Friday, September 29, 2006

Genetic Invariance: A Prerequisite to Life

In a response to the post entitled 'DNA Damage and a Kinase Signaling Pathway' Mike commented:

It seems strange that all these mechanism are devoted to restricting the number and diversity of DNA damage, yet 'random' mutation plus natural selection work best I think when theres a wide range of mutations to select for -antibiotic resistance a case in point.

Mechanisms that detect and repair faulty DNA occasioned by environmental causes or copying errors provide data supporting a change related paradigm but it is not evidence favoring the need for selected mutations but rather data favoring the need for genomic invariance. Bacterial adaptation includes non-mutational strategies. Adaptation in turn means that 99+% of genetic sequences remain unchanged. While these are not novel observations they present research opportunities for IDers.

Based on the universal presence of repair mechanisms, their essential functions and the existence of genetic impairment factors in all eras of natural history, one can reasonably hypothesize that living organisms could neither exist nor evolve without such mechanisms. This has implications for origin of life and evolutionary theories that are favorable to an intelligent inference.

It also seems as if there really isn't anything random about mutations -as these as Mike Gene says can be seen as a form of homeostasis -where in some instances of stress the organism can purposely increase the number of mutations, in a bit for survival. Interesting stuff,

Indeed. Gene does a good job of pointing out that biological data is amenable to telic interpretations.


Tuesday, September 26, 2006

Genetic Controls

A post by Cornelius Hunter entitled 'Cellular Software' can be found at ID the Future. The italicized article follows.

At first the information revolution in molecular biology consisted mainly of static data. Increasing numbers of protein and DNA sequences were scanned, followed by whole genomes. Then came the ability to detect genetic activity. The cellular response could be analyzed by observing which genes are active and which are dormant in response, for instance, to a particular environment. These data are now revealing a fascinating network of coordinated cellular responses, as exemplified in recent findings of how cells repair damaged DNA. [1]

DNA damage is not uncommon and so the cell's DNA repair capability is important. A variety of repair mechanisms and machinery have been elucidated in recent decades, but research published earlier this year illustrates how these different mechanisms work together, in a coordinated fashion. In the experiments, researchers used methyl-methanesulfonate to damage DNA in yeast cells, causing minor structural aberrations.

In the painstaking experiments, the exposed cells rapidly identified the damage, ceased several normal functions as if going into a lock-down mode, removed the damaged DNA, and coordinated a battery of mechanisms to insert a fresh copy of the DNA segment. As one researcher put it, "it’s almost as if cells have something akin to a computer program that becomes activated by DNA damage, and that program enables the cells to respond very quickly." Indeed, what was discovered is an elaborate system of genetic control that is triggered by DNA damage.

A result of the research is that various pathways that had been known to be associated with DNA damage are now explained in a single circuit diagram. As is often the case, however, these valuable results are really just the tip of the iceberg. There are many more questions to be answered about the cell's operations manual. As one researcher reflected, "the point of this is to generate novel ideas that then lead to more hypothesis-driven experiments."

This is empirical science. The goal is to figure out how nature works (the cell in this case), and this is done by generating hypotheses about the cell's design.

1. C.T. Workman, et. al., "A Systems Approach to Mapping DNA Damage Response Pathways," Science, 312:1054-1059, 2006.

Could a cell function in the absence of "an elaborate system of genetic control that is triggered by DNA damage?" How would such as system evolve when genomic safeguards do not exist? If the genome of a putative precursor cell could not function without the genetic controls then how does a stochastic/selection process generate life?


DNA Damage and a Kinase Signaling Pathway

'A new effector pathway links ATM kinase with the DNA damage response' was published in Nature Cell Biology 6, 968 - 976 (2004). The article is focused on a signaling pathway. Identified kinases phosphorylate proteins in response to DNA damage.

A new pathway was reported. In this pathway ATM kinase targets Strap (a transcriptional cofactor) in signaling the DNA damage response. Like a row of falling dominos the kinase phosphorylation of Strap leads to the formation of a complex of proteins. There is also a regulatory effect resulting from Strap's enhancement of p53 acetylation. Strap's function, when phosphorylated, is to augment the DNA damage response. A conclusion drawn was that accumulation of Strap in the nucleus was a critical damage response regulator.

In a comment on a previous post Doug asked:

"How many separate processes and enzymes are utilized to safe-guard against the degradation of genomic information?"

The cited pathway reveals the effects of specific kinase enzymes in a signaling pathway of a DNA damage response.


Monday, September 25, 2006

DNA Polymerase Lambda

An article entitled 'Unusual Mechanism Keeps Repair Protein Accurate' appeared in Science Daily on July 28, 2006. It describes a protein known as DNA polymerase lambda. The italicized article follows along with my comments in bold print.

Cancer researchers have discovered that a recently identified protein critical for repairing damaged genes uses an unusual mechanism to keep its repairs accurate.

The protein, called DNA polymerase lambda, is one of a group of proteins known as DNA polymerases that are vital for accurately making and repairing DNA.

Here is another example of a cellular mechanism which maintains genomic integrity.

But while other DNA-repair proteins insure their accuracy with the help of so-called proof-reading regions or accessory molecules, this protein maintains its accuracy using an otherwise ordinary-looking portion of its molecular structure.

The study was led by Zucai Suo, assistant professor of biochemistry and a researcher with the Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute. The research, published in the July 14 issue of The Journal of Biological Chemistry, provides new insights into how cells repair damaged DNA.

“DNA is constantly attacked and damaged by a variety of agents,” Suo says. “The body must properly repair that damage, or it can lead to cell death or to cancer, birth defects and other diseases.

The consequences of unchecked damage can be clearly severe.

“There are six families of DNA polymerases,” Suo says, “and this is the first polymerase to use this mechanism to maintain its accuracy when making new DNA. It is both surprising and unprecedented.”

The repair protein itself was first discovered by scientists studying DNA sequence data produced by the Human Genome Project. Suo and his colleagues then became interested in learning how the repair protein worked.

The protein has four distinct regions, or domains. Three of the regions had molecular structures that strongly suggest the task they performed.

For example, regions three and four closely resemble a well-known repair protein called DNA polymerase beta. In fact, it was this similarity that tipped off scientists that the new protein was probably involved in DNA repair.

Region one also had a predicted structure that should allow it to “dock” with other proteins. “This suggests that this protein may do more than just fix DNA damage,” Suo says.

Region two held the surprise. It is called the proline-rich domain because it has high levels of the amino acid proline.

“There was no known function for a structure like the proline-rich domain, so we at first thought it did nothing more than connect the docking region of the protein with regions three and four,” Suo says.

“Then by accident we learned that this was not just a structural connection, but that it is critical to the protein's ability to replicate DNA with very few mistakes.”

For this study, Suo and his colleagues wanted to learn how efficiently the new protein made new DNA. But the researchers initially considered the protein too large and difficult to produce in the laboratory. So instead of making the entire protein, the researchers made only the part that does the repair work, regions three and four.

When they tested this short version of the protein, however, they found that it made up to a 100 times more mistakes than did the similar repair protein, DNA polymerase beta.

“That error rate is too high,” Suo says. “If the entire repair protein produced that many errors, it would cause more problems than it would fix.”

Next, the researchers made the entire protein and found that it could repair DNA as accurately as the comparison protein.

Last, they tested a version of the protein that lacked the docking region. This shortened molecule also accurately made DNA.

“To find that the proline-rich domain was responsible for this repair protein's high fidelity came as a complete surprise,” Suo says.

Presently the scientists are studying the three-dimensional structure of the entire protein to learn how the presence of a proline-rich region influences the ability of the protein to accurately make DNA.

Funding from the National Institutes of Health Chemistry and Biology Interface Program and from the American Heart Association Predoctoral Fellowship program supported this research.

Note that the fidelity of the repair protein, having the proline-rich domain, is described as high. This indicates the essential nature of the domain and raises the question of whether survival would be possible without it.

Saturday, September 23, 2006

DNA Repair and the Enzyme OGG1

A HUM-MOLGEN article 'DNA Repair Enzyme Caught In The Act' reveals another cellular mechanism that helps to maintain genomic integrity. The italicized article is interspersed with my comments.

In the 31 March 2005 issue of Nature (Vol. 434, No. 7033, pp 612-618), researchers report the chemical structure of an enzyme vital for repairing routine damage to our DNA that is caused by oxidative damage. Their snap-shot of the protein captures it in the act of testing DNA for errors.

When oxidants attack DNA they can subtly alter the molecular building block guanine (G), creating a variation called 8-oxoguanine that can cause permanent mutations. The enzyme 8-oxoguanine DNA glycosylase 1 (OGG1) recognizes and repairs 8-oxoguanine, and mutations in it have been linked to lung and possibly kidney cancer.

Note that the cause of the mutations is traced to effects of normal cellular activities. Normal cellular activities and environmental factors occasion the need for mechanisms that remedy damage to DNA and the effects of inevitable errors. Remedial functions are not optional. They are needed to maintain genomic function.

By determining the X-ray structure of human OGG1 bound to undamaged DNA, Gregory Verdine and his colleagues reveal how the enzyme efficiently scans for abnormal guanine residues embedded in a vast expanse of normal DNA, and how it removes them from the DNA helix without damaging normal bases.

The function specificity is clear but a precursor function of a homologous protein candidate is not.


Friday, September 15, 2006

The PCNA Protein and Mismatch Repair

Italicized portions of this news release from Duke University Medical Center- How DNA Repair Machinery is a 'Two-Way Street'- are posted below with my comments.

DURHAM, N.C. -- Biochemists at Duke University Medical Center have discovered key components that enable the cell's DNA repair machinery to adeptly launch its action in either direction along a DNA strand to strip out faulty DNA. Such flexibility exemplifies the power of the repair machinery, which guards cells against mutations by editing out errors that occur during the process of chromosome replication. Malfunction of the "mismatch repair" machinery is the cause of several types of cancer, including relatively common forms of colon cancer.

DNA repair functions are essential to the survival of living organisms. When they malfunction consequences are generally disastrous for the affected organism. Cancer is a mentioned effect.

Modrich and his colleagues have long studied the mismatch repair machinery of the cell. This machinery detects and corrects errors in DNA replication in which the wrong DNA unit is stitched into place in a newly forming DNA strand. Normally such units -- called nucleotides -- on one strand of the double-stranded DNA molecule bond with complementary nucleotides on the other strand, like complementary pieces of a puzzle. Thus, an adenine on one strand is normally paired with a thymine on the other, and a guanine on one strand with a cytosine on another.

The process of mismatch repair involves first recognizing the mismatch -- for example of an adenine with a cytosine. The machinery then recognizes a break in the newly synthesized DNA strand, which triggers the machinery to excise the section including the mismatch, starting at the strand break and working toward the mismatch and slightly beyond. The system then replaces the mismatched strand with one containing the correct complementary nucleotide.

A central mystery is how the mismatch repair system is flexible enough to recognize such a triggering strand break on either side of the mismatch along the DNA strand, said Modrich. In the Molecular Cell paper, he and his colleagues have defined the protein components of the machinery that allows such bidirectionality and figured out how those components assemble at the strand break to direct the excision.

Importantly, the researchers' biochemical experiments and analyses of mutations in the repair proteins revealed how the machinery for excising the faulty DNA strand "knows" which way to go from the strand break to the mismatch.

Basically, they found that a protein called PCNA is clamped onto the DNA at the strand break. PCNA, together with the protein that clamps PCNA onto the DNA double helix, regulate the enzyme whose job it is to snip out the segment containing the mismatch, by "aiming" the enzyme -- called exonuclease I -- in the right direction to work itself along the strand, stripping out the segment containing the mismatch.

Exonuclease I, while essential, is insufficient to accomplish the function at hand without assistence. The assistence comes from two clamping proteins one of which is identified as PCNA. Skeptics of mainstream evolutionary theory point to mechanisms like this as inadaquately explained by gene duplication and protein homology.

"A surprising feature of the repair system that it can evaluate the placement of the strand signal to one side or the other of the mismatch and work from there," said Modrich. According to Modrich placement of the strand break that directs repair to one side or the other of the mismatch is likely a consequence of the mechanism by which DNA is copied by the replication machinery.

"This system does more than just repair DNA biosynthetic errors," he said. "Many cancer chemotherapeutic drugs work by damaging DNA, which selectively kills cancer cells because they are proliferating more than resting cells. The mismatch repair machinery senses certain types of DNA damage, which leads to activation of the cell's suicide machinery, called apoptosis, resulting in cell death. Inactivation of the mismatch repair system not only predisposes cells to tumor development, but also renders them resistant to certain anti-tumor drugs.

The study of DNA repair mechanisms is interesting from an intelligent design perspective. However it also yields many practical medical benefits.


Archaea XPB Helicase and Nucleotide Excision Repair

An indicator of intelligent causality is an outcome that would not otherwise occur through natural forces alone. Nucleic acid sequences naturally become disordered with time. In the absence of error detection and repair mechanisms the rate of decay will exceed possible increases in genomic information resulting from selected changes. Experimental verification of this hypothesis would establish the alluded to indicator of intelligence.

This post focuses on some DNA repair mechanisms.

The following portion of a press release of The Scripps Research Institute is based on studies showing effects resulting from the breakdown of DNA repair mechanisms. The press release quotes are italicized.

All the information for heredity is encoded in DNA molecules that are constantly under attack from sources inside and outside the body—by sunlight, ionizing radiation, other environmental carcinogens, and free radicals from the normal cellular metabolism. Surprisingly, most of this damage comes from the chemical reactions that are the normal processes needed for life, so life is impossible without DNA repair even in the absence of environmental toxins.

DNA damage ranges from one or a few altered nucleotides in a single strand of the double helix, to breaks in one or both strands and crosslinks between the two strands. To prevent accumulation of mutations and the production of altered proteins, cells must deploy an arsenal of repair mechanisms to excise and replace defective nucleotides, reconnect broken strands, and patch up other kinds of damage. As most damage comes from endogenous sources generated by the cellular metabolism, the impact of environmental and other mutagens depends upon the cell's ability to repair DNA damage, and this processes depends upon the accurate assembly of molecular machines for DNA repair such as the newly characterized XPB helicase.

Mutations that cause changes in these machines can block these DNA repair processes or even uncouple their normally coordinated actions to result in cancer and degenerative diseases associated with aging. This relationship is reflected by the extremely high cancer predisposition of individuals with hereditary defects in DNA-repair processes.

It is important to note that a certain level of damage to DNA is inevitable. Life is made possible by biological mechanisms that identify and repair damaged DNA.

In xeroderma pigmentosum patients, for example, exposure to sunlight typically causes hyper-pigmented skin that is dry and parchment-like, and is followed by multiple skin cancers. If carefully shielded from ultraviolet light, for example by window filters and protective clothing, many xeroderma pigmentosum sufferers can lead seemingly normal lives. Xeroderma pigmentosum results from mutations in any one of seven genes, labeled XPA through XPG, which are involved in the well-understood DNA repair mechanism called nucleotide-excision repair.

"XPB was initially identified as the gene responsible for nucleotide-excision repair defects in xeroderma pigmentosumpatients, who are hypersensitive to light and have a dramatically increased risk of skin cancer," says Tainer. "This reflects the fact that XPB plays a key role in unwinding damaged DNA during nucleotide-excision repair, which removes a broad spectrum of DNA lesions, including those caused by exposure to ultraviolet light."

Cockayne Syndrome is another disease of faulty DNA repair—this time of "transcription-coupled repair," which is repair to genes that are actively being transcribed into messenger RNA. Cockayne Syndrome is marked by severe physical and mental retardation — victims have an unusually small brain and fail to grow and develop normally after birth; pronounced wasting usually begins in the first year of life. As they grow older, Cockayne Syndrome sufferers look increasingly aged, with faces marked by sunken eyes. Average life expectancy is only 12 years and few survive their teens. Mutations in three XP-associated genes— XPB, XPD, and XPG — can lead to this syndrome.

A New Model

The research reported by this new study approached the complex repair machinery by looking at a simpler system involving the XPB helicase from an archaea, a single-cell organism analogous to bacteria, in many ways resembling the nucleus or core of human cells. Helicases are enzymes that unwind or separate the strands of the nucleic acid double helix, an action that is critical to transcription and nucleotide excision repair, as well as other cell processes.

Nucleotide excision repair, a critical defense mechanism that removes DNA lesions caused by the mutating effects of sunlight (ultraviolet light) and toxic chemicals is also central to the success of the anticancer drug cisplatin, since cisplatin works by initiating the process of DNA repair, in turn activating apoptosis or programmed cell death when the repair process fails. "Because chemotherapeutic agents like the chemotherapy drug cisplatin and radiation therapy work by essentially damaging DNA, any new understanding of the DNA repair mechanism could mean potential improvements in the treatment of cancer," Tainer says.

There is an alternative biological strategy to correcting damaged DNA. If the damage is extensive or cannot be remedied the alternative cellular suicide (apoptosis) option is available.

Prior to this study, there were no specific models for how XPB acts in DNA separation either to initiate transcription or to begin nucleotide excision repair. There were also no models for the role that XPB, which is an essential subunit of Transcription Factor IIH (TFIIH) functional assembly complex, might play in changing conformations for TFIIH's alternate roles in either transcription or DNA repair.

The XPB crystal structures developed by the researchers identified unexpected functional domains for XPB. Research Associate Li Fan of Scripps Research, the first author of the study, notes, "We were surprised when we found that XPB contains a domain structurally similar to the mismatch recognition domain of a bacterial DNA repair protein MutS. MutS helps recognize and repair mismatched DNA in E. coli. These two proteins have little sequence similarity. Biochemical assays following this discovery indicate that this domain allows XPB to interact with damaged DNA and enhances its unwinding activity on damaged DNA."

The report suggests that unknown protein and DNA interactions at transcription sites activate XPB within the TFIIH complex to allow it to start the DNA unwinding process.

"Even though TFIIH does not act directly in initial damage recognition, the interaction of XPB with the DNA lesion suggests that XPB plays a role in switching TFIIH from transcription mode to nucleotide excision repair," Tainer says. "The structural biochemistry of XPB that we discovered shows an unexpected molecular mechanism by which XPB plays a key role in determining exactly how TFIIH functions, whether in transcription or repair mode."

A new interacting function has been suggested for XPB. It involves influencing a role switch from transcription to repair.


Wednesday, September 13, 2006

Axoneme Structure

A linked article entitled 'Secrets of a Cellular Machine New Clues to the Architecture of Flagella and Cilia' provides information about axoneme structure. The article provoked more than the usual interest because of a recent paper co-authored by Nick Matzke. It was the subject of a blog post at Telic Thoughts. Portions of 'Secrets of a Cellular Machine New Clues to the Architecture of Flagella and Cilia' follow in italics accompanied by my comments in block print.

Kenneth Downing and Haixin Sui of Berkeley Lab's Life Sciences Division have pioneered the use of cryo-electron tomography to examine the ubiquitous protein structures called axonemes, which form the cores of the cilia and flagella of eukaryotic cells.

A new model of axoneme structure reveals the roles of specific proteins in organizing microtubule doublets. The model, above, incorporates known tubulin structures docked within the constituent microtubules. Cryo-electron microscope images of doublets in axonemes, like those used for tomography, are shown at bottom.

Axonemes are some of nature's largest molecular machines. Their principal structural elements are microtubules, tough and versatile protein assemblies that perform many cellular roles, notably as major components of the cell skeleton. In 1998 Downing and Eva Nogales, then a scientist in his group, with colleague Sharon Wolf, first revealed the structure of alpha and beta tubulins, the protein dimers from which microtubules are constructed. In 2002 Downing and Huilin Li, also a scientist in his group, published details of a microtubule's structure at eight-angstrom resolution, better than twice that ever obtained before.

"In the present work Haixin Sui and I were initially looking to follow up the earlier work on tubulin," Downing says. "In mammals tubulin comes in many forms, so we intended to isolate the simple form in sea urchin eggs in hopes of making better crystals. It turned out that we also collected a lot of sea urchin sperm, which are an excellent source of axonemes."

Whips and eyelashes
Lacking legs or flippers, many single-celled eukaryotes (eukaryotic cells are those with nuclei) get around using flagella and cilia, Latin for "small whips" and "eyelashes." Nor could complex creatures, including human beings, survive without these powerful molecular machines. The cilia that sprout thickly from cells that line the lungs and other organs wave as rhythmically as sea grass in the tide to dislodge and sweep away litter. Flagella thrash energetically to propel sperm.

Except for length and number per cell, flagella and cilia are similar and share a common structure. At the center of each is the axoneme, a tough, flexible bundle of microtubules encased by a membrane. Other proteins connect the microtubules in the axoneme together or move over them, causing them to bend and slide against each other in a rhythmic beating motion.

"The basic axoneme plan has been known for forty years, from biochemistry and low-resolution electron microscopy," says Sui. "But finding out which proteins are located where, and even learning the identities of many of the proteins, has long frustrated researchers."

"Resolution was the challenge," Downing says. "Conventional electron microscopy just couldn't see the details." The latest high-resolution results with cryo-electron tomography offer new insights and promise new understanding of these vital cellular structures.

Axonemes are the giant molecular machines that make up cilia and flagella. The axonemes used in the present study were taken from the sperm cells of purple sea urchins.

Despite the battle lines drawn over Behe's irreducibly complex cilia and flagella the article reminds us that there is much unknown data relating to the issue. Interestingly, although science involves the testing of hypotheses and the incorporation of newly gained knowledge resulting from such testing, advocates for and against Behe's views behave as if any new data could not matter.

Says Downing, "The axoneme is a basic structure in all eukaryotes. Our eventual goal is to find out how it evolved and why it has been conserved since the beginning."

I'd like to see this approached with a truly open mind that is has not predisposed to the idea that there are always plausible pathways without intermediates lacking selective value.

Sunday, September 10, 2006

Science and Faith

Many articles have been written about Dr. Francis Collins recently. One entitled 'He trusts science, puts faith in God' appeared in 'Pioneer Press.' The following quote is taken from the article.

"Tall and trim, with gray hair, blue eyes, a self-effacing manner and just the barest hint of a Southern twang, Collins, 56, has set himself up as an emissary between two clashing worldviews.

He urges his fellow scientists to give up the arrogant assumption that the only questions worth asking are those science can answer. He entreats his fellow believers to recognize it's not blasphemous to learn about the world."

Collins feeds the stereotyping of the Darwinist fringe of science with the implication that his fellow believers think it blasphemous to learn about the world. A strange comment to believers who have made the effort to obtain degrees in scientific fields and have studied the natural world since then. Where believers depart from their critics lies with the philosophical assumption that matter and energy is all there is. Throwing this bone avails Collins little as this quote from the same article shows.

"From the other camp, some scientists ridicule Collins' effort to find a place for God in the scientific framework.

"I could just as well say that there are 70 pink elephants revolving around the Earth," said Herbert Hauptman, a Nobel laureate in chemistry. Science and faith "are simply incompatible," he added. "There's no getting around it."

The writer suggests that Collins has been ridiculed for attempting to integrate God into science. Collins has argued that there are questions worth asking that science cannot answer according to this same writer in this article. That's hardly an attempt to "find a place for God in the scientific framework." Of course one could argue that nothing is beyond our capacity to observe and test but that is a philosophical position; not an empirical one.

Hauptman's comment is inane. Science and faith are different. That does not make them incompatible. Faith does not signify that the object of faith is inconsistent with science. Pink elephant references are generally shorthand for a negative personal opinion of divine possibilities. Oddly, mainstream versions of natural history require no small amount of faith in conclusions not supported by empirical data. Hauptman would be hard pressed to present a case for "man evolving from primordial muck" not based on presumptions extending well beyond supporting data. Belief, despite the evidence, rather than based on it, is not even sound faith much less sound science. But then Collins is right about this not being a case of science contravening faith. Rather it is the unacknowledged convictions of scientism that contravenes the faith of Collins's fellow believers.

Here is more from the article:

"Maybe God intended mutations in DNA over the millennia to lead to the emergence of homo sapiens. Once man arrived, maybe God set him apart from the other creatures by endowing him with knowledge of right and wrong, a sense of altruism and a yearning for spiritual nourishment.

Collins knew he could never prove any of these ideas, but that no longer troubled him the way it once had.

Science could reel back time 14 billion years to postulate a big bang that created the universe. But it could not explain what came before that singular moment — or how the energy that fueled the cosmic explosion came to be. Science clearly had limits. So it seemed unfair to Collins to reject the divine simply because God's existence could not be proved.

That argument frustrates Nobel-prize winning physicist Steven Weinberg. Yes, he said, science does have limits. But attributing the unknown to God doesn't advance human knowledge or serve a useful purpose, except to give believers a "warm, fuzzy, reassuring feeling."

This is another misconception. Attributing causation to God predates the advent of modern science by many centuries. It also is not refuted by science since science has limits as was correctly noted. David Heddle has pointed out that while the Bible may not make claims that are subject to scientific testing it makes many historic and archeological claims that can be tested against evidence available from these disciplines. It may not be about evidence dealt with within Weinberg's field of expertise however, archeological and historic evidence are not warm, fuzzy feelings either.

"And given all the violence done in the name of religion, Weinberg argues that the world is better off without it."

Although Weinberg's criticism is not scientific in nature, neither is it accurate. The most horrendous violence in history, accounting for the most deaths, stems from non-religious causes. In many cases they involved leaders who were avowed atheists. Stalin, Mao and Pol Pot have the blood of tens of millions on their hands and all three had about as much disdain for religion as Weinberg.

"It's something we have to grow out of," he said. "There will always be mystery, always things we don't fully understand. We just have to resign ourselves to that."

Weinberg and Collins's fellow believers would concur that there will always be mysteries we will not fully understand. They part company in their approach to atheism as the only suitable paradigm within which to view that reality.

Friday, September 08, 2006

Reverse Evolution

Have you heard it said that evolution is a directionless process? Merely a change in allele frequency? The People's Cube excels at parody. This time it is known as the Case Of Backward Evolution: New Hope For Democrats. From the site:

Scientists: If your mouth is already on the floor, you have an evolutionary advantage over those who need to bend over Progressive researchers and politicians alike are encouraged by last month's discovery of a genetic mutation that reverses human evolution to its starting point. Those affected by the Backward Evolution Syndrome (BES) walk on all fours and speak a primitive language. The mutation that has afflicted a family in Turkey has stripped them of the genes that let humans walk upright, returning them to the pre-human state of quadrupedalism, or four-limbed walking. Many scientists hope that BES will reveal the secrets of human origins. But researchers at the Karl Marx Treatment Center see it as an exciting opportunity to correct human evolution, which has gone terribly wrong.

"Humankind has made a wrong turn somewhere in its development," says the Center's Chief Scientist Dr. Fuku. "It has evolved individualism, greed, competition, and private property. Ever wondered why socialism never worked anywhere it's been tried? Bad genes."

Quadrupedals are welcome in New Orleans
Scientists: "Occasionally, reverse evolution may require a little human help."

$$ Halliburton: "We've seen this syndrome before in welfare recipients."

"Wrongly evolved humanity breeds monsters like capitalism, global warming, and George Bush. But a pre-human DNA will enable us to start an alternative evolution from scratch, breeding a politically correct human race that's fit to live in a socialist utopia. We will succeed where Stalin's scientists failed," Dr. Fuku added.

"This is what the idyllic Golden Age looked like," says known environmental scientist Al Gore. "Imagine Earth populated by quadrupedal people incapable of drilling for oil, driving cars, or cultivating fields. We must immediately spend millions of taxpayers' dollars on genetic research to replicate the syndrome on a broader scale. Anything less will be a crime against nature."

Some members of the academia, however, argue that "reverse evolution" is not a glitch in the DNA but a product of successful adaptation to a progressive world that increasingly leans towards socialism. Natural selection prefers people who can do things like menial agricultural labor, scrounging for food scraps, etc. If your mouth is already on the floor, you'll have an evolutionary advantage over those who need to bend over.

Protein Folding News

A news release entitled 'Cornell and Scripps researchers propose theory of how proteins fold into their critical shapes' details some recent findings related to the mystery of protein folding. Part of the story follows in italics interspersed with my comments in standard form.

Experimental evidence provided by a Cornell researcher and colleagues at the Scripps Research Institute in La Jolla, Calif., supports a long-held theory of how and where proteins fold to create their characteristic shapes and biological functions.

The theory proposes that proteins start to fold in specific places along an amino acid chain (called a polypeptide chain) that contains nonpolar groups, or groups of molecules without a charge, and continue to fold by aggregation, i.e., as several individuals of these nonpolar groupings combine. Using the same principle that separates oil and water, these molecules are hydrophobic -- they avoid water and associate with each other.

In the water-based cell fluid, where long polypeptide chains are manufactured and released by ribosomes, the polypeptide chains rapidly fold up into their biologically functional structure. The theory proposes that there are sites along the polypeptide chains where hydrophobic groups initially fold in on themselves, creating small nonpolar (hydrophobic) pockets that are protected from the water.

These pockets tend to be found in the core of proteins. Cellular membrane proteins are ready examples.

The first method used supercomputers to calculate the energy required to convert a polypeptide chain into a collapsed hydrophobic pocket. The folds occur in several places that require the least possible energy to maintain. By finding these places where the nonpolar groups exist, the researchers better understand where folding occurs along a linear polypeptide chain.

Search criteria includes both the minimal energy and non-polar amino acid side chain factors.

The second method involved mapping a folded protein by tracing the folding steps required to arrive at the protein's native structure. This method mapped three stages of folding. First, the short-range contacts between amino acids that are very close to each other were mapped, revealing the initial nonpolar (hydrophobic) folds. The next two stages show folds that occur between points that are farther from each other along the polypeptide chain. These secondary folds may attach two or three hydrophobic pockets.

These two methods were used together in this study to pinpoint where on a polypeptide chain the nonpolar segments occur and where initial folding takes place and then propagates to the final folded form.

Each protein contains a massive amount of information. Yet this problem appears to be slowly yielding to research efforts. A recent post discussed the chaperone role played by some proteins in the folding of others. Since misfolding leads to malfunction and disease the importance of the topic is evident.

Monday, September 04, 2006

Front Loading

In a post entitled 'Another Protozoan and Front-Loading' Mike Gene argued: "Singled-celled eukaryotic organisms known as Tetrahymena contain many features that make them a good candidate model for front-loading evolution." Gene subsequently refers to front-loading evolution as FLE. In a linked reference Gene writes the following:

In this paper, Ausio covers a lot of evidence whereby histone H1, which functions to link nucleosomes and thus more efficiently package DNA in eukaryotes, is not essential for survival and reproduction in filamentous fungi. If we eliminate H1 function in Ascolobus and Aspergillus, the cells are perfectly viable with no deleterious consequence on the sexual reproduction cycle. The same results were previously seen in the protozoan Tetrahymena. However, in the fungi mentioned, elimination of H1 does result in the cessation of growth within a week or two. In other words, elimination of H1 does not affect viability or reproduction, but only the life-span of the individual organism (however, with Aspergillus, elimination of H1 does not even effect the life span of the organism and has no apparent effect).

Three more points. First, thus far H1 is ubiquitous in eukaryotes. Secondly, H1 may not be crucial in single-celled organisms; in addition to the Tetrahymena data, Ausio observes, "These results suggest that while linker histones may be dispensable for the relatively short life span of an individual cell, they are most likely indispensable for survival of higher eukaryote organisms." Thirdly, Ausio argues that this is probably not true for multi-cellular organisms, where compaction of the genome is an important ingredient in the regulatory schemes used in generating and maintaining a multicellular body plan. Why is all this significant?

If H1 was indeed designed, given its minimal role in protozoa, it might constitute a very good example of front-loading evolution such that the initial eukaryotic state was prepared to evolve a multicellular state. In other words, the existence of H1 in protozoa may best be explained by the existence of H1 in metazoans. And that is one hypothesis that simply cannot be entertained, for the briefest of all moments, from a non-teleological perspective.

An important caveat is in order, however. Tetrahymena are fairly specialized protozoa and may not be representative of most protists. However, given that H1 is not essential in simple metazoans, such as filamentous fungi and also in specialized protozoa, we have good reason to suspect it might likewise be nonessential for less specialized protozoa. Here is yet another example where a teleological approach can generate experimental research. Instead of assuming Tetrahymena is unusual, and thus irrelevant, with regard to its lack of need for H1, we need to go into the lab and knock out H1 genes from other protozoans. And in keeping with the general argument of my speculation, we have yet another example of using a teleological approach to generate a prediction - if there is something to my hypothesis, then we will find other protists where H1 is not essential. In fact, we might even find some protists without H1.

Finally, keep in mind that "nonessential" does not mean H1 will have no role. Useless H1 is not a way to front-load (as useless things decay into nonexistence). Front-loading may entail giving a higher eukaryotic protein some role in protozoa to ensure it persists until something like higher eukaryotes evolve. But it is not until it is coopted into its primary designed role that it becomes essential.

Gene zeroes in on a histone protein known as H1 and notes that this protein plays an essential role in most eukaryotic organisms involving efficient packaging of DNA.

A commentator posted this in connection with Gene's original post: "So if the only prediction that you can make is a negative one like "natural selection is not enough," then you are at a dead end. To have a viable research program, you need to come up with positive predictions that diverge from those of natural selection."

Note the criticism. It is not unusual to see critics of ID contend that research grounded in ID based assumptions are practically indistinguishable from evolutionary counterparts. The specific complain in this instance is based on the belief that a telic based hypothesis would not diverge from those customarilly attributed to natural selection. But is that the case. Based on Gene's comments the criticism does not stand. Gene's front loaded concept is intrinsically linked to function and therefore natural selection. However, in a twist on the usual natural selection paradigms, in this case an absence of function, indicating a parallel absence of selective value, would signal the need for another explanation as to why a protein, lacking functional utility, is nevertheless found in an organism. Front loading is an attempt to offer a rational explanation for a circumstance that defies natural selection expectations. Why would functionless genes and proteins be retained by an organism? There is a metabolic cost associated with their synthesis without the yield of a benefit to the organism. That is unless the benefit is presently a potential and is to be accrued through subsequent genetic changes. Planning is the obvious inference and biological data the supporting evidence.

Critics can argue that H1 has yet undiscovered functional utility. That is a matter for further research but it does not mitigate the argument associated with the front-loading hypothesis. It merely poses a suggestion as to how the front loading concept can be falsified.

Note this quote of Mike gene:

Finally, keep in mind that "nonessential" does not mean H1 will have no role. Useless H1 is not a way to front-load (as useless things decay into nonexistence). Front-loading may entail giving a higher eukaryotic protein some role in protozoa to ensure it persists until something like higher eukaryotes evolve.

Do "useless things" really decay into nonexistence. If so how would we account for the existence of pseudogenes? If the H1 in question truly is without functional value then the front loading hypothesis would be strengthened. Front loading would then provide an explanation natural selection fails to provide.

Saturday, September 02, 2006

A 'Nucleic Acids Research' Article Review

An article entitled 'Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms' appeared in 'Nucleic Acids Research.' A review follows.

Research, focused on six prokaryotic and five eukaryotic genomes, was the basis for determining whether the termination signal for protein synthesis has common determinants. In the words of the authors: "Four of the six prokaryotic and all of the eukaryotic genomes investigated demonstrated a similar pattern of nucleotide bias both 5' and 3' of the stop codon. A preferred core signal of 4 nt was evident, encompassing the stop codon and the following nucleotide. Codons decoded by hyper-modified tRNAs were over-represented in the region 5' to the stop codon in genes from both kingdoms."

Experiments were aimed at determining whether there existed a correlation between termination efficiency and signal abundance bias. Escherichia coli, one of the prokaryotic organisms studied, showed a correlation between termination efficiency and signal abundance as related to the stop codons UAA and UGA. Such was not the case with mammalian cells.

The paper notes the interactive nature of protein synthesis termination. There is evolutionary significance to the data. There are differences between prokaryotes and eukaryotes with regard to translation termination. As noted in the paper, protein synthesis termination involves release factors (RFs). The function of these RF proteins entails release of the polypeptide chain from the ribosome. Whereas prokaryotes contain two release factors eukaryotes only contain one. As expected the decoding capacity of the eukaryotic RF extends to all three stop codons. The two prokaryotic RFs are both effective with the UAA stop codon but RF1 only decodes UAG and RF2, UGA.

[An article entitled 'Endless possibilities: translation termination and stop codon recognition' provides some background information about release factors that could be helpful. The following passage is from this cited article.]

During translation termination, a stop codon located in the ribosomal A-site is recognized by a release factor or release factor complex, which binds the ribosome and triggers release of the nascent peptide. In eukaryotes, translation is terminated by a heterodimer consisting of two proteins, release factors eRF1 and eRF3, which interact in vivo (Frolova et al., 1994 ; Zhouravleva et al., 1995 ; Stansfield et al., 1995 ). eRF1 recognizes all three stop codons and triggers peptidyl-tRNA hydrolysis by the ribosome, releasing the nascent peptide (Frolova et al., 1994 ; Drugeon et al., 1997 ). Eukaryote termination efficiency is enhanced by the GTPase release factor eRF3, the second component of the heterodimer eRF complex. In response to a stop codon in the ribosomal A-site, formation of a quaternary complex comprising the ribosome, eRF1, GTP and eRF3 triggers GTP hydrolysis and enhances the rate of peptidyl release

In contrast to eukaryotes, the role of stop codon recognition during translation termination in eubacteria is divided between two so-called class 1 release factors, RF1 and RF2, which in Escherichia coli are encoded by the essential prfA and prfB genes, respectively (Scolnick et al., 1968 ; Caskey et al., 1984 ; Weiss et al., 1984 ). RF1 catalyses translation termination at UAA and UAG codons, and RF2 at UAA and UGA codons

[Back to the review]

The authors state that the differences in prokaryotic/eukaryotic release factors are consistent with independent evolution. The absence of sequence and structural homology among the prokaryotic and eukaryotic release factors is additional data in support of their conclusion.

The paper devotes attention to the issue of termination efficiency. Experimental evidence was cited testing nucleotide sequence changes in E.coli- both 5' and 3' of stop codons.

Results indicate that there is bias in occurence of specific nucleotide sequences which affects bacterial termination efficiency. Translation termination efficiency was also studied in yeast and mammalian cells. In the words of the authors- "these studies have revealed that the nucleotide sequences both 5' and 3' of the stop codon can modulate termination efficiency."

The prokaryotic and eukaryotic genomes studied both shared similar relationships in their level of gene expression and nucleotide sequence bias. Highly expressed genes show nucleotide bias in the area around stop codons while the bias of genes with the lowest expression was insignificant. Specific nucleotide biases have been identified- TAAT (E.coli K12 and M.genitalium), TAAA and TAAT (B.subtilis), TAGC (M.tuberculosis) and in the words of the authors: "All five eukaryotic genomes showed preferred tetra-nucleotide signals of a stop codon followed by a purine (G or A)."

The paper states that a correlation exists between tRNA abundance and translation efficiency for both prokaryotes and eukaryotes. However, insofar as termination efficiency was concerned the data gave differing interpretations for prokaryotes and eukaryotes. The number of termination codons UAA, UGA and UAG are not equally abundant in E.coli; UAG terminating the smallest percentage of genes. There was a correlation observed in the abundance of termination signals and the efficiency of termination in E.coli. Inefficient signals in E.coli were linked to gene expression. This was most pronounced with low mRNA levels and smaller genes where termination and initiation signals were closer. Initiation of mRNA was said to be influenced by ribosomal pausing and queuing which in turn can result from inefficient termination.

In contrast the same relationship between abundance of termination codons and efficiency of termination was not found in the eukaryotes studied. As the authors stated:

"Indeed, the abundant UAA signal was the least efficient and, generally, the rare signals were among the most efficient."

There were efforts made to determine the importance of release factors to stop signal efficiency. To do so the concentration of RF was increased by as much as five-fold and a dramatic increase in termination efficiency at rare signals was observed. More abundant signals were not as impacted. The authors had this to say about RFs and protein synthesis termination:

The recognition and binding of the decoding RFs for termination of protein synthesis may be the major, if not the sole determinant of the extended length of the stop signal in prokaryotes. In prokaryotes, transcription and translation are spatially and temporally linked, and efficient recognition of stop codons by the decoding factors is correlated with translation rate.

As was the case with prokaryotes increased concentration of decoding RF resulted in improved signal efficiency for eukaryotes and even influenced gene expression with reference to particular genes. Eukaryotic signal sequences were investigated to determine termination efficiency and in the words of the authors:

The results indicated that differences in the nucleotide sequences in both 3' and 5' contexts could affect signal efficiency but this did not correlate with bias and/or abundance.

I found interesting the analysis related to an observation of a lack of direct correlation between termination efficiency in eukaryotes and the bias 5' and 3' of stop codons. The implication, according to the authors, is that the function of the translation termination signal is broader than termination of protein synthesis. They then speculate that the translation termination sequence may be connected with an mRNA recycling loop which lessens the rate of mRNA decay and increases protein expression efficiency. The existence of extended termination signals may be a means by which mature and premature stop codons are distinguished.

In concluding remarks the authors noted that greater regulation of gene expression exists in eukaryotic organisms. New roles for eukaryotic translation termination mechanisms exist that are not found in prokaryotes. The authors surmise that this may explain some of the divergence in translational termination signals.