mellowtigger: (dna mouse)
Most people know that they get half of their dna from their mother and half from their father. What most people don't know, however, is that they also inherit another kind of dna exclusively from their mother. The mother provides the "egg", and the egg is very special. It includes extra material that every cell needs to survive and replicate. One vital feature inside our cells is the mitochondrion, a small factory that produces the chemical energy that we need to thrive. Mitochondria have their own dna, separate from our regular dna, and we inherit it entirely from the egg.

Without mitochondria, we would slowly die. Our cells individually would simply run out of fuel to function. I kept up with news in the early 1990s about medical trials because I knew college students who participated in this "job" sector as volunteer medical test subjects. I remember that one study was terminated prematurely because its participants died. They discovered that the drug was destroying human mitochondrial dna (although it did not harm dogs in previous tests), so their test volunteers were slowly starving to death, cell by cell, throughout their bodies. The point being that the health of our mitochondria affects our bodies profoundly, so our maternal heritage of mitochondrial dna is an important part of our genetic lineage.

One side-effect of these powerhouses doing their normal function is the production of hydrogen peroxide, H2O2. As any child who's seen hydrogen peroxide bubble on their wounds would know, this chemical is highly reactive. Since mitochondria produce it, our cells need a way to harness the chemical before it reacts with other chemicals in our cells (like our dna) and causes harm. This destructive reaction by oxygen-containing molecules or free radicals is known in a very generic way as "oxidative stress". We need antioxidants to defend against that damage.

Oxidative stress is now linked to a great many disorders, from Parkinson's to Autism and more. Of particular interest to me is the realization that it can trigger mitochondrial dysfunction in some people with autism, separate from the known long-term dysfunction comorbidity. Mitochondrial dysfunction would leave me feeling tired, unfocused, and thoroughly exhausted by physical activity... which matches nicely with my symptoms.  We've ruled out multiple sclerosis to explain my own health problems, so I've separated the symptoms of muscle twitches/cramps (which is responding very positively to a gluten-free diet) from the symptoms of exhaustion, brain fog, and apparent dopamine depletion. I am considering oxidative stress as an explanation for this second set of symptoms which has not responded to Ropinarole.

I've spent a lot of money on medical bills this year. Now that I'm earning a poor person's wages again, I have to get my spending under control. There are expensive tests for objectively measuring mitochondrial dysfunction, but doctor visits will have to wait while I slowly accumulate more discretionary funds. Instead, I'm experimenting more cheaply by taking supplements that affect mitochondrial function and oxidative stress. Most diet supplement pills are known to be ineffective, so I'm trying to stick with ones already proven to have some effect in reputable journals.

I bought some pills containing:
  • glutathione,
  • coenzyme Q-10,
  • vitamin E, and
  • selenium.
I can get more vitamin C and beta-carotene just by eating some carrots. I'll try adding plenty of turmeric spice to my meals too. I hope this combination will improve my energy level, memory/concentration, and dopamine. In theory, it should; but in practice, we'll see.
mellowtigger: (dna mouse)
I am 3.0% Neanderthal. 

Scientists have been slowly gathering testable dna samples from Neanderthal remains, but the best sample came from a 130,000-year-old toe bone.  It allowed sequencing for the entire genome, published just a month ago.  Various companies that do genetic testing are able to offer this comparison now, but my results are from 23 And Me.  Apparently interbreeding between human species happened a very long time ago, so Neanderthal genes are found in both European and Asian populations today.  Supposedly the typical European holds only about 1.7% similarity.  I'm placed in the 88th percentile among Europeans, according to 23 And Me.

I figure it's only a matter of time until somebody tries to revive the species, just as predicted in the book "Existence" (which I liked).  I'd like to meet them.  I think I'd have more in common with them than the typical Homo sapiens, besides just the eyebrows and bigger skull.  I suspect that Neanderthal psychology will have a lot more in common with modern autistics than modern neurotypicals.  I guess we'll all find out soon enough.

Slightly less dramatic, but another patron at 23 And Me might actually be a blood relative.  The website has long notified people of distant ancestry relations based on their genetic sequencing, but they added a new feature where people can build an actual family tree with names and dates.  Someone contacted me recently, and we share a suspiciously similar name in our pasts.  One of his ancestors is a "William B Walker" (born 1789) and one of mine is "Willie Burkes Walker" (born 1889).  Both family lines include tales of Tennessee before relocating to Texas.  Alone, those similarities are just coincidences, but the genetic similarity suggests that my "Willie B" might have been named after somebody's memory of a related "Willie B".  Again, time will tell.  This technology will just keep improving as the years go by.

Someday, as in the movie "Gattaca", babies will be sequenced routinely by the time of their birth.  Probably, they'll be sequenced soon after conception, so potential diseases can be addressed while the body is still in development.

Strange.  Someday, genetics might allow me to meet kin from ancestors a few centuries ago or a few hundred millenia ago.  Throw in an uplifted chimpanzee, then we'll hold a proper family reunion.
mellowtigger: (sleepy)
I have mentioned before that I have an "off switch". I first encountered it by accident in 10th grade geometry class. Luckily, it's something quite easy to avoid. My last boyfriend (some 14 years ago?) also found it once, although I never explained to him what he triggered.

Recent news about autism genetics and neuron function had me searching tonight for mention of any link between autism and neuron degeneration similar to multiple sclerosis.  There seem to be plenty of anecdotal accounts about autism and MS, so I kept searching.  To my surprise, I found the trifecta: "Possible Connection between Autism, Narcolepsy and Multiple Sclerosis" at http://aut.sagepub.com/content/2/4/425.extract.

I can't tell, though, if the findings were ever duplicated in other studies.

( Hint for the title: http://www.fireflyfans.net/mthread.asp?b=14&t=13463 )
mellowtigger: (dna)
On April 25th, 57 years ago, Watson and Crick published their article in Nature magazine about the structure of DNA.  To celebrate the 50th anniversary (7 years ago), the US Congress established April 25th as "DNA Day".

Since my last gattaca post, the company that did my own dna testing has further specified my maternal haplogroup.  I am now officially a member of the U5b2c segment of humanity.  Here's an image showing the geographic distribution of the encompassing U5 group.
U5b2c

About 44-55 thousand years ago, a woman was born within the R haplogroup. This woman had a mutation in her mitochondrial dna that allows us to distinguish her from other humans of the time.  Her descendants became the U haplogroup, and U5 may be the oldest sub-group in the European region.  This wikipedia chart shows how the main maternal group names are related.


Human mitochondrial DNA (mtDNA) haplogroups
  Mitochondrial Eve (L)    
L0 L1 L2 L3   L4 L5 L6
  M N  
CZ D E G Q   A S   R   I W X Y
C Z B F R0   pre-JT P  U
HV JT K
H V J T Former Clusters IWX

Semi-related, there is recent news that Homo sapiens may have interbred with other species of hominids.  And you probably thought that family trees these days were complicated because of all the trans-continental adoptions, illegitimate births, and serial marriages!
mellowtigger: (Default)
I've mentioned epigenetics before. Our genes contain information about everything that our cells CAN build. Wrapped around dna, however, are other chemicals that determine which of those things ARE built.  This extra signaling is inherited from our parents, and it also changes within our lifetimes in response to our environment.

Today, I see the announcement that someone has finally mapped a complete human epigenome.
http://www.physorg.com/news174744415.html

I expect useful medical knowledge to follow quickly.
mellowtigger: (dna)
Testing such as I had done at 23andme.com is not quite as useful as researchers (and afficionados like me) had once hoped.  They're finding that creatures are much more complex than just the programming in their dna.  Part of the problem is that genetics includes lots and lots of evolutionary baggage.  Study of the machinery that decides which parts gets used (instead of locked into "cold storage" indefinitely) is now called the science of epigenetics.  It's a second layer of inherited information.

Genetics covers the 4 main bases of dna, the chemicals that encode every protein that the body CAN produce.  Epigenetics covers additional chemical markers that are latched onto dna, "methylated" bases, that determine which of these possible proteins that a body actually WILL produce.

"One key epigenetic player is DNA methylation, which targets sites where cytosine precedes guanine in the DNA code. An enzyme called DNA methyltransferase affixes a methyl group to cytosine, creating a different but stable nucleotide called 5-methylcytosine. This modification in the promoter region of a gene results in gene silencing."
- http://www.physorg.com/news159111225.html

Quoting David Goldstein of Duke University, "With only a few exceptions, what the genomics companies are doing right now is recreational genomics... the information has little or in many cases no clinical relevance.
- http://blogs.wsj.com/health/2009/04/16/genetic-testing-provides-few-easy-answers/

So I added $400 to my Visa bill (in addition to about $1500 recently for car repairs *SIGH*) for entertainment.  I knew it was such when I did it, but I succumbed to curiosity.  That happens sometimes.  :)  I don't mind going into debt for that kind of entertainment.  I learn a lot from the process eventually.  I just need to get back onto this project, after other recent distractions are finally over.
mellowtigger: (dna)
First draft, but I just want to get something "finished" enough to post, because I have other tasks to work on this week and need to try getting this one out of my head for a short while.  Summary:  I have 4 autism markers, 2 uncertain, several normal markers, and many that remain untested or unexplained.

geneaddressnormalautism riskmereference
METrs1858830GGCC x 2.27, CG x 1.67CCPubMed
ADRB2rs1042714
CCGG x 1.33 - 1.60 (or even twice that)GGPubMed
GABRB2rs2617503CC or TTCT x ?CTScienceDirect
APCrs1804197AACC x ?CCPubMed
NPAS2rs1811399?C (unspecified heterozygous risk)ACNature
EN2rs1861973?C (unspecified heterozygous risk)CTNature

For many autism markers, I have the typical dna pattern instead.  There are a lot of markers that are not tested by 23andme.  There are many studies which mention specific SNP addresses but their summaries do not indicate which base pairs were involved (and I can't afford to purchase all of those articles for their details).

Some markers were tested, but I had results not indicated in any expected combination.  For example, I have AA at rs2710102 (CNTNAP2 gene) but expected values according to the article are CC, CT, and TT for Caucasian Europeans.  Similar shenanigans occur at rs1322784 (DISC1 gene).  What these differences are supposed to mean, I have no idea.  Are they:
  1. bad gene chip results (disappointing),
  2. contamination (also disappointing),
  3. brand new mutation (exciting!), or
  4. a data mixup in how the SNP addresses are reported (confusing)?
Apparently there's some kind of left-hand versus right-hand notation involved in naming the "rs#" addresses, so it could easily be a translation problem there.   Some texts, however, were just plain confusing, like rs1861972 and rs1861973 which seem to simultaneously associate for and against autism, unless I'm misreading that somehow.  I didn't get enough sleep last night, so maybe I should try again in a few days with a fresher mind.

I still have more references to check.  There are so many autism markers!  More to say in the second draft later, I guess.

mellowtigger: (dna)
I know nothing about my family heritage other than "Irish".  Someone once mentioned: Tennessee, 1800s, Irish.  Someone else would mention Irish marrying other Irish, and later more Irish marrying into the family, and later some more Irish.  Mind you, I never once heard a name associated with any of these cases.  There was only the word Irish.  That, plus we'd always been poor and there was alcoholism in the family too.  Not that racist stereotypes are to always be believed, of course.  *big shrug*  I'm just saying that the little bit I'd heard seemed to fit with the reality of American history, where the Irish lived and worked on plantations with the slaves... in Tennessee... in the mid-1800s, I think.

Well, the haplogroup testing seems to confirm it.
http://en.wikipedia.org/wiki/Human_mitochondrial_DNA_haplogroup
http://en.wikipedia.org/wiki/Human_Y-chromosome_DNA_haplogroup

maternal U5b2paternal R1b1c7

The maternal haplogroup U5b2 (left photo) is generally northern European, but it is also commonly found throughout Europe.  The paternal haplogroup R1b1c7 (right photo) is much more specific though.  The text at 23andme even says, "R1b1c7 reaches its peak in Ireland".

So, yes, I am Irish.
mellowtigger: (dna)
The email arrived at 11:07pm.  My genetic results are in.

Slight detour first, there was news yesterday about a new technology that may make sequencing much faster in the future.
http://www.physorg.com/news156953933.html

First glance at my "generic" results for specific conditions that they evaluate for people:

Research confidence:Condition:Their take:My take:
4 starsmultiple sclerosisI have 2 markers for increased risk. 0.52 out of 100 people of European heritage get MS.  0.71 out of 100 of them who have my genetic markers get MS.The neuropathy in my feet was considered several years ago to be a result of low B12 value, causing myelination problems. Something to investigate, perhaps, if I ever get health insurance again.
3 starsabdominal aortic aneurysm"Slightly increased" odds for me, based on 1 marker tested.There are only 36.5 cases per 100,000 people each year.  I'm not worried.
3 starsbrain aneurysm"Slightly increased" odds for me, based on 1 marker tested.Up to 5% of all people have one eventually.  I'm still not too worried.
3 starschronic lymphocytic leukemiaI have 2 of 6 markers.  One of them gives 1.5 X the odds, and the other gives 1.4 X the odds.I wouldn't dismiss the possibility someday, but it's not something I'm worried about.
2 starsdevelopmental dyslexia"Slightly higher" odds for me, based on 1 marker tested.If it hasn't been a problem by now, I don't think it will be.

I also have higher odds for gallstones, gout, and statin response.  I have decreased odds for cluster headaches, various cancers (bladder, esophageal, larynx, oral and throat, breast, and skin), Lou Gehrig's disease, and schizophrenia.  I also have decreased odds for Restless Leg Syndrome, but I know that I've had exactly those symptoms many times over the years.  It's all a matter of playing the odds, obviously, not a matter of certainty.

On various traits, I am typical in many ways.  I have average odds of living to age 100, typical caffeine metabolism, typical odds of male pattern baldness, typical progression of HIV-1 infection, typical response to antidepressants, and typical sensitivity to pain.  I have typical odds of blond hair or brown hair, and typical odds of blue-vs-green eye color.  Men in my family actually start out blond and grow darker soon after.  My eyes seem to change between their blue and green hue, plus I have yellow in there too.

I have one marker that suggests I eat more sugar per day than the average person, and I heartily disagree.  Sweets I easily ignore, but it's the high-fat foods that I get cravings for. 

I have one marker for reduced sensitivity to sweat odor.  Woe is me.  ;)   I have one marker for 0.16 inch (0.4 cm) shorter height than the average person.

I also have a genetic marker that was found in Dutch families to be associated with 3 IQ points higher in non-verbal scores.  I have 1 marker that's associated with 4-5 point increase if I'd been breastfed as a child.  I have 1 other marker associated with 6-7 point increase in IQ if I'd been breastfed.  (I think I was, but I don't know for sure.)

I'll examine specific markers next.  The initial review is not really anything very remarkable except for the Multiple Sclerosis risk.
mellowtigger: (dna)
The group called "Autism Speaks" has a really bad reputation amongst the autistic rabble rousers (otherwise known as self-advocates), about the same reputation as "Cure Autism Now" does.  The usual complaint is that they want to eliminate autism, and they have no autistic people on their board or in their programs.  The rallying cry is, "Autism Speaks does not speak for me!"

Well, I ran into another problem with the group.  They solicit genetic information from autistic people (and their neurotypical families), but they don't seem to offer their results to the autistic population either.  They host the project called "Autism Genetic Resource Exchange" (AGRE), but I can't tell what's being offered in exchange for our dna data.  I wanted to use their database to check for SNP addresses that I can then compare to my results from 23andme.com.  They publish no such information that I can find.
http://www.autismspeaks.org/science/programs/agre/index.php

They do have a webpage form where I can apply for access to AGRE data.
http://www.agre.org/application/app.cfm?do=app

For "Project Abstract", I submitted:
I will compare my genotype data against the database of known SNP addresses for autism susceptibility.

For "Intended Use of database", I submitted:
I have an autism diagnosis.  I am being genotyped by 23andme.com.  I want to compare my results against known autism-related SNP addresses.  Your website solicits autism information from people with the diagnosis, but it doesn't advertise how to get information back out from these studies.  I'm filling out this research form trying to gain a list of those genetic addresses that you've identified from the autistic population.  Your name does suggest that you are an "Exchange", so I'm hoping that you provide information back to the population from which you get your data.

Afterwards, I found that they have a 10-page contract that I have to print, sign, and mail off to them.  The application does say, "AGRE shall notify Principal Investigator in writing when action has been taken on said Application."  Guess I'll force them to answer my request by printing it out and mailing it off.

Their website does have a link for downloading data.  It leads to a site called ISAAC.  It says that ISAAC is founded and funded by "Cure Autism Now".  Remember them from the introductory paragraph?  *sigh*
https://www.autismtools.org/

All I want is a SNP list to add to my own compilation.  Criminy. 
mellowtigger: (dna)
I (mistakenly) thought that 23andme was sequencing my dna and sending me the "deltas", all the places in my dna that differed from the reference template.  I was wrong.

Instead, they are genotyping me, meaning that they are testing only specific locations of their choosing.  Granted, they are testing over half a million of these locations, but I'll likely find that they aren't testing every location that would be of interest to me.  Anticipating my results to arrive in 3-4 weeks, I am beginning to compile a list of SNP (single nucleotide polymorphism) addresses that interest me.  This activity is what led to me finally understand the limitations of the 23andme test process.
https://www.23andme.com/you/faqwin/sequencing/

I'm very disappointed, but I'm still very very curious about the results that I get back.  They will have some autism SNPs tested, they will have my HIV resistance tested.  So there will be plenty of data for me to pore over, just not as much as I'd hoped.
mellowtigger: (Default)
Saturday morning, I mailed off a tube of my spit.  It will take about 8 weeks to get back my results.  When the results are posted online, I will be able to view a vast number of specific points of my DNA to see how they compare against known differences in the human genome.  I'll be using the tag "gattaca" here on LiveJournal to follow my results of this personal journey.  I suspect that I will be learning a great deal about the human genome starting about 8 weeks from now.  *laugh*

"Gattaca", for those who don't know, was a great movie about the dangers of predicting human life outcomes based on the results of genetic testing.  The name of the movie is built using the same letters as the 4 chemical parts used to build a dna molecule: guanine, adenine, thymine, cytosine.

I first learned about 23andme.com a few months ago.  (Hello, [livejournal.com profile] lordalfredhenry .)  I did not feel any overwhelming urge to run my own DNA through their system, but I confess that pure unadulterated curiosity finally got the better of me.  I added $400 to my credit card debt, and now here I am waiting for results.  I've already created my community profile there, although I think you have to have paid your money and claimed your special test kit code in order to participate.
https://www.23andme.com/user/?community_profile=92caa46f527ff773

Using their sample result data set as an example, I will get about 633,000 data points from my DNA.  These data points are called SNPs ("snips"), Single Nucleotide Polymorphisms.  These are places in the long strand of DNA code that a single difference is found.  So instead of getting my complete genetic code back, I'll be getting the "deltas", the differences.  They are using as a reference template, the published "human genome, build 36".
http://www.ncbi.nlm.nih.gov/projects/mapview/map_search.cgi?taxid=9606&build=36

8 weeks until I see results.   That's 56 days.  Or 1,344 hours.  Or even 80,640 minutes.

*twiddle*
mellowtigger: (dna)
While I do believe that autism represents a different kind of human rather than just an inferior human, I make no attempt to hide the fact that evolution is messy business. Change requires experimentation, and experimentation in this context means that there will be casualties. For every creature in history that benefited from sprouting effective wings, there are countless hordes of kin that died as a direct result of their malformed bodies that failed to achieve such grace. Blind experimentation is effective. It is not, however, efficient.

So I have mixed reactions to news, like a recent article from the Times of London, about how genes associated with autism are also associated with great mental gifts. I dunno, do serious artists feel like they're being merely "artsy-craftsy" when their life accomplishments are compared to the results of people like Cezanne, Monet, or Picasso? How many times do autistics have to be compared to Einstein and Newton before we can get past this stage of our understanding?

Anyway, this story describes a study involving hundreds of students at Cambridge University that showed autistics (and relatives of autistics) were several times more likely to be found amongst mathematicians than amongst students of other studies.
The fact that autism runs in families shows that it is partly genetic in origin, but evolutionary theory suggests genes causing such a debilitating conditions ought to have been weeded out of the population. The Cambridge study hints at why this has not happened, suggesting that with variations in the way they are combined, such genes are beneficial.

On their own, such studies have to be treated cautiously because the numbers involved are small. In the Cambridge study, seven of 378 maths students were found to be autistic, compared with only one among the 414 students in the control group.
Other studies show similar patterns, so a trend is certainly developing. Eventually there will be a definitive list of autism genes, and expect soon afterwards a definitive list of autism-gene associations.
Patricia Howlin, professor of clinical child psychology at the Institute of Psychiatry at King’s College London, studied 137 people with autism; 39 of them (29%) possessed an exceptional mental skill. The most common was outstanding memory.

She said: “It had been thought that only about 5%-10% of people with autism had such skills, but nobody had measured it properly, and it seems the number is far higher. If we could foster these skills, many more people with autism could live independently and even become high achievers.”
I have my moments, sure, but I'm not exactly making much progress on my physics grand unification theories. I have to devote a lot of attention to keeping a roof over my head and food in my belly, after all.

*digs exhaustively into the (proverbial) cereal box*

Where's my prize?
mellowtigger: (Default)
Remember the tv show Hercules that presented tales of the adventures of Hercules and Iolaus? Well, they had more interesting adventures than even that good series was capable of showing. According to Plutarch, the fidelity of Iolaus to Hercules (but not vice versa) was so famed that male couples would use him as an example and profess their fidelity to each other at the tomb of Iolaus.
"And as to the loves of Hercules, it is difficult to record them because of their number; but those who think that Iolaus was one of them do to this day worship and honor him, and make their loved ones swear fidelity at his tomb."
- Plutarch, "Eroticus", par. 17

"It is a tradition likewise that Iolaus, who assisted Hercules in his labors and fought at his side, was beloved of him; and Aristotle observes that even in his time lovers plighted their faith at Iolaus' tomb."
- Plutarch, "Life of Pelopidas", Clough translation
Sexual fidelity, however, is such a rare thing. Not just among humans but also other animals. Rare, though, is not the same thing as absent. According to a PubMed article:
"The Wandering Albatross provides a striking exception to partner infidelity. This albatross is one of the most remarkable animals in the world (Figure 13). These enormous birds, with a wingspan that measures 11 feet, the longest of any bird (one wing is as long as your outstretched arms), mate for life, which is often 6 decades or longer."
I had originally thought that maybe "til death do us part" would have made a lot more sense for humans back when we only lived to our 30s, but this albatross proves that it is natural (for them) even across long lifetimes. A few days ago, news broke about a study that found what seems to be an infidelity gene that was linked statistically to the strength of the bond that a male (human) feels to his partner. Men without the gene had higher fidelity and higher relationship satisfaction (as reported by their partner).  Men with one copy of the gene had lower scores on those attributes.  Men with two copies of the gene had even lower scores.  The researchers looked at this gene after it was previously found to play a role in the fidelity of male voles (a small rodent).

When talking about the feature in humans, it's much too easy to get caught up in political maneuvering instead of rational inquiry.  Since that article, though, I've been pondering what sexual reproductive strategy would be "best" for a species (any species) given a few starting conditions:
  1. males and females have comparable abilities (no significant disparity in survival skills individually)
  2. long lifespan (>60 years)
  3. long child development (>15 years)
  4. one adult is designated primary caregiver for each child born
  5. permanent sexual fertility (not annual/seasonal like many animals) across lifespan
  6. pathogens that can kill "quickly" (<2 years)
Given those simplistic terms, what reproductive strategy yields the highest number of healthy children?

I find that #3 takes precedence.  Since child rearing takes so very long, it requires more resources than can reasonably be expected from only one adult.  (Let's call that Corollary 3a.)  I see some kind of fidelity involved in arranging for these long relationships.  Why?  If sexual attraction is responsible for creating children, then anyone who creates a child will want to ensure that another adult can be relied upon to continue providing resources.  If sexual attraction produced one child, then it can produce another with a different sexual partner, leading to loss of resources to the first child's primary caregiver.

At first, I kept thinking that some form of group fidelity would be an excellent arrangement.  If the group remains small, then problems introduced by #6 can still be minimized.  Even if one particular partner dies, then the cost of child rearing can still be shared amongst the other available (and committed) adults.  Sounds great.  But then I realized the complication that appears across generations.  The group must continually bring in new members to avoid inbreeding.  In return, it must continuously shed old members to other groups.  So the pathogen issue comes up again.  Unless (cruelty alert) newcomers are quarantined for the 2 years during which pathogens can make their presence apparent.

So I was back to shrinking the group down to only a couple.  Pathogen involvement is limited (with fidelity).  Except, of course, when one partner dies and the remaining partner looks for a new caregiver to share in child rearing.  But at least risk affects only one adult and their children rather than an entire group.

Promiscuity is excellent at avoiding the inbreeding problem (thereby introducing necessary genetic variety) but loses its luster when faced with the pathogen problem.  The only way I can get it to "work" is if transmission of genetic material (mating) happens only once and then the receiving partner maintains the genetic material to use slowly across time.  Some animals can do that for short periods of time.  In this scenario, pathogen exposure (sexually transmitted, anyway) happens only once.  If the receiving partner survives, then they can continuously produce offspring from that one encounter.  No additional risk necessary.  Then finding someone to share resources during child development would likely occur in groups only with other surviving child-producers (since they have proven themselves free of deadly pathogen).  It could be the females (like mammals) or the males (like the seahorse), whichever protects the fetus during development.

So that's the best that I can come up with, examining things without involving religious tradition or political propaganda.  My 6 starting rules seem to yield 3 possible outcomes that are very good for the stated goal of producing lots of healthy children.
  1. binary couples with fidelity
  2. group structure with fidelity and newcomer sequestration
  3. random promiscuity during sole lifetime encounter, followed by parent-group association
Did I miss something?

HHV-6

Sep. 4th, 2008 10:02 am
mellowtigger: (dna)
I was going to start by saying that herpes is a fascinating virus. But then I realized that I thought the same of the cold virus... and HIV. So maybe I'm just fascinated in general by the simple complexity of any virus. Maybe it helps that I don't have the same "ooh, ick" reaction to herpes that other people do. I never learned of it as a sexually transmitted disease ("unclean! filthy!", as taught in high school health class, I suppose). To me, it's just another socially transmitted virus.

In my family, we get canker sores in our mouths. Usually, canker sores are a result of HHV-1 or HHV-2 (aka herpes simplex) infection.  (edit: Correction is found in comments section.)  It was interesting, though, that children always got it but spouses never did.  So although I consider my canker sores to be a source of concern for my exposure to other pathogens, I rarely conceive of it as a source of infection to somebody else.  I would, however, warn my last boyfriend when I felt one coming on, so we could avoid contact until it healed... just in case it was transmissible.  I never fully believed it was transmissible in my case though, because spouses in my family seemed never to have the same issue as the children did.

I remember one relative who wasn't even old enough to speak yet, but I saw her point in her mouth at the sore there and then whimper to express her discomfort. My father would go to the doctor to have silver nitrate sticks used to burn out the sores in his mouth, they got so bad.  I (of necessity) do a far better job at monitoring and regulating my stress level than other people in my family, so I seemed to have the lightest case of it in my extended family.  I think it was sometime in the 1970s (during one of those silver nitrate visits) that my father was told he had "genetic herpes". I found the concept interesting, but I dismissed it since I could never find any medical validation of this diagnosis.

It turns out, though, that there is such a thing as genetic herpes.

In recent news, researchers at the University of Rochester Medical Center (Rochester, NY) have shown that HHV-6 infection (which causes roseola) in a parent can bury itself into the germ line, resulting in children who carry the code within their dna. Their study included 254 children, and they found:
"Of the infants who had congenital infections, 86 percent of them (37) had the virus integrated into their chromosomes."
and
"HHV-6 DNA was found in the hair of one parent of all children with integrated virus with available parental samples (18 mothers and 11 fathers), which means the children acquired the integrated infections through their mother's egg or father's sperm at conception."

So, there could be a whole lot of people with herpetic "infection" who were never actually infected. Now that it's been shown with HHV-6, I look forward to studies that examine the possibility with other herpetic viruses.
mellowtigger: (Default)
New research from the Children's Hospital of Boston finds several new genes implicated in some forms of autism. They ran a study involving 104 Middle Eastern families (88 of which had cousin marriages, increasing the likelihood of transmission for rare mutations), looking for recessive genes that could be linked to autism diagnoses. They found that 6% of the families had DNA deletions (5 were identified) linked to autism. One of those genes was also found mutated in European and American children (especially those with autism and seizures).

In most of these "deletions", however, it wasn't the gene itself that was missing but instead it was nearby "switches" adjacent to it, suggesting the possibility that someday science could find a way to reactivate the dormant genes. The report notes:
It is the refinement of these synaptic connections that is the basis of learning and memory, suggesting that autism at its heart may represent molecular defects of learning. ... The findings also support the use of behavioral therapies in autism, which expose children to a rich environment and highly repetitive activities that may help turn on the genes and strengthen synaptic connections, Morrow adds.
I'm still not real keen on the idea that one person could decide for someone else whether to "change" them in such a way or not, but I still think it's fine for any person to make the decision only for their own self.  Anyone who suffers deserves relief.  It does make me ponder, though, what "normal" could even be in such a world.  Suppose I want to reactivate some long-buried gene that would give me a fur coat like a dog or a tail like a monkey or gills in my neck like a fish?

If it's not a matter of adding new protein encoding but merely reactivating what codes are already in my body, then it still counts as "my natural self", doesn't it?

This kind of stuff strikes me as odd in the same way as gender reassignment surgery on infants.  You don't like the body/mind that chance gave you, so you exchange that person for a different one.  Seems really dangerous to do that sort of thing to another person, but acceptable if they choose to do it for themselves.

cassava

Jul. 2nd, 2008 09:21 am
mellowtigger: (Default)
As I mentioned earlier in my daydream list, I thought it would be a good idea to genetically engineer a plant to become a self-contained complete source of nutrients for humans. It turns out, someone is doing exactly that. They're working on a plant called cassava which looks something like a yam. It's an interesting choice as a food source, since it's also potentially deadly because of its cyanide yield. Apparently preparation of the cassava as food involves many hours of airing out so that the cyanide gas can escape. Strange, eh?

The story from Ohio State University says:
The researchers have further engineered the cassava plant so it can resist the crop’s most damaging viral threats and are refining methods to reduce cyanogens, substances that yield poisonous cyanide if they are not properly removed from the food before consumption. The reduction of cyanogens also can shorten the time it takes to process the plant into food, which typically requires three to six days to complete.
This is important news not just for humans on earth but for humans leaving the planet too. Information that I can't yet find is the B12 content of this newly engineered cassava plant. As I found out during my own health troubles, B12 is manufactured only by bacteria and not by larger life forms. Even on their more-detailed webpage, though, I can't find mention of B12 content. Worse, it seems that cassava is already known to actually reduce the B12 in the body.

epigenetics

May. 8th, 2008 08:36 am
mellowtigger: (dna)
Everything that your cells are capable of producing is recorded in your genetics, the arrangement of base pairs in the spiral-staircase-shaped molecule of your DNA. The sequence of those base pairs are step-by-step recipes for producing the molecules that your body needs to exist.   The DNA, however, is a junked up basement chock full of recipes. It includes some remnants of our entire evolutionary development for the last billion years or so. What makes the recipes useful and active, however, is another chemical signal that piggybacks onto the DNA molecule.

DNA doesn't exist by itself, you see.  It comes packaged with other chemicals that scientists are discovering will code for other useful information. The parts of your DNA library that are actually produced are marked differently by chemicals called methyl groups. These extra markers identify sections of DNA as being "heavy use" (easily pulled out for use by your cells) or "light use" (requiring more time and effort to unlock and use). So, for instance (and oversimplified), the cells in your heart are actively using only the muscle recipes while the cells in your brain are actively using only the neuron recipes. All of your cells have the same DNA, but they have different methylation patterns so they behave differently. Exposure to stressors can even activate some old sections of DNA, and leave them active for future use. Post-it notes for DNA... provided by methylation patterns attached to the DNA.

The DNA and these other markers is altogether called chromatin. Scientists have discovered that it's not just DNA information that is passed down along generations. The whole chromatin passes information from parent to child. So the environment and lifestyle of the parent shapes both the genetics (DNA) and the epigenetics (methylation) of the child.

Which brings me to today's news...
A team of McGill University scientists has discovered important differences between the brains of suicide victims and so-called normal brains. Although the genetic sequence was identical in the suicide and non-suicide brains, there were differences in their epigenetic marking – a chemical coating influenced by environmental factors.
It appears that humans abused as children can undergo epigenetic change. Their brains are functionally different. Moreover, since we keep finding evidence that epigenetic changes can be inherited, it could very well be true that the trauma will remain with the family line for generations after the initial incident. Mother Nature, she tries to keep future generations prepared for the hardships of previous generations. A different way of arguing "original sin", perhaps.

It is my personal theory that autism represents an epigenetic response to the current chemical environment (altered by modern human society). I claim that autistics are humans with an awakened genetic machinery from our recent (in evolutionary terms) past. There's still a lot of research to be done, but so far I think the results are already very promising.

My favorite epigenetic database is in New Zealand, the catalog of imprinted genes and related effects. I like their database because it's easy to search across species and for particular effects. Go ahead, search for autism. They have several curiosities identified already.
http://igc.otago.ac.nz/Search.html

PubMed talks about a new database under development called MethDB. I don't like its search features as well, but I suppose that can improve in the future. For general information, there's Epigenetics Station.  (*sing* Conjunction junction, what's your function?)

So there you have it, gentle students. A short introduction to the new science of epigenetics.  It's going to change a lot of our thinking about product safety.  What medicines or manufacturing chemicals have tested safe against genetics but may still alter our epigenetics?  Nobody knows.... yet.
mellowtigger: (Default)
Well, a new study shows that there is actually a link of some kind between autism diagnosis and proximity to environmental mercury exposure. Not only that, but it shows a statistically significant link between risk level and distance from the mercury source such that "... community autism prevalence is reduced by 1 percent to 2 percent with each 10 miles of distance from the pollution source."

The study was done on data from Texas, where I grew up. They looked at influence from coal-fired power plants and other industrial facilities. They did not consider mercury contamination from the water supply, where decades of defoliant use on cotton crops has made the groundwater into a known health hazard during dry seasons.  Thankfully, the author is apparently aware of another issue (individual response to mercury) and stated plainly that, “This study was not designed to understand which individuals in the population are at risk due to mercury exposure."

I'm a bit of an agnostic in this debate. I do not believe that autism is just another word for mercury poisoning. I do not believe that autistics respond the same way to mercury as the rest of the population. I could fairly be called a fence sitter, just waiting for more information. That's fine. My own thoughts are more specific but just harder to classify in the usual dichotomy.

My pet theory: Autism results when an environmental factor (edit: mercury? zinc?) triggers an awakening (via epigenetic influence) of long-dormant genes, specifically genes related to the metabolism of metals (mercury and others) that were never quite "completed" successfully whenever they were last being worked on by evolutionary pressures. How soon and how fully the old genetic machinery awakens may influence the constellation of symptoms experienced by the individual.

Shorter translation: Mother Nature is experimenting again with an old, previously shelved model of human, and we call the results autism.

*goes back to sitting on the fence, waiting for more information, mulling more thoughts about my quack theory*
mellowtigger: (Default)
Two important genetic discoveries announced today.

1) It's happened before with TRIM5 gene

Monkeys have, more than once, evolved a genetic defense to lentiviruses (which includes HIV). "An intriguing possibility is that the newly formed genes prevented infection by prehistoric viruses related to modern AIDS viruses. If so, this could mean that AIDS-like epidemics are not unique to our time, but in fact may have plagued our primate ancestors long before the modern AIDS epidemic. " Which, if their idea is correct, means that we can definitively beat this epidemic this time, since it's been done multiple times before by nature.

2) It's happening now with TRIM22 gene

Researchers find a gene that can prevent a cell from assembling more copies of HIV.  "This means that TRIM22 is an essential part of our body's ability to fight off HIV. The results are very exciting because they show that our bodies have a gene that is capable of stopping the spread of HIV."

Good to hear.  :)

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