Sandwalk: March 2017

Monday, March 27, 2017

How to define evolution?

Do you think this video is helpful? [see "What Is Evolution?"] Is it important to know that evolution requires genetic changes and that it's populations that evolve? Is it important to have a definition of evolution that covers antibiotic resistance in bacteria and blood types in humans?

Monday, March 20, 2017

Correcting the correction of a video about evolution

Charlie McDonnell is the author of a book called Fun Science: A Guide To Life, The Universe And Why Science Is So Awesome. He made a video on misconceptions about the theory of evolution (see below). Sally Le Page (below left) is an evolutionary biologist working on her Ph.D. at Oxford (UK). She noticed a few problems with the McDonnell video so she made one of her own to correct the misconception in the first video. Now it's my turn to correct the misconception in the video that corrects the first video!

Sally Le Page highlights six misconceptions in the McDonnell video. She points out that none of them are very important—they are "little niggles"—but she still thinks a comment is necessary. (I agree.)

What's in Your Genome? Chapter 4: Pervasive Transcription

I'm working (slowly) on a book called What's in Your Genome?: 90% of your genome is junk! The first chapter is an introduction to genomes and DNA [What's in Your Genome? Chapter 1: Introducing Genomes ]. Chapter 2 is an overview of the human genome. It's a summary of known functional sequences and known junk DNA [What's in Your Genome? Chapter 2: The Big Picture]. Chapter 3 defines "genes" and describes protein-coding genes and alternative splicing [What's in Your Genome? Chapter 3: What Is a Gene?].

Chapter 4 is all about pervasive transcription and genes for functional noncoding RNAs.

Chapter 4: Pervasive Transcription

How much of the genome is transcribed?

How do we know about pervasive transcription?

Different kinds of noncoding RNAs

        Box 4-1: Long noncoding RNAs (lncRNAs)

Understanding transcription

        Box 4-2: Revisiting the Central Dogma

What the scientific papers don’t tell you

        Box 4-3: John Mattick proves his hypothesis?

On the origin of new genes

The biggest blow to junk?

        Box 4-4: How do you tell if it’s functional?

Biochemistry is messy

Evolution as a tinkerer

        Box 4-5: Dealing with junk RNA

Change your worldview

What's in Your Genome? Chapter 3: What Is a Gene?

I'm working (slowly) on a book called What's in Your Genome?: 90% of your genome is junk! The first chapter is an introduction to genomes and DNA [What's in Your Genome? Chapter 1: Introducing Genomes ]. Chapter 2 is an overview of the human genome. It's a summary of known functional sequences and known junk DNA [What's in Your Genome? Chapter 2: The Big Picture]. Here's the TOC entry for Chapter 3: What Is a Gene?. The goal is to define "gene" and determine how many protein-coding genes are in the human genome. (Noncoding genes are described in the next chapter.)

Chapter 3: What Is a Gene?

Defining a gene

        Box 3-1: Philosophers and genes

Counting Genes

Misleading statements about the number of genes

Introns and the evolution of split genes

Introns are mostly junk

        Box 3-2: Yeast loses its introns

Alternative splicing

        Box 3-2: Competing databases

Alternative splicing and disease

        Box 3-3: The false logic of the argument from         complexity

Gene families

The birth & death of genes

        Box 3-4: Real orphans in the human genome

Different kinds of pseudogenes

        Box 3-5: Conserved pseudogenes and Ken Miller’s         argument against intelligent design

Are they really pseudogenes?

How accurate is the genome sequence?

The Central Dogma of Molecular Biology

ENCODE proposes a “new” definition of “gene”

What is noncoding DNA?

Dark matter

Monday, March 06, 2017

What's in Your Genome? Chapter 2: The Big Picture

I'm working (slowly) on a book called What's in Your Genome?: 90% of your genome is junk! I thought I'd post the TOC for each chapter as I finish the first drafts. Here's chapter 2.

Chapter 2: The Big Picture
How much of the genome has been sequenced?

Whose genome was sequenced?

How many genes?

Pseudogenes

Regulatory sequences

Origins of replication

Centromeres

Telomeres

Scaffold Attachment regions (SARs)

Transposons

Viruses

Mitochondrial DNA (NumtS)

How much of our genome is functional?

What's in Your Genome? Chapter 1: Introducing Genomes

I'm working (slowly) on a book called What's in Your Genome?: 90% of your genome is junk! I thought I'd post the TOC for each chapter as I finish the first drafts. Here's chapter 1.

Chapter 1: Introducing Genomes
The genome war

What is DNA?

Chromatin

How big is your genome?

Active genes?

What do you need to know?

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)

Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)

Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Peter Atkins

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake. Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory. Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change. Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance. Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change. Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat. Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is True

I once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000

It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma

One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick

There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner

An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins

Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod

The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.

Richard Lewontin

Sandwalk

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Monday, March 27, 2017

How to define evolution?

Monday, March 20, 2017

Correcting the correction of a video about evolution

Wednesday, March 08, 2017

What's in Your Genome? Chapter 4: Pervasive Transcription

What's in Your Genome? Chapter 3: What Is a Gene?

Monday, March 06, 2017

What's in Your Genome? Chapter 2: The Big Picture

What's in Your Genome? Chapter 1: Introducing Genomes