You MUST read this paper if you are interested in evolution

A reader alerted me to a paper that was just published in BMC Biology.¹ The author is Eugene Koonin. He makes the case for neutral evolution (random genetic drift) and against adaptationism. You may not agree with his take on evolutionary theory but you better be aware of it if you claim to be knowledgeable about evolution.

Koonin, E.V. (2016) Splendor and misery of adaptation, or the importance of neutral null for understanding evolution. BMC biology, 14:114. [doi: 10.1186/s12915-016-0338-2]

The study of any biological features, including genomic sequences, typically revolves around the question: what is this for? However, population genetic theory, combined with the data of comparative genomics, clearly indicates that such a “pan-adaptationist” approach is a fallacy. The proper question is: how has this sequence evolved? And the proper null hypothesis posits that it is a result of neutral evolution: that is, it survives by sheer chance provided that it is not deleterious enough to be efficiently purged by purifying selection. To claim adaptation, the neutral null has to be falsified. The adaptationist fallacy can be costly, inducing biologists to relentlessly seek function where there is none.

The Edge question 2017

Every year John Brockman asks his stable of friends an interesting question. Brockman is a literary agent and most of the people who respond are clients of his. (I want to be one.) The question and responses are posted on his website Edge. This year's question is, "What scientific term or concept ought to be more widely known?"

This year, the introduction is more interesting than the responses. Here's part of what Brokman wrote,

The most popular Sandwalk post of 2016

My most popular post last year was: An Intelligent Design Creationist disputes the evolution of citrate utilization in the LTEE ... Lenski responds. It had almost 20,000 views and 227 comments.

The article discussed a paper by Intelligent Design Creationist Scott Minnich who criticized Richard Lenski's ongoing evolution experiment on the grounds that no new information had been created in the evolution of ability to use citrate.

Intelligent Design Creationists reveal their top story of 2016

Yesterday I posted an article on: Creationists list the top ten stories of 2016 . Some of you may have noticed that there were only nine stories. That's because Evolution News & Views didn't post their top story until today. I was pretty sure what it would be.

Let me remind you of the main point I made yesterday. Intelligent Design Creationists claim to have scientific evidence of intelligent design. They claim their movement is focused on demonstrating intelligent design but not on proving anything about who the designer might be.

But that's not what the movement is all about. Most of their writings and speeches are focused on attacking evolution. They hope that by discrediting evolution and science they will, by default, support the case for gods (false dichotomy). They also hope that by promoting gaps in our knowledge they will lend support to those who want to insert gods into the gaps.

You don't need to take my word for it. Just look at what they think are the top stories of 2016. Most of their top nine stories were critiques of science in one way or another. There wasn't a single top story that advanced the case for intelligent design.

So, what about the #1 story? Is it going to be different?

Creationists list the top ten stories of 2016

Intelligent Design Creationists are still trying to promote their views. They consistently claim to have positive evidence of intelligent design and they consistently complain whenever we point out what they actually do; they attack evolution/science. Their main talking point relies on the fallacy known as "false dichotomy." They assume that by casting doubt on evolution/science they lend support to their religious viewpoint.

Each year, the IDiots on Evolution News & Views (sic) publish their top ten stories. The series is linked to a fund-raising campaign so it's safe to assume they think these stories advance their cause. Let's see how many of the top stories promote intelligent design and how many are just criticisms of evolution/science. That should be revealing ...

Is the high frequency of blood type O in native Americans due to random genetic drift?

The frequency of blood type O is very high in some populations of native Americans. In many North American tribes, for example, the frequency is over 90% and often approaches 100%. A majority of individuals in those populations have blood type O (homozygous for the O allele). [see Theme: ABO Blood Types]

Since there's no solid evidence that blood types are adaptive,¹ the standard explanation is random genetic drift.

Jerry Coyne explains it in Why Evolution Is True.

One example of evolution by drift may be the unusual frequencies of blood types (as in the ABO system) in the Old Order Amish and Dunker religious communities in America. These are small, isolated, religious groups whose members intermarry—just the right circumstances for rapid evolution by genetic drift.

Accidents of sampling can also happen when a population is founded by just a few immigrants, as occurs when individuals colonize an island or a new area. The almost complete absence of genes producing the B blood type in Native American populations, for example, may reflect the loss of this gene in a small population of humans that colonized North America from Asia around twelve thousand years ago.

Nature opposes misinformation (pot, kettle, black)

The lead editorial in last week's issue of Nature (Dec. 8, 2016) urges us to Take the time and effort to correct misinformation. The author (Phil Williamson) is a scientist whose major research interest is climate change and the issue he's addressing is climate change denial. That's a clear example of misinformation but there are other, more subtle, examples that also need attention. I like what he says in the opening paragraphs,

Most researchers who have tried to engage online with ill-informed journalists or pseudoscientists will be familiar with Brandolini’s law (also known as the Bullshit Asymmetry Principle): the amount of energy needed to refute bullshit is an order of magnitude bigger than that needed to produce it. Is it really worth taking the time and effort to challenge, correct and clarify articles that claim to be about science but in most cases seem to represent a political ideology?

I think it is. Challenging falsehoods and misrepresentation may not seem to have any immediate effect, but someone, somewhere, will hear or read our response. The target is not the peddler of nonsense, but those readers who have an open mind on scientific problems. A lie may be able to travel around the world before the truth has its shoes on, but an unchallenged untruth will never stop.

I've had a bit of experience trying to engage journalists who appear to be ill-informed. I've had little success in convincing them that their reporting leaves a lot to be desired.

I agree with Phil Williamson that challenging falsehoods and misrepresentation is absolutely necessary even if it has no immediate effect. Recently I posted a piece on the misrepresentations of the ENCODE results in 2007 and pointed a finger at Nature and their editors [The ENCODE publicity campaign of 2007]. They are responsible because they did not ensure that the main paper (Birney et al., 2007) was subjected to appropriate peer review. They are responsible because they promoted misrepresentations in their News article and they are responsible because they published a rather silly News & Views article that did little to correct the misrepresentations.

That was nine years ago. Nature never admitted they were partly to blame for misrepresenting the function of the human genome.

The ENCODE publicity campaign of 2007

ENCODE¹ published the results of a pilot project in 2007 (Birney et al., 2007). They looked at 1% (30Mb) of the genome with a view to establishing their techniques and dealing with large amounts of data from many different groups. The goal was to "provide a more biologically informative representation of the human genome by using high-throughput methods to identify and catalogue the functional elements encoded."

The most striking result of this preliminary study was the confirmation of pervasive transcription. Here's what the ENCODE Consortium leaders said in the abstract,

Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap with one another.

ENCODE concluded that 93% of the genome is transcribed in one tissue or another. There are two possible explanations that account for pervasive transcription.

The proteome complexity myth

A reader pointed me to the ThermoFisher Scientific website. ThermoFisher Scientific is a major supply of scientific equipment and supplies. They created their life sciences wesite to help inform their customers and sell more products. The page I'm interested in is: Overview of Post-Translational Modifications (PTMs). It begins with,

Within the last few decades, scientists have discovered that the human proteome is vastly more complex than the human genome. While it is estimated that the human genome comprises between 20,000 and 25,000 genes (1), the total number of proteins in the human proteome is estimated at over 1 million (2). These estimations demonstrate that single genes encode multiple proteins. Genomic recombination, transcription initiation at alternative promoters, differential transcription termination, and alternative splicing of the transcript are mechanisms that generate different mRNA transcripts from a single gene (3).

The increase in complexity from the level of the genome to the proteome is further facilitated by protein post-translational modifications (PTMs). PTMs are chemical modifications that play a key role in functional proteomics, because they regulate activity, localization and interaction with other cellular molecules such as proteins, nucleic acids, lipids, and cofactors.

Revisiting Michael Behe's challenge and revealing a closed mind

It's been twenty years since Michael Behe published Darwin's Black Box and Intelligent Design Creationists are flagellating themselves over the fact that it had so little impact on creationism. The USA is becoming more secular with each passing year. Religion is on the decline.

In their attempt to deal with their defeat, the main ID blog has been publishing "Behe's Greatest Hits," which is a euphemistic way of saying "Behe's Greatest Failures." The latest one caught my eye. It's Best of Behe: An Open Letter to Professors Kenneth Miller and PZ Myers.

It takes you back more than two years to July 21, 2014. That's when Michael Behe issued his challenge to PZ Myers and Ken Miller. The challenge was based on his book The Edge of Evolution and specifically on the development of chloroquine resistance in Plasmodium falciparum. Behe starts with the assumption that cloroquine resistance is extremely rare—it occurs with a probability of roughly 10^-20. He concludes that resistance requires at least two different mutations that must occur simultaneously in an individual suffering from malaria while being treated with chloroquine.

The first assumption is approximately correct. Chloroquine resistance is rare. He was criticized for the second assumption; namely, that the overall probability of chloroquine resistance is just the probability of two mutations occurring simultaneously (e.g. 10^-10 × 10^-10 = 10^-20).

The best countries for atheists

The International Humanist and Ethical Union (IHEU) is a collection of Humanist, atheist, secular and similar organizations from many countries. It publishes the Freedom of Thought Report, which purports to be, "A global report on discrimination against humanists, atheists, and the nonreligious." The group intends to highlight systemic discrimination.

We believe it is important to document discriminatory national laws and state authorities which violate freedom of religion or belief and freedom of expression. As well as affecting the overtly nonreligious, such as atheists and Humanists, such systemic discrimination also often affects the religious, in particular minorities and non-conformists, and the unaffiliated (those who hold no particular religion or worldview-level belief).

Systemic, legal discrimination can include such things as established state churches (resulting in religious privilege), religious instruction provided without secular ethical alternative classes in schools, through to severe punishments such as prison for crimes of “insulting” religion, or death merely for expressing your atheism.

There are four categories of systemic discrimination: Constitution and government; Education and children’s rights; Family, community, society, religious courts and tribunals; and Freedom of expression advocacy of humanist values. For each category there are six possible rankings [see Ratings System]:

Black = Grave Violations
Red = Severe Discrimination
Orange = Systemic Discrimination
Yellow = Mostly Satisfactory
Green = Free and Equal
Gray = No Rating

Here's the result for the entire world.

Canada is ranked as "Systemic Discrimination" in all four categories. The USA gets the best rating (Free and Equal) in two categories: "Education and children’s rights" and "Freedom of expression advocacy of humanist values." It gets the second highest rating (Mostly Satisfactory) in: "Constitution and government" and "Family, community, society, religious courts and tribunals."

The conclusion is obvious. If you are an atheist you are much better off living in the USA than in Canada!

Hemant Mehta, better known as The Friendly Atheist, published the same figure on his blog a few days ago [New Report Highlights the Worst Countries in the World for Atheist Citizens. Many Canadians responded in the comments. One of them, CanuckAmuck, said,

I am dubious about some of the standards of this report. Not to appear butthurt, but to equate Canada to Russia in terms of "Constitution and the Government" is to say the least, asinine. And to report that "Society and Community" is "graver" for the atheist here than in the U.S. is likewise so.

I agree completely. Read the other comments to see what others think of this report.

Respond in the comments if you think atheists are better off in the USA than in Canada.

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Using conservation to determine whether splice variants are functional

We've been having a discussion about function and how to recognize it. This is important when it comes to determining how much junk is in our genome [see Restarting the function wars (The Function Wars Part V)]. There doesn't seem to be any consensus on how to define "function" although there's general agreement on using sequence conservation as a first step. If some sequence under investigation is conserved in other species then that's a good sign that it's under negative selection and has a biological function. What if it's not conserved? Does that rule out function? The correct answer is "no" because one can always come up with explanations/excuses for such an observation. We discussed the example of de novo genes, which, by definition, are not conserved.

Let's look at another example: splice variants. Splice variants are different forms of RNA produced from the same gene. If they are biologically relevant then they will produce different forms of the protein (for protein-coding genes). This is an example of alternative splicing if, and only if, relevance has been proven.

Restarting the function wars (The Function Wars Part V)

The term "function wars" refers to debates over the meaning of the word "function" in biology. It refers specifically to the discussion about junk DNA because junk DNA is defined as DNA that does not have a biological function. The wars were (re-)started when the ENCODE Consortium decided to use a stupid definition of function in order to prove that most of our genome was functional. This prompted a number of papers attempting to create a more meaningful definition.

None of them succeeded, in my opinion, because biology is messy and doesn't lend itself to precise definitions. Look how difficult it is to define a "gene," for example. Or "evolution."

Nevertheless, some progress was made. Dan Graur has recently posted a summary of the two most important definitions of function [What does “function” mean in the context of evolution & what absurd situations may arise by using the wrong definition?]. The two definitions are "selected-effect" and "causal-role" (there are synonyms).

How many proteins in the human proteome?

Humans have about 25,000 genes. About 20,000 of these genes are protein-coding genes.¹ That means, of course, that humans make at least 20,000 proteins. Not all of them are different since the number of protein-coding genes includes many duplicated genes and gene families. We would like to know how many different proteins there are in the human proteome.

The latest issue of Science contains an insert with a chart of the human proteome produced by The Human Protein Atlas. Publication was timed to correspond with release of a new version of the Cell Atlas at the American Society of Cell Biology meeting in San Francisco. The Cell Atlas maps the location of about 12,000 proteins in various tissues and organs. Mapping is done primarily by looking at whether or not a gene is transcribed in a given tissue.

A total of 7367 genes (60%) are expressed in all tissues. These "housekeeping" genes correspond to the major metabolic pathways and the gene expression pathway (e.g. RNA polymerase subunits, ribosomal proteins, DNA replication proteins). Most of the remaining genes are tissue-specific or developmentally specific.

Suzan Mazur doesn't like Carl Zimmer

There weren't many science writers are the Royal Society meeting in London (UK) [New trends in evolutionary biology: biological, philosophical and social science perspectives]. Carl Zimmer was there and so was Suzan Mazur. Carl was there to learn and do some research. Suzan was there to promote herself as the main publicist of the paradigm shifters.

Carl Zimmer wrote a news article about the meeting for Quanta: Scientists Seek to Update Evolution. The subtitle was "Recent discoveries have led some researchers to argue that the modern evolutionary synthesis needs to be amended." It was a pretty fair article and pretty good reporting on what went on at the meeting. I would have been a bit more harsh about the success of the so-called "paradigm shifters" but Carl did a good job of conveying the skepticism exhibited by many at the meeting. [See Kevin Laland's new view of evolution for my take on these "revolutionaries."]