Tuesday, July 29, 2014

The Function Wars: Part III

This is Part III of several "Function Wars"1 posts.

How much of the human genome is conserved?

The first post in this series covered the various definitions of "function" [Quibbling about the meaning of the word "function"]. In the second post I tried to create a working definition of "function" and I discussed whether active transposons count as functional regions of the genome or junk [The Function Wars: Part II]. I claim that junk DNA is DNA that is nonfunctional and it can be deleted from the genome of an organism without affecting its survival, or the survival of its descendants.

The best way to define "function" is to rely on evolution. DNA that is under selection is functional. But how can you determine whether a given stretch of DNA is being preserved by natural selection? The easiest way is to look at sequence conservation. If the sequence has not changed at the rate expected of neutral changes fixed by random genetic drift then it is under negative selection. Unfortunately, sequence conservation only applies to regions of the genome where the sequence is important. It doesn't apply to DNA that is selected for its bulk properties.

The most important rule for publishing a paper on alternative splicing

I'm not a big fan of alternative splicing. I think it falls into the same category as pervasive transcrition—most of it is accidental [see Alternative Splicing and Why IDiots Don't Understand How Science Works and A Challenge to Fans of Alternative Splicing ]. The error rate for splicing is known to be high [Splicing Error Rate May Be Close to 1% ].

I just read a paper about alternative splicing in Science (Lo et al., 2014) and it annoys me that a key piece of data was left out. The missing data is the abundance of the rare transcripts that are presumed to be genuine, alternatvely spliced, variants. Are they present at more than one copy per cell?

We need to know this in order to decide whether the detection of alternatively spiced variant is biologically significant. You should not be able to publish a paper on this topic without presenting your data on relative and absolute abundance [see Extraordinary Claims about Human Genes and How to Evaluate Genome Level Transcription Papers]. Surely this is obvious, having just been through the ENCODE publicity hype disaster.


Lo, W.-S., Gardiner, E., Xu, Z., Lau, C.-F., Wang, F., Zhou, J. J., Mendlein, J. D., Nangle, L. A., Chiang, K. P. X-L, Yang, K-F. Au, W. H. Wong, M. Guo, M. Zhang, and P. Schimmel1 (2014) Human tRNA synthetase catalytic nulls with diverse functions. Science 345:328-332. [doi: 10.1126/science.1252943]

Walter Gehring (1939 - 2014)

I just learned today that Walter Gehring died in a car accident in Greece on May 29th. I learned of his death from the obituary by Michael Levine in Science [Walter Gehring (1939–2014)]. There's another obituary on the Biozentrum (Basel, Switzerland) website [Obituary for Walter Gehring (1939 – 2014)]. He was only seven years older than me.

I first met Walter Gerhing when I was a post-doc in Alfred Tissières lab in Geneva (Switzerland) in the mid-1070s. The two labs collaborated on cloning and characterizing the major heat shock gene (Hsp70) of Drosophila melanogaster. Paul Schedl and Spyros Artavanis-Tsakonis made the library in Gehring's lab in 1976-1977 and Marc-Edouard Mirault and I isolated the mRNA for screening and then identified the genes we cloned. The result was three papers in Cell (see below). (John Lis, then in David Hogness' lab, was cloning the same gene.)

I met Gerhing dozens of times but I only had a few conversations with him one-on-one. We always talked about evolution. I always found him to be very charming and very curious and not embarrassed to admit that he didn't know something. Other post-docs and students in his lab have different impressions.

As Michael Levine puts it ...
An amazing group of students and postdocs was attracted to the Gehring lab over the years: Eric Wieschaus (Nobelist), Christianne Nüsslein-Volhard (Nobelist), David Ish-Horowicz, Spyros Artavanis-Tsakonas, Paul Schedl, Alex Schier, Georg Halder, Hugo Bellen, and Markus Affolter, to mention just a few. I worked closely with two of my future lifelong friends and colleagues: Ernst Hafen and Bill McGinnis. The lab was an absolute blast, but a strange mix of anarchy and oppression. Walter permitted considerable independence, but was hardly laissez-faire. He could be confrontational, and did not hesitate to call us out (particularly me) when he felt we were misbehaving.

I found Walter to be a complicated character. He had the mannerisms of an authoritative Herr Doktor Professor, but was also folksy and unaffected and always ready to laugh and joke. He sometimes felt competitive with his students and postdocs, but was also highly supportive and proud of our independent careers. In short, I believe the key to Walter's success was his yin and yang embodiment of old-world scholar and modern competitive scientist. He was able to exude charm and empathy, but nothing we did seemed to be quite good enough. In other words, tough love, possibly the perfect prescription for eliciting the very best efforts from his students and postdocs.
Walter Gehring was one of a small group people who changed the way I think about science.


Artavanis-Tsakonas, S., Schedl, P., Mirault, M.-E., Moran, L. and J. Lis (1979) Genes for the 70,000 dalton heat shock protein in two cloned D. melanogaster DNA segments. Cell 17, 9-18. [doi: 10.1016/0092-8674(79)90290-3]

Moran, L., Mirault, M.-E., Tissières, A., Lis, J., Schedl, P., Artavanis-Tsakonas, S. and W.J. Gehring (1979) Physical map of two D. melanogaster DNA segments containing sequences coding for the 70,000 dalton heat shock protein. Cell 17, 1-8. [doi: 10.1016/0092-8674(79)90289-7]

Schedl, P., Artavanis-Tsakonas, S., Steward, R., Gehring, W. J., Mirault, M.-E., Goldschmidt-Clermont, M., Moran, L. and A. Tissières (1978) Two hybrid plasmids with D. melanogaster DNA sequences complementary to mRNA coding for the major heat shock protein. Cell 14, 921-929. [doi: 10.1016/0092-8674(78)90346-X]

Monday, July 28, 2014

How many genes do we have and what happened to the orphans?

How many genes in the human genome? There's only one correct answer to that question and that's "we don't know."

The main problem is counting the number of genes that produce functional RNA molecules. The latest Ensembl results are based on build CRch37 from February 2009 and the GENCODE annotation from last year (GENCODE 19) [see Human assembly and gene annotation and Harrow et al., 2014]

The most recent estimates are 20,807 protein-encoding genes, 9,096 genes for short RNAs, and 13,870 genes for long RNAs. This gives 43,773 genes. Nobody knows for sure how many of the putative genes for RNAs actually exist. They may only be a few thousand functional genes in this category.

It's a lot easier to figure out whether a gene really encodes a functional protein so most of the annotation effort is focused on those genes. I want to draw your attention to a recent paper by Ezkurdia et al. (2014) that discusses this issue. The authors begin with a bit of history ...

Transcription Initiation Sites: Do You Think This Is Reasonable? (revisited)

I'm curious about how different people read the scientific literature. My way of thinking about science is to mentally construct a model of how I think things work. The more I know about a subject, the more sophisticated the model becomes.

When I read a new paper I immediately test it against my model of how things are supposed to work. If the conclusions of the paper don't fit with my views, I tend to be very skeptical of the paper. Of course I realize that my model could be wrong and I'm always on the lookout for new results that challenge the current dogma, but, in most cases, if the paper conflicts with current ideas then it's probably flawed.

This is what people mean when they talk about making sense of biology. The ENCODE papers don't make sense, according to my model of how genomes work so I was immediately skeptical of the reported claims. The arseniclife paper conflicted with my understanding of the structure of DNA and how it evolved so I knew it was wrong even before Rosie Redfield pointed out the flaws in the methodology.

Finding the "perfect" enzyme

I got an email message yesterday from a student who is taking a summer course in biochemistry. His professor asked the class to find "most efficient enzyme known to man." The professor gave them a hint by telling them that the enzyme had something to do with nucleotide biosynthesis. The student contacted me because some of my blog posts popped up on Goggle. He (the student) was a bit confused about how to define the "perfect" enzyme.

There are two different ways of defining the "perfect" enzyme and both of them are wrong because there's no such thing. The common textbook definition picks up on the idea that the "perfect" enzyme catalyzes a reaction every time it encounters a substrate(s). These enzyme rates are referred to as "diffusion-controlled" rates since the rate is limited only by the rate at which substrate diffuses into the reaction site on the enzyme. Some enzymes can even catalyze reactions that are slightly faster than the diffusion-controlled limit.

Here's what Voet & Voet (4th edition) say (page 490) ...

Friday, July 25, 2014

The Central Dogma according to Riken

You may never have heard of Riken. Here's what they say on their website [Riken] ...
RIKEN is Japan's largest comprehensive research institution renowned for high-quality research in a diverse range of scientific disciplines. Founded in 1917 as a private research foundation in Tokyo, RIKEN has grown rapidly in size and scope, today encompassing a network of world-class research centers and institutes across Japan.
They've published a video on the Central Dogma. Here's how they describe it ...
The 'Central Dogma' of molecular biology is that 'DNA makes RNA makes protein'. This anime shows how molecular machines transcribe the genes in the DNA of every cell into portable RNA messages, how those messenger RNA are modified and exported from the nucleus, and finally how the RNA code is read to build proteins.

The video was made by RIKEN Omics Science Center (RIKEN OSC) for the exhibition titled 'Beyond DNA' held at National Science Museum of Japan. RIKEN OSC has published in Nature Genetics on the regulation of RNA expression in human cancer cells.
Most of you know that I have a different view of The Central Dogma of Molecular Biology but that's not what I want to discuss here. Watch the video. Do you think it's a good idea to show this process as well-designed little machines and ships? It sure gets the IDiots excited {RIKEN’s 10-minute antidote to atheism: see for yourself].



Wednesday, July 02, 2014

Carnival of Evolution #73: World Cup Edition

This month's Carnival of Evolution is hosted by none other than the King of the Carnival, Bjørn Østman Pleiotropy . Read it at 73rd Carnival of Evolution: World Cup Edition .
Welcome to the 2014 Carnival of Evolution World Cup of evolution blog posts.

We have an exciting post ahead of us today where we will find the winner of the inaugural CoE World Cup. Entered posts will be scored based on several parameters, and matches will be determined probabilistically.

The scoring system works like this:

+1 for mentioning "evolution" or "evolve"
+1 for posts about biological evolution
-1 for saying "develop" or "development" when meaning "evolve" or "evolution"
-1 for being very short
-2 for being very long
0 to +5 points based on the interest of the referee (the CoE host)
+2 for posts about peer-reviewed articles
+4 for posts whose authors clearly present opinions of their own
+1 per picture (up to three) included in the post
+1 for attracting any comments
+1 extra for each original picture (max 3)
+3 for showing videos
+25 for reports on rabbit fossils from the Cambrian
-5 for any hint of panadaptationism
-2 for each logical fallacy
-4 for any mention of aquatic ape theory
-7 for agreeing with Lynn Margulis that everything is endosymbiosis
-3 if talking about the work of others without citation
-5 to -1 for any wrong statements about evolution - See more at: http://pleiotropy.fieldofscience.com/2014/07/73rd-carnival-of-evolution-world-cup.html#sthash.75w1XHA6.dpuf
It was a tough battle. My own entry, The Function Wars: Part I, had a fairly low score but managed to squeak out a victory in the early rounds in spite of the fact that it had a severe disadvantage (too long).

My post beat out Was Fisher (W)right? in the semi-final thanks to an own goal in extra time. In the final, Function Wars was up against a better post Of Population Structure and the Adaptive Landscapes but Function Wars won on penalty kicks. Yeah!!!!

If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Bjørn is threatening to name YOU as host even if you don't volunteer! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission. Please alert Bjørn or the upcoming host if you see an article that should be included in next month's. You don't have to be the author to nominate a post.

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Tuesday, July 01, 2014

The Function Wars: Part II

This is Part II of several "Function Wars"1 posts. The first one is on Quibbling about the meaning of the word "function" [The Function Wars: Part I].

The ENCODE legacy

I addressed the meaning of "function" in Part I It is apparent that philosophers and scientists are a long way from agreeing on an acceptable definition. There has been a mini-explosion of papers on this topic in the past few years, stimulated by the ENCODE Consortium publicity campaign where the ENCODE leaders clearly picked a silly definition of "function" in order to attract attention.

Unfortunately, the responses to this mistake have not clarified the issue at all. Indeed, some philosophers have even defended the ENCODE Consortium definition (Germain et al., 2014). Some have opposed the ENCODE definition but come under attack from other scientists and philosophers for using the wrong definition (see Elliott et al, 2014). The net effect has been to lend credence to the ENCODE Consortium’s definition, if only because it becomes one of many viable alternatives.

Saturday, June 28, 2014

Ann Gauger's old facts

Some of you are probably watching Saturday morning cartoons but for those of you looking for other forms of entertainment I offer a list of six "old facts" that Ann Gauger says have been proven to be wrong [Why Does Biology Still Have the Ability to Surprise Us?].

Since I'm at least as old as Ann Gauger, I offer my own interpretation under each one. If you want to see how she interprets them you'll have to go to the IDiot website.

1. Old fact: DNA is stable and genes don't hop around.
I suppose there was a time when scientists might have thought that "DNA was stable." I was taught about "jumping genes" in my second year genetics class in 1965. I think that's before many of you were born so it's a pretty old fact.
2. New "old" fact: Mobile genetic elements are selfish DNA that replicate themselves without benefit to the organism, thus cluttering the genome with garbage.
That's still pretty much true today.
3. Old fact: A gene is an uninterrupted stretch of DNA that encodes a single protein. Genes are arranged like beads on a string.
I learned in 1965 that some genes produced tRNA and ribosomal RNA. I learned in 1975 that some protein-encoding genes had introns. (That one was a surprise.) I still think that genes are lined up one-after-another on their chromosomes although there are some minor exceptions. I learned about overlapping genes, for example, when the φX174 genome was sequenced in 1978. That's how old her facts are.
4. Old fact: There are only 3 forms of RNA: messenger RNA, transfer RNA, and ribosomal RNA.
Scientists have known about RNA viruses for at least 70 years. That's long before the discovery of messenger RNA and tRNA. It wasn't until the early 1970s that molecular biologists became aware of regulatory RNAs, RNA primers on Okazaki fragments, and antisense RNAs. This was followed quickly by the discovery of many other types of RNAs. Ann Gauger says these are "new" discoveries. I guess that depends on whether something that's been known for forty years (or seventy years) counts as "new."
5. Old fact: Pseudogenes are useless broken remnants of former genes.
Still true today. The fact that some of the sequence of one-in-a-million pseudogenes may have secondarily acquired another function doesn't change the fact that it is a pseudogene.
6. Old fact: The genome is full of junk, the remnants of wasteful evolutionary processes and selfish DNA (see #1, #2 and #5 above).
Still a fact in the 21st century.

Friday, June 27, 2014

This is my little boy playing in the mud

My son, Gordon, ran in a 19km race at Whistler (British Columbia) last weekend. There were lots of obstacles and a 10,000 volt electric shock at the end. He said it was "Super fun!"

I remember when playing in the mud meant something a lot different.


UPDATE Ms. Sandwalk has posted more pictures, and more words at: Oh My Goodness.


Wednesday, June 25, 2014

The Function Wars: Part I

This is Part I of the "Function Wars: posts. The second one is on The ENCODE legacy.1

Quibbling about the meaning of the word "function"

The world is not inhabited exclusively by fools and when a subject arouses intense interest and debate, as this one has, something other than semantics is usually at stake.
Stephan Jay Gould (1982)
The ENCODE Consortium tried to redefine the word “function” to include any biological activity that they could detect using their genome-wide assays. This was not helpful since it included a huge number of sites and sequences that result from spurious (nonfunctional) binding of transcription factors or accidental transcription of random DNA sequences to make junk RNA [see What did the ENCODE Consortium say in 2012?]..

I believe that this strange way of redefining biological function was a deliberate attempt to discredit junk DNA. It was quite successful since much of the popular press interpreted the ENCODE results as refuting or disproving junk DNA. I believe that the leaders of the ENCODE Consortium knew what they were doing when they decided to hype their results by announcing that 80% of the human genome is functional [see The Story of You: Encode and the human genome – video, Science Writes Eulogy for Junk DNA]..

The ENCODE Project, today, announces that most of what was previously considered as 'junk DNA' in the human genome is actually functional. The ENCODE Project has found that 80 per cent of the human genome sequence is linked to biological function.

[Google Earth of Biomedical Research]

Monday, June 16, 2014

A bun bargain

We were at our local supermarket yesterday and I wanted to buy some large Kaiser rolls. Unfortunately, the bins were empty.

I guess the customers couldn't resist the bargain if they bought half-a-dozen buns.


Friday, June 13, 2014

Ontario elects a Liberal government under Kathleen Wynne

The people of Ontario (Canada) voted in a provincial election yesterday and the Liberal Party won a majority of the seats. The leader of the party is Kathleeen Wynne and she becomes the first woman to be elected Premier of Ontario. (She has been Premier for the past sixteen months since she became leader of the Liberal Party.) Not only is she the first woman, she is the first openly gay politican to be elected Premier of any province in Canada. (According to Wikipedia, she is the first openly gay head of any government in the Commonwealth.)

The results are:

Liberals: 59 seats, 39% of the vote
Progressive Conservatives: 27 seats, 31%
New Democratic Party: 21 seats, 24%
Green Party: 0 seats, 5%.

The results are going to be poured over with a fine-tooth comb in the next few weeks but it's clear that the Tea-Party agenda of the Progressive Conservatives did not work. (He hired American Republican strategists to help with his campaign.) They should have won the election handily after 11 years of Liberal government plagued by scandal but, instead, they lost 10 seats and their leader Tim Hudak resigned last night when the results became clear.




Friday, June 06, 2014

June 6, 1944

Today is the 70th anniversary of D-Day—the day British, Canadian, and American troops landed on the beaches of Normandy.1

For baby boomers it means a day of special significance for our parents. In my case, it was my father who took part in the invasions. That's him on the right as he looked in 1944. He was an RAF pilot flying rocket firing typhoons in close support of the ground troops. During the initial days his missions were limited to quick strikes and reconnaissance since Normandy was at the limit of their range from southern England. During the second week of the invasion (June 14th) his squadron landed in Crepon, Normandy and things became very hectic from then on with several close support missions every day.

I have my father's log book and here (below) are the pages from June 1944. The red letters on June 6 say "DER TAG." It was his way of announcing D-Day. On the right it says "Followed SQN across channel. Saw hundreds of ships ... jumped by 190s. LONG AWAITED 2nd FRONT IS HERE." Later that day they shot up German vehicles south-east of Caen where there was heavy fighting by British and Canadian troops. The next few weeks saw several sorties over the allied lines. These were attack missions using rockets to shoot up German tanks, vehicles, and trains.


The photograph on the right shows a crew loading rockets onto a typhoon based just a few kilometers from the landing beaches in Normandy. You can see from the newspaper clipping in my father's log book that his squadron was especially interested in destroying German headquarter units and they almost got Rommel. It was another RAF squadron that wounded Rommel on July 17th.

The log book entry (above) for June 10th says, "Wizard show. Recco area at 2000' south west of Caen F/S Moore and self destroyed 2 flak trucks, 2 arm'd trucks, and i arm'd command vehicle, Every vehicle left burning but one. Must have been a divisional headquarters? No casualties."

Here's another description of that rocket-firing typhoon raid [Air Power Over the Normandy Beaches and Beyond].
Intelligence information from ULTRA set up a particularly effective air strike on June 10. German message traffic had given away the location of the headquarters of Panzergruppe West on June 9, and the next evening a mixed force of forty rocket-armed Typhoons and sixty-one Mitchells from 2 TAF struck at the headquarters, located in the Chateau of La Caine, killing the unit's chief of staff and many of its personnel and destroying fully 75 percent of its communications equipment as well as numerous vehicles. At a most critical point in the Normandy battle, then, the Panzer group, which served as a vital nexus between operating armored forces, was knocked out of the command, control, and communications loop; indeed, it had to return to Paris to be reconstituted before resuming its duties a month later.

My father was awarded the Distinguished Flying Cross (DFC) for his efforts during the war.



1. The British landed at Sword Beach and Gold Beache, the Canadians at Juno Beach, and American troops landed at Omaha and Utah Beaches.