Fishing for meaning in a dictionary of genes

I disagree with you here P.Z.

Mass murder is not normal for most of the human population. The examples you gave had many other factors, including cultural differences, pressure from authority figures, institutionalized fear, and other mitigating circumstances.

The overwhelming majority of people do NOT go on mass killing sprees. Most adults are sickened at the thought of harming other human beings, especially children. There is ample evidence that mental illness has genetic components and a history of mental illness is a common factor in these kinds of incidents. Mental illness is also more common in some families than others.

So, examining Adam Lanza's DNA alone will probably yield no useful results, examining the DNA of several mass murderers might come up with genetic markers more prevalent in them than in the general population. It would point to certain kinds of mental illness being at least partially genetic and giving those individuals higher chances of violent actions.

Not every mentally ill person is going to become violent and hurt people. For that, it we would have to look at the environmental triggers and circumstances (access to weapons, lack of mental health care, stress, etc).

So biology is a precursor to whether one chooses to behave violently or not? Supposing one is inclined to go with that belief and find that people like Adam and him exhibit a tendency to show gene duplications, deletions or unexpected mutations, are we to now infer that people with such apparitions are now a danger to society? Isn’t that like saying people with curly hair or blue eyes are now more prone to violence? Or how about people who live in one part of the world who over time have exhibited a certain genetical strain, are we to now suppose those individuals are more prone to anti social behavior or even the opposite, better able to adapt to stress in the environment?

http://scallywagandvagabond.com/2012/12/geneticists-hope-to-uncover-sec…

I think you could also reflect on what the article suggests about the state of general science education in the population--though, in addition to that, it suggests that scientifically-educated people also exhibit an astounding degree of misunderstaning.

"Standard" ( i.e. the accepted and dominant paradigmatic views, the basic dogma taught in university departments everywhere, in ) genetic theory is truly a spectacle of people wandering in a theoretical wilderness, lost and grasping desperately at even ridiculous concepts--numerous of them throw-backs to Aristotelian conceptions of essence in things.

My recommendation as an antidote to the reigning stupidity is the work of Jean-Jacques Kupiec, Pierre Sonigo, Thomas Heames and their associates in the biological sciences.

Otherwise, get used to more insane bright ideas driven by vitalist -thinking, essentialist-thinking, finalist-thinking: the reintroduction once through the back-door (but now, again, right through the front-door ) of theology dressed up in science-y clothing.

"Garbage-in, garbage-out." !!!!!

Ooops. Spelled "Heams," not "Heames" --no final "e" in that.

from the site, "Slate", on Richard C. Francis's book, "Epigenetics: The Ultimate Mystery of Inheritance"

Goodbye, Genetic Blueprint
What the new field of epigenetics reveals about how DNA really works

By Christine Kenneally|Posted Monday, June 20, 2011, at 9:52 AM ET
link: http://www.slate.com/articles/arts/books/2011/06/goodbye_genetic_bluepr…

@scallywag: No, but we can tell people that they may be more predisposed to mental illness that can lead to violence.

Doctors already warn people when their family history indicates a genetic proclivity for heart disease, diabetes, hemophilia, asthma, and many other diseases and disorders. What's the difference?

mmm .. Excellent and timely post .. thoughtful comments

Family, peer group(s), culture, community. Environment.. Of course we are somewhat hard-wired by the time we are born.. then it all comes together, gets shaped, evolves, blown in the wind. Experience and that great shaper of people and events come into play ... time.

My genetics are unknown to me or to the public or the world of medicine or speculation. To think science might foresee that I would grow up without being able to remember my mother or my father, would excel at sports, flail scholastically, be hired at age 20 as a maximum security guard, work with drug addicted juveniles, become a photographer, own a number of guns, become a father, work with the emotionally disturbed as a youth worker, write a novel, grow up on a farm, buy an iPad is... well .. laughable.

Would those genetic markers foretell that a cemetery monument would break free and fall on me at age three? And that I did not die because the piled earth of a recent grave prevented the damn thing from completely crushing me? (whereby my genetics beyond age 3 would be moot .. null n void)

I'm not a scientist or a biologist (neither of which is acceptable in Canada currently) but I am a realist, and an idealist... and the thought of any single one of us having our genetic data paraded for the Russian or Canadian judge to give me a score of 6.4 on the psycho rating is pretty whacko

Just think of it.. 'We think young Jimmy is OK till age 11 based on the genetic evidence.. certainly he will gravitate towards guns, ammo and dark thoughts by age 12. Friends and family will see his as a normal warm and caring... ' Well .. you get the idea.

It would likely be better to aim science to search the world for a sea lion that will rule the world justly ... or a sea gull.. a cockroach or mushroom

A better angle would be to search for similarities in the DNA of Wayne LaPierre and other mass murder brokers with that of people who follow the meme of the NRA.

Ah .. well said, Don ....

@darth_borehead
There's a big difference between inferring inherited traits from a history of common or similar behavior in a family (i.e., a family history) and imputing genetic eftects by looking at the genome of a single person, especially when we have no idea what most of the sequence codes for.

If they're going to look for genetic causes, then they need to look at the entire human race. The Jewish people don't like to admit it, it's not politically correct to point it out, and it does not mitigate the pain they suffered in the Holocaust or the actions of the German people who were involved or who knew and looked the other way, but the Torah records the massacre of the Canaanites because "God said." The Christians and the Muslims happily butchered one another for hundreds of years, as did the French and the English.

The Mongols invented biological warfare - a hideous idea only refined today by the US military. (It is worth noting that Mongol genes can be found in several hundred million people worldwide, and the world has seldom seen a people so devoted to warfare. ) The Chinese came up with brutal forms of torture, yet were nationally enraged by the Rape of Nanking. Still, it was a Chinese guy who, within days of the Sandy hook shooting, took out just as many people in China with a KNIFE.

The Romans based their kalends and their entire way of life upon war, and they were good at it. When they were not at war, the population was soothed by the bloody shows of the Coliseum (and other, lesser-known gladiatorial arenas scattered all over the Roman world). Public execution was a common scene throughout the medieval world, often accompanied or preceded by scenes of horrific torture - which also continues to this day. Abu Ghraib should sound familiar.

The hundreds of tribes native to Africa have been busy with their own wars for millenia as well - witness the Rwandan genocide, the war in the Congo, and the atrocities that continue every day in Darfur.

A hospital in Syria that pushed itself to the limit every day to serve the Hippocratic Oath every day, with limited supplies and little hope, was bombed to rubble for the crime of serving life, regardless of what uniform that life wore.

In Saudi Arabia today, it is considered fair and acceptable for a woman to be stoned to death for being a rape victim. But to some, it is also perfectly acceptable to go blow up a bunch of innocents - in the words of a famous commander, "Kill them all, let God sort it out" - because they worship a different god, or that you have to restore the family honor by brutally murdering your daughter because she kissed a guy without your permission.

The Westboro Baptists, who hide behind religion and use the image of God to promote their brand of vicious hate - the KKK, infamous for the racially-motivated hate crimes, now saying even the Westboros have gone too far.

And what about the complete lack of morals, ethics, or even basic human regard for the situation of another that drives the capitalist chase for money and power in the Westernized world? The willingness to countenance the suffering of thousands, or even millions, of other human beings, or to poison or steal their resources, or lie, or knowingly create great hardship for them, all for the sake of maximizing one's own (or company's) profit? Or the warlords who are willing to deny their own people food and medicine to maintain their power base, and directly cause millions of deaths among their own people that way. This is in any way NOT pathological?

Of all these examples - and I could easily go on - the idea that one American crazy's brain holds the keys, or even any keys, to what makes mass murder possible is utter bosh. As cruel as it sounds, the shooting rampage in Sandy Hook that left 26 lives ended and countless more ravaged was only one more word in the sorry story of human violence against other humans.

The potential for murder lurks in ALL of us - it is the dark shadow of the psyche that nobody wants to confront. We raise our children, across cultures, to value war and violence. War will not end, nor the desire to see many people dead, dying, or suffering, until we AS ONE PLANET move beyond the desire to wage war and death and suffering upon one another.

@darth_borehd
some features are associated with the DNA (in deed), but I think mental diseases are more related with the expression of some genes (RNA not DNA), since the expression of some genes is related with the environment, is the environment the thing we need to study for avoid this horrible events and this is what scientists have been doing the last years. So studying the mass killer's DNA with this reason in mint is a waist of time and money. money that need for improve the life of some people and avoid a bad environment.

No doubt, study of any individual's genetic markers will reflect the fact that all of us have evolved (?) from forebears to whom the ability to purposely harm other humans, whether individuals or whole tribes of "others", had survival value. That this propensity has become institutionalized at the group level (i.e. family, tribe, nation...) will not be on the basis of genetics, but on the "evolution" of so-called "civilization". Biology will neither account for nor explain this behavior, although a study of anthropology and history might. Unfortunately, none of this seems to suggest any viable ways to change this behavior.

A complex behavior is not rooted in a gene. Does nobody actually understand cell biology nowadays? There's so much research out there that emphatically disagrees with our mistaken concept that a complex trait is decided by a single gene.

Genes code for products, be they ultimately RNA or protein. That's all. There's not a single RNA or protein product that "causes" a behavior.

What with all the research which has been done, we should really be lightyears beyond this simplistic concept that gene = trait. And the sad thing is it isn't just the layperson who's latched onto this concept but scientist alike. I swear, sometimes I think people just don't look at the evidence before their eyes. Any person who studies a single cell can could see how complex it is, let alone whole tissues and entire multicellular organisms!

Hypotheses (turned into "theory) leading the data. :/

RE: E.L. Williams's comment @ 28 Dec. :

"What with all the research which has been done, we should really be lightyears beyond this simplistic concept that gene = trait. And the sad thing is it isn’t just the layperson who’s latched onto this concept but scientist alike."

Amen to that. My question: why aren't we far beyond such simplistic beliefs?

Do "Genes code for products"? Are genes "carriers of information"? In what sense? How does a cell, let alone a molecule of a cell "read," or "interpret," the "code" or its "information"? Are these terms simply regarded as very loose metaphors? Peter Godfrey-Smith (Harvard) discusses the question in an essay, "Information in Biology" contained in Hull & Ruse, "The Cambridge Companion to the Philosophy of Biology (2007).

It's seems to me beyond question that people--both expertly trained scientists and, moreover, many, many lay-people, assume that genes "code," they transmit "information" in the computing sense of the term--as though there is some data file and it is in some real sense "uploaded" and "downloaded" in the processes of cells' activities.

For example, writing in Self Comes to Mind: Constructing the Conscious Brain, professor and researcher in neurosciences (Univ. of Southern Calif. and Salk Institute, La Jolla, Calif.) tells us (in part IV, chap. 11), in a brief side-note entitled, "Note on the Genomic Unconscious," (my translation from the French edition so I vouch here only for the main gist of the points as presented)

"What is meant by the genomic unconscious? Quite simply the collossal number of instructions which are contained in our genome and which command the construction of our organism, indicating to it which are the distinctive traits of our phenotype in the body properly speaking and in the brain, to then participate in its operations."

There is no question that Damasio is a brilliant sceintist or that he has many extremely important insights to offer readers in understanding the physiology and operation of the brain and the ways in which consciousness emerges from it. That said, how are we to understand and explain that such a brilliant and experienced scientist can seem to credit the idea that genes possess coded information which, when apparently "read" by and through the workings of cells and their components, prescribe a predetermined physiological outcome as though by design and intent somehow, somewhere?

revision/correction:

..."writing in Self Comes to Mind: Constructing the Conscious Brain, professor and researcher in neurosciences Antonio Damasio (Univ. of Southern Calif. and Salk Institute, La Jolla, Calif.) "....

RE: (NY Times: "Scientists Seek Clues" / "News Analysis
Seeking Answers in Genome of Gunman")

link: http://www.nytimes.com/2012/12/25/science/scientists-to-seek-clues-to-v…;

"Some researchers, like Dr. Arthur Beaudet, a professor at the Baylor College of Medicine and the chairman of its department of molecular and human genetics, applaud the effort. He believes that the acts committed by men like Mr. Lanza and the gunmen in other rampages in recent years — at Columbine High School and in Aurora, Colo., in Norway, in Tucson and at Virginia Tech — are so far off the charts of normal behavior that there must be genetic changes driving them. "

So, if the article represented him correctly, Dr. Beaudet apparently hypothesizes that cases such as this are in some sense what one could regard as "outliers"--extremes; and that there could be valid reason to search for exceptional indicators in the subjects' biological make-up.

Wise or wacky, both or neither, Dr. Beaudet's credentials are impeccable :

Professor and Chairman, Department of Molecular and Human Genetics
Professor, Departments of Pediatrics and Molecular and Cellular Biology
B.S., College of the Holy Cross
M.D., Yale University School of Medicine
Resident in Pediatrics, John Hopkins Hospital
Postdoc, National Institutes of Health

http://www.bcm.edu/cmb/?pmid=2040

>>Amen to that. My question: why aren’t we far beyond such simplistic beliefs?

Do “Genes code for products”? Are genes “carriers of information”? In what sense? How does a cell, let alone a molecule of a cell “read,” or “interpret,” the “code” or its “information”? Are these terms simply regarded as very loose metaphors?<<

I really do think that we've allowed ourselves to be carried away by metaphor. Probably for a variety of reasons. I'm no scientific historian, but I would imagine what with the advent of computers around the same time that Genetics was being popularized, the metaphor of "code" was in early use and the two have, essentially, "grown up" together. And nowadays, most of our society has been raised with such concepts. It pervades our medical science, our media, even our colloquialisms: "It's in our genes!" And being human, a combination of both scientist and poet at heart, we do seem to love our metaphors.

Probably until there's a truly unique paradigm shift away from the "blueprint DNA" metaphor, we'll continue to have these problems. I admit, I have difficulty myself not switching back and forth. Why? I'm not sure. The metaphor is just so enticing, so easy to envision. And so engrained.

Re, the issue of "coding", I think it's just an illusion. Life is based on a certain replicability. "Duplication with variation" as Weiss & Buchanan (2009) say. And according to most Origins of Life scientists, the ability to replicate is the defining element to Life. And so in order to replicate, one generally needs a template so that one might ensure heritability. In the case of modern cells, that basic template for replication is DNA, although there are obviously huge numbers of regulatory elements and post-transcriptional/translational modifications. But at the basis of modern life is a template (although there's debate in OoL science what was in fact the original template, be it nucleic acid or something metabolic like the Citric Acid Cycle). So even though calling it a "code" is kind of like putting the chicken before the egg, it's only wrong in the way we've gotten it turned around and given a sense of "design" and "purpose" to it, when if it weren't some sort of template formatting, it wouldn't have evolved at all.

Note that a literal nucleotide template is only one possibility for replication, but the benefit being that it allows a variety of products to be made based on modularity, simply mixing and matching. A metabolic system like the Citric Acid Cycle simply produces more of the same or similar product, which ultimately ends up as a limiting factor concerning evolution. While simple metabolism may've been a first step towards life, having a nucleotide template has underlain variety through modularity.

RE : Emily L. Williams @ December 30, 2012

For me, your comments exemplify what is best in a scientists' (or "even" a non-scientist's) ability to examine critically the most basic presuppositions that inform one's daily work and to admit where and how they may be lakcing in rigor. The comments are also exemplary of what I find so needed-- but too often missing from comments by scientists who address the general non-specialist reader--needed by people who, like myself, look to science for sound reason.

Thank you for so thoughtful a reply to my own post.

The following article caught my attention recently; you might find it interesting in the light of these issues---

"Cancer scientists identify a new layer of complexity within human colon cancer"

http://www.eurekalert.org/pub_releases/2012-12/uhn-csi121212.php

My personal view is that, while the observations described are immensely important, there is little or nothing actually "new" in these findings; what's being described there as a paradigm-shift is, I agree, just that. However, properly credited, it occurred first some decades ago in the work--I mentioned previously--pioneered (but negelected by angophone scientists) by Jean-Jacques Kupiec.

(from less recent to more recent)

http://www.ncbi.nlm.nih.gov/pubmed/9236778
http://www.ncbi.nlm.nih.gov/pubmed/19917305
http://www.sciencedirect.com/science/article/pii/S0079610712000387

Meh, there's pretty good evidence for genetic differences as an underlyng causative factor in mental illnesses. As one commenter noted, a gene codes for a single product, often transcribed into a protein (although PZ would probably correctly point out that it could just as easily code for an ribozyme or a transcription factor of some sort).

The thing is, this can still have an effect om behavior if the gene codes for one of the many complex proteins that are present on the cell membranes of neurons. A mutation in genes that code for a particular ligand receptor are going to alter how neurons react to certain electrochemical signals. A mutation to a gene that codes for a VMAT protein is going to directly affect how readily neurons clear certain neurotransmitters from the synapse. Other proteins and transcription factors may influence the densities of such proteins on the cell membrane itself.

However, PZ is ultimately correct in that Adam Lanza represents n=1, which is useless for a GWAS...especially in the absence of a known diagnosis and without comparing his DNA to family members. Even if he is found to have a genetic mutation known to be associated with schizophrenia or some other serious mental illness, that doesn't confirm that he must have had such an illness. There are better ways to make that determination anyways by having forensic psychiatrists speak to friends and family members and examine any diaries if available, although even then that's a bit of a crapshoot without being able to examine the patient.

Tl;dnr: There's nothing silly about the idea that genetic differences may lead to behavioral differences. It is ridiculous to bekieve that one can reach any sort of conclusions from a sample of n=1, however, and the research so far is not conclusive enough to be appropriate for diagnostic use anyways.

I have a suspicion that it might be something altogether different than presumed. I have been doing research on http://epa.gov/endo/pubs/edspoverview/finalrpt.htm not a doctor nor a scientist. This study was first started in 98 by the Clinton administration. I suspect it is more far reaching than even they are aware of. In a nutshell different chemicals steal your hormonal key which means yours no longer works correctly. Kinda like being hacked by a computer hacker and you've downloaded a computer virus.. We have regular hormones and releasing hormones like a stop and go system. Obama has reopened this study to include more testing on more chemicals. One would have to take past ancestral history of exposures into account as well as present history of exposure. I started it as a hobby. My family and my husbands grew up in a farming community 50 years ago next to an Air Force Base and many of us are now ill. I also started noticing the increase in sex offenders including police officers. Looked at the fact that over 150 of our army committed suicide last year and started reading stuff Toxtown Epa stuff you name it.. Map it out look at the areas they come from look at superfunds and surrounding area toxic spill stuff etc. Now look at the clusters whether it is mass murder suicides etc and what chemicals they were all exposed to and you start to see patterns. Perchlorate pops up alot in regards to suicides. Mass murder I havent encountered a connection but if someone who knew what they were doing was to check it out maybe they would see what I have been seeing. Releasing hormones are tested differently than regular ones and who thinks to look at that when studying genomes is so much more fascinating. Don't get me started on the ion channel research going on dare I say it "The ultimate signal in excitable cells is a change in intracellular Ca2+, which mediates the effect of cellular electricity". Investigating something this complex is going to take way more than just researching genetics. Your right PZ Meyers thanks for writing this it was an interesting read! Happy New Years!

DNA has nothing to do with sin. Evil influences people, but mind altering drugs also cause events such as this.

There is a dangerous mind altering drug called scopolamine which eliminates free will if inhaled. Basically you could blow this stuff in someone's face and they could be influenced to do just about anything you want them to do. Deros?

Besides litle is being said about the second shooter in this incident. Is it not very convenient that all of the eyewitnesses who saw Lanza and a potential second shooter are all dead now? These mass shootings ALL have one thing in common - every single shooter was on mind altering drugs prior to the event. Every single one of them.

Now, I am not sure wether these shooting were random acts of violence caused by evil influence and mind altering drugs OR wether government forces picked these suspects out to do carry out these acts in order to gain more control and disarm the citizenry to get ready for the upcoming global government rule.

Sure I will be called a so called "conspiracy theorists" since I am willing to question authority and question reality, but I would be willing to put money on the fact that these events are all have federal involvement somehow. Looks like the illuminati still runs things as tightly as ever. I am willing to bet money that this whole thing was a staged event.

The government tried mass shootings before in Arizona, Colorado, and other places hoping to get the public angry enough to demand that guns be banned. They finally pulled it off. Congradulations, my hairy palmed overlords.

Gun control has little to do with guns and alot to do with CONTROL.

Lanza's DNA is not going to help anyone, unless they plan on building more of him or soemthing.

Plants get used alot in these federal endeavors
http://www.infowars.com/fanapt-hoax-hides-real-connection-between-shoot…

"Why? Because some scientists are stupid."

more importantly, some guys with big money are stupid, and they're willing to give a grant to any scientist who will somehow reach the findings that they want.

Specifically, there's lots of gun aficionados (i'm trana be polite here) who think, Well Guns aren't the problem, it must be the other main scapegoat, Mental Illness. And for any quality of a human, some people think you can find a gene for it. Like for instance, tallness is dictated by like 400 genes, none more powerful than a tenth of an inch. But, you know, if they could find a gene, that might postpone gun control legislation, cuz most voters and politicians are similarly uninformed.

Actually Stanley Milgram proved in the 1950s that like half of all people could be coerced into killing, given the right authority figure and situation. Look up 'Milgram Experiment' in Wikipedia.

'Do “Genes code for products”? Are genes “carriers of information”? In what sense? How does a cell, let alone a molecule of a cell “read,” or “interpret,” the “code” or its “information”? '

Genes are carriers of information just like any computer file or piece of paper or lecture over the radio.

DNA is a string of molecules; there's four different ones, A T G and C. We've got like 3 billion of these bases. Machinery in the cell transcribes groups of 3 bases into different amino acids. There's about 21 different amino acids.

For instance, TGG makes Tryptophan. AGG and CGG both make Arginine. These amino acids string together to make proteins and hormones. Different parts of the protein string attract or repel other parts, so it can fold to make a sheet or just about any other shape. These proteins then float around the cell somehow and make it grow. and divide. or whatever the cell is supposed to do.

A 'gene' is a string of DNA that codes for one protein, some thousands of bases long. Most mutations are just a change in one base. Many of them have no effect at all, but some disable/enable the whole protein. so for instance, then you get blue or gray eyes cuz the pigments are proteins.

"Machinery in the cell transcribes groups of 3 bases into different amino acids. "

So, there's this "machinery" in the cell

--but my question was how (in this instance, according to you, this machinery in the cell) this "machinery" can "read "interpret" the "information".

Isn't all such "explanatory" verbage simply descibing via ex post facto attribution things which were not and still are not able to allow us to predict, from a coherent theoretical standing, what happens (and why) when we concern ourselves with things we haven't already observed ?

and it recognizes the bases? Understands what they are, what they're "for," and then "transcribes" accordingly?

The "machinery" must have recognized that, when presented with with either AGG or CGG, the "product" should be the same---namely, arginine.

Why do genes bother to handle "code" which is without any effect at all?

revision / correction:

... "which we're (not "were") not and still are not able to allow us to predict" ...