‘Epigenetics’ Explained, in the Context of Descendants of Holocaust and Slavery Victims

A renowned psychologist asked us by email:

It has been posited that the trauma involved in genocide has altered gene expression not only of Holocaust survivors (as well as descendents of African slaves and conquered Native American) but of their descendents. is there any theoretical or empirical basis for that proposal?

We are posting the [...]

Posted on 23 July 2014 | 2:36 pm

Using Mathematical Induction to Design Algorithms

We are revisiting the 1980s, thanks to Gene Myers, and came across this elegant 1988 paper by Udi Manber that our readers may find helpful. Manber later wrote a book “Introduction to Algorithms – A Creative Approach”, where he expanded on the same ideas (more on that later).

This article presents a methodology, based [...]

Posted on 23 July 2014 | 12:09 pm

Minia’s New Home – GATB (Genome Assembly & Analysis Tool Box)

The readers of our blog should be very familiar with parts of this project through their introduction with Minia assembler and DSK k-mer counter. Minia uses the same idea as diginorm (Bloom filters), but builds an entire assembler with it. Now Rayan Chikhi, Guillaume Rizk, Dominique Lavenier and their collaborators have converted those programs into [...]

Posted on 16 July 2014 | 2:56 am

On the Ongoing Scripps Saga – President Resigns

Scripps Research Institute is broke and the biggest reasons are – (i) declining funding for basic research (mathematics, physics, chemistry, basic biology) and (ii) the need to sustain >80% overhead as a purely research institute. We earlier reported about its possible merger with USC, which could have reduced the overhead cost, if not anything else.


Posted on 23 July 2014 | 1:36 pm

Dimitry Orlov Discusses the ‘Education Delusion’

Dimitry Orlov became well known in 2006 by highlighting the similarities between collapsed Soviet Union and collapsing United States. At that time, he was ridiculed, because the housing bubble was going strong, Lehman Brothers was still alive and US president was exporting democracy to Iraq and Afganistan. Eight years later, he appears far more prescient [...]

Posted on 23 July 2014 | 12:50 pm

Are Universities Going the Way of Record Labels?

Why did the businesses of record labels peak in 2000 and then went into decline? Martin Smith at The Atlantic shows four similarities between the record labels delivering music and the universities delivering ‘educational content’.

1. The price of content will freefall over the next seven years. We heard the first rumblings last year [...]

Posted on 23 July 2014 | 12:40 pm

BioXSD: the common data-exchange format for everyday bioinformatics web services

A paper on common standards came out in 2010 in Bioinformatics. It is being discussed in #socbin14 conference. Isn’t JSON more appropriate?

Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more [...]

Posted on 12 June 2014 | 3:43 am

d3.js – Tutorials, Books, Examples

d3.js is a SVG-based framework.

1. mbostock/d3 github gallery

This is the best source for hands on learning and comes from the author of d3.js. There are many examples to choose from and study their codes. We have been going through those examples one by one.


2. Next you need quick tutorials. Please try [...]

Posted on 6 May 2014 | 11:28 am

We Plan to Be Early Adopters of Meteorchart

Earlier we talked about HTML5 and SVG, as well as kinetic.js, raphael and d3.js. Eric Rowell, the author of kinetic.js, developed a new program called Meteorchart, which seems interesting. We plan to use it for our bioinformatics applications.

The program is not free for everyone, but it has the type of license that we [...]

Posted on 3 May 2014 | 7:21 am

Benchmark Analysis of RNA-Seq is an Excellent Confirmation of ‘Short Read’ Noise

In the past, we talked about ‘short read noise’, which is the noise introduced by clean short reads due to being short. Readers may take at these two of our earlier commentaries for details.

End of Short-Read Era? – (Part I)

End of Short-Read Era? – (Part II)

An excellent biorxiv paper analyzing RNA-seq assemblies [...]

Posted on 16 July 2014 | 3:14 am

‘Transcriptome Assembly is Hard’, but Not Any More with Richard Smith’s Transrate

Richard Smith-Una, whose work was covered in our blog, releases a new quality assessment program (transrate) that we surely like to check out.

Transcriptome assembly is hard. The algorithms are complex, the data are messy, and it’s often not clear how to determine whether an assembly is suitable for answering a biological question.

Transrate [...]

Posted on 8 July 2014 | 7:53 am

Efficient Algorithms for de novo Assembly of Alternative Splicing Events from RNA-seq Data

Readers may enjoy this new arxiv paper from Gustavo Sacomoto (h/t: haldane’s sieve)

Efficient Algorithms for de novo Assembly of Alternative Splicing Events from RNA-seq Data

In this thesis, we address the problem of identifying and quantifying variants (alternative splicing and genomic polymorphism) in RNA-seq data when no reference genome is available, without assembling the [...]

Posted on 25 June 2014 | 8:21 am

A Textbook-free ‘Introduction to Biological Anthropology’

Holly Dunsworth at Mermaid’s tale blog put together an wonderful commentary with free and online materials. Her audience is anthropology students, but others can also benefit from the materials on evolution. Especially, pay attention to unit 2.

Here are the topics. You can access the links from her blog post.

Unit 2. Explaining the similarities [...]

Posted on 23 June 2014 | 11:12 pm

A single female-specific piRNA is the primary determiner of sex in the silkworm


The silkworm Bombyx mori uses a WZ sex determination system that is analogous to the one found in birds and some reptiles. In this system, males have two Z sex chromosomes, whereas females have Z and W sex chromosomes. The silkworm W chromosome has a dominant role in female determination1, 2, suggesting the existence [...]

Posted on 28 May 2014 | 5:00 pm

Sponge Jelly Genome is Studied to Find Evolutionary Origins of Neural Systems

Two months back, we mentioned about an upcoming paper, where Friday Harbor lab was a collaborator (“Animal Ancestors – Sponges or Comb Jellies?“). It just came out in Nature today.

The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These [...]

Posted on 22 May 2014 | 9:05 am

Non-random DNA fragmentation in next-generation sequencing


Next Generation Sequencing (NGS) technology is based on cutting DNA into small fragments, and their massive parallel sequencing. The multiple overlapping segments termed “reads” are assembled into a contiguous sequence. To reduce sequencing errors, every genome region should be sequenced several dozen times. This sequencing approach is based on the assumption that genomic DNA [...]

Posted on 10 June 2014 | 6:08 am

PacBio P4-C2, P5-C3, etc. – What Do They Mean?

We had been pondering about those cryptic terms and found by asking some people around that the P stands for polymerase and C stands for chemistry. Therefore, P4-C2 means polymerase of fourth generation and chemistry of second generation.


That got us curious about what the actual DNA polymerase sequences are for 2nd, 3rd or [...]

Posted on 4 April 2014 | 4:58 am

Three Amazing Applications of CRISPR/cas9

Changing genome in plants used to be incredibly difficult, but not any more. Here is an excellent review -

Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system

Targeted genome engineering (also known as genome editing) has emerged as an alternative to classical plant breeding and transgenic (GMO) [...]

Posted on 31 March 2014 | 9:58 pm

Early Evolution of Fish – A Primitive Fish from the Cambrian of North America

New Nature paper -

Knowledge of the early evolution of fish largely depends on soft-bodied material from the Lower (Series 2) Cambrian period of South China1, 2. Owing to the rarity of some of these forms and a general lack of comparative material from other deposits, interpretations of various features remain controversial3, 4, as do [...]

Posted on 12 June 2014 | 3:48 am

The Fishiest Story Ever – (ii)

This is a follow up of previous commentary – The Fishiest Story Ever – (i).

All orders of fish are shown below based on the following phylogeny (courtesy: Professor James Albert). Please note that we (humans, tetrapods) are also a part of the phylogeny tree shown below.

———————————————————— ———————————————————— ———————————————————— Argentiniformes

———————————————————— Salmoniformes


Posted on 7 May 2014 | 7:48 pm

Rare Megamouth Shark Caught in Japan



Megamouth shark was first seen in 1976 and is so rare that -

According to WPTV, it was only the 58th megamouth to have been captured or sighted by man.

The Florida Museum of Natural History states that the first known capture of a megamouth shark was in 1976. It was [...]

Posted on 7 May 2014 | 7:38 pm

Immune System in Plants – A Good Review from 2011

We earlier posted on the possibility of LRR-type immune system of Ectocarpus. Readers may find the following review useful in that context.

Arabidopsis and the Plant Immune System


1. The first challenge was to dispel the notion that Arabidopsis does have enemies.

2. Achievement in early (pre-genome) years -

The biggest accomplishment of these [...]

Posted on 8 July 2014 | 10:55 am

Bacterial Tricks for Turning Plants into Zombies

Here is another interesting paper along the same line as previous commentary. It was published by Saskia A. Hogenhout and colleagues, and we meant to cover it some time back, but did not get time.

Phytoplasma Effector SAP54 Hijacks Plant Reproduction by Degrading MADS-box Proteins and Promotes Insect Colonization in a RAD23-Dependent Manner

Pathogens that [...]

Posted on 16 May 2014 | 10:24 am

A gene horizontally transferred from bacteria protects arthropods from host plant cyanide poisoning

Elife published this interesting paper on co-evolution -

Cyanogenic glucosides are among the most widespread defense chemicals of plants. Upon plant tissue disruption, these glucosides are hydrolyzed to a reactive hydroxynitrile that releases toxic hydrogen cyanide (HCN). Yet many mite and lepidopteran species can thrive on plants defended by cyanogenic glucosides. The nature of the [...]

Posted on 16 May 2014 | 7:15 am

Rain in Seattle and MH17 Tragedy over Ukraine

After a number of beautiful sunny days, it is raining again in Seattle. Cloudy skies remind us that we are getting closer to winter every day.

What does that have to do with the plane crash in Ukraine? Simple. Here is the world map and you can see where Seattle is located, where Kiev is [...]

Posted on 23 July 2014 | 4:46 pm

Funny Do-it-yourself Guide to Creating Your Own Caliphate

From zerohedge-

and not so funny news from real Caliphate -

Acting-man blog provides a lot of interesting details –

The decisive passage in which the ‘caliph’ announces his claim to henceforth lead international djihadism is this one:

“I am the wali (leader) who presides over you, though I am not the [...]

Posted on 8 July 2014 | 8:25 am

An Experience with American Prison

Readers may find the following comment in James Kunstler’s blog thought-provoking.

…Long time no see. Been in jail for my illegal tree house, PHONEHENGE….While in the Twin Towers jail I found out first hand how far down the rabbit hole our society has gone. The first thing they do when they process you is to [...]

Posted on 7 July 2014 | 1:35 pm