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.
Unfortunately, according to paleontologist David Krause, from Stony Brook University, "The fossil record for Madagascar stinks." He should know: He's been going on fossil hunting expeditions in Madagascar for about a dozen years. Many of the rocks and sediments in Madagascar are not suitable for preserving fossils; there are virtually no fossils between 26,000 years old and 65 million years old. Krause digs up fossils about 70 million years old. What he's found indicates that the faunal community living in Madagascar then was not as endemic nor as imbalanced as today. Many are similar to fossils of the same age found in South America and India. Most do not appear to be ancestors of the animals in Madagascar today. Some people speculate that many of Madagascar's animals became extinct 65 million years ago as a result of the same meteor impact that doomed the dinosaurs, but there's currently no solid evidence for this.
Molecular clocks help date divergence of species.
In the absence of fossils, scientists sometimes use "molecular clocks" to put dates on evolutionary trees. The assumption is that mutations in DNA occur at more or less regular rates through time, so the number of differences in the DNA between two species can be used to infer the amount of time that has passed since the two species diverged from one another. In recent years, it's become obvious that most mutations do not occur at regular rates, so this method is not infallible. However, modern statistical methods have allowed scientists to use molecular clock data in conjunction with fossil data to produce ever more precise age estimates. ### Comparing sister groups
Sister groups may provide missing data.
Even when fossil or DNA dates are not available, scientists can look at sister groups to figure out where a Malagasy species arose. Sister groups are different branches of an evolutionary tree that share a common ancestor. (All life forms share a common ancestor, but evolutionary scientists are usually looking at the most recent one for two or more particular groups.) If a sister group of a particular Malagasy species lives in South America, for example, scientists speculate that both groups evolved from an ancestor that lived on Gondwana before it split apart. If the only sister group is in Africa, and the divergence between the two groups appears to have occurred fairly recently, then the species likely evolved from individuals that arrived in Madagascar by means of waif dispersal. ### The results so far
Most species emigrated from Africa.
Scientists think there are only a handful of terrestrial groups in Madagascar today that evolved from Gondwanan animals--some turtles, boas, and iguanas. These animals are most closely related to animals that live in South America. Most other Malagasy animals appear to have descended from animals that arrived on the island from Africa in the more recent past. For example, there are four main groups of nonflying mammals in Madagascar: * tenrecs (insect-eating shrewlike mammals) * lemurs * carnivorans (such as the fossa, a catlike relative of the mongoose) * a subset of rodents Each of these groups has been shown, through DNA analysis, to be the direct descendents of groups of animals in Africa. Dating techniques, including fossil work and molecular clock data, indicate that the species in all four groups most likely arose after Madagascar became isolated.
This explains imbalances in biodiversity.
If waif dispersal explains the presence of most organisms present on the island today, then it is not surprising that the biota is so imbalanced. It would be more surprising if representatives from all common tropical taxonomic groups had managed to make the unlikely trip, survive, and flourish. ### Working together to fill in the blanks
Plant evolution may shed light on some animal groups.
Evolutionary scientists would like to know more about the sequence of arrival of various groups in Madagascar, which would help explain the unusual present-day collection and evolutionary processes in general. What if a plant washes up on shore, but its natural pollinator is not present? What if a newly arrived animal finds its preferred niche already filled or is faced with a new predator? As scientists continue to refine the evolutionary trees of different organisms, a sequence of arrival will start to emerge, and some of these questions can be addressed. Sometimes the evolutionary tree of one organism can illuminate something about another organism. Plants and their specialist herbivores are a good example. David Lees, a butterfly specialist from the Natural History Museum in London, said, "We don't know when butterflies originated. Recently people have made claims for early origins of butterflies--84 million years ago, or between 82.5 million and 95 million years ago. This seems to me to ignore that the fossil record of the host plants is far better. The plants that some of these butterflies feed on are not that old."
Scientists are collaborating to solve riddles.
Lees and other meeting attendees plan to form a working group to compare the evolution of plants and their pollinators in Madagascar. Another member of the working group, Michelle Zjhra, asked, "Do the [evolutionary] patterns in the trees correspond to the patterns of the lemurs that disperse the fruit?" Lemurs, who eat the fleshy fruit of many trees, are significant pollinators and dispersers of trees in Madagascar. By synthesizing the evolutionary data available so far on Malagasy plants and their pollinators or dispersers, be they butterflies, hawkmoths, or lemurs, the researchers hope to address questions about how the evolution of one group affects or responds to the evolution of other groups. Lees and Zjhra also hope their work will inspire others to do research in Madagascar. ### Sharing data leads to discoveries
Dated pollen data showed where a rain forest had been.
One of the most exciting moments in the meeting came when David Vieites, of the University of California-Berkeley, presented his brand-new reconstruction of past habitats in Madagascar. ("This is all new stuff," he said. "I just finished working on it last night.") Using information about worldwide climate inferred from dated pollen samples from all over the world, Vieites assembled maps of Madagascar in different geologic time periods, showing the changing locations and extents of habitats. When Vieites showed the group the maps, someone shouted out, "There's Brian's lost rain forest!" Indeed, the Pleistocene map showed a tiny patch of rain forest at the southern tip of Madagascar. Just the day before, ant expert Brian Fisher had told the group about some rain forest ants that live deep in rock crevasses in southern Madagascar, an area that's currently arid. He had speculated a rain forest must have been there in the past. Vieites said of his maps: "It's very preliminary. We need to calculate the error. But it is very promising. The ant people, the plant people, the butterfly people were happy with it." ### Improving conservation plans
Which information will benefit conservation most?
Claire Kremen studies Malagasy butterflies and computer habitat modeling at the University of California-Berkeley. She is particularly interested in using computer models to help prioritize areas for preservation. It's an endeavor fraught with unknowns. Scientists are trying to work out which attributes are most important when evaluating the value of a piece of land as a preserve: * size * shape * connections to other preserves * number of species that live there * number of individual organisms that live there * ratio of rare to common species * diversity of habitats * stability or fluctuation of habitat type over geologic time * presence or absence of habitat degradation by humans * presence or absence of features that encourage the development of new species
What groups should conservation strategies protect?
There are other questions as well. Does protecting land for the benefit of one species protect other species too? It has long been assumed that protecting large "charismatic" species, such as tigers, would automatically help smaller species. Recent computer modeling by Craig Moritz of the University of California-Berkeley indicates that preserving parcels of land to best protect large vertebrates would not necessarily do a good job protecting invertebrates, whereas conserving habitat for invertebrates might have a positive impact on larger organisms.
Evolutionary histories help inform conservation efforts for the long term.
And what about global climate change, which will likely disrupt many habitats whether they are in national parks or not? Craig Moritz asked, "Should we prepare for recovery from climate change? Can we locate geographical areas that might drive diversification of species?" No one knows the answers to these questions. But as these scientists and others continue to piece together the evolutionary history of Madagascar, what they learn will help predict the conditions that are necessary to protect Madagascar's plants and animals--and the evolutionary processes that produced them--in the future. Anne Yoder summed up her hopes this way: "How are we going to take this magnificent biota and save it? That's my dream for what's going to come out of this meeting."

© 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/roberson.html http://staging.actionbioscience.org/evolution/roberson.html 5-overpopulation impacts Original evolution evolution and the history of life Madagascar Sun, 01 Oct 2006 12:28:34 -0500 Coping with Climate Change Climate change is known to affect ecosystems.
The problem is amplified by changes to the landscape.
What have we learned so far about how climate change is affecting our global environment? Studies show that it adversely affects human and natural systems by * reducing biodiversity * altering hydrological systems * impairing biological and chemical cycles * making it more difficult to restore degraded ecosystems Climate is not the only factor in the deterioration of natural systems. We are making big changes to the landscape, altering land use and land cover in major ways. These changes combined present a challenge to environmental management. Adaptive management is a scientific approach to managing the adverse impacts of climate and landscape change. ### Nature and impacts of climate change Every week it seems there is an article about global warming in the news media. It may be difficult for some to grasp the big picture of the issue, but in general, climate change has already or is expected to * increase temperatures, particularly in the interior of continents, toward the poles and in winter * boost precipitation in wetter areas and suppress precipitation in drier areas
Climate change is affecting weather and temperature.
* increase rain and decrease snow * lessen peak spring runoff and cause more even year-round flows of water, thereby reducing water availability during summer irrigation and navigation seasons * increase evaporation of water during the summer * enhance the likelihood of lower mean lake levels, drier wetlands, and water shortages, particularly in mountain regions * raise the frequency and magnitude of extreme weather events, such as hurricanes, tornadoes, and floods * raise global sea levels causing some populated coastal areas to become inundated * reduce the extent and duration of Arctic sea ice with adverse consequences for marine mammals * increase permafrost melting, thereby altering soil stability and limiting modes of transportation * increase the loss of glaciers in middle and equatorial latitudes, including premier mountain ecosystems such as Glacier National Park in Montana
It's 6°C warmer now than 100 years ago.
Global average temperature has increased by about 0.6°C over the past 100 years, with a major warming upswing in the 1970s. Warming is the result, in part, of rapid increases in emissions of greenhouse gases (GHG), particularly carbon dioxide (CO2), which is a byproduct of the combustion of fossil fuels, such as coal, oil, and natural gas, used for power generation and transportation. When global temperatures rise and precipitation patterns change, it is expected there will be consequences on ecosystems, such as an increase in the spread of exotic species; redistribution of plants, animals, energy, water, and nutrients; alteration of natural processes and the structure and function of ecosystems.
The Arctic is warming faster than the rest of the world.
Northerly latitudes are particularly vulnerable to climate change. The Arctic Council, an intergovernmental forum for Arctic nations and indigenous people, reported that the northern ice cap is warming at twice the global rate and the Arctic region is expected to warm at two to three times the rate for the rest of the world. Arctic warming will have serious human and ecological consequences. ### Nature and impacts of landscape change
Both nature and humans contribute to landscape change.
Landscape change results from natural disturbances and human activities. Natural disturbances include fire, windstorms, avalanches, landslides, tree fall, floods, and insect epidemics. Human activities causing landscape change include urban sprawl, conversion of forestland to agriculture, drainage of wetlands, and forest fragmentation from road construction and timber harvesting.
Humans have a big impact on landscapes.
Human activities often have a more significant effect on landscapes than natural disturbances because they alter the availability of energy, water, and nutrients to ecosystems; increase the spread of exotic species; accelerate natural processes of ecosystem change; and adversely affect the structure and functioning of ecosystems. Human-induced landscape change has accelerated during the past several decades because of rapid population and economic growth, particularly in countries such as China, India, and Brazil.
Most of the contiguous United States has been altered since its settlement.
* Landscape change has contributed to a dramatic 1,000-fold increase in species extinction over the past 400 years. * On a global basis, nearly 1.2 million km2 of forest and woodland and 5.6 million km2 of grassland and pastureland have been converted to other uses. * During the last three centuries, 12 million km2 of cropland were lost. Between 1982 and 1997, 121,000 km2 of non-federal land were urbanized in the United States. * More than 90 percent of the land in the lower 48 states has been logged, plowed, mined, grazed, paved, or otherwise modified from presettlement conditions.
Development in parts of the Yellowstone ecosystem has increased fourfold.
Human-induced landscape change significantly affects wildlife. For example, between 1970 and 2000, rural residential development in the Montana and Wyoming portions of the Greater Yellowstone Ecosystem increased 400 percent. Consequently, current and potential grizzly bear habitat on private lands in the ecosystem has been degraded and fragmented. Double-digit growth in residential subdivisions adjacent to the National Elk Refuge in Jackson, Wyoming, has diminished winter range for the 10,000 elk that use the refuge and displaced corridors that elk use to reach summer range in Yellowstone and Grand Teton National Parks. Another example of significant impacts from landscape change is the Crown of the Continent Ecosystem. This ecosystem straddles the Rocky Mountains in British Columbia and Alberta, Canada, and western Montana, United States. Here are some specifics:
Most old-growth forests on unprotected lands in the Rockies are gone.
* Most old growth forests that once existed outside of protected park and wilderness areas have been harvested. * Many rivers in the region have been altered by hydroelectric power development. * Significant farm, ranch, and forest acreage has been converted to homes and commercial developments. * Lakes and streams have been polluted by agricultural and urban runoff. * Fish and wildlife habitats have been degraded. * Active and proposed energy developments threaten protected areas. * Large areas have been invaded by nonnative species. The desire to preserve the outstanding wildlife (especially large carnivores) and environmental amenities from the negative effects of rapid economic growth and development in the northern Rocky Mountain region prompted creation of the Yellowstone to Yukon Conservation Initiative. The initiative involves 300 conservation organizations and covers an area larger than the states of California and Texas combined, including the Greater Yellowstone and Crown of the Continent Ecosystems. ### Coping with climate and landscape change Although climate and landscape change has positive effects on human and natural systems, it is expected to have many adverse impacts that deserve attention. Ecosystems have an inherent capacity to resist climate and landscape change, known as ecological resilience. When this capacity is exceeded, the ecosystem can change in ways that may not be socially and ecologically acceptable.
There are ways to help ecosystems adjust to the changes.
So what can be done? Mitigation strategies can reduce ecosystem vulnerability, and adaptation strategies can increase ecological resilience to climate and landscape change. Mitigation strategies are actions to prevent, reduce, or slow climate and/or landscape change. Adaptation strategies are actions to counteract the adverse consequences of climate and landscape change. Natural resource managers can use both strategies to reduce adverse ecosystem effects of climate and landscape change. The Kyoto Protocol to the United Nations Framework Convention on Climate Change, which took effect in February 2005, is a prime example of a climate change mitigation strategy. The protocol commits 36 industrialized countries to curb GHG emissions, especially CO2. Limiting increases in global temperature by 2°C would require keeping atmospheric concentrations of CO2 below 400 parts per million (ppm). Current concentrations are about 375 ppm. Benefits of the Kyoto Protocol may be limited because it does not include some developed countries, which emit substantial GHGs, and developing countries where rapid population and economic growth is expected to dramatically increase GHG emissions.
The Kyoto Protocol is a mitigation strategy to slow climate change.
Other mitigation strategies include increasing the use of alternative energy sources and technologies (clean coal, renewable energy, ethanol, hybrid vehicles, and nuclear power). Although the United States did not sign the Kyoto Protocol, 28 states have programs to curb CO2 emissions, and at least 166 US cities have agreed to apply the Kyoto emission reduction standards to their communities. Other initiatives, like the Apollo Alliance, bring together labor unions, environmental and business groups, and activist organizations with the mission of sharply reducing US dependence on fossil fuels. The alliance is seeking ways to do the following: * increase the use of solar and wind energy * power the economy with hydrogen produced from renewable energy resources * implement green construction codes * revitalize urban centers to reduce urban sprawl * determine how industry can store rather than emit carbon into the atmosphere
The Apollo Alliance is working to mitigate the energy crisis.
The Apollo Alliance expects to invest $300 billion in new energy technologies and energy conservation over 10 years as a way to eliminate US dependence on foreign oil and create millions of good-paying jobs. These funds would be raised using tax incentives, public bonds, capital strategies, and other mechanisms. Communities, too, can adapt. The Inuvialuit people of Sachs Harbor in the Canadian Arctic illustrate an example of social adaptation to climate change. They adapted by changing both the species they hunted and the timing and methods of hunting. Other adaptation strategies for climate change include:
Communities can devise their own solutions.
* moving people out of low-lying coastal areas bound to be inundated by rising sea levels * switching to more drought tolerant agricultural crops * increasing use of irrigation in crop production in areas expected to become more arid * installing snowmaking machines at ski resorts * conserving biodiversity * maintaining landscape connectivity to aid vegetation and wildlife migration * reducing habitat fragmentation * actively managing species that can adapt to climate change Some adaptation strategies are likely to involve tradeoffs. For example, greater use of irrigation in crop production could reduce the amount of water available for other human uses and natural systems. Several strategies are suitable for mitigating adverse effects of natural landscape change. Consider wildfire. It is a dominant natural driver of landscape change and is likely to increase with global warming. Wildfire can be mitigated by reducing fuel loads in the urban-wildland interface and extinguishing wildfires that threaten human life and property. Because wildfire has positive ecological benefits, extinguishing all wildfires is not appropriate. As it is unacceptable to some (at least in democratic societies) to control population and economic growth--the primary drivers of landscape change--options for mitigating human-induced landscape change are limited. However, we can take these steps:
There are ways to limit human impacts.
* enact zoning regulations to limit residential and commercial development in environmentally sensitive areas, such as wildlife migration corridors, riparian areas, wetlands, river corridors, groundwater recharge areas, and critical habitat for threatened and endangered species * purchase conservation easements to prevent development of agricultural and ranch properties * purchase environmentally sensitive private land and manage it for conservation uses (as with, for example, lands purchased by The Nature Conservancy) * restore degraded ecosystems (the Comprehensive Everglades Restoration Plan is an example) When considering adaptation strategies to reduce adverse consequences of human-induced landscape change on natural resources, especially vulnerable species, we may choose to do the following:
Adaptation strategies can help protect vulnerable species and their habitat.
* restrict development in buffer zones for protected areas (as is done in Biosphere Reserves) * improve connectivity by creating wildlife corridors between protected areas (for example, Yellowstone to Yukon Conservation Initiative) * move species at risk to zoological parks and more favorable habitats * decommission roads in national forests that contain critical habitat for species adversely affected by roads, such as grizzly bear (the policy adopted by Flathead National Forest in Montana is an example) * restrict the form of angling to catch and release only, and lower bag limits and shorten seasons for game species * support natural migration of species to more favorable habitats Many adaptation strategies, just like mitigation strategies, involve tradeoffs in terms of the benefits and costs to both human (economic) and natural systems. For example, restricting development in buffer zones for protected areas would reduce the amount of land available for development, but it would increase conservation of protected areas and maintain open spaces. ### The adaptive management approach
Resource management faces many challenges.
The writing is on the wall: Resource managers must implement effective mitigation and adaptation strategies well in advance of expected impacts of climate and landscape change. This task is challenging for two reasons: First, most natural resource managers do not have the personnel and budget to manage their areas for potentially adverse impacts of climate and landscape change. Second, there is considerable uncertainty regarding the nature and extent of future climate and landscape change, and how natural and human systems are likely to respond to those changes, with or without mitigation and adaptation strategies. The capacity of managers to make more informed and sound policy and management decisions related to climate and landscape change can be enhanced by (1) increasing managers' access to and understanding of the causes and consequences of climate and landscape change, and (2) providing managers with tools that allow them to identify and compare mitigation and adaptation strategies. Adaptive management (AM) is a science- and information-based approach that is well suited for managing natural resources for climate and landscape change. It does the following:
AM is a scientific approach to managing natural resources.
* embraces the uncertainties inherent in climate and landscape change * employs scientific methods (modeling, experiments, and hypothesis testing) * adjusts mitigation and adaptation strategies based on new knowledge and information * fosters ecosystem stability and institutional flexibility * facilitates collaborative decision-making AM has been used in a variety of natural resource management settings, including these:
AM has been employed in Canada and the United States.
* site-specific management of the state of Washington's timber, fish, and wildlife resources * implementation of a human use management strategy for Banff National Park in Alberta, Canada * management of ungulates and snow machine use in Yellowstone National Park * management of the Missouri River System * salmon recovery in the Columbia River Basin and British Columbia * restoration of the Florida Everglades ecosystem * improved understanding of how water releases from Glen Canyon Dam influence human and environmental values in the lower Colorado River There are two forms of AM, passive and active. Passive AM formulates predictive models of ecosystem responses to management actions, makes management decisions based on those models, and revises the models using monitoring data. Passive AM is relatively simple and inexpensive, but it does not yield reliable information about ecosystem responses to management actions due to statistical deficiencies. Active AM overcomes these deficiencies by employing experimental data to test hypotheses about the effects of management actions, such as mitigation and adaptation strategies. However, AM is challenging to apply because it
AM may be challenging to implement.
* may not be possible to satisfy prerequisites for successful application * is more time consuming, complex, and costly than other forms of management, such as passive AM, trial-and-error, and deferred action * can give faulty results when relevant variables are either ignored or not held constant * has certain application pitfalls (i.e., using linear systems models, discounting nonscientific forms of knowledge, and giving inadequate attention to policy processes that promote the development of shared understandings among diverse stakeholders) * runs the risk of implementing management actions that fail to achieve desired outcomes Several of these limitations can be alleviated by incorporating knowledge from multiple sources, using several systems models, implementing new forms of cooperative decision-making, and educating politicians and managers about the benefits and risks of AM. ### Decision support tool Natural resource managers are unlikely to use the AM approach to manage adverse impacts of climate and landscape change unless the approach is made understandable and accessible. This can be achieved by incorporating the approach in an Internet-based decision support tool that integrates the following elements for specific management areas:
Managers have tools available to try AM.
* geospatial datasets such as GIS (geographic information system), GPS (global positioning system), and remote sensing * models that simulate the impacts of climate and landscape change on selected indicators (e.g., using the Environmental Policy Integrated Climate model to simulate agricultural impacts, or using the FIRE-BGC model to simulate long-term changes in fuels, fire hazard, and fire behavior for different climate and landscape change scenarios) * concepts and methods of AM * alternative decision criteria for evaluating mitigation and adaptation strategies (e.g., minimax regret criteria, precautionary principle, safe minimum standard, and limits of acceptable change) The decision support tool would allow managers to identify best mitigation and adaptation strategies for alternative climate and landscape change scenarios. A pilot program to evaluate the pros and cons of the proposed AM approach to managing adverse impacts of climate and landscape change would provide valuable information. It would develop and evaluate the AM approach and decision support tool for a sample of managed ecosystems that encompasses a range of natural resource and environmental conditions, human uses and values, and availabilities of scientific information and technical expertise. Results of the pilot program could be used to identify conditions under which the approach is most likely to be feasible (that is, when expected benefits exceed expected costs).

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]]> http://staging.actionbioscience.org/environment/prato_fagre.html http://staging.actionbioscience.org/environment/prato_fagre.html 1-climate change Original environment Climate Change Sun, 01 Oct 2006 12:28:10 -0500 Genomic Puzzles Old and New Are common genomic characteristics universal?
Genomes are highly diverse.
> "Most problems have either many answers or no answer. Only a few problems have a single answer." Edmund C. Berkeley The search for genetic differences among people represents one of the most active areas of research made possible by the completion of the human genome sequence. Yet the notion that there is such a thing as "the human genome" carries with it the implication that there are fundamental genomic characteristics that are universal among all members of a species. The most obvious of these relate to the quantity and arrangement of genetic material. We now know that: * One copy of a human's genome contains about 3.5 picograms (pg, or 10-12 grams) of DNA packaged into 23 chromosomes. * Chimpanzees, the closest living relatives of _Homo sapiens_, carry around a slightly heavier genome (3.75 pg) apportioned into 24 chromosomes. * An aardvark genome, by contrast, is contained within only 10 chromosomes but weighs in at 5.8 pg.1
DNA content is constant within a species.
The basic idea that the amount of DNA per chromosome set might be consistent across cells within bodies and among individuals within species was hinted at as early as 1885. An explicit "DNA constancy hypothesis," however, was not developed until the mid-20th century,2 stemming from a 1948 report of "a remarkable constancy in the nuclear DNA content of all the cells in all the individuals within a given animal species,"3 which was interpreted as evidence in favour of DNA, rather than proteins, as the molecule responsible for inheritance. ### The DNA constancy hypothesis In the simplest terms, the DNA constancy hypothesis that emerged in the late 1940s and early 1950s consisted of two central ideas:
This hypothesis emerged in the mid 1900s.
* The amount of DNA per chromosome set within an individual organism is constant. * The DNA content of a single set of chromosomes is largely invariant among members of the same species.
It remains an important idea in modern genomics.
The underlying notion of DNA constancy persists more than a half-century later, even though there are interesting exceptions to both of these postulates (which are beyond the scope of this article). In fact, DNA constancy is an important assumption in modern genome size research, because the two dominant methods of DNA quantification both rely on the use of standards of "known" DNA content for certain conversions.4-6 ### The C-value paradox It is due to its constancy that the amount of DNA contained within a haploid chromosome set is commonly referred to as the "C value," a term coined by Hewson Swift in 1950.7 One year later, scientists provided the first taxonomically broad survey of C values and noted that:
More complex species don't necessarily have more DNA.
> Comparing the largest and one of the smallest examples among vertebrates, one finds that a cell of _Amphiuma_, a urodele, contains 70 times as much DNA as is found in a cell of the domestic fowl, a far more highly developed animal. It seems most unlikely that _Amphiuma_ contains 70 times as many different genes as does the fowl or that a gene of _Amphiuma_ contains 70 times as much DNA as does one in the fowl. To make a somewhat different comparison: a cell of _Amphiuma_ contains 170 times as much DNA as does a cell of a relatively closely related animal, the trigger fish, whereas a cell of the latter contains only nine times as much DNA as does a cell of a sponge, which is far removed phylogenetically from any vertebrate.8
This finding was deemed a confusing paradox.
It is not difficult to understand why observations such as these engendered considerable confusion for the next two decades. As C. A. Thomas put it in 1971, "It was argued that mammals display a greater developmental complexity than primitive fish, therefore, they must have more genes, yet why should the lower forms have more DNA, if DNA is the chemical basis of the gene?"9 To early researchers this seemed downright paradoxical--and indeed, Thomas dubbed the disconnect between genome size and organismal complexity the "C-value paradox."
Even species with similar complexity exhibit the so-called "paradox".
The C-value paradox has traditionally been described in three different ways: * _More complex organisms do not always have larger genomes than simpler ones_. "The quantity of DNA does not seem to be related to the number of genes, for the amount of DNA does not increase unequivocally with the complexity and number of hereditary characters."10 * _Any given genome seems to contain more DNA than would be needed for the predicted gene number._ "One of the problems of eukaryotic genetics is that higher organisms possess much more DNA in their genome than they are likely to need as genetic information."11 * _Some closely related species exhibit divergent DNA contents_. "The paradox is the fact that organisms at the same general level of morphological complexity, which presumably have the same genetic requirements, nevertheless often have genomes whose DNA contents differ by orders of magnitude."12 Consider, for example, the reported genome sizes versus semi-subjective notions of complexity for some well-known organisms:
The human genome is not the largest genome.
* Nematode worm (_Caenorhabditis elegans_): 0.1 pg * Thale cress (_Arabidopsis thaliana_): 0.16 pg * Fruit fly (_Drosophila melanogaster_): 0.18 pg * Pufferfish (_Takifugu rubripes_): 0.4 pg * Rice (_Oryza sativa_): 0.5 pg * Human (_Homo sapiens_): 3.5 pg * Leopard frog (_Rana pipiens_): 6.7 pg * Onion (_Allium cepa_): 16.75 pg * Mountain grasshopper (_Podisma pedestris_): 16.9 pg * Tiger salamander (_Ambystoma tigrinum_): 32 pg * Easter lily (_Lilium longiflorum_): 35.2 pg * Marbled lungfish (_Protopterus aethiopicus_): 132 pg
Humans have less DNA than a tiny salamander.
The human genome, it turns out, is thoroughly average in size for a mammal and significantly smaller than that of various plants, amphibians, insects, and even some single-celled protozoa. Some authors apparently found this revelation bruising to the human ego, as reflected in this complaint: > Being a little chauvinistic toward our own species, we like to think that man is surely one of the most complicated species on earth and thus needs just about the maximum number of genes. However, the lowly liverwort has 18 times as much DNA as we, and the slimy, dull salamander known as _Amphiuma_ has 26 times our complement of DNA. To further add to the insult, the unicellular _Euglena_ has almost as much DNA as man.13 ### Noncoding DNA and the end of the paradox
Today, C-value differences are no longer paradoxical.
In spite of its label, the "paradox" was not so much the lack of a correlation with complexity, per se, but rather the inability of early researchers to reconcile the constancy of DNA content within species (which occurs because it is the stuff of genes) with the variation in quantity of DNA among species (which does not relate to the number of genes). Today, the solution to the paradox is widely recognized: Most eukaryotic DNA does not code for proteins, so there is no reason to expect a complex organism to have a large genome or a simple organism to have a small one. To put it succinctly, the C-value paradox vanished the moment geneticists abandoned the concept of the genome consisting of the genes, all the genes, and nothing but the genes.
The real puzzle lies in "excess" or noncoding DNA.
Stanley K. Sessions may have said it best 20 years ago when, in a review of the influential volume _The Evolution of Genome Size_,14 he pointed out that: > The C-value paradox is the observation that genome size does not correspond to the amount of DNA needed for protein-coding functions. This observation is a paradox only under the expectation that genome size should be equal or proportional to gene number and should therefore increase with "organismal complexity." This paradox has literally disappeared with the discovery that genomes contain "excess" (largely repetitive) DNA that is not transcribed into functional products. Thus it is no longer mysterious that salamanders (for example) have larger genomes than humans. The origin and precise function of the "excess" DNA (which may constitute more than 99% of the genomic DNA) remains an unsolved problem, but it is not a paradox.15 Comparatively modest in size though it is, the human genome provides an excellent illustration of the overwhelming abundance of noncoding DNA and thus the solution to the old "C-value paradox." In 2001, the International Human Genome Sequencing Consortium revealed that each copy of the human genome consists of the following:
The human genome has been sequenced and analyzed.
* 1.5% protein-coding genes * 25.9% introns (noncoding regions within gene sequences) * 20.4% long interspersed nuclear elements (LINEs), including 516,000 copies of the transposable element known as_LINE-1_ * 13.1% short interspersed nuclear elements (SINEs), including 1,090,000 copies of the Alu element * 2.9% DNA transposons (mobile DNA elements) * 8.3% long terminal repeat (LTR) retrotransposons (transposons copied from RNA and flanked by repeated sequences) * 5% segmental duplications * 3% simple sequence repeats * 11.6% miscellaneous unique sequences * 8% miscellaneous compacted DNA, or heterochromatin ### The C-value enigma
The C-value "enigma" is more apt and indicates a complex puzzle.
As Wendell L. Wilkie once quipped, "a good catchword can obscure analysis for 50 years." Despite its obvious obsolescence, and in a clear case of linguistic inertia taking precedence over scientific precision, the term "C-value paradox" continues to enjoy widespread use--often with confusion and miscommunication as the outcome. Variation in genome size is not the least bit paradoxical, but as Sessions and many others have noted, it remains a long-standing puzzle in need of resolution. As an alternative to the outdated term "C-value paradox," which tends to inspire one-dimensional attempts at explanation, the new term "C-value enigma" has been offered in its place.17-19 As an enigma--a complex puzzle--the issue of genome size variation can be explicitly divided into several component questions, each of which must be answered if a complete understanding is to be achieved:
More intruiguing questions about DNA remain.
* What are the sources of all this noncoding DNA? * In what proportions are different types of noncoding DNA represented in the genomes of different species? * By what mechanisms is noncoding DNA gained and lost over evolutionary time? * What are the phenotypic implications, or in some cases perhaps even functions, of noncoding DNA? * Why are the genomes of some species, such as nematodes or rice, streamlined while others, such as those of lungfishes or lilies, are positively enormous? ### Unraveling the enigma While a great deal of work remains to be conducted in terms of each of the component questions of the C-value enigma, research spanning the past 50 years--from the origin of the DNA constancy hypothesis to the modern era of complete genome sequencing--has revealed many important insights regarding the nature and impacts of noncoding DNA. Among the most notable are these findings:
We now have new insights into noncoding DNA.
* A very large fraction of many eukaryotic genomes is composed of "genomic parasites" in the form of transposable elements; in humans, nearly half of the genome consists of such "selfish DNA." Moreover, large genomes contain a larger proportion of transposable elements and a lower proportion of protein-coding genes than smaller genomes. * The abundances and/or lengths of several types of both single-copy and repetitive noncoding DNA appear to increase along with genome size, including all types of transposable elements, introns, microsatellites (repetitive short nucleotide sequences), and ribosomal RNA genes. The amplification and loss of these sequence types varies, suggesting that there may be a general mechanism for DNA content modulation that applies across the genome. Mechanisms exist that are capable of increasing or decreasing genome size over both short and long evolutionary timescales. For example, duplicative transposition of transposable elements and small- and large-scale duplications (from single genes to entire genomes) can add DNA to genomes, sometimes in large amounts and often very rapidly in evolutionary terms. Other processes can either add or remove DNA at a range of scales, such as the insertion or deletion of one or a few nucleotides during DNA replication, recombination events leading to the addition or loss of chromosome segments, and gains or losses of entire chromosomes.
Genome size may increase or decrease through evolution.
* Genome size correlates positively with nucleus and cell size, and negatively with cell division rate, in a wide range of cell types and organisms. The preponderance of the evidence indicates that genome size exerts a causative influence on these cellular parameters. * Depending on the biology of the group in question, the cell-level effects of genome size variation may result in correlations between DNA content and body size, metabolic rate, developmental rate, organ complexity, geographical distribution, and ecological niche. ### A new paradox?
The human genome contains a mere 20,000 to 25,000 genes.
Most of the early discussion surrounding the C-value paradox was predicated on the assumption that gene number and organismal complexity would be closely linked. In light of the extraordinary complexity of its bearer, the human genome in particular was expected to contain an exceptionally high number of protein-coding genes. Prior to the completion of the draft genome sequence, 100,000 genes was a common estimate; as it turns out, the human genome contains a mere 20,000 to 25,000 genes.20 Comparing this with the more than 3,000,000 copies of transposable elements present in each human genome, including more than one million copies of the SINE_Alu_, it is no wonder that W. Ford Doolittle once suggested, only partly facetiously, that our genomes "might be ironically viewed as vehicles for the replication of_Alu_sequences."21 An examination of the genomes of other species shows that, like genome size, gene number is a poor predictor of organismal complexity:
Rice has twice as many genes as humans.
* Fruit fly (_Drosophila melanogaster_): 13,500 genes * Nematode worm (_Caenorhabditis elegans_): 20,000 genes * Human (_Homo sapiens_): 20,000 to 25,000 genes * Pufferfish (_Takifugu rubripes_): 21,000 genes * Thale cress (_Arabidopsis thaliana_): 25,500 genes * Rice (_Oryza sativa_): 40,000 to 50,000 genes
Such findings led to the G-value "paradox".
As with C-values, this observation has been the source of significant surprise among genome researchers. "How can our own supremely sophisticated species be governed by just 50% to 100% more genes than the nematode worm?" some wondered.22 Following the same formula as with genome size (simplistic expectation + contradictory data = "paradox"), this disparity between gene number and complexity has been labeled as the "G-value paradox" or "N-value paradox."23-25 ### The G-value enigma
How an organism is constructed is puzzling.
Perhaps it should go without saying that the G-value "paradox," like its C-value predecessor, is not paradoxical at all. What the data currently emerging from comparative genomics indicate is that the mechanisms by which the genome specifies the construction of an organism is complex and, for the time being, puzzling: a "G-value enigma." And, like the C-value enigma, this new puzzle is most likely to be solved when the pieces are clearly delineated. In this case, some of the pertinent questions include these: * By what mechanisms are genes regulated, and how does this contribute to the high diversity of tissues constructed from a low number of genes? The recent suggestion of a second, nongenic "code" in DNA based on the positions of packaging structures called nucleosomes provides an exciting example of the sorts of discoveries that will be forthcoming in this area.26
What roles do noncoding DNA play?
* What roles, if any, does noncoding DNA play in the link between genome and phenotype? Insights from the study of genome size in general, such as those described above, are directly relevant to this issue, as are other influences such as the position and configuration of DNA, the level of DNA compaction, and other such non-genic factors. * In what ways do interactions among genes account for the emergence of complex wholes from a relatively limited number of parts? * How many different protein products can a single gene region encode through such processes as alternative splicing, and to what extent could this explain the diverse protein products that can result from even a relatively simple protein-encoding genome?
Solving the enigma is a step toward understanding genomic form, function, and evolution.
### Future perspectives Although they may not yet be recognized explicitly as parts of a larger puzzle, each of the component questions in the G-value enigma is the subject of an increasing amount of study. To the extent that co-opted transposable elements play a role in gene regulation, that other noncoding DNA influences gene expression, that introns are involved in alternative splicing, and that bulk DNA content exerts an impact on cellular and organismal phenotypes, it is clear that the C-value and G-value enigmas are themselves part of an overarching quest to understand the form, function, and evolution of genomes. To advance this cause, a few key steps might be taken by the scientific community:
There are ways to improve the study of genomes.
* Consider findings that contradict simplistic assumptions about genomes--most notably that one or a few linear genomic parameters should determine the complexity of organisms--as exciting challenges, rather than framing them as "paradoxical." * Think of genomes as complex biological entities with their own inherent properties and evolutionary histories. * Characterize both the coding and noncoding components of genomes and their relative proportions in complete sequencing projects.
Problems with many answers are more stimulating than paradoxes.
* Create greater linkages between researchers who study genome size (the C-value enigma) and those dealing with the sequences and functions of genes (the G-value enigma), and make a stronger effort to combine insights derived from the study of each of the major groups of living things and to move well beyond the current cast of model organisms. The lesson from the past 50 years, and the most productive guiding principle for the next phase of genomic science, is that genomes are complex and strongly resistant to one-dimensional explanations. Put more simply, those wishing to shed light on the causes and consequences of genomic variation at any level should bear the following in mind: Paradoxes are frustrating, but clearly defined puzzles are stimulating.

© 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/genomic/gregory.html http://staging.actionbioscience.org/genomic/gregory.html 5-understanding genomes Original genomics science and technology in the 21st century Genomic Puzzles Tue, 01 Aug 2006 12:28:43 -0500 Ecology and Economics Ecologists study natural systems and economists study human systems. **Polasky:** I have a joint position in ecology and economics in Minnesota, so I see lots of similarities. Besides just sharing the first three letters "eco," they are formally very similar because both ecology and economics are studies of systems. Ecology is the study of natural systems, and economics is the study of a human system or human market systems. In both you are talking about interactions between components or processes of the systems and how those lead to knowing how the system works as a whole. In economics we talk about market prices and the interaction of supply and demand. In ecology we talk about interactions between various species, predators and prey, and how they lead to the diversity of the system and to differences in system stability and productivity. So there are striking similarities--different terms and sometimes different questions that people think of as interesting--but the mechanics that underlie both ecology and economics are quite similar. ### What perspective could both an ecologist and economist bring to the challenges of conservation?
Conservation must take people's needs into account.
**Polasky:** I have been too immersed in this for a while, so I don't think that you can do it without both ecology and economics. Let me give you one example. Suppose that habitat loss is the leading conservation problem in an area. Why is habitat being threatened? Typically it is because humans are making decisions about land use, because they want to grow crops, they want to cut trees, they want to do something that will lead to some improvement in their material well-being, or they want to increase income from the land. Now from an economic perspective you have to understand why they are doing what they are doing. What are their incentives? On the ecological side you need to know what to do for habitat protection in order to conserve species. What does the species need to survive? What is going to lead to a viable population? Knowing this you can then work back to the economics on what we need to do in order to provide incentives to people to actually get conservation of that habitat in place. Again, you need both perspectives. ### What do you mean by ecosystem services? Do economists view these services similarly or differently from ecologists?
Nature provides valuable services to people.
**Polasky:** What I use as my definition of ecosystem services is this: It is the contribution of ecological systems to the production of goods and services that people care about. It is clear that natural systems provide services that are useful to people. We are not talking about some manufactured item but something that is coming from a natural, or let's say managed, system. I prefer to get away from the use of "natural system" because who knows what that means, but clearly an ecological biological system is contributing value to our lives, such as the fish we eat or the filtration of water.
These services can be measured economically.
To answer the second part of the question, I actually think we see ecosystem services in the same light. Ecosystem services is the bridging concept between the natural sciences and economics because the idea of goods and services is a pretty standard way for an economist to approach this concept: by the quantities of goods and services and the values, which are the prices that we attach to those goods and services. Occasionally there are some differences in opinions. I don't think they are insurmountable by any means. Sometimes ecologists will talk about ecosystem functions or ecosystem processes almost synonymously with services, and in my mind what makes it a service is that it has to be of value somehow to people. It could be that the production of net primary productivity in an ecosystem is of interest to an ecologist, but does it have value to people? ### What factors do economists consider when they place a value on an ecosystem service?
Economic valuation includes looking at the big picture.
**Polasky:** When economists try to place a value on a service, we are really asking, in a sense, How important is this ecosystem service relative to other things? Is it more important to have more wetlands, which then create habitat and nutrient cycling and all the consequences of that, or, for example, to have more cropland? This asks you to look at the question Is society better off with the wetland as a wetland or converted to cropland? When you transform the system, you have to think of the consequences of making that change, such as do I have to worry about the nitrogen that had been retained by the wetland? If the wetland is in Minnesota, what are the consequences of nitrogen going down the Mississippi River and down into the Gulf of Mexico and adding to the hypoxic [dead] zone in the Gulf? On the human side, how much do these consequences matter to people? ### Is it possible to put a monetary value on ecosystem services?
Putting a monetary value on services is not always easy.
**Polasky:** Yes and no. For certain ecosystem services, I would have no problem putting a dollar value on it, for example, if we are talking about pollination services for growing crops. If ecological science is good enough to explain how crop yields change with the availability or absence of pollinators, then the economic step of putting a dollar value on this is fairly easy because we are assessing crops that are traded in markets. A simple way is to take the change in quantity and multiply that by the market price and that is your value. It gets a little more complicated than that when you are talking about large changes because the prices will change as the availability of crops change, but it's still a standard supply and demand curve analysis. Where you get into trouble is with issues beyond basics. Suppose we are considering the protection of species. Are these species that people really seem to care about? If they don't seem to care about them, is it because they don't know much about them? In the U.S. we have an Endangered Species Act that protects certain species. It is based on a moral and ethical consideration that people shouldn't cause extinctions. How do you place a dollar value on preventing extinction? We may be better off just talking in strictly ecological terms about what amount of habitat is necessary to protect the species and how we can do that cost effectively. I don't know that we will ever be able to, or should, put a dollar value on that. ### The figure "$33 trillion" was once projected as the value of ecosystems globally. What do you think of this type of economic analysis?
Are nature's services worth trillions?
**Polasky:** The $33-trillion figure refers to one of the earliest studies that was done on the value of ecosystem services. The lead author was Robert Costanza. He and his coauthors tried to get at the notion of how we can establish on a global basis what the value of ecosystem services is. They came up with a number 33 trillion [USD] plus or minus a few trillion. There are a number of problems with the study. The most basic one is the question of what you are talking about when you consider all the ecosystem services of Earth. The entire system is our life support system. So what is our life support system worth? You don't really have to have a scientific study in order to answer that question. The real value of the study was not the $33-trillion figure, which who knows what that means, but that it spurred people to focus on these issues. ### Have you come up with some monetary values on a small scale?
Another study showed people would pay more for a home near a nature area.
**Polasky:** I have worked on several such studies. I worked with a graduate student who was very interested in wetlands. We conducted a study on whether wetlands in Portland, Oregon, make any appreciable impact on something we could observe. We looked at property prices, and we controlled for how close properties were to a wetland. We considered other things as well, such as parks, neighborhoods, and school quality. We considered things like the square footage of property, how many bathrooms there were, did it have a view, and so on. We had a great data set--15,000 observations. I was initially skeptical that we would find anything because I didn't think we would find that people in Portland would value wetlands. But they did. We found that if you moved the house closer to wetlands by something like a quarter mile, you increased the value of the house by some $400 to $500, on average. To get the gross value in Portland, then, of living near wetlands, you would multiply the $500 per household times the number of households in Portland. Other studies support the view that people find value in living next to natural areas. ### The economist Richard Norgaard said that an evaluation of ecosystem services should also consider the moral factor of investing in future generations. Can this be done?
Ethical factors are not always part of the equation.
**Polasky:** There is a lot of interest within economics about sustainability and about issues of the welfare of current versus future generations. There isn't a clear answer in economics about how to deal with such a moral question. In many ways it is outside economics. Economists don't have a monopoly on ethics, just as natural sciences don't have a monopoly on ethics. I can give you personal views. But Norgaard has brought out an important point, that decisions we make do have important ethical components to them. Clearly, when we are talking about trying to prevent extinction of a species, that has an ethical component both in our relationship to other species as well as our relationship to other generations of humans. ### Since we can put a value on ecosystem services, what does that imply for policymakers or conservation management?
Good science is essential to making good decisions.
**Polasky:** Having good information on which to base decisions is necessary but it is not sufficient for good decision making. Just because we know that there is climate change does not mean that we have actually done anything about it. There is another step to take, which is considering the incentives and the institutions. Are they actually adequate for making decisions? I'll give a fisheries example to illustrate this point. We know that humans have overfished, causing massive declines in some species. Fishermen are very aware of that, but the individual fisherman has little incentive to stop fishing; it is a tragedy of the commons. The individual fishermen don't have the incentive to take on the world's problems. They have to put food on the table, so they continue to go out and fish. Just knowing that the fish has value isn't sufficient to cure the tragedy of the commons problem. What are the institutions that society has to manage these problems? Valuation is necessary for good information, and good information is necessary for good decision making, but there is more to good decision making than just information.

© 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/environment/polasky.html http://staging.actionbioscience.org/environment/polasky.html 4-health of humans and ecosystems Original Interview environment Eco-economics Sat, 01 Jul 2006 12:28:09 -0500 Computational Skills for Biology Students Understanding quantitative research is critical to grasping biology. **Gross:** A good fraction of modern biology is heavily quantitative, and one of the main complaints that I have heard for a very long time from biologists is that students do not have the capability to carry out the basic quantitative research that is critical to all modern biology across the spectrum.
Graphing is a required basic skill.
One of the most distressing comments has been about the simplest things: reading, interpreting, and producing graphs--simple graphs that students have seen again and again since they were in elementary and middle school. Things like bar charts and histograms are common, but certainly the kinds of graphs that come up again and again in science include those that have logarithmic and exponential scalings. These are the ones that are typically called log-log or semi-log graphs. These are used throughout biology and the rest of science to describe systems, particularly those in which there is an exponential component. An exponential response is something students learn in high school and, from my experience, they never really get an understanding of it. What educators need are good data sets and good ways to explain why these kinds of graphs arise. That includes what are called allometric relationships, such as the relationship between body size and weight in mammals, or that of diameter, breast height, and tree height. Such scaling relationships occur in biological systems from the level of individuals to that of entire global systems. Perhaps the simplest illustration of this point is the basic way we communicate science, which requires a quantitative framework for understanding. I gave the example of graphs, but we also communicate science through symbolic means, from simple equations to more complicated ones. ### How do teachers go about helping students become more computer savvy?
The ability to compute and analyze data is essential.
**Gross:** The students that are coming into upper high school and college level now are computer savvy in a variety of ways. Certainly they have the capability to use programs such as Word, PowerPoint, and even Excel to a certain extent to carry out analysis because they have been using them for other tasks. Perhaps the easiest way to help is to build on students' own experience. That means having them carry out some variation of observations or experiments themselves, then having them enter their data into a program like Excel or one of a wide variety of others and carry out some level of analysis. That level of analysis could be very simple, for example, creating scatterplots that relate two variables like length and width or heart rate before and after exercise. One thing that you can do here is to make sure that students are invested in some sense in the data sets that they have collected. There are now lots of tools that are useful in providing sensor input into data loggers, and calculators that directly connect to them, allowing students to collect real time data on a variety of things. ### What key skills should a teacher help students develop so that they can become good computational biologists?
Students need to understand what algorithms are and how to use them.
**Gross:** First I should say that being a good computational biologist is not going to come from just a few exposures. It is going to require considerable exposure to lots of different areas of what we generally call computational science. Just because someone learns what an algorithm is is not enough. Working with algorithms is key. It helps you gain an understanding of how any computer program operates, that is, by one step following another in a logical sequence of operations. It is possible to teach computational biology from a wide variety of perspectives, including the cellular level. There are great websites and collections of materials, such as the ones produced by BioQUEST, that provide ways to introduce students to a logical sequence of operations. Even in Excel there is sort of a logical construct for what goes first and what goes next. It is kind of hidden in that people are not running programs in the same way they would if they were using basic computer language, but they are good things to start with.
Essential quantitative concepts are listed in Math & Bio 2010.
Beyond that there are a good variety of resources available on what computational biologists need to know. I even have something on my website about this, but it is not a one shot kind of thing. It requires a long-term, sustained exposure of students to a variety of computational science issues. My preference is to focus on the general biology student and not to target students that are going on to do computational biology. I focus on the key concepts that underlie quantitative approaches in the life sciences and across the board. The _Math & Bio 2010_ report has a listing of these concepts, if an educator wants to know how to train what we could call "fearless biologists." Fearless biologists can go off and do a wide variety of research related to the basic biological questions that they are interested in and not be constrained by their lack of understanding in some discipline.
Equilibria and homeostasis are two such concepts.
What you are aiming for is a conceptual foundation for undergraduate education. For example, most science undergraduates take some kind of course in which they learn about catalysts and what an instantaneous rate of change is in a very formalized way. But there are other kinds of rates of change, rates of change over a time period, say, and these are not instantaneous at all. A very different underlying mathematical framework is required for analyzing things like the change in population size from one generation to the next, the change in inset populations as the population changes through time, or the change of a number of individuals in a population affected by a disease such as HIV or rabies. That is not something students pick up in a calculus course. What we can do in our biology courses is reinforce these basic quantitative concepts that occur again and again throughout the life sciences. Rates of change are just one example, but there are many others. The whole notion of homeostasis and what equilibrium is in a biological system are concepts that you would hope every undergraduate in life sciences has some conceptual foundation for understanding. Even if they can't do the underlying mathematics, they should at least understand the notion of equilibrium in a process for which there is no change through time. We hope they have some understanding of what we call dynamic equilibrium, such as a distinct increase in heart rate. Just those basic concepts are important: equilibria, dynamic equilibria, and associated issues of homeostasis. Again, _Math & Bio 2010_ report has a listing of the key conceptual foundations for biology that have quantitative components, and I think that serves as a good guide to what one could encourage students to grasp throughout undergraduate studies or in a general biology program. ### What advantages does a biology student with some computational skills have?
Many biology jobs require quantitative skills.
**Gross:** One is, of course, just an expansion of the skill set, in that anytime you learn a new skill you have the potential to utilize that skill. Much of the job opportunities in modern biology require quantitative training, so graduate students should be encouraged to use quantitative skills. In fact, many of my colleagues would argue that it is much easier for students to learn biology if they have quantitative training. It is certainly easier if you develop the skill along the way. There is a movement toward developing programs that train students at the undergraduate level in both quantitative skills and in biological skills.
Math skills are also important for technical jobs.
Pick up any issue of _Science_ and _Nature_ and you will see that the job ads for people with PhDs are looking for people with quantitative skills. In addition to ads for computational biologists, there are technical jobs that require an understanding of what is going on inside machines, if nothing else. Admittedly, there are many technicians who don't understand what is going on in the machine that they use, but I think that those who are most in demand would be those who have an understanding beyond just pushing a certain button to produce a particular result. Technicians need to know why a result arises, and often that involves sitting down and analyzing the techniques that the piece of equipment utilizes. A piece of equipment can be simple or complicated; for example, in ecology we use a wide variety of photosynthetic measuring devices. The underlying mathematics is not outrageously complicated, but it requires some thought to understand what you are measuring when you measure photosynthesis. ### Any suggestions for high school teachers about adding computational biology skills to the curriculum?
There are many quantitative resources for the high-school level.
**Gross:** There are wonderful resources, including computer programs and free programs, which are designed to assist students at the high school level [see "learn more links" below]. The vast majority of students entering college programs in biology already have had calculus. They often have already taken a course viewed as a college-level course, and students realize quite well that they need this kind of background. Good biology students today, whether they are interested in the health sciences or in veterinary medicine, ecology, or other areas, realize that quantitative skills will enhance their ability to work in the future.
Linking experiments or statistical methods with biology courses helps.
Therefore, I would encourage students at the high school level to think about data. Having students collect and analyze data gives them quantitative skills that will serve them well in the long term no matter what they do. In addition, many of the students entering college now have had a statistics course in high school. Coupling that statistics course with their biology courses or any lab experience would also be beneficial. Much of what we call bioinformatics relates to statistical methods, and a good grounding in statistics is critical in life science research as well.
Math adds a new dimension to a biological question.
I have an entire website devoted to modules aimed at incorporating the basic high-school-level mathematics into a general biology framework (). The set of modules is applicable for both college-level biology as well as the high-school level because the mathematics that underlies the activities is at the high-school level. The objective in that set of modules is to have cases in which the mathematics adds something that was not possible to see from biological data sets by themselves, that is, to devise a new way of thinking about a biological question.

© 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/education/gross.html http://staging.actionbioscience.org/education/gross.html Original Interview curriculum content education Thu, 01 Jun 2006 12:27:40 -0500 Primer on Ethics and Crossing Species Boundaries Part-human animals are the stuff of myths and movies.
Experiments with such creatures are causing concern.
Ancient Greek mythology is replete with references to part-human animals. There is the monstrous half-human, half-bull Minotaur; the Gorgon sisters (one of whom is Medusa) with hair of writhing snakes; the Sirens who are sweet singing sea nymphs each with the head of a woman and the body of a bird; and, not to be forgotten, there is the infamous Sphinx with the head and breasts of a woman, the body of a lion, and the wings of a bird. Part-human creatures are also a staple of modern science fiction, as in H. G. Wells' _The Island of Dr Moreau_,1 where animals are vivisected into part-human creatures, or George Langelaan's _The Fly_, in which a scientist emerges from his disintegrator-reintegrator machine with the head and arms of a fly.2 But part-human animals are not only science fiction--they are also science fact. While not as monstrous as the creatures of lore, part-human laboratory animals raise some important ethical and societal issues. ### What does it mean to cross species boundaries? First, from a biological perspective, it is surprisingly difficult to answer the question What does it mean to cross species boundaries? This is true not only because of the number of species concepts (according to some, as many as 22),3 but also because species boundaries are not fixed.
How do we define a species?
Is the boundary between species real or artificial?
* **Species concepts:** One classic definition of species is the biological species concept. This definition emphasizes the importance of reproductive isolation or lack of genetic exchange that separates species.4 By this account, crossing species boundaries would involve the transfer of genetic materials between populations of organisms that do not interbreed. In cases where such interbreeding can be achieved artificially, as in the laboratory, the raison d'�tre of the biological species concept is undermined. Other accounts of species may be brought to bear in place of the biological species concept, but the consensus among biologists is that no single species concept will be sufficient for all situations. * **Species boundaries:** One of the consequences of our evolutionary past is that genes, gene regulatory networks, epigenetic developmental processes, and features of the biophysical environment are widely shared by different kinds of creatures. The idea of fixed or rigid breaks between species plays no role whatsoever in contemporary biology. Indeed, the fluidity of species boundaries has been revealed through the techniques of comparative genomics, warning against the interpretation of species as unique types.
Crossing the boundary implies combining genetic or cellular material from two organisms.
Given the difficulty in defining species once and for all, and also the flexibility of species boundaries,5 what does it mean to cross species boundaries? When we refer to species and the crossing of species boundaries,5 we do so based on the following simple idea: Every individual human contains a human genome. In all likelihood, this genome will not be representative of other human genomes and will contain a lot of DNA that is contained in many other kinds of organisms, thanks to our evolution from a common ancestor. The same will be true with nonhuman organisms, such as a rose or a rat or a _Rhesus macaque_. As such, when we refer to crossing species boundaries, we refer to the combination of genetic or cellular material from two organisms that would generally be understood, in lay terms, as belonging to different species: a human as understood by most lay people, a _Rhesus macaque_ as understood by most lay people, and so on.6
Parents of hybrids are different species.
Genetically modified food is a transgenic product.
Chimeras have cells from two genetically distinct organisms.
### Hybrids, transgenics, and chimeras There are many types of interspecies organisms including hybrids, transgenics, and chimeras, each of which is created through different sorts of processes. Hybrids are created through breeding. Transgenics are produced through genetic manipulation and modification. Chimeras are the result of cell or tissue transplants. * _Hybrids_ are created by breeding across species. Hybrids are generally the result of combining an egg from one species with sperm from another to form a single embryo. Hybrids contain recombined genetic material throughout their genome and throughout all the tissues in their body. * _Transgenics_ are the result of gene transfer. Typically, transgenics contain transferred or manipulated genes in addition to the host nuclear and mitochondrial DNA. One exception may be a transgenic embryo comprised of the entire complement of nuclear DNA from one organism fused with an enucleated egg cell from another. * _Chimeras_ comprise a mixture of cells from two or more genetically distinct organisms of the same or different species. They are mosaics at the cellular level; individual cells are derived from either the host or the donor but not both.7 Note that chimeras and transgenics need not cross species boundaries, whereas hybrids are always interspecific. ### Multiple applications Crossing species boundaries happens all the time in nature and in agricultural settings, and it has a long history in developmental biology and immunology laboratories. Consider just a few examples:
Nature and breeding programs cross boundaries.
* lateral gene transfer between bacteria, whereby genetic material is transmitted horizontally from one organism to another8 * the crossing of strains of wheat; the insertion of genes from a plant (or an animal) into a plant to improve crop yield and robustness9 * the mating of a horse with a donkey to create a mule; the fusion of sheep and goat cells to create a "geep"10 * the transplantation of cells and tissues from one species of frog to another, and of neural tissue from quails to chickens, to study the complex processes of development11-13
Gene transfer from animals to humans and vice versa is common.
Crossing species boundaries between human and nonhuman animals is also commonplace: * Animal tissues, cells, and their derivatives are often transferred to humans, whether by using insulin produced from pig or cow pancreases, injecting flu vaccines cultured in fertilized chicken eggs, or transplanting heart valves from pigs into humans. * Human genes and cells are often transferred to animal hosts to create humanized animal models (such as OncoMouse, which develops human cancers14), to grow humanized tissues that can be transplanted back into humans (such as sheep with human livers15), or to test the developmental potential of transplants.16 ### Stem cell research
Stem cell research and cloning ignited debate.
In the first few years of human stem cell research, most of the ethics discussions centered on the use of human embryos as sources of stem cells. Research to derive human embryonic stem (hES) cells involves removing cells from the inner cell mass of a human blastocyst, which destroys the developing embryo. While this debate continued, further debate on the ethics of cloning to produce children, and cloning for biomedical research, emerged. This debate arose in response to claims about the anticipated benefit of future stem cell therapies using cells from cloned embryos, which would allow patients to receive transplants of cells containing their own DNA.17
The debate has encompassed part-human animals.
While these issues remain ethically contentious, a new debate has recently emerged concerning the ethics of crossing species boundaries to make part-human chimeras. Stem cell scientists and others insist that this cross-species work is important to basic science and a necessary step on the path to regenerative medicine. They maintain that it would be unethical to involve humans in stem cell transplantation research without first having studied the safety and efficacy of the human cells in nonhuman animals. ### Ethical controversy Issues of health and safety, especially given the possibility of zoonosis, or the transfer of a disease from nonhuman animals to humans, have long been front and center in the ethics debate about cross-species work.18 In the last decade or so, with the increase in science options for the crossing of species boundaries, other ethical issues have come to the fore.
Attempts to patent a humanzee failed but caused a stir.
In 1997, Stuart Newman, a developmental biologist sponsored by biotechnology activist Jeremy Rifkin, sought to preclude the creation of a humanzee--a part-human, part-chimpanzee chimera. Together, Newman and Rifkin tried to patent the relevant technology so that they would be able to restrict its use and to promote a vigorous social dialogue about the desirability of such part-human beings.19 They were unsuccessful in obtaining the patent, leaving open the possibility that humanzees may soon walk among us, with or without patent protection. Examples of recent research involving the transplantation of cells and tissues into prenatal nonhuman animals (embryos and fetuses), the transplantation of cells and tissues into nonhuman animal brains, and the transplantation of cells and tissues into the brains of nonhuman primates, serve to make this point:
Part-human animals already exist.
Scientists want to test human cells in other primates.
* Scientists at Harvard University have published their research involving the transfer of human neural stem cells into the developing fetal brain of bonnet monkeys.20 * Scientists in Israel have reported that human embryonic stem cells transplanted into chick embryos differentiated into neurons.21 * Scientists in Nevada have reported on inserting human neural stem cells into fetal sheep to assess their developmental potential.22 * Scientists in California have reported on the development of functional neurons in mouse brains, where the neurons were derived from human embryonic stem cells.23 While this research is ongoing, a debate has erupted about the ethics of creating part-human beings in response to proposals from some stem cell scientists to use nonhuman primates as an assay system for testing the developmental potential of human stem cells. The fact that biologists are especially interested in transplanting human neural stem cells into the brains of nonhuman primates24 intensifies the controversy about humanzee-like chimeras. ### The ethics of creating part-human beings
Is it natural and moral to develop part-human animals?
The ethical debate has been multivocal, with moral considerations raised from many perspectives, both religious and secular. The central moral concerns with creating part-human beings include worries about the following: * the unnaturalness and intuitive repugnance of certain kinds of creatures, such as part-human combinations25 * the threat of intensified moral confusion regarding the creation of novel part-human beings who violate the pragmatically clear moral demarcation line between species upon which current institutions, structures, and social practices are based5 * the potential for transferring moral status to nonhuman animals by conferring on them characteristically human cognitive capacities, which may or may not threaten human dignity24,26 * the possibility that enhanced animals would deserve to be treated as if they were human subjects but would continue being treated as if they were unenhanced nonhuman animals27 * the moral status of nonhuman animals, especially primates, as experimental animals28
Some see the medical benefits of the research.
Others see it as a way to improve humans.
Scientists and others who advocate cross-species work argue that the part-human animals will be useful as disease models, assay systems, or organ sources.16,29 They dismiss the worries about repugnance, deny the potential for moral confusion, and endeavor to sidestep concerns about moral status and potential threats to human dignity. They also rely heavily on current norms for research involving humans to legitimate preclinical cross-species research in nonhuman animals. Additionally, advocates of _transhumanism_, the movement to enhance humans using biotechnology, argue that the creation of hybrids, transgenics, and chimeras may be useful in the quest to radically alter humans.30 They see an opportunity to improve upon human nature and to enhance cognitive and physical performance--an idea that is itself morally controversial.31
More debate is needed about the value and ethics of such research.
### Toward a constructive public debate Unfortunately, much of the public debate on the ethics of crossing species boundaries is characterized by sensationalism and political posturing. While some commentators have attempted to explore the moral dimensions of interspecies research in careful and respectful terms, many of the media reports have exaggerated the conflict, providing more heat than light. Even so, attempts at public education and public engagement have tended to reveal the persistence of the moral controversy. This suggests the need for scientists, ethicists, and others to take seriously the ethical concerns that have been raised. The voluntary guidelines for human embryonic stem cell research recently published by the National Academy of Sciences arguably are an attempt to do just this.32 As we have argued elsewhere, however, considerably more debate and discussion is needed about the fundamental underlying values.33,34

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]]> http://staging.actionbioscience.org/biotech/baylis_robert.html http://staging.actionbioscience.org/biotech/baylis_robert.html 4-technology and ethics Original biotechnology science and technology in the 21st century Interspecies Mon, 01 May 2006 12:27:18 -0500