genotype-phenotype gap

intro’d/intrigued via:

rt via Caleb Harper – saying this is awesome


5/1/16 2:32 AM
Deep learning can help predict the phenotype from the genotype.…

and i keep returning to it… in the shower.. while i’m running.. while i’m taping my foot for running… while i’m reading.. eating.. not eating…what tiny little move leads us to ie: cancer, misunderstanding, war (queen noor et al)

wondering/thinking.. Caleb learned plant language.. why haven’t we yet learned human language..

why can’t i hear the ways my body really wants/needs to go..?

is it that we’re more complex than plants… or is it deeper/simpler than that…

so – this – all – very resonating to a nother way to live.. where we are quiet enough.. to hear (the plant) us…

ie: hosting life bits (or whatever) to hear/see/be


deep dive.. (one) author

In 2014, Frey co-founded Deep Genomics, a Toronto company that develops machine learning methods to model the deep biological architectures that relate genetic mutations to disease. The company’s goal is to bridge the genotype-phenotype gap, which is a pain point in genetic testing, pharmaceuticals, personalized medicine and health insurance.

from article tweeted:

DB: What does it mean to develop computational models that sufficiently account for the underlying biology?

BF: One of the most popular ways of relating genotype to phenotype is to look for mutations that correlate with disease, in what’s called a genome-wide association study (GWAS). This approach is also shallow in the sense that it discounts the many biological steps involved in going from a mutation to the disease phenotype. GWAS methods can identify regions of DNA that may be important, but most of the mutations they identify aren’t causal. In most cases, if you could “correct” the mutation, it wouldn’t affect the phenotype.


DB: Is genomics different from other applications of machine learning?

BF: We discovered that genomics entails unique challenges, compared to vision, speech, and text processing. A lot of the success in vision rests on the assumption that the object to be classified occupies a substantial part of the input image. In genomics, the difficulty emerges because the object of interest occupies only a tiny fraction—say, one millionth—of the input. Put another way, your classifier acts on trace amounts of signal. Everything else is noise—and a lot of it. Worse yet, it’s relatively structured noise comprised of other, much larger objects irrelevant to the classification task. That’s genomics for you.

entropy ness..?
on….everything else us noise……?

The more concerning complication is that we don’t ourselves really know how to interpret the genome. When we inspect a typical image, we naturally recognize its objects, and by extension, we know what we want the algorithm to look for. This applies equally well to text analysis and speech processing, domains in which we have some handle on the truth. In stark contrast, humans are not naturally good at interpreting the genome. In fact, they’re very bad at it.

All this is to say that we must turn to truly superhuman artificial intelligence to overcome our limitations.


Going forward, many emerging technologies in this space will require the ability to understand the inner workings of the genome. Take, for example, gene editing using the CRISPR/Cas9 system. This technique let’s us “write” to DNA and, as such, could be a very big deal down the line. That said, knowing how to write is not the same as knowing what to write. If you edit DNA, it may make the disease worse, not better. Imagine instead if you could use a computational “engine” to determine the consequences of gene editing writ large. That is, to be fair, a ways off. Yet ultimately, that’s what we want to build.
knowing how to write vs what to write


deep div .. topic

wikipedia small

The genotype–phenotype distinction is drawn in genetics. “Genotype” is an organism’s full hereditary information. “Phenotype” is an organism’s actual observed properties, such as morphology, development, or behavior. This distinction is fundamental in the study of inheritance of traits and their evolution.

It is the organism’s physical properties which directly determine its chances of survival and reproductive output, while the inheritance of physical properties occurs only as a secondary consequence of the inheritance of genes. Therefore, to properly understand the theory of evolution via natural selection, one must understand the genotype–phenotype distinction. The genes contribute to a trait, and the phenotype is the observable expression of the genes (and therefore the genotype that affects the trait). Say a white mouse had the recessive genes that caused the genes that cause the color of the mouse to be inactive (so “cc”). Its genotype would be responsible for its phenotype (the white color).

An organism’s genotype is a major (the largest by far for morphology) influencing factor in the development of its phenotype, but it is not the only one. Even two organisms with identical genotypes normally differ in their phenotypes. One experiences this in everyday life with monozygous (i.e. identical) twins. Identical twins share the same genotype, since their genomes are identical; but they never have the same phenotype, although their phenotypes may be very similar. This is apparent in the fact that their mothers and close friends can always tell them apart, even though others might not be able to see the subtle differences. Further, identical twins can be distinguished by their fingerprints, which are never completely identical.

The concept of phenotypic plasticity defines the degree to which an organism’s phenotype is determined by its genotype. A high level of plasticity means that environmental factors have a strong influence on the particular phenotype that develops. If there is little plasticity, the phenotype of an organism can be reliably predicted from knowledge of the genotype, regardless of environmental peculiarities during development.


In contrast to phenotypic plasticity, the concept of genetic canalization addresses the extent to which an organism’s phenotype allows conclusions about its genotype. A phenotype is said to be canalized if mutations (changes in the genome) do not noticeably affect the physical properties of the organism. This means that a canalized phenotype may form from a large variety of different genotypes, in which case it is not possible to exactly predict the genotype from knowledge of the phenotype (i.e. the genotype–phenotype map is not invertible). If canalization is not present, small changes in the genome have an immediate effect on the phenotype that develops.

The terms “genotype” and “phenotype” were created by Wilhelm Johannsen in 1911.



Genetics is the study of genes, genetic variation, and heredity in living organisms. It is generally considered a field of biology, but it intersects frequently with many of the life sciences and is strongly linked with the study of information systems.

The father of genetics is Gregor Mendel, a late 19th-century scientist and Augustinian friar. Mendel studied ‘trait inheritance’, patterns in the way traits were handed down from parents to offspring. He observed that organisms (pea plants) inherit traits by way of discrete “units of inheritance”. This term, still used today, is a somewhat ambiguous definition of what is referred to as a gene.

Trait inheritance and molecular inheritance mechanisms of genes are still primary principles of genetics in the 21st century, but modern genetics has expanded beyond inheritance to studying the function and behavior of genes. Gene structure and function, variation, and distribution are studied within the context of the cell, the organism (e.g.dominance) and within the context of a population. Genetics has given rise to a number of sub-fields includingepigenetics and population genetics. Organisms studied within the broad field span the domain of life, includingbacteria, plants, animals, and humans.


The word genetics stems from the Ancient Greek γενετικός genetikos meaning “genitive”/”generative”, which in turn derives from γένεσις genesis meaning “origin”


The modern working definition of a gene is a portion (or sequence) of DNA that codes for a known cellular function or process (e.g. the function “make melanin molecules”). A single ‘gene’ is most similar to a single ‘word’ in the English language. The nucleotides (molecules) that make up genes can be seen as ‘letters’ in the English language.


Although genes were known to exist on chromosomes, chromosomes are composed of both protein and DNA, and scientists did not know which of the two is responsible for inheritance.


Although the structure of DNA showed how inheritance works, it was still not known how DNA influences the behavior of cells. In the following years, scientists tried to understand how DNA controls the process of protein production. It was discovered that the cell uses DNA as a template to create matching messenger RNA, molecules with nucleotides very similar to DNA. The nucleotide sequence of a messenger RNA is used to create an amino acid sequence in protein; this translation between nucleotide sequences and amino acid sequences is known as the genetic code.

With the newfound molecular understanding of inheritance came an explosion of research. ….. One important development was chain-termination DNA sequencing in 1977 by Frederick Sanger. This technology allows scientists to read the nucleotide sequence of a DNA molecule. In 1983, Kary Banks Mullis developed the polymerase chain reaction, providing a quick way to isolate and amplify a specific section of DNA from a mixture. The efforts of the Human Genome Project, Department of Energy, NIH, and parallel private efforts by Celera Genomics led to the sequencing of the human genome in 2003.


At its most fundamental level, inheritance in organisms occurs by passing discrete heritable units, called genes, from parents to progeny. This property was first observed by Gregor Mendel, who studied the segregation of heritable traits in pea plants.


On 19 March 2015, a leading group of biologists urged a worldwide ban on clinical use of methods, particularly the use of CRISPR and zinc finger, to edit the human genome in a way that can be inherited. In April 2015, Chinese researchers reported results of basic research to edit the DNA of non-viable human embryos using CRISPR.



recent twitter convos/shares (just a sampling)


“There are no ‘genes for education”

like saying.. no water for ed. why are we assuming ed outcomes is natural/desirable phenom. we’re missing it/us.


Right. Are there genes for learning? Definitely. @monk51295

perhaps if we let go (of managing) what’s natural (no template/genome needed) we’d quit spinning wheels on what’s artificial

– – –


5/14/16 7:15 AM
Genes Play a Role in #Teen #Impulsivity v @PsychCentral #parenting

more of crazy genome… template… obsession
New research suggests excessive teenage binge-drinking may be influenced, as least in part, by genetics.
oh my… article worse than title from first sentence…
research shows… teen binge drinking from genes..
oh my…

Alcohol and drug abuse are major health issues that often begin during adolescence. The teenage years are known to be an impulsive time as emerging adults expand their boundaries. Some teens, however, seem to especially prone to impulsive behaviors leading to binge-drinking.

Researchers at the University of Sussex, working as part of a team of researchers from across Europe, have discovered a new genetic link between impulsivity and teenage binge-drinking.


“Alcohol and drug abuse are well documented as being major public health issues in today’s society. By uncovering a particular gene that links impulsive behavior with binge-drinking we may be an important step closer to understanding why some young people face a struggle to control their urges to engage in risky behavior like binge drinking.”

or perhaps rather.. genes suffering because of our supposed to… pre planned day/life..
called… survival genes…
not… what is this kid capable of… genes
is this a genes thing.. or is this an artificial/deadly/suffocating environment thing..

Investigators identified a variant of a specific gene, called KALRN, which is seen in teenagers who act impulsively and also binge-drink. Researchers believe the link suggests people can be predisposed to impulsive behavior, and perhaps also to early-life alcohol abuse.

Learning how these gene variations predispose people to impulsive behavior, may help professionals intervene to control binge-drinking and other disorders linked to impulsivity, like drug addiction and ADHD, explains Stephens

johann – chasing the scream
carl – high price
brucerat park


from  Robert Sapolsky‘s behave:


genotype: someones genetic makeup.. phenotype: the traits observable to the outside world produced by that genotype




dna ness

rna ness