Humans have about 22,000 separate genes; each gene codes for a protein that functions as part of the body, whether as an enzyme, a hormone, or a part of the body’s structure. Single-celled organisms have fewer genes, and there are some organisms that have many more genes. No-one knows for sure how many of these genes are really needed, and it is possible that some could be removed without impairing our function.
How many genes are essential for survival as a single free-living organism? Less than 500. Scientists have built a free-living bacterium related to the Mycoplasma family that has only 473 genes. This report in Science News describes the research that led to the production of this synthetic Mycoplasma. The Mycoplasma mycoides bacterium that the scientists used as the starting point for this experiment had 901 genes. Of the 473 essential genes, they were unable to determine the exact function of 149; of these, some 79 are completely mysterious.
At first, the research tried to create a genome with only known genetic parts, but it didn’t work. Once they added the genes with uncertain functions, the cell began to work properly. Of the genes with known functions, there were four broad classes: those that kept the cell membrane intact, those that expressed information from the genome, those that ran the metabolism (breaking down “food” and obtaining energy ), and finally those that helped preserve the genome in one piece.
While this accomplishment is less than perfect (over 17% of the basic genes have unknown functions) it is nonetheless dramatic. The people responsible are the J. Craig Venter Institute in La Jolla, CA; this nonprofit foundation was started by Venter for the express purpose of studying genomes. According to their web site, the Institute was formed in 2006 from the merger of five separate research organizations. It has 250 scientists at two sites: Rockville, MD, and La Jolla CA. Dr. Venter was at the National Institutes of Health (NIH) in 1991 when he started deciphering genes and discovered new tools for rapidly analyzing genomes. He started a group called The Institute for Genomic Research, a nonprofit dedicated to reading genomes. In 1995, the NIH team read the genome of Hemophilus influenzae, the first free-living organism to have its genome sequenced. The human genome was sequenced in 2001.
Now the group (and others) can focus on discovering the functions of the unknown genes, and more importantly, on discovering how multicellular organisms structure themselves through their genomes. The last fifty or sixty years have seen amazing advances in genetic research, from the discovery of the structure of DNA by Watson and Crick to the sequencing of the human genome by Celera Genomics and the National Institutes of Health through the Human Genome Project. In the last fifteen years since the human genome was sequenced, research has continued apace, and the minimal synthetic organism is the latest product.
Sunset at about 7 PM Today
Drumpf (Trump) is a Loser
This comment struck me so hard that I couldn’t resist passing it on:
amboycharlie
Nagoya, Japan August 4, 2015
A friend, who is fairly astute about such things, pointed out that Donald Trump, had he put his inheritance in an index fund and done nothing more in business, would be worth 20 billion today, not somewhere between 4 and 9 billion. His father built the fortune and he is squandering it on hotels, casinos and golf courses, at a time when such such [sic] things are losing their appeal. So how does that make him a winner?
Here’s a controversial issue: if your two-year-old is so severely disabled that she will never walk, talk, read, or eat on her own, what should you do to keep her at home as long as possible? One radical treatment, detailed in a New York Times article, involves administering estrogen (regardless of the person’s gender) starting at the age of two or three until about age six to induce the epiphyses (growing ends) of the bones to close up prematurely, limiting their eventual “stature” (or length, since they will never stand.) Combined with calorie limitation to prevent obesity, ideally this treatment can result in an “adult” who is a foot shorter and half as heavy as normal.
In females, this therapy is usually combined with bilateral subcutaneous mastectomy (removal of the breast buds) and hysterectomy to prevent maturation of the sexual organs. In males, this surgery is unnecessary, but mastectomy may be performed for cosmetic reasons. The resulting medical dwarfism makes the patient much easier to handle for the parents, who are generally the full-time caregivers. Compared with picking up a patient who weighs over a hundred pounds, a fifty pound end weight makes it relatively simple to transfer the patient from bed to wheelchair and into and out of the bathtub. The contrast in size and portability is remarkable and saves tremendous effort in care-giving.
Besides the advantage in transportability, there is a sense that the child is more “cuddle-able.” The child seems more an object of affection or even a pet.
The most serious error that could result from this treatment would be the restriction of growth of someone who would eventually be ambulatory and able to care for themselves. This is relatively simple to avoid because the only patients considered for this treatment are profoundly, permanently disabled, usually with grossly shrunken brains and undeveloped visual and speech centers.
In the 1960’s, estrogen treatment was considered for a few normal girls who were predicted to grow to be “too tall.” This idea was abandoned after a few girls were treated, partially because the idea of being “too tall” fell out of favor. In the present time, girls who undergo precocious puberty are also not treated, partly because many of them are intellectually disabled and the early maturation limits their adult stature. Another group of those who undergo precocious puberty do so because they are relatively obese, and there seems to be a threshold weight of about a hundred pounds at which a girl will undergo puberty, regardless of age.
Another objection is the theoretical lack of medical justification for inducing premature epiphyseal closure. Many people, none of whom have had to care for a profoundly disabled, full-sized adult, object to the treatment on the grounds that it is “medically unnecessary” and violates the patient’s rights. In fact, the degree of moral objection to this treatment is dramatic and there are individuals who describe it with disgust as deeply inhumane.
The alternative, in many cases, is placing the person in an institution when he becomes too large to lift. Institutions are, first, unavailable, and second, grossly abusive warehouses when they can be found. Many parents would find institutionalizing their child unacceptable, and find themselves trapped with an adult-sized but totally dependent vegetable in their homes. They are forced to use lifting devices to remove the person from bed for placement in a wheelchair, or, even more difficult, to place the person in a bathtub or remove him after washing.
The response to moral objections is simply that the patient has no awareness of his or her individual size or physical configuration because he or she is so profoundly disabled. The advantages of smaller size are so great to the caregiver that they justify any theoretical impairment of the patient’s personal “space.” In fact, the idea that “bigger is better” and that increasing size represents maturation and eventual graduation to adult status is really backward thinking. In the business world, being taller is an advantage, but to a minimally self-aware, profoundly disabled person, size is likely to be a drawback.
A commenter responded to the article by describing her/his personal situation. He/she is an adult with severe autism who functions at an adult level in some situations but is unable to hold down a job because of regressive behavior in some circumstances. He/she states that it would be much preferable for social reasons if he/she were not five foot eleven inches tall and 170 pounds. If he/she were childlike in stature, he/she states that others would treat him/her like a child and not expect completely adult behavior. In other words, a childlike appearance would elicit childlike treatment from others. As it is, he/she states that the only people who he/she can relate to and be friendly with are other children and older adults, who are more tolerant.
For this reason, both self-image and management by others, it would be preferable for growth of severely disabled children to be greatly limited. There is no advantage for a profoundly disabled, nonambulatory person to be full-sized because the person is unable to stand up in the first place. Provided that patients are carefully evaluated for potential maturation and reversal of the profound disabilities noted in early childhood, there are many advantages to be had by limiting growth to a manageable size.
An article in the New York Times (NYT) describes the dysfunction of Louisiana’s court system thanks to Governor Bobby Jindal’s efforts to cut taxes and state services in order to look good for a run for the Republican Presidential nomination. A commenter mentions that there is a $2 billion hole in the state’s budget. As a result, infrastructure and all state services are being cut back. The worst affected is the criminal defender’s office, which exists to support the indigent defendant’s right to representation by a lawyer.
Indigent defendants are being told that they cannot have a trial date set because they there is no public defender available to represent them. For some, this means being in limbo indefinitely; for others, this means being in jail indefinitely because they cannot afford bail. The state has attempted to draft lawyers to be public defenders, but many of those picked have no criminal experience and make weak trial lawyers.
In Louisiana, unlike almost all other states, defender’s fees are paid out of collected court fines. Police have been writing fewer tickets and smaller fines are being assessed, but there are still more prisoners in Louisiana than any other state. Many defendants, for lack of a lawyer, have no court dates set. Some are at liberty, but others are imprisoned because they cannot pay excessive bails. Without lawyers, they cannot negotiate lower bails, so they sit in jail indefinitely.
Louisiana was rated in a Politico article recently as the lowest state in the country for quality of life. The state receives $1.78 for every dollar it pays in to the federal government, typical of Republican-controlled states, most of which do not pay enough in taxes to support the services that the federal government provides. In addition, state taxes are highly regressive: for example, the state sales tax is 10%. Meantime, the chemical industry is heavily represented in Louisiana, and pays little or nothing in taxes.
Here are some typical comments posted in response to this article:
Dallee of Florida: No right to speedy trial, one constitutional protection gone. No abiding by Miranda rights, right to self incrimination gone — did you notice that police interrogation was going on without counsel after charges were filed? Right to counsel in a felony denied, Gideon rights gone. Bail set seemingly without regard for community ties and likelihood of appearing on an adjourned date, so the bail standards are unreasonable. Court economics based on fines collected, a problematic system which lead to federal action in Ferguson. Hard to find anything going right in the criminal courts of Louisiana. Shameful.
We can ask, with sarcasm, whether the GOP sure does know how to run a government? No, it doesn’t and the rights of our citizens are being trampled into the ground and their lives destroyed. The Way of the Tea Party is a path to destruction.
infrederick of maryland: It is really simple. The sixth Amendment says they must get a speedy trial and the Supreme court has ruled that if they do not get one they must be released, with the charges dismissed with prejudice. Evidently Louisiana needs to have the Federal Courts tell them flatly: either pay the necessary costs to have a system of Justice so that defendants get a speedy trial with a competent attorney or they go free. Leave it up to Louisiana if they want to raise the needed revenue or not. However if they refuse to raise the more revenue to pay for trials, then they will have to prioritize which cases to try and let the rest go.
Chris Bradfield of Kansas: The poor lack the means to legal defend themselves across the nation.
Amend the laws to state that the government can not spend more the. The defense.
The state has unlimited resources to prosecute a person, who’s life is destroyed as they do not have unlimited resources to defend themselves.
This has become a nation where the justice you receive is based on the amount you can pay…Paying Attention of Portland, Oregon: This is one side of a very sad and troubling coin; endemic poverty. There is a lot of money in Louisiana, it is just not very evenly distributed. Moreover, the haves have extreme contempt for the have nots. The public education system is an abomination, there are few jobs available for the multitudes of unskilled and poorly educated potential workers and, in a pull yourself up by the bootstrap culture, the rich and the poor blame the poor for their failures.
In sum, it is a third world economy right here in the middle of the USA. And it is not unique to Louisiana. The anger, frustration and fear experienced by those the high tech global economy has left behind is what is fueling Trumpism. The number of voters who support Trump should be a HUUUUGGGEEE wake up call that it is time for some major socialist redistribution. Sanders will never win the election, but his ideas must take root. The accumulation of wealth by the top 5%, let alone the top 0.1%, is unsustainable and will lead to social disorder on a scale that will make Louisiana’s substantial problems look insignificant.
kalpal of Columbus OH: Once upon a time a few decades ago there were lawyers who practiced in storefronts and were funded by the government. Due to their successes at vanquishing evil slumlords and various other wealthy miscreants, their storefronts were shuttered and they were dismissed. After all why should the poor and disenfranchised be represented by willing and competent attorneys at the expense of the miscreants who created the poverty and disenfranchisement?
ccg of New Orleans: Being a Louisiana resident for the last 30 plus years, the real problem is that we just finished 8 years of suffering thru the worst governor in our history – Bobby Jindal. He was basically our George W. Bush in that Jindal followed the neoconservative playbook to a T – cut income taxes and raise sales taxes, give corporations anything they want, and slash all social programs and public services to the bone. Jindal left Louisiana last month with a $900 million hole in this fiscal year’s budget and $2 billion hole in next year’s budget. For a poor state like we are, that is a ton of debt. State colleges and universities have already been cut to the bone to where professors and students are leaving the state, public healthcare has been slashed after Jindal refused to take Obamacare dollars (the new Democratic governor took Obamacare his second day in office), and all law enforcement for the indigent has been decimated as this article describes. Same thing W did to the country and Gov. Brownback has done to Kansas. The worst part in La. now is the Republican controlled House is refusing to raise taxes so is trying to continued Jindal’s failed policies which may result in private hospitals refusing to treat indigent or even Medicaid patients and a new billion dollar LSU teaching hospital could be shuttered. Yet the GOP still cannot figure out why they can’t win presidential elections and their party is in shambles with a blatantly incompetent Trump about to be their leader.
winthropo muchaco of Durham, NC: The article doesn’t mention the fact that all the judges of the Orleans Parish Criminal District Court were sued last year in federal court in New Orleans for using “court” fees they extort from indigent defendants upon pain of languishing indefinitely in jail to pay for as many 19 supplemental medical insurance policies for themselves.
One judge, Camille Buras, formerly chief judge of the court, had a pitifully lax punishment for her role in the scheme handed down by the judicial disciplinary committee of the Louisiana “Supreme” Court: she was required to publish an apology buried in the classified legal notices of the Times Pickyournose and agree to repay the monies she had scammed. Leave it to the Louisiana Supremes to make the characters in Confederacy of Dunces look like geniuses.
Judge Jerry Winsberg, quoted in the article, now retired from the Criminal District Court benefitted for many years from the scheme as well. Crocodile tears for Louisiana’s indigent defendants.
melissa: This story never mentions Gov. Jindal, whose disastrous anti-revenue crusade is behind Louisiana’s fiscal problems. From Eric Levitz, NY Magazine: “When Bobby Jindal moved into the governor’s mansion in 2008, he inherited a $1 billion surplus. When he moved out last year, Louisiana faced a $1.6 billion projected deficit. Part of that budgetary collapse can be put on the past year’s plummeting oil prices. The rest should be placed on Jindal passing the largest tax cut in the state’s history and then refusing to reverse course when the state’s biggest industry started tanking.”
PMJ of Lafayette, LA: Let’s not miss the lining here, which is tarnished but silver. I and other lawyers are devoting countless pro bono hours to the crisis. We were not ordered; we were asked, and we responded. While few of us have done significant criminal work, more experienced members of the bar are mentoring us. You don’t need to work in criminal courts long to know that there is a larger crisis here that goes beyond the justice system. A whole generation of lawyers here will see firsthand what they might otherwise never have experienced, namely, how the really poor live, and how the odds are stacked against them. Call me an unreasoning optimist, but I think it just might lead to progressive change.
Zika Virus Invades Puerto Rico
According to the Centers for Disease Control (CDC), Puerto Rico is about to experience an epidemic of Zika virus. A quarter of the population of the island will have Zika within the next year; eventually eighty percent of the 3.5 million residents will have been infected. Puerto Rico is a very dangerous spot for mosquito-borne infections because its sub-tropical climate is perfect for mosquitoes. There are also many people on the island who are exposed to mosquitoes due to lack of screening on windows and lack of air-conditioned spaces indoors. Most people living in Puerto Rico are poor and unable to afford any defenses against mosquitoes.
The New York Times, in the article cited above, states that thousands of workers needed to control mosquitoes have been laid off. In addition, the chemical used to fight adult mosquitoes no longer works, and the one used to attack larvae has been taken off the market. Nonetheless, the island’s health agencies have been doing their best to install screens in schools and clean up trash where standing pools of water can incubate mosquito larvae. Insecticide spraying has begun in many communities, although it is unlikely to be very effective.
Puerto Rico is in better shape than Brazil was because of the early warning that health officials have received. Only 249 confirmed cases of Zika virus have been reported so far, but officials believe many more cases have gone unreported. Workers are emphasizing protection of pregnant women, including wearing pants and using DEET insect repellent regularly. Putting screens on the windows in high schools can help because many girls in high school are already pregnant.
An agent in use since 1965 was discontinued by the manufacturer recently. The drug, temephos, is effective against mosquito larvae, but it didn’t have sufficient safety data on hand according to the Environmental Protection Agency. When the testing, which would cost $3 million, was demanded, the company that makes it decided to simply stop making it. Apparently the profit from making the drug wasn’t sufficient to justify the testing. There is still a nine month supply on hand in Puerto Rico, and the EPA could issue an emergency decree to make more.
The other problem besides mosquitoes is that Zika is transmitted sexually, and distribution of condoms is being tried to help block this method of spread. However, most islanders are Catholic, and the Church prohibits the use of “artificial” birth control methods. Instead, the Church has told its members to practice self-restraint. This is a particular problem because even pregnant women need to be protected from sexual transmission with condoms.
CDC Announces New Opioid Prescribing Guidelines; Naloxone Pen Distribution is Best Life Saver
There has been a big controversy over the release of the new guidelines by the Centers for Disease Control (CDC) but it seems to be an over-reaction. The guidelines advise that Vicodin or Norco are not first-line treatment for acute pain, nor for mild chronic pain. The guidelines do allow for some patients to use some quantities of opioids, but with caution. There is no prohibition on using opioids when a patient has severe, chronic, noncancer pain. The condition must be evaluated and properly diagnosed; efforts to correct orthopedic problems that cause wear and tear with chronic inflammation are very important.
If a patient has pain, it must be controlled well enough to continue with the activities necessary to daily living. Going to work is necessary for many people, and if it causes pain that can’t be controlled with non-steroidal anti-inflammatory drugs, then sometimes hydrocodone is necessary. The problem is that there are many people who say they have pain, who really don’t have significant pain. There are other people who have started taking opioids and are dependent on them, even though they don’t have significant pain.
The primary care provider, the receptionist, and the nurse take the brunt of patient demands for opioids. The patient is sure to be dissatisfied if their demands are not met. In some cases, the patient may become violent and there are stories about patients brandishing firearms in their efforts to get drugs. I know of more than one fatal shooting that occurred because the patient demanded, and was denied, a common narcotic pain killer.
What is just as bad, is the overdoses. The number of fatal opioid overdoses has increased by 200% since 2000 and is now at a record level, parallel with the increase in prescriptions and sales of narcotics. The exact mechanism for the increase in overdoses is not completely clear, but it appears that patients sometimes take an unexpectedly potent form of a known drug such as heroin, or take a larger than normal dose because of prior shortage. Perhaps the overdoses are in part intentional and reflective of a suicidal predisposition; that possibility has not been completely ruled out.
According to the CDC’s Morbidity and Mortality Weekly Report for January 1, 2016, there has been a dramatic rise in overdose deaths due to fentanyl because of the production of illicit fentanyl by underground chemists. In 2014, there were 47,055 deaths from all drug overdoses, exceeding deaths from motor vehicle crashes by one and a half times. There were significant increases in death rates in both sexes, all age groups, ethnic groups, and regions of the country. West Virginia had the highest rate of deaths from drug overdoses. 61% of drug overdose deaths were from all opioids, including heroin. Heroin overdose death rates increased 26% in one year and have more than tripled since 2010.
It seems that heroin use has also increased dramatically in the last few years and that the biggest factor in the increase has been the transition from prior use of prescription opiates. The relative cost of heroin and its high purity has contributed to the patients’ switches from prescription to illicit opioids. Illicit fentanyl has also been available and is sometimes mixed with heroin. Pure heroin and fentanyl are probably contributing to accidental overdoses due to product potency.
The fact that the quantity of opioids prescribed has increased four times since 2000 has a great deal to do with the epidemic of opioid overdose deaths. Patients receive significant amounts of drugs from doctors but are eventually cut off or find the drugs inadequate, so they switch to heroin. The high quality, nearly pure heroin cheaply available on the street is satisfying the desire to “get high” but puts the user at risk of accidental overdose.
Illicit fentanyl is being mixed with high purity heroin and sold as “China White”; since fentanyl is 50 times as potent as morphine, the chance of overdose increases further.
Based on this reasoning, the single action most likely to reduce overdose deaths is the widespread distribution of naloxone injectable pens to addicts, emergency workers, and anyone else who is likely to run into a patient who has overdosed. Naloxone can temporarily reverse the respiratory suppression caused by overdose and could save the life of a patient who has lapsed into a coma and stopped breathing after using too much heroin or fentanyl.
Zika Vaccine Not Soon
An article in the New York Times states that the World Health Organization (WHO) has announced that a vaccine against Zika virus will probably take years to develop and will not be in time to help with the current epidemic. Although many organizations are researching potential vaccines, the furthest along is six months from human trials and probably three years from widespread release.
Research has also shown that spraying insecticides against mosquitoes is ineffective at reducing the incidence of dengue fever, a closely related virus. Nonetheless, spraying will continue as there is no other effective approach. The use of genetically engineered mosquitoes to reduce the population is promising, but the numbers are still small and again there is likely to be several years delay before a large enough number of mosquitoes can be produced.
The most effective approach at present is to stay in air-conditioned residences and to wear mosquito repellent on exposed areas whenever outdoors.
At the current rate, Zika is expected to spread to the southern US within two years.
Anonymity and Anonymous
“Hacker, Hoaxer, Whistleblower, Spy: the many faces of Anonymous” written by Gabriella Coleman, is an account of her mostly online encounters with many personalities, most of them unidentified, collected over the period from 2010 to the present. It discusses what the writer describers as the “culture” of hackers. This “culture” includes a number of people who were arrested for Internet crimes such as the “theft” of information up to and including credit card numbers and passwords. The period of time referred to in the book runs from about 2010 to early 2015. A number of the people are identified by name only because they were arrested and imprisoned. During that time, the writer, acting as an anthropologist, communicated with many other, unidentified people who described themselves as hackers. She eventually did obtain a graduate degree in anthropology and now teaches.
The entire culture could be described as the Anonymous group or web, a large and very loosely associated group or groups of individuals who communicated over the Internet. Many of these groups claimed to be able to obtain information on a group that could be vulnerable, sometimes security firms. In more than one case, secret information was obtained from sensitive sites. A number of people were indicted and imprisoned for obtaining unauthorized information in the US. One young man, indicted for a wholesale downloading of an open-access journal, committed suicide after the prosecution demanded decades of imprisonment.
Many of these people were sincere in the belief that the vast majority of this information should be public and the government is in the wrong to punish people harshly for this kind of disobedience. Others felt that exposing oneself to danger in this fashion would be unwise in the long run. Fortunately for Anonymous as a movement, the most important members of the movement have managed to keep their identity, in fact their very existence, hidden from the government. Anonymous could only survive by being fully hidden from view.
The conclusion that the book makes is that any survivors have melted away and are saving their strength for a later occasion.
Conrad Theodore Seitz 