Musings on Biofuels

A spatially explicit whole-system model of the lignocellulosic bioethanol supply chain: an assessment of decentralised processing potential which is authored by Alex J Dunnett, Claire S Adjiman and Nilay Shah, was published in the journal Biotechnology for Biofuels. It details factors needing to be considered when evaluating both the environmental impact and the economic feasibility of biofuel solutions. The paper notes that the current market for biofuels can be described as the application of fermentation processes to sugar and starch crops. The efficiency of these processes with respect to environmental concerns involves assessing the energy input needed to produce biofuel output, including a measure of CO2 emissions inherent to the processing of crops and production of biofuels. In addition, consideration needs to given to the diversion of land and food resources to generate ethanol.

The authors note that the next generation of pretreatment and fermentation technologies could relieve resource constraints by utilizing lignocellulosic biomass. This would include what is currently considered waste and would provide a secondary benefit to biofuel production- the transformation of waste into productive output.

However promising the waste transformation and increased output efficiency appears, I believe this approach should supplement a resource supply adjustment which is currently unavailable in the United States because of legal and political factors. The specific resource would be hemp and the conversion of land resources to its production should yield financial and environmental benefits while lessening U.S. dependence on foreign sources of fossil fuels. Further articles will delve into the specific properties of hemp which make its useage likely to alleviate biofuel problems.

A Lioness with a Taste for Italian Cuisine

Lea, the spaghetti lioness is a Creation on the Web article. Lea is a lioness who was born and raised in Italy. When she was six weeks old she was taken and cared for by Antonio Vincenzo who lived in the Italian village of Nettuno. Lea acquired the nickname "Spaghetti Lioness" by virtue of her diet. She was fed potatoes, green vegetables and cheesy pasta and managed to thrive in spite of it. But before being dubbed "Spaghetti Lioness" Lea was called the "Spaghetti Kid" because her favorite food was spaghetti, which she preferred flavored with Neapolitan sauce.

When Antonio Vincenzo could no longer care for her Lea was taken to a zoo on the outskirts of Rome. Her concrete living quarters were not ideal and Vincenzo, after years of searching, eventually located a permanent home for Lea in South Africa. Her present home includes outdoor grassy enclosures and a diet of raw meat to which she has grown accustomed. Quoting the author of the article "Lea’s new caretakers at The Rhino & Lion Nature Reserve have advised us that she was weaned from spaghetti in one week and now has ‘absolutely no problem’ with fresh red meat, which is fed to her—she does not hunt." The author also made this point (quoting):

...the Bible tells us that felines were originally created vegetarian (Genesis 1:30) and it also speaks of a time when ‘the lion will eat straw like the ox’ (Isaiah 11:7, 65:25). So, from the Bible, vegetarian ‘carnivores’ make much more sense.

Accessing DNA and Kissing Ass

Scripps Research scientists shed light on how DNA is unwound so that its code can be read is a Biology News Net article. Discussed is a macromolecular machine, dubbed RSC, which is able to alter chromatin so as to allow enzyme access and resultant gene expression. Researchers from The Scripps Research Institute have discovered how this is done. They published their findings in the November 23, 2008 online issue of Nature Structural & Molecular Biology.

RSC is a very large protein complex consisting of thirteen different proteins. Its signature property is a capacity to hold individual nucleosomes in what the author describes as what looks like a vise grip. Nucleosomes are subunits of chromatin. Chromatin consists of a DNA coiled around a core of proteins known as histones. Chromatin plays an important role in regulating gene expression. Whether a gene, coding for a particular protein, is transcribed depends on the capacity of enzymes, involved in the transcription function, to access the gene. Chromatin can prevent access. RSC can reverse that condition. RSC activity requires an input of energy supplied by ATP.

The article concludes (quoting):

The structure RSC interacting with a nucleosome explains how previously observed DNA bulges formed by chromatin remodeling complexes are formed, and why a single intact nucleosome appears to be left on a fully activated gene before other cellular machinery scoop up the histones and repack the DNA until it needs to be read again.

"Every time your cell expresses a gene, it goes through this remarkable unpacking and repacking," he says. "We are happy to have provided some clarity to the process."

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PS: One of my uncles sent me this poem:

No Hard Feelings...to the democrats
The election day is over,
The talking is done.
My party lost, your party won.
So let us be friends,
Let arguments pass.
I'll hug my elephant,
You kiss your ass.

Evolutionary Constraints

Development Puts An End To Evolution Of Endless Forms is the title of the linked blog entry at Design Watch. The first paragraph:

The notion that evolution is completely random, that there is no plan or constraint harmonizes well with the atheistic world view. The fact however is that the commonality of convergent evolution suggests that evolution is a highly constrained process.

We don't hear enough about evolutionary constraints. Mainstreamers often give the impression that evolution is capable of producing any outcome. Yet constraints tend to multiply with the degree of complexity found in a given system. Single mutation routes to genetic change are well documented. Multiple mutations are inferred. It's not only a matter of time frames. It's the engineering problem posed by purposeless changes; selection being a passive sifter. Constraints is a theme IDists need to devote more attention to.

More on Materialism and Consciousness

Denyse O'Leary posted A philosopher confronts the errors of debunkers at Mindful Hack. Denyse cites philosopher Neal Grossman's take on committed materialists who he refers to as fundamentalists. Grossman notes the position that an afterlife is such an extraordinary claim that almost any other explanation is preferable. However, he points out this view is not shared by most people for whom an afterlife is entirely credible.

The last paragraph's promissory note-like approach to consciousness reminds me of similar approaches to origin of life issues. The materialist approach to the afterlife conjures up another well worn phrase usually flung by materialists namely, the argument from personal incredulity. If personal incredulity is a factor how can materialists objectively assess the case for mind/brain duality?

Beckwith and Design

I'm re-posting a blog entry posted at Telic Thoughts because I believe it gets to the heart of not only the source of disagreements but the reason for the vitrioloc nature of the exchanges. The post:

Frank Beckwith wrote The truth about me and Intelligent Design which has been panned by some IDists. Beckwith wrote this:

Despite my interest in this subject and my sympathy for the ID movement’s goal to dismantle materialism and its deleterious implications on our understanding of what is real and what counts as knowledge, I am not, and have never been, a proponent of ID. My reasons have to do with my philosophical opposition to the ID movement’s acquiescence to the modern idea that an Enlightenment view of science is the paradigm of knowledge.

Beckwith identifies what may be the most underrated idea motivating both supporters and opponents of ID. Perhaps the most frequent charge leveled against ID is that it is not a scientific theory. That tends to confirm Beckwith's allegation that ID critics view science as the determinant of authentic knowledge in accordance with a worldview deemed modern even as its roots go back centuries. It is not that IDists and their critics disagree about the utility of science or even the validity of the data itself in most cases. The bone of contention centers around the belief that truth is pegged to empirical results. Yet if both sides value science for its practical utility why are there disputes? Disputes center around issues that a scientific approach is ill-equipped to resolve. Whether the issue is mind/brain duality, the origin of life or the anthropic principle, empirical testing is unlikely to render definitive answers fully supporting either IDists or their critics. Critics can complain about God in the gaps but the truth is that an inability to produce conclusive scientific data is attributable to limitations inherent to scientific methodology rather than IDists exploiting a temporary absence of scientific knowledge.

Why would one complain about God in the gaps? Complainers tout themselves as defenders of science, as if a belief in divine causality jeopardizes good science. It doesn't of course. One can correctly identify a scientific law with the cause of a physical event and still attribute a divine hand to the process. Theistic beliefs are not negated by scientific knowledge. Science is ill-equipped to even define valid knowledge or resolve epistemological questions.

Beckwith has a point in that some IDists unintentionally validate the philosophical underpinnings of critics when they engage critics on their own terms. The antithesis of ID is not science. Its antithesis lies in the belief that it is more rational to believe that the physical world supports an ateleological perspective. Scientific data, as opposed to the scientism embraced by many critics, does not support ID's antithesis.

Unicellular Predatory Tactics

Predatory bacterial swarm uses rippling motion to reach prey is a Biology Blog entry focused on a bacterium known as Myxococcus xanthus (M. xanthus); a fearsome predator among the world of unicellular organisms. A specific function is discussed namely, an ability of many M. xanthus to act in concert in generating parallel waves which move in the direction of bacteria they prey on. A paper discussing this phenomeon was published in the October 24th edition of PNAS.

Chemotaxis is an ability to control movement in response to an environmental stimulus. Amusingly the research team described M. xanthus behavior in response to prey as predataxis.

Amino Acids

In the coming weeks this blog will feature a series of entries about amino acids. More specifically the focus will be on non-canonical amino acids with a view toward a truer understanding of the so called chemical affinity concept. Chemical affinity advocates contend that tRNA, essential to the genetic code translation function, paired with amino acid cognates during the formation of the code itself because of a chemical affinity between amino acids and corresponding codons. This in turn is offered as an explanation for how a coding system became fixated during the origin of life. I believe the explanation is fundamentally flawed. Coming blog entries are intended to show why.

An Ancient Hebrew Inscription

Oldest Hebrew Text Uncovered By Israeli Archaeologists is the title of an article appearing at Red Orbit. The article cites the discovery of a piece of pottery said to be 3,000 years old which contains an inscription in Hebrew. There is much significance to the find because it is very good evidence that the ancient Israelites were literate. This in turn makes it plausible to assume that Biblical accounts could have been recorded in writing as well as preserved through an oral tradition. Written recordings made soon after the occurences of described events would be evidence against the contention that events were mythological.

Tilting Toward Socialism

Obama Stands for Socialism is the title of a David Limbaugh article. Obama supporters take offense at the very linkage of him to socialism but are there grounds for the charge? Obama has made no secret of his income redistribution plans. Income redistribution invokes thoughts of socialism because that goal is known to be a prominent policy of socialist governments. Obama supporters claim this is merely about tax reform i.e. making taxes more progressive. Tax reform is nothing new. Progressive tax advocates have been around for a long time. What's new is the call by a presidential candidate for income redistribution. It's a phrase most commonly uttered by leftists in other nations.

In the USA the poor pay little taxes. Generally no state or federal income taxes. They do pay state sales taxes. The top two percent of income earners in America pay a huge share of federal income taxes collected. Middle income people pay much less and the poor virtually nothing. If you don't pay taxes then do you merit a tax rebate? If Obama thinks so he is departing from precedent and earning the socialist label. Shifting tax burdens have previously been described as restoring fairness etc. Obama invites the socialist label when he insists on framing the issue as income redistribution. Tax policies are a poor vehicle for income redistribution. Sound enhancement of one's earning capabilities is needed. That involves much more than a transfer of tax money. So describing tax reform as income redistribution is either an exagerration or merely part of a real income redistribution program about which Obama will be more forthcoming after he is elected. There is no point in discouraging voters with details.

One more thing needs to be mentioned. The recent bailout resulted in the U.S. government buying shares of financial institutions. That is quintessential socialism. Is it any wonder that Americans would be wary of creeping socialism, knowing that a Democratic president, allied with a congress controlled Democrats, could pursue further direct control of business enterprises? There are reasons for wariness that have nothing to do with hate and everything to do with reading the tea leaves properly.