cells today is too complex to have arisen without guidance by a Creator. Looking at the reality of RNA hairpins, we can see that this is not true. A key piece of our current replication machinery is cobbled together from smaller parts that could easily have formed by chance, and then been retained for their function.

RNA vs. Jenga!

I recently spent some time talking about binding affinities in molecules such as DNA, RNA, and proteins. I said previously that there wasn't any differential binding affinity from one base pair to the next.

That turns out not to be the case. (aka FAIL) There _are_ base stacking interactions that can stabilize DNA and RNA molecules. These means that some sequences will be more likely than others in the real world.

The situation can be explained with an analogy to human language. This is good, because Polanyi worshipers love this analogy. In English, Q is followed by U consistently. That is a complete affinity. We can also talk about an affinity between two classes of letters, those representing consonant sounds and those representing vowel sounds. A string of letters is more likely if it contains alternations between these two classes.

Why is that? Well, in written English you'd be wrong to imagine that the choice of letter order was entirely arbitrary, it obviously isn't. (If it was, we wouldn't be able to compress English text very well, which is obviously not the case.) Written English derives from spoken English, and it is a lot easier to transition from one consonant to another through a vowel sound rather than directly. If you disagree, try the Czech phrase "StrĨ prst skrz krk" which translates roughly as "stick a finger in your throat".

From here, we can see that Polanyi's analogy was a FAIL to begin with, since the thing he wanted to analogize to, human language, does show constraints based on physical properties of the world and is not an arbitrary symbol system.

And Jenga!? Obviously, the choices you make in this block stacking game are not arbitrary, either. Every player knows that a stack built of "middle" bricks is going to be very unstable.

Friday, April 13, 2012

No error bars, no science

There is a meme circulating in the skeptics of global warming blogosphere - "no error bars, no science" which is meant as a criticism of papers they disagree with. A laudable concern in general, but what is good for the goose is good for the gander. 

Apply the same idea to ID, friends. What is the error bar on "Goddidit"? If ID would like to be considered a scientific topic, what error bars will Dembski, et al. attach to their work?

Tuesday, April 10, 2012

Moshe Averick Helps Meyer Hide the Afikoman of Understanding


Signature in the Cell, Stephen Meyer's gift that keeps on giving. Published in 2009, this book stirred up some controversy at the time over its review of Origin Of Life (OOL) theories and crowning of ID as the "best explanation".

Recently, the book was reviewed by British geneticist Richard Saunders on his blog, Wonderful Life. This review attracted the attention of the Discovery Institute and one of the DI's pilot fish, Moshe Averick. Averick wrote a scolding rejoinder to Saunders, earning him a pat on the head from David Klinghoffer over on Evolution News and Views.

(An aside. Averick deserves some respect, not for the validity of his opinions or his choice of culture war bedmates, but for having the guts to write in a forum that accepts comments. Most of the DI propaganda machine operates in the criticism free zone of their own web sites, no comments allowed. The same tip of the hat goes to Cornelius Hunter, the Baghdad Bob of anti-Darwinian creationists. Hunter's agit-prop is completely disengaged from the stated moral code of his religion, but he does allow comments to his blog!)

I'm not going to try to fisk Averick's piece, it doesn't deserve that much attention. I am going to focus on the issue of Meyer's discussion of differential binding affinities, since it was one of the points about Saunder's review that Averick jumped on.

Wow, "differential binding affinities"... I can hear your eyes glazing over already. Half my readership just left to check their Facebook pages, and there was only two of you in the first place!

Yes friend, "differential binding affinities" is actually one of those important places in Signature in the Cell where Meyer connects his philosophy to real world science, showing the roots of the Intelligent Design movement.

Stepping back for a moment, one of the big ID arguments is that everything has to be explained by one of three drivers, chance, necessity, or Design. If we can eliminate chance and necessity, we are forced to choose Design as the best explanation.

So what are differential binding affinities? We know that DNA uses a four letter alphabet, ACGT. In a real DNA molecule, A and T pair up, as do C and G. These pairs are on the inside of the famous double helix shape. They are the rungs of the twisting ladder. The outside of the helix, where each pair is connected to the next pair, is made of phosphate molecules.

If I told you that one 'rung' of the helix was A-T, could you predict the next rung? Not really. There are four possibilities (A-T, T-A, C-G, and G-C) and they are all equally probable. That is the opposite of a differential affinity. In a differential affinity, A-T might be followed 50% the time by T-A, and never by G-C.

Meyer connects this idea to two different strands of thought. One is the idea that either the proteins or DNA sequences of life exist by necessity - because there is no other way to make the pieces fit together. Meyer attributes this idea to Dean Kenyon as an early (1980s) OOL explanation. My research can't confirm whether this idea actually had any followers. 

I admit that I am a bit suspicious since Kenyon, now a creationist, works with Stephen Meyer at the Discovery Institute. Bringing in Kenyon's work gives Meyer a strawman to knock down and an opportunity to play the sympathy card for Kenyon, who faced some strong criticism for mixing in creationism in his evolution courses.

The other connection is with the philosophy of Michael Polanyi. Polanyi was a well respected chemist and philosopher of science, but apparently had a thing about evolution. He wrote an essay, "Life's Irreducible Structure", that is very influential to the ID movement. It is to this essay that Meyer links the binding affinities issue, since to him it affirms the position of Polanyi that information is not reducible to structure, the "physico-chemical" laws of the universe.

This is (finally!) the important point of this section of Meyer's book. It is important to Meyer, and that is why it gets the "revelation from on high" treatment that Saunders objects to in his review, mentioned above.

Sorry, your afikoman is in another castle!

Since Averick is not shy about his rabbinic degree, I'll use a timely Jewish analogy. During the Passover seder, the leader hides the afikoman, a piece of matzah that will be used to complete the rituals later in the evening. Meyer (not Jewish, BTW) is also hiding something, and Averick is only too happy to help him do it. What is that something?

Meyer's book is about the origin of the genetic code. That is the "signature in the cell". The genetic code maps triplets of RNA nucleotides (AGC, for example) to the 20 or so amino acids that are used to build proteins. But Meyer is hiding something about nucleotide triplets and amino acids, and if you guessed "differential binding affinities" you win!

Here's the basic idea. Make some long repeating strands of RNA, such as ACTACTACT... . Now stir in different amino acids. In water, all the RNA and amino acid molecules will be in constant motion, bumping into each other in various ways. Sometimes they might stick briefly to each other before the water molecules push them apart. That length of time is their biding affinity and it is not the same for all combinations. Some combinations of triplet and amino acid are much more likely to stick together than others.

What does this mean? Say we had a little OOL scenario, warm pond, all the amino acids floating around and some short random RNA sequences as well. One of those RNAs is AUGGCC, for example. The AUG will prefer to stick to the amino acid Methionone, while the GCC will prefer to stick to Alanine. At some point, both a Methionone and an Alanine are sticking to this little RNA long enough for them to link together spontaneously. Now instead of two amino acids we have one small protein. 

The point here is that the differential stickiness of RNA and amino acids did not have to be "Designed". It is inherent in the physics and chemistry of the world. Polanyi was wrong. The genetic code was not "Designed", it flows naturally from these differential binding affinities.

What I've sketched out in the preceding paragraphs is called the "stereochemical hypothesis", and is an active research topic for OOL scientists such as Michael Yarus. (It is active because more evidence keeps accumulating that it is correct.) Meyer claims to be giving a thorough survey of all OOL work in his book, as a matter of fact his argument _requires_ him to survey all possible options and find them inadequate before he can conclude that Design is the best explanation. But just like the seder leader hiding the afikoman, Meyer has hidden any discussion of the stereochemical hypothesis (and most of the rest of the modern research on the RNA World) from view in his book.

Averick, the cheerleader and pilot fish, is only too happy to help do the hiding. He doesn't know the stereochemical hypothesis from a hole in the wall, but if Meyer is going to pound on about no differential binding affinities in DNA, Averick is there pounding also.

Wednesday, March 14, 2012

The Hyperbolic Lens

My interest in photography has led me off into some research into lens design. Why are camera lenses so darn complicated?

There are lots of issues, but the one I'd like to focus on is the shape of the lens. The shape of two objects rubbed against each other gradually becomes a sphere and a spherical hollow to match it. Most lens grinding is based on this, and so the surfaces of lens elements in a composite lens design are either flat, convex, or concave parts of a sphere.

Unfortunately, a sphere is not the perfect shape to focus light. That shape is a hyperbola. This has been known since the 17th century, and several great thinkers have tried to come up with ways to  create hyperbolic surfaces on lenses.

A wonderful monograph on the subject is "Descartes And The Hyperbolic Quest", by D. Graham Burnett. I've linked to a page showing the solution of Christopher Wren, the great architect. I really like this image!

Now some of you might be thinking that this solution is cheating. Sure, you can create a hyperbolic surface if you've already got one handy, in the form of the hyperboloid. All you've done is push off the problem one step. But creating the hyperboloid is easy, as one of the other illustrations shows. If you have two skew lines, and rotate one around the other, you trace out the surface of a hyperboloid.

Even today, manufacturing costs dictate that most lens elements are spherical. Hyperbolic lenses are used in specialty applications such as copying machines. Aspherical elements are incorporated into sophisticated lens designs for cameras, but they are not to my knowledge hyperbolic.

Tuesday, February 14, 2012

Talisman: the Game

When my son Daniel was 9 or 10, we played the board game Talisman with his friends. It was a lot of fun, and I was sad when I found out that it was no longer in print.

Well, I am sad no longer!

While browsing the ever enlarging Games section at Barnes and Noble, I noticed that Talisman is back on the shelves in a handsome new edition. Yay! As with the version we played, there are several add-ons for it as well. I didn't see Talisman Dungeon on the shelf, but it is available through Amazon.

According to reviews on Amazon, the rules have been tweaked slightly from the classic 2nd edition. For example, the mighty Prophetess no longer dominates the game as a character. Looks like a new generation is going to get hooked by this game.

Sunday, January 15, 2012

Review: First Life, by David Deamer

Just finished David Deamer's First Life.

The main point of the book is to expound on Deamer's theory that lipid based vesicles were important to the Origin Of Life (OOL). Lipids are the oils and fatty acids we use today as cell walls in our bodies. They are 'polar' molecules, with a different charge at each end of the chain of atoms. This makes one end attracted to water and the other end repelled by water (hydrophobic). When dispersed in water, the hydrophobic ends wind up crowded together, while the hydrophillic ends stick out, so the lipid molecules naturally form surfaces that are two molecules thick. Under the natural physical forces found in water, the most stable shape for these layers is a sphere -a vesicle or bubble.

A key property of these vesicles is that small molecules can work through the layer separating the inside from the environment, but a large molecule inside can't get out. Therefore, a chemical reaction that built up large molecules from small ones inside the vesicle would build up a concentration of large molecules far faster than the same reaction happening in the open, where the reaction products would get mixed and diluted quickly. It just so happens that life is full of these kind of reactions.

Having read a lot of pop sci literature (Zimmer, Ridley, etc.) it shows that Deamer is a working scientist, not a professional writer. At times the book felt padded by reviews of everything from the Big Bang onward, and an explanation of what name comes first in an article reference. And there was a fair bit of chemistry porn, in which the author gives a bit too much detail on lab procedures.

Deamer's take home message is that OOL requires some minimum complexity, and most scientists are not willing to attempt the messy experiments necessary. In a football analogy, grant funded science is a "three yards and down" ground game, and OOL needs some Hail Mary passing. 

His last chapter describes his ideal update of the famous Miller-Urey experiment, which showed that a combination of small molecules and energy could lead to biologically important molecules such as amino acids. It's big, throws a lot into the mix, and would cost a couple million dollars to run. At the same time, he acknowledges that it would have to run over and over, with multiple changes in atmosphere, temperature, pressure, etc. which would increase the cost. But at the same same time, he mentions that robotic experimentation runs hundreds of experiments at the same time. However, the two ideas never connect - that you have to reduce OOL experiments to something that can be done on a microfluidics chip in large batches.

Recommended.