Tag Archive | "molecular biology"

A New Genetic Code?

An old Discovery News article has recently been making its rounds on Facebook, which was claiming that “new nucleotides” were identified in human DNA. Users were quick to rant and rave about how game-changing this piece of news is. I read claims about how they’d need to retake biology courses now and how this could have implications on artificial life.

DNA is composed of four canonical bases. Canonical, because they are the classic bases in Watson and Crick’s double helix. That is, four chemical letters that compose genes—adenine (A), thymine (T), guanine (G), and cytosine (C). These are the A’s, T’s, G’s, and C’s you see in biology textbooks. What users took the news to be was that there were new letters to add to these. To be fair to those misled, the title was technically accurate (New Nucleotides Identified in Human DNA from Discovery News on July 27, 2011). There are two new nucleotides previously unknown. However, contrary to the subsequent speculations of those I read, the discovery doesn’t demolish or revolutionize anything that we’ve already known about what genes are. A’s will still always pair with T’s and G’s will always pair with C’s. There are no secret letters strewn throughout the genome (at least, for life here on Earth).

The finding, as the article later explains, is that there are two new modifications discovered of the canonical nucleotide cytosine and not that there are somehow new forms of genes that code for alien proteins. This is in addition to the two previously known modifications.

Cytosine has long been known to incorporate chemical groups that influence how genes are expressed. The study of this is called epigenetics. By altering the shape of DNA molecules, the modifications of cytosine can change how enzymes in the body access genes, preventing some genes from being read. As researcher Yi Zhang of the Howard Hughes Medical Institute opined, their work could lead to better control of how stem cells develop.

At the end of the day, your genetics classes don’t need to revamp their curricula and, no, you don’t have to forget what you learned in school. Surely, epigenetics is a fascinating field that is needed to augment our current understanding of how simple chemicals order each other around to make thinking human beings. And, while speculation is at the root of all scientific discovery, we must always be careful to temper it with skepticism and fact-checking.

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Gonorrhea Takes Human DNA

Just in time for Valentine’s Day, researchers from Northwestern Medicine have discovered that the bacterium that causes the sexually transmitted infection of Gonorrhea, Neisseria gonorrhoeae, has taken up human DNA and incorporated it into its own genome. A gene sequence identical to an L1 DNA element found in Homo sapiens has been observed in Neisseria isolates from a laboratory in the Northwestern University Feinberg School of Medicine.

CC BY-NA-SA Pembleton

Certain viruses readily insert their genes into their hosts. In fact, over 50% of our DNA came from viruses—a fact interesting enough on its own. Unlike viruses and their hosts, however, bacteria and complex multicellular organisms are not known to be able to trade genes. This discovery, led by postdoctoral fellow Mark Anderson, reveals an evolutionary mechanism previously unheard of. Bacteria are normally only capable of acquiring genes from other bacteria in a process of genetic recombination similar in some respects with a popular method of celebrating Valentine’s Day. In doing so, bacteria obtain novel genes from their bacterial neighbors, which, if fortunate enough, could aid in their adaptation to their environment. As to what Neisseria, a pathogen found only in humans, is doing with the genetic fragment that it took, that is still currently unknown.

The research, which was published in the journal mBio, goes to further show that species barriers aren’t as cut and dry as most people would like to think. What are commonly seen as boundaries between dogs and wolves, monkeys and men, aren’t clear and distinct. Evolution shows our kinship to even the simplest of organisms.

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Teleporting DNA

While it has been stunningly predictive and useful, quantum mechanics, because of its inherent peculiarity, has been a gold mine for new age hucksters such as Deepak Chopra. Albert Einstein himself couldn’t accept the theory which allowed for particles to take all possible paths from point A to point B and for cats to be both dead and alive at the same time. His aversion to this theory was immortalized in the quote, “God doesn’t play dice,” alluding to the strange universe ruled by random events that quantum mechanics was describing. To quote the physicist Richard Feynman, who made great strides in the field of quantum mechanics, “If you think you understand quantum theory, then you don’t understand quantum theory.”

Feynman’s fellow Nobel laureate, Luc Montagnier, who won the prize for establishing that AIDS was caused by HIV, recently published a paper, entitled “DNA waves and water,” which claims that through the use of electromagnetic fields, DNA molecules, the stuff of life, can “teleport” from one test tube to another. The mechanism this takes is, according to the paper, within the “framework of quantum field theory.”

Montagnier’s experimental setup included two test tubes, one containing pure water, and the other containing a highly diluted sample of a fragment of DNA from the human immunodeficiency virus (HIV). After applying a 7 Hz electromagnetic field for 18 hours to both the tube that contained pure water, and the other tube that contained DNA, the tubes were then subjected to a process called polymerase chain reaction (PCR). This procedure takes DNA molecules present in a sample and copies them continuously, based on a particular defined DNA sequence. Their results showed that the pure water miraculously produced DNA, when there should have been none.

Here the two tubes (with DNA on the left, pure water on the right) are shown being exposed to a 7 Hz electromagnetic field inside a µmetal cylinder.

This is a stunning result—so stunning that it seems rather dubious. The claim posited here is that dilute quantities of DNA can somehow emit “DNA waves” via its natural electromagnetic field and that this signal mimics the exact DNA sequence of the source in water. This signal can supposedly imprint itself into water. Such an outlandish declaration just cannot avoid comparisons to homeopathy. The paper’s conclusion also favors a rather convoluted solution (DNA waves) over a much more simple explanation: contamination. The retention of an electromagnetic field in the absence of the signal source is, however, entirely possible within quantum mechanics, though only in the order of picoseconds (one trillionth of a second)—certainly not enough time for a PCR reaction to take place (which usually takes about an hour).

The nature of PCR is that it is so effective at making copies of DNA that even just one molecule of DNA can be amplified. Imagine thousands of photocopiers that randomly take any page in their vicinity and copy them. Even if you just had one page to be copied, such a sheet containing the letter “X”, you could create millions of copies of this letter in no time since the copies of that page will be used by the other photocopiers to make even more copies—a chain reaction. Now, let’s say that just one stray sheet with the letter “Y” accidentally flew into the copier room. By the end of your copying, you’d have yourself billions of sheets with either “X” or “Y”. That’s how even one tiny splatter of contaminating DNA (from instruments used or even one’s own hands) can ruin an experiment.

Messing up a PCR experiment is so easy that Montagnier’s observation has to be reproduced by other scientists before it can even be taken seriously. The only reason it seems to be grabbing headlines is that Montagnier is a Nobel laureate. But, Nobel laureates are vulnerable to the dreaded “Nobel disease,” when noted scientists who have won the prize later support pseudoscientific ideas.

The originator of PCR, Kary Mullis, also won the Nobel prize, only to go on to deny the link between HIV and AIDS. Another laureate, Linus Pauling, who won two Nobel prizes, promoted the quackery that vitamin C treated cancers and prevented colds, late in his career.

However, regardless of accusations of Nobel disease, Montagnier’s ideas shouldn’t be dismissed offhand. If his observations can be consistently replicated by other researchers (and contamination is ruled out), then a revolution will occur in biology and all of science. It’s a prospect one can’t help but be excited about, but wonder should always be coupled with skepticism.

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The Genetic Case Against God

Image credit: http://www.flickr.com/photos/gravitywave/7715395/

Upon the completion of the first draft of the Human Genome Project in 2000, United States President Bill Clinton called the three billion letters that compose the human genome “the language in which God created life.” Indeed, the head of the HGP, current director of the National Institutes of Health, and devout Christian Francis Collins alludes to genetics as the “language of God”—the same title of his book-length presentation of supposed evidence for Christianity—and “God’s instruction book”.1

If there was any branch of science that could have ever vindicated the doctrine of vitalism (the belief that something nonphysical is the force behind the phenomenon of life), it would have been molecular biology and its study of the genetic and chemical underpinnings of life. It would also have been the prime candidate for debunking On the Origin of Species, which was published a hundred years before Avery, McLeod, and McCarty provided Darwin’s theory with DNA as the hereditary unit of life2 and Watson and Crick discovered its double helical structure3. A failure of molecular biology to reflect the wastefulness of natural selection and its reliance on ad hoc solutions for survival would have been proof positive that a physical description of the basis of life is intrinsically impossible. If genes were found to be too complex to have been the product of simpler parents, materialism would instantly cease to be a viable perspective. Scientists would then be forced to let go of their naturalistic premises. And yet, with junk DNA4 and genes co-opted for other functions5, we clearly see the fingerprints not of an intelligent God that deftly sculpted life, but of random chance whittled down by billions of years of natural selection.

Unfortunately for the religious intelligentsia, materialistic biology has only brought the hammer down more strongly against metaphysical and supernatural conceptions of life and consciousness. This is not to say that the religious have not tried to put on the white coat and the credibility of science in a counterintuitive attempt at showing that their beliefs are based on evidence and not on faith claims. Science is currently being assailed by unscrupulous hucksters and obscurantists trying to peddle the Bronze Age hokum of the Bible as scientific—thinly disguised as nondenominational under “Intelligent Design.” Less delusional believers adeptly see through this canard and rely on the self-refuting “theistic evolution” to ease their doubts about Adam and Eve while paying lip service to scientific consensus.6 Today, the claim that life and the human mind has no basis on physical events and the neurophysiology of the brain, respectively, is on par with the belief that demons are the generative cause of epilepsy. In this stage of human scientific progress, it is safe to announce that vitalism and its variants are intellectually indefensible and thoroughly deserve the muffled laughs they elicit. Despite its use by respectable scientists such as Dr. Collins, the “language of God” metaphor used for DNA is no less ridiculous. And, as we shall see after an inventory of genes and genetic disorders, believers may want to refrain from implicating God as the writer of the mess we call the human genome.

After the sperm and egg meet

The development of a human embryo involves a complex interplay between the genes it inherits from the much obsessed about union of the 23 chromosomes of the father’s sperm and the 23 chromosomes of the mother’s egg.7 These genes direct the development of embryonic structures at specific points in time and in specific amounts. Any error in the process will derail the entire endeavor and will have catastrophic consequences. Now, it often escapes the religious mind how such an intricate crosstalk between genes could ever have arisen by itself without the forethought of a designer. Of course, as the watchmaker argument goes, this failure of imagination necessitates that God must have carefully designed each gene to turn on at the right time and at the right amounts in order to produce each one of God’s precious little children. As Rick Warren says, “[God] carefully mixed the DNA cocktail that created you.”8 However, a moment’s additional thinking will reveal the vacuity of such an argument. Alternatively, what will be revealed by a little critical thinking is that God is either inept or cruel.

Once the embryo develops into a child, is born, and the doctor hands off the child to the mother, the next step, after a well-deserved embrace, is to look over the child for obvious defects. The parents check if the child has all its toes, if its head is round, and if its face possesses all the standard features. Once inspection confirms a healthy child, the parents breathe a sigh of relief over their little bundle of joy. This image is the best-case scenario for expectant parents. This is what happens when everything goes well with the 46 chromosomes of the child. However, in spite of the omnipotence and goodness of God, the alternative happens a little too often for someone who doesn’t make mistakes.

As much as 20% of all recognized conceptions result in spontaneous abortion—also known as miscarriages.9 This number does not include women who never even knew they were pregnant. Miscarriages occur for many reasons. Some of these reasons are embryonic developmental problems such as those involving errors in the inheritance of parental DNA (e.g., missing chromosomes, embryonic fatal genetic mutations, etc.). These problems arise by sheer chance because of the nature of DNA. Right at the get go, God’s perfect design seems to fail at least 20% of the time, without discrimination. And since the Catholic Church claims that the soul enters the embryo at the point of conception, then the Church must concede that God is the most prolific mass murderer of all.

Divinely mandated seclusion

While miscarriages are horrifying for expectant mothers, there is at least a modicum of comfort to be had in knowing that the fetus, lacking the neurological structures, did not suffer its own death. If a random mutation is lucky (or unlucky, as the case may be) enough to cross the threshold of birth, a human child with a functioning capacity for suffering will be involved in its ravages.

Severe Combined Immunodeficiency (SCID) is a genetic disease that is caused by various mutations, one of which involves the mutation of a gene on the X chromosome that codes for a protein that recognizes cell signals.10 Having this variant of SCID means that mothers that carry this mutation will pass it on to 50% of their offspring, since females carry two X chromosomes. Because of the two X chromosomes of females, they are unaffected by the disease since the defective copy on one X is compensated for by a working copy on the other. Therefore, the mutation is recessive, which means that since males only carry one X chromosome, males will have no functioning copy of the gene and will absolutely have the disease, regardless of environmental situation. The result is that the child with these genetic errors will have such a crippled immune system that he will need to live in an aseptic plastic bubble for all of his brief years on God’s green Earth. He will never even feel the touch of his mother’s uncovered skin until his body begins to fail catastrophically due to a chance infection and the sterile equipment that protects him is discarded as it will be of no use in a few minutes.

The curse of Huntington


Image credit: http://www.watchinghouse.com/wp-content/uploads/2008/05/househead5.jpg

Some genetic diseases remain benign until a certain point in adulthood. While many of these are largely environmentally determined such as heart disease and certain forms of cancer, some are completely deterministic. If you happen to have inherited a particular mutation in your huntingtin gene from your parents, there is no amount of vitamin C or exercise that will prevent you from becoming a quivering and demented shadow of your former self. This is Huntington’s chorea, a neurodegenerative disorder that affects adults at around 35 years of age. If it sounds familiar, it may be because the character Olivia Wilde plays on House has it. Huntington’s is caused by several repetitions of a DNA base triplet of CAG in the huntingtin gene. The more CAG repeats in your copy of huntingtin, the earlier the devastating effects of Huntington’s will be for you.11 You just need one disordered copy of the gene since the disease is dominant. This means that carriers of the mutated gene have a 50/50 chance of passing on their dreadful disease to their children. Many people who have a history of Huntington’s in the family opt not to be tested for the gene. Since there is no cure for the disease, many people would rather not have a ticking time bomb alert them of their guaranteed dementia and prefer to live in ignorance until the symptoms finally kick in.

This is but a sampling of the horrific genetic mishaps that follow the indifferent laws of statistics. They affect the lives of conscious creatures through no fault of anyone but chance. There are about 25,000 genes in the human genome.12 All of them are subject to mutation and failure. Most mutations are fatal; a tiny few are beneficial. This is the raw material in which evolution works.  This is how cruel natural selection is. The facts can’t be ignored by anyone defending the Christian idea of God. It takes a colossal amount of callousness to square evolution with a benevolent Creator. It takes an even greater amount of doublethink to use genetics as evidence for a loving God.


1 Collins, F. S. The Language of God: A Scientist Presents Evidence for Belief.  109 (Free Press, 2006).

2 Avery, O. T., MacLeod, C. M. & McCarty, M. Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III. Journal of Experimental Medicine 79, 137-158 (1944).

3 Watson, J. D. & Crick, F. A structure for deoxyribose nucleic acid. Nature 171, 737-738 (1954).

4 Ohno, S. So much ‘junk’ DNA in our genome. Evolution of Genetic Systems 23, 366-370 (1972).

5 Fraser, G. J. et al. An Ancient Gene Network Is Co-opted for Teeth on Old and New Jaws. PLoS Biology 7, e1000031 (2009).

6 Trese, L. J. The Faith Explained.  50-52 (Sinag-Tala Publishers, Inc., 2003).

7 Gilbert, S. F. Developmental Biology.  (Sinauer Associates, 2000).

8 Warren, R. The Purpose-Driven Life.  235 (OMF Literature Inc., 2001).

9 Griebel, C. P., Halvorsen, J., Golemon, T. B. & Day, A. A. Management of spontaneous abortion. American Family Physician 72, 1243-1250 (2005).

10 Davis, J. & Puck, J. X-Linked Severe Combined Immunodeficiency, <http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gene&part=x-scid> (2003).

11 Watson, J. D. DNA: The Secret of Life.  323-324 (Arrow Books, 2003).

12 ibid., p. 201

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