Tuesday, August 23, 2016

Splice variants of the human triose phosphate isomerase gene: is alternative splicing real?

Triose phosphate isomerase (TIM) is one of the enzymes in the gluconeogenesis pathway leading to the synthesis of glucose from simple precursors. It also plays a role in the degradation of glucose (glycolysis). The enzyme catalyzes the following reaction ....

Triose phosphate isomerase is found in almost all species. The structure and sequence of the enzyme is well-conserved. It is a classic β-barrel enzyme that usually forms a dimer. The overall structure of a single subunit is classic example of an αβ-barrel known as a TIM-barrel in reference to this enzyme.

To the best of my knowledge, no significant variants of this enzyme due to alternative promoters, alternative splicing, or proteolytic cleavage are known.1 The enzyme has been actively studied in biochemistry laboratories for at least eighty years.

Saturday, August 20, 2016

Understanding Michael Behe's edge of evolution

It's been about twenty years since Intelligent Design Creationism rose to prominence. Just last week the Center for Science and Culture celebrated it's 20th birthday [Twenty Years Ago Today, Did This Change the Evolution Debate Forever?]. In all that time, the best that ID proponents can come up with is some work by Michael Behe that attempts to discredit evolution.

The first book by Behe was Darwin's Black Box where he developed the notion of irreducible complexity. The definition of irreducible complexity has changed over the years but the basic idea is that some biological structures are very complex and the removal of any one part will render the complex nonfunctional. This presents an enormous problem for evolution, according to Behe, because all the presumptive intermediates will be nonfunctional.

The conclusion is that it's impossible to evolve an irreducibly complex structure. Evolutionary biologists have no problem accepting the existence of irreducibly complex structures. They see them all the time. What they object to is the idea that irreducibly complex structures cannot have arisen by evolution. Behe's conclusion has been shown to be false and he has admitted on multiple occasions that irreducibly complex structures can arise by purely natural means (evolution).

Thursday, August 18, 2016

Do you believe what's written in the introduction to this paper?

I came across this paper while doing research on alternative splicing. The introduction annoyed me. It illustrates what to my mind are some serious problems with modern scholarship.

Scotti, M.M. and Swanson, M.S. (2016) RNA mis-splicing in disease. Nature Reviews Genetics 17:19–3 [doi: 10.1038/nrg.2015.3]
Here's part of the first paragraph in the paper.
Recent analysis from the Encyclopedia of DNA Elements (ENCODE) project (GRCh38, Ensembl79) indicates that most of the human genome is transcribed and consists of ~60,000 genes (~20,000 protein-coding genes, ~16,000 long non-coding RNAs (lncRNAs), ~10,000 small non-coding RNA and 14,000 pseudogenes). Although this gene inventory will change with further analysis, the number of protein-coding genes is surprisingly low given the proteomic complexity that is evident in many tissues, particularly the central nervous system (CNS). High resolution mass spectrometry studies have identified peptides encoded by most of these annotated genes, but the number of isoforms expressed from this gene set has been estimated to be at least 5–10-fold higher. For example, long-read sequence analysis of adult mouse prefrontal cortex neurexin (Nrxn) mRNAs indicates that only three Nrxn genes produce thousands of isoform variants. This diversity is primarily generated by alternative splicing, with >90% of human protein-coding genes producing multiple mRNA isoforms.
Here are some of the problems I have with this introduction. My opinions on these issues differ from those of the authors.
  1. I think that pseudogenes are not genes.
  2. I think there are NOT ~16,000 lncRNAs and ~10,000 small-noncoding RNA genes. Instead, there are approximately this many putative or predicted genes, many of which will undoubtedly turn out not to be genes. Some of them will be pseudogenes.
  3. I don't think there's a discrepancy between the known number of protein-coding genes and proteomic complexity; therefore, it is misleading to say that the number of protein-coding genes is "surprisingly low."
  4. I'm pretty sure that nobody has ever proposed a truly scientific "estimate" of isoforms showing that the number should be 5-10-fold higher than the number of genes. This is all speculation and guesswork based mostly on deflated egos.
  5. It is not true that >90% of human genes produce multiple mRNA isoforms by alternative splicing. What IS true is that for every human gene researchers have detected low levels of non-canonical splice events upon careful analysis of the transcriptome. We do not know whether these represent true biologically relevant alternative splicing or simply splicing errors. All available evidence suggests that the vast majority are splicing errors.
The authors are certainly entitled to their opinion ... even if it differs from mine!

But surely there has to be a better way of expressing this opinion to make it clear that they aren't stating facts but just their own personal views based on their own interpretation of the literature? This becomes very important if there's widespread scientific controversy over some of these opinions. (It's not so important if there's widespread agreement, or consensus, in the scientific community. In those cases, you aren't obliged to mentions alternative views held by kooks.)

I believe that scientists have an ethical obligation to distinguish between fact and opinion and to make it very clear in their writings which is which. I don't know whether Scotti and Swanson know about the controversial aspect of their statements and are deliberately avoiding any mention of them, or whether they actually believe that their statements are factual. Either way, we have a problem.

Saturday, August 13, 2016

Twenty "sciencey" questions for Trump and Clinton

ScienceDebate.org is a group that wants a "science" debate between Presidential candidates in the upcoming American election. That's not going to happen so the next best thing is to demand that the candidates answer their 20 questions about Science, Engineering, Technology, Health, and the Environment. I would not answer these questions if I were a candidate. Many of them require extraordinarily complex answers. Some of them are based on false premises. Several are loaded. Some of the problems can't be dealt with in any realistic way by a President of the United States. Quite a few cannot be answered in any meaningful way without writing a book.

I'm not sure what this group expects. This seems to be a colossal waste of time. It also seems to be very low on the priority list given all the other problems with Trump and Clinton. The questions don't inspire confidence in ScienceDebate, in my opinion. Here are the questions from: 20 Questions.
  1. Science and engineering have been responsible for over half of the growth of the U.S. economy since WWII. But some reports question America’s continued leadership in these areas. What policies will best ensure that America remains at the forefront of innovation?
  2. Many scientific advances require long-term investment to fund research over a period of longer than the two, four, or six year terms that govern political cycles. In the current climate of budgetary constraints, what are your science and engineering research priorities and how will you balance short-term versus long-term funding?
  3. The Earth’s climate is changing and political discussion has become divided over both the science and the best response. What are your views on climate change, and how would your administration act on those views?
  4. Biological diversity provides food, fiber, medicines, clean water and many other products and services on which we depend every day. Scientists are finding that the variety and variability of life is diminishing at an alarming rate as a result of human activity. What steps will you take to protect biological diversity?
  5. The Internet has become a foundation of economic, social, law enforcement, and military activity. What steps will you take to protect vulnerable infrastructure and institutions from cyber attack, and to provide for national security while protecting personal privacy on electronic devices and the internet?
  6. Mental illness is among the most painful and stigmatized diseases, and the National Institute of Mental Health estimates it costs America more than $300 billion per year. What will you do to reduce the human and economic costs of mental illness?
  7. Strategic management of the US energy portfolio can have powerful economic, environmental, and foreign policy impacts. How do you see the energy landscape evolving over the next 4 to 8 years, and, as President, what will your energy strategy be?
  8. American students have fallen in many international rankings of science and math performance, and the public in general is being faced with an expanding array of major policy challenges that are heavily influenced by complex science. How would your administration work to ensure all students including women and minorities are prepared to address 21st century challenges and, further, that the public has an adequate level of STEM literacy in an age dominated by complex science and technology?
  9. Public health efforts like smoking cessation, drunk driving laws, vaccination, and water fluoridation have improved health and productivity and save millions of lives. How would you improve federal research and our public health system to better protect Americans from emerging diseases and other public health threats, such as antibiotic resistant superbugs?
  10. The long-term security of fresh water supplies is threatened by a dizzying array of aging infrastructure, aquifer depletion, pollution, and climate variability. Some American communities have lost access to water, affecting their viability and destroying home values. If you are elected, what steps will you take to ensure access to clean water for all Americans?
  11. Nuclear power can meet electricity demand without producing greenhouse gases, but it raises national security and environmental concerns. What is your plan for the use, expansion, or phasing out of nuclear power, and what steps will you take to monitor, manage and secure nuclear materials over their life cycle?
  12. Agriculture involves a complex balance of land and energy use, worker health and safety, water use and quality, and access to healthy and affordable food, all of which have inputs of objective knowledge from science. How would you manage the US agricultural enterprise to our highest benefit in the most sustainable way?
  13. We now live in a global economy with a large and growing human population. These factors create economic, public health, and environmental challenges that do not respect national borders. How would your administration balance national interests with global cooperation when tackling threats made clear by science, such as pandemic diseases and climate change, that cross national borders?
  14. Science is essential to many of the laws and policies that keep Americans safe and secure. How would science inform your administration's decisions to add, modify, or remove federal regulations, and how would you encourage a thriving business sector while protecting Americans vulnerable to public health and environmental threats?
  15. Public health officials warn that we need to take more steps to prevent international epidemics from viruses such as Ebola and Zika. Meanwhile, measles is resurgent due to decreasing vaccination rates. How will your administration support vaccine science?
  16. There is a political debate over America’s national approach to space exploration and use. What should America's national goals be for space exploration and earth observation from space, and what steps would your administration take to achieve them?
  17. There is a growing opioid problem in the United States, with tragic costs to lives, families and society. How would your administration enlist researchers, medical doctors and pharmaceutical companies in addressing this issue?
  18. There is growing concern over the decline of fisheries and the overall health of the ocean: scientists estimate that 90% of stocks are fished at or beyond sustainable limits, habitats like coral reefs are threatened by ocean acidification, and large areas of ocean and coastlines are polluted. What efforts would your administration make to improve the health of our ocean and coastlines and increase the long-term sustainability of ocean fisheries?
  19. There is much current political discussion about immigration policy and border controls. Would you support any changes in immigration policy regarding scientists and engineers who receive their graduate degree at an American university? Conversely, what is your opinion of recent controversy over employment and the H1-B Visa program?
  20. Evidence from science is the surest basis for fair and just public policy, but that is predicated on the integrity of that evidence and of the scientific process used to produce it, which must be both transparent and free from political bias and pressure. How will you foster a culture of scientific transparency and accountability in government, while protecting scientists and federal agencies from political interference in their work?

Thursday, August 11, 2016

A refreshing admission on Uncommon Descent

Some of us have been debating Intelligent Design Creationists for many years. Some of us have even visited the creationist blogs like Uncommon Descent where we discover that no facts and no logic will ever shake their obsession with proving evolution wrong and promoting their gods. That's why it was refreshing to read the following comment by William J. Murray in his post on "The Benefit of Arguments at UD." I only had time to read the first few lines but you get the gist ...

Probably one of the most daunting aspects of carrying on debates either about proper critical thinking, theism vs atheism, or intelligent design and its implications is the seeming implacable nature of those we debate here and elsewhere. It most often seems that no amount of logic, evidence or even reasonable discourse makes one iota of difference ...

Thursday, August 04, 2016

This anti-science creationist could be Vice-President of the United States of America

Thanks to PZ Myers for digging up this speech by Mike Pence in the House of Representatives [Mike Pence, creationist]. I think Pence is trying to make America great again by returning the country to the stone age.

Why are academics such bad writers?

Not all academics are bad writers but the exceptions are few and far between. Several recent articles in The Chronicle of Higher Education have attempted to explain why we can't write. There are two types of academic writing. The style you use in your academic papers differs from the style you use in writing for a general audience. There's absolutely no debate about the style of writing in the academic literature: it is horrible and it needs to change.

I want to talk about the other kind of writing; the kind where academics try to explain things to non-academics. I'll concentrate on science writing although I'm sure the same issues apply to history, philosophy, and all the other academic disciplines. I'm particularly sensitive to this problem since I'm working on a book about genomes and junk DNA and it's very different than writing a biochemistry textbook.

The latest (Aug. 1, 2016) article is an interview with Steven Pinker, the well-known Harvard psychologist. He's published seven trade books and is widely perceived to be a good example of how academics should write for a general audience [Scholars Talk Writing: Steven Pinker].

Wednesday, August 03, 2016

More junk science in Science

The latest issue of the journal Science (Aug. 1, 2016) has an article on a recent paper by Aires et al. (2016) published in Developmental Cell. Here's the abstract of the paper ...

Vertebrates exhibit a remarkably broad variation in trunk and tail lengths. However, the evolutionary and developmental origins of this diversity remain largely unknown. Posterior Hox genes were proposed to be major players in trunk length diversification in vertebrates, but functional studies have so far failed to support this view. Here we identify the pluripotency factor Oct4 as a key regulator of trunk length in vertebrate embryos. Maintaining high Oct4 levels in axial progenitors throughout development was sufficient to extend trunk length in mouse embryos. Oct4 also shifted posterior Hox gene-expression boundaries in the extended trunks, thus providing a link between activation of these genes and the transition to tail development. Furthermore, we show that the exceptionally long trunks of snakes are likely to result from heterochronic changes in Oct4 activity during body axis extension, which may have derived from differential genomic rearrangements at the Oct4 locus during vertebrate evolution.
... those ignorant of history are not condemned to repeat it; they are merely destined to be confused.

Stephen Jay Gould
Ontogeny and Phylogeny (1977)
The results were written up by a freelance journalist named Diana Crow [‘Junk DNA’ tells mice—and snakes—how to grow a backbone]. She writes ...
‘Junk DNA’ tells mice—and snakes—how to grow a backbone

Why does a snake have 25 or more rows of ribs, whereas a mouse has only 13? The answer, according to a new study, may lie in "junk DNA," large chunks of an animal’s genome that were once thought to be useless. The findings could help explain how dramatic changes in body shape have occurred over evolutionary history.

Scientists began discovering junk DNA sequences in the 1960s. These stretches of the genome—also known as noncoding DNA—contain the same genetic alphabet found in genes, but they don’t code for the proteins that make us who we are. As a result, many researchers long believed this mysterious genetic material was simply DNA debris accumulated over the course of evolution. But over the past couple decades, geneticists have discovered that this so-called junk is anything but. It has important functions, such as switching genes on and off and setting the timing for changes in gene activity.
Sandwalk readers will see all the mistakes and misconceptions in these paragraphs. She's talking about regulatory sequences that were never, ever, thought to be junk. The paper being discussed has nothing to do with junk DNA and the results do not in any way alter our understanding of developmental gene regulation.

If you look carefully at the abstract, you'll see the word "heterochronic." This is one of Stephen Jay Gould's favorite words. He wrote about it in Ontogeny and Phylogeny.
I wish to emphasize one other distinction. Evolution occurs when ontogeny is altered in one of two ways: when new characters are introduced at any stage of development with varying effects upon subsequent stages, or when characters already present undergo changes in developmental timing. Together, these two processes exhaust the formal concept of phyletic change.; the second process is heterochrony. [my emphasis ... LAM] If change in developmental timing is important in evolution, then this second process must be very common.
This was written in 1977—that's almost 40 years ago! These ideas were around for decades before Gould wrote his book1 and they have been shown to be correct by numerous studies in the 1980s.

What's going on here? Science is supposed to be one of the leading science journals. How could it publish an article that misrepresents the field so badly? Do the editors send these "Latest News" articles out for review?

1. Ed Lewis shared the Nobel Prize in 1995 for his contribution to "the genetic control of early embryonic development" [The Nobel Prize in Physiology or Medicine 1995].

Saturday, July 30, 2016

Siddhartha Mukherjee tries to correct his book

There are lots of things wrong with Mukherjee's best-selling book The Gene. I've listed a few things that I know about [What is a "gene" and how do genes work according to Siddhartha Mukherjee?]. Others have come up with different problems.

The biggest problem is that Mukherjee misrepresents the current state of knowledge in genetics, biochemistry, and molecular biology. His misleads his readers by promoting silly viewpoints that conflict with the consensus view. He doesn't mention that there are other views that are well supported by tons of scientific evidence.

The best example is regulation of gene expression. He fails to explain the standard textbook understanding of transcriptional regulation by transcription factors—a view that's solidly backed by decades of work in biochemistry, developmental genetics, molecular biology, and genomics. Instead, he promotes a flaky epigenetic theory that, according to him, threatens to overthrow Darwinian evolution.

The most important thing about nature according to Bill Martin

My friend and colleague, Alex Palazzo, alerted me to an interview of Bill Martin published in the July 11, 2016 issue of Current Biology [Bill Martin]. I loved all his answers—Bill Martin is one of my scientific heroes—but his answer to the last question was particularly insightful. The question was, "What’s the single most important thing that you have come to realize about nature?"

His answer was ....
Life is an exergonic chemical reaction. It’s the energy releasing redox reaction at the core of metabolism that makes life run, and throughout all of life’s history it is one and the same reaction that has been running in uninterrupted continuity from life’s onset. Everything else is secondary, manifestations of what is possible when the energy is harnessed to make genes that pass the torch.
I'm a biochemist so you might think I'm a little bit biased but let me tell you why this answer is so important.

Thursday, July 28, 2016

You are junk

There's an article about junk DNA in the latest issue of New Scientist (July 27, 2016) [You are junk: Why it’s not your genes that make you human]. I've already discussed the false meme at the beginning of the article [False history and the number of genes: 2016]. Now it's time to look at the main argument.

The subtitle is ...
Genes make proteins make us – that was the received wisdom. But from big brains to opposable thumbs, some of our signature traits could come from elsewhere.
You can see where this is going. You start with a false paradigm, "Genes make proteins make us," then proceed to refute it. This is called "paradigm shafting."1

False history and the number of genes: 2016

There's an article about junk DNA in the latest issue of New Scientist. The title is: You are junk: Why it’s not your genes that make you human. The author is Colin Barras, a science writer from Michigan with a Ph.D. in paleontology.

He begins with .....
IT WAS a discovery that threatened to overturn everything we thought about what makes us human. At the dawn of the new millennium, two rival teams were vying to be the first to sequence the human genome. Their findings, published in February 2001, made headlines around the world. Back-of-the-envelope calculations had suggested that to account for the sheer complexity of human biology, our genome should contain roughly 100,000 genes. The estimate was wildly off. Both groups put the actual figure at around 30,000. We now think it is even fewer – just 20,000 or so.

"It was a massive shock," says geneticist John Mattick. "That number is tiny. It’s effectively the same as a microscopic worm that has just 1000 cells."

What is "THE" theory of evolution?

I wish people would stop referring to "THE" Theory of Evolution. What they really mean, of course, is "The Theory of Natural Selection"—part of modern evolutionary theory. There's no question about the importance of natural selection and the major contribution of Charles Darwin in discovering it and promoting it to the general public. However, in 2016 there's a lot more to evolutionary theory than just natural selection and the public needs to know this. Many scientists need to know this.

There's also no debate about Darwin's contribution to promoting the evidence of evolution and descent with modification. He made a brilliant case for evolution in his books. Subsequent discoveries have demonstrated beyond a reasonable doubt that modern life is the product of billions of years of evolution. Descent with modification is a scientific fact. The fact that evolution has occurred is not a theory. It is not a "theory" that humans and the other apes have descended form a common ancestor ... it is a fact [Evolution Is a Fact and a Theory].

We perpetuate confusion in the minds of the general public if we don't make it abundantly clear that modern evolution theory is not about whether evolution occurred and it's not just about natural selection.

I was prompted to write this blog post by a recent article in New Scientist: Darwin’s discovery: The remarkable history of evolution.1 The author is John van Wyhe of the National University of Singapore. He is a historian of science with a special interest in Charles Darwin and Alfred Russel Wallace.

The article contains a box that says ...
Evolution in a nutshell

Darwin’s and Wallace’s theory of evolution maintains that new species are descended from earlier ones. This long-term process happens because all organisms vary. The tiny variations are naturally “selected” by virtue of whether or not they help an organism to survive the brutal struggle for existence in nature. Many are born, but few survive; fortuitous variations are preferentially passed on. This process of endless filtering works to adapt organisms to their environment.
This is misleading in two ways. First, it states that common descent is part of the the theory of evolution. Second, it only talks about natural selection as a mechanism of evolution.

We wish to question a deeply engrained habit of thinking among students of evolution. We call it the adaptationist programme, or the Panglossian paradigm.

S.J. Gould & R.C. Lewontin (1979) p. 584
Fortunately, the main body of the article is quite a bit better. Here's what John van Wyhe actually says about evolution.
Despite its baptism of fire, On the Origin of Species almost single-handedly convinced the international scientific community that evolution was a fact. In his 1889 book Darwinism, Wallace wrote of the revolution Darwin effected: "this totally unprecedented change in public opinion has been the result of the work of one man, and was brought about in the short space of twenty years!"

The theory of evolution has come a long way since. Today we think of it in terms of genes and DNA, but Darwin and Wallace had no idea of their existence. It was only in the 1930s and 1940s that genetics was incorporated into evolutionary theory. Even now, new discoveries are shaking up our understanding, but at the core of the modern theory remains Darwin’s idea of descent with modification.

Today evolution has many critics outside the scientific community, especially in the US, where a significant percentage of the population are creationists. What is forgotten is that the scientific debate over evolution was over by the 1870s and has never again been a matter of serious dispute.
Darwin showed that evolution is a fact and it's good that van Wyhe made this point in a article aimed at the general public. It's not good when he says "the core of the modern theory remains Darwin’s idea of descent with modification."

It's not good that he still refers to "THE" theory of evolution instead of "evolutionary theory," which encompasses all kinds of things other than natural selection.

1. The title in the print edition is: "The Evolution Revolution."

Thursday, July 14, 2016

The seven biggest problems in science

Here's an interesting article about the biggest problems in (American) science: The 7 biggest problems facing science, according to 270 scientists. Most of them apply to science in other countries.

I've added brief comments under six of the headings. Those are MY opinions, not necessarily those of the authors. The comment under #6 is a direct quote from the article.
  1. Academia has a huge money problem.
    There's not enough money to do high quality science, especially basic science.
  2. Too many studies are poorly designed. Blame bad incentives.
    Some experiments are poorly designed. All scientists are under pressure to make their results seem important.
  3. Replicating results is crucial. But scientists rarely do it.
    Replication is important—especially in medical studies—but I think this problem is exaggerated.
  4. Peer review is broken.
    The system (peer review) isn't working well. That doesn't mean there's a better system.
  5. Too much science is locked behind paywalls.
    This was never a problem in the past when you had to go to the library to read science journals. You could photocopy whatever you wanted. Now it's a problem because we want instant access from our laptops.
  6. Science is poorly communicated to the public.
    "But not everyone blamed the media and publicists alone. Other respondents pointed out that scientists themselves often oversell their work, even if it's preliminary, because funding is competitive and everyone wants to portray their work as big and important and game-changing.

    'You have this toxic dynamic where journalists and scientists enable each other in a way that massively inflates the certainty and generality of how scientific findings are communicated and the promises that are made to the public,' writes Daniel Molden, an associate professor of psychology at Northwestern University. 'When these findings prove to be less certain and the promises are not realized, this just further erodes the respect that scientists get and further fuels scientists desire for appreciation.'
  7. Life as a young academic is incredibly stressful.
    This is not just a problem for my younger colleagues. It affects all of us. It affects morale in an academic department and it affects the way science is done.

Bastille Day

Today is the Fête Nationale in France known also as "le quatorze juillet" or Bastille Day.

This is the day in 1789 when French citizens stormed and captured the Bastille—a Royalist fortress in Paris. It marks the symbolic beginning of the French revolution although the real beginning is when the Third Estate transformed itself into the National Assembly on June 17, 1789 [Tennis Court Oath].

Ms. Sandwalk and I visited the site of the Bastille (Place de la Bastille) when we were in Paris in 2008. There's nothing left of the former castle but the site still resonates with meaning and history.

One of Ms Sandwalk's ancestors, William Playfair witnessed the storming of the Bastille.

In honor of the French national day I invite you to sing the French national anthem, La Marseillaise. An English translation is provided so you can see that La Marseillaise is truly a revolutionary call to arms. (A much better translation can be found here.)

Check out Uncertain Principles for another version of La Marseillaise—this is the famous scene in Casablanca.

Reposted from 2009.