Tangled Bank #117

 
The latest issue of Tangled Bank has been published on Pro-Science [Tangled Bank #117].

Welcome everybody to the 117th edition of the blogosphere’s premiere science and medicine blogcarnival, Tangled Bank. Tangled Bank started out as a sort of Carnival of the Vanities for science bloggers taking it’s name from Charles Darwin’s famous metaphor:

It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the conditions of life and from use and disuse: a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms.

It’s fitting that this edition should itself present such a tangled bank of blog posts intertwining many different fields of science and medicine. Unfortunately, that means it becomes almost impossible to find a common theme or even group together the posts in any meaningful way. So I’m going to take the easy way out and simply list them in no particular order, although we’ll try to group related posts together.

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Send an email message to host@tangledbank.net if you want to submit an article to Tangled Bank. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger.

The Best Invention of 2008

 
According to Time magazine it's "The DNA Retail Test." Especially the one marketed by 23andMe.

We are at the beginning of a personal-genomics revolution that will transform not only how we take care of ourselves but also what we mean by personal information. In the past, only élite researchers had access to their genetic fingerprints, but now personal genotyping is available to anyone who orders the service online and mails in a spit sample. Not everything about how this information will be used is clear yet — 23andMe has stirred up debate about issues ranging from how meaningful the results are to how to prevent genetic discrimination — but the curtain has been pulled back, and it can never be closed again. And so for pioneering retail genomics, 23andMe's DNA-testing service is Time's 2008 Invention of the Year.

1. It's not an invention. The technology has been in place for years. It depends on the work done by hundreds of labs who are investigating the human genome. They deposit their results in public databases.


2. The profit making company is emphasizing genealogy as much as health. For $1000 (now $399) you can find out how your haplotyes compare to others. This is the best invention of 2008?


3. There are serious ethical concerns about genetic testing that have not been resolved.


4. Other companies are selling tests that are just as good and The Genographic Project from National Geographic deserves just as much, if not more, credit than any private company.


5. Many of the people who buy these products are scientifically literate, and responsible, adults. But there's plenty of opportunity to exploit others who might not understand what the test means.

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What the Heck Is This?

 
You must go to Botany Photo of the Day to find out. Be thankful that we can't reproduce smells on our blogs.

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32 Nearby Stars

 
Check out this interactive star map of the 32 nearest stars [32 Nearby Stars].

Imagine that humans could establish colonies on several of these stars in the next 10,000 years. This means that we would have reached out 10 light years in that time. Continuing at that pace, in one million years we would have colonies that are 1000 light years away. In one hundred million years we will have covered more than half the galaxy.

If there are other civilizations like ours, they would have to be less than one hundred million years older than us or they would likely be here by now. Maybe we are alone in the galaxy/universe?

UPDATE: I've been reminded that this argument against the high probability of life is known as the Fermi Paradox.

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[Hat Tip: Bad Astronomy]

On Assuming that God Obeys the Laws of Physics and Chemstry

 
John Pieret admires a recent posting by Steven Novella on NeuroLogica Blog where he (Novella) writes about More on Methodological Naturalism.

This methodoligical approach also deals with the problem of whether or not science can deal with God. The answer is - yes and no. If a supernatural (meaning inaccessible to science) power were meddling with our universe (with stuff science could access), science could detect it, document it, and even describe it. We could say that something was happening.

However (by the premises of this hypothetical situation) if the ultimate cause of these physical effects were beyond scientific methodology, the best science could do would be to describe anomalies. Science comes across anomalies all the time, and the typical approach is to assume (because we really have no choice) that the anomalies are due to either errors in observation, errors in our current theories, or incompleteness in our current theories, meaning there is some new phenomenon to discover.

So far the scientific approach (assuming anomalies will lead to a deeper understanding of reality) has worked out pretty well. This is the best evidence we have that our universe if mostly rational and does not include “supernatural” (by my definition) forces that will remain forever “mysterious.” If it did, then we would run across anomalies that we could never explain scientifically. All we could do would be to describe them, but we could never come up with a testable theory of mechanism.

I pretty much agree with what Steven Novella says here, although I note that he gets a bit fuzzy in other parts of the same posting. The basic point is that scientists are capable of detecting things that are not explainable by naturalistic explanations. In other words, if something isn't obeying the laws of physics and chemistry,¹ then we''ll know about it, even if we have to put it down as an unexplained anomaly.

The fact that there aren't any known mysteries that fall into this category means that there is no evidence for a God that acts in a supernatural manner. This is not the God of Francis Collins. Collins is a scientist who presents "evidence" that God exists.

The fact that most other scientists do not find such evidence is not proof that all types of God don't exist. It merely defines limits to the types of God that are possible if you use scientific reasoning.

John Pieret seems to knows this since in his posting Natural Method he asks:

I would quibble that divine action would not necessarily produce anomalies. For example, how could we tell the difference between a random mutation and a miraculous one?

Claiming that we can see no pattern in mutations, or the evolution it powers, does no good because that requires that you make an assertion about what God wants to do and how he, she or it would go about it -- and how could you know that?

John is doing exactly what he says is wrong. In light of the fact that several testable hypotheses about God have been refuted, John then speculates about what God might be doing to get around the conflict between science and religion. He imagines that God could, if he so wished, disguise his actions so that they were indistinguishable from actions that were entirely natural.

None of us can refute that possibility but I note that the goalposts have moved just about as far as they can go. We're left with a God who is so careful to avoid revealing himself that he might as well not exist. What's the point?

Why in the world did anyone start believing in such a God in the first place?²

If we weren't talking about religion, this kind of "logic" would be quickly dismissed. Imagine, for example, that someone claimed the stock market was being manipulated by clever gremlins. Pointing out that there was no evidence of such manipulation provokes the response, "These are very clever gremlins who go to extraordinary lengths to disguise their manipulations. That's why we can't detect them."

Since we can't disprove the existence of such gremlins, is that a reason to believe in them? Should we treat the gremlin-believers in the same way that we treat everyone else or are we right to be a little concerned about their psychological well-being? Is it okay to tentatively conclude that they are deluded?

Why does belief in God always get special privileges that we never grant to any other superstitions?

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1. It's a metaphor, John, not the be taken literally.

2. The answer, of course, is that nobody ever believed in such a God. This sort of God is merely the last refuge of those who used to believe in a personal, interventionist God but now find that they can't defend such a belief in a modern skeptical society. It's also the fallback position for those strange people who call themselves true agnostics. They have almost as much at stake in trying to show that we can't "prove" the nonexistence of God. They desperately want to avoid being a non-believer (atheist).

Citing Blogs

 
Some of my students have been asking how to cite blogs and other internet sources. I found a set of instructions on the NCBI website and I thought Id share them with you [26. Electronic Mail and Discussion Forums].

According to those instructions, you should cite Pharyngula like this:

Myers PZ (University of Minnesota, Morris, MN). Pharyngula [blog on the Internet]. New York: ScienceBlogs LLC. [2006 Jan] - [cited 2007 May 16]. Available from: http://scienceblogs.com/pharyngula/.

I'm not sure I agree with everything that's there. For example, I don't think it's useful to have the date when the blog started (2006, Jan). I don't think we need the affiliation of the author, or where the blog is published—unless it's part of a collective. I think it's important to cite a specific posting if that's what you're referring to.

Here's how I would cite today's posting on worshiping golden cows.

Myers, P.Z. (2008) Pharyngula [Internet blog] - "Where's Charlton Heston when you need him?" (Oct. 29, 2008) [cited Oct. 30, 2008]. ScienceBlogs LLC, New York. Available from: http://scienceblogs.com/pharyngula/2008/10/wheres_charlton_heston_when_yo.php

Here are some examples of how to cite comments on blogs [Examples of Citations to Blogs]. In the first example the author is unknown. In the second example the comment author is identified by affiliation.

Teresa. Comment on: "Flo's pledge: deal or no deal?" 2007 May 12 [cited 2007 May 16]. In: Kim. Emergiblog: The Life & Times of an ER Nurse [Internet]. San Francisco: Emergiblog. c2005-2007 - . [about 1 screen]. Available from: http://www.emergiblog.com/2007/05/flos-pledge-deal-or-no-deal.html scroll down to comments.

Lanard J (Western Pacific Regional Office of the World Health Organization, Manila, Philippines). Comment on: "This blog can save your life!" and "Health Communication: Science and Art." 2006 Oct 15 [cited 2007 May 17]. In: Bernhardt JM. Director's Blog [Internet]. Atlanta: Centers for Disease Control and Prevention (US), National Center for Health Marketing. [2006 Jul 13] - . [about 2 screens]. Available from: http://www.cdc.gov/healthmarketing/blog_101106.htm scroll down to locate comment.

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The Meat-Robots Are Stirring

 
The mind-body problem is one of the more serious problems in philosophy. At the risk of over-simplifying, the two main camps can be described as dualism and monism. A dualist thinks that there's more to the mind than just neurons—the word that comes up most often is consciousness. The monist rejects the idea that there is some vitalist component to the mind. It can all be explained by the structure of the brain and the laws of physics and chemistry.

Monists are materialists, for the most part. Dualists often believe in supernatural beings.

Michael Egnor writes articles on Intelligent Design Creationism for the Evolution News & Views website at the Discovery Institute. He thinks the materialists have been winning but it's time for the zombies meat-robots to strike back.

As a general anti-science strategy, it's easy to see why the mind-body problem is resurfacing. The IDiots have lost the battle over evolution so they have to look around for something else to attack. We (scientists) don't understand exactly how the mind works. That's a perfect gap to shove God into, for now.

The materialist project to explain the mind reads less like a compendium of scientific and philosophical investigation than like a psychiatrist’s case log. Succinctly, the materialist project is batsh*t. The mind is a catastrophe for materialism. Materialism doesn’t explain the mind, and it probably can’t explain the mind. Materialism flounders on the hard problem of consciousness — the problem of understanding how it is that we are subjects and not just objects. Now a number of scientists and other academics are challenging this repellent materialist nonsense. There’s no scientific or even logical justification for the inference that the mind is merely the brain, without remainder, and the philosophical and sociological implications of the materialist view of the mind are abhorrent. Now there’s a reality-based push-back to materialist superstition, and the materialists have an insurrection on their hands.

The meat-robots are stirring.

I wonder if the meat-robots have something substantial to contribute to the discussion or whether they'll just be complaining about science, as they always do?

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Voting Machines

 
We just had a Federal Election in Canada. We used paper ballots and the results were in by midnight. I had only one choice to make.

This isn't possible in the USA because American vote for many different candidates when they have an election. The ballots can be very complicated but you can always vote "straight Republican" or "straight Democrat" to simplify the process. Here's how voting machines work .... or not.

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[Hat Tip: Mike the Mad Biologist]

Nobel Laureate: Albrecht Kossel

 

The Nobel Prize in Physiology or Medicine 1910.

"in recognition of the contributions to our knowledge of cell chemistry made through his work on proteins, including the nucleic substances"

Albrecht Kossel (1853 - 1927) won the Noble Prize for his studies on proteins, especially those proteins that bind to nucleic acids. He was the first to characterize protamines and histones.

The significance of Kossel's work was not fully appreciated because at the time proteins were thought to be the information carrying molecules and nucleic acids were merely structural components of the nucleus. One gets the impression that the simplicity of the protamines, and to a lesser extent, the histones, was a disappointment.

The flavor of thinking in 1910 is captured by the presentation speech on the Nobel rize website.

THEME:
Nobel Laureates

There are several kinds of proteins. One group which is included here are the so-called protamines obtained from the milt of fish. Kossel has made a detailed study of these. For these a relatively simple structure has been discovered inasmuch as the number of dissimilar atom groups in them is not very great. They therefore present simpler relationships than proteins in general, and consist mainly of substances belonging to the group which I have just called basic breakdown products of protein. For certain protamines Kossel, thanks to his methods of determination, has in fact been able to establish the quantitative relationships of the building blocks making up these protamines, a goal which we seem to be far from attaining where the other proteins are concerned.

Work on these most simple protein bodies, i.e. the protamines, is however not only of great importance because it has explained the structure of such protein bodies. The protamines are also of direct interest for the knowledge of certain cells and their life, because they are in fact characteristic of certain transformation products of the cells and are formed from ordinary protein.

One protein group, first observed by Kossel, consists of the so-called histones. They stand between the protamines and what is termed ordinary protein. This group, again, is important because of its occurrence as a component of certain cells, and has also been studied in detail by Kossel.

Professor Kossel has made an extensive and important study of the problem of the protein compounds in cells. As we have already mentioned, the proteins are very complex bodies. Within the cells the relationships are further complicated by the fact that the proteins there are combined in varying degrees with other substances such as those grouped under the name of «nucleic acids.

It is clear from Kossel's Nobel Lecture that he recognized the importance of chromatin in heredity but was unclear about which component corresponded to genes.

If we now summarize the results of the investigations of loosely bound nuclein substances, the result is a follows: A composition of the chromatin substance of the cell nucleus from two components, the one rich in bound phosphoric acid and having the qualities of an acid; the second showing a protein with the qualities of a base. In their chemical structure both components show a notable similarity based on the remarkable accumulation of nitrogen atoms and because of this chemical structure the chromatin formations can be sharply differentiated from the remaining cell components; and this quality must obviously be associated with the function of the chromatin substances. These atom groups rich in nitrogen and containing phosphorus are those whose deposits in the chromosomes are first set in motion during cell division and whose transmission to other cells forms an essential part of the reproductive process.

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Translation at CSH

 
My co-author, Marc Perry, is at the Cold Spring Harbor Laboratories on Long Island (NY, USA). He sent me this photograph. I think it may be a Henry Moore.

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This Book Don't Need Reviews

 
Book Description (from Dembski at Uncommon Descent):

Although atheism might have been logically tenable before Darwin, writes Richard Dawkins, Darwin made it possible to be an intellectually fulfilled atheist. This little book shows that atheism must seek intellectual fulfillment elsewhere decisively demonstrating the need for intelligence in explaining life’s origin. This is the best overview of why traditional origin-of-life research has crashed and burned and why intelligent design is necessary to explain the high-tech engineering inside the cell.

Author William A. Dembski worked closely as an advisor with the producers of the Spring 2008 documentary Expelled: No Intelligence Allowed starring Ben Stein. How to Be an Intellectually Fulfilled Atheist (Or Not) is the intellectual argument that helped inform significant elements of the movie. This controversial feature-length documentary film about researchers, professors, and academics who claim to have been marginalized, silenced, or threatened with academic expulsion because of their challenges to some or all parts of Darwin’s theory of evolution is one of the top twelve highest grossing documentary’s of all time. It has attracted both praise and controversy in its challenge against Darwinism.

If you liked the previous books by Jonathan Wells and William Dembski then you'll love this one. If you didn't, then you won't.

Did he really say "Ben Stein" and "intellectual argument" in the same sentence?

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Junk DNA Opponents Are at It Again

 
Nils Reinton has just posted a provocative piece on Sciphu entitled Hammering nails in the “junk-DNA” coffin. Here's what he says,

Below you will find a list of references that I hope will contribute to the fall of the term “junk-DNA“, - some of it may (currently) lack a known function, but it is not junk !!!

Disclaimer: This is a list of useful references when arguing against the common overestimation of the amount of “junk”-DNA. By listing these I am not claiming anything beyond what I have already posted on this blog or in a comment somewhere. Also and importantly, I have not myself had the time to review these articles as thoroughly as I would have wanted to, - some have been read carefully, others lightly and yet others just skimmed through. Thus, you are more than welcome to comment on these references if you have opinions on any of them, or find them unsuited for this list.

You are more than welcome to visit Sciphu and make comments. I can't be bothered.

The articles are just the same-old, same-old, litany of occasional discoveries of functional bits of DNA coupled with a fanatical belief in the biological significance of every single transcript that has ever been reported in the literature.

Oh yes, I almost forgot. Nils also throws in some papers about the number of binding sites for transcription factors. I guess he hasn't read any of my postings on the importance of non-specific binding [see Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm].

THEME

Genomes & Junk DNA

Total Junk so far

    54%
I think there's good reason to assume that up to 90% of our genomes consist of junk DNA where the word "junk" means that it does not have a biological function. I haven't been able to keep up my series of postings analyzing the human genome but so far there's very good reason to believe that more than half is junk.

I've never seen an anti-junkie address the genetic load argument. Has anyone else? I wonder how they think we can survive if a substantial amount of our DNA is essential?

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Schizophyllum commune Has 28,000 Distinct Sexes

 
This is the Botany Photo of the Day from The University of British Columbia Botanical Garden and Centre for Plant Research. The organism is the fungus Schizophyllum commune which is reported to have 28,000 sexes according to Tom Volk's Fungus of the Month for February 2000. Check out the Botany Photo of the Day blog for a much better picture.

In some parts of the world sex is legally restricted to arrangements involving single members of specified gender. I wonder which sexes of Schizophyllum commune would qualify? Personally, I think that members of sex 408 should be allowed to marry members of sex 12,105 but all other marriages are immoral and should be illegal.

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Definitions Matter: Negative Selection and Postive Selection

 
In recent issues of the Proceedings of the National Academy of Sciences (USA) we have an interesting example of misuse of a key term in evolution.

The paper in question is by Sun et al. (2008a) of the University of California, San Francisco. The title of the paper is important: "Experimental evidence for negative selection in the evolution of a Yersinia pestis pseudogene." Here's how they describe this negative selection in the abstract,

Yersinia pestis, the agent of bubonic plague, evolved from the enteric pathogen Yersinia pseudotuberculosis within the past 20,000 years. Because ancestor and descendant both exist, it is possible to infer steps in molecular evolution by direct experimental approaches. The Y. pestis life cycle includes establishment of a biofilm within its vector, the flea. Although Y. pseudotuberculosis makes biofilms in other environments, it fails to do so in the insect. We show that rcsA, a negative regulator of biofilms that is functional in Y. pseudotuberculosis, is a pseudogene in Y. pestis. Replacement of the pseudogene with the functional Y. pseudotuberculosis rcsA allele strongly represses biofilm formation and essentially abolishes flea biofilms. The conversion of rcsA to a pseudogene during Y. pestis evolution, therefore, was a case of negative selection rather than neutral genetic drift.

Hmmm ... something about this form of "negative selection" seems puzzling. Does anyone see what it is?

The article was published online on June 3, 2008 and appeared in the June 10, 2008 issue of PNAS. It was communicated by National Academy member Stanley Falkow of Stanford University.

In this week's issue (Oct. 21, 2008) we see a letter from Jianzhi Zhang of the Department of Ecology and Evolutionary Biology, University of Michigan (Zhang, 2008).

There are two types of natural selection in biological evolution: Positive (Darwinian) selection promotes the spread of beneficial alleles, and negative (or purifying) selection hinders the spread of deleterious alleles (1). Pseudogenization is normally detrimental and prevented by negative selection. However, changes in genetic background or environment may render a formerly useful gene worthless, leading to the relaxation of the negative selection. Consequently, mutations disrupting the gene are fixed by genetic drift, and the gene becomes a pseudogene. This is the common type of pseudogenization by neutral evolution. Sometimes, however, a previously useful gene may become harmful to an organism. In this case, mutations destroying the gene would be beneficial and would be fixed by positive selection. Thus, pseudogenization can be adaptive (2). Recently, Sun et al. (3) reported an excellent example of adaptive pseudogenization, convincingly demonstrating that gene loss can also serve as an “engine” of evolution (4). Nevertheless, instead of calling it “positive selection,” they mistakenly used “negative selection.” The case involves Yersinia pestis, the agent of bubonic plague that is frequently transmitted by fleas. The authors found that the rcsA gene of Y. pestis became a pseudogene in the last 20,000 years (3). Replacing the rcsA pseudogene with its functional version represses the formation of biofilms in fleas (3), which would reduce the transmission rate of the bacteria. That is, the pseudogenization of rcsA allowed the formation of Y. pestis biofilms, which enhances the transmission of the bacteria, and hence was likely driven by positive selection.

That looks like a pretty devastating criticism to me. I'm convinced that the title of the paper was inaccurate. They were publishing an example of positive selection and not negative selection as claimed.

The authors replied in the same issue (Sun et al., 2008b).

In our article (1) we used “negative selection” to succinctly convey that a previously functional allele became deleterious and therefore was removed by natural selection. However, Zhang (2) is correct that our usage was contrary to the usual meaning. Olson's term, “adaptive gene loss” (3), would have been more appropriate. We are gratified that Zhang agrees with our conclusion that the pseudogenization of rcsA was adaptive.

Translation: "We really screwed up."

How did this happen? Normally, before a paper is published the work is presented at meetings and in lab group meetings. Was there nobody who recognized that the authors were using the wrong term? Clearly the authors themselves (all three) never questioned what they were putting into the title. Clearly the person who communicated the article didn't either, and neither did any of the reviewers.

What's happening to science these days? Now, don't get me wrong. These sorts of things happened in the "olden days" as well but I'm convinced that the problem is much more serious today. There is too much stuff being published that should never have made it past the lab group, let alone past reviewers.

Here's a question for everyone who has read this far. What should be done with the original paper? The title is wrong. How do we alert people to the fact that the authors have agreed that they made an error?

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Sun, Y-C., Hinnebusch, J.B. and Darby, C. (2008a) Experimental evidence for negative selection in the evolution of a Yersinia pestis pseudogene. Proc. Natl. Acad. Sci. (USA) 105:8097-8101. [DOI: 10.1073/pnas.0803525105]

Sun, Y-C., Hinnebusch, J.B. and Darby, C. (2008b) Reply to Zhang: Adaptive gene loss in Yersinia pestis rcsA pseudogenization. Proc. Natl. Acad. Sci. (USA) 105:E70; published ahead of print October 15, 2008. [doi:10.1073/pnas.0807434105]

Zhang, J. (2008) Positive selection, not negative selection, in the pseudogenization of rcsA in Yersinia pestis. Proc. Natl. Acad. Sci. (USA) 105:E69; published ahead of print October 15, 2008 [doi:10.1073/pnas.0806419105]

Guns and Kids Don't Mix

 
From an Associated Press report: Boy, 8, shoots himself to death at Mass. gun show.

WESTFIELD, Mass. (AP) — With an instructor watching, an 8-year-old boy at a gun fair aimed an Uzi at a pumpkin and pulled the trigger as his dad reached for a camera.

It was his first time shooting a fully automatic machine gun, and the recoil of the weapon was too much for him. He lost control and fatally shooting himself in the head.

I'm mostly interested in the comment further down in the press release.

"This accident was truly a mystery to me," said Bizilj, director of emergency medicine at Johnson Memorial Hospital in Stafford, Conn. "This is a horrible event, a horrible travesty, and I really don't know why it happened."

Canadian Cynic says exactly what we all must be thinking.

Yeah, it's a puzzler, all right. A real stumper. Children and fully automatic weapons -- what could possibly go wrong?

This is why I love Canadian Cynic!

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