Thursday, April 28, 2016

Fun and games with Otangelo Grasso about photosynthesis

Otangelo Grasso just posted another one of his screeds. This time it's on photosynthesis. All of his "essays' conform to the same pattern. He looks for some complex set of biochemical reactions, usually in complex animals, then claims that it couldn't possibly have evolved because the whole thing is irreducibly complex according to his understanding of biochemistry and evolution.

It's a classic argument from ignorance.

In this case it's photosynthesis in flowering plants. He posted this figure from the Kegg database ....

Then he says,
In photosynthesis , 26 protein complexes and enzymes are required to go through the light and light independent reactions, a chemical process that transforms sunlight into chemical energy, to get glucose as end product , a metabolic intermediate for cell respiration. A good part of the protein complexes are uniquely used in photosynthesis. The pathway must go all the way through, and all steps are required, otherwise glucose is not produced. Also, in the oxygen evolving complex, which splits water into electrons, protons, and CO2, if the light-induced electron transfer reactions do not go all the five steps through, no oxygen, no protons and electrons are produced, no advanced life would be possible on earth. So, photosynthesis is a interdependent system, that could not have evolved, since all parts had to be in place right from the beginning. It contains many interdependent systems composed of parts that would be useless without the presence of all the other necessary parts. In these systems, nothing works until all the necessary components are present and working. So how could someone rationally say, the individual parts, proteins and enzymes, co-factors and assembly proteins not present in the final assemblage, all happened by a series of natural events that we can call ad hoc mistake "formed in one particular moment without ability to consider any application." , to then somehow interlink in a meaningful way, to form electron transport chains, proton gradients to " feed " ATP synthase nano motors to produce ATP , and so on ? Such independent structures would have not aided survival. Consider the light harvesting complex, and the electron transport chain, that did not exist at exactly the same moment--would they ever "get together" since they would neither have any correlation to each other nor help survival separately? Repair of PSII via turnover of the damaged protein subunits is a complex process involving highly regulated reversible phosphorylation of several PSII core subunits. If this mechanism would not work starting right from the beginning, various radicals and active oxygen species with harmful effects on photosystem II (PSII) would make it cease to function. So it seems that photosynthesis falsifies the theory of evolution, where all small steps need to provide a survival advantage.
I responded on Facebook, pointing out that the cytochrome bc complex and ATP synthase pre-date photosynthesis [Facebook: Photosynthesis]. I also pointed out that there are many living species that use only simpler versions of photsystem I or only photosystem II to carry out photosynthesis [e.g. A Simple Version of Photosynthesis]. Those nasty little facts don't seem to fit with his claim that, "In these systems, nothing works until all the necessary components are present and working."

I probably should have known better. Otangelo Grasso's standard response to such criticism is to avoid dealing directly with his false statements and shift the goalposts on to some other topic. He then posts all kinds of links to websites that seem to back up his claims even if they have nothing to do with the criticisms. You can see him at work on the Facebook thread.

It's pretty frustrating. I probably shouldn't respond to kooks, especially those who think they are experts in biochemistry.

Monday, April 25, 2016

Theme: Genealogy

Monday, April 11, 2016
My DNA ancestry

I sent a DNA sample off to a few weeks ago and here are the results.

Monday, November 30, 2015
Celebrating Lucy Maud Montgomery

Today Google celebrates the birthday of Lucy Maud Montgomery (November 30, 1874 – April 24, 1942). She is the author of Anne of Green Gables. ...

Lucy Maud Montgomery is a distant cousin of mine. I descend from James Cole and his wife Mary (maiden name unknown) who came to North America from Bletchley, England. Their son, Benjamin Cole, is my great4-grandfather. James Cole died sometime around 1765 and Mary married George Penman. The history is confusing, they may have lived in New England and fled to P.E.I. after the American Revolution. They self-identify as United Empire Loyalists.

Friday, November 27, 2015
Hawker Hurricanes and Typhoons in World War II

My father, F/L Laurence Victor "Vic" Kirsch,1 was a fighter pilot in World War II and he flew Hurricanes and, later, rocket-firing Hawker Typhoons with the RAF 164 Squadron known as the Argentine British Squadron because of the volunteers from Argentina. (My father was seconded from the RCAF (Canada)).

Here's a picture of him in the cockpit of one of his planes.

Wednesday, August 19, 2015
The Burghers of Calais at the Metropolitan Museum of Art in New York

The burghers thought they were sacrificing their lives to save the inhabitants of Calais, which was being starved into submission by Edward III of England in 1347. Their lives were spared after Queen Philippa convinced her husband to be lenient.

One of my ancestors is Paon de Roet. He was a knight in Queen Phillippa's retinue and was one of two knights assigned to protect the burghers of Calais. I descend from Paon de Roet's daughter, Katherine. Her sister, Philippa (named after the Queen), married a poet named Geoffrey Chaucer [My Connection to Geoffrey Chaucer and Medieval Science].

Thursday, May 14, 2015
James Hutton and John Playfair and a genealogical connection

Hutton's work would not have been widely known if it hadn't been promoted by an Edinburgh professor named John Playfair (left). He published Illustrations of the Huttonian Theory of the Earth in 1802.

John Playfair's brother was William Playfair who was a friend of James Watt and Erasmus Darwin and the inventor of the bar graph and the pie chart [see Bar Graphs, Pie Charts, and Darwin and Bastille Day]. William Playfair is Ms Sandwalk's great5 grandfather and my childrens' great6 grandfather. William's son founded Playfairville in Eastern Ontario.

Tuesday, November 3, 2015
We are all Irish according to

One of my wife's relatives just had her DNA tested by and the results show that she is 61% Irish.1 She was (pleasantly) surprised so she shared the information with her relatives, including Ms. Sandwalk.

I was also surprised because I have a pretty extensive genealogy of my wife's side of the family and there's no ancestor from Ireland. Her grandparents—the aunt's parents—have typically Scottish surnames and they are the product of several generations of Scottish ancestors from a small community in Eastern Ontario.

Sunday, November 10, 2013
I'm Related to a Philosopher! Edwin Proctor Robins (1872-1899)

This was intriguing. I know I am related to all the Robins (Robbins) descendants from Prince Edward Island but I'd never heard of Edwin Proctor Robins. His great-grandfather, Robert Robbins, is a United Empire Loyalist who came to PEI from New Jersey when the American Revolution ended. Edwin Proctor Robins and I are fourth cousins, three times removed. Why did he die at Cornell University?

Sunday, October 6, 2013
Dr. Azor Betts vs Smallpox and George Washington

Dr. Azor Betts (1740-1809) is a distant cousin of mine. His mother was Mary Beldon and I descend from another Mary Beldon who is a cousin of Dr. Azor Betts' mother. Our common ancestor is Daniel Belden (1648-1732) of Deerfield, Massachusetts.

Dr. Betts' father was Nathan Betts and I'm also related to him through my ancestor Tama Betts (1754 - ).

Wednesday, September 4, 2013
James Hood (1776-1859)

James Hood is my wife's great, great, great, great, grandfather (and the great5 grandfather of Gordon and Jane). He is also the great, great, great grandfather of Mitt Romney.

Sunday, July 28, 2013
My Connection to Geoffrey Chaucer and Medieval Science

Katherine's sister, also called Philippa (1346-1387) [Philippa Roet] was a prominent member of Queen Philippa's court in England. At first, she was a child companion of the children of Elizabeth of Ulster and the Queen but later on she was a lady-in-waiting. Geoffrey Chaucer became a page in the household of Elizabeth of Ulster in 1357 when he was 14 and Phillipa was 11.

Sunday, March 23, 2013
Happy Saint Patrick's Day!

One of the cool things about studying your genealogy is that you can find connections to almost everyone. This means you can celebrate dozens of special days. In my case it was easy to find ancestors from England, Scotland, Netherlands, Germany, France, Spain, Poland, Lithuania, Belgium, Ukraine, Russia, United States, and, of course, Ireland.

We will be celebrating St. Patrick's Day today. It's rather hectic keeping up with all the national holidays but somebody has to keep the traditions alive!

Here's my Irish connection.1 The shortest connection is to the parents of my grandmother. My great-grandfather was Thomas (Keys) Foster, born in County Tyrone on September 5, 1852. He immigrated to Canada in 1876. Thomas married Eliza Ann Job, born in Fintona, County Tyrone on August 18, 1852. She immigrated to Canada in 1877.

My wife and our children are cousins of Mitt Romney. This is the story of their common ancestor James Hood and his Mormon descendants.Thursday, February 2, 2012
A Mormon Tale: The Romney Connection

Hannah Hood Hill arrived in Salt Lake City when she was eight years old. She lived there with her father Archibald Newell Hill and his four wives. (Hannah’s mother, Isabella Hood, died at Winters Quarters in 1847.)

On May 10, 1862 Hannah Hood Hill married Miles Park Romney. Miles was born on August 18, 1843 in Nauvoo. His parents had been converted to the Church of the Latter Day Saints while living in England.

Wednesday, February 1, 2012
A Mormon Tale: Navoo to Utah

Archibald Hill returned to Nauvoo and brought his family out to Winter Quarters. They arrived in early autumn. Presumably the advance party had already built houses and planted crops in preparation for winter.

Isabella Hood Hill was 25 years old. Samuel Hood Hill was six, Hannah Hood Hill was four, and Rebeccah Hood Hill was only one year old.

About 1000 settlers died that winter of illness or starvation. One of them was Isabella Hood Hill. She died on March 20, 1847 and she is buried in the Mormon Cemetery in Florence, Nebraska [grave #109].

Tuesday, January 31, 2012
A Mormon Tale: Ontario to Nauvoo

By the time of Smith’s murder, the population of Nauvoo and its suburbs was over 20,000. Vigilante gangs from other parts of the state harassed the outlying settlements forcing the Mormon inhabitants to move into Nauvoo. The Illinois militia shelled the city in September 1846 ("Battle of Nauvoo").3 The Saints had already decided that they needed to move west. Once Brigham Young became leader (after considerable infighting), preparations began in earnest for the trek westward and the Hill family was very involved in that effort. The future Mormon "Kingdom" would be in Utah.

Rebecca Hood Hill was born in Nauvoo on April 2, 1845 and the following year the entire ill family left Nauvoo for Utah. Hannah Hood Hill was four years old. In her autobiography she remembers her stay in Nauvoo ...

Thursday, November 24, 2011
What William the Conqueror's Companions Teach Us about Effective Population Size
My mother has been working on genealogy for several decades. She recently gave me a little book called My Ancestors Came with the Conqueror by Anthony J. Camp, first published in 1988. Camp is a professional genealogist. Before discussing this book, I should let you know that the relationship between professional genealogists and the amateur genealogy found on is similar to the relationship between scientists and Intelligent Design Creationism.

It's estimated that half the population of Great Britain claims to have descended from William the Conqueror who defeated King Harold at the Battle of Hastings in 1066. Not all claims meet the rigorous standards of professional genealogists but it's quite reasonable that there are millions of direct descendants of William.

Sunday, October 22, 2011
Daniel Belden and the Deerfield Massacre

William Beldon (1609-1655) was born in Heptonstall Parish, Yorkshire, England. He settled in Wethersfield in the Colony of Connecticut in 1641. (Wethersfield is just south of Hartford.)

William Beldon married Thomasine Sherwood (1615-1655) and they had the following children.
  1. Samuel Beldon (1647-1737)
  2. Daniel Belden (Belding) (1648-1732)
  3. John Belden (1650-1713)
  4. Susannah Beldon (1651-1706)
  5. Mary Beldon (1653-1724)
  6. Nathaniel Beldon (1654- )
I descend from John Beldon (1659-1713) and his wife Ruth Hale Hayes (1646-1700). But this is story about his brother, Daniel Beldon (sometimes known as Daniel Belding).

Friday, August 5, 2011
Cousin Lucy

We've been at the Chautauqua Institution in upstate New York for the past few days learning about Iran. On Wednesday afternoon we took a short trip to nearby Jamestown and visited the cemetery where Lucille Ball is buried.

Lucille Désirée Ball was born in Jamestown, New York, in 1911 and she died in Los Angeles in 1989. Her ancestors moved to Chautauqua County in the early 1800's from Connecticut. Lucy and her mother, Désirée Evelyn Hunt, are descendants of Thomas Sherwood (~1586 - 1655) and his second wife Mary Onge (?).

I descend on my mother's side from Thomas Sherwood and his first wife Alice Tiler (1585 - 1635).

Wednesday, June 29, 2011
Losing Charlemagne
Back in October 2009 I published my genealogical connection to Emperor Charlemagne [My Family and Other Emperors]. It is wrong. I relied too much on the information found in and much of that information is unreliable.

In my case the connection was through Ruhamah Hill (b ~1708) who married John Belden (1728 - ). They were British citizens who lived in Norwalk, Fairfield Country, Connecticut (a colony of Great Britain). The parents of Ruhamah Hill are often listed as William Hill and Abigail Barlow of Greenfield Connecticut but there's no evidence to support this connection. On the other hand, historical records say that Ruhamah Hill is the daughter of Captain John Hill (1669 - 1768?) of Westerley, Rhode Island and this seems much more reasonable since Captain John Hill married Ruhamah Wyer (1670 - ).

Saturday, October 24, 2010
The Pillars of the Earth

Matilda married Henry V, Holy Roman Emperor, when she was 13 years old and she became known as Empress Matilda at that point. She returned to England when her husband, Henry V, died in 1125. In the movie she is depicted as a young girl who is present when the King learns of his son's death on the White Ship. In fact, she was already 18 years old and married to the Holy Roman Emperor when the ship went down.

Empress Matilda, known as Maud in the movie, married Geoffrey Plantagenet, Count of Anjou in 1128. They had a son who eventually becomes Henry II of England and founds the Plantagenet dynasty. (Oops, I just gave away the ending!

I descend from Geoffrey and Matilda through my Scottish Stewart ancestors.

Friday, September 24, 2010
Our Ancestor Charlemagne: Taller than Average?

John Hawks found a paper analyzing the height of Charlemagne (742-814). Rühli et al. (2010) looked at measurements of Charlemagne's left tibia in order to determine his total height and robustness. The result indicates that he was 1.84 m tall (6' 0"). This is considerably taller than the average height of his male contemporaries at 1.69 m (5' 6"). Thus Charlemagne was taller than 99% of the men around him and qualifies as "great" in more ways than one.

The average height of Germans today is 1.78 m (5' 10") and Belgians are a bit taller at 1.795 (5' 10½"). (Charlemagne comes from the area around Liege in Belgium and Aachen in Germany.) Charlemagne would be taller than average in today's society but not notably taller.

Thursday, July 22, 2010
Godfrey was the son of Eustace II, Count of Boulogne and Ida of Lorraine. Eustace II fought with William the Conqueror at the Battle of Hastings. His father was Eustace I, Count of Boulogne who married Matilda of Leuven (Louvain). (She was the daughter of Lambert I, Count of Leuven (~950-1015). We have many Belgian ancestors.)

Eustace I and Matilda are Zoë's direct ancestors via their other son Lambert II, Count of Lens (1025-1054). We descend from his daughter Judith of Lens whose mother (wife of Lambert II) was Adelaide of Normandy, sister of William the Conqueror.

The majority of people reading this blog are also descendants of these people. You just don't know it.

Monday, April 12, 2010
Lance Corporal Robert Alexander Hood (1895 - 1917)

Robert Alexander Hood was born in 1895 in a small village north-west of Waterloo, Ontario, Canada. He went to France in 1916 when he was only 21 years old. Robert fought with the 73rd Battalion and he was killed in action at Vimy Ridge on this day, April 12, in 1917. He was a cousin of Ms. Sandwalk's grandfather.

Canadians "celebrate" the battle of Vimy Ridge as a great Canadian victory. It was part of the larger Battle of Arras, which in turn was a diversionary attack in support of the larger Nivelle Offensive carried out by the French Army. About 3,600 young Canadian men were killed during the four day battle and 7,000 more were wounded. This is just a small fraction of the casualties on both sides during World War I.

Thursday, October 15, 2009
Are You a Descendant of Charlemagne?
Thousands of amateur genealogists have contributed to a huge database of family relationships, including genetic analyses. What does this teach us about human populations and evolution?

It may seem like a ridiculous question to ask whether you are a descendant of Charlemagne, who was crowned Emperor on December 25, 800. If you live in Asia or Africa, or your ancestors are from Asia or Africa, then you are probably not a descendant of Charlemagne.

Tuesday, September 22, 2009
The Hanging of Goodwife Knapp in 1653

The remarkable thing about the Goodwife Knapp execution is not the trial itself but the aftermath. Roger Ludlow, the Deputy Governor of Connecticut, had been fighting on and off for several years with his neighbor Mary Staples (wife of Thomas Staples, also known as Staplies). In 1651 Ludlow won a suit against Mary Staples for slander but this did not put and end to their dispute.

The reason for my interest in this trial is that many of my ancestors lived in Fairfield at the time and their names are mentioned in the account. Some of my ancestors were friends of the Staples and defended Mary Staples while others sided with Roger Ludlow. Ludlow lost the case and he left Fairfield the following year (1654), making his way eventually back to England and then to Ireland where he remained for the rest of his life.

By an extraordinary coincidence, my good friend and former best man at my wedding, Charles Beach, is a descendant of Mary Staples and Thomas Staples. Their daughter, Mary Nicol Staples (1630-1677) married John Beach (1623-1677).

Saturday, January 31, 2009
My New York Ancestors

Arbraham Rycken and his wife owned a lot of property on Long Island, including a small island off the coast near their farms. Their children adopted several names including "van Lent" and "Riker." The small island remained in the family for several hundred years and it is still known as Rikers Island—now the site of a large prison.

Their daughter, Aeltje, married Captain Jan Harmse, a descendant of German/Dutch immigrants. Captain Harmse was born in New Amsterdam (New York) in 1657. Their son, Harmen Harmse (1684-1720), married Margaret Montras (1691-1739) thus uniting my French and Dutch ancestors. Harmen took his wife's last name. They moved to Tarrytown New York and joined the congregation of the Dutch Reformed Church of Sleepy Hollow.

The son of Harman and Margaret Montras is Peter Montras (1715-1790). He was my great6 grandfather.

Thursday, October 23, 2008
Niall Nóigiallach - Niall of the Nine Hostages

Niall is also famous for another reason. DNA studies indicate that one in twelve Irish men carry a Y chromosome haplotype that traces back to Niall. The haplotype is also common in Scotland and England, and on the continent. This makes Niall one of only a handful of men who have millions of direct male descendants. (Genghis Khan was another [Genghis Khan a Prolific Lover, DNA Data Implies].)

Families that trace their ancestry back to Niall of the Nine Hostages include: (O')Neill, (O')Gallagher, (O')Boyle, (O')Doherty, O'Donnell, Connor, Cannon, Bradley, O'Reilly, Flynn, (Mc)Kee, Campbell, Devlin, Donnelly, Egan, Gormley, Hynes, McCaul, McGovern, McLoughlin, McManus, McMenamin, Molloy, O'Kane, O'Rourke and Quinn.

My mother's maiden name is Doherty. We are descendants of the O'Dochartaigh's of Donegal in the north-west part Ireland.

Thursday, October 23, 2008
Bar Graphs, Pie Charts, and Darwin

One of Ms. Sandwalk's ancestors is William Playfair (1789 - 1823). Her great grandfather—the great-great-grandfather of my children—was John Playfair Leslie. John's mother is a direct descendant of William Playfair.

William Playfair was an interesting man for many reasons. He is most famous for inventing statistical graphs; especially pie charts and bar graphs. These were printed in his famous book, Commercial and Political Atlas, published in 1786. Two examples of figures from that book are shown here.

Sunday, September 28, 2008
Sleepy Hollow

This is a view of the cemetery of the Old Dutch Church of Sleepy Hollow. It was taken by a visitor who posted it on the Friends of the Old Dutch Burying Gorund website.

When Harman married Margaret Montras he took her name as his surname and became known as Harmen Montras. Their fourth child, Peter (Petrus) Montras, was baptized on March 6, 1715 in the Dutch Church of Sleepy Hollow. He is my great- great- great- great- great- great-grandfather. Peter's descendants changed their last name to Montrose or Montross.

Harmen Montras and his wife Margaret Montras are almost certainly buried in the Old Dutch Church of Sleepy Hollow cemetery in unmarked graves and so are Harmen's parents Jan Harmse and Aeltje. That's four direct ancestors of mine. Part of the house built by Jan Harmse is still standing in Irvington, New York.

Monday, August 11, 2008
Horse Thieves, Skeletons and Black Sheep in the Family
After serving his eight years as an indentured servant, Daniel Robins married Hope Potter in New Haven Conn. in 1641. Now here's the interesting part. Hope Potter's father was William Potter (b. 1608) who first came to New England in 1635. When searching for information about William Potter, my mother came across this opening paragraph on a listserve.
Every amateur genealogist has in the back of his or her mind that someday an ancestral skeleton will appear, perhaps the legendary "horse thief". For those who are descendants of William Potter, the skeleton has appeared, but he did not steal the horses.
Hmmm ....

Saturday, December 8, 2007
The DNA Genealogy Scam

CBC News has a show on television called Marketplace. It often covers scams and commercial frauds that Canadians need to be wary of. Last week they ran a segment on home DNA testing kits and the claims of those who sell them to the general public. You can watch the entire segment on their website [Who's Your Grand Daddy?].

I Think We Have the Same Eyes ( has this neat feature where they combine all their family trees into a big "One World" tree. If you know your ancestors, you can access the "one world" tree and check to see who you're related to. It's especially fun to see which famous people are your distance cousins.

There's only one problem. You really have to know something about your ancestors before you trust the results. Most of the relationships are wrong because someone has entered the wrong data and it gets propagated to the "one world" tree. This is a problem with all such databases—including scientific ones.

Here's one of the reliable hits. It shows how Bette Davis is a distant cousin. She descends from my great10 grandparents Captain Richard Norman and his wife Margaret Alford. They were born in Orchard Portman, Somerset, England (midway between Exeter and Bristol) and came to Massachusetts Colony in 1626.

UPDATE: This is wrong. There's a mistake on the internet! I am NOT a descendant of Richard Norman and Margaret Alford.

Saturday, April 23, 2016

Proponents of the Extended Evolutionary Synthesis (EES) explain their logic using the Central Dogma as an example

There's a group of biologists who think that the current version of evolutionary theory is insufficient. They want to create an extended evolutionary synthesis that incorporates evo-devo, plasticity, niche construction, evolvability, epigenetics, and other things.

You might be wondering how these things could be incorporated and what that would do to "classic" evolutionary theory. Fortunately, we have a road map provided by Massimo Pigliucci and Gerd Müller in chapter one of Evolution: The Extened Synthesis. They help us out by providing an analogy.
As we will see in the rest of this volume, several of these tenets [of the Modern Synthesis] are being challenged as either inaccurate or incomplete. It is important, however, to understand the kind of challenge being posed here, in order to avoid wasting time on unproductive discussions that missed the point of an extended evolutionary synthesis. Perhaps a parallel with another branch of biology will be helpful. After Watson and Crick discovered the double-helix structure of DNA, and the molecular revolution got started in earnest, one of the first principles to emerge from the new discipline was the unfortunately named "central dogma" of molecular biology. The dogma (a word that arguably should never be used in science) stated that the flow of information in biological systems is always one way, from DNA to RNA to proteins. Later on, however, it was discovered that the DNA > RNA flow can be reversed by the appropriately named process of reverse transcription, which takes place in a variety of organisms, including some viruses and eukaryotes (through retrotransposons). Moreover, we now know that some viruses replicate their RNA directly by means of RNA dependent RNA polymerases, enzymes also found in eukaryotes, where they mediate RNA silencing. Prions have shown us how some proteins can catalyze conformational changes in similar proteins, a phenomenon that is not a case of replication, but certainly qualifies as information transfer. Finally, we also have examples of direct DNA translation to protein in cell-free experimental systems in the presence of ribosomes but not of mRNA. All of these molecular processes clearly demolish the alleged central dogma, and yet do not call for the rejection of any of the empirical discoveries or conceptual advances made in molecular biology since the 1950s. Similarly, we argue, individual tenets of the Modern Synthesis can be modified, or even rejected, without generating a fundamental crisis in the structure of evolutionary theory—just as the Modern Synthesis itself improved upon but did not cause rejection of either Darwinism or neo-Darwinism.
I thank Pigliucci and Müller for giving us a clear idea of the logic behind their attack on the Modern Synthesis.

... I must correct a wrong idea that has been spreading for the past three or four years. It was discovered some years ago that in some cases, the transcription step from DNA to RNA works in the reverse direction. That is nothing surprising. ... it could be predicted that such events could occur. They do occur, indeed, but this must not be taken to mean that information from protein could possibly go back to the genome. ... I am ready to take any bet you like that this is never going to turn out to be the case.

Jacques Monod (1974) p.394
The original, and correct, version of the Central Dogma of Molecular Biology was stated clearly by Francis Crick in 1958. Crick restated the Central Dogma of Molecular Biology in a famous paper published in 1970 at a time when the premature slaying of the Central Dogma by reverse transcriptase was being announced (Crick, 1970). According to Crick, the correct, concise version of the Central Dogma is ...
... once (sequential) information has passed into protein it cannot get out again (F.H.C. Crick, 1958)
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid. (F.H.C. Crick, 1970)
Jim Watson published the well-known, but incorrect, version in his 1960s textbook but anyone who does even a little bit of research will discover that the Crick version is the original [see: The Central Dogma of Molecular Biology].

Here's the summary provided by Francis Crick in his 1970 Nature paper.

Fig. 1. Information flow and the sequence hypothesis. These diagrams of potential information flow were used by Crick (1958) to illustrate all possible transfers of information (left) and those that are permitted (right). The sequence hypothesis refers to the idea that information encoded in the sequence of nucleotides specifies the sequence of amino acids in the protein.
This is important because whenever someone attacks the Central Dogma you can get a good idea of their academic ability by seeing if they understand the concept they attack. In this case, there's a question about proponents of the extended evolutionary synthesis and whether they have a sufficient grasp of evolutionary theory to be challenging it. Pigliucci and Müller have tried to convince us that they know what they are talking about by giving us an analogy; namely, the "demolition" of the Central Dogma of Molecular Biology.

They didn't do their homework. That doesn't inspire confidence in their ability to overthrow modern evolutionary theory.

Crick, F.H.C. (1958) On protein synthesis. Symp. Soc. Exp. Biol. XII:138-163. [PDF]
Crick, F. (1970) Central Dogma of Molecular Biology. Nature 227, 561-563. [PDF file]
Monod, J. (1974) "On the Molecular Theory of Evolution" reprinted in Mark Ridley (editor) Evolution (1997) p. 389

Friday, April 22, 2016

Don't call it "The Theory of Evolution"

By now, we all know that a "theory" in science is much more than idle speculation, a point that has been made repeatedly over the past century. With respect to evolution, the most famous essay is by Stephen Jay Gould: "Evolution as Fact and Theory" and the latest explanation is an article in the New York Times by Carl Zimmer: In Science, It’s Never ‘Just a Theory’.

Unfortunately, it's not that simple and there are many scientists who use "theory" in the sense of hypothesis or speculation [see Facts and theories of evolution according to Dawkins and Coyne]. That's not what I want to talk about today.

What do scientists really mean when they refer to "The Theory of Evolution"? There is no single theory of evolution that covers all the mechanisms of evolution. There's the Theory of Natural Selection, and Neutral Theory, and the Theory of Random Genetic Drift, and a lot of theoretical population genetics. Sometimes you can lump them all together by referring to the Modern Synthesis or Neo-Darwinism. These terms are much more accurate than simply saying "The Theory of Evolution" as long as we all understand what those theories mean.

The problem with "The Theory of Evolution" is not only that it's ambiguous but it's misleading. It implies that there's only one theory to explain evolution. Another problem is that it sounds too much like we're talking about the history of life and saying that it's a "theory" that can be explained by evolution.

Instead of using the phrase "The Theory of Evolution," I think we should be referring to "evolutionary theory," which may come in different flavors. The term "evolutionary theory" encompasses a bunch of different ideas about the mechanisms of evolution and conveys a much more accurate description of the theoretical basis behind evolution. Douglas Futuyma prefers "evolutionary theory" in his textbook Evolution and I think he's right. It allows him to devote individual chapters to "The Theory of Random Genetic Drift" and "The Theory Natural Selection."

Here's how Futuyma explains the concept of theory in his book Evolution 2nd ed. p. 613.
So is evolution a fact or a theory? In light of these definitions, evolution is a scientific fact. That is, descent of all species, with modification, from common ancestors is a hypothesis that in the past 150 years or so has been supported by so much evidence, and so successfully resisted all challenges, that it has become a fact. But this history of evolutionary change is explained by evolutionary theory, the body of statements (about mutation, selection, genetic drift, developmental constraints, and so forth) that together account for the various changes that organisms have undergone. [my emphasis ... LAM]
He makes the same point in the opening pages of his book where he uses both terms when discussing the history of evolutionary theory. (Note that when Darwin used the word "theory" to describe natural selection he was not using it in the same sense as Gould and Zimmer to describe a modern scientific theory. That's why Futuyma uses "hypothesis" in the quote below.)
We now know that Darwin's hypothesis of natural selection on hereditary variation was correct, but we also know that there are more causes of evolution than Darwin realized, and that natural selection and hereditary variation themselves are more complex than he imagined. A body of ideas about the causes of evolution, including mutation, recombination, gene flow, isolation, random genetic drift, the many forms of natural selection, and other factors, constitute our current theory of evolution, or "evolutionary theory." Like all theories in science, it is a work in progress, for we do not yet know the causes of all of evolution, or all the biological phenomena that evolutionary biology will have to explain. Indeed, some details may turn out to be wrong. But the main tenets of the theory, as far as it goes, are so well supported that most biologists confidently accept evolutionary theory as the foundation of the science of life. p. 14 [my emphasis ... LAM]
When you're talking about the mechanisms of evolution, please use "evolutionary theory" instead of "the theory of evolution."

I wish the proponents of the Extended Evolutionary Synthesis would agree that the version of evolutionary theory they wish to extend is the one described by Douglas Futuyma. This would make it easier for them to explain what's wrong with that version and why their proposals are an improvement [see Templeton gives $8 million to prove that there's more to evolution than natural selection].

Templeton gives $8 million to prove that there's more to evolution than natural selection

The Templeton Foundation will fund a group of researchers who promote something called "The Extended Evolutionary Synthesis" (EES). The grant is for $8 million (US). The project is headed by Kevin N, Laland of the University of St. Andrews (Scotland, UK) and Tobias Uller of Lund University in Sweden. You can read all about it at: Putting the Extended Evolutionary Synthesis to the Test.

There are two problems with this funding. The first is the source of the funds. I agree with Jerry Coyne and many others that Templeton Fund money is tainted because the clear purpose of the fund is to lend credence to religion [Templeton keeps up the woo]. Templeton will only fund projects that advance that objective.

The second problem is the science. The advocates of EES promote things like "developmental plasticity," "niche construction," "evo-devo," and "epigenetics"—all of these phenomena are supposed to play a major role in evolutionary theory, a role that is not covered by the Modern Synthesis.

I think that all of these processes may play a role in explaining the history of life on Earth1 but so do plate tectonics, asteroid impacts, and endosymbiosis. The problem is that there's a difference between explaining the events behind the history of life and evolutionary theory. They are not the same thing.

The real question is whether any of these things need to be incorporated into modern evolutionary theory and whether they extend the Modern Synthesis. Personally, I don't think any of them make a significant contribution to evolutionary theory.

But my real beef is with the outdated view of evolution held by EES proponents. To a large extent they are fighting a strawman version of evolution. They think that the "Modern Synthesis" or "Neo-Darwinism" is the current view of evolutionary theory. They are attacking the old-fashioned view of evolutionary theory that was common in the 1960s but was greatly modified by the incorporation of Neutral Theory and increased emphasis on random genetic drift. The EES proponents all seem to have been asleep when the real revolution occurred.

When you listen to them, you get the distinct impression they have never read The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. I have no confidence in biologists who want to overthrow a view of evolutionary theory that's already been dead for half a century. I have no confidence in biologists who aren't at ease talking about non-adaptive evolution. This is the 21st century.2

Elizabeth Pennisi is all over this. She wrote an article for the April 22 (2016) edition of Science: Templeton grant funds evolution rethink. The opening sentence is very revealing ....
For many evolutionary biologists, nothing gets their dander up faster than proposing that evolution is anything other than the process of natural selection, acting on random mutations.
Damn right! I'm not an evolutionary biologist but my dander gets up whenever scientists make such a ridiculous claim.

Help is one the way, according to Elizabeth Pennisi because the Templeton Foundation is funding research to show that there's more to evolution than natural selection. Unfortunately, the "extended" version doesn't include random genetic drift and modern population genetics.
No wonder some evolutionary biologists are uneasy with an $8.7 million grant to U.K., Swedish, and U.S. researchers for experimental and theoretical work intended to put a revisionist view of evolution, the so-called extended evolutionary synthesis, on a sounder footing. Using a variety of plants, animals, and microbes, the researchers will study the possibility that organisms can influence their own evolution and that inheritance can take place through routes other than the genetic material.
I don't object to work on those subjects. My beef is with the idea that they pose a problem for our current understanding of evolutionary theory. More importantly, my main complaint is that the biologists who will spend all this money missed the real revolution that took place 50 years ago.

Here's how Pennisi describes the extended evolutionary synthesis. Her description is pretty accurate.
The extended evolutionary synthesis is a term coined in 2007 to imply that the preeminent current evolutionary theory, the so-called modern synthesis, needed to broaden its focus because it concentrated too much on the role of genes in evolution and lacked adequate incorporation of new insights from development and other areas of biology. The idea has gradually gathered momentum since its advocates first met in Germany in 2008 (Science, 11 July 2008, p. 196). Later, Kevin Laland, an evolutionary biologist at the University of St. Andrews in the United Kingdom, and several colleagues took up the cause, arranging for a point-counterpoint discussion in Nature in 2014 and a comprehensive review last year in the Proceedings of the Royal Society B's annual Darwin Review.

Advocates stress that animals, plants, and even microbes modify their environments, exhibit plasticity in their physical traits, and behave differently depending on the conditions they face. Chemical modifications of the DNA that affect gene activity—so-called epigenetic changes—seem to explain some of this flexibility. These and other factors suggest to some biologists that an organism's development is not simply programmed by the genetic sequences it inherits. For them, such plasticity implies that parents can influence offspring not just through their DNA but by passing on the microorganisms they host or by transmitting epigenetic marks to subsequent generations. “Innovation may be a developmental response that becomes stabilized through genetic changes,” explains Armin Moczek, an evolutionary developmental biologist at Indiana University, Bloomington.

Nor is evolution controlled only by natural selection, the winnowing process by which the fittest survive and reproduce, Laland and others argue. Organisms, by transforming their environments and responding to environmental factors, help control its course, they contend. As such, the extended synthesis “represents a nascent alternative conceptual framework for evolutionary biology,” Laland and dozens of colleagues wrote in a funding proposal to the Templeton Foundation last year.
This is a profoundly adaptationist view of evolutionary theory. The "extended" version merely adds a few more mechanisms that might improve adaptation.

Most of the EES proponents are working on animals, many are physiologists. They share an evo-devo view of evolution that emphasizes the role of natural selection. I share Michael Lynch's view that we live in a post-Darwinian world and nothing in evolution makes sense except in the light of population genetics. I agree with him that most scientists think of evolution as a soft science and that includes many biologists. It includes most of the EES proponents who probably couldn't tell you anything about population genetics beyond the fact that it's too mathematical. That doesn't stop them from criticizing modern evolutionary theory.

Natural selection is just one of several evolutionary mechanisms, and the failure to realize this is probably the most significant impediment to a fruitful integration of evolutionary theory with molecular, cellular, and developmental biology.

Michael Lynch
Here's a quote from Michael Lynch's book The Origins of Genome Architecture. In my view, it describes the group who were awarded $8 million to overthrow modern evolutionary theory.
Despite the tremendous theoretical and physical resources now available, the field of evolutionary biology continues to be widely perceived as a soft science. Here I am referring not to the problems associated with those pushing the view that life was created by an intelligent designer, but to a more significant internal issue: a subset of academics who consider themselves strong advocates of evolution but who see no compelling reason to probe the substantial knowledge base of the field. Although this is a heavy charge, it is easy to document. For example, in his 2001 presidential address to the Society for the Study of Evolution, Nick Barton presented a survey that demonstrated that about half of the recent literature devoted to evolutionary issues is far removed from mainstream evolutionary biology.

With the possible exception of behavior, evolutionary biology is treated unlike any other science. Philosophers, sociologists, and ethicists expound on the central role of evolutionary theory in understanding our place in the world. Physicists excited about biocomplexity and computer scientists enamored with genetic algorithms promise a bold new understanding of evolution, and similar claims are made in the emerging field of evolutionary psychology (and its derivatives in political science, economics, and even the humanities). Numerous popularizers of evolution, some with careers focused on defending the teaching of evolution in public schools, are entirely satisfied that a blind adherence to the Darwinian concept of natural selection is a license for such activities. A commonality among all these groups is the near-absence of an appreciation of the most fundamental principles of evolution. Unfortunately, this list extends deep within the life sciences.
The real revolution was the incorporation of nonadaptive mechanisms into evolutionary theory and the overthrow of adaptationism. That revolution is not complete. There are still thousands of biologists who remain strict Darwinists even as they try to promote different ways of achieving adaptation. Those biologists still dominate the popular press (e.g. Elizabeth Pennisi) and they are largely responsible for skepticism about junk DNA. That has to change. Evo-devo types need to listen to Michael Lynch when he says ...
Unfortunately, the emerging field of evolutionary developmental biology is based almost entirely on a paradigm of natural selection, and the near-absence of the concept of nonadaptive processes from the lexicon of those concerned with cellular and developmental evolution does not follow from any formal demonstration of the negligible contribution of such mechanisms but simply reflects the failure to consider them. [my emphasis ... LAM] There is no fundamental reason why cellular and developmental features should be uniquely immune to nonadaptive evolutionary forces. One could even argue that the stringency of natural selection is reduced in complex organisms with behavioral and/or growth from flexibilities that allow individuals to match their phenotypic capabilities to the local environment.

1. Some of them are trivial and some are ineffective but that's been debated many times. I want to emphasize the fact that EES proponents don't understand modern evolutionary theory.

2. To be fair, some of these proponents do pay lip-service to non-adaptive evolution from time to time but it's clear that they don't really get it.

Monday, April 11, 2016

My DNA ancestry

I sent a DNA sample off to a few weeks ago and here are the results.

Ancestry has a peculiar way of identifying haplotypes. When they say "Ireland," they mean Ireland and Scotland.1 When they say Great Britain, they mean that they don't distinguish between England, most of Scotland, and most of Normandy.

The results look fairly accurate. My maternal grandmother is Irish—both her parents immigrated to Canada from Ireland in the late 1800s. They descend mostly from English settlers who moved to Ireland in the 1600s. That's why I'm not 25% Irish.

My maternal grandfather is a mixture of English, Scottish, French and Dutch ancestors. The dominant DNA markers should be Scottish and English.

My paternal grandfather is from Russia, near the Volga river north of Volgograd and south of Saratov. He was German ... descended from German immigrants brought in my Catherine the Great in the late 1700s. The German communities on the Volga did not mix genes with the local Russians so the haplotypes will be German. This is mostly why I'm almost 25% German.

My paternal grandmother is from Volhynia in northern Ukraine. Many of her ancestors were German having recently (1700s) settled in the regions from Germany and German-speaking parts of Poland. Those families mixed with the local populations of Poland, Lithuania (now Belarus), and northern Ukraine.

The trace Scandinavian haplotypes could come from either side of my family through Poland/Germany or through Scotland/Ireland. identifies all my DNA relatives who have had their DNA tested. There are 73 of them in all but none closer than 4th cousin. Fortunately, some of them seem to related to my paternal grandfather. That's the link I wanted to explore so I'll be getting in touch with them.

If you add in the other bits then I've got all of Europe covered except Italy. That doesn't explain why I like spaghetti & meatballs and pizza.

1. The DNA analysis is done in a lab in Ireland!

Sunday, March 27, 2016

Georgi Marinov reviews two books on junk DNA

The December issue of Evolution: Education and Outreach has a review of two books on junk DNA. The reviewer is Georgi Marinov, a name that's familiar to Sandwalk readers. He is currently working with Michael Lynch at Indiana University in Bloomington, Indiana, USA. You can read the review at: A deeper confusion.

The books are ...
The Deeper Genome: Why there is more to the human genome than meets the eye, by John Parrington, (Oxford, United Kingdom: Oxford University Press), 2015. ISBN:978-0-19-968873-9.

Junk DNA: A Journey Through the Dark Matter of the Genome, by Nessa Carey, (New York, United States: Columbia University Press), 2015. ISBN:978-0-23-117084-0.
You really need to read the review for yourselves but here's a few teasers.
If taken uncritically, these texts can be expected to generate even more confusion in a field that already has a serious problem when it comes to communicating the best understanding of the science to the public.
Parrington claims that noncoding DNA was thought to be junk and Georgi replies,
However, no knowledgeable person has ever defended the position that 98 % of the human genome is useless. The 98 % figure corresponds to the fraction of it that lies outside of protein coding genes, but the existence of distal regulatory elements, as nicely narrated by the author himself, has been at this point in time known for four decades, and there have been numerous comparative genomics studies pointing to a several-fold larger than 2% fraction of the genome that is under selective constraint.
I agree. That's a position that I've been trying to advertise for several decades and it needs to be constantly reiterated since there are so many people who have fallen for the myth.

Georgi goes on to explain where Parringtons goes wrong about the ENCODE results. This critique is devastating, coming, as it does, from an author of the most relevant papers.1 My only complaint about the review is that George doesn't reveal his credentials. When he quotes from those papers—as he does many times—he should probably have mentioned that he is an author of those quotes.

Georgi goes on to explain four main arguments for junk DNA: genetic load, the C-value Paradox, transposons (selfish DNA), and modern evolutionary theory. I like this part since it's similar to the Five Things You Should Know if You Want to Participate in the Junk DNA Debate. The audience of this journal is teachers and this is important information that they need to know, and probably don't.

His critique of Nessa Carey's book is even more devastating. It begins with,
Still, despite a few unfortunate mistakes, The Deeper Genome is well written and gets many of its facts right, even if they are not interpreted properly. This is in stark contrast with Nessa Carey’s Junk DNA: A Journey Through the Dark Matter of the Genome. Nessa Carey has a PhD in virology and has in the past been a Senior Lecturer in Molecular Biology at Imperial College, London. However, Junk DNA is a book not written at an academic level but instead intended for very broad audience, with all the consequences that the danger of dumbing it down for such a purpose entails.
It gets worse. Nessa Carey claims that scientists used to think that all noncoding DNA was junk but recent discoveries have discredited that view. Georgi sets her straight with,
Of course, scientists have had a very good idea why so much of our DNA does not code for proteins, and they have had that understanding for decades, as outlined above. Only by completely ignoring all that knowledge could it have been possible to produce many of the chapters in the book. The following are referred to as junk DNA by Carey, with whole chapters dedicated to each of them (Table 3).

The inclusion of tRNAs and rRNAs in the list of “previously thought to be junk” DNA is particularly baffling given that they have featured prominently as critical components of the protein synthesis machinery in all sorts of basic high school biology textbooks for decades, not to mention the role that rRNAs and some of the other noncoding RNAs on that list play in many “RNA world” scenarios for the origin of life. How could something that has so often been postulated to predate the origin of DNA as the carrier of genetic information (Jeffares et al. 1998; Fox 2010) and that must have been of critical importance both before and after that be referred to as “junk”?
You would think that this is something that doesn't have to be explained to biology teachers but the evidence suggests otherwise. One of those teachers recently reviewed Nessa Carey's book very favorably in the journal The American Biology Teacher and another high school teacher reveals his confusion about the subject in the comments to my post [see Teaching about genomes using Nessa Carey's book: Junk DNA].

It's good that Georgi Marinov makes this point forcibly.

Now I'm going to leave you with an extended quote from Georgi Marinov's review. Coming from a young scientist, this is very potent and it needs to be widely disseminated. I agree 100%.
The reason why scientific results become so distorted on their way from scientists to the public can only be understood in the socioeconomic context in which science is done today. As almost everyone knows at this point, science has existed in a state of insufficient funding and ever increasing competition for limited resources (positions, funding, and the small number of publishing slots in top scientific journals) for a long time now. The best way to win that Darwinian race is to make a big, paradigm shifting finding. But such discoveries are hard to come by, and in many areas might actually never happen again—nothing guarantees that the fundamental discoveries in a given area have not already been made. ... This naturally leads to a publishing environment that pretty much mandates that findings are framed in the most favorable and exciting way, with important caveats and limitations hidden between the lines or missing completely. The author is too young to have directly experienced those times, but has read quite a few papers in top journals from the 1970s and earlier, and has been repeatedly struck by the difference between the open discussion one can find in many of those old articles and the currently dominant practices.

But that same problem is not limited to science itself, it seems to be now prevalent at all steps in the chain of transmission of findings, from the primary literature, through PR departments and press releases, and finally, in the hands of the science journalists and writers who report directly to the lay audience, and who operate under similar pressures to produce eye-catching headlines that can grab the fleeting attention of readers with ever decreasing ability to concentrate on complex and subtle issues. This leads to compound overhyping of results, of which The Deeper Genome is representative, and to truly surreal distortion of the science, such as what one finds in Nessa Carey’s Junk DNA.

The field of functional genomics is especially vulnerable to these trends, as it exists in the hard-to-navigate context of very rapid technological changes, a potential for the generation of truly revolutionary medical technologies, and an often difficult interaction with evolutionary biology, a controversial for a significant portion of society topic. It is not a simple subject to understand and communicate given all these complexities while in the same time the potential and incentives to mislead and misinterpret are great, and the consequences of doing so dire. Failure to properly communicate genomic science can lead to a failure to support and develop the medical breakthroughs it promises to deliver, or what might be even worse, to implement them in such a way that some of the dystopian futures imagined by sci-fi authors become reality. In addition, lending support to anti-evolutionary forces in society by distorting the science in a way that makes it appear to undermine evolutionary theory has profound consequences that given the fundamental importance of evolution for the proper understanding of humanity’s place in nature go far beyond making life even more difficult for teachers and educators of even the general destruction of science education. Writing on these issues should exercise the needed care and make sure that facts and their best interpretations are accurately reported. Instead, books such as The Deeper Genome and Junk DNA are prime examples of the negative trends outlined above, and are guaranteed to only generate even deeper confusion.
It's not easy to explain these things to a general audience, especially an audience that has been inundated with false information and false ideas. I'm going to give it a try but it's taking a lot more effort than I imagined.

1. Georgi Marinov is an author on the original ENCODE paper that claimed 80% of our genome is functional (ENCODE Project Consortium, 2012) and the paper where the ENCODE leaders retreated from that claim (Kellis et al., 2014).

ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 48957-74. [doi: 10.1038/nature11247]

Kellis, M., Wold, B., Snyder, M.P., Bernstein, B.E., Kundaje, A., Marinov, G.K., Ward, L.D., Birney, E., Crawford, G.E., and Dekker, J. (2014) Defining functional DNA elements in the human genome. Proc. Natl. Acad. Sci. (USA) 111:6131-6138. [doi: 10.1073/pnas.1318948111]

When philosophers write about evolution

The latest issue of Evolution: Education and Outreach contains a review of two books about evolution written by philosophers. The author of the review is Egbert Giles Leigh Jr. You can read it for free at: Questions about NeoDarwinism: a review of two books.

The books are,
Mind and Cosmos: Why the Materialist NeoDarwinian Conception of Nature is Almost Certainly False by Thomas Nagel. New York: Oxford University Press, 2012. ISBN 978-0-19-991975-8.

Are You an Illusion? by Mary Midgley. New York, NY: Routledge. 2014. ISBN 978-1-84465-792-6.
Both of these books challenge the idea that random mutation and natural selection can explain the world we see around us today.

The reviewer responds with a defense of natural selection from an adaptationist perspective.

I think Nagel and Midgley are wrong but for different reasons. I think that the history of life is the culmination of many random and accidental events and it could easily have gone in different directions [see Replaying life's tape]. I also think that lots of modern features are epiphenomena and not adaptations. Consciousness, to the extent that it actually exists, is one of them.

Nevertheless, Leigh's review is interesting and informative and I urge you to read it if you are interested in knowing why philosophers attack evolution. It helps us understand, once again, where philosophy is going wrong.

Friday, March 25, 2016

Teaching about genomes using Nessa Carey's book: Junk DNA

Nessa Carey's book about junk DNA is an embarrassment to the scientific community [Nessa Carey doesn't understand junk DNA] [The "Insulation Theory of Junk DNA"].

Today, while searching for articles on junk DNA, I came across a review of Nessa Carey's book published in The American Biology Teacher: DNA. The review was written by teacher in Colorado and she liked the book very much. Here's the opening paragraph,
The term junk DNA has been used to describe DNA that does not code for proteins or polypeptides. Recent research has made this term obsolete, and Nessa Carey elaborates on a wide spectrum of examples of ways in which DNA contributes to cell function in addition to coding for proteins. As in her earlier book, The Epigenetics Revolution (reviewed by ABT in 2013), Carey uses analogies and diagrams to relate complicated information. Although she unavoidably uses some jargon, she provides the necessary background for the nonbiologist.
The author of the review does not question or challenge the opinions of Nessa Carey and, if you think about it, that's understandable. The average biology teacher will assume that a book written by a scientist must be basically correct or it wouldn't have been published.

That's not true, as most Sandwalk readers know. You would think that biology educators should know this and exercise a little skepticism when reviewing books. Ideally, the book reviews should be written by experts who can evaluate the material in the book.

Now we have a problem. The way to correct false information about genomes and junk DNA is to teach it correctly in high school and university courses. But that means we first have to teach the teachers. Here's a case where professional teachers have been bamboozled by a bad book and that's going of make it even more difficult to correct the problem.

The last paragraph of the review shows us what influence a bad book can have,
As a biology teacher who enjoys sharing with students some details that go beyond the textbook or that challenge dogma, I enthusiastically read multiple chapters at each sitting, making note of what I cannot wait to add to class discussions. “Junk DNA” may be a misnomer, but Junk DNA is an excellent way of finding out why.
Oh dear. It's going to be hard to re-educate those students once their misconceptions have been reinforced by a teacher they respect.

Tuesday, March 22, 2016

How do you characterize these scientists?

We've been having a discussion on another thread about ID proponents. Are some of them acting in good faith or are they all lying and deceiving their followers?

I have similar problems about many scientists. I've been reading up on pervasive transcription and the potential number of genes for noncoding, functional, RNAs in the human genome. As far as I can tell, there are only a few hundred examples that have any supporting evidence. There are good scientific reasons to believe that most of the detected transcripts are junk RNA produced as the result of accidental, spurious, transcription.

There are about 20,000 protein-coding genes in the human genome. I think it's unlikely that there are more than a few thousand genes for functional RNAs for a total of less than 25,000 genes.

Here's one of the papers I found.
Guil, S. and Esteller, M. (2015) RNA–RNA interactions in gene regulation: the coding and noncoding players. Trends in Biochemical Sciences 40:248-256. [doi: 10.1016/j.tibs.2015.03.001]
Trends in Biochemical Sciences is a good journal and this is a review of the field by supposed experts. The authors are from the Department of Physiological Sciences II at the University of Barcelona School of Medicine in Barcelona, Catalonia, Spain. The senior author, Manel Esteller, has a Wikipedia entry [Manel Esteller].

Here's the first paragraph of the introduction.
There are more genes encoding regulatory RNAs than encoding proteins. This evidence, obtained in recent years from the sum of numerous post-genomic deep-sequencing studies, give a good clue of the gigantic step we have taken from the years of the central dogma: one gene gives rise to one RNA to produce one protein.
The first sentence is not true by any stretch of the imagination. The best that could be said is that there "may" be more genes for regulatory RNAs (> 20,000) but there's no strong consensus yet. Since the first sentence is an untruth, it follows that it is incorrect to say that the evidence supports such a claim.

It's also untrue to distort the real meaning of the Central Dogma of Molecular Biology, which never said that all genes have to encode proteins. The authors don't understand the history of their field in spite of the fact they are writing a review of that field.

Here's the problem. Are these scientists acting in good faith when they say such nonsense? Does acting in "good faith" require healthy criticism and critical thinking or is "honesty" the only criterion? The authors are clearly deluded about the controversy since they assume that it has been resolved in favor of their personal biases but they aren't lying. Can we distinguish between competent science and bad science based on such statements? Can we say that these scientists are incompetent or is that too harsh?

Furthermore, what ever happened to peer review? Isn't the system supposed to prevent such mistakes?

Sunday, March 20, 2016

Another failure: "The Mysterious World of the Human Genome"

The Mysterious World of the Human Genome
by Frank Ryan
William Collins, an imprint of Harper Collins, London UK (2015)
ISBN 978-0-00-754906-1

This is just another "gosh, gee whiz" book on the amazing and revolutionary (not!) discoveries about the human genome. The title tells you what to expect: The Mysterious World of the Human Genome.

The author is Frank P. Ryan, a physician who was employed as an "Honorary Senior Lecturer" in the Department of Medical Education at the University of Sheffield (UK). He's a member of The Third Way group. You can read more about him at their website: Frank P. Ryan.

You need to understand biology if you are going to debate an Intelligent Design Creationist

Last night's debate between Lawrence Krauss, Stephen Meyer, and Denis Lamoureux was very entertaining. I finally got to meet Stephen Meyer in person. (My photographer wasn't very good at focusing.)

There were some interesting exchanges during the debate. I want to talk about one of them.

Krauss tried to hammer Meyer on the "ID is not science" issue using quotes from a judge based on things said by lawyers in the Dover trial.1 Krauss tried to dismiss ID by saying that it never makes predictions but Meyer countered effectively by pointing out that ID predicts that most of our genome is functional and claiming that the prediction was confirmed by the ENCODE study.

The ID position is that Darwinists predicted that our genome would be full of junk while Intelligent Design Creationists predicted that most of our genome would be functional. ID was correct and Darwinism was wrong, according to this story.

Both Lawrence Krauss and Denis Lamoureux accepted the "fact" that ENCODE was right and most of the DNA in our genome has a function. Krauss was also hampered by his misunderstanding of evolution. It's obvious that he accepts the Richard Dawkins view of evolution so he tried to accommodate the ENCODE results by saying it's what you would expect of natural selection. This is the Richard Dawkins position.

Krauss tried to downplay the issue by saying that ID had not predicted what those functional parts of the genome would be doing but this was a weak rebuttal.

The facts are these ....
  • "Darwinists"—those who claim that natural selection is the only game in town—were opposed to the idea that most of our genome is junk. They still are.
  • Today, the majority of experts believe that most of our genome is junk in spite of the ENCODE publicity campaign from 2012.
  • The ENCODE Consortium has backed off it's original claim and now agrees that they misused the word "function." Some of them blame the media for distorting their position.
  • The ID "prediction" has been falsified.
A competent biologist would have known all this and could have challenged Meyer's statement. A biologist would have then demanded that Meyer explain how a genome that is 90% junk fits with Intelligent Design Creationism.

I talked to Denis Lamoureux after the debate to let him know that he was wrong about ENCODE and he was very gracious. I promised to send him more information. A genome full of junk DNA poses no threat to his version of Theistic Evolution.

Lawrence Krauss is an expert on cosmology but he's very weak on biology. I know it's common for physicists to think they are experts in everything but that's just not true. It was demonstrated in last night's debate.

1. This is a bad strategy. It's better to accept that ID proponents are doing science but just doing it very badly. Meyer ignored the issue of whether ID counted as science. He just presented the scientific case for ID and forced Krauss to respond to his "evidence."