The Panda's Thumb

Evangelicals talking sense to creationists

2013-05-22T14:00:00Z

Yesterday, I received a letter and a booklet from an organization called Day Star Research. The booklet was written by the president of Day Star, Fred Heeren, who writes, among other things,

Day Star Research is committed to

* Promoting healthy dialogue between the religious and non-religious.

* Fighting irrational extremism with rationality.…

* Encouraging Christians to reverse their reputation for anti-intellectualism, insensitivity, and judgmentalism.…

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Heeren goes on to explain that his “work on science news stories” has acquainted him with the work of cosmologists, paleontologists, and biologists, and helped him “see the way their discoveries are misunderstood by those who view them as a threat to their faith [my italics].” Heeren says he was “grounded” in young-earth creationism and later in intelligent-design creationism, clearly implying that he has given up those beliefs. He has

learned something from [his] conservative Christian friends who are skeptical about evolution or big bang cosmology: we need to not only convince them of their validity. We need to show them how we know what we know: we need to tell them the true stories of how the discoveries were made and connect the evidence with the conclusions [italics in original].

A few more quotations:

Once Christians learn that their Bible is not a science book, they can become less defensive and more open to what science reveals.

***

We want to show that becoming a Christian does not mean that we must buy into some agenda-driven, dishonest, Christianized brand of science. And we want to show Christians that they need not be afraid of the evidence—we can let it lead us where it will.

***

The movement called “Intelligent Design,” as Eugenie Scott [!] points out, is both bad science and bad theology.

Heeren has evidently come a long way in the last few years. Reports of the National Center for Science Education characterized him thus in its September-October 2000 issue:

It is perhaps inevitable that those motivated by a nonscientific agenda will seek to extract snippets and sound bites from the scientific arguments, package them out of context, and feed them to the general public. This is what Fred Heeren did. Heeren is an anti-evolutionist writer who attended the Chengjiang meeting and then peddled his distorted version of the Cambrian radiation to the popular media, with obvious success.

No longer is Heeren “an anti-evolutionist writer,” but he is still an evangelical, and I found the last part of the booklet disappointing. First, Heeren notes,

There are really only two steps between an atheist and me. Once we take the first step to recognize the purpose this universe clearly displays [my italics], then the next step we can take, the one I’ve taken, is to commit ourselves to the best [italics in original] we can find to explain that purpose.…

The best, of course, is Christianity, for a variety of simplistic and very debatable reasons.

Heeren talks of “a different kind of evangelism and a different kind of evangelistic organization, recognizing the importance of being peacemakers, of educating polarized groups so that they might stop talking past each other, and ending the Christian war on science and culture.” The last pages of the booklet, perhaps not surprisingly, invite you to make a tax-deductible contribution—not to explain evolution to Christians, but to help “reach skeptics with the good news of Jesus Christ.”

Impressed though I am with Heeren’s conversion, I suddenly felt underwhelmed.

The world's rarest birds

2013-05-20T18:00:00Z

Photograph by Huajin Sun.

Grus japonensis – red-crowned crane. This photograph, which adorns the dust jacket of The World’s Rarest Birds, earned second prize in the “endangered or data-deficient” category of a worldwide photo contest. I will review the book briefly, below the fold.

Note added May 21, 11:00 a.m., MDT: You may see the contest winners here and the winners of a second contest here.

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The editors of this splendid book sought photographs of as many endangered bird species as possible. To that end, they organized a photography contest and garnered over 3500 entries from more than 300 photographers and selected more than 500 photographs for inclusion in the book. The 7 contest winners are displayed in the frontispiece to the book, but frankly they have little or nothing over a great many of the other photographs in the book.

The World’s Rarest Birds is a big book at 8.5 x 11 in (approximately A4) and 330 pages, not counting acknowledgments, index, and whatnot. It is well printed on slick, heavy paper. All but perhaps a dozen or two pages display at least one stunning photograph, and often many. The plumage on many of the birds is remarkable; if you thought that feathers initially evolved for sexual selection, some of these pictures, at a minimum, will reinforce your opinion.

Those who read the book will be like the blind men and the elephant. Photographers will see a photography book. Birdwatchers will see a field guide to rare birds. Conservationists will see extinction. And dilettantes will see a coffee-table book. All will be in some measure correct.

The first chapter is a catchall that outlines the threats to endangered birds, from agriculture, to habitat loss and invasive species, to pollution and mining. The rest of the book is organized by region and provides thumbnail descriptions of each species, its range, its estimated population, and the threats against it. Many of the species are numbered at “<50.” The California condor, for example, numbers 44, but a little green upward-pointing arrow indicates increasing population. The majority of species, unfortunately, are shown with little red downward-pointing arrows that indicate decreasing population.

Like those who Google themselves or look themselves up in the Web of Science, I looked up North America and found in my area the Gunnison sage grouse, which was only recently recognized as a distinct species and which (according to the New York Times) is going extinct, right before our eyes; and the whooping crane, which reportedly has not been seen in Colorado since 2002.

Many of these birds have never had their pictures published before; 75 were drawn so meticulously that you cannot tell them from a photograph. I am afraid that many of these species will be gone by the time this book goes into a second edition.

My breasts. My genes.

2013-05-16T13:05:37Z

Angelina Jolie wrote about her decision to have a double mastectomy after learning that she carries a version of the BRCA1 gene with mutations that are significantly associated with developing breast cancer, speaking with her doctor, and considering the risks and benefits to herself, and for her family.

By ILA-boy

Many people have reacted, but I particularly like this response from Judith Soal that introduces the complexity of understanding the genetic component of diseases. We still have quite a lot to learn about the relationship between genes, environment, and disease, but we do know that some genetic mutations increase susceptibility to disease, but also that people without known genetic mutants are often affected by diseases due to environment, to novel mutations, or, by chance. Moreover, rarely is the culprit of a disease a single gene. But, for now, we’ll leave this to others.

I want to focus on something else. Something that is relevant to every person. Something that both of these articles touch on.

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Let me highlight them for you.

From Jolie’s article:

“The cost of testing for BRCA1 and BRCA2, at more than $3,000 in the United States, remains an obstacle for many women.”

From Soal’s article:

“Fortunately I live in the UK, where the NHS offers free genetic screening…”

Both of these articles mention the cost of the genetic screening. In the United Kingdom, this cost is covered, while in the United States, it is quite expensive, at least for health insurance plans in place prior to the passing of the Healthcare Law. But even if covered by insurance, someone is paying a lot of money for this testing.

BRCA1 is on chromosome 17
BRCA2 is on chromosome 13
Wikimedia Commons

Why?
Because a company called Myriad (and their BRCAnalysis) owns the right to know what the DNA sequence is of your (or mine, or anyone’s) BRCA1 and BRCA2 genes.

Owns?
Yes, they own it. Myriad holds a patent on the sequence of those genes. This means, even if you wanted to sequence your own BRCA1 and/or BRCA2 genes, you would have to pay a fee ($3,000-$4,000 to Myriad) because Myriad owns the right to know the sequence of every human BRCA1 and BRCA2 gene. All 7.1 Billion people (yes, we all have chromosome 17 an chromosome 13, and regardless of the genetic component are all susceptible to breast cancer, as well as many other associated cancers). This patent is currently being disputed in the Supreme Court.

If it’s a patent, what did they develop?
Myriad did not develop the BRCA1 or BRCA2 genes. Myriad did not create the mutations in BRCA1 or BRCA2 that are associated with breast, or other cancers. Myriad has no right to prevent anyone from knowing what the sequence of our genes are.

This patent gives Myriad ownership of information about my body that has always been a part of me. is akin to giving them the right to know (and to tell me, or not) what color my eyes are, even though I could use a mirror to figure it out. Using the mirror (doing it myself), would violate the patent unless I paid Myriad money. It is like allowing Myrad to to charge me thousands of dollars to know what my blood type is (even though I can order a couple, super-nifty, blood-typing cards for twenty bucks ).

Sure, Myriad can offer their test (which uses technology that is no different than thousands of labs around the world use daily). But, they have no right to prevent other people, or companies, or ourselves, from conducting tests to answer the same questions. Questions about ourselves.

Myriad does not own our genes.

A friend texted me the other day:

“What do you think about gene patenting? Seems douchey to me.”

I couldn’t agree more.

Accessible research: A tiny bladderwort (that's a plant with little "bladders") genome

2013-05-14T16:22:20Z

The genome from a species of bladderwort (Utricularia gibba) was recently published. Ed Yong has a wonderful summary about the bladderwort genome paper and its relationship with current debates regarding what is functional (introduction to the ENCODE project). Here’s my accessible research introduction:

The bladderwort is a carnivorous plant with beautiful yellow flowers on top:


This is a captivating “horned bladderwort” (Utricularia cornuta), by Jacopo Werther

And curious “bladders” on its roots that it uses to trap its prey.

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Bladder traps on the roots of the “common bladderwort” (Utricularia vulgaris), by pellaea.

The genome of this plant is so interesting because it is quite small. The authors go so far as to call it a “minimal” genome.

What makes it minimal?
Often, when talking about genetics, we usually talk about the genes. These are the pieces of DNA that code for proteins. These are “coding” regions. There are also pieces of DNA that do not code for proteins. We call these “non-coding”. The genome is the full set of coding and non-coding DNA. Some species have lots of non-coding DNA (like humans, and onions). Other species have very little non-coding DNA, including this bladderwort.

Although the bladderwort has nearly 10,000 more genes than a human, these genes are very compressed and overlapping so that the bladderwort genome and the human genome have about the same amount of coding DNA sites. But, the bladderwort genome has a lot less non-coding DNA, for a total genome size of 87 million bases, while the human genome has bloated amount of non-coding DNA a total genome size of 3,164.7 million bases. That’s over 36 times more total DNA than the bladderwort! (Note: the total DNA content does not indicate complexity - whatever that is. Check out the range in genome size of “flowering plants” at the top of this plot.)

Was the bladderwort genome always so slim?
No. By comparing with other yummy plant genomes (papaya, grape, tomato and Arabidopsis, a flowering mustard weed), and by analyzing the gene content within the bladderwort genome, Ibarra-Laclette et al. concluded that the bladderwort genome, like many plants, experienced duplications of its whole genome. Afterward there were some losses of large regions of DNA, but much of the reduction in DNA content from these duplications occured through what they call “microdeletions”, where small pieces of DNA here and there were deleted.

Are all bladderworts the same?
Just like there are many species in the taxonomic family Hominidae (orangutans, gorillas, bonobos, chimpanzees and humans), there are many species in the the taxonomic family of bladderworts (called Lentibulariaceae). Genome shrinking is not unique to this species of bladderwort, but is also not shared across all species of bladderworts. Curiously, genome size in the whole family of bladderworts varies from 60 million base pairs to 1,500 million base pairs. That is a lot of variation considering that genome sizes across all Hominidae are all within the range of 3,000 million base pairs (plants genomes get no respect).

Although genome size varies quite a bit, the bladderworts look and function in similar ways. So, while some of the noncoding sequence is functional (providing instructions for how and when to turn the genes on and off, in time, in response to the environment, and in particular tissues), it seems highly unlikely that there would be so many more instructions in the bladderwort with 1,500 million base pairs than in the bladderwort with 60 million base pairs. A lot of the non-coding DNA, therefore, is likely also non-functional.

bladderwort (Utricularia vulgaris) in the water. by H. Zell.

In the closing line of the bladderwort genome paper:

In summary, U. gibba genome architecture demonstrates that angiosperms can evolve diverse gene landscapes while overall genome size contracts, not only during expansions. Furthermore, in contrast to recent publications that highlight a crucial functional role of non-coding DNA in complex organisms such as animals²⁴, the necessary genomic context required to make a flowering plant may not require substantial hidden regulators in the non-coding ‘dark matter’ of the genome.

Enrique Ibarra-Laclette, Eric Lyons, Gustavo Hernández-Guzmán, Claudia Anahí Pérez-Torres, Lorenzo Carretero-Paulet, Tien-Hao Chang, Tianying Lan, Andreanna J. Welch, María Jazmín Abraham Juárez, June Simpson, Araceli Fernández-Cortés, Mario Arteaga-Vázquez, Elsa Góngora-Castillo, Gustavo Acevedo-Hernández, Stephan C. Schuster, Heinz Himmelbauer, André E. Minoche, Sen Xu, Michael Lynch, Araceli Oropeza-Aburto, Sergio Alan Cervantes-Pérez, María de Jesús Ortega-Estrada, Jacob Israel Cervantes-Luevano, Todd P. Michael, Todd Mockler, Douglas Bryant, Alfredo Herrera-Estrella, Victor A. Albert, & Luis Herrera-Estrella.
Architecture and evolution of a minute plant genome. 2013. Nature
http://dx.doi.org/10.1038/nature12132

John Searle's homunculus announces phased retirement

2013-05-13T18:29:48Z

Those who know John Searle’s “Chinese Room” critique of the possibility of genuine consciousness in artificial/machine intelligences will enjoy this:

John Searle’s homunculus announces phased retirement

After 54 years of teaching at Berkeley, the man inside John Searle’s head has announced he will be entering a three-year phased retirement after the end of the current semester. The diminutive Zhu Tao made the announcement at a press conference Monday in a rare out-of-costume appearance.

At the conference Zhu said he is retiring from his current position in order to spend more time with Searle’s family. “I have become quite attached to these people,” Zhu said through a translator. “Although, admittedly, not being able to understand a word they say has limited the intimacy of our relationships.”

…

While he expressed sadness at the end of an era, Zhu looked back with pride at his time inside John Searle’s head. Zhu is popularly credited with sparking the shift away from brain-based cognition. Today that shift continues apace, with figures such as Andy Clark and David Chalmers outsourcing their thinking to call centers in India as part of a growing movement of philosophers who believe cognition can extend beyond the boundaries of one’s skull.

Drosera rotundifolia

2013-05-13T18:00:00Z

Photograph by Dennis Venema.

Photography contest, Honorable Mention.

Drosera rotundifolia – round-leaved sundew, Fort Langley Bog, British Columbia.

Mark Perakh dies

2013-05-12T19:02:09Z

I was very saddened to receive the following a few minutes ago:

It is with great sorrow that Talk Reason announces the death of TR co-founder and major contributor Mark Perakh on May 7, 2013, following a brief illness. He was 88 years old.

Mark Perakh was a professor emeritus of mathematics and statistical mechanics at California State University in Fullerton, CA. Perakh taught physics and wrote some 300 scientific papers. His work in physics focused on superconductivity and his book on thin films was translated into eight languages. He also wrote and published the novel Man in a Wire Cage.

Perakh’s fame particularly comes from writing about science and religion on Talk Reason (a website he helped found) and from his regular contributions to the blog The Panda’s Thumb. He also wrote a book critical of pseudo-science, Unintelligent Design.

His death is a great loss to the scientific blogging community.

Mark also contributed considerably to Why Intelligent Design Fails (which I edited with Taner Edis) and was available any time I needed advice. I will miss him greatly.

Press Release: The Genomic Signature of Crop-Wild Introgression in Maize

2013-05-10T22:50:41Z

Introgression or genetic exchange between crops and their wild relatives is of broad interest due to concern regarding the escape of transgenes from genetically engineered crops. Many fear the potential deleterious effects of such introgression including decreased fitness or diversity of wild relatives and/or the creation of “superweeds” that are resistant to the current arsenal of herbicides. But there is another side to crop-wild gene exchange. A paper published in the open-access journal PLoS Genetics this week reveals that crop-wild introgression is likely a longstanding and potentially beneficial phenomenon in some agroecosystems. Matthew Hufford, Jeffrey Ross-Ibarra and colleagues describe how introgression from wild relatives has shaped the genome of corn, potentially providing essential adaptations as it spread from a narrow center of domestication into novel environments.

Corn was domesticated in the lowlands of southwest Mexico ~10,000 years ago from a wild grass known as teosinte. A few thousand years later corn colonized the high altitudes of the Mexican Central Plateau. There, it came into contact with a different wild teosinte, one presumably well adapted to the new environment. Both corn and teosinte in the highlands have characteristics such as purple pigmentation and hairy stalks and leaves that are believed to help these plants tolerate the lower temperatures and higher ultra-violet radiation of the highlands. For some time, biologists have been stumped as to whether corn and teosinte obtained these highland adaptations independently or through introgression, with some arguing that the shared characteristics were a good example of maize genes escaping into the wild.

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Through analysis of genetic markers from across the corn genome, Hufford and co-authors provide evidence that the shared characteristics of teosinte and highland corn are due to introgression, but with gene exchange occurring predominantly in one direction — from the wild teosinte into corn. Introgression was particularly common in regions of the genome previously linked to highland adaptation traits. When corn with and without introgression in these genomic regions was grown at low temperature, plants with teosinte introgression showed pigmentation and hairy leaves, consistent with highland adaptation, whereas those without introgression lacked these traits. These results suggest that the successful spread of corn to the highlands may have been enabled by gene exchange with highland teosinte.

In contrast, regions of the corn genome selected by early farmers during domestication appeared particularly resistant to introgression in either direction of gene flow, indicating continued selection against wild traits in corn as well as selection against corn genes in the wild teosinte.

In addition to corn, a number of crops have spread from small domestication centers into novel environments, often populated with locally-adapted wild relatives. The work by Hufford and coauthors suggests genomic data in other systems may reveal that introgression from wild relatives has provided crops with adaptations such as drought tolerance, acclimation to extreme temperature and disease resistance. Rather than focus solely on the biosafety aspects of crop-wild introgression, we can also begin to assess how crop-wild introgression may have contributed to — and continue to be harnessed for — crop improvement.

Reference: Hufford MB, Lubinksy P, Pyhäjärvi T, Devengenzo MT, Ellstrand NC, et al. (2013) The Genomic Signature of Crop-Wild Introgression in Maize. PLoS Genet 9(5): e1003477. doi:10.1371/journal.pgen.1003477

Eugenie Scott to retire from NCSE

2013-05-10T21:53:14Z

The National Center for Science Education announced that its executive director, Eugenie Scott, will retire at the end of the year:

NCSE’s executive director Eugenie C. Scott announced on May 6, 2013, that she was planning to retire by the end of the year, after more than twenty-six years at NCSE’s helm. “It’s a good time to retire, with our new climate change initiative off to a strong start and with the staff energized and excited by the new challenges ahead,” she commented. “The person who replaces me will find a strong staff, a strong set of programs, and a strong board of directors.”

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NCSE continues,

During Scott’s time at NCSE, she was honored with no fewer than eight honorary degrees as well as the Public Welfare Medal from the National Academy of Science, the inaugural Stephen Jay Gould Prize from the Society for the Study of Evolution, the Public Service Award from the National Science Board, and the Scientific Freedom and Responsibility Award from the American Association for the Advancement of Science.

“It’s not going to be easy to fill the shoes of someone who has done so much to make NCSE into the respected and admired organization it is,” remarked Brian Alters, the president of NCSE’s board of directors. “We look forward with working with Genie to find the best possible successor.” A job announcement is now available; members and friends of NCSE are encouraged to spread the word that what Scott once described as “the best job in the world” will soon be open.

Science Insider (May 6, 2013) reported on the announcement, quoting Kenneth R. Miller of Brown University as saying of Scott, “She’s incomparable, irreplaceable, and indispensable,” and Sean B. Carroll of the Howard Hughes Medical Institute as saying, “The entire scientific community, legions of teachers, and millions of students owe her a great debt for her dedication and passionate advocacy. She has established a remarkable legacy at NCSE.”

I could not agree more – we all owe Dr. Scott our gratitude for her tireless and eloquent defense of science and rational thinking.

If you want the job, click here.

Accessible Research: Rhesus Sperm Stem Cell Transplants

2013-05-09T14:45:40Z

I was going to update a previous post about sperm stem cell transplants in boars, when I came across a very recent paper with a similar technique in the Rhesus monkey, and I couldn’t pass it up. So a little of the background content here is duplicated from that previous post.

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Sperm cells are the vesicles used by male mammals to pass on their DNA to their offspring

Sperm are made from sperm stem cells. Each healthy cell in our body has a finite life, so we need stem cells (adult stem cells) to make more cells when the old one dies. There are many kinds of adult stem cells that can only make more of a certain kind of tissue. For example, there are skin stem cells to make more skin cells, there are blood stem cells to make more blood cells, and there are sperm stem cells to make more sperm cells. For the paper I’m talking about today by, it is the sperm stem cells that are important.

Hermann et al. worked with male rhesus monkeys that had undergone chemotherapy, which can permanently damage fertility.

They took healthy sperm stem cells from donor monkeys, and implanted them into the testes of chemotherapy-treated recipient monkeys. It is important that they transplanted sperm stem cells, which will keep replicating and making new sperm throughout the recipient monkey’s life, versus just sperm cells, which will die and not continue to replicate. This transplant wasn’t 100% successful, but in over half of the cases, there was evidence that the donor sperm stem cells were, in fact, replicating and producing sperm. Further, the researchers were able to confirm that donor-derived sperm could fertilize an egg (although, curiously, of the sample of sperm from the chemotherapy-treated monkey, only about 9% of the fertilized eggs were genetically similar to the donor, suggesting that not all spermatogenic function was lost during the chemotherapy treatment).

In the boar study, the scientists were looking to add functional sperm, where none (or very, very few) had previously existed, meaning that nearly all of the sperm generated would be from the donor. This would mean that if applied to genetically infertile XY-individual, that person’s offspring would be more genetically similar to the donor, than to the transplant recipient.

However, this study allows for a different approach, and application in humans. Considering the case when a sperm-making individual knows that they will be undergoing a procedure (such as chemotherapy) that affects their ability to make functional sperm. That person could, in theory, have some of their own sperm stem cells extracted, then transplanted back after the fertility-affecting procedure was completed.

Wow.

Cell Stem Cell. 2012 Nov 2;11(5):715-26. doi: 10.1016/j.stem.2012.07.017.

Spermatogonial stem cell transplantation into rhesus testes regenerates spermatogenesis producing functional sperm.

Loxodonta africana

2013-05-06T18:00:00Z

Photograph by Paul Ruggeri.

Photography contest, Honorable Mention.

Loxodonta africana – African elephant. Mud dries on the back of the elephant. The mud in the furrows between the folds remains moist, helping the elephant to keep cool in the heat. The dried mud on the folds helps protect against sunburn.

Ken hams it up, parodizes self

2013-05-06T14:00:00Z

My old friend, the Alert Reader, sent me a cartoon that he claimed had appeared on Ken Ham’s Facebook page. Captioned “Famous sayings of Ken Ham,” the cartoon shows a caricature of Ham and three balloons, including this one:

It’s designed to do what it does do.

What it does do it does do well.

Doesn’t it?

Yes, it does.

I think it does.

Do you? I do.

Hope you do, too. Do you?

I found it hard to believe that the cartoon was not a parody and wondered why it is found on Ham’s own Facebook page. The Alert Reader responded with the following, also reportedly from Ham’s Facebook page:

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Yesterday I spoke to hundreds of children and adults at the Homeschool Convention (Teach Them Diligently Convention) in Spartanburg, South Carolina. To help children remember what I teach them, I now give them two cards with colorful information on the front and back of each card that summarizes what is taught during the presentation. This is the back of one of these cards. The atheists have already had emotional meltdowns across the [I]nternet because I teach students how to think correctly about origins by asking ‘Were You There?’–so they can continue to have their meltdowns as thousands upon thousands of children are given these cards across the nation. I will be giving these out to the hundreds of kids who will be attending the AiG conference in the Atlanta area today and tomorrow.

OK, I have to agree that the cartoon is real. I have yet to see a better example of Poe’s law. Ken Ham, once again, commits autoparody.

Challenge: research in the 1000 most common words

2013-05-05T04:07:22Z

Here is a list of the 1000 most commonly used words in the English language.

Check it out. See if you can explain your research in these 1000 words.

My try:

I study how things that are different between men and women change over time.

Please add the description of your research in the comments!

Classical liberalism and evolution

2013-05-03T16:48:55Z

Stephen Dilley’s new book, Darwinian Evolution And Classical Liberalism: Theories in Tension, is now available, at least on Kindle. Chapter 12 is by me; it’s entitled, somehwat dully, “Classical Liberalism And Evolution.” In it, I argue that evolution, far from undercutting the premises of classical liberalism, is at least compatible with them, and, as I think, provides a stronger foundation for them than any variety of creationism. But, as I contend at the outset, it doesn’t much matter, because evolution is true. So if it’s incompatible with libertarianism, then so much the worse for libertarianism.

Chapter 11 is by my friend Shawn Klein; it’s called, somewhat more interestingly, “Volitional Consciousness and Evolution.” Other contributors include Roger Masters and Michael J. White.

Gene survival and death on the human Y chromosome

2013-05-02T15:36:07Z

I opened my mailbox last week, and what should appear before my wondering eyes, but the new issue of Molecular Biology and Evolution. Inside is our recent (and open access!!) paper: Gene survival and evolution on the human Y chromosome. Here’s my summary of our work. (Editorial Note: it is so, so much easier to distill down research articles that I haven’t spent years of my life on.)

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In humans, genetic females have two X chromosomes and genetic males have one X chromosome and one Y chromosome:

You might have noticed from the cartoon above that the human Y is much smaller than the human X. But, it wasn’t always this way. Ancestrally, the human X and Y were the same size, and had the same genes. Over time, however, the Y has shrunk, but both the X and Y have also gained some genes. To better understand how the X and Y became so different, and how the evolution of the two sex chromosomes are correlated, we asked three main questions:

1. What has been lost from the Y?
To know which genes were lost, we first had to identify which genes were on the ancestral sex chromosome pair. By comparing the genes on the human X with the genes the X in other species, we identified a set of genes that were likely on the ancestral X chromosome: 600 in total. Then, by searching the Y chromosome for the relics of all of these genes, we identified three classes of sex-linked genes. We should think of each of the 600 ancestral genes as a pair (with one copy on the X, and one on the Y). All of these pairs have a working copy on the human X. Some pairs have a working (functional) copy on the Y, some have a broken copy on the Y (degraded), and some are missing their Y-copy.

Many genes have been lost from the ancestral Y, but a few persist.

So, while some Y-linked genes have survived (I have another paper discussing this), and there have been some unique additions to the Y chromosome, we can see that the Y has lost functional capabilities for 96.83% of the genes that it once shared with the X. Wow!

2. Are there indicators of whether a Y-linked gene will be retained?
We can learn about the evolution of the sex chromosomes by studying differences between classes of sex-linked genes defined above. Specifically we asked, do features of X-linked genes suggest whether their Y-linked partner are retained or lost? In some cases, yes, they do.

First, we found that human X-linked genes with very few changes across mammals were more likely to have a working Y copy. So, if a gene is important enough to survive over long evolutionary time in roughly the same condition across very different species, then it might be very useful to the organism, so it would be important to have that gene in a working form in both males and females in the same species (human).

Second, we looked at expression. Genes can sometimes be “on” (which we would call expressed) or “off” (not expressed), but more often they can fall within a range. It’s like a light with a dimmer switch. The light can be turned on very brightly, but can also dimmed to a very low level without being “off”. We found that X-linked genes that were highly expressed (bright) were more likely to have a working Y copy. This might mean that, for these genes, the level of “brightness” or expression is important, so that it is highly beneficial for these genes to be working very hard in both females and in males.

3. Does gene loss on the Y affect the evolution the X?

Okay, so some features of the X-linked partner might predict whether it’s Y-linked partner will survive, but is there any feedback from the Y back to the X chromosome? Yes!

Let’s think back to that first picture: females have two “big” X chromosomes, while males have one “big” X and one “little” Y. And, I’ve shown you that the Y chromosome has lost (either because of broken copies, or completely lost) almost 97% of the genes that it once shared with the X. This might lead you to believe that there are more genes expressed in females than in males. But, in many mammals, females silence most of the genes on one of their X chromosomes (X-inactivation), to equalize the dosage of genes expressed between males and females.

Although it has been hypothesized, we showed that the pattern of genes subject to silencing in females among the three classes above is consistent with a process whereby silencing evolves in response to gene loss on the Y chromosome. Moreover, this pattern suggests that some amount of time must pass to allow the signal (that the Y-linked partner is no longer working) to reach the X-chromosome before silencing can occur.

The paper is open access, so if you are curious, you can read it here.

Mol Biol Evol. 2013 Apr;30(4):781-7. doi: 10.1093/molbev/mss267. Epub 2012 Dec 4.

Gene survival and death on the human Y chromosome.

Sayres MA, Makova KD.