Orphan Genes Part 1: Unexpected Results in DNA Sequencing

In his book, Why Evolution is True, biologist Jerry A. Coyne describes modern evolutionary theory with the following statement:

Life on earth evolved gradually beginning with one primitive species—perhaps a self-replicating molecule—that lived more than 3.5 billion years ago; it then branched out over time, throwing off many new and diverse species.”

Based on this foundational principle, various species are expected to share similar (or homologous) structures due to common ancestry. Berkeley’s Evolution 101 page notes, “Evolutionary theory predicts that related organisms will share similarities that are derived from common ancestors. Similar characteristics due to relatedness are known as homologies.”

Wikipedia’s homology entry lists the following example: “…the forelimbs of vertebrates, where the wings of bats, the arms of primates, the front flippers of whales and the forelegs of dogs and horses are all derived from the same ancestral tetrapod structure.”

Image via wikipedia: “The principle of homology: The biological relationships (shown by colours) of the bones in the forelimbs of vertebrates were used by Charles Darwin as an argument in favor of evolution.”

The Berkeley source provides the following example in the case of plants:

However, the relatively recent advent of DNA sequencing has produced some very unexpected results- surprisingly contrary to this evolutionary theory prediction.

DNA Sequencing- We’ve Come a Long Way Baby

DNA is the blueprint, or instruction manual, containing the instructions which make every species unique. DNA (pictured below) is defined as, “…a thread-like chain of nucleotides carrying the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses.”

In the 1960’s scientists developed the ability to “read” this DNA instruction manual in a process called DNA sequencing. This was a monumental scientific breakthrough. Britannica defines DNA sequencing and reveals its significance with the following entry:

…technique used to determine the nucleotide sequence of DNA… The nucleotide sequence is the most fundamental level of knowledge of a gene or genome. It is the blueprint that contains the instructions for building an organism, and no understanding of genetic function or evolution could be complete without obtaining this information.” (emphasis mine)

The last sentence is imperative. While Darwin and his predecessors could hypothesize that common ancestry is the most reasonable explanation for similarities shared among various species based on visual comparison, common ancestry cannot be proven and the very concept of evolution cannot be understood without the ability to “read” an organism’s instruction manual (DNA).

For several decades DNA sequencing was a very slow and expensive process. However, the Human Genome Project, initiated in 1990 and completed in 2003, had a revolutionary effect. The goal of this international project, to map the entire human genome, spurred tremendous technological advances in gene sequencing which has continued far beyond the project’s completion. James Heather concludes his History of Sequencing DNA by stating, “Over the years, innovations in sequencing protocols, molecular biology and automation increased the technological capabilities of sequencing while decreasing the cost, allowing the reading of DNA hundreds of basepairs in length, massively parallelized to produce gigabases of data in one run.”

It is this burgeoning wealth of genetics information that has revealed the “mystery” of orphan genes.

What are Orphan Genes and Why are They Problematic for Evolutionary Theory?

Cornelius Hunter, writing for Evolution News, provides the following definition, “The term orphan refers to a DNA open reading frame, or ORF, without any known similar sequence in other species or lineages. Hence ORFan, or ‘orphan.’” The author of this article in Uncommon Descent explains orphan genes this way, “Orphan genes are presumed protein coding genes that exist in only one species and have such non-similarity to anything in any other species they are called orphans…”

Why is this troubling? If the theory of evolution and (by default) common ancestry are true, a coding gene that is species specific, with no recognizable counterpart in other species should be an extreme rarity. Ann Gauger writes in Orphan Genes: A Guide for the Perplexed, “The working assumption had been that, given common descent and the fact that most housekeeping genes are shared among living things, and the assumption hitherto that evolution occurs by incremental small changes, orphan genes…should be rare if not non-existent.”

So, just how common are they? This 2009 study published in Trends in Genetics found, “Comparative genome analyses indicate that every taxonomic group so far studied contains 10-20% of genes that lack recognizable homologs in other species.” According to Richard Buggs (writing for Ecology and Nature), researchers originally believed that the mystery of these orphan genes would be resolved over time as more genomes were sequenced, finding precursors for the sequences that are now categorized as orphans. However, the opposite has proven true.

For example, Dr. Jeffrey Tompkins discusses ants, “When comparing the ant genes to other insects, researchers discovered 28,581 genes that were unique only to ants and not found in other insects. While the various ant species shared many groups of genes, only 64 genes were common to all seven ant species…The researchers concluded that on average, each ant species contained 1,715 unique genes—orphan genes.”

In Buggs’ 2017 ash tree genome paper published in Nature, he and his colleagues report that of the over 38,000 protein-coding genes found, “…one quarter (9,604) were unique to ash. On the basis of our research so far, I cannot suggest shared evolutionary ancestry for these genes with those in ten other plants we compared ash to: coffee, grape, loblolly pine, monkey flower, poplar, tomato, Amborella, Arabidopsis, barrel medic, and bladderwort. This is despite the fact that monkey flower and bladderwort are in the same taxonomic order (Lamiales) as ash.”

Not only are orphan genes common, they also appear to be functional. Dr.Tompkins writes, “These orphan genes are also being found to be particularly important for specific biological adaptations that correspond with ecological niches in relation to the creature’s interaction with its environment. The problem for the evolutionary model of animal origins is the fact that these DNA sequences appear suddenly and fully functional without any trace of evolutionary ancestry (DNA sequence precursors in other seemingly related organisms).”

Conclusion

Orphan genes are certainly a fly in the ointment for evolutionary theory, but no surprise to either creation science or intelligent design. As Gauger points out, “ Then there is the elephant in the room that evolutionary biologists don’t want to acknowledge. Perhaps we see so many species- and clade-specific orphan genes because they are uniquely designed for species- and clade-specific functions. Certainly, this runs contrary to the expectation of common descent.”

In Part 2 of this series, we’ll take a look at how evolutionary biology responds to orphan genes.

Ethical Guidelines for Clinical Trials Prevent Many Vaccines From Being Adequately Tested For Safety

The CDC (Centers for Disease Control), the WHO (World Health Organization), the National Institutes of Health (NIH), and the FDA (Food and Drug Administration) are considered by most Americans to be the most credible, trusted sources of “unbiased” information regarding disease, medical treatment, and the safety of pharmaceuticals. Your doctor and the entire medical community base their decisions about your care on recommendations from these organizations, which are theoretically based on the studies brilliant, highly-qualified scientists perform for these organizations. These organizations publicly publish this information so that anyone who wishes to educate themselves can do so.

That is precisely what millions of Americans, including myself, are now doing when it comes to the subject of vaccine safety. Unfortunately we are finding that these “trusted” recommendations are not adding up with the information provided by their own sources and many times are blatantly at odds with this publicly published information. I’m going to clearly demonstrate that to you today.

The focus of this article is the following claim publicly stated by the CDC:

“Before vaccines are approved by the Food and Drug Administration (FDA), they are tested extensively by scientists to ensure they are effective and safe.”

How do scientists test vaccine safety?

There are 3 phases in prelicensure vaccine safety testing as described by the FDA. According to the FDA, “Clinical trials are conducted according to plans that FDA reviews to ensure the highest scientific and ethical standards. The results of the clinical trials are a part of FDA’s evaluation to assess the safety and effectiveness of each vaccine.” Herein lies the rub.

What are the highest scientific standards when it comes to determining safety?

According to the NIH, randomized double blind placebo control studies are the “gold standard.” The NIH goes on to state that, “RDBPC studies remain the most convincing research design in which randomly assigning the intervention can eliminate the influence of unknown or immeasurable confounding variables that may otherwise lead to biased and incorrect estimate of treatment effect.”

The problem is, most vaccine studies are not RDBPC due to the ethical standards that must be maintained.

The fact is most vaccine safety clinical trials do not and cannot use a placebo in the truest sense of the word. According to the CDC’s own glossary of terms, a placebo is, “a substance or treatment that has no effect on human beings.” In the case of vaccine testing, a true placebo would have to be an injectable substance that is completely inert, such as saline solution for example. However, that is NOT what is predominantly used in vaccine trials.

If they aren’t using true placebos, what are they using?

According to the 2013 WHO Expert Consultation on the Use of Placebos in Vaccine Trials, the following replacements are used in lieu of a true placebo:

    • “In place of a placebo, a vaccine against a disease that is not the focus of the trial is given to participants who do not receive the trial vaccine.”

Or, an “add-on” vaccine can be used:

    • “In this design, the trial vaccine or placebo product is mixed with an existing vaccine not studied in the trial, and the subjects are given either (a) the trial vaccine mixed with the existing unrelated vaccine or (b) the combination of a placebo and the existing unrelated vaccine.”

Yes, you read those correctly! These vaccines are not being tested for safety against substances that are known to be safe. They are tested against other vaccines which contain the same or similar toxic ingredients common to all vaccines. Some trials are performed using “add-on” vaccines as a placebo. In these cases, potentially everyone in the trial is injected with the actual vaccine being tested! It doesn’t take a rocket scientist to deduce that these methods are unacceptable when the goal is to ascertain safety.

The WHO freely admits this:

“A methodological disadvantage, however, is that trials using these types of placebos provide a less perfect control. It may be difficult or impossible to assess fully the safety and reactogenicity of the trial vaccine, although its efficacy can usually be assessed satisfactorily.” (emphasis mine)

(Reactogenicity is the ability of the vaccine to cause adverse reactions.)

“Methodological disadvantage!?” That’s the understatement of the century!

Let’s look at some very disturbing clinical trial data for a few of the vaccines the CDC recommends. Each vaccine is linked to its package insert so that you can read this information for yourselves:

Engerix B Hepatitis B vaccine (Recombinant) GlaxoSmithKline

“Ten double-blind studies involving 2,252 subjects showed no significant difference in the frequency or severity of adverse experiences between ENGERIX-B and plasma-derived vaccines…All subjects were monitored for 4 days post-administration.”

This study doesn’t prove that this vaccine is safe. Plasma derived vaccines were used in the control group instead of a placebo. It demonstrates that this vaccine doesn’t cause any more or any worse adverse effects than other vaccines cause- at least within the 4 day time frame the subjects were monitored.

This vaccine is given to babies on their very first day of life whether they are at risk for Hep B or not. Only babies born to Hep B positive mothers are at risk for Hep B. For millions of babies this vaccine is a completely unnecessary risk that provides them with absolutely zero benefit.

Infanrix (DTaP) GlaxoSmithKline

Table 4, on page 18 shows that Infanrix was not compared to a placebo, it was compared to the whole cell DTP vaccine.

According to WHO, acellular vaccines (like Infanrix) were introduced “to address the adverse reactions observed with whole cell vaccines…” This WHO report also notes that acellular vaccines have replaced whole cell vaccines in industrialized countries. However, due to the increased cost of acellular vaccines, the whole cell is still used in many developing countries. This vaccine is being tested against a control vaccine that we already know to be more dangerous than the type of vaccine being studied!

**Note figure 8.1 on page 18: “Pregnancy Category C Animal reproduction studies have not been conducted with INFANRIX. It is not known whether INFANRIX can cause fetal harm when administered to pregnant women or can affect reproduction capacity.

Despite this information listed in the product packaging, the CDC routinely recommends the DTaP vaccine to pregnant women. You can read about that on the CDC’s website in their article, Pregnant? Get Tdap in your 3rd trimester.

The CDC recommends either the BOOSTRIX vaccine or the Adacel vaccine (both DTaP) to pregnant women. While BOOSTRIX is rated one category safer than Adacel (Category B),the packaging still notes, “A developmental toxicity study has been performed in female rats at a dose approximately 40 times the human dose (on a mL/kg basis) and revealed no evidence of harm to the fetus due to BOOSTRIX. Animal fertility studies have not been conducted with BOOSTRIX. There are no adequate and well controlled studies in pregnant women. Because animal production studies are not always predictive of human response, BOOSTRIX should be given to a pregnant woman only if clearly needed.”

Still feeling safe? Still feeling like the CDC has your back?

GARDASIL- Merck

In 7 clinical trials (5 Amorphous Aluminum Hydroxyphosphate Sulfate [AAHS]- controlled, and 1 uncontrolled), 18,083 individuals were administered GARDASIL or AAHS control or saline placebo on the day of enrollment, and approximately 2 and 6 months thereafter, and safety was evaluated using vaccine report cards (VRC)- aided surveillance for 14 days after each injection of GARDASIL or AAHS control or saline placebo in these individuals.”

In these Gardasil trials, there actually WAS a control group which was given a true saline placebo. However there was another (much larger) control group given AAHS, which is the adjuvant in the Gardasil vaccine (the toxic portion that triggers immune response.) According to the insert, 15,706 subjects received Gardasil, 13,023 received AAHS and 594 received the placebo. However, they did not compare the three groups separately; they combined the AAHS and placebo group together and compared them to the Gardasil group. This means that the whole Gardasil vaccine was tested primarily against an injection containing its own toxic ingredients and determined to be “safe.”

Furthermore, 40 deaths occurred in the entire study which were broken down by cause. When you subtract the number of deaths that were due to car wrecks, overdoses/suicides and gunshot wounds, and compare the number of subjects who died: 18 subjects who were given either Gardasil or AAHS died and only 1 who had been given the placebo died.  Think about that! Subjects who received Gardasil or AAHS instead of placebo, died at a rate of 18 to 1!

Why Don’t Scientists Use Appropriate Placebos in Trials?

The “gold standard” in clinical trials cannot be implemented because the use of a placebo in many cases is unethical. The purpose of the 2013 WHO Expert Consultation on the Use of Placebos in Vaccine Trials was to detail the guidelines placed on the ethical use of placebos in vaccine trials. If using a traditional, inert placebo in the control group doesn’t “add any risk of serious or irreversible harm,” then clearly there is nothing unethical about using it. But what about when it does?

For example, according to WHO reports, in 2008 rotavirus was responsible for about 5% of all child deaths globally, with 90% of these deaths occurring in Africa and Asia. In a 2011-12 clinical trial in India for a new rotavirus vaccine, 2/3 of the infants received the test vaccine while 1/3 got a saline placebo injection. At the time, two approved oral rotavirus vaccines were already available. Not giving 1/3 of the Indian children in the trial a vaccine already known to be effective against rotavirus, constituted a human research violation that would not have been allowed in the US. Allowing preventable harm to occur in the name of research is unethical.

This means, for very legitimate ethical reasons, using true placebos according to the “gold standard” of clinical testing is not feasible. However, this in no way negates the fact that due to ethical constraints, it is impossible to accurately assess vaccine safety in many cases. It is also unethical to fail to provide this information to parents when discussing vaccine safety.

It crosses the line of unethical and meanders into the territory of illegal, when this information is intentionally censored from vaccine education sheets given to parents in the pediatrician’s office (as well as from conversations with your pediatrician) assuring that vaccines are “extensively tested for safety” knowing full well that safety and reactogenicity are “difficult or impossible to assess” by their own publicly published standards.

The next time someone tells you that vaccines have been proven safe in numerous extensive studies you can tell them that information is blatantly false, and the CDC, WHO, NIH, and FDA know it. Vaccines cannot be both adequately and ethically tested for safety.

Do Vaccines Contain Aborted Fetal Cells?

Do vaccines contain aborted fetal cells?

The short answer is: Yes, some do, but not all. I’ve heard a lot of people actually argue about this. Some people will argue emphatically and call you an idiot if you truly believe the “conspiracy theory” that vaccines contain aborted fetal cells. These people have clearly never bothered to read the list of ingredients printed in the vaccine package inserts. Nor have they visited the CDC website where aborted fetal cells are listed in the ingredients lists of various vaccines.

I don’t know, maybe it’s because they are looking for the words, “aborted fetal cells” which obviously aren’t there. It takes a little reading into the subject to discover that the words you should be looking for are “human diploid fibroblast cell structures” (which come in two strains- WI-38 and MRC-5).

The following vaccines were developed using one of the two aborted fetal strains above and do contain DNA from them:

      • Hepatitis A
      • Rubella (Rubella is a part of the MMR combination vaccine)
      • Varicella (chicken pox)
      • Zoster (shingles)
      • Adenovirus
      • Rabies
      • Polio
      • Enbrel (Rheumatoid Arthritis)

The following vaccines that are in development come from additional aborted fetal strains and contain DNA:

    • Ebola
    • Flu and Avian Flu
    • HIV

Why are aborted babies needed to produce these vaccines?

In order to make a vaccine, scientists must be able to grow the bacteria or virus they wish to create a vaccine for. In order to grow the bacteria or virus, they must have tissue to grow it on. While many vaccines are created using the tissue of various animals (cows, monkeys, chickens to name a few) and animal products (such as eggs), the use of tissue from aborted babies is superior for a number of reasons.

Cowpox found on the udders of infected cows used to manufacture the smallpox vaccine.

*You can thank me later for posting a pic of an artist rendering instead of a photo…

First, vaccines derived from animal sources carry a higher risk of contamination from other bacteria and viruses. For example, the polio vaccines that our parents were vaccinated with in the 50’s and 60’s were later found to be contaminated with a monkey virus referred to as SV40 or Simian Virus 40. (Whoops!) Now, the CDC claims that SV40 didn’t cause any adverse effects. So, it’s very ironic that according to laboratory findings, “ SV40 DNA has been detected in several human tumors, including osteosarcoma, mesothelioma, and non-Hodgkin’s lymphoma. Similar tumors are induced by the virus in hamsters.” And no…the individuals whose tumors were found to contain SV40 DNA had no possible exposure to SV40 other than the polio vaccine. It’s not exactly something you come across on regular ole’ day in the US of A.

Rhesus Macaque. Monkey used to develop the polio vaccine used in the 50’s and 60’s. Later found to have been contaminated with Simian 40 virus.

Second, some pathogens just don’t grow as well on animal tissue (like chicken pox) because they don’t infect animals. However, the most important advantage to using tissue from aborted babies is that fetal cells can go through many more divisions than other cells before they die. A biologist named Hayflick determined that normal human cells can only reproduce a finite number of times (usually around 50) before they stop reproducing. Fetal cells, however, are capable of going through many more divisions before dying.

Let’s get acquainted with the two aborted babies that the vaccines we inject our children with are grown on. (I sincerely hope that sentence makes you cringe as much I did when I typed it.)Believe it or not, the background information is actually available. WI-38 is a 3 month old female fetus who belonged to two married parents living in Stockholm, Sweden in 1962. Reportedly, her father was a “drunk” who was “gone a lot.” According to Dr. Rene Leive in her “Brief History of Human Diploid Strains,” her parents “felt they already had too many children”, so they decided to abort her. MRC-5 is a fourteen week old male fetus who was murdered inside his 27 year old mother in 1970 for “psychiatric reasons.”

Before we continue, let’s take a minute to see what a 15 week old baby (the average age of the aborted babies used to create these fetal strains) looks like in utero.

15 week old fetus in utero

And here we come to the next misleading argument that is posited to rationalize or justify the use of aborted babies in the production of vaccines. If you’ll notice in the list of vaccine ingredients above, the vaccines that are currently in use today are all derived from two fetal cell strains: WI-38 and MRC-5. Our vaccines come from “only” two aborted babies. Again, Megan over at Whole Living puts it best with her “This Wasn’t Just a One-Night Stand” analogy, “You might have also heard that only two babies were used and it was a really long time ago, which justifies the continued use of shooting up live babies with dead babies.” Sometimes a little perspective goes a long way…

It may seem like common sense to some to realize that to arrive at WI number 38, numbers 1-37 logically preceded. You would be correct in this logical assumption. Hayflick also references WI-44 in his report, so you can be sure, very many more than one aborted baby has gone into the development of the WI-38 cell line that is still used today. The same holds true for the MRC-5 strain. Hayflick also makes mention of the MRC-9 strain which is derived from a 15 week old female fetus in 1974. Her mother was an unwed 14 year old who aborted her baby for “therapeutic” reasons according to the documentation (taken from the history of diploid strains linked above).

Our Rubella vaccine comes from another cell line, RA 27/3, which was developed by a man named Plotkin. It is derived from a female fetus whose mother contracted Rubella in 1964. She was aborted for this reason (rubella is only harmful to babies in utero and causes some severe birth defects). According to Plotkin’s documentation, over 40 aborted babies were cultured. RA 27/3 was not the first fetus to test positive for Rubella or the last and he doesn’t specify why he continued with the series. Interestingly, Dr. Leive notes, “It is documented that there were other effective virus strains already made at the time which had been obtained from other non-abortion-related methods.”

Can We Use These Same Cell Lines Forever?

No. They aren’t immortal and they’ll eventually die out. Scientists have never stopped developing new strains and new vaccines. In fact, they already have new human diploid cell strains to back up the current strains. IMR-90 is a 16 week old fetus from a 38 year old mother of six who decided the baby she was carrying in 1975 would be too inconvenient. Cell strain 293 is derived from kidney cells from a baby aborted in 1972. The PER C6 line, which is being used right now to develop the new ebola, flu, malaria, tuberculosis, and HIV vaccines, is derived from an 18 week old fetus aborted in 1985. The main researcher for the PER C6 line, Van der Eb, stated that, “the woman wanted to get rid of the fetus and the father was unkown.”

In fact, the American Congress of Obstetricians and Gynecologists is “distressed” that Congress is investigating fetal tissue researchers and procurement companies to make sure they aren’t profiting from the sale of tissue from aborted babies (which is illegal.) They released this statement, “Unfortunately, some state and federal politicians are working hard to obstruct- or even criminalize- fetal tissue research, limiting the ability of America’s leading scientists and researchers to develop new vaccines and medicines to prevent and treat disease. The ACOG warns that if this interference continues, “fetal research bans will stymie US based medical progress, leaving us to rely on other countries to develop medicines for our own patients.”

Apparently, without legal abortion to provide the scientific community with an endless supply of murdered babies, medical progress will virtually cease. Eye opening statement to say the least. There are some powerful players backing the pro-choice movement and their motivation has very little to do with a woman’s “right to choose.”

I’ll end with one last quote from Megan at Whole Living, “If science can’t advance without abortions, we need to go back to the drawing board.”