Love work of @billgates but "mosquitoes kill more people than people do" is just wrong

I truly love the work Bil Gates and the Gates Foundation have been doing over the last years.  Absolutely wonderful stuff.  But I have a bone (or perhaps a proboscis) to pick with this latest effort: The Deadliest Animal in the World | Bill Gates.  The article discusses some “facts” about how many people different animals kill.  And it uses this to argue for the need for more attention to be placed on mosquitoes.  I agree with the conclusion.  Mosquitoes are a big deal and need much much much more work and attention.  But the data is just, well, not sound.  Here is the problem I have

1. Many of the animals, including mosquitoes, are on the list are there because of the diseases they transmit.  For example, dogs are there (for rabies), and tsetse flies are there for sleeping sickness.  That is, they do not kill people directly but indirectly because of a disease they transmit.

2. If we follow that logic, which I am fine with, then we need to add a whole lot of deaths to the “human” column.  After all, humans transmit a whole heck of a lot of diseases that kill humans.  One source I found has the following #s

  • HIV/AIDS: 1.78 million per year
  • Tuberculosis: 1.34 million per year
  • Flu: 250-500,000 per year
  • HAIs: >100,000
  • Syphilis: 100,000
  • Measles: 600,000

and many many many more.   The totals are probably greater than 5 million per year that are killed by infectious diseases where it was humans who transmitted the agent to other humans.  Way more than the mosquitoes.  Again, I agree with the conclusion.  We need lots more attention on mosquitoes.  But there seems little doubt to me which animal is most responsible for the spread of deadly pathogens to humans.  And that animal is us.


Am kind of annoyed at the press coverage of this Gates – mosquitoes are the deadliest animal – concept.  Here are some examples where people just ate up the idea without really asking any questions about its accuracy

And many many more.  It is a cute concept.  And an important one.  It just happens to be wrong.

UPDATE 5/4. Some Tweets of relevance






See Vox post: No, mosquitoes aren’t deadlier than humans

Also see these posts which run with the Gates meme


Twisted Tree of Life Award: NPR on the Evolution of Crying

Well, normally I really like NPR science stories. But this one dug into my anti adaptationism feelings. Adaptationism is, in essence, the practice of saying something must be adaptive (i.e., beneficial), simply because it is there in an organism. Such cases are also referred to as “just so stories” – a play on the old Kipling “Just So Stories“.  That is, in essence, people who claim something is adaptive just because it is there are in essence telling you something is this way because it is just so.   I am actually not sure of the whole history of using the just-so analogy to refer to adaptationist stories – I know Stephen Jay Gould discussed this a lot in his books and lectures, but not sure who first did it. 
Anyway – NPR has an adaptationistic doozy from Morning Edition: 

Teary-Eyed Evolution: Crying Serves A Purpose : NPR

Basically, it seems the gist of the argument here is the following line:

Scientists who study evolution say crying probably conferred some benefit and did something to advance our species — because it’s stayed with us.

Wow – that is like straight out of the adaptationist playbook.  The problem with this argument is that many things exist and persist in organisms even when they are not adaptive.  There are many reasons why this can happen from constraints (e.g., if bones were not adaptive in humans it would be pretty hard to get rid of them) to  invisibility to selection (e.g., some features that only show up after reproductive age may not really influence fitness) and so on.

In essence the NPR story is one of the worst examples of adaptationism in the good science press I have seen in a while.  Sure this shows up all over the place.  But rarely this bad at NPR.  The story ends with an even worse line than the rest

Maybe that’s another reason evolution kept humans weeping: Tears help reveal the truth. And that’s because along with the tears, we’ve evolved a very sophisticated ability to interpret them.

Yes that is right.  Crying has been maintained in humans because we also evolved another adaptive feature – the ability to interpret tears.  So the logic here is that crying is adaptive because it is needed for another adaptive trait for which there is no evidence it is adaptive.

So for their story on crying and for in essence inventing some just so stories to explain why they think it is adaptive, NPR is the recipient of my Twisted Tree of Life Award.  Previous recipients are

See also these things for some stuff on evolution of crying:

Best genomics news article title …6 Billion Bits of Data About Me, Me, Me!

Gotta love the title of this article. It captures the essence of the new race to sequence ones own genome pretty well (with Jim Watson and Craig Venter leading the way). Clearly, this type of personal genomic medicine is coming whether we like it or not but, for those interested in getting ones own genome sequenced, here are some things to consider:

1. There will be many mistakes, at least with current methods. Get ready for lots of false positives and negatives relating to risk.

2. People will use it against you. Companies. Friends. Relatives. The government. This is not to discourage people from doing it (well, maybe a little bit). But given our current inability to keep anything important private in this country and our apparent inability to not snoop into people’s lives, this is going to be one overwhelming temptation for many people. Now is clearly the time to move forward with anti-discrimination laws.

3. Having your genome sequence will not automatically improve your health. It could even make it worse (e.g., see false positives above)

4. If you REALLY want to understand some of your biology from your genome, you are going to want to take a peak at the genomes of relatives. Good luck on all the family issues that will come up.

5. Just because Watson and Venter are releasing their genomes to the public does not mean you have to (for medicine it is VERY useful to have a genome associated with an individual … even many individuals, but there is no real need for names to be there)

6. The methods being used may not recover the haplotypes well (e.g., see Keith Robison’s blog).

ALSO check out some other articles on this topic

“I think this is a stunner,” Dr. Collins said. “This is like the seat of the soul of the genome.”

OK. I could not help myself with this one after I was sent the quote by Francis Collins in this New York Times Article. Dr. Collins, in relation to a new study that showed that one region of one human chromosome apparently plays roles in heart disease and diabetes, said

I think this is a stunner,” Dr. Collins said. “This is like the seat of the soul of the genome.”

Now, I have commented before about how Dr. Collins is doing a pretty good job about keeping his religious beliefs separate from his work. And since he is a strong supporter of evolutionary biology I like to give him the benefit of the doubt (I personally agree with him that there is no need for a conflict between evolutionary biology and non fundamentalist religious beliefs). But I think “the seat of the soul of the genome” is a bit much.

I frequently criticize researchers who observe something in the genome and immediately come up with an adaptive explanation for the observation. Such adaptationist, just so story responses, are common in molecular biology and many areas of biology and were written about extensively by Gould and Lewontin and others. But now I guess we have a new category of adaptationist-like explanations. Striking findings in a genome can now be called “just soul stories.”

More on the Human Microbiome Program Workshop – Day1

As a follow up to my previous blog I am posting some additional information here about the NIH Roadmap Human Microbiome Project Workshop, which was held in Bethesda, MD.

The general outline of the meeting was as follows:

  • Sunday Night
    • Introduction
      • Welcome by Francis Collins (NHGRI), Hugh Auchincloss (NIAID) and Griffin Rodgers (NIDDK)
      • Comments by Gary Schoolnik
      • Overview of the NAS report on metagenomics by Jim Tiedje
      • Overview of the NIH Roadmap program by Francis Collins
    • Introductory talks on human microbiome
      • Jeff Gordon
      • David Relman
      • Gary Huffnagle
      • Jo Handelsman
  • Monday AM
    • Technological issues
      • Elaine Mardis
      • Jill Banfield
      • Deirdre Meldrum
    • Bioinformatics issues
      • Lior Pachter
      • Rolf Apweiler
      • Peer Bork
    • ELSI Issues Pilar Ossorio
  • Lunch
  • Monday PM – Breakout sessions and discussion
    • Group 1 – Reference microbiome (Claire Fraser and Martin Blaser)
    • Group 2 – Changes in microbiome and human health (Rita Colwell and Martin Rosenberg)
    • Group 3 – Enabling technologies (Bruce Birren and Mary Lidstrom)
    • Group 4 – Bioinformatics tools (Ewan Birney and Owen White)
    • Group 5 – Ethical legal and social issues (Midred Cho)
  • Wrap up

Overall, I found the Sunday night talks very useful to set the stage. The introductory talks by the representatives from NHGRI, NIAID, and NIDDK clearly indicated that NIH as well as others consider the human microbiome an incredibly important research area. Then Jim Tiedje gave a nice overview of the recent NAS report on metagenomics (which was about metagenomics in general, not specifically for the human microbiome). The main points of the report are basically: microbes rule the world, metagenomics is a very powerful tool in studying them, and there is a need for a more coordinated effort among funding agencies to push metagenomics as a tool and a field. (My only complaint about Tiedje’s presentation was he kept using the term “higher organisms” for those multicellular species with nuclei. But otherwise, he did a good job of concicely summarizing the report and the benefits as well as challenges of metagenomics).

Francis Collins then gave an overview of the NIH Roadmap Program. The Roadmap was started in ~2003 as an initaitive to identify projects that would need coordination across multiple NIH agencies. These projects should meet certain characteristics: truly transforming, require all NIH, must need incubator scape, and the outcome should produce material into the public domain. Collins then discussed how, from among hundreds of suggestions, the Human Microbiome was picked as one of five topic areas for in depth consideration for the new round of Roadmap competition. Thus the point of this workshop was to discuss this in more detail and help provide material and ideas for the full consideration of an HMP program.

I should note, I found one thing disappointing in the introduction which was a response to my question concerning whether this project would be limited only to studies of humans or would allow for studies of model systems that inform human work. The answer was basically that this would likely be limited to humans. I think this is a big mistake. The human genome project came to the realization that comparative studies with other species were critical to understanding and interpreting studies of the human genome. The same will be true of the human microbiome program.

Jeff Gordon then gave an overview of human microbiome studies, and focused on what are the key questions that need to be answered. Among the key questions: Do we share a core set of microbes? How should we view differences in microbes between people and over time? How do we relate communities of microbes to health and disease? How should we sample microbial communities to characterize them? What determines robustness of microbial communities in people?

To start to answer these and other questions, he suggested that we have three tiers of data collection: (1) deep draft assemblies of microbial communities and reference genomes, (2) reference microbiome work (deep characterization of individuals including information about the familiy history and genetics) (3) 16s surveys of communities (a global human microbial diversity survey). I basically liked all of his ideas. He did talk about work in model organisms too. His work has shown just how important this is … and I think as I said above it needs to be emphasized more in the HMP.

David Relman, from Stanford, then talked about patterns in human microbial diversity. He talked about some of the challenges in such studies as well as results of his and others work. He discussed many interesting aspects of the diversity of samples, and the shapes of diversity. Some of the patterns he emphasized were that history plays a role in the diversity, that archaea generally seem to have limited presence, that diversity is uneven and complex.

Then Gary Huffnagle discussed in more detail the interaction of microbes with the host immune system. And Jo Handelsman discussed what she calls functional metagenomics, which involves focusing on the functions of genes found in the environment on top of examining the phylogenetic diversity of communities. Unfortauntely, I did not take extensive notes for these two talks so do not have much to base my comments on here. In addition, I confess, the fact that the room in which the meeting was held was incredibly crowded and boiling hot, and the fact that I had flown in from California earlier in the day, made taking notes challenging at this point. However, that did not stop me from going out afterwards for a beer with Julian Parkhill, Ewan Birney, Owen White, and Jacques Ravel. The worst part of going out for the beer – I grew up in Bethesda but I made multiple wrong turns in the two blocks to the brew pub. I am sure from now on Julian and Ewan will never trust my directions. Fortunately, the fact that the pub had the RedSox pummeling the Yankees on TV made up for my direction problems.

I will post more about the second day soon.

Scientist Reveals Secret of the Ocean: It’s Him

Published: April 1, 2007

Maverick scientist J. Craig Venter has done it again. It was just a few years ago that Dr. Venter announced that the human genome sequenced by Celera Genomics was in fact, mostly his own. And now, Venter has revealed a second twist in his genomic self-examination. Venter was discussing his Global Ocean Voyage, in which he used his personal yacht to collect ocean water samples from around the world. He then used large filtration units to collect microbes from the water samples which were then brought back to his high tech lab in Rockville, MD where he used the same methods that were used to sequence the human genome to study the genomes of the 1000s of ocean dwelling microbes found in each sample. In discussing the sampling methods, Venter let slip his latest attack on the standards of science – some of the samples were in fact not from the ocean, but were from microbial habitats in and on his body.

“The human microbiome is the next frontier,” Dr. Venter said. “The ocean voyage was just a cover. My main goal has always been to work on the microbes that live in and on people. And now that my genome is nearly complete, why not use myself as the model for human microbiome studies as well. ”

It is certainly true that in the last few years, the microbes that live in and on people have become a hot research topic. So hot that the same people who were involved in the race to sequence the human genome have been involved in this race too. Francis Collins, Venter main competitor and still the director of the National Human Genome Research Institute (NHGRI), recently testified before Congress regarding this type of work. He said, “There are more bacteria in the human gut than human cells in the entire human body… The human microbiome project represents an exciting new research area for NHGRI.” Other minor players in the public’s human genome effort, such as Eric Lander at the Whitehead Institute and George Weinstock at Baylor College of Medicine are also trying to muscle their way into studies of the human microbiome.

But Venter was not going to have any of this. “This time, I was not going to let them know I was coming. There would be no artificially declared tie. We set up a cutting edge human microbiome sampling system on the yacht, and then headed out to sea. They never knew what hit them. Now I have finished my microbiome.”

Reactions among scientists range from amusement to indifference, most saying that it is unimportant whose microbiome was sequenced. But a few scientists expressed disappointment that Dr. Venter had once again subverted the normal system of anonymity. Recent human microbome studies by other researchers have all involved anonymous donors. Jeff Gordon, at the Washington University in St. Louis expressed astonishment, “I have to fill out about 200 forms for every sample. It takes years to get anything done. And now Venter sails away with the prize. All I can say is, I will never listen to one of my review boards again.”

Venter had hinted at the possibility that something was amiss in an interview he gave last week for the BBC News. He said “Most of the samples we studied were from the ocean but a few were from people.” When the interviewer seemed stunned, Doug Rusch, one of Venter’s collaborators stepped in and said “Collected with the help of other people.”

Venter was apparently spurred to make the admission today that many of the samples were in fact from his own microbiome due to a video that surfaced on YouTube showing Jeff Hoffman, the person responsible for collecting the water samples, performing a tooth scraping of Venter and then replacing the ocean water filter with Venter’s tooth sample.

Venter said the YouTube video was immaterial, “Well, we wanted to wait a few more weeks to have the papers describing the human microbiome published. But in the interest of human health we are deciding to make the announcement today.”

Unlike with the human genome data however, Venter says all of the data from his personal microbiome will be made publicly available with no restrictions. “If there is one lesson I have learned it is that open access is better than closed access. The more people can access my microbiome, the more they will help me understand myself. Plus, unlike Collins and Lander, who publish only in fee-for access journals, we will be publishing our analysis in the inaugural issue of a new Open Access journal that is a joint effort between the Public Library of Science and Nature. It will be called PLoN, the Public Library of Nature.”

In making his microbiome available, Venter has yet again abandoned his genetic privacy as he did when making his own genome available. Interestingly, the microbiome helps explain one of the first findings that was announced regarding his own genome. Venter said that analysis of the samples that came from his intestine reveal that microbes may explain why even though he has an apoE4 allele in his own genome (which is associated with abnormal fat metabolism) he does not need to take fat-lowering drugs. “Apparently, I have some really good fat digesters living in my gut. They make up for what is missing in my own genome.”

Dr. Venter’s reason for having his own microbiome sequenced, he said in the interview was in part scientific curiosity — ”How could one not want to know about one’s own microbes?” As to opening himself to the accusation of egocentricity, he said, ”I’ve been accused of that so many times, I’ve gotten over it.”

The key question that remains is – which of the samples were really from the ocean and which are from Venter. Venter said “Our funding agencies, including the DOE and the Moore Foundation, have agreed that we should not explicitly reveal which samples are which as this will encourage people to develop better methods of analyzing such complex mixtures of different microbes. Next week we will be announcing an X-prize award for the person who can identify which samples are mine and where they came from in me.”

Rob Edwards, a freelance microbial genomics expert says “It won’t be difficult to tell which are which. In fact, we had already identified an anomalous sample from Venter’s previous ocean sampling work, but nobody would listen to us.”

Jonathan Eisen, an evolutionary biologist who used to work for Venter says “I am certain that a few creative evolutionary analyses can reveal which sample is which. In fact, we are starting analyzing the samples already in anticipation of the X-prize announcement.”

Others are not so confident. Ed Delong, an ocean microbiology expert from MIT says “We have spent years carefully selecting our ocean samples to make sure they are not contaminated with sewage from cruise ships or from city drains. And now this – a purposeful mixture of ocean and human. It could take years to clean up the mess.”

Venter does not seem concerned. “If nobody can figure out which sample is from me and which is from the ocean, then we have no hope of making any progress in studies of either human microbiomes or oceans.”

More importantly, many scientists want to know what Venter will do next. Some want to know so that they can make sure to stay out of the way. Others probably relish the potential to go head to head with Venter. In this regard, Venter is not shy. “Biofuels. There is a great future in biofuels.”

Neanderthals and Humans

So – we now have data and papers relating to some genome sequencing of DNA apparently from a Neanderthal fossil. I must say, even though I am a skeptic of much of the work on ancient DNA, I find the idea of sequencing the genome of a Neanderthal to be pretty cool. Perhaps more importantly than the scientific uses of this information, the sequencing is a brilliant public relations coup for genome sequencing. It is also a potentially useful tool in science and evolution education.

I will spare everyone my worries the scientific value of this work for now and am just using this post to collect links that I have found to be useful regarding Neandethal ancient DNA.

I will add more links in the next few days – or people can add them with comments