ActionBioscience http://staging.actionbioscience.org/ en Copyright 2008 Thu, 06 Dec 2007 11:11:57 -0500 http://www.sixapart.com/movabletype/ http://blogs.law.harvard.edu/tech/rss Genetic Testing to Predict Disease: Ethical, Legal, and Social Implications (ELSI) The Human Genome Project enabled genomic understanding. Will a genetic test change your life for the better? Predictive Genetic Testing (PGT) is the use of a genetic test to predict future risk of disease. Although PGT is relatively new, arising from the mapping of the human genome, it has rapidly emerged as a technology that carries many benefits, but many risks, as well. Considerable debate surrounds the moral and ethical issues regarding persons who have undergone predictive genetic testing.
X-linked recessive manner means that the inherited trait almost exclusively affects males.
PGT is utilized commonly in the following circumstances: * carrier testing1, which identifies persons with a genetic mutation for a disorder inherited in an autosomal recessive2 or X-linked recessive manner3; * prenatal diagnosis, in which testing determines whether a fetus is affected with a particular disorder4; and * predictive testing, which is offered to asymptomatic persons who, based on their family history, are at risk for developing a disorder. Each one of these circumstances carries a particular set of ethical, legal, or social implications, depending on the reasoning behind the testing. For example: * For medical purposes, is the testing diagnostic, or predictive with a treatment? * Are you having the testing done for personal decision-making reasons? That is, predictive without a treatment, carrier, or prenatal?
Genetic results are directly related to an individual’s identity.
In any circumstance, privacy and confidentiality are critical because the genetic results are directly related to an individual’s identity.5 Not only is confidentiality an issue for health care, but to prevent genetic discrimination in insurance coverage and employment, as well. Information from a genetic test can affect an entire family. If the disorder is either genetically dominant or carried by an individual, that person’s parents, children, brothers, sisters, and even extended family may also be affected. Questions that arise may be: * Should family members be informed of the test results? * Should the individual diagnosed with a genetic disorder inform his/her family they may be at risk? * Alternatively, should the physician who has diagnosed the patient inform the family of the disorder and recommend testing? Furthermore, a person may make life-altering decisions based on the results of a genetic test.6
Family history serves as a guide for genetic testing.
Disclosure of genetic test results can be critical in all aspects of an individual’s life. When a person is identified through family history as being at risk for an inherited condition, a genetic test may be available to clarify their chances of their developing that disease; in addition, the genetic test results may also reveal information regarding risk for disease of other biological family members. ### Marybeth: a case study At age 37, Marybeth is pregnant with her second child, in her first trimester. She discloses to her family physician that she had a severely mentally and physically handicapped younger brother who died shortly before she was born. Ashamed, Marybeth’s mother told her that her younger brother’s death was caused due to injuries resulting from a loss of oxygen when he was born. Marybeth has a healthy four-year-old daughter.
CVS is a prenatal test to detect chromosomal and genetic abnormalities.
Marybeth pursues genetic testing, and she is found to be the carrier of fragile X-gene mutation (a genetic mutation associated with mental retardation and developmental disabilities). She decides to have chorionic villus sampling (CVS), and the results show that her fetus is a boy who has not inherited the fragile X gene mutation. At her follow-up visit, she tells the clinician that she understands that it is likely that her mother is a carrier of this condition]]> http://staging.actionbioscience.org/genomic/glenn2.html http://staging.actionbioscience.org/genomic/glenn2.html 3-genetic information and privacy Original genomics Thu, 06 Dec 2007 11:11:57 -0500 Talking Past Each Other: Genetic Testing and Indigenous Populations Population genetics focuses on groups, not individuals. Although blood samples have been collected from indigenous or native peoples since the early 1920s, genetic testing of the world’s indigenous populations has been a source of heated controversy in the past two decades. Since the development of technology for decoding the genetic sequence of living organisms, geneticists and researchers have predicted that insights into human genes will enable scientists to better understand the genetic bases of numerous human diseases and disorders. Excited talk about possible cures has inspired a gene rush reminiscent of the California gold rush. According to the UNESCO Bioethics Committee, population genetics is a discipline of genetics which “considers the characteristics of genes within a population as opposed to a description of the genes in a particular individual.”1 In the quest for a holistic understanding of gene-environment interactions, several large-scale population genetic research studies have been initiated. Only Ashkenazi Jews have previously been the subject of such an intense and sustained scientific scrutiny. ### Why focus on indigenous groups? Why focus on indigenous peoples, and why has genetic testing of indigenous populations been such a heated and emotive issue? From the scientific standpoint, the increased homogeneity of the gene pool in populations perceived to be endogamous, or isolated from large-scale crossbreeding with other populations of dissimilar genetic background, makes it easier to identify perceived genetic peculiarities.
Native isolation supports a homogenous gene pool.
* It is easier to identify genetic triggers of inherited diseases when one studies the genetic pool of endogamous communities as opposed to communities with greater genetic variety. * Many isolated, culturally and linguistically distinct populations are currently in imminent danger of merging with other communities, making genetic testing an urgent need.2 Nevertheless, some populations perceived to be genetically homogenous may not in fact be so.3
Some target projects may help trace human history.
In 2005, the National Geographic Society and IBM launched the “Genographic Project,” a genetics research project targeting indigenous populations. Members of the general public are invited to send their DNA to National Geographic for analysis. The project is expected to last for five years. The project states that it involves no medical research, but will rather study human migrations.4
Others hope to gain medical insights.
The Genographic Project was preceded by two other projects that did explicitly involve genetic testing of indigenous peoples for medical research: the Human Genome Diversity Project [the HGDP]5 and the international HapMap6 (designed to study genetic markers called “haplotypes,” which consist of closely linked groups of alleles that tend to be inherited together7). Despite the high expectations surrounding the projects, the HGDP and the international HapMap floundered, or at least, found themselves the target of bitter and inflammatory rhetoric. The failure of the HGDP to achieve its target may be attributed to the vociferous opposition of indigenous groups, inspired by perceived historical injustice to and exploitation of indigenous populations. The crucial source of resentment was that critics argued the project treated indigenous peoples as mere sources of useful information while failing to recognize adequately their right to determine their own course. Whereas the arguments of those in support of genetic testing of indigenous populations largely focus on the vaunted medical benefits of such research findings, there is a firestorm of protests from groups, individuals, and stakeholders skeptical of the legal, ethical, and socio-cultural implications of genetic testing of indigenous peoples. ### Why is there opposition? Genetic testing is a controversial technological breakthrough largely because it involves the following issues: * the ownership of genetic samples * the patentability of the information gleaned from the testing, and * whether researchers obtained prior informed consent of the person from whom the genetic material was extracted.
Genetic testing is often controversial.
These concerns become more contentious when genetic technology is applied to individuals or groups with historical and contemporary claims of injustice and racialization.8 In such cases, the issues broaden into serious questions about international human rights laws9, ethics, and cultural self-determination of peoples.10
Native peoples have been exploited in the past.
They carry a mistrust of Western intentions.
At the core of the opposition to this testing from indigenous peoples is the memory of the racist and culturally insensitive dimensions of Western technologies, particularly those deployed during the height of Western colonialism and conquest. The backdrop to the unfolding debate is the increasing empowerment of indigenous populations since the demise of formal colonialism. Increasing political and legal power for indigenous groups over the past thirty years has put the ethical, legal, and cultural ramifications of genetic testing near the top of their agenda. At the height of colonialism, medical experimentation on indigenous populations was common, as was the “scientific” justification for racial denigration and depredation on such groups in the Americas, Australia, New Zealand, and other parts of the world.11 It is not surprising, then, that the announcement of the commencement of the Genographic Project was met with indignation and condemnation by a swathe of indigenous peoples, organizations, and human rights activists.12 ### What legal considerations influence patentability? The development of technologies and markets for gene therapy and products of biotechnology are factors that have made the search for commercially useful genes very lucrative. This in turn has led to the widespread use of patents as legal instruments for the control and merchandising of genetic information. It is therefore important to understand the legal requirements for a valid patent on genetic subject-matter and how patent law has been significantly modified to suit commercial interests.
DNA patent seekers must disclose intention of use.
Patent law requires that an inventor wishing to obtain patent protection for a new invention must disclose the industrial applicability of the alleged invention. This is generally referred to as the requirement of utility or industrial applicability. In patent law, regardless of the social, religious or cultural construction of genetic material, DNA sequences are considered to be like other complex chemical substances, such as paints, drugs, et cetera. Accordingly, anyone wishing to patent a genetic sequence obtained from a person, indigenous or non-indigenous, must disclose the utility of the DNA sequence. According to section 112 of the US Patent Act, this specification shall “contain a written description of the invention.”13 Judicial interpretation of section 112 of the US Patent law and similar legislation throughout the world shows that the utility requirement has three components, each of which must be met by an applicant.
Applying legal rules to genetic material is difficult.
* The “written description” requirement – the invention itself must be described. * The “enablement” requirement —the specification must describe the manner and process of making and using the invention. * The “best mode” requirement — the specification must describe the best mode contemplated by the inventor for practicing the invention. To the extent that an applicant for patent protection has shown that the DNA sequence is new, involved an inventive step, and is capable of industrial application, the DNA sequence is a patentable subject matter. The legal issue is therefore whether the applicant has met the three disclosure requirements. Patents can be issued only for sequences with known and proven utility. Patented sequences, unlike other chemicals with known utility, often have unknown functions even when scientists know the function of a similar gene sequence.14 Evidence suggests that in the past decade, many patent offices, especially those of the United States, Canada, United Kingdom, and European Patent Convention, have issued thousands of patents on the basis of homology instead of specific and ascertained utility and function.15 This practice is inconsistent with patent law. Even in the absence of proven utility, selling and licensing the use of genetic data are very lucrative.16 However, as the United States National Institutes of Health (NIH) and the Association of American Medical Colleges (AAMC) have recently argued, patents on homologous gene sequences (as they are called) are flawed because “a difference in a single base pair in a gene sequence can have important functional implications.”17 In simpler terms, gene sequences may be homologous on paper and yet have different pharmacological expressions when deployed or used therapeutically. Such small differences in supposedly homologous sequences are not uncommon. As noted above, patent offices and recent judicial attitude suggest a gradual return is in progress to a more conservative and rational approach to the test of utility in genetic patent applications. In this regard, the decision of the court in the case of _Regents of the University of California v. Eli Lilly & Co._18 is an instructive example:
In one case, a patent claimed medical use across species.
* One of the patents at issue in Eli Lilly issued from an application filed in 1977 and claimed recombinant plasmids and recombinant microorganisms containing a cDNA (a complementary DNA [Cdna] is DNA that has been synthesized from fully spliced ribonucleic acid [RNA] in a reaction catalyzed by the enzyme reverse transcriptase.] in essence, an isolated copy of an expressed gene—coding for a vertebrate insulin, such as rat or human insulin. * The patent describes a method of obtaining the cDNA sequence for rat insulin and discloses the sequence of the cDNA of rat insulin. The patent also describes the amino acid sequence of human insulin and discloses how the same method used to obtain the cDNA for rat insulin may be used to obtain human insulin cDNA. Because a patent on a genetic sequence may preclude subsequent patents on or uses of the sequence, patents are central source of contention. The patent does not, however, recite the sequence of the cDNA for human insulin.19 * Judge Lourie of the US Federal Circuit affirmed the district court’s invalidation of a claim directed to a microorganism containing a cDNA for human insulin and claims generically reciting cDNAs for vertebrate or mammalian insulin.20 With respect to the claim reciting a cDNA for human insulin, the court reasoned that: "While the example provides a process for obtaining human insulin-encoding cDNA, there is no further information in the patent pertaining to that cDNA's relevant structural or physical characteristics; in other words, it thus does not describe human insulin cDNA. Describing a method of preparing a cDNA or even describing the protein that the cDNA encodes, as the example does, does not necessarily describe the cDNA itself."21 In claims involving chemical materials, generic formulae usually indicate with specificity what the generic claims encompass. A person skilled in the art can distinguish such a formula from others and can identify many of the species that the claims encompass. Accordingly, such a formula is normally an adequate description of the claimed genus. In claims to genetic material, however, a generic statement such as “vertebrate insulin cDNA” or “mammalian insulin cDNA,” without more, is not an adequate written description of the genus because it does not distinguish the claimed genus from others, except by function.
Such claims can lead to patent abuse.
The court therefore held that “a cDNA is not defined or described by the mere name “cDNA,” even if accompanied by the name of the protein that it encodes, but requires a kind of specificity usually achieved by means of the recitation of the sequence of nucleotides that make up the cDNA.”22 This and similar decisions evidence a shift towards a stronger scrutiny of genetic patent applications. It is fair to say that the granting of speculative genetic patents that fail the requirement of the rules on specification of inventions brings the patent system into disrepute, especially when the victims of patent law sloppiness—people whose future actions and opportunities are constrained by over-broad patents—are already marginalised populations. ### What are the ethical implications of testing?
Racialization is a real concern in genetic testing.
The arguments against genetic testing of indigenous populations are not limited to the legality or patentability of genetic materials. Opponents have also marshalled formidable arguments regarding the ethics of genetic testing, especially the potential for racialization of indigenous groups. This assertion cannot be dismissed with vague assurances of propriety and changed circumstances. At the dawn of Western colonization, indigenous peoples were treated like objects, excluded from the dominant segments of humanity. The mummies and graves of indigenous peoples were often looted for “scientific studies” by Western colonizers. It follows, then, that current attempts at genetic testing of such groups, especially studies performed without legitimate prior informed consent, could easily reawaken the humiliation and dispossession of indigenous peoples.23
Should groups studied share in the benefits of discovery?
In spite of assurances that indigenous populations will receive equal benefits of genetic testing, evidence shows that on several occasions, scholars and researchers who collected samples from indigenous peoples enjoyed academic and professional advancement, while few benefits trickled down to the indigenous populations who provided the genetic materials.24 Researchers, academic institutions, and some drug companies, such as Harvard University, Boerhringer Institute, and Sequana Therapeutics Inc, have profited immensely from the gene sequences obtained from indigenous populations.25 Such allegations have swirled in particular around the blood samples taken from the Yanomami Indians of Brazil26 and the Havasupai Tribe of Arizona.27 Opposition to genetic testing of indigenous populations has gained significant resonance in several quarters because of unequal sharing of benefits (to both reputations and finances)28 between the populations and researchers.29 Some opposition from indigenous populations to the Genographic Project and similar projects is partly on the basis of the activities of the International Board for Plant Genetic Resources (IBPGR). In the 1970s, the IBPGR collected more than 125,000 plant germplasm specimens with the purported objective of holding them in trust for humanity. More than 80 percent of the specimens held in IBPGR storage sites were identified by indigenous peoples across the world. This immense database, however, became the source for billions of dollars worth of patented plant hybrids controlled by Western powers and agri-business giants.30 Indigenous populations thus have a long and painful history of being forgotten by dominant segments of humanity as soon as any perceived worth has expired.
Tests may cast doubt on an individual's heritage.
Genetic testing of indigenous groups could also raise divisive questions about membership in indigenous groups.31 In this context, it must be considered that the parameters for membership in an indigenous community may be different from what pertains in other societies. It is often the case that indigenous communities share common beliefs of origin, cultural affinities, and linguistic characteristics that may transcend genetic differences. Population genetics has the potential to confirm or refute long-held notions of common genetic and ancestral origins of many populations by exploring human migratory pathways. For indigenous peoples, the possibility of the revision or shattering of cherished lore and narratives of ancestral origins among various groups is a serious factor affecting their quest for self-determination. This fear is stoked equally by the fact that virtually all the personnel and instruments for the population genetics exercise are from communities and institutions historically associated with the subordination and dispossession of indigenous peoples. In an age when the concept of “indigeneity” has assumed potency in the struggle for political, economic, cultural, and social self-determination, however, the results of genetic testing of indigenous populations could spur significant social conflicts and divisions unless guidelines are established for how such information should be handled. ### In conclusion
Native peoples have support from human rights groups.
Beyond ethics, indigenous populations and human rights activists have found support in emerging international human rights jurisprudence on the need to protect indigenous peoples from racial discrimination and the emerging imperative of safeguarding indigenous peoples’ knowledge. For example, article 8(j) of the Convention on Biological Diversity obliges states to “respect, preserve and maintain knowledge, innovation and practices of indigenous communities and promote their wider application with the approval and involvement of the holders of such knowledge.”
Native culture must figure into ethical considerations.
In sum, although it is true that “population-based genetic research has the potential to affect human good, especially by further medical science,”32 researchers and their sponsors must consider seriously the concerns of indigenous populations about the ethics of genetic testing,33 the law and ethics of testing, and of course, the spiritual and historical arguments canvassed by indigenous populations. In this regard, it is comforting to note that the global community is increasingly aware of the need for an ethical approach. Even so, more work needs to be done on the politics of genetic testing, and especially the disempowerment of indigenous peoples.

© 2007, American Institute of Biological Sciences. Educators have permission to reprint articles for classroom use; other users, please contact editor@actionbioscience.org for reprint permission. See reprint policy.

]]> http://staging.actionbioscience.org/genomic/mgbeoji.html http://staging.actionbioscience.org/genomic/mgbeoji.html 2-ethics in genomics genomics Genetic Testing Mon, 17 Sep 2007 14:25:46 -0500 Looking for Ms or Mr Gene Right: Premarital Genetic Screening Should you consider genetic fitness as a partner? Should your choice of spouse be left solely to your heart, or should the choice incorporate some genetic fitness phase? Obviously, if one is to regard marriage (or any other equivalent arrangement such as cohabitation) as a joint decision to share your life with someone you love, incorporating genetic criteria might seem rather troubling, if not inappropriate. But, on the other hand, if you hold the view that the main reason for your union is procreation, then worrying about genetic compatibility and avoiding inheritance of grave genetic diseases becomes a serious consideration. ### The landscape
Many countries already conduct genetic screening.
Genetic testing and genetic screening have become part of contemporary medicine and public health initiatives. These terms are usually used interchangeably, but the term "testing" denotes a genetic test done on an individual voluntary basis, while "screening" implies large-scale, public health initiatives. Examples of genetic testing in clinical settings include testing for the presence of _BRCA1_ and _BRCA2_ genes, to identify increased risk for breast and ovarian cancer, or prenatal genetic testing for Huntington disease. Examples of public health initiatives in screening programs include newborn genetic screening programs instituted in all states in the United States (these panels of tests range among states from 6 to 50 diseases) and in other developed countries.1,2 The impetus to identifying the genetic cause of a disease or a susceptibility implies, or should imply, the ability to act upon this knowledge: * providing timely treatment * avoiding exposure to environmental risks * influencing reproductive choices
Screening should be restricted to lethal or severely debilitating diseases.
Importantly, we are not dealing here with genetic enhancement but rather avoiding the birth of babies with lethal or severely debilitating diseases. Screening for a genetic condition should also meet reasonable probability. It doesn’t make much sense to screen for a condition that is likely to occur in one case out of a million, as opposed to testing for a gene that could be carried by one in fifty. Therefore, discussion and decision with respect to a suggested test is highly dependent on the targeted population and its genetic susceptibilities. The subject of large-scale genetic screening, however, brings to mind notorious past precedents in this field, known as eugenics concepts (i.e., cleansing society's genetic pool of unfit genes). Thus, it is imperative to restrict such programs to lethal or severely debilitating diseases.
A newborn is at risk when both parents carry the same recessive gene.

Autosomal Recessive Inheritance. Photo: Wikimedia Commons

Another observation relates to the inheritance pattern of a genetic disease: dominant genes will manifest themselves (depending on their penetrance), while the heterozygote carrier state (having two different alleles) of recessive genes is asymptomatic and usually has no significance to the carrier or offspring. Only if both parents are heterozygous for the same ailment is there a 25 percent risk for every pregnancy that their offspring might receive both recessive genes and exhibit the disease. This latter possibility is the thrust for creating premarital genetic screening programs as we show below. X-linked recessive disorders, caused by mutations in genes on the X chromosome, are not amended to premarital genetic screening. Many countries have been struggling with the proper way to handle genetic information that has no immediate implication, such as a heterozygote carrier state that is identified during newborn screening.1,2 Should the information be revealed to parents? To tested individuals? If not, why not? ### What are the options?
Sometimes this combination is lethal.
In some populations, the likelihood of mating with a person with one's same faulty recessive gene is quite high. Since being a carrier doesn't carry any morbidity and is not manifested (i.e., no phenotype), the only material risk to carriers is that they might conceive a child with a partner who shares the same carrier status. If the genetic condition is a lethal one (e.g., Tay-Sachs disease), or seriously debilitating (e.g., Fanconi's anemia), one might wish to engage in preventive measures. What are the options? * One could remain in genetic ignorance with respect to his/her own carrier state, as well as the partner’s, and hope that the risk does not materialize. * One could resort to prenatal testing (e.g., amniocentesis, chorionic villus sampling), with the only true option in case of an affected embryo being an abortion. It should be noted that abortions carry certain risks to the mother (physical as well as psychological), are fraught with moral issues, and in some societies or subpopulations are strictly prohibited.
One option is to screen the embryo.
What should follow from such an analysis is an effort to avoid such conceptions, if possible. It is now possible to examine embryos prior to gestation in a procedure, called pregestational diagnosis (PGD), in which DNA from a cell of the developing pre-embryo is screened, and the pre-embryo is only returned to the mother-to-be’s womb if it doesn't bear the suspected gene for which it is tested. However, this procedure is still nascent, is expensive and, above all, necessitates in vitro fertilization with its embodied risks (e.g., invasive egg procurement, hyperstimulation syndrome, success rate of less than 20 percent per cycle) and substantial costs.
Another is to take premarital genetic tests.
But what if it would be possible to avoid the problem altogether? One way to do this is by performing premarital genetic testing (PGT) and informing prospective spouses about their carrier status, allowing potential partners who are both carriers of a particular recessive trait the option not to marry or not to procreate if they so wish. Several PGT programs have been instituted around the globe. The two most cited ones are the Dor Yeshorim (DY) program3,4 and the Cyprus thalassemia screening project. Although their means of operation are different, as are their outcomes, these programs share the same goals: * abolishing particular autosomal recessive diseases through a comprehensive testing program * targeting a given population in its entirety * situating in societies where abortions are regarded as highly undesirable Example 1: Dor Yeshorim If one is to fully appreciate PGT in the Orthodox Jewish community, some preliminary remarks are needed: * Some recessive genetic diseases such as Tay-Sachs are prevalent among Ashkenazi Jews (those originating from the Western and Eastern Europe diaspora), who make up more than 80 percent of world Jewry and are believed to be descended from about 1,500 Jewish families dating back to the 14th century. * In Jewish communities, secular as well as orthodox, reproduction represents a most significant social and religious obligation. As a result, the utilization of scientific technology in general, and genetics in particular, in the process of procreation is regarded favorably.5 Additionally, as abortions are seriously objectionable in Judaic ethics, a preference for prevention over termination of pregnancy is clear. * DY operates in ultra-orthodox communities, where arranged marriages are the norm. * Lastly, Jewish communities are generally tight-knit social groups, with numerous self-imposed, self-executed institutions (welfare, education, religious). All of these factors played out in the design and operation of DY’s premarital genetic screening program.6
The community established screening of teens.
Established by Rabbi Joseph Ekstein (who lost four children to Tay-Sachs disease), DY operates among ultra-orthodox communities and screens young adolescents for a panel of 10 recessive diseases that are lethal or severely debilitating (Tay-Sachs disease, cystic fibrosis, Gaucher disease type I, Canavan disease, familial dysautonomia, Bloom syndrome, Fanconi anemia, glycogen storage disease type 1a, mucolipidosis type IV, and Niemann-Pick disease type A). Most of these genetic screening takes place in high schools or religious academia (_Yeshivot_). For most members of Jewish populations outside the ultra-orthodox communities, Tay-Sachs disease screening occurs outside the Dor Yeshorim program and involves prenatal diagnosis of Tay-Sachs disease, followed by selective abortion when the fetus is found to have Tay-Sachs disease.
Testers are advised if they should or should not marry.
Generally, individuals consent to be tested, while parental consent is given in cases of underage minors. Each tested individual receives a coded identification (ID) number. When a proposed match is being considered, both individuals' IDs are checked in the DY database. The only result that the tested individuals receive is either “advisable” or “nonadvisable” for marriage. They do not receive their specific carrier status, neither at the time of the examination nor at the time of a match test. In this way, most carriers never find out what gene they carry and thereby avoid being seen as defective or a damaged good. If marriage is deemed inadvisable, genetic counseling (by phone only) is available to these individuals. Couples can still get married, but the overwhelming majority do not pursue the match and cancel their wedding plans. Fortunately, this carries a light emotional burden, as consulting the DY database transpires very early in the matchmaking. Stigmatization of individuals and their families is avoided by maintaining strict confidentiality in regard to carrier status. As mentioned, DY has been endorsed by religious community leaders and became a standard prerequisite in ultra-orthodox matchmaking. The results of DY are regarded as a huge success: Since its inception, over 220,000 individuals have been tested, over 500 incompatible couples identified, and virtually no afflicted children were born. Consequently, DY has aimed at increasing its activities, reaching out to other communities within Jewish society (including modern orthodox) and to non-Jewish communities. PGT is not restricted to Orthodox Jewish communities. Other important projects focusing on a single disease, thalassemia, were instituted in Cyprus, a Mediterranean island, and Iran. A short description of the Cypriot project follows, and the interested reader may find more information with respect to Iran elsewhere.7,8
Cypriots have a high genetic risk for a blood disorder.
Example 2: Cyprus thalassemia screening project The population of Cyprus has a very high ratio of carriers of thalassemia (1 in 7), a group of blood disorders resulting from underproduction of globin proteins. The treatment of afflicted individuals is based on blood transfusion and expensive medication or procedures (bone marrow transplantation). The overall health and pecuniary burden on the Cypriot community was extensive: It was estimated that without intervention, over a period of 40 years, 40 percent of the population would have to become blood donors to meet the expected 78,000 blood units needed annually, consuming resources equal to the entire health budget.9
Marriage licenses require genetic testing.
This fate was averted by a national program of PGT, set in motion in the 1970s with the support of the World Health Organization. Individuals who wish to marry must present documentation of thalassemia screening to obtain a marriage license. Laboratory services and know-how were introduced to meet the needs of this comprehensive project. Upon testing, individuals learn their personal carrier status, although typically at a later stage in the mating process than in DY. As a result, most couples (some 95 percent) do not revoke their marriage plans and resort to prenatal diagnosis (mainly amniocentesis) and abortion of embryos diagnosed with thalassemia. To complement this social transformation, the Orthodox Church of Cyprus has adopted a lenient approach regarding abortion of afflicted embryos, though not without criticism from abroad. Here again, the overall success of the program is impressive, with near zero births of afflicted newborns.10 ### Will these programs work in the United States and elsewhere?
Some societies have a moral dilemma with screening.
Prenatal screening is routinely offered in most countries today. This entails the need for selective abortions of embryos with lethal or severely debilitating diseases. Abortions are not risk- or cost-free, and in light of PGT-demonstrated successes, the question arises as to whether PGT can be instituted in other communities, especially in the United States and some Western countries. Indeed, the social, legal, and ethical challenges are not simple: * Most westerners do not engage in matchmaking, and creating a system for secure predating genetic scrutiny, as in the case of DY, would seem to be unacceptable and not feasible. Yet, some point to the growing acceptance of HIV testing as a prerequisite for serious dating in the United States as an example of a possible change of concept. * DY maintains strict confidentiality and limits access to test results even from the tested individual, which is very different from Western ethical paradigms. The former approach is intended to avoid unnecessary life-long knowledge if a recessive carrier doesn't end up marrying an individual with the same recessive gene.
Individual freedom is one concern.
* Importantly, social cohesion is far tighter in communities served by DY and in Cyprus, a key factor to the successful implementation of PGT. DY and the Cyprus programs are contingent on a powerful trust between the constituents and the governance of the project, a feature seemingly missing in the American context (notably, DY is not imposed by a governmental agency but rather by a social compact). Both programs exert a powerful social pressure, which some term “quasi-coercive.” As PGT programs became accepted practices, either by requiring a proof of testing in Cyprus or by the inability to participate in matchmaking in the ultra-orthodox Jewish community, the individual seems to have lost the freedom to choose whether to be tested or not. Such ostensible curtailments of individual freedom are a hard sell in the United States and some other Western countries. * Indeed, PGT may create a new concept of genetic identity. With PGT, individual responsibility with respect to genetic identity may manifest itself in different ways. In Cyprus, individual carriers also bear the burden of knowing their own genetic risk and are expected either to avoid marriage (which doesn’t usually happen) or to have an abortion if necessary. People tested by DY assume only the responsibility to make a genetically responsible decision with regard to their future spouse. They are not informed of their particular carrier status, as it lacks any relevance unless matched with another carrier. This creates what Prainsack and Siegal term “genetic couplehood.”6 This in turn is a stark presentation of a non-individualistic notion of one's genetic makeup--you are only part of a larger genetic identity. This could be a major leap for Western and American cultures, where accentuated individualism prevails.
These societies should address these concerns.
In summary, it would be safe to speculate that in the United States and some other Western nations widespread premarital genetic testing is not around the corner. However, one can envision a future genetic inquiry that is evidence-based and focused on population-specific diseases. The transformation to large-scale initiatives, or the creation of a public health initiative, could create substantial resistance. To this end, resolutions with respect to the public's genetic and health education, data management and protection, and genetic testing are all needed.

© 2007, American Institute of Biological Sciences. Educators have permission to reprint articles for classroom use; other users, please contact editor@actionbioscience.org for reprint permission. See reprint policy.

]]> http://staging.actionbioscience.org/genomic/siegal.html http://staging.actionbioscience.org/genomic/siegal.html 2-ethics in genomics Original genomics DNA Patents Fri, 01 Jun 2007 12:28:36 -0500 Why Do We Need an Amphibian Ark? About half of all amphibians are suffering declines. * nearly half of all amphibian species are declining * one-third to one-half are threatened with extinction * over 120 species have become extinct in recent years1 Amphibians seem to be faring worse than other taxa; for every threatened species of bird or mammal, there are two to three species of amphibian threatened with extinction.

Figure 1.

The Golden Toad, once abundant in Costa Rica, has not been seen since the late 1980s. Photo: U.S. Fishery and Wildlife Service.

### Why are amphibians important to our well-being? Amphibians profoundly enhance our lives and our world in countless ways:
Amphibians keep ecosystems healthy.
* They provide vital biomedicines, including analgesics and antibiotics.2 A compound capable of preventing HIV infection has been found in the skin of the Australian red-eyed tree frog (_Litoria chloris_) and several related species.3 * Amphibians are also indicators of environmental health. Trace amounts of the herbicide atrazine in the environment and in our drinking water are capable of chemically sterilizing developing tadpoles.4 Are amphibians modern-day canaries in the coal mine, warning us of worsening conditions that may one day threaten us? * Amphibians are also vital components of their ecosystems, and in some regions a single amphibian species can exceed the biomass of all the bird or mammal species combined.5 * Amphibians have also played an important role in human culture, from religion to fables and traditional medicines.6,7 ### Why are amphibian populations declining? Amphibian extinctions are caused by diverse factors, with habitat loss as one of the most significant threats impacting 90 percent of those species currently considered threatened. But a recently described fungus, _Batrachochytrium dendrobatidis_, has been receiving much scientific scrutiny in the past decade.
An infectious chytrid fungus is killing them.

Figure 2.

Southern Corroboree Frog populations, once numerous in Australia, have declined by 80% in the last decade. Photo: Taronga Zoo.

This parasite was previously thought to infect only vascular plants and invertebrates, but now it has been connected to dying amphibians on every amphibian-inhabited continent. For example, scientists have observed how amphibian populations in the mountains of Central America quickly suffered a 50 percent loss of species and an 80 percent loss of individuals after arrival of the fungus, and that the disease is spreading southeast through the isthmus at about 28 kilometers per year.8
The disease cannot be stopped in the wild.
### Can the killer fungus be stopped? It has been posited that amphibian chytrid is native to South Africa where it lives symbiotically with the African clawed frog.9 Since the 1930s, these frogs have been distributed around the world by the tens of thousands, initially for use in human pregnancy tests. Although it is easily treated in captivity, the disease cannot be stopped in the wild, and massive extinctions are predicted as it continues to spread around the world. Amphibian chytridiomycosis has been called "the worst infectious disease ever recorded among vertebrates in terms of the number of species impacted and its propensity to drive them to extinction."10
The world reacted in 2005 with a response plan.
Although the scientific community has been aware of and is monitoring the developing problem for several decades, intervention has not been a unified priority. In 2005, the global conservation community united and stated, "it is morally irresponsible to document amphibian declines and extinctions without also designing and promoting a response to this global crisis."4,10 An Amphibian Conservation Summit was convened with the world's amphibian authorities from academia, zoos, governments, veterinary medicine, and other diverse disciplines. A declaration was produced calling for an Amphibian Conservation Action Plan (ACAP) to address the extinction crisis and establish the Amphibian Specialist Group (ASG) to carry out that plan.11 The ACAP calls for four lines of action: * **Research**--expand understanding of causes of declines * **Assessment**--document amphibian diversity and its changes * **Conservation**--develop long-term conservation programs * **Rapid response**--intervene against imminent extinctions
It will cost about $400 million.
The overall budget for these initiatives in the first five years is estimated at $400 million. Although this seems like an impossibly large sum, it is less than the cost of two 747 airplanes and just 0.1 percent of the US war budget in the Middle East. It is only about a quarter of what US federal and state agencies currently spend on endangered and threatened species in a year ($1.4 billion), and it's just three times what these agencies spent on their top recipient, the Chinook salmon ($161,309,500), a single sport and commercial fish species that is being deliberately introduced in parts of North America.
Amphibian survival depends on captive management.
While the ACAP's greatest conservation priority is _in situ_ action, that is, in the wild (as opposed to _ex situ_, in a controlled situation such as a lab), some threats like chytrid fungus cannot be addressed in the wild. Without immediate captive management as a stopgap component of an integrated conservation effort, hundreds of species will become extinct. The World Conservation Union, IUCN, has urged that "all critically endangered and extinct in the wild taxa should be subject to _ex situ_ management to ensure recovery of wild populations," and the ACAP white papers echo that assertion: "Survival assurance colonies are mandatory for amphibian species that will not persist in the wild long enough to recover naturally once environments are restored; these species need to be saved now through _ex situ_ measures so that more complete restoration of ecosystems is possible in the future."10 Comparable calls to action are included in the Global Amphibian Assessment and other documents. ### What can the Amphibian Ark do? Fortunately, a thriving industry already exists that specializes in captive management of animals. Zoos and related facilities number over 1200 institutions with more than 100,000 employees and attract about 600 million visitors per year. Zoos have the capability to assist with the following:
Zoos already have the means to help amphibians.
* rapid response rescues * captive assurance colonies * providing animals for release and research * conservation education * capacity building * fundraising * helping to develop recovery plans The World Association of Zoos and Aquariums (WAZA) has joined with the Conservation Breeding Specialist Group (CBSG) and ASG to form the Amphibian Ark, or AArk for short. The AArk vision is the world's amphibians safe in nature. Its mission is to work with partners to ensure the global survival of amphibians, focusing on those that cannot be safeguarded in nature. AArk is rapidly developing capacity to coordinate _ex situ_ programs implemented by partners around the world, with the first emphasis on programs within the range countries of the species. At the same time, it maintains constant attention on its obligation to couple _ex situ_ conservation measures with necessary efforts to protect or restore species in their natural habitats. Its activities include these:
AArk will work with zoos and others on conservation.
* provide strategic guidance on activities to all stakeholders, such as zoos, wildlife agencies, universities * consult on species-specific issues, for example, reintroduction, gene banking, and veterinary, legal, and ethical concerns * coordinate all aspects of implementation within the AArk initiative * assist AArk partners in identifying priority taxa and regions for _ex situ_ conservation work * lead development and implementation of training programs for building capacity of individuals and institutions * develop communications strategies, messages, and materials to promote understanding and action on behalf of amphibian conservation The AArk's Conservation Plan is one part of the comprehensive ACAP; the _ex situ_ component may help stave off many extinctions, but safeguarding these species _in situ_ will be the ultimate measure of success. In 2008, AArk will lead zoos in a globally coordinated public awareness campaign, "The Year of the Frog." The publicity campaign will help leverage a simultaneous worldwide capital campaign managed at the level of the individual institutions. ### What are the challenges?
Zoos can manage only 10 percent of species that need help.
The _ex situ_ conservation community faces many challenges to meet expectations, first and foremost of which is rapidly increasing capacity. It is estimated that the global zoo community can currently manage viable populations of around 50 amphibian species, which amounts to perhaps 10 percent of those requiring _ex situ_ intervention. One solution is to have zoos construct additional biosecure facilities where needed, ensuring that keepers are trained and resources are appropriately allocated to support this action. Of course, some zoos are already making valuable contributions to amphibian conservation. Some are constructing dedicated facilities on grounds, and some are helping to develop facilities in other regions of the world. Zoos are leading dozens of amphibian conservation programs, including habitat restoration, translocations, conservation education and research,12 and region-wide amphibian community rescues.13 There are now several zoo-led courses designed to develop husbandry expertise, including AZA's amphibian biology and management course, which has spawned similar courses in Mexico, Ecuador, and Colombia. Amphibians are vitally important as * integral components of ecosystems5 * indicators of environmental health4,14 * contributors to human health2,3
Amphibians are today's greatest conservation challenge.
Amphibians persisted as the dinosaurs came and went, but today as many as half of all species are threatened with extinction. We are only just beginning to understand the impacts of their disappearance.15,16 Addressing the amphibian extinction crisis represents the greatest species conservation challenge in the history of humanity. The global conservation community has formulated a response, and an integral part of that response is the Amphibian Ark, in which select species that would otherwise go extinct will be maintained in captivity until they can be secured in the wild. Without immediate captive management as a stopgap component of an integrated conservation effort, hundreds of species may become extinct.

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]]> http://staging.actionbioscience.org/biodiversity/zippel.html http://staging.actionbioscience.org/biodiversity/zippel.html Original biodiversity endangered species global threats Amphibians Tue, 01 May 2007 12:27:13 -0500 Rewilding Megafauna: Lions and Camels in North America? Rewilding is about restoring biodiversity. **Barlow:** Rewilding is a concept that works with restoration ecology and evolution combined. One type of rewilding deals with restoring lost biodiversity. Restoration ecology is when you look at a landscape and ask how we can bring it back to conditions that are more natural, say, before Europeans arrived in North America. Another type of rewilding has to do with climate change, for example, creating a park corridor from Yellowstone to the Yukon to give movement to animals as climate changes.
Rewilding also attempts to replace species that have gone extinct in North America.
In 2005, a top science journal published an article by a dozen prominent conservation biologists proposing a shift in the benchmark that is commonly used for restoring lost wildlife to former habitats.1 Most parklands and wilderness areas in North America will continue to be restored to conditions that prevailed just prior to the arrival of Columbus in 1492 [the "pre-Columbian" benchmark]. But what about rewilding a small portion of America's natural heritage to conditions just prior to the first human incursion on the landscape some 13,000 years ago? This idea of rewilding from a deep time perspective is going back to a time before the first humans began to migrate to the Americas in the late Pleistocene [about 10,000 years ago] and asking how we can restore the ecological landscape. Current trends in rewilding North America have to do with restoration of species displaced or endangered since the first European settlers arrived, for example, bringing back gray wolves to Yellowstone, reintroducing the lynx to Colorado, and bringing the peregrine falcon to the Midwest. That is standard practice restoration ecology. What I would like to address is the controversial subject of rewilding North America as proposed a few years ago by looking at a deep time perspective and saying lets not just stop with the wolves. What species were here before humans invaded the landscape, and is it still possible to bring them back? ### Why restore animals from the Pleistocene era and not those that have disappeared since Columbus? **Barlow:** This is a conservation question as well as an ethical one. Why should we do it? For several reasons:
We lost major megafauna about 13,000 years ago.
An ecological history park would have many benefits.
* It was at the end of the Pleistocene that many large vertebrate [backboned] animals disappeared. The majority view in mainstream science now is that humans were the main cause of the extinction of these large animals, called _megafauna_. These large animals did not coevolve with humans in the way that large African and Asian animals did. So if humans were the cause for the loss of these animals, such as the mammoths, mastodons, and the big carnivores that depended on them, then it behooves us to do our best to restore them. * I think it's possible to manage rewilding efforts. A Pleistocene park, or an ecological history park, has been suggested, that is, some representative landscapes where we bring back these large creatures. * The plants and the landscapes that we have here in North America lost their coevolved animal partners just 13,000 years ago. Plants take longer to adjust to environmental changes. By bringing back some of the big animals of the Pleistocene--the big browsers and the big carnivores--to control and evolve with plants, we would see what the American landscape really looks like. * It is good for the economy. Tourists would visit the park and other rewilded areas, promoting the local economies, mostly in rural areas. * Josh Donlan, one of the authors of the paper I mentioned, states that evidence shows when large animals disappear from ecosystems, the ecosystem biodiversity collapses and society is the lesser for this loss. The disappearance of megafauna had a domino affect on ecosystems. ### Which large animals are suggested for rewilding? **Barlow:** If one adopts an end-Pleistocene benchmark, then it is time to bring back the American cheetah, the American camel, the American plains lion, the American mastodons and mammoths, and other species by using proxies from the Old World to restart their evolution in the New, and to restore their vital roles as shapers of ecological landscapes. Let's take the camel as an example. Camels originated here in North America, not in the Old World, around 50 million years ago. They spent most of their time here, but then around 3 million years ago they crossed from Alaska to Siberia and moved down into Asia and into the African continent.
The camel is a good candidate for rewilding.

A Bactrian Camel in the Kyzyl Kum desert in Uzbekistan, Central Asia. Photo by Dmitriy Pitrimov.

If we were to bring back camels, the Bactrian camel for example, as well as elephants, these animals would probably do very well in controlling what is called shrub invasion of the arid West. Cattle and horses cannot eat mesquite, juniper, creocote, but the big browsers can. Camels are especially good at eating toxic shrubs. If you're worried about your lawn, they cannot eat grass.
The elephant is another.
By introducing the Indian [Asian] elephant we have a replacement for the extinct mammoths. Indian elephants enjoy knocking over trees to browse, but when they leave an area, the grasses that grow after their departure will attract the grazers. You establish a dance between the grazers and the browsers. So the thought is that if we were to bring back some of the large browsers in particular, we would be able then to see the true ecological landscapes of North America. ### Why choose megafauna over other animals; many animals have gone extinct.
Humans hunted the megafauna to extinction.
**Barlow:** Whenever humans have set foot in a landscape, since the time when they could kill at a distance with stones and spears, they killed off megafauna. Humans hunted the megafauna to extinction. Spears were particularly lethal because you don't even have to kill the animal. All you have to do is puncture its gut and wait till it dies of infection. The littler creatures could hide from humans; they also had the advantages of small populations and higher reproduction rates. Take the extinct moa of New Zealand. Its extinction is completely correlated to the arrival of the first Maoris. It's the same with the elephant birds and the giant turtles of Madagascar. ### Aren't the animals that you are suggesting for rewilding genetically different from those extant species? **Barlow:** Absolutely. The plan calls for rewilding proxies of native species in many cases. One of the closest genetic ties between today's large animal and one that disappeared from North America would be the horse. Horses have already been rewilded. They originated in North America 50 million years ago and disappeared. Some horses went across into Alaska and Siberia, and down into Africa, and guess what they became? Zebras!
Proxy species would be used.

Przewalski's horses numbered around 1500 in the wild in 2005. Creative Commons photo.

The Spaniards, as most schoolchildren know, brought back horses. Some escaped confinement and went wild. Plains Indians co-evolved a culture of hunting buffalo and riding horses. Our modern horses are the same genus as those of the Pleistocene, _Equus caballus_. The rewilding proposal suggests reintroducing modern horses as well as wild horses, such as Przewalski's horse.
Asian elephants are relatives of mammoths.
Let me give you an example of an elephant because an elephant is considered the most outrageous to some. Elephants evolved in the Old World, and then periodically some migrated from Africa into the western hemisphere millions of years ago. There were gomphotheres, mastodons, and several waves of mammoths that came in, most recently woolly mammoths. The mammoths that we had in North America, including in Florida, are more closely related to the Indian [Asian] elephant than the Indian elephant is related to the African elephant. ### Why not work with the species you have in North America, such as the native puma, before they go extinct, instead of reintroducing the cheetah from Africa?
The cheetah originated in North America and migrated to Africa.
**Barlow:** We can do both. Sure, the pumas are close relatives to African cheetahs. Mountain lions, cougars, pumas, and cheetahs evolved from related lineages. All of them, except the cheetah, still roam various parts of the Americas. But did you know cheetahs originated here in North America? They are now found only in Africa. While they were here they coevolved with the fastest land herbivore on the planet--the American pronghorn. The American pronghorn runs 60 miles an hour, faster than any of the gazelles in Africa. Our wolves run 40 miles an hour. Evolution does not build in excess. The pronghorn that is running 60 miles an hour in Wyoming is still running from the American cheetah that went extinct here. So we are suggesting bringing back the cheetah because it not only belongs here but it is nature's natural predator of the pronghorn. ### How would these new megafauna survive, and would they destroy the native habitats that have evolved to be what they are now?
Today's ecosystem is almost the same as 13,000 years ago.
**Barlow:** The ecosystems haven't evolved much in 13,000 years. You have different mixes of populations in different areas, but we have no new plant species other than exotic introductions and we didn't lose most plant species. Thirteen thousand years to plants is nothing. It is just a question of how would things be reconfigured with the native species that we have. The point is that we are not suggesting repopulating all of North America. The natural history ecological park would be somewhere out in the great plains, say Nebraska or Kansas or perhaps in northern New Mexico, where we have some good grassland habitat and semiarid areas. It would be a scientific experiment to see if it works and how far we could go with the idea. ### Some of the predators and other species considered for the park are migratory or need large areas to forage and to hunt. How could a park provide them with what they need and contain them as well?
The parks would be big Texas-style ranches.
**Barlow:** We're not talking about a Hollywood-style Jurassic Park. Humans were not around at the time of the dinosaurs. The larger, more dangerous animals we propose to bring back would be contained in a big Texas-style ranch. Elephants would be the most difficult in that regard, but good grassland in eastern Texas is an ideal grazing area. These animals are all slow-reproducing megafauna, and they were once natives. It's not like we are introducing an exotic, such as the troublesome Brazilian peppertree or the Cuban anole, that's almost impossible to eradicate. If something goes wrong with the park and the new animals are destroying the landscape, we will be able to find them alternate arrangements.
In some areas the predators would be very useful.
Here's an example of the imbalance that happens if you don't manage rewilding well. Wild horses, introduced by the Spaniards after they disappeared from North America, are destroying a portion of the American west because people don't want to have them shot and killed. These wild horses are breeding like fruit flies because this was always their native landscape. They have no natural predators here. All you need is to bring in the African lion. What is the primary food of the African lion in Africa? The zebra! Wolves can't take down horses well, and neither can mountain lions. When you bring in the African lions to control the wild horses, you've actually created a balance of predator and prey. ### Many American farmers and ranchers protested the recent reintroduction of wolves. What would you say to them about the introduction of large predators such as lions and cheetahs?
Rewilding would be done on private land.
**Barlow:** First of all, this would not happen on public lands. They would be rewilded on private lands. Right now, the bolson tortoise is being reintroduced on Ted Turner's private ranch in New Mexico. We are hoping to get to the point where a large private rancher, perhaps in Texas, will work with us on other efforts. There are already all kinds of African game in Texas ranches. There are more lions on Texas ranches than there are in all the zoos in the United States. ### Do you view this park as a tourist attraction or solely a natural history experiment?
Rewilding would help improve our ecosystems.
**Barlow:** The main idea is conservation and evolution. The proponents for this idea are thinking over the long term. Let's say humans don't go extinct in the next few million years, what sort of evolution is going to happen in North America if we bring back the species that were here before humans, or at least bring back founder populations that were here and give them a chance to evolve? Unless we do that we are going to just keep the same impoverished megafauna that we had when the Europeans arrived. We used to have as much megafauna here as we now see in Africa, for example, four species of camel, three species of horses, and five species of elephants. People were not native to North America. Even the ancient Clovis people from Siberia, the mammoth hunters, were native to the Asian landscape and not to this land, just as the ancestors of the Maori people who came to New Zealand were not native to New Zealand. These cultures crashed because the large creatures crashed. Out of the ashes came the indigenous peoples and the Native Americans. They were not the cause of the destruction of the Pleistocene megafauna. The frontier ancestors were the ones that did this.
It would also be a boon to ecotourism.
A secondary advantage is the potential economic boon to areas where these megafauna would be rewilded. An ecological history park, say in Kansas, would bring in huge ecotourism benefits. Incidentally, there is already a ranch in Kansas that has camels. The camels are thriving just fine, even in winter. I personally foresee elephants and people working together. In the Old World, humans follow herds of elephants. You would let the elephants explore the landscape, even asking ranchers to open their gates and let the heard pass through. It could become a tourist activity where people follow elephants to see how they move to different landscapes seasonally to forage for food. Could be great for the economy, just like the buffalo commons.

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]]> http://staging.actionbioscience.org/newfrontiers/barlow.html http://staging.actionbioscience.org/newfrontiers/barlow.html Original Interview evolution and the future management and conservation new frontiers Pleistocene rewilding Thu, 01 Mar 2007 12:28:48 -0500 Evidence and the Cambrian Explosion Explanations depend on observation and evidence. * There are facts that command explanation. A simple example is Why does the sun rise daily? * It allows us to test hypotheses, or ideas that explain the facts. An example of a hypothesis is that the sun seems to rise every day because of Earth's rotation. Observation and hypothesis are both important. Accidental discovery is crucial. People finding fossils has gone on for hundreds of years. But using fossil evidence to test a hypothesis is what ensures that science will present accurate statements, research, and theories. ### Some people do not understand the difference between "theory" as used in science and "theory" as used in general conversation. So, would you clarify the concept?
"Theory" may have different meanings.
**Levinton:** In general conversation, people might say "I have a theory" when they mean they have an idea or are making an assumption. In science, a theory is not based on speculation. There are many steps to take before a theory is established.
"Theory" in science is not a hunch; it is based on fact.
* A hypothesis is a testable statement explaining observations about phenomena occurring in the natural world. * A theory is a hypothesis or group of related hypotheses that have been repeatedly tested and which scientists generally agree conform to all known data/observations or a major set of observations about the world. ### The Cambrian explosion is an important event in Earth's history. What have we learned about it so far?
The Cambrian explosion produced a rich variety of species.
**Levinton:** The Cambrian explosion is a brief time in the Early Cambrian when most major groups of animals that have bilateral symmetry first appear in the fossil record. A bilateral animal is one whose body plan is such that it has two mirror-image halves. Modern examples are lobsters, people, dogs, and butterflies. The event is referred to as an "explosion" because a rich diversity of species appeared in a relatively short amount of time.
There is growing evidence for a common ancestor.
The hypothesis is that all these animal groups arose from a common ancestor and diverged at or near the beginning of the Cambrian period, which spans 543 million to 490 million years ago. Evidence is growing to support this hypothesis, at least from evidence derived from fossil occurrences. After that period, very few additional animal phyla, or large animal categories, arose.

A trilobite (Parkaspis decamera) from the Cambrian Period found in the Burgess Shale, Canada.
Image © Oklahoma University, Photographer Albert Copley; Source: Earth Science World Image Bank

### How do we know all of this happened? **Levinton:** We know it from evidence. There are two things we need to know:
Fossils and dating methods provide the evidence.
* You have to have a series of rocks from natural sites that are dated scientifically. Rocks are dated by their relative location and other methods but also by radiometric dating. Radiometric dating involves the use of radioactive isotope series that have half-lives up to many billions of years, such as uranium/lead. * The occurrence of the fossils. What we know now is that many of the animal groups go back in time but not past the Cambrian period.
Most Cambrian organisms are not found in rocks of other periods.
Fossils are not always preserved perfectly. Sometimes you will come across a lack of good preservation factors for 200 million years, say, for an appropriate fossil to occur. Evidence shows that the rocks before the explosion were suitable for fossils to be formed but most of the Cambrian animals do not appear in these rocks. Other groups are found before the Cambrian, but not the bilaterian groups participating in the Cambrian explosion, except for a few still controversial specimens.
Scientist must take care to calibrate data to ensure accuracy.
So the date of the rock in which a fossil is found is the date of the fossil. However, it's possible that a rock can be transported by natural events, for example, eroded out of a rock, transported downstream by a strong current, and deposited somewhere else. Scientists have to be careful about that possibility. Even the famous Burgess Shale in the Rocky Mountains of Canada, where Cambrian fossils were found, may consist of some animal fossils that were transported a few thousand yards. Scientists have to calibrate the data to make sure they are dated correctly.
Molecular clocks are used to determine how long ago two species diverged.
### Can molecular clocks determine the lineage of a fossil from such distant times as the Cambrian? **Levinton:** You can never date rocks with molecular clocks, but you can ask certain questions. If you have two organisms and the DNA sequence of a certain type of molecule that evolved slowly enough so that you can see the difference in DNA sequence in the two organisms, you can go back in time to see when they diverged on the tree of life. However, you must have a way to calibrate the difference in DNA sequence against an absolute time scale.
They are not accurate enough for analysis of very distant periods.
Molecular clocks are not that accurate going back to such distant periods as the Cambrian, for several reasons: * There are different ways you can make an analysis, but the calibration points are not that abundant. Let's say you have a 400-million-year-old fossil and another one that arose 430 million years ago. But which age do you use in your evolutionary calculations? It could be a source of error. * There is also a lot of variation in rates of evolution and that has to be compensated for. There are statistical challenges here. When looking at shorter spans of time, say 5 to 10 million years before the present, scientists are a lot more confident. There's a lot more to be learned about molecular clocks to use them accurately for older times such as the Cambrian explosion. ### Did the Cambrian explosion happen because it followed an extinction event?
Some environmental factors may explain why the explosion happened.
**Levinton:** Maybe. There are groups of organisms that seem to have some major overturns just before the Cambrian. There are also some physical changes on Earth that are well known, but no one can pinpoint the time. There's an idea, bolstered by data, that the whole of the Earth was covered by ice, which suggests that the oceans were anoxic, that is, life in the oceans was nonexistent. That would have been an extinction event, which, as history shows, is often followed by a burst of new species. But it would be difficult to connect this possible extinction event to the Cambrian explosion. There are other changes that occurred just before the Cambrian, but these include everything from a lowering of ocean temperature to an increase in oxygen in the atmosphere. There are too many variables that are too poorly timed to help us very much at this time. ### Why is the Cambrian explosion so pivotal as an example of macroevolution?
The Cambrian explosion is evolution at its most creative.
**Levinton:** Macroevolution is about natural processes on a grand scale of geological time, such as origins and extinctions. The Cambrian explosion is the mother of all animal radiations. All the major body plans--for example, arthropods, brachiopods, and so on--they all arose in a short window of time, if the current fossil record is to be taken at face value. Scientists are still searching for evidence to add to the wealth of knowledge about this period so we can all agree that this hypothesis is absolutely accurate. If it proves to be absolutely true, it means that most of life's diversity pretty much started then. It's _the_ moment of animal evolution's creativity.

© 2007, American Institute of Biological Sciences. Educators have permission to reprint articles for classroom use; other users, please contact editor@actionbioscience.org for reprint permission. See reprint policy.

]]> http://staging.actionbioscience.org/evolution/levinton.html http://staging.actionbioscience.org/evolution/levinton.html Original Interview evolution the fossil record Cambrian Explosion Mon, 01 Jan 2007 12:28:28 -0500 Animals: Tracing Their Heritage All animals have a common ancestor. **King:** Yes. All animals, from sponges to jellyfish to vertebrates [animals with a backbone], can be traced to a common ancestor. So far, molecular and fossil evidence indicate that animals evolved at least 600 million years ago. The fossil record does not reveal what the first animals looked like or how they lived. Therefore, my lab and other research groups around the world are investigating the nature of the first animals by studying diverse living organisms.
Most organisms on Earth have only one cell.
### You study multicellularity. Is there a connection to animal origins? **King:** Eukaryotes [organisms with membrane-bound nuclei] range from those with a single cell, such as the amoeba, to complex multicellular animals, including humans. The vast majority of life on Earth has been dominated by unicellular life. At some point in the lineage leading to animals, multicellularity evolved. Multicellular organisms are those that have many cells. Their cells depend on each other, functioning in concert to sustain the life of the organism. So, the common ancestor of animals was a single cell.
A single-celled organism gave rise to multicellular organisms.
It was that event--the origin of multicellularity-- that was seminal to the evolutionary history of animals. We have yet to discover what this unicellular ancestor of multicellular animals was, but we have gathered clues about its genetic complexity. We don't have a fossil record regarding the rise of multicellularity, but we can deduce the shared characteristics, using molecular and other data, among animals that are extinct and their living relatives.
A phylogenetic tree details the relationships among organisms.
Databases help us construct phylogenetic trees.
### How does a phylogenetic tree allow you to make these connections? **King:** A phylogenetic tree, or tree of life, is a diagram of the relationships among organisms. It is a hypothesis, always evolving as more data is added to it. Phylogeneticists take sequences of genes or other regions of genomes from diverse organisms and align them with each other to identify positions in the sequences that suggest shared ancestry. Those that have changed in concert with each other may suggest a common ancestor within that group to the exclusion of other groups. This process used to be done by hand, but now computers have vastly accelerated the process. We now have publicly accessible databases of phylogenetic information that allow us to view and analyze gene sequences of diverse organisms. ### Why have you chosen to work with choanoflagellates?
Choanoflagellates may hold clues to animal evolution.
**King:** Choanoflagellates are a window on early animal evolution. Both cell biological and molecular evidence indicate that choanoflagellates are the closest living relatives of multicellular animals.

Figure 1.

A choanoflagellate typically has a collar of tentacles and a single flagellum.
Image courtesy of the King Lab, University of California-Berkeley.

Choanoflagellates are a unique group of single-celled and colony-forming eukaryotes. There are at least 150 species of choanoflagellates, living in almost all aquatic habitats. Choanoflagellates use flagella to swim and trap food, mostly bacteria, in the walls of their collar (see image).
They may shed light on the transition to multicellularity.
The relationship of choanoflagellates to animals and the fact that they are unicellular suggest that they might help us understand the prehistory of multicellular animals. Their biology is similar to the hypothesized state of the unicellular ancestor of animals, so we think they have preserved this ancestral data better than other organisms. Genes shared by choanoflagellates and animals were likely present in their common ancestor and may shed light on the transition to multicellularity. Our lab has already provided evidence for the expression in choanoflagellates of protein families required for animal cell signaling [how cells communicate] and adhesion [how cells stick]. ### Did multicellularity evolve once or many times?
Each multicellular lineage arose independently.
**King:** Scientists have observed that the cell biology of multicellularity is radically different in different groups of organisms. So it suggests that different multicellular organisms arose from unicellular organisms numerous times. Animals, fungi, plants, and other multicellular lineages evolved multicellularity separately, and each lineage has a different common ancestor. This means that the mechanism by which multicellularity developed in each lineage is evolutionarily different and unique. When we focus on animals, however, we see that multicellularity evolved in this lineage only once.
Choanoflagellate genomes are evolutionarily unique.
Genomics research also benefits humans, in this case, cancer research.
### Will you attempt to reconstruct the genome of the ancestor of choanoflagellates? **King:** I don't know if it will be technically feasible to do so entirely, but it's something I like to think about. It's a wonderful challenge for a scientist. Reconstructing the genome of the ancestor of animals and choanoflagellates would allow us to test whether we understand important components of the process by which animals evolved. One major challenge right now is to assemble choanoflagellate genomes. It is very interesting to work with an organism that is so distant from other organisms whose genomes have already been sequenced. There are no markers about where to go and how to proceed. Our research into genome comparisons promises new insights into the last common ancestor of choanoflagellates and metazoans as well as the early evolutionary history of animals. Our research is in fact a study in macroevolution--trying to understand how major changes happened over large spans of time. Beyond that, there may be some direct benefit to humankind. There is some interest in our work by people involved in cancer research. Many of the proteins that we are finding in choanoflagellates are ones that contribute to cancer development in humans. Our work may shed light on the cellular functions of some of these proteins.

© 2007, American Institute of Biological Sciences. Educators have permission to reprint articles for classroom use; other users, please contact editor@actionbioscience.org for reprint permission. See reprint policy.

]]> http://staging.actionbioscience.org/evolution/king.html http://staging.actionbioscience.org/evolution/king.html Original Interview evolution evolution and the history of life Animal Evolution Mon, 01 Jan 2007 12:28:26 -0500 The Foja Mountains of Indonesia: Exploring the Lost World The author and his team ventured into new territory.

Figure 1.

The Foja Mountains on the island of New Guinea are host to a dazzling variety of new and rare animal species.
© 2006 Conservation International.

Spending a month in the Fojas, the 20-person team inventoried plants, frogs, reptiles, butterflies, mammals, and birds, documenting more than 40 new species in this little-studied corner of the tropical world. These amazing discoveries were the culmination of years of effort and planning. The senior project co-leader began planning this expedition in 1982--the 23-year project timeline should adequately convey a sense of the political challenges to obtaining permission for the field research as well as the nature of this area's near-absolute inaccessibility. The team members all agreed the stunning results proved the project was worth the long wait, and that all the hard work that went into making it happen was well and truly worthwhile. ### The search for a lost world
The story begins with a woman's feathered hat.
The Fojas' story begins back in the mid-1890s, when a shipment of stuffed birds, intended to adorn women's hats, arrived in Europe from New Guinea. Some of the more peculiar specimens in this shipment were removed by the Dutch trader who received them and forwarded to prominent European naturalists. An unusual bowerbird was sent to Lord Walter Rothschild in England, and a black-and-white bird of paradise was forwarded to a German natural history collection. Shortly thereafter, these were described as new species by Rothschild and renowned ornithologist Otto Kleinschmidt, respectively. They noted the following:
The feathers were from unknown birds.
* The bowerbird was distinct in sporting a large erectile crest of golden plumes that stretched from forehead to nape. * The bird of paradise exhibited a curious mix of characters found in two already-described species of six-wired birds of paradise. * Most importantly, neither specimen came from an identified locality, but it was assumed that both originated from somewhere in the mountains of western New Guinea, then a Dutch colony.
Many attempts to find their origins failed.
In the decades to follow, a number of ornithologists were to make expeditions to western New Guinea trying to discover the homeland of these two unique species. Certainly, the researchers wanted to know more about these two "lost" forms, but undoubtedly a greater motivating force was the thought that whoever found the homeland of these mysterious birds might find additional species new to science--the prime goal of most expeditions. Those who ventured to New Guinea in search of this mountain habitat scoured a number of isolated mountain ranges and adjacent mountainous islands, but to no avail.1 The mystery of the golden-fronted bowerbird was finally solved in 1979 by biologist Jared Diamond, who helicoptered with a small team into the uplands of the Foja Mountains of northern Papua (then called Irian Jaya). He observed that this species
The bowerbird was traced to the Foja Mountains in 1979.
* creates distinctive terrestrial display bowers made of moss and sticks and decorated with blue and yellow fruit * builds dozens of these bowers on mid-elevation ridge tops in the Fojas Diamond's wonderful discovery was met with considerable coverage in the Western press, and his paper reporting the rediscovery of the bowerbird was featured as a cover article in _Science_.2 Diamond also collected evidence hinting that the missing bird of paradise might inhabit the Foja Mountains, but the solution to this mystery had to await our visit to the Fojas in 2005.
It took over 20 years to prepare for the 2005 trip.
### The 2005 expedition I began making plans to conduct a comprehensive biological survey of the Foja Mountains shortly after Diamond's discovery. With this in mind, I visited Indonesia several times, made three overflights of the mountain range, and held discussions with a range of governmental and nongovernmental stakeholders. Thus began more than two decades of on-again, off-again efforts to pull all the pieces together to conduct such a complex, expensive, and difficult mission.
The logistics of organizing the expedition were complex.
In 2003 I met with project co-leader Stephen Richards of the South Australian Museum to reformulate our plans in light of evidence of improvement in the political climate in Indonesia. Our redoubled efforts produced results in 2005, when our multi-institutional team received preliminary approval for our plan from Indonesia. We then pushed into high gear, pressing for government permits, making an extra effort to raise additional funds, and clearing personal travel schedules to make way for this once-in-a-lifetime opportunity. In October, local village landowners granted us their approval for the field trip. The international team arrived in Jakarta in November, and the final national and provincial authorizations were finalized shortly thereafter. One final hurdle remained. The team would not be able to get into the misty montane uplands of the Fojas without a helicopter, and helicopters were rare and expensive in Papua in November 2005. Through some indirect negotiations with several institutional partners, the evangelical service organization Helimission agreed to a charter of one of its helicopters, providing its incomparable bush pilots for the challenging mountain-top drop-off and retrieval. At that point we were set to go.
The expedition team divided into hill and mountain groups.
The team and its copious supplies and equipment were ferried by a single-engine Cessna aircraft into the Kwerba airstrip at the foot of the mountain range in mid-November. We divided this large party into a hill forest survey group and a montane survey group: * The hill group established camps on foot in the hill forest northeast of Kwerba. * On 22 November, the mountain team got its helicopter ride up to a boggy clearing in the montane forest at 1,650 meters above sea level, in the heart of the Foja's interior.
The montane team was dropped in an area devoid of human impact.
Being at 1,650 meters in the Foja Mountains was a dream come true for the research team of six: botanist Wayne Takeuchi, lepidopterist Henk van Mastrigt, herpetologists Steve Richards and Burhan Tjaturadi, mammalogist Kris Helgen, and ornithologist Bruce Beehler. A 30-minute helicopter ride transported us into a montane forest tract of humid tropical forest that showed no evidence of human impact: no road, no trail, no trash, no village, no TV, no radio. Only rarely did a passenger jet overhead disturb our isolated wilderness environment. Our six local guides, from the villages of Kwerba and Papasena, were just as amazed as we were. They assured us that they had never visited this interior region of the Foja Range. And the wildlife in many instances was remarkably unwary (unusual in a place like New Guinea, where subsistence hunting is chronic and all pervasive). Birds flitted around our campsite and sang lustily from nearby trees. A giant rat visited nightly to collect scraps. Most remarkably, the long-lost bird of paradise carried out an elaborate display on the ground within view of our rough dining table on a drizzly afternoon. Our team of 12 worked night and day for 15 days, to learn as much as we could about the natural history of this remarkably pristine and isolated mountain range.3 Whereas the hill forest team found that the forest in their area supported mainly common and widespread species (their five apparently new species of palms were an exception to this rule), our montane team found a world of biological novelties:
They discovered over 40 new species.

Figure 2.

Berlepsch's six-wired bird of paradise (Parotia berlepschi) is named for the curious wires that extend from its head in place of a crest.
© 2006 Conservation International, Bruce Beehler.

* up to 20 new species of frogs * 5 to 10 new species of plants * 5 new butterflies * several possible new mammal species, including a large mammal (golden-mantled tree kangaroo) new to the Indonesian national list * a new bird species: the wattled smoky honeyeater * the "lost" Berlepsch's bird of paradise (see Figure 2) Moreover, we believe that there are dozens of additional new species from these focal taxonomic groups that will be found with additional effort. ### A call for conservation Finding new species in the tropical rainforest is no rare event. What, then, is so remarkable about this expedition and its findings? Why should we ensure this lost world's biodiversity remains intact?
Many species are yet to be discovered.
* When coupled with the remarkable recent discovery of more than 50 new marine species in the waters just west of the Foja Mountains,4 the scale of the biodiversity discoveries coming from Indonesian New Guinea is remarkable. Conservation International, which sponsored and led both the marine and terrestrial field research, is proposing additional field studies, and these are clearly justified. Today, Papua might well be considered a "lost world" for novel biodiversity, and the situation is such that a province-wide biological survey (both marine and terrestrial) is warranted. Perhaps as little as 50 percent of New Guinea's frog species have been described.5
Indonesia can profit from ecotourism in the area.
* This offers an opportunity for institutional collaboration and training of new field students, benefiting Indonesia and tropical field science. A large-scale multi-year program of field surveys, matching Indonesian and international scientists with local research students, would set the stage for a renaissance of field study in this important but little-studied part of the tropical world. This, in turn, could lead to greatly expanded ecotourism in the Province, providing local economic benefits.
Issues like logging and poaching need attention.
* The expanded field research and ecotourism could drive a conservation-planning process that could help Papua design and manage a network of forest and marine parks that could become the envy of the tropical world. This would go a long way toward addressing the growing threats of poaching, over-hunting, and unconstrained industrial logging and plantation development. There is room for both development and nature conservation in Papua, if guided by thoughtful planning and management of these resources. It is not too late to make these steps. The good news is that the Foja Mountains are already part of Indonesia's system of national wildlife sanctuaries. It should be noted, however, that the Fojas are also the traditional lands of several forest-dwelling peoples who inhabit the range's surrounding foothills. The forests constitute these communities' patrimony--their main source of wealth. From the upland forests of the Fojas the local people obtain
The local people depend on the area and its wildlife.
* their pure drinking water * their wild game in the form of pigs, cassowaries, wallabies, and tree kangaroos * fish from the rivers * fiber and building materials from the forests * stories, legends, and myths as a product of their long interaction with the hills, woodlands, plants, and animals
Future conservation plans should include local stakeholders.
It is safe to say that these local forest peoples are the true stewards of the pristine forests of the Foja Mountains. Any sustainable conservation plan for this remarkable region must place these local stakeholders at the center of any future agreements and plans. These are the voices who can speak with authority about the forests, and these are the people in place to protect these natural resources from the relentless pressure of large-scale development that is bound to arrive at their doorstep in the decades to come. It is the mandate of conservation organizations, such as Conservation International and counterpart government agencies, to work closely with these local stakeholders for the good of this globally significant resource.

© 2007, American Institute of Biological Sciences. Educators have permission to reprint articles for classroom use; other users, please contact editor@actionbioscience.org for reprint permission. See reprint policy.

]]> http://staging.actionbioscience.org/biodiversity/beehler.html http://staging.actionbioscience.org/biodiversity/beehler.html Original biodiversity diversity of species Lost world Mon, 01 Jan 2007 12:26:57 -0500 Fossils and the Origin of Whales The concept of evolution was known before Darwin. **Gingerich:** Keith Thomson's book _Before Darwin: Reconciling God and Nature_ gives an excellent history of the concept of evolution before Darwin arrived on the scene. He does a marvelous job of outlining how much was known about evolution before the 1850's. It's fascinating to read. Darwin didn't invent evolution. Darwin developed the current and viable explanation of how it works as a process. Evolution was well established in the decades and even a century before Darwin in the sense of knowing that life changed through time. ### What does the fossil record look like on the microevolutionary scale [within a species]?
Microevolution happens on a small time scale.
**Gingerich:** It is one of continuity and discontinuity. We know that some species don't change much over time, others exhibit changes, some get bigger or smaller, and so on. We see lineages appear suddenly in the fossil record--ones that we can't explain--while in other cases, early primates for instance, we have been able to trace successive species through time. So there are many different patterns in microevolution. ### Is this pattern the same or different on the macroevolutionary scale [at or above the species level]?
Macroevolution happens on a grand time scale.
**Gingerich:** Macroevolution and microevolution are parts of a continuum that are distinguished more by the scale of time on which they are studied. Macroevolution, generally speaking, is what paleontologists study on time scales of thousands to millions of generations. Macroevolution is evolution that happens on a grand time scale and explores questions such as the origin of major groups of plants and animals, and the development of novel innovations like sexual reproduction. Microevolution is what people can study in laboratories or in the field from a few up to a thousand generations. The evolutionary process itself, though, is not even microevolutionary--the process takes place on a generation-to-generation time scale. ### Are you saying that the rate of evolution is fast?
Generation- to- generation evolution is a relatively fast process.
**Gingerich:** Evolution takes place on short time scales, from one generation to the next. When you study evolution, macroevolution or microevolution, over many generations, it is often slow, but when you study evolution on the time scale of the process, a generation at a time, the change you can measure is generally fast. An example would be the evolutionary history of the horse, whose history starts in the early part of the Eocene. We have hundreds and hundreds of fossils that trace its early history. It appeared the size of a Siamese cat, then it was replaced by an animal the size of a fox, then one the size of a coyote--in incremental steps--until it reached today's size. These changes were slow, but when you measure the difference between successive fossil samples, you see that evolution was faster on shorter time scales. This is what happens when morphology is constrained and time [geological time] is long.
With each generation, children have generally gotten taller.
Evolution is a much more dynamic process than most people think. If you study it on short time scales, it's very fast. It doesn't take millions of years to make new structures or to adapt to new conditions. It takes a few generations--not even hundreds or thousands of generations. It's well known, for example, that students have gotten taller during the last few human generations. I think I can see this in the students I have taught for the past generation. Anthropologists have studied human stature and call this increase over time the secular trend in human physical growth. This means the fossil record is more the record of the environmental conditions during which change took place than it is a record of the evolutionary process itself. This is why the fossil record looks punctuated, that is, exhibiting periods of intense evolution and periods when nothing much seems to happen. ### How do you calculate the rate of evolution?
The rate of evolution is largely influenced by the time scale.
**Gingerich:** In mathematical terms, a rate of evolution depends not so much on the numerator of the ratio but rather on the denominator. A rate is a ratio with a numerator [in this case, change] and denominator [time]. If you study a long-term fossil record, you will see slow rates because that's all you can see on this macroevolutionary time scale. But on a microevolutionary scale, where the time frame is shorter, rates are systematically faster. When you do lab experiments, they are faster still. When you plot all of these time scales together, you see a perfectly continuous distribution. You can then examine evolution on a generation-to-generation time scale; evidence shows it's fast. It doesn't mean evolution cannot be slower, but the upper limit is very fast. Knowing the rate of evolution is important because rates: * quantify, or measure, evolutionary change in relation to time, and * indicate how the process of evolution works.
The rate can be calculated in darwins or haldanes.
Some scientists use a rate in darwins, which uses a standard of one million years. I prefer to use a rate using haldanes, which uses a standard of one generation. Both calculate rates in terms of proportional change divided by elapsed time. What we are really interested in, from the point of view of the process, is generation-to-generation rates or rates calculated on one-generation time scales.

Philip Gingerich working on a fossil whale in the field in Egypt.
Photo by Jeffrey A. Wilson

### Your team was the first to find skeletons linking whales to land mammals. Does the fossil record to date indicate a rapid change from land to sea? **Gingerich:** Whales have not been collected on a fine enough time scale to see rapid change. This will be revealed through more fieldwork. So far we have fossils illustrating three or four steps that bridge the precursor of whales to today's mammals.
Whales share a common ancestor with hippos.
Fossils document biological change through geological time. The fossil record, of course, is supported by molecular and other studies showing that whales share a common ancestor with four-footed, hoofed mammals such as cows and hippos. Their evolution is particularly interesting because early vertebrates came from the sea to live on land, and whales then returned to an aquatic life. My research focuses on archaeocetes, or "archaic" whales that were the ones that evolved from land. We find whale fossils from the Eocene epoch, which lasted from about 54.8 to 33.7 million years ago [mya]. These include:
Archaic whales lived between 54.8 and 33.7 million years ago.
* complete skeletons of middle-to-late Eocene Basilosauridae (e.g., _Dorudon_ and _Basilosaurus_) that were the first known to retain hand limbs, feet, and toes * exceptionally complete skeletons of middle Eocene Protocetidae (e.g., _Rodhocetus_ and _Artiocetus_) that connect whales to an artiodactyl ancestry * a partial skull of earliest middle Eocene Pakicetidae (the _Pakicetus_) that was at the time the first skull of the oldest known whale ### What are some of the key discoveries about whale history?
The earliest whales were semi-aquatic.
**Gingerich:** The oldest whale fossil, _Himalayacetus_, was found in India in Eocene marine strata, indicating it was about 53 million years old. It has the misfortune of being represented only by a lower jaw with two teeth in it. It shows one interesting characteristic: It doesn't yet exhibit the enlarged mandibular canal later linked to hearing in water. That happens soon afterward. Another interesting characteristic is that this fossil is found in marine rocks. This puts other whale fossils that were contemporaries, such as those of the riverine _Pakicetus_, in perspective. All of the earliest whales that we know about so far were semi-aquatic. I am sure that they were still coming on land to give birth, to rest, and to mate, very much like modern sea lions.
They used their webbed feet for swimming.
Other fossil examples provide additional evidence. For example, nearly complete skeletons of _Rodhocetus_ and _Artiocetus_ from the early middle Eocene represent foot-powered swimmers with large webbed feet. We now have a complete skeleton of _Rodhocetus_. It's an important find because it illustrates and allows us to quantify the whale's transition from land to water. The proportions of _Rodhocetus_ ' limbs, skull, neck, and thorax indicate it was a foot-powered swimmer. It would take subsequent generations to evolve into tail-powered swimmers. By the mid- to late Eocene, ancient whales such as the _Dorudon_ were swimming like the whales of today, using their tail.
They later swam using their tails and diverged.
At the close of the Eocene, or early in the next epoch, the Oligocene [33.7 to 23.8 mya], the archaic whale lineage began to divide into two groups leading to the toothed whales and the baleen whales, and these in turn evolved into the wonderful whale diversity we see today. ### What have we learned so far from whale fossils? **Gingerich:** Whale fossil finds enable us to document the evolutionary history of whales, a history we were postulating from theory before:
Whale fossils show that evolution is opportunistic.
* Whales are warm-blooded mammals that evolved backwards, from land to sea, which shows that evolution can go both ways; it is opportunistic, not deterministic. * It hasn't been a smooth transition for whales. There is a stage between specialized foot-powered swimmers like _Rodhocetus_ and modern whales: the stage of tail-powered swimmers like _Dorudon_ that still retain vestigial hind limbs. * Modern whales that are carnivorous today evolved from ancient artiodactyls [the mammalian order including cows, deer, hippos, etc.] that were plant eaters. It's an interesting change in feeding strategy, from eating plants to eating animals.

© 2006, American Institute of Biological Sciences.Educators have permission to reprint articles for classroom use; other users,please contact editor@actionbioscience.org for reprint permission. See reprint policy.

]]> http://staging.actionbioscience.org/evolution/gingerich.html http://staging.actionbioscience.org/evolution/gingerich.html Original Interview evolution the fossil record Whale Fossils Fri, 01 Dec 2006 12:28:22 -0500 Evolutionary Biologists Aim to Protect Madagascar’s Plants and Animals Scientists meet to focus on Madagascar. "It's a dream come true to me to have this kind of group assembled," said Anne Yoder, speaking to 26 scientists who had come from all over the United States as well as England, France, Finland, Germany, and Madagascar to meet for three days in June 2006 in Durham, North Carolina.1 The group included botanists, zoologists, ecologists, paleontologists, molecular biologists, statisticians, computer modelers, and taxonomists. What drew this diverse group together? A fascination with Madagascar and with evolution. ### Madagascar: Evolutionary hotspot In Yoder's words, "Madagascar has often been described as one of the world's greatest natural laboratories for the study of evolution." An island 400 kilometers off the eastern coast of South Africa, Madagascar is only about the size of Texas, yet it contains an astonishing collection of plants and animals that are characterized by
The island is ideal for the study of evolution.
* diversity: an estimated 200,000 animal species are present2 * endemism: most Madagascar species occur only in Madagascar; 7 of at least 160 plant_families_on the island live nowhere else3 * imbalance: some globally widespread taxonomic groups are absent, while others are unusually diverse
Many animal species exist nowhere else.
All of the island's mammals, not counting bats, are endemic. Madagascar supports at least 50 different species of lemurs, which are primates that live nowhere else on Earth, but no monkeys or apes live there. More than 95 percent of Madagascar's reptile and amphibian species are endemic. Out of 28 frog families worldwide, only three live on the island. But within these three families, there are more than 300 species. Some amphibians and reptiles are conspicuously absent: No salamanders or vipers live in Madagascar.4
New plant species are found every year.
There are at least 12,000 different plant species and more are identified every year. The endemic Madagascar periwinkle plant has become well known because it is used in medicine to treat childhood leukemia. According to George Schatz of the Missouri Botanical Gardens, "We really don't have any idea how many plant species are in Madagascar. It may go to 14,000 or 16,000." Texas, by comparison, contains about 5,500 plant species. ### Threats to Madagascar's flora and fauna
Impoverished people destroy forests to make a living.
Madagascar is one of the poorest countries in the world. More than 18 million people live there, and the population is growing rapidly. The vast majority of Malagasy people (as inhabitants of Madagascar are called) eke out an existence supported by slash-and-burn agriculture. Farmers clear a plot of land, cultivate it for a few years until the soil is depleted, then move on to clear another patch of forest. Forest is also burned to provide grazing areas for cattle and logged for construction materials, firewood, and charcoal production.5 Humans arrived on the island only about 2,000 years ago but have already left a heavy mark:
Less than 15 percent of the island is undisturbed.
Less than 10 percent will be protected by 2008.
* It is estimated that only 10 to 15 percent of the island's habitat remains undisturbed. * Deforestation has caused massive erosion, as the island's soils wash into the ocean. * To add to the ecological disaster, many animals are illegally hunted for meat or for the international pet trade. * On top of it all, global climate change looms as a serious threat. Michelle Zjhra, of Georgia Southern University, who studies Madagascar's trees, said, "Since I've been collecting, the number of these species has gone way up, which means we're only just finding the tip of the iceberg. We're racing against the clock to document the diversity." To date about 2.7 percent of Madagascar's land area (16,131 km�) is officially protected.6 In response to the ecological crisis, in 2003 the president of Madagascar, Marc Ravalomanana, announced he would triple the amount of land under protection in his country before 2008. ### Scientists convene Ravalomanana's announcement has generated a lot of interest in the scientific community; scientists hope their knowledge of the evolutionary history of the island's biota will help identify the best areas to protect.
NESCent is spearheading scientific meetings.
Yoder, professor of biology at Duke University and director of the Duke Lemur Center, and Claire Kremen, assistant professor in the department of environmental science, policy, and management at the University of California-Berkeley, called together the international group in June at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, with these goals: * to share and compare their research on the evolutionary history of Madagascar's plants and animals * to organize small collaborative working groups * to apply their knowledge to help identify conservation priorities in Madagascar
Its goal is to foster collaborations.
Like birds of a feather, scientists tend to spend most of their professional meeting time with their own kind, gathering at conferences sponsored by groups such as the Geological Society of America and the American Society for Microbiology. The NESCent meeting, in contrast, brought together a variety of different specialists. Joel Kingsolver, NESCent's associate director, explained, "We're interested in getting people together who may not have met before and fostering new collaborations."
How did such unusual creatures evolve in Madagascar?
### Studying the unusual Yoder and Kremen hope the NESCent meeting will jumpstart data-sharing among scientists to help figure out in more detail what geological events, climatic conditions, and evolutionary processes led to Madagascar's present-day assemblage of plants and animals. There's no easy answer to how evolutionary processes led to such an unusual biota, but several factors clearly play a role: * geographic isolation * size--Madagascar is the fourth largest island in the world * variety of habitats, including desert, rain forest, mountainous regions, and seashore * tropical location
The island's geography is one clue.
Because of the island's isolation, Madagascar's organisms follow their own evolutionary paths with little or no competition or genetic exchange with the world's other plants and animals. The size of the island and wide variety of habitats provide many different niches for different species to fill. The tropical location may allow evolution to proceed faster: Scientists in New Zealand announced this spring that among the 45 plant species they studied, molecular changes in DNA (which drive evolution) occur at a faster rate in tropical climates compared to temperate ones.7 ### The geological story of Madagascar's isolation
Madagascar separated from India millions of years ago.
Millions of years ago, Madagascar was part of a large continent called Gondwana. What would later become Madagascar was nestled between parts of what would later become South America, Africa, India, Antarctica, and Australia. About 165 million years ago, Gondwana began to break up. After separating from Africa and the other continents, Madagascar and India remained joined until 88 million years ago, when India split away and headed on a collision course to Asia. Since then, Madagascar has been on its own. This is currently the most widely accepted theory, but new fossil evidence has led some scientists to speculate that land bridges connected Antarctica to the southern tip of South America as well as to the southern tip of India-Madagascar for 40 million years or more after Madagascar and Africa parted ways.
The Mozambique Channel separates it from Africa.
The Mozambique Channel, which separates Madagascar and Africa, is so deep that even during times of low sea level there was no land bridge between the two. That means that plants and animals living in Madagascar today have either evolved from what was there when it first became isolated or evolved from individuals that arrived on Madagascar's shores after floating, swimming, rafting, or flying across the Mozambique Channel--a mechanism called "waif dispersal."
Did some species arrive via the channel?
"Entire trees may have been dislodged from a west African mangrove [forest], rafted across, and germinated on the Madagascar shore," said Kobinah Abdul-Salim, a botanist at Ohio State University. Other plants and animals could have hitched rides on rafting trees. Animals might have flown or swum. While waif dispersal seems highly unlikely, it only has to happen once or twice for a particular organism to establish a new colony. Once established, the new colony has virtually no contact with the parent colony in Africa, allowing the daughter colony to follow a different evolutionary path.
Evolutionary trees and sister groups help explain origins.
Given any particular plant or animal in Madagascar, how do scientists figure out whether it evolved from an organism that was present on the island when it first became isolated, or from an organism that arrived by means of waif dispersal? Here are the first steps: * construct an evolutionary tree of the organism and related groups * add dates to different branches of the tree, if possible * pinpoint the geographic locations of relatives, called "sister groups," living in other parts of the world today
Technology makes it easier to construct such trees.
### Constructing evolutionary trees using genetic analysis New genetic techniques have given scientists new ways to construct evolutionary trees. In the past, scientists primarily compared physical characteristics of organisms. Those that shared similar physical characteristics were assumed to be more closely related than those that didn't. Fossils were placed on the tree the same way. Today, scientists compare DNA samples from living species. The molecular structure of DNA from closely related species is more alike than the DNA of distantly related species.
Look-alike species are not necessarily closely related.
Genetic studies uncover surprising relationships. Bart Buyck, of the National Museum of Natural History in Paris, who studies fungi, said, "For two centuries, the whole systematics [of fungi] has been based on what they look like. With the arrival of molecular techniques, we know now this system is worthless. For example, what were supposed to be different families before are now a single genus." Even for animals such as frogs and ants, genetic analysis is showing that some look-alike species are not as closely related as previously believed, whereas some species have one or more very different forms (males and females, for example). Genetic analysis is quickly being adopted by more and more evolutionary scientists. Miguel Vences, an expert on Malagasy frogs who works at the Technical University of Braunschweig in Germany, said, "It's amazing to see how much has been done in the past five years. In the next couple of years, if we work on it, we could get a lot more [data]." ### Assigning dates to evolutionary trees The two most common ways of putting ages on the branches of an evolutionary tree are to use fossil ages or the more recent method using DNA evidence.
The island's lack of fossils presents a challenge.